RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8220
(161 letters)
>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 = 103 bits (260), Expect = 7e-29
Identities = 56/134 (41%), Positives = 72/134 (53%), Gaps = 21/134 (15%)
Query: 26 DVILEVVDARDPMGTRCKVAEDLVVGT-PGKKLVIVINKAGK-PSTKIQSGSMAQIFQTW 83
DVILEV+DARDP+G RC E V+ P KKLV+V+NK P + + W
Sbjct: 1 DVILEVLDARDPLGCRCPQVERAVLVLGPNKKLVLVLNKIDLVPK---------ENVEKW 51
Query: 84 IPYNSIQ--------SIYSSPRFSSRSQKDAQTERDLKAINVSSCVGAELLMLLLGNYTR 135
+ Y + S + SR K + DL + S+C+GA+ L+ LL NY R
Sbjct: 52 LKYLRNEFPTVAFKASTQQQKKNLSRKSKKVKASDDLLS--SSACLGADALLKLLKNYAR 109
Query: 136 NKDIKTSITVGVVG 149
NK IKTSITVGVVG
Sbjct: 110 NKGIKTSITVGVVG 123
>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 = 59.3 bits (144), Expect = 8e-12
Identities = 25/49 (51%), Positives = 35/49 (71%), Gaps = 1/49 (2%)
Query: 16 EIERSVVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKA 64
+ R +++ ADV+LEVVDARDP TR + E + + GKKL+IV+NKA
Sbjct: 3 RLVRRIIKEADVVLEVVDARDPELTRSRKLERMAL-ELGKKLIIVLNKA 50
>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 = 58.1 bits (141), Expect = 2e-11
Identities = 24/44 (54%), Positives = 34/44 (77%), Gaps = 1/44 (2%)
Query: 21 VVEAADVILEVVDARDPMGTRCK-VAEDLVVGTPGKKLVIVINK 63
V++++DVI++V+DARDPMGTRCK V + L P K L+ V+NK
Sbjct: 5 VIDSSDVIIQVLDARDPMGTRCKHVEKYLRKEKPHKHLIFVLNK 48
>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 = 55.1 bits (133), Expect = 2e-10
Identities = 20/39 (51%), Positives = 28/39 (71%), Gaps = 1/39 (2%)
Query: 26 DVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKA 64
DV++EVVDARDP+ +R E L+ KKL++V+NKA
Sbjct: 1 DVVVEVVDARDPLSSRNPDIEVLIN-EKNKKLIMVLNKA 38
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 55.9 bits (135), Expect = 6e-10
Identities = 37/138 (26%), Positives = 67/138 (48%), Gaps = 20/138 (14%)
Query: 19 RSVVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKAGKPSTKIQSGSMAQ 78
+ V+++ DV++EVVDARDP+GTR E +V K ++V+NKA ++ +
Sbjct: 29 KEVLKSVDVVVEVVDARDPLGTRNPELERIV---KEKPKLLVLNKADLAPKEV----TKK 81
Query: 79 IFQTWIPYNSIQSIYSSPRFSSRSQKDAQTERDLKAINVSSCVGAELLMLLLGNYTRNKD 138
+ + I+ I+ S++S++ ++ KA+ +L + +
Sbjct: 82 WKKYFKKEEGIKPIFV----SAKSRQG--GKKIRKAL-------EKLSEEKIKRLKKKGL 128
Query: 139 IKTSITVGVVGECNIAGS 156
+K I VGVVG N+ S
Sbjct: 129 LKRKIRVGVVGYPNVGKS 146
>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 = 47.2 bits (113), Expect = 2e-07
Identities = 19/45 (42%), Positives = 31/45 (68%), Gaps = 1/45 (2%)
Query: 21 VVEAADVILEVVDARDPMGTRCKVAEDLVVGT-PGKKLVIVINKA 64
V+E +DV++++VDAR+P+ RC E V P K+ V+++NKA
Sbjct: 8 VIERSDVVVQIVDARNPLFFRCPDLEKYVKEVDPSKENVLLLNKA 52
>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 = 37.5 bits (88), Expect = 8e-04
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 25 ADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKA 64
DV++EV DAR P+ +R + + K +IV+NKA
Sbjct: 20 VDVVIEVRDARIPLSSRNPDLDKI---LGNKPRLIVLNKA 56
>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 = 37.5 bits (88), Expect = 0.001
Identities = 15/40 (37%), Positives = 26/40 (65%), Gaps = 3/40 (7%)
Query: 25 ADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKA 64
DV++EV+DAR P+ +R + +++ K +IV+NKA
Sbjct: 22 VDVVIEVLDARIPLSSRNPMIDEIR---GNKPRLIVLNKA 58
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 37.1 bits (87), Expect = 0.002
Identities = 13/51 (25%), Positives = 30/51 (58%), Gaps = 7/51 (13%)
Query: 14 VQEIERSVVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKA 64
++E + V DV++EV+DAR P+ + + + ++ K ++++NK+
Sbjct: 18 IKENLKLV----DVVIEVLDARIPLSSENPMIDKII---GNKPRLLILNKS 61
>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 = 33.8 bits (78), Expect = 0.011
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 5 KPMEMRGVVVQEIERSVVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINK 63
K +E ++ I AD+IL VVDA + + + + + P K +++V+NK
Sbjct: 64 KGVEGFNRFLEAIRE-----ADLILLVVDASEGLTEDDEEILEELEKLPKKPIILVLNK 117
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 34.7 bits (81), Expect = 0.014
Identities = 17/50 (34%), Positives = 32/50 (64%), Gaps = 5/50 (10%)
Query: 17 IERS--VVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKA 64
IERS +E AD++L V+DA +P+ + ++++ K +++V+NKA
Sbjct: 285 IERSREAIEEADLVLLVLDASEPLT---EEDDEILEELKDKPVIVVLNKA 331
>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 = 32.5 bits (75), Expect = 0.042
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 9/52 (17%)
Query: 17 IERSV--VEAADVILEVVDARDPMGTRCKVAEDLVVG--TPGKKLVIVINKA 64
IER+ +E AD++L VVDA + + EDL + K +++V+NK+
Sbjct: 73 IERAREAIEEADLVLLVVDASEGLD-----EEDLEILELPAKKPVIVVLNKS 119
>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 = 32.0 bits (74), Expect = 0.10
Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 16/65 (24%)
Query: 10 RGVVVQEIER-SVV------EAADVILEVVDARDPMGTRCKVAEDLVVGT----PGKKLV 58
+G V + +E+ SV+ E ADV+L V+DA + + +DL + GK LV
Sbjct: 233 KGKVTEGVEKYSVLRTLKAIERADVVLLVLDATEGI-----TEQDLRIAGLALEAGKALV 287
Query: 59 IVINK 63
IV+NK
Sbjct: 288 IVVNK 292
Score = 31.3 bits (72), Expect = 0.19
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 9/47 (19%)
Query: 22 VEAADVILEVVDARDPMGTRCKVAEDLVVG----TPGKKLVIVINKA 64
+E ADVIL VVD R+ + ED + GK +++V NK
Sbjct: 76 IEEADVILFVVDGREGL-----TPEDEEIAKWLRKSGKPVILVANKI 117
>gnl|CDD|206676 cd01889, SelB_euk, SelB, the dedicated elongation factor for
delivery of selenocysteinyl-tRNA to the ribosome. SelB
is an elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains eukaryotic SelBs and some from archaea.
Length = 192
Score = 31.6 bits (72), Expect = 0.12
Identities = 19/49 (38%), Positives = 31/49 (63%), Gaps = 6/49 (12%)
Query: 19 RSVVEAA---DVILEVVDARDPMGTRCKVAEDLVVGT-PGKKLVIVINK 63
R+++ A D++L VVDA+ G + + AE LV+G K L++V+NK
Sbjct: 83 RTIIGGAQIIDLMLLVVDAKK--GIQTQTAECLVIGELLCKPLIVVLNK 129
>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 = 30.1 bits (69), Expect = 0.33
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 9/47 (19%)
Query: 22 VEAADVILEVVDARDPMGTRCKVAEDLVVGT----PGKKLVIVINKA 64
+E ADVIL VVD R+ + D + K +++V+NK
Sbjct: 74 IEEADVILFVVDGREGL-----TPADEEIAKYLRKSKKPVILVVNKI 115
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 30.4 bits (70), Expect = 0.41
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 9/47 (19%)
Query: 22 VEAADVILEVVDARDPMGTRCKVAEDLVVG----TPGKKLVIVINKA 64
+E ADVIL VVD R + D + K +++V+NK
Sbjct: 78 IEEADVILFVVDGRAGL-----TPADEEIAKILRKSNKPVILVVNKV 119
Score = 29.2 bits (67), Expect = 0.86
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 16/65 (24%)
Query: 10 RGVVVQEIER-SVV------EAADVILEVVDARDPMGTRCKVAEDLVVG----TPGKKLV 58
+G V + +E+ SV+ E ADV+L V+DA + + +DL + G+ LV
Sbjct: 234 KGKVTEGVEKYSVIRTLKAIERADVVLLVIDATEGI-----TEQDLRIAGLALEAGRALV 288
Query: 59 IVINK 63
IV+NK
Sbjct: 289 IVVNK 293
>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 = 29.4 bits (67), Expect = 0.53
Identities = 14/50 (28%), Positives = 24/50 (48%)
Query: 15 QEIERSVVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKA 64
EI S + AD ++ V+ A P+ + ++ GKK+ V+NK
Sbjct: 64 TEITESFLPRADAVIFVLSADQPLTESEREFLKEILKWSGKKIFFVLNKI 113
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 29.8 bits (68), Expect = 0.58
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 10/53 (18%)
Query: 17 IERS--VVEAADVILEVVDARDPMGTRCKVAEDLV---VGTPGKKLVIVINKA 64
IER+ +E AD++L V+DA P+ EDL + K +++V+NKA
Sbjct: 287 IERAKKAIEEADLVLFVLDASQPL-----DKEDLALIELLPKKKPIIVVLNKA 334
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 29.5 bits (67), Expect = 0.70
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 16/65 (24%)
Query: 10 RGVVVQEIER-SVV------EAADVILEVVDARDPMGTRCKVAEDLVVGT----PGKKLV 58
+G + + +E+ SV E ADV+L V+DA + + +DL + G+ +V
Sbjct: 239 KGKITESVEKYSVARTLKAIERADVVLLVIDATEGI-----SEQDLRIAGLIEEAGRGIV 293
Query: 59 IVINK 63
IV+NK
Sbjct: 294 IVVNK 298
Score = 28.3 bits (64), Expect = 1.7
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 14/61 (22%)
Query: 8 EMRGVVVQEIERSVVEAADVILEVVDARDPMGTRCKVAEDLVVG----TPGKKLVIVINK 63
+R + IE ADVIL VVD R+ + D + K +++V+NK
Sbjct: 72 LIREQALIAIEE-----ADVILFVVDGREGI-----TPADEEIAKILRRSKKPVILVVNK 121
Query: 64 A 64
Sbjct: 122 I 122
>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 = 28.9 bits (66), Expect = 0.75
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 16/65 (24%)
Query: 10 RGVVVQEIERSVV-------EAADVILEVVDARDPMGTRCKVAEDLVVGTP----GKKLV 58
+G V + IE+ V E ADV+L V+DA + + +DL + GK L+
Sbjct: 63 KGKVTEGIEKYSVLRTLKAIERADVVLLVLDASEGI-----TEQDLRIAGLILEEGKALI 117
Query: 59 IVINK 63
IV+NK
Sbjct: 118 IVVNK 122
>gnl|CDD|206678 cd01891, TypA_BipA, Tyrosine phosphorylated protein A (TypA)/BipA
family belongs to ribosome-binding GTPases. BipA is a
protein belonging to the ribosome-binding family of
GTPases and is widely distributed in bacteria and
plants. BipA was originally described as a protein that
is induced in Salmonella typhimurium after exposure to
bactericidal/permeability-inducing protein (a cationic
antimicrobial protein produced by neutrophils), and has
since been identified in E. coli as well. The properties
thus far described for BipA are related to its role in
the process of pathogenesis by enteropathogenic E. coli.
It appears to be involved in the regulation of several
processes important for infection, including
rearrangements of the cytoskeleton of the host,
bacterial resistance to host defense peptides,
flagellum-mediated cell motility, and expression of K5
capsular genes. It has been proposed that BipA may
utilize a novel mechanism to regulate the expression of
target genes. In addition, BipA from enteropathogenic E.
coli has been shown to be phosphorylated on a tyrosine
residue, while BipA from Salmonella and from E. coli K12
strains is not phosphorylated under the conditions
assayed. The phosphorylation apparently modifies the
rate of nucleotide hydrolysis, with the phosphorylated
form showing greatly increased GTPase activity.
Length = 194
Score = 28.7 bits (65), Expect = 0.92
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 6/59 (10%)
Query: 16 EIERSVVEAADVILEVVDARD-PM-GTRCKVAEDLVVGTPGKKLVIVINKAGKPSTKIQ 72
E+ER V+ D +L +VDA + PM TR + + L G K ++VINK +P + +
Sbjct: 81 EVER-VLSMVDGVLLLVDASEGPMPQTRFVLKKALEAG---LKPIVVINKIDRPDARPE 135
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 29.2 bits (67), Expect = 0.92
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 19 RSVVEAADVILEVVDARDPMGTR-CKVAEDLVVGTPGKKLVIVINK 63
S ++ D++L VVDA + +G + E L +++V+NK
Sbjct: 79 WSSLKDVDLVLFVVDADEKIGPGDEFILEKL--KKVKTPVILVLNK 122
>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 = 27.4 bits (62), Expect = 2.5
Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 3/43 (6%)
Query: 25 ADVILEVVDARDP-MGTRCKVAEDLV--VGTPGKKLVIVINKA 64
AD++L VVDA DP + + E+++ +G +++V+NK
Sbjct: 121 ADLLLHVVDASDPDREEQIETVEEVLKELGADDIPIILVLNKI 163
>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 = 27.3 bits (61), Expect = 2.6
Identities = 11/46 (23%), Positives = 21/46 (45%)
Query: 19 RSVVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKKLVIVINKA 64
R ++ AD++L ++DA D L + L+ V+N+
Sbjct: 70 RRLLPEADLVLWLLDADDRALAADHDFYLLPLAGHDAPLLFVLNQV 115
>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 = 27.4 bits (62), Expect = 2.6
Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 5 KPMEMRGVVVQEIERSVVEAADVILEVVDARDPMGTR-CKVAEDLVVGTPGKKLVIVINK 63
KP + G + + S ++ D++L VVDA + +G + E ++ +++V+NK
Sbjct: 63 KPKKKLGERMVKAAWSALKDVDLVLFVVDASEWIGEGDEFILE--LLKKSKTPVILVLNK 120
>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 = 26.8 bits (60), Expect = 3.7
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 19 RSVVEAADVILEVVDARDPMGTRCKVAEDLVVGT---PGKKLVIVINKA 64
R V + AD++L VVD V E+ +G GK +++V+NK
Sbjct: 71 RQVADRADLVLLVVD-----SDLTPVEEEAKLGLLRERGKPVLLVLNKI 114
>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 = 27.0 bits (61), Expect = 4.4
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 7/48 (14%)
Query: 22 VEAADVILEVVDARDP-----MGTRCKVAEDLVVGTPGKKLVIVINKA 64
V AD++L VVDA DP + KV E+L G ++V NK
Sbjct: 266 VREADLLLHVVDASDPDREEQIEAVEKVLEEL--GAEDIPQLLVYNKI 311
>gnl|CDD|233603 TIGR01862, N2-ase-Ialpha, nitrogenase component I, alpha chain.
This model represents the alpha chain of all three
varieties (Mo-Fe, V-Fe, and Fe-Fe) of component I of
nitrogenase [Central intermediary metabolism, Nitrogen
fixation].
Length = 443
Score = 26.6 bits (59), Expect = 6.2
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 134 TRNKDIKTSITVGVVGECNIAG 155
TR K+I T V ++GE NI G
Sbjct: 183 TREKEITTEYDVNIIGEYNIGG 204
>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 = 26.3 bits (58), Expect = 6.9
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 16 EIERSVVEAADVILEVVDARDP-MGTRCKVAEDLVVGTPGKKLVIVINKA 64
E+ R ++ AD+IL VVD+ D K+ + G +++V NK
Sbjct: 67 ELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGNKI 116
>gnl|CDD|238080 cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region)
or GLGF (after a conserved sequence motif). Many PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. Heterodimerization
through PDZ-PDZ domain interactions adds to the
domain's versatility, and PDZ domain-mediated
interactions may be modulated dynamically through
target phosphorylation. Some PDZ domains play a role in
scaffolding supramolecular complexes. PDZ domains are
found in diverse signaling proteins in bacteria,
archebacteria, and eurkayotes. This CD contains two
distinct structural subgroups with either a N- or
C-terminal beta-strand forming the peptide-binding
groove base. The circular permutation placing the
strand on the N-terminus appears to be found in
Eumetazoa only, while the C-terminal variant is found
in all three kingdoms of life, and seems to co-occur
with protease domains. PDZ domains have been named
after PSD95(post synaptic density protein), DlgA
(Drosophila disc large tumor suppressor), and ZO1, a
mammalian tight junction protein.
Length = 70
Score = 25.0 bits (55), Expect = 7.4
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 3 SVKPMEMRGVVVQEI------ERSVVEAADVILEVVDARDPMGTRCKVAEDLVVGTPGKK 56
S++ GVVV + ER+ ++A DVIL V+ D + +L+ G+K
Sbjct: 6 SIRGGTEGGVVVLSVEPGSPAERAGLQAGDVILA-VNGTDVKNLTLEDVAELLKKEVGEK 64
Query: 57 LVIVI 61
+ + +
Sbjct: 65 VTLTV 69
>gnl|CDD|198449 cd10481, EphR_LBD_A3, Ligand Binding Domain of Ephrin type-A
Receptor 3. Ephrin receptors (EphRs) comprise the
largest subfamily of receptor tyrosine kinases (RTKs).
Class EphA receptors bind GPI-anchored ephrin-A ligands.
There are ten vertebrate EphA receptors (EphA1-10),
which display promiscuous interactions with six ephrin-A
ligands. EphA3 has been implicated in leukemia, lung and
other cancers. EphRs contain a ligand binding domain and
two fibronectin repeats extracellularly, a transmembrane
segment, and a cytoplasmic tyrosine kinase domain.
Binding of the ephrin ligand to EphR requires cell-cell
contact since both are anchored to the plasma membrane.
The resulting downstream signals occur bidirectionally
in both EphR-expressing cells (forward signaling) and
ephrin-expressing cells (reverse signaling). Ephrin/EphR
interaction mainly results in cell-cell repulsion or
adhesion.
Length = 173
Score = 26.2 bits (57), Expect = 8.4
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 83 WIPYNSIQSIYSSPRFSSR 101
WIP NS Q IY +F+ R
Sbjct: 58 WIPRNSAQKIYVELKFTLR 76
>gnl|CDD|233394 TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA. This
bacterial (and Arabidopsis) protein, termed TypA or
BipA, a GTP-binding protein, is phosphorylated on a
tyrosine residue under some cellular conditions. Mutants
show altered regulation of some pathways, but the
precise function is unknown [Regulatory functions,
Other, Cellular processes, Adaptations to atypical
conditions, Protein synthesis, Translation factors].
Length = 594
Score = 26.1 bits (58), Expect = 9.3
Identities = 22/58 (37%), Positives = 34/58 (58%), Gaps = 6/58 (10%)
Query: 16 EIERSVVEAADVILEVVDARD-PM-GTRCKVAEDLVVGTPGKKLVIVINKAGKPSTKI 71
E+ER V+ D +L +VDA + PM TR + + L +G K ++VINK +PS +
Sbjct: 80 EVER-VLGMVDGVLLLVDASEGPMPQTRFVLKKALELGL---KPIVVINKIDRPSARP 133
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.131 0.361
Gapped
Lambda K H
0.267 0.0736 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,805,629
Number of extensions: 687257
Number of successful extensions: 705
Number of sequences better than 10.0: 1
Number of HSP's gapped: 684
Number of HSP's successfully gapped: 47
Length of query: 161
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 72
Effective length of database: 6,990,096
Effective search space: 503286912
Effective search space used: 503286912
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: 55 (24.9 bits)