RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15907
(260 letters)
>gnl|CDD|239657 cd03685, ClC_6_like, ClC-6-like chloride channel proteins. This CD
includes ClC-6, ClC-7 and ClC-B, C, D in plants.
Proteins in this family are ubiquitous in eukarotes and
their functions are unclear. They are expressed in
intracellular organelles membranes. This family belongs
to the ClC superfamily of chloride ion channels, which
share the unique double-barreled architecture and
voltage-dependent gating mechanism. The gating is
conferred by the permeating anion itself, acting as the
gating charge. ClC chloride ion channel superfamily
perform a variety of functions including cellular
excitability regulation, cell volume regulation,
membrane potential stabilization, acidification of
intracellular organelles, signal transduction, and
transepithelial transport in animals.
Length = 466
Score = 282 bits (724), Expect = 2e-93
Identities = 119/214 (55%), Positives = 146/214 (68%), Gaps = 3/214 (1%)
Query: 2 PRLVRIKTLVVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFKY 61
P ++R+KTL+VK +GVI +V GGLA GKEGPMIH GA +AAG+SQG STS DF+ F+Y
Sbjct: 121 PHILRLKTLLVKIVGVILSVSGGLALGKEGPMIHIGACIAAGLSQGGSTSLRLDFRWFRY 180
Query: 62 FREDHEKRDFVSGGAAAGVAAAFGAPVGGVLFSLEEGASFWNQSLTWRIFFGTIVTTFTL 121
FR D +KRDFV+ GAAAGVAAAFGAPVGGVLFSLEE ASFWNQ+LTWR FF +++ TFTL
Sbjct: 181 FRNDRDKRDFVTCGAAAGVAAAFGAPVGGVLFSLEEVASFWNQALTWRTFFSSMIVTFTL 240
Query: 122 NVVLSAYYGHPGELTNSGLLNFGKFYD--LRYDLLEMFFYVGAGVFGGLTGALYNSLNHK 179
N LS L G L Y E+ ++ GV GGL GAL+N LNHK
Sbjct: 241 NFFLSGCNSGKCGLFGPGGLIMFDGSSTKYLYTYFELIPFMLIGVIGGLLGALFNHLNHK 300
Query: 180 LTVFRIRYMSAR-YVKVLEAVLVAMVSACVPIIM 212
+T FR R +KVLEA+LV++V++ V
Sbjct: 301 VTRFRKRINHKGKLLKVLEALLVSLVTSVVAFPQ 334
>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 = 162 bits (413), Expect = 1e-47
Identities = 77/211 (36%), Positives = 117/211 (55%), Gaps = 4/211 (1%)
Query: 2 PRLVRIKTLVVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFKY 61
P + I+TL+ KTI I V GL GKEGP++H GA++ AG+ QG+S + G +F+
Sbjct: 80 PMYLSIRTLIAKTISCICAVASGLPLGKEGPLVHLGAMIGAGLLQGRSRTLGCHVHLFQL 139
Query: 62 FREDHEKRDFVSGGAAAGVAAAFGAPVGGVLFSLEEGASFWNQSLTWRIFFGTIVTTFTL 121
FR ++RDF+ GAAAGVA+AFGAP+GG+LF LEE ++F+ L WR+FF +V+ F +
Sbjct: 140 FRNPRDRRDFLVAGAAAGVASAFGAPIGGLLFVLEEVSTFFPVRLAWRVFFAALVSAFVI 199
Query: 122 NVVLS--AYYGHPGELTNSGLLNFGKFYDLRYDLLEMFFYVGAGVFGGLTGALYNSLNHK 179
+ S + + + L + +L E V GV GL AL+ L+
Sbjct: 200 QIYNSFNSGFELLDRSSAMFLSLTVFELHVPLNLYEFIPTVVIGVICGLLAALFVRLSII 259
Query: 180 LTVFRIRYM--SARYVKVLEAVLVAMVSACV 208
+R R + +VLE VL ++ + +
Sbjct: 260 FLRWRRRLLFRKTARYRVLEPVLFTLIYSTI 290
>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 = 140 bits (355), Expect = 6e-39
Identities = 82/258 (31%), Positives = 129/258 (50%), Gaps = 32/258 (12%)
Query: 1 MPRLVRIKTLVVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFK 60
+ + TL++K++G++ V GL+ GKEGP++H V IS+ +F
Sbjct: 70 IRGFLGKWTLLIKSVGLVLAVASGLSLGKEGPLVHIATCVGNIISR-----------LFP 118
Query: 61 YFREDH-EKRDFVSGGAAAGVAAAFGAPVGGVLFSLEEGASFWNQSLTWRIFFGTIVTTF 119
+R + ++R+ +S AAAGVA AFGAP+GGVLFSLEE + ++ WR FF +V F
Sbjct: 119 KYRRNEAKRREILSAAAAAGVAVAFGAPIGGVLFSLEEVSYYFPLKTLWRSFFCALVAAF 178
Query: 120 TLNVVLSAYYGHPGELTNSGLLNFGKFYDLRYDLLEMFFYVGAGVFGGLTGALYNSLNHK 179
TL + G L+ F YD + E+ ++ G+FGGL GA + N K
Sbjct: 179 TLKSLNPFGTGR--------LVLFEVEYDRDWHYFELIPFILLGIFGGLYGAFFIKANIK 230
Query: 180 LTVFRIRYMSARYVKVLEAVLVAMVSACV----------PIIMIYSI-DDCRPLGEDPTE 228
FR + + RY VLE +LVA+++A + ++ + ++C P ++
Sbjct: 231 WARFRKKSLLKRY-PVLEVLLVALITALISFPNPYTRLDMTELLELLFNECEPGDDNSLC 289
Query: 229 HAVQMYCGDGEYNTLAAL 246
GDG Y L +L
Sbjct: 290 CYRDPPAGDGVYKALWSL 307
>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 = 119 bits (300), Expect = 9e-32
Identities = 51/207 (24%), Positives = 89/207 (42%), Gaps = 27/207 (13%)
Query: 2 PRLVRIKTLVVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFKY 61
+ ++ L+VK +G + T+ G + G+EGP + GA + +G+ + K
Sbjct: 32 KGPLPLRVLLVKFLGTLLTLGSGGSLGREGPSVQIGAAIGSGLGR-----------RLKL 80
Query: 62 FREDHEKRDFVSGGAAAGVAAAFGAPVGGVLFSLEEGASFWNQSLTWRIFFGTIVTTFTL 121
R D +R ++ GAAAG+AAAF AP+ GVLF+LEE + ++ + ++V
Sbjct: 81 SRND--RRRLIAAGAAAGIAAAFNAPLAGVLFALEELSRSFSYRALLPVLVASVVAALVS 138
Query: 122 NVVLSAYYGHPGELTNSGLLNFGKFYDLRYDLLEMFFYVGAGVFGGLTGALYNSLNHKLT 181
++ F LLE+ ++ G+ GL GAL+ L K+
Sbjct: 139 RLLFGNE------------PLFEVPSLPPLSLLELPLFILLGILCGLLGALFVRLLLKVE 186
Query: 182 VFRIRYMSARYVKVLEAVLVAMVSACV 208
R +L L ++ +
Sbjct: 187 RLFRRLKKLP--PILRPALGGLLVGLL 211
>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 = 112 bits (282), Expect = 1e-28
Identities = 64/212 (30%), Positives = 105/212 (49%), Gaps = 14/212 (6%)
Query: 1 MPRLVRIKTLVVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFK 60
+P + KTLV K IG+ + GL GKEGP +H +IVAA +S+ + G
Sbjct: 87 LPEYLTFKTLVAKVIGLTCALGSGLPLGKEGPFVHISSIVAALLSKLTTFFSG------- 139
Query: 61 YFREDHEKRDFVSGGAAAGVAAAFGAPVGGVLFSLEEGASFWNQSLTWRIFFGTIVTTFT 120
+ + + + ++ A GVA FGAP+GGVLFS+E ++++ WR FF FT
Sbjct: 140 IYENESRRMEMLAAACAVGVACTFGAPIGGVLFSIEVTSTYFAVRNYWRGFFAATCGAFT 199
Query: 121 LNVVLSAYYGHPGELTNSGLLNFGKFYDLRYDLLEMFFYVGAGVFGGLTGALYNSLNHKL 180
+L+ ++ +T F F D +D+ E+ + G+ GL GAL+ L+ K+
Sbjct: 200 FR-LLAVFFSDQETITALFKTTF--FVDFPFDVQELPIFALLGIICGLLGALFVFLHRKI 256
Query: 181 TVFRIRYMSARYV----KVLEAVLVAMVSACV 208
FR + +L +VA+++A +
Sbjct: 257 VRFRRKNRLFSKFLKRSPLLYPAIVALLTAVL 288
>gnl|CDD|223116 COG0038, EriC, Chloride channel protein EriC [Inorganic ion
transport and metabolism].
Length = 443
Score = 87.4 bits (217), Expect = 1e-19
Identities = 47/196 (23%), Positives = 79/196 (40%), Gaps = 24/196 (12%)
Query: 1 MPRLVRIKTLVVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFK 60
+ + L VK + + T+ G + G+EGP + GA + + + + + K
Sbjct: 104 RKGRISPRVLPVKLVATLLTIGSGASLGREGPSVQIGAAIGSLLGR-----------LLK 152
Query: 61 YFREDHEKRDFVSGGAAAGVAAAFGAPVGGVLFSLEEGASFWNQSLTWRIFFGTIVTTFT 120
RED +R ++ GAAAG+AAAF AP+ G LF++E + L +R +V
Sbjct: 153 LSRED--RRILLAAGAAAGLAAAFNAPLAGALFAIEVLYG---RFLEYRALVPVLVAAVV 207
Query: 121 LNVVLSAYYGHPGELTNSGLLNFGKFYDLRYDLLEMFFYVGAGVFGGLTGALYNSLNHKL 180
+V + G L L ++ Y+ G+ GL G L + L
Sbjct: 208 ALLVAGLFGGPHFLLPIV--------TTPHMSLWDLLLYLVLGIIAGLFGVLLSRLLALS 259
Query: 181 TVFRIRYMSARYVKVL 196
F R ++
Sbjct: 260 RRFFRRLPLPPLLRPA 275
>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 = 81.8 bits (203), Expect = 6e-18
Identities = 52/213 (24%), Positives = 92/213 (43%), Gaps = 27/213 (12%)
Query: 1 MPRLVRIKTLVVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFK 60
+ + L VK +G + + GL+ G+EGP + GA + G+S+
Sbjct: 77 LLPPNWWRVLPVKFVGGVLALGSGLSLGREGPSVQIGAAIGQGVSK-------------W 123
Query: 61 YFREDHEKRDFVSGGAAAGVAAAFGAPVGGVLFSLEEGASFWNQSLTWRIFFGTIVTTFT 120
+ E+R ++ GAAAG+AAAF AP+ GVLF LEE S + +V +
Sbjct: 124 FKTSPEERRQLIAAGAAAGLAAAFNAPLAGVLFVLEE----LRHSFSPLALLTALVASIA 179
Query: 121 LNVVLSAYYGHPGELTNSGLLNFGKFYDLRYDLLEMFFYVGAGVFGGLTGALYN-SLNHK 179
+ V ++G +L+ L L + + G+ GL G L+N SL
Sbjct: 180 ADFVSRLFFG------LGPVLSIPPLPALP--LKSYWLLLLLGIIAGLLGYLFNRSLLKS 231
Query: 180 LTVF-RIRYMSARYVKVLEAVLVAMVSACVPII 211
++ +++ + +L +L+ + +P
Sbjct: 232 QDLYRKLKKLPRELRVLLPGLLIGPLGLLLPEA 264
>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 = 78.4 bits (194), Expect = 9e-17
Identities = 45/194 (23%), Positives = 82/194 (42%), Gaps = 25/194 (12%)
Query: 3 RLVRIKTLVVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFKYF 62
+ ++ +VK + T+ G + G+EGP++ GA + + + + +
Sbjct: 78 GRLPLRVALVKFLASALTLGSGGSVGREGPIVQIGAAIGSWLGR-----------RLRLS 126
Query: 63 REDHEKRDFVSGGAAAGVAAAFGAPVGGVLFSLEEGASFWNQSLTWRIFFGTIVTTFTLN 122
R D +R V+ GAAAG+AAAF AP+ G LF++E + + ++ +
Sbjct: 127 RND--RRILVACGAAAGIAAAFNAPLAGALFAIEVLLGEY----SVASLIPVLLASVAAA 180
Query: 123 VVLSAYYGHPGELTNSGLLNFGKFYDLRYDLLEMFFYVGAGVFGGLTGALYNSLNHKLTV 182
+V +G FG LLE+ Y+ G+ GL G L+ L +K+
Sbjct: 181 LVSRLLFGAEPA--------FGVPLYDPLSLLELPLYLLLGLLAGLVGVLFVRLLYKIER 232
Query: 183 FRIRYMSARYVKVL 196
R +++
Sbjct: 233 LFRRLPIPPWLRPA 246
>gnl|CDD|235385 PRK05277, PRK05277, chloride channel protein; Provisional.
Length = 438
Score = 58.0 bits (141), Expect = 9e-10
Identities = 31/88 (35%), Positives = 46/88 (52%), Gaps = 12/88 (13%)
Query: 10 LVVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFKYFREDHEKR 69
L VK G + T+ G+ G+EGP + G + + IF+ R D +
Sbjct: 93 LPVKFFGGLGTLGSGMVLGREGPTVQMGGNIGRMVLD-----------IFR-LRSDEARH 140
Query: 70 DFVSGGAAAGVAAAFGAPVGGVLFSLEE 97
++ GAAAG+AAAF AP+ G+LF +EE
Sbjct: 141 TLLAAGAAAGLAAAFNAPLAGILFVIEE 168
>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 = 57.2 bits (139), Expect = 2e-09
Identities = 46/178 (25%), Positives = 73/178 (41%), Gaps = 30/178 (16%)
Query: 2 PRLVRIKTLVVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFKY 61
RL+ ++T V K + + ++GG + G+EGP + GA V I + G
Sbjct: 72 RRLLSLRTAVGKILLTLLGLLGGASVGREGPSVQIGAAVMLAIGRRLPKWGGLS------ 125
Query: 62 FREDHEKRDFVSGGAAAGVAAAFGAPVGGVLFSLEEGASFWNQSLTWRIFFGTIVTTFTL 121
+R + G AAG+AAAF P+ G++F++EE + + + + I
Sbjct: 126 ------ERGLILAGGAAGLAAAFNTPLAGIVFAIEELSRDFELRFSGLVLLAVIAAGLVS 179
Query: 122 NVVL--SAYYGHPGELTNSGLLNFGKFYDLRYDLLEMFFYVGA-GVFGGLTGALYNSL 176
VL Y+G + L E + V GV GGL G L+ L
Sbjct: 180 LAVLGNYPYFGVA---------------AVALPLGEAWLLVLVCGVVGGLAGGLFARL 222
>gnl|CDD|234963 PRK01610, PRK01610, putative voltage-gated ClC-type chloride
channel ClcB; Provisional.
Length = 418
Score = 47.8 bits (114), Expect = 2e-06
Identities = 46/169 (27%), Positives = 73/169 (43%), Gaps = 37/169 (21%)
Query: 11 VVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFKYFREDHEKRD 70
+VK++ + V G A G+EG MI A+ A+ +Q F E +
Sbjct: 101 LVKSLASLLVVTSGSAIGREGAMILLAALAASCFAQ--------------RFTPRQEWKL 146
Query: 71 FVSGGAAAGVAAAFGAPVGGVLFSLEEGASFWNQSLTWRIFFGTIVTTFTLNVVLSAYYG 130
+++ GAAAG+A+A+ AP+ G LF E I FGT++ VV+SA
Sbjct: 147 WIACGAAAGMASAYHAPLAGSLFIAE-------------ILFGTLMLASLGPVVISAVVA 193
Query: 131 HPGELTNSGLLNFGK--FYDLRYDL----LEMFFYVGAGVFGGLTGALY 173
L + LLN Y+++ + + + G+ GL G L
Sbjct: 194 ----LLTTNLLNGSDALLYNVQLSVTVQARDYALIISTGLLAGLCGPLL 238
>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 = 46.8 bits (112), Expect = 5e-06
Identities = 50/210 (23%), Positives = 77/210 (36%), Gaps = 38/210 (18%)
Query: 17 VITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFKYFREDHEKRD-FVSGG 75
V+T + GG AG +EG + G +A + F+ E R + G
Sbjct: 86 VLTHLFGGSAG-REGTAVQMGGSLADAFG--------------RVFKLPEEDRRILLIAG 130
Query: 76 AAAGVAAAFGAPVGGVLFSLEEGASFWNQSLTWRIFFGTIVTTFTLNVVLSAYYGHPGEL 135
AAG AA FG P+ G +F+LE L + +V + V A
Sbjct: 131 IAAGFAAVFGTPLAGAIFALEVLVL---GRLRYSALIPCLVAAIVADWVSHAL------- 180
Query: 136 TNSGLLNFGKFY--DLRYDLLEMFFYVGAGVFGGLTGALYNSLNHKLTVFRIRYMSARYV 193
GL + D L + AG+ GL G L+ L H L + + Y+
Sbjct: 181 ---GLEHTHYHIVFIPTLDPLLFVKVILAGIIFGLAGRLFAELLHFLKKLLKKRIKNPYL 237
Query: 194 KVLEAVLVAMVSACVPIIMIYSIDDCRPLG 223
+ V + I+++Y + R LG
Sbjct: 238 R-------PFVGGLLIILLVYLLGSRRYLG 260
>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 = 38/173 (21%), Positives = 65/173 (37%), Gaps = 35/173 (20%)
Query: 5 VRIKTLVVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFKYFRE 64
VR ++ + T+ G + G+EGPM+ A+ A S F F R
Sbjct: 115 VRQSLW--RSASSLLTIGSGGSIGREGPMVQLAALAA---------SLVGRFAHFDPPR- 162
Query: 65 DHEKRDFVSGGAAAGVAAAFGAPVGGVLFSLEEGASFWNQSLTWRIFFGTIVTTFTLNVV 124
R V+ GAAAG+ +A+ AP+ G F E I G+I +V
Sbjct: 163 ---LRLLVACGAAAGITSAYNAPIAGAFFVAE-------------IVLGSIAMESFGPLV 206
Query: 125 LSAYYGHPGELTNSGLLNFGKFYDLRY--DL--LEMFFYVGAGVFGGLTGALY 173
+++ + + + Y++ + E+ +V GV G +
Sbjct: 207 VASVVAN---IVMREFAGYQPPYEMPVFPAVTGWEVLLFVALGVLCGAAAPQF 256
>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 = 35.0 bits (81), Expect = 0.030
Identities = 23/79 (29%), Positives = 33/79 (41%), Gaps = 13/79 (16%)
Query: 18 ITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFKYFREDHEKRDFVSGGAA 77
I TV G G+E GA++A S ++R V+ A
Sbjct: 93 IVTVGLGAPLGREVAPREVGALLAQRFSD-------------WLGLTVADRRLLVACAAG 139
Query: 78 AGVAAAFGAPVGGVLFSLE 96
AG+AA + P+ G LF+LE
Sbjct: 140 AGLAAVYNVPLAGALFALE 158
>gnl|CDD|119038 pfam10518, TAT_signal, TAT (twin-arginine translocation) pathway
signal sequence.
Length = 26
Score = 27.9 bits (64), Expect = 0.40
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 68 KRDFVSGGAAAGVAAAFGAPVGG 90
+R F+ GGAAA AAA G
Sbjct: 4 RRQFLKGGAAAAAAAALGGAAAA 26
>gnl|CDD|176454 cd01700, PolY_Pol_V_umuC, umuC subunit of DNA Polymerase V. umuC
subunit of Pol V. Pol V is a bacterial translesion
synthesis (TLS) polymerase that consists of the
heterotrimer of one umuC and two umuD subunits.
Translesion synthesis is a process that allows the
bypass of a variety of DNA lesions. TLS polymerases
lack proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. Pol V, RecA,
single stranded DNA-binding protein, beta sliding clamp,
and gamma clamp loading complex are responsible for
inducing the SOS response in bacteria to repair
UV-induced DNA damage.
Length = 344
Score = 31.4 bits (72), Expect = 0.42
Identities = 17/68 (25%), Positives = 25/68 (36%), Gaps = 19/68 (27%)
Query: 177 NHKLTVFRIRY-----MSARYVKVLEAVLVAMVSACVPIIMIYSIDDC------RPLGED 225
H + VF Y MS R + +LE P + +YSID+ D
Sbjct: 62 RHGVAVFSSNYALYGDMSRRIMSILERF--------SPDVEVYSIDESFLDLTGSLRFGD 113
Query: 226 PTEHAVQM 233
E A ++
Sbjct: 114 LEELARKI 121
>gnl|CDD|233399 TIGR01409, TAT_signal_seq, Tat (twin-arginine translocation)
pathway signal sequence. Proteins assembled with
various cofactors or by means of cytosolic molecular
chaperones are poor candidates for translocation across
the bacterial inner membrane by the standard general
secretory (Sec) pathway. This model describes a family
of predicted long, non-Sec signal sequences and
signal-anchor sequences (uncleaved signal sequences).
All contain an absolutely conserved pair of arginine
residues, in a motif approximated by (S/T)-R-R-X-F-L-K,
followed by a membrane-spanning hydrophobic region.
Members with small amino acid side chains at the -1 and
-3 positions from the C-terminus of the model should be
predicted to be cleaved as are Sec pathway signal
sequences. Members are almost exclusively bacterial,
although archaeal sequences are also found. A large
fraction of the members of this family may have bound
redox-active cofactors [Protein fate, Protein and
peptide secretion and trafficking].
Length = 29
Score = 27.9 bits (63), Expect = 0.45
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 69 RDFVSGGAAAGVAAAFGAPVGGV 91
RDF+ G AAAG AA GA +
Sbjct: 4 RDFLKGAAAAGAAAGLGALLPSP 26
>gnl|CDD|214015 cd12871, Bacuni_01323_like, Uncharacterized protein conserved in
Bacteroidetes. A well-conserved family of 16-stranded
beta barrels resembling outer membrane porins. The
interior of the barrels is mostly occupied by an insert
with partially helical structure.
Length = 231
Score = 30.9 bits (70), Expect = 0.54
Identities = 17/76 (22%), Positives = 25/76 (32%), Gaps = 12/76 (15%)
Query: 113 GTIVTTFTLNVVLS----AYY---GHPGELTNSGLLNFGKFYDLRYDLLEMFFYVGAGVF 165
G IV+ T + Y + N G L L YDL ++F+ +
Sbjct: 124 GDIVSISTKSNTEENESKITYTSDKVYNPIVNKGCLMLF-GLTLGYDLSDLFYA----YY 178
Query: 166 GGLTGALYNSLNHKLT 181
GL G L +
Sbjct: 179 AGLLGKATKHLPESII 194
>gnl|CDD|237883 PRK14991, PRK14991, tetrathionate reductase subunit A;
Provisional.
Length = 1031
Score = 30.0 bits (68), Expect = 1.6
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 65 DHEKRDFVSGGAAAGVAAAFGA 86
D +R + GG AAG AAF A
Sbjct: 2 DKTRRQLLKGGLAAGGLAAFAA 23
>gnl|CDD|221425 pfam12110, Nup96, Nuclear protein 96. Nup96 (often known by the
name of its yeast homolog Nup145C) is part of the Nup84
heptameric complex in the nuclear pore complex. Nup96
complexes with Sec13 in the middle of the heptamer. The
function of the heptamer is to coat the curvature of the
nuclear pore complex between the inner and outer nuclear
membranes. Nup96 is predicted to be an alpha helical
solenoid. The interaction between Nup96 and Sec13 is the
point of curvature in the heptameric complex.
Length = 290
Score = 28.9 bits (65), Expect = 2.8
Identities = 18/93 (19%), Positives = 34/93 (36%), Gaps = 18/93 (19%)
Query: 78 AGVAAAFGAPVGGVLFSLEEGASFWNQSLTWRIFFGTIVTTFTLNVVLSAY--------- 128
AG G F L+ W Q+L R+++G I ++ + ++
Sbjct: 75 AGNVFRSLGDSGENEFELD-----WLQALGLRLWYG-ISDDLSIEDAVQSFLDALSSGEE 128
Query: 129 ---YGHPGELTNSGLLNFGKFYDLRYDLLEMFF 158
P E + + F D +DLL+++
Sbjct: 129 PAPPPPPTEGVADDVNSGEPFEDPLFDLLKLYA 161
>gnl|CDD|221355 pfam11981, DUF3482, Domain of unknown function (DUF3482). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria and eukaryotes. This domain
is typically between 289 to 301 amino acids in length.
This domain is found associated with pfam01926. THe
central region of these proteins contains a hydrophobic
region that is similar to pfam05433.
Length = 293
Score = 27.6 bits (62), Expect = 6.2
Identities = 11/25 (44%), Positives = 12/25 (48%)
Query: 70 DFVSGGAAAGVAAAFGAPVGGVLFS 94
D GG G AAA GA GG +
Sbjct: 164 DLAVGGLTLGAAAALGALAGGGWQT 188
>gnl|CDD|227315 COG4982, COG4982, 3-oxoacyl-[acyl-carrier protein].
Length = 866
Score = 27.5 bits (61), Expect = 8.5
Identities = 24/88 (27%), Positives = 30/88 (34%)
Query: 3 RLVRIKTLVVKTIGVITTVVGGLAGGKEGPMIHSGAIVAAGISQGKSTSFGTDFQIFKYF 62
RL K K G I V G G EG H G +G S G+ +
Sbjct: 143 RLRSSKGPGGKRPGAIAERVTGTWGLGEGWADHVLVEALLGTREGPSVRGGSLADLKAAL 202
Query: 63 REDHEKRDFVSGGAAAGVAAAFGAPVGG 90
+K D + A + VAA G V
Sbjct: 203 DSSAQKVDALIDAAVSSVAARQGVSVAL 230
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.324 0.141 0.425
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,699,770
Number of extensions: 1348965
Number of successful extensions: 2201
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2166
Number of HSP's successfully gapped: 66
Length of query: 260
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 165
Effective length of database: 6,723,972
Effective search space: 1109455380
Effective search space used: 1109455380
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 58 (26.2 bits)