RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6781
(534 letters)
>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 = 348 bits (895), Expect = e-119
Identities = 126/157 (80%), Positives = 147/157 (93%)
Query: 236 ELYKVIDSSDVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVPIWVTQRW 295
ELYKVIDSSDV++ VLD RDPMGTRC H+E +LR+EKPHKHL F+LNK DLVP WVT+RW
Sbjct: 1 ELYKVIDSSDVIIQVLDARDPMGTRCKHVEKYLRKEKPHKHLIFVLNKCDLVPTWVTKRW 60
Query: 296 VAILSKEYPTIAFHASMTHPFGKGSIINLLRQFSKLHTERKQISVGFIGYPNVGKSSIIN 355
V +LSKEYPT+AFHAS+T+PFGKG++INLLRQF+KLH+++KQISVGFIGYPNVGKSS+IN
Sbjct: 61 VKVLSKEYPTLAFHASITNPFGKGALINLLRQFAKLHSDKKQISVGFIGYPNVGKSSVIN 120
Query: 356 ALRNKKVCKTAPVPGETKVWQYITLMRRIYLIDCPGV 392
LR+KKVCK AP+PGETKVWQYITLM+RIYLIDCPGV
Sbjct: 121 TLRSKKVCKVAPIPGETKVWQYITLMKRIYLIDCPGV 157
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 224 bits (572), Expect = 6e-69
Identities = 101/287 (35%), Positives = 144/287 (50%), Gaps = 28/287 (9%)
Query: 228 GQSKRIWGELYKVIDSSDVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLV 287
G K+ +L +V+ S DVVV V+D RDP+GTR +E ++ EKP +LNK DL
Sbjct: 19 GHMKKAKRQLKEVLKSVDVVVEVVDARDPLGTRNPELERIVK-EKPK---LLVLNKADLA 74
Query: 288 PIWVTQRWVAILSKEYPTIAFHASMTHPFGKGSII--------NLLRQFSKLHTERKQIS 339
P VT++W KE S G I +++ K +++I
Sbjct: 75 PKEVTKKWKKYFKKEEGIKPIFVSAKSRQGGKKIRKALEKLSEEKIKRLKKKGLLKRKIR 134
Query: 340 VGFIGYPNVGKSSIINALRNKKVCKTAPVPGETKVWQYITLMRRIYLIDCPGVVYDMTNV 399
VG +GYPNVGKS++IN L KKV KT+ PG TK Q+I L IYL+D PG++
Sbjct: 135 VGVVGYPNVGKSTLINRLLGKKVAKTSNRPGTTKGIQWIKLDDGIYLLDTPGII---PPK 191
Query: 400 ETDTEKVLRGVVRVENIDDPVQYIDAVLERIKKV-----HLVKTYGIDEWE-------DT 447
D E VL + I DPV D V ER+ H + I +E D
Sbjct: 192 FDDDELVLLKLAPKGEIKDPVLPADEVAERLLGGLLIDEHYGEKLNITRYESNPIHRTDP 251
Query: 448 EDFLKKLAFKWGK-IKKKGEPVITASAKMVLNDWQRGKLPYYTVPEG 493
E+FL+ +A K G + K GEP + +A+ +L D + GKL ++++ E
Sbjct: 252 EEFLELIAKKRGWLLLKGGEPDLERAAETILKDIRNGKLGWFSLEEP 298
>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 = 173 bits (440), Expect = 7e-52
Identities = 64/148 (43%), Positives = 84/148 (56%), Gaps = 2/148 (1%)
Query: 245 DVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVPIWVTQRWVAILSKEYP 304
DVVV V+D RDP+ +R IE + +K L +LNK DLVP V ++WVA LS+ Y
Sbjct: 1 DVVVEVVDARDPLSSRNPDIEVL--INEKNKKLIMVLNKADLVPKEVLRKWVAELSELYG 58
Query: 305 TIAFHASMTHPFGKGSIINLLRQFSKLHTERKQISVGFIGYPNVGKSSIINALRNKKVCK 364
T F S T+ G + + + +K I VG +G PNVGKSS INAL NK K
Sbjct: 59 TKTFFISATNGQGILKLKAEITKQKLKLKYKKGIRVGVVGLPNVGKSSFINALLNKFKLK 118
Query: 365 TAPVPGETKVWQYITLMRRIYLIDCPGV 392
+PG TK+ Q + L + IYL D PG+
Sbjct: 119 VGSIPGTTKLQQDVKLDKEIYLYDTPGI 146
>gnl|CDD|149291 pfam08153, NGP1NT, NGP1NT (NUC091) domain. This N terminal domain
is found in a subfamily of hypothetical nucleolar
GTP-binding proteins similar to human NGP1.
Length = 130
Score = 168 bits (428), Expect = 2e-50
Identities = 63/132 (47%), Positives = 92/132 (69%), Gaps = 3/132 (2%)
Query: 71 MYRCFKAKRDKTGKIIHPAPFQGWVPSGTQSRVEPNRKWFDNTRVISQNSLQKFQEEFGK 130
MY+ KAKR+ GKII APFQ G +R+EP+RKWF NTRVISQ++LQKF+EE G+
Sbjct: 1 MYKSGKAKRNAKGKIIKAAPFQ--SKEGPVARIEPDRKWFGNTRVISQDALQKFREEMGE 58
Query: 131 AIKNPYDVIMKPTNLPITLLNEV-RKHERVHVLDTESYESVFGKKKQRKKANLSITNESE 189
K+PY V++K + LP++LL + +K ++V +L+TE +E FG K QRK+ L++++ E
Sbjct: 59 KKKDPYSVLLKRSKLPMSLLKDSTKKQKKVKILETEPFEDTFGPKAQRKRPKLAVSSLEE 118
Query: 190 LAALVQTSNENY 201
LA + S + Y
Sbjct: 119 LAKKAEESADTY 130
>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 = 168 bits (429), Expect = 7e-50
Identities = 61/171 (35%), Positives = 92/171 (53%), Gaps = 23/171 (13%)
Query: 245 DVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVPIWVTQRWVAILSKEYP 304
DV++ VLD RDP+G RC +E + P+K L +LNK+DLVP ++W+ L E+P
Sbjct: 1 DVILEVLDARDPLGCRCPQVERAVLVLGPNKKLVLVLNKIDLVPKENVEKWLKYLRNEFP 60
Query: 305 TIAFHASMTHP-----------------------FGKGSIINLLRQFSKLHTERKQISVG 341
T+AF AS G +++ LL+ +++ + I+VG
Sbjct: 61 TVAFKASTQQQKKNLSRKSKKVKASDDLLSSSACLGADALLKLLKNYARNKGIKTSITVG 120
Query: 342 FIGYPNVGKSSIINALRNKKVCKTAPVPGETKVWQYITLMRRIYLIDCPGV 392
+GYPNVGKSS+IN+L+ + C PG TK Q + L + + L+D PGV
Sbjct: 121 VVGYPNVGKSSVINSLKRSRACNVGATPGVTKSMQEVHLDKHVKLLDSPGV 171
>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 = 131 bits (331), Expect = 3e-36
Identities = 59/162 (36%), Positives = 85/162 (52%), Gaps = 23/162 (14%)
Query: 233 IWGELYKVIDSSDVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVPIWVT 292
+W +L++VI+ SDVVV ++D R+P+ RC +E +++ P K +LNK DLV
Sbjct: 1 VWRQLWRVIERSDVVVQIVDARNPLFFRCPDLEKYVKEVDPSKENVLLLNKADLVTEEQR 60
Query: 293 QRWVAILSKEYPTIAFHASMTHPFGKGSIINLLRQFSKLHTERKQISVGFIGYPNVGKSS 352
+ W KE + F FS L + ++G +GYPNVGKSS
Sbjct: 61 KAWARYFKKEGIVVLF-------------------FSAL----NEATIGLVGYPNVGKSS 97
Query: 353 IINALRNKKVCKTAPVPGETKVWQYITLMRRIYLIDCPGVVY 394
+INAL K + PG+TK +Q I L I L DCPG+V+
Sbjct: 98 LINALVGSKKVSVSSTPGKTKHFQTIFLEPGITLCDCPGLVF 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 = 125 bits (316), Expect = 7e-34
Identities = 63/159 (39%), Positives = 86/159 (54%), Gaps = 13/159 (8%)
Query: 239 KVIDSSDVVVYVLDVRDPMGTRCAHIENF-LRREKPHKHLFFILNKVDLVPIWVTQRWVA 297
++I +DVV+ V+D RDP TR +E L K L +LNK DLVP V ++W
Sbjct: 7 RIIKEADVVLEVVDARDPELTRSRKLERMALELGKK---LIIVLNKADLVPREVLEKWKE 63
Query: 298 ILSKE-YPTIAFHASMTHPFGKGSIINLLRQFSKLHTERKQISVGFIGYPNVGKSSIINA 356
+ E P + A G+ I L R +L + K + VG +GYP VGKSSIINA
Sbjct: 64 VFESEGLPVVYVSARER----LGTRI-LRRTIKELAIDGKPVIVGVVGYPKVGKSSIINA 118
Query: 357 LRNKKVCKTAPVPGE---TKVWQYITLMRRIYLIDCPGV 392
L+ + T+P+PG TK Q + + +IYLID PGV
Sbjct: 119 LKGRHSASTSPIPGSPGYTKGIQLVRIDSKIYLIDTPGV 157
>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 = 106 bits (266), Expect = 1e-25
Identities = 80/254 (31%), Positives = 130/254 (51%), Gaps = 19/254 (7%)
Query: 245 DVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVPIWVTQRWVAILSKEYP 304
DVV+ VLD R P+ +R I+ +R KP +LNK DL VT++W+ +E
Sbjct: 23 DVVIEVLDARIPLSSRNPMIDE-IRGNKPR---LIVLNKADLADPAVTKQWLKYF-EEKG 77
Query: 305 TIAFHASMTHPFGKGSIINLLRQFSKLHTER--------KQISVGFIGYPNVGKSSIINA 356
A + G II ++ K E+ + I +G PNVGKS++IN
Sbjct: 78 IKALAINAKKGKGVKKIIKAAKKLLKEKNEKLKAKGLLNRPIRAMIVGIPNVGKSTLINR 137
Query: 357 LRNKKVCKTAPVPGETKVWQYITLMRRIYLIDCPGVVYDMTNVETDTEK-VLRGVVRVE- 414
L KKV K PG TK Q+I L + L+D PG+++ + K G ++ E
Sbjct: 138 LAGKKVAKVGNRPGVTKGQQWIKLSDGLELLDTPGILWPKFEDQEVGLKLAATGAIKDEA 197
Query: 415 -NIDDPVQY-IDAVLERIKKVHLVKTYGIDE-WEDTEDFLKKLAFKWGKIKKKGEPVITA 471
+++D + ++ +LE ++ L + Y +DE ED + L+ +A K G + K GE +
Sbjct: 198 LDLEDVALFLLEYLLEHYPEL-LKERYKLDELPEDIVELLEAIAKKRGCLLKGGELDLDR 256
Query: 472 SAKMVLNDWQRGKL 485
+A+++LND+++GKL
Sbjct: 257 AAEILLNDFRKGKL 270
>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 = 101 bits (255), Expect = 3e-25
Identities = 49/158 (31%), Positives = 74/158 (46%), Gaps = 18/158 (11%)
Query: 245 DVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVPIWVTQRWVAILSKEYP 304
DVV+ V D R P+ +R ++ L KP +LNK DL T++W+ K +
Sbjct: 21 DVVIEVRDARIPLSSRNPDLDKILGN-KPR---LIVLNKADLADPAKTKKWL----KYFK 72
Query: 305 TIAFHASMTHPFGKGSIINLLRQFSKLHTER----------KQISVGFIGYPNVGKSSII 354
+ + + LL++ KL E + + +G PNVGKS++I
Sbjct: 73 SQGEPVLFVNAKNGKGVKKLLKKAKKLLKENEKLKAKGLLPRPLRAMVVGIPNVGKSTLI 132
Query: 355 NALRNKKVCKTAPVPGETKVWQYITLMRRIYLIDCPGV 392
N LR KKV K PG T+ Q+I + I L+D PG+
Sbjct: 133 NRLRGKKVAKVGNKPGVTRGQQWIRIGPNIELLDTPGI 170
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 103 bits (259), Expect = 1e-24
Identities = 83/280 (29%), Positives = 136/280 (48%), Gaps = 33/280 (11%)
Query: 236 ELYKVIDSSDVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVPIWVTQRW 295
E+ + + DVV+ VLD R P+ + I+ + KP ILNK DL VT++W
Sbjct: 17 EIKENLKLVDVVIEVLDARIPLSSENPMIDK-IIGNKPR---LLILNKSDLADPEVTKKW 72
Query: 296 VAIL-SKEYPTIAFHASMTHPFGKGSIINLLRQFSKLHTER--------KQISVGFIGYP 346
+ + +A +A G I+ ++ K ER + I IG P
Sbjct: 73 IEYFEEQGIKALAINAK--KGQGVKKILKAAKKLLKEKNERRKAKGMRPRAIRAMIIGIP 130
Query: 347 NVGKSSIINALRNKKVCKTAPVPGETKVWQYITLMRRIYLIDCPGVVY-DMTNVETDTEK 405
NVGKS++IN L KK+ KT PG TK Q+I L + + L+D PG+++ + + E +
Sbjct: 131 NVGKSTLINRLAGKKIAKTGNRPGVTKAQQWIKLGKGLELLDTPGILWPKLEDQEVGLKL 190
Query: 406 VLRGVVRVENIDDPVQYIDAV----LERIKKV---HLVKTYGIDEWEDT-EDFLKKLAFK 457
L G ++ E +D ++ V LE + K L + Y +DE + + L+ +A K
Sbjct: 191 ALTGAIKDEALD-----LEEVAIFALEYLSKHYPERLKERYKLDELPEDILELLEAIARK 245
Query: 458 WGKIKKKGEPVITASAKMVLNDWQRGKLPYYTVPEGFEVP 497
G ++K GE +++++LN+++ GKL T E P
Sbjct: 246 RGALRKGGEIDYERASELLLNEFRNGKLGKIT----LETP 281
>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 = 75.0 bits (185), Expect = 2e-16
Identities = 24/56 (42%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 340 VGFIGYPNVGKSSIINALRNKKVCKTAPVPGETKVWQY--ITLMRRIYLIDCPGVV 393
V +G PNVGKS++INAL KV + PG T+ + L R+I L+D PG++
Sbjct: 2 VALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVLGLGRQIILVDTPGLI 57
Score = 34.6 bits (80), Expect = 0.031
Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 228 GQSKRIWGELY----KVIDSSDVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNK 283
G S+ E + + I +D+++ V+D + + I L + K + +LNK
Sbjct: 59 GASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEELEKLP-KKPIILVLNK 117
>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 = 68.1 bits (167), Expect = 3e-13
Identities = 40/169 (23%), Positives = 68/169 (40%), Gaps = 21/169 (12%)
Query: 239 KVIDSSDVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVP----IWVTQR 294
+++ + +VV+V+D+ D G+ + + + + + NK+DL+P ++
Sbjct: 29 TLLNDNALVVHVVDIFDFPGSLIPGLAELIGAKP----VILVGNKIDLLPKDVKPNRLKQ 84
Query: 295 WVAILSKEYPTIAFHASMTHPFGKGSIINLLRQFSKLHTERKQISVGFIGYPNVGKSSII 354
WV K + + L+ + KL R V +G NVGKS++I
Sbjct: 85 WVKKRLKIGGLKIKDVILVSAKKGWGVEELIEEIKKLAKYRGD--VYVVGATNVGKSTLI 142
Query: 355 NALRNKKVCK-----------TAPVPGETKVWQYITLMRRIYLIDCPGV 392
NAL K +P+PG T I L L D PG+
Sbjct: 143 NALLKSNGGKVQAQALVQRLTVSPIPGTTLGLIKIPLGEGKKLYDTPGI 191
>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 = 64.2 bits (157), Expect = 3e-12
Identities = 41/152 (26%), Positives = 58/152 (38%), Gaps = 25/152 (16%)
Query: 341 GFIGYPNVGKSSIINALRNKKVCKTAPVPGETKVWQY----ITLMRRIYLIDCPGVVYDM 396
G PNVGKSS++NAL + V +P+PG T+ + + + LID PG+ D
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGL--DE 58
Query: 397 TNVETD-----TEKVLRG------VVRV-ENIDDPVQYIDAVLERIKKVHLV--KTYGID 442
+V VV + + + ER K V LV K ID
Sbjct: 59 EGGLGRERVEEARQVADRADLVLLVVDSDLTPVEEEAKLGLLRERGKPVLLVLNK---ID 115
Query: 443 EWEDTEDFLKKLAFKWGKIKKKGEPVITASAK 474
++E+ K PVI SA
Sbjct: 116 LVPESEEEELLRERK--LELLPDLPVIAVSAL 145
Score = 39.5 bits (93), Expect = 0.001
Identities = 30/130 (23%), Positives = 49/130 (37%), Gaps = 21/130 (16%)
Query: 202 KEEKDFDIVRDNGGVTDAPRDWVMAAGQSKRIWGELYKVIDSSDVVVYVLDVRDPMGTRC 261
++ D G+ + G + E +V D +D+V+ V+D
Sbjct: 43 LPLGPVVLI-DTPGLDEE-------GGLGRERVEEARQVADRADLVLLVVDSDLTPVEEE 94
Query: 262 AHIENFLRREKPHKHLFFILNKVDLVP----IWVTQRWVAILSKEYPTIAFHASMTHPFG 317
A + R KP + +LNK+DLVP + + L + P IA A
Sbjct: 95 AKLGLLRERGKP---VLLVLNKIDLVPESEEEELLRERKLELLPDLPVIAVSAL------ 145
Query: 318 KGSIINLLRQ 327
G I+ LR+
Sbjct: 146 PGEGIDELRK 155
>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 = 62.1 bits (151), Expect = 2e-11
Identities = 42/152 (27%), Positives = 62/152 (40%), Gaps = 23/152 (15%)
Query: 341 GFIGYPNVGKSSIINALRNKKVCKTAPVPGET-----KVWQYITLMRRIYLIDCPGVV-Y 394
+G VGKSS++NAL +V + + VPG T V + ++ L+D PG+ +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF 60
Query: 395 DMTNVETDTEKVLRG------VVRV---ENIDDPVQYIDAVLERIKKVHLV---KTYGID 442
E +LRG VV E+ +D I L + ++ K ID
Sbjct: 61 GGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGNK---ID 117
Query: 443 EWEDTEDFLKKLAFKWGKIKKKGEPVITASAK 474
E+ E + KI G PV SAK
Sbjct: 118 LLEEREVEELLRLEELAKI--LGVPVFEVSAK 147
Score = 34.0 bits (78), Expect = 0.086
Identities = 9/64 (14%), Positives = 23/64 (35%), Gaps = 6/64 (9%)
Query: 228 GQSKRIWGELYKVIDSSDVVVYVLDVRDP---MGTRCAHIENFLRREKPHKHLFFILNKV 284
++ +D+++ V+D D + + + P + + NK+
Sbjct: 60 FGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIP---IILVGNKI 116
Query: 285 DLVP 288
DL+
Sbjct: 117 DLLE 120
>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 = 64.2 bits (157), Expect = 4e-11
Identities = 46/167 (27%), Positives = 73/167 (43%), Gaps = 16/167 (9%)
Query: 236 ELYKVIDSSDVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVPIWVT--- 292
L + DS+ ++VYV+D+ D G+ ++ F+ + + NK+DL+P V
Sbjct: 56 LLNSLGDSNALIVYVVDIFDFEGSLIPELKRFVGG----NPVLLVGNKIDLLPKSVNLSK 111
Query: 293 -QRWVAILSKEYPTIAFHASMTHPFGKGSIINLLRQFSKLHTERKQISVGFIGYPNVGKS 351
+ W+ +KE + I LL + K ++ +G NVGKS
Sbjct: 112 IKEWMKKRAKELGLKPVDIILVSAKKGNGIDELLDKIKKARNKKDVY---VVGVTNVGKS 168
Query: 352 SIINAL-----RNKKVCKTAPVPGETKVWQYITLMRRIYLIDCPGVV 393
S+IN L +K V T+P PG T I L L D PG++
Sbjct: 169 SLINKLLKQNNGDKDVITTSPFPGTTLDLIEIPLDDGHSLYDTPGII 215
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 64.1 bits (157), Expect = 6e-11
Identities = 52/209 (24%), Positives = 88/209 (42%), Gaps = 44/209 (21%)
Query: 205 KDFDIVRDNGGVTDAPRDWVMAAGQSKRIWGELYKVIDSSDVVVYVLDVRDPMGTRCAHI 264
++F ++ D GG+ D D + + I + I+ +DV+++V+D R+ + I
Sbjct: 51 REFILI-DTGGLDDGDEDELQ-----ELIREQALIAIEEADVILFVVDGREGITPADEEI 104
Query: 265 ENFLRREKPHKHLFFILNKVDLVPIWVTQRWVAI-------LSKEYPTIAFHASMTHPFG 317
LRR K K + ++NK+D + + P A H G
Sbjct: 105 AKILRRSK--KPVILVVNKID-----NLKAEELAYEFYSLGFGEPVPISAEH-------G 150
Query: 318 KGSIINLLRQFSKL---------HTERKQISVGFIGYPNVGKSSIINALRNKKVCKTAPV 368
+G I +LL +L E I + IG PNVGKSS+INA+ ++ + +
Sbjct: 151 RG-IGDLLDAVLELLPPDEEEEEEEETDPIKIAIIGRPNVGKSSLINAILGEERVIVSDI 209
Query: 369 PGET-----KVWQYITLMRRIYLIDCPGV 392
G T ++ R+ LID G+
Sbjct: 210 AGTTRDSIDIEFER--DGRKYVLIDTAGI 236
Score = 37.2 bits (87), Expect = 0.018
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 343 IGYPNVGKSSIINALRNKKVCKTAPVPGETKVWQYITLM---RRIYLIDCPGVV 393
+G PNVGKS++ N L +++ + PG T+ Y R LID G+
Sbjct: 9 VGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDAEWLGREFILIDTGGLD 62
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 60.0 bits (146), Expect = 2e-09
Identities = 34/98 (34%), Positives = 47/98 (47%), Gaps = 7/98 (7%)
Query: 336 KQISVGFIGYPNVGKSSIINALRNKKVCKTAPVPG---ETKVWQYITLMRRIYLIDCPGV 392
K+++V +G PNVGK+++ NAL K PG E K + I ++D PG
Sbjct: 2 KKLTVALVGNPNVGKTTLFNALTGANQ-KVGNWPGVTVEKKEGKLKYKGHEIEIVDLPG- 59
Query: 393 VYDMTNVETDTEKVLRGVVRVENIDDPVQYIDAV-LER 429
Y +T D EKV R + D V +DA LER
Sbjct: 60 TYSLTAYSED-EKVARDFLLEGKPDLIVNVVDATNLER 96
>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 = 59.4 bits (145), Expect = 2e-09
Identities = 62/295 (21%), Positives = 119/295 (40%), Gaps = 67/295 (22%)
Query: 205 KDFDIVRDNGGVTDAPRDWVMAAGQSKRIWGELYKVIDSSDVVVYVLDVRDPMGTRCAHI 264
++F ++ D GG+ + G K+I + I+ +DV+++V+D R+ + I
Sbjct: 47 REFILI-DTGGIEED------DDGLDKQIREQAEIAIEEADVILFVVDGREGLTPEDEEI 99
Query: 265 ENFLRREKPHKHLFFILNKVDLVPIWVTQRWVAILSKEYPTIAFHA---------SMTHP 315
+LR+ K + + NK+D ++ F++ S H
Sbjct: 100 AKWLRKSG--KPVILVANKIDG------------KKEDAVAAEFYSLGFGEPIPISAEHG 145
Query: 316 FGKGSIIN-LLRQFSK----LHTERKQISVGFIGYPNVGKSSIINALRNKKVCKTAPVPG 370
G G +++ +L + E I + IG PNVGKS+++NAL ++ + + G
Sbjct: 146 RGIGDLLDAILELLPEEEEEEEEEDGPIKIAIIGRPNVGKSTLVNALLGEERVIVSDIAG 205
Query: 371 ETK--VWQYITLM-RRIYLIDCPGVVYDMTNVETDTEK--VLRGVVRVENIDDPVQYIDA 425
T+ + ++ LID G+ V EK VLR
Sbjct: 206 TTRDSIDIPFERNGKKYTLIDTAGIR-RKGKVTEGVEKYSVLR----------------- 247
Query: 426 VLERIKKVHLVKTYGIDEWEDTEDFLKKLAFKWGKIKKKGEPVITASAKMVLNDW 480
L+ I++ +V +D E + ++A G + G+ ++ +V+N W
Sbjct: 248 TLKAIERADVV-LLVLDATEGITEQDLRIA---GLALEAGKALV-----IVVNKW 293
Score = 34.3 bits (80), Expect = 0.16
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 343 IGYPNVGKSSIINALRNKKVCKTAPVPGET--KVWQYITLM-RRIYLIDCPGVV 393
+G PNVGKS++ N L K+ + PG T + + R LID G+
Sbjct: 5 VGRPNVGKSTLFNRLTGKRDAIVSDTPGVTRDRKYGDAEWGGREFILIDTGGIE 58
Score = 34.3 bits (80), Expect = 0.17
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 239 KVIDSSDVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLV 287
K I+ +DVV+ VLD + + + I K L ++NK DLV
Sbjct: 250 KAIERADVVLLVLDATEGITEQDLRIAGLALEAG--KALVIVVNKWDLV 296
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 59.3 bits (145), Expect = 2e-09
Identities = 44/183 (24%), Positives = 80/183 (43%), Gaps = 34/183 (18%)
Query: 203 EEKDFDIVRDNGGVTDAPRDWVMAAGQSKRIWGELYKVIDSSDVVVYVLDVRDPMGTRCA 262
++F ++ D GG+ + K+I + I+ +DV+++V+D R +
Sbjct: 47 LGREFILI-DTGGIEPDDDGF------EKQIREQAELAIEEADVILFVVDGRAGLTPADE 99
Query: 263 HIENFLRREKPHKHLFFILNKVDLVPIWVTQRWVAILSKEYPTIAFHA-SMTHPF----- 316
I LR+ K + ++NKVD +E F++ + P+
Sbjct: 100 EIAKILRKSN--KPVILVVNKVD------------GPDEEADAYEFYSLGLGEPYPISAE 145
Query: 317 -GKG------SIINLLRQFSKLHTERKQISVGFIGYPNVGKSSIINALRNKKVCKTAPVP 369
G+G +I+ L + + E + I + IG PNVGKSS+INAL ++ + +
Sbjct: 146 HGRGIGDLLDAILEELPEEEEEDEEDEPIKIAIIGRPNVGKSSLINALLGEERVIVSDIA 205
Query: 370 GET 372
G T
Sbjct: 206 GTT 208
Score = 31.9 bits (74), Expect = 0.96
Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 343 IGYPNVGKSSIINALRNKKVCKTAPVPGETKVWQY--ITLM-RRIYLIDCPGVVYD 395
+G PNVGKS++ N L K+ A PG T+ Y + R LID G+ D
Sbjct: 7 VGRPNVGKSTLFNRLTGKRDAIVADTPGVTRDRIYGEAEWLGREFILIDTGGIEPD 62
Score = 31.6 bits (73), Expect = 1.0
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 239 KVIDSSDVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVP 288
K I+ +DVV+ V+D + + + I + L ++NK DLV
Sbjct: 251 KAIERADVVLLVIDATEGITEQDLRIAGLALEAG--RALVIVVNKWDLVD 298
>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 = 56.0 bits (136), Expect = 3e-09
Identities = 23/53 (43%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 340 VGFIGYPNVGKSSIINAL-RNKKVCKTAPVPGETKVWQYITLMRRIYLIDCPG 391
V F G NVGKSS+INAL KK+ +T+ PG T++ + + + L+D PG
Sbjct: 2 VAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFFNVGDKFRLVDLPG 54
>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 = 51.3 bits (124), Expect = 1e-07
Identities = 33/92 (35%), Positives = 46/92 (50%), Gaps = 7/92 (7%)
Query: 342 FIGYPNVGKSSIINALRNKKVCKTAPVPG---ETKVWQYITLMRRIYLIDCPGVVYDMTN 398
+G PNVGK+++ NAL + K PG E K ++ + I ++D PG Y +T
Sbjct: 2 LVGNPNVGKTTLFNALTGARQ-KVGNWPGVTVEKKEGEFKLGGKEIEIVDLPG-TYSLTP 59
Query: 399 VETDTEKVLRGVVRVENIDDPVQYIDAV-LER 429
D EKV R + E D V +DA LER
Sbjct: 60 YSED-EKVARDFLLGEEPDLIVNVVDATNLER 90
>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 = 50.5 bits (122), Expect = 2e-07
Identities = 22/53 (41%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 340 VGFIGYPNVGKSSIINAL-RNKKVCKTAPVPGETKVWQYITLMRRIYLIDCPG 391
+ F G NVGKSS+INAL KK+ +T+ PG T++ + + L+D PG
Sbjct: 21 IAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFFEVNDGFRLVDLPG 73
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 49.5 bits (119), Expect = 6e-07
Identities = 21/53 (39%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 340 VGFIGYPNVGKSSIINAL-RNKKVCKTAPVPGETKVWQYITLMRRIYLIDCPG 391
+ F G NVGKSS+INAL K + +T+ PG T++ + + + L+D PG
Sbjct: 27 IAFAGRSNVGKSSLINALTNQKNLARTSKTPGRTQLINFFEVDDELRLVDLPG 79
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of the
cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 47.9 bits (115), Expect = 2e-06
Identities = 30/96 (31%), Positives = 46/96 (47%), Gaps = 7/96 (7%)
Query: 338 ISVGFIGYPNVGKSSIINALRNKKVCKTAPVPG---ETKVWQYITLMRRIYLIDCPGVVY 394
I++ +G PNVGK+++ NAL + PG E K + I ++D PG Y
Sbjct: 1 ITIALVGNPNVGKTTLFNALTGARQ-HVGNWPGVTVEKKEGTFKYKGYEIEIVDLPG-TY 58
Query: 395 DMTNVETDTEKVLRGVVRVENIDDPVQYIDAV-LER 429
++ + EKV R + E D + +DA LER
Sbjct: 59 SLSPYSEE-EKVARDYLLEEKPDVIINVVDATNLER 93
>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 = 50.1 bits (120), Expect = 2e-06
Identities = 31/90 (34%), Positives = 42/90 (46%), Gaps = 7/90 (7%)
Query: 344 GYPNVGKSSIINALRNKKVCKTAPVPGET---KVWQYITLMRRIYLIDCPGVVYDMTNVE 400
G PNVGKS++ NAL PG T K + I ++D PG +Y +T
Sbjct: 1 GNPNVGKSTLFNALTGANQ-TVGNWPGVTVEKKEGKLGFQGEDIEIVDLPG-IYSLTTFS 58
Query: 401 TDTEKVLRGVVRVENIDDPVQYIDA-VLER 429
+ E+V R + E D V +DA LER
Sbjct: 59 LE-EEVARDYLLNEKPDLVVNVVDASNLER 87
>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 = 46.4 bits (111), Expect = 5e-06
Identities = 24/64 (37%), Positives = 33/64 (51%), Gaps = 8/64 (12%)
Query: 344 GYPNVGKSSIINALRNKKVCKTAPVPGETK---VWQYITLMRRIYLIDCPGV----VYDM 396
GYPNVGKSS++N L K + AP P TK V + R +ID PG+ + +
Sbjct: 7 GYPNVGKSSLVNKLTRAKP-EVAPYPFTTKSLFVGHFDYKYLRWQVIDTPGILDRPLEER 65
Query: 397 TNVE 400
+E
Sbjct: 66 NTIE 69
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 46.4 bits (111), Expect = 6e-06
Identities = 38/163 (23%), Positives = 70/163 (42%), Gaps = 23/163 (14%)
Query: 340 VGFIGYPNVGKSSIINALRNKKVCKTAPVPGETKVWQYIT--LMRRIYLIDCPGVVYDMT 397
+ +G + GKS+++NAL ++V T P T V + L++ + L+D PG+ + T
Sbjct: 3 LAVVGEFSAGKSTLLNALLGEEVLPTGVTP-TTAVITVLRYGLLKGVVLVDTPGL--NST 59
Query: 398 NVETD--TEKVLR---GVVRVENIDDP-----VQYIDAVLER-IKKVHLVKTYGID---- 442
TE L V+ V + D P +++ +L+ KK+ V ID
Sbjct: 60 IEHHTEITESFLPRADAVIFVLSADQPLTESEREFLKEILKWSGKKIFFVLNK-IDLLSE 118
Query: 443 -EWEDTEDFLKKLAFKWGKIKKKGEPVITASAKMVLNDWQRGK 484
E E+ ++ ++ ++ + SAK L +G
Sbjct: 119 EELEEVLEYSREELGV-LELGGGEPRIFPVSAKEALEARLQGD 160
Score = 37.9 bits (89), Expect = 0.005
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 7/53 (13%)
Query: 238 YKVIDSSDVVVYVLDVRDPMGTRCAHIE-NFLR--REKPHKHLFFILNKVDLV 287
+ +D V++VL P+ E FL+ + K +FF+LNK+DL+
Sbjct: 68 ESFLPRADAVIFVLSADQPLT----ESEREFLKEILKWSGKKIFFVLNKIDLL 116
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 45.5 bits (109), Expect = 2e-05
Identities = 21/53 (39%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 340 VGFIGYPNVGKSSIINAL-RNKKVCKTAPVPGETKVWQYITLMRRIYLIDCPG 391
+ F G NVGKSS+INAL K + +T+ PG T++ + + ++ L+D PG
Sbjct: 27 IAFAGRSNVGKSSLINALTNRKNLARTSKTPGRTQLINFFEVNDKLRLVDLPG 79
>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 = 44.7 bits (107), Expect = 2e-05
Identities = 38/148 (25%), Positives = 63/148 (42%), Gaps = 32/148 (21%)
Query: 338 ISVGFIGYPNVGKSSIINALRNKKVCKTAPVPGETKVWQYITLMR---RIYLIDCPGVVY 394
I + IG PNVGKSS++NAL ++ + + G T+ + + LID G+
Sbjct: 3 IKIAIIGRPNVGKSSLLNALLGEERVIVSDIAGTTRDSIDVPFEYDGQKYTLIDTAGIR- 61
Query: 395 DMTNVETDTEK--VLRGVVRVENIDDPVQYIDAVLERIKKVHLVKTYGIDEWEDTEDFLK 452
V EK VLR L+ I++ +V +D E +
Sbjct: 62 KKGKVTEGIEKYSVLR-----------------TLKAIERADVV-LLVLDASEGITEQDL 103
Query: 453 KLAFKWGKIKKKGEPVITASAKMVLNDW 480
++A G I ++G+ +I +V+N W
Sbjct: 104 RIA---GLILEEGKALI-----IVVNKW 123
Score = 33.9 bits (79), Expect = 0.10
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 239 KVIDSSDVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVP 288
K I+ +DVV+ VLD + + + I + E K L ++NK DLV
Sbjct: 80 KAIERADVVLLVLDASEGITEQDLRIAGLILEE--GKALIIVVNKWDLVE 127
>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 = 43.2 bits (103), Expect = 7e-05
Identities = 42/157 (26%), Positives = 62/157 (39%), Gaps = 32/157 (20%)
Query: 340 VGFIGYPNVGKSSIINALRNKKVCKTAPVPGETKVWQYITLMRRIY--------LIDCPG 391
V IG PNVGKS+++NAL +K+ +P P T+ +R IY +D PG
Sbjct: 6 VAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTR-----NRIRGIYTDDDAQIIFVDTPG 60
Query: 392 VVYDMTNVE----TDTEKVLRGV----VRVENIDDPVQYIDAVLERIKKVH----LV--K 437
+ + L+ V V+ + + + +LE +KK LV K
Sbjct: 61 IHKPKKKLGERMVKAAWSALKDVDLVLFVVDASEWIGEGDEFILELLKKSKTPVILVLNK 120
Query: 438 TYGIDEWEDTEDFLKKLAFKWGKIKKKGEPVITASAK 474
ID +D ED L L K + SA
Sbjct: 121 ---IDLVKDKEDLLPLLEKL--KELHPFAEIFPISAL 152
Score = 36.3 bits (85), Expect = 0.014
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 238 YKVIDSSDVVVYVLDVRDPMGTRCAHIENFLRREKPHKH-LFFILNKVDLVP 288
+ + D+V++V+D + +G E L K K + +LNK+DLV
Sbjct: 77 WSALKDVDLVLFVVDASEWIG---EGDEFILELLKKSKTPVILVLNKIDLVK 125
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 44.7 bits (106), Expect = 9e-05
Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 3/70 (4%)
Query: 336 KQISVGFIGYPNVGKSSIINALR--NKKVCKTAPVPGETKVWQYITLMRRIYLIDCPGVV 393
K++++G IG PN GK+++ N L ++V A V E K Q+ T ++ L+D PG
Sbjct: 2 KKLTIGLIGNPNSGKTTLFNQLTGARQRVGNWAGVTVERKEGQFSTTDHQVTLVDLPG-T 60
Query: 394 YDMTNVETDT 403
Y +T + + T
Sbjct: 61 YSLTTISSQT 70
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ 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. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 42.8 bits (102), Expect = 1e-04
Identities = 27/90 (30%), Positives = 40/90 (44%), Gaps = 13/90 (14%)
Query: 280 ILNKVDLVPIWVTQRWVAILSK-EYPTIAFHASMTHPFGKGSIINLLRQFSKLHTERKQI 338
+LNK DLV + + I K YP +A S G + LL+ +
Sbjct: 39 VLNKADLVDDEELEELLEIYEKLGYPVLA--VSAKTGEGLDELRELLK---------GKT 87
Query: 339 SVGFIGYPNVGKSSIINALRNKKVCKTAPV 368
SV +G VGKS+++NAL + V T +
Sbjct: 88 SV-LVGQSGVGKSTLLNALLPELVLATGEI 116
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 43.8 bits (104), Expect = 2e-04
Identities = 24/87 (27%), Positives = 42/87 (48%), Gaps = 14/87 (16%)
Query: 344 GYPNVGKSSIINALRNKKVCKTAPVPGETK---VWQYITLMRRIYLIDCPGV----VYDM 396
GYPNVGKSS++ L K + AP P TK V + RI +ID PG+ + +
Sbjct: 175 GYPNVGKSSLVRKLTTAKP-EVAPYPFTTKGIHVGHFERGYLRIQVIDTPGLLDRPLEER 233
Query: 397 TNVETDTEKVLRGVVRVENIDDPVQYI 423
+E + ++ + ++ + ++
Sbjct: 234 NEIE------RQAILALRHLAGVILFL 254
>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 = 41.2 bits (97), Expect = 3e-04
Identities = 21/58 (36%), Positives = 34/58 (58%), Gaps = 7/58 (12%)
Query: 341 GFIGYPNVGKSSIINALRNKKVCKTAPVPGETK-----VWQYITLMRRIYLIDCPGVV 393
G +G PNVGKS++++AL + KV + A P T V+++ I +ID PG++
Sbjct: 1 GLVGLPNVGKSTLLSALTSAKV-EIASYPFTTLEPNVGVFEFGDG-VDIQIIDLPGLL 56
>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 = 40.9 bits (97), Expect = 4e-04
Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 9/81 (11%)
Query: 205 KDFDIVRDNGGVTDAPRDWVMAAGQSKRIWGELYKVIDSSDVVVYVLDVRDPMGTRCAHI 264
++F ++ D GG+ SK I + I+ +DV+++V+D R+ + I
Sbjct: 45 REFILI-DTGGIEPDDEGI------SKEIREQAEIAIEEADVILFVVDGREGLTPADEEI 97
Query: 265 ENFLRREKPHKHLFFILNKVD 285
+LR+ K K + ++NK+D
Sbjct: 98 AKYLRKSK--KPVILVVNKID 116
Score = 38.6 bits (91), Expect = 0.002
Identities = 29/125 (23%), Positives = 47/125 (37%), Gaps = 17/125 (13%)
Query: 343 IGYPNVGKSSIINALRNKKVCKTAPVPGET--KVWQYITLM-RRIYLIDCPGVVYDMTNV 399
+G PNVGKS++ N L ++ + PG T + + R LID G+ D +
Sbjct: 3 VGRPNVGKSTLFNRLTGRRDAIVSDTPGVTRDRKYGEAEWGGREFILIDTGGIEPDDEGI 62
Query: 400 ETD-TEKVLRGV-----------VRVENIDDPVQYIDAVLERIKKVHLV--KTYGIDEWE 445
+ E+ + R + + + K V LV K I E E
Sbjct: 63 SKEIREQAEIAIEEADVILFVVDGREGLTPADEEIAKYLRKSKKPVILVVNKIDNIKEEE 122
Query: 446 DTEDF 450
+ +F
Sbjct: 123 EAAEF 127
>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 = 40.9 bits (97), Expect = 5e-04
Identities = 14/30 (46%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 340 VGFIGYPNVGKSSIINALRNKKVCKTAPVP 369
VG +G PN GKS++++A+ N K K A P
Sbjct: 3 VGLVGLPNAGKSTLLSAISNAKP-KIADYP 31
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 42.5 bits (100), Expect = 5e-04
Identities = 33/125 (26%), Positives = 53/125 (42%), Gaps = 16/125 (12%)
Query: 244 SDVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVPIW--VTQRWVAILSK 301
+D VV+V+D + + + I LRR K + +NK+D + W L +
Sbjct: 355 ADAVVFVVDGQVGLTSTDERIVRMLRRAG--KPVVLAVNKIDDQASEYDAAEFWKLGLGE 412
Query: 302 EYPTIAFHASMTHPFGKGSIINLLRQFSKLHTERKQIS-------VGFIGYPNVGKSSII 354
YP S H G G +++ K+ + V +G PNVGKSS++
Sbjct: 413 PYPI-----SAMHGRGVGDLLDEALDSLKVAEKTSGFLTPSGLRRVALVGRPNVGKSSLL 467
Query: 355 NALRN 359
N L +
Sbjct: 468 NQLTH 472
Score = 28.6 bits (64), Expect = 9.6
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 340 VGFIGYPNVGKSSIINALRNKKVCKTAPVPGETK 373
V +G PNVGKS+++N + ++ PG T+
Sbjct: 278 VAIVGRPNVGKSTLVNRILGRREAVVEDTPGVTR 311
>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 = 41.0 bits (97), Expect = 0.001
Identities = 17/39 (43%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 334 ERKQISVGFIGYPNVGKSSIINALRNKKVCKTAPVPGET 372
R I G G N GKSS+INAL + + + VPG T
Sbjct: 5 NRLHI--GIFGRRNAGKSSLINALTGQDIAIVSDVPGTT 41
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 40.3 bits (95), Expect = 0.002
Identities = 32/129 (24%), Positives = 53/129 (41%), Gaps = 24/129 (18%)
Query: 241 IDSSDVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVPIW--VTQRWVAI 298
+ ++D V++V+D + LRR K + NKVD W
Sbjct: 115 MRTADAVLFVVDATVGATATDEAVARVLRRSG--KPVILAANKVDDERGEADAAALWSLG 172
Query: 299 LSKEYPTIAFHASMTHPFGKGS------IINLLRQFSKLHTE----RKQISVGFIGYPNV 348
L + +P A H G+G ++ L + ++ + R+ V +G PNV
Sbjct: 173 LGEPHPVSALH-------GRGVGDLLDAVLAALPEVPRVGSASGGPRR---VALVGKPNV 222
Query: 349 GKSSIINAL 357
GKSS++N L
Sbjct: 223 GKSSLLNKL 231
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 40.2 bits (95), Expect = 0.002
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 331 LHTERKQIS-VGFIGYPNVGKSSIINALRNKKVCKTAPVPGETKV 374
L E K ++ VG +G PN GKS++++A+ K K A P T V
Sbjct: 152 LRLELKLLADVGLVGLPNAGKSTLLSAVSAAKP-KIADYPFTTLV 195
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 40.5 bits (96), Expect = 0.002
Identities = 11/22 (50%), Positives = 18/22 (81%)
Query: 340 VGFIGYPNVGKSSIINALRNKK 361
VG +G+PNVGKS++++ + N K
Sbjct: 161 VGLVGFPNVGKSTLLSVVSNAK 182
>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 = 39.7 bits (94), Expect = 0.002
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 330 KLHTERKQIS-VGFIGYPNVGKSSIINALRNKKVCKTAPVP 369
L E K ++ VG +G PN GKS++I+A+ K K A P
Sbjct: 149 WLRLELKLLADVGLVGLPNAGKSTLISAVSAAKP-KIADYP 188
>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 = 39.1 bits (92), Expect = 0.003
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 22/68 (32%)
Query: 338 ISVGFIGYPNVGKSSIINALRNKKVCKTA--------PVPGETKVWQYITLMR----RIY 385
V +G+P+VGKS++++ L N K + A VPG +M +I
Sbjct: 1 ARVALVGFPSVGKSTLLSKLTNTKS-EVAAYEFTTLTCVPG---------VMEYKGAKIQ 50
Query: 386 LIDCPGVV 393
L+D PG++
Sbjct: 51 LLDLPGII 58
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 39.9 bits (94), Expect = 0.003
Identities = 18/55 (32%), Positives = 26/55 (47%)
Query: 318 KGSIINLLRQFSKLHTERKQISVGFIGYPNVGKSSIINALRNKKVCKTAPVPGET 372
+ LL + R+ + V IG PNVGKSS++NAL + + G T
Sbjct: 198 IAELDELLATAKQGKILREGLKVVIIGRPNVGKSSLLNALLGRDRAIVTDIAGTT 252
Score = 34.1 bits (79), Expect = 0.18
Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 5/51 (9%)
Query: 239 KVIDSSDVVVYVLDVRDPMGTR-CAHIENFLRREKPHKHLFFILNKVDLVP 288
K I+ +D+V++VLD P+ A IE L ++KP +LNK DLV
Sbjct: 292 KAIEEADLVLFVLDASQPLDKEDLALIEL-LPKKKPI---IVVLNKADLVS 338
>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 = 37.9 bits (89), Expect = 0.004
Identities = 16/38 (42%), Positives = 22/38 (57%)
Query: 335 RKQISVGFIGYPNVGKSSIINALRNKKVCKTAPVPGET 372
R+ I V G PNVGKSS++NAL + + + G T
Sbjct: 1 REGIKVVIAGKPNVGKSSLLNALAGRDRAIVSDIAGTT 38
Score = 35.2 bits (82), Expect = 0.032
Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 10/71 (14%)
Query: 238 YKVIDSSDVVVYVLDVRDPMGTRCAHIENFLRREKP-HKHLFFILNKVDLVPIWVTQRWV 296
+ I+ +D+V+ V+D + + E+ E P K + +LNK DL+
Sbjct: 77 REAIEEADLVLLVVDASEGLD-----EEDLEILELPAKKPVIVVLNKSDLLS----DAEG 127
Query: 297 AILSKEYPTIA 307
P IA
Sbjct: 128 ISELNGKPIIA 138
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 39.2 bits (92), Expect = 0.004
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 12/65 (18%)
Query: 338 ISVGFIGYPNVGKSSIINALRNKKV-------CKTAPVPGETKVWQYITLMRRIYLIDCP 390
+V +G+P+VGKS+++N L N K PVPG + +Y +I L+D P
Sbjct: 64 ATVALVGFPSVGKSTLLNKLTNTKSEVADYPFTTLEPVPG---MLEYKGA--QIQLLDLP 118
Query: 391 GVVYD 395
G++
Sbjct: 119 GIIEG 123
>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 = 38.5 bits (90), Expect = 0.005
Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 340 VGFIGYPNVGKSSIINALRNKKVCKTAPVPGETK---VWQYITLMRRIYLIDCPG 391
V +G PNVGKS+++N L +K+ T+P T+ + T +I ID PG
Sbjct: 3 VAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFIDTPG 57
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 38.7 bits (91), Expect = 0.005
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 336 KQISVGFIGYPNVGKSSIINALRNKKVCKTAPVPGETK---VWQYITLMRRIYLIDCPGV 392
K V IG PNVGKS+++NAL +K+ +P P T+ T +I +D PG+
Sbjct: 5 KSGFVAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNAQIIFVDTPGI 64
Score = 29.5 bits (67), Expect = 4.7
Identities = 11/44 (25%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 245 DVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVP 288
D++++V+D + G I L++ K + ++NK+D V
Sbjct: 87 DLILFVVDADEGWGPGDEFILEQLKKTK--TPVILVVNKIDKVK 128
>gnl|CDD|206743 cd11383, YfjP, YfjP GTPase. The Era (E. coli Ras-like
protein)-like YfjP subfamily includes several
uncharacterized bacterial GTPases that are similar to
Era. They 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. Era is
characterized by a distinct derivative of the KH domain
(the pseudo-KH domain) which is located C-terminal to
the GTPase domain.
Length = 140
Score = 36.2 bits (84), Expect = 0.012
Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 7/57 (12%)
Query: 341 GFIGYPNVGKSSIINALRNKKVCKTAPVPGETK-----VWQYITLMRRIYLIDCPGV 392
G +G GKSS+ NAL +V T+ VWQ T + L+D PGV
Sbjct: 1 GLMGKTGAGKSSLCNALFGTEVAAVGDRRPTTRAAQAYVWQ--TGGDGLVLLDLPGV 55
>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 = 37.1 bits (86), Expect = 0.021
Identities = 15/53 (28%), Positives = 25/53 (47%)
Query: 321 IINLLRQFSKLHTERKQISVGFIGYPNVGKSSIINALRNKKVCKTAPVPGETK 373
+ + KL + +G PNVGKSS++NAL + + + G T+
Sbjct: 187 ELKDILNSYKLEKLDDGFKLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTR 239
Score = 35.9 bits (83), Expect = 0.054
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 238 YKVIDSSDVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVP 288
+K I +D+V+YVLD P+ I + + +KP +LNK+DL
Sbjct: 277 FKAIKQADLVIYVLDASQPLTKDDFLIIDLNKSKKP---FILVLNKIDLKI 324
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 37.0 bits (87), Expect = 0.022
Identities = 16/37 (43%), Positives = 22/37 (59%), Gaps = 3/37 (8%)
Query: 321 IINLLRQFSKLHTERKQISVGFIGYPNVGKSSIINAL 357
++ RQ L R+ + V G PNVGKSS++NAL
Sbjct: 202 LLASARQGEIL---REGLKVVIAGRPNVGKSSLLNAL 235
Score = 37.0 bits (87), Expect = 0.025
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 238 YKVIDSSDVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVP 288
+ I+ +D+V+ VLD +P+ ++ + E K + +LNK DL
Sbjct: 289 REAIEEADLVLLVLDASEPLTEE----DDEILEELKDKPVIVVLNKADLTG 335
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 36.0 bits (84), Expect = 0.022
Identities = 44/147 (29%), Positives = 65/147 (44%), Gaps = 34/147 (23%)
Query: 342 FIGYPNVGKSSIINALRNKKVCKTAPVPGET-KVWQYITLMRRIYLIDCPGVVYDMTNVE 400
F+G NVGKS+++ L KKV + PG T K Y L D PG + M+ V
Sbjct: 14 FVGRSNVGKSTLVRELTGKKV-RVGKRPGVTRKPNHY--DWGDFILTDLPGFGF-MSGVP 69
Query: 401 TDTEKVLRGVVRVENIDDPVQYIDAVLERIK-KVHLVKTYG----IDEWE-------DTE 448
+ ++ ++ D+ V+YI+ +RI V +V I+ WE D E
Sbjct: 70 KEVQEKIK--------DEIVRYIEDNADRILAAVLVVDGKSFIEIIERWEGRGEIPIDVE 121
Query: 449 --DFLKKL-------AFKWGKIKKKGE 466
DFL++L K KIK + E
Sbjct: 122 MFDFLRELGIPPIVAVNKMDKIKNRDE 148
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 36.6 bits (86), Expect = 0.025
Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 238 YKVIDSSDVVVYVLDVRDPMGTRCAHIENFLRREKPHKHLFFILNKVDLVP 288
+ + D+V++V+D + +G I L++ K + +LNK+DLV
Sbjct: 79 WSSLKDVDLVLFVVDADEKIGPGDEFILEKLKKVK--TPVILVLNKIDLVK 127
Score = 35.8 bits (84), Expect = 0.039
Identities = 14/30 (46%), Positives = 21/30 (70%)
Query: 340 VGFIGYPNVGKSSIINALRNKKVCKTAPVP 369
V +G PNVGKS+++NAL +K+ +P P
Sbjct: 8 VAIVGRPNVGKSTLLNALVGQKISIVSPKP 37
>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 = 35.0 bits (81), Expect = 0.036
Identities = 32/153 (20%), Positives = 60/153 (39%), Gaps = 14/153 (9%)
Query: 338 ISVGFIGYPNVGKSSIINALRNKKVCKTAPVPG-----ETKVWQYITLMRRIYLIDCPG- 391
I + +G PNVGKS+++N L K+ T PG T V + + L+D G
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQ 61
Query: 392 -----VVYDMTNVETDTEKVLRGVVRVENIDDPVQYIDAVLERIKKVHLVKTYGIDEWE- 445
+ + +V V+ V ++++ ++ + + + ++ +
Sbjct: 62 EDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVGNKIDL 121
Query: 446 DTEDFLKKLAFKWGKIKKKGEPVITASAKMVLN 478
+AF K GEP+I SA+ N
Sbjct: 122 RDAKLKTHVAFL--FAKLNGEPIIPLSAETGKN 152
>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 = 35.5 bits (83), Expect = 0.047
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 340 VGFIGYPNVGKSSIINALRNKKV 362
+G +G PNVGKS++ NAL
Sbjct: 1 IGIVGLPNVGKSTLFNALTKSNA 23
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 34.5 bits (79), Expect = 0.052
Identities = 26/148 (17%), Positives = 50/148 (33%), Gaps = 11/148 (7%)
Query: 314 HPFGKGSIINLLRQFSKLHTERKQISVGFIGYPNVGKSSIINALRNKKVCKTAPVPGETK 373
G+ + L + SV G GK+S++ L + +
Sbjct: 1 RLVGREEELERLLDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAER 60
Query: 374 VWQY--ITLMRRIYLIDCPGVVYDMTNVETDTEKVLRGVVRVENIDDPVQYIDAVLERIK 431
Y +R + + ++ + L +E + D V+ ++ +L R +
Sbjct: 61 NPPYAFSQALRELLRQLLRELAAELLLLREALLAALGA-ELIEGLQDLVELLERLLARAR 119
Query: 432 KVHLVKTYGIDE--WEDTE--DFLKKLA 455
+ LV +D+ W D E D L L
Sbjct: 120 PLVLV----LDDLQWADEESLDLLAALL 143
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 35.3 bits (82), Expect = 0.066
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 339 SVGFIGYPNVGKSSIINALRNKKV 362
+G +G PNVGKS+ NAL ++V
Sbjct: 23 KMGIVGLPNVGKSTTFNALCKQQV 46
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 35.2 bits (82), Expect = 0.080
Identities = 24/62 (38%), Positives = 32/62 (51%), Gaps = 8/62 (12%)
Query: 338 ISVGFIGYPNVGKSSIINALRNKKVCKTAPVPGETKVWQYITLMRRIY-------LIDCP 390
IS+ F+G VGKSS+INAL + V + + Q+ T R+Y LID P
Sbjct: 207 ISI-FVGQSGVGKSSLINALLPEAEILVGDVSDNSGLGQHTTTAARLYHFPHGGDLIDSP 265
Query: 391 GV 392
GV
Sbjct: 266 GV 267
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 34.8 bits (81), Expect = 0.090
Identities = 51/192 (26%), Positives = 74/192 (38%), Gaps = 44/192 (22%)
Query: 237 LYKVIDSSDVVVYVLDVRDPMGTRCAHIENFLRR---EKPHKHLFFIL--NKVDLVPI-- 289
L + DS +VV V+D+ D G+ L R P +L NK DL+P
Sbjct: 63 LNGIGDSDALVVNVVDIFDFNGS----WIPGLHRFVGNNP-----VLLVGNKADLLPKSV 113
Query: 290 -------WVTQRWVAILSKEY---PTIAFHASMTHPFGKGSIINLLRQFSKLHTERKQIS 339
W+ Q +KE P S G I LL + R+
Sbjct: 114 KKNKVKNWLRQE-----AKELGLRPVDVVLISAQKGHG---IDELL---EAIEKYREGRD 162
Query: 340 VGFIGYPNVGKSSIINAL-----RNKKVCKTAPVPGETKVWQYITLMRRIYLIDCPGVVY 394
V +G NVGKS++IN + K V T+ PG T I L +L D PG+++
Sbjct: 163 VYVVGVTNVGKSTLINRIIKEITGEKDVITTSRFPGTTLDKIEIPLDDGSFLYDTPGIIH 222
Query: 395 D--MTNVETDTE 404
M + + +
Sbjct: 223 RHQMAHYLSAKD 234
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 34.7 bits (81), Expect = 0.099
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 340 VGFIGYPNVGKSSIINALRNKK 361
VG +G PN GKS++I+A+ K
Sbjct: 161 VGLVGLPNAGKSTLISAVSAAK 182
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 34.8 bits (81), Expect = 0.10
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 338 ISVGFIGYPNVGKSSIINALRNKKV 362
+ +G +G PNVGKS++ NAL
Sbjct: 3 LKIGIVGLPNVGKSTLFNALTKAGA 27
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 34.7 bits (79), Expect = 0.10
Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 4/79 (5%)
Query: 317 GKGSIINLLRQFSKLHTERKQISVGFIGYPNVGKSSIINALRNKKVCKTAPVPGETK--V 374
G S + L +F K+ + +K +SV IG PN GKS+++N + +K+ P T+ +
Sbjct: 33 GSTSKLPLEVKFGKM-SNQKTVSVCIIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSII 91
Query: 375 WQYITLM-RRIYLIDCPGV 392
ITL ++ L D PG+
Sbjct: 92 TGIITLKDTQVILYDTPGI 110
>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 = 0.11
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 10/47 (21%)
Query: 321 IINLLRQFSKLHTERKQI----------SVGFIGYPNVGKSSIINAL 357
I L ++ K+ +R+ +V +GY N GKS++ NAL
Sbjct: 15 IAKLRKELEKVKKQRELQRARRKRSGVPTVALVGYTNAGKSTLFNAL 61
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 33.7 bits (78), Expect = 0.11
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 335 RKQISVGFIGYPNVGKSSIINALRNKKVCKTAPVPGETKVWQYITLMRRIY-------LI 387
+ + SV G VGKS+++NAL + +T + + ++ T ++ LI
Sbjct: 34 KGKTSV-LAGQSGVGKSTLLNALLPELDLRTGEISEKLGRGRHTTTHVELFPLPGGGLLI 92
Query: 388 DCPGV 392
D PG
Sbjct: 93 DTPGF 97
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 34.3 bits (80), Expect = 0.14
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 338 ISVGFIGYPNVGKSSIINALRNKKV 362
+ G +G PNVGKS++ NAL
Sbjct: 3 LKCGIVGLPNVGKSTLFNALTKAGA 27
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 34.5 bits (80), Expect = 0.14
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 340 VGFIGYPNVGKSSIINALRNKKVCKTAPVPGETKV 374
VG +G PN GKS+ I A+ K K A P T V
Sbjct: 162 VGLLGLPNAGKSTFIRAVSAAKP-KVADYPFTTLV 195
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 32.6 bits (74), Expect = 0.35
Identities = 8/45 (17%), Positives = 17/45 (37%)
Query: 336 KQISVGFIGYPNVGKSSIINALRNKKVCKTAPVPGETKVWQYITL 380
K+ + +G VGK++++N L + + P
Sbjct: 4 KEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIE 48
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 32.9 bits (76), Expect = 0.46
Identities = 11/18 (61%), Positives = 16/18 (88%)
Query: 340 VGFIGYPNVGKSSIINAL 357
VG +G+P+ GKSS+I+AL
Sbjct: 162 VGLVGFPSAGKSSLISAL 179
>gnl|CDD|232848 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
Members of this protein were designated YjeQ and are now
designated RsgA (ribosome small subunit-dependent GTPase
A). The strongest motif in the alignment of these
proteins is GXSGVGKS[ST], a classic P-loop for
nucleotide binding. This protein has been shown to
cleave GTP and remain bound to GDP. A role as a
regulator of translation has been suggested. The Aquifex
aeolicus ortholog is split into consecutive open reading
frames. Consequently, this model was build in fragment
mode (-f option) [Protein synthesis, Translation
factors].
Length = 245
Score = 32.4 bits (74), Expect = 0.51
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 335 RKQISVGFIGYPNVGKSSIINALRNKKVCKTAPVPGETKVWQYITLMRRIY------LID 388
+ +ISV F G VGKSS+INAL + + + + ++ T ++ + D
Sbjct: 119 QNRISV-FAGQSGVGKSSLINALDPSVKQQVNDISSKLGLGKHTTTHVELFHFHGGLIAD 177
Query: 389 CPGV-VYDMTNVE 400
PG + + ++E
Sbjct: 178 TPGFNEFGLWHLE 190
>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 = 32.4 bits (75), Expect = 0.60
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 334 ERKQI-SVGFIGYPNVGKSSIINALRNKKV 362
+R + +V +GY N GKS++ NAL V
Sbjct: 185 KRADVPTVALVGYTNAGKSTLFNALTGADV 214
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 32.1 bits (73), Expect = 0.61
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 321 IINLLRQFSKLHTERKQISVGFIGYPNVGKSSIINALRNKKVCKTAPVPG----ETKVWQ 376
I+ LR TE++ ++V +G GKSS+INAL +V + + V T++
Sbjct: 25 ILEQLRMLQL--TEKEPVNVLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLRL 82
Query: 377 YITLMRRIYLIDCPGV 392
+ L D PG+
Sbjct: 83 SYDG-ENLVLWDTPGL 97
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 31.9 bits (73), Expect = 0.75
Identities = 29/123 (23%), Positives = 48/123 (39%), Gaps = 22/123 (17%)
Query: 280 ILNKVDLVPIWVTQRWVA---ILSKEYPTIAFHASMTHPFGKGSIINLLRQFSKLHTERK 336
+LNK+DL+ YP + S + G + LL
Sbjct: 116 VLNKIDLLDDEEAAVKELLREYEDIGYPVLFV--SAKNGDGLEELAELLA---------G 164
Query: 337 QISVGFIGYPNVGKSSIINALRNKKVCKTAPVPGETKVWQYITLMRRIY-------LIDC 389
+I+V +G VGKS++INAL + KT + + ++ T ++ +ID
Sbjct: 165 KITV-LLGQSGVGKSTLINALLPELNQKTGEISEKLGRGRHTTTHVELFPLPGGGWIIDT 223
Query: 390 PGV 392
PG
Sbjct: 224 PGF 226
>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 = 31.8 bits (73), Expect = 0.90
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 340 VGFIGYPNVGKSSIINALRNKKVCKTAPVP 369
+G +G PNVGKS+ NA V + A P
Sbjct: 1 IGLVGKPNVGKSTFFNAATLADV-EIANYP 29
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 31.3 bits (72), Expect = 1.2
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 337 QISVGFIGYPNVGKSSIINALRNKKVCKTAPV 368
+++V G VGKS+++NAL KT +
Sbjct: 165 KVTV-LAGQSGVGKSTLLNALAPDLELKTGEI 195
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 31.1 bits (71), Expect = 1.4
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 10/52 (19%)
Query: 321 IINLLRQFSKLHTERKQI----------SVGFIGYPNVGKSSIINALRNKKV 362
I L R+ + R+ V +GY N GKS++ NAL V
Sbjct: 166 IAKLKRELENVEKAREPRRKKRSRSGIPLVALVGYTNAGKSTLFNALTGADV 217
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 30.0 bits (68), Expect = 1.9
Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 18/70 (25%)
Query: 340 VGFIGYPNVGKSSIINAL----------RNKKVCKTAPVPGE--------TKVWQYITLM 381
VG IG+ + GK+++ +L +K + E T V ++
Sbjct: 2 VGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWPK 61
Query: 382 RRIYLIDCPG 391
RRI ID PG
Sbjct: 62 RRINFIDTPG 71
>gnl|CDD|206721 cd04155, Arl3, Arf-like 3 (Arl3) GTPase. Arl3 (Arf-like 3) is an
Arf family protein that differs from most Arf family
members in the N-terminal extension. In is inactive,
GDP-bound form, the N-terminal extension forms an
elongated loop that is hydrophobically anchored into the
membrane surface; however, it has been proposed that
this region might form a helix in the GTP-bound form.
The delta subunit of the rod-specific cyclic GMP
phosphodiesterase type 6 (PDEdelta) is an Arl3 effector.
Arl3 binds microtubules in a regulated manner to alter
specific aspects of cytokinesis via interactions with
retinitis pigmentosa 2 (RP2). It has been proposed that
RP2 functions in concert with Arl3 to link the cell
membrane and the cytoskeleton in photoreceptors as part
of the cell signaling or vesicular transport machinery.
In mice, the absence of Arl3 is associated with abnormal
epithelial cell proliferation and cyst formation.
Length = 174
Score = 30.1 bits (68), Expect = 2.1
Identities = 11/50 (22%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 321 IINLLRQFSKLHTERKQISVGFIGYPNVGKSSIINALRNKKVCKTAPVPG 370
++++LR+ + R+++ + +G N GK++I+ L ++ + P G
Sbjct: 1 LLSILRKLKP--SSRQEVRILLLGLDNAGKTTILKQLASEDISHITPTQG 48
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 29.0 bits (66), Expect = 4.2
Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 25/88 (28%)
Query: 338 ISVGFIGYPNVGKSSIINALRNKK-------------VCKTAPVPGET---KVW------ 375
+ IG VGK+S++ + K KT V G+ ++W
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQE 60
Query: 376 QYITLMRRIYLIDCPGV--VYDMTNVET 401
++ + + Y G VYD+TN E+
Sbjct: 61 RFRS-ITSSYYRGAHGAILVYDVTNRES 87
>gnl|CDD|206652 cd01853, Toc34_like, Translocon at the Outer-envelope membrane of
Chloroplasts 34-like (Toc34-like). The Toc34-like
(Translocon at the Outer-envelope membrane of
Chloroplasts) family contains several Toc proteins,
including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125,
and Toc90. The Toc complex at the outer envelope
membrane of chloroplasts is a molecular machine of ~500
kDa that contains a single Toc159 protein, four Toc75
molecules, and four or five copies of Toc34. Toc64 and
Toc12 are associated with the translocon, but do not
appear to be part of the core complex. The Toc
translocon initiates the import of nuclear-encoded
preproteins from the cytosol into the organelle. Toc34
and Toc159 are both GTPases, while Toc75 is a
beta-barrel integral membrane protein. Toc159 is equally
distributed between a soluble cytoplasmic form and a
membrane-inserted form, suggesting that assembly of the
Toc complex is dynamic. Toc34 and Toc75 act sequentially
to mediate docking and insertion of Toc159 resulting in
assembly of the functional translocon.
Length = 248
Score = 29.2 bits (66), Expect = 4.4
Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 348 VGKSSIINALRNKKVCKTAPVPGETKVWQYITLMR---RIYLIDCPGVV 393
VGKSS IN++ ++ + ET + ++ ++ +ID PG++
Sbjct: 42 VGKSSTINSIFGERKVSVSAFQSETLRPREVSRTVDGFKLNIIDTPGLL 90
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 29.0 bits (66), Expect = 4.6
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 18/72 (25%)
Query: 338 ISVGFIGYPNVGKSSIINALR------NKKVCKTAPV----PGE--------TKVWQYIT 379
++G IG+ + GK+++ +AL +K+ K A V E + T
Sbjct: 4 RNIGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVSFET 63
Query: 380 LMRRIYLIDCPG 391
R I +ID PG
Sbjct: 64 KKRLINIIDTPG 75
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 28.5 bits (63), Expect = 4.7
Identities = 21/142 (14%), Positives = 39/142 (27%), Gaps = 30/142 (21%)
Query: 339 SVGFIGYPNVGKSSIINALRNKKVCKTAPVPGETKVWQYITLMRRIYLIDCPGVVYDMTN 398
+ +G P GK+++ AL + + ID +
Sbjct: 4 VILIVGPPGSGKTTLARAL----------------ARELGPPGGGVIYIDG-----EDIL 42
Query: 399 VETDTEKVLRGVVRVENIDDPVQYIDAVLERIKKVHLVKTYGIDE--------WEDTEDF 450
E + +L V + + L +K +DE E
Sbjct: 43 EEVLDQLLLIIVGGKKASGSGELRLRLALALARK-LKPDVLILDEITSLLDAEQEALLLL 101
Query: 451 LKKLAFKWGKIKKKGEPVITAS 472
L++L +K VI +
Sbjct: 102 LEELRLLLLLKSEKNLTVILTT 123
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 29.4 bits (67), Expect = 4.7
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 338 ISVGFIGYPNVGKSSIINA 356
I++G +G PNVGKS+ NA
Sbjct: 2 ITIGLVGKPNVGKSTFFNA 20
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 28.3 bits (64), Expect = 6.7
Identities = 13/47 (27%), Positives = 24/47 (51%)
Query: 324 LLRQFSKLHTERKQISVGFIGYPNVGKSSIINALRNKKVCKTAPVPG 370
L +KL K++ + +G N GK++I+ L+ ++ T P G
Sbjct: 1 FLSILAKLFGWNKEMRILILGLDNAGKTTILYKLKLGEIVTTIPTIG 47
>gnl|CDD|213323 cd12115, A_NRPS_Sfm_like, The adenylation domain of nonribosomal
peptide synthetases (NRPS), including Saframycin A gene
cluster from Streptomyces lavendulae. The adenylation
(A) domain of NRPS recognizes a specific amino acid or
hydroxy acid and activates it as an (amino) acyl
adenylate by hydrolysis of ATP. The activated acyl
moiety then forms a thioester to the enzyme-bound
cofactor phosphopantetheine of a peptidyl carrier
protein domain. NRPSs are large multifunctional enzymes
which synthesize many therapeutically useful peptides in
bacteria and fungi via a template-directed, nucleic acid
independent nonribosomal mechanism. These natural
products include antibiotics, immunosuppressants, plant
and animal toxins, and enzyme inhibitors. NRPS has a
distinct modular structure in which each module is
responsible for the recognition, activation, and in some
cases, modification of a single amino acid residue of
the final peptide product. The modules can be subdivided
into domains that catalyze specific biochemical
reactions. This family includes the saframycin A gene
cluster from Streptomyces lavendulae which implicates
the NRPS system for assembling the unusual tetrapeptidyl
skeleton in an iterative manner. It also includes
saframycin Mx1 produced by Myxococcus xanthus NRPS.
Length = 449
Score = 29.2 bits (66), Expect = 6.9
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 477 LNDWQRGKLPYYTVPEGFEV----PLSKQGEADKEA 508
L +LP Y VP F PL+ G+ D++A
Sbjct: 413 LRARLATRLPAYMVPSRFVRLDALPLTPNGKIDRKA 448
>gnl|CDD|173938 cd08179, NADPH_BDH, NADPH-dependent butanol dehydrogenase involved
in the butanol and ethanol formation pathway in
bacteria. NADPH-dependent butanol dehydrogenase (BDH)
is involved in the butanol and ethanol formation pathway
of some bacteria. The fermentation process is
characterized by an acid producing growth phase,
followed by a solvent producing phase. The latter phase
is associated with the induction of solventogenic
enzymes such as butanol dehydrogenase. The activity of
the enzymes require NADPH as cofactor, as well as
divalent ions zinc or iron. This family is a member of
the iron-containing alcohol dehydrogenase superfamily.
Protein structure has a dehydroquinate synthase-like
fold.
Length = 375
Score = 28.8 bits (65), Expect = 7.0
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 10/58 (17%)
Query: 400 ETDTEKVLRGVVRVENIDDPVQYIDAVLERIKKVHL---VKTYGIDEWEDTEDFLKKL 454
+ + +K G+ + E ++D I+AV E KK+ + K YGIDE ++FL+KL
Sbjct: 290 DAEAKKRYAGLAKEEGVED---LIEAVRELNKKLGIPACFKEYGIDE----QEFLEKL 340
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 28.4 bits (64), Expect = 7.0
Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 2/77 (2%)
Query: 339 SVGFIGYPNVGKSSIINALRNKKVCKTAP--VPGETKVWQYITLMRRIYLIDCPGVVYDM 396
+V +G + GK+++ L KV T P + + +++ L+D PG
Sbjct: 2 TVLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKGKKLTLVDVPGHEKLR 61
Query: 397 TNVETDTEKVLRGVVRV 413
+ + L+ +V V
Sbjct: 62 DKLLEYLKASLKAIVFV 78
>gnl|CDD|205379 pfam13198, DUF4014, Protein of unknown function (DUF4014). This is
a bacterial and viral family of uncharacterized
proteins.
Length = 72
Score = 26.6 bits (59), Expect = 8.0
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 265 ENFLRREKPHKHLFFILNKVDLVPI 289
+N+ R+ + + LF IL V +VPI
Sbjct: 7 KNYPRKSRTTEFLFLILFLVLMVPI 31
>gnl|CDD|182388 PRK10337, PRK10337, sensor protein QseC; Provisional.
Length = 449
Score = 28.5 bits (64), Expect = 9.8
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 468 VITASAKMVLNDWQRGK-LPYYTVPEGF 494
+ T KMVLND G+ +PY EGF
Sbjct: 90 IFTRDGKMVLNDGDNGEDIPYSYQREGF 117
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 0.133 0.395
Gapped
Lambda K H
0.267 0.0684 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,044,254
Number of extensions: 2644834
Number of successful extensions: 2801
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2745
Number of HSP's successfully gapped: 139
Length of query: 534
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 433
Effective length of database: 6,457,848
Effective search space: 2796248184
Effective search space used: 2796248184
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: 61 (27.4 bits)