RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 018809
(350 letters)
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 564 bits (1455), Expect = 0.0
Identities = 213/346 (61%), Positives = 272/346 (78%), Gaps = 3/346 (0%)
Query: 4 KASKSKEAPAERPILGRFSSHLKIGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNE 63
K K ++ +LGR ++LK+GIVGLPNVGKST FN L K +PAENFPFCTI+PN
Sbjct: 1 MPPKKKMEEEKKVLLGRPGNNLKMGIVGLPNVGKSTTFNALCKQQVPAENFPFCTIDPNT 60
Query: 64 ARVNIPDERFEWLCQLFKPKSAVPAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIF 123
ARVN+PDERF+WLC+ FKPKS VPA L+I DIAGLV+GA EG+GLGN+FLSHIRAVDGI+
Sbjct: 61 ARVNVPDERFDWLCKHFKPKSIVPAQLDITDIAGLVKGASEGEGLGNAFLSHIRAVDGIY 120
Query: 124 HVLRAFEDPDIIHVDDSVDPVRDLEVISAELRLKDIEFMERRIEDVEKSMKRSN-DKQLK 182
HV+RAFED DI HV+ +DPVRDLE+IS+EL LKD+EF+E+R++++ K K+ K+ K
Sbjct: 121 HVVRAFEDEDITHVEGEIDPVRDLEIISSELILKDLEFVEKRLDELTKKRKKKKKKKEEK 180
Query: 183 IEHELCQRVKAWLQDGKDVRLGDWKAADIEILNTFQLLTAKPVVYLVNMNEKDYQRKKNK 242
+E ++ ++V WL++GK VR GDW +IEILN +QLLTAKP++YLVNM+EKD+ R+KNK
Sbjct: 181 VELDVLKKVLEWLEEGKPVRDGDWTDKEIEILNEYQLLTAKPMIYLVNMSEKDFIRQKNK 240
Query: 243 FLPKIHAWVQEHGGEQIIPFSCALERNLADMPPDEA-AKYCEENKV-QSALPKIIKTGFS 300
+L KI WV E GG IIP+S E LA++ +E +Y EE + QS L KIIKTG+
Sbjct: 241 WLAKIKEWVGEKGGGPIIPYSAEFEEELAELGSEEERKEYLEEYGIKQSMLDKIIKTGYK 300
Query: 301 AINLIYFFTAGPDEVKCWQIRRQTKAPQAAGTIHTDFERGFICAEV 346
+NLI+FFTAGPDEV+CW I++ TKAPQAAG IH+DFE+GFICAEV
Sbjct: 301 LLNLIHFFTAGPDEVRCWTIQKGTKAPQAAGVIHSDFEKGFICAEV 346
>gnl|CDD|206687 cd01900, YchF, YchF GTPase. YchF is a member of the Obg family,
which includes four other subfamilies of GTPases: Obg,
DRG, Ygr210, and NOG1. Obg is an essential gene that is
involved in DNA replication in C. crescentus and
Streptomyces griseus and is associated with the
ribosome. Several members of the family, including YchF,
possess the TGS domain related to the RNA-binding
proteins. Experimental data and genomic analysis suggest
that YchF may be part of a nucleoprotein complex and may
function as a GTP-dependent translational factor.
Length = 274
Score = 431 bits (1111), Expect = e-153
Identities = 143/276 (51%), Positives = 189/276 (68%), Gaps = 4/276 (1%)
Query: 27 IGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPDERFEWLCQLFKPKSAV 86
IGIVGLPNVGKSTLFN LTK A N+PFCTIEPN V +PDER + L ++ KPK V
Sbjct: 1 IGIVGLPNVGKSTLFNALTKSNAEAANYPFCTIEPNVGIVPVPDERLDKLAEIVKPKKIV 60
Query: 87 PAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRAFEDPDIIHVDDSVDPVRD 146
PA +E DIAGLV+GA +G+GLGN FLSHIR VD I HV+R FED DI HV+ SVDPVRD
Sbjct: 61 PATIEFVDIAGLVKGASKGEGLGNKFLSHIREVDAIAHVVRCFEDDDITHVEGSVDPVRD 120
Query: 147 LEVISAELRLKDIEFMERRIEDVEKSMKRSNDKQLKIEHELCQRVKAWLQDGKDVRLGDW 206
+E+I+ EL L D+E +E+R+E +EK K S DK+ K E EL +++K L++GK R +
Sbjct: 121 IEIINTELILADLETIEKRLERLEKKAK-SGDKEAKEELELLEKIKEHLEEGKPARTLEL 179
Query: 207 KAADIEILNTFQLLTAKPVVYLVNMNEKDYQRKKNKFLPKIHAWVQEHGGEQIIPFSCAL 266
+I+IL + QLLTAKPV+Y+ N++E D R NK L + G ++IP S L
Sbjct: 180 TDEEIKILKSLQLLTAKPVIYVANVSEDDLIRGNNKVL--KVREIAAKEGAEVIPISAKL 237
Query: 267 ERNLADMPPDEAAKYCEENKVQ-SALPKIIKTGFSA 301
E LA++ +EAA++ EE ++ S L K+I+ G+
Sbjct: 238 EAELAELDEEEAAEFLEELGLEESGLDKLIRAGYEL 273
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 427 bits (1102), Expect = e-150
Identities = 154/325 (47%), Positives = 220/325 (67%), Gaps = 4/325 (1%)
Query: 25 LKIGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPDERFEWLCQLFKPKS 84
LK GIVGLPNVGKSTLFN LTK A N+PFCTIEPN V +PD R + L ++ KPK
Sbjct: 3 LKCGIVGLPNVGKSTLFNALTKAGAEAANYPFCTIEPNVGVVPVPDPRLDKLAEIVKPKK 62
Query: 85 AVPAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRAFEDPDIIHVDDSVDPV 144
VPA +E DIAGLV+GA +G+GLGN FL++IR VD I HV+R FED +I HV+ VDP+
Sbjct: 63 IVPATIEFVDIAGLVKGASKGEGLGNQFLANIREVDAIVHVVRCFEDDNITHVEGKVDPI 122
Query: 145 RDLEVISAELRLKDIEFMERRIEDVEKSMKRSNDKQLKIEHELCQRVKAWLQDGKDVRLG 204
RD+E I+ EL L D+E +E+R+E +EK + DK+ K E EL +++ L++GK R
Sbjct: 123 RDIETINTELILADLETVEKRLERLEK-KAKGGDKEAKAELELLEKLLEHLEEGKPARTL 181
Query: 205 DWKAADIEILNTFQLLTAKPVVYLVNMNEKDYQRKKNKFLPKIHAWVQEHGGEQIIPFSC 264
+ + ++L + QLLTAKPV+Y+ N++E D N ++ K+ + G +++
Sbjct: 182 ELTDEEEKLLKSLQLLTAKPVLYVANVDEDDLA-DGNPYVKKVREIAAKE-GAEVVVICA 239
Query: 265 ALERNLADMPPDEAAKYCEENKVQ-SALPKIIKTGFSAINLIYFFTAGPDEVKCWQIRRQ 323
+E +A++ +E A++ EE ++ S L ++I+ G+ + LI +FTAGP EV+ W I++
Sbjct: 240 KIEAEIAELDDEEKAEFLEELGLEESGLDRLIRAGYELLGLITYFTAGPKEVRAWTIKKG 299
Query: 324 TKAPQAAGTIHTDFERGFICAEVVA 348
T APQAAG IHTDFE+GFI AEV++
Sbjct: 300 TTAPQAAGVIHTDFEKGFIRAEVIS 324
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 388 bits (1000), Expect = e-135
Identities = 150/334 (44%), Positives = 206/334 (61%), Gaps = 10/334 (2%)
Query: 24 HLKIGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPDERFEWLCQLFK-P 82
LKIGIVGLPNVGKSTLFN LTK N+PFCTIEPN V +PD R + L ++ K P
Sbjct: 2 SLKIGIVGLPNVGKSTLFNALTKAGAEIANYPFCTIEPNVGVVYVPDCRLDELAEIVKCP 61
Query: 83 KSAVPAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRAFEDPDIIHVDDSVD 142
PA +E DIAGLV+GA +G+GLGN FL +IR VD I HV+R F D DI HV+ VD
Sbjct: 62 PKIRPAPVEFVDIAGLVKGASKGEGLGNKFLDNIREVDAIIHVVRCFGDTDIEHVEGKVD 121
Query: 143 PVRDLEVISAELRLKDIEFMERRIEDVEKSMKRSN--DKQLKIEHELCQRVKAWLQDGKD 200
PV D+E+I+ EL L D+E +E+R E +EK K DK+LK E L +++ L++GK
Sbjct: 122 PVEDIEIINTELILWDLESLEKRWERLEKRAKAGKKLDKELKEELSLLGKLEEHLEEGKP 181
Query: 201 VR---LGDWKAADIEILNTFQLLTAKPVVYLVNMNEKDYQRKKNKFLPKIHAWVQEHGGE 257
R L W D+E L + LLTAKP++Y+ N++E D N+++ ++ +
Sbjct: 182 ARGLDLSKWSEEDLEALASLNLLTAKPMLYVANVSEDDLA-NLNEYVKRLKELAAKE-NA 239
Query: 258 QIIPFSCALERNLADMPPDEAAKYCEENKVQ--SALPKIIKTGFSAINLIYFFTAGPDEV 315
+++P S A+E L ++ E Q S L ++I+ G+ + L +FTAG EV
Sbjct: 240 EVVPVSAAIELELRELADAEEKGEFLIELGQKESGLNELIRAGYGLLGLQTYFTAGVKEV 299
Query: 316 KCWQIRRQTKAPQAAGTIHTDFERGFICAEVVAC 349
+ W I+ +KAP AAG IH DFE+GFI AEV++
Sbjct: 300 RAWTIKDGSKAPDAAGVIHPDFEKGFIRAEVISY 333
>gnl|CDD|129200 TIGR00092, TIGR00092, GTP-binding protein YchF. This predicted
GTP-binding protein is found in a single copy in every
complete bacterial genome, and is found in Eukaryotes. A
more distantly related protein, separated from this
model, is found in the archaea. It is known to bind GTP
and double-stranded nucleic acid. It is suggested to
belong to a nucleoprotein complex and act as a
translation factor [Unknown function, General].
Length = 368
Score = 253 bits (649), Expect = 4e-82
Identities = 130/329 (39%), Positives = 169/329 (51%), Gaps = 8/329 (2%)
Query: 25 LKIGIVGLPNVGKSTLFNTLTKLAI-PAENFPFCTIEPNEARVNIPDERFEWLCQLFKPK 83
L GIVGLPNVGKSTLF T L A N PF TIEPN VN D R + L KP+
Sbjct: 3 LSGGIVGLPNVGKSTLFAATTNLLGNEAANPPFTTIEPNAGVVNPSDPRLDLLAIYIKPE 62
Query: 84 SAVPAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRAFEDPDIIHVDDSVDP 143
P E DIAGLV GA +G+GLGN FL++IR VD I HV+R FED I HV + DP
Sbjct: 63 KVPPTTTEFVDIAGLVGGASKGEGLGNQFLANIREVDIIQHVVRCFEDDIIHHVGNVDDP 122
Query: 144 VRDLEVISAELRLKDIEFMERRIEDVEKSMKRSNDKQLKIEHELCQRVKAWLQDGKDVRL 203
D E+I E LK EF+ + + +S K + + K E L + L +G +
Sbjct: 123 RDDFEIID-EELLKADEFLVEKR--IGRSKKSAEGGKDKKEELLLLEIILPLLNGGQMAR 179
Query: 204 GDWKAADIEILNTFQLLTAKPVVYLVNMNEKDYQRKKNKFLPKIHAWVQEHG-GEQIIPF 262
+ + IL L K + L+ +DY R N I W+ + G+ + F
Sbjct: 180 HVDLSKEELILIKSLNLLTKKPIILIANVSEDYLRNLNNNYLLIVEWIAAYSKGDPKVVF 239
Query: 263 SCALERNLADMPPDEAAKYCEENKVQ--SALPK-IIKTGFSAINLIYFFTAGPDEVKCWQ 319
CALE + DE + + SA II+ + + L +FFT G +EV+ W
Sbjct: 240 VCALEESELSELDDEERQEFLQKLGLTESAGLNIIIRARYKLLLLSFFFTGGKEEVRAWT 299
Query: 320 IRRQTKAPQAAGTIHTDFERGFICAEVVA 348
+ APQAAG IHTDFE GFI AEV++
Sbjct: 300 RKGGWAAPQAAGIIHTDFETGFIAAEVIS 328
>gnl|CDD|133440 cd04867, TGS_YchF_C, TGS_YchF_C: This subfamily represents TGS
domain-containing YchF GTP-binding protein, a
universally conserved GTPase whose function is unknown.
The N-terminal domain of the YchF protein belongs to the
Obg-like family of GTPases, and some members of the
family contain a C-terminal TGS domain. TGS is a small
domain of about 50 amino acid residues with a
predominantly beta-sheet structure. There is no direct
information on the function of the TGS domain, but its
presence in two types of regulatory proteins (the
GTPases and guanosine polyphosphate
phosphohydrolases/synthetases) suggests a ligand (most
likely nucleotide)-binding, regulatory role.
Length = 83
Score = 103 bits (259), Expect = 1e-27
Identities = 34/46 (73%), Positives = 38/46 (82%)
Query: 304 LIYFFTAGPDEVKCWQIRRQTKAPQAAGTIHTDFERGFICAEVVAC 349
LI FFTAGPDEV+ W IR+ TKAPQAAG IHTDFE+GFI AEV+
Sbjct: 1 LISFFTAGPDEVRAWTIRKGTKAPQAAGVIHTDFEKGFIRAEVMKY 46
>gnl|CDD|206686 cd01899, Ygr210, Ygr210 GTPase. Ygr210 is a member of Obg-like
family and present in archaea and fungi. They are
characterized by a distinct glycine-rich motif
immediately following the Walker B motif. The Ygr210 and
YyaF/YchF subfamilies appear to form one major branch of
the Obg-like family. Among eukaryotes, the Ygr210
subfamily is represented only in fungi. These fungal
proteins form a tight cluster with their archaeal
orthologs, which suggests the possibility of horizontal
transfer from archaea to fungi.
Length = 318
Score = 110 bits (276), Expect = 1e-27
Identities = 71/227 (31%), Positives = 105/227 (46%), Gaps = 28/227 (12%)
Query: 27 IGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEA----RVNIPDERFEWLCQLFKP 82
IG+VG PNVGKST FN T + N+PF TI+PN RV P + C P
Sbjct: 1 IGLVGKPNVGKSTFFNAATLADVEIANYPFTTIDPNVGVGYVRVECPCKELGVSC---NP 57
Query: 83 KSA--------VPAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRA--FEDP 132
+ VP +E+ D+AGLV GAHEG+GLGN FL +R D + HV+ A D
Sbjct: 58 RYGKCIDGKRYVP--VELIDVAGLVPGAHEGKGLGNQFLDDLRDADVLIHVVDASGGTDA 115
Query: 133 DIIHVD-DSVDPVRDLEVISAELRL-------KDIEFMERRIEDVEKSMKRSNDKQLKIE 184
+ V+ DP+ D+E + E+ + ++ E + R+ + + + + +QL
Sbjct: 116 EGNGVETGGYDPLEDIEFLENEIDMWIYGILERNWEKIVRKAKAEKTDIVEALSEQLSGF 175
Query: 185 HELCQRVKAWLQDGK-DVRLGDWKAADIEILNTFQLLTAKPVVYLVN 230
V L++ + L W D+ L KP+V N
Sbjct: 176 GVNEDVVIEALEELELPADLSKWDDEDLLRLARELRKRRKPMVIAAN 222
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 108 bits (273), Expect = 9e-27
Identities = 76/263 (28%), Positives = 118/263 (44%), Gaps = 57/263 (21%)
Query: 25 LKIGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNE----ARVNIPDERFEWLCQLF 80
+ IG+VG PNVGKST FN T + N+PF TI+PN RV P + C
Sbjct: 2 ITIGLVGKPNVGKSTFFNAATLADVEIANYPFTTIDPNVGVAYVRVECPCKELGVKCN-- 59
Query: 81 KPKSA--------VPAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRAF--E 130
P++ +P +E+ D+AGLV GAHEG+GLGN FL +R D + HV+ A
Sbjct: 60 -PRNGKCIDGTRFIP--VELIDVAGLVPGAHEGRGLGNQFLDDLRQADALIHVVDASGST 116
Query: 131 DPDIIHVD-DSVDPVRDLEVISAELRLKDIEFMERRIE---------DVEKSMKRSNDKQ 180
D + V+ S DPV +DI+F+E ++ + EK +++ ++
Sbjct: 117 DEEGNPVEPGSHDPV------------EDIKFLEEELDMWIYGILEKNWEKFSRKAQAEK 164
Query: 181 LKIEHELCQRV-----------KAWLQDGKDVRLGDWKAADIEILNTFQLLTAKPVVYLV 229
IE L +++ +A + G W D+ L +KP+V
Sbjct: 165 FDIEEALAEQLSGLGINEEHVKEALRELGLPEDPSKWTDEDLLELARELRKISKPMVIAA 224
Query: 230 NM-----NEKDYQRKKNKFLPKI 247
N E++ +R K + +
Sbjct: 225 NKADLPPAEENIERLKEEKYYIV 247
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 100 bits (252), Expect = 9e-26
Identities = 50/140 (35%), Positives = 67/140 (47%), Gaps = 28/140 (20%)
Query: 28 GIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPDERFEWLCQLFKPKSAVP 87
G+VGLPNVGKSTL + LT + ++PF T+EPN D
Sbjct: 1 GLVGLPNVGKSTLLSALTSAKVEIASYPFTTLEPNVGVFEFGD----------------G 44
Query: 88 AFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRAFEDPDIIHVDDSVDPVRDL 147
++I D+ GL+ GA EG+GLG L+H+ D I HV+ A E D DP+ D
Sbjct: 45 VDIQIIDLPGLLDGASEGRGLGEQILAHLYRSDLILHVIDASE-------DCVGDPLEDQ 97
Query: 148 -----EVISAELRLKDIEFM 162
EV + L LK+ M
Sbjct: 98 KTLNEEVSGSFLFLKNKPEM 117
>gnl|CDD|203386 pfam06071, YchF-GTPase_C, Protein of unknown function (DUF933).
This domain is found at the C terminus of the YchF
GTP-binding protein and is possibly related to the
ubiquitin-like and MoaD/ThiS superfamilies.
Length = 84
Score = 95.7 bits (239), Expect = 8e-25
Identities = 31/46 (67%), Positives = 37/46 (80%)
Query: 304 LIYFFTAGPDEVKCWQIRRQTKAPQAAGTIHTDFERGFICAEVVAC 349
LI FFTAGP EV+ W IR+ T APQAAG IH+DFE+GFI AEV++
Sbjct: 1 LITFFTAGPKEVRAWTIRKGTTAPQAAGVIHSDFEKGFIRAEVISY 46
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 93.3 bits (233), Expect = 2e-21
Identities = 53/144 (36%), Positives = 72/144 (50%), Gaps = 31/144 (21%)
Query: 27 IGIVGLPNVGKSTLFNTLT----KLAIPAENFPFCTIEPNEARVNIPDERFEWLCQLFKP 82
+G+VGLPN GKSTL + ++ K+A ++PF T+ PN V + D R
Sbjct: 160 VGLVGLPNAGKSTLISAVSAAKPKIA----DYPFTTLVPNLGVVRVDDGR---------- 205
Query: 83 KSAVPAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRAFEDPDIIHVDDSVD 142
S V A DI GL+ GA EG GLG+ FL HI + H++ DI D S D
Sbjct: 206 -SFVIA-----DIPGLIEGASEGAGLGHRFLKHIERTRVLLHLI------DISPEDGS-D 252
Query: 143 PVRDLEVISAELRLKDIEFMERRI 166
P+ D E+I EL+ E E+
Sbjct: 253 PIEDYEIIRNELKKYSPELAEKPR 276
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 89.0 bits (222), Expect = 2e-21
Identities = 51/142 (35%), Positives = 69/142 (48%), Gaps = 33/142 (23%)
Query: 27 IGIVGLPNVGKSTLFNTLT----KLAIPAENFPFCTIEPNEARVNIPDERFEWLCQLFKP 82
+G+VGLPN GKSTL + ++ K+A ++PF T+ PN V + D R
Sbjct: 3 VGLVGLPNAGKSTLLSAISNAKPKIA----DYPFTTLVPNLGVVRVDDGR---------- 48
Query: 83 KSAVPAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRAFEDPDIIHVDDSVD 142
S V A DI GL+ GA EG+GLG+ FL HI + HV+ D+ D
Sbjct: 49 -SFVIA-----DIPGLIEGASEGKGLGHRFLRHIERTRVLLHVI------DL---SGEDD 93
Query: 143 PVRDLEVISAELRLKDIEFMER 164
PV D E I EL + E+
Sbjct: 94 PVEDYETIRNELEAYNPGLAEK 115
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 91.1 bits (227), Expect = 1e-20
Identities = 48/142 (33%), Positives = 68/142 (47%), Gaps = 31/142 (21%)
Query: 27 IGIVGLPNVGKSTLFNTLT----KLAIPAENFPFCTIEPNEARVNIPDERFEWLCQLFKP 82
+G+VGLPN GKSTL + ++ K+A ++PF T+ PN V +
Sbjct: 162 VGLVGLPNAGKSTLLSAVSAAKPKIA----DYPFTTLVPNLGVVRVDGG----------- 206
Query: 83 KSAVPAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRAFEDPDIIHVDDSVD 142
+S V A DI GL+ GA EG GLG FL HI + HV+ D+ +D D
Sbjct: 207 ESFVVA-----DIPGLIEGASEGVGLGLRFLRHIERTRVLLHVI------DLSPIDGR-D 254
Query: 143 PVRDLEVISAELRLKDIEFMER 164
P+ D + I EL + E+
Sbjct: 255 PIEDYQTIRNELEKYSPKLAEK 276
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 88.6 bits (221), Expect = 7e-20
Identities = 51/145 (35%), Positives = 71/145 (48%), Gaps = 40/145 (27%)
Query: 27 IGIVGLPNVGKSTLFNTLT----KLAIPAENFPFCTIEPNEARVNIPDERFEWLCQLFKP 82
+G+VGLPN GKSTL + ++ K+A ++PF T+ PN V + D +
Sbjct: 161 VGLVGLPNAGKSTLISAVSAAKPKIA----DYPFTTLHPNLGVVRVDDYK---------- 206
Query: 83 KSAVPAFLEIHDIAGLVRGAHEGQGLGNSFLSHI-RAVDGIFHVLRAFEDPDIIHVDD-- 139
S V A DI GL+ GA EG GLG+ FL HI R +L +H+ D
Sbjct: 207 -SFVIA-----DIPGLIEGASEGAGLGHRFLKHIERT-----RLL--------LHLVDIE 247
Query: 140 SVDPVRDLEVISAELRLKDIEFMER 164
+VDPV D + I EL E ++
Sbjct: 248 AVDPVEDYKTIRNELEKYSPELADK 272
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 82.3 bits (204), Expect = 2e-19
Identities = 37/112 (33%), Positives = 53/112 (47%), Gaps = 23/112 (20%)
Query: 26 KIGIVGLPNVGKSTLFNTLT--KLAIPAENFPFCTIEPNEARVNIPDERFEWLCQLFKPK 83
++ +VG PNVGKSTL N LT K+AI ++P T +P + + +
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAI-VSDYPGTTRDPILGVLGLGRQ------------ 47
Query: 84 SAVPAFLEIHDIAGLVRGAHEGQGLG--NSFLSHIRAVDGIFHVLRAFEDPD 133
+ + D GL+ GA EG+G+ N FL IR D I V+ A E
Sbjct: 48 ------IILVDTPGLIEGASEGKGVEGFNRFLEAIREADLILLVVDASEGLT 93
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 87.5 bits (218), Expect = 4e-19
Identities = 56/151 (37%), Positives = 74/151 (49%), Gaps = 41/151 (27%)
Query: 25 LKI----GIVGLPNVGKSTLFNTLT----KLAIPAENFPFCTIEPNEARVNIPDERFEWL 76
LK+ G+VG PNVGKSTL + ++ K+A N+ F T+ PN V D R
Sbjct: 155 LKLLADVGLVGFPNVGKSTLLSVVSNAKPKIA----NYHFTTLVPNLGVVETDDGR---- 206
Query: 77 CQLFKPKSAVPAFLEIHDIAGLVRGAHEGQGLGNSFLSHI---RAVDGIFHVLRAFEDPD 133
S V A DI GL+ GA EG GLG+ FL HI R I HV+ D
Sbjct: 207 -------SFVMA-----DIPGLIEGASEGVGLGHQFLRHIERTRV---IVHVI------D 245
Query: 134 IIHVDDSVDPVRDLEVISAELRLKDIEFMER 164
+ + DP+ D E I+ EL+L + +ER
Sbjct: 246 MSGSEGR-DPIEDYEKINKELKLYNPRLLER 275
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 79.9 bits (198), Expect = 1e-16
Identities = 48/133 (36%), Positives = 66/133 (49%), Gaps = 31/133 (23%)
Query: 27 IGIVGLPNVGKSTLFNTLT----KLAIPAENFPFCTIEPNEARVNIPDERFEWLCQLFKP 82
+G++GLPN GKST ++ K+A ++PF T+ PN V + DER
Sbjct: 162 VGLLGLPNAGKSTFIRAVSAAKPKVA----DYPFTTLVPNLGVVRVDDER---------- 207
Query: 83 KSAVPAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRAFEDPDIIHVDDSVD 142
S V A DI GL+ GA EG GLG FL H+ + H++ DI +D S D
Sbjct: 208 -SFVVA-----DIPGLIEGASEGAGLGIRFLKHLERCRVLLHLI------DIAPIDGS-D 254
Query: 143 PVRDLEVISAELR 155
PV + +I EL
Sbjct: 255 PVENARIIINELE 267
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 73.0 bits (180), Expect = 4e-14
Identities = 44/134 (32%), Positives = 65/134 (48%), Gaps = 33/134 (24%)
Query: 27 IGIVGLPNVGKSTLFNTLT----KLAIPAENFPFCTIEPNEARVNIPDERFEWLCQLFKP 82
+G+VG P+ GKS+L + L+ K+A ++PF T+ PN V D RF
Sbjct: 162 VGLVGFPSAGKSSLISALSAAKPKIA----DYPFTTLVPNLGVVQAGDTRFT-------- 209
Query: 83 KSAVPAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLR-AFEDPDIIHVDDSV 141
+ D+ GL+ GA EG+GLG FL HI + HV+ A +P
Sbjct: 210 ---------VADVPGLIPGASEGKGLGLDFLRHIERCAVLVHVVDCATLEPG-------R 253
Query: 142 DPVRDLEVISAELR 155
DP+ D++ + AEL
Sbjct: 254 DPLSDIDALEAELA 267
>gnl|CDD|206683 cd01896, DRG, Developmentally Regulated GTP-binding protein (DRG).
The developmentally regulated GTP-binding protein (DRG)
subfamily is an uncharacterized member of the Obg
family, an evolutionary branch of GTPase superfamily
proteins. GTPases act as molecular switches regulating
diverse cellular processes. DRG2 and DRG1 comprise the
DRG subfamily in eukaryotes. In view of their widespread
expression in various tissues and high conservation
among distantly related species in eukaryotes and
archaea, DRG proteins may regulate fundamental cellular
processes. It is proposed that the DRG subfamily
proteins play their physiological roles through RNA
binding.
Length = 233
Score = 59.9 bits (146), Expect = 2e-10
Identities = 29/114 (25%), Positives = 45/114 (39%), Gaps = 31/114 (27%)
Query: 27 IGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPDERFEWLCQLFKPKSAV 86
+ +VG P+VGKSTL + LT + F T+ V
Sbjct: 3 VALVGFPSVGKSTLLSKLTNTKSEVAAYEFTTLTC------------------------V 38
Query: 87 PAFLE-------IHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRAFEDPD 133
P +E + D+ G++ GA +G+G G ++ R D I VL A +
Sbjct: 39 PGVMEYKGAKIQLLDLPGIIEGASDGKGRGRQVIAVARTADLILIVLDATKPEG 92
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 60.8 bits (148), Expect = 2e-10
Identities = 36/109 (33%), Positives = 50/109 (45%), Gaps = 17/109 (15%)
Query: 27 IGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPDERFEWLCQLFKPKSAV 86
+ +VG P+VGKSTL N LT ++PF T+EP +
Sbjct: 66 VALVGFPSVGKSTLLNKLTNTKSEVADYPFTTLEPVPGMLEYKG---------------- 109
Query: 87 PAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRAFEDPDII 135
A +++ D+ G++ GA G+G G LS R D I VL FEDP
Sbjct: 110 -AQIQLLDLPGIIEGASSGRGRGRQVLSVARNADLIIIVLDVFEDPHHR 157
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 51.1 bits (123), Expect = 7e-08
Identities = 25/131 (19%), Positives = 36/131 (27%), Gaps = 28/131 (21%)
Query: 28 GIVGLPNVGKSTLFNTLTKLAI-PAENFPFCTIEPNEARVNIPDERFEWLCQLFKPKSAV 86
I G PNVGKS+L N L + P T +P + P
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLG---------P---- 47
Query: 87 PAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRAFEDPDIIHVDDSVDPVRD 146
+ + D GL G+ D + V VD + PV +
Sbjct: 48 ---VVLIDTPGLDEEGGLGRERVEEARQVADRADLVLLV-----------VDSDLTPVEE 93
Query: 147 LEVISAELRLK 157
+
Sbjct: 94 EAKLGLLRERG 104
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 51.9 bits (125), Expect = 3e-07
Identities = 20/50 (40%), Positives = 27/50 (54%)
Query: 25 LKIGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPDERFE 74
L + +VG PNVGK+TLFN LT N+P T+E E ++ E
Sbjct: 4 LTVALVGNPNVGKTTLFNALTGANQKVGNWPGVTVEKKEGKLKYKGHEIE 53
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane
protein. The N terminus contains a P-loop motif
suggesting that iron transport may be ATP dependent.
Length = 159
Score = 47.8 bits (115), Expect = 1e-06
Identities = 19/46 (41%), Positives = 25/46 (54%)
Query: 29 IVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPDERFE 74
+VG PNVGK+TLFN LT N+P T+E E + + E
Sbjct: 2 LVGNPNVGKTTLFNALTGARQKVGNWPGVTVEKKEGEFKLGGKEIE 47
>gnl|CDD|206681 cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.
This EngA1 subfamily CD represents the first GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to
other GTPases, it is likely that an ancient gene
duplication, rather than a fusion of evolutionarily
distinct GTPases, gave rise to this family. Although
the exact function of these proteins has not been
elucidated, studies have revealed that the E. coli EngA
homolog, Der, and Neisseria gonorrhoeae EngA are
essential for cell viability. A recent report suggests
that E. coli Der functions in ribosome assembly and
stability.
Length = 157
Score = 47.0 bits (113), Expect = 1e-06
Identities = 18/29 (62%), Positives = 20/29 (68%), Gaps = 3/29 (10%)
Query: 29 IVGLPNVGKSTLFNTLT--KLAIPAENFP 55
IVG PNVGKSTLFN LT + AI + P
Sbjct: 2 IVGRPNVGKSTLFNRLTGRRDAI-VSDTP 29
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 48.8 bits (117), Expect = 2e-06
Identities = 18/46 (39%), Positives = 26/46 (56%)
Query: 27 IGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPDER 72
+ +VG N GKSTLFN LT + + F T++P R+ + D R
Sbjct: 195 VALVGYTNAGKSTLFNALTGADVYVADQLFATLDPTTRRIELGDGR 240
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of
the cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 47.1 bits (113), Expect = 3e-06
Identities = 20/50 (40%), Positives = 25/50 (50%)
Query: 25 LKIGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPDERFE 74
+ I +VG PNVGK+TLFN LT N+P T+E E E
Sbjct: 1 ITIALVGNPNVGKTTLFNALTGARQHVGNWPGVTVEKKEGTFKYKGYEIE 50
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 48.2 bits (116), Expect = 3e-06
Identities = 20/51 (39%), Positives = 23/51 (45%), Gaps = 3/51 (5%)
Query: 26 KIGIVGLPNVGKSTLFNTLTK--LAIPAENFPFCTIEPNEARVNIPDERFE 74
+ IVG PNVGKSTLFN LT AI + P T + F
Sbjct: 1 VVAIVGRPNVGKSTLFNRLTGKRDAI-VSDTPGVTRDRKYGDAEWGGREFI 50
Score = 44.4 bits (106), Expect = 5e-05
Identities = 36/146 (24%), Positives = 53/146 (36%), Gaps = 46/146 (31%)
Query: 12 PAERPILGRFSSHLKIGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARV---NI 68
P E +KI I+G PNVGKSTL N L E RV +I
Sbjct: 160 PEEEEEEEEEDGPIKIAIIGRPNVGKSTLVNALL----------------GEERVIVSDI 203
Query: 69 P-------DERFEWLCQLFKPKSAVPAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDG 121
D FE + + + D AG+ R +G+ S +R
Sbjct: 204 AGTTRDSIDIPFERNGKKYT----------LIDTAGIRRKGKVTEGV--EKYSVLRT--- 248
Query: 122 IFHVLRAFEDPDI-IHVDDSVDPVRD 146
L+A E D+ + V D+ + + +
Sbjct: 249 ----LKAIERADVVLLVLDATEGITE 270
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 45.5 bits (108), Expect = 6e-06
Identities = 22/102 (21%), Positives = 35/102 (34%), Gaps = 18/102 (17%)
Query: 28 GIVGLPNVGKSTLFNTLTKLAIPA-ENFPFCTIEPNEARVNIPDERFEWLCQLFKPKSAV 86
+VG VGKS+L N L + + P T +P+ + + +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVK------------ 48
Query: 87 PAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRA 128
L + D GL G G +R D I V+ +
Sbjct: 49 ---LVLVDTPGLDEF--GGLGREELARLLLRGADLILLVVDS 85
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 47.4 bits (114), Expect = 6e-06
Identities = 17/26 (65%), Positives = 19/26 (73%), Gaps = 2/26 (7%)
Query: 26 KIGIVGLPNVGKSTLFNTLT--KLAI 49
+ IVG PNVGKSTLFN LT + AI
Sbjct: 3 VVAIVGRPNVGKSTLFNRLTGKRDAI 28
Score = 42.3 bits (101), Expect = 2e-04
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 24 HLKIGIVGLPNVGKSTLFNTLTK 46
+KI I+G PNVGKS+L N L
Sbjct: 173 PIKIAIIGRPNVGKSSLINALLG 195
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 47.1 bits (113), Expect = 7e-06
Identities = 19/47 (40%), Positives = 28/47 (59%)
Query: 26 KIGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPDER 72
+ +VG N GKSTLFN LT + A + F T++P R+++PD
Sbjct: 191 TVALVGYTNAGKSTLFNALTGADVYAADQLFATLDPTTRRLDLPDGG 237
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 45.9 bits (110), Expect = 7e-06
Identities = 20/46 (43%), Positives = 28/46 (60%)
Query: 27 IGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPDER 72
+ +VG N GKSTLFN LT + AE+ F T++P R+ +P R
Sbjct: 44 VALVGYTNAGKSTLFNALTGADVLAEDQLFATLDPTTRRIKLPGGR 89
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except
some eubacteria. It binds to the 16S ribosomal RNA
(rRNA) of the 30S subunit and appears to play a role in
the assembly of the 30S subunit, possibly by
chaperoning the 16S rRNA. It also contacts several
assembly elements of the 30S subunit. Era couples cell
growth with cytokinesis and plays a role in cell
division and energy metabolism. Homologs have also been
found in eukaryotes. Era contains two domains: the
N-terminal GTPase domain and a C-terminal domain KH
domain that is critical for RNA binding. Both domains
are important for Era function. Era is functionally
able to compensate for deletion of RbfA, a cold-shock
adaptation protein that is required for efficient
processing of the 16S rRNA.
Length = 168
Score = 44.0 bits (105), Expect = 2e-05
Identities = 14/27 (51%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 25 LKIGIVGLPNVGKSTLFNTL--TKLAI 49
+ I+G PNVGKSTL N L K++I
Sbjct: 4 GFVAIIGRPNVGKSTLLNALVGQKISI 30
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 45.5 bits (108), Expect = 3e-05
Identities = 20/44 (45%), Positives = 24/44 (54%)
Query: 31 GLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPDERFE 74
G PNVGKSTLFN LT N+P T+E E ++ E E
Sbjct: 1 GNPNVGKSTLFNALTGANQTVGNWPGVTVEKKEGKLGFQGEDIE 44
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 43.1 bits (102), Expect = 4e-05
Identities = 33/126 (26%), Positives = 45/126 (35%), Gaps = 21/126 (16%)
Query: 26 KIGIVGLPNVGKSTLFNTLTKLAI-PAENFPFCTIEPNEARVNIPDERFEWLCQLFKPKS 84
KI IVG PNVGKSTL N L I E P T + + ++
Sbjct: 3 KIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYK---------- 52
Query: 85 AVPAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRAFE-----DPDIIHVDD 139
+ D AG + + S +R D + VL E +IIH +
Sbjct: 53 -----FNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAE 107
Query: 140 SVDPVR 145
S P+
Sbjct: 108 SGVPII 113
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 43.2 bits (103), Expect = 4e-05
Identities = 33/133 (24%), Positives = 52/133 (39%), Gaps = 46/133 (34%)
Query: 25 LKIGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARV---NIP-------DERFE 74
+KI I+G PNVGKS+L N L E RV +I D FE
Sbjct: 3 IKIAIIGRPNVGKSSLLNALL----------------GEERVIVSDIAGTTRDSIDVPFE 46
Query: 75 WLCQLFKPKSAVPAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRAVDGIFHVLRAFEDPDI 134
+ Q + + D AG+ + +G+ S +R L+A E D+
Sbjct: 47 YDGQKYT----------LIDTAGIRKKGKVTEGI--EKYSVLRT-------LKAIERADV 87
Query: 135 -IHVDDSVDPVRD 146
+ V D+ + + +
Sbjct: 88 VLLVLDASEGITE 100
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 44.1 bits (105), Expect = 7e-05
Identities = 20/50 (40%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 26 KIGIVGLPNVGKSTLFNTLT--KLAIPAENFPFCTIEPNEARVNIPDERF 73
+ IVG PNVGKSTLFN LT ++AI + P T + F
Sbjct: 5 VVAIVGRPNVGKSTLFNRLTGRRIAI-VSDTPGVTRDRIYGDAEWLGREF 53
Score = 41.4 bits (98), Expect = 5e-04
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 12 PAERPILGRFSSHLKIGIVGLPNVGKSTLFNTLTK 46
P E + +KI I+G PNVGKS+L N +
Sbjct: 166 PDEEEEEEEETDPIKIAIIGRPNVGKSSLINAILG 200
>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 = 42.0 bits (99), Expect = 8e-05
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 2 PPKASKSKEAPAERPILGRFSSHLKIGIVGLPNVGKSTLFNTL-TKLAIPAENFP 55
K K ++ + ++ +++G+VGLPNVGKS+ N L K + + P
Sbjct: 69 GQGILKLKAEITKQKLKLKYKKGIRVGVVGLPNVGKSSFINALLNKFKLKVGSIP 123
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. Proteins of the
YlqF family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases. The YlqF subfamily is represented in all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 41.7 bits (99), Expect = 1e-04
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 4 KASKSKEAPAERPILGRFSSHLKIGIVGLPNVGKSTLFNTLTK 46
K K E + +L R L+ +VG+PNVGKSTL N L
Sbjct: 98 KLLKENEKLKAKGLLPRP---LRAMVVGIPNVGKSTLINRLRG 137
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 42.0 bits (100), Expect = 2e-04
Identities = 15/25 (60%), Positives = 18/25 (72%), Gaps = 2/25 (8%)
Query: 27 IGIVGLPNVGKSTLFNTL--TKLAI 49
+ IVG PNVGKSTL N L K++I
Sbjct: 8 VAIVGRPNVGKSTLLNALVGQKISI 32
Score = 28.9 bits (66), Expect = 4.4
Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 6/65 (9%)
Query: 206 WKAADIEILNTFQLLTAKPVVYLVNMNEK-DYQRKKNKFLPKIHAWVQEHGGEQIIPFSC 264
D IL + PV+ ++N K D + K + LP + + +I+P S
Sbjct: 98 IGPGDEFILEKLKK-VKTPVILVLN---KIDLVKDKEELLPLLEELSELMDFAEIVPIS- 152
Query: 265 ALERN 269
AL+ +
Sbjct: 153 ALKGD 157
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes.
TrmE contains a GTPase domain that forms a canonical
Ras-like fold. It functions a molecular switch GTPase,
and apparently uses a conformational change associated
with GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 40.6 bits (96), Expect = 3e-04
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 25 LKIGIVGLPNVGKSTLFNTLTK 46
+K+ I G PNVGKS+L N L
Sbjct: 4 IKVVIAGKPNVGKSSLLNALAG 25
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 41.6 bits (99), Expect = 4e-04
Identities = 15/27 (55%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 25 LKIGIVGLPNVGKSTLFNTLTK--LAI 49
LK+ I G PNVGKS+L N L AI
Sbjct: 216 LKVVIAGRPNVGKSSLLNALLGEERAI 242
>gnl|CDD|206753 cd04178, Nucleostemin_like, A circularly permuted subfamily of the
Ras GTPases. Nucleostemin (NS) is a nucleolar protein
that functions as a regulator of cell growth and
proliferation in stem cells and in several types of
cancer cells, but is not expressed in the differentiated
cells of most mammalian adult tissues. NS shuttles
between the nucleolus and nucleoplasm bidirectionally at
a rate that is fast and independent of cell type.
Lowering GTP levels decreases the nucleolar retention of
NS, and expression of NS is abruptly down-regulated
during differentiation prior to terminal cell division.
Found only in eukaryotes, NS consists of an N-terminal
basic domain, a coiled-coil domain, a GTP-binding
domain, an intermediate domain, and a C-terminal acidic
domain. Experimental evidence indicates that NS uses its
GTP-binding property as a molecular switch to control
the transition between the nucleolus and nucleoplasm,
and this process involves interaction between the basic,
GTP-binding, and intermediate domains of the protein.
Length = 171
Score = 39.9 bits (94), Expect = 6e-04
Identities = 11/23 (47%), Positives = 18/23 (78%)
Query: 22 SSHLKIGIVGLPNVGKSTLFNTL 44
+ + +G+VG PNVGKS++ N+L
Sbjct: 114 KTSITVGVVGYPNVGKSSVINSL 136
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 40.3 bits (95), Expect = 8e-04
Identities = 14/25 (56%), Positives = 18/25 (72%), Gaps = 2/25 (8%)
Query: 27 IGIVGLPNVGKSTLFNTL--TKLAI 49
+ I+G PNVGKSTL N L K++I
Sbjct: 9 VAIIGRPNVGKSTLLNALVGQKISI 33
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 39.7 bits (93), Expect = 0.002
Identities = 19/47 (40%), Positives = 26/47 (55%)
Query: 24 HLKIGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPD 70
L IG++G PN GK+TLFN LT N+ T+E E + + D
Sbjct: 3 KLTIGLIGNPNSGKTTLFNQLTGARQRVGNWAGVTVERKEGQFSTTD 49
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 39.3 bits (92), Expect = 0.002
Identities = 17/44 (38%), Positives = 28/44 (63%)
Query: 27 IGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPD 70
+ +VG N GKSTLFN +T+ + A + F T++P R+++ D
Sbjct: 200 VSLVGYTNAGKSTLFNRITEARVYAADQLFATLDPTLRRIDVAD 243
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 39.0 bits (92), Expect = 0.002
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 25 LKIGIVGLPNVGKSTLFNTLTK 46
++ IVG+PNVGKSTL N L
Sbjct: 119 IRAMIVGIPNVGKSTLINRLAG 140
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 39.1 bits (92), Expect = 0.002
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 25 LKIGIVGLPNVGKSTLFNTLTK 46
LK+ I+G PNVGKS+L N L
Sbjct: 218 LKVVIIGRPNVGKSSLLNALLG 239
>gnl|CDD|206750 cd01857, HSR1_MMR1, A circularly permuted subfamily of the Ras
GTPases. Human HSR1 is localized to the human MHC class
I region and is highly homologous to a putative
GTP-binding protein, MMR1 from mouse. These proteins
represent a new subfamily of GTP-binding proteins that
has only eukaryote members. This subfamily shows a
circular permutation of the GTPase signature motifs so
that the C-terminal strands 5, 6, and 7 (strand 6
contains the G4 box with sequence NKXD) are relocated to
the N-terminus.
Length = 140
Score = 37.6 bits (88), Expect = 0.002
Identities = 16/28 (57%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 20 RFSSHLK---IGIVGLPNVGKSTLFNTL 44
F S L IG+VG PNVGKS+L N L
Sbjct: 75 LFFSALNEATIGLVGYPNVGKSSLINAL 102
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 38.6 bits (91), Expect = 0.003
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 29 IVGLPNVGKSTLFNTLTK 46
I+G+PNVGKSTL N L
Sbjct: 126 IIGIPNVGKSTLINRLAG 143
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 38.5 bits (90), Expect = 0.004
Identities = 13/22 (59%), Positives = 17/22 (77%)
Query: 25 LKIGIVGLPNVGKSTLFNTLTK 46
+++G+VG PNVGKSTL N L
Sbjct: 133 IRVGVVGYPNVGKSTLINRLLG 154
>gnl|CDD|133441 cd04938, TGS_Obg-like, TGS_Obg-like: The C-terminal TGS domain of
Obg-like GTPases such as those present in DRG
(developmentally regulated GTP-binding protein), and
GTP-binding proteins Ygr210 and YchF. The TGS domain
(named after the ThrRS, GTPase, and SpoT proteins where
it occurs) is a small domain of about 50 amino acid
residues with a predominantly beta-sheet structure.
There is no direct information on the function of the
TGS domain, but its presence in two types of regulatory
proteins (the GTPases and guanosine polyphosphate
phosphohydrolases/synthetases) suggests a ligand (most
likely nucleotide)-binding, regulatory role.
Length = 76
Score = 35.5 bits (82), Expect = 0.004
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 309 TAGPDEVKCWQIRRQTKAPQAAGTIHTDFERGFICAEV 346
+ G C +++ T A IH D E+GFI A
Sbjct: 17 SGGNVFRDCVLVKKGTTVGDVARKIHGDLEKGFIEAVG 54
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus,
defects in NOG1 can lead to defects in 60S biogenesis.
The S. cerevisiae NOG1 gene is essential for cell
viability, and mutations in the predicted G motifs
abrogate function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 37.2 bits (87), Expect = 0.004
Identities = 15/30 (50%), Positives = 18/30 (60%)
Query: 29 IVGLPNVGKSTLFNTLTKLAIPAENFPFCT 58
I G PNVGKS+L N LT+ +PF T
Sbjct: 5 IAGYPNVGKSSLVNKLTRAKPEVAPYPFTT 34
>gnl|CDD|206751 cd01858, NGP_1, A novel nucleolar GTP-binding protein, circularly
permuted subfamily of the Ras GTPases. Autoantigen
NGP-1 (Nucleolar G-protein gene 1) has been shown to
localize in the nucleolus and nucleolar organizers in
all cell types analyzed, which is indicative of a
function in ribosomal assembly. NGP-1 and its homologs
show a circular permutation of the GTPase signature
motifs so that the C-terminal strands 5, 6, and 7
(strand 6 contains the G4 box with NKXD motif) are
relocated to the N terminus.
Length = 157
Score = 36.1 bits (84), Expect = 0.010
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 24 HLKIGIVGLPNVGKSTLFNTLTK 46
+ +G +G PNVGKS++ NTL
Sbjct: 102 QISVGFIGYPNVGKSSVINTLRS 124
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 35.7 bits (83), Expect = 0.015
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 29 IVGLPNVGKSTLFNTLTK 46
+VG NVGKSTL N L K
Sbjct: 130 VVGATNVGKSTLINALLK 147
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 36.2 bits (84), Expect = 0.016
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 25 LKIGIVGLPNVGKSTLFNTL 44
+ I+G PNVGKSTL N L
Sbjct: 1 GFVAILGRPNVGKSTLLNQL 20
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 36.8 bits (86), Expect = 0.016
Identities = 16/49 (32%), Positives = 19/49 (38%), Gaps = 4/49 (8%)
Query: 8 SKEAPAERPILGRFSSHL----KIGIVGLPNVGKSTLFNTLTKLAIPAE 52
SK R +L S + +I IVG GKSTL L P
Sbjct: 328 SKGYDGGRLLLKDLSFRIDRGDRIAIVGPNGAGKSTLLKLLAGELGPLS 376
Score = 30.7 bits (70), Expect = 1.2
Identities = 18/55 (32%), Positives = 23/55 (41%), Gaps = 14/55 (25%)
Query: 26 KIGIVGLPNV-GKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIP-DERFEWLCQ 78
+IG+VG N GKSTL L +EP+ V P R +L Q
Sbjct: 31 RIGLVG-RNGAGKSTLLKILAGE-----------LEPDSGEVTRPKGLRVGYLSQ 73
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA,
an essential protein involved in cell division control.
YihA and its orthologs are small proteins that
typically contain less than 200 amino acid residues and
consists of the GTPase domain only (some of the
eukaryotic homologs contain an N-terminal extension of
about 120 residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 35.2 bits (82), Expect = 0.018
Identities = 17/44 (38%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 27 IGIVGLPNVGKSTLFNTLT---KLAIPAENFPFCTIEPNEARVN 67
+ G NVGKS+L N LT KLA P T N V
Sbjct: 2 VAFAGRSNVGKSSLINALTNRKKLA-RTSKTPGRTQLINFFNVG 44
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 35.3 bits (81), Expect = 0.025
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 21 FSSHLKIGIVGLPNVGKSTLFNTLTK 46
F KI ++G VGK+TL N L
Sbjct: 2 FMKEFKIVVLGDGGVGKTTLLNRLVG 27
>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 = 34.7 bits (81), Expect = 0.025
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 4/43 (9%)
Query: 14 ERPILGRFSSHL----KIGIVGLPNVGKSTLFNTLTKLAIPAE 52
+ +L S + +IG+VG GKSTL + P E
Sbjct: 12 GKLLLKDISLTINPGDRIGLVGRNGAGKSTLLKLIAGELEPDE 54
>gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an
ATPase enzyme and as a kinase, and phosphorylates
periplasmic binding proteins involved in the LAO
(lysine, arginine, ornithine)/AO transport systems.
Length = 267
Score = 35.0 bits (81), Expect = 0.041
Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 12 PAERPILGRFSSH----LKIGIVGLPNVGKSTLFNTLTKLAI 49
P R +L R ++GI G+P GKSTL L
Sbjct: 13 PEARELLRRLMPLTGRAHRVGITGVPGAGKSTLIEALGMELR 54
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted subfamily
of the Ras GTPases. This family represents archaeal
GTPase typified by the protein MJ1464 from Methanococcus
jannaschii. The members of this family show a circular
permutation of the GTPase signature motifs so that
C-terminal strands 5, 6, and 7 (strands 6 contain the
NKxD motif) are relocated to the N terminus.
Length = 157
Score = 33.4 bits (77), Expect = 0.068
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 26 KIGIVGLPNVGKSTLFNTLTK 46
+G+VG P VGKS++ N L
Sbjct: 101 IVGVVGYPKVGKSSIINALKG 121
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation
GTPase HydF. This model describes the family of the
[Fe] hydrogenase maturation protein HypF as
characterized in Chlamydomonas reinhardtii and found,
in an operon with radical SAM proteins HydE and HydG,
in numerous bacteria. It has GTPase activity, can bind
an 4Fe-4S cluster, and is essential for hydrogenase
activity [Protein fate, Protein modification and
repair].
Length = 391
Score = 34.4 bits (80), Expect = 0.069
Identities = 13/21 (61%), Positives = 14/21 (66%)
Query: 25 LKIGIVGLPNVGKSTLFNTLT 45
L IGI G N GKS+L N LT
Sbjct: 7 LHIGIFGRRNAGKSSLINALT 27
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 33.8 bits (78), Expect = 0.11
Identities = 24/85 (28%), Positives = 31/85 (36%), Gaps = 30/85 (35%)
Query: 4 KASKSKEAPAE--RPILGRFSS-----------------HLK-----------IGIVGLP 33
KA+K + + R GR +S HLK I + G P
Sbjct: 118 KAAKDPKEANQLRRQAFGRVASIIKKIDDDLEFLRKARDHLKKLPAIDPDLPTIVVAGYP 177
Query: 34 NVGKSTLFNTLTKLAIPAENFPFCT 58
NVGKS+L LT +PF T
Sbjct: 178 NVGKSSLVRKLTTAKPEVAPYPFTT 202
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and
related GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 33.8 bits (78), Expect = 0.11
Identities = 13/47 (27%), Positives = 17/47 (36%), Gaps = 4/47 (8%)
Query: 7 KSKEAPAERPILGRFSSH----LKIGIVGLPNVGKSTLFNTLTKLAI 49
+ R +L IGI G+P GKSTL L +
Sbjct: 30 RPDHRALARELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRELR 76
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 34.0 bits (78), Expect = 0.13
Identities = 34/113 (30%), Positives = 49/113 (43%), Gaps = 25/113 (22%)
Query: 9 KEAPAERPILGRFSSHL-KIGIVGLPNVGKSTLFNTLT--KLAIPAENFPFCTIEPNEAR 65
K A L S L ++ +VG PNVGKS+L N LT + A+ + T +P +
Sbjct: 436 KVAEKTSGFLT--PSGLRRVALVGRPNVGKSSLLNQLTHEERAV-VNDLAGTTRDPVDEI 492
Query: 66 VNIPDERFEWLCQLFKPKSAVPAFLEIHDIAGLVRGAHEGQGLGNSFLSHIRA 118
V I E +WL F+ D AG+ R H + G + S +R
Sbjct: 493 VEIDGE--DWL------------FI---DTAGIKRRQH--KLTGAEYYSSLRT 526
Score = 34.0 bits (78), Expect = 0.13
Identities = 16/33 (48%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 27 IGIVGLPNVGKSTLFNT-LTKLAIPAENFPFCT 58
+ IVG PNVGKSTL N L + E+ P T
Sbjct: 278 VAIVGRPNVGKSTLVNRILGRREAVVEDTPGVT 310
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 33.6 bits (77), Expect = 0.13
Identities = 14/22 (63%), Positives = 16/22 (72%)
Query: 25 LKIGIVGLPNVGKSTLFNTLTK 46
K+ IVG PNVGKS+L N L K
Sbjct: 204 FKLAIVGSPNVGKSSLLNALLK 225
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 33.8 bits (78), Expect = 0.14
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 7/38 (18%)
Query: 10 EAPAERPILG--RFSSHLKIGIVGLPNVGKSTLFNTLT 45
E P G R ++ +VG PNVGKS+L N L
Sbjct: 200 EVPRVGSASGGPR-----RVALVGKPNVGKSSLLNKLA 232
Score = 32.6 bits (75), Expect = 0.26
Identities = 11/14 (78%), Positives = 12/14 (85%)
Query: 29 IVGLPNVGKSTLFN 42
+VG PNVGKSTL N
Sbjct: 43 VVGRPNVGKSTLVN 56
>gnl|CDD|206641 cd00157, Rho, Ras homology family (Rho) of small guanosine
triphosphatases (GTPases). Members of the Rho (Ras
homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1,
RhoBTB, and Rop. There are 22 human Rho family members
identified currently. These proteins are all involved
in the reorganization of the actin cytoskeleton in
response to external stimuli. They also have roles in
cell transformation by Ras in cytokinesis, in focal
adhesion formation and in the stimulation of
stress-activated kinase. These various functions are
controlled through distinct effector proteins and
mediated through a GTP-binding/GTPase cycle involving
three classes of regulating proteins: GAPs
(GTPase-activating proteins), GEFs (guanine nucleotide
exchange factors), and GDIs (guanine nucleotide
dissociation inhibitors). Most Rho 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 Rho proteins. Since crystal structures often lack
C-terminal residues, this feature is not available for
annotation in many of the CDs in the hierarchy.
Length = 171
Score = 32.1 bits (74), Expect = 0.20
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 25 LKIGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPN-EARVNIPDERFE 74
+KI +VG VGK+ L + T P E P T+ N A V + ++
Sbjct: 1 IKIVVVGDGAVGKTCLLISYTTNKFPTEYVP--TVFDNYSANVTVDGKQVN 49
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 32.2 bits (74), Expect = 0.24
Identities = 16/41 (39%), Positives = 19/41 (46%)
Query: 26 KIGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARV 66
+I VG NVGKSTL LT + P T +PN
Sbjct: 11 EIVFVGRSNVGKSTLVRELTGKKVRVGKRPGVTRKPNHYDW 51
>gnl|CDD|213835 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members
commonly are called EngB based on homology to EngA, one
of several other GTPases of ribosome biogenesis.
Cutoffs as set find essentially all bacterial members,
but also identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about
80 percent of bacterial genomes [Protein synthesis,
Other].
Length = 178
Score = 31.7 bits (73), Expect = 0.29
Identities = 14/25 (56%), Positives = 15/25 (60%), Gaps = 3/25 (12%)
Query: 27 IGIVGLPNVGKSTLFNTLT---KLA 48
I G NVGKS+L N LT KLA
Sbjct: 21 IAFAGRSNVGKSSLINALTNRKKLA 45
>gnl|CDD|107141 PHA02128, PHA02128, hypothetical protein.
Length = 151
Score = 31.6 bits (71), Expect = 0.29
Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 1/62 (1%)
Query: 199 KDVRLGDWKAADIEILNTFQLLTAKPVVYLVNMNEKDYQRKKNKFLPKIHAWVQEHGGEQ 258
+D+ W+ DI I +L P V + ++E +Y +I+ W HG E
Sbjct: 89 QDMVSYQWRG-DIRISTISELTDRCPKVKFLMIDESEYTLTSRHQRQEIYDWAGTHGVEF 147
Query: 259 II 260
+I
Sbjct: 148 VI 149
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component
of iron-siderophores, vitamin B12 and hemin
transporters and related proteins. ABC transporters,
involved in the uptake of siderophores, heme, and
vitamin B12, are widely conserved in bacteria and
archaea. Only very few species lack representatives of
the siderophore family transporters. The E. coli BtuCD
protein is an ABC transporter mediating vitamin B12
uptake. The two ATP-binding cassettes (BtuD) are in
close contact with each other, as are the two
membrane-spanning subunits (BtuC); this arrangement is
distinct from that observed for the E. coli lipid
flippase MsbA. The BtuC subunits provide 20
transmembrane helices grouped around a translocation
pathway that is closed to the cytoplasm by a gate
region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 31.6 bits (73), Expect = 0.35
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 14 ERPILGRFSSHLK----IGIVGLPN-VGKSTLFNTLTKL 47
R +L S ++ +GI+G PN GKSTL TL L
Sbjct: 11 GRTVLDDLSLSIEAGEIVGILG-PNGAGKSTLLKTLAGL 48
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 31.4 bits (72), Expect = 0.42
Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 8/42 (19%)
Query: 5 ASKSKEAPAERPILGRFSSHLKIGIVGLPNVGKSTLFNTLTK 46
A K+ P + +I G NVGKS+L N LT
Sbjct: 13 APDIKQYPEDDLP--------EIAFAGRSNVGKSSLINALTN 46
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. 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 = 157
Score = 31.1 bits (71), Expect = 0.45
Identities = 14/43 (32%), Positives = 17/43 (39%), Gaps = 4/43 (9%)
Query: 14 ERPILGRFSSHLK----IGIVGLPNVGKSTLFNTLTKLAIPAE 52
R L S LK + +VG GKSTL + L P
Sbjct: 11 GRTALDNVSLTLKAGEIVALVGPNGSGKSTLLRAIAGLLKPTS 53
>gnl|CDD|236992 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
Reviewed.
Length = 556
Score = 32.0 bits (74), Expect = 0.53
Identities = 13/21 (61%), Positives = 15/21 (71%), Gaps = 3/21 (14%)
Query: 28 GIVGL--PN-VGKSTLFNTLT 45
GIVG+ PN GKSTLF +T
Sbjct: 351 GIVGIIGPNGAGKSTLFKMIT 371
Score = 29.7 bits (68), Expect = 2.6
Identities = 17/37 (45%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 8 SKEAPAERPILGRFS-SHL---KIGIVGLPNVGKSTL 40
SK P ++ IL S S KIG++GL GKSTL
Sbjct: 13 SKVVPPKKQILKDISLSFFPGAKIGVLGLNGAGKSTL 49
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 31.2 bits (72), Expect = 0.55
Identities = 11/18 (61%), Positives = 12/18 (66%), Gaps = 3/18 (16%)
Query: 34 NVGKSTLFNTLT---KLA 48
NVGKS+L N LT LA
Sbjct: 34 NVGKSSLINALTNRKNLA 51
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 31.1 bits (71), Expect = 0.63
Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 4/50 (8%)
Query: 12 PAERPILGRFSSHLK----IGIVGLPNVGKSTLFNTLTKLAIPAENFPFC 57
P + L S ++ + ++G GKSTL L L P
Sbjct: 14 PGRKAALKDVSLEIEKGERVLLIGPNGSGKSTLLKLLNGLLKPTSGEVLV 63
>gnl|CDD|129833 TIGR00750, lao, LAO/AO transport system ATPase. In E. coli,
mutation of this kinase blocks phosphorylation of two
transporter system periplasmic binding proteins and
consequently inhibits those transporters. This kinase
is also found in Gram-positive bacteria, archaea, and
the roundworm C. elegans. It may have a more general,
but still unknown function. Mutations have also been
found that do not phosphorylate the periplasmic binding
proteins, yet still allow transport. The ATPase
activity of this protein seems to be necessary, however
[Transport and binding proteins, Amino acids, peptides
and amines, Regulatory functions, Protein
interactions].
Length = 300
Score = 31.3 bits (71), Expect = 0.71
Identities = 11/35 (31%), Positives = 15/35 (42%)
Query: 15 RPILGRFSSHLKIGIVGLPNVGKSTLFNTLTKLAI 49
I+ + ++GI G P GKSTL L
Sbjct: 25 DRIMPYTGNAHRVGITGTPGAGKSTLLEALGMELR 59
>gnl|CDD|187550 cd05239, GDP_FS_SDR_e, GDP-fucose synthetase, extended (e) SDRs.
GDP-fucose synthetase (aka 3, 5-epimerase-4-reductase)
acts in the NADP-dependent synthesis of GDP-fucose from
GDP-mannose. Two activities have been proposed for the
same active site: epimerization and reduction. Proteins
in this subgroup are extended SDRs, which have a
characteristic active site tetrad and an NADP-binding
motif, [AT]GXXGXXG, that is a close match to the
archetypical form. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
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, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, 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. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. 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.
Length = 300
Score = 30.6 bits (70), Expect = 1.0
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 14/69 (20%)
Query: 93 HDIAGLVRGAHEGQGLGNS-------------FLSHIRAVDGIFHVLRAFEDPDIIHVDD 139
H I L+R HE + G FL I +L +++P I++V
Sbjct: 175 HVIPALIRKFHEAKLRGGKEVTVWGSGTPRREFLYSDDLARAIVFLLENYDEPIIVNVGS 234
Query: 140 SVD-PVRDL 147
V+ +R+L
Sbjct: 235 GVEISIREL 243
>gnl|CDD|221521 pfam12307, DUF3631, Protein of unknown function (DUF3631). This
protein is found in bacteria. Proteins in this family
are typically between 180 to 701 amino acids in length.
Length = 183
Score = 29.9 bits (68), Expect = 1.4
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 162 MERRI--EDVEKSMKRSNDKQLKIEHELCQRVKAWLQDGKDVRLGDWKAADIEILN 215
M RR E VE R ++ + L R+ AWL+D D L D + A + L
Sbjct: 2 MRRRAPGETVEPFRHRRDEPEA---AALRDRLAAWLEDVAD-TLEDARPAMPDGLE 53
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 29.2 bits (65), Expect = 1.4
Identities = 9/15 (60%), Positives = 9/15 (60%)
Query: 26 KIGIVGLPNVGKSTL 40
I I G P GKSTL
Sbjct: 1 IILITGPPGSGKSTL 15
>gnl|CDD|239388 cd03114, ArgK-like, The function of this protein family is
unkown. The protein sequences are similar to the ArgK
protein in E. coli. ArgK protein is a membrane ATPase
which is required for transporting arginine, ornithine
and lysine into the cells by the arginine and ornithine
(AO system) and lysine, arginine and ornithine (LAO)
transport systems.
Length = 148
Score = 29.6 bits (67), Expect = 1.5
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 27 IGIVGLPNVGKSTLFNTLTK 46
IGI G+P GKSTL + L
Sbjct: 2 IGITGVPGAGKSTLIDALIT 21
>gnl|CDD|163431 TIGR03719, ABC_ABC_ChvD, ATP-binding cassette protein, ChvD
family. Members of this protein family have two copies
of the ABC transporter ATP-binding cassette, but are
found outside the common ABC transporter operon
structure that features integral membrane permease
proteins and substrate-binding proteins encoded next to
the ATP-binding cassette (ABC domain) protein. The
member protein ChvD from Agrobacterium tumefaciens was
identified as both a candidate to interact with VirB8,
based on yeast two-hybrid analysis, and as an apparent
regulator of VirG. The general function of this protein
family is unknown.
Length = 552
Score = 30.7 bits (70), Expect = 1.5
Identities = 17/37 (45%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 8 SKEAPAERPILGRFS-SHL---KIGIVGLPNVGKSTL 40
SK P ++ IL S S KIG++GL GKSTL
Sbjct: 11 SKVVPPKKEILKDISLSFFPGAKIGVLGLNGAGKSTL 47
Score = 29.1 bits (66), Expect = 3.5
Identities = 14/26 (53%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 28 GIVGL--PN-VGKSTLFNTLTKLAIP 50
GIVG+ PN GKSTLF +T P
Sbjct: 349 GIVGVIGPNGAGKSTLFRMITGQEQP 374
>gnl|CDD|184198 PRK13638, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 271
Score = 30.0 bits (67), Expect = 1.5
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 21 FSSHLKIGIVGLPNVGKSTLFNTLTKLAIPAE 52
FS G+VG GKSTLF L+ L P +
Sbjct: 24 FSLSPVTGLVGANGCGKSTLFMNLSGLLRPQK 55
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to
as the Sar1-N-terminal activation recruitment (STAR)
motif. The STAR motif mediates the recruitment of Sar1
to ER membranes and facilitates its interaction with
mammalian Sec12 GEF leading to activation.
Length = 191
Score = 29.6 bits (67), Expect = 1.6
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 18 LGRFSSHLKIGIVGLPNVGKSTLFNTL 44
LG + KI +GL N GK+TL + L
Sbjct: 13 LGLYKKEAKIVFLGLDNAGKTTLLHML 39
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 30.2 bits (69), Expect = 1.6
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 10/47 (21%)
Query: 29 IVGLPNVGKSTLFNTLTKLAIPAEN------FPFCTIEPNEARVNIP 69
+VG+ NVGKSTL N + K ++ FP T++ ++ IP
Sbjct: 165 VVGVTNVGKSTLINRIIKEITGEKDVITTSRFPGTTLD----KIEIP 207
>gnl|CDD|215595 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 30.5 bits (69), Expect = 1.6
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 11/45 (24%)
Query: 26 KIGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPD 70
K+GIVG GKS++ N L F +E R+ I
Sbjct: 1267 KVGIVGRTGAGKSSMLNAL-----------FRIVELERGRILIDG 1300
>gnl|CDD|206724 cd04159, Arl10_like, Arf-like 9 (Arl9) and 10 (Arl10) GTPases.
Arl10-like subfamily. Arl9/Arl10 was identified from a
human cancer-derived EST dataset. No functional
information about the subfamily is available at the
current time, but crystal structures of human Arl10b
and Arl10c have been solved.
Length = 159
Score = 29.2 bits (66), Expect = 1.7
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 27 IGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARV 66
I +VGL N GK+TL N + + P T+ N +V
Sbjct: 2 ITLVGLQNSGKTTLVNVIASGQFSEDTIP--TVGFNMRKV 39
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They
belong to the subfamily C of the ATP-binding cassette
(ABC) superfamily of transport proteins. The ABCC
subfamily contains transporters with a diverse
functional spectrum that includes ion transport, cell
surface receptor, and toxin secretion activities. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains, each composed of six
transmembrane (TM) helices, and two nucleotide-binding
domains (NBD). 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 = 171
Score = 29.3 bits (67), Expect = 2.0
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 12 PAERPILGRFSSHL----KIGIVGLPNVGKSTLFNTLTKL 47
+P+L S + K+ IVG GKSTL L +L
Sbjct: 12 GRPKPVLKDVSLTIKPGEKVAIVGPSGSGKSTLLKLLLRL 51
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 29.8 bits (67), Expect = 2.0
Identities = 10/49 (20%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 24 HLKIGIVGLPNVGKSTLFNTLTKLAI-PAENFPFCTIEPNEARVNIPDE 71
+ + ++G GKS+L N L + + T R++ E
Sbjct: 39 PVNVLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLRLSYDGE 87
>gnl|CDD|217842 pfam04010, DUF357, Protein of unknown function (DUF357). Members
of this family are short (less than 100 amino acid)
proteins found in archaebacteria. The function of these
proteins is unknown.
Length = 75
Score = 27.6 bits (62), Expect = 2.0
Identities = 9/43 (20%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 157 KDIEFMERRIEDVEKSMKRSNDKQLKIEHELCQRVKAWLQDGK 199
+ I +E + V+ + + E E+ + K++L+D K
Sbjct: 2 RYIRLLEEALSKVKIAPPEGSPLHAAAE-EVLEMAKSYLEDAK 43
>gnl|CDD|216919 pfam02181, FH2, Formin Homology 2 Domain.
Length = 372
Score = 29.9 bits (68), Expect = 2.2
Identities = 11/68 (16%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 132 PDIIHVDDSVDPVRDLEVISAELRLKDIEFMERRIEDVEKSMKRSNDKQLKIEHELCQRV 191
PD++ + V + E KD++ +E+ ++ +E+ ++ S + + +++
Sbjct: 258 PDLLDFSSELSHVEKAAKVDLEQLEKDVKELEKGLKKLERELELSA-LDEHPDDKFVEKM 316
Query: 192 KAWLQDGK 199
K +L++ +
Sbjct: 317 KEFLEEAE 324
>gnl|CDD|237475 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 29.1 bits (66), Expect = 2.4
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 25 LKIGIVGLPNVGKSTL 40
+KIGI G P VGK+TL
Sbjct: 1 MKIGITGPPGVGKTTL 16
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 29.6 bits (67), Expect = 2.7
Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 4/41 (9%)
Query: 14 ERPILGRFSSHL----KIGIVGLPNVGKSTLFNTLTKLAIP 50
+ L F+ L K+ I+G GKSTL L P
Sbjct: 350 QTKALKNFNLTLAQGEKVAILGRSGSGKSTLLQLLAGAWDP 390
>gnl|CDD|236515 PRK09435, PRK09435, membrane ATPase/protein kinase; Provisional.
Length = 332
Score = 29.4 bits (67), Expect = 2.7
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 25 LKIGIVGLPNVGKSTLFNTL 44
L+IGI G+P VGKST L
Sbjct: 57 LRIGITGVPGVGKSTFIEAL 76
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 29.1 bits (66), Expect = 2.9
Identities = 13/27 (48%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 27 IGIVGLPN-VGKSTLFNTLTKLAIPAE 52
GI+G PN GKSTL L L P
Sbjct: 31 TGILG-PNGSGKSTLLKCLAGLLKPKS 56
>gnl|CDD|233305 TIGR01189, ccmA, heme ABC exporter, ATP-binding protein CcmA.
This model describes the cyt c biogenesis protein
encoded by ccmA in bacteria. An exception is, an
arabidopsis protein. Quite likely this is encoded by an
organelle. Bacterial c-type cytocromes are located on
the periplasmic side of the cytoplasmic membrane.
Several gene products encoded in a locus designated as
'ccm' are implicated in the transport and assembly of
the functional cytochrome C. This cluster includes
genes: ccmA;B;C;D;E;F;G and H. The posttranslational
pathway includes the transport of heme moiety, the
secretion of the apoprotein and the covalent attachment
of the heme with the apoprotein. The proteins ccmA and
B represent an ABC transporter; ccmC and D participate
in heme transfer to ccmE, which function as a
periplasmic heme chaperone. The presence of ccmF, G and
H is suggested to be obligatory for the final
functional assembly of cytochrome c [Protein fate,
Protein and peptide secretion and trafficking,
Transport and binding proteins, Other].
Length = 198
Score = 28.9 bits (65), Expect = 3.4
Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 14 ERPILGRFSSHLKIG----IVGLPN-VGKSTLFNTLTKLAIPAE 52
ER + S L G + G PN +GK+TL L L P
Sbjct: 12 ERMLFEGLSFTLNAGEALQVTG-PNGIGKTTLLRILAGLLRPDS 54
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a
nonhistone chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 28.5 bits (64), Expect = 3.4
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 22 SSHLKIGIVGLPNVGKST-LFNTLTKLAI 49
K+ IVGL N GK+T L+ L +
Sbjct: 13 RKEYKVIIVGLDNAGKTTILYQFLLGEVV 41
>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 = 28.5 bits (63), Expect = 3.5
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 26 KIGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNIPDERFE 74
I IVG P GK+TL L + P I+ + + D+
Sbjct: 4 VILIVGPPGSGKTTLARALARELGP-PGGGVIYIDGEDILEEVLDQLLL 51
>gnl|CDD|213269 cd03369, ABCC_NFT1, ATP-binding cassette domain 2 of NFT1,
subfamily C. Domain 2 of NFT1 (New full-length
MRP-type transporter 1). NFT1 belongs to the MRP
(multidrug resistance-associated protein) family of ABC
transporters. Some of the MRP members have five
additional transmembrane segments in their N-terminus,
but the function of these additional membrane-spanning
domains is not clear. The MRP was found in the
multidrug-resisting lung cancer cell in which
p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions such as
glutathione, glucuronate, and sulfate.
Length = 207
Score = 28.5 bits (64), Expect = 3.6
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 11/49 (22%)
Query: 20 RFSSHLKIGIVGLPNVGKSTLFNTLTKLAIPAENFPFCTIEPNEARVNI 68
+ + KIGIVG GKSTL L F +E E ++ I
Sbjct: 30 KVKAGEKIGIVGRTGAGKSTLILAL-----------FRFLEAEEGKIEI 67
>gnl|CDD|213223 cd03256, ABC_PhnC_transporter, ATP-binding cassette domain of the
binding protein-dependent phosphonate transport system.
Phosphonates are a class of organophosphorus compounds
characterized by a chemically stable
carbon-to-phosphorus (C-P) bond. Phosphonates are
widespread among naturally occurring compounds in all
kingdoms of wildlife, but only prokaryotic
microorganisms are able to cleave this bond. Certain
bacteria such as E. coli can use alkylphosphonates as a
phosphorus source. 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 = 241
Score = 28.7 bits (65), Expect = 3.7
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 27 IGIVGLPNVGKSTLFNTLTKLAIPAE 52
+ ++G GKSTL L L P
Sbjct: 30 VALIGPSGAGKSTLLRCLNGLVEPTS 55
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 28.7 bits (65), Expect = 4.1
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 29 IVGLPNVGKSTLFNTLTKL 47
+VG+ NVGKS+L N L K
Sbjct: 159 VVGVTNVGKSSLINKLLKQ 177
>gnl|CDD|213211 cd03244, ABCC_MRP_domain2, ATP-binding cassette domain 2 of
multidrug resistance-associated protein. The ABC
subfamily C is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resistance lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 221
Score = 28.6 bits (65), Expect = 4.3
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 26 KIGIVGLPNVGKSTLFNTL 44
K+GIVG GKS+L L
Sbjct: 32 KVGIVGRTGSGKSSLLLAL 50
>gnl|CDD|130262 TIGR01194, cyc_pep_trnsptr, cyclic peptide transporter. This model
describes cyclic peptide transporter in bacteria.
Bacteria have elaborate pathways for the production of
toxins and secondary metabolites. Many such compounds,
including syringomycin and pyoverdine are synthesized on
non-ribosomal templates consisting of a multienzyme
complex. On several occasions the proteins of the
complex and transporter protein are present on the same
operon. Often times these compounds cross the biological
membrane by specific transporters. Syringomycin is an
amphipathic, cylclic lipodepsipeptide when inserted into
host causes formation of channels, permeable to variety
of cations. On the other hand, pyoverdine is a cyclic
octa-peptidyl dihydroxyquinoline, which is efficient in
sequestering iron for uptake [Transport and binding
proteins, Amino acids, peptides and amines, Transport
and binding proteins, Other].
Length = 555
Score = 28.8 bits (64), Expect = 4.5
Identities = 21/52 (40%), Positives = 24/52 (46%)
Query: 1 MPPKASKSKEAPAERPILGRFSSHLKIGIVGLPNVGKSTLFNTLTKLAIPAE 52
M PKA + E A PI R + + IVG GKSTL L IP E
Sbjct: 345 MNPKAPEGSEGFALGPIDLRIAQGDIVFIVGENGCGKSTLAKLFCGLYIPQE 396
>gnl|CDD|151404 pfam10957, DUF2758, Protein of unknown function (DUF2758). This
family of proteins has no known function.
Length = 60
Score = 26.2 bits (58), Expect = 5.4
Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 11/42 (26%)
Query: 233 EKDYQRKKNKFLPKIH-----------AWVQEHGGEQIIPFS 263
EKD + + N FL KI A + E GEQI FS
Sbjct: 12 EKDLEDEVNVFLKKIDDDQLIDIKYNVAAMCEPEGEQIYCFS 53
>gnl|CDD|206709 cd04137, RheB, Ras Homolog Enriched in Brain (RheB) is a small
GTPase. Rheb (Ras Homolog Enriched in Brain)
subfamily. Rheb was initially identified in rat brain,
where its expression is elevated by seizures or by
long-term potentiation. It is expressed ubiquitously,
with elevated levels in muscle and brain. Rheb
functions as an important mediator between the tuberous
sclerosis complex proteins, TSC1 and TSC2, and the
mammalian target of rapamycin (TOR) kinase to stimulate
cell growth. TOR kinase regulates cell growth by
controlling nutrient availability, growth factors, and
the energy status of the cell. TSC1 and TSC2 form a
dimeric complex that has tumor suppressor activity, and
TSC2 is a GTPase activating protein (GAP) for Rheb. The
TSC1/TSC2 complex inhibits the activation of TOR kinase
through Rheb. Rheb has also been shown to induce the
formation of large cytoplasmic vacuoles in a process
that is dependent on the GTPase cycle of Rheb, but
independent of the TOR kinase, suggesting Rheb plays a
role in endocytic trafficking that leads to cell growth
and cell-cycle progression. 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 = 180
Score = 28.0 bits (63), Expect = 5.4
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 24 HLKIGIVGLPNVGKSTL 40
KI ++G +VGKS+L
Sbjct: 1 QRKIAVLGSRSVGKSSL 17
>gnl|CDD|199871 cd06251, M14_ASTE_ASPA_like_1, Peptidase M14 Succinylglutamate
desuccinylase (ASTE)/aspartoacylase (ASPA)-like;
uncharacterized subgroup. A functionally
uncharacterized subgroup of the Succinylglutamate
desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily
which is part of the M14 family of
metallocarboxypeptidases. ASTE catalyzes the fifth and
last step in arginine catabolism by the arginine
succinyltransferase pathway, and aspartoacylase (ASPA,
also known as aminoacylase 2, and ACY-2; EC:3.5.1.15)
cleaves N-acetyl L-aspartic acid (NAA) into aspartate
and acetate. NAA is abundant in the brain, and
hydrolysis of NAA by ASPA may help maintain white
matter. ASPA is an NAA scavenger in other tissues.
Mutations in the gene encoding ASPA cause Canavan
disease (CD), a fatal progressive neurodegenerative
disorder involving dysmyelination and spongiform
degeneration of white matter in children. This enzyme
binds zinc which is necessary for activity. Measurement
of elevated NAA levels in urine is used in the diagnosis
of CD.
Length = 287
Score = 28.3 bits (64), Expect = 5.7
Identities = 27/117 (23%), Positives = 35/117 (29%), Gaps = 30/117 (25%)
Query: 48 AIPAENFPFCTIEPNEARVNIPDERFEWLCQLFKPKSAVPAFLEIHDIAGLVRGAHEGQG 107
AI N P R ++ + L + F P L+ G +R A G
Sbjct: 118 AIGRTNLPQI-------RADLDNPEVLELARAFGA----PVILDSPGRDGSLRTAAVDAG 166
Query: 108 -------LGNSF---LSHIRA-VDGIFHVLRAF------EDPDIIHV--DDSVDPVR 145
G + IRA V GI +VLR P S VR
Sbjct: 167 IPVITYEAGEALRFDEDAIRAGVKGILNVLRHLGMLDGRRTPKRPPPVIARSSKWVR 223
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 27.8 bits (62), Expect = 5.9
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 29 IVGLPNVGKSTLFNTLT 45
I GL + GK++LF LT
Sbjct: 8 IAGLCDSGKTSLFTLLT 24
>gnl|CDD|224057 COG1134, TagH, ABC-type polysaccharide/polyol phosphate transport
system, ATPase component [Carbohydrate transport and
metabolism / Cell envelope biogenesis, outer membrane].
Length = 249
Score = 28.4 bits (64), Expect = 6.0
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 4/45 (8%)
Query: 4 KASKSKEAPAERPILGRFSSHL----KIGIVGLPNVGKSTLFNTL 44
+K AE L S + ++GI+G GKSTL +
Sbjct: 29 GLAKGGRKVAEFWALKDISFEIYKGERVGIIGHNGAGKSTLLKLI 73
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 28.1 bits (63), Expect = 6.0
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 10/44 (22%)
Query: 3 PKASKSKEAPAERPILGRFSSHLKIGIVGLPNVGKSTLFNTLTK 46
P ++ E P P++ + +VG P VGKSTL +L K
Sbjct: 28 PVVDRTPEEPP--PLV--------VVVVGPPGVGKSTLIRSLIK 61
>gnl|CDD|233477 TIGR01575, rimI, ribosomal-protein-alanine acetyltransferase.
Members of this model belong to the GCN5-related
N-acetyltransferase (GNAT) superfamily. This model
covers prokarotes and the archaea. The seed contains a
characterized accession for Gram negative E. coli. An
untraceable characterized accession (PIR|S66013) for
Gram positive B. subtilis scores well (205.0) in the
full alignment. Characterized members are lacking in the
archaea. Noise cutoff (72.4) was set to exclude M. loti
paralog of rimI. Trusted cutoff (80.0) was set at next
highest scoring member in the mini-database [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 131
Score = 27.3 bits (61), Expect = 6.8
Identities = 9/25 (36%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 91 EIHDIAGLVRGAHEGQGLGNSFLSH 115
I +IA V+ ++GQG+G + L
Sbjct: 56 HILNIA--VKPEYQGQGIGRALLRE 78
>gnl|CDD|213212 cd03245, ABCC_bacteriocin_exporters, ATP-binding cassette domain
of bacteriocin exporters, subfamily C. Many
non-lantibiotic bacteriocins of lactic acid bacteria
are produced as precursors which have N-terminal leader
peptides that share similarities in amino acid sequence
and contain a conserved processing site of two glycine
residues in positions -1 and -2. A dedicated
ATP-binding cassette (ABC) transporter is responsible
for the proteolytic cleavage of the leader peptides and
subsequent translocation of the bacteriocins across the
cytoplasmic membrane.
Length = 220
Score = 27.9 bits (63), Expect = 7.0
Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 6/49 (12%)
Query: 26 KIGIVGLPNVGKSTLFNTLTKLAIPAE------NFPFCTIEPNEARVNI 68
K+ I+G GKSTL L L P ++P + R NI
Sbjct: 32 KVAIIGRVGSGKSTLLKLLAGLYKPTSGSVLLDGTDIRQLDPADLRRNI 80
>gnl|CDD|225183 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 28.3 bits (64), Expect = 7.2
Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 4/43 (9%)
Query: 12 PAERPILGRFSSHLK----IGIVGLPNVGKSTLFNTLTKLAIP 50
P + P+L S + + IVG GKSTL L L P
Sbjct: 483 PDDPPVLEDLSLEIPPGEKVAIVGRSGSGKSTLLKLLLGLYKP 525
>gnl|CDD|213186 cd03219, ABC_Mj1267_LivG_branched, ATP-binding cassette component
of branched chain amino acids transport system. The
Mj1267/LivG ABC transporter subfamily is involved in
the transport of the hydrophobic amino acids leucine,
isoleucine and valine. MJ1267 is a branched-chain amino
acid transporter with 29% similarity to both the LivF
and LivG components of the E. coli branched-chain amino
acid transporter. MJ1267 contains an insertion from
residues 114 to 123 characteristic of LivG
(Leucine-Isoleucine-Valine) homologs. The
branched-chain amino acid transporter from E. coli
comprises a heterodimer of ABCs (LivF and LivG), a
heterodimer of six-helix TM domains (LivM and LivH),
and one of two alternative soluble periplasmic
substrate binding proteins (LivK or LivJ).
Length = 236
Score = 27.8 bits (63), Expect = 7.3
Identities = 11/24 (45%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 28 GIVGLPN-VGKSTLFNTLTKLAIP 50
G++G PN GK+TLFN ++ P
Sbjct: 30 GLIG-PNGAGKTTLFNLISGFLRP 52
>gnl|CDD|224533 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 179
Score = 27.7 bits (62), Expect = 7.5
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 25 LKIGIVGLPNVGKSTL 40
+KI I G P VGK+TL
Sbjct: 6 MKIFITGRPGVGKTTL 21
>gnl|CDD|223434 COG0357, GidB, Predicted S-adenosylmethionine-dependent
methyltransferase involved in bacterial cell division
[Cell envelope biogenesis, outer membrane].
Length = 215
Score = 27.6 bits (62), Expect = 7.7
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 147 LEVISAELRLKDIEFMERRIEDVEKSMK 174
L + EL L+++E + R E+ + K
Sbjct: 107 LREVKKELGLENVEIVHGRAEEFGQEKK 134
>gnl|CDD|224847 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 27.7 bits (62), Expect = 7.7
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 26 KIGIVGLPNVGKSTLFNTLTKLAIP 50
I I G P VGK+T+ L +L
Sbjct: 2 LIAITGTPGVGKTTVCKLLRELGYK 26
>gnl|CDD|213197 cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the
drug resistance transporter and related proteins,
subfamily A. This family of ATP-binding proteins
belongs to a multi-subunit transporter involved in drug
resistance (BcrA and DrrA), nodulation, lipid
transport, and lantibiotic immunity. In bacteria and
archaea, these transporters usually include an
ATP-binding protein and one or two integral membrane
proteins. Eukaryotic systems of the ABCA subfamily
display ABC domains that are quite similar to this
family. The ATP-binding domain shows the highest
similarity between all members of the ABC transporter
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 = 173
Score = 27.4 bits (62), Expect = 7.9
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 27 IGIVGLPN-VGKSTLFNTLTKLAIP 50
G++G PN GK+TL + L P
Sbjct: 29 YGLLG-PNGAGKTTLIKIILGLLKP 52
>gnl|CDD|223315 COG0237, CoaE, Dephospho-CoA kinase [Coenzyme metabolism].
Length = 201
Score = 27.6 bits (62), Expect = 8.2
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 25 LKIGIVGLPNVGKSTLFNTLTKLAIP 50
L IG+ G GKST+ L +L P
Sbjct: 3 LIIGLTGGIGSGKSTVAKILAELGFP 28
>gnl|CDD|197556 smart00178, SAR, Sar1p-like members of the Ras-family of small
GTPases. Yeast SAR1 is an essential gene required for
transport of secretory proteins from the endoplasmic
reticulum to the Golgi apparatus.
Length = 184
Score = 27.6 bits (61), Expect = 8.2
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 18 LGRFSSHLKIGIVGLPNVGKSTLFNTL 44
LG ++ H KI +GL N GK+TL + L
Sbjct: 11 LGLWNKHAKILFLGLDNAGKTTLLHML 37
>gnl|CDD|175986 cd04019, C2C_MCTP_PRT_plant, C2 domain third repeat found in
Multiple C2 domain and Transmembrane region Proteins
(MCTP); plant subset. MCTPs are involved in Ca2+
signaling at the membrane. Plant-MCTPs are composed of
a variable N-terminal sequence, four C2 domains, two
transmembrane regions (TMRs), and a short C-terminal
sequence. It is one of four protein classes that are
anchored to membranes via a transmembrane region; the
others being synaptotagmins, extended synaptotagmins,
and ferlins. MCTPs are the only membrane-bound C2 domain
proteins that contain two functional TMRs. MCTPs are
unique in that they bind Ca2+ but not phospholipids. C2
domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the third C2
repeat, C2C, and has a type-II topology.
Length = 150
Score = 27.2 bits (61), Expect = 8.3
Identities = 17/40 (42%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 129 FEDPDIIHVDDSVDPVRDLEVISAELRLKDIEFMERRIED 168
FED I+ V+D V P +D + A + L DI ERR++D
Sbjct: 60 FEDHLILSVEDRVGPNKDEPLGRAVIPLNDI---ERRVDD 96
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl)
small GTPases. Arf (ADP-ribosylation factor)/Arl
(Arf-like) small GTPases. Arf proteins are activators
of phospholipase D isoforms. Unlike Ras proteins they
lack cysteine residues at their C-termini and therefore
are unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a
unique structural device, interswitch toggle, that
implements front-back communication from N-terminus to
the nucleotide binding site. Arf-like (Arl) proteins
are close relatives of the Arf, but only Arl1 has been
shown to function in membrane traffic like the Arf
proteins. Arl2 has an unrelated function in the folding
of native tubulin, and Arl4 may function in the
nucleus. Most other Arf family proteins are so far
relatively poorly characterized. Thus, despite their
significant sequence homologies, Arf family proteins
may regulate unrelated functions.
Length = 158
Score = 27.2 bits (61), Expect = 8.4
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 26 KIGIVGLPNVGKSTLFNTL 44
+I ++GL GK+T+ L
Sbjct: 1 RILMLGLDGAGKTTILYKL 19
>gnl|CDD|226210 COG3685, COG3685, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 167
Score = 27.3 bits (61), Expect = 8.5
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 156 LKDIEFMERRIEDVEKSM-KRSNDKQLK--IEHELCQ 189
L+DI E++I M +R+ +LK IE L +
Sbjct: 14 LRDIYAAEKQILKALPKMARRAQYPELKAAIEKHLEE 50
>gnl|CDD|223998 COG1072, CoaA, Panthothenate kinase [Coenzyme metabolism].
Length = 283
Score = 27.6 bits (62), Expect = 8.6
Identities = 11/22 (50%), Positives = 11/22 (50%)
Query: 27 IGIVGLPNVGKSTLFNTLTKLA 48
IGI G VGKST L L
Sbjct: 85 IGIAGSVAVGKSTTARILQALL 106
>gnl|CDD|217340 pfam03055, RPE65, Retinal pigment epithelial membrane protein.
This family represents a retinal pigment epithelial
membrane receptor which is abundantly expressed in
retinal pigment epithelium, and binds plasma retinal
binding protein. The family also includes the sequence
related neoxanthin cleavage enzyme in plants and
lignostilbene-alpha,beta-dioxygenase in bacteria.
Length = 469
Score = 28.0 bits (63), Expect = 8.7
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 122 IFHVLRAFEDPDIIHVD 138
+FH A+E+ I +D
Sbjct: 278 VFHTANAWEEGGEIVLD 294
>gnl|CDD|184130 PRK13545, tagH, teichoic acids export protein ATP-binding
subunit; Provisional.
Length = 549
Score = 27.9 bits (62), Expect = 9.1
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 27 IGIVGLPNVGKSTLFNTLTKLAIPAE 52
+GI+GL GKSTL N + + +P +
Sbjct: 53 VGIIGLNGSGKSTLSNLIAGVTMPNK 78
>gnl|CDD|213202 cd03235, ABC_Metallic_Cations, ATP-binding cassette domain of the
metal-type transporters. This family includes
transporters involved in the uptake of various metallic
cations such as iron, manganese, and zinc. The ATPases
of this group of transporters are very similar to
members of iron-siderophore uptake family suggesting
that they share a common ancestor. The best
characterized metal-type ABC transporters are the
YfeABCD system of Y. pestis, the SitABCD system of
Salmonella enterica serovar Typhimurium, and the
SitABCD transporter of Shigella flexneri. Moreover
other uncharacterized homologs of these metal-type
transporters are mainly found in pathogens like
Haemophilus or enteroinvasive E. coli isolates.
Length = 213
Score = 27.5 bits (62), Expect = 9.9
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 27 IGIVGLPN-VGKSTLFNTLTKLAIPAE 52
+ IVG PN GKSTL + L P
Sbjct: 28 LAIVG-PNGAGKSTLLKAILGLLKPTS 53
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.138 0.418
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,380,302
Number of extensions: 1806879
Number of successful extensions: 2438
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2386
Number of HSP's successfully gapped: 177
Length of query: 350
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 252
Effective length of database: 6,590,910
Effective search space: 1660909320
Effective search space used: 1660909320
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.2 bits)