RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014450
(424 letters)
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 651 bits (1683), Expect = 0.0
Identities = 226/370 (61%), Positives = 285/370 (77%), Gaps = 6/370 (1%)
Query: 55 MSLRAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSK 114
M L+ GIVGLPNVGKSTLFNA+ + G A+AAN+PFCTIEPNVG+V VPDPRL L+ + K
Sbjct: 1 MGLKCGIVGLPNVGKSTLFNALTKAG-AEAANYPFCTIEPNVGVVPVPDPRLDKLAEIVK 59
Query: 115 SQKAVPASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFEDNDIVHVNGKV 174
+K VPA++EFVDIAGLVKGAS+GEGLGN+FL++IREVD+I+ VVRCFED++I HV GKV
Sbjct: 60 PKKIVPATIEFVDIAGLVKGASKGEGLGNQFLANIREVDAIVHVVRCFEDDNITHVEGKV 119
Query: 175 DPKSDVDVINLELVFSDLDQIEKRMEKLKKGKAKDSQSKLKEDAEKAALEKIQQALMDGK 234
DP D++ IN EL+ +DL+ +EKR+E+L+K KAK + K AE LEK+ + L +GK
Sbjct: 120 DPIRDIETINTELILADLETVEKRLERLEK-KAKGGDKEAK--AELELLEKLLEHLEEGK 176
Query: 235 PARSVTLNDFERDSIKQLCLLTMKPIIYVANVAESDLADPGSNPHVNEVMNLASDLQSGR 294
PAR++ L D E +K L LLT KP++YVANV E DLAD NP+V +V +A+ +
Sbjct: 177 PARTLELTDEEEKLLKSLQLLTAKPVLYVANVDEDDLAD--GNPYVKKVREIAAKEGAEV 234
Query: 295 VTISAQVEAELTELPSEERVEYLASLGVSESGLGNLIRSTYSLLGLRTYFTSGEKETKAW 354
V I A++EAE+ EL EE+ E+L LG+ ESGL LIR+ Y LLGL TYFT+G KE +AW
Sbjct: 235 VVICAKIEAEIAELDDEEKAEFLEELGLEESGLDRLIRAGYELLGLITYFTAGPKEVRAW 294
Query: 355 TIRAGMTAPQAAGVIHSDFEKGFIRAETVAYDDFVAAGSLAAAREKGLLRSEGKDYIVQE 414
TI+ G TAPQAAGVIH+DFEKGFIRAE ++YDD + GS A A+E G +R EGKDYIVQ+
Sbjct: 295 TIKKGTTAPQAAGVIHTDFEKGFIRAEVISYDDLIEYGSEAGAKEAGKVRLEGKDYIVQD 354
Query: 415 GDVMLFRFNV 424
GDVM FRFNV
Sbjct: 355 GDVMHFRFNV 364
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 515 bits (1328), Expect = 0.0
Identities = 213/376 (56%), Positives = 273/376 (72%), Gaps = 10/376 (2%)
Query: 55 MSLRAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSK 114
MSL+ GIVGLPNVGKSTLFNA+ + G A+ AN+PFCTIEPNVG+V VPD RL L+ + K
Sbjct: 1 MSLKIGIVGLPNVGKSTLFNALTKAG-AEIANYPFCTIEPNVGVVYVPDCRLDELAEIVK 59
Query: 115 -SQKAVPASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFEDNDIVHVNGK 173
K PA VEFVDIAGLVKGAS+GEGLGNKFL +IREVD+I+ VVRCF D DI HV GK
Sbjct: 60 CPPKIRPAPVEFVDIAGLVKGASKGEGLGNKFLDNIREVDAIIHVVRCFGDTDIEHVEGK 119
Query: 174 VDPKSDVDVINLELVFSDLDQIEKRMEKLKKGKAKDSQSKLKEDAEK-AALEKIQQALMD 232
VDP D+++IN EL+ DL+ +EKR E+L+K +AK + KE E+ + L K+++ L +
Sbjct: 120 VDPVEDIEIINTELILWDLESLEKRWERLEK-RAKAGKKLDKELKEELSLLGKLEEHLEE 178
Query: 233 GKPARSV---TLNDFERDSIKQLCLLTMKPIIYVANVAESDLADPGSNPHVNEVMNLASD 289
GKPAR + ++ + +++ L LLT KP++YVANV+E DLA+ N +V + LA+
Sbjct: 179 GKPARGLDLSKWSEEDLEALASLNLLTAKPMLYVANVSEDDLANL--NEYVKRLKELAAK 236
Query: 290 LQSGRVTISAQVEAELTELP-SEERVEYLASLGVSESGLGNLIRSTYSLLGLRTYFTSGE 348
+ V +SA +E EL EL +EE+ E+L LG ESGL LIR+ Y LLGL+TYFT+G
Sbjct: 237 ENAEVVPVSAAIELELRELADAEEKGEFLIELGQKESGLNELIRAGYGLLGLQTYFTAGV 296
Query: 349 KETKAWTIRAGMTAPQAAGVIHSDFEKGFIRAETVAYDDFVAAGSLAAAREKGLLRSEGK 408
KE +AWTI+ G AP AAGVIH DFEKGFIRAE ++Y D + G AAA+E G R EGK
Sbjct: 297 KEVRAWTIKDGSKAPDAAGVIHPDFEKGFIRAEVISYADLIHYGGEAAAKEAGKRRLEGK 356
Query: 409 DYIVQEGDVMLFRFNV 424
DYIVQ+GDV+ F+FNV
Sbjct: 357 DYIVQDGDVIHFKFNV 372
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 472 bits (1216), Expect = e-166
Identities = 183/372 (49%), Positives = 241/372 (64%), Gaps = 7/372 (1%)
Query: 56 SLRAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKS 115
+L+ GIVGLPNVGKST FNA+ + A NFPFCTI+PN V VPD R L K
Sbjct: 21 NLKMGIVGLPNVGKSTTFNAL-CKQQVPAENFPFCTIDPNTARVNVPDERFDWLCKHFKP 79
Query: 116 QKAVPASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFEDNDIVHVNGKVD 175
+ VPA ++ DIAGLVKGAS+GEGLGN FLSHIR VD I VVR FED DI HV G++D
Sbjct: 80 KSIVPAQLDITDIAGLVKGASEGEGLGNAFLSHIRAVDGIYHVVRAFEDEDITHVEGEID 139
Query: 176 PKSDVDVINLELVFSDLDQIEKRMEKLKKGKAKDSQSKLKEDAEKAALEKIQQALMDGKP 235
P D+++I+ EL+ DL+ +EKR+++L K K K + K +E E L+K+ + L +GKP
Sbjct: 140 PVRDLEIISSELILKDLEFVEKRLDELTK-KRKKKKKKKEEKVELDVLKKVLEWLEEGKP 198
Query: 236 ARSVTLNDFERDSIKQLCLLTMKPIIYVANVAESDLADPGSNPHVNEVMNLASDLQSGRV 295
R D E + + + LLT KP+IY+ N++E D N + ++ + G
Sbjct: 199 VRDGDWTDKEIEILNEYQLLTAKPMIYLVNMSEKDFIRQK-NKWLAKIKE-WVGEKGGGP 256
Query: 296 TI--SAQVEAELTELPS-EERVEYLASLGVSESGLGNLIRSTYSLLGLRTYFTSGEKETK 352
I SA+ E EL EL S EER EYL G+ +S L +I++ Y LL L +FT+G E +
Sbjct: 257 IIPYSAEFEEELAELGSEEERKEYLEEYGIKQSMLDKIIKTGYKLLNLIHFFTAGPDEVR 316
Query: 353 AWTIRAGMTAPQAAGVIHSDFEKGFIRAETVAYDDFVAAGSLAAAREKGLLRSEGKDYIV 412
WTI+ G APQAAGVIHSDFEKGFI AE + Y+DF+ GS AA + +G R EGKDY+V
Sbjct: 317 CWTIQKGTKAPQAAGVIHSDFEKGFICAEVMKYEDFLELGSEAAVKAEGKYRQEGKDYVV 376
Query: 413 QEGDVMLFRFNV 424
Q+GD++ F+FNV
Sbjct: 377 QDGDIIFFKFNV 388
>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 = 429 bits (1107), Expect = e-151
Identities = 166/280 (59%), Positives = 207/280 (73%), Gaps = 6/280 (2%)
Query: 59 AGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQKA 118
GIVGLPNVGKSTLFNA+ ++ A+AAN+PFCTIEPNVGIV VPD RL L+ + K +K
Sbjct: 1 IGIVGLPNVGKSTLFNALTKSN-AEAANYPFCTIEPNVGIVPVPDERLDKLAEIVKPKKI 59
Query: 119 VPASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFEDNDIVHVNGKVDPKS 178
VPA++EFVDIAGLVKGAS+GEGLGNKFLSHIREVD+I VVRCFED+DI HV G VDP
Sbjct: 60 VPATIEFVDIAGLVKGASKGEGLGNKFLSHIREVDAIAHVVRCFEDDDITHVEGSVDPVR 119
Query: 179 DVDVINLELVFSDLDQIEKRMEKLKKGKAKDSQSKLKEDAEKAALEKIQQALMDGKPARS 238
D+++IN EL+ +DL+ IEKR+E+L+K KAK + KE E LEKI++ L +GKPAR+
Sbjct: 120 DIEIINTELILADLETIEKRLERLEK-KAKSGDKEAKE--ELELLEKIKEHLEEGKPART 176
Query: 239 VTLNDFERDSIKQLCLLTMKPIIYVANVAESDLADPGSNPHVNEVMNLASDLQSGRVTIS 298
+ L D E +K L LLT KP+IYVANV+E DL N V +V +A+ + + IS
Sbjct: 177 LELTDEEIKILKSLQLLTAKPVIYVANVSEDDLIRG--NNKVLKVREIAAKEGAEVIPIS 234
Query: 299 AQVEAELTELPSEERVEYLASLGVSESGLGNLIRSTYSLL 338
A++EAEL EL EE E+L LG+ ESGL LIR+ Y LL
Sbjct: 235 AKLEAELAELDEEEAAEFLEELGLEESGLDKLIRAGYELL 274
>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 = 387 bits (995), Expect = e-133
Identities = 184/373 (49%), Positives = 243/373 (65%), Gaps = 8/373 (2%)
Query: 55 MSLRAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSK 114
M L GIVGLPNVGKSTLF A +AAN PF TIEPN G+V DPRL +L+ K
Sbjct: 1 MGLSGGIVGLPNVGKSTLFAATTNLLGNEAANPPFTTIEPNAGVVNPSDPRLDLLAIYIK 60
Query: 115 SQKAVPASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFEDNDIVHVNGKV 174
+K P + EFVDIAGLV GAS+GEGLGN+FL++IREVD I VVRCFED+ I HV
Sbjct: 61 PEKVPPTTTEFVDIAGLVGGASKGEGLGNQFLANIREVDIIQHVVRCFEDDIIHHVGNVD 120
Query: 175 DPKSDVDVINLELVFSDLDQIEKRMEKLKKGKAKDSQSKLKEDAEKAALEKIQQALMDGK 234
DP+ D ++I+ EL+ +D +EKR+ + KK A+ + K +E LE I L G+
Sbjct: 121 DPRDDFEIIDEELLKADEFLVEKRIGRSKK-SAEGGKDKKEEL---LLLEIILPLLNGGQ 176
Query: 235 PARSVTLNDFERDSIKQLCLLTMKPIIYVANVAESDLADPGSNPHVNEVMNLASDLQSGR 294
AR V L+ E IK L LLT KPII +ANV+E L + +N ++ V +A+ +
Sbjct: 177 MARHVDLSKEELILIKSLNLLTKKPIILIANVSEDYLRN-LNNNYLLIVEWIAAYSKGDP 235
Query: 295 --VTISAQVEAELTELPSEERVEYLASLGVSES-GLGNLIRSTYSLLGLRTYFTSGEKET 351
V + A E+EL+EL EER E+L LG++ES GL +IR+ Y LL L +FT G++E
Sbjct: 236 KVVFVCALEESELSELDDEERQEFLQKLGLTESAGLNIIIRARYKLLLLSFFFTGGKEEV 295
Query: 352 KAWTIRAGMTAPQAAGVIHSDFEKGFIRAETVAYDDFVAAGSLAAAREKGLLRSEGKDYI 411
+AWT + G APQAAG+IH+DFE GFI AE +++DDF+ S A++ GL+R EGK Y+
Sbjct: 296 RAWTRKGGWAAPQAAGIIHTDFETGFIAAEVISWDDFIYKKSSQGAKKGGLMRLEGKYYV 355
Query: 412 VQEGDVMLFRFNV 424
V +GDV+ F FNV
Sbjct: 356 VDDGDVLFFAFNV 368
>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 = 176 bits (450), Expect = 3e-55
Identities = 59/84 (70%), Positives = 69/84 (82%)
Query: 340 LRTYFTSGEKETKAWTIRAGMTAPQAAGVIHSDFEKGFIRAETVAYDDFVAAGSLAAARE 399
L T+FT+G KE +AWTIR G TAPQAAGVIHSDFEKGFIRAE ++YDD + GS A A+E
Sbjct: 1 LITFFTAGPKEVRAWTIRKGTTAPQAAGVIHSDFEKGFIRAEVISYDDLIEYGSEAKAKE 60
Query: 400 KGLLRSEGKDYIVQEGDVMLFRFN 423
G LR EGKDYIVQ+GD++ FRFN
Sbjct: 61 AGKLRLEGKDYIVQDGDIIHFRFN 84
>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 = 166 bits (423), Expect = 4e-51
Identities = 52/83 (62%), Positives = 65/83 (78%)
Query: 340 LRTYFTSGEKETKAWTIRAGMTAPQAAGVIHSDFEKGFIRAETVAYDDFVAAGSLAAARE 399
L ++FT+G E +AWTIR G APQAAGVIH+DFEKGFIRAE + Y+D V GS AAA+E
Sbjct: 1 LISFFTAGPDEVRAWTIRKGTKAPQAAGVIHTDFEKGFIRAEVMKYEDLVELGSEAAAKE 60
Query: 400 KGLLRSEGKDYIVQEGDVMLFRF 422
G R EGKDY+VQ+GD++ F+F
Sbjct: 61 AGKYRQEGKDYVVQDGDIIFFKF 83
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 132 bits (335), Expect = 8e-35
Identities = 119/434 (27%), Positives = 183/434 (42%), Gaps = 117/434 (26%)
Query: 56 SLRAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGI--VAVPDPRLHVLSGLS 113
+ G+VG PNVGKST FNA + AN+PF TI+PNVG+ V V P G+
Sbjct: 1 MITIGLVGKPNVGKSTFFNAATLA-DVEIANYPFTTIDPNVGVAYVRVECP--CKELGVK 57
Query: 114 KSQKA---------VPASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVV----R 160
+ + +P VE +D+AGLV GA +G GLGN+FL +R+ D+++ VV
Sbjct: 58 CNPRNGKCIDGTRFIP--VELIDVAGLVPGAHEGRGLGNQFLDDLRQADALIHVVDASGS 115
Query: 161 CFEDNDIVHVNGKVDPKSDVDVINLELVFSDLDQIEKRMEKLKKGKAKDSQSKLKEDAEK 220
E+ + V G DP D+ + EL +EK EK ++ +Q++ K D E+
Sbjct: 116 TDEEGNPVEP-GSHDPVEDIKFLEEELDMWIYGILEKNWEKF----SRKAQAE-KFDIEE 169
Query: 221 AALEK----------IQQALMDGKPARSVTLNDFERDSIKQLCLLTM---KPIIYVANVA 267
A E+ +++AL + + + + + +L KP++ AN A
Sbjct: 170 ALAEQLSGLGINEEHVKEALRELGLPED--PSKWTDEDLLELARELRKISKPMVIAANKA 227
Query: 268 ESDLADPGSNPHVNEVMNLASDLQSGRVTISAQVEAELT--------------------- 306
DL N + L + V SA EAEL
Sbjct: 228 --DLPPAEEN-----IERLKEEKYYIVVPTSA--EAELALRRAAKAGLIDYIPGDSDFEI 278
Query: 307 --ELPSEER--VEYLASL-------GVSESGLGNLIRSTYSLLGLRTYFTSGEKETKAWT 355
EL +++ +EY+ + GV E+ + + + LL + + E E K T
Sbjct: 279 LGELSEKQKKALEYIREVLKKYGGTGVQEA----INTAVFDLLDMIVVY-PVEDENK-LT 332
Query: 356 ------------IRAGMTAPQAAGVIHSDFEKGFIRAETVAYDDFVAAGSLAAAREKGLL 403
+ G TA A IH+D +GF+ A D AR K
Sbjct: 333 DKKGNVLPDAFLLPKGSTARDLAYKIHTDIGEGFLY----AID----------ARTK--- 375
Query: 404 RSEGKDYIVQEGDV 417
R G+DY +++GDV
Sbjct: 376 RRIGEDYELKDGDV 389
>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 = 128 bits (325), Expect = 5e-34
Identities = 84/285 (29%), Positives = 133/285 (46%), Gaps = 45/285 (15%)
Query: 60 GIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQKA- 118
G+VG PNVGKST FNA + AN+PF TI+PNVG+ V G+S + +
Sbjct: 2 GLVGKPNVGKSTFFNAATLAD-VEIANYPFTTIDPNVGVGYVRVECPCKELGVSCNPRYG 60
Query: 119 --------VPASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVV----RCFEDND 166
VP VE +D+AGLV GA +G+GLGN+FL +R+ D ++ VV + +
Sbjct: 61 KCIDGKRYVP--VELIDVAGLVPGAHEGKGLGNQFLDDLRDADVLIHVVDASGGTDAEGN 118
Query: 167 IVHVNGKVDPKSDVDVINLELVFSDLDQIEKRMEKLKKGKAKDSQSKLKEDAEKAALEK- 225
V G DP D++ + E+ +E+ EK+ + KAK K D +A E+
Sbjct: 119 GVET-GGYDPLEDIEFLENEIDMWIYGILERNWEKIVR-KAK----AEKTDIVEALSEQL 172
Query: 226 ---------IQQALMDGK-PARSVTLNDFERDSIKQLCLLTM---KPIIYVANVAESDLA 272
+ +AL + + PA L+ ++ + + +L KP++ AN A D+
Sbjct: 173 SGFGVNEDVVIEALEELELPAD---LSKWDDEDLLRLARELRKRRKPMVIAANKA--DIP 227
Query: 273 DPGSNPHVNEVMNLASDLQSGRVTISAQVEAELTELPSEERVEYL 317
D N + + V SA+ E L + ++Y+
Sbjct: 228 DAEENISKLRLKYPDEIV----VPTSAEAELALRRAAKQGLIKYV 268
>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 = 109 bits (275), Expect = 1e-28
Identities = 55/165 (33%), Positives = 79/165 (47%), Gaps = 29/165 (17%)
Query: 60 GIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQKAV 119
G+VGLPNVGKSTL +A+ K + A++PF T+EPNVG+ D
Sbjct: 1 GLVGLPNVGKSTLLSALTS-AKVEIASYPFTTLEPNVGVFEFGDGV-------------- 45
Query: 120 PASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFEDNDIVHVNGKVDPKSD 179
++ +D+ GL+ GAS+G GLG + L+H+ D IL V+ ED DP D
Sbjct: 46 --DIQIIDLPGLLDGASEGRGLGEQILAHLYRSDLILHVIDASEDCVG-------DPLED 96
Query: 180 VDVINLELVFSDLDQIEKR----MEKLKKGKAKDSQSKLKEDAEK 220
+N E+ S L K K+ ++ +LK D K
Sbjct: 97 QKTLNEEVSGSFLFLKNKPEMIVANKIDMASE-NNLKRLKLDKLK 140
>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 = 99.0 bits (248), Expect = 1e-24
Identities = 60/162 (37%), Positives = 84/162 (51%), Gaps = 42/162 (25%)
Query: 59 AGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQKA 118
G+VGLPN GKSTL +A+ N K + A++PF T+ PN+G+V V D R
Sbjct: 3 VGLVGLPNAGKSTLLSAIS-NAKPKIADYPFTTLVPNLGVVRVDDGR------------- 48
Query: 119 VPASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFEDNDIVHVNGKVDPKS 178
S DI GL++GAS+G+GLG++FL HI +L V+ D+ +G+ DP
Sbjct: 49 ---SFVIADIPGLIEGASEGKGLGHRFLRHIERTRVLLHVI------DL---SGEDDPVE 96
Query: 179 DVDVINLEL--------------VFS--DLDQIEKRMEKLKK 204
D + I EL V + DL E+R EKLK+
Sbjct: 97 DYETIRNELEAYNPGLAEKPRIVVLNKIDLLDAEERFEKLKE 138
>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 = 97.1 bits (243), Expect = 2e-22
Identities = 51/128 (39%), Positives = 70/128 (54%), Gaps = 24/128 (18%)
Query: 60 GIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQKAV 119
G+VGLPN GKSTL +AV K + A++PF T+ PN+G+V V D R
Sbjct: 161 GLVGLPNAGKSTLISAV-SAAKPKIADYPFTTLVPNLGVVRVDDGR-------------- 205
Query: 120 PASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFEDNDIVHVNGKVDPKSD 179
S DI GL++GAS+G GLG++FL HI +L ++ DI +G DP D
Sbjct: 206 --SFVIADIPGLIEGASEGAGLGHRFLKHIERTRVLLHLI------DISPEDGS-DPIED 256
Query: 180 VDVINLEL 187
++I EL
Sbjct: 257 YEIIRNEL 264
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 96.1 bits (240), Expect = 7e-22
Identities = 61/204 (29%), Positives = 89/204 (43%), Gaps = 47/204 (23%)
Query: 59 AGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQKA 118
G+VGLPN GKSTL + V K + A++PF T+ PN+G+V V
Sbjct: 162 VGLVGLPNAGKSTLLS-AVSAAKPKIADYPFTTLVPNLGVVRVDGGE------------- 207
Query: 119 VPASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFEDNDIVHVNGKVDPKS 178
S DI GL++GAS+G GLG +FL HI +L V+ D+ ++G+ DP
Sbjct: 208 ---SFVVADIPGLIEGASEGVGLGLRFLRHIERTRVLLHVI------DLSPIDGR-DPIE 257
Query: 179 DVDVINLEL--------------VFSDLDQI--EKRMEKLKKGKAKDSQ-------SKLK 215
D I EL V + +D E+ +E+LKK A+ S L
Sbjct: 258 DYQTIRNELEKYSPKLAEKPRIVVLNKIDLPLDEEELEELKKALAEALGWEVFYLISALT 317
Query: 216 EDAEKAALEKIQQALMDGKPARSV 239
+ L + + L + K
Sbjct: 318 REGLDELLRALAELLEETKAEAEA 341
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 95.9 bits (240), Expect = 1e-21
Identities = 58/164 (35%), Positives = 80/164 (48%), Gaps = 44/164 (26%)
Query: 59 AGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQKA 118
G+VG PNVGKSTL +VV N K + AN+ F T+ PN+G+V D R
Sbjct: 161 VGLVGFPNVGKSTLL-SVVSNAKPKIANYHFTTLVPNLGVVETDDGR------------- 206
Query: 119 VPASVEFV--DIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFEDNDIVHVNGKVDP 176
FV DI GL++GAS+G GLG++FL HI I+ V+ D+ G+ DP
Sbjct: 207 -----SFVMADIPGLIEGASEGVGLGHQFLRHIERTRVIVHVI------DMSGSEGR-DP 254
Query: 177 KSDVDVINLELVF----------------SDLDQIEKRMEKLKK 204
D + IN EL DL + E+ +E+ K+
Sbjct: 255 IEDYEKINKELKLYNPRLLERPQIVVANKMDLPEAEENLEEFKE 298
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 94.4 bits (236), Expect = 2e-21
Identities = 55/173 (31%), Positives = 80/173 (46%), Gaps = 45/173 (26%)
Query: 59 AGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQKA 118
G+VGLPN GKSTL + V K + A++PF T+ PN+G+V V D +
Sbjct: 161 VGLVGLPNAGKSTLI-SAVSAAKPKIADYPFTTLHPNLGVVRVDDYK------------- 206
Query: 119 VPASVEFV--DIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFEDNDIVHVNGKVDP 176
FV DI GL++GAS+G GLG++FL HI +L +V DI VDP
Sbjct: 207 -----SFVIADIPGLIEGASEGAGLGHRFLKHIERTRLLLHLV------DIEA----VDP 251
Query: 177 KSDVDVINLEL--------------VFSDLDQIEKRMEKLKKGKAKDSQSKLK 215
D I EL V + +D +++ E+ K+ + +
Sbjct: 252 VEDYKTIRNELEKYSPELADKPRILVLNKIDLLDEEEEREKRAALELAALGGP 304
>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 = 87.7 bits (218), Expect = 4e-21
Identities = 41/130 (31%), Positives = 63/130 (48%), Gaps = 22/130 (16%)
Query: 58 RAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQK 117
R +VG PNVGKSTL NA+ A +++P T +P +G++ +
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVLGLGRQ------------- 47
Query: 118 AVPASVEFVDIAGLVKGASQGEGLG--NKFLSHIREVDSILQVVRCFE--DNDIVHVNGK 173
+ VD GL++GAS+G+G+ N+FL IRE D IL VV E D + +
Sbjct: 48 -----IILVDTPGLIEGASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEE 102
Query: 174 VDPKSDVDVI 183
++ +I
Sbjct: 103 LEKLPKKPII 112
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 80.3 bits (199), Expect = 2e-16
Identities = 54/162 (33%), Positives = 79/162 (48%), Gaps = 44/162 (27%)
Query: 60 GIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQKAV 119
G++GLPN GKST AV K + A++PF T+ PN+G+V V D R
Sbjct: 163 GLLGLPNAGKSTFIRAV-SAAKPKVADYPFTTLVPNLGVVRVDDER-------------- 207
Query: 120 PASVEFV--DIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFEDNDIVHVNGKVDPK 177
FV DI GL++GAS+G GLG +FL H+ +L ++ DI ++G DP
Sbjct: 208 ----SFVVADIPGLIEGASEGAGLGIRFLKHLERCRVLLHLI------DIAPIDG-SDPV 256
Query: 178 SDVDVINLEL--------------VFSDLDQI--EKRMEKLK 203
+ +I EL VF+ +D + E+ E+ K
Sbjct: 257 ENARIIINELEKYSPKLAEKPRWLVFNKIDLLDEEEAEERAK 298
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 74.5 bits (184), Expect = 2e-14
Identities = 47/135 (34%), Positives = 66/135 (48%), Gaps = 38/135 (28%)
Query: 60 GIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQKAV 119
G+VG P+ GKS+L + + K + A++PF T+ PN+G+V D R V
Sbjct: 163 GLVGFPSAGKSSLI-SALSAAKPKIADYPFTTLVPNLGVVQAGDTRFTV----------- 210
Query: 120 PASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFEDNDIVHV-------NG 172
D+ GL+ GAS+G+GLG FL HI RC +VHV G
Sbjct: 211 ------ADVPGLIPGASEGKGLGLDFLRHIE---------RC---AVLVHVVDCATLEPG 252
Query: 173 KVDPKSDVDVINLEL 187
+ DP SD+D + EL
Sbjct: 253 R-DPLSDIDALEAEL 266
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 70.4 bits (173), Expect = 2e-13
Identities = 37/107 (34%), Positives = 57/107 (53%), Gaps = 18/107 (16%)
Query: 58 RAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQK 117
+VG P+VGKSTL N + N K++ A++PF T+EP G++
Sbjct: 65 TVALVGFPSVGKSTLLNKLT-NTKSEVADYPFTTLEPVPGMLEYKG-------------- 109
Query: 118 AVPASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFED 164
A ++ +D+ G+++GAS G G G + LS R D I+ V+ FED
Sbjct: 110 ---AQIQLLDLPGIIEGASSGRGRGRQVLSVARNADLIIIVLDVFED 153
>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 = 68.7 bits (169), Expect = 3e-13
Identities = 30/107 (28%), Positives = 53/107 (49%), Gaps = 18/107 (16%)
Query: 58 RAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQK 117
R +VG P+VGKSTL + + N K++ A + F T+ G++
Sbjct: 2 RVALVGFPSVGKSTLLSKLT-NTKSEVAAYEFTTLTCVPGVMEYKG-------------- 46
Query: 118 AVPASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFED 164
A ++ +D+ G+++GAS G+G G + ++ R D IL V+ +
Sbjct: 47 ---AKIQLLDLPGIIEGASDGKGRGRQVIAVARTADLILIVLDATKP 90
>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 = 50.5 bits (121), Expect = 2e-08
Identities = 23/81 (28%), Positives = 31/81 (38%), Gaps = 18/81 (22%)
Query: 342 TYFTSGEKETKAWTIRAGMTAPQAAGVIHSDFEKGFIRAETVAYDDFVAAGSLAAAREKG 401
T + G ++ G T A IH D EKGFI A G
Sbjct: 14 TNGSGGNVFRDCVLVKKGTTVGDVARKIHGDLEKGFIEAVG------------------G 55
Query: 402 LLRSEGKDYIVQEGDVMLFRF 422
R EGKD I+ + D++ F+
Sbjct: 56 RRRLEGKDVILGKNDILKFKT 76
>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 = 49.9 bits (120), Expect = 2e-07
Identities = 23/102 (22%), Positives = 33/102 (32%), Gaps = 16/102 (15%)
Query: 60 GIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQKAV 119
I G PNVGKS+L NA++ + P T +P +
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLG-------------- 46
Query: 120 PASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRC 161
V +D GL + G + D +L VV
Sbjct: 47 --PVVLIDTPGLDEEGGLGRERVEEARQVADRADLVLLVVDS 86
>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 = 45.4 bits (108), Expect = 8e-07
Identities = 17/70 (24%), Positives = 23/70 (32%), Gaps = 19/70 (27%)
Query: 353 AWTIRAGMTAPQAAGVIHSDFEKGFIRAETVAYDDFVAAGSLAAAREKGLLRSEGKDYIV 412
A + G TA A IH+D KGFI A + Y +
Sbjct: 10 AVELPKGATAMDFALKIHTDLGKGFIGALVNG-------------------QLVDLSYTL 50
Query: 413 QEGDVMLFRF 422
Q+GD +
Sbjct: 51 QDGDTVSIVT 60
>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 = 47.1 bits (112), Expect = 2e-06
Identities = 33/144 (22%), Positives = 57/144 (39%), Gaps = 27/144 (18%)
Query: 60 GIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQKAV 119
+VG VGKS+L NA++ + ++ P T +P+V + + ++
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKV------------- 47
Query: 120 PASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVV-----RCFEDNDIVHVNGKV 174
+ VD GL + G G +R D IL VV ED ++ +
Sbjct: 48 --KLVLVDTPGLDEF--GGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLR 103
Query: 175 DPKSDVDVINLELVFSDLDQIEKR 198
I + LV + +D +E+R
Sbjct: 104 KEG-----IPIILVGNKIDLLEER 122
>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 = 46.0 bits (110), Expect = 5e-06
Identities = 17/33 (51%), Positives = 21/33 (63%)
Query: 56 SLRAGIVGLPNVGKSTLFNAVVENGKAQAANFP 88
LRA +VG+PNVGKSTL N + A+ N P
Sbjct: 115 PLRAMVVGIPNVGKSTLINRLRGKKVAKVGNKP 147
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 46.2 bits (110), Expect = 1e-05
Identities = 17/50 (34%), Positives = 26/50 (52%)
Query: 39 TTTSSRRRFSSASKISMSLRAGIVGLPNVGKSTLFNAVVENGKAQAANFP 88
+ +R + +R G+VG PNVGKSTL N ++ A+ +N P
Sbjct: 115 LSEEKIKRLKKKGLLKRKIRVGVVGYPNVGKSTLINRLLGKKVAKTSNRP 164
>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 = 43.2 bits (103), Expect = 4e-05
Identities = 15/26 (57%), Positives = 17/26 (65%), Gaps = 7/26 (26%)
Query: 61 IVGLPNVGKSTLFN-------AVVEN 79
IVG PNVGKSTLFN A+V +
Sbjct: 2 IVGRPNVGKSTLFNRLTGRRDAIVSD 27
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 45.0 bits (107), Expect = 6e-05
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 54 SMSLRAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVL 109
L +VG PNVGK+TLFNA+ + N+P T+E G + + ++
Sbjct: 1 MKKLTVALVGNPNVGKTTLFNALT-GANQKVGNWPGVTVEKKEGKLKYKGHEIEIV 55
>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 = 43.7 bits (104), Expect = 9e-05
Identities = 17/33 (51%), Positives = 21/33 (63%)
Query: 56 SLRAGIVGLPNVGKSTLFNAVVENGKAQAANFP 88
+RA IVG+PNVGKSTL N + A+ N P
Sbjct: 118 PIRAMIVGIPNVGKSTLINRLAGKKVAKVGNRP 150
>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 = 43.2 bits (103), Expect = 2e-04
Identities = 15/26 (57%), Positives = 17/26 (65%), Gaps = 7/26 (26%)
Query: 61 IVGLPNVGKSTLFN-------AVVEN 79
IVG PNVGKSTLFN A+V +
Sbjct: 4 IVGRPNVGKSTLFNRLTGKRDAIVSD 29
Score = 36.7 bits (86), Expect = 0.018
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 56 SLRAGIVGLPNVGKSTLFNA 75
++ I+G PNVGKSTL NA
Sbjct: 172 PIKIAIIGRPNVGKSTLVNA 191
>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 = 40.9 bits (97), Expect = 3e-04
Identities = 14/23 (60%), Positives = 16/23 (69%)
Query: 56 SLRAGIVGLPNVGKSTLFNAVVE 78
S I+G PNVGKSTL NA+V
Sbjct: 3 SGFVAIIGRPNVGKSTLLNALVG 25
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 42.1 bits (100), Expect = 3e-04
Identities = 16/32 (50%), Positives = 21/32 (65%)
Query: 57 LRAGIVGLPNVGKSTLFNAVVENGKAQAANFP 88
+RA I+G+PNVGKSTL N + A+ N P
Sbjct: 122 IRAMIIGIPNVGKSTLINRLAGKKIAKTGNRP 153
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 42.3 bits (101), Expect = 4e-04
Identities = 13/14 (92%), Positives = 13/14 (92%)
Query: 61 IVGLPNVGKSTLFN 74
IVG PNVGKSTLFN
Sbjct: 6 IVGRPNVGKSTLFN 19
Score = 37.0 bits (87), Expect = 0.017
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 57 LRAGIVGLPNVGKSTLFNA 75
++ I+G PNVGKS+L NA
Sbjct: 174 IKIAIIGRPNVGKSSLINA 192
>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 = 4e-04
Identities = 17/37 (45%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 61 IVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVG 97
I G PNVGKS+L N + K + A +PF T VG
Sbjct: 5 IAGYPNVGKSSLVN-KLTRAKPEVAPYPFTTKSLFVG 40
>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 = 40.5 bits (96), Expect = 5e-04
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 57 LRAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHV 108
+ +VG PNVGK+TLFNA+ + N+P T+E G + +
Sbjct: 1 ITIALVGNPNVGKTTLFNALT-GARQHVGNWPGVTVEKKEGTFKYKGYEIEI 51
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 41.8 bits (99), Expect = 5e-04
Identities = 30/101 (29%), Positives = 39/101 (38%), Gaps = 19/101 (18%)
Query: 61 IVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQKAVP 120
IVG PNVGKSTLFN + A ++ P T + G + +
Sbjct: 8 IVGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDA-----------------EWLG 50
Query: 121 ASVEFVDIAGLVKGASQ--GEGLGNKFLSHIREVDSILQVV 159
+D GL G E + + L I E D IL VV
Sbjct: 51 REFILIDTGGLDDGDEDELQELIREQALIAIEEADVILFVV 91
Score = 34.9 bits (81), Expect = 0.081
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 57 LRAGIVGLPNVGKSTLFNA 75
++ I+G PNVGKS+L NA
Sbjct: 179 IKIAIIGRPNVGKSSLINA 197
>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 = 39.7 bits (94), Expect = 7e-04
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 61 IVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVL 109
+VG PNVGK+TLFNA+ + + N+P T+E G + + ++
Sbjct: 2 LVGNPNVGKTTLFNALT-GARQKVGNWPGVTVEKKEGEFKLGGKEIEIV 49
>gnl|CDD|206753 cd04178, Nucleostemin_like, A circularly permuted subfamily of the
Ras GTPases. Nucleostemin (NS) is a nucleolar protein
that functions as a regulator of cell growth and
proliferation in stem cells and in several types of
cancer cells, but is not expressed in the differentiated
cells of most mammalian adult tissues. NS shuttles
between the nucleolus and nucleoplasm bidirectionally at
a rate that is fast and independent of cell type.
Lowering GTP levels decreases the nucleolar retention of
NS, and expression of NS is abruptly down-regulated
during differentiation prior to terminal cell division.
Found only in eukaryotes, NS consists of an N-terminal
basic domain, a coiled-coil domain, a GTP-binding
domain, an intermediate domain, and a C-terminal acidic
domain. Experimental evidence indicates that NS uses its
GTP-binding property as a molecular switch to control
the transition between the nucleolus and nucleoplasm,
and this process involves interaction between the basic,
GTP-binding, and intermediate domains of the protein.
Length = 171
Score = 39.9 bits (94), Expect = 8e-04
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 51 SKISMSLRAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCT 91
I S+ G+VG PNVGKS++ N++ + P T
Sbjct: 111 KGIKTSITVGVVGYPNVGKSSVINSLKRSRACNVGATPGVT 151
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 40.7 bits (96), Expect = 0.001
Identities = 29/109 (26%), Positives = 46/109 (42%), Gaps = 17/109 (15%)
Query: 60 GIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSG-------- 111
+VG N GKSTLFNA+ A+ F T++P + + D R +L+
Sbjct: 196 ALVGYTNAGKSTLFNALTGADVY-VADQLFATLDPTTRRIELGDGRKVLLTDTVGFIRDL 254
Query: 112 ---LSKSQKAVPASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQ 157
L ++ K+ V+ D+ V AS E L + V+ +L
Sbjct: 255 PHPLVEAFKSTLEEVKEADLLLHVVDASDPE-----ILEKLEAVEDVLA 298
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 40.3 bits (95), Expect = 0.001
Identities = 41/145 (28%), Positives = 62/145 (42%), Gaps = 32/145 (22%)
Query: 56 SLRAGIVGLPNVGKSTLFNAVVE------NGKAQAANFPFCTI--EPNVGIVAVPDPRLH 107
S I+G PNVGKSTL NA+V + K Q I N I+ V P
Sbjct: 6 SGFVAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNAQIIFVDTP--- 62
Query: 108 VLSGLSKSQ--------KAVPASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVV 159
G+ K + KA ++++ VD+ V A +G G G++F IL+ +
Sbjct: 63 ---GIHKPKHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEF---------ILEQL 110
Query: 160 RCFEDNDIVHVNGKVDPKSDVDVIN 184
+ + I+ VN K+D V+
Sbjct: 111 KKTKTPVILVVN-KIDKVKPKTVLL 134
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 40.0 bits (95), Expect = 0.001
Identities = 16/26 (61%), Positives = 19/26 (73%), Gaps = 3/26 (11%)
Query: 55 MSLRAG---IVGLPNVGKSTLFNAVV 77
M ++G IVG PNVGKSTL NA+V
Sbjct: 1 MGFKSGFVAIVGRPNVGKSTLLNALV 26
>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 = 39.3 bits (92), Expect = 0.002
Identities = 26/119 (21%), Positives = 46/119 (38%), Gaps = 10/119 (8%)
Query: 57 LRAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLS--GLSK 114
I+G PNVGKSTL N + + + T GI ++ + G +
Sbjct: 1 GFVAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFIDTPGFHE 60
Query: 115 SQ--------KAVPASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFEDN 165
+ K +++ VD+ V + Q G G L+ ++ + + + R DN
Sbjct: 61 KKHSLNRLMMKEARSAIGGVDLILFVVDSDQWNGDGEFVLTKLQNLKRPVVLTRNKLDN 119
>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 = 37.5 bits (88), Expect = 0.004
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 61 IVGLPNVGKSTLFNA 75
I G PNVGKS+L NA
Sbjct: 8 IAGKPNVGKSSLLNA 22
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 38.6 bits (91), Expect = 0.005
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 61 IVGLPNVGKSTLFNA 75
I G PNVGKS+L NA
Sbjct: 220 IAGRPNVGKSSLLNA 234
>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 = 36.6 bits (85), Expect = 0.006
Identities = 15/32 (46%), Positives = 22/32 (68%)
Query: 57 LRAGIVGLPNVGKSTLFNAVVENGKAQAANFP 88
+R G+VGLPNVGKS+ NA++ K + + P
Sbjct: 92 IRVGVVGLPNVGKSSFINALLNKFKLKVGSIP 123
>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 = 37.8 bits (88), Expect = 0.010
Identities = 27/117 (23%), Positives = 50/117 (42%), Gaps = 24/117 (20%)
Query: 47 FSSASKISMSLRAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCT---IEPNVGIVAVPD 103
K+ + IVG PNVGKS+L NA+++ +A ++ T +E + + +
Sbjct: 194 SYKLEKLDDGFKLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGIL- 252
Query: 104 PRLHVLSGLSKSQKAVPASVEFVDIAGLVKGASQGEGLG-NKFLSHIREVDSILQVV 159
++ +D AG+ + A E LG K I++ D ++ V+
Sbjct: 253 -------------------IKLLDTAGIREHADFVERLGIEKSFKAIKQADLVIYVL 290
>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 = 36.3 bits (85), Expect = 0.014
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 56 SLRAGIVGLPNVGKSTLFNA 75
++ I+G PNVGKS+L NA
Sbjct: 2 PIKIAIIGRPNVGKSSLLNA 21
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 36.5 bits (85), Expect = 0.018
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 61 IVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVL 109
+ G PNVGKS+L + K + A +PF T +VG R+ V+
Sbjct: 173 VAGYPNVGKSSLVRKLT-TAKPEVAPYPFTTKGIHVGHFERGYLRIQVI 220
>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 = 37.0 bits (86), Expect = 0.020
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 63 GLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHV 108
G PNVGKSTLFNA+ N+P T+E G + + +
Sbjct: 1 GNPNVGKSTLFNALT-GANQTVGNWPGVTVEKKEGKLGFQGEDIEI 45
>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 = 34.9 bits (81), Expect = 0.020
Identities = 17/36 (47%), Positives = 22/36 (61%), Gaps = 3/36 (8%)
Query: 46 RFSSASKISMSLRAGIVGLPNVGKSTLFNAVVENGK 81
F SA + G+VG PNVGKS+L NA+V + K
Sbjct: 75 LFFSALNEAT---IGLVGYPNVGKSSLINALVGSKK 107
>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 = 35.4 bits (82), Expect = 0.022
Identities = 23/106 (21%), Positives = 35/106 (33%), Gaps = 16/106 (15%)
Query: 60 GIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLSGLSKSQKAV 119
IVG PNVGKSTL N ++ N + P T ++
Sbjct: 5 VIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEE---------------DGK 49
Query: 120 PASVEFVDIAGLVKGASQGEGLGNKFLSHIREVDSILQVVRCFEDN 165
+D AG + S +R D ++ V+ E+
Sbjct: 50 TYKFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLD-VEEI 94
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 36.4 bits (85), Expect = 0.024
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 7/35 (20%)
Query: 45 RRFSSASKISMSLRAG----IVGLPNVGKSTLFNA 75
+ KI LR G I+G PNVGKS+L NA
Sbjct: 205 LATAKQGKI---LREGLKVVIIGRPNVGKSSLLNA 236
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA,
an essential protein involved in cell division control.
YihA and its orthologs are small proteins that
typically contain less than 200 amino acid residues and
consists of the GTPase domain only (some of the
eukaryotic homologs contain an N-terminal extension of
about 120 residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 35.2 bits (82), Expect = 0.024
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 61 IVGLPNVGKSTLFNAVVENGK-AQAANFPFCTIEPN 95
G NVGKS+L NA+ K A+ + P T N
Sbjct: 4 FAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLIN 39
>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 = 35.9 bits (84), Expect = 0.030
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 7/68 (10%)
Query: 43 SRRRFSSASKISMSLRAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVP 102
RR+ + ++ +VG N GKSTLFNA+ AA+ F T++P + +P
Sbjct: 182 RRRKRADVPTVA------LVGYTNAGKSTLFNALTGAD-VYAADQLFATLDPTTRRLDLP 234
Query: 103 DPRLHVLS 110
D +L+
Sbjct: 235 DGGEVLLT 242
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 35.3 bits (82), Expect = 0.031
Identities = 24/107 (22%), Positives = 45/107 (42%), Gaps = 20/107 (18%)
Query: 16 LLPKPMESSLFTR------NANLIGVLGITTTSSRRRF---SSASKISMSLRAG----IV 62
LLPK ++ + + + + + S+++ + +I + +V
Sbjct: 72 LLPKDVKPNRLKQWVKKRLKIGGLKIKDVILVSAKKGWGVEELIEEIKKLAKYRGDVYVV 131
Query: 63 GLPNVGKSTLFNAVVE--NGKAQAANFPFCTIE---PN--VGIVAVP 102
G NVGKSTL NA+++ GK QA P +G++ +P
Sbjct: 132 GATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPGTTLGLIKIP 178
>gnl|CDD|178768 PLN03229, PLN03229, acetyl-coenzyme A carboxylase carboxyl
transferase subunit alpha; Provisional.
Length = 762
Score = 35.6 bits (82), Expect = 0.046
Identities = 21/57 (36%), Positives = 35/57 (61%), Gaps = 2/57 (3%)
Query: 174 VDPKSDVDVINLELVFSDLDQIEKRMEKLKKG--KAKDSQSKLKEDAEKAALEKIQQ 228
VDP+ V++ E V + + ++E +EKLK+ KAK+S SK E A +EK+++
Sbjct: 413 VDPERKVNMKKREAVKTPVRELEGEVEKLKEQILKAKESSSKPSELALNEMIEKLKK 469
>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 = 34.0 bits (79), Expect = 0.078
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 60 GIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDPRLHVLS 110
+VG N GKSTLFNA+ A + F T++P + +P R +L+
Sbjct: 45 ALVGYTNAGKSTLFNALTGAD-VLAEDQLFATLDPTTRRIKLPGGREVLLT 94
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 34.9 bits (81), Expect = 0.081
Identities = 15/25 (60%), Positives = 16/25 (64%), Gaps = 7/25 (28%)
Query: 61 IVGLPNVGKSTLFN-------AVVE 78
+VG PNVGKSTL N AVVE
Sbjct: 43 VVGRPNVGKSTLVNRILGRREAVVE 67
Score = 30.7 bits (70), Expect = 1.4
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 58 RAGIVGLPNVGKSTLFN 74
R +VG PNVGKS+L N
Sbjct: 213 RVALVGKPNVGKSSLLN 229
>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 = 32.7 bits (75), Expect = 0.16
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 8/58 (13%)
Query: 31 NLIGVLGITTTSSRRRFSSASKISMSLRAGIVGLPNVGKSTLFNAVVENGKAQAANFP 88
LI +L R+F+ + G +G PNVGKS++ N + + A P
Sbjct: 85 ALINLL--------RQFAKLHSDKKQISVGFIGYPNVGKSSVINTLRSKKVCKVAPIP 134
>gnl|CDD|203471 pfam06518, DUF1104, Protein of unknown function (DUF1104). This
family consists of several hypothetical proteins of
unknown function which appear to be found largely in
Helicobacter pylori.
Length = 93
Score = 31.5 bits (72), Expect = 0.16
Identities = 19/95 (20%), Positives = 41/95 (43%), Gaps = 16/95 (16%)
Query: 164 DNDIVHVNGKVDPKSDVDVINLELVFSDLDQIEKRMEKLKKGKAKDSQSKLKEDAEKAAL 223
+ +++ + G V PK D +I+KR+ K+K+ +AK+ ++ K K L
Sbjct: 8 NEELLKMAGSVAPKELADYAF---------EIDKRLGKMKEKEAKNFKAGFKAAMRK-NL 57
Query: 224 EKIQQALMDGKPARSVTLNDFERDSIKQLCLLTMK 258
K+ R + + K++ +++K
Sbjct: 58 SKMSVE------DRRKFRKEVREEMNKKVDAMSVK 86
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 33.9 bits (78), Expect = 0.17
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 61 IVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPD 103
+VG N GKSTLFN + E AA+ F T++P + + V D
Sbjct: 202 LVGYTNAGKSTLFNRITEAR-VYAADQLFATLDPTLRRIDVAD 243
>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 = 32.3 bits (74), Expect = 0.20
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 58 RAGIVGLPNVGKSTLFNAV 76
G+VG P VGKS++ NA+
Sbjct: 101 IVGVVGYPKVGKSSIINAL 119
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 33.6 bits (77), Expect = 0.23
Identities = 16/26 (61%), Positives = 17/26 (65%), Gaps = 7/26 (26%)
Query: 61 IVGLPNVGKSTLFN-------AVVEN 79
IVG PNVGKSTL N AVVE+
Sbjct: 280 IVGRPNVGKSTLVNRILGRREAVVED 305
Score = 30.1 bits (68), Expect = 2.7
Identities = 16/46 (34%), Positives = 23/46 (50%)
Query: 58 RAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPD 103
R +VG PNVGKS+L N + +A + T +P IV +
Sbjct: 452 RVALVGRPNVGKSSLLNQLTHEERAVVNDLAGTTRDPVDEIVEIDG 497
>gnl|CDD|224032 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
DnaJ-type Zn finger domain [DNA replication,
recombination, and repair].
Length = 715
Score = 33.2 bits (76), Expect = 0.27
Identities = 22/84 (26%), Positives = 43/84 (51%), Gaps = 15/84 (17%)
Query: 166 DIVHVNGKVDP---KSDVDVINLE-LVFSDLDQIEKRMEKLKKGKAK--------DSQ-- 211
DIV V G+V + +++ +E L + ++ KR+++ +A+ DS+
Sbjct: 263 DIVEVIGEVTRRDGRLQIEIEAMEKLTGDEAAEVRKRIDEALDRRAEPADVGFLVDSEVL 322
Query: 212 SKLKEDAEKAALEKIQQALMDGKP 235
LK D A E I++A+++G+P
Sbjct: 323 EALKPDMVDVAKE-IRRAVLEGRP 345
>gnl|CDD|215490 PLN02903, PLN02903, aminoacyl-tRNA ligase.
Length = 652
Score = 32.8 bits (75), Expect = 0.41
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 152 VDSILQVVRCFEDNDIVHVNGKVDPKSDVDVINLELVFSDLDQIEKRMEKL 202
D Q+ RCF D D+ + D + + +++EL F+ L+ + K E L
Sbjct: 272 FDRYYQIARCFRDEDL-----RADRQPEFTQLDMELAFTPLEDMLKLNEDL 317
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 32.1 bits (74), Expect = 0.50
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 61 IVGLPNVGKSTLFNAVVE 78
+VG+ NVGKSTL N +++
Sbjct: 165 VVGVTNVGKSTLINRIIK 182
>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 = 32.1 bits (74), Expect = 0.52
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 54 SMSLRAGIVGLPNVGKSTLFNAVV 77
L GI G N GKS+L NA+
Sbjct: 4 GNRLHIGIFGRRNAGKSSLINALT 27
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA ternary
complex to the ribosomal A site by facilitated release
of the deacylated tRNA from the E site. The reaction
requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 30.9 bits (71), Expect = 0.60
Identities = 19/73 (26%), Positives = 29/73 (39%), Gaps = 17/73 (23%)
Query: 51 SKISMSL----RAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAV-PDPR 105
IS+++ R G+VG GKSTL + +EP+ GIV +
Sbjct: 17 KDISLTINPGDRIGLVGRNGAGKSTLLKLIAGE------------LEPDEGIVTWGSTVK 64
Query: 106 LHVLSGLSKSQKA 118
+ LS +K
Sbjct: 65 IGYFEQLSGGEKM 77
>gnl|CDD|233546 TIGR01725, phge_HK97_gp10, phage protein, HK97 gp10 family. This
model represents an uncharacterized, highly divergent
bacteriophage family. The family includes gp10 from
HK022 and HK97. It appears related to TIGR01635, a phage
morphogenesis family believed to be involved in tail
completion [Mobile and extrachromosomal element
functions, Prophage functions].
Length = 119
Score = 30.5 bits (69), Expect = 0.66
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 4/63 (6%)
Query: 189 FSDLDQIEKRMEKLKKGKAKDSQSKLKEDAEKAALEKIQQALMDGKPARSVTLNDFERDS 248
F+ LD++ +++EKL K K + A KA I+ L P + RDS
Sbjct: 1 FTGLDELLQKLEKLGKKVDK----EKVRKALKAGANVIRAKLKSNAPVSKGKKHGSLRDS 56
Query: 249 IKQ 251
I +
Sbjct: 57 IVK 59
>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 = 28.7 bits (65), Expect = 1.0
Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 17/65 (26%)
Query: 353 AWTIRAGMTAPQAAGVIHSDFEKGFIRAETVAYDDFVAAGSLAAAREKGLLRSEGKDYIV 412
A+ + G TA A IH+D GF+ A AR R G+DY +
Sbjct: 24 AFLLPKGSTARDLAYAIHTDIGDGFLHA--------------IDARTG---RRVGEDYEL 66
Query: 413 QEGDV 417
+ DV
Sbjct: 67 KHRDV 71
>gnl|CDD|203270 pfam05532, CsbD, CsbD-like. CsbD is a bacterial general stress
response protein. It's expression is mediated by
sigma-B, an alternative sigma factor. The role of CsbD
in stress response is unclear.
Length = 53
Score = 28.2 bits (64), Expect = 1.1
Identities = 9/35 (25%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 186 ELVFSDLDQIEKRMEKLKKGKAKDSQSKLKEDAEK 220
+ D + E + ++LK GKA++ K+ A+
Sbjct: 20 KATGDDKLEAEGKADQLK-GKAQEKYGDAKDAAKD 53
>gnl|CDD|237619 PRK14135, recX, recombination regulator RecX; Provisional.
Length = 263
Score = 31.0 bits (71), Expect = 1.2
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 12/57 (21%)
Query: 179 DVDVINLELV-FSDLDQIE---KRMEKLKKGKAKDSQSKLKEDAEKAALEKIQQALM 231
+ ++I L +++ DQIE K EKL K K LK +KI Q+L+
Sbjct: 138 EDEIIEEALSEYTEEDQIEVAQKLAEKLLKKYQKLPFKALK--------QKIIQSLL 186
>gnl|CDD|236992 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
Reviewed.
Length = 556
Score = 30.9 bits (71), Expect = 1.5
Identities = 15/24 (62%), Positives = 16/24 (66%), Gaps = 4/24 (16%)
Query: 54 SMSL-RAGIVGL--PN-VGKSTLF 73
S SL GIVG+ PN GKSTLF
Sbjct: 344 SFSLPPGGIVGIIGPNGAGKSTLF 367
>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 = 30.1 bits (69), Expect = 1.6
Identities = 15/28 (53%), Positives = 19/28 (67%), Gaps = 4/28 (14%)
Query: 53 ISMSLRAG-IVGL--PN-VGKSTLFNAV 76
+S S+R G I GL PN GK+TLFN +
Sbjct: 19 VSFSVRPGEIHGLIGPNGAGKTTLFNLI 46
>gnl|CDD|236515 PRK09435, PRK09435, membrane ATPase/protein kinase; Provisional.
Length = 332
Score = 30.2 bits (69), Expect = 1.8
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 56 SLRAGIVGLPNVGKSTLFNA 75
+LR GI G+P VGKST A
Sbjct: 56 ALRIGITGVPGVGKSTFIEA 75
>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 140
Score = 29.1 bits (66), Expect = 2.0
Identities = 9/49 (18%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 182 VINLELVFSDLDQIEKRMEKLKKGKAKDSQSKLKEDAEKAALEKIQQAL 230
V++++ + + + ++L+K + K Q++L+ + L+K+++ L
Sbjct: 3 VVDVQKILQESPAGKAAQKQLEK-EFKKRQAELE--KLEKELQKLKEKL 48
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 30.5 bits (69), Expect = 2.1
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 57 LRAGIVGLPNVGKSTLFNAVVENGKAQ-AANFPFCTIEPNVGIVAVPD 103
L G++G PN GK+TLFN + G Q N+ T+E G + D
Sbjct: 4 LTIGLIGNPNSGKTTLFNQL--TGARQRVGNWAGVTVERKEGQFSTTD 49
>gnl|CDD|224340 COG1422, COG1422, Predicted membrane protein [Function unknown].
Length = 201
Score = 29.6 bits (67), Expect = 2.1
Identities = 13/68 (19%), Positives = 31/68 (45%), Gaps = 14/68 (20%)
Query: 197 KRMEKLKKGKA--KDSQSKLKEDAEKAALEKIQQALMDGKPARSVTLNDFERDSIKQLCL 254
++M++L+K + + +E + L+K+Q+ M + D ++L
Sbjct: 72 EKMKELQKMMKEFQKEFREAQESGDMKKLKKLQEKQM-----------EMMDDQ-RELMK 119
Query: 255 LTMKPIIY 262
+ KP++Y
Sbjct: 120 MQFKPMLY 127
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 29.9 bits (67), Expect = 2.3
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 56 SLRAGIVGLPNVGKSTLFNAVVEN 79
+ ++G VGK+TL N +V +
Sbjct: 5 EFKIVVLGDGGVGKTTLLNRLVGD 28
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 30.2 bits (68), Expect = 2.5
Identities = 29/137 (21%), Positives = 58/137 (42%), Gaps = 9/137 (6%)
Query: 143 NKFLSHIREVDSI-LQVVRCFEDNDIVHVNGKVDPKSDVDVINLELVFSDLDQIEKRMEK 201
N + EV+ I ++ R D+ + +N + KS + +E D+DQ++K M K
Sbjct: 1150 NLEDITLNEVNEIEIEYERILIDHIVEQINNEAK-KSKTIMEEIESYKKDIDQVKKNMSK 1208
Query: 202 LKKGKAKDSQSKLKEDAEKAALEKIQQAL-----MDGKPARSVTLNDFERDSIKQLCLLT 256
+ + D A+ E I++ + G+ RS +++ + IK
Sbjct: 1209 ERNDHLTTFEYNAYYDKATASYENIEELTTEAKGLKGEANRSTNVDELKE--IKLQVFSY 1266
Query: 257 MKPIIYVANVAESDLAD 273
++ +I N E+ L +
Sbjct: 1267 LQQVIKENNKMENALHE 1283
>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 = 29.9 bits (68), Expect = 2.6
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 61 IVGLPNVGKSTLFNAVVE 78
+VG+ NVGKS+L N +++
Sbjct: 159 VVGVTNVGKSSLINKLLK 176
>gnl|CDD|237050 PRK12305, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 575
Score = 30.1 bits (69), Expect = 2.6
Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 190 SDLDQIEKRMEKLKKGKAKDSQSKLKEDAEKAAL--EKIQQALMDGKPARSVTL 241
DL +IEK+M+K+ K + ++ + + E + L+D P +T+
Sbjct: 53 EDLKKIEKKMKKIIKRGLPFEREEVSREEAREEFANEPYKLELIDDIPEEGITI 106
>gnl|CDD|239570 cd03488, Topoisomer_IB_N_htopoI_like, Topoisomer_IB_N_htopoI_like :
N-terminal DNA binding fragment found in eukaryotic DNA
topoisomerase (topo) IB proteins similar to the
monomeric yeast and human topo I. Topo I enzymes are
divided into: topo type IA (bacterial) and type IB
(eukaryotic). Topo I relaxes superhelical tension in
duplex DNA by creating a single-strand nick, the broken
strand can then rotate around the unbroken strand to
remove DNA supercoils and, the nick is religated,
liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit religation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. This family may represent more than
one structural domain.
Length = 215
Score = 29.2 bits (66), Expect = 2.8
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 189 FSDLDQIEKRMEKLKKGKAKDSQSKLKEDAEKAALEKIQQ-ALMDG 233
F+ + K ++ KK +K + K AEK LE+ ++DG
Sbjct: 87 FTQMFAYFKAQKEEKKAMSK--EEKKAIKAEKEKLEEEYGFCILDG 130
>gnl|CDD|238356 cd00660, Topoisomer_IB_N, Topoisomer_IB_N: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the monomeric yeast and human topo I
and heterodimeric topo I from Leishmania donvanni. Topo
I enzymes are divided into: topo type IA (bacterial)
and type IB (eukaryotic). Topo I relaxes superhelical
tension in duplex DNA by creating a single-strand nick,
the broken strand can then rotate around the unbroken
strand to remove DNA supercoils and, the nick is
religated, liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit re-ligation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topos I play putative roles
in organizing the kinetoplast DNA network unique to
these parasites. This family may represent more than
one structural domain.
Length = 215
Score = 29.5 bits (67), Expect = 2.9
Identities = 17/60 (28%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 177 KSDVDVINLELVFSDLDQIEKRMEKLK-KGKAKDSQSKLKEDAEKAALEKIQQ-ALMDGK 234
+ I +L D I + E+ K K KA + K EK LE+ L+DG
Sbjct: 72 TKEEKHIIKKLSKCDFTPIYQYFEEEKEKKKAMSKEEKKAIKEEKEKLEEPYGYCLVDGH 131
>gnl|CDD|184281 PRK13729, PRK13729, conjugal transfer pilus assembly protein TraB;
Provisional.
Length = 475
Score = 29.8 bits (67), Expect = 3.0
Identities = 10/39 (25%), Positives = 20/39 (51%)
Query: 192 LDQIEKRMEKLKKGKAKDSQSKLKEDAEKAALEKIQQAL 230
++I + ++ L K + D + K + AAL + +AL
Sbjct: 85 YEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKAL 123
>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 = 29.6 bits (67), Expect = 3.0
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 56 SLRAGIVGLPNVGKSTLFNAVVEN 79
+ R GI G+P GKSTL A+
Sbjct: 29 AHRVGITGVPGAGKSTLIEALGME 52
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 28.8 bits (65), Expect = 3.1
Identities = 12/49 (24%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 182 VINLELVFSDLDQIEKRMEKLKKGKAKDSQSKLKEDAEKAALEKIQQAL 230
V++++ V S+ + ++L+K + K Q++L ++ L+K +Q L
Sbjct: 20 VVDVQKVLSESPAGKAAQKQLEK-EFKKLQAEL--QKKEKELQKEEQKL 65
>gnl|CDD|107088 PHA01818, PHA01818, hypothetical protein.
Length = 458
Score = 29.7 bits (66), Expect = 3.5
Identities = 10/54 (18%), Positives = 20/54 (37%)
Query: 273 DPGSNPHVNEVMNLASDLQSGRVTISAQVEAELTELPSEERVEYLASLGVSESG 326
D G + L + G I A+ A L + P E ++ + + ++
Sbjct: 56 DKGLTKSYGNITALRDIKEPGYYYIGARTLATLLDRPDMESLDVVLHVVPLDTS 109
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 29.2 bits (66), Expect = 3.6
Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 10/49 (20%)
Query: 56 SLRAGIVGLPNVGKSTLFNAVVENGKAQAANFPFCTIEPNVGIVAVPDP 104
+ GI G+P GKSTL A+ V ++AV DP
Sbjct: 51 AHVIGITGVPGAGKSTLIEALGRE---------LRERGHRVAVLAV-DP 89
>gnl|CDD|227082 COG4739, COG4739, Uncharacterized protein containing a ferredoxin
domain [Function unknown].
Length = 182
Score = 29.1 bits (65), Expect = 3.7
Identities = 28/79 (35%), Positives = 43/79 (54%), Gaps = 8/79 (10%)
Query: 167 IVHVNGKVDPKSD-VDVINLELVF-SDLDQIEKRMEKLKKGKAKDSQSKLKEDAEKAALE 224
I+ + PKS +D I + LV ++++I RME+L + K KD LK DAE +
Sbjct: 16 IMAEAARTAPKSKGIDDIVIVLVEGEEMEKIAARMEELAEEKDKDF---LKRDAE--NVR 70
Query: 225 KIQQALMDG-KPARSVTLN 242
K Q ++ G K + +V LN
Sbjct: 71 KSQAIVLIGVKASGTVGLN 89
>gnl|CDD|234618 PRK00078, PRK00078, Maf-like protein; Reviewed.
Length = 192
Score = 28.9 bits (65), Expect = 3.9
Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 8/42 (19%)
Query: 184 NLELVFSDLDQ--------IEKRMEKLKKGKAKDSQSKLKED 217
+ +++ SD D+ IE + L +GKA+ KL ++
Sbjct: 22 DFQVIVSDFDESSVPFKGNIESYVMNLAEGKARSVSKKLDQE 63
>gnl|CDD|236134 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated.
Length = 394
Score = 29.1 bits (66), Expect = 4.2
Identities = 9/33 (27%), Positives = 13/33 (39%)
Query: 296 TISAQVEAELTELPSEERVEYLASLGVSESGLG 328
A+ +A E E E +LG +G G
Sbjct: 249 AAEAEAKALTAERDEAETEELRTALGAGGTGKG 281
>gnl|CDD|213191 cd03224, ABC_TM1139_LivF_branched, ATP-binding cassette domain of
branched-chain amino acid transporter. LivF (TM1139)
is part of the LIV-I bacterial ABC-type two-component
transport system that imports neutral, branched-chain
amino acids. The E. coli branched-chain amino acid
transporter comprises a heterodimer of ABC transporters
(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).
ABC transporters are a large family of proteins
involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides, and
more complex organic molecules.
Length = 222
Score = 28.9 bits (66), Expect = 4.3
Identities = 10/29 (34%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 53 ISMSLRAG-IVGL--PN-VGKSTLFNAVV 77
+S+++ G IV L N GK+TL ++
Sbjct: 19 VSLTVPEGEIVALLGRNGAGKTTLLKTIM 47
>gnl|CDD|222030 pfam13291, ACT_4, ACT domain. ACT domains bind to amino acids and
regulate associated enzyme domains. These ACT domains
are found at the C-terminus of the RelA protein.
Length = 77
Score = 27.1 bits (61), Expect = 4.5
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 166 DIVHVNGKVDPKSDVDVINLELVFSDLDQIEKRMEKLKK 204
+I+ VN + + + INL L DL+ + + + KL+K
Sbjct: 31 NILSVNAESK-DNGIATINLTLEVKDLEHLARLIRKLRK 68
>gnl|CDD|232931 TIGR00344, alaS, alanine--tRNA ligase. The model describes
alanine--tRNA ligase. This enzyme catalyzes the reaction
(tRNAala + L-alanine + ATP = L-alanyl-tRNAala +
pyrophosphate + AMP) [Protein synthesis, tRNA
aminoacylation].
Length = 851
Score = 29.3 bits (66), Expect = 4.6
Identities = 23/118 (19%), Positives = 51/118 (43%), Gaps = 16/118 (13%)
Query: 190 SDLDQIEKRMEKLKKGKAKDSQSKLKEDAEKAALEKIQQALMDGKPARSVTLNDFERDSI 249
+++ K++E+ + + K Q +L+ K A +KI + L D ++ T+N + +
Sbjct: 719 VTPNELPKKIERFFE-EWKALQKELESLKLKIADQKIDE-LKD----KAETINGVKVL-V 771
Query: 250 KQLCLLTMKPIIYVANVAESDLADPGSNPHVNEVMNLASDLQSGRVTISAQVEAELTE 307
+ + MK + +AD + + + LAS G+V + V ++
Sbjct: 772 EVVDAKDMKSL--------KTMADRLKSKLGSAIYVLASFAN-GKVKLVCGVSNDVLN 820
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 28.7 bits (65), Expect = 4.9
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 62 VGLPNVGKSTLFNAVVENGKAQA 84
G NVGKS+L NA+ N K A
Sbjct: 30 AGRSNVGKSSLINALT-NQKNLA 51
>gnl|CDD|143439 cd07121, ALDH_EutE, Ethanolamine utilization protein EutE-like.
Coenzyme A acylating aldehyde dehydrogenase (ACDH), an
NAD+ and CoA-dependent acetaldehyde dehydrogenase,
acetylating (EC=1.2.1.10), converts acetaldehyde into
acetyl-CoA. This CD is limited to such monofunctional
enzymes as the Ethanolamine utilization protein, EutE,
in Salmonella typhimurium. Mutations in eutE abolish
the ability to utilize ethanolamine as a carbon source.
Length = 429
Score = 29.1 bits (66), Expect = 5.0
Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 5/62 (8%)
Query: 312 ERVEYLASLGVSESGLGNLIRSTYSLLGLRTYFTSGEK--ETKAWTIRAGMTAPQAA--G 367
E LA + V E+G+G + T G + T AW+ G+T + A G
Sbjct: 41 SNAEELAEMAVEETGMGRVEDKIAKNHLAAEK-TPGTEDLTTTAWSGDNGLTLVEYAPFG 99
Query: 368 VI 369
VI
Sbjct: 100 VI 101
>gnl|CDD|238288 cd00520, RRF, Ribosome recycling factor (RRF). Ribosome recycling
factor dissociates the posttermination complex, composed
of the ribosome, deacylated tRNA, and mRNA, after
termination of translation. Thus ribosomes are
"recycled" and ready for another round of protein
synthesis. RRF is believed to bind the ribosome at the
A-site in a manner that mimics tRNA, but the specific
mechanisms remain unclear. RRF is essential for
bacterial growth. It is not necessary for cell growth
in archaea or eukaryotes, but is found in mitochondria
or chloroplasts of some eukaryotic species.
Length = 179
Score = 28.4 bits (64), Expect = 5.0
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 198 RMEKLKKGKAKDSQSKLKEDAEKAALEKIQQA 229
R + K K + + ++ ED K A E +Q+
Sbjct: 128 RRDANDKIKKLEKEKEISEDEVKKAEEDLQKL 159
>gnl|CDD|218905 pfam06125, DUF961, Bacterial protein of unknown function (DUF961).
This family consists of several hypothetical bacterial
proteins of unknown function.
Length = 103
Score = 27.3 bits (61), Expect = 5.7
Identities = 11/31 (35%), Positives = 14/31 (45%)
Query: 285 NLASDLQSGRVTISAQVEAELTELPSEERVE 315
NL S +Q + +S EA E P VE
Sbjct: 43 NLYSSVQGDDIQVSIPAEAGEKEFPYNAEVE 73
>gnl|CDD|223394 COG0317, SpoT, Guanosine polyphosphate
pyrophosphohydrolases/synthetases [Signal transduction
mechanisms / Transcription].
Length = 701
Score = 29.1 bits (66), Expect = 5.9
Identities = 8/42 (19%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 163 EDNDIVHVNGKVDPKSDVDVINLELVFSDLDQIEKRMEKLKK 204
E +++ VN + D K + + +L+ + + + +LK+
Sbjct: 651 EKINVLGVNTRSD-KDQFATMQFTIEVKNLNHLGRVLARLKQ 691
>gnl|CDD|179798 PRK04239, PRK04239, hypothetical protein; Provisional.
Length = 110
Score = 27.5 bits (62), Expect = 6.2
Identities = 10/43 (23%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 190 SDLDQI-EKRMEKLKKGKAKDSQSKLKEDAEKAALEKIQQALM 231
+L++I +++E+L+K + Q++ +++ +A E +QA++
Sbjct: 1 EELEEIRRRKLEELQKQAQEQQQAQEEQEEAQAQAEAQKQAIL 43
>gnl|CDD|224415 COG1498, SIK1, Protein implicated in ribosomal biogenesis, Nop56p
homolog [Translation, ribosomal structure and
biogenesis].
Length = 395
Score = 28.9 bits (65), Expect = 6.2
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 194 QIEKRMEKLKKGKAKDSQSKLKEDAEKAALEKIQQALMDGKPARS 238
++EKR+EKLK+ K E +K + + K A+S
Sbjct: 345 ELEKRIEKLKEKPPKPPTKAKPERDKKERPGR-YRRKKKEKKAKS 388
>gnl|CDD|211576 TIGR00459, aspS_bact, aspartyl-tRNA synthetase, bacterial type.
Asparate--tRNA ligases in this family may be
discriminating (6.1.1.12) or nondiscriminating
(6.1.1.23). In a multiple sequence alignment of
representative asparaginyl-tRNA synthetases (asnS),
archaeal/eukaryotic type aspartyl-tRNA synthetases
(aspS_arch), and bacterial type aspartyl-tRNA
synthetases (aspS_bact), there is a striking similarity
between asnS and aspS_arch in gap pattern and in
sequence, and a striking divergence of aspS_bact.
Consequently, a separate model was built for each of the
three groups. This model, aspS_bact, represents
aspartyl-tRNA synthetases from the Bacteria and from
mitochondria. In some species, this enzyme aminoacylates
tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently
transamidated to Asn-tRNA(asn). This model generates
very low scores for the archaeal type of aspS and for
asnS; scores between the trusted and noise cutoffs
represent fragmentary sequences [Protein synthesis, tRNA
aminoacylation].
Length = 583
Score = 28.9 bits (65), Expect = 6.4
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 152 VDSILQVVRCFEDNDIVHVNGKVDPKSDVDVINLELVFSDLDQIEKRMEKL 202
VD Q+ RCF D D+ + D + + I++E+ F + + + +EKL
Sbjct: 206 VDRYYQIARCFRDEDL-----RADRQPEFTQIDMEMSFMTQEDVMELIEKL 251
>gnl|CDD|218188 pfam04641, Rtf2, Replication termination factor 2. It is vital for
effective cell-replication that replication is not
stalled at any point by, for instance, damaged bases.
Rtf2 stabilizes the replication fork stalled at the
site-specific replication barrier RTS1 by preventing
replication restart until completion of DNA synthesis by
a converging replication fork initiated at a flanking
origin. The RTS1 element terminates replication forks
that are moving in the cen2-distal direction while
allowing forks moving in the cen2-proximal direction to
pass through the region. Rtf2 contains a C2HC2 motif
related to the C3HC4 RING-finger motif, and would appear
to fold up, creating a RING finger-like structure but
forming only one functional Zn2+ ion-binding site.
Length = 254
Score = 28.5 bits (64), Expect = 6.6
Identities = 10/62 (16%), Positives = 27/62 (43%), Gaps = 16/62 (25%)
Query: 162 FEDNDIVHVNGKVDPKSDVDVINLELVFSDLDQIEKRMEKLK-KGKAKDSQSKLKEDAEK 220
+ + D+V +N + +++ ++ R+E+ + K K K + K K++
Sbjct: 154 YSEEDVVPLNPTEE---------------EVELLKARLEEERAKKKKKKKKKKTKKNNAT 198
Query: 221 AA 222
+
Sbjct: 199 GS 200
>gnl|CDD|227554 COG5229, LOC7, Chromosome condensation complex Condensin, subunit H
[Chromatin structure and dynamics / Cell division and
chromosome partitioning].
Length = 662
Score = 28.6 bits (63), Expect = 6.9
Identities = 32/171 (18%), Positives = 55/171 (32%), Gaps = 14/171 (8%)
Query: 190 SDLDQIEKRMEKLKKGKAKDS----QSKLKEDAEKAALEKIQQALMDGKPARSV--TLND 243
S +D + KL G A DS L D E K R TL
Sbjct: 62 SRVDSVSTETGKLLSGLANDSNGGNGEGLGGDIEIDD-PDRNNTEERRKKQRVGKTTLVK 120
Query: 244 FERDSIKQL-CLLTMKPIIYVANVAESDLADPGSNPHVNEVMNLASDLQSGRVTISAQVE 302
FE+ +IK+ C L + P+ D + ++N + + R+ +
Sbjct: 121 FEKITIKKNICELNIDPLFKKR------CVDFDEGGAKSLLLNTLNIDNTKRLYFDSSPI 174
Query: 303 AELTELPSEERVEYLASLGVSESGLGNLIRSTYSLLGLRTYFTSGEKETKA 353
+ + + L +S + +L+ + SL T + A
Sbjct: 175 KDTENVGQGKLQRKEEELIERDSLVDDLMIDSQSLGISSNDSTVNDSVISA 225
>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 = 28.2 bits (63), Expect = 7.3
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 56 SLRAGIVGLPNVGKSTLFNAVVE 78
+ R GI G P GKSTL A+
Sbjct: 34 AHRVGITGTPGAGKSTLLEALGM 56
>gnl|CDD|218391 pfam05029, TIMELESS_C, Timeless protein C terminal region. The
timeless (tim) gene is essential for circadian function
in Drosophila. Putative homologues of Drosophila tim
have been identified in both mice and humans (mTim and
hTIM, respectively). Mammalian TIM is not the true
orthologue of Drosophila TIM, but is the likely
orthologue of a fly gene, timeout (also called tim-2).
mTim has been shown to be essential for embryonic
development, but does not have substantiated circadian
function. Some family members contain a SANT domain in
this region.
Length = 507
Score = 28.5 bits (63), Expect = 8.2
Identities = 29/134 (21%), Positives = 48/134 (35%), Gaps = 16/134 (11%)
Query: 173 KVDPKSDVDVINLELVFSDLDQIEKRMEKLKKGKAKDSQSKLKEDAEKAALEKIQQALMD 232
+ + K DVD + + + K + K G A + L E+ +KA +K Q +
Sbjct: 386 EDELKDDVDGEQADESEHETLALRKNARQRKAGLASPEEEALGEEEQKAPPKKKQLNQKN 445
Query: 233 GKPARSVTLNDFERDSIKQLCLLTMKPIIYVANVAESDLADPGSNP--HVNEVMNLASDL 290
+ S T +D ERD + + DLAD G P H ++ +
Sbjct: 446 KQQTGSGTNSDEERDDT--------------SLDEDRDLADDGGLPRIHKDKRAGASLTQ 491
Query: 291 QSGRVTISAQVEAE 304
VE +
Sbjct: 492 SPLSRRRLKVVEDD 505
>gnl|CDD|119001 pfam10481, Cenp-F_N, Cenp-F N-terminal domain. Mitosin or
centromere-associated protein-F (Cenp-F) is found bound
across the centromere as one of the proteins of the
outer layer of the kinetochore. Most of the
kinetochore/centromere functions appear to depend upon
binding of the C-terminal par to f the molecule, whereas
the N-terminal part, here, may be a cytoplasmic player
in controlling the function of microtubules and dynein.
Length = 288
Score = 28.2 bits (62), Expect = 8.3
Identities = 14/43 (32%), Positives = 28/43 (65%), Gaps = 3/43 (6%)
Query: 192 LDQIEKRMEKLKKGKAKDSQSKLKEDAEKAALEKIQQALMDGK 234
+ ++E +++KLKK K Q + + D+ +AAL+K +Q + + K
Sbjct: 20 IQELEGQLDKLKKEK---QQRQFQLDSLEAALQKQKQKVENEK 59
>gnl|CDD|237937 PRK15304, PRK15304, putative fimbrial outer membrane usher protein;
Provisional.
Length = 801
Score = 28.2 bits (63), Expect = 9.6
Identities = 8/47 (17%), Positives = 20/47 (42%), Gaps = 1/47 (2%)
Query: 354 WTIRAGMTAPQAAGVIHSDFEKGFIRAETVAYDDFVAAGSLAAAREK 400
W + M A GV+ +++ R + V + + S+ +++
Sbjct: 364 WRLTPWMNL-LAGGVLAENYQAAGARLDWVPLPKWTVSASMLGSQDS 409
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
0.315 0.132 0.362
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,273,152
Number of extensions: 2091162
Number of successful extensions: 3139
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3064
Number of HSP's successfully gapped: 178
Length of query: 424
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 324
Effective length of database: 6,502,202
Effective search space: 2106713448
Effective search space used: 2106713448
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: 60 (26.8 bits)