RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16230
(292 letters)
>gnl|CDD|233513 TIGR01657, P-ATPase-V, P-type ATPase of unknown pump specificity
(type V). These P-type ATPases form a distinct clade
but the substrate of their pumping activity has yet to
be determined. This clade has been designated type V in.
Length = 1054
Score = 196 bits (499), Expect = 1e-56
Identities = 91/243 (37%), Positives = 132/243 (54%), Gaps = 14/243 (5%)
Query: 63 INVKKLMYVWSDQEQNFIKLV-----GLDKGLTNSQLHQFNGFTFEEQFMRGIVYGKNEI 117
+ +K + + ++E + G+ ++ NG T + R YGKNEI
Sbjct: 98 FDFRKQRFSYHEKELKIFSPLPYLFKEKSFGVYSTCAGHSNGLTTGDIAQRKAKYGKNEI 157
Query: 118 NVPIQNISSLFVLEALNPFYIFQVFTLCVWFAEAYYYYTGAIICMSVFGIVSSVIQTRQK 177
+P+ + L E L+PFY+FQVF++ +W + YYYY+ I+ MS I SV Q R++
Sbjct: 158 EIPVPSFLELLKEEVLHPFYVFQVFSVILWLLDEYYYYSLCIVFMSSTSISLSVYQIRKQ 217
Query: 178 S--LHDTVNTVDKVTVKRSKGLYEEVPTTHLVPGDIIVIPK-HGCTLACDATLLQGNCIV 234
L D V+ V V R+ G + + + LVPGDI+ IP+ T+ CD+ LL G+CIV
Sbjct: 218 MQRLRDMVHKPQSVIVIRN-GKWVTIASDELVPGDIVSIPRPEEKTMPCDSVLLSGSCIV 276
Query: 235 NESMLTGESVPVMKTALP----SQSDFYNEKEDVNHTLYCGTVILQAR-YHGDEYLHAVV 289
NESMLTGESVPV+K +P D + + H L+ GT ILQ R Y GD A+V
Sbjct: 277 NESMLTGESVPVLKFPIPDNGDDDEDLFLYETSKKHVLFGGTKILQIRPYPGDTGCLAIV 336
Query: 290 IRT 292
+RT
Sbjct: 337 VRT 339
Score = 62.4 bits (152), Expect = 8e-11
Identities = 27/60 (45%), Positives = 34/60 (56%), Gaps = 5/60 (8%)
Query: 1 MLTGESVPVMKTALP----SQSDFYNEKEDVNHTLYCGTVILQAR-YHGDEYLHAVVIRT 55
MLTGESVPV+K +P D + + H L+ GT ILQ R Y GD A+V+RT
Sbjct: 280 MLTGESVPVLKFPIPDNGDDDEDLFLYETSKKHVLFGGTKILQIRPYPGDTGCLAIVVRT 339
>gnl|CDD|233438 TIGR01494, ATPase_P-type, ATPase, P-type (transporting), HAD
superfamily, subfamily IC. The P-type ATPases are a
large family of trans-membrane transporters acting on
charged substances. The distinguishing feature of the
family is the formation of a phosphorylated intermediate
(aspartyl-phosphate) during the course of the reaction.
Another common name for these enzymes is the E1-E2
ATPases based on the two isolable conformations: E1
(unphosphorylated) and E2 (phosphorylated). Generally,
P-type ATPases consist of only a single subunit
encompassing the ATPase and ion translocation pathway,
however, in the case of the potassium (TIGR01497) and
sodium/potassium (TIGR01106) varieties, these functions
are split between two subunits. Additional small
regulatory or stabilizing subunits may also exist in
some forms. P-type ATPases are nearly ubiquitous in life
and are found in numerous copies in higher organisms (at
least 45 in Arabidopsis thaliana, for instance ).
Phylogenetic analyses have revealed that the P-type
ATPase subfamily is divided up into groups based on
substrate specificities and this is represented in the
various subfamily and equivalog models that have been
made: IA (K+) TIGR01497, IB (heavy metals) TIGR01525,
IIA1 (SERCA-type Ca++) TIGR01116, IIA2 (PMR1-type Ca++)
TIGR01522, IIB (PMCA-type Ca++) TIGR01517, IIC (Na+/K+,
H+/K+ antiporters) TIGR01106, IID (fungal-type Na+ and
K+) TIGR01523, IIIA (H+) TIGR01647, IIIB (Mg++)
TIGR01524, IV (phospholipid, flippase) TIGR01652 and V
(unknown specificity) TIGR01657. The crystal structure
of one calcium-pumping ATPase and an analysis of the
fold of the catalytic domain of the P-type ATPases have
been published. These reveal that the catalytic core of
these enzymes is a haloacid dehalogenase(HAD)-type
aspartate-nucleophile hydrolase. The location of the
ATP-binding loop in between the first and second HAD
conserved catalytic motifs defines these enzymes as
members of subfamily I of the HAD superfamily (see also
TIGR01493, TIGR01509, TIGR01549, TIGR01544 and
TIGR01545). Based on these classifications, the P-type
ATPase _superfamily_ corresponds to the IC subfamily of
the HAD superfamily.
Length = 543
Score = 94.7 bits (236), Expect = 8e-22
Identities = 46/144 (31%), Positives = 71/144 (49%), Gaps = 13/144 (9%)
Query: 159 IICMSVFGIVSSVIQT-----RQKSLHDTVNTVDKVTVKRSKGLYEEVPTTHLVPGDIIV 213
I+ + + ++ V Q +SL D + TV R+ +E+P LVPGD+++
Sbjct: 2 ILFLVLVFVLLVVKQKLKAEDILRSLSDRLVNTRPATVLRNGW--KEIPAKDLVPGDVVL 59
Query: 214 IPKHGCTLACDATLLQGNCIVNESMLTGESVPVMKTALPSQSDFYNEKEDV--NHTLYCG 271
+ G T+ D LL G+C V+ES LTGES PV+KTAL + V ++ G
Sbjct: 60 VKS-GETVPADGVLLSGSCFVDESNLTGESNPVLKTALKETQSGTITGDLVFAGTYVFGG 118
Query: 272 TVILQARYHG---DEYLHAVVIRT 292
T+I+ G AVV++T
Sbjct: 119 TLIVVVTPTGILTTVGRIAVVVKT 142
Score = 43.9 bits (104), Expect = 5e-05
Identities = 25/90 (27%), Positives = 39/90 (43%), Gaps = 11/90 (12%)
Query: 1 MLTGESVPVMKTALPSQSDFYNEKEDV--NHTLYCGTVILQARYHG---DEYLHAVVIRT 55
LTGES PV+KTAL + V ++ GT+I+ G AVV++T
Sbjct: 83 NLTGESNPVLKTALKETQSGTITGDLVFAGTYVFGGTLIVVVTPTGILTTVGRIAVVVKT 142
Query: 56 EVTELKVINVKKLMYVWSDQEQNFIKLVGL 85
+ + D+ +NFI ++ L
Sbjct: 143 GF------ETRTPLQSKRDRLENFIFILFL 166
>gnl|CDD|223550 COG0474, MgtA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 917
Score = 93.6 bits (233), Expect = 3e-21
Identities = 51/213 (23%), Positives = 84/213 (39%), Gaps = 35/213 (16%)
Query: 98 NGFTFEEQFMRGIVYGKNEINVPIQNISSLFV---------------LEALNPFYIFQVF 142
G + EE R YG NE+ P + SL + AL ++
Sbjct: 43 TGLSEEEVKRRLKKYGPNEL--PEEKKRSLLKKFLRQFKDPFIILLLVAALLSAFVGDWV 100
Query: 143 TLCVWFAEAYYYYTGAIICMSVFGIVSSVIQTRQ--KSLHDTVNTVDKVTVKRSKGLYEE 200
V ++ ++ + + ++L + K V R E
Sbjct: 101 DAGV-----DAIVILLVVVINALLGFVQEYRAEKALEALKKMSSP--KAKVLRDGKF-VE 152
Query: 201 VPTTHLVPGDIIVIPKHGCTLACDATLLQGNC-IVNESMLTGESVPVMKTALPSQSDFYN 259
+P + LVPGDI+++ + G + D LL+ + V+ES LTGES+PV K ALP
Sbjct: 153 IPASELVPGDIVLL-EAGDVVPADLRLLESSDLEVDESALTGESLPVEKQALPLTKSDAP 211
Query: 260 EKEDVNHTLYCGTVILQARYHGDEYLHAVVIRT 292
D ++ L+ GT ++ R +V+ T
Sbjct: 212 LGLDRDNMLFSGTTVVSGR------AKGIVVAT 238
Score = 42.3 bits (100), Expect = 2e-04
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 1 MLTGESVPVMKTALPSQSDFYNEKEDVNHTLYCGTVILQARYHGDEYLHAVVIRT 55
LTGES+PV K ALP D ++ L+ GT ++ R +V+ T
Sbjct: 190 ALTGESLPVEKQALPLTKSDAPLGLDRDNMLFSGTTVVSGR------AKGIVVAT 238
>gnl|CDD|215733 pfam00122, E1-E2_ATPase, E1-E2 ATPase.
Length = 222
Score = 81.5 bits (202), Expect = 2e-18
Identities = 38/140 (27%), Positives = 61/140 (43%), Gaps = 28/140 (20%)
Query: 158 AIICMSVFGIVSSVIQTRQ-----KSLHDTVNTVDKVTVKRSKGLYEEVPTTHLVPGDII 212
I+ + + + Q + K+L + TV R EE+P LV GDI+
Sbjct: 1 IILLLVLINALLEAYQEYRARKALKALKKLLPPT-AATVIRDGKE-EEIPADELVVGDIV 58
Query: 213 VIPKHGCTLACDATLLQGNCIVNESMLTGESVPVMKTALPSQSDFYNEKEDVNHTLYCGT 272
++ K G + D +++G+ V+ES LTGES+PV K+ T++ GT
Sbjct: 59 LL-KPGDRVPADGRIIEGSLEVDESALTGESLPVEKS--------------RGDTVFAGT 103
Query: 273 VILQARYHGDEYLHAVVIRT 292
V+L L +V T
Sbjct: 104 VVLSGE------LKVIVTAT 117
Score = 34.8 bits (81), Expect = 0.032
Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 20/55 (36%)
Query: 1 MLTGESVPVMKTALPSQSDFYNEKEDVNHTLYCGTVILQARYHGDEYLHAVVIRT 55
LTGES+PV K+ T++ GTV+L L +V T
Sbjct: 83 ALTGESLPVEKS--------------RGDTVFAGTVVLSGE------LKVIVTAT 117
>gnl|CDD|225127 COG2217, ZntA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 713
Score = 66.5 bits (163), Expect = 3e-12
Identities = 26/64 (40%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 187 DKVTVKRSKGLYEEVPTTHLVPGDIIVIPKHGCTLACDATLLQGNCIVNESMLTGESVPV 246
TV R G EEVP + GDI+++ + G + D ++ G+ V+ESMLTGES+PV
Sbjct: 211 KTATVVRGDGEEEEVPVEEVQVGDIVLV-RPGERIPVDGVVVSGSSSVDESMLTGESLPV 269
Query: 247 MKTA 250
K
Sbjct: 270 EKKP 273
Score = 30.3 bits (69), Expect = 1.3
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 1 MLTGESVPVMKTA 13
MLTGES+PV K
Sbjct: 261 MLTGESLPVEKKP 273
>gnl|CDD|233447 TIGR01525, ATPase-IB_hvy, heavy metal translocating P-type ATPase.
This model encompasses two equivalog models for the
copper and cadmium-type heavy metal transporting P-type
ATPases (TIGR01511 and TIGR01512) as well as those
species which score ambiguously between both models. For
more comments and references, see the files on TIGR01511
and 01512.
Length = 556
Score = 60.3 bits (147), Expect = 2e-10
Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 187 DKVTVKRSKGLYEEVPTTHLVPGDIIVIPKHGCTLACDATLLQGNCIVNESMLTGESVPV 246
V + G EEVP L GDI+++ + G + D ++ G V+ES LTGES+PV
Sbjct: 55 STARVLQGDGSEEEVPVEELQVGDIVIV-RPGERIPVDGVVISGESEVDESALTGESMPV 113
Query: 247 MK 248
K
Sbjct: 114 EK 115
>gnl|CDD|211664 TIGR01512, ATPase-IB2_Cd, heavy
metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase.
This model describes the P-type ATPase primarily
responsible for translocating cadmium ions (and other
closely-related divalent heavy metals such as cobalt,
mercury, lead and zinc) across biological membranes.
These transporters are found in prokaryotes and plants.
Experimentally characterized members of the seed
alignment include: SP|P37617 from E. coli, SP|Q10866
from Mycobacterium tuberculosis and SP|Q59998 from
Synechocystis PCC6803. The cadmium P-type ATPases have
been characterized as Type IB based on a phylogenetic
analysis which combines the copper-translocating ATPases
with the cadmium-translocating species. This model and
that describing the copper-ATPases (TIGR01511) are well
separated, and thus we further type the copper-ATPases
as IB1 and the cadmium-ATPases as IB2. Several sequences
which have not been characterized experimentally fall
just below trusted cutoff for both of these models
(SP|Q9CCL1 from Mycobacterium leprae, GP|13816263 from
Sulfolobus solfataricus, OMNI|NTL01CJ01098 from
Campylobacter jejuni, OMNI|NTL01HS01687 from
Halobacterium sp., GP|6899169 from Ureaplasma
urealyticum and OMNI|HP1503 from Helicobacter pylori)
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 536
Score = 60.4 bits (147), Expect = 2e-10
Identities = 28/62 (45%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 187 DKVTVKRSKGLYEEVPTTHLVPGDIIVIPKHGCTLACDATLLQGNCIVNESMLTGESVPV 246
D V R G EEV L GD++V+ K G + D +L G V+ES LTGESVPV
Sbjct: 55 DTARVLRG-GSLEEVAVEELKVGDVVVV-KPGERVPVDGVVLSGTSTVDESALTGESVPV 112
Query: 247 MK 248
K
Sbjct: 113 EK 114
>gnl|CDD|130587 TIGR01524, ATPase-IIIB_Mg, magnesium-translocating P-type ATPase.
This model describes the magnesium translocating P-type
ATPase found in a limited number of bacterial species
and best described in Salmonella typhimurium, which
contains two isoforms. These transporters are active in
low external Mg2+ concentrations and pump the ion into
the cytoplasm. The magnesium ATPases have been
classified as type IIIB by a phylogenetic analysis
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 867
Score = 59.5 bits (144), Expect = 6e-10
Identities = 51/209 (24%), Positives = 81/209 (38%), Gaps = 28/209 (13%)
Query: 99 GFTFEEQFMRGIVYGKNEINVPIQNISS---LFVLEALNPFYIFQVFTLCVWFAEAYYYY 155
G T E R +G N+ + L + NPF + V +
Sbjct: 33 GLTNVEVTERLAEFGPNQ--TVEEKKVPNLRLLIRAFNNPFIYILAMLMGVSYLTDDLEA 90
Query: 156 TGAIICM-SVFGIVSSVIQTRQ-------KSLHDTVNTVDKVTVKRSKGLYEEVPTTHLV 207
T I M G++ + ++R K++ TV +V + G +EVP LV
Sbjct: 91 TVIIALMVLASGLLGFIQESRAERAAYALKNMVKNTATVLRVINENGNGSMDEVPIDALV 150
Query: 208 PGDIIVIPKHGCTLACDATLLQG-NCIVNESMLTGESVPVMK---TALPSQSDFYNEKED 263
PGD+I + G + DA ++ + +N+S LTGES+PV K E +
Sbjct: 151 PGDLIELAA-GDIIPADARVISARDLFINQSALTGESLPVEKFVEDKRARD----PEILE 205
Query: 264 VNHTLYCGTVILQARYHGDEYLHAVVIRT 292
+ + GT +L AVV+ T
Sbjct: 206 RENLCFMGTNVLSGH------AQAVVLAT 228
>gnl|CDD|237914 PRK15122, PRK15122, magnesium-transporting ATPase; Provisional.
Length = 903
Score = 52.3 bits (126), Expect = 1e-07
Identities = 51/195 (26%), Positives = 90/195 (46%), Gaps = 41/195 (21%)
Query: 84 GLDKGLTNSQLH-QFNGFTFEEQFMRGIVYGKNEI---NVP---IQNISSLFVLEAL-NP 135
L++ L N L+ G T E+ R YG NE+ P +Q +L+A NP
Sbjct: 31 SLEETLAN--LNTHRQGLTEEDAAERLQRYGPNEVAHEKPPHALVQ------LLQAFNNP 82
Query: 136 F-YIFQVFTLCVWFAEAYYY---------YTGAIICMSVFGIVSSVIQTRQ--------- 176
F Y+ V +F + Y+ TG II +++ + S +++ Q
Sbjct: 83 FIYVLMVLAAISFFTD-YWLPLRRGEETDLTGVIIILTMVLL-SGLLRFWQEFRSNKAAE 140
Query: 177 --KSLHDTVNTVDKVTVKRSKGLYEEVPTTHLVPGDIIVIPKHGCTLACDATLLQG-NCI 233
K++ T TV + ++ + E+P LVPGDI+ + G + D L++ +
Sbjct: 141 ALKAMVRTTATVLRRGHAGAEPVRREIPMRELVPGDIVHLSA-GDMIPADVRLIESRDLF 199
Query: 234 VNESMLTGESVPVMK 248
+++++LTGE++PV K
Sbjct: 200 ISQAVLTGEALPVEK 214
>gnl|CDD|233506 TIGR01647, ATPase-IIIA_H, plasma-membrane proton-efflux P-type
ATPase. This model describes the plasma membrane proton
efflux P-type ATPase found in plants, fungi, protozoa,
slime molds and archaea. The best studied representative
is from yeast.
Length = 754
Score = 51.9 bits (125), Expect = 2e-07
Identities = 26/62 (41%), Positives = 40/62 (64%), Gaps = 3/62 (4%)
Query: 188 KVTVKRSKGLYEEVPTTHLVPGDIIVIPKHGCTLACDATLLQGNCI-VNESMLTGESVPV 246
K V R G ++E+P + LVPGD++ + K G + D L +G+ I V+++ LTGES+PV
Sbjct: 93 KARVLRD-GKWQEIPASELVPGDVVRL-KIGDIVPADCRLFEGDYIQVDQAALTGESLPV 150
Query: 247 MK 248
K
Sbjct: 151 TK 152
>gnl|CDD|225126 COG2216, KdpB, High-affinity K+ transport system, ATPase chain B
[Inorganic ion transport and metabolism].
Length = 681
Score = 51.5 bits (124), Expect = 2e-07
Identities = 22/56 (39%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 193 RSKGLYEEVPTTHLVPGDIIVIPKHGCTLACDATLLQGNCIVNESMLTGESVPVMK 248
R+ G E VP T L GDI+++ + G + D +++G V+ES +TGES PV++
Sbjct: 110 RADGSIEMVPATELKKGDIVLV-EAGEIIPSDGEVIEGVASVDESAITGESAPVIR 164
>gnl|CDD|234905 PRK01122, PRK01122, potassium-transporting ATPase subunit B;
Provisional.
Length = 679
Score = 50.6 bits (122), Expect = 4e-07
Identities = 23/56 (41%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 193 RSKGLYEEVPTTHLVPGDIIVIPKHGCTLACDATLLQGNCIVNESMLTGESVPVMK 248
R G EEVP T L GDI+++ + G + D +++G V+ES +TGES PV++
Sbjct: 110 REPGAAEEVPATELRKGDIVLV-EAGEIIPADGEVIEGVASVDESAITGESAPVIR 164
>gnl|CDD|130561 TIGR01497, kdpB, K+-transporting ATPase, B subunit. This model
describes the P-type ATPase subunit of the complex
responsible for translocating potassium ions across
biological membranes in microbes. In E. coli and other
species, this complex consists of the proteins KdpA,
KdpB, KdpC and KdpF. KdpB is the ATPase subunit, while
KdpA is the potassium-ion translocating subunit. The
function of KdpC is unclear, although cit has been
suggested to couple the ATPase subunit to the
ion-translocating subunit , while KdpF serves to
stabilize the complex. The potassium P-type ATPases have
been characterized as Type IA based on a phylogenetic
analysis which places this clade closest to the
heavy-metal translocating ATPases (Type IB). Others
place this clade closer to the Na+/K+ antiporter type
(Type IIC) based on physical characteristics. This model
is very clear-cut, with a strong break between trusted
hits and noise. All members of the seed alignment, from
Clostridium, Anabaena and E. coli are in the
characterized table. One sequence above trusted,
OMNI|NTL01TA01282, is apparently mis-annotated in the
primary literature, but properly annotated by TIGR
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 675
Score = 50.7 bits (121), Expect = 5e-07
Identities = 30/91 (32%), Positives = 49/91 (53%), Gaps = 7/91 (7%)
Query: 170 SVIQTRQKSLHDTVNTVDKVTVKR---SKGLYEEVPTTHLVPGDIIVIPKHGCTLACDAT 226
+V + R K+ D++ K T + G ++VP L GDI+++ + G + CD
Sbjct: 85 AVAEGRGKAQADSLKGTKKTTFAKLLRDDGAIDKVPADQLKKGDIVLV-EAGDVIPCDGE 143
Query: 227 LLQGNCIVNESMLTGESVPVMKTALPSQSDF 257
+++G V+ES +TGES PV+K S DF
Sbjct: 144 VIEGVASVDESAITGESAPVIKE---SGGDF 171
>gnl|CDD|236827 PRK11033, zntA, zinc/cadmium/mercury/lead-transporting ATPase;
Provisional.
Length = 741
Score = 50.4 bits (121), Expect = 5e-07
Identities = 24/56 (42%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 196 GLYEEVPTTHLVPGDII-VIPKHGCTLACDATLLQGNCIVNESMLTGESVPVMKTA 250
G EEV L PGD+I V G L D LL +ES LTGES+PV +
Sbjct: 251 GEREEVAIADLRPGDVIEVAA--GGRLPADGKLLSPFASFDESALTGESIPVERAT 304
>gnl|CDD|233445 TIGR01511, ATPase-IB1_Cu, copper-(or silver)-translocating P-type
ATPase. This model describes the P-type ATPase
primarily responsible for translocating copper ions
accross biological membranes. These transporters are
found in prokaryotes and eukaryotes. This model
encompasses those species which pump copper ions out of
cells or organelles (efflux pumps such as CopA of
Escherichia coli ) as well as those which pump the ion
into cells or organelles either for the purpose of
supporting life in extremely low-copper environments
(for example CopA of Enterococcus hirae ) or for the
specific delivery of copper to a biological complex for
which it is a necessary component (for example FixI of
Bradyrhizobium japonicum, or CtaA and PacS of
Synechocystis). The substrate specificity of these
transporters may, to a varying degree, include silver
ions (for example, CopA from Archaeoglobus fulgidus).
Copper transporters from this family are well known as
the genes which are mutated in two human disorders of
copper metabolism, Wilson's and Menkes' diseases. The
sequences contributing to the seed of this model are all
experimentally characterized. The copper P-type ATPases
have been characterized as Type IB based on a
phylogenetic analysis which combines the
copper-translocating ATPases with the
cadmium-translocating species. This model and that
describing the cadmium-ATPases (TIGR01512) are well
separated, and thus we further type the copper-ATPases
as IB1 (and the cadmium-ATPases as IB2). Several
sequences which have not been characterized
experimentally fall just below the cutoffs for both of
these models. A sequence from Enterococcus faecalis
scores very high against this model, but yet is
annotated as an "H+/K+ exchanging ATPase". BLAST of this
sequence does not hit anything else annotated in this
way. This error may come from the characterization paper
published in 1987. Accession GP|7415611 from
Saccharomyces cerevisiae appears to be mis-annotated as
a cadmium resistance protein. Accession
OMNI|NTL01HS00542 from Halobacterium which scores above
trusted for this model is annotated as
"molybdenum-binding protein" although no evidence can be
found for this classification [Cellular processes,
Detoxification, Transport and binding proteins, Cations
and iron carrying compounds].
Length = 572
Score = 49.6 bits (119), Expect = 9e-07
Identities = 23/51 (45%), Positives = 33/51 (64%), Gaps = 1/51 (1%)
Query: 199 EEVPTTHLVPGDIIVIPKHGCTLACDATLLQGNCIVNESMLTGESVPVMKT 249
EEVP L PGDI+ + G + D T+++G V+ES++TGES+PV K
Sbjct: 103 EEVPVELLQPGDIVRV-LPGEKIPVDGTVIEGESEVDESLVTGESLPVPKK 152
>gnl|CDD|236705 PRK10517, PRK10517, magnesium-transporting ATPase MgtA;
Provisional.
Length = 902
Score = 48.9 bits (117), Expect = 2e-06
Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 185 TVDKVTVKRSKGLYEEVPTTHLVPGDIIVIPKHGCTLACDATLLQG-NCIVNESMLTGES 243
TV +V + + + E+P LVPGDII + G + D +LQ + V ++ LTGES
Sbjct: 162 TVLRVINDKGENGWLEIPIDQLVPGDIIKLAA-GDMIPADLRILQARDLFVAQASLTGES 220
Query: 244 VPVMKTALPSQSD 256
+PV K A Q +
Sbjct: 221 LPVEKFATTRQPE 233
Score = 28.1 bits (63), Expect = 6.7
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 2 LTGESVPVMKTALPSQSD 19
LTGES+PV K A Q +
Sbjct: 216 LTGESLPVEKFATTRQPE 233
>gnl|CDD|188151 TIGR01517, ATPase-IIB_Ca, plasma-membrane calcium-translocating
P-type ATPase. This model describes the P-type ATPase
responsible for translocating calcium ions across the
plasma membrane of eukaryotes , out of the cell. In some
organisms, this type of pump may also be found in
vacuolar membranes. In humans and mice, at least, there
are multiple isoforms of the PMCA pump with overlapping
but not redundant functions. Accordingly, there are no
human diseases linked to PMCA defects, although
alterations of PMCA function do elicit physiological
effects. The calcium P-type ATPases have been
characterized as Type IIB based on a phylogenetic
analysis which distinguishes this group from the Type
IIA SERCA calcium pump. A separate analysis divides Type
IIA into sub-types (SERCA and PMR1) which are modelled
by TIGR01116 and TIGR01522. This model is well separated
from those.
Length = 944
Score = 48.6 bits (116), Expect = 2e-06
Identities = 37/161 (22%), Positives = 63/161 (39%), Gaps = 23/161 (14%)
Query: 108 RGIVYGKNEINVPIQNISSLFVLEALNPFYIFQVFTLC--VWFAEAYYY----------- 154
R VYGKNE+ V AL+ + ++ V
Sbjct: 70 REKVYGKNELPEKPPKSFLQIVWAALSD-QTLILLSVAAVVSLVLGLPEPGEGKADTETG 128
Query: 155 -YTGAIICMSVFGIVS-SVIQTRQKSLH----DTVNTVDKVTVKRSKGLYEEVPTTHLVP 208
G I +SV +V + + +K L + + K+ V R G +++ +V
Sbjct: 129 WIEGVAILVSVILVVLVTAVNDYKKELQFRQLNREKSAQKIAVIRG-GQEQQISIHDIVV 187
Query: 209 GDIIVIPKHGCTLACDATLLQG-NCIVNESMLTGESVPVMK 248
GDI+ + G + D + G + ++ES +TGES P+ K
Sbjct: 188 GDIVSL-STGDVVPADGVFISGLSLEIDESSITGESDPIKK 227
>gnl|CDD|130586 TIGR01523, ATPase-IID_K-Na, potassium and/or sodium efflux P-type
ATPase, fungal-type. Initially described as a calcium
efflux ATPase , more recent work has shown that the S.
pombe CTA3 gene is in fact a potassium ion efflux pump.
This model describes the clade of fungal P-type ATPases
responsible for potassium and sodium efflux. The degree
to which these pumps show preference for sodium or
potassium varies. This group of ATPases has been
classified by phylogentic analysis as type IID. The
Leishmania sequence (GP|3192903), which falls between
trusted and noise in this model, may very well turn out
to be an active potassium pump.
Length = 1053
Score = 46.2 bits (109), Expect = 1e-05
Identities = 41/160 (25%), Positives = 73/160 (45%), Gaps = 11/160 (6%)
Query: 98 NGFTFEEQFMRGIVYGKNEINVPIQNISSLFVL-EALNPFYIFQVFTLCVWFAEAYYYYT 156
G T +E R G+N + + +L + N + + + FA +
Sbjct: 25 EGLTHDEAQHRLKEVGENRLEADSGIDAKAMLLHQVCNAMCMVLIIAAAISFAMHDWIEG 84
Query: 157 GAIICMSVFGIVSSVIQTRQKSLHDTVNTVDKVT-----VKRSKGLYEEVPTTHLVPGDI 211
G I + I+ IQ + T++++ + V R+ G + + + LVPGDI
Sbjct: 85 GVISAIIALNILIGFIQEYKAE--KTMDSLKNLASPMAHVIRN-GKSDAIDSHDLVPGDI 141
Query: 212 IVIPKHGCTLACDATLLQG-NCIVNESMLTGESVPVMKTA 250
++ K G T+ D L++ N +E++LTGES+PV+K A
Sbjct: 142 CLL-KTGDTIPADLRLIETKNFDTDEALLTGESLPVIKDA 180
>gnl|CDD|184448 PRK14010, PRK14010, potassium-transporting ATPase subunit B;
Provisional.
Length = 673
Score = 40.8 bits (95), Expect = 6e-04
Identities = 36/140 (25%), Positives = 60/140 (42%), Gaps = 26/140 (18%)
Query: 126 SLFVLEALNPFYIFQVFTLCVW------FAEAYYYYTGAIICMSVFGIVSSVIQTRQKSL 179
LF E+++ Y+F +F + + F+EA G + + +L
Sbjct: 53 DLFHQESVSRLYVFSIFIILLLTLVFANFSEALAEGRG---------------KAQANAL 97
Query: 180 HDTVNTVDKVTVKRSKGLYEEVPTTHLVPGDIIVIPKHGCTLACDATLLQGNCIVNESML 239
T + +K G YE + + L G I+ + G + D +++G V+ES +
Sbjct: 98 RQTQTEMKARRIK-QDGSYEMIDASDLKKGHIVRV-ATGEQIPNDGKVIKGLATVDESAI 155
Query: 240 TGESVPVMKTALPSQSDFYN 259
TGES PV+K S DF N
Sbjct: 156 TGESAPVIKE---SGGDFDN 172
>gnl|CDD|233277 TIGR01116, ATPase-IIA1_Ca, sarco/endoplasmic reticulum
calcium-translocating P-type ATPase. This model
describes the P-type ATPase responsible for
translocating calcium ions across the endoplasmic
reticulum membrane of eukaryotes , and is of particular
importance in the sarcoplasmic reticulum of skeletal and
cardiac muscle in vertebrates. These pumps transfer Ca2+
from the cytoplasm to the lumen of the endoplasmic
reticulum. In humans and mice, at least, there are
multiple isoforms of the SERCA pump with overlapping but
not redundant functions. Defects in SERCA isoforms are
associated with diseases in humans. The calcium P-type
ATPases have been characterized as Type IIA based on a
phylogenetic analysis which distinguishes this group
from the Type IIB PMCA calcium pump modelled by
TIGR01517. A separate analysis divides Type IIA into
sub-types, SERCA and PMR1 the latter of which is
modelled by TIGR01522 [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 917
Score = 40.5 bits (95), Expect = 8e-04
Identities = 30/100 (30%), Positives = 53/100 (53%), Gaps = 13/100 (13%)
Query: 196 GLYEEVPTTHLVPGDIIVIPKHGCTLACDATLLQGNCI-VNESMLTGESVPVMKT--ALP 252
G + + LVPGDI+ + G + D +L + V++S+LTGESV V K ++P
Sbjct: 81 GRWSVIKAKDLVPGDIVEL-AVGDKVPADIRVLSLKTLRVDQSILTGESVSVNKHTESVP 139
Query: 253 SQSDFYNEKEDVNHTLYCGTVILQARYHGDEYLHAVVIRT 292
+ +K+++ L+ GT+++ + G VV+RT
Sbjct: 140 DERAVNQDKKNM---LFSGTLVVAGKARG------VVVRT 170
Score = 30.1 bits (68), Expect = 1.6
Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 12/66 (18%)
Query: 1 MLTGESVPVMKT--ALPSQSDFYNEKEDVNHTLYCGTVILQARYHGDEYLHAVVIRTEV- 57
+LTGESV V K ++P + +K+++ L+ GT+++ + G VV+RT +
Sbjct: 123 ILTGESVSVNKHTESVPDERAVNQDKKNM---LFSGTLVVAGKARG------VVVRTGMS 173
Query: 58 TELKVI 63
TE+ I
Sbjct: 174 TEIGKI 179
>gnl|CDD|130585 TIGR01522, ATPase-IIA2_Ca, golgi membrane calcium-translocating
P-type ATPase. This model describes the P-type ATPase
responsible for translocating calcium ions across the
golgi membrane of fungi and animals , and is of
particular importance in the sarcoplasmic reticulum of
skeletal and cardiac muscle in vertebrates. The calcium
P-type ATPases have been characterized as Type IIA based
on a phylogenetic analysis which distinguishes this
group from the Type IIB PMCA calcium pump modelled by
TIGR01517. A separate analysis divides Type IIA into
sub-types, SERCA and PMR1 the former of which is
modelled by TIGR01116.
Length = 884
Score = 34.8 bits (80), Expect = 0.056
Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 2/80 (2%)
Query: 196 GLYEEVPTTHLVPGDIIVIPKHGCTLACDATLLQG-NCIVNESMLTGESVPVMKTALPSQ 254
G E V + LVPGD+ V G + D +++ + ++ES LTGE+ PV K P
Sbjct: 125 GKLEHVLASTLVPGDL-VCLSVGDRVPADLRIVEAVDLSIDESNLTGETTPVSKVTAPIP 183
Query: 255 SDFYNEKEDVNHTLYCGTVI 274
+ + + ++ + GT++
Sbjct: 184 AATNGDLAERSNIAFMGTLV 203
>gnl|CDD|182635 PRK10671, copA, copper exporting ATPase; Provisional.
Length = 834
Score = 33.6 bits (77), Expect = 0.13
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 224 DATLLQGNCIVNESMLTGESVPVMKTA 250
D + QG ++E+MLTGE +P K
Sbjct: 358 DGEITQGEAWLDEAMLTGEPIPQQKGE 384
>gnl|CDD|233397 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain,
Gram-positive type. This model describes a polypeptide
chain of DNA polymerase III. Full-length homologs of
this protein are restricted to the Gram-positive
lineages, including the Mycoplasmas. This protein is
designated alpha chain and given the gene symbol polC,
but is not a full-length homolog of other polC genes.
The N-terminal region of about 200 amino acids is rich
in low-complexity sequence, poorly alignable, and not
included n this model [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1213
Score = 29.3 bits (66), Expect = 2.9
Identities = 17/78 (21%), Positives = 33/78 (42%), Gaps = 19/78 (24%)
Query: 148 FAEAYYYYTGAIICM---SVFGIVSSVIQTRQKSLHDTVNTVDKVT-----VKRSKGLYE 199
F E + + G I + + +G V + + H ++++ VKR+ G +
Sbjct: 761 FGEDHTFRAGTIGTVAEKTAYGYVKKYFED--QGKHYRDAEIERLVQGCTGVKRTTGQH- 817
Query: 200 EVPTTHLVPGDIIVIPKH 217
PG II++PK+
Sbjct: 818 --------PGGIIIVPKY 827
>gnl|CDD|233509 TIGR01652, ATPase-Plipid, phospholipid-translocating P-type ATPase,
flippase. This model describes the P-type ATPase
responsible for transporting phospholipids from one
leaflet of bilayer membranes to the other. These ATPases
are found only in eukaryotes.
Length = 1057
Score = 29.3 bits (66), Expect = 2.9
Identities = 21/79 (26%), Positives = 31/79 (39%), Gaps = 6/79 (7%)
Query: 188 KVTVKRSKGLYEEVPTTHLVPGDIIVIPKHGCTLACDATLLQ-----GNCIVNESMLTGE 242
V G + E+P L GDI+ + K + D LL G C V + L GE
Sbjct: 86 LTEVLEGHGQFVEIPWKDLRVGDIVKVKKDE-RIPADLLLLSSSEPDGVCYVETANLDGE 144
Query: 243 SVPVMKTALPSQSDFYNEK 261
+ ++ AL +E
Sbjct: 145 TNLKLRQALEETQKMLDED 163
>gnl|CDD|218300 pfam04870, Moulting_cycle, Moulting cycle. This family of proteins
plays a role in the moulting cycle of nematodes, which
involves the synthesis of a new collagen-rich cuticle
underneath the existing cuticle and the subsequent
removal of the old cuticle.
Length = 323
Score = 29.0 bits (65), Expect = 2.9
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 74 DQEQNFIKLV-GLDKGLTNSQLHQFN--GFTFEEQFMRGIVYGK 114
E I+L+ LDK + QL + N G+T ++YG+
Sbjct: 240 PYEARKIELMEKLDKSYSKEQLKEMNSTGYTIMTPKQMELLYGE 283
>gnl|CDD|184523 PRK14125, PRK14125, cell division suppressor protein YneA;
Provisional.
Length = 103
Score = 27.7 bits (62), Expect = 3.0
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 202 PTTHLVPGDIIVIPKH 217
P+ H+ GD +VIP
Sbjct: 76 PSGHIKAGDKLVIPVL 91
>gnl|CDD|130176 TIGR01106, ATPase-IIC_X-K, sodium or proton efflux -- potassium
uptake antiporter, P-type ATPase, alpha subunit. This
model describes the P-type ATPases responsible for the
exchange of either protons or sodium ions for potassium
ions across the plasma membranes of eukaryotes. Unlike
most other P-type ATPases, members of this subfamily
require a beta subunit for activity. This model
encompasses eukaryotes and consists of two functional
types, a Na/K antiporter found widely distributed in
eukaryotes and a H/K antiporter found only in
vertebrates. The Na+ or H+/K+ antiporter P-type ATPases
have been characterized as Type IIC based on a published
phylogenetic analysis. Sequences from Blastocladiella
emersonii (GP|6636502, GP|6636502 and PIR|T43025), C.
elegans (GP|2315419, GP|6671808 and PIR|T31763) and
Drosophila melanogaster (GP|7291424) score below trusted
cutoff, apparently due to long branch length (excessive
divergence from the last common ancestor) as evidenced
by a phylogenetic tree. Experimental evidence is needed
to determine whether these sequences represent ATPases
with conserved function. Aside from fragments, other
sequences between trusted and noise appear to be
bacterial ATPases of unclear lineage, but most likely
calcium pumps [Energy metabolism, ATP-proton motive
force interconversion].
Length = 997
Score = 29.0 bits (65), Expect = 4.2
Identities = 17/61 (27%), Positives = 23/61 (37%), Gaps = 18/61 (29%)
Query: 200 EVPTTHLVPGDIIVIPKHGCTLACDATLLQGNCIVNESMLTGESVPVMKTALPSQSDFYN 259
EV +P D+ +I GC V+ S LTGES P +F +
Sbjct: 166 EVKGGDRIPADLRIISAQGCK-------------VDNSSLTGESEP-----QTRSPEFTH 207
Query: 260 E 260
E
Sbjct: 208 E 208
>gnl|CDD|214521 smart00115, CASc, Caspase, interleukin-1 beta converting enzyme
(ICE) homologues. Cysteine aspartases that mediate
programmed cell death (apoptosis). Caspases are
synthesised as zymogens and activated by proteolysis of
the peptide backbone adjacent to an aspartate. The
resulting two subunits associate to form an
(alpha)2(beta)2-tetramer which is the active enzyme.
Activation of caspases can be mediated by other caspase
homologues.
Length = 241
Score = 27.6 bits (62), Expect = 8.2
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 108 RGIVYGKNEINVPIQNISSLF 128
G +YG + +P+ I SLF
Sbjct: 86 EGGIYGTDGDPLPLDEIFSLF 106
>gnl|CDD|237997 cd00032, CASc, Caspase, interleukin-1 beta converting enzyme (ICE)
homologues; Cysteine-dependent aspartate-directed
proteases that mediate programmed cell death
(apoptosis). Caspases are synthesized as inactive
zymogens and activated by proteolysis of the peptide
backbone adjacent to an aspartate. The resulting two
subunits associate to form an (alpha)2(beta)2-tetramer
which is the active enzyme. Activation of caspases can
be mediated by other caspase homologs.
Length = 243
Score = 27.2 bits (61), Expect = 8.6
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 108 RGIVYGKNEINVPIQNISSLF 128
G +YG + VPI I+SLF
Sbjct: 87 EGGIYGTDGDVVPIDEITSLF 107
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
0.321 0.137 0.407
Gapped
Lambda K H
0.267 0.0767 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,612,654
Number of extensions: 1354813
Number of successful extensions: 1039
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1016
Number of HSP's successfully gapped: 46
Length of query: 292
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 196
Effective length of database: 6,679,618
Effective search space: 1309205128
Effective search space used: 1309205128
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 (21.9 bits)
S2: 59 (26.4 bits)