RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 013262
(447 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 = 220 bits (564), Expect = 5e-67
Identities = 83/127 (65%), Positives = 103/127 (81%), Gaps = 3/127 (2%)
Query: 119 PSSILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSY---TNIDQGLY 175
P ++LIFF+LY L TFGIAVPSGLF+P+IL+G+AYGRL+G+ +GSY T+ID GLY
Sbjct: 333 PQTLLIFFVLYYFLACWTFGIAVPSGLFIPMILIGAAYGRLVGILLGSYFGFTSIDPGLY 392
Query: 176 AVLGAASLMAGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIAKTVGDSFNPSIYEIILE 235
A+LGAA+ + G MRMTVSL VI LELTNNL LP M+VL+IAK VGD FN IY+II++
Sbjct: 393 ALLGAAAFLGGVMRMTVSLTVILLELTNNLTYLPPIMLVLMIAKWVGDYFNEGIYDIIIQ 452
Query: 236 LKGLPFL 242
LKG+PFL
Sbjct: 453 LKGVPFL 459
Score = 33.4 bits (77), Expect = 0.21
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 31 KGKMHKLLLALSVSVFTSVCQYCLPFL 57
KGK+ K+L AL VS+ TSV + L
Sbjct: 311 KGKLLKVLEALLVSLVTSVVAFPQTLL 337
>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 = 127 bits (321), Expect = 1e-32
Identities = 47/122 (38%), Positives = 77/122 (63%), Gaps = 11/122 (9%)
Query: 121 SILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAM-----------GSYTN 169
++L+F ++Y + + FGIAVP G F+P +++G+A GRL+G+ + +
Sbjct: 295 TLLLFLLIYFWMSALAFGIAVPGGTFIPSLVIGAAIGRLVGLLVHRIAVAGIGAESATLW 354
Query: 170 IDQGLYAVLGAASLMAGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIAKTVGDSFNPSI 229
D G+YA++GAA+ + G+ R+T S+CVI +ELT +L L M+ +LIAK V D+F S+
Sbjct: 355 ADPGVYALIGAAAFLGGTTRLTFSICVIMMELTGDLHHLLPLMVAILIAKAVADAFCESL 414
Query: 230 YE 231
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 = 115 bits (290), Expect = 4e-28
Identities = 50/140 (35%), Positives = 78/140 (55%), Gaps = 18/140 (12%)
Query: 121 SILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTN----------- 169
S+L+ I+ +L + TFGI VP+G+F+P + +G+ +GR++G+ +
Sbjct: 306 SLLLALIIKLLLTIFTFGIKVPAGIFVPSMAVGALFGRIVGILVEQLAYSYPDSIFFACC 365
Query: 170 ------IDQGLYAVLGAASLMAGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIAKTVGD 223
I GLYA++GAA+ + G RMTVSL VI ELT L + MI ++++K V D
Sbjct: 366 TAGPSCITPGLYAMVGAAAFLGGVTRMTVSLVVIMFELTGALNYILPLMIAVMVSKWVAD 425
Query: 224 SFNP-SIYEIILELKGLPFL 242
+ IY+ + L G PFL
Sbjct: 426 AIGKEGIYDAHIHLNGYPFL 445
>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 (254), Expect = 2e-23
Identities = 47/133 (35%), Positives = 80/133 (60%), Gaps = 13/133 (9%)
Query: 121 SILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLG----------MAMGSYTNI 170
++ +F ++ +L + + VP+G+F+P+ ++G+A GRL+G + G I
Sbjct: 294 TLFLFIVVKFVLTALAITLPVPAGIFMPVFVIGAALGRLVGEIMAVLFPEGIRGGISNPI 353
Query: 171 DQGLYAVLGAASLMAGSMRMTVSLCVIFLELTNNL-LLLPITMIVLLIAKTVGDSFNPSI 229
G YAV+GAA+ +G++ TVS+ VI ELT + LLP+ +I +LI+ V PSI
Sbjct: 354 GPGGYAVVGAAAF-SGAVTHTVSVAVIIFELTGQISHLLPV-LIAVLISNAVAQFLQPSI 411
Query: 230 YEIILELKGLPFL 242
Y+ I+++K LP+L
Sbjct: 412 YDSIIKIKKLPYL 424
>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 = 94.5 bits (236), Expect = 2e-21
Identities = 34/124 (27%), Positives = 62/124 (50%), Gaps = 6/124 (4%)
Query: 103 DAVRNIFSSNTPTEFQPSSILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGM 162
++ + + +T + +L+ +L + ++ G P G+F P + +G+A GRLLG+
Sbjct: 224 GLIQLLLNGSTLS---LLLLLLLLLLKLLATALSLGSGAPGGIFAPSLFIGAALGRLLGL 280
Query: 163 AMGSY---TNIDQGLYAVLGAASLMAGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIAK 219
+ G +A+LG A+ +AG R ++ V+ ELT + LL M+ +LIA
Sbjct: 281 LLPLLFPGIAPSPGAFALLGMAAFLAGVTRAPLTAIVLVFELTGSYSLLLPLMLAVLIAY 340
Query: 220 TVGD 223
V
Sbjct: 341 LVSR 344
>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 = 81.9 bits (203), Expect = 4e-19
Identities = 50/168 (29%), Positives = 66/168 (39%), Gaps = 63/168 (37%)
Query: 262 KPPVITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVVPPSGLANVATELHGLILRAHLVLA 321
P V+ L V + +L T+HNGFPV+D P L G ILR+ LV+A
Sbjct: 1 VPLVVLLPEGMTVEDLESLLSTTSHNGFPVVDSTEESP--------RLVGYILRSQLVVA 52
Query: 322 LKKKWFLQEKRRTEEWEVREKFSWVELAEREGKIEEVAVTSEEMEMYIDLHPLTNTTPYT 381
LK YID +P+T
Sbjct: 53 LKN-------------------------------------------YID------PSPFT 63
Query: 382 VIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLRAF 429
V S+ K LFR++GLRHLLVV + +VGI+TR+DL
Sbjct: 64 VSPRTSLEKVHQLFRKLGLRHLLVVDE------GRLVGIITRKDLLKA 105
>gnl|CDD|223116 COG0038, EriC, Chloride channel protein EriC [Inorganic ion
transport and metabolism].
Length = 443
Score = 77.8 bits (192), Expect = 2e-15
Identities = 41/138 (29%), Positives = 67/138 (48%), Gaps = 4/138 (2%)
Query: 116 EFQPSSILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYT---NIDQ 172
E +L+ F+L + L+++G P G+F P + +G+A G G +G ++
Sbjct: 306 EGGLLVLLLLFLLKLLATLLSYGSGAPGGIFAPSLFIGAALGLAFGALLGLLFPPSILEP 365
Query: 173 GLYAVLGAASLMAGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIAKTVGDSFNP-SIYE 231
GL+A+LG A+ +A + R ++ V+ LE+T N LL +I LIA V IY
Sbjct: 366 GLFALLGMAAFLAATTRAPLTAIVLVLEMTGNYQLLLPLLIACLIAYLVSRLLGGRPIYT 425
Query: 232 IILELKGLPFLDAHPEPW 249
+L +G P L
Sbjct: 426 QLLARRGAPILREERAEP 443
>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 = 72.6 bits (179), Expect = 6e-14
Identities = 29/100 (29%), Positives = 54/100 (54%), Gaps = 3/100 (3%)
Query: 122 ILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSY---TNIDQGLYAVL 178
+L+ +L + +T G P G+F P + +G+A G G+ + + G YA++
Sbjct: 283 LLLLLLLKLLATALTLGSGFPGGVFAPSLFIGAALGAAFGLLLPALFPGLVASPGAYALV 342
Query: 179 GAASLMAGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIA 218
G A+L+A +R ++ ++ LELT + LL M+ ++IA
Sbjct: 343 GMAALLAAVLRAPLTAILLVLELTGDYSLLLPLMLAVVIA 382
>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 = 69.5 bits (171), Expect = 8e-13
Identities = 39/125 (31%), Positives = 65/125 (52%), Gaps = 6/125 (4%)
Query: 116 EFQPSSILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTNIDQGL- 174
F S +L+ F+L I ++++G P G+F P++ +G+ G L G + I
Sbjct: 279 NFSISLLLLIFVLRFIFTMLSYGSGAPGGIFAPMLALGALLGLLFGTILVQLGPIPISAP 338
Query: 175 --YAVLGAASLMAGSMRMTVSLCVIFLELTNNL-LLLPITMIVLLIAKTVGDSFN-PSIY 230
+A+ G A+ A +R ++ ++ E+T N LLLP+ M+V L+A V D IY
Sbjct: 339 ATFAIAGMAAFFAAVVRAPITAIILVTEMTGNFNLLLPL-MVVCLVAYLVADLLGGKPIY 397
Query: 231 EIILE 235
E +LE
Sbjct: 398 EALLE 402
>gnl|CDD|235385 PRK05277, PRK05277, chloride channel protein; Provisional.
Length = 438
Score = 60.3 bits (147), Expect = 7e-10
Identities = 37/120 (30%), Positives = 64/120 (53%), Gaps = 10/120 (8%)
Query: 123 LIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSY---TNIDQGLYAVLG 179
L F+ I L+ FG P G+F P++ +G+ G GM + +I+ G +A+ G
Sbjct: 299 LFIFVARFITTLLCFGSGAPGGIFAPMLALGTLLGLAFGMVAAALFPQYHIEPGTFAIAG 358
Query: 180 AASLMAGSMRMTVSLCVIFLELTNN-LLLLPITMIVL---LIAKTVGDSFNPSIYEIILE 235
+L A ++R ++ V+ LE+T+N L+LP+ + L L+A+ +G IY +LE
Sbjct: 359 MGALFAATVRAPLTGIVLVLEMTDNYQLILPLIITCLGATLLAQFLG---GKPIYSALLE 415
>gnl|CDD|234987 PRK01862, PRK01862, putative voltage-gated ClC-type chloride
channel ClcB; Provisional.
Length = 574
Score = 50.5 bits (121), Expect = 1e-06
Identities = 36/151 (23%), Positives = 66/151 (43%), Gaps = 12/151 (7%)
Query: 135 ITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSY---TNIDQGLYAVLGAASLMAGSMRMT 191
T G G+F P + +G+ G L G+AM + YA++G + +AG+ +
Sbjct: 329 ATAGSGAVGGVFTPTLFVGAVVGSLFGLAMHALWPGHTSAPFAYAMVGMGAFLAGATQAP 388
Query: 192 VSLCVIFLELT-NNLLLLPITMIVLLIAKTVGDSFNP-SIYEIILELKGLPFLDAHPEPW 249
+ ++ E+T + ++LP M+ ++A + S+YEI L D
Sbjct: 389 LMAILMIFEMTLSYQVVLP-LMVSCVVAYFTARALGTTSMYEITLRRHQ----DEAERER 443
Query: 250 MRTLTVGELIDAKPPVITLSGIEKVSQIVDV 280
+RT + ELI V+ + V+ + V
Sbjct: 444 LRTTQMRELIQPAQTVVPPTA--SVADMTRV 472
>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 = 42.8 bits (101), Expect = 3e-05
Identities = 33/164 (20%), Positives = 59/164 (35%), Gaps = 54/164 (32%)
Query: 263 PPVITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVVPPSGLANVATELHGLILRAHLVLAL 322
V+T+S + V++ + ++ +G PV+D+ L G++ L+ AL
Sbjct: 1 RDVVTVSPDDTVAEALRLMLEHGISGLPVVDD-----------DGRLVGIVTERDLLRAL 49
Query: 323 KKKWFLQEKRRTEEWEVREKFSWVELAEREGKIEEVAVTSEEMEMYIDLHPLTNTTPYTV 382
EG ++ + + M TV
Sbjct: 50 A----------------------------EGGLDPLVTVGDVM----------TRDVVTV 71
Query: 383 IESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 426
S+ +A L + G+R L VV + G +VGI+TR D+
Sbjct: 72 SPDTSLEEAAELMLEHGIRRLPVV---DDEGR--LVGIVTRSDI 110
Score = 36.3 bits (84), Expect = 0.005
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 377 TTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLRAF 429
TV +VA+A+ L + G+ L VV + G +VGI+T +DL
Sbjct: 1 RDVVTVSPDDTVAEALRLMLEHGISGLPVV---DDDGR--LVGIVTERDLLRA 48
>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 = 41.4 bits (98), Expect = 7e-04
Identities = 30/103 (29%), Positives = 53/103 (51%), Gaps = 3/103 (2%)
Query: 125 FFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTNIDQGLYAVLGAASLM 184
F +L + L+++ +P GLF P + +G+ G LL +GS + QG +LG A+ +
Sbjct: 286 FGLLKFLATLLSYWSGIPGGLFAPSLAVGAGLGSLLAALLGS---VSQGALVLLGMAAFL 342
Query: 185 AGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIAKTVGDSFNP 227
AG + ++ VI +E+T + +L + L+A V P
Sbjct: 343 AGVTQAPLTAFVIVMEMTGDQQMLLPLLAAALLASGVSRLVCP 385
>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 = 38.2 bits (89), Expect = 0.001
Identities = 14/33 (42%), Positives = 22/33 (66%)
Query: 265 VITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVV 297
VIT+S V ++ +++ T H+GFPV+D G V
Sbjct: 4 VITVSPDNTVKDVIKLIKETGHDGFPVVDNGKV 36
>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 = 36.0 bits (84), Expect = 0.002
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 376 NTTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLR 427
TV S+ +A+ L R+ G+ L VV + +VGI+T +DL
Sbjct: 6 TPDVVTVPPDTSLEEALELMRENGISRLPVVDEDGK-----LVGIVTLRDLL 52
Score = 28.3 bits (64), Expect = 1.1
Identities = 14/70 (20%), Positives = 32/70 (45%), Gaps = 13/70 (18%)
Query: 255 VGELIDAKPPVITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVVPPSGLANVATELHGLIL 314
V +++ P V+T+ + + ++++R + PV+DE +L G++
Sbjct: 1 VKDIM--TPDVVTVPPDTSLEEALELMRENGISRLPVVDED-----------GKLVGIVT 47
Query: 315 RAHLVLALKK 324
L+ AL +
Sbjct: 48 LRDLLRALLE 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 = 39.2 bits (92), Expect = 0.003
Identities = 26/100 (26%), Positives = 49/100 (49%), Gaps = 3/100 (3%)
Query: 119 PSSILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTNIDQ-GLYAV 177
S +LI +L + L+ GL P + +G+ G LLG+ + +A+
Sbjct: 278 LSLLLILLVLKIVATLLALRAGAYGGLLTPSLALGALLGALLGIVWNALLPPLSIAAFAL 337
Query: 178 LGAASLMAGSMRMTVSLCVIFLELT--NNLLLLPITMIVL 215
+GAA+ +A + + ++ ++ LE T N L L+P+ + V
Sbjct: 338 IGAAAFLAATQKAPLTALILVLEFTRQNPLFLIPLMLAVA 377
>gnl|CDD|234963 PRK01610, PRK01610, putative voltage-gated ClC-type chloride
channel ClcB; Provisional.
Length = 418
Score = 38.6 bits (90), Expect = 0.005
Identities = 34/118 (28%), Positives = 55/118 (46%), Gaps = 6/118 (5%)
Query: 119 PSSILIFFILYCIL--GLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTNIDQG--- 173
P +LI I C L L + G P G+F P + +G A G L G ++G + +
Sbjct: 293 PLLMLIAGIFLCKLLAVLASSGSGAPGGVFTPTLFVGLAIGMLYGRSLGLWLPDGEEITL 352
Query: 174 LYAVLGAASLMAGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIAKTVGDSFNP-SIY 230
L + G A+L+A + + ++ E+T LLP +I +IA + + SIY
Sbjct: 353 LLGLTGMATLLAATTHAPIMSTLMICEMTGEYQLLPGLLIACVIASVISRTLRRDSIY 410
>gnl|CDD|239984 cd04611, CBS_pair_PAS_GGDEF_DUF1_assoc, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains in association with a PAS domain, a GGDEF
(DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain
downstream. PAS domains have been found to bind ligands,
and to act as sensors for light and oxygen in signal
transduction. The GGDEF domain has been suggested to be
homologous to the adenylyl cyclase catalytic domain and
is thought to be involved in regulating cell surface
adhesiveness in bacteria. 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 = 111
Score = 36.0 bits (84), Expect = 0.007
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 10/57 (17%)
Query: 372 HPLTNTTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLRA 428
PL TV S+ A L R+ G+RHL+VV + G ++G+L++ DL
Sbjct: 64 SPL-----LTVPADTSLYDARQLMREHGIRHLVVV---DDDGE--LLGLLSQTDLLQ 110
>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 = 34.0 bits (79), Expect = 0.007
Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 5/48 (10%)
Query: 379 PYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 426
TV ++ +A+ L R+ G+R L VV + G +VGI+TR+D+
Sbjct: 2 VVTVSPDTTLEEALELLRENGIRRLPVV---DEEGR--LVGIVTRRDI 44
Score = 28.2 bits (64), Expect = 0.92
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 264 PVITLSGIEKVSQIVDVLRNTTHNGFPVLDE 294
V+T+S + + +++LR PV+DE
Sbjct: 1 DVVTVSPDTTLEEALELLRENGIRRLPVVDE 31
>gnl|CDD|239985 cd04612, CBS_pair_SpoIVFB_EriC_assoc, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains in association with either the SpoIVFB domain
(sporulation protein, stage IV cell wall formation, F
locus, promoter-distal B) or the chloride channel
protein EriC. SpoIVFB is one of 4 proteins involved in
endospore formation; the others are SpoIVFA (sporulation
protein, stage IV cell wall formation, F locus,
promoter-proximal A), BofA (bypass-of-forespore A ), and
SpoIVB (sporulation protein, stage IV cell wall
formation, B locus). SpoIVFB is negatively regulated by
SpoIVFA and BofA and activated by SpoIVB. It is thought
that SpoIVFB, SpoIVFA, and BofA are located in the
mother-cell membrane that surrounds the forespore and
that SpoIVB is secreted from the forespore into the
space between the two where it activates SpoIVFB. EriC
is involved in inorganic ion transport and metabolism.
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 = 111
Score = 34.9 bits (81), Expect = 0.018
Identities = 31/164 (18%), Positives = 55/164 (33%), Gaps = 56/164 (34%)
Query: 263 PPVITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVVPPSGLANVATELHGLILRAHLVLAL 322
P V+T+ V +++ ++ H G+PV+D+G L G++ A +
Sbjct: 1 PDVVTVPVDLTVDEVLALMFGERHRGYPVVDDG------------RLVGIVTLADI---- 44
Query: 323 KKKWFLQEKRRTEEWEVREKFSWVELAEREGKIEEVAVTSEEMEMYIDLHPLTNTTPYTV 382
RR V RE + V + + P T
Sbjct: 45 ---------RR------------VPAEGREATVLVGDVMTRD--------------PVTA 69
Query: 383 IESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 426
++ A+ + + L VV +VGI++R DL
Sbjct: 70 SPDETLRDALKRMAERDIGRLPVV-----DDSGRLVGIVSRSDL 108
>gnl|CDD|240006 cd04635, CBS_pair_22, 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 = 122
Score = 34.8 bits (80), Expect = 0.022
Identities = 32/167 (19%), Positives = 61/167 (36%), Gaps = 51/167 (30%)
Query: 263 PPVITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVVPPSGLANVATELHGLILRAHLVLAL 322
+T + + VS++ D++ + G PV+ + A EL G+I R ++
Sbjct: 1 REPVTCTPDDPVSKVWDLMLESGFTGLPVVQK-----------AGELIGIITRRDII--- 46
Query: 323 KKKWFLQEKRRTEEWEVREKFSWVELA-EREGKIEEVAVTSEEMEMYIDLHPLTNTTPYT 381
+ V + E + + + A + E M +T Y+
Sbjct: 47 -------------------RAGSVRTSVEDQQRTQTKASPTVEKIM--------STPVYS 79
Query: 382 VIESMSVAKA--MVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 426
V S+A A ++L +G +P +VGI+ R D+
Sbjct: 80 VTPDDSIATAVELMLEHDIGR-----LPVVNEKDQ--LVGIVDRHDV 119
>gnl|CDD|239958 cd04585, CBS_pair_ACT_assoc2, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains in
the acetoin utilization proteins in bacteria. Acetoin
is a product of fermentative metabolism in many
prokaryotic and eukaryotic microorganisms. They produce
acetoin as an external carbon storage compound and then
later reuse it as a carbon and energy source during
their stationary phase and sporulation. In addition
these CBS domains are associated with a downstream ACT
domain, which is linked to a wide range of metabolic
enzymes that are regulated by amino acid concentration.
Pairs of ACT domains bind specifically to a particular
amino acid leading to regulation of the linked enzyme.
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 = 122
Score = 34.2 bits (79), Expect = 0.036
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 377 TTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLR 427
P TV S+ +A+ L ++ +R L VV + + +VGI+T +DL+
Sbjct: 1 KNPITVTPDTSLMEALKLMKENSIRRLPVVDRGK------LVGIVTDRDLK 45
>gnl|CDD|239962 cd04589, CBS_pair_CAP-ED_DUF294_assoc_bac, This cd contains two
tandem repeats of the cystathionine beta-synthase (CBS
pair) domains associated with the bacterial CAP_ED (cAMP
receptor protein effector domain) family of
transcription factors and the DUF294 domain. Members of
CAP_ED, include CAP which binds cAMP, FNR (fumarate and
nitrate reductase) which uses an iron-sulfur cluster to
sense oxygen, and CooA a heme containing CO sensor. In
all cases binding of the effector leads to
conformational changes and the ability to activate
transcription. DUF294 is a putative
nucleotidyltransferase with a conserved DxD motif. 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.
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 = 111
Score = 32.6 bits (75), Expect = 0.095
Identities = 18/50 (36%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 378 TPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLR 427
P V S S+ A L R+ G LLV P +GI+TR DL
Sbjct: 2 PPLIVDASTSIRDAARLMREHGADALLV------RDGDPRLGIVTRTDLL 45
>gnl|CDD|239963 cd04590, CBS_pair_CorC_HlyC_assoc, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains associated with the CorC_HlyC domain. CorC_HlyC
is a transporter associated domain. This small domain is
found in Na+/H+ antiporters, in proteins involved in
magnesium and cobalt efflux, and in association with
some proteins of unknown function. The function of the
CorC_HlyC domain is uncertain but it might be involved
in modulating transport of ion substrates. 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.
The second CBS domain in this CD is degenerate.
Length = 111
Score = 32.5 bits (75), Expect = 0.13
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 5/48 (10%)
Query: 379 PYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 426
P V ES + + R+ +VV +Y G++T +D+
Sbjct: 66 PLFVPESTPLDDLLEEMRKERSHMAIVVDEYGG-----TAGLVTLEDI 108
>gnl|CDD|109527 pfam00474, SSF, Sodium:solute symporter family. Membership of this
family is supported by a significant blast score.
Length = 406
Score = 34.2 bits (79), Expect = 0.13
Identities = 22/131 (16%), Positives = 42/131 (32%), Gaps = 23/131 (17%)
Query: 121 SILIFFILYCILGLI--------TFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTNIDQ 172
S+L++F Y + ++ G+ + + L L Y G S+T+ Q
Sbjct: 92 SLLLYFFTYMSVQIVGGARLIELALGLNYYTAVLLLGALTA-IYTFFGGFLAVSWTDTIQ 150
Query: 173 GLYAVLGAASLMAGSMRMTVSLCVIFLELTN--------------NLLLLPITMIVLLIA 218
+ + G LM + ++L P+T + L
Sbjct: 151 AVLMLFGTIILMIIVFHEVGGYSSAVEKYMTADPNGVDLYTPDGLHILRDPLTGLSLWPG 210
Query: 219 KTVGDSFNPSI 229
+G + P I
Sbjct: 211 LVLGTTGLPHI 221
>gnl|CDD|240114 cd04801, CBS_pair_M50_like, This cd contains two tandem repeats of
the cystathionine beta-synthase (CBS pair) domains in
association with the metalloprotease peptidase M50. 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 = 114
Score = 32.2 bits (74), Expect = 0.16
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 381 TVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLRAF 429
TV+ S+A+ + L + GL L VV E +G V+G++T DL
Sbjct: 71 TVLSEESLAEVLKLLEEQGLDELAVV---EDSGQ--VIGLITEADLLRR 114
>gnl|CDD|223591 COG0517, COG0517, FOG: CBS domain [General function prediction
only].
Length = 117
Score = 31.7 bits (72), Expect = 0.23
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 6/51 (11%)
Query: 379 PYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLRAF 429
TV SV A++L + G+ + VV + +VGI+T +D+
Sbjct: 9 VITVKPDTSVRDALLLMSENGVSAVPVVDDGK------LVGIITERDILRA 53
>gnl|CDD|239994 cd04622, CBS_pair_9, 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 = 31.7 bits (73), Expect = 0.23
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 377 TTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 426
TV E V +A L R+ +R L VV + G +VGI++ DL
Sbjct: 66 RGVVTVTEDDDVDEAARLMREHQVRRLPVV---DDDGR--LVGIVSLGDL 110
>gnl|CDD|239996 cd04624, CBS_pair_11, 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 = 112
Score = 31.4 bits (72), Expect = 0.25
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 5/46 (10%)
Query: 381 TVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 426
TV VA+A L R+ +RH LVV K +VG+++ +DL
Sbjct: 69 TVDPDEPVAEAAKLMRKNNIRHHLVVDKGGE-----LVGVISIRDL 109
>gnl|CDD|239957 cd04584, CBS_pair_ACT_assoc, This cd contains two tandem repeats of
the cystathionine beta-synthase (CBS pair) domains in
the acetoin utilization proteins in bacteria. Acetoin is
a product of fermentative metabolism in many prokaryotic
and eukaryotic microorganisms. They produce acetoin as
an external carbon storage compound and then later reuse
it as a carbon and energy source during their stationary
phase and sporulation. In addition these CBS domains are
associated with a downstream ACT domain, which is linked
to a wide range of metabolic enzymes that are regulated
by amino acid concentration. Pairs of ACT domains bind
specifically to a particular amino acid leading to
regulation of the linked enzyme. 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 = 121
Score = 31.4 bits (72), Expect = 0.32
Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 5/51 (9%)
Query: 377 TTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLR 427
T+ + ++A+A+ L R+ +RHL VV + G +VGI+T +DLR
Sbjct: 1 RDVVTITPTTTIAEALELMREHKIRHLPVV---DEEGR--LVGIVTDRDLR 46
>gnl|CDD|239973 cd04600, CBS_pair_HPP_assoc, This cd contains two tandem repeats of
the cystathionine beta-synthase (CBS pair) domains
associated with the HPP motif domain. These proteins are
integral membrane proteins with four transmembrane
spanning helices. The function of these proteins is
uncertain, but they are thought to be transporters. 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 = 124
Score = 31.5 bits (72), Expect = 0.35
Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 6/72 (8%)
Query: 377 TTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL-RAFNILTAF 435
TV S+ +A L R+ ++ L VV + +VGI+T++DL R
Sbjct: 2 RDVVTVTPDTSLEEAWALLRRHRIKALPVV---DGDRR--LVGIVTQRDLLRHARPDGRR 56
Query: 436 PHLERSKSGQKH 447
P R + K
Sbjct: 57 PLRGRLRGRDKP 68
>gnl|CDD|240116 cd04803, CBS_pair_15, 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 = 122
Score = 31.1 bits (71), Expect = 0.37
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 379 PYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 426
T+ E S+A A L R+ +RHL VV +VG+LT++DL
Sbjct: 3 VVTLSEDDSLADAEELMREHRIRHLPVV-----NEDGKLVGLLTQRDL 45
>gnl|CDD|214589 smart00261, FU, Furin-like repeats.
Length = 45
Score = 29.4 bits (66), Expect = 0.39
Identities = 14/49 (28%), Positives = 18/49 (36%), Gaps = 9/49 (18%)
Query: 47 TSVCQYCLPFLADCKACDPSFPETCPTNGRSGNFKQFN-----CPNGHY 90
C+ C P C C P+ C T+ + G F CP G Y
Sbjct: 1 DGECKPCHPE---CATCTGPGPDDC-TSCKHGFFLDGGKCVSECPPGTY 45
>gnl|CDD|240001 cd04630, CBS_pair_17, 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 = 114
Score = 30.7 bits (70), Expect = 0.48
Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 4/47 (8%)
Query: 380 YTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 426
T+ +VA+A+ L ++ G+ L+V + E S GI+T +D+
Sbjct: 4 VTIDGLATVAEALQLMKEHGVSSLVVEKRRE----SDAYGIVTMRDI 46
Score = 27.6 bits (62), Expect = 5.8
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 6/47 (12%)
Query: 380 YTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 426
+V M + L + +R VV E ++GI++ D+
Sbjct: 71 ISVSPDMDIKYCARLMERTNIRRAPVVENNE------LIGIISLTDI 111
>gnl|CDD|240113 cd04800, CBS_pair_CAP-ED_DUF294_PBI_assoc2, This cd contains two
tandem repeats of the cystathionine beta-synthase (CBS
pair) domains associated with either the CAP_ED (cAMP
receptor protein effector domain) family of
transcription factors and the DUF294 domain or the PB1
(Phox and Bem1p) domain. Members of CAP_ED, include CAP
which binds cAMP, FNR (fumarate and nitrate reductase)
which uses an iron-sulfur cluster to sense oxygen, and
CooA a heme containing CO sensor. In all cases binding
of the effector leads to conformational changes and the
ability to activate transcription. DUF294 is a putative
nucleotidyltransferase with a conserved DxD motif. The
PB1 domain adopts a beta-grasp fold, similar to that
found in ubiquitin and Ras-binding domains. A motif,
variously termed OPR, PC and AID, represents the most
conserved region of the majority of PB1 domains, and is
necessary for PB1 domain function. This function is the
formation of PB1 domain heterodimers, although not all
PB1 domain pairs associate. 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 = 111
Score = 30.5 bits (70), Expect = 0.52
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 379 PYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 426
P T+ +V +A++L + G+ HL VV +VG+++ DL
Sbjct: 67 PITIPPDATVFEALLLMLERGIHHLPVVDD------GRLVGVISATDL 108
>gnl|CDD|239995 cd04623, CBS_pair_10, 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 = 30.2 bits (69), Expect = 0.79
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 377 TTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGV 414
TV +V +AM L + RHL VV + G+
Sbjct: 67 RNVITVTPDDTVDEAMALMTERRFRHLPVVDGGKLVGI 104
>gnl|CDD|225321 COG2524, COG2524, Predicted transcriptional regulator, contains
C-terminal CBS domains [Transcription].
Length = 294
Score = 31.2 bits (71), Expect = 0.96
Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 10/63 (15%)
Query: 377 TTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLRAFNILTAFP 436
T+ E + A+ L + + LLV ++ G VGI+TR D ILT
Sbjct: 242 KNVITINEDEDIYDAIRLMNKNNVGRLLVT---DSNGK--PVGIITRTD-----ILTRIA 291
Query: 437 HLE 439
LE
Sbjct: 292 GLE 294
>gnl|CDD|239980 cd04607, CBS_pair_NTP_transferase_assoc, This cd contains two
tandem repeats of the cystathionine beta-synthase (CBS
pair) domain associated with the NTP (Nucleotidyl
transferase) 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 = 113
Score = 29.8 bits (68), Expect = 1.1
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 376 NTTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 426
N P T S + + L R+ +RHL ++ + G VVG+ T DL
Sbjct: 65 NRNPITAKVGSSREEILALMRERSIRHLPIL---DEEGR--VVGLATLDDL 110
>gnl|CDD|225457 COG2905, COG2905, Predicted signal-transduction protein containing
cAMP-binding and CBS domains [Signal transduction
mechanisms].
Length = 610
Score = 31.2 bits (71), Expect = 1.2
Identities = 31/128 (24%), Positives = 47/128 (36%), Gaps = 19/128 (14%)
Query: 318 LVLALKKKWFLQEKRRTEEWEVREKFSWVELAEREGKIEEVAVTSEEMEMYID------L 371
L L K F+Q E E + F LA+R I + E E +
Sbjct: 100 LCYLLPKSVFMQ--LMEENPEFADFFL-RSLAKRLRDIADRLAEQGESEFILTRVGEVKT 156
Query: 372 HPLTNTTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLRAFNI 431
P +P I A+ M G+ L+V+ P++GI+TR+DLR+ I
Sbjct: 157 LPAVTVSPQASI--QDAARKMKDE---GVSSLVVLDDSG-----PLLGIVTRKDLRSRVI 206
Query: 432 LTAFPHLE 439
+
Sbjct: 207 ADGRSKTQ 214
>gnl|CDD|151203 pfam10710, DUF2512, Protein of unknown function (DUF2512).
Proteins in this family are predicted to be integral
membrane proteins, and many of them are annotated as
being YndM protein. They are all found in Firmicutes.
The true function is not known.
Length = 136
Score = 30.0 bits (68), Expect = 1.3
Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 122 ILIFFILYCILGLITFGIAVPSGLFLPIILMGSAY 156
I+ +LY +LGL FG++ L + ++L +Y
Sbjct: 12 IMTLAVLYIVLGLF-FGVSFGDVLLISLVLTLVSY 45
>gnl|CDD|219185 pfam06808, DctM, DctM-like transporters. This family contains a
diverse range of predicted transporter proteins.
Including the DctM subunit of the bacterial and archaeal
TRAP C4-dicarboxylate transport (Dct) system permease.
In general, C4-dicarboxylate transport systems allow
C4-dicarboxylates like succinate, fumarate, and malate
to be taken up. TRAP C4-dicarboxylate carriers are
secondary carriers that use an electrochemical H+
gradient as the driving force for transport. DctM is an
integral membrane protein that is one of the
constituents of TRAP carriers. Note that many family
members are hypothetical proteins.
Length = 412
Score = 31.1 bits (71), Expect = 1.3
Identities = 25/112 (22%), Positives = 45/112 (40%), Gaps = 17/112 (15%)
Query: 119 PSSILIFFILYCILGLITFGIAVPS-----GLFLPIILMGSAYGRL----LGMAMGSYTN 169
P+ +L F IL I GI P+ + +++ Y RL + A+
Sbjct: 214 PALLLPFIIL----IGILLGIFTPTEAGAYAVVYALLIGVLVYRRLTLEEVAAALLQTAR 269
Query: 170 IDQGLYAVLGAASLMAGSMRMT---VSLCVIFLELT-NNLLLLPITMIVLLI 217
+ +L AA + A + +T ++ L L LL L + ++LL+
Sbjct: 270 TTAAVLFILAAAGIFAWLLTLTGVPFAVSDWLLSLGGGKLLFLILVNLLLLV 321
>gnl|CDD|240005 cd04634, CBS_pair_21, 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 = 143
Score = 30.0 bits (68), Expect = 1.3
Identities = 35/164 (21%), Positives = 58/164 (35%), Gaps = 24/164 (14%)
Query: 263 PPVITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVVPPSGLANVATELHGLILRAHLVLAL 322
IT + + +S +LR +G PVLD G L + +E IL+ +
Sbjct: 1 KNPITCNADDTISDAARLLRENKISGAPVLDGGK-----LVGIVSE--SDILKLLVTHDP 53
Query: 323 KKKWFLQEKRRTEEWEVREKFSWVELAEREGKIEEVAVTSEEMEMYIDLHPLTNTTPYTV 382
+L E +RE +W E + + M + T+
Sbjct: 54 SGNLWLPSPLELIELPLREFINWEETKR---ALTDAGKMKVRDIMTKKVI--------TI 102
Query: 383 IESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 426
S+ A L + ++ L VV +VGI+TR D+
Sbjct: 103 SPDASIEDAAELMVRHKIKRLPVVED------GRLVGIVTRGDI 140
>gnl|CDD|218505 pfam05216, UNC-50, UNC-50 family. Gmh1p from S. cerevisiae is
located in the Golgi membrane and interacts with ARF
exchange factors.
Length = 232
Score = 30.7 bits (70), Expect = 1.4
Identities = 25/109 (22%), Positives = 44/109 (40%), Gaps = 27/109 (24%)
Query: 125 FFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTNIDQGLYAV---LGAA 181
FF ++ +L ++ F LP+++ S +G + Y I G Y LG
Sbjct: 141 FFPIFVLLYVLQF-------FLLPLLIRDSFISLFVGNTL--YL-IALGYYFYITFLGYN 190
Query: 182 SLMAGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIAKTVGDSFNPSIY 230
+L FL+ T LL PI ++ +L ++ FN + +
Sbjct: 191 ALP-------------FLKNTQ-FLLYPIPLLFILYLLSLLFGFNVARH 225
>gnl|CDD|240010 cd04639, CBS_pair_26, 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 = 111
Score = 29.2 bits (66), Expect = 1.6
Identities = 22/86 (25%), Positives = 30/86 (34%), Gaps = 17/86 (19%)
Query: 267 TLSGIEKVSQIVDVLRNTTHNGFPVLDEGVVPPSGLANVATELHGLILRAHLVLALKKKW 326
TLS + + D L TT + FPV+D L GL+ R L+ AL +
Sbjct: 5 TLSPADTLDDAADALLATTQHEFPVVDG-----------DGHLVGLLTRDDLIRALAEG- 52
Query: 327 FLQEKRRTEEWEV-REKFSWVELAER 351
V R F V +
Sbjct: 53 ----GPDAPVRGVMRRDFPTVSPSAT 74
>gnl|CDD|179585 PRK03511, minC, septum formation inhibitor; Reviewed.
Length = 228
Score = 30.4 bits (69), Expect = 1.7
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 10/50 (20%)
Query: 234 LELKGLPFLDAHPEPWMRTLTVGELIDAKPPVITLSGIEKVSQIVDVLRN 283
+ELKG F TL+V L DA+P VI + +K++Q L+N
Sbjct: 6 IELKGSSF----------TLSVVHLHDAEPEVIRQALEDKIAQAPAFLKN 45
>gnl|CDD|225407 COG2851, CitM, H+/citrate symporter [Energy production and
conversion].
Length = 433
Score = 30.4 bits (69), Expect = 2.0
Identities = 27/97 (27%), Positives = 42/97 (43%), Gaps = 15/97 (15%)
Query: 122 ILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTNIDQGLYAVLGAA 181
+L+F IL+ FGI + SGLF P+I ++L + G + G AVL A
Sbjct: 63 MLMFAILF-------FGIMIDSGLFDPLI------RKILSIVKGDPVKVVIGT-AVLAAV 108
Query: 182 SLMAGSMRMTVSLCV-IFLELTNNLLLLPITMIVLLI 217
+ G T + + L L L + P + +L
Sbjct: 109 VSLDGDGATTFLITIPALLPLYKRLGMNPYLLALLAT 145
>gnl|CDD|233156 TIGR00861, MIP, MIP family channel proteins. 1.A.8 The Major
Intrinsic Protein (MIP) FamilyThe MIP family is large
and diverse, possessing over 100 members that all form
transmembrane channels. These channel proteins function
in water, smallcarbohydrate (e.g., glycerol), urea, NH3,
CO2 and possibly ion transport by an energy independent
mechanism. They are found ubiquitously in bacteria,
archaeaand eukaryotes. The MIP family contains two major
groups of channels: aquaporins and glycerol
facilitators.The known aquaporins cluster loosely
together as do the known glycerol facilitators. MIP
family proteins are believed to form aqueous pores that
selectively allow passive transport of their solute(s)
across the membrane with minimal apparent recognition.
Aquaporins selectively transport water (but not
glycerol) while glycerol facilitators selectively
transport glycerol but not water. Some aquaporins can
transport NH3 and CO2. Glycerol facilitators function as
solute nonspecific channels, and may transport glycerol,
dihydroxyacetone, propanediol, urea and other small
neutral molecules in physiologically importantprocesses.
Some members of the family, including the yeast FPS
protein (TC #1.A.8.5.1) and tobacco NtTIPA may transport
both water and small solutes [Transport and binding
proteins, Unknown substrate].
Length = 216
Score = 30.0 bits (68), Expect = 2.1
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 122 ILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTN 169
I ++ I VP G F P+ +G L+ ++MG YT
Sbjct: 130 IGTAILVLVIFATTDDRNRVPRGGFAPLA-IGLLVF-LIHLSMGPYTG 175
>gnl|CDD|163494 TIGR03782, Bac_Flav_CT_J, Bacteroides conjugative transposon TraJ
protein. Members of this protein family are designated
TraM and are found in a proposed transfer region of a
class of conjugative transposon found in the Bacteroides
lineage. This family is related conjugation system
proteins in the Proteobacteria, including TrbL of
Agrobacterium Ti plasmids and VirB6 [Cellular processes,
DNA transformation].
Length = 322
Score = 30.1 bits (68), Expect = 2.6
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 105 VRNIFSSNTPTEFQPSSILI------FFILYCILGLITFGIAVPSGL 145
VR+ F FQ ++++I F I+ ILG I F I+V G
Sbjct: 164 VRDWFRELLELLFQAAALVIDTLRTFFLIVLSILGPIAFAISVYDGF 210
>gnl|CDD|233951 TIGR02614, ftsW, cell division protein FtsW. This family consists
of FtsW, an integral membrane protein with ten
transmembrane segments. In general, it is one of two
paralogs involved in peptidoglycan biosynthesis, the
other being RodA, and is essential for cell division.
All members of the seed alignment for this model are
encoded in operons for the biosynthesis of
UDP-N-acetylmuramoyl-pentapeptide, a precursor of murein
(peptidoglycan). The FtsW designation is not used in
endospore-forming bacterial (e.g. Bacillus subtilis),
where the member of this family is designated SpoVE and
three or more RodA/FtsW/SpoVE family paralogs are
present. SpoVE acts in spore cortex formation and is
dispensible for growth. Biological rolls for FtsW in
cell division include recruitment of penicillin-binding
protein 3 to the division site [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan, Cellular processes, Cell division].
Length = 356
Score = 29.8 bits (68), Expect = 2.9
Identities = 21/96 (21%), Positives = 39/96 (40%), Gaps = 19/96 (19%)
Query: 125 FFILYCILGLITFGIAV--PSGLFLPIILMGSAYGRLLGMAMGSYTNIDQGLYAVLGAAS 182
+L+ +L L+ G+ + + + + L G + Y Q YA+LG
Sbjct: 2 RLLLFVVLLLLGIGLVMVYSASAAVALRLGGDPF----------YFLKRQLFYALLGLI- 50
Query: 183 LMAGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIA 218
LM + R+ + F + +L + IVLL+
Sbjct: 51 LMFVASRLPLR----FWRKLSVPIL--LIAIVLLVL 80
>gnl|CDD|221721 pfam12698, ABC2_membrane_3, ABC-2 family transporter protein. This
family is related to the ABC-2 membrane transporter
family pfam01061.
Length = 278
Score = 29.6 bits (67), Expect = 3.4
Identities = 22/122 (18%), Positives = 46/122 (37%), Gaps = 12/122 (9%)
Query: 121 SILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRL---LGMAMGSYTNIDQGLYAV 177
+L+ I I+ L+ FG+ +P G L ++L+ YG LG +GS + V
Sbjct: 147 DLLVGLIQLLIILLLLFGLGIPFGNLLLLLLLFLLYGLAYIALGALLGSLFKNSEAAILV 206
Query: 178 LGAASLMAGSMRMTVSLCVIFLELTNNLL-----LLPITMIVLLIAKTVGDSFNPSIYEI 232
+ L+ + L + L ++P + + + + + +
Sbjct: 207 ISILILLL----SGFFGGLFPLPNMPSFLQWIFSIIPFFAPIDGLLRIIYGDLAEILLSL 262
Query: 233 IL 234
I+
Sbjct: 263 II 264
>gnl|CDD|224173 COG1253, TlyC, Hemolysins and related proteins containing CBS
domains [General function prediction only].
Length = 429
Score = 29.2 bits (66), Expect = 4.5
Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 7/49 (14%)
Query: 379 PYTVIESMSVAKAMVLFRQVGLRHL-LVVPKYEAAGVSPVVGILTRQDL 426
P V E++S++ + FR+ H+ +VV +Y V G++T +D+
Sbjct: 281 PLFVPETLSLSDLLEEFREER-THMAIVVDEYGG-----VEGLVTLEDI 323
>gnl|CDD|147812 pfam05858, BIV_Env, Bovine immunodeficiency virus surface protein
(SU). The bovine lentivirus also known as the bovine
immunodeficiency-like virus (BIV) has conserved and
hypervariable regions in the surface envelope gene. This
family corresponds to the SU surface protein.
Length = 548
Score = 29.3 bits (65), Expect = 5.0
Identities = 39/157 (24%), Positives = 60/157 (38%), Gaps = 34/157 (21%)
Query: 95 TLLLTTNDDAVRNIFSSNT---PTEFQPSSILIFFILYCILGLITFGIA----------- 140
T+ T D ++ N P + LI L CILGL+ IA
Sbjct: 117 TMAGTALADDDQSSVPENITKIPIKDTDPWTLILLGLVCILGLLGVIIAMRRSNPEGILA 176
Query: 141 --------------VPSGLFLPIILMGSAYGRLLG-MAMGSYTNIDQGLYAVLGAASLMA 185
+P +PIIL+ S ++G M Y+ I +G G+ SLM
Sbjct: 177 ARDAVDWWLSANKEIPLKFTVPIILISSPLAGIMGYFVMERYSKILKGGCQFCGSLSLMW 236
Query: 186 GSMRMTVSLCVIFLELTNNLLLLPITMIVLLIAKTVG 222
G + L I LT+ + +++LLI+ + G
Sbjct: 237 GML-----LEEIGRRLTHREWSVSRVVVILLISFSWG 268
>gnl|CDD|240004 cd04633, CBS_pair_20, 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 = 121
Score = 27.6 bits (62), Expect = 5.5
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 243 DAHPEPWMRTLTVGELIDAKPPVITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVV 297
D H E +R L V +++ PVIT+ VS + ++ G PV+D+G +
Sbjct: 57 DRHQERRIRNLPVSDIM--TRPVITIEPDTSVSDVASLMLENNIGGLPVVDDGKL 109
>gnl|CDD|235507 PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase;
Reviewed.
Length = 486
Score = 29.0 bits (66), Expect = 6.2
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 14/77 (18%)
Query: 352 EGKIEEVA-VTSEEMEMYIDLHPLTNTTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYE 410
E + EEV V E + D P TV ++A+A+ L + G+ + VV +
Sbjct: 77 EEQAEEVRKVKRSESGVVTD--------PVTVTPDTTLAEALALMARYGISGVPVV---D 125
Query: 411 AAGVSPVVGILTRQDLR 427
G +VGI+T +D+R
Sbjct: 126 ENGK--LVGIITNRDVR 140
>gnl|CDD|216266 pfam01051, Rep_3, Initiator Replication protein. This protein is
an initiator of plasmid replication. RepB possesses
nicking-closing (topoisomerase I) like activity. It is
also able to perform a strand transfer reaction on ssDNA
that contains its target. This family also includes RepA
which is an E.coli protein involved in plasmid
replication. The RepA protein binds to DNA repeats that
flank the repA gene.
Length = 218
Score = 28.4 bits (64), Expect = 6.2
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 319 VLALKKKWFLQEKRRTEEWEVREKFSWVELAEREGKIEEVAVTSEEMEMYIDL 371
+ L KK F E + E+ WV +EGK+ E+ + + ++L
Sbjct: 69 LERLMKKDFEIEDEEEKGGEIINIVLWVGYIIKEGKV-ELEFSPDLKPYLLEL 120
>gnl|CDD|239960 cd04587, CBS_pair_CAP-ED_DUF294_PBI_assoc, This cd contains two
tandem repeats of the cystathionine beta-synthase (CBS
pair) domains associated with either the CAP_ED (cAMP
receptor protein effector domain) family of
transcription factors and the DUF294 domain or the PB1
(Phox and Bem1p) domain. Members of CAP_ED, include CAP
which binds cAMP, FNR (fumarate and nitrate reductase)
which uses an iron-sulfur cluster to sense oxygen, and
CooA a heme containing CO sensor. In all cases binding
of the effector leads to conformational changes and the
ability to activate transcription. DUF294 is a putative
nucleotidyltransferase with a conserved DxD motif. The
PB1 domain adopts a beta-grasp fold, similar to that
found in ubiquitin and Ras-binding domains. A motif,
variously termed OPR, PC and AID, represents the most
conserved region of the majority of PB1 domains, and is
necessary for PB1 domain function. This function is the
formation of PB1 domain heterodimers, although not all
PB1 domain pairs associate. 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 = 113
Score = 27.2 bits (61), Expect = 6.9
Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 5/51 (9%)
Query: 376 NTTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 426
P V +A+ L Q RHL VV + +G VVG+L L
Sbjct: 65 TPNPVCATSDTPVLEALHLMVQGKFRHLPVV---DKSG--QVVGLLDVTKL 110
>gnl|CDD|240011 cd04640, CBS_pair_27, 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 = 126
Score = 27.2 bits (61), Expect = 8.4
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 377 TTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 426
P + S+ +A+ L + G+R LLVV + +G++T DL
Sbjct: 1 VKPIVIPADTSIDEALELMIKHGVRLLLVVDSDDN-----FIGVITAVDL 45
>gnl|CDD|239972 cd04599, CBS_pair_GGDEF_assoc2, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains in
association with the GGDEF (DiGuanylate-Cyclase (DGC))
domain. The GGDEF domain has been suggested to be
homologous to the adenylyl cyclase catalytic domain and
is thought to be involved in regulating cell surface
adhesiveness in bacteria. 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 = 105
Score = 27.0 bits (60), Expect = 9.3
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 6/51 (11%)
Query: 379 PYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLRAF 429
P T+ SV +A L + + L VV +VGI+T +D+R
Sbjct: 3 PITIDPLDSVGRAARLMEKHRIGGLPVVED------GKLVGIITSRDVRRA 47
>gnl|CDD|239986 cd04613, CBS_pair_SpoIVFB_EriC_assoc2, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains in association with either the SpoIVFB domain
(sporulation protein, stage IV cell wall formation, F
locus, promoter-distal B) or the chloride channel
protein EriC. SpoIVFB is one of 4 proteins involved in
endospore formation; the others are SpoIVFA (sporulation
protein, stage IV cell wall formation, F locus,
promoter-proximal A), BofA (bypass-of-forespore A ), and
SpoIVB (sporulation protein, stage IV cell wall
formation, B locus). SpoIVFB is negatively regulated by
SpoIVFA and BofA and activated by SpoIVB. It is thought
that SpoIVFB, SpoIVFA, and BofA are located in the
mother-cell membrane that surrounds the forespore and
that SpoIVB is secreted from the forespore into the
space between the two where it activates SpoIVFB. EriC
is involved in inorganic ion transport and metabolism.
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 = 114
Score = 27.2 bits (61), Expect = 9.4
Identities = 9/32 (28%), Positives = 21/32 (65%)
Query: 264 PVITLSGIEKVSQIVDVLRNTTHNGFPVLDEG 295
V+T+ +++++DV+ ++ N FPV+D+
Sbjct: 2 DVVTIPEDTPLNELLDVIAHSPENNFPVVDDD 33
>gnl|CDD|239974 cd04601, CBS_pair_IMPDH, 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 = 110
Score = 26.7 bits (60), Expect = 9.8
Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 5/49 (10%)
Query: 379 PYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLR 427
P TV +VA+A+ L + G+ L VV + G +VGI+T +DLR
Sbjct: 4 PITVSPDATVAEALELMAEYGISGLPVV---DDDGK--LVGIVTNRDLR 47
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
0.323 0.138 0.413
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,011,913
Number of extensions: 2319966
Number of successful extensions: 2658
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2605
Number of HSP's successfully gapped: 151
Length of query: 447
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 347
Effective length of database: 6,502,202
Effective search space: 2256264094
Effective search space used: 2256264094
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 61 (27.5 bits)