RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031293
(162 letters)
>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 = 160 bits (408), Expect = 4e-51
Identities = 66/156 (42%), Positives = 97/156 (62%), Gaps = 1/156 (0%)
Query: 2 LNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGFAYAKEEVKDAWEELVKEY 61
+NALT + + RTS PG TQ INFF +G K LVDLPGYG+A +EV++ W +L++EY
Sbjct: 16 INALTNRKKLARTSKTPGRTQLINFFNVGDKFRLVDLPGYGYAKVSKEVREKWGKLIEEY 75
Query: 62 VSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQI 121
+ R +LK V LLID + G P D E++ +E + +VLTK D + ++A+ +I
Sbjct: 76 LENRENLKGVVLLIDARHGPTPIDLEMLEFLEELGIPFLIVLTKADKLKKSELAKVLKKI 135
Query: 122 EESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIA 157
+E L N L PV++ SSK G GI LR ++++
Sbjct: 136 KEELNLFNIL-PPVILFSSKKGTGIDELRALIAEWL 170
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 146 bits (371), Expect = 4e-45
Identities = 59/156 (37%), Positives = 94/156 (60%), Gaps = 3/156 (1%)
Query: 2 LNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGFAYAKEEVKDAWEELVKEY 61
+NALT + + RTS PG TQ INFF++ KL LVDLPGYG+A +E K+ W++L++EY
Sbjct: 41 INALTNRKNLARTSKTPGRTQLINFFEVNDKLRLVDLPGYGYAKVSKEEKEKWQKLIEEY 100
Query: 62 VSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQI 121
+ TR +LK V LLID++ +K D ++I ++ +VLTK D + + ++ ++
Sbjct: 101 LRTRENLKGVVLLIDSRHPLKELDLQMIEWLKEYGIPVLIVLTKADKLKKGERKKQLKKV 160
Query: 122 EESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIA 157
++LK + V++ SS GI LR ++K
Sbjct: 161 RKALKFGDD---EVILFSSLKKQGIDELRAAIAKWL 193
>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 = 134 bits (339), Expect = 1e-40
Identities = 54/145 (37%), Positives = 85/145 (58%), Gaps = 2/145 (1%)
Query: 2 LNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGFAYAKEEVKDAWEELVKEY 61
+NALT + + RTS PG TQ INFF++ LVDLPGYG+A +E K+ W++L++EY
Sbjct: 35 INALTNRKKLARTSKTPGRTQLINFFEVNDGFRLVDLPGYGYAKVSKEEKEKWQKLIEEY 94
Query: 62 VSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQI 121
+ R +LK V LL+D + +K D E+I + +VLTK D + ++ ++ +I
Sbjct: 95 LEKRENLKGVVLLMDIRHPLKELDLEMIEWLRERGIPVLIVLTKADKLKKSELNKQLKKI 154
Query: 122 EESLKANNSLVQPVMMVSSKSGAGI 146
+++LK + V + SS GI
Sbjct: 155 KKALKKDADD--SVQLFSSLKKTGI 177
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 132 bits (335), Expect = 8e-40
Identities = 61/152 (40%), Positives = 88/152 (57%)
Query: 2 LNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGFAYAKEEVKDAWEELVKEY 61
+NALT Q + RTS PG TQ INFF++ +L LVDLPGYG+A +EVK+ W++L++EY
Sbjct: 41 INALTNQKNLARTSKTPGRTQLINFFEVDDELRLVDLPGYGYAKVPKEVKEKWKKLIEEY 100
Query: 62 VSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQI 121
+ R +LK V LLID + K D E+I + VVLTK D + + ++ ++
Sbjct: 101 LEKRANLKGVVLLIDARHPPKDLDREMIEFLLELGIPVIVVLTKADKLKKSERNKQLNKV 160
Query: 122 EESLKANNSLVQPVMMVSSKSGAGIRSLRTVL 153
E LK Q V++ SS GI L+ +
Sbjct: 161 AEELKKPPPDDQWVVLFSSLKKKGIDELKAKI 192
>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 = 56.9 bits (138), Expect = 3e-11
Identities = 27/107 (25%), Positives = 45/107 (42%), Gaps = 8/107 (7%)
Query: 2 LNALTRQWGVVRTSDKPGLTQ--TINFFKLGTKLCLVDLPGYGFAYAKEEVKDAWEELVK 59
+NALT V SD PG T+ + LG ++ LVD PG + + E
Sbjct: 16 INALTGA-KVAIVSDYPGTTRDPILGVLGLGRQIILVDTPGLI----EGASEGKGVEGFN 70
Query: 60 EYVSTRVSLKRVCLLIDTKWGVKPRDHELIS-LMERSQTKYQVVLTK 105
++ + L++D G+ D E++ L + + +VL K
Sbjct: 71 RFLEAIREADLILLVVDASEGLTEDDEEILEELEKLPKKPIILVLNK 117
>gnl|CDD|206734 cd04171, SelB, 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 bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 49.1 bits (118), Expect = 6e-08
Identities = 40/148 (27%), Positives = 65/148 (43%), Gaps = 22/148 (14%)
Query: 17 KPGLTQTINF----FKLGTKLCLVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVC 72
K G+T + F G +L +D+PG+ E+ VK ++ + V
Sbjct: 32 KRGITIDLGFAYLDLPDGKRLGFIDVPGH-------------EKFVKNMLAGAGGIDAVL 78
Query: 73 LLIDTKWGVKP--RDH-ELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANN 129
L++ G+ P R+H E++ L+ + VVLTK D V + +I E L
Sbjct: 79 LVVAADEGIMPQTREHLEILELLGIKKG--LVVLTKADLVDEDRLELVEEEILELLAGTF 136
Query: 130 SLVQPVMMVSSKSGAGIRSLRTVLSKIA 157
P+ VSS +G GI L+ L ++A
Sbjct: 137 LADAPIFPVSSVTGEGIEELKNYLDELA 164
>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 = 49.0 bits (117), Expect = 6e-08
Identities = 36/156 (23%), Positives = 59/156 (37%), Gaps = 20/156 (12%)
Query: 2 LNALTRQWGVVRTSDKPGLTQTINFFKLGT-----KLCLVDLPGYGFAYAKEEVKDAWEE 56
LNAL V SD PG T+ + + KL LVD PG +E E
Sbjct: 14 LNALLGGE-VGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGL------DEFGGLGRE 66
Query: 57 LVKEYVSTRVSLKRVCLLID-TKWGVKPR-DHELISLMERSQTKYQVVLTKTDTVFPIDV 114
+ + L + L++D T + ++ + + +V K D + +V
Sbjct: 67 ELARLLLRGADL--ILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGNKIDLLEEREV 124
Query: 115 ARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLR 150
++ + L PV VS+K+G G+ L
Sbjct: 125 E----ELLRLEELAKILGVPVFEVSAKTGEGVDELF 156
>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 = 46.9 bits (112), Expect = 4e-07
Identities = 40/163 (24%), Positives = 64/163 (39%), Gaps = 22/163 (13%)
Query: 2 LNALTRQWGVVRTSDKPGLTQTIN----FFKLGTKLCLVDLPGY--GFAYAKEEVKDAWE 55
LNAL Q V S PG T+ + L+D PG +E V++A +
Sbjct: 14 LNALLGQN-VGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGLDEEGGLGRERVEEARQ 72
Query: 56 ELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHEL-ISLMERSQTKYQVVLTKTDTVFPIDV 114
R L V L++D+ + P + E + L+ +VL K D V +
Sbjct: 73 VA------DRADL--VLLVVDS--DLTPVEEEAKLGLLRERGKPVLLVLNKIDLVPESEE 122
Query: 115 ARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIA 157
+ + L PV+ VS+ G GI LR ++++
Sbjct: 123 EELLRERKLEL----LPDLPVIAVSALPGEGIDELRKKIAELL 161
>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 = 42.7 bits (101), Expect = 1e-05
Identities = 30/143 (20%), Positives = 51/143 (35%), Gaps = 21/143 (14%)
Query: 19 GLTQTINFFKLGTKLC---LVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLI 75
G+T + +D PG+ E+ KE V L++
Sbjct: 47 GITIKTGVVEFEWPKRRINFIDTPGH-------------EDFSKETVRGLAQADGALLVV 93
Query: 76 DTKWGVKPRDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQ-- 133
D GV+P+ E +++ V + K D V D +I+E LK
Sbjct: 94 DANEGVEPQTREHLNIALAGGLPIIVAVNKIDRVGEEDFDEVLREIKELLKLIGFTFLKG 153
Query: 134 ---PVMMVSSKSGAGIRSLRTVL 153
P++ +S+ +G GI L +
Sbjct: 154 KDVPIIPISALTGEGIEELLDAI 176
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 42.2 bits (100), Expect = 3e-05
Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 12 VRTSDKPGLTQTINFFKLGTKLCLVDLPGYGF-AYAKEEVKDAWEELVKEYV 62
VR +PG+T+ N + G + L DLPG+GF + +EV++ ++ + Y+
Sbjct: 34 VRVGKRPGVTRKPNHYDWGDFI-LTDLPGFGFMSGVPKEVQEKIKDEIVRYI 84
>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 = 39.8 bits (94), Expect = 2e-04
Identities = 15/87 (17%), Positives = 35/87 (40%), Gaps = 4/87 (4%)
Query: 71 VCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNS 130
V ++D + D ++ L+++S+T +VL K D V + ++ + L
Sbjct: 86 VLFVVDASEWIGEGDEFILELLKKSKTPVILVLNKIDLVKDKEDLLPLLEKLKELHPF-- 143
Query: 131 LVQPVMMVSSKSGAGIRSLRTVLSKIA 157
+ +S+ G + L + +
Sbjct: 144 --AEIFPISALKGENVDELLEYIVEYL 168
>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 = 38.3 bits (90), Expect = 7e-04
Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 9/85 (10%)
Query: 73 LLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLV 132
L++D G + ELI ++ + Y VV+ K D + +
Sbjct: 91 LVVDAGVGPGEYELELIEELKERKIPYIVVINKIDLGEESAELEKLEKKFG--------- 141
Query: 133 QPVMMVSSKSGAGIRSLRTVLSKIA 157
P + VS+ +G GI L+ + ++
Sbjct: 142 LPPIFVSALTGEGIDELKEAIIELL 166
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 38.1 bits (89), Expect = 0.001
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 2 LNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGF 43
+N L + V +TS++PG T+ I + KL + L+D PG
Sbjct: 149 INRLLGK-KVAKTSNRPGTTKGIQWIKLDDGIYLLDTPGIIP 189
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 38.1 bits (89), Expect = 0.001
Identities = 31/145 (21%), Positives = 60/145 (41%), Gaps = 20/145 (13%)
Query: 17 KPGLTQTINF--FKLGTK-LCLVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVCL 73
K G+T + F KL + +D+PG+ + + ++ + L
Sbjct: 33 KRGITIDLGFYYRKLEDGVMGFIDVPGH-------------PDFISNLLAGLGGIDYALL 79
Query: 74 LIDTKWGVKPRDHELISLMERSQTKYQ-VVLTKTDTVFPIDVARRAMQIEESLKANNSLV 132
++ G+ + E + +++ K +VLTK D V D AR +I++ L +
Sbjct: 80 VVAADEGLMAQTGEHLLILDLLGIKNGIIVLTKADRV---DEARIEQKIKQILADLSLAN 136
Query: 133 QPVMMVSSKSGAGIRSLRTVLSKIA 157
+ S+K+G GI L+ L +
Sbjct: 137 AKIFKTSAKTGRGIEELKNELIDLL 161
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 37.7 bits (89), Expect = 0.001
Identities = 17/87 (19%), Positives = 40/87 (45%), Gaps = 8/87 (9%)
Query: 71 VCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNS 130
V ++D + P D ++ +++ +T +VL K D V + ++ L+ +
Sbjct: 88 VLFVVDADEKIGPGDEFILEKLKKVKTPVILVLNKIDLVKDKE------ELLPLLEELSE 141
Query: 131 LVQP--VMMVSSKSGAGIRSLRTVLSK 155
L+ ++ +S+ G + L V++K
Sbjct: 142 LMDFAEIVPISALKGDNVDELLDVIAK 168
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes [Protein synthesis, Translation factors].
Length = 581
Score = 36.0 bits (83), Expect = 0.005
Identities = 31/164 (18%), Positives = 64/164 (39%), Gaps = 23/164 (14%)
Query: 4 ALTRQWGVVRTSDKP-----GLTQTINFFKL---GTKLCLVDLPGYGFAYAKEEVKDAWE 55
L + + P G+T + F +L +D+PG+ E
Sbjct: 15 TLLKALTGIAADRLPEEKKRGMTIDLGFAYFPLPDYRLGFIDVPGH-------------E 61
Query: 56 ELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKYQ-VVLTKTDTVFPIDV 114
+ + ++ + L++D GV + E +++++ + VV+TK D V ++
Sbjct: 62 KFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIPHTIVVITKADRVNEEEI 121
Query: 115 ARRAMQIEESL-KANNSLVQPVMMVSSKSGAGIRSLRTVLSKIA 157
R M +++ L + S+K+G GI L+ L +
Sbjct: 122 KRTEMFMKQILNSYIFLKNAKIFKTSAKTGQGIGELKKELKNLL 165
>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 = 34.8 bits (81), Expect = 0.009
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 2 LNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPG 40
+N L + V + +KPG+T+ + ++G + L+D PG
Sbjct: 132 INRLRGK-KVAKVGNKPGVTRGQQWIRIGPNIELLDTPG 169
>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 = 33.9 bits (79), Expect = 0.020
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 101 VVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSK 155
+VL K D V ++ E L PV+ VS+K+G G+ LR +L
Sbjct: 38 IVLNKADLVDDEELEELLEIYE-------KLGYPVLAVSAKTGEGLDELRELLKG 85
>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 = 33.4 bits (77), Expect = 0.030
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 101 VVLTKTDTVFP-IDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIARF 159
+V K D + + R +++ LK ++ V++VS+K G G+ L + +I +
Sbjct: 65 LVGNKIDLLPKDVKPNRLKQWVKKRLKIGGLKIKDVILVSAKKGWGVEEL---IEEIKKL 121
Query: 160 AK 161
AK
Sbjct: 122 AK 123
Score = 28.0 bits (63), Expect = 2.1
Identities = 10/28 (35%), Positives = 11/28 (39%)
Query: 14 TSDKPGLTQTINFFKLGTKLCLVDLPGY 41
S PG T + LG L D PG
Sbjct: 164 VSPIPGTTLGLIKIPLGEGKKLYDTPGI 191
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 33.5 bits (78), Expect = 0.031
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 15/88 (17%)
Query: 70 RVCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANN 129
V L++D + D E++ E VVL K D + +
Sbjct: 297 LVLLVLDASEPLTEEDDEILE--ELKDKPVIVVLNKAD-------------LTGEIDLEE 341
Query: 130 SLVQPVMMVSSKSGAGIRSLRTVLSKIA 157
+PV+ +S+K+G GI LR + ++A
Sbjct: 342 ENGKPVIRISAKTGEGIDELREAIKELA 369
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 33.3 bits (77), Expect = 0.035
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 101 VVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLS-KIARF 159
+VL K D +D RA + E L ++ V+MVSS +G G+ L L+ +I+ F
Sbjct: 155 IVLNKIDL---LDDEGRA-FVNEQLDIYRNIGYRVLMVSSHTGEGLEELEAALTGRISIF 210
Query: 160 A 160
Sbjct: 211 V 211
>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 = 32.1 bits (74), Expect = 0.066
Identities = 32/141 (22%), Positives = 47/141 (33%), Gaps = 27/141 (19%)
Query: 19 GLTQTINFFKLGTKLC---LVDLPGYGFAYAKEEVKDAWEELVKE-YVSTRVSLKRVCLL 74
G+T I TK ++D PG+ + KE L+
Sbjct: 51 GITIKIAAVSFETKKRLINIIDTPGH-------------VDFTKEMIRGASQ-ADGAILV 96
Query: 75 IDTKWGVKPRDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEE------SLKAN 128
+D GV P+ E + L + V + K D V D A +EE
Sbjct: 97 VDAVEGVMPQTREHLLLAKTLGVPIIVFINKIDRV---DDAELEEVVEEISRELLEKYGF 153
Query: 129 NSLVQPVMMVSSKSGAGIRSL 149
PV+ S+ +G GI L
Sbjct: 154 GGETVPVVPGSALTGEGIDEL 174
>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 = 32.4 bits (75), Expect = 0.079
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 12/70 (17%)
Query: 90 SLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSL 149
L E+ + VVL K D + ++ +++E+L +PV +S+ +G G+ L
Sbjct: 270 ELAEKPRI---VVLNKIDLLDEEELEELLKELKEALG------KPVFPISALTGEGLDEL 320
Query: 150 RTVLSKIARF 159
L +A
Sbjct: 321 ---LYALAEL 327
>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 = 31.7 bits (73), Expect = 0.099
Identities = 21/87 (24%), Positives = 42/87 (48%), Gaps = 14/87 (16%)
Query: 71 VCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNS 130
V L++D G+ D E++ L ++ VVL K+D + ++ +
Sbjct: 86 VLLVVDASEGLDEEDLEILEL--PAKKPVIVVLNKSDL------------LSDAEGISEL 131
Query: 131 LVQPVMMVSSKSGAGIRSLRTVLSKIA 157
+P++ +S+K+G GI L+ L ++A
Sbjct: 132 NGKPIIAISAKTGEGIDELKEALLELA 158
>gnl|CDD|178633 PLN03084, PLN03084, alpha/beta hydrolase fold protein; Provisional.
Length = 383
Score = 32.2 bits (73), Expect = 0.11
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 38 LPGYGFAYAKEEVKDAWEELVKEYVSTRVSL 68
PGYGF Y +E + E L+ E S +VSL
Sbjct: 171 QPGYGFNYTLDEYVSSLESLIDELKSDKVSL 201
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 31.8 bits (73), Expect = 0.12
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 11/88 (12%)
Query: 70 RVCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANN 129
V ++D + D LI L + VVL K D V I+ ES K N
Sbjct: 299 LVLFVLDASQPLDKEDLALIEL-LPKKKPIIVVLNKADLVSKIE--------LESEKLAN 349
Query: 130 SLVQPVMMVSSKSGAGIRSLRTVLSKIA 157
++ +S+K+G G+ +LR + ++
Sbjct: 350 G--DAIISISAKTGEGLDALREAIKQLF 375
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 30.1 bits (69), Expect = 0.28
Identities = 19/83 (22%), Positives = 32/83 (38%), Gaps = 6/83 (7%)
Query: 80 GVKPRDHELISLMERSQTKYQVVLTKTD-----TVFPIDVARRAMQIEESLKANNSLVQP 134
GV P+ E I+ + + V + K D P V ++ + V
Sbjct: 85 GVMPQTIEAINHAKAANVPIIVAINKIDKPYGTEADPERVKNELSELGLVGEEWGGDVSI 144
Query: 135 VMMVSSKSGAGIRSLRTVLSKIA 157
V +S+K+G GI L + +A
Sbjct: 145 VP-ISAKTGEGIDDLLEAILLLA 166
>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 = 30.0 bits (68), Expect = 0.38
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 84 RDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSG 143
R +L + K +VL K D V P +V + ++ ES PV+ VS++
Sbjct: 28 RSRKLERMALELGKKLIIVLNKADLV-PREVLEKWKEVFESEGL------PVVYVSARER 80
Query: 144 AGIRSLRTVLSKIA 157
G R LR + ++A
Sbjct: 81 LGTRILRRTIKELA 94
Score = 28.8 bits (65), Expect = 0.86
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 3 NALTRQWGVVRTS---DKPGLTQTINFFKLGTKLCLVDLPG 40
NAL + TS PG T+ I ++ +K+ L+D PG
Sbjct: 117 NALKGR-HSASTSPIPGSPGYTKGIQLVRIDSKIYLIDTPG 156
>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 = 30.0 bits (68), Expect = 0.42
Identities = 27/125 (21%), Positives = 52/125 (41%), Gaps = 17/125 (13%)
Query: 34 CLVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLME 93
LVD PG+ L++ + + + L++D K G++ + E + + E
Sbjct: 71 TLVDCPGHA-------------SLIRTIIGGAQIIDLMLLVVDAKKGIQTQTAECLVIGE 117
Query: 94 RSQTKYQVVLTKTDTVFPIDVARRAMQ----IEESLKANNSLVQPVMMVSSKSGAGIRSL 149
VVL K D + + R+ + ++++L+ P++ VS+K G G L
Sbjct: 118 LLCKPLIVVLNKIDLIPEEERKRKIEKMKKRLQKTLEKTRLKDSPIIPVSAKPGEGEAEL 177
Query: 150 RTVLS 154
L
Sbjct: 178 GGELK 182
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 30.2 bits (69), Expect = 0.45
Identities = 15/85 (17%), Positives = 40/85 (47%), Gaps = 4/85 (4%)
Query: 71 VCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNS 130
+ ++D G P D ++ +++++T +V+ K D V P +++ LK
Sbjct: 89 ILFVVDADEGWGPGDEFILEQLKKTKTPVILVVNKIDKVKP---KTVLLKLIAFLKKLLP 145
Query: 131 LVQPVMMVSSKSGAGIRSLRTVLSK 155
+ ++ +S+ G + +L ++ +
Sbjct: 146 -FKEIVPISALKGDNVDTLLEIIKE 169
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 29.8 bits (68), Expect = 0.56
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 101 VVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSL 149
+V K D + + RA I E+L PV ++S+ SG G++ L
Sbjct: 280 LVFNKIDLLDEEEAEERAKAIVEALGW----EGPVYLISAASGLGVKEL 324
>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 = 29.2 bits (66), Expect = 0.57
Identities = 34/160 (21%), Positives = 50/160 (31%), Gaps = 39/160 (24%)
Query: 1 MLNALTRQWGVVRTSDKPGLTQTINFFKLGTK---LCLVDLPGYGFAYAKEEVKDAW-EE 56
+ NAL V D+ T+ + T L L+DLPG G +D EE
Sbjct: 13 LCNALFGT-EVAAVGDRRPTTRAAQAYVWQTGGDGLVLLDLPGVGERG----RRDREYEE 67
Query: 57 LVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISL-MERSQTKYQVVLTKTDTVFPIDVA 115
L + + V L+D DH+ L + VL + D V
Sbjct: 68 LYRRLLPE---ADLVLWLLDADDRALAADHDFYLLPLAGHDAPLLFVLNQVDPVLA---- 120
Query: 116 RRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSK 155
VS+++G G+ L L
Sbjct: 121 ----------------------VSARTGWGLDELAEALIT 138
>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 = 29.4 bits (67), Expect = 0.69
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 11 VVRTSDKPGLTQTINFFKLGTKLCLVDLPG 40
V + ++PG+T+ + KL L L+D PG
Sbjct: 143 VAKVGNRPGVTKGQQWIKLSDGLELLDTPG 172
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 29.6 bits (67), Expect = 0.81
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 101 VVLTKTDTVFPIDVARRA---MQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIA 157
V LTK D V D AR A Q++ L+ + + ++ G GI +LR L ++
Sbjct: 109 VALTKADRV---DEARIAEVRRQVKAVLREYGFAEAKLFVTAATEGRGIDALREHLLQLP 165
>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 = 28.2 bits (64), Expect = 1.3
Identities = 20/100 (20%), Positives = 43/100 (43%), Gaps = 14/100 (14%)
Query: 14 TSDKPGLT---QTINFFKLGTKLCLVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKR 70
SD PG+T + G + L+D G E + + ++E ++++
Sbjct: 25 VSDTPGVTRDRKYGEAEWGGREFILIDTGGI------EPDDEGISKEIRE--QAEIAIEE 76
Query: 71 ---VCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTD 107
+ ++D + G+ P D E+ + +S+ +V+ K D
Sbjct: 77 ADVILFVVDGREGLTPADEEIAKYLRKSKKPVILVVNKID 116
>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 = 28.9 bits (66), Expect = 1.3
Identities = 22/102 (21%), Positives = 43/102 (42%), Gaps = 18/102 (17%)
Query: 14 TSDKPGLT-----QTINFFKLGTKLCLVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSL 68
SD PG+T + G + L+D G EE D ++ ++E +++
Sbjct: 27 VSDTPGVTRDRKYGDAEW--GGREFILIDTGGI------EEDDDGLDKQIRE--QAEIAI 76
Query: 69 K---RVCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTD 107
+ + ++D + G+ P D E+ + +S +V K D
Sbjct: 77 EEADVILFVVDGREGLTPEDEEIAKWLRKSGKPVILVANKID 118
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 28.5 bits (65), Expect = 1.4
Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 8/61 (13%)
Query: 101 VVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIARFA 160
+VL K D + + R + L A PV ++S+ +G G+ L L +
Sbjct: 276 LVLNKIDLL--DEEEEREKRAALELAALG---GPVFLISAVTGEGLDEL---LRALWELL 327
Query: 161 K 161
+
Sbjct: 328 E 328
>gnl|CDD|152022 pfam11586, DUF3242, Protein of unknown function (DUF3242). This
protein from Thermotoga maritima is a hypothetical
ORFan protein, TM1622, whose structure has been
determined. The protein is composed of seven beta
strands and three alpha helices.
Length = 127
Score = 27.5 bits (61), Expect = 1.8
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 36 VDLPGYGFAYAKEEVKDAWEELVKEY 61
+ P Y F Y EE K W+++ K
Sbjct: 44 ENGPFYVFKYKDEEAKKIWKKINKRA 69
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated with
diverse processes in dividing and non-dividing cells.
They were first discovered in the budding yeast S.
cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of the
cell cortex and exocytosis. In humans, 12 septin genes
generate dozens of polypeptides, many of which comprise
heterooligomeric complexes. Since septin mutants are
commonly defective in cytokinesis and formation of the
neck formation of the neck filaments/septin rings,
septins have been considered to be the primary
constituents of the neck filaments. Septins belong to
the GTPase superfamily for their conserved GTPase motifs
and enzymatic activities.
Length = 275
Score = 28.3 bits (64), Expect = 1.9
Identities = 32/126 (25%), Positives = 52/126 (41%), Gaps = 29/126 (23%)
Query: 25 NFFKLGTKLCLVDLPGYGFAYAKEEVKDAWEELVK-------EYVSTRVSLKRVCLLIDT 77
N KL KL ++D PG+G D W+ +V Y+ + R + DT
Sbjct: 58 NGVKL--KLTVIDTPGFGDNINNS---DCWKPIVDYIDDQFESYLREESRINRNRRIPDT 112
Query: 78 K------------WGVKPRDHELISLMERSQTKYQV--VLTKTDTVFPIDVARRAMQIEE 123
+ G+KP D I M++ K + V+ K DT+ P ++ +I E
Sbjct: 113 RVHCCLYFIPPTGHGLKPLD---IEFMKKLSKKVNIIPVIAKADTLTPEELTEFKKRIME 169
Query: 124 SLKANN 129
++ NN
Sbjct: 170 DIEENN 175
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 28.3 bits (64), Expect = 2.1
Identities = 28/114 (24%), Positives = 54/114 (47%), Gaps = 20/114 (17%)
Query: 3 NALTRQWGVVR---TSDKPGLTQTINFFK---LGTKLCLVDLPGYGFAYAKEEVKDAWEE 56
N LT + R SD PG+T+ + LG + L+D G + +D +E
Sbjct: 21 NRLTGR----RIAIVSDTPGVTRDRIYGDAEWLGREFILIDTGGL-----DDGDEDELQE 71
Query: 57 LVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTD 107
L++E ++++ + ++D + G+ P D E+ ++ RS+ +V+ K D
Sbjct: 72 LIRE--QALIAIEEADVILFVVDGREGITPADEEIAKILRRSKKPVILVVNKID 123
>gnl|CDD|130988 TIGR01933, hflK, HflK protein. HflK and HflC are paralogs encoded
by tandem genes in Proteobacteria, spirochetes, and some
other bacterial lineages. The HflKC complex is anchored
in the membrane and exposed to the periplasm. The
complex is not active as a protease, but rather binds to
and appears to modulate the ATP-dependent protease FtsH.
The overall function of HflKC is not fully
described.//Regulation of FtsH by HflKC appears to be
negative (PMID:8947034,PMID:96367) [SS 8/27/03].
Length = 261
Score = 28.1 bits (63), Expect = 2.1
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 1 MLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGFAYAKEEVKDAWEELVK 59
M + LT +R K L + I+ + LG + V+ A EEVK+A+++++
Sbjct: 105 MDDILTEGRSQIREDTKERLNEIIDNYDLGITVTDVNFQS---ARPPEEVKEAFDDVII 160
>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 = 27.6 bits (62), Expect = 2.1
Identities = 13/33 (39%), Positives = 14/33 (42%), Gaps = 6/33 (18%)
Query: 11 VVRTSDKPGLT---QTINFFKLGTKLCLVDLPG 40
V S PG T QTI L + L D PG
Sbjct: 107 KVSVSSTPGKTKHFQTIF---LEPGITLCDCPG 136
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 27.9 bits (63), Expect = 2.4
Identities = 24/72 (33%), Positives = 32/72 (44%), Gaps = 9/72 (12%)
Query: 85 DHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGA 144
D L L ER + VVL K D P D A + L+A PV VS+ S
Sbjct: 276 DLGLGDLAERPRL---VVLNKIDV--P-DARELAEFVRPELEARG---WPVFEVSAASRE 326
Query: 145 GIRSLRTVLSKI 156
G+R L L+++
Sbjct: 327 GLRELSFALAEL 338
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 27.7 bits (63), Expect = 2.6
Identities = 26/116 (22%), Positives = 51/116 (43%), Gaps = 25/116 (21%)
Query: 3 NALTRQWGVVR---TSDKPGLT-----QTINFFKLGTKLCLVDLPGYGFAYAKEEVKDAW 54
N LT + R +D PG+T + LG + L+D G E D +
Sbjct: 19 NRLTGK----RDAIVADTPGVTRDRIYGEAEW--LGREFILIDTGGI------EPDDDGF 66
Query: 55 EELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTD 107
E+ ++E ++++ + ++D + G+ P D E+ ++ +S +V+ K D
Sbjct: 67 EKQIRE--QAELAIEEADVILFVVDGRAGLTPADEEIAKILRKSNKPVILVVNKVD 120
>gnl|CDD|226469 COG3960, COG3960, Glyoxylate carboligase [General function
prediction only].
Length = 592
Score = 27.9 bits (62), Expect = 2.6
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 79 WGVKPRDHELISLMERSQTKYQ---VVLTKTDTVFPI 112
WG P DH L++ M QT ++ L +D VF I
Sbjct: 241 WGCIPDDHPLMAGMVGLQTSHRYGNATLLASDMVFGI 277
>gnl|CDD|234321 TIGR03708, poly_P_AMP_trns, polyphosphate:AMP phosphotransferase.
Members of this protein family contain a domain
duplication. The characterized member from Acinetobacter
johnsonii is polyphosphate:AMP phosphotransferase (PAP),
which can transfer the terminal phosphate from poly(P)
to AMP, yielding ADP. In the opposite direction, this
enzyme can synthesize poly(P). Each domain of this
protein family is homologous to polyphosphate kinase, an
enzyme that can run in the forward direction to extend a
polyphosphate chain with a new terminal phosphate from
ATP, or in reverse to make ATP (or GTP) from ADP (or
GDP) [Central intermediary metabolism, Phosphorus
compounds].
Length = 493
Score = 27.7 bits (62), Expect = 3.3
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 54 WEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTDT 108
W L K+ R LK++ +T+W V P D + + + +R + + +L T T
Sbjct: 150 WLHLSKKQQKER--LKKLEKDPETRWRVTPEDWKQLKVYDRYRKLAERMLRYTST 202
>gnl|CDD|211417 cd11576, GH99_GH71_like_2, Uncharacterized glycoside hydrolase
family 99-like domain. This family of putative
glycoside hydrolases resembles glycosyl hydrolase
families 71 and 99 (following the CAZY nomenclature) and
may share a similar catalytic site and mechanism. The
domain may co-occur with other domains involved in the
binding/processing of glycans.
Length = 378
Score = 26.8 bits (60), Expect = 6.4
Identities = 8/29 (27%), Positives = 11/29 (37%)
Query: 37 DLPGYGFAYAKEEVKDAWEELVKEYVSTR 65
DL G +K+ W LV +Y
Sbjct: 137 DLSGLNAGTVLSVIKNDWTNLVDKYKILD 165
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 26.4 bits (59), Expect = 6.8
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 7/55 (12%)
Query: 101 VVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSK 155
+VLTK D + ++ A V PV+ VS+ G G+ L LS
Sbjct: 147 IVLTKADLCEDAEEKIAEVE------ALAPGV-PVLAVSALDGEGLDVLAAWLSG 194
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 26.7 bits (60), Expect = 6.9
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 11 VVRTSDKPGLTQTINFFKLGTKLCLVDLPG 40
+ +T ++PG+T+ + KLG L L+D PG
Sbjct: 146 IAKTGNRPGVTKAQQWIKLGKGLELLDTPG 175
>gnl|CDD|112128 pfam03299, TF_AP-2, Transcription factor AP-2.
Length = 207
Score = 26.3 bits (58), Expect = 7.1
Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 12/62 (19%)
Query: 95 SQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLS 154
S +KY+V + +R + E L N SL+ V+ +KS G R LR L
Sbjct: 15 STSKYKVT---------VAEVQRRLSPPECL--NASLLGGVLR-RAKSKNGGRLLREKLD 62
Query: 155 KI 156
KI
Sbjct: 63 KI 64
>gnl|CDD|213633 TIGR01504, glyox_carbo_lig, glyoxylate carboligase. Glyoxylate
carboligase, also called tartronate-semialdehyde
synthase, releases CO2 while synthesizing a single
molecule of tartronate semialdehyde from two molecules
of glyoxylate. It is a thiamine pyrophosphate-dependent
enzyme, closely related in sequence to the large subunit
of acetolactate synthase. In the D-glycerate pathway,
part of allantoin degradation in the Enterobacteriaceae,
tartronate semialdehyde is converted to D-glycerate and
then 3-phosphoglycerate, a product of glycolysis and
entry point in the general metabolism.
Length = 588
Score = 26.8 bits (59), Expect = 7.1
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 79 WGVKPRDHELISLMERSQTKYQ---VVLTKTDTVFPI 112
WG P DHEL++ M QT ++ L ++D VF I
Sbjct: 240 WGCIPDDHELMAGMVGLQTSHRYGNATLLESDFVFGI 276
>gnl|CDD|217942 pfam04179, Init_tRNA_PT, Initiator tRNA phosphoribosyl transferase.
This enzyme (EC:2.4.2.-) modifies exclusively the
initiator tRNA in position 64 using
5'-phosphoribosyl-1'-pyrophosphate as the modification
donor. As the initiator tRNA participates both in the
initiation and elongation of translation, the
2'-O-ribosyl phosphate modification discriminates the
initiator tRNAs from the elongator tRNAs.
Length = 441
Score = 26.6 bits (59), Expect = 7.3
Identities = 28/119 (23%), Positives = 46/119 (38%), Gaps = 11/119 (9%)
Query: 43 FAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKYQVV 102
A ++E++ D EELV E S+ + VKP + I ++ + +
Sbjct: 251 LATSEEDLPDLIEELVAESSSSS-------TGSGAELIVKPTTNLYIGAIDTNLNASLLN 303
Query: 103 LTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIARFAK 161
+ + I+ + + E K L + SSK G+ R LR L I F K
Sbjct: 304 KEENEFDCVINCSESPTESETWEKQKKRLHLG--LGSSKKGS--RDLRKALPPICDFIK 358
>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 = 26.3 bits (58), Expect = 9.1
Identities = 38/155 (24%), Positives = 64/155 (41%), Gaps = 24/155 (15%)
Query: 1 MLNALTRQWGVVRTSDKPGLTQTI---NFFKLGTKLCLVDLPGYGFAYAKEEVKDAWEEL 57
+LNAL +Q + SD G T+ + +F G + L+D G E D E L
Sbjct: 219 LLNALLKQDRAI-VSDIKGTTRDVVEGDFELNGILIKLLDTAGI------REHADFVERL 271
Query: 58 VKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTDTVFPIDV 114
E + ++K+ V ++D + D LI + +S+ + +VL K ID+
Sbjct: 272 GIE--KSFKAIKQADLVIYVLDASQPLTKDD-FLIIDLNKSKKPFILVLNK------IDL 322
Query: 115 ARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSL 149
+++ S K NS + K A + L
Sbjct: 323 KINSLEFFVSSKVLNSSN--LSAKQLKIKALVDLL 355
>gnl|CDD|234313 TIGR03688, pupylate_PafA2, proteasome accessory factor PafA2. This
protein family is paralogous to (and distinct from) the
PafA (proteasome accessory factor) first described in
Mycobacterium tuberculosis (see TIGR03686). Members of
both this family and TIGR03686 itself tend to cluster
with each other, with the ubiquitin analog Pup
(TIGR03687) associated with targeting to the proteasome,
and with proteasome subunits themselves [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 485
Score = 26.3 bits (58), Expect = 9.6
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 20 LTQTINFFKLGTKLCLVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLID 76
+++T N+ KLGT ++D GF ++ + + + VS ++L + L D
Sbjct: 249 MSETSNYLKLGTTSLVLDAIEAGFDFSDLALANPVAAVHA--VSHDLTLTHLLRLAD 303
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
0.320 0.133 0.380
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,849,853
Number of extensions: 694408
Number of successful extensions: 767
Number of sequences better than 10.0: 1
Number of HSP's gapped: 753
Number of HSP's successfully gapped: 69
Length of query: 162
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 73
Effective length of database: 6,990,096
Effective search space: 510277008
Effective search space used: 510277008
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (24.8 bits)