RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17315
(561 letters)
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 370 bits (951), Expect = e-124
Identities = 158/287 (55%), Positives = 200/287 (69%), Gaps = 24/287 (8%)
Query: 267 RAFEDDDVTHVEGEVNPVRDIEIINEELRLKDVEHIEKEINKIEKLVQRGDKKLKPEYVS 326
RAFED+D+THVEGE++PVRD+EII+ EL LKD+E +EK ++++ K R KK K E
Sbjct: 124 RAFEDEDITHVEGEIDPVRDLEIISSELILKDLEFVEKRLDELTKK--RKKKKKKKEEKV 181
Query: 327 EVWFSFIYLFIKNGHIGHEDALVKIKAFVCEGDKRHARYGDWSNADIEHLNKLNLLTAKT 386
E+ D L K+ ++ EG + R GDW++ +IE LN+ LLTAK
Sbjct: 182 EL-----------------DVLKKVLEWLEEG--KPVRDGDWTDKEIEILNEYQLLTAKP 222
Query: 387 QIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDE-RQRYL 445
IYLVN+S KD+I++KNKWL KIKEWV G IIP+S FE +L ++ +E R+ YL
Sbjct: 223 MIYLVNMSEKDFIRQKNKWLAKIKEWVGEKGGG-PIIPYSAEFEEELAELGSEEERKEYL 281
Query: 446 DEQKAT-SVLDKIITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGF 504
+E S+LDKII GYK L L +FFTAG DEV+ WTIQKGTKAPQAAG IH+DFEKGF
Sbjct: 282 EEYGIKQSMLDKIIKTGYKLLNLIHFFTAGPDEVRCWTIQKGTKAPQAAGVIHSDFEKGF 341
Query: 505 IMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFNA 551
I AEVM ++DF E GSEAA +A GKYRQ+G+ Y V+DGDIIFFKFN
Sbjct: 342 ICAEVMKYEDFLELGSEAAVKAEGKYRQEGKDYVVQDGDIIFFKFNV 388
Score = 181 bits (462), Expect = 7e-52
Identities = 72/124 (58%), Positives = 83/124 (66%), Gaps = 19/124 (15%)
Query: 76 MGPKKTDEGEKKMLLGRVGTNLKVGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPNE 135
M PKK E EKK+LLGR G NLK+GIVG+PNVGKST FN L K AENFPFCTIDPN
Sbjct: 1 MPPKKKMEEEKKVLLGRPGNNLKMGIVGLPNVGKSTTFNALCKQQVPAENFPFCTIDPNT 60
Query: 136 -------------------NNKVPAFLNVVDIAGLVKGAAEGQGLGNAFLSHISACDAIF 176
+ VPA L++ DIAGLVKGA+EG+GLGNAFLSHI A D I+
Sbjct: 61 ARVNVPDERFDWLCKHFKPKSIVPAQLDITDIAGLVKGASEGEGLGNAFLSHIRAVDGIY 120
Query: 177 HLCK 180
H+ +
Sbjct: 121 HVVR 124
Score = 76.1 bits (188), Expect = 8e-15
Identities = 31/43 (72%), Positives = 34/43 (79%)
Query: 224 MGPKKTDEGEKKMLLGRVGTNLKVGIVGVPNVGKSTFFNVLTK 266
M PKK E EKK+LLGR G NLK+GIVG+PNVGKST FN L K
Sbjct: 1 MPPKKKMEEEKKVLLGRPGNNLKMGIVGLPNVGKSTTFNALCK 43
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 294 bits (755), Expect = 4e-95
Identities = 119/285 (41%), Positives = 174/285 (61%), Gaps = 27/285 (9%)
Query: 267 RAFEDDDVTHVEGEVNPVRDIEIINEELRLKDVEHIEKEINKIEKLVQRGDKKLKPEYVS 326
R FEDD++THVEG+V+P+RDIE IN EL L D+E +EK + ++EK + GDK+ K E
Sbjct: 105 RCFEDDNITHVEGKVDPIRDIETINTELILADLETVEKRLERLEKKAKGGDKEAKAEL-- 162
Query: 327 EVWFSFIYLFIKNGHIGHEDALVKIKAFVCEGDKRHARYGDWSNADIEHLNKLNLLTAKT 386
+ L K+ + EG + AR + ++ + + L L LLTAK
Sbjct: 163 -------------------ELLEKLLEHLEEG--KPARTLELTDEEEKLLKSLQLLTAKP 201
Query: 387 QIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLD 446
+Y+ N+ D + N ++ K++E A GA ++ E ++ ++ D+E+ +L+
Sbjct: 202 VLYVANVDEDD-LADGNPYVKKVREI--AAKEGAEVVVICAKIEAEIAELDDEEKAEFLE 258
Query: 447 EQKAT-SVLDKIITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFI 505
E S LD++I GY+ L L +FTAG EV+AWTI+KGT APQAAG IHTDFEKGFI
Sbjct: 259 ELGLEESGLDRLIRAGYELLGLITYFTAGPKEVRAWTIKKGTTAPQAAGVIHTDFEKGFI 318
Query: 506 MAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFN 550
AEV+ +DD E+GSEA + AGK R +G+ Y V+DGD++ F+FN
Sbjct: 319 RAEVISYDDLIEYGSEAGAKEAGKVRLEGKDYIVQDGDVMHFRFN 363
Score = 140 bits (356), Expect = 5e-37
Identities = 53/100 (53%), Positives = 63/100 (63%), Gaps = 19/100 (19%)
Query: 97 LKVGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPNE-------------------NN 137
LK GIVG+PNVGKST FN LTK+ A A N+PFCTI+PN
Sbjct: 3 LKCGIVGLPNVGKSTLFNALTKAGAEAANYPFCTIEPNVGVVPVPDPRLDKLAEIVKPKK 62
Query: 138 KVPAFLNVVDIAGLVKGAAEGQGLGNAFLSHISACDAIFH 177
VPA + VDIAGLVKGA++G+GLGN FL++I DAI H
Sbjct: 63 IVPATIEFVDIAGLVKGASKGEGLGNQFLANIREVDAIVH 102
Score = 52.0 bits (126), Expect = 4e-07
Identities = 18/22 (81%), Positives = 19/22 (86%)
Query: 245 LKVGIVGVPNVGKSTFFNVLTK 266
LK GIVG+PNVGKST FN LTK
Sbjct: 3 LKCGIVGLPNVGKSTLFNALTK 24
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 264 bits (678), Expect = 1e-83
Identities = 124/292 (42%), Positives = 168/292 (57%), Gaps = 32/292 (10%)
Query: 267 RAFEDDDVTHVEGEVNPVRDIEIINEELRLKDVEHIEKEINKIEKLVQRG---DKKLKPE 323
R F D D+ HVEG+V+PV DIEIIN EL L D+E +EK ++EK + G DK+LK E
Sbjct: 106 RCFGDTDIEHVEGKVDPVEDIEIINTELILWDLESLEKRWERLEKRAKAGKKLDKELKEE 165
Query: 324 YVSEVWFSFIYLFIKNGHIGHEDALVKIKAFVCEG-DKRHARYGDWSNADIEHLNKLNLL 382
L K++ + EG R WS D+E L LNLL
Sbjct: 166 L---------------------SLLGKLEEHLEEGKPARGLDLSKWSEEDLEALASLNLL 204
Query: 383 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPD-DER 441
TAK +Y+ N+S D N+++ ++KE A ++P S E +L ++ D +E+
Sbjct: 205 TAKPMLYVANVSEDDL-ANLNEYVKRLKELAAKE--NAEVVPVSAAIELELRELADAEEK 261
Query: 442 QRYLDE--QKATSVLDKIITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTD 499
+L E QK S L+++I GY L LQ +FTAG EV+AWTI+ G+KAP AAG IH D
Sbjct: 262 GEFLIELGQK-ESGLNELIRAGYGLLGLQTYFTAGVKEVRAWTIKDGSKAPDAAGVIHPD 320
Query: 500 FEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFNA 551
FEKGFI AEV+ + D +G EAA + AGK R +G+ Y V+DGD+I FKFN
Sbjct: 321 FEKGFIRAEVISYADLIHYGGEAAAKEAGKRRLEGKDYIVQDGDVIHFKFNV 372
Score = 141 bits (357), Expect = 4e-37
Identities = 51/103 (49%), Positives = 62/103 (60%), Gaps = 20/103 (19%)
Query: 95 TNLKVGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPNE------------------- 135
+LK+GIVG+PNVGKST FN LTK+ A N+PFCTI+PN
Sbjct: 1 MSLKIGIVGLPNVGKSTLFNALTKAGAEIANYPFCTIEPNVGVVYVPDCRLDELAEIVKC 60
Query: 136 -NNKVPAFLNVVDIAGLVKGAAEGQGLGNAFLSHISACDAIFH 177
PA + VDIAGLVKGA++G+GLGN FL +I DAI H
Sbjct: 61 PPKIRPAPVEFVDIAGLVKGASKGEGLGNKFLDNIREVDAIIH 103
Score = 50.6 bits (122), Expect = 1e-06
Identities = 18/24 (75%), Positives = 21/24 (87%)
Query: 243 TNLKVGIVGVPNVGKSTFFNVLTK 266
+LK+GIVG+PNVGKST FN LTK
Sbjct: 1 MSLKIGIVGLPNVGKSTLFNALTK 24
>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 = 201 bits (515), Expect = 8e-61
Identities = 81/200 (40%), Positives = 109/200 (54%), Gaps = 27/200 (13%)
Query: 267 RAFEDDDVTHVEGEVNPVRDIEIINEELRLKDVEHIEKEINKIEKLVQRGDKKLKPEYVS 326
R FEDDD+THVEG V+PVRDIEIIN EL L D+E IEK + ++EK + GDK+ K E
Sbjct: 101 RCFEDDDITHVEGSVDPVRDIEIINTELILADLETIEKRLERLEKKAKSGDKEAKEEL-- 158
Query: 327 EVWFSFIYLFIKNGHIGHEDALVKIKAFVCEGDKRHARYGDWSNADIEHLNKLNLLTAKT 386
+ L KIK + EG AR + ++ +I+ L L LLTAK
Sbjct: 159 -------------------ELLEKIKEHLEEGKP--ARTLELTDEEIKILKSLQLLTAKP 197
Query: 387 QIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLD 446
IY+ N+S D I+ NK L K A GA +IP S E +L ++ ++E +L+
Sbjct: 198 VIYVANVSEDDLIRGNNKVL---KVREIAAKEGAEVIPISAKLEAELAELDEEEAAEFLE 254
Query: 447 EQKAT-SVLDKIITQGYKSL 465
E S LDK+I GY+ L
Sbjct: 255 ELGLEESGLDKLIRAGYELL 274
Score = 159 bits (406), Expect = 4e-45
Identities = 54/100 (54%), Positives = 64/100 (64%), Gaps = 19/100 (19%)
Query: 99 VGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPNE-------------------NNKV 139
+GIVG+PNVGKST FN LTKS+A A N+PFCTI+PN V
Sbjct: 1 IGIVGLPNVGKSTLFNALTKSNAEAANYPFCTIEPNVGIVPVPDERLDKLAEIVKPKKIV 60
Query: 140 PAFLNVVDIAGLVKGAAEGQGLGNAFLSHISACDAIFHLC 179
PA + VDIAGLVKGA++G+GLGN FLSHI DAI H+
Sbjct: 61 PATIEFVDIAGLVKGASKGEGLGNKFLSHIREVDAIAHVV 100
Score = 50.5 bits (122), Expect = 7e-07
Identities = 16/20 (80%), Positives = 18/20 (90%)
Query: 247 VGIVGVPNVGKSTFFNVLTK 266
+GIVG+PNVGKST FN LTK
Sbjct: 1 IGIVGLPNVGKSTLFNALTK 20
>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 = 192 bits (489), Expect = 4e-56
Identities = 98/287 (34%), Positives = 138/287 (48%), Gaps = 28/287 (9%)
Query: 267 RAFEDDDVTHVEGEVNPVRDIEIINEELRLKDVEHIEKEINKIEKLVQRGDKKLKPEYVS 326
R FEDD + HV +P D EII+EEL D +EK I + +K + G K + +
Sbjct: 106 RCFEDDIIHHVGNVDDPRDDFEIIDEELLKADEFLVEKRIGRSKKSAEGGKDKKEELLLL 165
Query: 327 EVWFSFIYLFIKNGHIGHEDALVKIKAFVCEGDKRHARYGDWSNADIEHLNKLNLLTAKT 386
E I + G + + L K L K
Sbjct: 166 E----------------------IILPLLNGGQMARHV---DLSKEELILIKSLNLLTKK 200
Query: 387 QIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQ-LVDMPDDERQRYL 445
I L+ ++DY++ N I EW+ A G + F E L ++ D+ERQ +L
Sbjct: 201 PIILIANVSEDYLRNLNNNYLLIVEWIAAYSKGDPKVVFVCALEESELSELDDEERQEFL 260
Query: 446 DE--QKATSVLDKIITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKG 503
+ ++ L+ II YK L L +FFT G++EV+AWT + G APQAAG IHTDFE G
Sbjct: 261 QKLGLTESAGLNIIIRARYKLLLLSFFFTGGKEEVRAWTRKGGWAAPQAAGIIHTDFETG 320
Query: 504 FIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFN 550
FI AEV+ +DDF S + G R +G+ Y V+DGD++FF FN
Sbjct: 321 FIAAEVISWDDFIYKKSSQGAKKGGLMRLEGKYYVVDDGDVLFFAFN 367
Score = 75.6 bits (186), Expect = 9e-15
Identities = 45/101 (44%), Positives = 53/101 (52%), Gaps = 20/101 (19%)
Query: 97 LKVGIVGVPNVGKSTFFNVLTKSSAA-AENFPFCTIDPN------------------ENN 137
L GIVG+PNVGKST F T A N PF TI+PN +
Sbjct: 3 LSGGIVGLPNVGKSTLFAATTNLLGNEAANPPFTTIEPNAGVVNPSDPRLDLLAIYIKPE 62
Query: 138 KVPAFLNV-VDIAGLVKGAAEGQGLGNAFLSHISACDAIFH 177
KVP VDIAGLV GA++G+GLGN FL++I D I H
Sbjct: 63 KVPPTTTEFVDIAGLVGGASKGEGLGNQFLANIREVDIIQH 103
>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 = 176 bits (449), Expect = 9e-54
Identities = 62/83 (74%), Positives = 70/83 (84%)
Query: 467 LQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRA 526
L FFTAG DEV+AWTI+KGTKAPQAAG IHTDFEKGFI AEVM ++D E GSEAA +
Sbjct: 1 LISFFTAGPDEVRAWTIRKGTKAPQAAGVIHTDFEKGFIRAEVMKYEDLVELGSEAAAKE 60
Query: 527 AGKYRQQGRAYTVEDGDIIFFKF 549
AGKYRQ+G+ Y V+DGDIIFFKF
Sbjct: 61 AGKYRQEGKDYVVQDGDIIFFKF 83
>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 = 164 bits (418), Expect = 3e-49
Identities = 55/84 (65%), Positives = 66/84 (78%)
Query: 467 LQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRA 526
L FFTAG EV+AWTI+KGT APQAAG IH+DFEKGFI AEV+ +DD E+GSEA +
Sbjct: 1 LITFFTAGPKEVRAWTIRKGTTAPQAAGVIHSDFEKGFIRAEVISYDDLIEYGSEAKAKE 60
Query: 527 AGKYRQQGRAYTVEDGDIIFFKFN 550
AGK R +G+ Y V+DGDII F+FN
Sbjct: 61 AGKLRLEGKDYIVQDGDIIHFRFN 84
>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 = 92.7 bits (231), Expect = 1e-20
Identities = 40/106 (37%), Positives = 54/106 (50%), Gaps = 26/106 (24%)
Query: 99 VGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPN------------------ENNKVP 140
+G+VG PNVGKSTFFN T + N+PF TIDPN N +
Sbjct: 1 IGLVGKPNVGKSTFFNAATLADVEIANYPFTTIDPNVGVGYVRVECPCKELGVSCNPRYG 60
Query: 141 AFLN--------VVDIAGLVKGAAEGQGLGNAFLSHISACDAIFHL 178
++ ++D+AGLV GA EG+GLGN FL + D + H+
Sbjct: 61 KCIDGKRYVPVELIDVAGLVPGAHEGKGLGNQFLDDLRDADVLIHV 106
Score = 41.4 bits (98), Expect = 9e-04
Identities = 14/19 (73%), Positives = 16/19 (84%)
Query: 247 VGIVGVPNVGKSTFFNVLT 265
+G+VG PNVGKSTFFN T
Sbjct: 1 IGLVGKPNVGKSTFFNAAT 19
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 92.9 bits (232), Expect = 2e-20
Identities = 43/109 (39%), Positives = 56/109 (51%), Gaps = 30/109 (27%)
Query: 97 LKVGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPN---------------------E 135
+ +G+VG PNVGKSTFFN T + N+PF TIDPN
Sbjct: 2 ITIGLVGKPNVGKSTFFNAATLADVEIANYPFTTIDPNVGVAYVRVECPCKELGVKCNPR 61
Query: 136 NNK-------VPAFLNVVDIAGLVKGAAEGQGLGNAFLSHISACDAIFH 177
N K +P + ++D+AGLV GA EG+GLGN FL + DA+ H
Sbjct: 62 NGKCIDGTRFIP--VELIDVAGLVPGAHEGRGLGNQFLDDLRQADALIH 108
Score = 42.1 bits (100), Expect = 6e-04
Identities = 14/21 (66%), Positives = 17/21 (80%)
Query: 245 LKVGIVGVPNVGKSTFFNVLT 265
+ +G+VG PNVGKSTFFN T
Sbjct: 2 ITIGLVGKPNVGKSTFFNAAT 22
Score = 29.0 bits (66), Expect = 7.0
Identities = 62/310 (20%), Positives = 112/310 (36%), Gaps = 88/310 (28%)
Query: 279 GEVNPVRDIEIINEELRLKDVEHIEKEINKIEKLVQRGDKKLKPEYVSEVWFSFIYLFIK 338
G +PV DI+ + EEL + +EK K + Q ++ E ++E L I
Sbjct: 126 GSHDPVEDIKFLEEELDMWIYGILEKNWEKFSRKAQAEKFDIE-EALAEQ---LSGLGIN 181
Query: 339 NGHIGHEDALVKIKAFVCEGDKRHARYGDWSNADIEHLNKLNLLTAKTQIYLVN----LS 394
H+ ++AL ++ W++ D+ L + +K + N
Sbjct: 182 EEHV--KEALRELGL--------PEDPSKWTDEDLLELARELRKISKPMVIAANKADLPP 231
Query: 395 AKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLV-------------------- 434
A++ I++ +KE + ++P S E L
Sbjct: 232 AEENIER-------LKE-----EKYYIVVPTSAEAELALRRAAKAGLIDYIPGDSDFEIL 279
Query: 435 -DMPDDERQ------RYLDEQKATSVLDKIITQGYKSLQLQYFFTAGQDEVKAWTIQKGT 487
++ + +++ L + T V + I T + L + + +DE K T +KG
Sbjct: 280 GELSEKQKKALEYIREVLKKYGGTGVQEAINTAVFDLLDMIVVY-PVEDENK-LTDKKGN 337
Query: 488 KAPQA------------AGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGR 535
P A A +IHTD +GF+ A D + R+ G
Sbjct: 338 VLPDAFLLPKGSTARDLAYKIHTDIGEGFLYAI-----DARTK------------RRIGE 380
Query: 536 AYTVEDGDII 545
Y ++DGD+I
Sbjct: 381 DYELKDGDVI 390
>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 = 82.0 bits (203), Expect = 8e-19
Identities = 33/85 (38%), Positives = 47/85 (55%), Gaps = 4/85 (4%)
Query: 98 KVGIVGVPNVGKSTFFNVLTKSSAA-AENFPFCTIDPNENN-KVPAFLNVVDIAGLVKGA 155
+V +VG PNVGKST N LT + A ++P T DP + + +VD GL++GA
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVLGLGRQIILVDTPGLIEGA 60
Query: 156 AEGQGLG--NAFLSHISACDAIFHL 178
+EG+G+ N FL I D I +
Sbjct: 61 SEGKGVEGFNRFLEAIREADLILLV 85
Score = 44.6 bits (106), Expect = 1e-05
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 246 KVGIVGVPNVGKSTFFNVLTKR 267
+V +VG PNVGKST N LT
Sbjct: 1 RVALVGRPNVGKSTLINALTGA 22
>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 = 81.7 bits (202), Expect = 4e-18
Identities = 32/81 (39%), Positives = 49/81 (60%), Gaps = 3/81 (3%)
Query: 100 GIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPNE---NNKVPAFLNVVDIAGLVKGAA 156
G+VG+PNVGKST + LT + ++PF T++PN + ++D+ GL+ GA+
Sbjct: 1 GLVGLPNVGKSTLLSALTSAKVEIASYPFTTLEPNVGVFEFGDGVDIQIIDLPGLLDGAS 60
Query: 157 EGQGLGNAFLSHISACDAIFH 177
EG+GLG L+H+ D I H
Sbjct: 61 EGRGLGEQILAHLYRSDLILH 81
Score = 38.9 bits (91), Expect = 0.002
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 248 GIVGVPNVGKSTFFNVLTK 266
G+VG+PNVGKST + LT
Sbjct: 1 GLVGLPNVGKSTLLSALTS 19
>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 = 75.2 bits (186), Expect = 8e-16
Identities = 31/86 (36%), Positives = 51/86 (59%), Gaps = 9/86 (10%)
Query: 99 VGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPN------ENNKVPAFLNVVDIAGLV 152
VG+VG+PN GKST + ++ + ++PF T+ PN ++ + + DI GL+
Sbjct: 3 VGLVGLPNAGKSTLLSAISNAKPKIADYPFTTLVPNLGVVRVDDGRS---FVIADIPGLI 59
Query: 153 KGAAEGQGLGNAFLSHISACDAIFHL 178
+GA+EG+GLG+ FL HI + H+
Sbjct: 60 EGASEGKGLGHRFLRHIERTRVLLHV 85
Score = 46.3 bits (111), Expect = 6e-06
Identities = 30/147 (20%), Positives = 46/147 (31%), Gaps = 59/147 (40%)
Query: 247 VGIVGVPNVGKSTFFNVLTK--------------------RAFEDDDVT----------- 275
VG+VG+PN GKST + ++ R +
Sbjct: 3 VGLVGLPNAGKSTLLSAISNAKPKIADYPFTTLVPNLGVVRVDDGRSFVIADIPGLIEGA 62
Query: 276 ------------HVE------------GEVNPVRDIEIINEELRLKDVEHIEKE----IN 307
H+E GE +PV D E I EL + EK +N
Sbjct: 63 SEGKGLGHRFLRHIERTRVLLHVIDLSGEDDPVEDYETIRNELEAYNPGLAEKPRIVVLN 122
Query: 308 KIEKLVQRGDKKLKPEYVSEVWFSFIY 334
KI+ L + E + E+ ++
Sbjct: 123 KIDLLDAEERFEKLKELLKELKGKKVF 149
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 78.4 bits (194), Expect = 1e-15
Identities = 34/91 (37%), Positives = 48/91 (52%), Gaps = 19/91 (20%)
Query: 99 VGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPNENNKVPAFLNVV-----------D 147
VG+VG+PN GKST + ++ + ++PF T+ PN L VV D
Sbjct: 162 VGLVGLPNAGKSTLLSAVSAAKPKIADYPFTTLVPN--------LGVVRVDGGESFVVAD 213
Query: 148 IAGLVKGAAEGQGLGNAFLSHISACDAIFHL 178
I GL++GA+EG GLG FL HI + H+
Sbjct: 214 IPGLIEGASEGVGLGLRFLRHIERTRVLLHV 244
Score = 39.5 bits (93), Expect = 0.004
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 247 VGIVGVPNVGKSTFFNVLT 265
VG+VG+PN GKST + ++
Sbjct: 162 VGLVGLPNAGKSTLLSAVS 180
>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 = 77.9 bits (193), Expect = 1e-15
Identities = 40/111 (36%), Positives = 56/111 (50%), Gaps = 27/111 (24%)
Query: 83 EGEKKMLLGRVGTNLK----VGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPNENNK 138
GE++ L LK VG+VG+PN GKST + ++ + ++PF T+ PN
Sbjct: 144 PGEERWLR----LELKLLADVGLVGLPNAGKSTLISAVSAAKPKIADYPFTTLVPN---- 195
Query: 139 VPAFLNVV-----------DIAGLVKGAAEGQGLGNAFLSHISACDAIFHL 178
L VV DI GL++GA+EG GLG+ FL HI + HL
Sbjct: 196 ----LGVVRVDDGRSFVIADIPGLIEGASEGAGLGHRFLKHIERTRVLLHL 242
Score = 38.2 bits (90), Expect = 0.009
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 8/39 (20%)
Query: 231 EGEKKMLLGRVGTNLK----VGIVGVPNVGKSTFFNVLT 265
GE++ L LK VG+VG+PN GKST + ++
Sbjct: 144 PGEERWLR----LELKLLADVGLVGLPNAGKSTLISAVS 178
Score = 30.5 bits (70), Expect = 2.2
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 5/42 (11%)
Query: 273 DVTHVEGEVNPVRDIEIINEELRLKDVEHIEKE----INKIE 310
D++ +G +P+ D EII EL+ E EK +NKI+
Sbjct: 244 DISPEDGS-DPIEDYEIIRNELKKYSPELAEKPRIVVLNKID 284
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 76.6 bits (190), Expect = 3e-15
Identities = 42/115 (36%), Positives = 58/115 (50%), Gaps = 35/115 (30%)
Query: 83 EGEKKMLLGRVGTNLK----VGIVGVPNVGKSTFFNVLTKSSAAAE----NFPFCTIDPN 134
GE++ L LK VG+VG+PN GKST + ++ AA+ ++PF T+ PN
Sbjct: 145 PGEERWLRLE----LKLLADVGLVGLPNAGKSTLISAVS----AAKPKIADYPFTTLHPN 196
Query: 135 ENNKVPAFLNVV-----------DIAGLVKGAAEGQGLGNAFLSHISACDAIFHL 178
L VV DI GL++GA+EG GLG+ FL HI + HL
Sbjct: 197 --------LGVVRVDDYKSFVIADIPGLIEGASEGAGLGHRFLKHIERTRLLLHL 243
Score = 39.7 bits (94), Expect = 0.003
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 8/39 (20%)
Query: 231 EGEKKMLLGRVGTNLK----VGIVGVPNVGKSTFFNVLT 265
GE++ L LK VG+VG+PN GKST + ++
Sbjct: 145 PGEERWLRLE----LKLLADVGLVGLPNAGKSTLISAVS 179
Score = 29.3 bits (67), Expect = 6.1
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 280 EVNPVRDIEIINEELRLKDVEHIEKE----INKIEKLVQRGDKKLK 321
V+PV D + I EL E +K +NKI+ L + +++ +
Sbjct: 248 AVDPVEDYKTIRNELEKYSPELADKPRILVLNKIDLLDEEEEREKR 293
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 77.1 bits (191), Expect = 4e-15
Identities = 37/91 (40%), Positives = 49/91 (53%), Gaps = 19/91 (20%)
Query: 99 VGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPNENNKVPAFLNVV-----------D 147
VG+VG PNVGKST +V++ + N+ F T+ PN L VV D
Sbjct: 161 VGLVGFPNVGKSTLLSVVSNAKPKIANYHFTTLVPN--------LGVVETDDGRSFVMAD 212
Query: 148 IAGLVKGAAEGQGLGNAFLSHISACDAIFHL 178
I GL++GA+EG GLG+ FL HI I H+
Sbjct: 213 IPGLIEGASEGVGLGHQFLRHIERTRVIVHV 243
Score = 37.4 bits (88), Expect = 0.015
Identities = 12/20 (60%), Positives = 16/20 (80%)
Query: 247 VGIVGVPNVGKSTFFNVLTK 266
VG+VG PNVGKST +V++
Sbjct: 161 VGLVGFPNVGKSTLLSVVSN 180
Score = 33.2 bits (77), Expect = 0.32
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 10/62 (16%)
Query: 273 DVTHVEGEVNPVRDIEIINEELRLKDVEHIEKE----INKI-----EKLVQRGDKKLKPE 323
D++ EG +P+ D E IN+EL+L + +E+ NK+ E+ ++ +KL P+
Sbjct: 245 DMSGSEGR-DPIEDYEKINKELKLYNPRLLERPQIVVANKMDLPEAEENLEEFKEKLGPK 303
Query: 324 YV 325
Sbjct: 304 VF 305
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 68.4 bits (168), Expect = 2e-12
Identities = 41/119 (34%), Positives = 59/119 (49%), Gaps = 30/119 (25%)
Query: 78 PKKTD---EGEKKMLLGRVGTNLK----VGIVGVPNVGKSTFFNVLTKSSAAAENFPFCT 130
P++ GE++ L LK VG++G+PN GKSTF ++ + ++PF T
Sbjct: 138 PRQKTPGTPGEERELKLE----LKLLADVGLLGLPNAGKSTFIRAVSAAKPKVADYPFTT 193
Query: 131 IDPNENNKVPAFLNVV-----------DIAGLVKGAAEGQGLGNAFLSHISACDAIFHL 178
+ PN L VV DI GL++GA+EG GLG FL H+ C + HL
Sbjct: 194 LVPN--------LGVVRVDDERSFVVADIPGLIEGASEGAGLGIRFLKHLERCRVLLHL 244
Score = 32.5 bits (75), Expect = 0.63
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 11/47 (23%)
Query: 226 PKKTD---EGEKKMLLGRVGTNLK----VGIVGVPNVGKSTFFNVLT 265
P++ GE++ L LK VG++G+PN GKSTF ++
Sbjct: 138 PRQKTPGTPGEERELKLE----LKLLADVGLLGLPNAGKSTFIRAVS 180
>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 = 65.3 bits (160), Expect = 6e-12
Identities = 24/85 (28%), Positives = 43/85 (50%), Gaps = 12/85 (14%)
Query: 99 VGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPNENNKVPAFLN-------VVDIAGL 151
V +VG P+VGKST + LT + + + F T+ VP + ++D+ G+
Sbjct: 3 VALVGFPSVGKSTLLSKLTNTKSEVAAYEFTTLTC-----VPGVMEYKGAKIQLLDLPGI 57
Query: 152 VKGAAEGQGLGNAFLSHISACDAIF 176
++GA++G+G G ++ D I
Sbjct: 58 IEGASDGKGRGRQVIAVARTADLIL 82
Score = 33.7 bits (78), Expect = 0.17
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 247 VGIVGVPNVGKSTFFNVLTK 266
V +VG P+VGKST + LT
Sbjct: 3 VALVGFPSVGKSTLLSKLTN 22
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 64.9 bits (159), Expect = 4e-11
Identities = 37/94 (39%), Positives = 50/94 (53%), Gaps = 26/94 (27%)
Query: 99 VGIVGVPNVGKSTFFNVLTKSSAA----AENFPFCTIDPNENNKVPAFLNVV-------- 146
VG+VG P+ GKS+ + L SAA A+ +PF T+ PN L VV
Sbjct: 162 VGLVGFPSAGKSSLISAL---SAAKPKIAD-YPFTTLVPN--------LGVVQAGDTRFT 209
Query: 147 --DIAGLVKGAAEGQGLGNAFLSHISACDAIFHL 178
D+ GL+ GA+EG+GLG FL HI C + H+
Sbjct: 210 VADVPGLIPGASEGKGLGLDFLRHIERCAVLVHV 243
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 62.3 bits (152), Expect = 2e-10
Identities = 30/85 (35%), Positives = 46/85 (54%), Gaps = 12/85 (14%)
Query: 99 VGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPNENNKVPAFLN-------VVDIAGL 151
V +VG P+VGKST N LT + + ++PF T++P VP L ++D+ G+
Sbjct: 66 VALVGFPSVGKSTLLNKLTNTKSEVADYPFTTLEP-----VPGMLEYKGAQIQLLDLPGI 120
Query: 152 VKGAAEGQGLGNAFLSHISACDAIF 176
++GA+ G+G G LS D I
Sbjct: 121 IEGASSGRGRGRQVLSVARNADLII 145
Score = 31.1 bits (71), Expect = 1.5
Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 17/70 (24%)
Query: 200 LKLLETRIRDLRRSVDAKADSKKKMGP----KKTDEGEKKMLLGRVGTNLKVGIVGVPNV 255
+ LL+ ++ +LR ++ + G KK+ + V +VG P+V
Sbjct: 28 IGLLKAKLAELREELEKRKSKSGGGGSGFAVKKSGDA-------------TVALVGFPSV 74
Query: 256 GKSTFFNVLT 265
GKST N LT
Sbjct: 75 GKSTLLNKLT 84
>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 = 45.1 bits (107), Expect = 2e-06
Identities = 22/87 (25%), Positives = 33/87 (37%), Gaps = 18/87 (20%)
Query: 463 KSLQLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEA 522
K++ + G ++KGT A +IH D EKGFI A
Sbjct: 8 KNIHTFTNGSGGNVFRDCVLVKKGTTVGDVARKIHGDLEKGFIEAVG------------- 54
Query: 523 ACRAAGKYRQQGRAYTVEDGDIIFFKF 549
G+ R +G+ + DI+ FK
Sbjct: 55 -----GRRRLEGKDVILGKNDILKFKT 76
>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 = 47.5 bits (114), Expect = 1e-05
Identities = 17/36 (47%), Positives = 21/36 (58%)
Query: 98 KVGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDP 133
V +VG N GKST FN LT + A + F T+DP
Sbjct: 191 TVALVGYTNAGKSTLFNALTGADVYAADQLFATLDP 226
Score = 35.5 bits (83), Expect = 0.064
Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 246 KVGIVGVPNVGKSTFFNVLTK-RAFEDD 272
V +VG N GKST FN LT + D
Sbjct: 191 TVALVGYTNAGKSTLFNALTGADVYAAD 218
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 47.2 bits (113), Expect = 2e-05
Identities = 36/141 (25%), Positives = 54/141 (38%), Gaps = 38/141 (26%)
Query: 190 SLNTITIWRNLKLLETRIRDLRRSVDAKADSKKKMGPKKTDEGEKKMLLGRVGTNLKVGI 249
L I L+ L + +L + K EG LKV I
Sbjct: 184 ELVLEKIREKLEELIAELDELLATAKQG---------KILREG------------LKVVI 222
Query: 250 VGVPNVGKSTFFNVLTK--RAFEDDDVTHVEG------EVNPVRDIEIINEELRLKDVEH 301
+G PNVGKS+ N L RA VT + G E DI + +RL D
Sbjct: 223 IGRPNVGKSSLLNALLGRDRAI----VTDIAGTTRDVIEE----DINLNGIPVRLVDTAG 274
Query: 302 IEKEINKIEKL-VQRGDKKLK 321
I + + +E++ ++R K ++
Sbjct: 275 IRETDDVVERIGIERAKKAIE 295
Score = 36.4 bits (85), Expect = 0.038
Identities = 14/26 (53%), Positives = 16/26 (61%)
Query: 97 LKVGIVGVPNVGKSTFFNVLTKSSAA 122
LKV I+G PNVGKS+ N L A
Sbjct: 218 LKVVIIGRPNVGKSSLLNALLGRDRA 243
>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 = 45.5 bits (109), Expect = 2e-05
Identities = 18/35 (51%), Positives = 22/35 (62%)
Query: 99 VGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDP 133
V +VG N GKST FN LT + AE+ F T+DP
Sbjct: 44 VALVGYTNAGKSTLFNALTGADVLAEDQLFATLDP 78
Score = 36.7 bits (86), Expect = 0.014
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 13/67 (19%)
Query: 201 KLLETRIRDLRRSVDAKADSKKKMGPKKTDEGEKKMLLGRVGTNL-KVGIVGVPNVGKST 259
+L+ RI LR+ + +K+ KK E ++ R + + V +VG N GKST
Sbjct: 9 RLIRERIAKLRKEL-------EKV--KKQRELQRA---RRKRSGVPTVALVGYTNAGKST 56
Query: 260 FFNVLTK 266
FN LT
Sbjct: 57 LFNALTG 63
>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 = 46.3 bits (111), Expect = 2e-05
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 74 KKMGPKKTDEGEKKMLLGRVGTNLKVGIVGVPNVGKSTFFNVLTKSSAA 122
KK+ +K ++ + K G + ++ IVG+PNVGKST N L A
Sbjct: 99 KKLLKEKNEKLKAK---GLLNRPIRAMIVGIPNVGKSTLINRLAGKKVA 144
Score = 46.3 bits (111), Expect = 2e-05
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 3/46 (6%)
Query: 222 KKMGPKKTDEGEKKMLLGRVGTNLKVGIVGVPNVGKSTFFNVLTKR 267
KK+ +K ++ + K G + ++ IVG+PNVGKST N L +
Sbjct: 99 KKLLKEKNEKLKAK---GLLNRPIRAMIVGIPNVGKSTLINRLAGK 141
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 46.9 bits (112), Expect = 2e-05
Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 97 LKVGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTID 132
L V +VG PNVGK+T FN LT ++ N+P T++
Sbjct: 4 LTVALVGNPNVGKTTLFNALTGANQKVGNWPGVTVE 39
Score = 41.1 bits (97), Expect = 0.002
Identities = 14/22 (63%), Positives = 16/22 (72%)
Query: 245 LKVGIVGVPNVGKSTFFNVLTK 266
L V +VG PNVGK+T FN LT
Sbjct: 4 LTVALVGNPNVGKTTLFNALTG 25
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 45.5 bits (109), Expect = 3e-05
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 3/46 (6%)
Query: 222 KKMGPKKTDEGEKKMLLGRVGTNLKVGIVGVPNVGKSTFFNVLTKR 267
KK+ +K + + K + R ++ I+G+PNVGKST N L +
Sbjct: 102 KKLLKEKNERRKAKGMRPR---AIRAMIIGIPNVGKSTLINRLAGK 144
Score = 45.5 bits (109), Expect = 3e-05
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 74 KKMGPKKTDEGEKKMLLGRVGTNLKVGIVGVPNVGKSTFFNVLTKSSAA 122
KK+ +K + + K + R ++ I+G+PNVGKST N L A
Sbjct: 102 KKLLKEKNERRKAKGMRPR---AIRAMIIGIPNVGKSTLINRLAGKKIA 147
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 46.0 bits (110), Expect = 4e-05
Identities = 23/71 (32%), Positives = 29/71 (40%), Gaps = 11/71 (15%)
Query: 95 TNLKVGIVGVPNVGKSTFFNVLTKSSAA-AENFPFCTIDPNE------NNKVPAFLNVVD 147
+ V IVG PNVGKST FN LT A + P T D + ++D
Sbjct: 2 STPVVAIVGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDAEWLGREF----ILID 57
Query: 148 IAGLVKGAAEG 158
GL G +
Sbjct: 58 TGGLDDGDEDE 68
Score = 42.6 bits (101), Expect = 5e-04
Identities = 16/25 (64%), Positives = 17/25 (68%)
Query: 243 TNLKVGIVGVPNVGKSTFFNVLTKR 267
+ V IVG PNVGKST FN LT R
Sbjct: 2 STPVVAIVGRPNVGKSTLFNRLTGR 26
Score = 37.2 bits (87), Expect = 0.021
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 97 LKVGIVGVPNVGKSTFFNVLTK 118
+K+ I+G PNVGKS+ N +
Sbjct: 179 IKIAIIGRPNVGKSSLINAILG 200
Score = 37.2 bits (87), Expect = 0.021
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 245 LKVGIVGVPNVGKSTFFNVLTK 266
+K+ I+G PNVGKS+ N +
Sbjct: 179 IKIAIIGRPNVGKSSLINAILG 200
>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 = 45.5 bits (109), Expect = 5e-05
Identities = 17/31 (54%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 98 KVGIVGVPNVGKSTFFNVLTKSSAA-AENFP 127
V IVG PNVGKST FN LT A + P
Sbjct: 1 VVAIVGRPNVGKSTLFNRLTGKRDAIVSDTP 31
Score = 44.4 bits (106), Expect = 1e-04
Identities = 15/22 (68%), Positives = 16/22 (72%)
Query: 246 KVGIVGVPNVGKSTFFNVLTKR 267
V IVG PNVGKST FN LT +
Sbjct: 1 VVAIVGRPNVGKSTLFNRLTGK 22
Score = 38.6 bits (91), Expect = 0.008
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 97 LKVGIVGVPNVGKSTFFNVLTKS 119
+K+ I+G PNVGKST N L
Sbjct: 173 IKIAIIGRPNVGKSTLVNALLGE 195
Score = 38.2 bits (90), Expect = 0.010
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 245 LKVGIVGVPNVGKSTFFNVLTK 266
+K+ I+G PNVGKST N L
Sbjct: 173 IKIAIIGRPNVGKSTLVNALLG 194
>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 = 43.6 bits (104), Expect = 5e-05
Identities = 25/84 (29%), Positives = 31/84 (36%), Gaps = 12/84 (14%)
Query: 101 IVGVPNVGKSTFFNVLTKSSAA-AENFPFCTIDPNENNKVPAFLN-----VVDIAGLVKG 154
IVG PNVGKST FN LT A + P T D A ++D G+
Sbjct: 2 IVGRPNVGKSTLFNRLTGRRDAIVSDTPGVTRDRKYGE---AEWGGREFILIDTGGIEPD 58
Query: 155 AAEGQGL--GNAFLSHISACDAIF 176
A ++ I D I
Sbjct: 59 DEGISKEIREQAEIA-IEEADVIL 81
Score = 41.3 bits (98), Expect = 3e-04
Identities = 15/19 (78%), Positives = 15/19 (78%)
Query: 249 IVGVPNVGKSTFFNVLTKR 267
IVG PNVGKST FN LT R
Sbjct: 2 IVGRPNVGKSTLFNRLTGR 20
>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 = 43.7 bits (104), Expect = 6e-05
Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 10/82 (12%)
Query: 52 PKAPKRRKQHLSDKLRP--KADSKKKMGPKKTDEGEKKMLL--------GRVGTNLKVGI 101
P K+ ++ + P ++K G KK + KK+L G + L+ +
Sbjct: 61 PAKTKKWLKYFKSQGEPVLFVNAKNGKGVKKLLKKAKKLLKENEKLKAKGLLPRPLRAMV 120
Query: 102 VGVPNVGKSTFFNVLTKSSAAA 123
VG+PNVGKST N L A
Sbjct: 121 VGIPNVGKSTLINRLRGKKVAK 142
Score = 42.9 bits (102), Expect = 9e-05
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 219 DSKKKMGPKKTDEGEKKMLL--------GRVGTNLKVGIVGVPNVGKSTFFNVLTKR 267
++K G KK + KK+L G + L+ +VG+PNVGKST N L +
Sbjct: 82 NAKNGKGVKKLLKKAKKLLKENEKLKAKGLLPRPLRAMVVGIPNVGKSTLINRLRGK 138
>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 = 43.6 bits (104), Expect = 7e-05
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 97 LKVGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTID 132
+ + +VG PNVGK+T FN LT + N+P T++
Sbjct: 1 ITIALVGNPNVGKTTLFNALTGARQHVGNWPGVTVE 36
Score = 39.4 bits (93), Expect = 0.002
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 245 LKVGIVGVPNVGKSTFFNVLT 265
+ + +VG PNVGK+T FN LT
Sbjct: 1 ITIALVGNPNVGKTTLFNALT 21
>gnl|CDD|133435 cd01616, TGS, The TGS domain, named after the ThrRS, GTPase, and
SpoT/RelA proteins where it occurs, is structurally
similar to ubiquitin. 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 = 60
Score = 40.4 bits (95), Expect = 8e-05
Identities = 22/80 (27%), Positives = 29/80 (36%), Gaps = 22/80 (27%)
Query: 468 QYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAA 527
FT A + KG A A +IHTD KGFI A V
Sbjct: 1 MIIFTPDG---SAVELPKGATAMDFALKIHTDLGKGFIGALVNG---------------- 41
Query: 528 GKYRQQGRAYTVEDGDIIFF 547
+ +YT++DGD +
Sbjct: 42 ---QLVDLSYTLQDGDTVSI 58
>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 = 42.2 bits (100), Expect = 1e-04
Identities = 20/86 (23%), Positives = 28/86 (32%), Gaps = 8/86 (9%)
Query: 100 GIVGVPNVGKSTFFNVLTKS-SAAAENFPFCTIDPNE-----NNKVPAFLNVVDIAGLVK 153
I G PNVGKS+ N L P T DP P + ++D GL +
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGP--VVLIDTPGLDE 58
Query: 154 GAAEGQGLGNAFLSHISACDAIFHLC 179
G+ D + +
Sbjct: 59 EGGLGRERVEEARQVADRADLVLLVV 84
Score = 35.3 bits (82), Expect = 0.034
Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 8/51 (15%)
Query: 248 GIVGVPNVGKSTFFNVLTKR--------AFEDDDVTHVEGEVNPVRDIEII 290
I G PNVGKS+ N L + D E E+ P+ + +I
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLI 51
>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 = 42.4 bits (101), Expect = 1e-04
Identities = 15/32 (46%), Positives = 21/32 (65%)
Query: 101 IVGVPNVGKSTFFNVLTKSSAAAENFPFCTID 132
+VG PNVGK+T FN LT + N+P T++
Sbjct: 2 LVGNPNVGKTTLFNALTGARQKVGNWPGVTVE 33
Score = 38.6 bits (91), Expect = 0.003
Identities = 12/17 (70%), Positives = 14/17 (82%)
Query: 249 IVGVPNVGKSTFFNVLT 265
+VG PNVGK+T FN LT
Sbjct: 2 LVGNPNVGKTTLFNALT 18
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 43.9 bits (105), Expect = 2e-04
Identities = 16/25 (64%), Positives = 16/25 (64%)
Query: 98 KVGIVGVPNVGKSTFFNVLTKSSAA 122
V IVG PNVGKST FN LT A
Sbjct: 3 VVAIVGRPNVGKSTLFNRLTGKRDA 27
Score = 43.5 bits (104), Expect = 2e-04
Identities = 15/22 (68%), Positives = 16/22 (72%)
Query: 246 KVGIVGVPNVGKSTFFNVLTKR 267
V IVG PNVGKST FN LT +
Sbjct: 3 VVAIVGRPNVGKSTLFNRLTGK 24
Score = 37.7 bits (89), Expect = 0.014
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 96 NLKVGIVGVPNVGKSTFFNVLTK 118
+K+ I+G PNVGKS+ N L
Sbjct: 173 PIKIAIIGRPNVGKSSLINALLG 195
Score = 37.7 bits (89), Expect = 0.014
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 244 NLKVGIVGVPNVGKSTFFNVLTK 266
+K+ I+G PNVGKS+ N L
Sbjct: 173 PIKIAIIGRPNVGKSSLINALLG 195
>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 = 44.0 bits (104), Expect = 2e-04
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 103 GVPNVGKSTFFNVLTKSSAAAENFPFCTID 132
G PNVGKST FN LT ++ N+P T++
Sbjct: 1 GNPNVGKSTLFNALTGANQTVGNWPGVTVE 30
Score = 33.9 bits (78), Expect = 0.24
Identities = 12/16 (75%), Positives = 12/16 (75%)
Query: 251 GVPNVGKSTFFNVLTK 266
G PNVGKST FN LT
Sbjct: 1 GNPNVGKSTLFNALTG 16
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 43.0 bits (102), Expect = 3e-04
Identities = 16/35 (45%), Positives = 20/35 (57%)
Query: 99 VGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDP 133
V +VG N GKST FN LT + + F T+DP
Sbjct: 195 VALVGYTNAGKSTLFNALTGADVYVADQLFATLDP 229
Score = 33.4 bits (77), Expect = 0.31
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 203 LETRIRDLRRSVDAKADSKKKMGPKKTDEGEKKMLLGRVGTNLK-VGIVGVPNVGKSTFF 261
LET R +RR + A K+++ + ++ + R + + V +VG N GKST F
Sbjct: 155 LETDRRRIRRRI---AKLKREL--ENVEKAREPRRKKRSRSGIPLVALVGYTNAGKSTLF 209
Query: 262 NVLTK 266
N LT
Sbjct: 210 NALTG 214
>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 = 40.2 bits (95), Expect = 7e-04
Identities = 14/30 (46%), Positives = 18/30 (60%)
Query: 101 IVGVPNVGKSTFFNVLTKSSAAAENFPFCT 130
I G PNVGKS+ N LT++ +PF T
Sbjct: 5 IAGYPNVGKSSLVNKLTRAKPEVAPYPFTT 34
Score = 34.1 bits (79), Expect = 0.078
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 249 IVGVPNVGKSTFFNVLT 265
I G PNVGKS+ N LT
Sbjct: 5 IAGYPNVGKSSLVNKLT 21
>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 = 39.7 bits (93), Expect = 0.001
Identities = 25/86 (29%), Positives = 36/86 (41%), Gaps = 5/86 (5%)
Query: 98 KVGIVGVPNVGKSTFFNVLTKSSAA-AENFPFCTIDPN----ENNKVPAFLNVVDIAGLV 152
K+ IVG PNVGKST N L + + E P T + E + N++D AG
Sbjct: 3 KIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQE 62
Query: 153 KGAAEGQGLGNAFLSHISACDAIFHL 178
A + A S + D + +
Sbjct: 63 DYDAIRRLYYRAVESSLRVFDIVILV 88
Score = 33.9 bits (78), Expect = 0.11
Identities = 13/22 (59%), Positives = 14/22 (63%)
Query: 246 KVGIVGVPNVGKSTFFNVLTKR 267
K+ IVG PNVGKST N L
Sbjct: 3 KIVIVGDPNVGKSTLLNRLLGN 24
>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 = 39.0 bits (92), Expect = 0.002
Identities = 27/80 (33%), Positives = 41/80 (51%), Gaps = 17/80 (21%)
Query: 245 LKVGIVGVPNVGKSTFFNVLTKRAFEDDD---VTHVEGEVNPVRDI--EIINEE---LRL 296
+KV I G PNVGKS+ N L R D V+ + G RD+ E I+ +RL
Sbjct: 4 IKVVIAGKPNVGKSSLLNALAGR-----DRAIVSDIAGT---TRDVIEEEIDLGGIPVRL 55
Query: 297 KDVEHIEKEINKIEKL-VQR 315
D + + ++IEK+ ++R
Sbjct: 56 IDTAGLRETEDEIEKIGIER 75
Score = 38.6 bits (91), Expect = 0.002
Identities = 13/26 (50%), Positives = 15/26 (57%)
Query: 97 LKVGIVGVPNVGKSTFFNVLTKSSAA 122
+KV I G PNVGKS+ N L A
Sbjct: 4 IKVVIAGKPNVGKSSLLNALAGRDRA 29
>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 = 39.0 bits (91), Expect = 0.002
Identities = 22/85 (25%), Positives = 30/85 (35%), Gaps = 7/85 (8%)
Query: 100 GIVGVPNVGKSTFFNVLTKSS-AAAENFPFCTIDPNENNKVPAF----LNVVDIAGLVKG 154
+VG VGKS+ N L + P T DP+ K L +VD GL +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF 60
Query: 155 AAEGQGLGNAFLSHISACDAIFHLC 179
G G + D I +
Sbjct: 61 --GGLGREELARLLLRGADLILLVV 83
Score = 32.0 bits (73), Expect = 0.38
Identities = 12/60 (20%), Positives = 23/60 (38%), Gaps = 2/60 (3%)
Query: 248 GIVGVPNVGKSTFFNVLTKRAFEDDDVTHVE--GEVNPVRDIEIINEELRLKDVEHIEKE 305
+VG VGKS+ N L + V++++ +L L D +++
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF 60
>gnl|CDD|236515 PRK09435, PRK09435, membrane ATPase/protein kinase; Provisional.
Length = 332
Score = 40.2 bits (95), Expect = 0.002
Identities = 16/28 (57%), Positives = 18/28 (64%)
Query: 89 LLGRVGTNLKVGIVGVPNVGKSTFFNVL 116
LL G L++GI GVP VGKSTF L
Sbjct: 49 LLPHTGNALRIGITGVPGVGKSTFIEAL 76
Score = 40.2 bits (95), Expect = 0.002
Identities = 16/28 (57%), Positives = 18/28 (64%)
Query: 237 LLGRVGTNLKVGIVGVPNVGKSTFFNVL 264
LL G L++GI GVP VGKSTF L
Sbjct: 49 LLPHTGNALRIGITGVPGVGKSTFIEAL 76
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 39.7 bits (93), Expect = 0.003
Identities = 14/26 (53%), Positives = 17/26 (65%)
Query: 97 LKVGIVGVPNVGKSTFFNVLTKSSAA 122
++VG+VG PNVGKST N L A
Sbjct: 133 IRVGVVGYPNVGKSTLINRLLGKKVA 158
Score = 39.3 bits (92), Expect = 0.004
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 245 LKVGIVGVPNVGKSTFFNVLTKR 267
++VG+VG PNVGKST N L +
Sbjct: 133 IRVGVVGYPNVGKSTLINRLLGK 155
>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 = 38.3 bits (90), Expect = 0.003
Identities = 15/31 (48%), Positives = 21/31 (67%)
Query: 93 VGTNLKVGIVGVPNVGKSTFFNVLTKSSAAA 123
+ T++ VG+VG PNVGKS+ N L +S A
Sbjct: 113 IKTSITVGVVGYPNVGKSSVINSLKRSRACN 143
Score = 36.4 bits (85), Expect = 0.015
Identities = 15/28 (53%), Positives = 21/28 (75%), Gaps = 1/28 (3%)
Query: 241 VGTNLKVGIVGVPNVGKSTFFNVLTKRA 268
+ T++ VG+VG PNVGKS+ N L KR+
Sbjct: 113 IKTSITVGVVGYPNVGKSSVINSL-KRS 139
>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 = 38.1 bits (89), Expect = 0.004
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 98 KVGIVGVPNVGKSTFFNVLTKSSAA 122
VG+VG P VGKS+ N L +A
Sbjct: 101 IVGVVGYPKVGKSSIINALKGRHSA 125
Score = 37.3 bits (87), Expect = 0.006
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 246 KVGIVGVPNVGKSTFFNVLTKR 267
VG+VG P VGKS+ N L R
Sbjct: 101 IVGVVGYPKVGKSSIINALKGR 122
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 39.3 bits (93), Expect = 0.004
Identities = 14/26 (53%), Positives = 15/26 (57%)
Query: 97 LKVGIVGVPNVGKSTFFNVLTKSSAA 122
LKV I G PNVGKS+ N L A
Sbjct: 216 LKVVIAGRPNVGKSSLLNALLGEERA 241
Score = 38.9 bits (92), Expect = 0.006
Identities = 13/23 (56%), Positives = 14/23 (60%)
Query: 245 LKVGIVGVPNVGKSTFFNVLTKR 267
LKV I G PNVGKS+ N L
Sbjct: 216 LKVVIAGRPNVGKSSLLNALLGE 238
>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 = 37.4 bits (87), Expect = 0.004
Identities = 17/50 (34%), Positives = 25/50 (50%)
Query: 73 KKKMGPKKTDEGEKKMLLGRVGTNLKVGIVGVPNVGKSTFFNVLTKSSAA 122
+ K E K+ L + ++VG+VG+PNVGKS+F N L
Sbjct: 68 NGQGILKLKAEITKQKLKLKYKKGIRVGVVGLPNVGKSSFINALLNKFKL 117
Score = 36.2 bits (84), Expect = 0.012
Identities = 17/46 (36%), Positives = 25/46 (54%)
Query: 221 KKKMGPKKTDEGEKKMLLGRVGTNLKVGIVGVPNVGKSTFFNVLTK 266
+ K E K+ L + ++VG+VG+PNVGKS+F N L
Sbjct: 68 NGQGILKLKAEITKQKLKLKYKKGIRVGVVGLPNVGKSSFINALLN 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 = 37.8 bits (89), Expect = 0.006
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 96 NLKVGIVGVPNVGKSTFFNVLTKS 119
+K+ I+G PNVGKS+ N L
Sbjct: 2 PIKIAIIGRPNVGKSSLLNALLGE 25
Score = 37.4 bits (88), Expect = 0.007
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 244 NLKVGIVGVPNVGKSTFFNVLTK 266
+K+ I+G PNVGKS+ N L
Sbjct: 2 PIKIAIIGRPNVGKSSLLNALLG 24
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 38.1 bits (89), Expect = 0.010
Identities = 14/35 (40%), Positives = 16/35 (45%)
Query: 237 LLGRVGTNLKVGIVGVPNVGKSTFFNVLTKRAFED 271
L R G +GI GVP GKST L + E
Sbjct: 44 LYPRTGNAHVIGITGVPGAGKSTLIEALGRELRER 78
Score = 33.5 bits (77), Expect = 0.25
Identities = 13/30 (43%), Positives = 15/30 (50%)
Query: 89 LLGRVGTNLKVGIVGVPNVGKSTFFNVLTK 118
L R G +GI GVP GKST L +
Sbjct: 44 LYPRTGNAHVIGITGVPGAGKSTLIEALGR 73
>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 = 36.7 bits (86), Expect = 0.010
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 97 LKVGIVGVPNVGKSTFFNVL 116
V I+G PNVGKST N L
Sbjct: 4 GFVAIIGRPNVGKSTLLNAL 23
Score = 36.7 bits (86), Expect = 0.010
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 245 LKVGIVGVPNVGKSTFFNVL 264
V I+G PNVGKST N L
Sbjct: 4 GFVAIIGRPNVGKSTLLNAL 23
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 35.3 bits (81), Expect = 0.015
Identities = 21/118 (17%), Positives = 41/118 (34%), Gaps = 9/118 (7%)
Query: 98 KVGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPNENNKVPAFLNVVDIAGLVKGAAE 157
+ I G P GKST + AE I ++ + + D G +
Sbjct: 1 IILITGPPGSGKSTL------AKKLAEKLGIPVISLDDLLREEGLAELDD--GELDDIDI 52
Query: 158 GQGLGNAFLSHISACDAIFHLCKEKLRNIFFISLNTITIWRNLKLLETRIRDLRRSVD 215
L L ++ + + +E + + + ++ +L L R R L+R +
Sbjct: 53 DLELLEEILDELAKQEWVIDGVRESTLELRLEEADLV-VFLDLPLPACRFRLLKRRLQ 109
Score = 30.3 bits (68), Expect = 0.95
Identities = 16/94 (17%), Positives = 30/94 (31%), Gaps = 7/94 (7%)
Query: 246 KVGIVGVPNVGKSTFFNVLTKR----AFEDDDVTHVEGEVNPVRDIEIINEELRLKDVEH 301
+ I G P GKST L ++ DD+ EG + E
Sbjct: 1 IILITGPPGSGKSTLAKKLAEKLGIPVISLDDLLREEGLAELDDGELDDIDIDLELLEEI 60
Query: 302 IEKEINK---IEKLVQRGDKKLKPEYVSEVWFSF 332
+++ + I+ + + + E V+
Sbjct: 61 LDELAKQEWVIDGVRESTLELRLEEADLVVFLDL 94
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 37.5 bits (87), Expect = 0.018
Identities = 18/35 (51%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 99 VGIVGVPNVGKSTFFN-VLTKSSAAAENFPFCTID 132
V IVG PNVGKST N +L + A E+ P T D
Sbjct: 278 VAIVGRPNVGKSTLVNRILGRREAVVEDTPGVTRD 312
Score = 33.6 bits (77), Expect = 0.33
Identities = 21/51 (41%), Positives = 30/51 (58%), Gaps = 7/51 (13%)
Query: 246 KVGIVGVPNVGKSTFFNVLT--KRAFEDDDVTHVEG-EVNPVRDIEIINEE 293
+V +VG PNVGKS+ N LT +RA +D + G +PV +I I+ E
Sbjct: 452 RVALVGRPNVGKSSLLNQLTHEERAVVND----LAGTTRDPVDEIVEIDGE 498
Score = 32.5 bits (74), Expect = 0.72
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 98 KVGIVGVPNVGKSTFFNVLTKSS-AAAENFPFCTIDP 133
+V +VG PNVGKS+ N LT A + T DP
Sbjct: 452 RVALVGRPNVGKSSLLNQLTHEERAVVNDLAGTTRDP 488
Score = 30.9 bits (70), Expect = 2.3
Identities = 14/23 (60%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 247 VGIVGVPNVGKSTFFN-VLTKRA 268
V IVG PNVGKST N +L +R
Sbjct: 278 VAIVGRPNVGKSTLVNRILGRRE 300
>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 = 36.1 bits (84), Expect = 0.021
Identities = 12/27 (44%), Positives = 13/27 (48%)
Query: 246 KVGIVGVPNVGKSTFFNVLTKRAFEDD 272
V +VG NVGKST N L K
Sbjct: 127 DVYVVGATNVGKSTLINALLKSNGGKV 153
Score = 35.3 bits (82), Expect = 0.037
Identities = 13/22 (59%), Positives = 14/22 (63%)
Query: 98 KVGIVGVPNVGKSTFFNVLTKS 119
V +VG NVGKST N L KS
Sbjct: 127 DVYVVGATNVGKSTLINALLKS 148
>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 = 36.7 bits (85), Expect = 0.029
Identities = 28/89 (31%), Positives = 46/89 (51%), Gaps = 9/89 (10%)
Query: 238 LGRVGTNLKVGIVGVPNVGKSTFFNVLTK--RAFEDDDVTHVEGEVNPV--RDIEIINEE 293
L ++ K+ IVG PNVGKS+ N L K RA V+ ++G V D E+
Sbjct: 197 LEKLDDGFKLAIVGSPNVGKSSLLNALLKQDRAI----VSDIKGTTRDVVEGDFELNGIL 252
Query: 294 LRLKDVEHIEKEINKIEKL-VQRGDKKLK 321
++L D I + + +E+L +++ K +K
Sbjct: 253 IKLLDTAGIREHADFVERLGIEKSFKAIK 281
Score = 34.4 bits (79), Expect = 0.15
Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 90 LGRVGTNLKVGIVGVPNVGKSTFFNV-LTKSSAAAENFPFCTIDPNENNKV--PAFLNVV 146
L ++ K+ IVG PNVGKS+ N L + A + T D E + + ++
Sbjct: 197 LEKLDDGFKLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGILIKLL 256
Query: 147 DIAGLVKGAAEGQGLG 162
D AG+ + A + LG
Sbjct: 257 DTAGIREHADFVERLG 272
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 35.7 bits (82), Expect = 0.033
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 245 LKVGIVGVPNVGKSTFFNVLTKRAFEDDDVTHVEGEVNPVRDIEIINEELRL 296
K+ ++G VGK+T N L F + + P + IE ++L
Sbjct: 6 FKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLD-PAKTIEPYRRNIKL 56
Score = 30.3 bits (68), Expect = 2.1
Identities = 15/62 (24%), Positives = 20/62 (32%), Gaps = 12/62 (19%)
Query: 97 LKVGIVGVPNVGKSTFFNVLTK-------SSAAAENFP-FCTIDPNENNKVPAFLNVVDI 148
K+ ++G VGK+T N L P N K L + D
Sbjct: 6 FKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIK----LQLWDT 61
Query: 149 AG 150
AG
Sbjct: 62 AG 63
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 36.0 bits (84), Expect = 0.041
Identities = 14/28 (50%), Positives = 17/28 (60%)
Query: 247 VGIVGVPNVGKSTFFNVLTKRAFEDDDV 274
V +VGV NVGKST N + K + DV
Sbjct: 163 VYVVGVTNVGKSTLINRIIKEITGEKDV 190
Score = 36.0 bits (84), Expect = 0.043
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 6/40 (15%)
Query: 99 VGIVGVPNVGKSTFFNVLTKSSAAAEN------FPFCTID 132
V +VGV NVGKST N + K ++ FP T+D
Sbjct: 163 VYVVGVTNVGKSTLINRIIKEITGEKDVITTSRFPGTTLD 202
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 36.2 bits (84), Expect = 0.046
Identities = 16/35 (45%), Positives = 22/35 (62%)
Query: 99 VGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDP 133
V +VG N GKST FN +T++ A + F T+DP
Sbjct: 200 VSLVGYTNAGKSTLFNRITEARVYAADQLFATLDP 234
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 35.7 bits (83), Expect = 0.050
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 101 IVGVPNVGKSTFFNVLTKSSAAAENFPFCT 130
+ G PNVGKS+ LT + +PF T
Sbjct: 173 VAGYPNVGKSSLVRKLTTAKPEVAPYPFTT 202
Score = 30.7 bits (70), Expect = 1.8
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 249 IVGVPNVGKSTFFNVLTK 266
+ G PNVGKS+ LT
Sbjct: 173 VAGYPNVGKSSLVRKLTT 190
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 35.4 bits (83), Expect = 0.064
Identities = 13/18 (72%), Positives = 13/18 (72%)
Query: 99 VGIVGVPNVGKSTFFNVL 116
V IVG PNVGKST N L
Sbjct: 8 VAIVGRPNVGKSTLLNAL 25
Score = 35.4 bits (83), Expect = 0.064
Identities = 13/18 (72%), Positives = 13/18 (72%)
Query: 247 VGIVGVPNVGKSTFFNVL 264
V IVG PNVGKST N L
Sbjct: 8 VAIVGRPNVGKSTLLNAL 25
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 34.9 bits (81), Expect = 0.100
Identities = 17/35 (48%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 99 VGIVGVPNVGKSTFFN-VLTKSSAAAENFPFCTID 132
V +VG PNVGKST N +L + A E+ P T D
Sbjct: 41 VAVVGRPNVGKSTLVNRILGRREAVVEDVPGVTRD 75
Score = 31.9 bits (73), Expect = 0.90
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 246 KVGIVGVPNVGKSTFFNVLTKRAFEDDDVTH-VEG-EVNPVRD-IEIINEELRLKDVEHI 302
+V +VG PNVGKS+ N K A E+ V V G V+PV IE+ + R D +
Sbjct: 213 RVALVGKPNVGKSSLLN---KLAGEERSVVDDVAGTTVDPVDSLIELGGKTWRFVDTAGL 269
Query: 303 EKEIN 307
+ +
Sbjct: 270 RRRVK 274
Score = 31.5 bits (72), Expect = 1.2
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 247 VGIVGVPNVGKSTFFN 262
V +VG PNVGKST N
Sbjct: 41 VAVVGRPNVGKSTLVN 56
Score = 31.1 bits (71), Expect = 1.6
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 13/71 (18%)
Query: 98 KVGIVGVPNVGKSTFFNVLTKSS-AAAENFPFCTIDPNENNKVPAFLNV-------VDIA 149
+V +VG PNVGKS+ N L + ++ T+DP V + + + VD A
Sbjct: 213 RVALVGKPNVGKSSLLNKLAGEERSVVDDVAGTTVDP-----VDSLIELGGKTWRFVDTA 267
Query: 150 GLVKGAAEGQG 160
GL + + G
Sbjct: 268 GLRRRVKQASG 278
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 34.1 bits (79), Expect = 0.18
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 99 VGIVGVPNVGKSTFFNVL 116
V I+G PNVGKST N L
Sbjct: 9 VAIIGRPNVGKSTLLNAL 26
Score = 34.1 bits (79), Expect = 0.18
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 247 VGIVGVPNVGKSTFFNVL 264
V I+G PNVGKST N L
Sbjct: 9 VAIIGRPNVGKSTLLNAL 26
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 33.9 bits (78), Expect = 0.25
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 97 LKVGIVGVPNVGKSTFFNVLT 117
L +G++G PN GK+T FN LT
Sbjct: 4 LTIGLIGNPNSGKTTLFNQLT 24
Score = 33.9 bits (78), Expect = 0.25
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 245 LKVGIVGVPNVGKSTFFNVLT 265
L +G++G PN GK+T FN LT
Sbjct: 4 LTIGLIGNPNSGKTTLFNQLT 24
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 33.4 bits (77), Expect = 0.31
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 246 KVGIVGVPNVGKSTFFNVLTKRAFEDDDVTHVEGEVNPVRDIEI 289
++G+VG GKST +L D GEV + + +
Sbjct: 31 RIGLVGRNGAGKSTLLKILAGELEPD------SGEVTRPKGLRV 68
Score = 29.9 bits (68), Expect = 3.7
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 98 KVGIVGVPNVGKSTFFNVLT 117
++ IVG GKST +L
Sbjct: 350 RIAIVGPNGAGKSTLLKLLA 369
Score = 29.9 bits (68), Expect = 3.7
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 246 KVGIVGVPNVGKSTFFNVLT 265
++ IVG GKST +L
Sbjct: 350 RIAIVGPNGAGKSTLLKLLA 369
Score = 29.9 bits (68), Expect = 4.0
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 98 KVGIVGVPNVGKSTFFNVLT 117
++G+VG GKST +L
Sbjct: 31 RIGLVGRNGAGKSTLLKILA 50
>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 = 33.1 bits (76), Expect = 0.33
Identities = 13/30 (43%), Positives = 15/30 (50%)
Query: 89 LLGRVGTNLKVGIVGVPNVGKSTFFNVLTK 118
L+ G +VGI GVP GKST L
Sbjct: 22 LMPLTGRAHRVGITGVPGAGKSTLIEALGM 51
Score = 33.1 bits (76), Expect = 0.33
Identities = 13/30 (43%), Positives = 15/30 (50%)
Query: 237 LLGRVGTNLKVGIVGVPNVGKSTFFNVLTK 266
L+ G +VGI GVP GKST L
Sbjct: 22 LMPLTGRAHRVGITGVPGAGKSTLIEALGM 51
>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 = 32.8 bits (76), Expect = 0.38
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 10/39 (25%)
Query: 247 VGIVGVPN-VGKSTFFNVLTKRA--------FEDDDVTH 276
G++G PN GK+T FN+++ F+ +D+T
Sbjct: 29 HGLIG-PNGAGKTTLFNLISGFLRPTSGSVLFDGEDITG 66
Score = 31.3 bits (72), Expect = 1.2
Identities = 9/20 (45%), Positives = 15/20 (75%), Gaps = 2/20 (10%)
Query: 99 VGIVGVPN-VGKSTFFNVLT 117
G++G PN GK+T FN+++
Sbjct: 29 HGLIG-PNGAGKTTLFNLIS 47
>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 = 32.7 bits (75), Expect = 0.38
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 97 LKVGIVGVPNVGKSTFFNVL 116
V I+G PNVGKST N L
Sbjct: 1 GFVAILGRPNVGKSTLLNQL 20
Score = 32.7 bits (75), Expect = 0.38
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 245 LKVGIVGVPNVGKSTFFNVL 264
V I+G PNVGKST N L
Sbjct: 1 GFVAILGRPNVGKSTLLNQL 20
>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 = 32.8 bits (75), Expect = 0.40
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 87 KMLLGRVGTNLKVGIVGVPNVGKSTFFNVLTK 118
++ G +VGI G P GKST L
Sbjct: 25 DRIMPYTGNAHRVGITGTPGAGKSTLLEALGM 56
Score = 32.8 bits (75), Expect = 0.40
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 235 KMLLGRVGTNLKVGIVGVPNVGKSTFFNVLTK 266
++ G +VGI G P GKST L
Sbjct: 25 DRIMPYTGNAHRVGITGTPGAGKSTLLEALGM 56
>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 = 31.8 bits (73), Expect = 0.41
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 99 VGIVGVPNVGKSTFFNVL 116
+G+VG PNVGKS+ N L
Sbjct: 85 IGLVGYPNVGKSSLINAL 102
Score = 31.8 bits (73), Expect = 0.41
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 247 VGIVGVPNVGKSTFFNVL 264
+G+VG PNVGKS+ N L
Sbjct: 85 IGLVGYPNVGKSSLINAL 102
>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 = 31.5 bits (72), Expect = 0.53
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 247 VGIVGVPNVGKSTFFNVLTKR 267
+GI GVP GKST + L
Sbjct: 2 IGITGVPGAGKSTLIDALITA 22
Score = 30.4 bits (69), Expect = 1.2
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 99 VGIVGVPNVGKSTFFNVLTK 118
+GI GVP GKST + L
Sbjct: 2 IGITGVPGAGKSTLIDALIT 21
>gnl|CDD|215622 PLN03189, PLN03189, Protease specific for SMALL UBIQUITIN-RELATED
MODIFIER (SUMO); Provisional.
Length = 490
Score = 32.1 bits (73), Expect = 0.72
Identities = 35/138 (25%), Positives = 64/138 (46%), Gaps = 17/138 (12%)
Query: 210 LRRSVDAKADSKKKMGPKKTDEGEKKMLLGRVGTNLKVGIVGVPNVGKSTFFNVLTKRAF 269
LRR V A K K TD EKK LG V N + ++ K + + L +
Sbjct: 64 LRREVHAPCRILKFGRDKSTDSSEKKQGLGNVMGNF---LSRKYDMAKRSALDAL-RYYR 119
Query: 270 EDDDVTHVEGEVNPVRDIEIINEELRLKDVEHIEKEINKIEKLVQRGDKKLKPEYVSEVW 329
+D +V V E+ +E+I+++ +++VE +E +++++E+ ++ S+V
Sbjct: 120 KDKEVVDVGDELG---KVEMISDDSSIEEVEAVEMDVDEVEE-----KAEMGNGLSSDVK 171
Query: 330 FSFIYLFIKNGHIGHEDA 347
KNG++ ED
Sbjct: 172 IV-----TKNGNLRVEDT 184
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 31.4 bits (72), Expect = 0.88
Identities = 16/48 (33%), Positives = 18/48 (37%)
Query: 88 MLLGRVGTNLKVGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPNE 135
M R ++ VG NVGKST LT P T PN
Sbjct: 1 MFETRPDRKPEIVFVGRSNVGKSTLVRELTGKKVRVGKRPGVTRKPNH 48
Score = 29.9 bits (68), Expect = 2.7
Identities = 12/34 (35%), Positives = 15/34 (44%)
Query: 236 MLLGRVGTNLKVGIVGVPNVGKSTFFNVLTKRAF 269
M R ++ VG NVGKST LT +
Sbjct: 1 MFETRPDRKPEIVFVGRSNVGKSTLVRELTGKKV 34
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 31.5 bits (72), Expect = 0.90
Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 14/79 (17%)
Query: 247 VGIVGVPNVGKSTFFNVLTKRAFEDDDVTH---------VEGEVNPVRDIEIINEELRLK 297
VGIVG+ VGK+T L K+ + DD V V R + I +EL L
Sbjct: 22 VGIVGMGGVGKTT----LAKQIYNDDSVGGHFDSVAWVVVSKTYTEFRLQKDILQELGLD 77
Query: 298 DVEHIEKEINKI-EKLVQR 315
D + +EK +++ K+ +
Sbjct: 78 DSDWVEKNESELAVKIKEA 96
>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 = 31.8 bits (73), Expect = 0.96
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 11/71 (15%)
Query: 71 DSKKKMGPKKTDEGEKKMLLGRVGTNLKVGIVGVPNVGKSTFFNVLTKSSAAAEN----- 125
+KK G + + KK + V +VGV NVGKS+ N L K + ++
Sbjct: 134 SAKKGNGIDELLDKIKKARNKK-----DVYVVGVTNVGKSSLINKLLKQNNGDKDVITTS 188
Query: 126 -FPFCTIDPNE 135
FP T+D E
Sbjct: 189 PFPGTTLDLIE 199
Score = 30.7 bits (70), Expect = 2.1
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 5/56 (8%)
Query: 219 DSKKKMGPKKTDEGEKKMLLGRVGTNLKVGIVGVPNVGKSTFFNVLTKRAFEDDDV 274
+KK G + + KK + V +VGV NVGKS+ N L K+ D DV
Sbjct: 134 SAKKGNGIDELLDKIKKARNKK-----DVYVVGVTNVGKSSLINKLLKQNNGDKDV 184
>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 = 30.7 bits (70), Expect = 1.1
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 247 VGIVGVPNVGKSTFFNVLTKR 267
VG +G PNVGKS+ N L +
Sbjct: 105 VGFIGYPNVGKSSVINTLRSK 125
Score = 30.3 bits (69), Expect = 1.6
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 99 VGIVGVPNVGKSTFFNVLTK 118
VG +G PNVGKS+ N L
Sbjct: 105 VGFIGYPNVGKSSVINTLRS 124
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 30.1 bits (68), Expect = 1.2
Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 10/73 (13%)
Query: 247 VGIVGVPNVGKSTFFNVLTKR--------AFEDDDVTHVEGEVNPVRDIEIINEELRLKD 298
+ I G P GK+T L +R A E+ V ++ E+ + + ++E+ K
Sbjct: 1 ILITGTPGSGKTTLAKELAERLGDVLRDLAKENGLVLELDEEIT--DESKRLDEDKLAKL 58
Query: 299 VEHIEKEINKIEK 311
++ +EK I ++ +
Sbjct: 59 LDKLEKIIEELAE 71
>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 = 31.3 bits (72), Expect = 1.2
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 97 LKVGIVGVPNVGKSTFFNVLTKSSAA-AENFPFCTIDPNE 135
L +GI G N GKS+ N LT A + P T DP
Sbjct: 7 LHIGIFGRRNAGKSSLINALTGQDIAIVSDVPGTTTDPVY 46
Score = 29.0 bits (66), Expect = 7.3
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 245 LKVGIVGVPNVGKSTFFNVLT 265
L +GI G N GKS+ N LT
Sbjct: 7 LHIGIFGRRNAGKSSLINALT 27
>gnl|CDD|213180 cd03213, ABCG_EPDR, Eye pigment and drug resistance transporter
subfamily G of the ATP-binding cassette superfamily.
ABCG transporters are involved in eye pigment (EP)
precursor transport, regulation of lipid-trafficking
mechanisms, and pleiotropic drug resistance (DR). DR is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. Compared to other members of the
ABC transporter subfamilies, the ABCG transporter family
is composed of proteins that have an ATP-binding
cassette domain at the N-terminus and a TM
(transmembrane) domain at the C-terminus.
Length = 194
Score = 30.6 bits (70), Expect = 1.4
Identities = 13/35 (37%), Positives = 14/35 (40%), Gaps = 4/35 (11%)
Query: 247 VGIVGVPNVGKSTFFNVLTKRAFEDDDVTHVEGEV 281
I+G GKST N L R V GEV
Sbjct: 38 TAIMGPSGAGKSTLLNALAGRR----TGLGVSGEV 68
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 28.5 bits (64), Expect = 1.5
Identities = 8/33 (24%), Positives = 13/33 (39%), Gaps = 1/33 (3%)
Query: 247 VGIVGVPNVGKSTFFNVLTKRAFEDDDVTHVEG 279
+ I G GKST L ++ V ++
Sbjct: 2 IAITGGSGSGKSTVAKKLAEQ-LGGRSVVVLDE 33
>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 = 30.2 bits (69), Expect = 1.8
Identities = 11/21 (52%), Positives = 12/21 (57%)
Query: 247 VGIVGVPNVGKSTFFNVLTKR 267
V G NVGKS+ N LT R
Sbjct: 2 VAFAGRSNVGKSSLINALTNR 22
Score = 28.6 bits (65), Expect = 5.0
Identities = 11/25 (44%), Positives = 12/25 (48%)
Query: 99 VGIVGVPNVGKSTFFNVLTKSSAAA 123
V G NVGKS+ N LT A
Sbjct: 2 VAFAGRSNVGKSSLINALTNRKKLA 26
>gnl|CDD|220272 pfam09508, Lact_bio_phlase, Lacto-N-biose phosphorylase. The gene
which codes for this protein in gut-bacteria is located
in a novel putative operon for galactose metabolism. The
protein appears to be a carbohydrate-processing
phosphorolytic enzyme (EC:2.4.1.211), unlike either
glycoside hydrolases or glycoside lyase. Intestinal
colonisation by bifidobacteria is important for human
health, especially in pediatrics, because colonisation
seems to prevent infection by some pathogenic bacteria
that cause diarrhoea or other illnesses. The operon
seems to be involved in intestinal colonisation by
bifidobacteria mediated by metabolism of mucin sugars.
In addition, it may also resolve the question of the
nature of the bifidus factor in human milk as the
lacto-N-biose structure found in milk oligosaccharides.
Length = 716
Score = 30.8 bits (70), Expect = 2.2
Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 18/80 (22%)
Query: 367 DWSNADIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFS 426
DW D EH + KT+ ++ L + +W+ N P ++ F+
Sbjct: 167 DW--GDKEHEIPYDPRHPKTREHV---------------LEALDQWLKEN-PQVDVVRFT 208
Query: 427 GVFEHQLVDMPDDERQRYLD 446
F + + +++Y+D
Sbjct: 209 TFFYQFTLVFGEKAKEKYVD 228
>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 = 29.6 bits (67), Expect = 2.4
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 247 VGIVGVPNVGKSTFFNVLTKRAFEDD 272
+ +VG+ N GK+T NV+ F +D
Sbjct: 2 ITLVGLQNSGKTTLVNVIASGQFSED 27
Score = 27.7 bits (62), Expect = 9.6
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 99 VGIVGVPNVGKSTFFNVLTKSSAAAENFP 127
+ +VG+ N GK+T NV+ + + P
Sbjct: 2 ITLVGLQNSGKTTLVNVIASGQFSEDTIP 30
>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein
complex aNOP56 subunit; Provisional.
Length = 414
Score = 30.7 bits (70), Expect = 2.5
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 52 PKAPKRRKQHLSDKLRPKADSKKKMGPKKTDEGEK 86
PK PK++++ + R K +KK G K+ +G K
Sbjct: 380 PKPPKKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414
>gnl|CDD|236992 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
Reviewed.
Length = 556
Score = 30.5 bits (70), Expect = 2.5
Identities = 12/21 (57%), Positives = 15/21 (71%), Gaps = 3/21 (14%)
Query: 100 GIVGV--PN-VGKSTFFNVLT 117
GIVG+ PN GKST F ++T
Sbjct: 351 GIVGIIGPNGAGKSTLFKMIT 371
Score = 30.5 bits (70), Expect = 2.5
Identities = 12/21 (57%), Positives = 15/21 (71%), Gaps = 3/21 (14%)
Query: 248 GIVGV--PN-VGKSTFFNVLT 265
GIVG+ PN GKST F ++T
Sbjct: 351 GIVGIIGPNGAGKSTLFKMIT 371
>gnl|CDD|219974 pfam08696, Dna2, DNA replication factor Dna2. Dna2 is a DNA
replication factor with single-stranded DNA-dependent
ATPase, ATP-dependent nuclease, ( 5'-flap endonuclease)
and helicase activities. It is required for Okazaki
fragment processing and is involved in DNA repair
pathways.
Length = 209
Score = 29.9 bits (68), Expect = 2.6
Identities = 11/48 (22%), Positives = 22/48 (45%)
Query: 367 DWSNADIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVD 414
D+ +E L L ++YL+ S + ++ + LP I+ W +
Sbjct: 109 DFDLEFLEELLDAVLEKYLEELYLLGESQDEVREEVMEHLPAIEGWAE 156
>gnl|CDD|235210 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 29.5 bits (67), Expect = 3.0
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 246 KVGIVGVPNVGKSTFFNVLTKRAFEDDDVTHV 277
V + GVP VGK+T N ++ +D V
Sbjct: 4 VVVVTGVPGVGKTTVLNKALEKL--KEDYKIV 33
>gnl|CDD|111933 pfam03092, BT1, BT1 family. Members of this family are
transmembrane proteins. Several are Leishmania putative
proteins that are thought to be pteridine transporters.
One such protein, previously termed (and is still
annotated as) ORFG, was shown to encode a biopterin
transport protein using null mutants, thus being
subsequently renamed BT1. The significant similarity of
ORFG/BT1 to Trypanosoma brucei ESAG10 (a putative
transmembrane protein and another member of this family)
was previously noted. This family also contains five
putative Arabidopsis thaliana proteins of unknown
function. In addition, it also contains two predicted
prokaryotic proteins (from the cyanobacteria
Synechocystis and Synechococcus).
Length = 425
Score = 30.0 bits (68), Expect = 3.2
Identities = 19/90 (21%), Positives = 27/90 (30%), Gaps = 21/90 (23%)
Query: 111 TFFNVLTKSSAAAENFPFCTIDPNENNKVPAFLNVV----DIAGLVKGAAEGQGLGNAFL 166
F A A+ F + T + N +F V IAGL+ G L N FL
Sbjct: 218 ISFWAAPLVIAKADMFYYQTNELGGPNFSYSFYGTVKVIGSIAGLL-----GVTLYNRFL 272
Query: 167 SHISACDAIFHLCKEKLRNIFFISLNTITI 196
R F ++ +
Sbjct: 273 KKHP------------YRLTFGVTTVLQVL 290
>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 = 29.0 bits (66), Expect = 3.4
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 246 KVGIVGVPNVGKSTFFNVLTKRAFED 271
++G+VG GKST ++ D
Sbjct: 28 RIGLVGRNGAGKSTLLKLIAGELEPD 53
Score = 28.6 bits (65), Expect = 4.3
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 98 KVGIVGVPNVGKSTFFNVLT 117
++G+VG GKST ++
Sbjct: 28 RIGLVGRNGAGKSTLLKLIA 47
>gnl|CDD|133439 cd01669, TGS_Ygr210_C, TGS_Ygr210_C: The C-terminal TGS domain of
Ygr210 GTP-binding protein which is a member of Obg-like
family of GTPases, and present in archaea. Several
Obg-like 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. 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 = 76
Score = 27.6 bits (62), Expect = 3.6
Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 13/46 (28%)
Query: 474 GQDEVKAWTIQKGTKAPQA------------AGRIHTDFEKGFIMA 507
+DE K T ++G P A A IHTD GF+ A
Sbjct: 7 VEDENK-LTDKEGNVLPDAFLLPKGSTARDLAYAIHTDIGDGFLHA 51
>gnl|CDD|224847 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 29.2 bits (66), Expect = 3.7
Identities = 15/70 (21%), Positives = 33/70 (47%), Gaps = 6/70 (8%)
Query: 246 KVGIVGVPNVGKSTFFNVLTKRAFEDDDVTHVEGE------VNPVRDIEIINEELRLKDV 299
+ I G P VGK+T +L + ++ ++ + E + +R I++ + K +
Sbjct: 2 LIAITGTPGVGKTTVCKLLRELGYKVIELNELAKENGLYTEYDELRKSVIVDVDKLRKRL 61
Query: 300 EHIEKEINKI 309
E + +E + I
Sbjct: 62 EELLREGSGI 71
>gnl|CDD|213199 cd03232, ABCG_PDR_domain2, Second domain of the pleiotropic drug
resistance-like (PDR) subfamily G of ATP-binding
cassette transporters. The pleiotropic drug resistance
(PDR) is a well-described phenomenon occurring in fungi
and shares several similarities with processes in
bacteria and higher eukaryotes. This PDR subfamily
represents domain I of its (ABC-IM)2 organization. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds
including 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 = 192
Score = 29.1 bits (66), Expect = 4.0
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 8/55 (14%)
Query: 231 EGEKKMLL----GRVGTNLKVGIVGVPNVGKSTFFNVLTKRAFEDDDVTHVEGEV 281
+G K+ LL G V ++G GK+T +VL R + GE+
Sbjct: 16 KGGKRQLLNNISGYVKPGTLTALMGESGAGKTTLLDVLAGRK----TAGVITGEI 66
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 29.3 bits (67), Expect = 4.2
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 254 NVGKSTFFNVLTKR 267
NVGKS+ N LT R
Sbjct: 34 NVGKSSLINALTNR 47
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 29.1 bits (66), Expect = 4.2
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 250 VGVPNVGKSTFFNVLTKR 267
G NVGKS+ N LT +
Sbjct: 30 AGRSNVGKSSLINALTNQ 47
Score = 28.7 bits (65), Expect = 5.8
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 102 VGVPNVGKSTFFNVLTKSSAAA 123
G NVGKS+ N LT A
Sbjct: 30 AGRSNVGKSSLINALTNQKNLA 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 = 29.0 bits (66), Expect = 4.7
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 247 VGIVGVPNVGKSTFFNVLTKR 267
+ G NVGKS+ N LT R
Sbjct: 21 IAFAGRSNVGKSSLINALTNR 41
>gnl|CDD|219151 pfam06725, 3D, 3D domain. This short presumed domain contains
three conserved aspartate residues, hence the name 3D.
It has been shown to be part of the catalytic double psi
beta barrel domain of MltA.
Length = 72
Score = 27.2 bits (61), Expect = 4.7
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 511 HFDDFKEHGSEAACRAAGKYRQQGRAYTVE 540
D + G EA AG YR+ GR Y +
Sbjct: 44 RIDLYFGTGDEA-GNLAGLYRKTGRVYILL 72
>gnl|CDD|133478 cd07153, Fur_like, Ferric uptake regulator(Fur) and related
metalloregulatory proteins; typically iron-dependent,
DNA-binding repressors and activators. Ferric uptake
regulator (Fur) and related metalloregulatory proteins
are iron-dependent, DNA-binding repressors and
activators mainly involved in iron metabolism. A
general model for Fur repression under iron-rich
conditions is that activated Fur (a dimer having one
Fe2+ coordinated per monomer) binds to specific DNA
sequences (Fur boxes) in the promoter region of
iron-responsive genes, hindering access of RNA
polymerase, and repressing transcription. Positive
regulation by Fur can be direct or indirect, as in the
Fur repression of an anti-sense regulatory small RNA.
Some members sense metal ions other than Fe2+. For
example, the zinc uptake regulator (Zur) responds to
Zn2+, the manganese uptake regulator (Mur) responds to
Mn2+, and the nickel uptake regulator (Nur) responds to
Ni2+. Other members sense signals other than metal ions.
For example, PerR, a metal-dependent sensor of hydrogen
peroxide. PerR regulates DNA-binding activity through
metal-based protein oxidation, and co-ordinates Mn2+ or
Fe2+ at its regulatory site. Fur family proteins contain
an N-terminal winged-helix DNA-binding domain followed
by a dimerization domain; this CD spans both those
domains.
Length = 116
Score = 28.3 bits (64), Expect = 4.9
Identities = 13/37 (35%), Positives = 23/37 (62%), Gaps = 6/37 (16%)
Query: 168 HISACDAIFHLCKEKLRNIFFISLNTITIWRNLKLLE 204
H++A + I+ ++K +I SL T+ +R L+LLE
Sbjct: 16 HLTA-EEIYERLRKKGPSI---SLATV--YRTLELLE 46
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 28.6 bits (65), Expect = 5.0
Identities = 6/28 (21%), Positives = 13/28 (46%)
Query: 245 LKVGIVGVPNVGKSTFFNVLTKRAFEDD 272
K+ ++G VGK++ F ++
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSEN 28
>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 = 29.5 bits (67), Expect = 5.3
Identities = 13/21 (61%), Positives = 15/21 (71%), Gaps = 3/21 (14%)
Query: 100 GIVGV--PN-VGKSTFFNVLT 117
GIVGV PN GKST F ++T
Sbjct: 349 GIVGVIGPNGAGKSTLFRMIT 369
Score = 29.5 bits (67), Expect = 5.3
Identities = 13/21 (61%), Positives = 15/21 (71%), Gaps = 3/21 (14%)
Query: 248 GIVGV--PN-VGKSTFFNVLT 265
GIVGV PN GKST F ++T
Sbjct: 349 GIVGVIGPNGAGKSTLFRMIT 369
>gnl|CDD|168661 PRK06753, PRK06753, hypothetical protein; Provisional.
Length = 373
Score = 29.3 bits (66), Expect = 5.6
Identities = 13/53 (24%), Positives = 18/53 (33%), Gaps = 13/53 (24%)
Query: 297 KDVEHIEKEIN---KIEKLVQRGDK----------KLKPEYVSEVWFSFIYLF 336
V+H K I KI K+ Q K K P ++ F+Y
Sbjct: 319 IRVKHTAKVIKRSRKIGKIAQIESKLLVALRNRVMKRMPNALAAGQTKFLYKS 371
>gnl|CDD|223488 COG0411, LivG, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 250
Score = 29.1 bits (66), Expect = 5.9
Identities = 11/22 (50%), Positives = 16/22 (72%), Gaps = 2/22 (9%)
Query: 99 VGIVGVPN-VGKSTFFNVLTKS 119
VG++G PN GK+T FN++T
Sbjct: 33 VGLIG-PNGAGKTTLFNLITGF 53
Score = 28.7 bits (65), Expect = 6.5
Identities = 11/20 (55%), Positives = 16/20 (80%), Gaps = 2/20 (10%)
Query: 247 VGIVGVPN-VGKSTFFNVLT 265
VG++G PN GK+T FN++T
Sbjct: 33 VGLIG-PNGAGKTTLFNLIT 51
>gnl|CDD|224453 COG1536, FliG, Flagellar motor switch protein [Cell motility and
secretion].
Length = 339
Score = 29.2 bits (66), Expect = 6.1
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 18/73 (24%)
Query: 267 RAFEDDDVT-HVEGEVNPVRD----------IEIINEEL------RLKDVEHIEKEI-NK 308
R + +D+ ++G +R+ E++ EEL RL DVE +K I N
Sbjct: 260 REVDKEDLAIALKGASEELREKILSNMSKRAAEMLKEELEFLGPVRLSDVETAQKAILNI 319
Query: 309 IEKLVQRGDKKLK 321
+ +L + G+ +K
Sbjct: 320 VRRLAESGEIVIK 332
>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 = 28.3 bits (64), Expect = 6.4
Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 245 LKVGIVGVPNVGKSTFFNVLTKRAFEDDDV-THVEGEVNPVRDIEIINEELRL 296
+K+ +VG VGK+ T F + V T + N ++ + +++ L
Sbjct: 1 IKIVVVGDGAVGKTCLLISYTTNKFPTEYVPTVFD---NYSANVTVDGKQVNL 50
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated with
diverse processes in dividing and non-dividing cells.
They were first discovered in the budding yeast S.
cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of the
cell cortex and exocytosis. In humans, 12 septin genes
generate dozens of polypeptides, many of which comprise
heterooligomeric complexes. Since septin mutants are
commonly defective in cytokinesis and formation of the
neck formation of the neck filaments/septin rings,
septins have been considered to be the primary
constituents of the neck filaments. Septins belong to
the GTPase superfamily for their conserved GTPase motifs
and enzymatic activities.
Length = 275
Score = 28.7 bits (65), Expect = 7.2
Identities = 18/70 (25%), Positives = 25/70 (35%), Gaps = 13/70 (18%)
Query: 94 GTNLKVGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPN-------------ENNKVP 140
G + +VG +GKSTF N L + +P + E N V
Sbjct: 2 GFQFNIMVVGESGLGKSTFINTLFGTKLYPSKYPPAPGEHITKTVEIKISKAELEENGVK 61
Query: 141 AFLNVVDIAG 150
L V+D G
Sbjct: 62 LKLTVIDTPG 71
>gnl|CDD|189762 pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.
cryoelectron microscopy indicates that VP5 is a trimer
implying that there are 360 copies of VP5 per virion.
Length = 507
Score = 28.9 bits (65), Expect = 7.7
Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 6/73 (8%)
Query: 252 VPNVGKSTFFNVLTKRAFEDDDVTHVEGEVNPVRDIEIINEELRLKDVEHIEKEI-NKIE 310
P + T +L K D + +R +E E +EH+ +EI KI+
Sbjct: 269 TPKIQPKTLETLLEKPTDVIPDAALAVAVSSKLRHVEENKNE-----LEHLNEEILPKIK 323
Query: 311 KLVQRGDKKLKPE 323
K + + L
Sbjct: 324 KAAEEDKEILGIR 336
>gnl|CDD|215595 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 29.3 bits (66), Expect = 7.7
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 98 KVGIVGVPNVGKSTFFNVL 116
KVGIVG GKS+ N L
Sbjct: 1267 KVGIVGRTGAGKSSMLNAL 1285
Score = 29.3 bits (66), Expect = 7.7
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 246 KVGIVGVPNVGKSTFFNVL 264
KVGIVG GKS+ N L
Sbjct: 1267 KVGIVGRTGAGKSSMLNAL 1285
>gnl|CDD|238991 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible oxidation
of CO to CO2. CODH contains a nickel-iron-sulfur cluster
(C-center) and an iron-sulfur cluster (B-center). CO
oxidation occurs at the C-center. Three accessory
proteins encoded by cooCTJ genes are involved in nickel
incorporation into a nickel site. CooC functions as a
nickel insertase that mobilizes nickel to apoCODH using
energy released from ATP hydrolysis. CooC is a homodimer
and has NTPase activities. Mutation at the P-loop
abolishs its function.
Length = 116
Score = 27.6 bits (62), Expect = 7.9
Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 12/83 (14%)
Query: 98 KVGIVGVPNVGKSTFFNVLTKSSAAAENFPFCTIDPNENNKVPAF------LNVVDIAGL 151
K+ I G VGK+T +L + A ID + ++ + ++ + G+
Sbjct: 1 KIAITGKGGVGKTTIAALLARYLAEKGKPVLA-IDADPDDLPERLSVEVGEIKLLLVMGM 59
Query: 152 VKGAAEG-----QGLGNAFLSHI 169
+ EG L NA L H+
Sbjct: 60 GRPGGEGCYCPENALLNALLRHL 82
>gnl|CDD|216517 pfam01467, CTP_transf_2, Cytidylyltransferase. This family
includes: Cholinephosphate cytidylyltransferase.
Glycerol-3-phosphate cytidylyltransferase.
Length = 148
Score = 27.8 bits (62), Expect = 8.7
Identities = 11/46 (23%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 266 KRAFEDDDVTHVEGEVNPVRDI-EIINEELRLKDVEHIEKEINKIE 310
K F+ D + V + +P +D + + E RL+ +E + +E
Sbjct: 21 KELFDLDKIVGVPSDESPHKDTKNLFSAEERLEMLELALEVDPNLE 66
>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 = 28.5 bits (64), Expect = 9.5
Identities = 18/69 (26%), Positives = 22/69 (31%), Gaps = 12/69 (17%)
Query: 51 GPKAPKRRKQHLSDKLRPKADSKKKMGPKKTDEGEKKMLLGRVGTNLKVGIVGVPNVGKS 110
R+ Q D +KK+ D L V +VG P VGKS
Sbjct: 6 SAVRAARQFQRTQDL------EEKKLHVPVVDR------TPEEPPPLVVVVVGPPGVGKS 53
Query: 111 TFFNVLTKS 119
T L K
Sbjct: 54 TLIRSLIKR 62
>gnl|CDD|180696 PRK06793, fliI, flagellum-specific ATP synthase; Validated.
Length = 432
Score = 28.8 bits (64), Expect = 9.8
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 241 VGTNLKVGIVGVPNVGKSTFFNVLTKRAFEDDDVTHVEGE 280
+G K+GI VGKST ++ K A D +V + GE
Sbjct: 153 IGIGQKIGIFAGSGVGKSTLLGMIAKNAKADINVISLVGE 192
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
0.317 0.136 0.400
Gapped
Lambda K H
0.267 0.0581 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,133,396
Number of extensions: 2915648
Number of successful extensions: 3921
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3869
Number of HSP's successfully gapped: 253
Length of query: 561
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 459
Effective length of database: 6,413,494
Effective search space: 2943793746
Effective search space used: 2943793746
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 62 (28.0 bits)