RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy885
(270 letters)
>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 = 277 bits (709), Expect = 6e-87
Identities = 126/249 (50%), Positives = 156/249 (62%), Gaps = 12/249 (4%)
Query: 14 NPPNHCVSFSGRREQAIAVRQDVETKWKKEFTLEFSRDRKSMSSYCTPLKSSKLGSSGPK 73
P S +R A+ K+KK TLEFSRDRKSMS C P S+G K
Sbjct: 394 GLPATKNGVSSKRRPALGCNSVWNDKFKKLATLEFSRDRKSMSVLCKP-------STGNK 446
Query: 74 LFVKGAPEGVLERCTHARIG-SQKVSLKDFSANTRFENLRSLEPKSKVS----AIVPWGM 128
LFVKGAPEGVLERCTH G + V L D NT ++ + + A
Sbjct: 447 LFVKGAPEGVLERCTHILNGDGRAVPLTDKMKNTILSVIKEMGTTKALRCLALAFKDIPD 506
Query: 129 KPEDMNLADSTKFASYEVNLTFVGVVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNKAT 188
E+ L+D F + E +LTF+GVVGMLDPPR EV D+I +CR AGIRVI+ITGDNK T
Sbjct: 507 PREEDLLSDPANFEAIESDLTFIGVVGMLDPPRPEVADAIEKCRTAGIRVIMITGDNKET 566
Query: 189 AEAICRRIGVFTEEEDTTGKSYSGREFDDLPLSEQKAAVARARLFSRVEPAHKSKIVEFL 248
AEAICRRIG+F+ +ED T KS++GREFD++ ++Q+AA A LFSRVEP+HKS++VE L
Sbjct: 567 AEAICRRIGIFSPDEDVTFKSFTGREFDEMGPAKQRAACRSAVLFSRVEPSHKSELVELL 626
Query: 249 QGMNEISAM 257
Q EI AM
Sbjct: 627 QEQGEIVAM 635
>gnl|CDD|223550 COG0474, MgtA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 917
Score = 151 bits (384), Expect = 2e-41
Identities = 73/228 (32%), Positives = 101/228 (44%), Gaps = 28/228 (12%)
Query: 39 KWKKEF----TLEFSRDRKSMSSYCTPLKSSKLGSSGPKLFVKGAPEGVLERCTHARIGS 94
+ E+ + F +RK MS K LFVKGAPE +LERC
Sbjct: 435 GLEVEYPILAEIPFDSERKRMSVIV------KTDEGKYILFVKGAPEVILERCKS----- 483
Query: 95 QKVSLKDFSANTRFENLRSLEPK-----SKVSAIVPWGMKPEDMNLADSTKFASYEVNLT 149
E LR+LE S+ ++ K D D E +L
Sbjct: 484 -----IGELEPLTEEGLRTLEEAVKELASEGLRVLAVAYKKLDRAEKDDEV-DEIESDLV 537
Query: 150 FVGVVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGVFTEEEDTTGKS 209
F+G+ G+ DPPR++V ++I R AGI+V +ITGD+ TA AI + G+ E E +
Sbjct: 538 FLGLTGIEDPPREDVKEAIEELREAGIKVWMITGDHVETAIAIAKECGIEAEAE--SALV 595
Query: 210 YSGREFDDLPLSEQKAAVARARLFSRVEPAHKSKIVEFLQGMNEISAM 257
G E D L E V +F+RV P K++IVE LQ + AM
Sbjct: 596 IDGAELDALSDEELAELVEELSVFARVSPEQKARIVEALQKSGHVVAM 643
>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 = 109 bits (275), Expect = 3e-27
Identities = 58/217 (26%), Positives = 82/217 (37%), Gaps = 70/217 (32%)
Query: 41 KKEFTLEFSRDRKSMSSYCTPLKSSKLGSSGPKLFVKGAPEGVLERCTHARIGSQKVSLK 100
K FS K MS + LFVKGAPE +LERC + +
Sbjct: 309 KILDVFPFSSVLKRMSVIV------ETPDGSDLLFVKGAPEFILERCNNY-----EEKYL 357
Query: 101 DFSANTRFENLRSLEPKSKVSAIVPWGMKPEDMNLADSTKFASYEVNLTFVGVVGMLDPP 160
+ + LR L A E +L F+G++ DP
Sbjct: 358 ELARQG----LRVL-------AFA----------------SKELEDDLEFLGLITFEDPL 390
Query: 161 RKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGVFTEEEDTTGKSYSGREFDDLPL 220
R + ++I +AAGI+V++ITGDN TA+AI + +G+
Sbjct: 391 RPDAKETIEELKAAGIKVVMITGDNVLTAKAIAKELGID--------------------- 429
Query: 221 SEQKAAVARARLFSRVEPAHKSKIVEFLQGMNEISAM 257
+F+RV P K +IVE LQ I AM
Sbjct: 430 -----------VFARVSPEQKLQIVEALQKKGHIVAM 455
>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 = 106 bits (265), Expect = 8e-26
Identities = 62/224 (27%), Positives = 114/224 (50%), Gaps = 23/224 (10%)
Query: 34 QDVETKWKKEFTLEFSRDRKSMSSYCTPLKSSKLGSSGPKLFVKGAPEGVLERCTHARIG 93
D+ + + + FS +RK M+ C + F+KGA E VL+ CT+ +
Sbjct: 422 DDLRETYIRVAEVPFSSERKWMAVKCVHRQDRS-----EMCFMKGAYEQVLKYCTYYQ-- 474
Query: 94 SQKVSLKDFSANTRFENLRSLEPKSKVSAIVPWGMKPEDMNLADSTKFASYEVNLTFVGV 153
+ + R + ++ E +++++ G++ +A ++ + LTF+G+
Sbjct: 475 KKDGKTLTLTQQQR-DVIQ--EEAAEMASA---GLRV----IAFASGPEKGQ--LTFLGL 522
Query: 154 VGMLDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGVFTEEEDTTGKSYSGR 213
VG+ DPPR V +++ G+R+I+ITGD++ TA +I RR+G+ + T +S SG
Sbjct: 523 VGINDPPRPGVKEAVTTLITGGVRIIMITGDSQETAVSIARRLGMPS----KTSQSVSGE 578
Query: 214 EFDDLPLSEQKAAVARARLFSRVEPAHKSKIVEFLQGMNEISAM 257
+ D + + V + +F+R P HK KIV+ LQ ++ AM
Sbjct: 579 KLDAMDDQQLSQIVPKVAVFARASPEHKMKIVKALQKRGDVVAM 622
>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 = 91.8 bits (228), Expect = 6e-21
Identities = 64/218 (29%), Positives = 93/218 (42%), Gaps = 31/218 (14%)
Query: 48 FSRDRKSMSSYCTPLKSSKLGSSGPKLFVKGAPEGVLERCTH-------ARIGSQ--KVS 98
F+ +RK MS + G + F KGA E VL+ C A S K
Sbjct: 480 FNSERKFMSV----VVKHSGGKY--REFRKGASEIVLKPCRKRLDSNGEATPISDDDKDR 533
Query: 99 LKDFSANTRFENLRSLEPKSKVSAIVPWGMKPEDMNLADSTKFASYEVNLTFVGVVGMLD 158
D + LR++ + PE+ D LT +GVVG+ D
Sbjct: 534 CADVIEPLASDALRTI-------CLAYRDFAPEEFPRKDYP-----NKGLTLIGVVGIKD 581
Query: 159 PPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGVFTEEEDTTGKSYSGREFDDL 218
P R V +++ C+ AGI V ++TGDN TA+AI R G+ T G + G+EF L
Sbjct: 582 PLRPGVREAVQECQRAGITVRMVTGDNIDTAKAIARNCGILT----FGGLAMEGKEFRSL 637
Query: 219 PLSEQKAAVARARLFSRVEPAHKSKIVEFLQGMNEISA 256
E + + R+ +R P K +V L+ M E+ A
Sbjct: 638 VYEEMDPILPKLRVLARSSPLDKQLLVLMLKDMGEVVA 675
>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 = 86.8 bits (215), Expect = 3e-19
Identities = 64/222 (28%), Positives = 103/222 (46%), Gaps = 38/222 (17%)
Query: 69 SSGPK--LFVKGAPEGVLERCTHARIGSQKVSLKDFSA---NTRFENLRSLEPKSKVSAI 123
P+ L +KGAPE +LERC+ I ++ L + + L L +V
Sbjct: 472 PRDPRHLLVMKGAPERILERCSSILIHGKEQPLDEELKEAFQNAYLELGGL--GERVLGF 529
Query: 124 VPWGMKPEDMNLADSTKFASYEVN-----LTFVGVVGMLDPPRKEVFDSIARCRAAGIRV 178
P++ + +F + +VN L FVG++ M+DPPR V D++ +CR+AGI+V
Sbjct: 530 CHL-YLPDE-QFPEGFQFDTDDVNFPTDNLCFVGLISMIDPPRAAVPDAVGKCRSAGIKV 587
Query: 179 IVITGDNKATAEAICRRIGVFTE----EEDTTGK----------------SYSGREFDDL 218
I++TGD+ TA+AI + +G+ +E ED + G + D+
Sbjct: 588 IMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVVHGSDLKDM 647
Query: 219 PLSEQKAAVARAR---LFSRVEPAHKSKIVEFLQGMNEISAM 257
SEQ + + +F+R P K IVE Q I A+
Sbjct: 648 T-SEQLDEILKYHTEIVFARTSPQQKLIIVEGCQRQGAIVAV 688
>gnl|CDD|236705 PRK10517, PRK10517, magnesium-transporting ATPase MgtA;
Provisional.
Length = 902
Score = 85.9 bits (213), Expect = 7e-19
Identities = 54/228 (23%), Positives = 94/228 (41%), Gaps = 36/228 (15%)
Query: 33 RQDVETKWKKEFTLEFSRDRKSMSSYCTPLKSSKLGSSGPKLFVKGAPEGVLERCTHARI 92
+ + ++W+K + F +R+ MS + +L KGA E +L C+ R
Sbjct: 434 ARSLASRWQKIDEIPFDFERRRMSVVV------AENTEHHQLICKGALEEILNVCSQVRH 487
Query: 93 GSQKVSLKD--------FSANTRFENLRSLEPKSKVSAIVPWGMKP--EDMNLADSTKFA 142
+ V L D + + LR V A+ + D AD
Sbjct: 488 NGEIVPLDDIMLRRIKRVTDTLNRQGLR-------VVAVATKYLPAREGDYQRAD----- 535
Query: 143 SYEVNLTFVGVVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGVFTEE 202
E +L G + LDPP++ ++ +A+G+ V ++TGD++ A +C +G+
Sbjct: 536 --ESDLILEGYIAFLDPPKETTAPALKALKASGVTVKILTGDSELVAAKVCHEVGL---- 589
Query: 203 EDTTGKSYSGREFDDLPLSEQKAAVARARLFSRVEPAHKSKIVEFLQG 250
G+ G + + L E R LF+R+ P HK +IV L+
Sbjct: 590 --DAGEVLIGSDIETLSDDELANLAERTTLFARLTPMHKERIVTLLKR 635
>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 = 80.7 bits (199), Expect = 4e-17
Identities = 58/213 (27%), Positives = 95/213 (44%), Gaps = 20/213 (9%)
Query: 39 KWKKEFTLEFSRDRKSMSSYCTPLKSSKLGSSGPKLFVKGAPEGVLERCTHARIGSQKVS 98
+WKK + F DR+ +S + +L KGA E +L CTH R G V+
Sbjct: 405 RWKKVDEIPFDFDRRRLSVVVEN------RAEVTRLICKGAVEEMLTVCTHKRFGGAVVT 458
Query: 99 LKDFSANTRFENLRSLEPKSKVSAI--VPWGMKPEDMNLADSTKFASYEVNLTFVGVVGM 156
L + + L+ + + I + K + AD TK + E L G +G
Sbjct: 459 LSE----SEKSELQDMTAEMNRQGIRVIAVATKTLKVGEADFTK--TDEEQLIIEGFLGF 512
Query: 157 LDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGVFTEEEDTTGKSYSGREFD 216
LDPP++ ++IA GI V V+TGDN+ IC+ +G+ G + +
Sbjct: 513 LDPPKESTKEAIAALFKNGINVKVLTGDNEIVTARICQEVGI------DANDFLLGADIE 566
Query: 217 DLPLSEQKAAVARARLFSRVEPAHKSKIVEFLQ 249
+L E + + +F+R+ P KS+I+ L+
Sbjct: 567 ELSDEELARELRKYHIFARLTPMQKSRIIGLLK 599
>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 = 78.1 bits (192), Expect = 3e-16
Identities = 55/197 (27%), Positives = 91/197 (46%), Gaps = 13/197 (6%)
Query: 74 LFVKGAPEGVLERCT--HARIGSQKVSLKDFSANTRFENLRSLEPKS-KVSAIVPWGMKP 130
++ KGA E ++E C+ + + G + L+D N+ SL + +V A
Sbjct: 554 IYAKGAFERIIECCSSSNGKDGVKISPLEDCDRELIIANMESLAAEGLRVLAFASKSFDK 613
Query: 131 EDMN----LADSTKFASYEVNLTFVGVVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNK 186
D N ++ A+ E +L F+G++G+ DPPR E ++ +C AGI V ++TGD
Sbjct: 614 ADNNDDQLKNETLNRATAESDLEFLGLIGIYDPPRNESAGAVEKCHQAGINVHMLTGDFP 673
Query: 187 ATAEAICRRIGVFT------EEEDTTGKSYSGREFDDLPLSEQKAAVARARLFSRVEPAH 240
TA+AI + +G+ +E +G +FD L E A + +R P
Sbjct: 674 ETAKAIAQEVGIIPPNFIHDRDEIMDSMVMTGSQFDALSDEEVDDLKALCLVIARCAPQT 733
Query: 241 KSKIVEFLQGMNEISAM 257
K K++E L AM
Sbjct: 734 KVKMIEALHRRKAFCAM 750
>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 = 68.1 bits (167), Expect = 5e-13
Identities = 40/117 (34%), Positives = 61/117 (52%), Gaps = 13/117 (11%)
Query: 150 FVGVVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIG----VFTEEEDT 205
F+G++ + DPPR + ++I R R G+ V ++TGD+ A A+ RR+G ++T +
Sbjct: 433 FLGLLPLFDPPRHDTKETIERARHLGVEVKMVTGDHLAIAKETARRLGLGTNIYTADVLL 492
Query: 206 TGKSYSGREFDDLPLSEQKAAVARARLFSRVEPAHKSKIVEFLQGMNEISAMDSSTG 262
G + DDLP + V A F+ V P HK +IVE LQ + M TG
Sbjct: 493 KGDNR-----DDLPSGLGE-MVEDADGFAEVFPEHKYEIVEILQKRGHLVGM---TG 540
>gnl|CDD|237914 PRK15122, PRK15122, magnesium-transporting ATPase; Provisional.
Length = 903
Score = 67.7 bits (166), Expect = 8e-13
Identities = 51/185 (27%), Positives = 79/185 (42%), Gaps = 26/185 (14%)
Query: 74 LFVKGAPEGVLERCTHARIGSQKVSLKDFSANTRFENLRSL-----EPKSKVSAI----V 124
L KGA E +L TH R G L + R E L +L +V + +
Sbjct: 467 LICKGAVEEMLAVATHVRDGDTVRPLDE----ARRERLLALAEAYNADGFRVLLVATREI 522
Query: 125 PWGMKPEDMNLADSTKFASYEVNLTFVGVVGMLDPPRKEVFDSIARCRAAGIRVIVITGD 184
P G + AD E +L G + LDPP++ +IA R G+ V V+TGD
Sbjct: 523 PGGESRAQYSTAD-------ERDLVIRGFLTFLDPPKESAAPAIAALRENGVAVKVLTGD 575
Query: 185 NKATAEAICRRIGVFTEEEDTTGKSYSGREFDDLPLSEQKAAVARARLFSRVEPAHKSKI 244
N ICR +G+ G+ G E + + + V +F+++ P KS++
Sbjct: 576 NPIVTAKICREVGL------EPGEPLLGTEIEAMDDAALAREVEERTVFAKLTPLQKSRV 629
Query: 245 VEFLQ 249
++ LQ
Sbjct: 630 LKALQ 634
>gnl|CDD|222006 pfam13246, Hydrolase_like2, Putative hydrolase of
sodium-potassium ATPase alpha subunit. This is a
putative hydrolase of the sodium-potassium ATPase alpha
subunit.
Length = 91
Score = 61.9 bits (151), Expect = 1e-12
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 7/56 (12%)
Query: 35 DVETKWKKEFTLEFSRDRKSMSSYCTPLKSSKLGSSGPK-LFVKGAPEGVLERCTH 89
++ ++ + + F+ +RK MS+ KL LFVKGAPE +LERC+
Sbjct: 41 ELRARYPRVAEIPFNSERKRMSTVH------KLEDDDGYRLFVKGAPERILERCST 90
>gnl|CDD|225127 COG2217, ZntA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 713
Score = 60.3 bits (147), Expect = 2e-10
Identities = 22/53 (41%), Positives = 37/53 (69%)
Query: 146 VNLTFVGVVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGV 198
V+ VGV+ + D R + ++IA +A GI+V+++TGDN+ TAEAI + +G+
Sbjct: 524 VDGKLVGVIALADELRPDAKEAIAALKALGIKVVMLTGDNRRTAEAIAKELGI 576
>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 = 56.2 bits (136), Expect = 6e-09
Identities = 40/157 (25%), Positives = 65/157 (41%), Gaps = 23/157 (14%)
Query: 46 LEFSRDRKSMSSYCTPLKSSKLGSSGPKLFVKGAPEGVLERCTHARIGSQ-KVSLKDFSA 104
+FS + MS ++ S P FVKGAPE + C+ + S + LK ++
Sbjct: 558 FQFSSALQRMSVIV---STNDERS--PDAFVKGAPETIQSLCSPETVPSDYQEVLKSYTR 612
Query: 105 NTRFENLRSLEPKSKVSAIVPWGMKP-EDMNL--ADSTKFASYEVNLTFVGVVGMLDPPR 161
++ K + L A + E NLTF+G + +P +
Sbjct: 613 EG--------------YRVLALAYKELPKLTLQKAQDLSRDAVESNLTFLGFIVFENPLK 658
Query: 162 KEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGV 198
+ + I + A IR ++ITGDN TA + R G+
Sbjct: 659 PDTKEVIKELKRASIRTVMITGDNPLTAVHVARECGI 695
>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 = 51.5 bits (124), Expect = 2e-07
Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 142 ASYEVNLTFVGVVGMLDPPRKEVFDSIAR-CRAAGIRVIVITGDNKATAEAICRRIGV 198
V+ +GV+ + D R E ++IA RA GI+++++TGDN++ AEA+ +G+
Sbjct: 367 VFVAVDGELLGVIALRDQLRPEAKEAIAALKRAGGIKLVMLTGDNRSAAEAVAAELGI 424
>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 = 48.5 bits (116), Expect = 2e-06
Identities = 19/54 (35%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 146 VNLTFVGVVGMLDPPRKEVFDSIARCRAAGI-RVIVITGDNKATAEAICRRIGV 198
+ T++G + + D PR + ++IA +A GI +V+++TGD +A AE + R +G+
Sbjct: 349 RDGTYLGYILLSDEPRPDAAEAIAELKALGIEKVVMLTGDRRAVAERVARELGI 402
>gnl|CDD|216069 pfam00702, Hydrolase, haloacid dehalogenase-like hydrolase. This
family is structurally different from the alpha/beta
hydrolase family (pfam00561). This family includes
L-2-haloacid dehalogenase, epoxide hydrolases and
phosphatases. The structure of the family consists of
two domains. One is an inserted four helix bundle, which
is the least well conserved region of the alignment,
between residues 16 and 96 of Pseudomonas sp.
(S)-2-haloacid dehalogenase 1. The rest of the fold is
composed of the core alpha/beta domain. Those members
with the characteristic DxD triad at the N-terminus are
probably phosphatidylglycerolphosphate (PGP)
phosphatases involved in cardiolipin biosynthesis in the
mitochondria.
Length = 187
Score = 46.9 bits (111), Expect = 2e-06
Identities = 24/93 (25%), Positives = 48/93 (51%), Gaps = 2/93 (2%)
Query: 109 ENLRSLEPKSKVSAIVPWGMKPEDMNLADSTKFAS--YEVNLTFVGVVGMLDPPRKEVFD 166
ENL + V ++ + E++ A+ ++L +G++ + DP +
Sbjct: 42 ENLTKEGREELVRRLLLRALAGEELLEELLRAGATVVAVLDLVVLGLIALTDPLYPGARE 101
Query: 167 SIARCRAAGIRVIVITGDNKATAEAICRRIGVF 199
++ + AGI++ ++TGDN+ TA AI R +G+F
Sbjct: 102 ALKELKEAGIKLAILTGDNRLTANAIARLLGLF 134
>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 = 48.0 bits (115), Expect = 2e-06
Identities = 17/54 (31%), Positives = 31/54 (57%)
Query: 145 EVNLTFVGVVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGV 198
VN GV+ + D + E + I + GI +++TGDN+ TA+A+ + +G+
Sbjct: 400 AVNGELAGVLALADQLKPEAKEVIQALKRRGIEPVMLTGDNRKTAKAVAKELGI 453
>gnl|CDD|215623 PLN03190, PLN03190, aminophospholipid translocase; Provisional.
Length = 1178
Score = 44.1 bits (104), Expect = 5e-05
Identities = 48/162 (29%), Positives = 70/162 (43%), Gaps = 28/162 (17%)
Query: 47 EFSRDRKSMSSYCTPLKSSKLG--SSGPKLFVKGAPE---GVLERCTHAR-IGSQKVSLK 100
EF DRK MS LG K+FVKGA V++R + I + + L
Sbjct: 610 EFDSDRKRMSVI--------LGCPDKTVKVFVKGADTSMFSVIDRSLNMNVIRATEAHLH 661
Query: 101 DFSA---NTRFENLRSLEPKSKVSAIVPWGMKPEDMNLADSTKFA-------SYEVNLTF 150
+S+ T +R L S W E + A + A + E NLT
Sbjct: 662 TYSSLGLRTLVVGMRELND----SEFEQWHFSFEAASTALIGRAALLRKVASNVENNLTI 717
Query: 151 VGVVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAI 192
+G + D ++ V ++I R AGI+V V+TGD + TA +I
Sbjct: 718 LGASAIEDKLQQGVPEAIESLRTAGIKVWVLTGDKQETAISI 759
>gnl|CDD|182635 PRK10671, copA, copper exporting ATPase; Provisional.
Length = 834
Score = 42.0 bits (99), Expect = 2e-04
Identities = 16/41 (39%), Positives = 25/41 (60%)
Query: 158 DPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGV 198
DP R + ++ R AG R++++TGDN TA AI + G+
Sbjct: 649 DPLRSDSVAALQRLHKAGYRLVMLTGDNPTTANAIAKEAGI 689
>gnl|CDD|225126 COG2216, KdpB, High-affinity K+ transport system, ATPase chain B
[Inorganic ion transport and metabolism].
Length = 681
Score = 40.3 bits (95), Expect = 7e-04
Identities = 21/52 (40%), Positives = 28/52 (53%), Gaps = 6/52 (11%)
Query: 150 FVGVVGMLD---PPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGV 198
+GV+ + D P KE F + R GI+ ++ITGDN TA AI GV
Sbjct: 438 ILGVIYLKDIVKPGIKERFAEL---RKMGIKTVMITGDNPLTAAAIAAEAGV 486
>gnl|CDD|236827 PRK11033, zntA, zinc/cadmium/mercury/lead-transporting ATPase;
Provisional.
Length = 741
Score = 40.4 bits (95), Expect = 7e-04
Identities = 15/50 (30%), Positives = 29/50 (58%)
Query: 149 TFVGVVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGV 198
+G++ + D R + +I+ +A GI+ +++TGDN A AI +G+
Sbjct: 558 DVLGLIALQDTLRADARQAISELKALGIKGVMLTGDNPRAAAAIAGELGI 607
>gnl|CDD|234905 PRK01122, PRK01122, potassium-transporting ATPase subunit B;
Provisional.
Length = 679
Score = 40.2 bits (95), Expect = 8e-04
Identities = 21/52 (40%), Positives = 28/52 (53%), Gaps = 6/52 (11%)
Query: 150 FVGVVGMLD---PPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGV 198
+GV+ + D P KE F + R GI+ ++ITGDN TA AI GV
Sbjct: 436 VLGVIYLKDIVKPGIKERFAEL---RKMGIKTVMITGDNPLTAAAIAAEAGV 484
>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 = 40.1 bits (94), Expect = 0.001
Identities = 40/160 (25%), Positives = 63/160 (39%), Gaps = 23/160 (14%)
Query: 46 LEFSRDRKSMSSYCTPLKSSKLGSSGPKLFVKGAPE---GVLERCTHARIGSQKVSLKDF 102
LEF+ DRK MS + KL KGA L + K L+++
Sbjct: 515 LEFNSDRKRMSVIV------RNPDGRIKLLCKGADTVIFKRLSSGGNQVNEETKEHLENY 568
Query: 103 SANTRFENLRSLEPKSKV---SAIVPWGMKPEDMNLA------DSTKFASY-EVNLTFVG 152
++ E LR+L + W + + + A A E +L +G
Sbjct: 569 AS----EGLRTLCIAYRELSEEEYEEWNEEYNEASTALTDREEKLDVVAESIEKDLILLG 624
Query: 153 VVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAI 192
+ D ++ V ++I R AGI++ V+TGD TA I
Sbjct: 625 ATAIEDKLQEGVPETIELLRQAGIKIWVLTGDKVETAINI 664
>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 = 39.5 bits (92), Expect = 0.001
Identities = 37/122 (30%), Positives = 54/122 (44%), Gaps = 19/122 (15%)
Query: 94 SQKVSLKDFSANTR-----FENLRSLEPKSKVSAIVPW-----GMKPEDMNLA------- 136
S + +F+A TR +N R + K V AI G P D++ A
Sbjct: 366 SLHATFVEFTAQTRMSGINLDNGRMIR-KGAVDAIKRHVEANGGHIPTDLDQAVDQVARQ 424
Query: 137 DSTKFASYEVNLTFVGVVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRI 196
T E N + GV+ + D + + + A+ R GI+ I+ITGDN+ TA AI
Sbjct: 425 GGTPLVVCEDNRIY-GVIYLKDIVKGGIKERFAQLRKMGIKTIMITGDNRLTAAAIAAEA 483
Query: 197 GV 198
GV
Sbjct: 484 GV 485
>gnl|CDD|119389 cd01427, HAD_like, Haloacid dehalogenase-like hydrolases. The
haloacid dehalogenase-like (HAD) superfamily includes
L-2-haloacid dehalogenase, epoxide hydrolase,
phosphoserine phosphatase, phosphomannomutase,
phosphoglycolate phosphatase, P-type ATPase, and many
others, all of which use a nucleophilic aspartate in
their phosphoryl transfer reaction. All members possess
a highly conserved alpha/beta core domain, and many also
possess a small cap domain, the fold and function of
which is variable. Members of this superfamily are
sometimes referred to as belonging to the DDDD
superfamily of phosphohydrolases.
Length = 139
Score = 32.3 bits (74), Expect = 0.10
Identities = 5/44 (11%), Positives = 18/44 (40%)
Query: 160 PRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGVFTEEE 203
V +++ + GI++ + T ++ + +G+ +
Sbjct: 25 LYPGVKEALKELKEKGIKLALATNKSRREVLELLEELGLDDYFD 68
>gnl|CDD|184448 PRK14010, PRK14010, potassium-transporting ATPase subunit B;
Provisional.
Length = 673
Score = 33.5 bits (76), Expect = 0.12
Identities = 15/52 (28%), Positives = 26/52 (50%)
Query: 147 NLTFVGVVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGV 198
+ +GV+ + D + + + R GI ++ TGDN+ TA I + GV
Sbjct: 429 DNEILGVIYLKDVIKDGLVERFRELREMGIETVMCTGDNELTAATIAKEAGV 480
>gnl|CDD|236195 PRK08238, PRK08238, hypothetical protein; Validated.
Length = 479
Score = 33.3 bits (77), Expect = 0.12
Identities = 13/43 (30%), Positives = 25/43 (58%)
Query: 159 PPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGVFTE 201
P +EV D + RAAG ++++ T ++ A+A+ +G+F
Sbjct: 72 PYNEEVLDYLRAERAAGRKLVLATASDERLAQAVAAHLGLFDG 114
>gnl|CDD|222115 pfam13419, HAD_2, Haloacid dehalogenase-like hydrolase.
Length = 176
Score = 32.3 bits (74), Expect = 0.14
Identities = 7/41 (17%), Positives = 24/41 (58%)
Query: 159 PPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGVF 199
P +V + + R +A G+++++++ ++ E + ++G+
Sbjct: 77 EPFPDVVELLRRLKAKGVKLVILSNGSREAVERLLEKLGLL 117
>gnl|CDD|219386 pfam07364, DUF1485, Protein of unknown function (DUF1485). This
family consists of several hypothetical bacterial
proteins of around 300 residues in length. Members of
this family all appear to be in the Phylum
Proteobacteria. The function of this family is unknown.
Length = 292
Score = 32.9 bits (76), Expect = 0.15
Identities = 18/65 (27%), Positives = 24/65 (36%), Gaps = 13/65 (20%)
Query: 169 ARCRAAGIRVIVITGDNKATAEAICRRIG--VFTEEEDTTGKSYSGREFDDLPLSEQKAA 226
A G V+V T + A AEA + ++ +D LPL E A
Sbjct: 238 ADVPEMGPSVLVYTDGDPAAAEAAADELAAELWARRDDFVFPF--------LPLDE---A 286
Query: 227 VARAR 231
V RA
Sbjct: 287 VDRAL 291
>gnl|CDD|223634 COG0560, SerB, Phosphoserine phosphatase [Amino acid transport and
metabolism].
Length = 212
Score = 31.9 bits (73), Expect = 0.22
Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 3/81 (3%)
Query: 153 VVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGV---FTEEEDTTGKS 209
V + +A +AAG +V++I+G E I R+G+ E +
Sbjct: 71 VREEFLRLTPGAEELVAALKAAGAKVVIISGGFTFLVEPIAERLGIDYVVANELEIDDGK 130
Query: 210 YSGREFDDLPLSEQKAAVARA 230
+GR + E KA R
Sbjct: 131 LTGRVVGPICDGEGKAKALRE 151
>gnl|CDD|221729 pfam12710, HAD, haloacid dehalogenase-like hydrolase.
Length = 122
Score = 31.0 bits (70), Expect = 0.23
Identities = 6/61 (9%), Positives = 22/61 (36%)
Query: 147 NLTFVGVVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGVFTEEEDTT 206
+ + ++ L R+ ++ V++++G + + + +G+ T
Sbjct: 13 DTALLLLLEALAEDRRLGLLGLSDAEELLELVVIVSGSPEPLVRPVAKALGIDDVNVVGT 72
Query: 207 G 207
Sbjct: 73 E 73
>gnl|CDD|223162 COG0084, TatD, Mg-dependent DNase [DNA replication, recombination,
and repair].
Length = 256
Score = 31.8 bits (73), Expect = 0.29
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 157 LDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAI 192
D R EV IAR R AG++ +V+ G + +
Sbjct: 15 FDEDRDEV---IARAREAGVKKMVVVGTDLEDFKRA 47
>gnl|CDD|215200 PLN02350, PLN02350, phosphogluconate dehydrogenase
(decarboxylating).
Length = 493
Score = 31.2 bits (71), Expect = 0.56
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 3/65 (4%)
Query: 193 CRRIGVFTEEEDTTGKSYSGREFDDLPLSEQKAAVARARLFSRVEPA-HKSKIVEFLQGM 251
R + EE K + +D+ ++ V + +L V A + SKI + QGM
Sbjct: 292 ARYLSGLKEERVAAAKVFKEAGLEDILSADSG--VDKKQLIDDVRQALYASKICSYAQGM 349
Query: 252 NEISA 256
N I A
Sbjct: 350 NLIRA 354
>gnl|CDD|234176 TIGR03351, PhnX-like, phosphonatase-like hydrolase. This clade of
sequences are the closest homologs to the PhnX enzyme,
phosphonoacetaldehyde (Pald) hydrolase (phosphonatase,
TIGR01422). This phosphonatase-like enzyme and PhnX
itself are members of the haloacid dehalogenase (HAD)
superfamily (pfam00702) having a a number of distinctive
features that set them apart from typical HAD enzymes.
The typical HAD N-terminal motif DxDx(T/V) here is DxAGT
and the usual conserved lysine prior to the C-terminal
motif is instead an arginine. Also distinctive of
phosphonatase, and particular to its bi-catalytic
mechanism is a conserved lysine in the variable "cap"
domain. This lysine forms a Schiff base with the
aldehyde of phosphonoacetaldehyde, providing, through
the resulting positive charge, a polarization of the C-P
bond necesary for cleavage as well as a route to the
initial product of cleavage, an ene-amine. The
conservation of these elements in this
phosphonatase-like enzyme suggests that the substrate is
also, like Pald, a 2-oxo-ethylphosphonate. Despite this,
the genomic context of members of this family are quite
distinct from PhnX, which is almost invariably
associated with the 2-aminoethylphosphonate transaminase
PhnW (TIGR02326), the source of the substrate Pald.
Members of this clade are never associated with PhnW,
but rather associate with families of FAD-dependent
oxidoreductases related to deaminating amino acid
oxidases (pfam01266) as well as zinc-dependent
dehydrogenases (pfam00107). Notably, family members from
Arthrobacter aurescens TC1 and Nocardia farcinica IFM
10152 are adjacent to the PhnCDE ABC cassette
phosphonates transporter (GenProp0236) typically found
in association with the phosphonates C-P lyase system
(GenProp0232). These observations suggest two
possibilities. First, the substrate for this enzyme
family is also Pald, the non-association with PhnW not
withstanding. Alternatively, the substrate is something
very closely related such as
hydroxyphosphonoacetaldehyde (Hpald). Hpald could come
from oxidative deamination of
1-hydroxy-2-aminoethylphosphonate (HAEP) by the
associated oxidase. HAEP would not be a substrate for
PhnW due to its high specificity for AEP. HAEP has been
shown to be a constituent of the sphingophosphonolipid
of Bacteriovorax stolpii, and presumably has other
natural sources. If Hpald is the substrate, the product
would be glycoaldehyde (hydroxyacetaldehyde), and the
associated alcohol dehydrogenase may serve to convert
this to glycol.
Length = 220
Score = 30.5 bits (69), Expect = 0.60
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 166 DSIARCRAAGIRVIVITGDNKATAEAICRRIG 197
++ R++GI+V + TG ++ TAE + ++G
Sbjct: 94 EAFRSLRSSGIKVALTTGFDRDTAERLLEKLG 125
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 31.0 bits (71), Expect = 0.61
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 3/48 (6%)
Query: 154 VGMLDPP-RKEVFDSIARCRA-AGIRVIVITGDNKATAEAICRRIGVF 199
V LD + +V + + + G+ + I+ D A I R+ V
Sbjct: 457 VSALDVSVQAQVLNLLKDLQEELGLTYLFISHD-LAVVRYIADRVAVM 503
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 30.7 bits (70), Expect = 0.70
Identities = 11/43 (25%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 157 LDPP-RKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGV 198
LDP R+E+++ + G I+++ AE +C R+ +
Sbjct: 167 LDPESRREIWELLRELAKEGGVTILLSTHILEEAEELCDRVII 209
>gnl|CDD|233435 TIGR01488, HAD-SF-IB, Haloacid Dehalogenase superfamily, subfamily
IB, phosphoserine phosphatase-like. This model
represents a subfamily of the Haloacid Dehalogenase
superfamily of aspartate-nucleophile hydrolases.
Subfamily IA, B, C and D are distinguished from the rest
of the superfamily by the presence of a variable domain
between the first and second conserved catalytic motifs.
In subfamilies IA and IB, this domain consists of an
alpha-helical bundle. It was necessary to model these
two subfamilies separately, breaking them at a an
apparent phylogenetic bifurcation, so that the resulting
model(s) are not so broadly defined that members of
subfamily III (which lack the variable domain) are
included. Subfamily IA includes the enzyme phosphoserine
phosphatase (TIGR00338) as well as three hypothetical
equivalogs. Many members of these hypothetical
equivalogs have been annotated as PSPase-like or
PSPase-family proteins. In particular, the hypothetical
equivalog which appears to be most closely related to
PSPase contains only Archaea (while TIGR00338 contains
only eukaryotes and bacteria) of which some are
annotated as PSPases. Although this is a reasonable
conjecture, none of these sequences has sufficient
evidence for this assignment. If such should be found,
this model should be retired while the PSPase model
should be broadened to include these sequences [Unknown
function, Enzymes of unknown specificity].
Length = 177
Score = 30.0 bits (68), Expect = 0.80
Identities = 9/43 (20%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 156 MLDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRIGV 198
L P +E+ I+ + GI ++++G E + ++G+
Sbjct: 73 ALRPGAREL---ISWLKERGIDTVIVSGGFDFFVEPVAEKLGI 112
>gnl|CDD|236536 PRK09479, glpX, fructose 1,6-bisphosphatase II; Reviewed.
Length = 319
Score = 30.1 bits (69), Expect = 1.2
Identities = 16/33 (48%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 153 VVGMLDPPRKEVFDSIARCRAAGIRVIVIT-GD 184
V +LD PR E + IA R AG RV +I+ GD
Sbjct: 160 TVVVLDRPRHE--ELIAEIREAGARVKLISDGD 190
>gnl|CDD|200456 cd11317, AmyAc_bac_euk_AmyA, Alpha amylase catalytic domain found
in bacterial and eukaryotic Alpha amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes AmyA proteins from bacteria, fungi, mammals,
insects, mollusks, and nematodes. The Alpha-amylase
family comprises the largest family of glycoside
hydrolases (GH), with the majority of enzymes acting on
starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 329
Score = 29.8 bits (68), Expect = 1.2
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 161 RKEVFDSIARCRAAGIRVIV 180
E D + RC AAG+RV V
Sbjct: 65 EAEFRDMVNRCNAAGVRVYV 84
>gnl|CDD|201399 pfam00694, Aconitase_C, Aconitase C-terminal domain. Members of
this family usually also match to pfam00330. This domain
undergoes conformational change in the enzyme mechanism.
Length = 131
Score = 28.8 bits (65), Expect = 1.5
Identities = 12/81 (14%), Positives = 26/81 (32%), Gaps = 2/81 (2%)
Query: 107 RFENLRSLEPKSKVSAIVPWGMKPEDM-NLADSTKFASYEV-NLTFVGVVGMLDPPRKEV 164
+F LR + +S + + P+ + + + +
Sbjct: 3 KFLTLRGVCTPDFISNVDTDLIIPKQFLGTIANIGLGNILFDGWRANKTTHLPTGENPDF 62
Query: 165 FDSIARCRAAGIRVIVITGDN 185
D+ R + G ++VI G N
Sbjct: 63 VDAAERYKQHGAPILVIGGKN 83
>gnl|CDD|182523 PRK10530, PRK10530, pyridoxal phosphate (PLP) phosphatase;
Provisional.
Length = 272
Score = 29.2 bits (66), Expect = 1.8
Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 4/33 (12%)
Query: 155 GMLDPPRK----EVFDSIARCRAAGIRVIVITG 183
G L P+K E +++AR R AG +VI++TG
Sbjct: 12 GTLLTPKKTILPESLEALARAREAGYKVIIVTG 44
>gnl|CDD|238500 cd01018, ZntC, Metal binding protein ZntC. These proteins are
predicted to function as initial receptors in ABC
transport of metal ions. They belong to the TroA
superfamily of helical backbone metal receptor proteins
that share a distinct fold and ligand binding mechanism.
They are comprised of two globular subdomains connected
by a long alpha helix and bind their specific ligands in
the cleft between these domains. In addition, many of
these proteins possess a metal-binding histidine-rich
motif (repetitive HDH sequence).
Length = 266
Score = 29.3 bits (66), Expect = 2.0
Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 4/51 (7%)
Query: 162 KEVFDSIARCRAAGIRVIVI-TGDNKATAEAICRRIGVFTEEEDTTGKSYS 211
K + D + G+RV+ + + +AEAI R IG D +
Sbjct: 207 KRLIDL---AKEKGVRVVFVQPQFSTKSAEAIAREIGAKVVTIDPLAADWE 254
>gnl|CDD|221719 pfam12696, TraG-D_C, TraM recognition site of TraD and TraG. This
family includes both TraG and TraD as well as VirD4
proteins. TraG is essential for DNA transfer in
bacterial conjugation. These proteins are thought to
mediate interactions between the DNA-processing (Dtr)
and the mating pair formation (Mpf) systems. This domain
interacts with the relaxosome component TraM via the
latter's tetramerisation domain. TraD is a hexameric
ring ATPase that forms the cytoplasmic face of the
conjugative pore.
Length = 126
Score = 28.4 bits (64), Expect = 2.0
Identities = 19/95 (20%), Positives = 34/95 (35%), Gaps = 34/95 (35%)
Query: 153 VVGMLD-----PPRKEVFDSIARCRAAGIRVIVIT----------GDNKA---------- 187
V+ +LD ++ ++++ R+ GI +++I G + A
Sbjct: 2 VLFLLDEFANLGKIPDLEEALSTGRSRGISLVLILQSLAQLEELYGKDGAETILGNCDVK 61
Query: 188 ---------TAEAICRRIGVFTEEEDTTGKSYSGR 213
TAE I + +G T E T S G
Sbjct: 62 IFLGGNDPETAEYISKLLGKTTVEVKTRSSSSGGS 96
>gnl|CDD|161973 TIGR00639, PurN, phosphoribosylglycinamide formyltransferase,
formyltetrahydrofolate-dependent. This model describes
phosphoribosylglycinamide formyltransferase (GAR
transformylase), one of several proteins in
formyl_transf (Pfam family pfam00551). This enzyme uses
formyl tetrahydrofolate as a formyl group donor to
produce 5'-phosphoribosyl-N-formylglycinamide. PurT, a
different GAR transformylase, uses ATP and formate
rather than formyl tetrahydrofolate. Experimental proof
includes complementation of E. coli purN mutants by
orthologs from vertebrates (where it is a domain of a
multifunctional protein), Bacillus subtilis, and
Arabidopsis. No archaeal example was detected. In
phylogenetic analyses, the member from Saccharomyces
cerevisiae shows a long branch length but membership in
the family, while the formyltetrahydrofolate
deformylases form a closely related outgroup [Purines,
pyrimidines, nucleosides, and nucleotides, Purine
ribonucleotide biosynthesis].
Length = 190
Score = 28.9 bits (65), Expect = 2.3
Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 5/46 (10%)
Query: 82 GVLERCTHARIGSQKVSLKDFSANTRFEN-----LRSLEPKSKVSA 122
LER A I + +SLKDF + F+ LR+ E V A
Sbjct: 41 YGLERAAQAGIPTFVLSLKDFPSREAFDQAIIEELRAHEVDLVVLA 86
>gnl|CDD|225396 COG2840, COG2840, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 184
Score = 28.5 bits (64), Expect = 2.6
Identities = 13/24 (54%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 161 RKEVFDSIARCRAAGIR-VIVITG 183
R+E+ IAR RA G+R V+VI G
Sbjct: 110 RQELGAFIARARAEGLRCVLVIHG 133
>gnl|CDD|216658 pfam01713, Smr, Smr domain. This family includes the Smr (Small
MutS Related) proteins, and the C-terminal region of the
MutS2 protein. It has been suggested that this domain
interacts with the MutS1 protein in the case of Smr
proteins and with the N-terminal MutS related region of
MutS2. This domain exhibits nicking endonuclease
activity that might have a role in mismatch repair or
genetic recombination. It shows no significant double
strand cleavage or exonuclease activity. The full-length
human NEDD4-binding protein 2 also has the
polynucleotide kinase activity.
Length = 80
Score = 26.8 bits (60), Expect = 3.1
Identities = 8/24 (33%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 161 RKEVFDSIARCRAAGIR-VIVITG 183
+ D + A GIR V++I G
Sbjct: 12 LDALEDFLDEAWAKGIRCVLIIHG 35
>gnl|CDD|173902 cd00805, TyrRS_core, catalytic core domain of tyrosinyl-tRNA
synthetase. Tyrosinyl-tRNA synthetase (TyrRS) catalytic
core domain. TyrRS is a homodimer which attaches Tyr to
the appropriate tRNA. TyrRS is a class I tRNA
synthetases, so it aminoacylates the 2'-OH of the
nucleotide at the 3' end of the tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formationof the enzyme bound
aminoacyl-adenylate. It contains the class I
characteristic HIGH and KMSKS motifs, which are involved
in ATP binding.
Length = 269
Score = 28.7 bits (65), Expect = 3.3
Identities = 24/94 (25%), Positives = 35/94 (37%), Gaps = 23/94 (24%)
Query: 168 IARCRAAGIRVIVITGDNKATAEAICRRIGVFTEEEDTTGKSYSGREFDDLPLSEQKAAV 227
+ + AG VIV+ GD ATA IG D +GKS E L L +
Sbjct: 25 LRDFQQAGHEVIVLIGD--ATA-----MIG------DPSGKS---EERKLLDLELIRENA 68
Query: 228 ARARL----FSRVEPAHKSKIV---EFLQGMNEI 254
+ P K+K V ++L + +
Sbjct: 69 KYYKKQLKAILDFIPPEKAKFVNNSDWLLSLYTL 102
>gnl|CDD|216281 pfam01070, FMN_dh, FMN-dependent dehydrogenase.
Length = 302
Score = 28.6 bits (65), Expect = 3.5
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 161 RKEVFDSIARCRAAGIRVIVITGD 184
R+ D + R AAG + +V+T D
Sbjct: 122 RELTEDLLERAEAAGYKALVLTVD 145
>gnl|CDD|238868 cd01830, XynE_like, SGNH_hydrolase subfamily, similar to the
putative arylesterase/acylhydrolase from the rumen
anaerobe Prevotella bryantii XynE. The P. bryantii XynE
gene is located in a xylanase gene cluster. SGNH
hydrolases are a diverse family of lipases and
esterases. The tertiary fold of the enzyme is
substantially different from that of the alpha/beta
hydrolase family and unique among all known hydrolases;
its active site closely resembles the Ser-His-Asp(Glu)
triad found in other serine hydrolases.
Length = 204
Score = 28.0 bits (63), Expect = 3.9
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 168 IARCRAAGIRVIVIT 182
I R A GI+VI T
Sbjct: 112 IRRAHARGIKVIGAT 126
>gnl|CDD|240214 cd05710, SIS_1, A subgroup of the SIS domain. SIS (Sugar ISomerase)
domains are found in many phosphosugar isomerases and
phosphosugar binding proteins. SIS domains are also
found in proteins that regulate the expression of genes
involved in synthesis of phosphosugars.
Length = 120
Score = 27.2 bits (61), Expect = 4.3
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 162 KEVFDSIARCRAAGIRVIVITGD 184
KE + + G VI +T D
Sbjct: 61 KETVAAAKFAKEKGATVIGLTDD 83
>gnl|CDD|223390 COG0313, COG0313, Predicted methyltransferases [General function
prediction only].
Length = 275
Score = 28.3 bits (64), Expect = 4.3
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 168 IARCRAAGIRVIVITGDNKATA 189
+ R AGIRV+ + G +
Sbjct: 99 VRAAREAGIRVVPLPGPSALIT 120
>gnl|CDD|239772 cd04239, AAK_UMPK-like, AAK_UMPK-like: UMP kinase (UMPK)-like, the
microbial/chloroplast uridine monophosphate kinase
(uridylate kinase) enzyme that catalyzes UMP
phosphorylation and plays a key role in pyrimidine
nucleotide biosynthesis. Regulation of this process is
via feed-back control and via gene repression of
carbamoyl phosphate synthetase (the first enzyme of the
pyrimidine biosynthesis pathway). The UMP kinases of E.
coli (Ec) and Pyrococcus furiosus (Pf) are known to
function as homohexamers, with GTP and UTP being
allosteric effectors. Like other related enzymes
(carbamate kinase, aspartokinase, and N-acetylglutamate
kinase) the E. coli and most bacterial UMPKs have a
conserved, N-terminal, lysine residue proposed to
function in the catalysis of the phosphoryl group
transfer, whereas most archaeal UMPKs appear to lack
this residue and the Pyrococcus furiosus structure has
an additional Mg ion bound to the ATP molecule which is
proposed to function as the catalysis instead. Also
included in this CD are the alpha and beta subunits of
the Mo storage protein (MosA and MosB) characterized as
an alpha4-beta4 octamer containing an ATP-dependent,
polynuclear molybdenum-oxide cluster. These and related
sequences in this CD are members of the Amino Acid
Kinase Superfamily (AAK).
Length = 229
Score = 27.9 bits (63), Expect = 5.3
Identities = 11/40 (27%), Positives = 15/40 (37%), Gaps = 2/40 (5%)
Query: 163 EVFDSIA--RCRAAGIRVIVITGDNKATAEAICRRIGVFT 200
+V D+ A CR I +IV G + V T
Sbjct: 187 KVMDATALTLCRRNKIPIIVFNGLKPGNLLRALKGEHVGT 226
>gnl|CDD|181872 PRK09456, PRK09456, ?-D-glucose-1-phosphatase; Provisional.
Length = 199
Score = 27.7 bits (62), Expect = 5.8
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 7/37 (18%)
Query: 150 FVGVVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNK 186
FV + R EV + + R G RV+V++ N+
Sbjct: 82 FVAL-------RPEVIAIMHKLREQGHRVVVLSNTNR 111
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain I
of the ABC component of a cobalt transport family found
in bacteria, archaea, and eukaryota. The transition
metal cobalt is an essential component of many enzymes
and must be transported into cells in appropriate
amounts when needed. This ABC transport system of the
CbiMNQO family is involved in cobalt transport in
association with the cobalamin (vitamin B12)
biosynthetic pathways. Most of cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are encoded
by the conserved gene cluster cbiMNQO. Both the CbiM and
CbiQ proteins are integral cytoplasmic membrane
proteins, and the CbiO protein has the linker peptide
and the Walker A and B motifs commonly found in the
ATPase components of the ABC-type transport systems.
Length = 211
Score = 27.4 bits (62), Expect = 5.9
Identities = 9/28 (32%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 156 MLDPP-RKEVFDSIARCRAAGIRVIVIT 182
LDP R+E+ + + + +A G +I++T
Sbjct: 164 GLDPAGRRELLELLKKLKAEGKTIIIVT 191
>gnl|CDD|212507 cd11648, RsmI, Ribosomal RNA small subunit methyltransferase I,
also known as rRNA (cytidine-2'-O-)-methyltransferase
RsmI. Proteins in this family catalyze the
2-O-methylation of the ribose of cytidine 1402 (C1402)
in 16S rRNA using S-adenosyl-L-methionine (SAM or
Ado-Met) as the methyl donor. RsmI proteins employ the
30S subunit (not the 16S rRNA) as a substrate,
suggesting that the methylation reaction occurs at a
late step during 30S assembly in the cell.
Length = 218
Score = 27.7 bits (63), Expect = 6.1
Identities = 6/22 (27%), Positives = 9/22 (40%)
Query: 168 IARCRAAGIRVIVITGDNKATA 189
+ AGI V+ I G +
Sbjct: 93 VRAAIEAGIPVVPIPGPSALIT 114
>gnl|CDD|224419 COG1502, Cls,
Phosphatidylserine/phosphatidylglycerophosphate/cardioli
pin synthases and related enzymes [Lipid metabolism].
Length = 438
Score = 27.9 bits (62), Expect = 6.2
Identities = 8/33 (24%), Positives = 14/33 (42%)
Query: 160 PRKEVFDSIARCRAAGIRVIVITGDNKATAEAI 192
P +E+ ++ G+ V +I A AI
Sbjct: 295 PDRELLAALKAAARRGVDVRIIIPSLGANDSAI 327
>gnl|CDD|217491 pfam03320, FBPase_glpX, Bacterial fructose-1,6-bisphosphatase,
glpX-encoded.
Length = 308
Score = 27.8 bits (63), Expect = 6.3
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 153 VVGMLDPPRKEVFDSIARCRAAGIRVIVIT-GD 184
V +LD PR + I R AG RV +I+ GD
Sbjct: 156 TVVVLDRPRHA--ELIEEIREAGARVKLISDGD 186
>gnl|CDD|182449 PRK10425, PRK10425, DNase TatD; Provisional.
Length = 258
Score = 27.7 bits (62), Expect = 6.3
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 161 RKEVFDSIARCRAAGIRVIVITGDNKATAEAICR 194
K+ D +AR AAG+ ++ITG N ++ +
Sbjct: 14 AKDRDDVVARAFAAGVNGMLITGTNLRESQQAQK 47
>gnl|CDD|239203 cd02809, alpha_hydroxyacid_oxid_FMN, Family of homologous
FMN-dependent alpha-hydroxyacid oxidizing enzymes. This
family occurs in both prokaryotes and eukaryotes.
Members of this family include flavocytochrome b2
(FCB2), glycolate oxidase (GOX), lactate monooxygenase
(LMO), mandelate dehydrogenase (MDH), and long chain
hydroxyacid oxidase (LCHAO). In green plants, glycolate
oxidase is one of the key enzymes in photorespiration
where it oxidizes glycolate to glyoxylate. LMO catalyzes
the oxidation of L-lactate to acetate and carbon
dioxide. MDH oxidizes (S)-mandelate to phenylglyoxalate.
It is an enzyme in the mandelate pathway that occurs in
several strains of Pseudomonas which converts
(R)-mandelate to benzoate.
Length = 299
Score = 27.8 bits (63), Expect = 6.4
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 168 IARCRAAGIRVIVITGD 184
+ R AAG + +V+T D
Sbjct: 135 LRRAEAAGYKALVLTVD 151
>gnl|CDD|143493 cd06819, PLPDE_III_LS_D-TA, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Low Specificity D-Threonine
Aldolase. Low specificity D-threonine aldolase (Low
specificity D-TA, EC 4.3.1.18), encoded by dtaAS gene
from Arthrobacter sp. strain DK-38, is the prototype of
this subfamily. Low specificity D-TAs are fold type III
PLP-dependent enzymes that catalyze the interconversion
between D-threonine/D-allo-threonine and glycine plus
acetaldehyde. Both PLP and divalent cations (eg. Mn2+)
are required for catalytic activity. Members of this
subfamily show similarity to bacterial alanine racemase
(AR), which contains an N-terminal PLP-binding
TIM-barrel domain and a C-terminal beta-sandwich domain.
AR exists as homodimers with active sites that lie at
the interface between the TIM barrel domain of one
subunit and the beta-sandwich domain of the other
subunit. Based on its similarity to AR, it is possible
that low specificity D-TAs also form dimers in solution.
Experimental data show that the monomeric form of low
specificity D-TAs exhibit full catalytic activity.
Length = 358
Score = 27.6 bits (62), Expect = 6.6
Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 164 VFDSIARCRAAGIRVIVITGDNKATAEAICRRIGVFTE 201
+ + AAG+ ++TG T E GV+TE
Sbjct: 192 LQATRDALEAAGLPCEIVTGGGTGTYE-FEAASGVYTE 228
>gnl|CDD|180472 PRK06210, PRK06210, enoyl-CoA hydratase; Provisional.
Length = 272
Score = 27.4 bits (61), Expect = 7.1
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 10/54 (18%)
Query: 144 YEVNLTFVGVVGMLDPPR---------KEVFDSIARCRA-AGIRVIVITGDNKA 187
YEV + V V+ + P R EV+ ++ R A +RVIV+TG +
Sbjct: 9 YEVADSGVAVITLNRPDRLNAWTPVMEAEVYAAMDRAEADPAVRVIVLTGAGRG 62
>gnl|CDD|99976 cd03804, GT1_wbaZ_like, This family is most closely related to the
GT1 family of glycosyltransferases. wbaZ in Salmonella
enterica has been shown to possess the mannosyl
transferase activity. The members of this family are
found in certain bacteria and Archaea.
Length = 351
Score = 27.5 bits (62), Expect = 7.8
Identities = 26/107 (24%), Positives = 38/107 (35%), Gaps = 24/107 (22%)
Query: 147 NLTFVGVVGMLDPPRKEVFDSIARCR------------------AAGIRVIVITGDNKAT 188
N+TF+G V +E+ D AR R A+G VI G A
Sbjct: 243 NVTFLGRV-----SDEELRDLYARARAFLFPAEEDFGIVPVEAMASGTPVIAY-GKGGAL 296
Query: 189 AEAICRRIGVFTEEEDTTGKSYSGREFDDLPLSEQKAAVARARLFSR 235
I G+ EE+ + + F+ + +A A A FS
Sbjct: 297 ETVIDGVTGILFEEQTVESLAAAVERFEKNEDFDPQAIRAHAERFSE 343
>gnl|CDD|238514 cd01066, APP_MetAP, A family including aminopeptidase P,
aminopeptidase M, and prolidase. Also known as
metallopeptidase family M24. This family of enzymes is
able to cleave amido-, imido- and amidino-containing
bonds. Members exibit relatively narrow substrate
specificity compared to other metallo-aminopeptidases,
suggesting they play roles in regulation of biological
processes rather than general protein degradation.
Length = 207
Score = 27.0 bits (60), Expect = 8.0
Identities = 8/58 (13%), Positives = 23/58 (39%)
Query: 139 TKFASYEVNLTFVGVVGMLDPPRKEVFDSIARCRAAGIRVIVITGDNKATAEAICRRI 196
+ Y +LT V+G ++E+++++ + A + + + A +
Sbjct: 82 GVYDGYHADLTRTFVIGEPSDEQRELYEAVREAQEAALAALRPGVTAEEVDAAAREVL 139
>gnl|CDD|214881 smart00881, CoA_binding, CoA binding domain. This domain has a
Rossmann fold and is found in a number of proteins
including succinyl CoA synthetases, malate and
ATP-citrate ligases.
Length = 100
Score = 26.3 bits (59), Expect = 8.3
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 160 PRKEVFDSIARCRAAGIRVIVI 181
P + D+I AGI+ IV+
Sbjct: 74 PAEAAPDAIDEAIEAGIKGIVV 95
>gnl|CDD|107273 cd06278, PBP1_LacI_like_2, Ligand-binding domain of uncharacterized
DNA-binding regulatory proteins that are members of the
LacI-GalR family of bacterial transcription repressors.
This group includes the ligand-binding domain of
uncharacterized DNA-binding regulatory proteins that are
members of the LacI-GalR family of bacterial
transcription repressors. The LacI-GalR family
repressors are composed of two functional domains: an
N-terminal HTH (helix-turn-helix) domain, which is
responsible for the DNA-binding specificity, and a
C-terminal ligand-binding domain, which is homologous to
the sugar-binding domain of ABC-type transport systems
that contain the type I periplasmic binding protein-like
fold. As also observed in the periplasmic binding
proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding which in turn changes the DNA
binding affinity of the repressor.
Length = 266
Score = 27.1 bits (61), Expect = 9.1
Identities = 17/69 (24%), Positives = 21/69 (30%), Gaps = 25/69 (36%)
Query: 167 SIAR-CRAAGIRVIVI------------TGDNKATAEAI--------CRRIGVFTEEEDT 205
+A CR GI V++I DN CRRI DT
Sbjct: 68 ELAEECRRNGIPVVLINRYVDGPGVDAVCSDNYEAGRLAAELLLAKGCRRIAFIGGPADT 127
Query: 206 TGKSYSGRE 214
+ RE
Sbjct: 128 ----STSRE 132
>gnl|CDD|232780 TIGR00010, TIGR00010, hydrolase, TatD family. PSI-BLAST, starting
with a urease alpha subunit, finds a large superfamily
of proteins, including a number of different enzymes
that act as hydrolases at C-N bonds other than peptide
bonds (EC 3.5.-.-), many uncharacterized proteins, and
the members of this family. Several genomes have
multiple paralogs related to this family. However, a set
of 17 proteins can be found, one each from 17 of the
first 20 genomes, such that each member forms a
bidirectional best hit across genomes with all other
members of the set. This core set (and one other
near-perfect member), but not the other paralogs, form
the seed for this model. Additionally, members of the
seed alignment and all trusted hits, but not all
paralogs, have a conserved motif DxHxH near the amino
end. The member from E. coli was recently shown to have
DNase activity [Unknown function, Enzymes of unknown
specificity].
Length = 252
Score = 27.2 bits (61), Expect = 9.2
Identities = 8/33 (24%), Positives = 15/33 (45%)
Query: 157 LDPPRKEVFDSIARCRAAGIRVIVITGDNKATA 189
++V + I R +AAG+ +V G +
Sbjct: 10 FLDFEEDVEEVIERAKAAGVTAVVAVGTDLEDF 42
>gnl|CDD|107286 cd06291, PBP1_Qymf_like, Ligand binding domain of the lacI-like
transcription regulator from a novel metal-reducing
bacterium Alkaliphilus Metalliredigens (strain Qymf) and
its close homologs. This group includes the ligand
binding domain of the lacI-like transcription regulator
from a novel metal-reducing bacterium Alkaliphilus
Metalliredigens (strain Qymf) and its close homologs.
Qymf is a strict anaerobe that could be grown in the
presence of borax and its cells are straight rods that
produce endospores. This group is a member of the
LacI-GalR family repressors that are composed of two
functional domains: an N-terminal HTH (helix-turn-helix)
domain, which is responsible for the DNA-binding
specificity, and a C-terminal ligand-binding domain,
which is homologous to the sugar-binding domain of
ABC-type transport systems that contain the type I
periplasmic binding protein-like fold. As also observed
in the periplasmic binding proteins, the C-terminal
domain of the bacterial transcription repressor
undergoes a conformational change upon ligand binding
which in turn changes the DNA binding affinity of the
repressor.
Length = 265
Score = 27.1 bits (61), Expect = 9.7
Identities = 10/55 (18%), Positives = 17/55 (30%), Gaps = 2/55 (3%)
Query: 177 RVIVITGDNKATAEAICRRIGVFTEEEDTTGKSYSGREFD-DLPLSEQKAAVARA 230
+ I G N + R G F + G E + +E+K +
Sbjct: 114 HIAHIGGPNNTVSPTNLRYEG-FLDVLKENGLEVRIIEIQENFDDAEKKEEIKEL 167
>gnl|CDD|187585 cd05324, carb_red_PTCR-like_SDR_c, Porcine testicular carbonyl
reductase (PTCR)-like, classical (c) SDRs. PTCR is a
classical SDR which catalyzes the NADPH-dependent
reduction of ketones on steroids and prostaglandins.
Unlike most SDRs, PTCR functions as a monomer. This
subgroup also includes human carbonyl reductase 1 (CBR1)
and CBR3. CBR1 is an NADPH-dependent SDR with broad
substrate specificity and may be responsible for the in
vivo reduction of quinones, prostaglandins, and other
carbonyl-containing compounds. In addition it includes
poppy NADPH-dependent salutaridine reductase which
catalyzes the stereospecific reduction of salutaridine
to 7(S)-salutaridinol in the biosynthesis of morphine,
and Arabidopsis SDR1,a menthone reductase, which
catalyzes the reduction of menthone to neomenthol, a
compound with antimicrobial activity; SDR1 can also
carry out neomenthol oxidation. 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, 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 = 225
Score = 26.8 bits (60), Expect = 10.0
Identities = 6/23 (26%), Positives = 12/23 (52%)
Query: 177 RVIVITGDNKATAEAICRRIGVF 199
+V ++TG N+ I R++
Sbjct: 1 KVALVTGANRGIGFEIVRQLAKS 23
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
0.316 0.131 0.372
Gapped
Lambda K H
0.267 0.0829 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,397,460
Number of extensions: 1256720
Number of successful extensions: 1559
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1539
Number of HSP's successfully gapped: 90
Length of query: 270
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 175
Effective length of database: 6,723,972
Effective search space: 1176695100
Effective search space used: 1176695100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (25.9 bits)