RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 007694
(593 letters)
>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 = 294 bits (755), Expect = 1e-94
Identities = 140/316 (44%), Positives = 191/316 (60%), Gaps = 20/316 (6%)
Query: 33 IKAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFSLMMENNRERKIALVAAGAASGIASGF 92
+K + +A+TLG+G S+G EGP V IG + + + +R + LVA GAA+GIA+ F
Sbjct: 87 VKFLASALTLGSGGSVGREGPIVQIGAAIGSWLGRRLRLSRNDRRILVACGAAAGIAAAF 146
Query: 93 NAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLLGTQSAFTVPSYDLK 152
NA +AG FAIE +L + ++LASV ++ VS +L G + AF VP YD
Sbjct: 147 NAPLAGALFAIEVLLGEYSVA-----SLIPVLLASVAAALVSRLLFGAEPAFGVPLYDPL 201
Query: 153 SAAELPLYLILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAGIIAL 212
S ELPLYL+LG+L G+V V+F RL+ + F + +PP + PALGGL G++ L
Sbjct: 202 SLLELPLYLLLGLLAGLVGVLFVRLLYKIERLF----RRLPIPPWLRPALGGLLLGLLGL 257
Query: 213 RYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLM 272
P +L G+ + L A + LL L K++ATAL GSG GG++APSL
Sbjct: 258 FLPQVLGSGYGAILLAL-----AGELSLLLLLLLLLLKLLATALTLGSGFPGGVFAPSLF 312
Query: 273 IGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELT 332
IGAA+GA FG ++ + PG VA P AYALVGMAA LA+V PLT++LL+ ELT
Sbjct: 313 IGAALGAAFG----LLLPALFPG--LVASPGAYALVGMAALLAAVLRAPLTAILLVLELT 366
Query: 333 RDYRILLPLMGAVGLA 348
DY +LLPLM AV +A
Sbjct: 367 GDYSLLLPLMLAVVIA 382
Score = 54.1 bits (131), Expect = 9e-08
Identities = 47/198 (23%), Positives = 79/198 (39%), Gaps = 26/198 (13%)
Query: 164 GMLCGVVSVVFTRLVAWFTK-------SFDFIKEKFGLPPVVCPALGGLGAGIIALRYPG 216
G+L G+ +V+F L+ L ++ P +GGL G++
Sbjct: 1 GVLSGLGAVLFRLLIELLQNLLFGGLPGELAAGSLSPLYILLVPVIGGLLVGLL------ 54
Query: 217 ILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAA 276
+ G I + + G L ++A K +A+AL GSG G P + IGAA
Sbjct: 55 VRLLGPARGHGIPEVIEAIALGGGRLPLRVALVKFLASALTLGSGGSVGREGPIVQIGAA 114
Query: 277 VGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFE-LTRDY 335
+G+ G ++ + + G AA +A+ + PL L E L +Y
Sbjct: 115 IGSWLGR----------RLRLSRNDRRILVACGAAAGIAAAFNAPLAGALFAIEVLLGEY 164
Query: 336 RI--LLPLMGAVGLAIWV 351
+ L+P++ A A V
Sbjct: 165 SVASLIPVLLASVAAALV 182
>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 = 252 bits (646), Expect = 6e-79
Identities = 130/319 (40%), Positives = 191/319 (59%), Gaps = 18/319 (5%)
Query: 33 IKAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFSLMMENNRERKIALVAAGAASGIASGF 92
+K + +TLG+G SLG EGPSV IG + +G ++ +R + L+AAGAA+GIA+ F
Sbjct: 42 VKFLGTLLTLGSGGSLGREGPSVQIGAAIGSGLGRRLKLSRNDRRRLIAAGAAAGIAAAF 101
Query: 93 NAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLLGTQSAFTVPSYDLK 152
NA +AG FA+E + R +++ASV+++ VS +L G + F VPS
Sbjct: 102 NAPLAGVLFALEELSRSFSYR-----ALLPVLVASVVAALVSRLLFGNEPLFEVPSLPPL 156
Query: 153 SAAELPLYLILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAGIIAL 212
S ELPL+++LG+LCG++ +F RL+ + F + LPP++ PALGGL G++ L
Sbjct: 157 SLLELPLFILLGILCGLLGALFVRLLLKVERLF---RRLKKLPPILRPALGGLLVGLLGL 213
Query: 213 RYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLM 272
P +L G+ ++ +L+ S + LL L K++ATAL GSG GG++APSL
Sbjct: 214 FLPEVLGGGYGLIQLLLN----GSTLSLLLLLLLLLLKLLATALSLGSGAPGGIFAPSLF 269
Query: 273 IGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELT 332
IGAA+G + G ++ PG P A+AL+GMAA LA V PLT+++L+FELT
Sbjct: 270 IGAALGRLLG----LLLPLLFPGI--APSPGAFALLGMAAFLAGVTRAPLTAIVLVFELT 323
Query: 333 RDYRILLPLMGAVGLAIWV 351
Y +LLPLM AV +A V
Sbjct: 324 GSYSLLLPLMLAVLIAYLV 342
Score = 53.7 bits (130), Expect = 1e-07
Identities = 46/155 (29%), Positives = 64/155 (41%), Gaps = 23/155 (14%)
Query: 202 LGGLGAGIIALRYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSG 261
+GGL AG++ R+P G V LH K + L K + T L GSG
Sbjct: 1 IGGLLAGLLVKRFPEAAGSGIPEVIAALHGVK----GPLPLRV--LLVKFLGTLLTLGSG 54
Query: 262 LVGGLYAPSLMIGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALV--GMAATLASVCS 319
G PS+ IGAA+G+ G ++ L+ G AA +A+ +
Sbjct: 55 GSLGREGPSVQIGAAIGSGLGRRL------------KLSRNDRRRLIAAGAAAGIAAAFN 102
Query: 320 VPLTSVLLLFELTRD---YRILLPLMGAVGLAIWV 351
PL VL E YR LLP++ A +A V
Sbjct: 103 APLAGVLFALEELSRSFSYRALLPVLVASVVAALV 137
>gnl|CDD|223116 COG0038, EriC, Chloride channel protein EriC [Inorganic ion
transport and metabolism].
Length = 443
Score = 204 bits (520), Expect = 2e-59
Identities = 111/323 (34%), Positives = 180/323 (55%), Gaps = 25/323 (7%)
Query: 33 IKAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFSLMMENNRERKIALVAAGAASGIASGF 92
+K + +T+G+G SLG EGPSV IG + + +++ +RE + L+AAGAA+G+A+ F
Sbjct: 115 VKLVATLLTIGSGASLGREGPSVQIGAAIGSLLGRLLKLSREDRRILLAAGAAAGLAAAF 174
Query: 93 NAAVAGCFFAIETVLRPLRAENSPPFTTAMI---ILASVISSTVSTVLLGTQSAFTVPSY 149
NA +AG FAIE + + ++A+V++ V+ + G + +
Sbjct: 175 NAPLAGALFAIEVLYGRF-------LEYRALVPVLVAAVVALLVAGLFGGPHFLLPIVTT 227
Query: 150 DLKSAAELPLYLILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAGI 209
S +L LYL+LG++ G+ V+ +RL+A + F + LPP++ PALGGL G
Sbjct: 228 PHMSLWDLLLYLVLGIIAGLFGVLLSRLLALSRRFFRRLP----LPPLLRPALGGLLVGA 283
Query: 210 IALRYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAP 269
+ L +P +L G+ ++ L + L K++AT L GSG GG++AP
Sbjct: 284 LGLLFPEVLGNGYGLIQLALAGEGGLLVLLL-----LFLLKLLATLLSYGSGAPGGIFAP 338
Query: 270 SLMIGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLF 329
SL IGAA+G FG ++ P + + EP +AL+GMAA LA+ PLT+++L+
Sbjct: 339 SLFIGAALGLAFG----ALLGLLFPPS--ILEPGLFALLGMAAFLAATTRAPLTAIVLVL 392
Query: 330 ELTRDYRILLPLMGAVGLAIWVP 352
E+T +Y++LLPL+ A +A V
Sbjct: 393 EMTGNYQLLLPLLIACLIAYLVS 415
>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 = 196 bits (500), Expect = 8e-57
Identities = 97/319 (30%), Positives = 157/319 (49%), Gaps = 21/319 (6%)
Query: 34 KAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFS-LMMENNRERKIALVAAGAASGIASGF 92
K + + LG+G SLG EGPSV IG + G S + ER+ L+AAGAA+G+A+ F
Sbjct: 89 KFVGGVLALGSGLSLGREGPSVQIGAAIGQGVSKWFKTSPEERRQ-LIAAGAAAGLAAAF 147
Query: 93 NAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLLGTQSAFTVPSYDLK 152
NA +AG F +E + + P ++AS+ + VS + G ++P
Sbjct: 148 NAPLAGVLFVLEELRH-----SFSPLALLTALVASIAADFVSRLFFGLGPVLSIPPLPAL 202
Query: 153 SAAELPLYLILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAGIIAL 212
L L+LG++ G++ +F R + + +K LP + L GL G + L
Sbjct: 203 PLKSYWLLLLLGIIAGLLGYLFNRSLLKSQDLYRKLK---KLPRELRVLLPGLLIGPLGL 259
Query: 213 RYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLM 272
P L G + + I LL + + + T L GSG GG++AP L
Sbjct: 260 LLPEALGGGHGLILSLAGGN-----FSISLLLLIFVLRFIFTMLSYGSGAPGGIFAPMLA 314
Query: 273 IGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELT 332
+GA +G +FG ++ G + ++ P +A+ GMAA A+V P+T+++L+ E+T
Sbjct: 315 LGALLGLLFGTILVQL------GPIPISAPATFAIAGMAAFFAAVVRAPITAIILVTEMT 368
Query: 333 RDYRILLPLMGAVGLAIWV 351
++ +LLPLM +A V
Sbjct: 369 GNFNLLLPLMVVCLVAYLV 387
Score = 42.5 bits (101), Expect = 5e-04
Identities = 54/200 (27%), Positives = 78/200 (39%), Gaps = 25/200 (12%)
Query: 164 GMLCGVVSVVFTRLV----AWFTKSFDFIKEKFGLP---PVVCPALGGLGAGIIALRYPG 216
G+L G+V+V+F + +DF L P++ LG L ++ P
Sbjct: 2 GLLAGLVAVLFRLGIDKLGNLRLSLYDFAANNPPLLLVLPLISAVLGLLAGWLVKKFAPE 61
Query: 217 ILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAA 276
G VE +L G P W ++ K V L GSGL G PS+ IGAA
Sbjct: 62 AKGSGIPQVEGVL-AGLL---PPNWW--RVLPVKFVGGVLALGSGLSLGREGPSVQIGAA 115
Query: 277 VGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFE-LTRDY 335
+G S +A G AA LA+ + PL VL + E L +
Sbjct: 116 IGQGVSKWFKT---SPEERRQLIA-------AGAAAGLAAAFNAPLAGVLFVLEELRHSF 165
Query: 336 RILLPLMGAVGLAIWVPSVA 355
L L+ A+ +I V+
Sbjct: 166 SPLA-LLTALVASIAADFVS 184
>gnl|CDD|239965 cd04592, CBS_pair_EriC_assoc_euk, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains in the EriC CIC-type chloride channels in
eukaryotes. 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 = 133
Score = 180 bits (458), Expect = 2e-54
Identities = 71/133 (53%), Positives = 97/133 (72%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGD 485
++KV+ T TLKEA+ M D +Q+CVLVV+ +DFLEGILT GDI+R L + + +
Sbjct: 1 TKYIKVSPTTTLKEALNLMLDEKQSCVLVVDSDDFLEGILTLGDIQRFLFTNKTTRVQPE 60
Query: 486 SIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSRE 545
NTCLVSS+CT+GISY G+E GL TC PDTDL AK+LMEAKG+KQLPV+KR +
Sbjct: 61 DETKQTNTCLVSSVCTKGISYGGQECGLWTCTPDTDLTTAKKLMEAKGVKQLPVVKRGVD 120
Query: 546 LQRRRKQRIVAIL 558
+RR +++++ +L
Sbjct: 121 RRRRGRRKVLGLL 133
>gnl|CDD|234987 PRK01862, PRK01862, putative voltage-gated ClC-type chloride
channel ClcB; Provisional.
Length = 574
Score = 187 bits (476), Expect = 5e-52
Identities = 109/312 (34%), Positives = 169/312 (54%), Gaps = 26/312 (8%)
Query: 34 KAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFSLMMENNRERKIALVAAGAASGIASGFN 93
++ + +T+G+G S+G EGP V + A+ + R LVA GAA+GI S +N
Sbjct: 121 RSASSLLTIGSGGSIGREGPMVQLAALAASLVGRFAHFDPPRLRLLVACGAAAGITSAYN 180
Query: 94 AAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLLGTQSAFTVPSYDLKS 153
A +AG FF E VL + E+ P +++ASV+++ V G Q + +P + +
Sbjct: 181 APIAGAFFVAEIVLGSIAMESFGP-----LVVASVVANIVMREFAGYQPPYEMPVFPAVT 235
Query: 154 AAELPLYLILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFG---LPPVVCPALGGLGAGII 210
E+ L++ LG+LCG F + D K +F +P V ALGGL G+I
Sbjct: 236 GWEVLLFVALGVLCGA-------AAPQFLRLLDASKNQFKRLPVPLPVRLALGGLLVGVI 288
Query: 211 ALRYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPS 270
++ P + G++ V ILH T A L+ AK++ATA GSG VGG++ P+
Sbjct: 289 SVWVPEVWGNGYSVVNTILHAPWTWQALVAVLV-----AKLIATAATAGSGAVGGVFTPT 343
Query: 271 LMIGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFE 330
L +GA VG++FG + ++ PG + P AYA+VGM A LA PL ++L++FE
Sbjct: 344 LFVGAVVGSLFGLAM----HALWPG--HTSAPFAYAMVGMGAFLAGATQAPLMAILMIFE 397
Query: 331 LTRDYRILLPLM 342
+T Y+++LPLM
Sbjct: 398 MTLSYQVVLPLM 409
>gnl|CDD|235385 PRK05277, PRK05277, chloride channel protein; Provisional.
Length = 438
Score = 163 bits (416), Expect = 1e-44
Identities = 95/313 (30%), Positives = 153/313 (48%), Gaps = 19/313 (6%)
Query: 41 TLGTGCSLGPEGPSVDIGKSCANGF-SLMMENNRERKIALVAAGAASGIASGFNAAVAGC 99
TLG+G LG EGP+V +G + + + E + L+AAGAA+G+A+ FNA +AG
Sbjct: 103 TLGSGMVLGREGPTVQMGGNIGRMVLDIFRLRSDEARHTLLAAGAAAGLAAAFNAPLAGI 162
Query: 100 FFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLLGTQSAFTVPSYDLKSAAELPL 159
F IE +RP + + + ++++ V + G Q+ V + L L
Sbjct: 163 LFVIEE-MRPQFRYSLISIK--AVFIGVIMATIVFRLFNGEQAVIEVGKFSAPPLNTLWL 219
Query: 160 YLILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAGIIALRYPGILY 219
+L+LG++ G+ V+F +L+ FD + V+ G G++ L P +
Sbjct: 220 FLLLGIIFGIFGVLFNKLLLRTQDLFDRLHGGNKKRWVLMGGAVGGLCGLLGLLAPAAVG 279
Query: 220 WGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVGA 279
GF + L A I +L + A+ + T LC GSG GG++AP L +G +G
Sbjct: 280 GGFNLIPIAL-----AGNFSIGMLLFIFVARFITTLLCFGSGAPGGIFAPMLALGTLLGL 334
Query: 280 VFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELTRDYRILL 339
FG AA + EP +A+ GM A A+ PLT ++L+ E+T +Y+++L
Sbjct: 335 AFGMVAAALFPQYHI------EPGTFAIAGMGALFAATVRAPLTGIVLVLEMTDNYQLIL 388
Query: 340 PLM----GAVGLA 348
PL+ GA LA
Sbjct: 389 PLIITCLGATLLA 401
>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 = 140 bits (354), Expect = 2e-36
Identities = 100/320 (31%), Positives = 157/320 (49%), Gaps = 27/320 (8%)
Query: 40 VTLGTGCSLGPEGPSVDIGKSCANGFS-LMMENNRERKIALVAAGAASGIASGFNAAVAG 98
VT+G G LG E ++G A FS + +R++ LVA A +G+A+ +N +AG
Sbjct: 94 VTVGLGAPLGREVAPREVGALLAQRFSDWLGLTVADRRL-LVACAAGAGLAAVYNVPLAG 152
Query: 99 CFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLLGTQSAFTVPSYDLKSAAELP 158
FA+E +LR + + + S I++ V+++L G + +P L S L
Sbjct: 153 ALFALEILLRTISLRS-----VVAALATSAIAAAVASLLKGDHPIYDIPPMQL-STPLLI 206
Query: 159 LYLILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAGIIALRYPGIL 218
L+ G + GVV+ F RL + + + L L G++++ +P IL
Sbjct: 207 WALLAGPVLGVVAAGFRRLSQAARAK---RPKGKRILWQM--PLAFLVIGLLSIFFPQIL 261
Query: 219 YWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVG 278
G + T T S LL L K+VAT L +G GGL PSL +GA +G
Sbjct: 262 GNGRALAQLAFSTTLTLS-----LLLILLVLKIVATLLALRAGAYGGLLTPSLALGALLG 316
Query: 279 AVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELTR-DYRI 337
A+ G + N+ +P +++A A+AL+G AA LA+ PLT+++L+ E TR +
Sbjct: 317 ALLGI----VWNALLP-PLSIA---AFALIGAAAFLAATQKAPLTALILVLEFTRQNPLF 368
Query: 338 LLPLMGAVGLAIWVPSVANQ 357
L+PLM AV A+ V Q
Sbjct: 369 LIPLMLAVAGAVAVSRFILQ 388
>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 = 130 bits (330), Expect = 3e-33
Identities = 91/314 (28%), Positives = 140/314 (44%), Gaps = 35/314 (11%)
Query: 45 GCSLGPEGPSVDIGKSCANGFSLMMENNRERKIA-LVAAGAASGIASGFNAAVAGCFFAI 103
G S+G EGPSV IG + + L+ AG A+G+A+ FN +AG FAI
Sbjct: 94 GASVGREGPSVQIGAAVMLAIGRRLPKWGGLSERGLILAGGAAGLAAAFNTPLAGIVFAI 153
Query: 104 ETVLRPLRAENSPPFTTAMIILASVISSTVSTV-LLGTQSAFTVPSYDLKSAAELPLYLI 162
E + R + ++L +VI++ + ++ +LG F V + L L L+
Sbjct: 154 EELSR------DFELRFSGLVLLAVIAAGLVSLAVLGNYPYFGVAAVALPLGEAWLLVLV 207
Query: 163 LGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLP----PVVCPALGGLGAGIIALRYPGIL 218
G++ G+ +F RL+ + + PV+ AL GL +I L G+
Sbjct: 208 CGVVGGLAGGLFARLLVALSS---GLPGWVRRFRRRRPVLFAALCGLALALIGLVSGGLT 264
Query: 219 YW-GFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAV 277
+ G+ L G K +AT L SG+ GGL+APSL +GA +
Sbjct: 265 FGTGYLQARAALEGGGGLPL-------WFGLLKFLATLLSYWSGIPGGLFAPSLAVGAGL 317
Query: 278 GAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELTRDYRI 337
G++ A L+GMAA LA V PLT+ +++ E+T D ++
Sbjct: 318 GSLLAALLGS------------VSQGALVLLGMAAFLAGVTQAPLTAFVIVMEMTGDQQM 365
Query: 338 LLPLMGAVGLAIWV 351
LLPL+ A LA V
Sbjct: 366 LLPLLAAALLASGV 379
Score = 29.5 bits (67), Expect = 5.6
Identities = 32/106 (30%), Positives = 46/106 (43%), Gaps = 12/106 (11%)
Query: 246 LAAAKVVATALCKGSGLVGGLYAPSLMIGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAY 305
A K++ T L G G PS+ IGAAV G P ++E
Sbjct: 79 TAVGKILLTLLGLLGGASVGREGPSVQIGAAVMLAIGRRL--------PKWGGLSERG-L 129
Query: 306 ALVGMAATLASVCSVPLTSVLL-LFELTRDY--RILLPLMGAVGLA 348
L G AA LA+ + PL ++ + EL+RD+ R ++ AV A
Sbjct: 130 ILAGGAAGLAAAFNTPLAGIVFAIEELSRDFELRFSGLVLLAVIAA 175
>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 (291), Expect = 1e-27
Identities = 87/355 (24%), Positives = 142/355 (40%), Gaps = 48/355 (13%)
Query: 33 IKAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFSLMM---ENNRERKIALVAAGAASGIA 89
IK++ + + +G SLG EGP V I N S + N ++ +++A AA+G+A
Sbjct: 81 IKSVGLVLAVASGLSLGKEGPLVHIATCVGNIISRLFPKYRRNEAKRREILSAAAAAGVA 140
Query: 90 SGFNAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLL------GTQSA 143
F A + G F++E V S F + S + V+ L GT
Sbjct: 141 VAFGAPIGGVLFSLEEV--------SYYFPLKT-LWRSFFCALVAAFTLKSLNPFGTGRL 191
Query: 144 --FTVPSYDLK-SAAELPLYLILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCP 200
F V YD EL +++LG+ G+ F + + + K PV+
Sbjct: 192 VLFEV-EYDRDWHYFELIPFILLGIFGGLYGAFFIKANIKWARFRKKSLLKRY--PVLEV 248
Query: 201 ALGGLGAGIIALRYPGI-------LYWGFT-----NVEEILHTGKTASAPGIW-LLTQLA 247
L L +I+ P L F + + + G++ L L
Sbjct: 249 LLVALITALISFPNPYTRLDMTELLELLFNECEPGDDNSLCCYRDPPAGDGVYKALWSLL 308
Query: 248 AAKVVATALCK---GSGLVGGLYAPSLMIGAAVGAVFG--------GSAAEIINSAIPGN 296
A ++ L G + G++ PS+ +GA G + G I +
Sbjct: 309 LALIIKLLLTIFTFGIKVPAGIFVPSMAVGALFGRIVGILVEQLAYSYPDSIFFACCTAG 368
Query: 297 VAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELTRDYRILLPLMGAVGLAIWV 351
+ P YA+VG AA L V + ++ V+++FELT +LPLM AV ++ WV
Sbjct: 369 PSCITPGLYAMVGAAAFLGGVTRMTVSLVVIMFELTGALNYILPLMIAVMVSKWV 423
>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 = 108 bits (273), Expect = 2e-25
Identities = 87/339 (25%), Positives = 137/339 (40%), Gaps = 55/339 (16%)
Query: 34 KAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFSLMM------ENNRERKIALVAAGAASG 87
K I LG+G LG EGP V I A S + N R++ ++AA A G
Sbjct: 99 KVIGLTCALGSGLPLGKEGPFVHISSIVAALLSKLTTFFSGIYENESRRMEMLAAACAVG 158
Query: 88 IASGFNAAVAGCFFAIETVLRPLRAENS-PPFTTAMI------ILASVISSTVSTVLLGT 140
+A F A + G F+IE N F A +LA S + L
Sbjct: 159 VACTFGAPIGGVLFSIEVTSTYFAVRNYWRGFFAATCGAFTFRLLAVFFSDQETITALFK 218
Query: 141 QSAFTVPSYDLKSAAELPLYLILGMLCGVVSVVFTRLVAW---FTKSFDFIKEKFGLPPV 197
+ F +D++ ELP++ +LG++CG++ +F L F + + P+
Sbjct: 219 TTFFVDFPFDVQ---ELPIFALLGIICGLLGALFVFLHRKIVRFRRKNRLFSKFLKRSPL 275
Query: 198 VCPALGGLGAGIIALRYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALC 257
+ PA+ L ++ +P L K V TAL
Sbjct: 276 LYPAIVALLTAVL--TFP------------------------FLTLFLFIVVKFVLTALA 309
Query: 258 KGSGLVGGLYAPSLMIGAAVGAVFGGSAAEIINSAIP-----GNVAVAEPQAYALVGMAA 312
+ G++ P +IGAA+G + G EI+ P G P YA+VG AA
Sbjct: 310 ITLPVPAGIFMPVFVIGAALGRLVG----EIMAVLFPEGIRGGISNPIGPGGYAVVGAAA 365
Query: 313 TLASVCSVPLTSVLLLFELTRDYRILLPLMGAVGLAIWV 351
+V + ++ +++FELT LLP++ AV ++ V
Sbjct: 366 FSGAV-THTVSVAVIIFELTGQISHLLPVLIAVLISNAV 403
>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 = 105 bits (265), Expect = 1e-24
Identities = 92/352 (26%), Positives = 138/352 (39%), Gaps = 68/352 (19%)
Query: 33 IKAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFS--------------LMMENNRERKIA 78
K I + +G LG EGP V +G G + N R+R+
Sbjct: 90 AKTISCICAVASGLPLGKEGPLVHLGAMIGAGLLQGRSRTLGCHVHLFQLFRNPRDRR-D 148
Query: 79 LVAAGAASGIASGFNAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLL 138
+ AGAA+G+AS F A + G F +E V + + A+++S+ V +
Sbjct: 149 FLVAGAAAGVASAFGAPIGGLLFVLEEVSTFFPVRLA-----WRVFFAALVSAFVIQIYN 203
Query: 139 GTQSAFTVP-------SYDLKSAAELPLYL-------ILGMLCGVVSVVFTRLVAWFTK- 183
S F + +PL L ++G++CG+++ +F RL F +
Sbjct: 204 SFNSGFELLDRSSAMFLSLTVFELHVPLNLYEFIPTVVIGVICGLLAALFVRLSIIFLRW 263
Query: 184 --SFDFIKEKFGLPPVVCPALGGLGAGIIALRYPGILYWGFTNVEEILHTGKTASAPGIW 241
F K V+ P L L Y I Y
Sbjct: 264 RRRLLFRKTAR--YRVLEPVL-------FTLIYSTIHYAPT------------------- 295
Query: 242 LLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVGAVFGGSAAEIINSAIPGNVAV-- 299
LL L +AL G + GG + PSL+IGAA+G + G I + I A
Sbjct: 296 LLLFLLI-YFWMSALAFGIAVPGGTFIPSLVIGAAIGRLVGLLVHRIAVAGIGAESATLW 354
Query: 300 AEPQAYALVGMAATLASVCSVPLTSVLLLFELTRDYRILLPLMGAVGLAIWV 351
A+P YAL+G AA L + + +++ ELT D LLPLM A+ +A V
Sbjct: 355 ADPGVYALIGAAAFLGGTTRLTFSICVIMMELTGDLHHLLPLMVAILIAKAV 406
>gnl|CDD|234963 PRK01610, PRK01610, putative voltage-gated ClC-type chloride
channel ClcB; Provisional.
Length = 418
Score = 97.9 bits (244), Expect = 7e-22
Identities = 83/327 (25%), Positives = 160/327 (48%), Gaps = 25/327 (7%)
Query: 23 FDLVAGVFPTIKAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFSLMMENNRERKIALVAA 82
FD A + +K++ + + + +G ++G EG + + A+ F+ +E K+ +A
Sbjct: 95 FDYAASL---VKSLASLLVVTSGSAIGREGAMILLAALAASCFAQRFTPRQEWKL-WIAC 150
Query: 83 GAASGIASGFNAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLLGTQS 142
GAA+G+AS ++A +AG F E + L + P +++++V++ + +L G+ +
Sbjct: 151 GAAAGMASAYHAPLAGSLFIAEILFGTLMLASLGP-----VVISAVVALLTTNLLNGSDA 205
Query: 143 A-FTVPSYDLKSAAELPLYLILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCPA 201
+ V A + L + G+L G+ + L+ + F +K L P A
Sbjct: 206 LLYNVQLSVTVQARDYALIISTGLLAGLCGPLLLTLMNASHRGFVSLK----LAPPWQLA 261
Query: 202 LGGLGAGIIALRYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSG 261
LGGL G+++L P + G++ V+ L + P + L+ + K++A GSG
Sbjct: 262 LGGLIVGLLSLFTPAVWGNGYSVVQSFL-----TAPPLLMLIAGIFLCKLLAVLASSGSG 316
Query: 262 LVGGLYAPSLMIGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVP 321
GG++ P+L +G A+G ++G + +P + L GMA LA+ P
Sbjct: 317 APGGVFTPTLFVGLAIGMLYG----RSLGLWLPDGEEIT--LLLGLTGMATLLAATTHAP 370
Query: 322 LTSVLLLFELTRDYRILLPLMGAVGLA 348
+ S L++ E+T +Y++L L+ A +A
Sbjct: 371 IMSTLMICEMTGEYQLLPGLLIACVIA 397
>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 = 80.4 bits (199), Expect = 5e-16
Identities = 82/348 (23%), Positives = 139/348 (39%), Gaps = 69/348 (19%)
Query: 33 IKAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFS--------------LMMENNRERKIA 78
+K + +++ G +LG EGP + IG A G S N+R+++
Sbjct: 131 VKIVGVILSVSGGLALGKEGPMIHIGACIAAGLSQGGSTSLRLDFRWFRYFRNDRDKR-D 189
Query: 79 LVAAGAASGIASGFNAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLL 138
V GAA+G+A+ F A V G F++E V T +S+I + L
Sbjct: 190 FVTCGAAAGVAAAFGAPVGGVLFSLEEVASFWNQ-----ALTWRTFFSSMIVTFTLNFFL 244
Query: 139 -------------GTQSAFTVPS-YDLKSAAELPLYLILGMLCGVVSVVFTRLVAWFTKS 184
G F S L + EL ++++G++ G++ +F L T+
Sbjct: 245 SGCNSGKCGLFGPGGLIMFDGSSTKYLYTYFELIPFMLIGVIGGLLGALFNHLNHKVTR- 303
Query: 185 FDFIKEKFGLPPVVCPALGGLGAGIIA-LRYPGILYWGFTNVEEILHTGKTASAPGIWLL 243
F K ++ L + + + + +P L F + L W
Sbjct: 304 --FRKRINHKGKLLKVLEALLVSLVTSVVAFPQTL-LIFFVLYYFL---------ACW-- 349
Query: 244 TQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVGAVFGGSAAEIINSAIPGNVAVAEPQ 303
T G + GL+ P ++IGAA G + G I+ + G + +P
Sbjct: 350 ----------TF---GIAVPSGLFIPMILIGAAYGRLVG-----ILLGSYFGFTS-IDPG 390
Query: 304 AYALVGMAATLASVCSVPLTSVLLLFELTRDYRILLPLMGAVGLAIWV 351
YAL+G AA L V + ++ ++L ELT + L P+M + +A WV
Sbjct: 391 LYALLGAAAFLGGVMRMTVSLTVILLELTNNLTYLPPIMLVLMIAKWV 438
Score = 29.2 bits (66), Expect = 8.2
Identities = 15/46 (32%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 237 APGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVGAVFG 282
P I L L K+V L GL G P + IGA + A
Sbjct: 120 IPHILRLKTLLV-KIVGVILSVSGGLALGKEGPMIHIGACIAAGLS 164
>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 = 74.2 bits (183), Expect = 4e-14
Identities = 83/308 (26%), Positives = 129/308 (41%), Gaps = 53/308 (17%)
Query: 40 VTLGT------GCSLGPEGPSVDIGKSCANGFS-LMMENNRERKIALVAAGAASGIASGF 92
V GT G S G EG +V +G S A+ F + +R+I L+A G A+G A+ F
Sbjct: 81 VLFGTVLTHLFGGSAGREGTAVQMGGSLADAFGRVFKLPEEDRRILLIA-GIAAGFAAVF 139
Query: 93 NAAVAGCFFAIE-TVLRPLRAENSPPFTTAMI--ILASVISSTVSTVLLGTQSAFTVPSY 149
+AG FA+E VL LR A+I ++A++++ VS LG + +
Sbjct: 140 GTPLAGAIFALEVLVLGRLRYS-------ALIPCLVAAIVADWVSH-ALGLEHTHYHIVF 191
Query: 150 DLKSAAELPLYLILGMLC-GVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAG 208
L + +IL + G+ +F L+ + K +K P + P +GGL
Sbjct: 192 IPTLDPLLFVKVILAGIIFGLAGRLFAELLHFLKKLL----KKRIKNPYLRPFVGGLLII 247
Query: 209 IIAL-----RYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLV 263
++ RY G+ G T + E G T P WLL K++ T + G+G
Sbjct: 248 LLVYLLGSRRYLGL---G-TPLIEDSFFGGTVY-PYDWLL------KLIFTVITLGAGFK 296
Query: 264 GGLYAPSLMIGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLT 323
GG P IGA +G I+ + A +G A A + PL
Sbjct: 297 GGEVTPLFFIGATLGNALAP----ILGLPVS---------LLAALGFVAVFAGATNTPLA 343
Query: 324 SVLLLFEL 331
+++ EL
Sbjct: 344 CIIMGIEL 351
>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 = 63.6 bits (155), Expect = 2e-12
Identities = 35/121 (28%), Positives = 54/121 (44%), Gaps = 20/121 (16%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGD 485
+D V V+ T+ EA+ M + + + VV+ + L GI+T D+ R L++ D
Sbjct: 1 RDVVTVSPDDTVAEALRLMLEHGISGLPVVDDDGRLVGIVTERDLLRALAEGGLDPLVT- 59
Query: 486 SIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSRE 545
V + T R ++T PDT L A ELM GI++LPV+
Sbjct: 60 ----------VGDVMT---------RDVVTVSPDTSLEEAAELMLEHGIRRLPVVDDEGR 100
Query: 546 L 546
L
Sbjct: 101 L 101
Score = 44.7 bits (106), Expect = 9e-06
Identities = 22/61 (36%), Positives = 32/61 (52%)
Query: 410 AEEMLLEELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGD 469
AE L + V M++D V V+ +L+EA E M + + VV+ E L GI+T D
Sbjct: 50 AEGGLDPLVTVGDVMTRDVVTVSPDTSLEEAAELMLEHGIRRLPVVDDEGRLVGIVTRSD 109
Query: 470 I 470
I
Sbjct: 110 I 110
>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 = 56.4 bits (137), Expect = 6e-10
Identities = 27/135 (20%), Positives = 50/135 (37%), Gaps = 29/135 (21%)
Query: 429 VKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIA 488
+ V+ ++ +A+ + VLVV+ L G +T GDI+R L KG S+
Sbjct: 5 LLVSPDASILDALRKIDKNALRIVLVVDENGRLLGTVTDGDIRRAL-------LKGLSLD 57
Query: 489 SDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSRELQR 548
V+ + + +T + LM + I+ LP++
Sbjct: 58 DPVSEVMNRNP--------------ITAKVGSSREEILALMRERSIRHLPILDEEG---- 99
Query: 549 RRKQRIVAILHYDSI 563
R+V + D +
Sbjct: 100 ----RVVGLATLDDL 110
Score = 29.4 bits (67), Expect = 1.7
Identities = 9/54 (16%), Positives = 27/54 (50%)
Query: 417 ELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 470
+ VS M+++ + + + +E + M++ + +++ E + G+ T D+
Sbjct: 57 DDPVSEVMNRNPITAKVGSSREEILALMRERSIRHLPILDEEGRVVGLATLDDL 110
>gnl|CDD|239977 cd04604, CBS_pair_KpsF_GutQ_assoc, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains associated with KpsF/GutQ domains in the API
[A5P (D-arabinose 5-phosphate) isomerase] protein.
These APIs catalyze the conversion of the pentose
pathway intermediate D-ribulose 5-phosphate into A5P, a
precursor of 3-deoxy-D-manno-octulosonate, which is an
integral carbohydrate component of various glycolipids
coating the surface of the outer membrane of
Gram-negative bacteria, including lipopolysaccharide and
many group 2 K-antigen capsules. 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 = 56.3 bits (137), Expect = 7e-10
Identities = 38/130 (29%), Positives = 52/130 (40%), Gaps = 28/130 (21%)
Query: 430 KVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIAS 489
V+ +LK+A+ M VV+ + L GI T GD++R L K
Sbjct: 6 LVSPDTSLKDALLEMSRKGLGMTAVVDEDGRLVGIFTDGDLRRALEKG-----------L 54
Query: 490 DVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSRELQRR 549
D+ T V+ + TR + T PD A A ELME I LPV+
Sbjct: 55 DILTLPVADVMTRN----PK-----TIDPDALAAEALELMEENKITALPVVD-------- 97
Query: 550 RKQRIVAILH 559
R V +LH
Sbjct: 98 DNGRPVGVLH 107
>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 = 56.0 bits (136), Expect = 9e-10
Identities = 27/116 (23%), Positives = 46/116 (39%), Gaps = 20/116 (17%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGD 485
+D V + L E ++ + +N VV+ + L GI++ DI+ L S
Sbjct: 1 RDVVTIPEDTPLNELLDVIAHSPENNFPVVDDDGRLVGIVSLDDIREILFDPSLY---DL 57
Query: 486 SIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIK 541
+ASD+ T + + YP+ L A + E +QLPV+
Sbjct: 58 VVASDIMT-----------------KPPVVVYPEDSLEDALKKFEDSDYEQLPVVD 96
>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 = 55.6 bits (135), Expect = 1e-09
Identities = 33/123 (26%), Positives = 53/123 (43%), Gaps = 24/123 (19%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNC-VLVVNGEDFLEGILTYGDIK-RCLSKLSSDNSK 483
+D V V+ T++EA M++ + L V D L GI+T DI R +++
Sbjct: 1 RDVVTVSPDDTIREAARLMRE--HDVGALPVCENDRLVGIVTDRDIVVRAVAE------- 51
Query: 484 GDSIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRS 543
D +T V + TRG ++T D D+ A LM +++LPV+
Sbjct: 52 ----GRDPDTTTVGDVMTRG---------VVTVTEDDDVDEAARLMREHQVRRLPVVDDD 98
Query: 544 REL 546
L
Sbjct: 99 GRL 101
Score = 36.7 bits (86), Expect = 0.006
Identities = 17/61 (27%), Positives = 29/61 (47%)
Query: 410 AEEMLLEELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGD 469
AE + V M++ V V + EA M++ Q + VV+ + L GI++ GD
Sbjct: 50 AEGRDPDTTTVGDVMTRGVVTVTEDDDVDEAARLMREHQVRRLPVVDDDGRLVGIVSLGD 109
Query: 470 I 470
+
Sbjct: 110 L 110
>gnl|CDD|223591 COG0517, COG0517, FOG: CBS domain [General function prediction
only].
Length = 117
Score = 54.0 bits (130), Expect = 5e-09
Identities = 37/145 (25%), Positives = 62/145 (42%), Gaps = 30/145 (20%)
Query: 420 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSS 479
V M+KD + V ++++A+ M + + V VV+ L GI+T DI R L++
Sbjct: 1 VKDIMTKDVITVKPDTSVRDALLLMSENGVSAVPVVDDGK-LVGIITERDILR---ALAA 56
Query: 480 DNSKGDSIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELM-EAKGIKQLP 538
+ + +V T + ++T PDT L A ELM E I++LP
Sbjct: 57 GGKRLLPV-KEVMT-----------------KPVVTVDPDTPLEEALELMVERHKIRRLP 98
Query: 539 VIKRSRELQRRRKQRIVAILHYDSI 563
V+ ++V I+ I
Sbjct: 99 VVDDDGG-------KLVGIITLSDI 116
Score = 36.3 bits (84), Expect = 0.008
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 416 EELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQ-NCVLVVNGEDF-LEGILTYGDI 470
L V M+K V V L+EA+E M + + + VV+ + L GI+T DI
Sbjct: 60 RLLPVKEVMTKPVVTVDPDTPLEEALELMVERHKIRRLPVVDDDGGKLVGIITLSDI 116
>gnl|CDD|239998 cd04626, CBS_pair_13, 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 = 52.8 bits (127), Expect = 1e-08
Identities = 25/119 (21%), Positives = 51/119 (42%), Gaps = 21/119 (17%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGD 485
DF + +++EA+ M N ++V + E+ L+G++T+ DI L S +
Sbjct: 1 TDFPTIDEDASIREALHEMLKYNTNEIIVKDNEEKLKGVVTFTDI----LDLDLFESFLE 56
Query: 486 SIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSR 544
V +I ++ + Y + + A ++M K I +LPV+ ++
Sbjct: 57 K--------KVFNIVSQDVFYVN---------EEDTIDEALDIMREKQIGRLPVVDDNK 98
>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 = 49.5 bits (119), Expect = 5e-08
Identities = 19/57 (33%), Positives = 32/57 (56%)
Query: 420 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSK 476
V M+ D V V +L+EA+E M++ + + VV+ + L GI+T D+ R L +
Sbjct: 1 VKDIMTPDVVTVPPDTSLEEALELMRENGISRLPVVDEDGKLVGIVTLRDLLRALLE 57
Score = 32.1 bits (74), Expect = 0.065
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 511 RGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSREL 546
++T PDT L A ELM GI +LPV+ +L
Sbjct: 7 PDVVTVPPDTSLEEALELMRENGISRLPVVDEDGKL 42
>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 = 49.9 bits (120), Expect = 1e-07
Identities = 33/132 (25%), Positives = 56/132 (42%), Gaps = 30/132 (22%)
Query: 428 FVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI-KRCLSKLSSDNSKGDS 486
V+ T T++EA + M++ + +CVLV++G L GI T DI R +++
Sbjct: 3 PATVSPTTTVQEAAKLMREKRVSCVLVMDGNK-LVGIFTSKDIALRVVAQ---------- 51
Query: 487 IASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSREL 546
D + LV + T + DT + A LM + LPV+ +S +
Sbjct: 52 -GLDPESTLVERVMTPNP---------VCATSDTPVLEALHLMVQGKFRHLPVVDKSGQ- 100
Query: 547 QRRRKQRIVAIL 558
+V +L
Sbjct: 101 -------VVGLL 105
>gnl|CDD|239978 cd04605, CBS_pair_MET2_assoc, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains
associated with the MET2 domain. Met2 is a key enzyme in
the biosynthesis of methionine. It encodes a homoserine
transacetylase involved in converting homoserine to
O-acetyl homoserine. CBS is a small domain originally
identified in cystathionine beta-synthase and
subsequently found in a wide range of different
proteins. CBS domains usually come in tandem repeats,
which associate to form a so-called Bateman domain or a
CBS pair which is reflected in this model. The interface
between the two CBS domains forms a cleft that is a
potential ligand binding site. The CBS pair coexists
with a variety of other functional domains. It has been
proposed that the CBS domain may play a regulatory role,
although its exact function is unknown.
Length = 110
Score = 49.6 bits (119), Expect = 1e-07
Identities = 34/139 (24%), Positives = 59/139 (42%), Gaps = 32/139 (23%)
Query: 425 SKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKG 484
S+ V ++ ++KEA + M + N + VV+ + L GI+T DI +
Sbjct: 1 SRPVVTISEDASIKEAAKLMIEENINHLPVVDEDGRLVGIVTSWDISK------------ 48
Query: 485 DSIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSR 544
++A D + V I TR + +T PD + +A ME I LPV+
Sbjct: 49 -AVARDKKS--VEDIMTRNV---------ITATPDEPIDVAARKMERHNISALPVVD--- 93
Query: 545 ELQRRRKQRIVAILHYDSI 563
+ R++ I+ + I
Sbjct: 94 -----AENRVIGIITSEDI 107
>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 = 49.0 bits (118), Expect = 3e-07
Identities = 30/112 (26%), Positives = 46/112 (41%), Gaps = 19/112 (16%)
Query: 429 VKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIA 488
+ V T+ EA + M + V+VV+ L GI + DI R ++ +G S
Sbjct: 4 ITVRPDATVAEAAKLMAEKNIGAVVVVDDGGRLVGIFSERDIVRKVAL------RGASAL 57
Query: 489 SDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVI 540
VS I T R ++T PD + A LM + + LPV+
Sbjct: 58 DTP----VSEIMT---------RNVITVTPDDTVDEAMALMTERRFRHLPVV 96
>gnl|CDD|239966 cd04593, CBS_pair_EriC_assoc_bac_arch, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains in the EriC CIC-type chloride channels in
bacteria and archaea. 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 = 115
Score = 45.8 bits (109), Expect = 4e-06
Identities = 33/114 (28%), Positives = 54/114 (47%), Gaps = 20/114 (17%)
Query: 430 KVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIAS 489
++ T L+EA E + + + LVV+ + + GI+T D+ R L +D + S
Sbjct: 5 VLSATTPLREAAEQLIESKHGSALVVDRDGGVVGIITLPDLLRALE---ADEAGEPSAVD 61
Query: 490 DVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRS 543
+V T LLT +PD LA A + M ++G++QLPV+ R
Sbjct: 62 EVAT-----------------PPLLTVHPDEPLAHALDRMASRGLRQLPVVDRG 98
>gnl|CDD|240008 cd04637, CBS_pair_24, 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 = 44.6 bits (106), Expect = 1e-05
Identities = 16/72 (22%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 401 VENAADSEAAEEMLLEELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDF 460
+ A ++E L + + M++D + V+ + EA + + + +C+ VV+
Sbjct: 52 LGTAGETEKDLATLNR--RAHQIMTRDPITVSPDTPVDEASKLLLENSISCLPVVDENGQ 109
Query: 461 LEGILTYGDIKR 472
L GI+T+ D+ +
Sbjct: 110 LIGIITWKDLLK 121
Score = 31.2 bits (71), Expect = 0.57
Identities = 28/117 (23%), Positives = 50/117 (42%), Gaps = 15/117 (12%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGD 485
V V + L+E E + + + +LVV ++ L G+++ D + +S + G+
Sbjct: 1 TRVVTVEMDDRLEEVREIFEKHKFHHLLVVE-DNELVGVISDRDYLKAIS--PFLGTAGE 57
Query: 486 SIASDVNTCL--VSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVI 540
+ D+ T I TR +T PDT + A +L+ I LPV+
Sbjct: 58 T-EKDLATLNRRAHQIMTRD---------PITVSPDTPVDEASKLLLENSISCLPVV 104
>gnl|CDD|239959 cd04586, CBS_pair_BON_assoc, This cd contains two tandem repeats of
the cystathionine beta-synthase (CBS pair) domains
associated with the BON (bacterial OsmY and nodulation
domain) domain. BON is a putative phospholipid-binding
domain found in a family of osmotic shock protection
proteins. It is also found in some secretins and a group
of potential haemolysins. Its likely function is
attachment to phospholipid membranes. 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 = 135
Score = 43.3 bits (103), Expect = 4e-05
Identities = 34/138 (24%), Positives = 62/138 (44%), Gaps = 15/138 (10%)
Query: 425 SKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGD-IKRCLSKLSSDNSK 483
+ D V V+ ++ EA M D + + VV+ + L GI++ GD ++R ++
Sbjct: 1 TTDVVTVSPETSVAEAARLMLDNHISGLPVVDDDGRLVGIVSEGDLLRRAELGTERRRAR 60
Query: 484 GDSIASDVNTCLVSSICTRGISYRGRE---RGLLTCYPDTDLAIAKELMEAKGIKQLPVI 540
+ + + + + G + + R ++T DT LA ELME IK++PV+
Sbjct: 61 WLDLLAGAEELAAAFVRSHGR--KVADVMTRPVVTVGEDTPLAEVAELMEEHRIKRVPVV 118
Query: 541 KRSRELQRRRKQRIVAIL 558
R R+V I+
Sbjct: 119 ---------RGGRLVGIV 127
>gnl|CDD|235148 PRK03655, PRK03655, putative ion channel protein; Provisional.
Length = 414
Score = 45.5 bits (108), Expect = 5e-05
Identities = 82/327 (25%), Positives = 131/327 (40%), Gaps = 58/327 (17%)
Query: 42 LGTGCSLGPEGP--SVDIGKSCANGFSLMMENNRERKIALVAAGAASGIASGFNAAVAGC 99
L G SLGPE P +V+I + A G L+ NR L +AG I + F VA
Sbjct: 111 LAGGVSLGPEHPIMTVNIALAVAIGARLLPRVNRMDWTILASAGT---IGALFGTPVAAA 167
Query: 100 FFAIETVLRPLRAENSPPFTTAMI--ILASVISSTVSTVLLGTQSAFTVPSY------DL 151
+T L N P + ++A+ + + + + + Y D+
Sbjct: 168 LIFSQT----LNGSNEVPLWDRLFAPLMAAAAGALTTGLFFHPHFSLPIAHYGQMEMTDI 223
Query: 152 KSAAELPLYLILGMLCGVVSV-VFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAGII 210
S A + + + G+V+V RL A + +K PV+ +GG GI+
Sbjct: 224 LSGAIVAA---IAIAAGMVAVWCLPRLHALMHR----LKN-----PVLVLGIGGFILGIL 271
Query: 211 -ALRYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAP 269
+ P L+ G +++ + + SA +LL + A +V A G GG P
Sbjct: 272 GVIGGPLTLFKGLDEMQQ-MAANQAFSASDYFLLAVVKLAALVVAAAS---GFRGGRIFP 327
Query: 270 SLMIGAAVGA-----VFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTS 324
++ +G A+G V AA ++ AI G V V + + MAA + VP T+
Sbjct: 328 AVFVGVALGLMLHAHVPAVPAAITVSCAILGIVLVVTRDGWLSLFMAAVV-----VPDTT 382
Query: 325 VLLLFELTRDYRILLPLMGAVGLAIWV 351
LLPL+ V L W+
Sbjct: 383 -------------LLPLLCIVMLPAWL 396
>gnl|CDD|240115 cd04802, CBS_pair_3, 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 = 42.4 bits (100), Expect = 6e-05
Identities = 33/116 (28%), Positives = 50/116 (43%), Gaps = 20/116 (17%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGD 485
K+ + V T+ EA M + ++VV+ E GI+T D+ + K+ S N K
Sbjct: 1 KNVITVDPDTTVYEAANIMTENNIGRLIVVDNEK-PVGIITERDL---VKKVVSRNLK-- 54
Query: 486 SIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIK 541
+V V S L+T P+ L A +LM GIK+LPV+
Sbjct: 55 --PREVPVGEVMS------------TPLITIDPNASLNEAAKLMAKHGIKRLPVVD 96
>gnl|CDD|129488 TIGR00393, kpsF, KpsF/GutQ family protein. This model describes a
number of closely related proteins with the
phosphosugar-binding domain SIS (Sugar ISomerase)
followed by two copies of the CBS (named after
Cystathionine Beta Synthase) domain. One is GutQ, a
protein of the glucitol operon. Another is KpsF, a
virulence factor involved in capsular polysialic acid
biosynthesis in some pathogenic strains of E. coli
[Energy metabolism, Sugars].
Length = 268
Score = 44.4 bits (105), Expect = 7e-05
Identities = 29/124 (23%), Positives = 52/124 (41%), Gaps = 22/124 (17%)
Query: 418 LKVSRAM-SKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSK 476
+KV M + D +A T + K+A+ M + + +V + + L G+ T GD++R L
Sbjct: 155 VKVKDLMQTTDLPLIAPTTSFKDALLEMSEKRLGSAIVCDENNQLVGVFTDGDLRRAL-- 212
Query: 477 LSSDNSKGDSIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQ 536
G S+ S+V + +++ D L A E +E + I
Sbjct: 213 -----LGGGSLKSEVRDFMTLG----PKTFK----------LDALLLEALEFLERRKITS 253
Query: 537 LPVI 540
L V+
Sbjct: 254 LVVV 257
>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 = 41.1 bits (97), Expect = 2e-04
Identities = 32/113 (28%), Positives = 49/113 (43%), Gaps = 11/113 (9%)
Query: 434 TVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIASDVNT 493
+L +A E M++ + + VVN + L G+LT D+ R LSS + G+ +
Sbjct: 9 DDSLADAEELMREHRIRHLPVVNEDGKLVGLLTQRDLLRAA--LSSLSDNGEESLTKERD 66
Query: 494 CLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSREL 546
V+ + + LT PDT L A E+M I LPV+ L
Sbjct: 67 VPVAEVMKTDV---------LTVTPDTPLREAAEIMVENKIGCLPVVDDKGTL 110
Score = 32.6 bits (75), Expect = 0.18
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 411 EEMLLEE--LKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYG 468
EE L +E + V+ M D + V L+EA E M + + C+ VV+ + L GI+T
Sbjct: 58 EESLTKERDVPVAEVMKTDVLTVTPDTPLREAAEIMVENKIGCLPVVDDKGTLVGIITRS 117
Query: 469 DIKR 472
D R
Sbjct: 118 DFLR 121
Score = 32.2 bits (74), Expect = 0.23
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 518 PDTDLAIAKELMEAKGIKQLPVIKRSREL 546
D LA A+ELM I+ LPV+ +L
Sbjct: 8 EDDSLADAEELMREHRIRHLPVVNEDGKL 36
>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 = 39.0 bits (92), Expect = 2e-04
Identities = 18/48 (37%), Positives = 28/48 (58%)
Query: 427 DFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCL 474
D V V+ TL+EA+E +++ + VV+ E L GI+T DI + L
Sbjct: 1 DVVTVSPDTTLEEALELLRENGIRRLPVVDEEGRLVGIVTRRDIIKAL 48
Score = 32.5 bits (75), Expect = 0.044
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 513 LLTCYPDTDLAIAKELMEAKGIKQLPVIKRSREL 546
++T PDT L A EL+ GI++LPV+ L
Sbjct: 2 VVTVSPDTTLEEALELLRENGIRRLPVVDEEGRL 35
>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 = 40.7 bits (96), Expect = 3e-04
Identities = 31/139 (22%), Positives = 55/139 (39%), Gaps = 29/139 (20%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVV-NGEDFLEGILTYGDIKRCLSKLSSDNSKG 484
+ V + T+ EA++ MK+ + ++V E GI+T DI L K+ ++
Sbjct: 1 PNVVTIDGLATVAEALQLMKEHGVSSLVVEKRRESDAYGIVTMRDI---LKKVVAEGRDP 57
Query: 485 DSIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSR 544
D + V I T+ L++ PD D+ LME I++ PV+
Sbjct: 58 DRVN-------VYEIMTKP---------LISVSPDMDIKYCARLMERTNIRRAPVV---- 97
Query: 545 ELQRRRKQRIVAILHYDSI 563
++ I+ I
Sbjct: 98 -----ENNELIGIISLTDI 111
Score = 27.6 bits (62), Expect = 7.2
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 15/85 (17%)
Query: 400 VVENAADSEA--------------AEEMLLEELKVSRAMSKDFVKVALTVTLKEAIESMK 445
VVE +S+A AE + + V M+K + V+ + +K M+
Sbjct: 28 VVEKRRESDAYGIVTMRDILKKVVAEGRDPDRVNVYEIMTKPLISVSPDMDIKYCARLME 87
Query: 446 DGQQNCVLVVNGEDFLEGILTYGDI 470
VV + L GI++ DI
Sbjct: 88 RTNIRRAPVVENNE-LIGIISLTDI 111
>gnl|CDD|240007 cd04636, CBS_pair_23, 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 = 132
Score = 40.0 bits (94), Expect = 5e-04
Identities = 33/125 (26%), Positives = 55/125 (44%), Gaps = 18/125 (14%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSK--------- 476
KD + V TL++ +E + G+ + V VV+ E + GI++ GD+ R + K
Sbjct: 1 KDVITVKKDDTLRDVVEILLTGKISGVPVVDNEGRVVGIVSEGDLIRKIYKGKGLFYVTL 60
Query: 477 LSSDNSKGDSIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQ 536
L S +S + V I T+ + +T DT + +M K IK+
Sbjct: 61 LYSVIFLDESKIKKLLGKKVEEIMTKKV---------ITVDEDTTIEDVARIMSKKNIKR 111
Query: 537 LPVIK 541
LPV+
Sbjct: 112 LPVVD 116
Score = 33.9 bits (78), Expect = 0.081
Identities = 24/126 (19%), Positives = 48/126 (38%), Gaps = 12/126 (9%)
Query: 359 KETDASD--KRTLARGYSSLSPMEDKNEVLWRRTDG-----ADELELSVVENAADS---- 407
K+ D + L S + ++++ V+ ++G + + S
Sbjct: 8 KDDTLRDVVEILLTGKISGVPVVDNEGRVVGIVSEGDLIRKIYKGKGLFYVTLLYSVIFL 67
Query: 408 EAAEEMLLEELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTY 467
+ ++ L KV M+K + V T+++ M + VV+ L GI++
Sbjct: 68 DESKIKKLLGKKVEEIMTKKVITVDEDTTIEDVARIMSKKNIKRLPVVDD-GKLVGIISR 126
Query: 468 GDIKRC 473
GDI R
Sbjct: 127 GDIIRS 132
>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 = 39.6 bits (93), Expect = 7e-04
Identities = 20/59 (33%), Positives = 37/59 (62%)
Query: 414 LLEELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 472
LL ++KVS M++D + V+ +++EA E M + + + + VV+ + L GI+T D+ R
Sbjct: 63 LLSKIKVSDIMTRDPITVSPDASVEEAAELMLERKISGLPVVDDQGRLVGIITESDLFR 121
Score = 36.5 bits (85), Expect = 0.007
Identities = 35/117 (29%), Positives = 53/117 (45%), Gaps = 15/117 (12%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCL-SK-LSSDNSK 483
K+ + V +L EA++ MK+ + VV+ L GI+T D+K SK + D +
Sbjct: 1 KNPITVTPDTSLMEALKLMKENSIRRLPVVDRGK-LVGIVTDRDLKLASPSKATTLDIWE 59
Query: 484 GDSIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVI 540
+ S + VS I TR +T PD + A ELM + I LPV+
Sbjct: 60 LYYLLSKIK---VSDIMTRDP---------ITVSPDASVEEAAELMLERKISGLPVV 104
Score = 31.1 bits (71), Expect = 0.62
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 511 RGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSR 544
+ +T PDT L A +LM+ I++LPV+ R +
Sbjct: 1 KNPITVTPDTSLMEALKLMKENSIRRLPVVDRGK 34
>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 = 38.8 bits (91), Expect = 0.001
Identities = 28/111 (25%), Positives = 48/111 (43%), Gaps = 11/111 (9%)
Query: 434 TVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIASDVNT 493
T T+ EA+E M++ + + VV+ E L GI+T D++ + S+ +
Sbjct: 9 TTTIAEALELMREHKIRHLPVVDEEGRLVGIVTDRDLRDASPSPFTTLSEHELYLLLKMP 68
Query: 494 CLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSR 544
V I T+ + +T +P + A LM I LPV++ R
Sbjct: 69 --VKEIMTKDV---------ITVHPLDTVEEAALLMREHRIGCLPVVEDGR 108
Score = 35.3 bits (82), Expect = 0.022
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 404 AADSEAAEEMLLEELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEG 463
E LL ++ V M+KD + V T++EA M++ + C+ VV L G
Sbjct: 53 FTTLSEHELYLLLKMPVKEIMTKDVITVHPLDTVEEAALLMREHRIGCLPVVED-GRLVG 111
Query: 464 ILTYGDI 470
I+T D+
Sbjct: 112 IITETDL 118
Score = 33.0 bits (76), Expect = 0.11
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 511 RGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSRELQ 547
R ++T P T +A A ELM I+ LPV+ L
Sbjct: 1 RDVVTITPTTTIAEALELMREHKIRHLPVVDEEGRLV 37
>gnl|CDD|239982 cd04609, CBS_pair_PALP_assoc2, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains
associated with the pyridoxal-phosphate (PALP) dependent
enzyme domain upstream. The vitamin B6 complex
comprises pyridoxine, pyridoxal, and pyridoxamine, as
well as the 5'-phosphate esters of pyridoxal (PALP) and
pyridoxamine, the last two being the biologically active
coenzyme derivatives. The members of the PALP family
are principally involved in the biosynthesis of amino
acids and amino acid-derived metabolites, but they are
also found in the biosynthetic pathways of amino sugars
and other amine-containing compounds. CBS is a small
domain originally identified in cystathionine
beta-synthase and subsequently found in a wide range of
different proteins. CBS domains usually come in tandem
repeats, which associate to form a so-called Bateman
domain or a CBS pair which is reflected in this model.
The interface between the two CBS domains forms a cleft
that is a potential ligand binding site. The CBS pair
coexists with a variety of other functional domains. It
has been proposed that the CBS domain may play a
regulatory role, although its exact function is unknown.
Length = 110
Score = 37.9 bits (89), Expect = 0.002
Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 9/65 (13%)
Query: 511 RGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSRELQRRRKQRIVAILHYDSIWNCLREE 570
+++ PD ++ A E M G+ QLPV+ R+V + + + L E
Sbjct: 1 GDVVSVAPDDTVSQAIERMREYGVSQLPVV---------DDGRVVGSIDESDLLDALIEG 51
Query: 571 VNHRK 575
Sbjct: 52 KAKFS 56
Score = 30.6 bits (70), Expect = 0.72
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 417 ELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 470
L V M + V + E + + D V+V G F+ GI+T D+
Sbjct: 56 SLPVREVMGEPLPTVDPDAPI-EELSELLDRGNVAVVVDEGGKFV-GIITRADL 107
>gnl|CDD|240003 cd04632, CBS_pair_19, 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 = 128
Score = 37.9 bits (88), Expect = 0.003
Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 411 EEMLLEELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGED--FLEGILTYG 468
E ML +L V AMS + + ++++A++ M + + V+VV +D + GILT
Sbjct: 66 ERML--DLPVYDAMSSPVITASPNDSVRDAVDRMLENDDSSVVVVTPDDDTKVVGILTKK 123
Query: 469 DIKR 472
D+ R
Sbjct: 124 DVLR 127
Score = 28.6 bits (64), Expect = 3.8
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 470
+D + V ++ +AI +++ + + VV+ L GI+T DI
Sbjct: 1 EDVITVREDDSVGKAINVLREHGISRLPVVDDNGKLTGIVTRHDI 45
>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 = 37.2 bits (87), Expect = 0.003
Identities = 28/114 (24%), Positives = 44/114 (38%), Gaps = 22/114 (19%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGD 485
+ +L EA M++ + + ++VV+ L GI+T DI R L
Sbjct: 1 TQILTCPPDTSLAEAASRMRERRISSIVVVDDGRPL-GIVTERDILRLL----------- 48
Query: 486 SIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPV 539
+ V + + LLT DT L A++LM GI+ L V
Sbjct: 49 -ASGPDLQTPVGEVMS---------SPLLTVPADTSLYDARQLMREHGIRHLVV 92
>gnl|CDD|215230 PLN02418, PLN02418, delta-1-pyrroline-5-carboxylate synthase.
Length = 718
Score = 38.9 bits (91), Expect = 0.007
Identities = 34/102 (33%), Positives = 44/102 (43%), Gaps = 10/102 (9%)
Query: 349 IWVPSVANQAKETDASDKRTLARGYSSLSPMEDKNEVLWRRTDGADELE----LSVVENA 404
+W PS A+E A R +R +LS E K +L D AD LE L EN
Sbjct: 287 LWAPSKEVGAREM-AVAARESSRKLQALSSEERKKILL----DVADALEANEELIKAENE 341
Query: 405 ADSEAAEEMLLEELKVSRAMSKDFVKVALTVTLKEAIESMKD 446
D AA+E E+ VSR K K+A + M+D
Sbjct: 342 LDVAAAQEAGYEKSLVSRLTLKP-GKIASLAASIRQLADMED 382
>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 = 36.5 bits (85), Expect = 0.008
Identities = 24/89 (26%), Positives = 31/89 (34%), Gaps = 10/89 (11%)
Query: 453 LVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIASDVNTCLVSSICTRGISYRGRERG 512
L V L GI+T DI L + VS I TR
Sbjct: 27 LPVIEGGKLVGIVTEKDIADALRSFRPLVR-DRHQERRIRNLPVSDIMTRP--------- 76
Query: 513 LLTCYPDTDLAIAKELMEAKGIKQLPVIK 541
++T PDT ++ LM I LPV+
Sbjct: 77 VITIEPDTSVSDVASLMLENNIGGLPVVD 105
>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 = 36.1 bits (84), Expect = 0.009
Identities = 32/119 (26%), Positives = 53/119 (44%), Gaps = 23/119 (19%)
Query: 429 VKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIA 488
V V +++EA + M + V+VV+ ++ GI+T DI R ++A
Sbjct: 4 VTVDPDTSIREAAKLMAEENVGSVVVVDPDERPIGIVTERDIVR-------------AVA 50
Query: 489 SDVN-TCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSREL 546
+ ++ VS I TR L+T PD +A A +LM I+ V+ + EL
Sbjct: 51 AGIDLDTPVSEIMTRD---------LVTVDPDEPVAEAAKLMRKNNIRHHLVVDKGGEL 100
Score = 31.0 bits (71), Expect = 0.52
Identities = 16/54 (29%), Positives = 26/54 (48%)
Query: 420 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRC 473
VS M++D V V + EA + M+ LVV+ L G+++ D+ R
Sbjct: 59 VSEIMTRDLVTVDPDEPVAEAAKLMRKNNIRHHLVVDKGGELVGVISIRDLVRE 112
>gnl|CDD|225778 COG3238, COG3238, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 150
Score = 36.1 bits (84), Expect = 0.013
Identities = 25/99 (25%), Positives = 37/99 (37%), Gaps = 21/99 (21%)
Query: 77 IALVAAGAASGIASGFNAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTV 136
+ + AGA + + N +A R SP +LAS+IS V TV
Sbjct: 8 LFAILAGALLPLQAAINGRLA-------------RYLGSP-------LLASLISFLVGTV 47
Query: 137 LLGTQSAFTVPSYDLKSAAELPLYLILGMLCGVVSVVFT 175
LL L + A P + +G L G + V +
Sbjct: 48 LLLILLLIKQGHPGLAAVASAPWWAWIGGLLGAI-FVTS 85
>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 = 35.1 bits (82), Expect = 0.018
Identities = 32/121 (26%), Positives = 51/121 (42%), Gaps = 24/121 (19%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGD 485
+D + V+ T+ EA+E M + + + VV+ + L GI+T D+ R + L
Sbjct: 2 RDPITVSPDATVAEALELMAEYGISGLPVVDDDGKLVGIVTNRDL-RFETDLDKP----- 55
Query: 486 SIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSRE 545
VS + T LLT T L A EL+ I++LPV+ +
Sbjct: 56 ----------VSEVMTP--------ENLLTTVEGTSLEEALELLHEHKIEKLPVVDDEGK 97
Query: 546 L 546
L
Sbjct: 98 L 98
Score = 28.6 bits (65), Expect = 3.4
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 419 KVSRAM-SKDFVKVALTVTLKEAIESMKDGQQNCV---LVVNGEDFLEGILTYGDI 470
VS M ++ + +L+EA+E + ++ + VV+ E L+G++T DI
Sbjct: 55 PVSEVMTPENLLTTVEGTSLEEALELL---HEHKIEKLPVVDDEGKLKGLITVKDI 107
>gnl|CDD|218193 pfam04657, DUF606, Protein of unknown function, DUF606. This
family includes several uncharacterized bacterial
proteins.
Length = 139
Score = 35.5 bits (83), Expect = 0.019
Identities = 24/99 (24%), Positives = 38/99 (38%), Gaps = 20/99 (20%)
Query: 77 IALVAAGAASGIASGFNAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTV 136
+ + AGA + + NA + ++ SP +LAS++S V T+
Sbjct: 4 LLALLAGALLALQAAINARLG-------------KSLGSP-------LLASLVSFLVGTI 43
Query: 137 LLGTQSAFTVPSYDLKSAAELPLYLILGMLCGVVSVVFT 175
+L FT L + A P + LG L G V
Sbjct: 44 VLLLLLLFTRRPLSLGALASAPWWAWLGGLLGAFYVTLN 82
>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 = 35.0 bits (81), Expect = 0.022
Identities = 16/51 (31%), Positives = 26/51 (50%)
Query: 420 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 470
V M +DF V+ + TL + M+ G V VV+G L G++T ++
Sbjct: 58 VRGVMRRDFPTVSPSATLDAVLRLMQQGGAPAVPVVDGSGRLVGLVTLENV 108
Score = 33.4 bits (77), Expect = 0.083
Identities = 27/111 (24%), Positives = 40/111 (36%), Gaps = 22/111 (19%)
Query: 436 TLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIASDVNTCL 495
TL +A +++ Q+ VV+G+ L G+LT D+ R L A
Sbjct: 11 TLDDAADALLATTQHEFPVVDGDGHLVGLLTRDDLIRAL-------------AEGGPDAP 57
Query: 496 VSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSREL 546
V + R T P L LM+ G +PV+ S L
Sbjct: 58 VRGVMRRDFP---------TVSPSATLDAVLRLMQQGGAPAVPVVDGSGRL 99
>gnl|CDD|240014 cd04643, CBS_pair_30, 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 = 116
Score = 34.9 bits (81), Expect = 0.022
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 2/60 (3%)
Query: 411 EEMLLEELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 470
+ L +LKV M+ D + ++E + + D Q + VV+ + GI+T +I
Sbjct: 56 DLERLVDLKVIDVMNTDVPVIIDDADIEEILHLLID--QPFLPVVDDDGIFIGIITRREI 113
>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 = 34.9 bits (81), Expect = 0.026
Identities = 15/36 (41%), Positives = 19/36 (52%)
Query: 511 RGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSREL 546
R ++T PDT L A L+ IK LPV+ R L
Sbjct: 2 RDVVTVTPDTSLEEAWALLRRHRIKALPVVDGDRRL 37
Score = 32.6 bits (75), Expect = 0.17
Identities = 16/53 (30%), Positives = 24/53 (45%)
Query: 418 LKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 470
V MS V V + E + + DG + V VV+ + L GI+T D+
Sbjct: 69 ETVGDIMSPPVVTVRPDTPIAELVPLLADGGHHHVPVVDEDRRLVGIVTQTDL 121
>gnl|CDD|215936 pfam00478, IMPDH, IMP dehydrogenase / GMP reductase domain. This
family is involved in biosynthesis of guanosine
nucleotide. Members of this family contain a TIM barrel
structure. In the inosine monophosphate dehydrogenases 2
CBS domains pfam00571 are inserted in the TIM barrel.
This family is a member of the common phosphate binding
site TIM barrel family.
Length = 467
Score = 36.5 bits (85), Expect = 0.034
Identities = 16/61 (26%), Positives = 33/61 (54%)
Query: 412 EMLLEELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIK 471
L ++ V M++D V +TL+EA E + + + + +V+ + L G++T DI+
Sbjct: 137 IDFLSKVSVVMTMTEDLVTAPEGITLEEANEILHEHKIEKLPIVDDDGELVGLITRKDIE 196
Query: 472 R 472
+
Sbjct: 197 K 197
>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 = 0.051
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 511 RGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSREL 546
R +T PD L A + M + I +LPV+ S L
Sbjct: 64 RDPVTASPDETLRDALKRMAERDIGRLPVVDDSGRL 99
Score = 29.5 bits (67), Expect = 1.7
Identities = 11/37 (29%), Positives = 21/37 (56%)
Query: 436 TLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 472
TL++A++ M + + VV+ L GI++ D+ R
Sbjct: 74 TLRDALKRMAERDIGRLPVVDDSGRLVGIVSRSDLLR 110
>gnl|CDD|233128 TIGR00792, gph, sugar (Glycoside-Pentoside-Hexuronide) transporter.
The Glycoside-Pentoside-Hexuronide (GPH):Cation
Symporter Family (TC 2.A.2) GPH:cation symporters
catalyze uptake of sugars in symport with a monovalent
cation (H+ or Na+). Members of this family includes
transporters for melibiose, lactose, raffinose,
glucuronides, pentosides and isoprimeverose. Mutants of
two groups of these symporters (the melibiose permeases
of enteric bacteria, and the lactose permease of
Streptococcus thermophilus) have been isolated in which
altered cation specificity is observed or in which sugar
transport is uncoupled from cation symport (i.e.,
uniport is catalyzed). The various members of the family
can use Na+, H+ or Li, Na+ or Li+, H+ or Li+, or only H+
as the symported cation. All of these proteins possess
twelve putative transmembrane a-helical spanners
[Transport and binding proteins, Carbohydrates, organic
alcohols, and acids].
Length = 437
Score = 36.1 bits (84), Expect = 0.054
Identities = 46/225 (20%), Positives = 78/225 (34%), Gaps = 37/225 (16%)
Query: 122 MIILASVISSTVSTVLLGTQSAFTVPSYDLKSAAELPLYLILGMLCGVVSVVFT-RLVAW 180
++ LA + + + G Q + +Y L + + G++ V+ RLV
Sbjct: 226 ILCLAYLFYNLAFNIKNGVQVYYF--TYVLGDPELFSYMGSIAIGAGLIGVLLFPRLVKK 283
Query: 181 FTKSFDFIKEKFGLPPVVCPALGGLGAGIIALRYPGILYWGFTNVEEILHTGKTASAPGI 240
F + F GG+ ++ I ++ +N+ IL + G
Sbjct: 284 FGRKILF--------------AGGILLMVLGY---LIFFFAGSNLPLIL-VLIILAGFGQ 325
Query: 241 WLLTQLAAAKVVATA----LCKG---SGLVGGLYAPSLMIGAAVGAVFGGSAAEIINSAI 293
+T L A V T G GLV + +G A+ G II
Sbjct: 326 NFVTGLVWALVADTVDYGEWKTGVRAEGLVYSVRTFVRKLGQALAGFLVGLILGII---- 381
Query: 294 PGNVAVAEPQAYALVGMAATLASVCSVP-LTSVLLLFELTRDYRI 337
G VA A L G+ + +VP L +L + R Y++
Sbjct: 382 -GYVANAAQSPITLNGIKILM---FAVPALFLLLAAIIIGRFYKL 422
>gnl|CDD|240002 cd04631, CBS_pair_18, 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 = 125
Score = 33.8 bits (78), Expect = 0.059
Identities = 36/119 (30%), Positives = 49/119 (41%), Gaps = 16/119 (13%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVV-NGEDFLEGILTYGDIKRCL---SKLSSDN 481
KD V V T + EA + M + VV G L GI+T DI + L K +
Sbjct: 1 KDVVTVPPTTPIMEAAKIMVRNGFRRLPVVDEGTGKLVGIITATDILKYLGGGEKFNKIK 60
Query: 482 SKGDSIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVI 540
+ A + V SI TR ++T PD + A ELM K + LPV+
Sbjct: 61 TGNGLEAINEP---VRSIMTRN---------VITITPDDSIKDAAELMLEKRVGGLPVV 107
Score = 30.3 bits (69), Expect = 1.2
Identities = 13/55 (23%), Positives = 29/55 (52%)
Query: 419 KVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRC 473
V M+++ + + ++K+A E M + + + VV+ + L GI+T D+ +
Sbjct: 71 PVRSIMTRNVITITPDDSIKDAAELMLEKRVGGLPVVDDDGKLVGIVTERDLLKA 125
>gnl|CDD|118676 pfam10148, SCHIP-1, Schwannomin-interacting protein 1. Members of
this family are coiled coil protein involved in linking
membrane proteins to the cytoskeleton.
Length = 239
Score = 35.1 bits (80), Expect = 0.077
Identities = 24/97 (24%), Positives = 46/97 (47%), Gaps = 7/97 (7%)
Query: 341 LMGAVGLAIWVPSVANQAKETDASDKRTLARGYSSLSPMEDKNEVLWRRTDGADELELSV 400
L + L I + + K++DA D +T + LSPM ++ L R G ++L
Sbjct: 44 LQNGMNLQICFVNDSGSDKDSDADDSKTETSLDTPLSPMSKQSSSLSDRDTGEEDL---- 99
Query: 401 VENAADSE--AAEEMLLEELKVSRAMSKDFVKVALTV 435
++ D + ++ L E K++ A++K K+ + V
Sbjct: 100 -DSLDDMDFLRLQKKLQAEAKMALALAKPMAKMQVEV 135
>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 = 33.9 bits (78), Expect = 0.078
Identities = 30/131 (22%), Positives = 58/131 (44%), Gaps = 13/131 (9%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCL-SKLSSDN--- 481
K+ + T+ +A +++ + + V++G L GI++ DI + L + S N
Sbjct: 1 KNPITCNADDTISDAARLLRENKISGAPVLDG-GKLVGIVSESDILKLLVTHDPSGNLWL 59
Query: 482 -SKGDSIASDVNTCLVSSICTRGISYRGR-------ERGLLTCYPDTDLAIAKELMEAKG 533
S + I + + R ++ G+ + ++T PD + A ELM
Sbjct: 60 PSPLELIELPLREFINWEETKRALTDAGKMKVRDIMTKKVITISPDASIEDAAELMVRHK 119
Query: 534 IKQLPVIKRSR 544
IK+LPV++ R
Sbjct: 120 IKRLPVVEDGR 130
Score = 32.0 bits (73), Expect = 0.34
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 419 KVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 470
KV M+K + ++ ++++A E M + + VV L GI+T GDI
Sbjct: 90 KVRDIMTKKVITISPDASIEDAAELMVRHKIKRLPVVEDGR-LVGIVTRGDI 140
>gnl|CDD|239992 cd04620, CBS_pair_7, 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 = 115
Score = 33.5 bits (77), Expect = 0.081
Identities = 30/134 (22%), Positives = 52/134 (38%), Gaps = 28/134 (20%)
Query: 431 VALTVTLKEAIESM-KDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIAS 489
V + +AI M + G +CVLVV + L GI T DI R +I
Sbjct: 6 VTPDTPVADAIALMSQQGDSSCVLVVE-KGRLLGIFTERDIVR-----------LTAIGK 53
Query: 490 DVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSRELQRR 549
D++ + + T+ + L D+ A L I+ LPV+
Sbjct: 54 DLSDLPIGEVMTQPVV-------TLQESEIQDIFTALSLFRQHQIRHLPVLD-------- 98
Query: 550 RKQRIVAILHYDSI 563
+ +++ ++ +SI
Sbjct: 99 DQGQLIGLVTAESI 112
>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 = 33.2 bits (77), Expect = 0.086
Identities = 31/120 (25%), Positives = 51/120 (42%), Gaps = 23/120 (19%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI-KRCLSKLSSDNSKG 484
+ V + T++EA M + + + +LVV + L GI+T D+ R +++
Sbjct: 1 RPPVTCSPDTTIREAARLMTEHRVSSLLVV-DDGRLVGIVTDRDLRNRVVAE-------- 51
Query: 485 DSIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSR 544
D +T VS + T +T PD + A LM +GI LPV+ R
Sbjct: 52 ---GLDPDT-PVSEVMT---------APPITIPPDATVFEALLLMLERGIHHLPVVDDGR 98
>gnl|CDD|239956 cd04583, CBS_pair_ABC_OpuCA_assoc2, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains in association with the ABC transporter OpuCA.
OpuCA is the ATP binding component of a bacterial solute
transporter that serves a protective role to cells
growing in a hyperosmolar environment but the function
of the CBS domains in OpuCA remains unknown. In the
related ABC transporter, OpuA, the tandem CBS domains
have been shown to function as sensors for ionic
strength, whereby they control the transport activity
through an electronic switching mechanism. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. They are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
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 = 109
Score = 32.9 bits (76), Expect = 0.099
Identities = 27/112 (24%), Positives = 47/112 (41%), Gaps = 25/112 (22%)
Query: 436 TLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIASDVNTCL 495
TL EAI+ M+D + + +LVV+ ++ L GI++ +++ + S D + DV T
Sbjct: 12 TLAEAIKLMRDKKVDSLLVVDKDNKLLGIVSLESLEQAYKE---AKSLEDIMLEDVFTVQ 68
Query: 496 VSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSRELQ 547
PD L L+ +G K +PV+ +L
Sbjct: 69 ----------------------PDASLRDVLGLVLKRGPKYVPVVDEDGKLV 98
Score = 31.0 bits (71), Expect = 0.45
Identities = 13/63 (20%), Positives = 26/63 (41%)
Query: 406 DSEAAEEMLLEELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGIL 465
E+ E+ E + M +D V +L++ + + V VV+ + L G++
Sbjct: 42 SLESLEQAYKEAKSLEDIMLEDVFTVQPDASLRDVLGLVLKRGPKYVPVVDEDGKLVGLI 101
Query: 466 TYG 468
T
Sbjct: 102 TRS 104
>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 = 32.4 bits (74), Expect = 0.16
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 420 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCV--LVVNGEDFLEGILTYGDIKR 472
V+ AM+++ V ++ +L EA M ++ + L V E L GI+T G I
Sbjct: 53 VADAMTREVVTISPEASLLEAKRLM---EEKKIERLPVLRERKLVGIITKGTIAL 104
Score = 31.6 bits (72), Expect = 0.27
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 8/54 (14%)
Query: 511 RGLLTCYPDTDLAIAKELMEAKGIKQLPV--------IKRSRELQRRRKQRIVA 556
R +T P + A LME I LPV I SR+++R R+VA
Sbjct: 1 RDPITIDPLDSVGRAARLMEKHRIGGLPVVEDGKLVGIITSRDVRRAHPNRLVA 54
Score = 29.7 bits (67), Expect = 1.3
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 518 PDTDLAIAKELMEAKGIKQLPVIKRSR 544
P+ L AK LME K I++LPV++ +
Sbjct: 66 PEASLLEAKRLMEEKKIERLPVLRERK 92
>gnl|CDD|130254 TIGR01186, proV, glycine betaine/L-proline transport ATP binding
subunit. This model describes the glycine
betaine/L-proline ATP binding subunit in bacteria and
its equivalents in archaea. This transport system belong
to the larger ATP-Binding Cassette (ABC) transporter
superfamily. The characteristic feature of these
transporter is the obligatory coupling of ATP hydrolysis
to substrate translocation. The minimal configuration of
bacterial ABC transport system: an ATPase or ATP binding
subunit; An integral membrane protein; a hydrophilic
polypetpide, which likely functions as substrate binding
protein. Functionally, this transport system is involved
in osmoregulation. Under conditions of stress, the
organism recruits these transport system to accumulate
glycine betaine and other solutes which offer
osmo-protection. It has been demonstrated that glycine
betaine uptake is accompanied by symport with sodium
ions. The locus has been named variously as proU or
opuA. A gene library from L.lactis functionally
complements an E.coli proU mutant. The comlementing
locus is similar to a opuA locus in B.sutlis. This
clarifies the differences in nomenclature [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 363
Score = 34.1 bits (78), Expect = 0.18
Identities = 14/75 (18%), Positives = 35/75 (46%), Gaps = 3/75 (4%)
Query: 419 KVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLS 478
++++ M+ + + A++ M+D + + + VV+ ++ L G++ IK+ K
Sbjct: 243 RIAQRMNTGPITKTADKGPRSALQLMRDERVDSLYVVDRQNKLVGVVDVESIKQARKK-- 300
Query: 479 SDNSKGDSIASDVNT 493
D + D+ T
Sbjct: 301 -AQGLQDVLIDDIYT 314
>gnl|CDD|239993 cd04621, CBS_pair_8, 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 = 135
Score = 32.4 bits (74), Expect = 0.21
Identities = 28/135 (20%), Positives = 47/135 (34%), Gaps = 20/135 (14%)
Query: 436 TLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIASDVNTCL 495
+L ++ M+ V+VV+ G++TY D+ DN +G S
Sbjct: 11 SLLHVVDEMEKNGVGRVIVVDDNGKPVGVITYRDL---AFAEFEDNERGLPKKSIKMKRK 67
Query: 496 VSSICTRGISYR-------GRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSRELQR 548
R + E ++T P+ D+ A +LM I LPV+
Sbjct: 68 AGQKRYRYVKEVPLVAEDIMTEE-IITVSPNDDVVDAAKLMLEANISGLPVVD------- 119
Query: 549 RRKQRIVAILHYDSI 563
IV ++ I
Sbjct: 120 --NDNIVGVITKTDI 132
Score = 30.1 bits (68), Expect = 1.3
Identities = 12/55 (21%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 418 LKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 472
L M+++ + V+ + +A + M + + + VV+ ++ + G++T DI R
Sbjct: 81 LVAEDIMTEEIITVSPNDDVVDAAKLMLEANISGLPVVDNDNIV-GVITKTDICR 134
>gnl|CDD|239981 cd04608, CBS_pair_PALP_assoc, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains
associated with the pyridoxal-phosphate (PALP) dependent
enzyme domain upstream. The vitamin B6 complex
comprises pyridoxine, pyridoxal, and pyridoxamine, as
well as the 5'-phosphate esters of pyridoxal (PALP) and
pyridoxamine, the last two being the biologically active
coenzyme derivatives. The members of the PALP family
are principally involved in the biosynthesis of amino
acids and amino acid-derived metabolites, but they are
also found in the biosynthetic pathways of amino sugars
and other amine-containing compounds. 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 = 32.3 bits (74), Expect = 0.23
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 429 VKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIA 488
V V TVT EAIE +K+ + + VV+ + G++T G++ LS LSS +
Sbjct: 5 VTVLPTVTCAEAIEILKEKGFDQLPVVDESGKILGMVTLGNL---LSSLSSGKVQPSDPV 61
Query: 489 SDV 491
S
Sbjct: 62 SKA 64
Score = 30.8 bits (70), Expect = 0.79
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 514 LTCYPDTDLAIAKELMEAKGIKQLPVIKRS 543
+T P A A E+++ KG QLPV+ S
Sbjct: 5 VTVLPTVTCAEAIEILKEKGFDQLPVVDES 34
>gnl|CDD|239968 cd04595, CBS_pair_DHH_polyA_Pol_assoc, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains associated with an upstream DHH domain which
performs a phosphoesterase function and a downstream
polyA polymerase domain. CBS is a small domain
originally identified in cystathionine beta-synthase and
subsequently found in a wide range of different
proteins. CBS domains usually come in tandem repeats,
which associate to form a so-called Bateman domain or a
CBS pair which is reflected in this model. The interface
between the two CBS domains forms a cleft that is a
potential ligand binding site. The CBS pair coexists
with a variety of other functional domains. It has been
proposed that the CBS domain may play a regulatory role,
although its exact function is unknown.
Length = 110
Score = 31.4 bits (72), Expect = 0.34
Identities = 20/58 (34%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 415 LEELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 472
L V MS D V V L E E M + V VV L GI+T D+ R
Sbjct: 53 LGHAPVKDYMSTDVVTVPPDTPLSEVQELMVEHDIGRVPVVEDGR-LVGIVTRTDLLR 109
>gnl|CDD|239991 cd04619, CBS_pair_6, 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 = 31.7 bits (72), Expect = 0.34
Identities = 23/105 (21%), Positives = 45/105 (42%), Gaps = 19/105 (18%)
Query: 436 TLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIASDVNTCL 495
TL+ A + + + + V+V + L G+LT D+ R + A
Sbjct: 11 TLQRAAKILGEPGIDLVVVCDPHGKLAGVLTKTDVVRQMG----RCGGPGCTAP------ 60
Query: 496 VSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVI 540
V ++ TR + ++C P L ++M+ +G+K +PV+
Sbjct: 61 VENVMTRAV---------VSCRPGDLLHDVWQVMKQRGLKNIPVV 96
>gnl|CDD|235507 PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase;
Reviewed.
Length = 486
Score = 33.2 bits (77), Expect = 0.43
Identities = 14/32 (43%), Positives = 18/32 (56%)
Query: 515 TCYPDTDLAIAKELMEAKGIKQLPVIKRSREL 546
T PDT LA A LM GI +PV+ + +L
Sbjct: 99 TVTPDTTLAEALALMARYGISGVPVVDENGKL 130
Score = 30.9 bits (71), Expect = 1.9
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 419 KVSRAMSKD-FVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 472
VS M+K+ V V TL+EA+E + + + + VV+ L+G++T DI++
Sbjct: 148 PVSEVMTKERLVTVPEGTTLEEALELLHEHRIEKLPVVDDNGRLKGLITVKDIEK 202
>gnl|CDD|239979 cd04606, CBS_pair_Mg_transporter, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domain in the magnesium transporter, MgtE. MgtE and its
homologs are found in eubacteria, archaebacteria, and
eukaryota. Members of this family transport Mg2+ or
other divalent cations into the cell via two highly
conserved aspartates. 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 = 109
Score = 30.9 bits (71), Expect = 0.45
Identities = 14/55 (25%), Positives = 23/55 (41%)
Query: 416 EELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 470
+ VS M D + V+ +E + + VV+ E L GI+T D+
Sbjct: 51 PDTPVSDIMDTDVISVSADDDQEEVARLFEKYDLLALPVVDEEGRLVGIITVDDV 105
>gnl|CDD|225978 COG3447, COG3447, Predicted integral membrane sensor domain [Signal
transduction mechanisms].
Length = 308
Score = 32.4 bits (74), Expect = 0.54
Identities = 23/123 (18%), Positives = 34/123 (27%), Gaps = 6/123 (4%)
Query: 238 PGIWLLTQLAAAKVVATALCKGSGLVGGLYAP-----SLMIGAAVGAVFGGSAAEIINSA 292
+ L L + T G AP S+M+GA I S
Sbjct: 14 HPLLHLVSLGLVSFLFTLFSLELSQFGTQLAPLWFPTSIMMGAFYRHAG-RMWPGIALSC 72
Query: 293 IPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELTRDYRILLPLMGAVGLAIWVP 352
GN+A + A + +LL +L Y L L + +
Sbjct: 73 SLGNIAASILLFSTSSLNMAITTINILEAVVGAVLLRKLLPWYNPLQNLQDWLRFLLGGA 132
Query: 353 SVA 355
V
Sbjct: 133 IVP 135
>gnl|CDD|237843 PRK14869, PRK14869, putative manganese-dependent inorganic
pyrophosphatase; Provisional.
Length = 546
Score = 32.5 bits (75), Expect = 0.68
Identities = 15/58 (25%), Positives = 26/58 (44%)
Query: 417 ELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCL 474
+ +V V V+ +LKEA M + + VV+ E L G+++ D+ R
Sbjct: 67 KPQVRDLEIDKPVTVSPDTSLKEAWNLMDENNVKTLPVVDEEGKLLGLVSLSDLARAY 124
Score = 29.0 bits (66), Expect = 8.5
Identities = 15/75 (20%), Positives = 34/75 (45%), Gaps = 1/75 (1%)
Query: 393 ADELELSVVENAADSEAAEEMLLEELKVSRAMSK-DFVKVALTVTLKEAIESMKDGQQNC 451
A E ++V+ D+ ++ + + VS M+ D V + L++ E M +
Sbjct: 221 AKENGVTVISTPYDTFTTARLINQSIPVSYIMTTEDLVTFSKDDYLEDVKEVMLKSRYRS 280
Query: 452 VLVVNGEDFLEGILT 466
VV+ + + G+++
Sbjct: 281 YPVVDEDGKVVGVIS 295
>gnl|CDD|225321 COG2524, COG2524, Predicted transcriptional regulator, contains
C-terminal CBS domains [Transcription].
Length = 294
Score = 31.6 bits (72), Expect = 1.0
Identities = 16/59 (27%), Positives = 26/59 (44%)
Query: 419 KVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKL 477
KVS M K+ + + + +AI M +LV + GI+T DI ++ L
Sbjct: 235 KVSDYMRKNVITINEDEDIYDAIRLMNKNNVGRLLVTDSNGKPVGIITRTDILTRIAGL 293
Score = 28.5 bits (64), Expect = 9.9
Identities = 30/122 (24%), Positives = 46/122 (37%), Gaps = 23/122 (18%)
Query: 419 KVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLS 478
KV MSK + V TL+EA + + VV+ +D + GI+T DI
Sbjct: 173 KVKNLMSKKLITVRPDDTLREAAKLFYEKGIRGAPVVD-DDKIVGIITLSDI-------- 223
Query: 479 SDNSKGDSIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLP 538
+IA+ VS + ++T D D+ A LM + +L
Sbjct: 224 -----AKAIANGNLDAKVSDYMR---------KNVITINEDEDIYDAIRLMNKNNVGRLL 269
Query: 539 VI 540
V
Sbjct: 270 VT 271
>gnl|CDD|233166 TIGR00880, 2_A_01_02, Multidrug resistance protein.
Length = 141
Score = 30.3 bits (69), Expect = 1.4
Identities = 23/101 (22%), Positives = 34/101 (33%), Gaps = 5/101 (4%)
Query: 251 VVATALCKGSGLVGGLYAPSLMIGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGM 310
V++TA+ S + L + G AA I + P V A L+
Sbjct: 39 VLSTAMFALSSNITVLIIARFLQGFGAAFALVAGAALIADIYPPEERGV----ALGLMSA 94
Query: 311 AATLASVCSVPLTSVLLLFELTR-DYRILLPLMGAVGLAIW 350
L + PL VL F R + L L A + +
Sbjct: 95 GIALGPLLGPPLGGVLAQFLGWRAPFLFLAILALAAFILLA 135
>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 = 29.7 bits (67), Expect = 1.4
Identities = 25/122 (20%), Positives = 51/122 (41%), Gaps = 27/122 (22%)
Query: 425 SKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKG 484
++D + V+ T+K+ I+ +K+ + VV+ + GI++ D+
Sbjct: 1 TRDVITVSPDNTVKDVIKLIKETGHDGFPVVDN-GKVVGIVSARDL-------------- 45
Query: 485 DSIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSR 544
+ D + V I ++ L+ P+ D+ A +M GI +LPV+ +
Sbjct: 46 --LGKDPDE-TVEEIMSKD---------LVVAVPEMDIMDAARVMFRTGISKLPVVDENN 93
Query: 545 EL 546
L
Sbjct: 94 NL 95
>gnl|CDD|237537 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
Length = 440
Score = 31.4 bits (72), Expect = 1.5
Identities = 44/163 (26%), Positives = 58/163 (35%), Gaps = 38/163 (23%)
Query: 161 LILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPP-------VVCPALGGLGAGIIALR 213
L+L ++ G+ S +F++ FT F G P +V AL LG GI
Sbjct: 208 LVLAVIVGIGSTLFSQ----FTAGFG------GAEPTIDDAMAIVLAALSLLGLGIFG-- 255
Query: 214 YPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMI 273
PGI G + AP QL A V T L G V L
Sbjct: 256 -PGIA------------NGLVSGAP------QLGAGAAVGTGLAAGGAAVAAAAGAGLAA 296
Query: 274 GAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLAS 316
G A G +AA +A G + A A AA +A+
Sbjct: 297 GGGAAAAGGAAAAARGGAAAAGGASSAYSAGAAGGSGAAGVAA 339
>gnl|CDD|239961 cd04588, CBS_pair_CAP-ED_DUF294_assoc_arch, This cd contains two
tandem repeats of the cystathionine beta-synthase (CBS
pair) domains associated with the archaeal 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.
The interface between the two CBS domains forms a cleft
that is a potential ligand binding site. The CBS pair
coexists with a variety of other functional domains. It
has been proposed that the CBS domain may play a
regulatory role, although its exact function is unknown.
Length = 110
Score = 29.2 bits (66), Expect = 1.8
Identities = 19/58 (32%), Positives = 27/58 (46%)
Query: 415 LEELKVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 472
LE KV M+KD + + L +AI M ++V + E GI+T DI R
Sbjct: 52 LELAKVKDVMTKDVITIDEDEQLYDAIRLMNKHNVGRLIVTDDEGRPVGIITRTDILR 109
Score = 29.2 bits (66), Expect = 2.3
Identities = 25/115 (21%), Positives = 39/115 (33%), Gaps = 23/115 (20%)
Query: 426 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGD 485
K + + TL+EA + VV+ L GI+T DI
Sbjct: 1 KPLITLNPNATLREAARLFNTHHIHGAPVVDD-GKLVGIVTLSDI-------------AH 46
Query: 486 SIASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVI 540
+IA + V + T+ + +T D L A LM + +L V
Sbjct: 47 AIARGLELAKVKDVMTKDV---------ITIDEDEQLYDAIRLMNKHNVGRLIVT 92
>gnl|CDD|233350 TIGR01302, IMP_dehydrog, inosine-5'-monophosphate dehydrogenase.
This model describes IMP dehydrogenase, an enzyme of GMP
biosynthesis. This form contains two CBS domains. This
model describes a rather tightly conserved cluster of
IMP dehydrogenase sequences, many of which are
characterized. The model excludes two related families
of proteins proposed also to be IMP dehydrogenases, but
without characterized members. These are related
families are the subject of separate models [Purines,
pyrimidines, nucleosides, and nucleotides, Purine
ribonucleotide biosynthesis].
Length = 450
Score = 31.2 bits (71), Expect = 1.8
Identities = 14/55 (25%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 419 KVSRAMSK-DFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 472
VS M++ + + V + L+EA++ + + + + VV+ L G++T DI +
Sbjct: 144 PVSEVMTREEVITVPEGIDLEEALKVLHEHRIEKLPVVDKNGELVGLITMKDIVK 198
>gnl|CDD|225148 COG2239, MgtE, Mg/Co/Ni transporter MgtE (contains CBS domain)
[Inorganic ion transport and metabolism].
Length = 451
Score = 30.7 bits (70), Expect = 2.5
Identities = 37/198 (18%), Positives = 70/198 (35%), Gaps = 46/198 (23%)
Query: 388 RRTDGADELELSVVENAADSEAAEE-----MLLEELKVS--RAMSKDFVKVALTVTLKEA 440
D DEL V + EE LL + + R M+ +FV + VT+ EA
Sbjct: 95 DAADLLDELPDEVRDELLSLLDPEERARVRQLLSYPEDTAGRIMTTEFVTLPEDVTVDEA 154
Query: 441 IESMK-----DGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIASDVNTCL 495
++ ++ + VV+ + L G+++ D+ ++ D + D+
Sbjct: 155 LDRIRERAEDAETIYYLYVVDEKGKLLGVVSLRDLLT---------AEPDELLKDL---- 201
Query: 496 VSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSRELQRRRKQRIV 555
E +++ D D L E + +PV+ R++
Sbjct: 202 -------------MEDDVVSVLADDDQEEVARLFEKYDLLAVPVVDED--------NRLI 240
Query: 556 AILHYDSIWNCLREEVNH 573
I+ D I + + EE
Sbjct: 241 GIITIDDIIDVIEEEATE 258
>gnl|CDD|239967 cd04594, CBS_pair_EriC_assoc_archaea, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains associated with the EriC CIC-type chloride
channels in archaea. 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 = 104
Score = 28.9 bits (65), Expect = 2.8
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 431 VALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 470
V LT T +EA E M + VV+ F GI+T I
Sbjct: 63 VRLTSTAEEAWEVMMKNKTRWCPVVDDGKFK-GIVTLDSI 101
>gnl|CDD|226147 COG3620, COG3620, Predicted transcriptional regulator with
C-terminal CBS domains [Transcription].
Length = 187
Score = 29.7 bits (67), Expect = 3.4
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 511 RGLLTCYPDTDLAIAKELMEAKGIKQLPVI 540
+++ PD ++ LM KGI QLPVI
Sbjct: 73 SPVVSVSPDDSISDVVNLMRDKGISQLPVI 102
>gnl|CDD|130164 TIGR01092, P5CS, delta l-pyrroline-5-carboxylate synthetase. This
protein contains a glutamate 5-kinase (ProB, EC
2.7.2.11) region followed by a gamma-glutamyl phosphate
reductase (ProA, EC 1.2.1.41) region [Amino acid
biosynthesis, Glutamate family].
Length = 715
Score = 30.3 bits (68), Expect = 4.0
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 9/81 (11%)
Query: 352 PSVANQAKETDASDKRTLARGYSSLSPMEDKNEVLWRRTDGADELELS----VVENAADS 407
P+V + A R +R +LS E + E+L D AD LE + + EN D
Sbjct: 281 PTVEQTGERDMAVAARESSRMLQALSS-EQRKEIL---HDIADALEDNEDEILAENKKDV 336
Query: 408 EAAEEMLLEELKVSR-AMSKD 427
AA+ V+R +MS
Sbjct: 337 AAAQGAGYAASLVARLSMSPS 357
>gnl|CDD|181127 PRK07807, PRK07807, inosine 5-monophosphate dehydrogenase;
Validated.
Length = 479
Score = 29.9 bits (68), Expect = 4.0
Identities = 13/47 (27%), Positives = 22/47 (46%)
Query: 420 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILT 466
V MS D V + +EA + ++ + VV+ + L G+LT
Sbjct: 150 VRDVMSTDLVTLPAGTDPREAFDLLEAARVKLAPVVDADGRLVGVLT 196
>gnl|CDD|225365 COG2807, CynX, Cyanate permease [Inorganic ion transport and
metabolism].
Length = 395
Score = 29.9 bits (68), Expect = 4.1
Identities = 22/105 (20%), Positives = 38/105 (36%), Gaps = 15/105 (14%)
Query: 256 LCKGSGLVGGLYAPSLMIGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALV------- 308
+ G + P L +G + G+ +IN +P + P+ L+
Sbjct: 87 IAAGILIRSLGGLPLLF----LGTLLAGAGIAVINVLLPSLIKRDFPKRVGLMTGLYSTS 142
Query: 309 -GMAATLASVCSVPLTSVLLLFELTRDYRILLPLMGAVGLAIWVP 352
G A LA+ +VPL + L+ + L IW+P
Sbjct: 143 LGAGAALAAALAVPLAQHSGGWRGA---LGFWALLALLALLIWLP 184
>gnl|CDD|240009 cd04638, CBS_pair_25, 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 = 106
Score = 28.1 bits (63), Expect = 4.8
Identities = 29/118 (24%), Positives = 50/118 (42%), Gaps = 26/118 (22%)
Query: 427 DFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDS 486
+ V V L T + +E +K+ + + V VV L GI+T D+ R N + +
Sbjct: 2 NVVYVTLPGTRDDVLELLKEYKVSGVPVVKKSGELVGIITRKDLLR--------NPEEEQ 53
Query: 487 IASDVNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSR 544
+A L++ R T PD D+ A +LM I+++PV+ +
Sbjct: 54 LA-----LLMT-------------RDPPTVSPDDDVKEAAKLMVENNIRRVPVVDDGK 93
>gnl|CDD|237158 PRK12650, PRK12650, putative monovalent cation/H+ antiporter
subunit A; Reviewed.
Length = 962
Score = 30.0 bits (68), Expect = 4.8
Identities = 23/92 (25%), Positives = 38/92 (41%), Gaps = 5/92 (5%)
Query: 264 GGLYAPSLMIGAAVGAV--FGGSAAEIINSAIPGNVAVAE-PQAYALVGMAATLASVCSV 320
G L++GAA+GAV F SA ++ + + G ++ +A + + A L S+
Sbjct: 405 GNAGVVLLLVGAALGAVFTFAYSARLVLGAFVDGPRDMSHVKEAPVSLWLPAALPGALSL 464
Query: 321 PLTSVLLLFELTRDYRILLPLMGAVG--LAIW 350
PL V L + LA+W
Sbjct: 465 PLGLVPGLLDAPVSAAATAAAGEHAHTHLALW 496
>gnl|CDD|222896 PHA02592, 52, DNA topisomerase II medium subunit; Provisional.
Length = 439
Score = 29.6 bits (67), Expect = 5.0
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 6/49 (12%)
Query: 546 LQRRRKQRIVAI-----LH-YDSIWNCLREEVNHRKSVYQHSKDKNLEE 588
L R Q I I L Y++ + +R+ V RK+ Q ++E
Sbjct: 293 LIERVSQNITVINENGKLKVYENAEDLIRDFVEIRKTYVQKRIQYEIKE 341
>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 = 28.0 bits (63), Expect = 5.0
Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 419 KVSRAMS--KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRC 473
V + M+ V V +L E ++ +++ + + VV + G++T D+ R
Sbjct: 58 TVIQVMTPAAKLVTVLSEESLAEVLKLLEEQGLDELAVVEDSGQVIGLITEADLLRR 114
>gnl|CDD|212032 cd10322, SLC5sbd, Solute carrier 5 family, sodium/glucose
transporters and related proteins; solute-binding
domain. This family represents the solute-binding
domain of SLC5 proteins (also called the sodium/glucose
cotransporter family or solute sodium symporter family)
that co-transport Na+ with sugars, amino acids,
inorganic ions or vitamins. Family members include: the
human glucose (SGLT1, 2, 4, 5), chiro-inositol (SGLT5),
myo-inositol (SMIT), choline (CHT), iodide (NIS),
multivitamin (SMVT), and monocarboxylate (SMCT)
cotransporters, as well as Vibrio parahaemolyticus
glucose/galactose (vSGLT), and Escherichia coli proline
(PutP) and pantothenate (PutF) cotransporters. Vibrio
parahaemolyticus Na(+)/galactose cotransporter (vSGLT)
has 13 transmembrane helices (TMs): TM-1, an inverted
topology repeat: TMs1-5 and TMs6-10, and TMs 11-12 (TMs
numbered to conform to the solute carrier 6 family
Aquifex aeolicus LeuT). One member of this family, human
SGLT3, has been characterized as a glucose sensor and
not a transporter. Members of this family are important
in human physiology and disease.
Length = 455
Score = 29.4 bits (67), Expect = 5.7
Identities = 23/96 (23%), Positives = 36/96 (37%), Gaps = 18/96 (18%)
Query: 123 IILASVIS---STVSTVLLGTQSAFTVPSYDL-----KSAAELPLYLILGMLCGVVSVVF 174
++LA +++ ST ++LL + FT D+ A L +G + VV V
Sbjct: 312 LVLAGLLAAIMSTADSLLLAASTLFT---RDIYKRLINPKASDKKLLRVGRIATVVVGVL 368
Query: 175 TRLVAWFTKS-----FDFIKEKFGLPPVVCPALGGL 205
L+A F S + P L GL
Sbjct: 369 ALLLALFPPSIILLLSLAA--GLLAAALFPPLLLGL 402
>gnl|CDD|225457 COG2905, COG2905, Predicted signal-transduction protein containing
cAMP-binding and CBS domains [Signal transduction
mechanisms].
Length = 610
Score = 29.7 bits (67), Expect = 6.1
Identities = 13/54 (24%), Positives = 28/54 (51%)
Query: 419 KVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 472
+V + V V+ ++++A MKD + ++V++ L GI+T D++
Sbjct: 150 RVGEVKTLPAVTVSPQASIQDAARKMKDEGVSSLVVLDDSGPLLGIVTRKDLRS 203
>gnl|CDD|214688 smart00483, POLXc, DNA polymerase X family. includes vertebrate
polymerase beta and terminal
deoxynucleotidyltransferases.
Length = 334
Score = 29.3 bits (66), Expect = 6.6
Identities = 13/53 (24%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 522 LAIAKELMEAKGIKQLPVIKRSRELQRRRKQRIVAILHYDSIWNCL-REEVNH 573
A + KGI+ L +K+++EL+ ++Q+ + +Y+ I + R E
Sbjct: 99 PKTAAKWYR-KGIRTLEELKKNKELKLTKQQKA-GLKYYEDILKKVSRAEAFA 149
>gnl|CDD|215154 PLN02274, PLN02274, inosine-5'-monophosphate dehydrogenase.
Length = 505
Score = 29.3 bits (66), Expect = 6.9
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 417 ELKVSRAMSKD--FVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 472
E K+S M+ D V + L+EA +KD ++ + +VN + L ++T D+KR
Sbjct: 162 ETKLSEVMTSDDDLVTAPAGIDLEEAEAVLKDSKKGKLPLVNEDGELVDLVTRTDVKR 219
>gnl|CDD|178102 PLN02484, PLN02484, probable pectinesterase/pectinesterase
inhibitor.
Length = 587
Score = 29.1 bits (65), Expect = 7.0
Identities = 20/73 (27%), Positives = 22/73 (30%), Gaps = 9/73 (12%)
Query: 48 LGPEGPSVDIGKSCANGFSLMMENNRERKIALVAAGAASGIASGFNAAVAGCFFAIETVL 107
LGP G S S A E R RK LV I S A A F +
Sbjct: 6 LGPSGASGPNQTSTATALP---ELRRRRKTKLVLFSIVLLIVS---AVAAAIFAGVRAK- 58
Query: 108 RPLRAENSPPFTT 120
+ SP
Sbjct: 59 --ASGQTSPKSLH 69
>gnl|CDD|239173 cd02772, MopB_NDH-1_NuoG2, MopB_NDH-1_NuoG2: The second domain of
the NuoG subunit of the NADH-quinone oxidoreductase/NADH
dehydrogenase-1 (NDH-1), found in beta- and
gammaproteobacteria. The NDH-1 is the first
energy-transducting complex in the respiratory chain and
functions as a redox pump that uses the redox energy to
translocate H+ ions across the membrane, resulting in a
significant contribution to energy production. In
Escherichia coli NDH-1, the largest subunit is encoded
by the nuoG gene, and is part of the 14 distinct
subunits constituting the functional enzyme. The NuoG
subunit is made of two domains: the first contains three
binding sites for FeS clusters (the fer2 domain), the
second domain (this CD), is of unknown function or, as
postulated, has lost an ancestral formate dehydrogenase
activity that became redundant during the evolution of
the complex I enzyme. Although only vestigial sequence
evidence remains of a molybdopterin binding site, this
protein domain belongs to the molybdopterin_binding
(MopB) superfamily of proteins.
Length = 414
Score = 28.9 bits (65), Expect = 7.6
Identities = 24/98 (24%), Positives = 35/98 (35%), Gaps = 16/98 (16%)
Query: 231 TGKTASAPGIWL--LTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVGAVFGGSAAEI 288
+GK AP L Q+A A +A GL P AA +
Sbjct: 199 SGKAIVAPSALANALAQVAKA--LAEEK--------GLAVPDEDAKVEASEEARKIAASL 248
Query: 289 INSA----IPGNVAVAEPQAYALVGMAATLASVCSVPL 322
+++ GN+A PQA L +A +A + L
Sbjct: 249 VSAERAAVFLGNLAQNHPQAATLRALAQEIAKLTGATL 286
>gnl|CDD|236386 PRK09129, PRK09129, NADH dehydrogenase subunit G; Validated.
Length = 776
Score = 29.1 bits (66), Expect = 8.7
Identities = 27/96 (28%), Positives = 37/96 (38%), Gaps = 12/96 (12%)
Query: 231 TGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVGAVFGGSAAEIIN 290
+ AP W A VA A KG L L ++ AA A+ A + N
Sbjct: 417 AQRIIVAPSAWADALAGVAAAVAAA--KGVALPEAL--AKVLAAAAARAI----AQSLAN 468
Query: 291 SA----IPGNVAVAEPQAYALVGMAATLASVCSVPL 322
+ GN+AV PQA L +A +A + L
Sbjct: 469 GERAAILLGNLAVNHPQAATLRALAQWIAKLTGATL 504
>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 = 27.2 bits (61), Expect = 8.9
Identities = 30/129 (23%), Positives = 51/129 (39%), Gaps = 30/129 (23%)
Query: 431 VALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIASD 490
V + ++++A M++ + +LV +G+ L GI+T D+ L + D
Sbjct: 6 VDASTSIRDAARLMREHGADALLVRDGDPRL-GIVTRTDL---LDAVLLDG-------LP 54
Query: 491 VNTCLVSSICTRGISYRGRERGLLTCYPDTDLAIAKELMEAKGIKQLPVIKRSRELQRRR 550
+T V I T + L+T PD L A LM I ++ V R
Sbjct: 55 SST-PVGEIAT----FP-----LITVDPDDFLFNALLLMTRHRIHRVVV---------RE 95
Query: 551 KQRIVAILH 559
+V +L
Sbjct: 96 GGEVVGVLE 104
>gnl|CDD|239975 cd04602, CBS_pair_IMPDH_2, This cd contains two tandem repeats of
the cystathionine beta-synthase (CBS pair) domains in
the inosine 5' monophosphate dehydrogenase (IMPDH)
protein. IMPDH is an essential enzyme that catalyzes
the first step unique to GTP synthesis, playing a key
role in the regulation of cell proliferation and
differentiation. CBS is a small domain originally
identified in cystathionine beta-synthase and
subsequently found in a wide range of different
proteins. CBS domains usually come in tandem repeats,
which associate to form a so-called Bateman domain or a
CBS pair which is reflected in this model. The interface
between the two CBS domains forms a cleft that is a
potential ligand binding site. The CBS pair coexists
with a variety of other functional domains. It has been
proposed that the CBS domain may play a regulatory role,
although its exact function is unknown. Mutations of
conserved residues within this domain in IMPDH have been
associated with retinitis pigmentosa.
Length = 114
Score = 27.6 bits (62), Expect = 9.1
Identities = 15/59 (25%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 416 EELKVSRAMSK--DFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 472
E +S M+ V +TL+EA E +++ ++ + +VN + L ++T D+K+
Sbjct: 55 SETPLSEVMTPREVLVVAPTGITLEEANEILRESKKGKLPIVNDDGELVALVTRSDLKK 113
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 28.6 bits (65), Expect = 9.3
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 559 HYDSIWNCLREEVNHRKSVYQHSKDKNLEEISN 591
Y ++ L+E + HR VY+ K+ LE++
Sbjct: 302 KYLNLKEILKEFLEHRLEVYKRRKEYLLEKLEE 334
>gnl|CDD|216818 pfam01970, TctA, Tripartite tricarboxylate transporter TctA family.
This family, formerly known as DUF112, is a family of
bacterial and archaeal tripartite tricarboxylate
transporters of the extracytoplasmic solute binding
receptor-dependent transporter group of families,
distinct from the ABC and TRAP-T families. TctA is part
of the tripartite TctABC system which, as characterized
in S. typhimurium, is a secondary carrier that depends
for activity on the extracytoplasmic
tricarboxylate-binding receptor TctC as well as two
integral membrane proteins, TctA and TctB. complete
three-component systems are found only in bacteria. TctA
is a large transmembrane protein with up to 12 predicted
membrane spanning regions in bacteria and up to 11 such
in archaea, with the N-terminal within the cytoplasm.
TctA is thought to be a permease, and in most other
bacteria functions without TctB and TctC molecules.
Length = 418
Score = 28.6 bits (65), Expect = 9.5
Identities = 31/96 (32%), Positives = 42/96 (43%), Gaps = 23/96 (23%)
Query: 266 LYAPSLMIGAAVGAVFGGSAAEI-INSAIPG---NVAVAEP--------QAYALVGMAAT 313
L A L+ G GA +GGS I +N IPG + A +A +G+AA
Sbjct: 40 LSALILLAGIYYGATYGGSIPAILLN--IPGTPASAATVLDGYPMAKQGRAGEALGLAA- 96
Query: 314 LASVCSVPLTSVLLLFELTRDYRILLPLMGAVGLAI 349
+AS L SVLLL +L P++ V L
Sbjct: 97 IASFIGG-LISVLLLI-------LLAPVLAKVALKF 124
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
0.319 0.134 0.385
Gapped
Lambda K H
0.267 0.0701 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 30,002,254
Number of extensions: 3022440
Number of successful extensions: 4227
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4073
Number of HSP's successfully gapped: 254
Length of query: 593
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 491
Effective length of database: 6,413,494
Effective search space: 3149025554
Effective search space used: 3149025554
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 62 (27.7 bits)