RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15159
(238 letters)
>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 = 224 bits (573), Expect = 3e-68
Identities = 101/171 (59%), Positives = 120/171 (70%), Gaps = 24/171 (14%)
Query: 68 KGIDLAIDESSFTGETEPATKVTSPMLKTN--GHTSMRNIAFMGTLVRCGNGKAQLNHPE 125
+ +DL+IDES+ TGET P +KVT+P+ NIAFMGTLVRCG+GK
Sbjct: 157 EAVDLSIDESNLTGETTPVSKVTAPIPAATNGDLAERSNIAFMGTLVRCGHGK------- 209
Query: 126 DYTSMINYKERLIEKGVVVNTGEKSEFGEVFKMMQAEEAPKTPLQKSMDILGTQLSLYSF 185
G+VV TG +EFG VFKMMQA E PKTPLQKSMD+LG QLSL SF
Sbjct: 210 ---------------GIVVGTGSNTEFGAVFKMMQAIEKPKTPLQKSMDLLGKQLSLVSF 254
Query: 186 CIIGLIMLLGWFQGRPVLDMFTIGVSLAVAAIPEGLPIVVTVTLALGVMRI 236
+IG+I L+GWFQG+ L+MFTI VSLAVAAIPEGLPI+VTVTLALGV+R+
Sbjct: 255 GVIGVICLVGWFQGKDWLEMFTISVSLAVAAIPEGLPIIVTVTLALGVLRM 305
Score = 72.2 bits (177), Expect = 1e-14
Identities = 33/70 (47%), Positives = 44/70 (62%), Gaps = 2/70 (2%)
Query: 15 RPSQGIDLAIDESSFTGETEPATKVTSPMLKTN--GHTSMRNIAFMGTLVRCGNGKGIDL 72
R + +DL+IDES+ TGET P +KVT+P+ NIAFMGTLVRCG+GKGI +
Sbjct: 154 RIVEAVDLSIDESNLTGETTPVSKVTAPIPAATNGDLAERSNIAFMGTLVRCGHGKGIVV 213
Query: 73 AIDESSFTGE 82
++ G
Sbjct: 214 GTGSNTEFGA 223
>gnl|CDD|215733 pfam00122, E1-E2_ATPase, E1-E2 ATPase.
Length = 222
Score = 117 bits (296), Expect = 1e-32
Identities = 46/165 (27%), Positives = 75/165 (45%), Gaps = 34/165 (20%)
Query: 71 DLAIDESSFTGETEPATKVTSPMLKTNGHTSMRNIAFMGTLVRCGNGKAQLNHPEDYTSM 130
L +DES+ TGE+ P K + F GT+V G K
Sbjct: 76 SLEVDESALTGESLPVEKSRGDTV------------FAGTVVLSGELKV----------- 112
Query: 131 INYKERLIEKGVVVNTGEKSEFGEVFKMMQAEEAPKTPLQKSMDILGTQLSLYSFCIIGL 190
+V TGE +E G++ ++++ ++ KTPLQ+ +D L L + L
Sbjct: 113 -----------IVTATGEDTELGKIARLVEEAKSAKTPLQRLLDKLAKILVPIVLALAIL 161
Query: 191 IMLLGWFQGRPVLDMFTIGVSLAVAAIPEGLPIVVTVTLALGVMR 235
+ L+ +F+G L+ +++ VAA PE LP+ V + LA+G R
Sbjct: 162 VFLIWFFRGGDFLEALLRALAVLVAACPEALPLAVPLALAVGAGR 206
Score = 43.3 bits (103), Expect = 3e-05
Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 12/63 (19%)
Query: 21 DLAIDESSFTGETEPATKVTSPMLKTNGHTSMRNIAFMGTLVRCGNGKGIDLAIDESSFT 80
L +DES+ TGE+ P K + F GT+V G K I A E +
Sbjct: 76 SLEVDESALTGESLPVEKSRGDTV------------FAGTVVLSGELKVIVTATGEDTEL 123
Query: 81 GET 83
G+
Sbjct: 124 GKI 126
>gnl|CDD|223550 COG0474, MgtA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 917
Score = 122 bits (308), Expect = 7e-32
Identities = 59/170 (34%), Positives = 93/170 (54%), Gaps = 25/170 (14%)
Query: 71 DLAIDESSFTGETEPATKVTSPMLKTNG--HTSMRNIAFMGTLVRCGNGKAQLNHPEDYT 128
DL +DES+ TGE+ P K P+ K++ N+ F GT V G K
Sbjct: 183 DLEVDESALTGESLPVEKQALPLTKSDAPLGLDRDNMLFSGTTVVSGRAK---------- 232
Query: 129 SMINYKERLIEKGVVVNTGEKSEFGEVFKMMQAEEAPKTPLQKSMDILGTQLSLYSFCII 188
G+VV TG ++EFG++ +++ ++ KTPLQ+ ++ LG L + + +
Sbjct: 233 ------------GIVVATGFETEFGKIARLLPTKKEVKTPLQRKLNKLGKFLLVLALVLG 280
Query: 189 GLIMLLGWFQGRP-VLDMFTIGVSLAVAAIPEGLPIVVTVTLALGVMRIY 237
L+ ++G F+G +L+ F ++LAVAA+PEGLP VVT+ LALG R+
Sbjct: 281 ALVFVVGLFRGGNGLLESFLTALALAVAAVPEGLPAVVTIALALGAQRMA 330
Score = 48.1 bits (115), Expect = 2e-06
Identities = 28/101 (27%), Positives = 44/101 (43%), Gaps = 10/101 (9%)
Query: 18 QGIDLAIDESSFTGETEPATKVTSPMLKTNG--HTSMRNIAFMGTLVRCGNGKGIDLAI- 74
+ DL +DES+ TGE+ P K P+ K++ N+ F GT V G KGI +A
Sbjct: 180 ESSDLEVDESALTGESLPVEKQALPLTKSDAPLGLDRDNMLFSGTTVVSGRAKGIVVATG 239
Query: 75 DESSF---TGETEPATKVTSPMLKTNGHTSMRNIAFMGTLV 112
E+ F +V +P+ + + F+ L
Sbjct: 240 FETEFGKIARLLPTKKEVKTPLQR----KLNKLGKFLLVLA 276
>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 = 103 bits (259), Expect = 2e-25
Identities = 66/182 (36%), Positives = 85/182 (46%), Gaps = 45/182 (24%)
Query: 72 LAIDESSFTGETEPATKVTSPMLKTNG-HTSMRNIAFMGTLVRCGNGKAQLNHPEDYTSM 130
L +D+S TGE+ K T + + +N+ F GTLV GKA
Sbjct: 117 LRVDQSILTGESVSVNKHTESVPDERAVNQDKKNMLFSGTLV--VAGKA----------- 163
Query: 131 INYKERLIEKGVVVNTGEKSEFGEVFKMMQAEEAPKTPLQKSMDILGTQLSLYSFCIIGL 190
+GVVV TG +E G++ M+A E TPLQK +D G LS IGL
Sbjct: 164 ---------RGVVVRTGMSTEIGKIRDEMRAAEQEDTPLQKKLDEFGELLSKV----IGL 210
Query: 191 IMLL----------------GWFQGRPVLDMFTIGVSLAVAAIPEGLPIVVTVTLALGVM 234
I +L GW QG + F I V+LAVAAIPEGLP V+T LALG
Sbjct: 211 ICILVWVINIGHFNDPALGGGWIQG--AIYYFKIAVALAVAAIPEGLPAVITTCLALGTR 268
Query: 235 RI 236
++
Sbjct: 269 KM 270
Score = 33.6 bits (77), Expect = 0.080
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 22 LAIDESSFTGETEPATKVTSPMLKTNG-HTSMRNIAFMGTLVRCGNGKGI 70
L +D+S TGE+ K T + + +N+ F GTLV G +G+
Sbjct: 117 LRVDQSILTGESVSVNKHTESVPDERAVNQDKKNMLFSGTLVVAGKARGV 166
>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 = 79.4 bits (196), Expect = 5e-17
Identities = 46/187 (24%), Positives = 76/187 (40%), Gaps = 52/187 (27%)
Query: 68 KGIDLAIDESSFTGETEPATK--VTSPMLKTNGHTSMRNIAFMGTLVRCGNGKAQLNHPE 125
G+ L IDESS TGE++P K V P L + GT+V G+G+
Sbjct: 207 SGLSLEIDESSITGESDPIKKGPVQDPFLLS------------GTVVNEGSGR------- 247
Query: 126 DYTSMINYKERLIEKGVVVNTGEKSEFGEVFKMMQAEEAPKTPLQKSMDILGTQLSLYS- 184
+V G S G++ ++ TPLQ+ + L + +
Sbjct: 248 ---------------MLVTAVGVNSFGGKLMMELRQAGEDSTPLQEKLSELAGLIGKFGM 292
Query: 185 -FCIIGLIMLLGWF--------------QGRPVLDMFTIGVSLAVAAIPEGLPIVVTVTL 229
++ ++L + + LD F I V++ V A+PEGLP+ VT+ L
Sbjct: 293 GSAVLLFLVLSLRYVFRIIRGDGRDTEEDAQTFLDHFIIAVTIVVVAVPEGLPLAVTIAL 352
Query: 230 ALGVMRI 236
A + ++
Sbjct: 353 AYSMKKM 359
Score = 43.2 bits (102), Expect = 7e-05
Identities = 24/68 (35%), Positives = 35/68 (51%), Gaps = 14/68 (20%)
Query: 18 QGIDLAIDESSFTGETEPATK--VTSPMLKTNGHTSMRNIAFMGTLVRCGNGKGIDLAID 75
G+ L IDESS TGE++P K V P L + GT+V G+G+ + A+
Sbjct: 207 SGLSLEIDESSITGESDPIKKGPVQDPFLLS------------GTVVNEGSGRMLVTAVG 254
Query: 76 ESSFTGET 83
+SF G+
Sbjct: 255 VNSFGGKL 262
>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 = 70.0 bits (172), Expect = 6e-14
Identities = 40/171 (23%), Positives = 65/171 (38%), Gaps = 28/171 (16%)
Query: 71 DLAIDESSFTGETEPATKVTSPMLKTNGHTSMRNIAFMGTLVRCGNGKAQLNHPEDYTSM 130
+DES+ TGE+ P K ++ T ++ F GT V G + T++
Sbjct: 76 SCFVDESNLTGESNPVLKTALKETQSGTITG--DLVFAGTYVFGGTLIVVVTPTGILTTV 133
Query: 131 INYKERLIEKGVVVNTGEKSEFGEVFKMMQAEEAPKTPLQKSMDILGTQLSLYSFCIIGL 190
VVV TG ++ +TPLQ D L + + ++ L
Sbjct: 134 G-------RIAVVVKTGFET---------------RTPLQSKRDRLENFIFILFLLLLAL 171
Query: 191 I-MLLGWFQG---RPVLDMFTIGVSLAVAAIPEGLPIVVTVTLALGVMRIY 237
L + +G + + + V +P LP VTV LA+G R+
Sbjct: 172 AVFLYLFIRGWDPNSIFKALLRALIVLVIVVPPALPAAVTVALAVGDARLA 222
Score = 29.6 bits (67), Expect = 1.6
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 21 DLAIDESSFTGETEPATKVTSPMLKTNGHTSMRNIAFMGTLVRCGNGKGI 70
+DES+ TGE+ P K ++ T ++ F GT V G +
Sbjct: 76 SCFVDESNLTGESNPVLKTALKETQSGTITG--DLVFAGTYVFGGTLIVV 123
>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 = 69.3 bits (170), Expect = 1e-13
Identities = 40/165 (24%), Positives = 73/165 (44%), Gaps = 35/165 (21%)
Query: 69 GIDLAIDESSFTGETEPATKVTSPMLKTNGHTSMRNIAFMGTLVRCGNGKAQLNHPEDYT 128
G + +D+++ TGE+ P TK T +IA+ G+ V+ G
Sbjct: 133 GDYIQVDQAALTGESLPVTKKTG------------DIAYSGSTVKQG------------- 167
Query: 129 SMINYKERLIEKGVVVNTGEKSEFGEVFKMMQAEEAPKTPLQKSMDILGTQLSLYSFCII 188
E + VV TG + FG+ ++Q+ E LQK + +G L + ++
Sbjct: 168 ------EA---EAVVTATGMNTFFGKAAALVQSTETGSGHLQKILSKIGLFLIVLIGVLV 218
Query: 189 GLIMLLGWFQ-GRPVLDMFTIGVSLAVAAIPEGLPIVVTVTLALG 232
+ +++ +F G + + L V IP +P V++VT+A+G
Sbjct: 219 LIELVVLFFGRGESFREGLQFALVLLVGGIPIAMPAVLSVTMAVG 263
Score = 35.8 bits (83), Expect = 0.016
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 12/65 (18%)
Query: 19 GIDLAIDESSFTGETEPATKVTSPMLKTNGHTSMRNIAFMGTLVRCGNGKGIDLAIDESS 78
G + +D+++ TGE+ P TK T +IA+ G+ V+ G + + A ++
Sbjct: 133 GDYIQVDQAALTGESLPVTKKTG------------DIAYSGSTVKQGEAEAVVTATGMNT 180
Query: 79 FTGET 83
F G+
Sbjct: 181 FFGKA 185
>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 = 64.4 bits (157), Expect = 6e-12
Identities = 55/172 (31%), Positives = 76/172 (44%), Gaps = 36/172 (20%)
Query: 71 DLAIDESSFTGETEPATKVTSPMLKTNGHTSMRNIAFMGTLVRCGNGKAQLNHPEDYTSM 130
+D SS TGE+EP T+ SP RNIAF T C G A+
Sbjct: 184 GCKVDNSSLTGESEPQTR--SPEFTHENPLETRNIAFFST--NCVEGTAR---------- 229
Query: 131 INYKERLIEKGVVVNTGEKSEFGEVFKMMQAEEAPKTPLQKSMD-----ILGTQLSL-YS 184
G+VVNTG+++ G + + E KTP+ ++ I G + L S
Sbjct: 230 ----------GIVVNTGDRTVMGRIASLASGLENGKTPIAIEIEHFIHIITGVAVFLGVS 279
Query: 185 FCIIGLIMLLGWFQGRPVLDMFTIGVSLAVAAIPEGLPIVVTVTLALGVMRI 236
F I+ LI+ W + +F IG+ VA +PEGL VTV L L R+
Sbjct: 280 FFILSLILGYTWLEAV----IFLIGI--IVANVPEGLLATVTVCLTLTAKRM 325
Score = 35.2 bits (81), Expect = 0.027
Identities = 21/61 (34%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 21 DLAIDESSFTGETEPATKVTSPMLKTNGHTSMRNIAFMGTLVRCGNGKGIDLAIDESSFT 80
+D SS TGE+EP T+ SP RNIAF T G +GI + + +
Sbjct: 184 GCKVDNSSLTGESEPQTR--SPEFTHENPLETRNIAFFSTNCVEGTARGIVVNTGDRTVM 241
Query: 81 G 81
G
Sbjct: 242 G 242
>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 = 54.1 bits (130), Expect = 2e-08
Identities = 39/167 (23%), Positives = 70/167 (41%), Gaps = 24/167 (14%)
Query: 71 DLAIDESSFTGETEPATKVTSPM-LKTNGHTSMRNIAFMGTLVRCGNGKAQLNHPEDYTS 129
DL I++S+ TGE+ P K + N+ FMGT V G+ +A
Sbjct: 174 DLFINQSALTGESLPVEKFVEDKRARDPEILERENLCFMGTNVLSGHAQA---------- 223
Query: 130 MINYKERLIEKGVVVNTGEKSEFGEVFKMMQAEEAPKTPLQKSMDILGTQLSLYSFCIIG 189
VV+ TG + FG + E +T K + + L + ++
Sbjct: 224 ------------VVLATGSSTWFGSLAIAA-TERRGQTAFDKGVKSVSKLLIRFMLVMVP 270
Query: 190 LIMLLGWFQGRPVLDMFTIGVSLAVAAIPEGLPIVVTVTLALGVMRI 236
+++++ L+ F +++AV PE LP++V+ LA G + +
Sbjct: 271 VVLMINGLMKGDWLEAFLFALAVAVGLTPEMLPMIVSSNLAKGAINM 317
>gnl|CDD|236705 PRK10517, PRK10517, magnesium-transporting ATPase MgtA;
Provisional.
Length = 902
Score = 49.7 bits (119), Expect = 5e-07
Identities = 37/163 (22%), Positives = 69/163 (42%), Gaps = 23/163 (14%)
Query: 71 DLAIDESSFTGETEPATKVTSPM-LKTNGHTSMRNIAFMGTLVRCGNGKAQLNHPEDYTS 129
DL + ++S TGE+ P K + + + + FMGT V G +A
Sbjct: 208 DLFVAQASLTGESLPVEKFATTRQPEHSNPLECDTLCFMGTNVVSGTAQA---------- 257
Query: 130 MINYKERLIEKGVVVNTGEKSEFGEVFKMMQAEEAPKTPLQKSMDILGTQLSLYSFCIIG 189
VV+ TG + FG++ + +++ Q+ + + L + +
Sbjct: 258 ------------VVIATGANTWFGQLAGRVSEQDSEPNAFQQGISRVSWLLIRFMLVMAP 305
Query: 190 LIMLLGWFQGRPVLDMFTIGVSLAVAAIPEGLPIVVTVTLALG 232
+++L+ + + +S+AV PE LP++VT TLA G
Sbjct: 306 VVLLINGYTKGDWWEAALFALSVAVGLTPEMLPMIVTSTLARG 348
>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 = 39.2 bits (92), Expect = 0.001
Identities = 30/161 (18%), Positives = 46/161 (28%), Gaps = 35/161 (21%)
Query: 73 AIDESSFTGETEPATKVTSPMLKTNGHTSMRNIAFMGTLVRCGNGKAQLNHPEDYTSMIN 132
+DES+ TGE+ P K G V G IN
Sbjct: 99 TVDESALTGESVPVEKAP------------------GDEVFAG--------------AIN 126
Query: 133 YKERLIEKGVVVNTGEKSEFGEVFKMMQAEEAPKTPLQKSMDILGTQLSLYSFCIIGLIM 192
L VV S ++ +++ ++ K Q+ +D + I I
Sbjct: 127 LDGVL--TIVVTKLPADSTIAKIVNLVEEAQSRKAKTQRFIDRFARYYTPVVLAIALAIW 184
Query: 193 LLGWFQGRPVLDMFTIGVSLAVAAIPEGLPIVVTVTLALGV 233
L+ R + L V A P L I +
Sbjct: 185 LVPGLLKRW-PFWVYRALVLLVVASPCALVISAPAAYLSAI 224
>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 = 38.8 bits (91), Expect = 0.002
Identities = 33/163 (20%), Positives = 58/163 (35%), Gaps = 40/163 (24%)
Query: 74 IDESSFTGETEPATKVTSPMLKTNGHTSMRNIAFMGTLVRCGNGKAQLNHPEDYTSMINY 133
+DES+ TGE+ P K G F GT+ NG L
Sbjct: 101 VDESALTGESMPVEKKE-------GDE-----VFAGTI----NGDGSL------------ 132
Query: 134 KERLIEKGVVVNTGEKSEFGEVFKMMQAEEAPKTPLQKSMDILGTQLSLYSFCIIGLIML 193
V GE S ++ ++++ ++ K P+Q+ D + + I L +
Sbjct: 133 ------TIRVTKLGEDSTLAQIVELVEEAQSSKAPIQRLADRIASYYVPAVLAIALLTFV 186
Query: 194 LGWFQGRPVLDMFTIGVSLAVAAIPEGL----PIVVTVTLALG 232
+ G L +++ V A P L P+ + V + +
Sbjct: 187 VWLALG--ALGALYRALAVLVVACPCALGLATPVAILVAIGVA 227
>gnl|CDD|217052 pfam02465, FliD_N, Flagellar hook-associated protein 2 C-terminus.
The flagellar hook-associated protein 2 (HAP2 or FliD)
forms the distal end of the flagella, and plays a role
in mucin specific adhesion of the bacteria. This
alignment covers the N-terminal region of this family of
proteins.
Length = 99
Score = 34.4 bits (80), Expect = 0.009
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 157 KMMQAEEAPKTPLQKSMDILGTQLSLYS 184
++M AE AP L++ L +LS Y
Sbjct: 12 QLMAAERAPLDRLEQQKTKLEAKLSAYG 39
>gnl|CDD|237914 PRK15122, PRK15122, magnesium-transporting ATPase; Provisional.
Length = 903
Score = 36.5 bits (85), Expect = 0.009
Identities = 41/173 (23%), Positives = 71/173 (41%), Gaps = 34/173 (19%)
Query: 71 DLAIDESSFTGETEPATK---VTSPMLKTNGHTS--------MRNIAFMGTLVRCGNGKA 119
DL I ++ TGE P K + + K+ + + NI FMGT V G A
Sbjct: 197 DLFISQAVLTGEALPVEKYDTLGAVAGKSADALADDEGSLLDLPNICFMGTNVVSGTATA 256
Query: 120 QLNHPEDYTSMINYKERLIEKGVVVNTGEKSEFGEVFKMMQAEEAPKTPLQKSMDILGTQ 179
VVV TG ++ FG + K + +T + ++ +
Sbjct: 257 ----------------------VVVATGSRTYFGSLAKSI-VGTRAQTAFDRGVNSVSWL 293
Query: 180 LSLYSFCIIGLIMLLGWFQGRPVLDMFTIGVSLAVAAIPEGLPIVVTVTLALG 232
L + ++ +++L+ F L+ +++AV PE LP++V+ LA G
Sbjct: 294 LIRFMLVMVPVVLLINGFTKGDWLEALLFALAVAVGLTPEMLPMIVSSNLAKG 346
>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 = 36.1 bits (84), Expect = 0.013
Identities = 20/92 (21%), Positives = 39/92 (42%), Gaps = 6/92 (6%)
Query: 146 TGEKSEFGEVFKMMQAEEAPKTPLQKSMDILGTQLSLYSFCIIGLIMLLGW-FQGRPVLD 204
TGE + ++ ++++ + K P+Q+ D + + I LI + W G +
Sbjct: 175 TGEDTTLAQIVRLVRQAQQSKAPIQRLADKV-AGYFVPVVIAIALITFVIWLILGADFVF 233
Query: 205 MFTIGVSLAVAAIPEGL----PIVVTVTLALG 232
+ V++ + A P L P V+ V L
Sbjct: 234 ALEVAVTVLIIACPCALGLATPTVIAVATGLA 265
>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 = 35.4 bits (81), Expect = 0.022
Identities = 42/198 (21%), Positives = 66/198 (33%), Gaps = 66/198 (33%)
Query: 75 DESSFTGETEPATKVTSPMLKTNGHTSMR---NIAFMGTLVRCGNGKAQLNHPEDYTSMI 131
DE+ TGE+ P K T + N+AF + V G K
Sbjct: 165 DEALLTGESLPVIKDAHATFGKEEDTPIGDRINLAFSSSAVTKGRAK------------- 211
Query: 132 NYKERLIEKGVVVNTGEKSEFGEVFKMMQAE---------EAPK---------------- 166
G+ + T SE G + +Q + + P
Sbjct: 212 ---------GICIATALNSEIGAIAAGLQGDGGLFQRPEKDDPNKRRKLNKWILKVTKKV 262
Query: 167 ----------TPLQKSMDILGTQLSLYSFCI-IGLIMLLGWFQGRPVLDMFTI-GVSLAV 214
TPL + + L L FCI I +++ V I + LA+
Sbjct: 263 TGAFLGLNVGTPLHRKLSKLAVIL----FCIAIIFAIIVMAAHKFDVDKEVAIYAICLAI 318
Query: 215 AAIPEGLPIVVTVTLALG 232
+ IPE L V+++T+A+G
Sbjct: 319 SIIPESLIAVLSITMAMG 336
Score = 28.8 bits (64), Expect = 2.8
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 25 DESSFTGETEPATKVTSPMLKTNGHTSMR---NIAFMGTLVRCGNGKGI 70
DE+ TGE+ P K T + N+AF + V G KGI
Sbjct: 165 DEALLTGESLPVIKDAHATFGKEEDTPIGDRINLAFSSSAVTKGRAKGI 213
>gnl|CDD|225127 COG2217, ZntA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 713
Score = 32.6 bits (75), Expect = 0.17
Identities = 30/160 (18%), Positives = 52/160 (32%), Gaps = 39/160 (24%)
Query: 73 AIDESSFTGETEPATKVTSPMLKTNGHTSMRNIAFMGTLVRCGNGKAQLNHPEDYTSMIN 132
++DES TGE+ P K G F GT+ +G
Sbjct: 256 SVDESMLTGESLPV-------EKKPGDE-----VFAGTVN--LDG--------------- 286
Query: 133 YKERLIEKGVVVNTGEKSEFGEVFKMMQAEEAPKTPLQKSMDILGTQLSLYSFCIIGLIM 192
L + V G + + ++++ ++ K P+Q+ D + + I L
Sbjct: 287 ---SLTIR--VTRVGADTTLARIIRLVEEAQSSKAPIQRLADRVASYFVPVVLVIAALTF 341
Query: 193 LLGWFQGR-PVLDMFTIGVSLAVAAIPEGL----PIVVTV 227
L G +++ V A P L P + V
Sbjct: 342 ALWPLFGGGDWETALYRALAVLVIACPCALGLATPTAILV 381
>gnl|CDD|237391 PRK13473, PRK13473, gamma-aminobutyraldehyde dehydrogenase;
Provisional.
Length = 475
Score = 30.3 bits (69), Expect = 0.83
Identities = 11/28 (39%), Positives = 13/28 (46%)
Query: 104 NIAFMGTLVRCGNGKAQLNHPEDYTSMI 131
F RC GKA + E +TSMI
Sbjct: 107 VFRFFAGAARCLEGKAAGEYLEGHTSMI 134
>gnl|CDD|178763 PLN03224, PLN03224, probable serine/threonine protein kinase;
Provisional.
Length = 507
Score = 30.4 bits (68), Expect = 0.86
Identities = 22/101 (21%), Positives = 40/101 (39%), Gaps = 5/101 (4%)
Query: 124 PEDYTSMINYKERLIEKGVVVNTGEKSEFGEVFKMMQAEEAPKTPLQKSMDILGTQLSLY 183
PE+ ++ + ++I+ G V+ F ++ M+ +P L
Sbjct: 337 PENLLVTVDGQVKIIDFGAAVDMCTGINFNPLYGMLDPRYSPPEELVMPQSCPRAPAPA- 395
Query: 184 SFCIIGLIMLLGWFQGRP-VLDMFTIGVSLAVAAIPEGLPI 223
+ L+ W GRP + D +T GV L +PE P+
Sbjct: 396 ---MAALLSPFAWLYGRPDLFDSYTAGVLLMQMCVPELRPV 433
>gnl|CDD|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated.
Length = 244
Score = 29.7 bits (68), Expect = 1.0
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 6/37 (16%)
Query: 101 SM-RNIAFMGTLVRCGNGKAQLNHPEDYTSMINYKER 136
+M RNI +GTL+ G GK PED ++ K+R
Sbjct: 194 NMVRNI--VGTLLEVGKGKRP---PEDIKELLEAKDR 225
>gnl|CDD|99793 cd06196, FNR_like_1, Ferredoxin reductase-like proteins catalyze
electron transfer between an NAD(P)-binding domain of
the alpha/beta class and a discrete (usually
N-terminal) domain which varies in orientation with
respect to the NAD(P) binding domain. The N-terminal
region may contain a flavin prosthetic group (as in
flavoenzymes) or use flavin as a substrate. Ferredoxin
is reduced in the final stage of photosystem I. The
flavoprotein Ferredoxin-NADP+ reductase transfers
electrons from reduced ferredoxin to FAD (forming FADH2
via a semiquinone intermediate) which then transfers a
hydride ion to convert NADP+ to NADPH.
Length = 218
Score = 28.4 bits (64), Expect = 2.8
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 14 FRPSQGIDLAIDESSFTGETEPAT 37
F P Q ++AID+ + E P T
Sbjct: 28 FTPGQATEVAIDKPGWRDEKRPFT 51
>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 = 28.5 bits (64), Expect = 4.4
Identities = 30/170 (17%), Positives = 61/170 (35%), Gaps = 23/170 (13%)
Query: 74 IDESSFTGETEPATKVTSPMLKT------NGHTSMRNIAFMGTLVRCGNGKAQLNHPEDY 127
++ES TGE+ P K P TS +++ F GT + L
Sbjct: 276 VNESMLTGESVPVLKFPIPDNGDDDEDLFLYETSKKHVLFGGTKI--------LQI---- 323
Query: 128 TSMINYKERLIEKGVVVNTGEKSEFGE-VFKMMQAEEAPKTPLQKSMDILGTQLSLYSFC 186
Y +VV TG + G+ V ++ + + S + L++ +
Sbjct: 324 ---RPYPGDTGCLAIVVRTGFSTSKGQLVRSILYPKPRVFKFYKDSFKFILF-LAVLALI 379
Query: 187 IIGLIMLLGWFQGRPVLDMFTIGVSLAVAAIPEGLPIVVTVTLALGVMRI 236
++ GRP+ + + + +P LP +++ + + R+
Sbjct: 380 GFIYTIIELIKDGRPLGKIILRSLDIITIVVPPALPAELSIGINNSLARL 429
>gnl|CDD|217134 pfam02600, DsbB, Disulfide bond formation protein DsbB. This
family consists of disulfide bond formation protein DsbB
from bacteria. The DsbB protein oxidises the periplasmic
protein DsbA which in turn oxidises cysteines in other
periplasmic proteins in order to make disulfide bonds.
DsbB acts as a redox potential transducer across the
cytoplasmic membrane and is an integral membrane
protein. DsbB posses six cysteines four of which are
necessary for it proper function in vivo.
Length = 159
Score = 26.9 bits (60), Expect = 6.7
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 183 YSFCIIGLIMLLGWFQGRPVLDMFTIGVSLAVAAI 217
+ + LI LL GR L + ++L +A
Sbjct: 45 IAMLALALIGLLALLAGRRGLRRLALLLALLLALA 79
>gnl|CDD|184448 PRK14010, PRK14010, potassium-transporting ATPase subunit B;
Provisional.
Length = 673
Score = 27.4 bits (60), Expect = 9.8
Identities = 23/100 (23%), Positives = 45/100 (45%), Gaps = 12/100 (12%)
Query: 1 MLSVFLTLFFTKIFRP-SQGIDLAIDESSFTGETEPATKVTSPMLKTNGHTSMRNIAFM- 58
+ S+F+ L T +F S+ + ++ + T++ + +K +G M + + +
Sbjct: 65 VFSIFIILLLTLVFANFSEALAEGRGKAQANALRQTQTEMKARRIKQDGSYEMIDASDLK 124
Query: 59 -GTLVRCGNGKGID---------LAIDESSFTGETEPATK 88
G +VR G+ I +DES+ TGE+ P K
Sbjct: 125 KGHIVRVATGEQIPNDGKVIKGLATVDESAITGESAPVIK 164
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 0.136 0.391
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,945,020
Number of extensions: 1110181
Number of successful extensions: 1163
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1137
Number of HSP's successfully gapped: 58
Length of query: 238
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 144
Effective length of database: 6,768,326
Effective search space: 974638944
Effective search space used: 974638944
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: 57 (25.7 bits)