RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 007387
(605 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 = 351 bits (902), Expect = e-115
Identities = 121/215 (56%), Positives = 155/215 (72%)
Query: 1 MFGATTLIVKIIGSIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWQWLRYFN 60
+ TL+VKI+G I +V+ GL LGKEGP++HIG+CIA+ L QGG + R+ ++W RYF
Sbjct: 123 ILRLKTLLVKIVGVILSVSGGLALGKEGPMIHIGACIAAGLSQGGSTSLRLDFRWFRYFR 182
Query: 61 NDRDRRDLITCGSSSGVCAAFRAPVGGVLFSLEEVATWWRSALLWRTFFSTAVVVVVLRA 120
NDRD+RD +TCG+++GV AAF APVGGVLFSLEEVA++W AL WRTFFS+ +V L
Sbjct: 183 NDRDKRDFVTCGAAAGVAAAFGAPVGGVLFSLEEVASFWNQALTWRTFFSSMIVTFTLNF 242
Query: 121 FIEICTSGKCGLFGTGGLIMFDVSNVPVRYHVMDIIPVTLIGIIGGILGGLYNHILHKVL 180
F+ C SGKCGLFG GGLIMFD S+ Y ++IP LIG+IGG+LG L+NH+ HKV
Sbjct: 243 FLSGCNSGKCGLFGPGGLIMFDGSSTKYLYTYFELIPFMLIGVIGGLLGALFNHLNHKVT 302
Query: 181 RLYNLINQKGKMHKLLLALSVSVFTSVCQYCLPFL 215
R IN KGK+ K+L AL VS+ TSV + L
Sbjct: 303 RFRKRINHKGKLLKVLEALLVSLVTSVVAFPQTLL 337
Score = 216 bits (552), Expect = 1e-63
Identities = 83/127 (65%), Positives = 103/127 (81%), Gaps = 3/127 (2%)
Query: 277 PSSILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSY---TNIDQGLY 333
P ++LIFF+LY L TFGIAVPSGLF+P+IL+G+AYGRL+G+ +GSY T+ID GLY
Sbjct: 333 PQTLLIFFVLYYFLACWTFGIAVPSGLFIPMILIGAAYGRLVGILLGSYFGFTSIDPGLY 392
Query: 334 AVLGAASLMAGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIAKTVGDSFNPSIYEIILE 393
A+LGAA+ + G MRMTVSL VI LELTNNL LP M+VL+IAK VGD FN IY+II++
Sbjct: 393 ALLGAAAFLGGVMRMTVSLTVILLELTNNLTYLPPIMLVLMIAKWVGDYFNEGIYDIIIQ 452
Query: 394 LKGLPFL 400
LKG+PFL
Sbjct: 453 LKGVPFL 459
>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 = 240 bits (616), Expect = 3e-73
Identities = 131/429 (30%), Positives = 207/429 (48%), Gaps = 87/429 (20%)
Query: 2 FGATTLIVKIIGSIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWQWLRYFNN 61
G TL++K +G + AVA+GL LGKEGPLVHI +C+ +++ R+ + +Y N
Sbjct: 74 LGKWTLLIKSVGLVLAVASGLSLGKEGPLVHIATCVGNIIS-------RL---FPKYRRN 123
Query: 62 DRDRRDLITCGSSSGVCAAFRAPVGGVLFSLEEVATWWRSALLWRTFFSTAVVVVVLRAF 121
+ RR++++ +++GV AF AP+GGVLFSLEEV+ ++ LWR+FF V L++
Sbjct: 124 EAKRREILSAAAAAGVAVAFGAPIGGVLFSLEEVSYYFPLKTLWRSFFCALVAAFTLKSL 183
Query: 122 IEICTSGKCGLFGTGGLIMFDVSNVPVRYHVMDIIPVTLIGIIGGILGGLYNHILHKVLR 181
FGTG L++F+V +H ++IP L+GI GG+ G + K R
Sbjct: 184 ---------NPFGTGRLVLFEV-EYDRDWHYFELIPFILLGIFGGLYGAFFIKANIKWAR 233
Query: 182 LYNLINQKGKMHKLLLALSVSVFTSVCQYCLPFL------------ADCKACDPSFPETC 229
K + +L L V++ T++ + P+ +C+ D + C
Sbjct: 234 FR--KKSLLKRYPVLEVLLVALITALISFPNPYTRLDMTELLELLFNECEPGDDN--SLC 289
Query: 230 PTNGRSGNFKQFNCPNGHYNDLATLLLTTNDDAVRNIFSSNTPTEFQPSSILIFFILYCI 289
++ +G Y L +LLL I +L I
Sbjct: 290 -------CYRDPPAGDGVYKALWSLLLAL-----------------------IIKLLLTI 319
Query: 290 LGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTN-----------------IDQGL 332
TFGI VP+G+F+P + +G+ +GR++G+ + I GL
Sbjct: 320 ---FTFGIKVPAGIFVPSMAVGALFGRIVGILVEQLAYSYPDSIFFACCTAGPSCITPGL 376
Query: 333 YAVLGAASLMAGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIAKTVGDSFNP-SIYEII 391
YA++GAA+ + G RMTVSL VI ELT L + MI ++++K V D+ IY+
Sbjct: 377 YAMVGAAAFLGGVTRMTVSLVVIMFELTGALNYILPLMIAVMVSKWVADAIGKEGIYDAH 436
Query: 392 LELKGLPFL 400
+ L G PFL
Sbjct: 437 IHLNGYPFL 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 = 201 bits (514), Expect = 2e-59
Identities = 99/379 (26%), Positives = 168/379 (44%), Gaps = 76/379 (20%)
Query: 6 TLIVKIIGSIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWQWLRYFNNDRDR 65
L+VK +G++ + +G LG+EGP V IG+ I S LG+ L+ NDR
Sbjct: 39 VLLVKFLGTLLTLGSGGSLGREGPSVQIGAAIGSGLGR-----------RLKLSRNDR-- 85
Query: 66 RDLITCGSSSGVCAAFRAPVGGVLFSLEEVATWWRSALLWRTFFSTAVVVVVLRAFIEIC 125
R LI G+++G+ AAF AP+ GVLF+LEE++ + L ++ V +V R
Sbjct: 86 RRLIAAGAAAGIAAAFNAPLAGVLFALEELSRSFSYRALLPVLVASVVAALVSRL----- 140
Query: 126 TSGKCGLFGTGGLIMFDVSNVPVRYHVMDIIPVTLIGIIGGILGGLYNHILHKVLRLYNL 185
LFG L F+V ++P ++++ L+GI+ G+LG L+ +L KV RL+
Sbjct: 141 ------LFGNEPL--FEVPSLPP-LSLLELPLFILLGILCGLLGALFVRLLLKVERLFRR 191
Query: 186 INQKGKMHKLLLALSVSVFTSVCQYCLPFLADCKACDPSFPETCPTNGRSGNFKQFNCPN 245
+ + +L + + LP
Sbjct: 192 LKKL---PPILRPALGGLLVGLLGLFLP-------------------------------- 216
Query: 246 GHYNDLATLLLTTNDDAVRNIFSSNTPTEFQPSSILIFFILYCILGLITFGIAVPSGLFL 305
+L ++ + + +T + +L+ +L + ++ G P G+F
Sbjct: 217 --------EVLGGGYGLIQLLLNGSTLS---LLLLLLLLLLKLLATALSLGSGAPGGIFA 265
Query: 306 PIILMGSAYGRLLGMAMGSY---TNIDQGLYAVLGAASLMAGSMRMTVSLCVIFLELTNN 362
P + +G+A GRLLG+ + G +A+LG A+ +AG R ++ V+ ELT +
Sbjct: 266 PSLFIGAALGRLLGLLLPLLFPGIAPSPGAFALLGMAAFLAGVTRAPLTAIVLVFELTGS 325
Query: 363 LLLLPITMIVLLIAKTVGD 381
LL M+ +LIA V
Sbjct: 326 YSLLLPLMLAVLIAYLVSR 344
>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 = 186 bits (473), Expect = 9e-53
Identities = 75/220 (34%), Positives = 115/220 (52%), Gaps = 4/220 (1%)
Query: 1 MFGATTLIVKIIGSIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWQWLRYFN 60
TLI K I I AVA+GL LGKEGPLVH+G+ I + L QG + F
Sbjct: 82 YLSIRTLIAKTISCICAVASGLPLGKEGPLVHLGAMIGAGLLQGRSRTLGCHVHLFQLFR 141
Query: 61 NDRDRRDLITCGSSSGVCAAFRAPVGGVLFSLEEVATWWRSALLWRTFFSTAVVVVVLRA 120
N RDRRD + G+++GV +AF AP+GG+LF LEEV+T++ L WR FF+ V V++
Sbjct: 142 NPRDRRDFLVAGAAAGVASAFGAPIGGLLFVLEEVSTFFPVRLAWRVFFAALVSAFVIQI 201
Query: 121 FIEICTSGKCGLFGTGGLIMFDVSNVPVRYHVMDIIPVTLIGIIGGILGGLYNHILHKVL 180
+ + + + + V + V ++ + IP +IG+I G+L L+ + L
Sbjct: 202 YNSFNSGFELLDRSSAMFLSLTVFELHVPLNLYEFIPTVVIGVICGLLAALFVRLSIIFL 261
Query: 181 RLY-NLINQKGKMHKLLLALSVSVFTSVCQY---CLPFLA 216
R L+ +K +++L + ++ S Y L FL
Sbjct: 262 RWRRRLLFRKTARYRVLEPVLFTLIYSTIHYAPTLLLFLL 301
Score = 124 bits (313), Expect = 1e-30
Identities = 47/122 (38%), Positives = 77/122 (63%), Gaps = 11/122 (9%)
Query: 279 SILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAM-----------GSYTN 327
++L+F ++Y + + FGIAVP G F+P +++G+A GRL+G+ + +
Sbjct: 295 TLLLFLLIYFWMSALAFGIAVPGGTFIPSLVIGAAIGRLVGLLVHRIAVAGIGAESATLW 354
Query: 328 IDQGLYAVLGAASLMAGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIAKTVGDSFNPSI 387
D G+YA++GAA+ + G+ R+T S+CVI +ELT +L L M+ +LIAK V D+F S+
Sbjct: 355 ADPGVYALIGAAAFLGGTTRLTFSICVIMMELTGDLHHLLPLMVAILIAKAVADAFCESL 414
Query: 388 YE 389
Y
Sbjct: 415 YH 416
>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 = 141 bits (358), Expect = 5e-37
Identities = 86/374 (22%), Positives = 158/374 (42%), Gaps = 78/374 (20%)
Query: 6 TLIVKIIGSIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWQWLRYFNNDRDR 65
+VK + S + +G +G+EGP+V IG+ I S LG+ LR + DR
Sbjct: 84 VALVKFLASALTLGSGGSVGREGPIVQIGAAIGSWLGR-----------RLRL--SRNDR 130
Query: 66 RDLITCGSSSGVCAAFRAPVGGVLFSLEEVATWWRSALLWRTFFSTAVVVVVLRAFIEIC 125
R L+ CG+++G+ AAF AP+ G LF++E + + +++ V+L +
Sbjct: 131 RILVACGAAAGIAAAFNAPLAGALFAIEVLL---------GEYSVASLIPVLLASVAAAL 181
Query: 126 TSGKCGLFGTGGLIMFDVSNVPVRYHVMDIIPVTLIGIIGGILGGLYNHILHKVLRLYNL 185
S LFG F V ++++ L+G++ G++G L+ +L+K+ RL+
Sbjct: 182 VSR--LLFGAEPA--FGVPLYDPL-SLLELPLYLLLGLLAGLVGVLFVRLLYKIERLF-- 234
Query: 186 INQKGKMHKLLLALSVSVFTSVCQYCLPFLADCKACDPSFPETCPTNGRSGNFKQFNCPN 245
++ + L + + LP + +
Sbjct: 235 --RRLPIPPWLRPALGGLLLGLLGLFLPQV---------------------------LGS 265
Query: 246 GHYNDLATLLLTTNDDAVRNIFSSNTPTEFQPSSILIFFILYCILGLITFGIAVPSGLFL 305
G+ L L E +L+ +L + +T G P G+F
Sbjct: 266 GYGAILLAL-----------------AGELSLLLLLLLLLLKLLATALTLGSGFPGGVFA 308
Query: 306 PIILMGSAYGRLLGMAMGSY---TNIDQGLYAVLGAASLMAGSMRMTVSLCVIFLELTNN 362
P + +G+A G G+ + + G YA++G A+L+A +R ++ ++ LELT +
Sbjct: 309 PSLFIGAALGAAFGLLLPALFPGLVASPGAYALVGMAALLAAVLRAPLTAILLVLELTGD 368
Query: 363 LLLLPITMIVLLIA 376
LL M+ ++IA
Sbjct: 369 YSLLLPLMLAVVIA 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 = 134 bits (341), Expect = 1e-34
Identities = 102/399 (25%), Positives = 170/399 (42%), Gaps = 82/399 (20%)
Query: 1 MFGATTLIVKIIGSIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWQWLRYFN 60
L VK +G + A+ +GL LG+EGP V IG+ I + + W +
Sbjct: 80 PNWWRVLPVKFVGGVLALGSGLSLGREGPSVQIGAAIGQGVSK-----------WFK--T 126
Query: 61 NDRDRRDLITCGSSSGVCAAFRAPVGGVLFSLEEVATWWRSALLWRTFFSTAVVVVVLRA 120
+ +RR LI G+++G+ AAF AP+ GVLF LEE+ + L ++ V R
Sbjct: 127 SPEERRQLIAAGAAAGLAAAFNAPLAGVLFVLEELRHSFSPLALLTALVASIAADFVSRL 186
Query: 121 FIEICTSGKCGLFGTG-GLIMFDVSNVPVRYHVMDIIPVTLIGIIGGILGGLYNHILHKV 179
F FG G L + + +P++ + + ++ +GII G+LG L+N L K
Sbjct: 187 F-----------FGLGPVLSIPPLPALPLKSYWLLLL----LGIIAGLLGYLFNRSLLKS 231
Query: 180 LRLYNLINQKGKMHKLLLALSVSVFTSVCQYCLPFLADCKACDPSFPETCPTNGRSGNFK 239
LY + + + ++LL + + PE G
Sbjct: 232 QDLYRKLKKLPRELRVLLPGLLIGPLGL----------------LLPEA--LGG------ 267
Query: 240 QFNCPNGHYNDLATLLLTTNDDAVRNIFSSNTPTEFQPSSILIFFILYCILGLITFGIAV 299
GH + ++ N S +L+ F+L I ++++G
Sbjct: 268 ------GHGL-------------ILSLAGGNFS----ISLLLLIFVLRFIFTMLSYGSGA 304
Query: 300 PSGLFLPIILMGSAYGRLLGMAMGSYTNIDQGL---YAVLGAASLMAGSMRMTVSLCVIF 356
P G+F P++ +G+ G L G + I +A+ G A+ A +R ++ ++
Sbjct: 305 PGGIFAPMLALGALLGLLFGTILVQLGPIPISAPATFAIAGMAAFFAAVVRAPITAIILV 364
Query: 357 LELTNNL-LLLPITMIVLLIAKTVGDSFN-PSIYEIILE 393
E+T N LLLP+ M+V L+A V D IYE +LE
Sbjct: 365 TEMTGNFNLLLPL-MVVCLVAYLVADLLGGKPIYEALLE 402
>gnl|CDD|223116 COG0038, EriC, Chloride channel protein EriC [Inorganic ion
transport and metabolism].
Length = 443
Score = 131 bits (331), Expect = 5e-33
Identities = 100/408 (24%), Positives = 162/408 (39%), Gaps = 80/408 (19%)
Query: 5 TTLIVKIIGSIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWQWLRYFNNDRD 64
L VK++ ++ + +G LG+EGP V IG+ I SLLG + L+ + D
Sbjct: 111 RVLPVKLVATLLTIGSGASLGREGPSVQIGAAIGSLLG-----------RLLKL--SRED 157
Query: 65 RRDLITCGSSSGVCAAFRAPVGGVLFSLEEVA-TWWRSALLWRTFFSTAVVVVVLRAFIE 123
RR L+ G+++G+ AAF AP+ G LF++E + + L + V ++V F
Sbjct: 158 RRILLAAGAAAGLAAAFNAPLAGALFAIEVLYGRFLEYRALVPVLVAAVVALLVAGLF-- 215
Query: 124 ICTSGKCGLFGTGGLIMFDVSNVPVRYHVMDIIPVTLIGIIGGILGGLYNHILHKVLRLY 183
G + + P + D++ ++GII G+ G L + +L R +
Sbjct: 216 -----------GGPHFLLPIVTTP-HMSLWDLLLYLVLGIIAGLFGVLLSRLLALSRRFF 263
Query: 184 NLINQKGKMHKLLLALSVSVFTSVCQYCLPFLADCKACDPSFPETCPTNGRSGNFKQFNC 243
+ + L L V + FPE G Q
Sbjct: 264 RRLPLPPLLRPALGGLLVGALGLL-----------------FPEVL---GNGYGLIQLAL 303
Query: 244 PNGHYNDLATLLLTTNDDAVRNIFSSNTPTEFQPSSILIFFILYCILGLITFGIAVPSGL 303
G L LLL F+L + L+++G P G+
Sbjct: 304 -AGEGGLLVLLLL---------------------------FLLKLLATLLSYGSGAPGGI 335
Query: 304 FLPIILMGSAYGRLLGMAMGSYT---NIDQGLYAVLGAASLMAGSMRMTVSLCVIFLELT 360
F P + +G+A G G +G ++ GL+A+LG A+ +A + R ++ V+ LE+T
Sbjct: 336 FAPSLFIGAALGLAFGALLGLLFPPSILEPGLFALLGMAAFLAATTRAPLTAIVLVLEMT 395
Query: 361 NNLLLLPITMIVLLIAKTVGDSFNP-SIYEIILELKGLPFLDAHPEPW 407
N LL +I LIA V IY +L +G P L
Sbjct: 396 GNYQLLLPLLIACLIAYLVSRLLGGRPIYTQLLARRGAPILREERAEP 443
>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 = 106 bits (267), Expect = 1e-24
Identities = 65/217 (29%), Positives = 103/217 (47%), Gaps = 23/217 (10%)
Query: 6 TLIVKIIGSIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWQWLRYFNNDRDR 65
TL+ K+IG A+ +GL LGKEGP VHI S +A+LL ++ + + N+ R
Sbjct: 95 TLVAKVIGLTCALGSGLPLGKEGPFVHISSIVAALLS-------KLTTFFSGIYENESRR 147
Query: 66 RDLITCGSSSGVCAAFRAPVGGVLFSLEEVATWWRSALLWRTFFS---TAVVVVVLRAFI 122
+++ + GV F AP+GGVLFS+E +T++ WR FF+ A +L F
Sbjct: 148 MEMLAAACAVGVACTFGAPIGGVLFSIEVTSTYFAVRNYWRGFFAATCGAFTFRLLAVFF 207
Query: 123 EICTSGKCGLFGTGGLIMFDVSNVPVRYHVMDIIPVTLIGIIGGILGGLY---NHILHKV 179
T + P + V ++ L+GII G+LG L+ + + +
Sbjct: 208 ------SDQETITALFKTTFFVDFP--FDVQELPIFALLGIICGLLGALFVFLHRKIVRF 259
Query: 180 LRLYNLINQKGKMHKLLLALSVSVFTSVCQYCLPFLA 216
R L ++ K LL V++ T+V + PFL
Sbjct: 260 RRKNRLFSKFLKRSPLLYPAIVALLTAVLTF--PFLT 294
Score = 99.6 bits (249), Expect = 2e-22
Identities = 47/133 (35%), Positives = 80/133 (60%), Gaps = 13/133 (9%)
Query: 279 SILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLG----------MAMGSYTNI 328
++ +F ++ +L + + VP+G+F+P+ ++G+A GRL+G + G I
Sbjct: 294 TLFLFIVVKFVLTALAITLPVPAGIFMPVFVIGAALGRLVGEIMAVLFPEGIRGGISNPI 353
Query: 329 DQGLYAVLGAASLMAGSMRMTVSLCVIFLELTNNL-LLLPITMIVLLIAKTVGDSFNPSI 387
G YAV+GAA+ +G++ TVS+ VI ELT + LLP+ +I +LI+ V PSI
Sbjct: 354 GPGGYAVVGAAAF-SGAVTHTVSVAVIIFELTGQISHLLPV-LIAVLISNAVAQFLQPSI 411
Query: 388 YEIILELKGLPFL 400
Y+ I+++K LP+L
Sbjct: 412 YDSIIKIKKLPYL 424
>gnl|CDD|235385 PRK05277, PRK05277, chloride channel protein; Provisional.
Length = 438
Score = 99.6 bits (249), Expect = 3e-22
Identities = 94/398 (23%), Positives = 168/398 (42%), Gaps = 86/398 (21%)
Query: 7 LIVKIIGSIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWQWLRYFNNDRDRR 66
L VK G +G + +G+ LG+EGP V +G I ++ R +++ R
Sbjct: 93 LPVKFFGGLGTLGSGMVLGREGPTVQMGGNIGRMVL-----------DIFRLRSDEA-RH 140
Query: 67 DLITCGSSSGVCAAFRAPVGGVLFSLEEVATWWRSALL--WRTFFSTAVVVVVLRAFIEI 124
L+ G+++G+ AAF AP+ G+LF +EE+ +R +L+ F + +V R F
Sbjct: 141 TLLAAGAAAGLAAAFNAPLAGILFVIEEMRPQFRYSLISIKAVFIGVIMATIVFRLFN-- 198
Query: 125 CTSGKCGLFGTGGLI-MFDVSNVPVRYHVMDIIPVTLI-GIIGGILGGLYNHILHKVLRL 182
G +I + S P+ + + + L+ GII GI G L+N +L + L
Sbjct: 199 ---------GEQAVIEVGKFSAPPL-----NTLWLFLLLGIIFGIFGVLFNKLLLRTQDL 244
Query: 183 YNLINQKGKMHKLLLALSVSVFTSVCQYCLPFLADCKACDPSFPETCPTNGRSGNFKQFN 242
++ ++ K +L+ +V + P G
Sbjct: 245 FDRLHGGNKKRWVLMGGAVGGLCGLLGLLAPAAVG-----------------GG------ 281
Query: 243 CPNGHYNDLATLLLTTNDDAVRNIFSSNTPTEFQPSSILIFFILYCILGLITFGIAVPSG 302
+ + + N F +L F+ I L+ FG P G
Sbjct: 282 -----------------FNLIPIALAGN----FSIGMLLFIFVARFITTLLCFGSGAPGG 320
Query: 303 LFLPIILMGSAYGRLLGMAMGSY---TNIDQGLYAVLGAASLMAGSMRMTVSLCVIFLEL 359
+F P++ +G+ G GM + +I+ G +A+ G +L A ++R ++ V+ LE+
Sbjct: 321 IFAPMLALGTLLGLAFGMVAAALFPQYHIEPGTFAIAGMGALFAATVRAPLTGIVLVLEM 380
Query: 360 TNN-LLLLPITMIVL---LIAKTVGDSFNPSIYEIILE 393
T+N L+LP+ + L L+A+ +G IY +LE
Sbjct: 381 TDNYQLILPLIITCLGATLLAQFLG---GKPIYSALLE 415
>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 = 82.3 bits (204), Expect = 4e-19
Identities = 50/168 (29%), Positives = 66/168 (39%), Gaps = 63/168 (37%)
Query: 420 KPPVITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVVPPSGLANVATELHGLILRAHLVLA 479
P V+ L V + +L T+HNGFPV+D P L G ILR+ LV+A
Sbjct: 1 VPLVVLLPEGMTVEDLESLLSTTSHNGFPVVDSTEESP--------RLVGYILRSQLVVA 52
Query: 480 LKKKWFLQEKRRTEEWEVREKFSWVELAEREGKIEEVAVTSEEMEMYIDLHPLTNTTPYT 539
LK YID +P+T
Sbjct: 53 LKN-------------------------------------------YID------PSPFT 63
Query: 540 VIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLRAF 587
V S+ K LFR++GLRHLLVV + +VGI+TR+DL
Sbjct: 64 VSPRTSLEKVHQLFRKLGLRHLLVVDE------GRLVGIITRKDLLKA 105
>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 = 77.3 bits (191), Expect = 4e-15
Identities = 46/172 (26%), Positives = 79/172 (45%), Gaps = 26/172 (15%)
Query: 10 KIIGSIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWQWLRYFNNDRDRRDLI 69
KI+ ++ + G +G+EGP V IG+ + +G+ P KW L R LI
Sbjct: 83 KILLTLLGLLGGASVGREGPSVQIGAAVMLAIGRRLP-----KWGGLS-------ERGLI 130
Query: 70 TCGSSSGVCAAFRAPVGGVLFSLEEVATWWRSALLWRTFFSTAVVVVVLRAFIEICTSGK 129
G ++G+ AAF P+ G++F++EE++ R F +V+L +G
Sbjct: 131 LAGGAAGLAAAFNTPLAGIVFAIEELS---------RDFELRFSGLVLLAVIA----AGL 177
Query: 130 CGLFGTGGLIMFDVSNVPVRYHVMDIIPVTLIGIIGGILGGLYNHILHKVLR 181
L G F V+ V + + V + G++GG+ GGL+ +L +
Sbjct: 178 VSLAVLGNYPYFGVAAVALPLG-EAWLLVLVCGVVGGLAGGLFARLLVALSS 228
Score = 39.9 bits (94), Expect = 0.003
Identities = 30/103 (29%), Positives = 53/103 (51%), Gaps = 3/103 (2%)
Query: 283 FFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTNIDQGLYAVLGAASLM 342
F +L + L+++ +P GLF P + +G+ G LL +GS + QG +LG A+ +
Sbjct: 286 FGLLKFLATLLSYWSGIPGGLFAPSLAVGAGLGSLLAALLGS---VSQGALVLLGMAAFL 342
Query: 343 AGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIAKTVGDSFNP 385
AG + ++ VI +E+T + +L + L+A V P
Sbjct: 343 AGVTQAPLTAFVIVMEMTGDQQMLLPLLAAALLASGVSRLVCP 385
>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 = 57.7 bits (140), Expect = 6e-09
Identities = 72/362 (19%), Positives = 128/362 (35%), Gaps = 80/362 (22%)
Query: 15 IGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWQWLRYFNNDRDRRDLITCGSS 74
I V G LG+E +G+ +A WL DRR L+ C +
Sbjct: 93 IVTVGLGAPLGREVAPREVGALLAQRFSD-----------WLGL--TVADRRLLVACAAG 139
Query: 75 SGVCAAFRAPVGGVLFSLEEVATWWRSALLWRTFFSTAVVVVVLRAFIEICTSGKCGLFG 134
+G+ A + P+ G LF+LE +L RT +VV + + I +
Sbjct: 140 AGLAAVYNVPLAGALFALE---------ILLRTISLRSVVAALATSAIAAAVAS----LL 186
Query: 135 TGGLIMFDVSNVPVRYHVMDIIPVTLIGIIGGILGGLYNHILHKVLRLYNLINQKGKMHK 194
G ++D+ + + ++ I L G + G++ + + KGK
Sbjct: 187 KGDHPIYDIPPMQLSTPLL--IWALLAGPVLGVVAAGFRRLSQAARAK----RPKGK-RI 239
Query: 195 LLLALSVSVFTSVCQYCLPFLADCKACDPSFPETCPTNGRSGNFKQFNCPNGHYNDLATL 254
L + + FP+ NGR+ F+
Sbjct: 240 LWQMPLAFLVIGLLSI-------------FFPQI-LGNGRALAQLAFS------------ 273
Query: 255 LLTTNDDAVRNIFSSNTPTEFQPSSILIFFILYCILGLITFGIAVPSGLFLPIILMGSAY 314
T S +LI +L + L+ GL P + +G+
Sbjct: 274 ------------------TTLTLSLLLILLVLKIVATLLALRAGAYGGLLTPSLALGALL 315
Query: 315 GRLLGMAMGSYTNIDQ-GLYAVLGAASLMAGSMRMTVSLCVIFLELT--NNLLLLPITMI 371
G LLG+ + +A++GAA+ +A + + ++ ++ LE T N L L+P+ +
Sbjct: 316 GALLGIVWNALLPPLSIAAFALIGAAAFLAATQKAPLTALILVLEFTRQNPLFLIPLMLA 375
Query: 372 VL 373
V
Sbjct: 376 VA 377
>gnl|CDD|234987 PRK01862, PRK01862, putative voltage-gated ClC-type chloride
channel ClcB; Provisional.
Length = 574
Score = 49.7 bits (119), Expect = 3e-06
Identities = 34/137 (24%), Positives = 61/137 (44%), Gaps = 10/137 (7%)
Query: 293 ITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSY---TNIDQGLYAVLGAASLMAGSMRMT 349
T G G+F P + +G+ G L G+AM + YA++G + +AG+ +
Sbjct: 329 ATAGSGAVGGVFTPTLFVGAVVGSLFGLAMHALWPGHTSAPFAYAMVGMGAFLAGATQAP 388
Query: 350 VSLCVIFLELT-NNLLLLPITMIVLLIAKTVGDSFNP-SIYEIILELKGLPFLDAHPEPW 407
+ ++ E+T + ++LP M+ ++A + S+YEI L D
Sbjct: 389 LMAILMIFEMTLSYQVVLP-LMVSCVVAYFTARALGTTSMYEITLRRHQ----DEAERER 443
Query: 408 MRTLTVGELIDAKPPVI 424
+RT + ELI V+
Sbjct: 444 LRTTQMRELIQPAQTVV 460
Score = 42.0 bits (99), Expect = 8e-04
Identities = 25/84 (29%), Positives = 45/84 (53%), Gaps = 13/84 (15%)
Query: 12 IGSIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWQWLRYFNNDRDRRDLITC 71
S+ + +G +G+EGP+V + + ASL+G+ +F+ R R L+ C
Sbjct: 123 ASSLLTIGSGGSIGREGPMVQLAALAASLVGR------------FAHFDPPRLRL-LVAC 169
Query: 72 GSSSGVCAAFRAPVGGVLFSLEEV 95
G+++G+ +A+ AP+ G F E V
Sbjct: 170 GAAAGITSAYNAPIAGAFFVAEIV 193
>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 = 41.6 bits (98), Expect = 1e-04
Identities = 33/164 (20%), Positives = 59/164 (35%), Gaps = 54/164 (32%)
Query: 421 PPVITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVVPPSGLANVATELHGLILRAHLVLAL 480
V+T+S + V++ + ++ +G PV+D+ L G++ L+ AL
Sbjct: 1 RDVVTVSPDDTVAEALRLMLEHGISGLPVVDD-----------DGRLVGIVTERDLLRAL 49
Query: 481 KKKWFLQEKRRTEEWEVREKFSWVELAEREGKIEEVAVTSEEMEMYIDLHPLTNTTPYTV 540
EG ++ + + M TV
Sbjct: 50 A----------------------------EGGLDPLVTVGDVM----------TRDVVTV 71
Query: 541 IESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 584
S+ +A L + G+R L VV + G +VGI+TR D+
Sbjct: 72 SPDTSLEEAAELMLEHGIRRLPVV---DDEGR--LVGIVTRSDI 110
Score = 35.9 bits (83), Expect = 0.012
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 535 TTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLRAF 587
TV +VA+A+ L + G+ L VV + G +VGI+T +DL
Sbjct: 1 RDVVTVSPDDTVAEALRLMLEHGISGLPVV---DDDGR--LVGIVTERDLLRA 48
>gnl|CDD|234963 PRK01610, PRK01610, putative voltage-gated ClC-type chloride
channel ClcB; Provisional.
Length = 418
Score = 43.6 bits (103), Expect = 2e-04
Identities = 39/166 (23%), Positives = 75/166 (45%), Gaps = 29/166 (17%)
Query: 8 IVKIIGSIGAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWQ-WLRYFNNDRDRR 66
+VK + S+ V +G +G+EG ++ + + AS Q R +W+ W
Sbjct: 101 LVKSLASLLVVTSGSAIGREGAMILLAALAASCFAQRF--TPRQEWKLW----------- 147
Query: 67 DLITCGSSSGVCAAFRAPVGGVLFSLEEVATWWRSALLWRTFFSTAVVVVVLRAFIEICT 126
I CG+++G+ +A+ AP+ G LF E +L+ T ++ VV+ A + + T
Sbjct: 148 --IACGAAAGMASAYHAPLAGSLFIAE---------ILFGTLMLASLGPVVISAVVALLT 196
Query: 127 SGKCGLFGTGGLIMFDVSNVPVRYHVMDIIPVTLIGIIGGILGGLY 172
+ L ++++V + V D + G++ G+ G L
Sbjct: 197 T---NLLNGSDALLYNV-QLSVTVQARDYALIISTGLLAGLCGPLL 238
Score = 37.8 bits (88), Expect = 0.013
Identities = 34/118 (28%), Positives = 55/118 (46%), Gaps = 6/118 (5%)
Query: 277 PSSILIFFILYCIL--GLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTNIDQG--- 331
P +LI I C L L + G P G+F P + +G A G L G ++G + +
Sbjct: 293 PLLMLIAGIFLCKLLAVLASSGSGAPGGVFTPTLFVGLAIGMLYGRSLGLWLPDGEEITL 352
Query: 332 LYAVLGAASLMAGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIAKTVGDSFNP-SIY 388
L + G A+L+A + + ++ E+T LLP +I +IA + + SIY
Sbjct: 353 LLGLTGMATLLAATTHAPIMSTLMICEMTGEYQLLPGLLIACVIASVISRTLRRDSIY 410
>gnl|CDD|239654 cd03682, ClC_sycA_like, ClC sycA-like chloride channel proteins.
This ClC family presents in bacteria, where it
facilitates acid resistance in acidic soil. Mutation of
this gene (sycA) in Rhizobium tropici CIAT899 causes
serious deficiencies in nodule development, nodulation
competitiveness, and N2 fixation on Phaseolus vulgaris
plants, due to its reduced ability for acid resistance.
This family is part of the ClC chloride channel
superfamiy. These proteins catalyse the selective flow
of Cl- ions across cell membranes and Cl-/H+ exchange
transport. These proteins share two characteristics that
are apparently inherent to the entire ClC chloride
channel superfamily: a unique double-barreled
architecture and voltage-dependent gating mechanism. The
gating is conferred by the permeating anion itself,
acting as the gating charge.
Length = 378
Score = 42.6 bits (101), Expect = 5e-04
Identities = 44/161 (27%), Positives = 70/161 (43%), Gaps = 28/161 (17%)
Query: 25 GKEGPLVHIGSCIASLLGQGGPDNHRIKWQWLRYFN-NDRDRRDLITCGSSSGVCAAFRA 83
G+EG V +G +A G R F + DRR L+ G ++G A F
Sbjct: 96 GREGTAVQMGGSLADAFG--------------RVFKLPEEDRRILLIAGIAAGFAAVFGT 141
Query: 84 PVGGVLFSLEEVATWWRSALLWRTFFSTAVVVVVLRAFIEICTSGKCGLFGTGGLIMFDV 143
P+ G +F+LE + L R +S A++ ++ A + S GL T I+F
Sbjct: 142 PLAGAIFALEVLV-------LGRLRYS-ALIPCLVAAIVADWVSHALGLEHTHYHIVFIP 193
Query: 144 SNVPVRYHVMDIIPVTLIGIIGGILGGLYNHILHKVLRLYN 184
+ + + V L GII G+ G L+ +LH + +L
Sbjct: 194 T-----LDPLLFVKVILAGIIFGLAGRLFAELLHFLKKLLK 229
>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 = 0.002
Identities = 14/33 (42%), Positives = 22/33 (66%)
Query: 423 VITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVV 455
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 = 35.6 bits (83), Expect = 0.004
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 534 NTTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLR 585
TV S+ +A+ L R+ G+ L VV + +VGI+T +DL
Sbjct: 6 TPDVVTVPPDTSLEEALELMRENGISRLPVVDEDGK-----LVGIVTLRDLL 52
Score = 27.9 bits (63), Expect = 2.2
Identities = 14/70 (20%), Positives = 32/70 (45%), Gaps = 13/70 (18%)
Query: 413 VGELIDAKPPVITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVVPPSGLANVATELHGLIL 472
V +++ P V+T+ + + ++++R + PV+DE +L G++
Sbjct: 1 VKDIM--TPDVVTVPPDTSLEEALELMRENGISRLPVVDED-----------GKLVGIVT 47
Query: 473 RAHLVLALKK 482
L+ AL +
Sbjct: 48 LRDLLRALLE 57
>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 = 35.6 bits (83), Expect = 0.013
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 10/57 (17%)
Query: 530 HPLTNTTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLRA 586
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 = 33.6 bits (78), Expect = 0.017
Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 5/48 (10%)
Query: 537 PYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 584
TV ++ +A+ L R+ G+R L VV + G +VGI+TR+D+
Sbjct: 2 VVTVSPDTTLEEALELLRENGIRRLPVV---DEEGR--LVGIVTRRDI 44
Score = 27.9 bits (63), Expect = 1.7
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 422 PVITLSGIEKVSQIVDVLRNTTHNGFPVLDE 452
V+T+S + + +++LR PV+DE
Sbjct: 1 DVVTVSPDTTLEEALELLRENGIRRLPVVDE 31
>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 = 34.4 bits (79), Expect = 0.037
Identities = 32/167 (19%), Positives = 61/167 (36%), Gaps = 51/167 (30%)
Query: 421 PPVITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVVPPSGLANVATELHGLILRAHLVLAL 480
+T + + VS++ D++ + G PV+ + A EL G+I R ++
Sbjct: 1 REPVTCTPDDPVSKVWDLMLESGFTGLPVVQK-----------AGELIGIITRRDII--- 46
Query: 481 KKKWFLQEKRRTEEWEVREKFSWVELA-EREGKIEEVAVTSEEMEMYIDLHPLTNTTPYT 539
+ V + E + + + A + E M +T Y+
Sbjct: 47 -------------------RAGSVRTSVEDQQRTQTKASPTVEKIM--------STPVYS 79
Query: 540 VIESMSVAKA--MVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 584
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 = 0.046
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 535 TTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLR 585
P TV S+ +A+ L ++ +R L VV + + +VGI+T +DL+
Sbjct: 1 KNPITVTPDTSLMEALKLMKENSIRRLPVVDRGK------LVGIVTDRDLK 45
>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 = 33.7 bits (78), Expect = 0.052
Identities = 31/164 (18%), Positives = 55/164 (33%), Gaps = 56/164 (34%)
Query: 421 PPVITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVVPPSGLANVATELHGLILRAHLVLAL 480
P V+T+ V +++ ++ H G+PV+D+G L G++ A +
Sbjct: 1 PDVVTVPVDLTVDEVLALMFGERHRGYPVVDDG------------RLVGIVTLADI---- 44
Query: 481 KKKWFLQEKRRTEEWEVREKFSWVELAEREGKIEEVAVTSEEMEMYIDLHPLTNTTPYTV 540
RR V RE + V + + P T
Sbjct: 45 ---------RR------------VPAEGREATVLVGDVMTRD--------------PVTA 69
Query: 541 IESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 584
++ A+ + + L VV +VGI++R DL
Sbjct: 70 SPDETLRDALKRMAERDIGRLPVV-----DDSGRLVGIVSRSDL 108
>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 = 0.13
Identities = 18/50 (36%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 536 TPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLR 585
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 = 32.1 bits (74), Expect = 0.20
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 5/48 (10%)
Query: 537 PYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 584
P V ES + + R+ +VV +Y G++T +D+
Sbjct: 66 PLFVPESTPLDDLLEEMRKERSHMAIVVDEYGG-----TAGLVTLEDI 108
>gnl|CDD|214589 smart00261, FU, Furin-like repeats.
Length = 45
Score = 30.2 bits (68), Expect = 0.27
Identities = 14/49 (28%), Positives = 18/49 (36%), Gaps = 9/49 (18%)
Query: 205 TSVCQYCLPFLADCKACDPSFPETCPTNGRSGNFKQFN-----CPNGHY 248
C+ C P C C P+ C T+ + G F CP G Y
Sbjct: 1 DGECKPCHPE---CATCTGPGPDDC-TSCKHGFFLDGGKCVSECPPGTY 45
>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 = 31.9 bits (73), Expect = 0.29
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 539 TVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLRAF 587
TV+ S+A+ + L + GL L VV E +G V+G++T DL
Sbjct: 71 TVLSEESLAEVLKLLEEQGLDELAVV---EDSGQ--VIGLITEADLLRR 114
>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 = 0.41
Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 5/51 (9%)
Query: 535 TTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLR 585
T+ + ++A+A+ L R+ +RHL VV + G +VGI+T +DLR
Sbjct: 1 RDVVTITPTTTIAEALELMREHKIRHLPVV---DEEGR--LVGIVTDRDLR 46
>gnl|CDD|223591 COG0517, COG0517, FOG: CBS domain [General function prediction
only].
Length = 117
Score = 31.3 bits (71), Expect = 0.41
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 6/51 (11%)
Query: 537 PYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLRAF 587
TV SV A++L + G+ + VV + +VGI+T +D+
Sbjct: 9 VITVKPDTSVRDALLLMSENGVSAVPVVDDGK------LVGIITERDILRA 53
>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 = 0.51
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 537 PYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 584
T+ E S+A A L R+ +RHL VV +VG+LT++DL
Sbjct: 3 VVTLSEDDSLADAEELMREHRIRHLPVV-----NEDGKLVGLLTQRDL 45
>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 = 30.9 bits (71), Expect = 0.55
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 535 TTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 584
TV E V +A L R+ +R L VV + G +VGI++ DL
Sbjct: 66 RGVVTVTEDDDVDEAARLMREHQVRRLPVV---DDDGR--LVGIVSLGDL 110
>gnl|CDD|109527 pfam00474, SSF, Sodium:solute symporter family. Membership of this
family is supported by a significant blast score.
Length = 406
Score = 32.7 bits (75), Expect = 0.61
Identities = 22/131 (16%), Positives = 42/131 (32%), Gaps = 23/131 (17%)
Query: 279 SILIFFILYCILGLI--------TFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTNIDQ 330
S+L++F Y + ++ G+ + + L L Y G S+T+ Q
Sbjct: 92 SLLLYFFTYMSVQIVGGARLIELALGLNYYTAVLLLGALTA-IYTFFGGFLAVSWTDTIQ 150
Query: 331 GLYAVLGAASLMAGSMRMTVSLCVIFLELTN--------------NLLLLPITMIVLLIA 376
+ + G LM + ++L P+T + L
Sbjct: 151 AVLMLFGTIILMIIVFHEVGGYSSAVEKYMTADPNGVDLYTPDGLHILRDPLTGLSLWPG 210
Query: 377 KTVGDSFNPSI 387
+G + P I
Sbjct: 211 LVLGTTGLPHI 221
>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 = 30.7 bits (70), Expect = 0.62
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 5/46 (10%)
Query: 539 TVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 584
TV VA+A L R+ +RH LVV K +VG+++ +DL
Sbjct: 69 TVDPDEPVAEAAKLMRKNNIRHHLVVDKGGE-----LVGVISIRDL 109
>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 = 30.7 bits (70), Expect = 0.72
Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 6/72 (8%)
Query: 535 TTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL-RAFNILTAF 593
TV S+ +A L R+ ++ L VV + +VGI+T++DL R
Sbjct: 2 RDVVTVTPDTSLEEAWALLRRHRIKALPVV---DGDRR--LVGIVTQRDLLRHARPDGRR 56
Query: 594 PHLERSKSGQKH 605
P R + K
Sbjct: 57 PLRGRLRGRDKP 68
>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 = 30.3 bits (69), Expect = 0.82
Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 4/47 (8%)
Query: 538 YTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 584
T+ +VA+A+ L ++ G+ L+V + E S GI+T +D+
Sbjct: 4 VTIDGLATVAEALQLMKEHGVSSLVVEKRRE----SDAYGIVTMRDI 46
Score = 27.2 bits (61), Expect = 9.7
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 6/47 (12%)
Query: 538 YTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 584
+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 = 0.82
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 537 PYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 584
P T+ +V +A++L + G+ HL VV +VG+++ DL
Sbjct: 67 PITIPPDATVFEALLLMLERGIHHLPVVDD------GRLVGVISATDL 108
>gnl|CDD|225457 COG2905, COG2905, Predicted signal-transduction protein containing
cAMP-binding and CBS domains [Signal transduction
mechanisms].
Length = 610
Score = 31.6 bits (72), Expect = 1.2
Identities = 31/128 (24%), Positives = 47/128 (36%), Gaps = 19/128 (14%)
Query: 476 LVLALKKKWFLQEKRRTEEWEVREKFSWVELAEREGKIEEVAVTSEEMEMYID------L 529
L L K F+Q E E + F LA+R I + E E +
Sbjct: 100 LCYLLPKSVFMQ--LMEENPEFADFFL-RSLAKRLRDIADRLAEQGESEFILTRVGEVKT 156
Query: 530 HPLTNTTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLRAFNI 589
P +P I A+ M G+ L+V+ P++GI+TR+DLR+ I
Sbjct: 157 LPAVTVSPQASI--QDAARKMKDE---GVSSLVVLDDSG-----PLLGIVTRKDLRSRVI 206
Query: 590 LTAFPHLE 597
+
Sbjct: 207 ADGRSKTQ 214
>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 = 29.8 bits (68), Expect = 1.5
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 535 TTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGV 572
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 = 30.8 bits (70), Expect = 1.8
Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 10/63 (15%)
Query: 535 TTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDLRAFNILTAFP 594
T+ E + A+ L + + LLV ++ G VGI+TR D ILT
Sbjct: 242 KNVITINEDEDIYDAIRLMNKNNVGRLLVT---DSNGK--PVGIITRTD-----ILTRIA 291
Query: 595 HLE 597
LE
Sbjct: 292 GLE 294
>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 = 2.3
Identities = 22/86 (25%), Positives = 30/86 (34%), Gaps = 17/86 (19%)
Query: 425 TLSGIEKVSQIVDVLRNTTHNGFPVLDEGVVPPSGLANVATELHGLILRAHLVLALKKKW 484
TLS + + D L TT + FPV+D L GL+ R L+ AL +
Sbjct: 5 TLSPADTLDDAADALLATTQHEFPVVDG-----------DGHLVGLLTRDDLIRALAEG- 52
Query: 485 FLQEKRRTEEWEV-REKFSWVELAER 509
V R F V +
Sbjct: 53 ----GPDAPVRGVMRRDFPTVSPSAT 74
>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 = 29.6 bits (67), Expect = 2.4
Identities = 35/164 (21%), Positives = 58/164 (35%), Gaps = 24/164 (14%)
Query: 421 PPVITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVVPPSGLANVATELHGLILRAHLVLAL 480
IT + + +S +LR +G PVLD G L + +E IL+ +
Sbjct: 1 KNPITCNADDTISDAARLLRENKISGAPVLDGGK-----LVGIVSE--SDILKLLVTHDP 53
Query: 481 KKKWFLQEKRRTEEWEVREKFSWVELAEREGKIEEVAVTSEEMEMYIDLHPLTNTTPYTV 540
+L E +RE +W E + + M + T+
Sbjct: 54 SGNLWLPSPLELIELPLREFINWEETKR---ALTDAGKMKVRDIMTKKVI--------TI 102
Query: 541 IESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 584
S+ A L + ++ L VV +VGI+TR D+
Sbjct: 103 SPDASIEDAAELMVRHKIKRLPVVED------GRLVGIVTRGDI 140
>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 = 29.6 bits (67), Expect = 2.5
Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 280 ILIFFILYCILGLITFGIAVPSGLFLPIILMGSAY 314
I+ +LY +LGL FG++ L + ++L +Y
Sbjct: 12 IMTLAVLYIVLGLF-FGVSFGDVLLISLVLTLVSY 45
>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 = 29.0 bits (66), Expect = 2.6
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 534 NTTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 584
N P T S + + L R+ +RHL ++ + G VVG+ T DL
Sbjct: 65 NRNPITAKVGSSREEILALMRERSIRHLPIL---DEEGR--VVGLATLDDL 110
>gnl|CDD|239792 cd04259, AAK_AK-DapDC, AAK_AK-DapDC: Amino Acid Kinase Superfamily
(AAK), AK-DapDC; this CD includes the N-terminal
catalytic aspartokinase (AK) domain of the bifunctional
enzyme AK - DAP decarboxylase (DapDC) found in some
bacteria. Aspartokinase is the first enzyme in the
aspartate metabolic pathway, catalyzes the conversion of
aspartate and ATP to aspartylphosphate and ADP. DapDC,
which is the lysA gene product, catalyzes the
decarboxylation of DAP to lysine.
Length = 295
Score = 30.6 bits (69), Expect = 2.6
Identities = 26/140 (18%), Positives = 52/140 (37%), Gaps = 22/140 (15%)
Query: 4 ATTLIVKIIGSIGAVAAGLDLGKEGP------LVHIGSCIASLLGQGGPDNHRIKWQWLR 57
A L+ + + G+ L K+ ++ +G +++ LG + +K +WL
Sbjct: 82 ADALLANDLAQLQRWLTGISLLKQASPRTRAEVLALGELMSTRLGAAYLEAQGLKVKWL- 140
Query: 58 YFNNDRDRRDLITCGSSSGVCAAFRAPVGGVLFSLEEVATWWRSALLWRTFFSTAVVVVV 117
D R+L+T + G G + L + L + + +++
Sbjct: 141 ------DARELLTATPTLG---------GETMNYLSARCESEYADALLQKRLADGAQLII 185
Query: 118 LRAFIEICTSGKCGLFGTGG 137
+ FI G+ L G GG
Sbjct: 186 TQGFIARNAHGETVLLGRGG 205
>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 = 30.3 bits (69), Expect = 2.7
Identities = 25/109 (22%), Positives = 44/109 (40%), Gaps = 27/109 (24%)
Query: 283 FFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTNIDQGLYAV---LGAA 339
FF ++ +L ++ F LP+++ S +G + Y I G Y LG
Sbjct: 141 FFPIFVLLYVLQF-------FLLPLLIRDSFISLFVGNTL--YL-IALGYYFYITFLGYN 190
Query: 340 SLMAGSMRMTVSLCVIFLELTNNLLLLPITMIVLLIAKTVGDSFNPSIY 388
+L FL+ T LL PI ++ +L ++ FN + +
Sbjct: 191 ALP-------------FLKNTQ-FLLYPIPLLFILYLLSLLFGFNVARH 225
>gnl|CDD|179585 PRK03511, minC, septum formation inhibitor; Reviewed.
Length = 228
Score = 30.0 bits (68), Expect = 3.0
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 10/50 (20%)
Query: 392 LELKGLPFLDAHPEPWMRTLTVGELIDAKPPVITLSGIEKVSQIVDVLRN 441
+ELKG F TL+V L DA+P VI + +K++Q L+N
Sbjct: 6 IELKGSSF----------TLSVVHLHDAEPEVIRQALEDKIAQAPAFLKN 45
>gnl|CDD|227529 COG5202, COG5202, Predicted membrane protein [Function unknown].
Length = 512
Score = 29.9 bits (67), Expect = 4.3
Identities = 14/29 (48%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 34 GSCIASLLGQGGPDNHRIKWQWLRYFNND 62
GSCI LG GPD+ + K +W R N D
Sbjct: 283 GSCILFGLGYNGPDSTQ-KIRWDRVRNID 310
>gnl|CDD|220963 pfam11067, DUF2868, Protein of unknown function (DUF2868). Some
members in this family of proteins with unknown function
are annotated as putative membrane proteins. However,
this cannot be confirmed.
Length = 318
Score = 29.6 bits (67), Expect = 4.6
Identities = 17/90 (18%), Positives = 26/90 (28%), Gaps = 14/90 (15%)
Query: 16 GAVAAGLDLGKEGPLVHIGSCIASLLGQGGPDNHRIKWQWLRYFNNDRDRRDLITCGSSS 75
GA+ L+L P + D+ + Q L R +I
Sbjct: 213 GALLVALELDDALPW-------PAGGAASVADDREQRAQLLSELAAAPPARVVI------ 259
Query: 76 GVCAAFRAPVGGVLFSLEEVATWWRSALLW 105
A+ P G L L E+ + L
Sbjct: 260 -AVDAWEPPDRGTLRFLAELRRAAGATRLL 288
>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 = 29.7 bits (67), Expect = 4.9
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 263 VRNIFSSNTPTEFQPSSILI------FFILYCILGLITFGIAVPSGL 303
VR+ F FQ ++++I F I+ ILG I F I+V G
Sbjct: 164 VRDWFRELLELLFQAAALVIDTLRTFFLIVLSILGPIAFAISVYDGF 210
>gnl|CDD|225407 COG2851, CitM, H+/citrate symporter [Energy production and
conversion].
Length = 433
Score = 29.6 bits (67), Expect = 5.6
Identities = 27/97 (27%), Positives = 42/97 (43%), Gaps = 15/97 (15%)
Query: 280 ILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTNIDQGLYAVLGAA 339
+L+F IL+ FGI + SGLF P+I ++L + G + G AVL A
Sbjct: 63 MLMFAILF-------FGIMIDSGLFDPLI------RKILSIVKGDPVKVVIGT-AVLAAV 108
Query: 340 SLMAGSMRMTVSLCV-IFLELTNNLLLLPITMIVLLI 375
+ G T + + L L L + P + +L
Sbjct: 109 VSLDGDGATTFLITIPALLPLYKRLGMNPYLLALLAT 145
>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 = 29.5 bits (67), Expect = 6.0
Identities = 25/112 (22%), Positives = 45/112 (40%), Gaps = 17/112 (15%)
Query: 277 PSSILIFFILYCILGLITFGIAVPS-----GLFLPIILMGSAYGRL----LGMAMGSYTN 327
P+ +L F IL I GI P+ + +++ Y RL + A+
Sbjct: 214 PALLLPFIIL----IGILLGIFTPTEAGAYAVVYALLIGVLVYRRLTLEEVAAALLQTAR 269
Query: 328 IDQGLYAVLGAASLMAGSMRMT---VSLCVIFLELT-NNLLLLPITMIVLLI 375
+ +L AA + A + +T ++ L L LL L + ++LL+
Sbjct: 270 TTAAVLFILAAAGIFAWLLTLTGVPFAVSDWLLSLGGGKLLFLILVNLLLLV 321
>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 = 28.8 bits (65), Expect = 6.1
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 477 VLALKKKWFLQEKRRTEEWEVREKFSWVELAEREGKIEEVAVTSEEMEMYIDL 529
+ 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 = 27.6 bits (62), Expect = 8.4
Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 5/51 (9%)
Query: 534 NTTPYTVIESMSVAKAMVLFRQVGLRHLLVVPKYEAAGVSPVVGILTRQDL 584
P V +A+ L Q RHL VV + +G VVG+L L
Sbjct: 65 TPNPVCATSDTPVLEALHLMVQGKFRHLPVV---DKSG--QVVGLLDVTKL 110
>gnl|CDD|147496 pfam05341, DUF708, Protein of unknown function (DUF708). This
family consists of several uncharacterized
nucleopolyhedrovirus proteins of unknown function.
Length = 105
Score = 27.2 bits (61), Expect = 8.4
Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 5/68 (7%)
Query: 228 TCPTNGRSGNFKQFNCPNGHYNDLATLLLTTNDDAV-----RNIFSSNTPTEFQPSSILI 282
T TN R N + F+ Y DL L N+++V R ++ P I +
Sbjct: 38 TYRTNLRKANLENFDYKQPIYYDLKRKQLLINNESVNKALNRPRYAVLDTLNISPIHIFL 97
Query: 283 FFILYCIL 290
FIL +L
Sbjct: 98 AFILIVLL 105
>gnl|CDD|224173 COG1253, TlyC, Hemolysins and related proteins containing CBS
domains [General function prediction only].
Length = 429
Score = 28.8 bits (65), Expect = 8.4
Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 7/49 (14%)
Query: 537 PYTVIESMSVAKAMVLFRQVGLRHL-LVVPKYEAAGVSPVVGILTRQDL 584
P V E++S++ + FR+ H+ +VV +Y V G++T +D+
Sbjct: 281 PLFVPETLSLSDLLEEFREER-THMAIVVDEYGG-----VEGLVTLEDI 323
>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 = 28.4 bits (64), Expect = 9.6
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 280 ILIFFILYCILGLITFGIAVPSGLFLPIILMGSAYGRLLGMAMGSYTN 327
I ++ I VP G F P+ +G L+ ++MG YT
Sbjct: 130 IGTAILVLVIFATTDDRNRVPRGGFAPLA-IGLLVF-LIHLSMGPYTG 175
>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 = 9.6
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 401 DAHPEPWMRTLTVGELIDAKPPVITLSGIEKVSQIVDVLRNTTHNGFPVLDEGVV 455
D H E +R L V +++ PVIT+ VS + ++ G PV+D+G +
Sbjct: 57 DRHQERRIRNLPVSDIM--TRPVITIEPDTSVSDVASLMLENNIGGLPVVDDGKL 109
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
0.324 0.141 0.429
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: 31,871,722
Number of extensions: 3286524
Number of successful extensions: 5097
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5007
Number of HSP's successfully gapped: 169
Length of query: 605
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 502
Effective length of database: 6,369,140
Effective search space: 3197308280
Effective search space used: 3197308280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 62 (27.9 bits)