RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy880
(263 letters)
>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 = 212 bits (541), Expect = 2e-66
Identities = 95/169 (56%), Positives = 102/169 (60%), Gaps = 43/169 (25%)
Query: 137 DWVFLALLGIIMATISFFMDRGINIIGRS------------------------------- 165
DW+FLALLGI+MA IS MD + + +
Sbjct: 1 DWLFLALLGILMALISIAMDFAVEKLLNARRWLYSLLTGNSLLQYLVWVAYPVALVLFSA 60
Query: 166 ------------SGIPEMKTILRGVALKEYLTFNTLVAKIIGLTATLGSGLPLGKEGPFV 213
SGIPEMKTILRGV L EYLTF TLVAK+IGLT LGSGLPLGKEGPFV
Sbjct: 61 LFCKYISPQAVGSGIPEMKTILRGVVLPEYLTFKTLVAKVIGLTCALGSGLPLGKEGPFV 120
Query: 214 HIASIVATLLSKLVTSFQGIYENESRNSEMLAAACAVGVGSCFGAPIGA 262
HI+SIVA LLSKL T F GIYENESR EMLAAACAVGV FGAPIG
Sbjct: 121 HISSIVAALLSKLTTFFSGIYENESRRMEMLAAACAVGVACTFGAPIGG 169
>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 = 130 bits (328), Expect = 2e-35
Identities = 43/103 (41%), Positives = 56/103 (54%), Gaps = 7/103 (6%)
Query: 166 SGIPEMKTILRGVALKEYLTFNTLVAKIIGLTATLGSGLPLGKEGPFVHIASIVATLLSK 225
SGIPE+ L GV L YL+ TL+AK I + SGLPLGKEGP VH+ +++ L +
Sbjct: 65 SGIPEVMAYLNGVHLPMYLSIRTLIAKTISCICAVASGLPLGKEGPLVHLGAMIGAGLLQ 124
Query: 226 LVTSFQG-------IYENESRNSEMLAAACAVGVGSCFGAPIG 261
+ G ++ N + L A A GV S FGAPIG
Sbjct: 125 GRSRTLGCHVHLFQLFRNPRDRRDFLVAGAAAGVASAFGAPIG 167
>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 = 125 bits (315), Expect = 3e-33
Identities = 51/125 (40%), Positives = 76/125 (60%), Gaps = 3/125 (2%)
Query: 137 DWVFLALLGIIMATISFFMDRGINIIGRSSGIPEMKTILRGVALKEYLTFNTLVAKIIGL 196
+++ LL ++ A I+ + + + SGIPE+KTIL G ++ +L TL+ K +GL
Sbjct: 27 NYIIYVLLALLFAFIAVLLVKVVAPYAAGSGIPEIKTILSGFIIRGFLGKWTLLIKSVGL 86
Query: 197 TATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENESRNSEMLAAACAVGVGSCF 256
+ SGL LGKEGP VHIA+ V ++S+L + NE++ E+L+AA A GV F
Sbjct: 87 VLAVASGLSLGKEGPLVHIATCVGNIISRLFPKY---RRNEAKRREILSAAAAAGVAVAF 143
Query: 257 GAPIG 261
GAPIG
Sbjct: 144 GAPIG 148
>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 = 92.3 bits (230), Expect = 2e-21
Identities = 47/155 (30%), Positives = 73/155 (47%), Gaps = 14/155 (9%)
Query: 118 KFAAVFRFVWKHTFAKLGEDWVFLALLGI--IMATISFFMDRGINIIGRSSGIPEMKTIL 175
KF V ++ K FL LG+ ++ ++ + I SGIPE+K L
Sbjct: 61 KFLVVKNYIEKGRLFT-----AFLVYLGLNLVLVLVAALLVAYIAPTAAGSGIPEVKGYL 115
Query: 176 RGVALKEYLTFNTLVAKIIGLTATLGSGLPLGKEGPFVHIASIVATLLS-------KLVT 228
GV + L TL+ KI+G+ ++ GL LGKEGP +HI + +A LS +L
Sbjct: 116 NGVKIPHILRLKTLLVKIVGVILSVSGGLALGKEGPMIHIGACIAAGLSQGGSTSLRLDF 175
Query: 229 SFQGIYENESRNSEMLAAACAVGVGSCFGAPIGAT 263
+ + N+ + + A GV + FGAP+G
Sbjct: 176 RWFRYFRNDRDKRDFVTCGAAAGVAAAFGAPVGGV 210
>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 = 89.9 bits (224), Expect = 5e-21
Identities = 39/125 (31%), Positives = 58/125 (46%), Gaps = 17/125 (13%)
Query: 139 VFLALLGIIMATISFFMDRGINIIGRSSGIPEMKTILRGVALKEYLTFNTLVAKIIGLTA 198
+ L G++ F G SGIPE+ L GV K L L+ K +G
Sbjct: 1 IGGLLAGLL--VKRFPEAAG-------SGIPEVIAALHGV--KGPLPLRVLLVKFLGTLL 49
Query: 199 TLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENESRNSEMLAAACAVGVGSCFGA 258
TLGSG LG+EGP V I + + + L + + + N+ R ++AA A G+ + F A
Sbjct: 50 TLGSGGSLGREGPSVQIGAAIGSGLGRRL----KLSRNDRRR--LIAAGAAAGIAAAFNA 103
Query: 259 PIGAT 263
P+
Sbjct: 104 PLAGV 108
Score = 41.8 bits (99), Expect = 2e-04
Identities = 32/151 (21%), Positives = 56/151 (37%), Gaps = 15/151 (9%)
Query: 114 RCATKFAAVFRFVWKHTFAKLGEDWVFLALLGIIMATISFFMDRGINIIGRSSGIPEMKT 173
R K +FR + K + AL G+++ + F+ ++G G ++
Sbjct: 180 RLLLKVERLFRRLKKLPP------ILRPALGGLLVGLLGLFL---PEVLG--GGYGLIQL 228
Query: 174 ILRGVALKEYLTFNTLVAKIIGLTATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGI 233
+L G L L L+ K++ +LGSG P G P + I + + LL L+
Sbjct: 229 LLNGSTLSLLLLLLLLLLKLLATALSLGSGAPGGIFAPSLFIGAALGRLLGLLLPLLFPG 288
Query: 234 YENESRNSEMLAAACAVGV-GSCFGAPIGAT 263
+ + A AP+ A
Sbjct: 289 I---APSPGAFALLGMAAFLAGVTRAPLTAI 316
>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 = 71.0 bits (175), Expect = 3e-14
Identities = 36/128 (28%), Positives = 61/128 (47%), Gaps = 12/128 (9%)
Query: 138 WVFLALLGIIMATISFFMDRGI--NIIGRSSGIPEMKTILRGVALKEYLTFNTLVAKIIG 195
+ L L+ ++ ++ ++ + G SGIP+++ +L G L + L K +G
Sbjct: 37 LLVLPLISAVLGLLAGWLVKKFAPEAKG--SGIPQVEGVLAG--LLPPNWWRVLPVKFVG 92
Query: 196 LTATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENESRNSEMLAAACAVGVGSC 255
LGSGL LG+EGP V I + + +SK + E R ++AA A G+ +
Sbjct: 93 GVLALGSGLSLGREGPSVQIGAAIGQGVSKWFKT-----SPEERRQ-LIAAGAAAGLAAA 146
Query: 256 FGAPIGAT 263
F AP+
Sbjct: 147 FNAPLAGV 154
>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 = 69.1 bits (170), Expect = 1e-13
Identities = 33/146 (22%), Positives = 60/146 (41%), Gaps = 20/146 (13%)
Query: 124 RFVWKHTFAKLGED---WVFLALLGIIMATISFFM-DRGINIIGRSSGIPEMKTILRGVA 179
++ +L +++ L+ +I + + G GIPE ++ +A
Sbjct: 20 NLLFGGLPGELAAGSLSPLYILLVPVIGGLLVGLLVRLLGPARGH--GIPE---VIEAIA 74
Query: 180 LKE-YLTFNTLVAKIIGLTATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENES 238
L L + K + TLGSG +G+EGP V I + + + L + + S
Sbjct: 75 LGGGRLPLRVALVKFLASALTLGSGGSVGREGPIVQIGAAIGSWLGRRL--------RLS 126
Query: 239 RNS--EMLAAACAVGVGSCFGAPIGA 262
RN ++A A G+ + F AP+
Sbjct: 127 RNDRRILVACGAAAGIAAAFNAPLAG 152
Score = 38.7 bits (91), Expect = 0.002
Identities = 29/147 (19%), Positives = 53/147 (36%), Gaps = 16/147 (10%)
Query: 119 FAAVFRFVWKHTFAKLGEDWVFLALL-GIIMATISFFMDRGINIIGRSSGIPEMKTILRG 177
F + + + F +L L G+++ + F+ + SG + L G
Sbjct: 223 FVRLLYKIER-LFRRLPIPPWLRPALGGLLLGLLGLFLPQV-----LGSGYGAILLALAG 276
Query: 178 -VALKEYLTFNTLVAKIIGLTATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYEN 236
++L L L+ K++ TLGSG P G P + I + + L+ +
Sbjct: 277 ELSLLLLLLL--LLLKLLATALTLGSGFPGGVFAPSLFIGAALGAAFGLLLPALFPGLVA 334
Query: 237 ESRNSEMLAAACAVGVGSCFGAPIGAT 263
A VG+ + A + A
Sbjct: 335 SP------GAYALVGMAALLAAVLRAP 355
>gnl|CDD|223116 COG0038, EriC, Chloride channel protein EriC [Inorganic ion
transport and metabolism].
Length = 443
Score = 67.4 bits (165), Expect = 7e-13
Identities = 36/125 (28%), Positives = 61/125 (48%), Gaps = 11/125 (8%)
Query: 138 WVFLALLGIIMATISFFMDRGINIIGRSSGIPEMKTILRGVALKEYLTFNTLVAKIIGLT 197
+ AL G+++ + + + R SGIP+ L G + ++ L K++
Sbjct: 67 PLVPALGGLLV--GALLVYKFAPEA-RGSGIPQAIEALHGRKGR--ISPRVLPVKLVATL 121
Query: 198 ATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENESRNSEMLAAACAVGVGSCFG 257
T+GSG LG+EGP V I + + +LL +L+ + E R +LAA A G+ + F
Sbjct: 122 LTIGSGASLGREGPSVQIGAAIGSLLGRLLKLSR-----EDRR-ILLAAGAAAGLAAAFN 175
Query: 258 APIGA 262
AP+
Sbjct: 176 APLAG 180
Score = 30.4 bits (69), Expect = 1.1
Identities = 13/79 (16%), Positives = 26/79 (32%), Gaps = 10/79 (12%)
Query: 189 LVAKIIGLTATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENESRNSEMLAAAC 248
+ K++ + GSG P G P + I + + L+ +
Sbjct: 316 FLLKLLATLLSYGSGAPGGIFAPSLFIGAALGLAFGALLGLLFP------PSILEPGLFA 369
Query: 249 AVGVGSCFG----APIGAT 263
+G+ + AP+ A
Sbjct: 370 LLGMAAFLAATTRAPLTAI 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 = 53.4 bits (129), Expect = 4e-08
Identities = 35/145 (24%), Positives = 55/145 (37%), Gaps = 21/145 (14%)
Query: 129 HTFAKLGEDWVFLALL-------GIIMATISFFMDRGINIIGRSSGIPEMKTILR---GV 178
F +L +L LL I T FF SGIP++ L
Sbjct: 16 ALFQRLTATHPWLPLLLTPAGFALIAWLTRRFFPG------AAGSGIPQVIAALELPSAA 69
Query: 179 ALKEYLTFNTLVAKIIGLTATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENES 238
A + L+ T V KI+ L G +G+EGP V I + V + + + + G+
Sbjct: 70 ARRRLLSLRTAVGKILLTLLGLLGGASVGREGPSVQIGAAVMLAIGRRLPKWGGL----- 124
Query: 239 RNSEMLAAACAVGVGSCFGAPIGAT 263
++ A A G+ + F P+
Sbjct: 125 SERGLILAGGAAGLAAAFNTPLAGI 149
>gnl|CDD|235385 PRK05277, PRK05277, chloride channel protein; Provisional.
Length = 438
Score = 52.2 bits (126), Expect = 7e-08
Identities = 39/122 (31%), Positives = 63/122 (51%), Gaps = 7/122 (5%)
Query: 138 WVFLALLGIIMATISFFMDRGINIIGRSSGIPEMKTILRGVALKEYLTFNTLVAKIIGLT 197
W+ L+ ++A I +F+ R SGIPE++ L G L+ + L K G
Sbjct: 44 WIVAFLISAVLAMIGYFLVRRFAPEAGGSGIPEIEGALEG--LRPVRWWRVLPVKFFGGL 101
Query: 198 ATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENESRNSEMLAAACAVGVGSCFG 257
TLGSG+ LG+EGP V + + ++V + +E+R++ +LAA A G+ + F
Sbjct: 102 GTLGSGMVLGREGPTVQMGGNIG----RMVLDIFRLRSDEARHT-LLAAGAAAGLAAAFN 156
Query: 258 AP 259
AP
Sbjct: 157 AP 158
>gnl|CDD|234987 PRK01862, PRK01862, putative voltage-gated ClC-type chloride
channel ClcB; Provisional.
Length = 574
Score = 36.3 bits (84), Expect = 0.015
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 6/64 (9%)
Query: 199 TLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENESRNSEMLAAACAVGVGSCFGA 258
T+GSG +G+EGP V +A++ A+L+ + F + R ++A A G+ S + A
Sbjct: 128 TIGSGGSIGREGPMVQLAALAASLVGRFA-HF-----DPPRLRLLVACGAAAGITSAYNA 181
Query: 259 PIGA 262
PI
Sbjct: 182 PIAG 185
>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 = 35.3 bits (82), Expect = 0.026
Identities = 25/127 (19%), Positives = 52/127 (40%), Gaps = 17/127 (13%)
Query: 138 WVFLALLGIIMATISFFMDRGINIIGRSSGIPEMKTILRGVALKEYL-TFNTLVAKIIGL 196
+ L + G+I + + R + + +K +RG + T V +I+
Sbjct: 43 ALSLTVGGLIAGLGWYLLRR------KGKKLVSIKQAVRGKKRMPFWETIIHAVLQIV-- 94
Query: 197 TATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENESRNSEMLAAACAVGVGSCF 256
T+G G PLG+E + +++A S + G+ + R ++A A G+ + +
Sbjct: 95 --TVGLGAPLGREVAPREVGALLAQRFSDWL----GLTVADRR--LLVACAAGAGLAAVY 146
Query: 257 GAPIGAT 263
P+
Sbjct: 147 NVPLAGA 153
>gnl|CDD|222035 pfam13303, PTS_EIIC_2, Phosphotransferase system, EIIC. The
bacterial phosphoenolpyruvate: sugar phosphotransferase
system (PTS) is a multi-protein system involved in the
regulation of a variety of metabolic and transcriptional
processes. The sugar-specific permease of the PTS
consists of three domains (IIA, IIB and IIC). The IIC
domain catalyzes the transfer of a phosphoryl group from
IIB to the sugar substrate.
Length = 329
Score = 31.7 bits (73), Expect = 0.33
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 10/62 (16%)
Query: 177 GVALKEYLTFNTLVAKIIGLTATLGSGLPLGKEGPFVH----------IASIVATLLSKL 226
GV + L N LV+ G+ +GSG G FV IA+ +A L+ KL
Sbjct: 50 GVLVALQLKANPLVSFSAGIAGFIGSGAITFTNGGFVLAGTGDPINAFIAAAIAVLVGKL 109
Query: 227 VT 228
+
Sbjct: 110 IG 111
Score = 28.3 bits (64), Expect = 4.5
Identities = 17/66 (25%), Positives = 23/66 (34%), Gaps = 14/66 (21%)
Query: 194 IGLTATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENESRNSEMLAAACAVGVG 253
+G+ TL G LG G + I S L ++ T Q +L A V V
Sbjct: 9 LGIVVTLIPGAILGTIGKLLGILS----FLVQIGTLAQS----------LLGPAIGVLVA 54
Query: 254 SCFGAP 259
A
Sbjct: 55 LQLKAN 60
>gnl|CDD|180439 PRK06171, PRK06171, sorbitol-6-phosphate 2-dehydrogenase;
Provisional.
Length = 266
Score = 30.4 bits (69), Expect = 0.78
Identities = 25/70 (35%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 158 GINIIGRSSGIPEMKTILRGVALKEYL--TFNTLVAKI-IGLTATLGSGLPLGKEGPFVH 214
I ++G + GI E T LR +E L T V ++ G T T S +PLG+ G
Sbjct: 180 NIRVVGVAPGILE-ATGLRTPEYEEALAYTRGITVEQLRAGYTKT--STIPLGRSGKLSE 236
Query: 215 IASIVATLLS 224
+A +V LLS
Sbjct: 237 VADLVCYLLS 246
>gnl|CDD|218398 pfam05045, RgpF, Rhamnan synthesis protein F. This family consists
of a group of proteins which are related to the
Streptococcus rhamnose-glucose polysaccharide assembly
protein (RgpF). Rhamnan backbones are found in several O
polysaccharides of phytopathogenic bacteria and are
regarded as pathogenic factors.
Length = 498
Score = 30.1 bits (68), Expect = 1.2
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 5/50 (10%)
Query: 144 LGIIMATISFFMDRGINIIGRS--SGIPEMKTILRGVALKEYLTFNTLVA 191
+G+++ I IG + PEM + R + +K+ NT VA
Sbjct: 399 IGLVIPDIVHI---RYPTIGNAWNENAPEMNKLARRMGIKKKFDDNTPVA 445
>gnl|CDD|216188 pfam00916, Sulfate_transp, Sulfate transporter family. Mutations
in human SLC26A2 lead to several human diseases.
Length = 279
Score = 29.9 bits (68), Expect = 1.4
Identities = 29/152 (19%), Positives = 51/152 (33%), Gaps = 32/152 (21%)
Query: 116 ATKFAAVFRFVWKHTFAKLGEDWVF-----LALLGIIMATISFFMDR-GINIIGR-SSGI 168
F + W+ +A++ + + F DR G++IIG SG+
Sbjct: 71 GLSFLIFLLIIKLLPKRLKKLFWIPAPAPLVAVIVATVISYIFLADRYGVSIIGEIPSGL 130
Query: 169 PEMKTILRGVALKEYLTFNTLVAKI-IGLTATLGSGLPLGKEGPFVHIASIVATLLSKLV 227
P L ++ L+ + I L + + + + L +K
Sbjct: 131 PPPS------LPDVPLDWSLLLDLLPIALALAI--------------VGLLESILTAK-- 168
Query: 228 TSFQGIYENESR-NSEMLAAACAVGVGSCFGA 258
SF + N E++A A V S FG
Sbjct: 169 -SFAKKKGYKIDSNKELVAQGIANIVSSLFGG 199
>gnl|CDD|214684 smart00478, ENDO3c, endonuclease III. includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 149
Score = 28.8 bits (65), Expect = 1.7
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 51 YPCPP-PANLGESDELQEYDASPGMYGRYTKELGEFAKEEAKKLNKKRKKDR 101
+P P A E +EL+E G Y R + L E A+ ++ + DR
Sbjct: 21 FPTPEDLAAADE-EELEELIRGLGFYRRKARYLIELARILVEEYGGEVPDDR 71
>gnl|CDD|221173 pfam11702, DUF3295, Protein of unknown function (DUF3295). This
family is conserved in fungi but the function is not
known.
Length = 509
Score = 29.5 bits (66), Expect = 2.2
Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 22/84 (26%)
Query: 7 MLDTEWEDFDKLMTE-------YKRRRMHVTASPLLHRRHSSKHQTQSQSFYPCPPPANL 59
ML TE +TE ++R++ TA+ +L RRH+S H + YP PP A
Sbjct: 432 MLATE-------LTESLRRNLLWERQQKSATANAVLKRRHTS-HDVANLKQYPEPPGAK- 482
Query: 60 GESDELQEYDASPGMYGRYTKELG 83
++ D + +Y + G
Sbjct: 483 ------KDKDVKNSSWNQYFVDFG 500
>gnl|CDD|206315 pfam14146, DUF4305, Domain of unknown function (DUF4305). This
family includes the B. subtilis YdiK protein, which is
functionally uncharacterized. This is not a homologue of
E. coli YdiK, which belongs to pfam01594. This family of
proteins is found in bacteria. Proteins in this family
are approximately 60 amino acids in length.
Length = 38
Score = 26.4 bits (59), Expect = 2.3
Identities = 8/25 (32%), Positives = 10/25 (40%), Gaps = 2/25 (8%)
Query: 138 WVFLALLGIIMATISFFMDRGINII 162
W F L I A + F I +I
Sbjct: 16 WDFWTYLLIAFAALDFG--IAIRMI 38
>gnl|CDD|221498 pfam12263, DUF3611, Protein of unknown function (DUF3611). This
family of proteins is found in bacteria and eukaryotes.
Proteins in this family are typically between 180 and
205 amino acids in length. There are two completely
conserved residues (W and G) that may be functionally
important.
Length = 183
Score = 28.4 bits (64), Expect = 2.4
Identities = 21/101 (20%), Positives = 39/101 (38%), Gaps = 25/101 (24%)
Query: 139 VFLALLGIIMATISFFMDRGINIIGR------SSGIPEMKTILRGVALKEYLTFNTLVAK 192
+FL ++G+I S F +GR + P +R + L L+
Sbjct: 59 LFLTIIGLIALGFSIFFAFRYTRLGRRLRNPDPAKRPSRADTVRLLRL-------GLIIN 111
Query: 193 IIGLTATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGI 233
++G+ L +G + + V LL+K ++ GI
Sbjct: 112 LLGMFLAL-----IGAQ-------ATVGILLAKALSQPPGI 140
>gnl|CDD|224328 COG1410, MetH, Methionine synthase I, cobalamin-binding domain
[Amino acid transport and metabolism].
Length = 842
Score = 29.2 bits (66), Expect = 2.5
Identities = 27/115 (23%), Positives = 43/115 (37%), Gaps = 19/115 (16%)
Query: 12 WEDFDKLMTEYKRRRMHVTASPLLHRRHSSKHQTQSQSF----YPCPPPANLG----ESD 63
+ + EY+ R R S + + Y P P G ++
Sbjct: 537 ADYSEGFRKEYETVRTQHANRKARTRPLSIEAARDNAEAVWADYEPPVPPFWGTRILKNS 596
Query: 64 ELQEY----DASP-----GMYGRYTKELGEFAKEEAKKLNKKRK--KDRLQADEL 107
L E D +P G+ G+Y + L E+ EEA+KL + D+L A+ L
Sbjct: 597 SLAELRPYIDWTPFFMQWGLRGKYPRILEEYVGEEARKLFPDAQAWLDKLIAEGL 651
>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 = 29.1 bits (66), Expect = 2.6
Identities = 31/138 (22%), Positives = 48/138 (34%), Gaps = 34/138 (24%)
Query: 138 WVFLALLGIIMATISFFMDR-------GINII-----GRSSGIPEMKTILRGVALKEYLT 185
L L + I + + G N+I G GIP LR L +
Sbjct: 31 PWLLPFLPLAGLLIGYLYQKFGKNSEKGNNLIIEEIHGPEEGIP-----LRMAPL---VL 82
Query: 186 FNTLVAKIIGLTATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENESRNSEMLA 245
F T++ + G +A G+EG V + +A ++ E R +L
Sbjct: 83 FGTVLTHLFGGSA--------GREGTAVQMGGSLADAFGRVFKL-----PEEDRRI-LLI 128
Query: 246 AACAVGVGSCFGAPIGAT 263
A A G + FG P+
Sbjct: 129 AGIAAGFAAVFGTPLAGA 146
>gnl|CDD|215183 PLN02323, PLN02323, probable fructokinase.
Length = 330
Score = 28.8 bits (65), Expect = 2.8
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 217 SIVATLLSKLVTSFQGIYENESRNSEMLAAACAVG 251
+ V LLS+L + E+E R E L A A G
Sbjct: 269 AFVGGLLSQLAKD-LSLLEDEERLREALRFANACG 302
>gnl|CDD|133894 PHA00448, PHA00448, hypothetical protein.
Length = 70
Score = 26.8 bits (59), Expect = 3.3
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 89 EAKKLNKKRKKDRLQADELRNKYR 112
EAK+LN K +KD +A L + R
Sbjct: 19 EAKRLNDKARKDATRARRLAKQSR 42
>gnl|CDD|218337 pfam04939, RRS1, Ribosome biogenesis regulatory protein (RRS1).
This family consists of several eukaryotic ribosome
biogenesis regulatory (RRS1) proteins. RRS1 is a nuclear
protein that is essential for the maturation of 25 S
rRNA and the 60 S ribosomal subunit assembly in
Saccharomyces cerevisiae.
Length = 164
Score = 28.0 bits (63), Expect = 3.4
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 84 EFAKEEAKKLNKKRKKDRLQADELRNKYRGR 114
+FAK KK KKRKK +L DE ++ R
Sbjct: 85 KFAK---KKGIKKRKKSKLVYDEATGEWVPR 112
>gnl|CDD|220467 pfam09911, DUF2140, Uncharacterized protein conserved in bacteria
(DUF2140). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 187
Score = 27.5 bits (62), Expect = 4.9
Identities = 8/30 (26%), Positives = 12/30 (40%), Gaps = 9/30 (30%)
Query: 125 FVWKHTFAKLGEDWVFLALLGIIMATISFF 154
WK W F LL + +A+I+
Sbjct: 1 NKWK---------WAFFVLLALNLASIAVV 21
>gnl|CDD|226982 COG4635, HemG, Flavodoxin [Energy production and conversion /
Coenzyme metabolism].
Length = 175
Score = 27.4 bits (61), Expect = 5.5
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 56 PANLGESDELQEYDA----SPGMYGRYTKELGEFAKEEAKKLNKK 96
+ E L++YDA + YG + + + F K+ A+ L+ K
Sbjct: 36 DLHAVEEPALEDYDAVVIGASIRYGHFHEAVQSFVKKHAEALSTK 80
>gnl|CDD|216469 pfam01384, PHO4, Phosphate transporter family. This family
includes PHO-4 from Neurospora crassa which is a is a
Na(+)-phosphate symporter. This family also contains the
leukaemia virus receptor.
Length = 268
Score = 27.9 bits (63), Expect = 5.5
Identities = 32/129 (24%), Positives = 46/129 (35%), Gaps = 24/129 (18%)
Query: 138 WVFLALLGIIMATISFFMDRGINIIGRSSGIPEMKTILRGVALKEYLTFNTLVAKIIGL- 196
WV L+G + A +SF G N + + G I G + F L+ + +
Sbjct: 119 WVLSPLIGGVAALMSFA--HGANDVANAIGPIAAILISTGSVSSSVVPFWVLLLGALAIA 176
Query: 197 --TATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENESRNSEMLAAACAVGVGS 254
T T G I V ++KL T +G S L AA V + S
Sbjct: 177 LGTLTGGW-----------RIIKTVGNKITKL-TPSRGF-------SAELGAAITVLLAS 217
Query: 255 CFGAPIGAT 263
G P+ T
Sbjct: 218 LLGIPVSTT 226
>gnl|CDD|150037 pfam09221, Bacteriocin_IId, Bacteriocin class IId cyclical
uberolysin-like. Members of this family are
membrane-interacting peptides, produced by Enterococci
that display a broad anti-microbial spectrum against
Gram-positive and Gram-negative bacteria. They adopt a
helical structure, with five alpha helices forming a
Saposin-like fold. The structure has been found to be
cyclical. It should be pointed out that one reference
implies that both circularin A and gassericin A are
class V or IIc-type bacteriocins; however we find that
these two proteins fall into different Pfam families
families, this one and BacteriocIIc_cy, pfam12173.
Length = 69
Score = 25.6 bits (56), Expect = 7.2
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 184 LTFNTLVAKIIGLTATLGSGLPLGKEGPFVHIASIVATLLSKL 226
L +T+ I LTA L G+ + ++ AT+ L
Sbjct: 19 LAGSTVTTIISILTAILSGGVSALLAIGW---SAFKATVKKIL 58
>gnl|CDD|187604 cd05346, SDR_c5, classical (c) SDR, subgroup 5. These proteins are
members of the classical SDR family, with a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. 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 = 249
Score = 27.2 bits (61), Expect = 7.7
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 84 EFAKEEAKKLNKKRKKDRLQ--ADELRNKYRG 113
FAK AK + R+ +RLQ ADEL K+
Sbjct: 19 RFAKAGAKLILTGRRAERLQELADELGAKFPV 50
>gnl|CDD|184825 PRK14797, PRK14797, lipoprotein signal peptidase; Provisional.
Length = 150
Score = 26.8 bits (60), Expect = 9.0
Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 3/39 (7%)
Query: 119 FAAVFRFVWKHTFAKLGEDWVFLALLGIIMATISFFMDR 157
++WKH + W L L II I F+DR
Sbjct: 69 IGVAIYYLWKH---RYKNIWFLLGLTLIIAGGIGNFIDR 104
>gnl|CDD|192292 pfam09429, Wbp11, WW domain binding protein 11. The WW domain is a
small protein module with a triple-stranded beta-sheet
fold. This is a family of WW domain binding proteins.
Length = 78
Score = 25.7 bits (57), Expect = 9.1
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 84 EFAKEEAKKLNKKRKKDRLQADELRNKYR 112
+ KE+ KK KK K +R E + +
Sbjct: 9 AYRKEQKKKELKKNKAERQARREAKLAKK 37
>gnl|CDD|221736 pfam12724, Flavodoxin_5, Flavodoxin domain. This is a family of
flavodoxins. Flavodoxins are electron transfer proteins
that carry a molecule of non-covalently bound FMN.
Length = 141
Score = 26.4 bits (59), Expect = 9.2
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 4/41 (9%)
Query: 61 ESDELQEYDA----SPGMYGRYTKELGEFAKEEAKKLNKKR 97
E +L+ YDA + YG+ EL +F K+ LN K
Sbjct: 35 EELDLESYDAVIIGASIRYGKILPELAKFVKKHQDALNDKP 75
>gnl|CDD|227725 COG5438, COG5438, Predicted multitransmembrane protein [Function
unknown].
Length = 385
Score = 27.3 bits (61), Expect = 9.3
Identities = 32/141 (22%), Positives = 54/141 (38%), Gaps = 24/141 (17%)
Query: 129 HTFAKLGEDWVFLALLGIIMATISFFMDRGINIIGRSSGIPEMKTILRGVALKEYLTFNT 188
+ +G ++ L L G+I+ ++ MD I+I +S I E+ + +KE
Sbjct: 244 YLSKNVGINFSGLFLAGVIIGSLGAIMDVAISI---ASSINELHEQNPNITVKELFKSGM 300
Query: 189 LVAK-IIG------LTATLGSGLPLGKEGPFVHIASIVATLLSKLVTSFQGIYENESRNS 241
+ + I+G L A LG LPL L + S I ++
Sbjct: 301 NIGQDIMGTMTNTLLLAYLGGALPL-------------LILFLRNNYSLYYIINSKVLAL 347
Query: 242 EMLAAACAVGVGSCFGAPIGA 262
E+L + +G PI A
Sbjct: 348 ELLRSLLG-SIGIVLAIPITA 367
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 0.135 0.399
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,470,671
Number of extensions: 1286916
Number of successful extensions: 1791
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1770
Number of HSP's successfully gapped: 72
Length of query: 263
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 168
Effective length of database: 6,723,972
Effective search space: 1129627296
Effective search space used: 1129627296
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: 58 (26.1 bits)