RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17544
(266 letters)
>gnl|CDD|236447 PRK09280, PRK09280, F0F1 ATP synthase subunit beta; Validated.
Length = 463
Score = 380 bits (979), Expect = e-132
Identities = 142/201 (70%), Positives = 159/201 (79%), Gaps = 2/201 (0%)
Query: 51 KGNGRVVAVIGAVVDVQFDHD-LPPILNALEVE-GRSPRLVLEVAQHLGENTVRTIAMDG 108
G++V VIG VVDV+F LP I NALEVE G +LVLEVAQHLG+ VRTIAM
Sbjct: 1 MNTGKIVQVIGPVVDVEFPRGELPKIYNALEVEKGDGKKLVLEVAQHLGDGVVRTIAMGS 60
Query: 109 TEGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVE 168
T+GLVRG V D+G PI +PVG TLGRI NV+GEPIDE+GPI ++ IH AP F E
Sbjct: 61 TDGLVRGMEVIDTGAPISVPVGKATLGRIFNVLGEPIDEKGPIGAEERWPIHRKAPSFEE 120
Query: 169 MSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAG 228
+S + EIL TGIKV+DLLAPYAKGGKIGLFGGAGVGKTVLI ELINN+AK HGGYSVFAG
Sbjct: 121 LSTKTEILETGIKVIDLLAPYAKGGKIGLFGGAGVGKTVLIQELINNIAKEHGGYSVFAG 180
Query: 229 VGERTREGNDLYHEMIESGVI 249
VGERTREGNDLYHEM ESGV+
Sbjct: 181 VGERTREGNDLYHEMKESGVL 201
>gnl|CDD|223133 COG0055, AtpD, F0F1-type ATP synthase, beta subunit [Energy
production and conversion].
Length = 468
Score = 341 bits (878), Expect = e-116
Identities = 142/203 (69%), Positives = 160/203 (78%), Gaps = 5/203 (2%)
Query: 53 NGRVVAVIGAVVDVQFDHD--LPPILNALEVEGRSPR-LVLEVAQHLGENTVRTIAMDGT 109
G+VV VIG VVDV+F + LP I NALEV+ + LVLEVAQHLG+N VRTIAM T
Sbjct: 3 KGKVVQVIGPVVDVEFPEEDELPEIYNALEVQNGNQGTLVLEVAQHLGDNVVRTIAMGST 62
Query: 110 EGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPI--DTDKSAAIHADAPEFV 167
+GLVRG V D+G PI +PVG TLGRI NV+GEPIDE+GPI + + IH AP F
Sbjct: 63 DGLVRGLEVIDTGKPISVPVGKGTLGRIFNVLGEPIDEKGPIKAEDFEKWPIHRKAPSFE 122
Query: 168 EMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFA 227
E+S + EIL TGIKV+DLLAPYAKGGKIGLFGGAGVGKTVLI ELINN+AK HGGYSVFA
Sbjct: 123 ELSTKTEILETGIKVIDLLAPYAKGGKIGLFGGAGVGKTVLIQELINNIAKEHGGYSVFA 182
Query: 228 GVGERTREGNDLYHEMIESGVIS 250
GVGERTREGNDLYHEM ESGV+
Sbjct: 183 GVGERTREGNDLYHEMKESGVLD 205
>gnl|CDD|211621 TIGR01039, atpD, ATP synthase, F1 beta subunit. The sequences of
ATP synthase F1 alpha and beta subunits are related and
both contain a nucleotide-binding site for ATP and ADP.
They have a common amino terminal domain but vary at the
C-terminus. The beta chain has catalytic activity, while
the alpha chain is a regulatory subunit. Proton
translocating ATP synthase, F1 beta subunit is
homologous to proton translocating ATP synthase
archaeal/vacuolar(V1), A subunit [Energy metabolism,
ATP-proton motive force interconversion].
Length = 461
Score = 328 bits (842), Expect = e-111
Identities = 143/199 (71%), Positives = 159/199 (79%), Gaps = 2/199 (1%)
Query: 54 GRVVAVIGAVVDVQFDHD-LPPILNALEVEGR-SPRLVLEVAQHLGENTVRTIAMDGTEG 111
G+VV VIG VVDV+F+ LP I NAL+V+ R L LEVAQHLG++TVRTIAM T+G
Sbjct: 3 GKVVQVIGPVVDVEFEQGELPRIYNALKVQNRAESELTLEVAQHLGDDTVRTIAMGSTDG 62
Query: 112 LVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVEMSV 171
LVRG V D+G PI +PVG ETLGRI NV+GEPIDE+GPI + IH AP F E S
Sbjct: 63 LVRGLEVIDTGAPISVPVGKETLGRIFNVLGEPIDEKGPIPAKERWPIHRKAPSFEEQST 122
Query: 172 EQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGE 231
+ EIL TGIKV+DLLAPYAKGGKIGLFGGAGVGKTVLI ELINN+AK HGGYSVFAGVGE
Sbjct: 123 KVEILETGIKVIDLLAPYAKGGKIGLFGGAGVGKTVLIQELINNIAKEHGGYSVFAGVGE 182
Query: 232 RTREGNDLYHEMIESGVIS 250
RTREGNDLYHEM ESGVI
Sbjct: 183 RTREGNDLYHEMKESGVID 201
>gnl|CDD|214349 CHL00060, atpB, ATP synthase CF1 beta subunit.
Length = 494
Score = 297 bits (763), Expect = 5e-99
Identities = 128/220 (58%), Positives = 157/220 (71%), Gaps = 7/220 (3%)
Query: 46 AAPKGKGNGRVVAVIGAVVDVQF-DHDLPPILNALEVEGRSP-----RLVLEVAQHLGEN 99
+ + K GR+ +IG V+DV F +P I NAL V+GR + EV Q LG N
Sbjct: 9 STLEEKNLGRITQIIGPVLDVAFPPGKMPNIYNALVVKGRDTAGQEINVTCEVQQLLGNN 68
Query: 100 TVRTIAMDGTEGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAI 159
VR +AM T+GL+RG V D+G P+ +PVG TLGRI NV+GEP+D GP+DT ++ I
Sbjct: 69 RVRAVAMSATDGLMRGMEVIDTGAPLSVPVGGATLGRIFNVLGEPVDNLGPVDTRTTSPI 128
Query: 160 HADAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKA 219
H AP F+++ + I TGIKVVDLLAPY +GGKIGLFGGAGVGKTVLIMELINN+AKA
Sbjct: 129 HRSAPAFIQLDTKLSIFETGIKVVDLLAPYRRGGKIGLFGGAGVGKTVLIMELINNIAKA 188
Query: 220 HGGYSVFAGVGERTREGNDLYHEMIESGVISLKDKS-SKV 258
HGG SVF GVGERTREGNDLY EM ESGVI+ ++ + SKV
Sbjct: 189 HGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKV 228
>gnl|CDD|183615 PRK12597, PRK12597, F0F1 ATP synthase subunit beta; Provisional.
Length = 461
Score = 274 bits (704), Expect = 2e-90
Identities = 111/201 (55%), Positives = 139/201 (69%), Gaps = 1/201 (0%)
Query: 51 KGNGRVVAVIGAVVDVQFD-HDLPPILNALEVEGRSPRLVLEVAQHLGENTVRTIAMDGT 109
GR++ + G VVDV+F+ LPPI AL V +LEV QHL E TVR IA+ T
Sbjct: 1 MMIGRIIKIRGDVVDVEFEEGALPPINQALTVHDDGGPTLLEVKQHLDETTVRAIALGST 60
Query: 110 EGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVEM 169
GL RG V ++G PI++PVG LGR+++V+GEP+D P+ ++ IH+ P E
Sbjct: 61 SGLARGDEVRNTGGPIEVPVGEAVLGRLLDVLGEPLDGGPPLPAEERRPIHSTIPPLAEQ 120
Query: 170 SVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGV 229
EIL TGIKV+DLL P AKGGK GLFGGAGVGKTVL+MELI N++K H G SVFAGV
Sbjct: 121 DTSTEILETGIKVIDLLCPIAKGGKTGLFGGAGVGKTVLMMELIFNISKQHSGSSVFAGV 180
Query: 230 GERTREGNDLYHEMIESGVIS 250
GER+REG++LYHEM ESGV+
Sbjct: 181 GERSREGHELYHEMKESGVLD 201
>gnl|CDD|238553 cd01133, F1-ATPase_beta, F1 ATP synthase beta subunit,
nucleotide-binding domain. The F-ATPase is found in
bacterial plasma membranes, mitochondrial inner
membranes and in chloroplast thylakoid membranes. It has
also been found in the archaea Methanosarcina barkeri.
It uses a proton gradient to drive ATP synthesis and
hydrolyzes ATP to build the proton gradient. The
extrinisic membrane domain, F1, is composed of alpha,
beta, gamma, delta and epsilon subunits with a
stoichiometry of 3:3:1:1:1. The beta subunit of ATP
synthase is catalytic.
Length = 274
Score = 252 bits (645), Expect = 5e-84
Identities = 106/127 (83%), Positives = 114/127 (89%)
Query: 124 PIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVEMSVEQEILVTGIKVV 183
PI +PVG ETLGRI NV+GEPIDERGPI T K+ IH +APEFVE S + EIL TGIKV+
Sbjct: 1 PISVPVGPETLGRIFNVLGEPIDERGPIKTKKTWPIHREAPEFVEQSTKTEILETGIKVI 60
Query: 184 DLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEM 243
DLLAPYAKGGKIGLFGGAGVGKTVLIMELINN+AKAHGGYSVFAGVGERTREGNDLYHEM
Sbjct: 61 DLLAPYAKGGKIGLFGGAGVGKTVLIMELINNIAKAHGGYSVFAGVGERTREGNDLYHEM 120
Query: 244 IESGVIS 250
ESGV+S
Sbjct: 121 KESGVLS 127
>gnl|CDD|132348 TIGR03305, alt_F1F0_F1_bet, alternate F1F0 ATPase, F1 subunit beta.
A small number of taxonomically diverse prokaryotic
species have what appears to be a second ATP synthase,
in addition to the normal F1F0 ATPase in bacteria and
A1A0 ATPase in archaea. These enzymes use ion gradients
to synthesize ATP, and in principle may run in either
direction. This model represents the F1 beta subunit of
this apparent second ATP synthase.
Length = 449
Score = 216 bits (552), Expect = 5e-68
Identities = 96/196 (48%), Positives = 126/196 (64%), Gaps = 1/196 (0%)
Query: 54 GRVVAVIGAVVDVQFDHDLPPILNALEVEGRSPRLVLEVAQHLGENTVRTIAMDGTEGLV 113
G VVAV G++VDV+FD +LP I + L GR +V+EV L + VR IA+ T+GL
Sbjct: 1 GHVVAVRGSIVDVRFDGELPAIHSVLRA-GREGEVVVEVLSQLDAHHVRGIALTPTQGLA 59
Query: 114 RGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVEMSVEQ 173
RG V DSG P+K PVG TL R+ +V G ID R P + ++H P S +
Sbjct: 60 RGMPVRDSGGPLKAPVGKPTLSRMFDVFGNTIDRREPPKDVEWRSVHQAPPTLTRRSSKS 119
Query: 174 EILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERT 233
E+ TGIK +D+L P +GGK GLFGGAGVGKTVL+ E+I+N+ H G S+F G+GER
Sbjct: 120 EVFETGIKAIDVLVPLERGGKAGLFGGAGVGKTVLLTEMIHNMVGQHQGVSIFCGIGERC 179
Query: 234 REGNDLYHEMIESGVI 249
REG +LY EM E+GV+
Sbjct: 180 REGEELYREMKEAGVL 195
>gnl|CDD|224079 COG1157, FliI, Flagellar biosynthesis/type III secretory pathway
ATPase [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 441
Score = 99.6 bits (249), Expect = 5e-24
Identities = 59/196 (30%), Positives = 96/196 (48%), Gaps = 12/196 (6%)
Query: 53 NGRVVAVIGAVVDVQFDHDLPPI--LNALEVEGRSPRLVLEVAQHLGENTVRTIAMDGTE 110
GR+ V G +++ I L +E S +++ EV E + + + E
Sbjct: 25 RGRLTRVTGLLLEAVGPQ--ARIGELCKIERSRGSEKVLAEVVGFNEERVL-LMPFEPVE 81
Query: 111 GLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVEMS 170
G+ G V +G P+ +PVG LGR+++ +G P+D G D + + A P ++
Sbjct: 82 GVSPGAEVVPTGRPLSVPVGDALLGRVLDGLGRPLDGGGLPDGTERRPLDAPPPNPLKRR 141
Query: 171 VEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVG 230
+E L TG++ +D L KG +IG+F G+GVGK+ L + +I +A +V A +G
Sbjct: 142 PIEEPLDTGVRAIDGLLTCGKGQRIGIFAGSGVGKSTL-LGMIARNTEAD--VNVIALIG 198
Query: 231 ERTREGNDLYHEMIES 246
ER RE E IE
Sbjct: 199 ERGREVR----EFIEK 210
>gnl|CDD|169656 PRK09099, PRK09099, type III secretion system ATPase; Provisional.
Length = 441
Score = 94.8 bits (236), Expect = 3e-22
Identities = 64/196 (32%), Positives = 100/196 (51%), Gaps = 10/196 (5%)
Query: 43 AAKAAPKGKGNGRVVAVIGAVVDVQ-FDHDLPPILNALEVEGRSPRLVLEVAQHLG-ENT 100
A P + G+VV VIG ++ V D L + + +G +L+ A+ +G
Sbjct: 15 ELAALPAVRRTGKVVEVIGTLLRVSGLDVTLGELCELRQRDGT----LLQRAEVVGFSRD 70
Query: 101 VRTIAMDGT-EGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAI 159
V ++ G GL RG V G P+ +PVG LGR+I+ +GEPID GP+D D+ +
Sbjct: 71 VALLSPFGELGGLSRGTRVIGLGRPLSVPVGPALLGRVIDGLGEPIDGGGPLDCDELVPV 130
Query: 160 HADAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKA 219
A P+ + + + L TG+++VD L +G ++G+F AGVGK+ L+
Sbjct: 131 IAAPPDPMSRRMVEAPLPTGVRIVDGLMTLGEGQRMGIFAPAGVGKSTLMGMFARG---T 187
Query: 220 HGGYSVFAGVGERTRE 235
+V A +GER RE
Sbjct: 188 QCDVNVIALIGERGRE 203
>gnl|CDD|233237 TIGR01026, fliI_yscN, ATPase FliI/YscN family. This family of
ATPases demonstrates extensive homology with ATP
synthase F1, beta subunit. It is a mixture of members
with two different protein functions. The first group is
exemplified by Salmonella typhimurium FliI protein. It
is needed for flagellar assembly, its ATPase activity is
required for flagellation, and it may be involved in a
specialized protein export pathway that proceeds without
signal peptide cleavage. The second group of proteins
function in the export of virulence proteins;
exemplified by Yersinia sp. YscN protein an ATPase
involved in the type III secretory pathway for the
antihost Yops proteins [Energy metabolism, ATP-proton
motive force interconversion].
Length = 440
Score = 94.0 bits (234), Expect = 5e-22
Identities = 65/213 (30%), Positives = 109/213 (51%), Gaps = 16/213 (7%)
Query: 54 GRVVAVIGAVVDVQFDHDLPPILNALEVE--GRSPRLVLEVAQHLGENTVRTIAMDGTEG 111
GRV V G +++ + + +E G RLV EV GE V + + EG
Sbjct: 25 GRVTKVKGLLIEAVGPQ--ASVGDLCLIERRGSEGRLVAEVVGFNGEF-VFLMPYEEVEG 81
Query: 112 LVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERG-PIDTDKSAAIHADAPEFVEMS 170
+ G V +G + I VG LGR+++ +G+PID +G +D ++ + ++ +
Sbjct: 82 VRPGSKVLATGEGLSIKVGDGLLGRVLDGLGKPIDGKGKFLDNVETEGLITAPINPLKRA 141
Query: 171 VEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVG 230
+EIL TG++ +D L KG +IG+F G+GVGK+ L + +I +A +V A +G
Sbjct: 142 PIREILSTGVRSIDGLLTVGKGQRIGIFAGSGVGKSTL-LGMIARNTEAD--VNVIALIG 198
Query: 231 ERTREGND-LYHEMIESG------VISLKDKSS 256
ER RE + + H++ E G V++ D+S
Sbjct: 199 ERGREVREFIEHDLGEEGLKRSVVVVATSDQSP 231
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 88.3 bits (220), Expect = 3e-21
Identities = 29/73 (39%), Positives = 42/73 (57%), Gaps = 2/73 (2%)
Query: 178 TGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGN 237
TGI+ +DLL P KG +IG+FGG+G GKTVL+ + N V+ +GER RE
Sbjct: 1 TGIRAIDLLLPIGKGQRIGIFGGSGTGKTVLLGMIARNAKA--DVVEVYVLIGERGREVA 58
Query: 238 DLYHEMIESGVIS 250
+ E++ G +
Sbjct: 59 EFIEELLGEGALK 71
>gnl|CDD|233918 TIGR02546, III_secr_ATP, type III secretion apparatus
H+-transporting two-sector ATPase. [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 422
Score = 91.6 bits (228), Expect = 3e-21
Identities = 64/215 (29%), Positives = 103/215 (47%), Gaps = 20/215 (9%)
Query: 54 GRVVAVIGAVVDVQFDHDLPPI-LNAL-EVEGRSP-RLVLEVAQHLGENTVRTIAMDGTE 110
GRV V G ++ LP + L + R P +L+ EV G+ + + +
Sbjct: 7 GRVTEVSGTLLKAV----LPGARVGELCLIRRRDPSQLLAEVVGFTGDEALLS-PLGELH 61
Query: 111 GLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAA--IHADAPEFVE 168
G+ G V +G P+ I VG LGR+++ G P+D +G + + + AD P +
Sbjct: 62 GISPGSEVIPTGRPLSIRVGEALLGRVLDGFGRPLDGKGELPAGEIETRPLDADPPPPMS 121
Query: 169 MSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAG 228
+ L TG++ +D L +G +IG+F GAGVGK+ L+ + A A +V A
Sbjct: 122 RQPIDQPLPTGVRAIDGLLTCGEGQRIGIFAGAGVGKSTLLGMIARG-ASAD--VNVIAL 178
Query: 229 VGERTREGND-LYHEMIESG------VISLKDKSS 256
+GER RE + + H + E G V+S D+ S
Sbjct: 179 IGERGREVREFIEHHLGEEGRKRSVLVVSTSDRPS 213
>gnl|CDD|163293 TIGR03498, FliI_clade3, flagellar protein export ATPase FliI.
Members of this protein family are the FliI protein of
bacterial flagellum systems. This protein acts to drive
protein export for flagellar biosynthesis. The most
closely related family is the YscN family of bacterial
type III secretion systems. This model represents one
(of three) segment of the FliI family tree. These have
been modeled separately in order to exclude the type III
secretion ATPases more effectively.
Length = 418
Score = 90.8 bits (226), Expect = 5e-21
Identities = 63/210 (30%), Positives = 101/210 (48%), Gaps = 11/210 (5%)
Query: 54 GRVVAVIGAVVDVQFDHDLPPILNALEVEGRSPRLVLEVAQHLGENTVRTIAMDGTEGLV 113
GRV AV G +++V+ + + + R R VL + V + + EG+
Sbjct: 1 GRVTAVTGLLIEVRGLSRAVRLGDRCAIRARDGRPVLAEVVGFNGDRVLLMPFEPLEGVG 60
Query: 114 RGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPI-DTDKSAAIHADAPEFVEMSVE 172
G V P+ + LGR+IN +GEPID +GP+ ++ + A P + +
Sbjct: 61 LGCAVFAREGPLAVRPHPSWLGRVINALGEPIDGKGPLPQGERRYPLRASPPPAMSRARV 120
Query: 173 QEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGER 232
E L TG++V+D P +G ++G+F G+GVGK+ L+ L N V A VGER
Sbjct: 121 GEPLDTGVRVIDTFLPLCRGQRLGIFAGSGVGKSTLLSMLARN---TDADVVVIALVGER 177
Query: 233 TREGND-LYHEMIESG------VISLKDKS 255
RE + L ++ E G V++ D+S
Sbjct: 178 GREVREFLEDDLGEEGLKRSVVVVATSDES 207
>gnl|CDD|213817 TIGR03496, FliI_clade1, flagellar protein export ATPase FliI.
Members of this protein family are the FliI protein of
bacterial flagellum systems. This protein acts to drive
protein export for flagellar biosynthesis. The most
closely related family is the YscN family of bacterial
type III secretion systems. This model represents one
(of three) segment of the FliI family tree. These have
been modeled separately in order to exclude the type III
secretion ATPases more effectively [Cellular processes,
Chemotaxis and motility].
Length = 411
Score = 89.5 bits (223), Expect = 2e-20
Identities = 42/136 (30%), Positives = 74/136 (54%), Gaps = 5/136 (3%)
Query: 102 RTIAM--DGTEGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAI 159
R + M + EGL G V P+++PVG LGR+I+ +G P+D +GP+D + +
Sbjct: 45 RVLLMPLEDVEGLRPGARVFPLEGPLRLPVGDSLLGRVIDGLGRPLDGKGPLDAGERVPL 104
Query: 160 HADAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKA 219
+A ++ + E L G++ ++ L +G ++G+F G+GVGK+ L + ++ +A
Sbjct: 105 YAPPINPLKRAPIDEPLDVGVRAINGLLTVGRGQRMGIFAGSGVGKSTL-LGMMARYTEA 163
Query: 220 HGGYSVFAGVGERTRE 235
V +GER RE
Sbjct: 164 D--VVVVGLIGERGRE 177
>gnl|CDD|211826 TIGR03497, FliI_clade2, flagellar protein export ATPase FliI.
Members of this protein family are the FliI protein of
bacterial flagellum systems. This protein acts to drive
protein export for flagellar biosynthesis. The most
closely related family is the YscN family of bacterial
type III secretion systems. This model represents one
(of three) segment of the FliI family tree. These have
been modeled separately in order to exclude the type III
secretion ATPases more effectively [Cellular processes,
Chemotaxis and motility].
Length = 413
Score = 88.5 bits (220), Expect = 4e-20
Identities = 48/130 (36%), Positives = 74/130 (56%), Gaps = 3/130 (2%)
Query: 109 TEGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVE 168
EG+ G +V +G P+ I VG LGR+++ +G P+D GPI ++ + P ++
Sbjct: 54 VEGIGPGSLVIATGRPLAIKVGKGLLGRVLDGLGRPLDGEGPIIGEEPYPLDNPPPNPLK 113
Query: 169 MSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAG 228
++ L TGIK +D L KG ++G+F G+GVGK+ L + +I AKA +V A
Sbjct: 114 RPRIRDPLETGIKAIDGLLTIGKGQRVGIFAGSGVGKSTL-LGMIARNAKA--DINVIAL 170
Query: 229 VGERTREGND 238
+GER RE D
Sbjct: 171 IGERGREVRD 180
>gnl|CDD|233211 TIGR00962, atpA, proton translocating ATP synthase, F1 alpha
subunit. The sequences of ATP synthase F1 alpha and
beta subunits are related and both contain a
nucleotide-binding site for ATP and ADP. They have a
common amino terminal domain but vary at the C-terminus.
The beta chain has catalytic activity, while the alpha
chain is a regulatory subunit. The alpha-subunit
contains a highly conserved adenine-specific
noncatalytic nucleotide-binding domain. The conserved
amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton
translocating ATP synthase F1, alpha subunit is
homologous to proton translocating ATP synthase
archaeal/vacuolar(V1), B subunit [Energy metabolism,
ATP-proton motive force interconversion].
Length = 501
Score = 86.7 bits (215), Expect = 2e-19
Identities = 47/144 (32%), Positives = 79/144 (54%), Gaps = 1/144 (0%)
Query: 89 VLEVAQHLGENTVRTIAMDGTEGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDER 148
V +A +L E++V + M + G V +G +++PVG LGR++N +GEPID +
Sbjct: 58 VQGIALNLEEDSVGAVIMGDYSDIREGSTVKRTGRILEVPVGDGLLGRVVNALGEPIDGK 117
Query: 149 GPIDTDKSAAIHADAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVL 208
GPID+D+ + + AP +E E L TGIK +D + P +G + + G GKT +
Sbjct: 118 GPIDSDEFSPVEKIAPGVIERKSVHEPLQTGIKAIDAMIPIGRGQRELIIGDRQTGKTAV 177
Query: 209 IMELINNVAKAHGGYSVFAGVGER 232
++ I N K Y ++ +G++
Sbjct: 178 AIDTIIN-QKDSDVYCIYVAIGQK 200
>gnl|CDD|183987 PRK13343, PRK13343, F0F1 ATP synthase subunit alpha; Provisional.
Length = 502
Score = 83.8 bits (208), Expect = 2e-18
Identities = 49/156 (31%), Positives = 75/156 (48%), Gaps = 5/156 (3%)
Query: 78 ALEVEGRSPRLVLEVAQHLGENTVRTIAMDGTEGLVRGQVVADSGNPIKIPVGAETLGRI 137
L EG S A +L E V + +D T ++ G V +G +++PVG LGR+
Sbjct: 52 LLRFEGGS----RGFAFNLEEELVGAVLLDDTADILAGTEVRRTGRVLEVPVGDGLLGRV 107
Query: 138 INVIGEPIDERGPIDTDKSAAIHADAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGL 197
I+ +G P+D GP+ + AP +E E L TGIKVVD L P +G + +
Sbjct: 108 IDPLGRPLDGGGPLQATARRPLERPAPAIIERDFVTEPLQTGIKVVDALIPIGRGQRELI 167
Query: 198 FGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERT 233
G GKT + ++ I N K V+ +G++
Sbjct: 168 IGDRQTGKTAIAIDAIIN-QKDSDVICVYVAIGQKA 202
>gnl|CDD|181439 PRK08472, fliI, flagellum-specific ATP synthase; Validated.
Length = 434
Score = 82.0 bits (203), Expect = 7e-18
Identities = 47/126 (37%), Positives = 67/126 (53%), Gaps = 3/126 (2%)
Query: 110 EGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVEM 169
EG G V S + IPVG LGR+++ +G PID +G ID ++ A I ++
Sbjct: 75 EGFKIGDKVFISKEGLNIPVGRNLLGRVVDPLGRPIDGKGAIDYERYAPIMKAPIAAMKR 134
Query: 170 SVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGV 229
+ E+ G+K +D L KG K+G+F G+GVGK+ L M +I A V A +
Sbjct: 135 GLIDEVFSVGVKSIDGLLTCGKGQKLGIFAGSGVGKSTL-MGMIVKGCLAP--IKVVALI 191
Query: 230 GERTRE 235
GER RE
Sbjct: 192 GERGRE 197
>gnl|CDD|238556 cd01136, ATPase_flagellum-secretory_path_III, Flagellum-specific
ATPase/type III secretory pathway virulence-related
protein. This group of ATPases are responsible for the
export of flagellum and virulence-related proteins. The
bacterial flagellar motor is similar to the F0F1-ATPase,
in that they both are proton driven rotary molecular
devices. However, the main function of the bacterial
flagellar motor is to rotate the flagellar filament for
cell motility. Intracellular pathogens such as
Salmonella and Chlamydia also have proteins which are
similar to the flagellar-specific ATPase, but function
in the secretion of virulence-related proteins via the
type III secretory pathway.
Length = 326
Score = 81.2 bits (201), Expect = 8e-18
Identities = 39/112 (34%), Positives = 64/112 (57%), Gaps = 3/112 (2%)
Query: 124 PIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVEMSVEQEILVTGIKVV 183
P+ +PVG LGR+++ GEP+D +GP+ + + P ++ E+L TG++ +
Sbjct: 1 PLSVPVGDALLGRVLDAFGEPLDGKGPLGKEVRYPLLRTPPNPLKRRPIDEVLPTGVRAI 60
Query: 184 DLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTRE 235
D L KG ++G+F G+GVGK+ L + +I A +V A +GER RE
Sbjct: 61 DGLLTVGKGQRLGIFAGSGVGKSTL-LGMIARGTTAD--VNVIALIGERGRE 109
>gnl|CDD|223134 COG0056, AtpA, F0F1-type ATP synthase, alpha subunit [Energy
production and conversion].
Length = 504
Score = 79.2 bits (196), Expect = 9e-17
Identities = 53/183 (28%), Positives = 92/183 (50%), Gaps = 12/183 (6%)
Query: 53 NGRVVAVIGAVVDVQFDHDLPPILN--ALEVEGRSPRLVLEVAQHLGENTVRTIAMDGTE 110
G V++V + V L ++ +E G V +A +L E++V + +
Sbjct: 28 VGTVISVGDGIARV---SGLENVMAGELVEFPGG----VKGMALNLEEDSVGAVILGDYS 80
Query: 111 GLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVE-M 169
+ G V +G +++PVG E LGR+++ +G PID +GPID K+ + AP ++
Sbjct: 81 DIKEGDEVKRTGRILEVPVGEELLGRVVDALGNPIDGKGPIDATKTRPVEKKAPGVMDRK 140
Query: 170 SVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGV 229
SV + L TGIK +D L P +G + + G GKT + ++ I N K G ++ +
Sbjct: 141 SVNEP-LQTGIKAIDALIPIGRGQRELIIGDRQTGKTAIAIDTIIN-QKGSGVKCIYVAI 198
Query: 230 GER 232
G++
Sbjct: 199 GQK 201
>gnl|CDD|217261 pfam02874, ATP-synt_ab_N, ATP synthase alpha/beta family,
beta-barrel domain. This family includes the ATP
synthase alpha and beta subunits the ATP synthase
associated with flagella.
Length = 69
Score = 71.0 bits (175), Expect = 3e-16
Identities = 31/69 (44%), Positives = 40/69 (57%), Gaps = 2/69 (2%)
Query: 56 VVAVIGAVVDVQFDHD-LPPILNALEVEGRS-PRLVLEVAQHLGENTVRTIAMDGTEGLV 113
+V VIG VVDV+F LP + NALEVE +L +LG + VR + M GT+GL
Sbjct: 1 IVQVIGPVVDVEFGIGRLPGLYNALEVELVEFGNGLLGEVLNLGGDKVRVVVMGGTDGLS 60
Query: 114 RGQVVADSG 122
RG V +G
Sbjct: 61 RGDEVKRTG 69
>gnl|CDD|180526 PRK06315, PRK06315, type III secretion system ATPase; Provisional.
Length = 442
Score = 74.9 bits (184), Expect = 2e-15
Identities = 54/151 (35%), Positives = 85/151 (56%), Gaps = 12/151 (7%)
Query: 118 VADSGNPIKIPVGAETLGRIINVIGEPIDE--RGP-IDTDKSAAIHADAPEFVEMSVEQE 174
V +G P+ I G LGR++N +GEPID +GP + D++ I P+ + + +
Sbjct: 87 VIPTGLPLHIRAGNGLLGRVLNGLGEPIDTETKGPLENVDETYPIFRAPPDPLHRAKLRT 146
Query: 175 ILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTR 234
IL TG++ +D + A+G +IG+F GAGVGK+ L+ + N +A +V A +GER R
Sbjct: 147 ILSTGVRCIDGMLTVARGQRIGIFAGAGVGKSSLLGMIARNAEEAD--VNVIALIGERGR 204
Query: 235 E-----GNDLYHEMIESGVI--SLKDKSSKV 258
E DL E ++ VI S D+SS++
Sbjct: 205 EVREFIEGDLGEEGMKRSVIVVSTSDQSSQL 235
>gnl|CDD|236448 PRK09281, PRK09281, F0F1 ATP synthase subunit alpha; Validated.
Length = 502
Score = 73.9 bits (183), Expect = 5e-15
Identities = 36/105 (34%), Positives = 60/105 (57%), Gaps = 2/105 (1%)
Query: 89 VLEVAQHLGENTVRTIAMDGTEGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDER 148
V +A +L E+ V + + E + G V +G +++PVG LGR++N +G+PID +
Sbjct: 59 VYGIALNLEEDNVGAVILGDYEDIKEGDTVKRTGRILEVPVGEALLGRVVNPLGQPIDGK 118
Query: 149 GPIDTDKSAAIHADAPEFVE-MSVEQEILVTGIKVVDLLAPYAKG 192
GPI+ ++ + AP ++ SV E L TGIK +D + P +G
Sbjct: 119 GPIEATETRPVERKAPGVIDRKSVH-EPLQTGIKAIDAMIPIGRG 162
>gnl|CDD|236351 PRK08927, fliI, flagellum-specific ATP synthase; Validated.
Length = 442
Score = 73.5 bits (181), Expect = 6e-15
Identities = 60/188 (31%), Positives = 91/188 (48%), Gaps = 14/188 (7%)
Query: 54 GRVVAVIGAVVDVQFDHDLPPILNALEVEGRSPRLVL-EVAQHLGENTVRTIAM--DGTE 110
GRVVAV G +V+V + + VE R R V EV +G R + M E
Sbjct: 19 GRVVAVRGLLVEVAGPIHALSVGARIVVETRGGRPVPCEV---VGFRGDRALLMPFGPLE 75
Query: 111 GLVRG--QVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSA-AIHADAPEFV 167
G+ RG V+A++ ++ LGR++N +GEPID +GP+ + A P
Sbjct: 76 GVRRGCRAVIANAAAAVR--PSRAWLGRVVNALGEPIDGKGPLPQGPVPYPLRAPPPPAH 133
Query: 168 EMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFA 227
+ E L G++ ++ +G ++G+F G+GVGK+VL+ L N SV
Sbjct: 134 SRARVGEPLDLGVRALNTFLTCCRGQRMGIFAGSGVGKSVLLSMLARNADAD---VSVIG 190
Query: 228 GVGERTRE 235
+GER RE
Sbjct: 191 LIGERGRE 198
>gnl|CDD|235666 PRK06002, fliI, flagellum-specific ATP synthase; Validated.
Length = 450
Score = 72.3 bits (178), Expect = 2e-14
Identities = 55/189 (29%), Positives = 84/189 (44%), Gaps = 37/189 (19%)
Query: 95 HLGENTVRTIAMDGTEGLVRGQVVA-----------DSGNPIKI-----PVGAETL---- 134
LG+ +A+ G G+VV + I + G +
Sbjct: 48 RLGD----FVAIRADGGTHLGEVVRVDPDGVTVKPFEPRIEIGLGDAVFRKGPLRIRPDP 103
Query: 135 ---GRIINVIGEPIDERGPIDT-DKSAAIHADAPEFVEMSVEQEILVTGIKVVDLLAPYA 190
GR+IN +GEPID GP+ + +I A AP + + + L TG++V+D+ P
Sbjct: 104 SWKGRVINALGEPIDGLGPLAPGTRPMSIDATAPPAMTRARVETGLRTGVRVIDIFTPLC 163
Query: 191 KGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSV-FAGVGERTREGNDLYHEMIESGVI 249
G +IG+F G+GVGK+ L+ L A+A +V A VGER RE E +E +
Sbjct: 164 AGQRIGIFAGSGVGKSTLLAML----ARADAFDTVVIALVGERGRE----VREFLEDTLA 215
Query: 250 SLKDKSSKV 258
K+ V
Sbjct: 216 DNLKKAVAV 224
>gnl|CDD|238552 cd01132, F1_ATPase_alpha, F1 ATP synthase alpha, central domain.
The F-ATPase is found in bacterial plasma membranes,
mitochondrial inner membranes and in chloroplast
thylakoid membranes. It has also been found in the
archaea Methanosarcina barkeri. It uses a proton
gradient to drive ATP synthesis and hydrolyzes ATP to
build the proton gradient. The extrinisic membrane
domain, F1, is composed of alpha, beta, gamma, delta and
epsilon subunits with a stoichiometry of 3:3:1:1:1. The
alpha subunit of the F1 ATP synthase can bind
nucleotides, but is non-catalytic.
Length = 274
Score = 70.4 bits (173), Expect = 3e-14
Identities = 35/108 (32%), Positives = 58/108 (53%), Gaps = 1/108 (0%)
Query: 125 IKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVEMSVEQEILVTGIKVVD 184
+PVG LGR+++ +G PID +GPI+T + I + AP + E L TGIK +D
Sbjct: 2 ADVPVGEALLGRVVDALGNPIDGKGPIETKERRPIESKAPGIIPRKSVNEPLQTGIKAID 61
Query: 185 LLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGER 232
+ P +G + + G GKT + ++ I N K Y ++ +G++
Sbjct: 62 AMIPIGRGQRELIIGDRQTGKTAIAIDTIIN-QKGKKVYCIYVAIGQK 108
>gnl|CDD|180712 PRK06820, PRK06820, type III secretion system ATPase; Validated.
Length = 440
Score = 70.6 bits (173), Expect = 6e-14
Identities = 44/129 (34%), Positives = 69/129 (53%), Gaps = 4/129 (3%)
Query: 107 DGTEGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEF 166
++GL GQ V G+ ++ VGA+ GRI++ +G PID GP T + + P
Sbjct: 79 ASSDGLRCGQWVTPLGHMHQVQVGADLAGRILDGLGAPIDG-GPPLTGQWRELDCPPPSP 137
Query: 167 VEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVF 226
+ +++L TGI+ +D + +G +IG+F AGVGK+ L+ L A + V
Sbjct: 138 LTRQPIEQMLTTGIRAIDGILSCGEGQRIGIFAAAGVGKSTLLGML---CADSAADVMVL 194
Query: 227 AGVGERTRE 235
A +GER RE
Sbjct: 195 ALIGERGRE 203
>gnl|CDD|236166 PRK08149, PRK08149, ATP synthase SpaL; Validated.
Length = 428
Score = 70.0 bits (172), Expect = 9e-14
Identities = 50/181 (27%), Positives = 80/181 (44%), Gaps = 16/181 (8%)
Query: 89 VLEVAQHLGENTVRTI--AMDGTEGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPID 146
V+ AQ +G RTI + +GL R V+ +G P+ + VG LG +++ G+ ++
Sbjct: 42 VIARAQVVGFQRERTILSLIGNAQGLSRQVVLKPTGKPLSVWVGEALLGAVLDPTGKIVE 101
Query: 147 ERGPIDTDKSA----AIHADAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAG 202
T I P + E +E L+TG++ +D L G ++G+F AG
Sbjct: 102 RFDAPPTVGPISEERVIDVAPPSYAERRPIREPLITGVRAIDGLLTCGVGQRMGIFASAG 161
Query: 203 VGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESG-------VISLKDKS 255
GKT L+ LI + + V +GER RE + + S V + D S
Sbjct: 162 CGKTSLMNMLIEH---SEADVFVIGLIGERGREVTEFVESLRASSRREKCVLVYATSDFS 218
Query: 256 S 256
S
Sbjct: 219 S 219
>gnl|CDD|181599 PRK08972, fliI, flagellum-specific ATP synthase; Validated.
Length = 444
Score = 69.7 bits (171), Expect = 1e-13
Identities = 46/135 (34%), Positives = 70/135 (51%), Gaps = 5/135 (3%)
Query: 111 GLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVEMS 170
G++ G V G +PVG LGR+I+ +G P+D GPI TD+ A+ H+ +
Sbjct: 81 GVLPGARVTPLGEQSGLPVGMSLLGRVIDGVGNPLDGLGPIYTDQRASRHSPPINPLSRR 140
Query: 171 VEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLI-MELINNVAKAHGGYSVFAGV 229
E L G++ ++ + KG ++GLF G+GVGK+VL+ M A V V
Sbjct: 141 PITEPLDVGVRAINAMLTVGKGQRMGLFAGSGVGKSVLLGMMTRGTTADV----IVVGLV 196
Query: 230 GERTREGNDLYHEMI 244
GER RE + E++
Sbjct: 197 GERGREVKEFIEEIL 211
>gnl|CDD|132367 TIGR03324, alt_F1F0_F1_al, alternate F1F0 ATPase, F1 subunit alpha.
A small number of taxonomically diverse prokaryotic
species, including Methanosarcina barkeri, have what
appears to be a second ATP synthase, in addition to the
normal F1F0 ATPase in bacteria and A1A0 ATPase in
archaea. These enzymes use ion gradients to synthesize
ATP, and in principle may run in either direction. This
model represents the F1 alpha subunit of this apparent
second ATP synthase.
Length = 497
Score = 69.4 bits (170), Expect = 2e-13
Identities = 43/162 (26%), Positives = 75/162 (46%), Gaps = 11/162 (6%)
Query: 54 GRVVAVIGAVVDVQFDHDLPPILNALEVEGRSPRLVLEVAQHLGENTVRTIAMDGTEGLV 113
+A + + V F+ L R P +L +A ++ E+ V + + L
Sbjct: 35 STGIARVHGLPGVGFEELL-----------RFPGGLLGIAFNVDEDEVGVVLLGEYSHLQ 83
Query: 114 RGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVEMSVEQ 173
G V +G + +PVG LGR+++ +G P+D GP+ + I AP ++ +
Sbjct: 84 AGDEVERTGRVMDVPVGDGLLGRVVDPLGRPLDGGGPLASSPRLPIERPAPPIMDRAPVT 143
Query: 174 EILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINN 215
L TG+KV+D L P +G + + G GKT + ++ I N
Sbjct: 144 VPLQTGLKVIDALIPIGRGQRELILGDRQTGKTAIAIDTILN 185
>gnl|CDD|181092 PRK07721, fliI, flagellum-specific ATP synthase; Validated.
Length = 438
Score = 67.4 bits (165), Expect = 7e-13
Identities = 37/121 (30%), Positives = 66/121 (54%), Gaps = 3/121 (2%)
Query: 115 GQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVEMSVEQE 174
G +V +G P+++ VG+ +G++++ +GEP+D + D P ++ +E
Sbjct: 81 GCLVEATGKPLEVKVGSGLIGQVLDALGEPLDGSALPKGLAPVSTDQDPPNPLKRPPIRE 140
Query: 175 ILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTR 234
+ G++ +D L KG ++G+F G+GVGK+ L M +I A +V A +GER R
Sbjct: 141 PMEVGVRAIDSLLTVGKGQRVGIFAGSGVGKSTL-MGMIARNTSAD--LNVIALIGERGR 197
Query: 235 E 235
E
Sbjct: 198 E 198
>gnl|CDD|180762 PRK06936, PRK06936, type III secretion system ATPase; Provisional.
Length = 439
Score = 65.5 bits (160), Expect = 3e-12
Identities = 43/146 (29%), Positives = 77/146 (52%), Gaps = 10/146 (6%)
Query: 118 VADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVEMSVEQEILV 177
V+ +G ++ VG LGR+++ +G+P D P + ++ADAP + + + L
Sbjct: 88 VSPTGTMHQVGVGEHLLGRVLDGLGQPFDGGHPPEPAAWYPVYADAPAPMSRRLIETPLS 147
Query: 178 TGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGN 237
G++V+D L +G ++G+F AG GK+ L+ LI + A +V A +GER RE
Sbjct: 148 LGVRVIDGLLTCGEGQRMGIFAAAGGGKSTLLASLIRS---AEVDVTVLALIGERGREVR 204
Query: 238 D-LYHEMIESG------VISLKDKSS 256
+ + ++ E G V++ D+ S
Sbjct: 205 EFIESDLGEEGLRKAVLVVATSDRPS 230
>gnl|CDD|200071 TIGR01041, ATP_syn_B_arch, ATP synthase archaeal, B subunit.
Archaeal ATP synthase shares extensive sequence
similarity with eukaryotic and prokaryotic V-type
(H+)-ATPases [Energy metabolism, ATP-proton motive force
interconversion].
Length = 458
Score = 62.8 bits (153), Expect = 3e-11
Identities = 46/148 (31%), Positives = 68/148 (45%), Gaps = 6/148 (4%)
Query: 107 DGTEGLVR-GQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPE 165
+GT GL G V +G +K+PV + LGRI+N GEPID I D+ I+
Sbjct: 55 EGTTGLDPTGTKVRFTGETLKLPVSEDMLGRILNGSGEPIDGGPEIVPDERRDINGAPIN 114
Query: 166 FVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYS- 224
+E + TGI +D + +G K+ +F G+G+ L + I A G S
Sbjct: 115 PYAREYPEEFIQTGISAIDGMNTLVRGQKLPIFSGSGLPHNELAAQ-IARQATVRGEESE 173
Query: 225 ---VFAGVGERTREGNDLYHEMIESGVI 249
VFA +G E N + E+G +
Sbjct: 174 FAVVFAAMGITYEEANFFMKDFEETGAL 201
>gnl|CDD|136438 PRK07594, PRK07594, type III secretion system ATPase SsaN;
Validated.
Length = 433
Score = 62.3 bits (151), Expect = 4e-11
Identities = 43/127 (33%), Positives = 61/127 (48%), Gaps = 4/127 (3%)
Query: 109 TEGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVE 168
T GL GQ V ++PVG LGR+I+ G P+D R D P V
Sbjct: 73 TIGLHCGQQVMALRRRHQVPVGEALLGRVIDGFGRPLDGRELPDVCWKDYDAMPPPAMVR 132
Query: 169 MSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAG 228
+ Q L+TGI+ +D +A +G ++G+F GVGK+ L+ L N +V
Sbjct: 133 QPITQP-LMTGIRAIDSVATCGEGQRVGIFSAPGVGKSTLLAMLCN---APDADSNVLVL 188
Query: 229 VGERTRE 235
+GER RE
Sbjct: 189 IGERGRE 195
>gnl|CDD|180696 PRK06793, fliI, flagellum-specific ATP synthase; Validated.
Length = 432
Score = 61.5 bits (149), Expect = 6e-11
Identities = 46/143 (32%), Positives = 70/143 (48%), Gaps = 8/143 (5%)
Query: 109 TEGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVE 168
TE + G V + IP G LG++++ GE ++E + I DAP
Sbjct: 73 TEKVCYGDSVTLIAEDVVIPRGNHLLGKVLSANGEVLNE--EAENIPLQKIKLDAPPIHA 130
Query: 169 MSVEQ--EILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVF 226
E+ ++ TGIK +D + G KIG+F G+GVGK+ L+ + N A +V
Sbjct: 131 FEREEITDVFETGIKSIDSMLTIGIGQKIGIFAGSGVGKSTLLGMIAKN---AKADINVI 187
Query: 227 AGVGERTREGND-LYHEMIESGV 248
+ VGER RE D + E+ E G+
Sbjct: 188 SLVGERGREVKDFIRKELGEEGM 210
>gnl|CDD|235251 PRK04196, PRK04196, V-type ATP synthase subunit B; Provisional.
Length = 460
Score = 59.5 bits (145), Expect = 4e-10
Identities = 45/148 (30%), Positives = 69/148 (46%), Gaps = 6/148 (4%)
Query: 108 GTEGL-VRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEF 166
GT GL ++ V +G P+K+PV + LGRI + +G PID I +K I+
Sbjct: 58 GTTGLDLKDTKVRFTGEPLKLPVSEDMLGRIFDGLGRPIDGGPEIIPEKRLDINGAPINP 117
Query: 167 VEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYS-- 224
V +E + TGI +D L +G K+ +F G+G+ L ++ AK G
Sbjct: 118 VAREYPEEFIQTGISAIDGLNTLVRGQKLPIFSGSGLPHNELAAQIARQ-AKVLGEEENF 176
Query: 225 --VFAGVGERTREGNDLYHEMIESGVIS 250
VFA +G E N + E+G +
Sbjct: 177 AVVFAAMGITFEEANFFMEDFEETGALE 204
>gnl|CDD|224078 COG1156, NtpB, Archaeal/vacuolar-type H+-ATPase subunit B [Energy
production and conversion].
Length = 463
Score = 58.1 bits (141), Expect = 8e-10
Identities = 44/148 (29%), Positives = 64/148 (43%), Gaps = 6/148 (4%)
Query: 108 GTEGL-VRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEF 166
GT GL +G V +G +KIPV + LGRI N G+PID I + I+
Sbjct: 61 GTSGLDTKGTTVRFTGETLKIPVSEDLLGRIFNGSGKPIDGGPEIVPEDRLDINGAPINP 120
Query: 167 VEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYS-- 224
+E + TGI +D + +G K+ +F G+G+ L + I A G
Sbjct: 121 YARIYPEEFIQTGISAIDGMNTLVRGQKLPIFSGSGLPHNELAAQ-IARQATVDGEEEEF 179
Query: 225 --VFAGVGERTREGNDLYHEMIESGVIS 250
VFA +G E E E+G +
Sbjct: 180 AVVFAAMGITHEEALFFMDEFEETGALD 207
>gnl|CDD|102061 PRK05922, PRK05922, type III secretion system ATPase; Validated.
Length = 434
Score = 58.4 bits (141), Expect = 9e-10
Identities = 41/156 (26%), Positives = 71/156 (45%), Gaps = 6/156 (3%)
Query: 84 RSPRLVLEVAQHLGENTVRTIAMDGTEGLVRGQVVADSGNPIKIPVGAETLGRIINVIGE 143
+SP ++ EV T+ +++ + G V P + + LGR+++ G
Sbjct: 50 KSPPILAEVIGFHNRTTL-LMSLSPIHYVALGAEVLPLRRPPSLHLSDHLLGRVLDGFGN 108
Query: 144 PIDERGPIDTDKSAAIHADAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGV 203
P+D + + + + P + QEI TGIK +D KG +IG+F G
Sbjct: 109 PLDGKEQLPKTHLKPLFSSPPSPMSRQPIQEIFPTGIKAIDAFLTLGKGQRIGVFSEPGS 168
Query: 204 GKTVLIMELINNVAK-AHGGYSVFAGVGERTREGND 238
GK+ L++ +AK + +V A +GER RE +
Sbjct: 169 GKS----SLLSTIAKGSKSTINVIALIGERGREVRE 200
>gnl|CDD|180875 PRK07196, fliI, flagellum-specific ATP synthase; Validated.
Length = 434
Score = 58.0 bits (140), Expect = 1e-09
Identities = 37/125 (29%), Positives = 60/125 (48%), Gaps = 3/125 (2%)
Query: 111 GLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVEMS 170
G++ G V S ++ +G LGR+IN +GEP+D +G + ++
Sbjct: 74 GVLGGARVFPSEQDGELLIGDSWLGRVINGLGEPLDGKGQLGGSTPLQQQLPQIHPLQRR 133
Query: 171 VEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVG 230
L G+ ++ L KG ++GL G+GVGK+VL + +I +A V +G
Sbjct: 134 AVDTPLDVGVNAINGLLTIGKGQRVGLMAGSGVGKSVL-LGMITRYTQAD--VVVVGLIG 190
Query: 231 ERTRE 235
ER RE
Sbjct: 191 ERGRE 195
>gnl|CDD|168181 PRK05688, fliI, flagellum-specific ATP synthase; Validated.
Length = 451
Score = 55.9 bits (135), Expect = 5e-09
Identities = 35/126 (27%), Positives = 61/126 (48%), Gaps = 3/126 (2%)
Query: 110 EGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVEM 169
G+ G V + ++P+G LGR+++ G +D +GP+ + + +
Sbjct: 86 AGIAPGARVVPLADTGRLPMGMSMLGRVLDGAGRALDGKGPMKAEDWVPMDGPTINPLNR 145
Query: 170 SVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGV 229
E L GI+ ++ L +G ++GLF G GVGK+VL + ++ +A V +
Sbjct: 146 HPISEPLDVGIRSINGLLTVGRGQRLGLFAGTGVGKSVL-LGMMTRFTEAD--IIVVGLI 202
Query: 230 GERTRE 235
GER RE
Sbjct: 203 GERGRE 208
>gnl|CDD|176999 CHL00059, atpA, ATP synthase CF1 alpha subunit.
Length = 485
Score = 55.0 bits (133), Expect = 1e-08
Identities = 40/141 (28%), Positives = 66/141 (46%), Gaps = 1/141 (0%)
Query: 92 VAQHLGENTVRTIAMDGTEGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPI 151
+A +L N V + M + G V +G +IPV LGR++N + +PID +G I
Sbjct: 41 IALNLESNNVGVVLMGDGLMIQEGSSVKATGKIAQIPVSEAYLGRVVNALAKPIDGKGEI 100
Query: 152 DTDKSAAIHADAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIME 211
+S I + AP + E L TG+ +D + P +G + + G GKT + +
Sbjct: 101 SASESRLIESPAPGIISRRSVYEPLQTGLIAIDSMIPIGRGQRELIIGDRQTGKTAVATD 160
Query: 212 LINNVAKAHGGYSVFAGVGER 232
I N K V+ +G++
Sbjct: 161 TILN-QKGQNVICVYVAIGQK 180
>gnl|CDD|238555 cd01135, V_A-ATPase_B, V/A-type ATP synthase (non-catalytic)
subunit B. These ATPases couple ATP hydrolysis to the
build up of a H+ gradient, but V-type ATPases do not
catalyze the reverse reaction. The Vacuolar (V-type)
ATPase is found in the membranes of vacuoles, the golgi
apparatus and in other coated vesicles in eukaryotes.
Archaea have a protein which is similar in sequence to
V-ATPases, but functions like an F-ATPase (called
A-ATPase). A similar protein is also found in a few
bacteria. This subfamily consists of the non-catalytic
beta subunit.
Length = 276
Score = 53.1 bits (128), Expect = 3e-08
Identities = 35/131 (26%), Positives = 58/131 (44%), Gaps = 5/131 (3%)
Query: 124 PIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVEMSVEQEILVTGIKVV 183
+K+PV + LGRI N G+PID I ++ I+ V +E++ TGI +
Sbjct: 1 TLKVPVSEDMLGRIFNGSGKPIDGGPEILAEEYLDINGPPINPVARIYPEEMIQTGISAI 60
Query: 184 DLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYS----VFAGVGERTREGNDL 239
D + +G KI +F G+G+ L ++ A G VFA +G +
Sbjct: 61 DGMNTLVRGQKIPIFSGSGLPHNELAAQIARQ-AGVVGEEENFAVVFAAMGITMEDARFF 119
Query: 240 YHEMIESGVIS 250
+ E+G +
Sbjct: 120 KDDFEETGALE 130
>gnl|CDD|140212 PTZ00185, PTZ00185, ATPase alpha subunit; Provisional.
Length = 574
Score = 53.5 bits (128), Expect = 4e-08
Identities = 39/143 (27%), Positives = 67/143 (46%), Gaps = 14/143 (9%)
Query: 104 IAMDGTEGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPID------ERGPIDTDKS- 156
I MD + GQ V +G + IPVGA LG+++N +G + R ++++++
Sbjct: 94 ILMDNITEVQSGQKVMATGKLLYIPVGAGVLGKVVNPLGHEVPVGLLTRSRALLESEQTL 153
Query: 157 AAIHADAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINN- 215
+ A AP V S L+TG K VD + P +G + + G GKT + + I N
Sbjct: 154 GKVDAGAPNIVSRSPVNYNLLTGFKAVDTMIPIGRGQRELIVGDRQTGKTSIAVSTIINQ 213
Query: 216 ------VAKAHGGYSVFAGVGER 232
+ + S++ +G+R
Sbjct: 214 VRINQQILSKNAVISIYVSIGQR 236
>gnl|CDD|233244 TIGR01040, V-ATPase_V1_B, V-type (H+)-ATPase V1, B subunit. This
models eukaryotic vacuolar (H+)-ATPase that is
responsible for acidifying cellular compartments. This
enzyme shares extensive sequence similarity with
archaeal ATP synthase [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 466
Score = 52.0 bits (125), Expect = 1e-07
Identities = 34/116 (29%), Positives = 59/116 (50%), Gaps = 5/116 (4%)
Query: 89 VLEVAQHLGENTVRTIAMDGTEGL-VRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDE 147
VLEV+ G V + +GT G+ + +G+ ++ PV + LGR+ N G+PID+
Sbjct: 41 VLEVS---GNKAVVQV-FEGTSGIDAKKTTCEFTGDILRTPVSEDMLGRVFNGSGKPIDK 96
Query: 148 RGPIDTDKSAAIHADAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGV 203
P+ + I+ +E++ TGI +D++ A+G KI +F AG+
Sbjct: 97 GPPVLAEDYLDINGQPINPYARIYPEEMIQTGISAIDVMNSIARGQKIPIFSAAGL 152
>gnl|CDD|181182 PRK07960, fliI, flagellum-specific ATP synthase; Validated.
Length = 455
Score = 51.7 bits (124), Expect = 1e-07
Identities = 38/141 (26%), Positives = 73/141 (51%), Gaps = 12/141 (8%)
Query: 106 MDGTEGLVRGQVV-------ADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAA 158
++ EG++ G V + ++P+G LGR+++ G+P+D DT ++ A
Sbjct: 82 LEEVEGILPGARVYARNISGEGLQSGKQLPLGPALLGRVLDGSGKPLDGLPAPDTGETGA 141
Query: 159 IHADAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAK 218
+ ++ + + +L TG++ ++ L +G ++GLF G+GVGK+V L+ +A+
Sbjct: 142 LITPPFNPLQRTPIEHVLDTGVRAINALLTVGRGQRMGLFAGSGVGKSV----LLGMMAR 197
Query: 219 AHGGYSVFAG-VGERTREGND 238
+ G +GER RE D
Sbjct: 198 YTQADVIVVGLIGERGREVKD 218
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 46.0 bits (109), Expect = 3e-06
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 194 KIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLY 240
I +FG G GKT L ++L N+A GG V+ + E E +
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIAT-KGGKVVYVDIEEEIEELTERL 46
>gnl|CDD|179373 PRK02118, PRK02118, V-type ATP synthase subunit B; Provisional.
Length = 436
Score = 45.0 bits (107), Expect = 2e-05
Identities = 29/95 (30%), Positives = 46/95 (48%), Gaps = 1/95 (1%)
Query: 108 GTEGLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFV 167
GT G+ G V G P+++ LGR N G+PID GP + I + V
Sbjct: 57 GTRGISTGDEVVFLGRPMQVTYSESLLGRRFNGSGKPID-GGPELEGEPIEIGGPSVNPV 115
Query: 168 EMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAG 202
+ V +E++ TGI ++D+ + KI +F +G
Sbjct: 116 KRIVPREMIRTGIPMIDVFNTLVESQKIPIFSVSG 150
>gnl|CDD|224077 COG1155, NtpA, Archaeal/vacuolar-type H+-ATPase subunit A [Energy
production and conversion].
Length = 588
Score = 43.0 bits (102), Expect = 1e-04
Identities = 31/81 (38%), Positives = 39/81 (48%), Gaps = 8/81 (9%)
Query: 173 QEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGER 232
+ LVTG +V+D L P AKGG + G G GKTV L A G ++ G GER
Sbjct: 205 EIPLVTGQRVIDTLFPVAKGGTAAVPGPFGSGKTVSQHTLSKL---ADGDIVIYVGCGER 261
Query: 233 TREGNDLYHEMIESGVISLKD 253
E ++ E E LKD
Sbjct: 262 GNEMTEVLQEFPE-----LKD 277
>gnl|CDD|235248 PRK04192, PRK04192, V-type ATP synthase subunit A; Provisional.
Length = 586
Score = 42.8 bits (102), Expect = 1e-04
Identities = 29/77 (37%), Positives = 38/77 (49%), Gaps = 20/77 (25%)
Query: 174 EILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYS-----VFAG 228
E L+TG +V+D P AKGG + G G GKTV +L AK ++ ++ G
Sbjct: 209 EPLITGQRVIDTFFPVAKGGTAAIPGPFGSGKTVTQHQL----AK----WADADIVIYVG 260
Query: 229 VGERTREGNDLYHEMIE 245
GER GN EM E
Sbjct: 261 CGER---GN----EMTE 270
>gnl|CDD|238554 cd01134, V_A-ATPase_A, V/A-type ATP synthase catalytic subunit A.
These ATPases couple ATP hydrolysis to the build up of a
H+ gradient, but V-type ATPases do not catalyze the
reverse reaction. The Vacuolar (V-type) ATPase is found
in the membranes of vacuoles, the golgi apparatus and in
other coated vesicles in eukaryotes. Archaea have a
protein which is similar in sequence to V-ATPases, but
functions like an F-ATPase (called A-ATPase). A similar
protein is also found in a few bacteria.
Length = 369
Score = 42.2 bits (100), Expect = 1e-04
Identities = 30/77 (38%), Positives = 38/77 (49%), Gaps = 20/77 (25%)
Query: 174 EILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYS-----VFAG 228
E L+TG +V+D L P KGG + G G GKTV+ L +K YS ++ G
Sbjct: 139 EPLLTGQRVLDTLFPVVKGGTAAIPGPFGCGKTVIQQSL----SK----YSNSDIVIYVG 190
Query: 229 VGERTREGNDLYHEMIE 245
GER GN EM E
Sbjct: 191 CGER---GN----EMTE 200
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 38.9 bits (90), Expect = 6e-04
Identities = 14/61 (22%), Positives = 19/61 (31%)
Query: 191 KGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVIS 250
G I + G G GKT L L + GG G + L ++ S
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 251 L 251
Sbjct: 61 G 61
>gnl|CDD|130115 TIGR01043, ATP_syn_A_arch, ATP synthase archaeal, A subunit.
Archaeal ATP synthase shares extensive sequence
similarity with eukaryotic and prokaryotic V-type
(H+)-ATPases [Energy metabolism, ATP-proton motive force
interconversion].
Length = 578
Score = 40.5 bits (95), Expect = 6e-04
Identities = 27/78 (34%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 166 FVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAK-AHGGYS 224
+ E + L+TG +++D P AKGG + G G GKTV +L AK +
Sbjct: 196 YKEKLPPEVPLITGQRILDTFFPIAKGGTAAIPGPFGSGKTVTQHQL----AKWSDADIV 251
Query: 225 VFAGVGERTREGNDLYHE 242
V+ G GER E D+ E
Sbjct: 252 VYIGCGERGNEMTDVLEE 269
>gnl|CDD|184795 PRK14698, PRK14698, V-type ATP synthase subunit A; Provisional.
Length = 1017
Score = 39.2 bits (91), Expect = 0.002
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 4/74 (5%)
Query: 176 LVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTV----LIMELINNVAKAHGGYSVFAGVGE 231
L+TG +V+D P AKGG + G G GK V LI+ + K Y + G G+
Sbjct: 211 LITGQRVIDTFFPQAKGGTAAIPGPFGSGKCVDGDTLILTKEFGLIKIKDLYEILDGKGK 270
Query: 232 RTREGNDLYHEMIE 245
+T EGN+ + E+ E
Sbjct: 271 KTVEGNEEWTELEE 284
>gnl|CDD|233245 TIGR01042, V-ATPase_V1_A, V-type (H+)-ATPase V1, A subunit. This
models eukaryotic vacuolar (H+)-ATPase that is
responsible for acidifying cellular compartments. This
enzyme shares extensive sequence similarity with
archaeal ATP synthase [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 591
Score = 35.5 bits (82), Expect = 0.027
Identities = 27/75 (36%), Positives = 37/75 (49%), Gaps = 20/75 (26%)
Query: 176 LVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYS-----VFAGVG 230
L+TG +V+D L P +GG + G G GKTV ++++ YS V+ G G
Sbjct: 210 LLTGQRVLDALFPCVQGGTTAIPGAFGCGKTV--------ISQSLSKYSNSDAIVYVGCG 261
Query: 231 ERTREGNDLYHEMIE 245
ER GN EM E
Sbjct: 262 ER---GN----EMAE 269
>gnl|CDD|235951 PRK07165, PRK07165, F0F1 ATP synthase subunit alpha; Validated.
Length = 507
Score = 33.8 bits (78), Expect = 0.082
Identities = 30/123 (24%), Positives = 52/123 (42%), Gaps = 6/123 (4%)
Query: 132 ETLGRIINVIGEPIDERGPIDTDKSAAIHADAPEFVE---MSVE--QEILVTGIKVVDLL 186
E G+II++ G I K + + + M+V+ E L TGI +DLL
Sbjct: 78 EYFGKIIDIDGNIIYPEAQNPLSKKFLPNTSSIFNLAHGLMTVKTLNEQLYTGIIAIDLL 137
Query: 187 APYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIES 246
P KG + + G GKT + + I N K ++ +G++ + +Y + E
Sbjct: 138 IPIGKGQRELIIGDRQTGKTHIALNTIIN-QKNTNVKCIYVAIGQKRENLSRIYETLKEH 196
Query: 247 GVI 249
+
Sbjct: 197 DAL 199
>gnl|CDD|234402 TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC,
C-terminal domain. This model describes the C-terminal
domain, or longer subunit, of the Firmicutes type VII
secretion protein EssC. This protein (homologous to EccC
in Actinobacteria) and the WXG100 target proteins are
the only homologous parts of type VII secretion between
Firmicutes and Actinobacteria [Protein fate, Protein and
peptide secretion and trafficking].
Length = 1296
Score = 31.5 bits (72), Expect = 0.45
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 191 KGGKIGLFGGAGVGKTVLIMELINNVAKAH 220
K G + +FG G GK+ + LI ++A+ H
Sbjct: 809 KDGHLAIFGSPGYGKSTFLQTLIMSLARQH 838
>gnl|CDD|237150 PRK12608, PRK12608, transcription termination factor Rho;
Provisional.
Length = 380
Score = 30.8 bits (70), Expect = 0.62
Identities = 28/111 (25%), Positives = 44/111 (39%), Gaps = 8/111 (7%)
Query: 111 GLVRGQVVADSGNPIKIPVGAETLGRIINVIGEPIDE-RGPIDTDKSAAIHADAPEFVEM 169
L G VV P + L R+ +V G ++ D +H +E
Sbjct: 58 NLRTGDVVEGVARPRE---RYRVLVRVDSVNGTDPEKLARRPHFDDLTPLHPRERLRLET 114
Query: 170 SVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAH 220
+ + +VVDL+AP KG + + GKTVL+ ++ VA H
Sbjct: 115 GSDDLSM----RVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQIAAAVAANH 161
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family are
found in a variety of single stranded RNA viruses.
Length = 105
Score = 29.5 bits (67), Expect = 0.63
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 197 LFGGAGVGKTVLIMELINNVAKAHG 221
L+G G GK+ L L + K G
Sbjct: 3 LYGPPGCGKSTLAKYLARALLKHLG 27
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 29.5 bits (66), Expect = 0.96
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 181 KVVDLLAPYAKGGKIGLF--GGAGVGKTVLIMELINNVAKAHGGYS 224
+++D L GG + G +G GKT L+ EL+ + A G
Sbjct: 11 RLLDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCD 56
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 30.1 bits (68), Expect = 1.0
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 178 TGIKVVD--LLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKA 219
TGI +D L +G + + G G GKT+ ++ + A+
Sbjct: 7 TGIPGLDEILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGARE 50
>gnl|CDD|188631 cd00439, Transaldolase, Transaldolase. Transaldolase. Enzymes
found in the non-oxidative branch of the pentose
phosphate pathway, that catalyze the reversible transfer
of a dihydroxyacetone group from fructose-6-phosphate to
erythrose-4-phosphate yielding sedoheptulose-7-phosphate
and glyceraldehyde-3-phosphate. They are members of the
class I aldolases, who are characterized by using a
Schiff-base mechanism for stabilization of the reaction
intermediates.
Length = 252
Score = 30.0 bits (67), Expect = 1.2
Identities = 28/127 (22%), Positives = 46/127 (36%), Gaps = 11/127 (8%)
Query: 19 TLNPALLQGEASKAVAGFTINKHYAAKAAPKGKGNGRVVAVIGAVVDVQFDHDLPPILNA 78
T NP+++Q S + A + GK + PI +
Sbjct: 25 TTNPSIIQAAISTSNAYNDQFR----TLVESGKDIESAYWELVVKDIQDACKLFEPIYDQ 80
Query: 79 LEVEGRSPRLVLEVAQHLGENTVRTIAMDGTEGLVRGQVVADSGNPIKIPVGAETLGRII 138
E +G R+ +EV+ L ++T + +VV IKIP AE + I
Sbjct: 81 TEADG---RVSVEVSARLADDTQGMVE----AAKYLSKVVNRRNIYIKIPATAEGIPAIK 133
Query: 139 NVIGEPI 145
++I I
Sbjct: 134 DLIAAGI 140
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 29.0 bits (66), Expect = 1.4
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 194 KIGLFGGAGVGKTVLIMELINN 215
KI L G +GVGKT L++ ++N
Sbjct: 2 KIVLIGDSGVGKTSLLLRFVDN 23
>gnl|CDD|213264 cd03297, ABC_ModC_molybdenum_transporter, ATP-binding cassette
domain of the molybdenum transport system. ModC is an
ABC-type transporter and the ATPase component of a
molybdate transport system that also includes the
periplasmic binding protein ModA and the membrane
protein ModB. ABC transporters are a large family of
proteins involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides and
more complex organic molecules. The nucleotide binding
domain shows the highest similarity between all members
of the family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 214
Score = 29.6 bits (67), Expect = 1.5
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 190 AKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGV 229
G+FG +G GK+ L+ I + K GG V G
Sbjct: 21 LNEEVTGIFGASGAGKSTLL-RCIAGLEKPDGGTIVLNGT 59
>gnl|CDD|216619 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a
conserved P-loop motif that is involved in binding ATP.
This family is almost exclusively found in
archaebacteria and particularly in Methanococcus
jannaschii that encodes sixteen members of this family.
Length = 223
Score = 29.2 bits (66), Expect = 1.9
Identities = 9/41 (21%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 197 LFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGN 237
++G GKT L+ E + + + G ++ R E
Sbjct: 25 VYGPRRCGKTALLREFLEEL-RELGYRVIYYDPLRREFEEK 64
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 29.3 bits (66), Expect = 2.0
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 181 KVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVF 226
+ L+ + +G + L G GVGKT L + + N + KA G SV
Sbjct: 94 DLASLVEFFERGENLVLLGPPGVGKTHLAIAIGNELLKA--GISVL 137
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 28.8 bits (64), Expect = 2.3
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 194 KIGLFGGAGVGKTVLIMELINN 215
KI + G GVGKT L+ L+ +
Sbjct: 7 KIVVLGDGGVGKTTLLNRLVGD 28
>gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein;
Provisional.
Length = 445
Score = 29.0 bits (65), Expect = 2.4
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 195 IGLFGGAGVGKTVLIMELINNVAKAHG 221
I LFG G GKT L+ ++ + ++ G
Sbjct: 144 IYLFGPEGSGKTHLMQAAVHALRESGG 170
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 160
Score = 28.3 bits (64), Expect = 2.4
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 194 KIGLFGGAGVGKTVLIMELINNV 216
K+ + G GVGK+ L + ++
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGE 23
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 29.3 bits (66), Expect = 2.5
Identities = 10/30 (33%), Positives = 13/30 (43%)
Query: 197 LFGGAGVGKTVLIMELINNVAKAHGGYSVF 226
+ G G GKTVL+ L+ K V
Sbjct: 441 IIGPTGAGKTVLLSFLLAQALKYGNPQIVA 470
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 28.7 bits (65), Expect = 2.7
Identities = 13/28 (46%), Positives = 20/28 (71%), Gaps = 1/28 (3%)
Query: 183 VDLLAPYAKGGK-IGLFGGAGVGKTVLI 209
+D+LA + GGK + L G +GVGK+ L+
Sbjct: 185 LDVLAAWLSGGKTVALLGSSGVGKSTLV 212
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 29.1 bits (66), Expect = 2.8
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 86 PRLVLEVAQHLGENTVRTIAMDGTEG--LVRGQVVADSGNPIKIPVGAETLGRIINV 140
RLV+ + QH+G + G +++GQ + + +PV A T G ++ +
Sbjct: 35 QRLVIPLKQHIGAEGELCVK----VGDRVLKGQPLTQGDGRMSLPVHAPTSGTVVAI 87
>gnl|CDD|238687 cd01393, recA_like, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to DNA
strand exchange. While prokaryotes have a single RecA
protein, eukaryotes have multiple RecA homologs such as
Rad51, DMC1 and Rad55/57. Archaea have the RecA-like
homologs radA and radB.
Length = 226
Score = 28.7 bits (65), Expect = 2.9
Identities = 16/49 (32%), Positives = 20/49 (40%), Gaps = 4/49 (8%)
Query: 178 TGIKVVDLL--APYAKGGKIGLFGGAGVGKTVLIMELINNVAKA--HGG 222
TG K +D L G +FG G GKT L ++L GG
Sbjct: 3 TGSKALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGG 51
>gnl|CDD|221790 pfam12819, Malectin_like, Carbohydrate-binding protein of the ER.
Malectin is a membrane-anchored protein of the
endoplasmic reticulum that recognises and binds
Glc2-N-glycan. The domain is found on a number of plant
receptor kinases.
Length = 335
Score = 28.9 bits (65), Expect = 3.0
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 71 DLPPILNALEV 81
LPP+LNALE+
Sbjct: 322 TLPPLLNALEI 332
>gnl|CDD|188540 TIGR04025, PPOX_FMN_DR2398, PPOX class probable FMN-dependent
enzyme, DR_2398 family. Members of the PPOX family (see
pfam01243) may contain either FMN or F420 as cofactor.
This subfamily consists of proteins mostly from species
that lack the capability to synthesize F420, and
therefore most likely all bind FMN.
Length = 197
Score = 28.2 bits (64), Expect = 3.3
Identities = 14/41 (34%), Positives = 16/41 (39%), Gaps = 11/41 (26%)
Query: 53 NGRVVAVIGAVVDVQFDHDLPPILNALEVEGRSPRLVLEVA 93
NG A I D P +L V G+ PR VL V
Sbjct: 106 NGT--ARI--STD-------PDLLARFAVNGKRPRSVLVVT 135
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 28.3 bits (63), Expect = 3.4
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 194 KIGLFGGAGVGKTVLIMELINN 215
++ G AGVGKT LI + +
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYD 22
>gnl|CDD|176197 cd08235, iditol_2_DH_like, L-iditol 2-dehydrogenase. Putative
L-iditol 2-dehydrogenase based on annotation of some
members in this subgroup. L-iditol 2-dehydrogenase
catalyzes the NAD+-dependent conversion of L-iditol to
L-sorbose in fructose and mannose metabolism. This
enzyme is related to sorbitol dehydrogenase, alcohol
dehydrogenase, and other medium chain
dehydrogenase/reductases. The zinc-dependent alcohol
dehydrogenase (ADH-Zn)-like family of proteins is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. This group is
also called the medium chain dehydrogenases/reductase
family (MDR) to highlight its broad range of activities
and to distinguish from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal GroES-like catalytic
domain. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. Active site zinc has a catalytic
role, while structural zinc aids in stability. ADH-like
proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
generally have 2 tightly bound zinc atoms per subunit.
The active site zinc is coordinated by a histidine, two
cysteines, and a water molecule. The second zinc seems
to play a structural role, affects subunit interactions,
and is typically coordinated by 4 cysteines.
Length = 343
Score = 28.3 bits (64), Expect = 3.8
Identities = 23/66 (34%), Positives = 28/66 (42%), Gaps = 9/66 (13%)
Query: 190 AKGGKIGLFGGAGVGKTVLI-MELI-NNVAKAHGGYSVFAGVGERTREGNDLYHEMIESG 247
KGG+I FGG G TV I LI G Y+ + E E+I SG
Sbjct: 256 RKGGRILFFGGLPKGSTVNIDPNLIHYREITITGSYAA-------SPEDYKEALELIASG 308
Query: 248 VISLKD 253
I +KD
Sbjct: 309 KIDVKD 314
>gnl|CDD|233649 TIGR01945, rnfC, electron transport complex, RnfABCDGE type, C
subunit. The six subunit complex RnfABCDGE in
Rhodobacter capsulatus encodes an apparent NADH
oxidoreductase responsible for electron transport to
nitrogenase, necessary for nitrogen fixation. A closely
related complex in E. coli, RsxABCDGE (Reducer of SoxR),
reduces the 2Fe-2S-containing superoxide sensor SoxR,
active as a transcription factor when oxidized. This
family of putative NADH oxidoreductase complexes exists
in many of the same species as the related NQR, a
Na(+)-translocating NADH-quinone reductase, but is
distinct. This model describes the C subunit [Energy
metabolism, Electron transport].
Length = 435
Score = 28.5 bits (64), Expect = 3.9
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 87 RLVLEVAQHLGENTVRTIAMDGTEGLVRGQVVADSGNPIKIPVGAETLGRIINV 140
L++ ++QH+G I G + L GQ +A + + P+ A T G ++ +
Sbjct: 30 ELIVPLSQHIG-APAEPIVKVGDKVLK-GQKIAKADGFVSAPIHAPTSGTVVAI 81
>gnl|CDD|206746 cd01849, YlqF_related_GTPase, Circularly permuted YlqF-related
GTPases. These proteins are found in bacteria,
eukaryotes, and archaea. They all exhibit a circular
permutation of the GTPase signature motifs so that the
order of the conserved G box motifs is G4-G5-G1-G2-G3,
with G4 and G5 being permuted from the C-terminal region
of proteins in the Ras superfamily to the N-terminus of
YlqF-related GTPases.
Length = 146
Score = 27.7 bits (62), Expect = 4.2
Identities = 14/47 (29%), Positives = 19/47 (40%)
Query: 172 EQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAK 218
L I L Y KG ++G+ G VGK+ I L+N
Sbjct: 71 GILKLKAEITKQKLKLKYKKGIRVGVVGLPNVGKSSFINALLNKFKL 117
>gnl|CDD|180690 PRK06777, PRK06777, 4-aminobutyrate aminotransferase; Provisional.
Length = 421
Score = 28.2 bits (63), Expect = 4.2
Identities = 28/88 (31%), Positives = 36/88 (40%), Gaps = 12/88 (13%)
Query: 141 IGEPIDERGPIDTDKSAAIHADAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGG 200
+ E I+ PID A E VE +V+ TG + G I FGG
Sbjct: 88 LAERINALAPIDGPAKTAFFTTGAEAVENAVKIARAYTG-----------RPGVIA-FGG 135
Query: 201 AGVGKTVLIMELINNVAKAHGGYSVFAG 228
A G+T+L M L VA G+ F G
Sbjct: 136 AFHGRTLLTMALTGKVAPYKVGFGPFPG 163
>gnl|CDD|236466 PRK09325, PRK09325, coenzyme F420-reducing hydrogenase subunit
beta; Validated.
Length = 282
Score = 28.0 bits (63), Expect = 4.6
Identities = 6/22 (27%), Positives = 17/22 (77%)
Query: 232 RTREGNDLYHEMIESGVISLKD 253
RT++G +++++ +E+G++ K
Sbjct: 223 RTKKGEEIFNKAVEAGLLETKP 244
>gnl|CDD|236729 PRK10636, PRK10636, putative ABC transporter ATP-binding protein;
Provisional.
Length = 638
Score = 28.2 bits (63), Expect = 4.7
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 192 GGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGV 229
G +IGL G G GK+ LI L +A G + G+
Sbjct: 338 GSRIGLLGRNGAGKSTLIKLLAGELAPVSGEIGLAKGI 375
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 28.3 bits (64), Expect = 4.7
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 178 TGIKVVDLLAP--YAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVF 226
TGI+ D + KG + G AG GKT+ ++ + N K VF
Sbjct: 15 TGIEGFDDITHGGLPKGRPTLVSGTAGTGKTLFALQFLVNGIKRFDEPGVF 65
>gnl|CDD|224080 COG1158, Rho, Transcription termination factor [Transcription].
Length = 422
Score = 28.4 bits (64), Expect = 4.8
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 168 EMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAH 220
E L T +V+DL++P KG + + GKT L+ + N + H
Sbjct: 151 ERENGSTDLST--RVIDLISPIGKGQRGLIVAPPKAGKTTLLQNIANAITTNH 201
>gnl|CDD|238548 cd01128, rho_factor, Transcription termination factor rho is a
bacterial ATP-dependent RNA/DNA helicase. It is a
homohexamer. Each monomer consists of an N-terminal
domain of the OB fold, which is responsible for binding
to cysteine rich nucleotides. This alignment is of the
C-terminal ATP binding domain.
Length = 249
Score = 28.1 bits (63), Expect = 4.8
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 181 KVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAH 220
+VVDL AP KG + + GKT L+ + N + K H
Sbjct: 5 RVVDLFAPIGKGQRGLIVAPPKAGKTTLLQSIANAITKNH 44
>gnl|CDD|223544 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 27.6 bits (62), Expect = 5.8
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 3/51 (5%)
Query: 178 TGIKVVDLLAP--YAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVF 226
TG +D +G ++G GKT L ++L+ N K GG + F
Sbjct: 44 TGSLALDEALGGGLPRGRITEIYGPESSGKTTLALQLVANAQKP-GGKAAF 93
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA ternary
complex to the ribosomal A site by facilitated release
of the deacylated tRNA from the E site. The reaction
requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 27.0 bits (61), Expect = 5.9
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 191 KGGKIGLFGGAGVGKTVLIMELINNVAKAHGG 222
G +IGL G G GK+ L ++LI + G
Sbjct: 25 PGDRIGLVGRNGAGKSTL-LKLIAGELEPDEG 55
>gnl|CDD|237309 PRK13211, PRK13211, N-acetylglucosamine-binding protein A;
Reviewed.
Length = 478
Score = 27.7 bits (62), Expect = 6.6
Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 16/73 (21%)
Query: 26 QGEA---SKAVAGFTINKHYAAKAAPKGKGNGRVVAVIGA------------VVDVQFDH 70
QG+ S A+A IN+ A + +G++ V G V++ +D
Sbjct: 246 QGKKNNWSHALAS-KINQEQQQLRAGQLNADGQIEPVYGKNPIYLKAGSGLERVEIGYDI 304
Query: 71 DLPPILNALEVEG 83
+ P LEV G
Sbjct: 305 EAPAPDYELEVSG 317
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 27.1 bits (60), Expect = 6.6
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 197 LFGGAGVGKTVLIMELINNVAKAHGGYSVFA 227
L+G G GKT L + N + + G
Sbjct: 24 LYGPPGTGKTTLARAIANELFRP--GAPFLY 52
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 27.3 bits (61), Expect = 7.0
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 194 KIGLFGGAGVGKTVLIMELI 213
+I L G GVGK+ LIM L+
Sbjct: 4 RIVLIGDEGVGKSSLIMSLV 23
>gnl|CDD|100094 cd05801, PGM_like3, This bacterial PGM-like
(phosphoglucomutase-like) protein of unknown function
belongs to the alpha-D-phosphohexomutase superfamily.
The alpha-D-phosphohexomutases include several related
enzymes that catalyze a reversible intramolecular
phosphoryl transfer on their sugar substrates. Other
members of this superfamily include phosphoglucosamine
mutase (PNGM), phosphoacetylglucosamine mutase (PAGM),
the bacterial phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 522
Score = 27.6 bits (62), Expect = 7.1
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 199 GGAGVGKTVLIMELINNVAKAHG 221
AGVGKT++ +I+ VA A G
Sbjct: 324 KSAGVGKTLVSSSMIDRVAAALG 346
>gnl|CDD|237182 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 559
Score = 27.6 bits (61), Expect = 7.4
Identities = 14/33 (42%), Positives = 16/33 (48%)
Query: 188 PYAKGGKIGLFGGAGVGKTVLIMELINNVAKAH 220
P +GG I L G G GKT I +L A H
Sbjct: 346 PLERGGVIALVGPTGAGKTTTIAKLAQRFAAQH 378
>gnl|CDD|233193 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
VirB4 family. Type IV secretion systems are found in
Gram-negative pathogens. They export proteins, DNA, or
complexes in different systems and are related to
plasmid conjugation systems. This model represents
related ATPases that include VirB4 in Agrobacterium
tumefaciens (DNA export) CagE in Helicobacter pylori
(protein export) and plasmid TraB (conjugation).
Length = 785
Score = 27.7 bits (62), Expect = 8.2
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 197 LFGGAGVGKTVLIMELINNVAKAHGGYSVFA 227
+FG G GKT L+ L+ + K GG ++FA
Sbjct: 439 IFGPTGSGKTTLLNFLLAQMQKY-GGMTIFA 468
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 27.1 bits (60), Expect = 8.2
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 194 KIGLFGGAGVGKTVLIMELINN 215
K+ + GG GVGK+ L ++ I N
Sbjct: 7 KLVVVGGGGVGKSALTIQFIQN 28
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 26.1 bits (57), Expect = 9.6
Identities = 11/62 (17%), Positives = 25/62 (40%), Gaps = 10/62 (16%)
Query: 194 KIGLFGGAGVGKTVLIMEL----------INNVAKAHGGYSVFAGVGERTREGNDLYHEM 243
I + G G GK+ L +L ++++ + G + G + +L E+
Sbjct: 1 IILITGPPGSGKSTLAKKLAEKLGIPVISLDDLLREEGLAELDDGELDDIDIDLELLEEI 60
Query: 244 IE 245
++
Sbjct: 61 LD 62
>gnl|CDD|220739 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling protein
DNA-binding domain. The plasmid conjugative coupling
protein TrwB forms hexamers from six structurally very
similar protomers. This hexamer contains a central
channel running from the cytosolic pole (made up by the
AADs) to the membrane pole ending at the transmembrane
pore shaped by 12 transmembrane helices, rendering an
overall mushroom-like structure. The TrwB_AAD (all-alpha
domain) domain appears to be the DNA-binding domain of
the structure. TrwB, a basic integral inner-membrane
nucleoside-triphosphate-binding protein, is the
structural prototype for the type IV secretion system
coupling proteins, a family of proteins essential for
macromolecular transport between cells and export.
Length = 386
Score = 27.2 bits (61), Expect = 10.0
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 195 IGLFGGAGVGKTVLIMELI 213
I + G G GKT + EL+
Sbjct: 18 ILIVGTTGTGKTQALRELL 36
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 0.136 0.381
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,683,853
Number of extensions: 1381718
Number of successful extensions: 1872
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1811
Number of HSP's successfully gapped: 138
Length of query: 266
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 171
Effective length of database: 6,723,972
Effective search space: 1149799212
Effective search space used: 1149799212
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 (26.6 bits)