RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 005685
(683 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 = 320 bits (823), Expect = e-103
Identities = 163/408 (39%), Positives = 227/408 (55%), Gaps = 28/408 (6%)
Query: 98 GLASGLCVAFFNKGVHIIHEWAWAGTPNEGAAWLRLQRLADTWHRILLIPVTGGVIVGMM 157
G+ SGL F + ++ + G P E AA ILL+PV GG++VG++
Sbjct: 1 GVLSGLGAVLFRLLIELLQNLLFGGLPGELAAGSLS------PLYILLVPVIGGLLVGLL 54
Query: 158 HGLL--EILNQIKQSSSLDRQGFDLVAGVFPTIKAIQAAVTLGTGCSLGPEGPSVDIGKS 215
LL + I + G + +K + +A+TLG+G S+G EGP V IG +
Sbjct: 55 VRLLGPARGHGIPEVIEAIALGGGRLPLRVALVKFLASALTLGSGGSVGREGPIVQIGAA 114
Query: 216 CANGFSLMMENNRERKIALVAAGAASGIASGFNAAVAGCFFAIETVLRPLRAENSPPFTT 275
+ + +R + LVA GAA+GIA+ FNA +AG FAIE +L +
Sbjct: 115 IGSWLGRRLRLSRNDRRILVACGAAAGIAAAFNAPLAGALFAIEVLLGEYSVA-----SL 169
Query: 276 AMIILASVISSTVSTVLLGTQSAFTVPSYDLKSAAELPLYLILGMLCGVVSVVFTRLVAW 335
++LASV ++ VS +L G + AF VP YD S ELPLYL+LG+L G+V V+F RL+
Sbjct: 170 IPVLLASVAAALVSRLLFGAEPAFGVPLYDPLSLLELPLYLLLGLLAGLVGVLFVRLLYK 229
Query: 336 FTKSFDFIKEKFGLPPVVCPALGGLGAGIIALRYPGILYWGFTNVEEILHTGKTASAPGI 395
+ F + +PP + PALGGL G++ L P +L G+ + L A +
Sbjct: 230 IERLF----RRLPIPPWLRPALGGLLLGLLGLFLPQVLGSGYGAILLAL-----AGELSL 280
Query: 396 WLLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVGAVFGGSAAEIINSAIPGNVAVA 455
LL L K++ATAL GSG GG++APSL IGAA+GA FG ++ + PG VA
Sbjct: 281 LLLLLLLLLKLLATALTLGSGFPGGVFAPSLFIGAALGAAFG----LLLPALFPG--LVA 334
Query: 456 EPQAYALVGMAATLASVCSVPLTSVLLLFELTRDYRILLPLMGAVGLA 503
P AYALVGMAA LA+V PLT++LL+ ELT DY +LLPLM AV +A
Sbjct: 335 SPGAYALVGMAALLAAVLRAPLTAILLVLELTGDYSLLLPLMLAVVIA 382
>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 = 248 bits (637), Expect = 1e-76
Identities = 130/319 (40%), Positives = 191/319 (59%), Gaps = 18/319 (5%)
Query: 188 IKAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFSLMMENNRERKIALVAAGAASGIASGF 247
+K + +TLG+G SLG EGPSV IG + +G ++ +R + L+AAGAA+GIA+ F
Sbjct: 42 VKFLGTLLTLGSGGSLGREGPSVQIGAAIGSGLGRRLKLSRNDRRRLIAAGAAAGIAAAF 101
Query: 248 NAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLLGTQSAFTVPSYDLK 307
NA +AG FA+E + R +++ASV+++ VS +L G + F VPS
Sbjct: 102 NAPLAGVLFALEELSRSFSYR-----ALLPVLVASVVAALVSRLLFGNEPLFEVPSLPPL 156
Query: 308 SAAELPLYLILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAGIIAL 367
S ELPL+++LG+LCG++ +F RL+ + F + LPP++ PALGGL G++ L
Sbjct: 157 SLLELPLFILLGILCGLLGALFVRLLLKVERLF---RRLKKLPPILRPALGGLLVGLLGL 213
Query: 368 RYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLM 427
P +L G+ ++ +L+ S + LL L K++ATAL GSG GG++APSL
Sbjct: 214 FLPEVLGGGYGLIQLLLN----GSTLSLLLLLLLLLLKLLATALSLGSGAPGGIFAPSLF 269
Query: 428 IGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELT 487
IGAA+G + G ++ PG P A+AL+GMAA LA V PLT+++L+FELT
Sbjct: 270 IGAALGRLLG----LLLPLLFPGI--APSPGAFALLGMAAFLAGVTRAPLTAIVLVFELT 323
Query: 488 RDYRILLPLMGAVGLAIWV 506
Y +LLPLM AV +A V
Sbjct: 324 GSYSLLLPLMLAVLIAYLV 342
Score = 52.9 bits (128), Expect = 3e-07
Identities = 46/155 (29%), Positives = 64/155 (41%), Gaps = 23/155 (14%)
Query: 357 LGGLGAGIIALRYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSG 416
+GGL AG++ R+P G V LH K + L K + T L GSG
Sbjct: 1 IGGLLAGLLVKRFPEAAGSGIPEVIAALHGVK----GPLPLRV--LLVKFLGTLLTLGSG 54
Query: 417 LVGGLYAPSLMIGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALV--GMAATLASVCS 474
G PS+ IGAA+G+ G ++ L+ G AA +A+ +
Sbjct: 55 GSLGREGPSVQIGAAIGSGLGRRL------------KLSRNDRRRLIAAGAAAGIAAAFN 102
Query: 475 VPLTSVLLLFELTRD---YRILLPLMGAVGLAIWV 506
PL VL E YR LLP++ A +A V
Sbjct: 103 APLAGVLFALEELSRSFSYRALLPVLVASVVAALV 137
Score = 32.1 bits (74), Expect = 0.92
Identities = 44/226 (19%), Positives = 78/226 (34%), Gaps = 46/226 (20%)
Query: 79 SLTESAPPEWALLLIGCLLGLASGLCVAFFNKGVHIIHEWAWAGTPNEGAAWLRLQRLAD 138
+ P L + LLG+ GL A F + + + + RL++L
Sbjct: 149 EVPSLPPLSLLELPLFILLGILCGLLGALFVRLLLKVERL-----------FRRLKKL-- 195
Query: 139 TWHRILLIPVTGGVIV-----------GMMHGLLEILNQIKQSSSLDRQGFDLVAGVFPT 187
+L P GG++V G +GL+++L L+ +
Sbjct: 196 ---PPILRPALGGLLVGLLGLFLPEVLGGGYGLIQLLLN-------GSTLSLLLLLLLLL 245
Query: 188 IKAIQAAVTLGTGCSLGPEGPSVDIG----KSCANGFSLMMENNRERKIALVAAGAASGI 243
+K + A++LG+G G PS+ IG + L+ A G A+ +
Sbjct: 246 LKLLATALSLGSGAPGGIFAPSLFIGAALGRLLGLLLPLLFPGIAPSPGAFALLGMAAFL 305
Query: 244 ASGFNAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVS 289
A A + E S +++ A +I+ VS
Sbjct: 306 AGVTRAPLTAIVLVFELT-------GSYSLLLPLML-AVLIAYLVS 343
>gnl|CDD|223116 COG0038, EriC, Chloride channel protein EriC [Inorganic ion
transport and metabolism].
Length = 443
Score = 210 bits (536), Expect = 6e-61
Identities = 124/432 (28%), Positives = 208/432 (48%), Gaps = 50/432 (11%)
Query: 89 ALLLIGCLLGLASGLCVAFFNKGVHIIHEWAWAGTPNEGAAWLRLQRLADTWHRILLIPV 148
L+ I LG+ GL + + A L + W L+ +
Sbjct: 21 VLIGIAAALGVIVGLF--------AVALDLALLLLGRLRGGLLSAAQAPGPWLLPLVPAL 72
Query: 149 TGGVIVGMM----------HGLLEILNQIKQSSSLDRQGFDLVAGVFPTIKAIQAAVTLG 198
G ++ ++ G+ Q ++ + +K + +T+G
Sbjct: 73 GGLLVGALLVYKFAPEARGSGI----PQAIEALHGRKGRISPRVLP---VKLVATLLTIG 125
Query: 199 TGCSLGPEGPSVDIGKSCANGFSLMMENNRERKIALVAAGAASGIASGFNAAVAGCFFAI 258
+G SLG EGPSV IG + + +++ +RE + L+AAGAA+G+A+ FNA +AG FAI
Sbjct: 126 SGASLGREGPSVQIGAAIGSLLGRLLKLSREDRRILLAAGAAAGLAAAFNAPLAGALFAI 185
Query: 259 ETVLRPLRAENSPPFTTAMI---ILASVISSTVSTVLLGTQSAFTVPSYDLKSAAELPLY 315
E + + ++A+V++ V+ + G + + S +L LY
Sbjct: 186 EVLYGRF-------LEYRALVPVLVAAVVALLVAGLFGGPHFLLPIVTTPHMSLWDLLLY 238
Query: 316 LILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAGIIALRYPGILYW 375
L+LG++ G+ V+ +RL+A + F + LPP++ PALGGL G + L +P +L
Sbjct: 239 LVLGIIAGLFGVLLSRLLALSRRFFRRLP----LPPLLRPALGGLLVGALGLLFPEVLGN 294
Query: 376 GFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVGAV 435
G+ ++ L + L K++AT L GSG GG++APSL IGAA+G
Sbjct: 295 GYGLIQLALAGEGGLLVLLL-----LFLLKLLATLLSYGSGAPGGIFAPSLFIGAALGLA 349
Query: 436 FGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELTRDYRILLP 495
FG ++ P + + EP +AL+GMAA LA+ PLT+++L+ E+T +Y++LLP
Sbjct: 350 FG----ALLGLLFPPS--ILEPGLFALLGMAAFLAATTRAPLTAIVLVLEMTGNYQLLLP 403
Query: 496 LMGAVGLAIWVP 507
L+ A +A V
Sbjct: 404 LLIACLIAYLVS 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 = 193 bits (494), Expect = 2e-55
Identities = 97/319 (30%), Positives = 157/319 (49%), Gaps = 21/319 (6%)
Query: 189 KAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFS-LMMENNRERKIALVAAGAASGIASGF 247
K + + LG+G SLG EGPSV IG + G S + ER+ L+AAGAA+G+A+ F
Sbjct: 89 KFVGGVLALGSGLSLGREGPSVQIGAAIGQGVSKWFKTSPEERRQ-LIAAGAAAGLAAAF 147
Query: 248 NAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLLGTQSAFTVPSYDLK 307
NA +AG F +E + + P ++AS+ + VS + G ++P
Sbjct: 148 NAPLAGVLFVLEELRH-----SFSPLALLTALVASIAADFVSRLFFGLGPVLSIPPLPAL 202
Query: 308 SAAELPLYLILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAGIIAL 367
L L+LG++ G++ +F R + + +K LP + L GL G + L
Sbjct: 203 PLKSYWLLLLLGIIAGLLGYLFNRSLLKSQDLYRKLK---KLPRELRVLLPGLLIGPLGL 259
Query: 368 RYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLM 427
P L G + + I LL + + + T L GSG GG++AP L
Sbjct: 260 LLPEALGGGHGLILSLAGGN-----FSISLLLLIFVLRFIFTMLSYGSGAPGGIFAPMLA 314
Query: 428 IGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELT 487
+GA +G +FG ++ G + ++ P +A+ GMAA A+V P+T+++L+ E+T
Sbjct: 315 LGALLGLLFGTILVQL------GPIPISAPATFAIAGMAAFFAAVVRAPITAIILVTEMT 368
Query: 488 RDYRILLPLMGAVGLAIWV 506
++ +LLPLM +A V
Sbjct: 369 GNFNLLLPLMVVCLVAYLV 387
Score = 41.4 bits (98), Expect = 0.001
Identities = 54/200 (27%), Positives = 78/200 (39%), Gaps = 25/200 (12%)
Query: 319 GMLCGVVSVVFTRLV----AWFTKSFDFIKEKFGLP---PVVCPALGGLGAGIIALRYPG 371
G+L G+V+V+F + +DF L P++ LG L ++ P
Sbjct: 2 GLLAGLVAVLFRLGIDKLGNLRLSLYDFAANNPPLLLVLPLISAVLGLLAGWLVKKFAPE 61
Query: 372 ILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAA 431
G VE +L G P W ++ K V L GSGL G PS+ IGAA
Sbjct: 62 AKGSGIPQVEGVL-AGLL---PPNWW--RVLPVKFVGGVLALGSGLSLGREGPSVQIGAA 115
Query: 432 VGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFE-LTRDY 490
+G S +A G AA LA+ + PL VL + E L +
Sbjct: 116 IGQGVSKWFKT---SPEERRQLIA-------AGAAAGLAAAFNAPLAGVLFVLEELRHSF 165
Query: 491 RILLPLMGAVGLAIWVPSVA 510
L L+ A+ +I V+
Sbjct: 166 SPLA-LLTALVASIAADFVS 184
>gnl|CDD|234987 PRK01862, PRK01862, putative voltage-gated ClC-type chloride
channel ClcB; Provisional.
Length = 574
Score = 192 bits (490), Expect = 3e-53
Identities = 129/418 (30%), Positives = 208/418 (49%), Gaps = 42/418 (10%)
Query: 90 LLLIGCLLGLASGLCVAFFNKGVHIIHEWAWAGTPNEGAAWLRLQRLADTWHRILLIPVT 149
+L+ ++G+ F +G+ +I + + G+ + L R+ L P
Sbjct: 24 MLIWSAIVGIGGAFATTAFREGIELIQHLI---SGHSGSFVEMAKSLPWYV-RVWL-PAA 78
Query: 150 GGVIVGMMHGLLEILNQIKQSSSLDRQGFDLVA---GVFPT----IKAIQAAVTLGTGCS 202
GG + G +L + N+ + + VA GV P ++ + +T+G+G S
Sbjct: 79 GGFLAGC---VLLLANRGARKGG-KTDYMEAVALGDGVVPVRQSLWRSASSLLTIGSGGS 134
Query: 203 LGPEGPSVDIGKSCANGFSLMMENNRERKIALVAAGAASGIASGFNAAVAGCFFAIETVL 262
+G EGP V + A+ + R LVA GAA+GI S +NA +AG FF E VL
Sbjct: 135 IGREGPMVQLAALAASLVGRFAHFDPPRLRLLVACGAAAGITSAYNAPIAGAFFVAEIVL 194
Query: 263 RPLRAENSPPFTTAMIILASVISSTVSTVLLGTQSAFTVPSYDLKSAAELPLYLILGMLC 322
+ E+ P +++ASV+++ V G Q + +P + + E+ L++ LG+LC
Sbjct: 195 GSIAMESFGP-----LVVASVVANIVMREFAGYQPPYEMPVFPAVTGWEVLLFVALGVLC 249
Query: 323 GVVSVVFTRLVAWFTKSFDFIKEKFG---LPPVVCPALGGLGAGIIALRYPGILYWGFTN 379
G F + D K +F +P V ALGGL G+I++ P + G++
Sbjct: 250 GA-------AAPQFLRLLDASKNQFKRLPVPLPVRLALGGLLVGVISVWVPEVWGNGYSV 302
Query: 380 VEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVGAVFGGS 439
V ILH T A L+ AK++ATA GSG VGG++ P+L +GA VG++FG +
Sbjct: 303 VNTILHAPWTWQALVAVLV-----AKLIATAATAGSGAVGGVFTPTLFVGAVVGSLFGLA 357
Query: 440 AAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELTRDYRILLPLM 497
++ PG + P AYA+VGM A LA PL ++L++FE+T Y+++LPLM
Sbjct: 358 M----HALWPG--HTSAPFAYAMVGMGAFLAGATQAPLMAILMIFEMTLSYQVVLPLM 409
>gnl|CDD|235385 PRK05277, PRK05277, chloride channel protein; Provisional.
Length = 438
Score = 164 bits (418), Expect = 2e-44
Identities = 109/444 (24%), Positives = 182/444 (40%), Gaps = 74/444 (16%)
Query: 91 LLIGCLLGLASGLCVAFFNKGVHIIHEWAWAGTPNEGAAWLRLQRLADTWHRILLIPVTG 150
L + ++G +GL F V + L + L+
Sbjct: 1 LFMAAVVGTLTGLVGVAFELAVDWVQNQ--------------RLGLLASVADNGLLLWIV 46
Query: 151 GVIVGMMHGLLEILNQIKQSSSLDRQGFDLV-------------------AGVFPT---- 187
++ + ++ G+ LV G+ P
Sbjct: 47 AFLISAVLAMI---------------GYFLVRRFAPEAGGSGIPEIEGALEGLRPVRWWR 91
Query: 188 ---IKAIQAAVTLGTGCSLGPEGPSVDIGKSCANGF-SLMMENNRERKIALVAAGAASGI 243
+K TLG+G LG EGP+V +G + + + E + L+AAGAA+G+
Sbjct: 92 VLPVKFFGGLGTLGSGMVLGREGPTVQMGGNIGRMVLDIFRLRSDEARHTLLAAGAAAGL 151
Query: 244 ASGFNAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLLGTQSAFTVPS 303
A+ FNA +AG F IE +RP + + + ++++ V + G Q+ V
Sbjct: 152 AAAFNAPLAGILFVIEE-MRPQFRYSLISIK--AVFIGVIMATIVFRLFNGEQAVIEVGK 208
Query: 304 YDLKSAAELPLYLILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAG 363
+ L L+L+LG++ G+ V+F +L+ FD + V+ G G
Sbjct: 209 FSAPPLNTLWLFLLLGIIFGIFGVLFNKLLLRTQDLFDRLHGGNKKRWVLMGGAVGGLCG 268
Query: 364 IIALRYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYA 423
++ L P + GF + L A I +L + A+ + T LC GSG GG++A
Sbjct: 269 LLGLLAPAAVGGGFNLIPIAL-----AGNFSIGMLLFIFVARFITTLLCFGSGAPGGIFA 323
Query: 424 PSLMIGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLL 483
P L +G +G FG AA + EP +A+ GM A A+ PLT ++L+
Sbjct: 324 PMLALGTLLGLAFGMVAAALFPQYHI------EPGTFAIAGMGALFAATVRAPLTGIVLV 377
Query: 484 FELTRDYRILLPLM----GAVGLA 503
E+T +Y+++LPL+ GA LA
Sbjct: 378 LEMTDNYQLILPLIITCLGATLLA 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 = 137 bits (347), Expect = 3e-35
Identities = 100/320 (31%), Positives = 157/320 (49%), Gaps = 27/320 (8%)
Query: 195 VTLGTGCSLGPEGPSVDIGKSCANGFS-LMMENNRERKIALVAAGAASGIASGFNAAVAG 253
VT+G G LG E ++G A FS + +R++ LVA A +G+A+ +N +AG
Sbjct: 94 VTVGLGAPLGREVAPREVGALLAQRFSDWLGLTVADRRL-LVACAAGAGLAAVYNVPLAG 152
Query: 254 CFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLLGTQSAFTVPSYDLKSAAELP 313
FA+E +LR + + + S I++ V+++L G + +P L S L
Sbjct: 153 ALFALEILLRTISLRS-----VVAALATSAIAAAVASLLKGDHPIYDIPPMQL-STPLLI 206
Query: 314 LYLILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAGIIALRYPGIL 373
L+ G + GVV+ F RL + + + L L G++++ +P IL
Sbjct: 207 WALLAGPVLGVVAAGFRRLSQAARAK---RPKGKRILWQM--PLAFLVIGLLSIFFPQIL 261
Query: 374 YWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVG 433
G + T T S LL L K+VAT L +G GGL PSL +GA +G
Sbjct: 262 GNGRALAQLAFSTTLTLS-----LLLILLVLKIVATLLALRAGAYGGLLTPSLALGALLG 316
Query: 434 AVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELTR-DYRI 492
A+ G + N+ +P +++A A+AL+G AA LA+ PLT+++L+ E TR +
Sbjct: 317 ALLGI----VWNALLP-PLSIA---AFALIGAAAFLAATQKAPLTALILVLEFTRQNPLF 368
Query: 493 LLPLMGAVGLAIWVPSVANQ 512
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 = 127 bits (322), Expect = 6e-32
Identities = 91/314 (28%), Positives = 140/314 (44%), Gaps = 35/314 (11%)
Query: 200 GCSLGPEGPSVDIGKSCANGFSLMMENNRERKIA-LVAAGAASGIASGFNAAVAGCFFAI 258
G S+G EGPSV IG + + L+ AG A+G+A+ FN +AG FAI
Sbjct: 94 GASVGREGPSVQIGAAVMLAIGRRLPKWGGLSERGLILAGGAAGLAAAFNTPLAGIVFAI 153
Query: 259 ETVLRPLRAENSPPFTTAMIILASVISSTVSTV-LLGTQSAFTVPSYDLKSAAELPLYLI 317
E + R + ++L +VI++ + ++ +LG F V + L L L+
Sbjct: 154 EELSR------DFELRFSGLVLLAVIAAGLVSLAVLGNYPYFGVAAVALPLGEAWLLVLV 207
Query: 318 LGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLP----PVVCPALGGLGAGIIALRYPGIL 373
G++ G+ +F RL+ + + PV+ AL GL +I L G+
Sbjct: 208 CGVVGGLAGGLFARLLVALSS---GLPGWVRRFRRRRPVLFAALCGLALALIGLVSGGLT 264
Query: 374 YW-GFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAV 432
+ G+ L G K +AT L SG+ GGL+APSL +GA +
Sbjct: 265 FGTGYLQARAALEGGGGLPL-------WFGLLKFLATLLSYWSGIPGGLFAPSLAVGAGL 317
Query: 433 GAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELTRDYRI 492
G++ A L+GMAA LA V PLT+ +++ E+T D ++
Sbjct: 318 GSLLAALLGS------------VSQGALVLLGMAAFLAGVTQAPLTAFVIVMEMTGDQQM 365
Query: 493 LLPLMGAVGLAIWV 506
LLPL+ A LA V
Sbjct: 366 LLPLLAAALLASGV 379
>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 = 114 bits (288), Expect = 4e-27
Identities = 87/355 (24%), Positives = 142/355 (40%), Gaps = 48/355 (13%)
Query: 188 IKAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFSLMM---ENNRERKIALVAAGAASGIA 244
IK++ + + +G SLG EGP V I N S + N ++ +++A AA+G+A
Sbjct: 81 IKSVGLVLAVASGLSLGKEGPLVHIATCVGNIISRLFPKYRRNEAKRREILSAAAAAGVA 140
Query: 245 SGFNAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLL------GTQSA 298
F A + G F++E V S F + S + V+ L GT
Sbjct: 141 VAFGAPIGGVLFSLEEV--------SYYFPLKT-LWRSFFCALVAAFTLKSLNPFGTGRL 191
Query: 299 --FTVPSYDLK-SAAELPLYLILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCP 355
F V YD EL +++LG+ G+ F + + + K PV+
Sbjct: 192 VLFEV-EYDRDWHYFELIPFILLGIFGGLYGAFFIKANIKWARFRKKSLLKRY--PVLEV 248
Query: 356 ALGGLGAGIIALRYPGI-------LYWGFT-----NVEEILHTGKTASAPGIW-LLTQLA 402
L L +I+ P L F + + + G++ L L
Sbjct: 249 LLVALITALISFPNPYTRLDMTELLELLFNECEPGDDNSLCCYRDPPAGDGVYKALWSLL 308
Query: 403 AAKVVATALCK---GSGLVGGLYAPSLMIGAAVGAVFG--------GSAAEIINSAIPGN 451
A ++ L G + G++ PS+ +GA G + G I +
Sbjct: 309 LALIIKLLLTIFTFGIKVPAGIFVPSMAVGALFGRIVGILVEQLAYSYPDSIFFACCTAG 368
Query: 452 VAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELTRDYRILLPLMGAVGLAIWV 506
+ P YA+VG AA L V + ++ V+++FELT +LPLM AV ++ WV
Sbjct: 369 PSCITPGLYAMVGAAAFLGGVTRMTVSLVVIMFELTGALNYILPLMIAVMVSKWV 423
>gnl|CDD|234963 PRK01610, PRK01610, putative voltage-gated ClC-type chloride
channel ClcB; Provisional.
Length = 418
Score = 108 bits (271), Expect = 4e-25
Identities = 104/421 (24%), Positives = 195/421 (46%), Gaps = 36/421 (8%)
Query: 91 LLIGCLLGLASGLCVAFFNKGVHIIHEWAWAGTPNEGAAWLRLQRLADTWHRILLIPVTG 150
LLI ++G+ + L VA F H + W N+ + + W R LL P G
Sbjct: 5 LLIATVVGILAALAVAGF---RHAMLLLEWLFLSNDSGSLVNAATNLSPWRR-LLTPALG 60
Query: 151 GVIVGMMHGLLEILNQIKQSSSLDRQ-------GFDLVAGVFPTIKAIQAAVTLGTGCSL 203
G+ G++ + Q + + D FD A + +K++ + + + +G ++
Sbjct: 61 GLAAGLLLWGWQKFTQQRPHAPTDYMEALQTDGQFDYAASL---VKSLASLLVVTSGSAI 117
Query: 204 GPEGPSVDIGKSCANGFSLMMENNRERKIALVAAGAASGIASGFNAAVAGCFFAIETVLR 263
G EG + + A+ F+ +E K+ +A GAA+G+AS ++A +AG F E +
Sbjct: 118 GREGAMILLAALAASCFAQRFTPRQEWKL-WIACGAAAGMASAYHAPLAGSLFIAEILFG 176
Query: 264 PLRAENSPPFTTAMIILASVISSTVSTVLLGTQSA-FTVPSYDLKSAAELPLYLILGMLC 322
L + P +++++V++ + +L G+ + + V A + L + G+L
Sbjct: 177 TLMLASLGP-----VVISAVVALLTTNLLNGSDALLYNVQLSVTVQARDYALIISTGLLA 231
Query: 323 GVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAGIIALRYPGILYWGFTNVEE 382
G+ + L+ + F +K L P ALGGL G+++L P + G++ V+
Sbjct: 232 GLCGPLLLTLMNASHRGFVSLK----LAPPWQLALGGLIVGLLSLFTPAVWGNGYSVVQS 287
Query: 383 ILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVGAVFGGSAAE 442
L + P + L+ + K++A GSG GG++ P+L +G A+G ++G
Sbjct: 288 FL-----TAPPLLMLIAGIFLCKLLAVLASSGSGAPGGVFTPTLFVGLAIGMLYG----R 338
Query: 443 IINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELTRDYRILLPLMGAVGL 502
+ +P + L GMA LA+ P+ S L++ E+T +Y++L L+ A +
Sbjct: 339 SLGLWLPDGEEIT--LLLGLTGMATLLAATTHAPIMSTLMICEMTGEYQLLPGLLIACVI 396
Query: 503 A 503
A
Sbjct: 397 A 397
>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 = 107 bits (269), Expect = 1e-24
Identities = 87/339 (25%), Positives = 137/339 (40%), Gaps = 55/339 (16%)
Query: 189 KAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFSLMM------ENNRERKIALVAAGAASG 242
K I LG+G LG EGP V I A S + N R++ ++AA A G
Sbjct: 99 KVIGLTCALGSGLPLGKEGPFVHISSIVAALLSKLTTFFSGIYENESRRMEMLAAACAVG 158
Query: 243 IASGFNAAVAGCFFAIETVLRPLRAENS-PPFTTAMI------ILASVISSTVSTVLLGT 295
+A F A + G F+IE N F A +LA S + L
Sbjct: 159 VACTFGAPIGGVLFSIEVTSTYFAVRNYWRGFFAATCGAFTFRLLAVFFSDQETITALFK 218
Query: 296 QSAFTVPSYDLKSAAELPLYLILGMLCGVVSVVFTRLVAW---FTKSFDFIKEKFGLPPV 352
+ F +D++ ELP++ +LG++CG++ +F L F + + P+
Sbjct: 219 TTFFVDFPFDVQ---ELPIFALLGIICGLLGALFVFLHRKIVRFRRKNRLFSKFLKRSPL 275
Query: 353 VCPALGGLGAGIIALRYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALC 412
+ PA+ L ++ +P L K V TAL
Sbjct: 276 LYPAIVALLTAVL--TFP------------------------FLTLFLFIVVKFVLTALA 309
Query: 413 KGSGLVGGLYAPSLMIGAAVGAVFGGSAAEIINSAIP-----GNVAVAEPQAYALVGMAA 467
+ G++ P +IGAA+G + G EI+ P G P YA+VG AA
Sbjct: 310 ITLPVPAGIFMPVFVIGAALGRLVG----EIMAVLFPEGIRGGISNPIGPGGYAVVGAAA 365
Query: 468 TLASVCSVPLTSVLLLFELTRDYRILLPLMGAVGLAIWV 506
+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 = 103 bits (260), Expect = 9e-24
Identities = 92/352 (26%), Positives = 138/352 (39%), Gaps = 68/352 (19%)
Query: 188 IKAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFS--------------LMMENNRERKIA 233
K I + +G LG EGP V +G G + N R+R+
Sbjct: 90 AKTISCICAVASGLPLGKEGPLVHLGAMIGAGLLQGRSRTLGCHVHLFQLFRNPRDRR-D 148
Query: 234 LVAAGAASGIASGFNAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLL 293
+ AGAA+G+AS F A + G F +E V + + A+++S+ V +
Sbjct: 149 FLVAGAAAGVASAFGAPIGGLLFVLEEVSTFFPVRLA-----WRVFFAALVSAFVIQIYN 203
Query: 294 GTQSAFTVP-------SYDLKSAAELPLYL-------ILGMLCGVVSVVFTRLVAWFTK- 338
S F + +PL L ++G++CG+++ +F RL F +
Sbjct: 204 SFNSGFELLDRSSAMFLSLTVFELHVPLNLYEFIPTVVIGVICGLLAALFVRLSIIFLRW 263
Query: 339 --SFDFIKEKFGLPPVVCPALGGLGAGIIALRYPGILYWGFTNVEEILHTGKTASAPGIW 396
F K V+ P L L Y I Y
Sbjct: 264 RRRLLFRKTAR--YRVLEPVL-------FTLIYSTIHYAPT------------------- 295
Query: 397 LLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVGAVFGGSAAEIINSAIPGNVAV-- 454
LL L +AL G + GG + PSL+IGAA+G + G I + I A
Sbjct: 296 LLLFLLI-YFWMSALAFGIAVPGGTFIPSLVIGAAIGRLVGLLVHRIAVAGIGAESATLW 354
Query: 455 AEPQAYALVGMAATLASVCSVPLTSVLLLFELTRDYRILLPLMGAVGLAIWV 506
A+P YAL+G AA L + + +++ ELT D LLPLM A+ +A V
Sbjct: 355 ADPGVYALIGAAAFLGGTTRLTFSICVIMMELTGDLHHLLPLMVAILIAKAV 406
>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 = 86.1 bits (213), Expect = 6e-20
Identities = 31/80 (38%), Positives = 49/80 (61%)
Query: 591 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGD 650
++KV+ T TLKEA+ M D +Q+CVLVV+ +DFLEGILT GDI+R L + + +
Sbjct: 1 TKYIKVSPTTTLKEALNLMLDEKQSCVLVVDSDDFLEGILTLGDIQRFLFTNKTTRVQPE 60
Query: 651 SIASDVCNCCLTFLNSRSLS 670
C ++ + ++ +S
Sbjct: 61 DETKQTNTCLVSSVCTKGIS 80
>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 = 79.6 bits (197), Expect = 1e-15
Identities = 82/348 (23%), Positives = 139/348 (39%), Gaps = 69/348 (19%)
Query: 188 IKAIQAAVTLGTGCSLGPEGPSVDIGKSCANGFS--------------LMMENNRERKIA 233
+K + +++ G +LG EGP + IG A G S N+R+++
Sbjct: 131 VKIVGVILSVSGGLALGKEGPMIHIGACIAAGLSQGGSTSLRLDFRWFRYFRNDRDKR-D 189
Query: 234 LVAAGAASGIASGFNAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTVLL 293
V GAA+G+A+ F A V G F++E V T +S+I + L
Sbjct: 190 FVTCGAAAGVAAAFGAPVGGVLFSLEEVASFWNQ-----ALTWRTFFSSMIVTFTLNFFL 244
Query: 294 -------------GTQSAFTVPS-YDLKSAAELPLYLILGMLCGVVSVVFTRLVAWFTKS 339
G F S L + EL ++++G++ G++ +F L T+
Sbjct: 245 SGCNSGKCGLFGPGGLIMFDGSSTKYLYTYFELIPFMLIGVIGGLLGALFNHLNHKVTR- 303
Query: 340 FDFIKEKFGLPPVVCPALGGLGAGIIA-LRYPGILYWGFTNVEEILHTGKTASAPGIWLL 398
F K ++ L + + + + +P L F + L W
Sbjct: 304 --FRKRINHKGKLLKVLEALLVSLVTSVVAFPQTL-LIFFVLYYFL---------ACW-- 349
Query: 399 TQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVGAVFGGSAAEIINSAIPGNVAVAEPQ 458
T G + GL+ P ++IGAA G + G I+ + G + +P
Sbjct: 350 ----------TF---GIAVPSGLFIPMILIGAAYGRLVG-----ILLGSYFGFTS-IDPG 390
Query: 459 AYALVGMAATLASVCSVPLTSVLLLFELTRDYRILLPLMGAVGLAIWV 506
YAL+G AA L V + ++ ++L ELT + L P+M + +A WV
Sbjct: 391 LYALLGAAAFLGGVMRMTVSLTVILLELTNNLTYLPPIMLVLMIAKWV 438
>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 = 72.6 bits (179), Expect = 1e-13
Identities = 100/421 (23%), Positives = 161/421 (38%), Gaps = 97/421 (23%)
Query: 93 IGCLLGLASGLCVAFFNKGVHIIHEWAWAGTPNEGAAWLRLQRLADTWHRILLIPVTGGV 152
+ L+GL G A F + E+ A WL + +P+ G+
Sbjct: 1 LALLIGLLVGSASALFLWSLDWATEFREA------HPWL-----------LPFLPL-AGL 42
Query: 153 IVGMMHGLLEILNQIKQSSSLDRQGFDLVAGVFPTIKAIQAA-----------VTLGT-- 199
++G ++ + G + G I+ I V GT
Sbjct: 43 LIGYLY---------------QKFGKNSEKGNNLIIEEIHGPEEGIPLRMAPLVLFGTVL 87
Query: 200 ----GCSLGPEGPSVDIGKSCANGFS-LMMENNRERKIALVAAGAASGIASGFNAAVAGC 254
G S G EG +V +G S A+ F + +R+I L+A G A+G A+ F +AG
Sbjct: 88 THLFGGSAGREGTAVQMGGSLADAFGRVFKLPEEDRRILLIA-GIAAGFAAVFGTPLAGA 146
Query: 255 FFAIE-TVLRPLRAENSPPFTTAMI--ILASVISSTVSTVLLGTQSAFTVPSYDLKSAAE 311
FA+E VL LR A+I ++A++++ VS LG + +
Sbjct: 147 IFALEVLVLGRLRYS-------ALIPCLVAAIVADWVSH-ALGLEHTHYHIVFIPTLDPL 198
Query: 312 LPLYLILGMLC-GVVSVVFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAGIIAL--- 367
L + +IL + G+ +F L+ + K +K P + P +GGL ++
Sbjct: 199 LFVKVILAGIIFGLAGRLFAELLHFLKKLL----KKRIKNPYLRPFVGGLLIILLVYLLG 254
Query: 368 --RYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPS 425
RY G+ G T + E G T P WLL K++ T + G+G GG P
Sbjct: 255 SRRYLGL---G-TPLIEDSFFGGTVY-PYDWLL------KLIFTVITLGAGFKGGEVTPL 303
Query: 426 LMIGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFE 485
IGA +G I+ + A +G A A + PL +++ E
Sbjct: 304 FFIGATLGNALAP----ILGLPVS---------LLAALGFVAVFAGATNTPLACIIMGIE 350
Query: 486 L 486
L
Sbjct: 351 L 351
>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 = 50.6 bits (122), Expect = 2e-08
Identities = 19/57 (33%), Positives = 32/57 (56%)
Query: 585 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSK 641
V M+ D V V +L+EA+E M++ + + VV+ + L GI+T D+ R L +
Sbjct: 1 VKDIMTPDVVTVPPDTSLEEALELMRENGISRLPVVDEDGKLVGIVTLRDLLRALLE 57
>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 = 46.3 bits (110), Expect = 3e-06
Identities = 16/50 (32%), Positives = 28/50 (56%)
Query: 591 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLS 640
+D V V+ T+ EA+ M + + + VV+ + L GI+T D+ R L+
Sbjct: 1 RDVVTVSPDDTVAEALRLMLEHGISGLPVVDDDGRLVGIVTERDLLRALA 50
Score = 44.0 bits (104), Expect = 2e-05
Identities = 19/51 (37%), Positives = 28/51 (54%)
Query: 585 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 635
V M++D V V+ +L+EA E M + + VV+ E L GI+T DI
Sbjct: 60 VGDVMTRDVVTVSPDTSLEEAAELMLEHGIRRLPVVDDEGRLVGIVTRSDI 110
>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 = 45.1 bits (107), Expect = 8e-06
Identities = 18/86 (20%), Positives = 38/86 (44%), Gaps = 4/86 (4%)
Query: 591 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGD 650
DF + +++EA+ M N ++V + E+ L+G++T+ DI L S +
Sbjct: 1 TDFPTIDEDASIREALHEMLKYNTNEIIVKDNEEKLKGVVTFTDI----LDLDLFESFLE 56
Query: 651 SIASDVCNCCLTFLNSRSLSLLCLSI 676
++ + + ++N L I
Sbjct: 57 KKVFNIVSQDVFYVNEEDTIDEALDI 82
>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 = 43.7 bits (104), Expect = 2e-05
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 594 VKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIA 653
+ V+ ++ +A+ + VLVV+ L G +T GDI+R L K S D +
Sbjct: 5 LLVSPDASILDALRKIDKNALRIVLVVDENGRLLGTVTDGDIRRALLK---GLSLDDPV- 60
Query: 654 SDVCN 658
S+V N
Sbjct: 61 SEVMN 65
Score = 29.4 bits (67), Expect = 1.9
Identities = 9/53 (16%), Positives = 26/53 (49%)
Query: 583 CQVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 635
VS M+++ + + + +E + M++ + +++ E + G+ T D+
Sbjct: 58 DPVSEVMNRNPITAKVGSSREEILALMRERSIRHLPILDEEGRVVGLATLDDL 110
>gnl|CDD|223591 COG0517, COG0517, FOG: CBS domain [General function prediction
only].
Length = 117
Score = 43.6 bits (103), Expect = 3e-05
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 585 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 637
V M+KD + V ++++A+ M + + V VV+ L GI+T DI R
Sbjct: 1 VKDIMTKDVITVKPDTSVRDALLLMSENGVSAVPVVDDGK-LVGIITERDILR 52
Score = 36.7 bits (85), Expect = 0.007
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 585 VSRAMSKDFVKVALTVTLKEAIESMKDGQQ-NCVLVVNGEDF-LEGILTYGDI 635
V M+K V V L+EA+E M + + + VV+ + L GI+T DI
Sbjct: 64 VKEVMTKPVVTVDPDTPLEEALELMVERHKIRRLPVVDDDGGKLVGIITLSDI 116
>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 = 42.1 bits (100), Expect = 8e-05
Identities = 16/54 (29%), Positives = 25/54 (46%)
Query: 595 KVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSK 648
V+ +LK+A+ M VV+ + L GI T GD++R L K +
Sbjct: 6 LVSPDTSLKDALLEMSRKGLGMTAVVDEDGRLVGIFTDGDLRRALEKGLDILTL 59
>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 = 39.8 bits (94), Expect = 1e-04
Identities = 18/48 (37%), Positives = 28/48 (58%)
Query: 592 DFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCL 639
D V V+ TL+EA+E +++ + VV+ E L GI+T DI + L
Sbjct: 1 DVVTVSPDTTLEEALELLRENGIRRLPVVDEEGRLVGIVTRRDIIKAL 48
>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 = 41.0 bits (97), Expect = 2e-04
Identities = 13/49 (26%), Positives = 24/49 (48%)
Query: 591 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCL 639
+D V + L E ++ + +N VV+ + L GI++ DI+ L
Sbjct: 1 RDVVTIPEDTPLNELLDVIAHSPENNFPVVDDDGRLVGIVSLDDIREIL 49
>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 = 41.2 bits (97), Expect = 2e-04
Identities = 13/54 (24%), Positives = 30/54 (55%)
Query: 584 QVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 637
+ + M++D + V+ + EA + + + +C+ VV+ L GI+T+ D+ +
Sbjct: 68 RAHQIMTRDPITVSPDTPVDEASKLLLENSISCLPVVDENGQLIGIITWKDLLK 121
>gnl|CDD|235148 PRK03655, PRK03655, putative ion channel protein; Provisional.
Length = 414
Score = 43.2 bits (102), Expect = 4e-04
Identities = 82/327 (25%), Positives = 131/327 (40%), Gaps = 58/327 (17%)
Query: 197 LGTGCSLGPEGP--SVDIGKSCANGFSLMMENNRERKIALVAAGAASGIASGFNAAVAGC 254
L G SLGPE P +V+I + A G L+ NR L +AG I + F VA
Sbjct: 111 LAGGVSLGPEHPIMTVNIALAVAIGARLLPRVNRMDWTILASAGT---IGALFGTPVAAA 167
Query: 255 FFAIETVLRPLRAENSPPFTTAMI--ILASVISSTVSTVLLGTQSAFTVPSY------DL 306
+T L N P + ++A+ + + + + + Y D+
Sbjct: 168 LIFSQT----LNGSNEVPLWDRLFAPLMAAAAGALTTGLFFHPHFSLPIAHYGQMEMTDI 223
Query: 307 KSAAELPLYLILGMLCGVVSV-VFTRLVAWFTKSFDFIKEKFGLPPVVCPALGGLGAGII 365
S A + + + G+V+V RL A + +K PV+ +GG GI+
Sbjct: 224 LSGAIVAA---IAIAAGMVAVWCLPRLHALMHR----LKN-----PVLVLGIGGFILGIL 271
Query: 366 -ALRYPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAP 424
+ P L+ G +++ + + SA +LL + A +V A G GG P
Sbjct: 272 GVIGGPLTLFKGLDEMQQ-MAANQAFSASDYFLLAVVKLAALVVAAAS---GFRGGRIFP 327
Query: 425 SLMIGAAVGA-----VFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLASVCSVPLTS 479
++ +G A+G V AA ++ AI G V V + + MAA + VP T+
Sbjct: 328 AVFVGVALGLMLHAHVPAVPAAITVSCAILGIVLVVTRDGWLSLFMAAVV-----VPDTT 382
Query: 480 VLLLFELTRDYRILLPLMGAVGLAIWV 506
LLPL+ V L W+
Sbjct: 383 -------------LLPLLCIVMLPAWL 396
>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 = 36.8 bits (86), Expect = 0.005
Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 2/50 (4%)
Query: 593 FVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI-KRCLSK 641
V+ T T++EA + M++ + +CVLV++G L GI T DI R +++
Sbjct: 3 PATVSPTTTVQEAAKLMREKRVSCVLVMDGNK-LVGIFTSKDIALRVVAQ 51
>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 = 36.7 bits (85), Expect = 0.008
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 578 FSIPPCQVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGED--FLEGILTYGDI 635
+P V AMS + + ++++A++ M + + V+VV +D + GILT D+
Sbjct: 69 LDLP---VYDAMSSPVITASPNDSVRDAVDRMLENDDSSVVVVTPDDDTKVVGILTKKDV 125
Query: 636 KR 637
R
Sbjct: 126 LR 127
Score = 29.0 bits (65), Expect = 3.4
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 591 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 635
+D + V ++ +AI +++ + + VV+ L GI+T DI
Sbjct: 1 EDVITVREDDSVGKAINVLREHGISRLPVVDDNGKLTGIVTRHDI 45
>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 = 36.1 bits (84), Expect = 0.012
Identities = 24/92 (26%), Positives = 36/92 (39%), Gaps = 2/92 (2%)
Query: 545 TDGADELELSVVENAADSEAAEEMLLEELKL-LQFSIPPCQVSRAMSKDFVKVALTVTLK 603
DG L + +V A L+ L+ P V MS V V +
Sbjct: 31 VDGDRRL-VGIVTQRDLLRHARPDGRRPLRGRLRGRDKPETVGDIMSPPVVTVRPDTPIA 89
Query: 604 EAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 635
E + + DG + V VV+ + L GI+T D+
Sbjct: 90 ELVPLLADGGHHHVPVVDEDRRLVGIVTQTDL 121
>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 = 35.2 bits (82), Expect = 0.020
Identities = 15/52 (28%), Positives = 26/52 (50%)
Query: 584 QVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 635
V M++ V V + EA M++ Q + VV+ + L GI++ GD+
Sbjct: 59 TVGDVMTRGVVTVTEDDDVDEAARLMREHQVRRLPVVDDDGRLVGIVSLGDL 110
>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 = 0.024
Identities = 16/51 (31%), Positives = 26/51 (50%)
Query: 585 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 635
V M +DF V+ + TL + M+ G V VV+G L G++T ++
Sbjct: 58 VRGVMRRDFPTVSPSATLDAVLRLMQQGGAPAVPVVDGSGRLVGLVTLENV 108
>gnl|CDD|225778 COG3238, COG3238, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 150
Score = 35.3 bits (82), Expect = 0.038
Identities = 25/99 (25%), Positives = 37/99 (37%), Gaps = 21/99 (21%)
Query: 232 IALVAAGAASGIASGFNAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTV 291
+ + AGA + + N +A R SP +LAS+IS V TV
Sbjct: 8 LFAILAGALLPLQAAINGRLA-------------RYLGSP-------LLASLISFLVGTV 47
Query: 292 LLGTQSAFTVPSYDLKSAAELPLYLILGMLCGVVSVVFT 330
LL L + A P + +G L G + V +
Sbjct: 48 LLLILLLIKQGHPGLAAVASAPWWAWIGGLLGAI-FVTS 85
>gnl|CDD|218193 pfam04657, DUF606, Protein of unknown function, DUF606. This
family includes several uncharacterized bacterial
proteins.
Length = 139
Score = 34.8 bits (81), Expect = 0.043
Identities = 24/99 (24%), Positives = 38/99 (38%), Gaps = 20/99 (20%)
Query: 232 IALVAAGAASGIASGFNAAVAGCFFAIETVLRPLRAENSPPFTTAMIILASVISSTVSTV 291
+ + AGA + + NA + ++ SP +LAS++S V T+
Sbjct: 4 LLALLAGALLALQAAINARLG-------------KSLGSP-------LLASLVSFLVGTI 43
Query: 292 LLGTQSAFTVPSYDLKSAAELPLYLILGMLCGVVSVVFT 330
+L FT L + A P + LG L G V
Sbjct: 44 VLLLLLLFTRRPLSLGALASAPWWAWLGGLLGAFYVTLN 82
>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 = 34.6 bits (80), Expect = 0.043
Identities = 25/132 (18%), Positives = 50/132 (37%), Gaps = 14/132 (10%)
Query: 514 KETDASD--KRTLARGYSSLSPMEDKNEVLWRRTDG-----ADELELSVVENAADSEAAE 566
K+ D + L S + ++++ V+ ++G + + S
Sbjct: 8 KDDTLRDVVEILLTGKISGVPVVDNEGRVVGIVSEGDLIRKIYKGKGLFYVTLLYSV--- 64
Query: 567 EMLLEELKLLQFSIPPCQVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFL 626
+ L+E K+ + V M+K + V T+++ M + VV+ L
Sbjct: 65 -IFLDESKIKKLLGKK--VEEIMTKKVITVDEDTTIEDVARIMSKKNIKRLPVVDD-GKL 120
Query: 627 EGILTYGDIKRC 638
GI++ GDI R
Sbjct: 121 VGIISRGDIIRS 132
>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 = 35.9 bits (83), Expect = 0.044
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 583 CQVSRAM-SKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSK 641
+V M + D +A T + K+A+ M + + +V + + L G+ T GD++R L
Sbjct: 155 VKVKDLMQTTDLPLIAPTTSFKDALLEMSEKRLGSAIVCDENNQLVGVFTDGDLRRALLG 214
Query: 642 LSSDNS 647
S S
Sbjct: 215 GGSLKS 220
>gnl|CDD|239958 cd04585, CBS_pair_ACT_assoc2, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains in
the acetoin utilization proteins in bacteria. Acetoin
is a product of fermentative metabolism in many
prokaryotic and eukaryotic microorganisms. They produce
acetoin as an external carbon storage compound and then
later reuse it as a carbon and energy source during
their stationary phase and sporulation. In addition
these CBS domains are associated with a downstream ACT
domain, which is linked to a wide range of metabolic
enzymes that are regulated by amino acid concentration.
Pairs of ACT domains bind specifically to a particular
amino acid leading to regulation of the linked enzyme.
CBS is a small domain originally identified in
cystathionine beta-synthase and subsequently found in a
wide range of different proteins. CBS domains usually
come in tandem repeats, which associate to form a
so-called Bateman domain or a CBS pair which is
reflected in this model. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains. It has been proposed that the
CBS domain may play a regulatory role, although its
exact function is unknown.
Length = 122
Score = 34.2 bits (79), Expect = 0.061
Identities = 17/53 (32%), Positives = 32/53 (60%)
Query: 585 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 637
VS M++D + V+ +++EA E M + + + + VV+ + L GI+T D+ R
Sbjct: 69 VSDIMTRDPITVSPDASVEEAAELMLERKISGLPVVDDQGRLVGIITESDLFR 121
Score = 27.6 bits (62), Expect = 9.5
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 591 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 637
K+ + V +L EA++ MK+ + VV+ L GI+T D+K
Sbjct: 1 KNPITVTPDTSLMEALKLMKENSIRRLPVVDRGK-LVGIVTDRDLKL 46
>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 = 33.6 bits (78), Expect = 0.079
Identities = 14/48 (29%), Positives = 23/48 (47%)
Query: 594 VKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSK 641
+ V T+ EA + M + V+VV+ L GI + DI R ++
Sbjct: 4 ITVRPDATVAEAAKLMAEKNIGAVVVVDDGGRLVGIFSERDIVRKVAL 51
>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 = 35.7 bits (83), Expect = 0.083
Identities = 46/225 (20%), Positives = 78/225 (34%), Gaps = 37/225 (16%)
Query: 277 MIILASVISSTVSTVLLGTQSAFTVPSYDLKSAAELPLYLILGMLCGVVSVVFT-RLVAW 335
++ LA + + + G Q + +Y L + + G++ V+ RLV
Sbjct: 226 ILCLAYLFYNLAFNIKNGVQVYYF--TYVLGDPELFSYMGSIAIGAGLIGVLLFPRLVKK 283
Query: 336 FTKSFDFIKEKFGLPPVVCPALGGLGAGIIALRYPGILYWGFTNVEEILHTGKTASAPGI 395
F + F GG+ ++ I ++ +N+ IL + G
Sbjct: 284 FGRKILF--------------AGGILLMVLGY---LIFFFAGSNLPLIL-VLIILAGFGQ 325
Query: 396 WLLTQLAAAKVVATA----LCKG---SGLVGGLYAPSLMIGAAVGAVFGGSAAEIINSAI 448
+T L A V T G GLV + +G A+ G II
Sbjct: 326 NFVTGLVWALVADTVDYGEWKTGVRAEGLVYSVRTFVRKLGQALAGFLVGLILGII---- 381
Query: 449 PGNVAVAEPQAYALVGMAATLASVCSVP-LTSVLLLFELTRDYRI 492
G VA A L G+ + +VP L +L + R Y++
Sbjct: 382 -GYVANAAQSPITLNGIKILM---FAVPALFLLLAAIIIGRFYKL 422
>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 = 33.2 bits (76), Expect = 0.100
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 585 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCV--LVVNGEDFLEGILTYGDIKR 637
V+ AM+++ V ++ +L EA M ++ + L V E L GI+T G I
Sbjct: 53 VADAMTREVVTISPEASLLEAKRLM---EEKKIERLPVLRERKLVGIITKGTIAL 104
>gnl|CDD|215230 PLN02418, PLN02418, delta-1-pyrroline-5-carboxylate synthase.
Length = 718
Score = 35.5 bits (82), Expect = 0.11
Identities = 26/73 (35%), Positives = 33/73 (45%), Gaps = 9/73 (12%)
Query: 504 IWVPSVANQAKETDASDKRTLARGYSSLSPMEDKNEVLWRRTDGADELE----LSVVENA 559
+W PS A+E A R +R +LS E K +L D AD LE L EN
Sbjct: 287 LWAPSKEVGAREM-AVAARESSRKLQALSSEERKKILL----DVADALEANEELIKAENE 341
Query: 560 ADSEAAEEMLLEE 572
D AA+E E+
Sbjct: 342 LDVAAAQEAGYEK 354
>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 = 35.3 bits (82), Expect = 0.11
Identities = 15/53 (28%), Positives = 30/53 (56%)
Query: 585 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 637
V M++D V +TL+EA E + + + + +V+ + L G++T DI++
Sbjct: 145 VVMTMTEDLVTAPEGITLEEANEILHEHKIEKLPIVDDDGELVGLITRKDIEK 197
>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 = 32.7 bits (75), Expect = 0.19
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 594 VKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIA 653
V V TVT EAIE +K+ + + VV+ + G++T G++ LS LSS +
Sbjct: 5 VTVLPTVTCAEAIEILKEKGFDQLPVVDESGKILGMVTLGNL---LSSLSSGKVQPSDPV 61
Query: 654 SDVCN 658
S
Sbjct: 62 SKALY 66
>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 = 32.2 bits (74), Expect = 0.30
Identities = 18/53 (33%), Positives = 27/53 (50%)
Query: 585 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 637
V+ M D + V L+EA E M + + C+ VV+ + L GI+T D R
Sbjct: 69 VAEVMKTDVLTVTPDTPLREAAEIMVENKIGCLPVVDDKGTLVGIITRSDFLR 121
Score = 28.0 bits (63), Expect = 7.3
Identities = 16/51 (31%), Positives = 26/51 (50%)
Query: 599 TVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKG 649
+L +A E M++ + + VVN + L G+LT D+ R SDN +
Sbjct: 9 DDSLADAEELMREHRIRHLPVVNEDGKLVGLLTQRDLLRAALSSLSDNGEE 59
>gnl|CDD|239996 cd04624, CBS_pair_11, The CBS domain, named after human CBS, is a
small domain originally identified in cystathionine
beta-synthase and is subsequently found in a wide range
of different proteins. CBS domains usually occur in
tandem repeats. They associate to form a so-called
Bateman domain or a CBS pair based on crystallographic
studies in bacteria. The CBS pair was used as a basis
for this cd hierarchy since the human CBS proteins can
adopt the typical core structure and form an
intramolecular CBS pair. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains and this has been used to help
in its classification here. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown. Mutations of conserved
residues within this domain are associated with a
variety of human hereditary diseases, including
congenital myotonia, idiopathic generalized epilepsy,
hypercalciuric nephrolithiasis, and classic Bartter
syndrome (CLC chloride channel family members),
Wolff-Parkinson-White syndrome (gamma 2 subunit of
AMP-activated protein kinase), retinitis pigmentosa (IMP
dehydrogenase-1), and homocystinuria (cystathionine
beta-synthase).
Length = 112
Score = 31.8 bits (73), Expect = 0.32
Identities = 16/54 (29%), Positives = 26/54 (48%)
Query: 585 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRC 638
VS M++D V V + EA + M+ LVV+ L G+++ D+ R
Sbjct: 59 VSEIMTRDLVTVDPDEPVAEAAKLMRKNNIRHHLVVDKGGELVGVISIRDLVRE 112
>gnl|CDD|225148 COG2239, MgtE, Mg/Co/Ni transporter MgtE (contains CBS domain)
[Inorganic ion transport and metabolism].
Length = 451
Score = 33.8 bits (78), Expect = 0.33
Identities = 23/98 (23%), Positives = 41/98 (41%), Gaps = 8/98 (8%)
Query: 543 RRTDGADELELSVVENAADSEAAEEMLLEELKLLQFSIPPCQVSRAMSKDFVKVALTVTL 602
D DEL V + EE ++ L S P R M+ +FV + VT+
Sbjct: 95 DAADLLDELPDEVRDELLSLLDPEE--RARVRQLL-SYPEDTAGRIMTTEFVTLPEDVTV 151
Query: 603 KEAIESMK-----DGQQNCVLVVNGEDFLEGILTYGDI 635
EA++ ++ + VV+ + L G+++ D+
Sbjct: 152 DEALDRIRERAEDAETIYYLYVVDEKGKLLGVVSLRDL 189
>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 = 31.5 bits (72), Expect = 0.33
Identities = 15/46 (32%), Positives = 26/46 (56%)
Query: 590 SKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 635
S+ V ++ ++KEA + M + N + VV+ + L GI+T DI
Sbjct: 1 SRPVVTISEDASIKEAAKLMIEENINHLPVVDEDGRLVGIVTSWDI 46
>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 = 33.7 bits (77), Expect = 0.34
Identities = 13/72 (18%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 585 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSS 644
+++ M+ + + A++ M+D + + + VV+ ++ L G++ IK+ K
Sbjct: 244 IAQRMNTGPITKTADKGPRSALQLMRDERVDSLYVVDRQNKLVGVVDVESIKQARKK--- 300
Query: 645 DNSKGDSIASDV 656
D + D+
Sbjct: 301 AQGLQDVLIDDI 312
>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 = 31.4 bits (72), Expect = 0.41
Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 584 QVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 635
+V M+ D + ++E + + D Q + VV+ + GI+T +I
Sbjct: 64 KVIDVMNTDVPVIIDDADIEEILHLLID--QPFLPVVDDDGIFIGIITRREI 113
>gnl|CDD|237843 PRK14869, PRK14869, putative manganese-dependent inorganic
pyrophosphatase; Provisional.
Length = 546
Score = 33.3 bits (77), Expect = 0.44
Identities = 16/56 (28%), Positives = 25/56 (44%)
Query: 584 QVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCL 639
QV V V+ +LKEA M + + VV+ E L G+++ D+ R
Sbjct: 69 QVRDLEIDKPVTVSPDTSLKEAWNLMDENNVKTLPVVDEEGKLLGLVSLSDLARAY 124
Score = 32.1 bits (74), Expect = 0.96
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 4/59 (6%)
Query: 574 KLLQFSIPPCQVSRAMSK-DFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILT 631
+L+ SIP VS M+ D V + L++ E M + VV+ + + G+++
Sbjct: 240 RLINQSIP---VSYIMTTEDLVTFSKDDYLEDVKEVMLKSRYRSYPVVDEDGKVVGVIS 295
>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 = 0.56
Identities = 17/63 (26%), Positives = 27/63 (42%)
Query: 573 LKLLQFSIPPCQVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTY 632
L+ L + P VS M D + V+ +E + + VV+ E L GI+T
Sbjct: 43 LRDLLLADPDTPVSDIMDTDVISVSADDDQEEVARLFEKYDLLALPVVDEEGRLVGIITV 102
Query: 633 GDI 635
D+
Sbjct: 103 DDV 105
>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 = 31.0 bits (71), Expect = 0.59
Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 601 TLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKLSSDNSKGDSIASDV 656
TL EAI+ M+D + + +LVV+ ++ L GI++ +++ + S D + DV
Sbjct: 12 TLAEAIKLMRDKKVDSLLVVDKDNKLLGIVSLESLEQAYKE---AKSLEDIMLEDV 64
Score = 28.3 bits (64), Expect = 4.7
Identities = 10/46 (21%), Positives = 20/46 (43%)
Query: 588 AMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYG 633
M +D V +L++ + + V VV+ + L G++T
Sbjct: 59 IMLEDVFTVQPDASLRDVLGLVLKRGPKYVPVVDEDGKLVGLITRS 104
>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 = 31.0 bits (71), Expect = 0.66
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 591 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCL 639
+ +L EA M++ + + ++VV+ L GI+T DI R L
Sbjct: 1 TQILTCPPDTSLAEAASRMRERRISSIVVVDDGRPL-GIVTERDILRLL 48
>gnl|CDD|181127 PRK07807, PRK07807, inosine 5-monophosphate dehydrogenase;
Validated.
Length = 479
Score = 32.2 bits (74), Expect = 0.90
Identities = 14/48 (29%), Positives = 23/48 (47%)
Query: 584 QVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILT 631
QV MS D V + +EA + ++ + VV+ + L G+LT
Sbjct: 149 QVRDVMSTDLVTLPAGTDPREAFDLLEAARVKLAPVVDADGRLVGVLT 196
>gnl|CDD|240005 cd04634, CBS_pair_21, The CBS domain, named after human CBS, is a
small domain originally identified in cystathionine
beta-synthase and is subsequently found in a wide range
of different proteins. CBS domains usually occur in
tandem repeats. They associate to form a so-called
Bateman domain or a CBS pair based on crystallographic
studies in bacteria. The CBS pair was used as a basis
for this cd hierarchy since the human CBS proteins can
adopt the typical core structure and form an
intramolecular CBS pair. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains and this has been used to help
in its classification here. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown. Mutations of conserved
residues within this domain are associated with a
variety of human hereditary diseases, including
congenital myotonia, idiopathic generalized epilepsy,
hypercalciuric nephrolithiasis, and classic Bartter
syndrome (CLC chloride channel family members),
Wolff-Parkinson-White syndrome (gamma 2 subunit of
AMP-activated protein kinase), retinitis pigmentosa (IMP
dehydrogenase-1), and homocystinuria (cystathionine
beta-synthase).
Length = 143
Score = 30.8 bits (70), Expect = 0.94
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 584 QVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 635
+V M+K + ++ ++++A E M + + VV L GI+T GDI
Sbjct: 90 KVRDIMTKKVITISPDASIEDAAELMVRHKIKRLPVVEDGR-LVGIVTRGDI 140
>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 = 30.7 bits (70), Expect = 0.97
Identities = 13/54 (24%), Positives = 29/54 (53%)
Query: 585 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRC 638
V M+++ + + ++K+A E M + + + VV+ + L GI+T D+ +
Sbjct: 72 VRSIMTRNVITITPDDSIKDAAELMLEKRVGGLPVVDDDGKLVGIVTERDLLKA 125
>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 = 30.4 bits (69), Expect = 1.1
Identities = 14/46 (30%), Positives = 25/46 (54%)
Query: 595 KVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLS 640
++ T L+EA E + + + LVV+ + + GI+T D+ R L
Sbjct: 5 VLSATTPLREAAEQLIESKHGSALVVDRDGGVVGIITLPDLLRALE 50
>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 = 29.9 bits (68), Expect = 1.6
Identities = 11/37 (29%), Positives = 21/37 (56%)
Query: 601 TLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 637
TL++A++ M + + VV+ L GI++ D+ R
Sbjct: 74 TLRDALKRMAERDIGRLPVVDDSGRLVGIVSRSDLLR 110
>gnl|CDD|225978 COG3447, COG3447, Predicted integral membrane sensor domain [Signal
transduction mechanisms].
Length = 308
Score = 31.2 bits (71), Expect = 1.7
Identities = 23/123 (18%), Positives = 34/123 (27%), Gaps = 6/123 (4%)
Query: 393 PGIWLLTQLAAAKVVATALCKGSGLVGGLYAP-----SLMIGAAVGAVFGGSAAEIINSA 447
+ L L + T G AP S+M+GA I S
Sbjct: 14 HPLLHLVSLGLVSFLFTLFSLELSQFGTQLAPLWFPTSIMMGAFYRHAG-RMWPGIALSC 72
Query: 448 IPGNVAVAEPQAYALVGMAATLASVCSVPLTSVLLLFELTRDYRILLPLMGAVGLAIWVP 507
GN+A + A + +LL +L Y L L + +
Sbjct: 73 SLGNIAASILLFSTSSLNMAITTINILEAVVGAVLLRKLLPWYNPLQNLQDWLRFLLGGA 132
Query: 508 SVA 510
V
Sbjct: 133 IVP 135
>gnl|CDD|225321 COG2524, COG2524, Predicted transcriptional regulator, contains
C-terminal CBS domains [Transcription].
Length = 294
Score = 31.2 bits (71), Expect = 1.7
Identities = 15/59 (25%), Positives = 26/59 (44%)
Query: 584 QVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRCLSKL 642
+VS M K+ + + + +AI M +LV + GI+T DI ++ L
Sbjct: 235 KVSDYMRKNVITINEDEDIYDAIRLMNKNNVGRLLVTDSNGKPVGIITRTDILTRIAGL 293
Score = 30.4 bits (69), Expect = 2.6
Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 562 SEAAEEMLLEELKLLQFSIPPCQVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVN 621
+ A E+L++ K++ SIP +V MSK + V TL+EA + + VV+
Sbjct: 153 DDTANEILIDISKMV--SIPKEKVKNLMSKKLITVRPDDTLREAAKLFYEKGIRGAPVVD 210
Query: 622 GEDFLEGILTYGDI 635
+D + GI+T DI
Sbjct: 211 -DDKIVGIITLSDI 223
>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 = 29.4 bits (67), Expect = 1.9
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 591 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILT 631
+ V + T++EA M + + + +LVV + L GI+T
Sbjct: 1 RPPVTCSPDTTIREAARLMTEHRVSSLLVV-DDGRLVGIVT 40
>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 = 29.5 bits (67), Expect = 2.0
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 591 KDFVKVALTVTLKEAIESMKDGQQNCVLVV-NGEDFLEGILTYGDI 635
+ V + T+ EA++ MK+ + ++V E GI+T DI
Sbjct: 1 PNVVTIDGLATVAEALQLMKEHGVSSLVVEKRRESDAYGIVTMRDI 46
>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 = 29.3 bits (66), Expect = 2.0
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 596 VALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 635
V LT T +EA E M + VV+ F GI+T I
Sbjct: 63 VRLTSTAEEAWEVMMKNKTRWCPVVDDGKFK-GIVTLDSI 101
>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 = 29.6 bits (67), Expect = 2.2
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 596 VALTVTLKEAIESM-KDGQQNCVLVVNGEDFLEGILTYGDIKR 637
V + +AI M + G +CVLVV + L GI T DI R
Sbjct: 6 VTPDTPVADAIALMSQQGDSSCVLVVE-KGRLLGIFTERDIVR 47
>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 = 29.5 bits (67), Expect = 2.2
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 584 QVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDI 635
V M+KD + V T++EA M++ + C+ VV L GI+T D+
Sbjct: 68 PVKEIMTKDVITVHPLDTVEEAALLMREHRIGCLPVVED-GRLVGIITETDL 118
Score = 28.4 bits (64), Expect = 5.7
Identities = 14/39 (35%), Positives = 24/39 (61%)
Query: 599 TVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 637
T T+ EA+E M++ + + VV+ E L GI+T D++
Sbjct: 9 TTTIAEALELMREHKIRHLPVVDEEGRLVGIVTDRDLRD 47
>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 = 29.1 bits (66), Expect = 2.3
Identities = 19/53 (35%), Positives = 22/53 (41%), Gaps = 1/53 (1%)
Query: 585 VSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 637
V MS D V V L E E M + V VV L GI+T D+ R
Sbjct: 58 VKDYMSTDVVTVPPDTPLSEVQELMVEHDIGRVPVVEDGR-LVGIVTRTDLLR 109
>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 = 31.0 bits (70), Expect = 2.5
Identities = 23/87 (26%), Positives = 37/87 (42%), Gaps = 9/87 (10%)
Query: 504 IWVPSVANQAKETDASDKRTLARGYSSLSPMEDKNEVLWRRTDGADELELS----VVENA 559
+W V + A R +R +LS E + E+L D AD LE + + EN
Sbjct: 279 LWPT-VEQTGERDMAVAARESSRMLQALSS-EQRKEIL---HDIADALEDNEDEILAENK 333
Query: 560 ADSEAAEEMLLEELKLLQFSIPPCQVS 586
D AA+ + + S+ P ++S
Sbjct: 334 KDVAAAQGAGYAASLVARLSMSPSKIS 360
>gnl|CDD|237537 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
Length = 440
Score = 30.6 bits (70), Expect = 2.6
Identities = 44/163 (26%), Positives = 58/163 (35%), Gaps = 38/163 (23%)
Query: 316 LILGMLCGVVSVVFTRLVAWFTKSFDFIKEKFGLPP-------VVCPALGGLGAGIIALR 368
L+L ++ G+ S +F++ FT F G P +V AL LG GI
Sbjct: 208 LVLAVIVGIGSTLFSQ----FTAGFG------GAEPTIDDAMAIVLAALSLLGLGIFG-- 255
Query: 369 YPGILYWGFTNVEEILHTGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMI 428
PGI G + AP QL A V T L G V L
Sbjct: 256 -PGIA------------NGLVSGAP------QLGAGAAVGTGLAAGGAAVAAAAGAGLAA 296
Query: 429 GAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGMAATLAS 471
G A G +AA +A G + A A AA +A+
Sbjct: 297 GGGAAAAGGAAAAARGGAAAAGGASSAYSAGAAGGSGAAGVAA 339
>gnl|CDD|223678 COG0605, SodA, Superoxide dismutase [Inorganic ion transport and
metabolism].
Length = 204
Score = 29.9 bits (68), Expect = 2.9
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 3/63 (4%)
Query: 68 FDHHN-YVDARDSLTESAPPEWALLLIGCLLGLASGLCVA-FFNKGVHIIHEWAWAG-TP 124
HH YV+ ++ E E L + ++ +GL A F N G H H W +P
Sbjct: 30 DKHHQTYVNNLNAALEGLTEELEDLSLEEIIKKLAGLPAALFNNAGGHWNHSLFWENLSP 89
Query: 125 NEG 127
G
Sbjct: 90 GGG 92
>gnl|CDD|233166 TIGR00880, 2_A_01_02, Multidrug resistance protein.
Length = 141
Score = 29.5 bits (67), Expect = 3.2
Identities = 23/101 (22%), Positives = 34/101 (33%), Gaps = 5/101 (4%)
Query: 406 VVATALCKGSGLVGGLYAPSLMIGAAVGAVFGGSAAEIINSAIPGNVAVAEPQAYALVGM 465
V++TA+ S + L + G AA I + P V A L+
Sbjct: 39 VLSTAMFALSSNITVLIIARFLQGFGAAFALVAGAALIADIYPPEERGV----ALGLMSA 94
Query: 466 AATLASVCSVPLTSVLLLFELTR-DYRILLPLMGAVGLAIW 505
L + PL VL F R + L L A + +
Sbjct: 95 GIALGPLLGPPLGGVLAQFLGWRAPFLFLAILALAAFILLA 135
>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 = 30.4 bits (69), Expect = 3.4
Identities = 14/54 (25%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 585 VSRAMSK-DFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 637
VS M++ + + V + L+EA++ + + + + VV+ L G++T DI +
Sbjct: 145 VSEVMTREEVITVPEGIDLEEALKVLHEHRIEKLPVVDKNGELVGLITMKDIVK 198
>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 = 28.6 bits (65), Expect = 4.1
Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 7/55 (12%)
Query: 585 VSRAM-SKDFVKVALTVTLKEAIESMKDGQQNCV---LVVNGEDFLEGILTYGDI 635
VS M ++ + +L+EA+E + ++ + VV+ E L+G++T DI
Sbjct: 56 VSEVMTPENLLTTVEGTSLEEALELL---HEHKIEKLPVVDDEGKLKGLITVKDI 107
>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 = 28.9 bits (65), Expect = 4.2
Identities = 11/49 (22%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 589 MSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 637
M+++ + V+ + +A + M + + + VV+ ++ + G++T DI R
Sbjct: 87 MTEEIITVSPNDDVVDAAKLMLEANISGLPVVDNDNIV-GVITKTDICR 134
>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 = 28.4 bits (64), Expect = 5.3
Identities = 10/48 (20%), Positives = 22/48 (45%)
Query: 591 KDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKRC 638
V V +L E ++ +++ + + VV + G++T D+ R
Sbjct: 67 AKLVTVLSEESLAEVLKLLEEQGLDELAVVEDSGQVIGLITEADLLRR 114
>gnl|CDD|235507 PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase;
Reviewed.
Length = 486
Score = 29.8 bits (68), Expect = 5.4
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 585 VSRAMSKD-FVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 637
VS M+K+ V V TL+EA+E + + + + VV+ L+G++T DI++
Sbjct: 149 VSEVMTKERLVTVPEGTTLEEALELLHEHRIEKLPVVDDNGRLKGLITVKDIEK 202
>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 = 27.7 bits (62), Expect = 8.1
Identities = 16/54 (29%), Positives = 25/54 (46%)
Query: 584 QVSRAMSKDFVKVALTVTLKEAIESMKDGQQNCVLVVNGEDFLEGILTYGDIKR 637
+V M+KD + + L +AI M ++V + E GI+T DI R
Sbjct: 56 KVKDVMTKDVITIDEDEQLYDAIRLMNKHNVGRLIVTDDEGRPVGIITRTDILR 109
>gnl|CDD|237158 PRK12650, PRK12650, putative monovalent cation/H+ antiporter
subunit A; Reviewed.
Length = 962
Score = 29.2 bits (66), Expect = 8.1
Identities = 23/92 (25%), Positives = 38/92 (41%), Gaps = 5/92 (5%)
Query: 419 GGLYAPSLMIGAAVGAV--FGGSAAEIINSAIPGNVAVAE-PQAYALVGMAATLASVCSV 475
G L++GAA+GAV F SA ++ + + G ++ +A + + A L S+
Sbjct: 405 GNAGVVLLLVGAALGAVFTFAYSARLVLGAFVDGPRDMSHVKEAPVSLWLPAALPGALSL 464
Query: 476 PLTSVLLLFELTRDYRILLPLMGAVG--LAIW 505
PL V L + LA+W
Sbjct: 465 PLGLVPGLLDAPVSAAATAAAGEHAHTHLALW 496
>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 = 29.0 bits (66), Expect = 8.9
Identities = 23/96 (23%), Positives = 36/96 (37%), Gaps = 18/96 (18%)
Query: 278 IILASVIS---STVSTVLLGTQSAFTVPSYDL-----KSAAELPLYLILGMLCGVVSVVF 329
++LA +++ ST ++LL + FT D+ A L +G + VV V
Sbjct: 312 LVLAGLLAAIMSTADSLLLAASTLFT---RDIYKRLINPKASDKKLLRVGRIATVVVGVL 368
Query: 330 TRLVAWFTKS-----FDFIKEKFGLPPVVCPALGGL 360
L+A F S + P L GL
Sbjct: 369 ALLLALFPPSIILLLSLAA--GLLAAALFPPLLLGL 402
>gnl|CDD|178102 PLN02484, PLN02484, probable pectinesterase/pectinesterase
inhibitor.
Length = 587
Score = 29.1 bits (65), Expect = 9.0
Identities = 20/73 (27%), Positives = 22/73 (30%), Gaps = 9/73 (12%)
Query: 203 LGPEGPSVDIGKSCANGFSLMMENNRERKIALVAAGAASGIASGFNAAVAGCFFAIETVL 262
LGP G S S A E R RK LV I S A A F +
Sbjct: 6 LGPSGASGPNQTSTATALP---ELRRRRKTKLVLFSIVLLIVS---AVAAAIFAGVRAK- 58
Query: 263 RPLRAENSPPFTT 275
+ 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 = 9.0
Identities = 24/98 (24%), Positives = 35/98 (35%), Gaps = 16/98 (16%)
Query: 386 TGKTASAPGIWL--LTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVGAVFGGSAAEI 443
+GK AP L Q+A A +A GL P AA +
Sbjct: 199 SGKAIVAPSALANALAQVAKA--LAEEK--------GLAVPDEDAKVEASEEARKIAASL 248
Query: 444 INSA----IPGNVAVAEPQAYALVGMAATLASVCSVPL 477
+++ GN+A PQA L +A +A + L
Sbjct: 249 VSAERAAVFLGNLAQNHPQAATLRALAQEIAKLTGATL 286
>gnl|CDD|237817 PRK14791, PRK14791, lipoprotein signal peptidase; Provisional.
Length = 146
Score = 28.0 bits (63), Expect = 9.2
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 9/59 (15%)
Query: 125 NEGAAWLRLQRLADTWHRILLIPVTGGVIVGMMHGLLEILNQIKQSSSLDRQGFDLVAG 183
N GAA+ LQ + LI +T VI+G+++ ++ + K +S L + L+
Sbjct: 44 NRGAAFGILQN-----KTLFLILITIIVILGLIYYII----KYKPTSKLYKISLSLIIS 93
>gnl|CDD|236386 PRK09129, PRK09129, NADH dehydrogenase subunit G; Validated.
Length = 776
Score = 29.1 bits (66), Expect = 9.4
Identities = 27/96 (28%), Positives = 37/96 (38%), Gaps = 12/96 (12%)
Query: 386 TGKTASAPGIWLLTQLAAAKVVATALCKGSGLVGGLYAPSLMIGAAVGAVFGGSAAEIIN 445
+ AP W A VA A KG L L ++ AA A+ A + N
Sbjct: 417 AQRIIVAPSAWADALAGVAAAVAAA--KGVALPEAL--AKVLAAAAARAI----AQSLAN 468
Query: 446 SA----IPGNVAVAEPQAYALVGMAATLASVCSVPL 477
+ GN+AV PQA L +A +A + L
Sbjct: 469 GERAAILLGNLAVNHPQAATLRALAQWIAKLTGATL 504
>gnl|CDD|187591 cd05330, cyclohexanol_reductase_SDR_c, cyclohexanol reductases,
including levodione reductase, classical (c) SDRs.
Cyloclohexanol reductases,including
(6R)-2,2,6-trimethyl-1,4-cyclohexanedione (levodione)
reductase of Corynebacterium aquaticum, catalyze the
reversible oxidoreduction of hydroxycyclohexanone
derivatives. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 257
Score = 28.6 bits (64), Expect = 9.7
Identities = 8/33 (24%), Positives = 14/33 (42%)
Query: 503 AIWVPSVANQAKETDASDKRTLARGYSSLSPME 535
AI P V K+ + + S++PM+
Sbjct: 187 AILTPMVEGSLKQLGPENPEEAGEEFVSVNPMK 219
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.134 0.397
Gapped
Lambda K H
0.267 0.0828 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 34,649,921
Number of extensions: 3508771
Number of successful extensions: 4715
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4590
Number of HSP's successfully gapped: 208
Length of query: 683
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 580
Effective length of database: 6,369,140
Effective search space: 3694101200
Effective search space used: 3694101200
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 (27.5 bits)