RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 029158
(198 letters)
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 199 bits (509), Expect = 2e-65
Identities = 79/193 (40%), Positives = 118/193 (61%), Gaps = 3/193 (1%)
Query: 1 MNKLEFFAAAKVSSSFPAPDLPEIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTI 60
++ EF +A P D PEIAFAGRSNVGKSS++NALT + + RTS PG TQ I
Sbjct: 4 IHNAEFVTSAPKLEQLPPDDGPEIAFAGRSNVGKSSLINALTNRKNLARTSKTPGRTQLI 63
Query: 61 NFFKLGTKLCLVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPR 120
NFF++ KL LVDLPGYG+A +E K+ W++L++EY+ TR +LK V LLID++ +K
Sbjct: 64 NFFEVNDKLRLVDLPGYGYAKVSKEEKEKWQKLIEEYLRTRENLKGVVLLIDSRHPLKEL 123
Query: 121 DHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGA 180
D ++I ++ +VLTK D + + ++ ++ ++LK + V++ SS
Sbjct: 124 DLQMIEWLKEYGIPVLIVLTKADKLKKGERKKQLKKVRKALKFGDD---EVILFSSLKKQ 180
Query: 181 GIRSLRTVLSKIA 193
GI LR ++K
Sbjct: 181 GIDELRAAIAKWL 193
>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 = 198 bits (506), Expect = 2e-65
Identities = 79/171 (46%), Positives = 112/171 (65%), Gaps = 1/171 (0%)
Query: 23 EIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGFAYA 82
E+AFAGRSNVGKSS++NALT + + RTS PG TQ INFF +G K LVDLPGYG+A
Sbjct: 1 EVAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFFNVGDKFRLVDLPGYGYAKV 60
Query: 83 KEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKT 142
+EV++ W +L++EY+ R +LK V LLID + G P D E++ +E + +VLTK
Sbjct: 61 SKEVREKWGKLIEEYLENRENLKGVVLLIDARHGPTPIDLEMLEFLEELGIPFLIVLTKA 120
Query: 143 DTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIA 193
D + ++A+ +I+E L N L PV++ SSK G GI LR ++++
Sbjct: 121 DKLKKSELAKVLKKIKEELNLFNIL-PPVILFSSKKGTGIDELRALIAEWL 170
>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 = 184 bits (470), Expect = 7e-60
Identities = 74/178 (41%), Positives = 107/178 (60%), Gaps = 2/178 (1%)
Query: 5 EFFAAAKVSSSFPAPDLPEIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFK 64
EF +A P D PEIAFAGRSNVGKSS++NALT + + RTS PG TQ INFF+
Sbjct: 2 EFVKSAVKLKQLPPDDGPEIAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQLINFFE 61
Query: 65 LGTKLCLVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHEL 124
+ LVDLPGYG+A +E K+ W++L++EY+ R +LK V LL+D + +K D E+
Sbjct: 62 VNDGFRLVDLPGYGYAKVSKEEKEKWQKLIEEYLEKRENLKGVVLLMDIRHPLKELDLEM 121
Query: 125 ISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGI 182
I + +VLTK D + ++ ++ +I+++LK + V + SS GI
Sbjct: 122 IEWLRERGIPVLIVLTKADKLKKSELNKQLKKIKKALKKDADD--SVQLFSSLKKTGI 177
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 181 bits (462), Expect = 2e-58
Identities = 82/188 (43%), Positives = 114/188 (60%)
Query: 2 NKLEFFAAAKVSSSFPAPDLPEIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTIN 61
+K +F +A +P DLPEIAFAGRSNVGKSS++NALT Q + RTS PG TQ IN
Sbjct: 5 HKAKFITSAPDIKQYPEDDLPEIAFAGRSNVGKSSLINALTNQKNLARTSKTPGRTQLIN 64
Query: 62 FFKLGTKLCLVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRD 121
FF++ +L LVDLPGYG+A +EVK+ W++L++EY+ R +LK V LLID + K D
Sbjct: 65 FFEVDDELRLVDLPGYGYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPPKDLD 124
Query: 122 HELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAG 181
E+I + VVLTK D + + ++ ++ E LK Q V++ SS G
Sbjct: 125 REMIEFLLELGIPVIVVLTKADKLKKSERNKQLNKVAEELKKPPPDDQWVVLFSSLKKKG 184
Query: 182 IRSLRTVL 189
I L+ +
Sbjct: 185 IDELKAKI 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 = 85.8 bits (213), Expect = 6e-22
Identities = 35/122 (28%), Positives = 56/122 (45%), Gaps = 8/122 (6%)
Query: 23 EIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQ--TINFFKLGTKLCLVDLPGYGFA 80
+A GR NVGKS+++NALT V SD PG T+ + LG ++ LVD PG
Sbjct: 1 RVALVGRPNVGKSTLINALTGA-KVAIVSDYPGTTRDPILGVLGLGRQIILVDTPGLI-- 57
Query: 81 YAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELIS-LMERSQTKYQVVL 139
+ + E ++ + L++D G+ D E++ L + + +VL
Sbjct: 58 --EGASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEELEKLPKKPIILVL 115
Query: 140 TK 141
K
Sbjct: 116 NK 117
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 72.6 bits (179), Expect = 4e-16
Identities = 31/78 (39%), Positives = 49/78 (62%), Gaps = 4/78 (5%)
Query: 22 PEIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGF-A 80
PEI F GRSNVGKS+++ LT + VR +PG+T+ N + G + L DLPG+GF +
Sbjct: 10 PEIVFVGRSNVGKSTLVRELTGKK--VRVGKRPGVTRKPNHYDWGDFI-LTDLPGFGFMS 66
Query: 81 YAKEEVKDAWEELVKEYV 98
+EV++ ++ + Y+
Sbjct: 67 GVPKEVQEKIKDEIVRYI 84
>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 = 71.7 bits (176), Expect = 5e-16
Identities = 43/169 (25%), Positives = 67/169 (39%), Gaps = 20/169 (11%)
Query: 25 AFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGT-----KLCLVDLPGYGF 79
GR VGKSS+LNAL V SD PG T+ + + KL LVD PG
Sbjct: 1 VVVGRGGVGKSSLLNALLGGE-VGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGL-- 57
Query: 80 AYAKEEVKDAWEELVKEYVSTRVSLKRVCLLID-TKWGVKPR-DHELISLMERSQTKYQV 137
+E E + + L + L++D T + ++ + + +
Sbjct: 58 ----DEFGGLGREELARLLLRGADL--ILLVVDSTDRESEEDAKLLILRRLRKEGIPIIL 111
Query: 138 VLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLR 186
V K D + +V ++ + L PV VS+K+G G+ L
Sbjct: 112 VGNKIDLLEEREVE----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 = 68.4 bits (168), Expect = 7e-15
Identities = 49/176 (27%), Positives = 74/176 (42%), Gaps = 22/176 (12%)
Query: 25 AFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTIN----FFKLGTKLCLVDLPGY--G 78
A GR NVGKSS+LNAL Q V S PG T+ + L+D PG
Sbjct: 1 AIFGRPNVGKSSLLNALLGQN-VGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGLDEE 59
Query: 79 FAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHEL-ISLMERSQTKYQV 137
+E V++A + R L V L++D+ + P + E + L+ +
Sbjct: 60 GGLGRERVEEARQVA------DRADL--VLLVVDS--DLTPVEEEAKLGLLRERGKPVLL 109
Query: 138 VLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIA 193
VL K D V + + + L PV+ VS+ G GI LR ++++
Sbjct: 110 VLNKIDLVPESEEEELLRERKLEL----LPDLPVIAVSALPGEGIDELRKKIAELL 161
>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 = 64.1 bits (157), Expect = 2e-12
Identities = 49/180 (27%), Positives = 74/180 (41%), Gaps = 32/180 (17%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLT-----QTINFFKLGTKLCLVDLPGYG 78
I GR N GKSS++NALT Q + SD PG T + + LG + L+D G
Sbjct: 9 IGIFGRRNAGKSSLINALTGQ-DIAIVSDVPGTTTDPVYKAMELLPLGPVV-LIDTAG-- 64
Query: 79 FAYAKEEVKDAWE--ELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERSQT 133
+ D E EL E TR L + L++D G + ELI ++ +
Sbjct: 65 -------LDDEGELGELRVE--KTREVLDKTDLALLVVDAGVGPGEYELELIEELKERKI 115
Query: 134 KYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIA 193
Y VV+ K D + + P + VS+ +G GI L+ + ++
Sbjct: 116 PYIVVINKIDLGEESAELEKLEKKFG---------LPPIFVSALTGEGIDELKEAIIELL 166
>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 = 60.6 bits (148), Expect = 8e-12
Identities = 43/179 (24%), Positives = 75/179 (41%), Gaps = 25/179 (13%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLG------TKLCLVDLPGY 77
+A GR NVGKS++LNAL Q + S KP T+ G ++ VD PG
Sbjct: 6 VAIIGRPNVGKSTLLNALVGQ-KISIVSPKPQTTRNRI---RGIYTDDDAQIIFVDTPGI 61
Query: 78 GFAYAKEEVKDAWEELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERSQTK 134
+ ++ E +VK S +LK V ++D + D ++ L+++S+T
Sbjct: 62 ---HKPKKKLG--ERMVKAAWS---ALKDVDLVLFVVDASEWIGEGDEFILELLKKSKTP 113
Query: 135 YQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIA 193
+VL K D V + ++ + L + +S+ G + L + +
Sbjct: 114 VILVLNKIDLVKDKEDLLPLLEKLKELHPF----AEIFPISALKGENVDELLEYIVEYL 168
>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 = 59.2 bits (144), Expect = 3e-11
Identities = 48/178 (26%), Positives = 79/178 (44%), Gaps = 23/178 (12%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKP-GLTQTINF----FKLGTKLCLVDLPGYG 78
I AG + GK++++ ALT +K G+T + F G +L +D+PG+
Sbjct: 2 IGTAGHIDHGKTTLIKALTGIETDRLPEEKKRGITIDLGFAYLDLPDGKRLGFIDVPGH- 60
Query: 79 FAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKP--RDH-ELISLMERSQTKY 135
E+ VK ++ + V L++ G+ P R+H E++ L+ +
Sbjct: 61 ------------EKFVKNMLAGAGGIDAVLLVVAADEGIMPQTREHLEILELLGIKKG-- 106
Query: 136 QVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIA 193
VVLTK D V + +I E L P+ VSS +G GI L+ L ++A
Sbjct: 107 LVVLTKADLVDEDRLELVEEEILELLAGTFLADAPIFPVSSVTGEGIEELKNYLDELA 164
>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 = 52.0 bits (125), Expect = 6e-09
Identities = 36/140 (25%), Positives = 53/140 (37%), Gaps = 14/140 (10%)
Query: 25 AFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTK---LCLVDLPGYGFAY 81
G++ GKSS+ NAL V D+ T+ + T L L+DLPG G
Sbjct: 1 GLMGKTGAGKSSLCNALFGT-EVAAVGDRRPTTRAAQAYVWQTGGDGLVLLDLPGVGERG 59
Query: 82 AKEEVKDAW-EELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISL-MERSQTKYQVVL 139
+D EEL + + V L+D DH+ L + VL
Sbjct: 60 ----RRDREYEELYRRLLPE---ADLVLWLLDADDRALAADHDFYLLPLAGHDAPLLFVL 112
Query: 140 TKTDTVFPIDVARRAMQIEE 159
+ D V + AR ++E
Sbjct: 113 NQVDPVLAV-SARTGWGLDE 131
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 53.9 bits (130), Expect = 8e-09
Identities = 21/52 (40%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 28 GRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGF 79
G NVGKS+++N L + V +TS++PG T+ I + KL + L+D PG
Sbjct: 139 GYPNVGKSTLINRLLGK-KVAKTSNRPGTTKGIQWIKLDDGIYLLDTPGIIP 189
>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 = 52.3 bits (126), Expect = 9e-09
Identities = 37/188 (19%), Positives = 66/188 (35%), Gaps = 35/188 (18%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVV--------RTSD------KPGLTQTINFFKLGTKL 69
+ G + GK+++ +L Q G + D + G+T +
Sbjct: 2 VGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWPK 61
Query: 70 C---LVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELIS 126
+D PG+ E+ KE V L++D GV+P+ E ++
Sbjct: 62 RRINFIDTPGH-------------EDFSKETVRGLAQADGALLVVDANEGVEPQTREHLN 108
Query: 127 LMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQ-----PVMMVSSKSGAG 181
+ V + K D V D +I+E LK P++ +S+ +G G
Sbjct: 109 IALAGGLPIIVAVNKIDRVGEEDFDEVLREIKELLKLIGFTFLKGKDVPIIPISALTGEG 168
Query: 182 IRSLRTVL 189
I L +
Sbjct: 169 IEELLDAI 176
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 53.1 bits (129), Expect = 1e-08
Identities = 41/190 (21%), Positives = 72/190 (37%), Gaps = 51/190 (26%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKP-------------GLTQTINFFKLGTKLC 70
+A GR NVGKS++LNAL Q + S KP Q I
Sbjct: 8 VAIVGRPNVGKSTLLNALVGQ-KISIVSPKPQTTRHRIRGIVTEDDAQII---------- 56
Query: 71 LVDLPGYGFA-------YAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHE 123
VD PG + + ++ V L V ++D + P D
Sbjct: 57 FVDTPGI-HKPKRALNRAMNKAAWSSLKD---------VDL--VLFVVDADEKIGPGDEF 104
Query: 124 LISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQP--VMMVSSKSGAG 181
++ +++ +T +VL K D V + ++ L+ + L+ ++ +S+ G
Sbjct: 105 ILEKLKKVKTPVILVLNKIDLVKDKE------ELLPLLEELSELMDFAEIVPISALKGDN 158
Query: 182 IRSLRTVLSK 191
+ L V++K
Sbjct: 159 VDELLDVIAK 168
>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 = 51.4 bits (124), Expect = 2e-08
Identities = 17/46 (36%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 31 NVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPG 76
NVGKS+++N L + V + +KPG+T+ + ++G + L+D PG
Sbjct: 125 NVGKSTLINRLRGK-KVAKVGNKPGVTRGQQWIRIGPNIELLDTPG 169
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 52.6 bits (127), Expect = 2e-08
Identities = 37/132 (28%), Positives = 66/132 (50%), Gaps = 20/132 (15%)
Query: 21 LPEIAFAGRSNVGKSSMLNALTRQWGVVR---TSDKPGLTQTINFFK---LGTKLCLVDL 74
P +A GR NVGKS++ N LT + R SD PG+T+ + LG + L+D
Sbjct: 3 TPVVAIVGRPNVGKSTLFNRLTGR----RIAIVSDTPGVTRDRIYGDAEWLGREFILIDT 58
Query: 75 PGYGFAYAKEEVKDAWEELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERS 131
G + +D +EL++E ++++ + ++D + G+ P D E+ ++ RS
Sbjct: 59 GGL-----DDGDEDELQELIRE--QALIAIEEADVILFVVDGREGITPADEEIAKILRRS 111
Query: 132 QTKYQVVLTKTD 143
+ +V+ K D
Sbjct: 112 KKPVILVVNKID 123
Score = 40.6 bits (96), Expect = 2e-04
Identities = 48/170 (28%), Positives = 83/170 (48%), Gaps = 16/170 (9%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQ---TINFFKLGTKLCLVDLPGYGFA 80
IA GR NVGKSS++NA+ + V+ SD G T+ I F + G K L+D G
Sbjct: 181 IAIIGRPNVGKSSLINAILGEERVI-VSDIAGTTRDSIDIEFERDGRKYVLIDTAG---I 236
Query: 81 YAKEEVKDAWEELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERSQTKYQV 137
K ++ ++ E+ T +++R V L+ID G+ +D + L+E + +
Sbjct: 237 RRKGKITESVEKY--SVARTLKAIERADVVLLVIDATEGISEQDLRIAGLIEEAGRGIVI 294
Query: 138 VLTKTDTVFPIDVARRAMQIEESLKANNSLV--QPVMMVSSKSGAGIRSL 185
V+ K D V D A + ++ L+ + P++ +S+ +G G+ L
Sbjct: 295 VVNKWDLVEE-DEATME-EFKKKLRRKLPFLDFAPIVFISALTGQGLDKL 342
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 52.6 bits (127), Expect = 2e-08
Identities = 49/184 (26%), Positives = 76/184 (41%), Gaps = 42/184 (22%)
Query: 24 IAFAGRSNVGKSSMLNALTRQ-WGVVRTSDKPGLTQTI--NFFKL-GTKLCLVDLPGY-- 77
+ GR NVGKSS+LNAL + +V +D G T+ + L G + LVD G
Sbjct: 220 VVIIGRPNVGKSSLLNALLGRDRAIV--TDIAGTTRDVIEEDINLNGIPVRLVDTAGIRE 277
Query: 78 --------GFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLME 129
G AK+ +++A V ++D + D LI L
Sbjct: 278 TDDVVERIGIERAKKAIEEA---------------DLVLFVLDASQPLDKEDLALIEL-L 321
Query: 130 RSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVL 189
+ VVL K D V I+ ES K N ++ +S+K+G G+ +LR +
Sbjct: 322 PKKKPIIVVLNKADLVSKIE--------LESEKLANG--DAIISISAKTGEGLDALREAI 371
Query: 190 SKIA 193
++
Sbjct: 372 KQLF 375
>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 = 50.5 bits (122), Expect = 4e-08
Identities = 47/174 (27%), Positives = 78/174 (44%), Gaps = 24/174 (13%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQ---TINFFKLGTKLCLVDLPGYGFA 80
IA GR NVGKSS+LNAL + V+ SD G T+ + F G K L+D G
Sbjct: 5 IAIIGRPNVGKSSLLNALLGEERVI-VSDIAGTTRDSIDVPFEYDGQKYTLIDTAG---I 60
Query: 81 YAKEEVKDAWEELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERSQTKYQV 137
K +V + E+ + T +++R V L++D G+ +D + L+ +
Sbjct: 61 RKKGKVTEGIEKYS--VLRTLKAIERADVVLLVLDASEGITEQDLRIAGLILEEGKALII 118
Query: 138 VLTKTDTVFPIDVARRAM--QIEESLK----ANNSLVQPVMMVSSKSGAGIRSL 185
V+ K D V + + ++ L A P++ +S+ +G G+ L
Sbjct: 119 VVNKWDLVEKDEKTMKEFEKELRRKLPFLDYA------PIVFISALTGQGVDKL 166
>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 = 49.4 bits (119), Expect = 9e-08
Identities = 31/125 (24%), Positives = 57/125 (45%), Gaps = 21/125 (16%)
Query: 28 GRSNVGKSSMLNALTRQWGVVR---TSDKPGLT---QTINFFKLGTKLCLVDLPGYGFAY 81
GR NVGKS++ N LT + R SD PG+T + G + L+D G
Sbjct: 4 GRPNVGKSTLFNRLTGR----RDAIVSDTPGVTRDRKYGEAEWGGREFILIDTGGI---- 55
Query: 82 AKEEVKDAWEELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERSQTKYQVV 138
E + + ++E ++++ + ++D + G+ P D E+ + +S+ +V
Sbjct: 56 --EPDDEGISKEIRE--QAEIAIEEADVILFVVDGREGLTPADEEIAKYLRKSKKPVILV 111
Query: 139 LTKTD 143
+ K D
Sbjct: 112 VNKID 116
>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 = 49.3 bits (118), Expect = 1e-07
Identities = 37/172 (21%), Positives = 67/172 (38%), Gaps = 27/172 (15%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTIN--FFKLG---TKLCLVDLPGYG 78
I G NVGKS++LN L + T KPG T+ + K L+D G
Sbjct: 4 IVIVGDPNVGKSTLLNRLLGNKISI-TEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG-- 60
Query: 79 FAYAKEEVKDAWEELVKEYVSTRVSLKRVC----LLIDTKWGVKPRDHELISLMERSQTK 134
++ ++ + + Y S RV L++D + ++ + E+I E S
Sbjct: 61 --------QEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAE-SGVP 111
Query: 135 YQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLR 186
+V K D ++ + +P++ +S+++G I S
Sbjct: 112 IILVGNKIDLRD------AKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSAF 157
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 50.5 bits (122), Expect = 1e-07
Identities = 46/189 (24%), Positives = 72/189 (38%), Gaps = 56/189 (29%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVR----TSDKPG-----LTQTINFFKLGTKLCLVDL 74
+ AGR NVGKSS+LNAL +D G + + IN G L L+D
Sbjct: 218 VVIAGRPNVGKSSLLNALLG-----EERAIVTDIAGTTRDVIEEHINL--DGIPLRLIDT 270
Query: 75 PGY----------GFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHEL 124
G G ++E +++A V L++D + D E+
Sbjct: 271 AGIRETDDEVEKIGIERSREAIEEA---------------DLVLLVLDASEPLTEEDDEI 315
Query: 125 ISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRS 184
+ E VVL K D + + +PV+ +S+K+G GI
Sbjct: 316 LE--ELKDKPVIVVLNKAD-------------LTGEIDLEEENGKPVIRISAKTGEGIDE 360
Query: 185 LRTVLSKIA 193
LR + ++A
Sbjct: 361 LREAIKELA 369
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 50.0 bits (121), Expect = 1e-07
Identities = 35/134 (26%), Positives = 63/134 (47%), Gaps = 25/134 (18%)
Query: 21 LPEIAFAGRSNVGKSSMLNALTRQWGVVR---TSDKPGLT-----QTINFFKLGTKLCLV 72
P +A GR NVGKS++ N LT + R +D PG+T + LG + L+
Sbjct: 1 KPVVAIVGRPNVGKSTLFNRLTGK----RDAIVADTPGVTRDRIYGEAEW--LGREFILI 54
Query: 73 DLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLME 129
D G E D +E+ ++E ++++ + ++D + G+ P D E+ ++
Sbjct: 55 DTGGI------EPDDDGFEKQIRE--QAELAIEEADVILFVVDGRAGLTPADEEIAKILR 106
Query: 130 RSQTKYQVVLTKTD 143
+S +V+ K D
Sbjct: 107 KSNKPVILVVNKVD 120
Score = 44.7 bits (107), Expect = 1e-05
Identities = 24/73 (32%), Positives = 34/73 (46%), Gaps = 11/73 (15%)
Query: 11 KVSSSFPAPDLPE-------IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQ---TI 60
+ P + + IA GR NVGKSS++NAL + V+ SD G T+
Sbjct: 156 AILEELPEEEEEDEEDEPIKIAIIGRPNVGKSSLINALLGEERVI-VSDIAGTTRDSIDT 214
Query: 61 NFFKLGTKLCLVD 73
F + G K L+D
Sbjct: 215 PFERDGQKYTLID 227
>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 = 48.0 bits (115), Expect = 2e-07
Identities = 26/64 (40%), Positives = 30/64 (46%), Gaps = 7/64 (10%)
Query: 16 FPAPDLPEIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLT---QTINFFKLGTKLCLV 72
F A + I G NVGKSS++NAL V S PG T QTI L + L
Sbjct: 77 FSALNEATIGLVGYPNVGKSSLINALVGS-KKVSVSSTPGKTKHFQTIF---LEPGITLC 132
Query: 73 DLPG 76
D PG
Sbjct: 133 DCPG 136
>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 = 49.7 bits (120), Expect = 2e-07
Identities = 34/131 (25%), Positives = 59/131 (45%), Gaps = 25/131 (19%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVR---TSDKPGLT-----QTINFFKLGTKLCLVDLP 75
+A GR NVGKS++ N LT + R SD PG+T + G + L+D
Sbjct: 2 VAIVGRPNVGKSTLFNRLTGK----RDAIVSDTPGVTRDRKYGDAEW--GGREFILIDTG 55
Query: 76 GYGFAYAKEEVKDAWEELVKEYVSTRVSLK---RVCLLIDTKWGVKPRDHELISLMERSQ 132
G EE D ++ ++E ++++ + ++D + G+ P D E+ + +S
Sbjct: 56 GI------EEDDDGLDKQIRE--QAEIAIEEADVILFVVDGREGLTPEDEEIAKWLRKSG 107
Query: 133 TKYQVVLTKTD 143
+V K D
Sbjct: 108 KPVILVANKID 118
Score = 48.2 bits (116), Expect = 7e-07
Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 12/74 (16%)
Query: 11 KVSSSFPAPDLPE--------IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQ---T 59
+ P + E IA GR NVGKS+++NAL + V+ SD G T+
Sbjct: 154 AILELLPEEEEEEEEEDGPIKIAIIGRPNVGKSTLVNALLGEERVI-VSDIAGTTRDSID 212
Query: 60 INFFKLGTKLCLVD 73
I F + G K L+D
Sbjct: 213 IPFERNGKKYTLID 226
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 48.3 bits (116), Expect = 5e-07
Identities = 42/173 (24%), Positives = 77/173 (44%), Gaps = 17/173 (9%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLT----QTINFFKLGTKLCLVDLPGYGF 79
+A GR NVGKS++LNAL Q + S KP T + I ++ VD PG
Sbjct: 9 VAIIGRPNVGKSTLLNALVGQ-KISIVSPKPQTTRNRIRGIVTTD-NAQIIFVDTPGI-- 64
Query: 80 AYAKEEVKDAWEE-LVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKYQVV 138
+ K A E + K S + + ++D G P D ++ +++++T +V
Sbjct: 65 ----HKPKHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLKKTKTPVILV 120
Query: 139 LTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSK 191
+ K D V P +++ LK + ++ +S+ G + +L ++ +
Sbjct: 121 VNKIDKVKP---KTVLLKLIAFLKKLLP-FKEIVPISALKGDNVDTLLEIIKE 169
>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 = 46.1 bits (110), Expect = 2e-06
Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 10/62 (16%)
Query: 26 FAGRSNVGKSSMLNALTRQWGVVR----------TSDKPGLTQTINFFKLGTKLCLVDLP 75
G +NVGKS+++NAL + G S PG T + LG L D P
Sbjct: 130 VVGATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPGTTLGLIKIPLGEGKKLYDTP 189
Query: 76 GY 77
G
Sbjct: 190 GI 191
Score = 33.8 bits (78), Expect = 0.031
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 137 VVLTKTDTVFP-IDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIARF 195
+V K D + + R +++ LK ++ V++VS+K G G+ L + +I +
Sbjct: 65 LVGNKIDLLPKDVKPNRLKQWVKKRLKIGGLKIKDVILVSAKKGWGVEEL---IEEIKKL 121
Query: 196 AK 197
AK
Sbjct: 122 AK 123
>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 = 45.2 bits (108), Expect = 2e-06
Identities = 47/189 (24%), Positives = 81/189 (42%), Gaps = 55/189 (29%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVR----TSDKPG-----LTQTINFFKLGTKLCLVDL 74
+ AG+ NVGKSS+LNAL R SD G + + I+ G + L+D
Sbjct: 6 VVIAGKPNVGKSSLLNALAG-----RDRAIVSDIAGTTRDVIEEEIDLG--GIPVRLIDT 58
Query: 75 PGY----------GFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHEL 124
G G A+E +++A +L V L++D G+ D E+
Sbjct: 59 AGLRETEDEIEKIGIERAREAIEEA--DL-------------VLLVVDASEGLDEEDLEI 103
Query: 125 ISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRS 184
+ L ++ VVL K+D + ++ + +P++ +S+K+G GI
Sbjct: 104 LEL--PAKKPVIVVLNKSDL------------LSDAEGISELNGKPIIAISAKTGEGIDE 149
Query: 185 LRTVLSKIA 193
L+ L ++A
Sbjct: 150 LKEALLELA 158
>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 = 45.2 bits (108), Expect = 3e-06
Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 11/70 (15%)
Query: 24 IAFAGRSNVGKSSMLNALT--RQWGVVRTSDKPGLTQTIN--FFKL-GTKLCLVDLPG-Y 77
IA G NVGK+++ NALT RQ + PG+T FK G ++ +VDLPG Y
Sbjct: 3 IALVGNPNVGKTTLFNALTGARQ----HVGNWPGVTVEKKEGTFKYKGYEIEIVDLPGTY 58
Query: 78 GF-AYAKEEV 86
Y++EE
Sbjct: 59 SLSPYSEEEK 68
>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 = 45.9 bits (109), Expect = 4e-06
Identities = 46/168 (27%), Positives = 73/168 (43%), Gaps = 24/168 (14%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTI---NFFKLGTKLCLVDLPGYGFA 80
+A G NVGKSS+LNAL +Q + SD G T+ + +F G + L+D G
Sbjct: 206 LAIVGSPNVGKSSLLNALLKQDRAI-VSDIKGTTRDVVEGDFELNGILIKLLDTAGI--- 261
Query: 81 YAKEEVKDAWEELVKEYVSTRVSLKR---VCLLIDTKWGVKPRDHELISLMERSQTKYQV 137
E D E L E + ++K+ V ++D + D LI + +S+ + +
Sbjct: 262 ---REHADFVERLGIE--KSFKAIKQADLVIYVLDASQPLTKDD-FLIIDLNKSKKPFIL 315
Query: 138 VLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSL 185
VL K ID+ +++ S K NS + K A + L
Sbjct: 316 VLNK------IDLKINSLEFFVSSKVLNSSN--LSAKQLKIKALVDLL 355
>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 = 45.3 bits (108), Expect = 6e-06
Identities = 21/56 (37%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 26 FAGRSNVGKSSMLNALTRQWG----VVRTSDKPGLTQTINFFKLGTKLCLVDLPGY 77
G +NVGKSS++N L +Q V+ TS PG T + L L D PG
Sbjct: 159 VVGVTNVGKSSLINKLLKQNNGDKDVITTSPFPGTTLDLIEIPLDDGHSLYDTPGI 214
>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 = 44.2 bits (105), Expect = 6e-06
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTS---DKPGLTQTINFFKLGTKLCLVDLPG 76
+ G VGKSS++NAL + TS PG T+ I ++ +K+ L+D PG
Sbjct: 102 VGVVGYPKVGKSSIINALKGR-HSASTSPIPGSPGYTKGIQLVRIDSKIYLIDTPG 156
Score = 30.4 bits (69), Expect = 0.32
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 120 RDHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSG 179
R +L + K +VL K D V P +V + ++ ES PV+ VS++
Sbjct: 28 RSRKLERMALELGKKLIIVLNKADLV-PREVLEKWKEVFESEGL------PVVYVSARER 80
Query: 180 AGIRSLRTVLSKIA 193
G R LR + ++A
Sbjct: 81 LGTRILRRTIKELA 94
>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 = 45.6 bits (108), Expect = 6e-06
Identities = 40/180 (22%), Positives = 76/180 (42%), Gaps = 27/180 (15%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKP-----GLTQTINFFKL---GTKLCLVDLP 75
IA AG + GK+++L ALT + P G+T + F +L +D+P
Sbjct: 3 IATAGHVDHGKTTLLKALTG----IAADRLPEEKKRGMTIDLGFAYFPLPDYRLGFIDVP 58
Query: 76 GYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKY 135
G+ E+ + ++ + L++D GV + E +++++ +
Sbjct: 59 GH-------------EKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIPH 105
Query: 136 Q-VVLTKTDTVFPIDVARRAMQIEESL-KANNSLVQPVMMVSSKSGAGIRSLRTVLSKIA 193
VV+TK D V ++ R M +++ L + S+K+G GI L+ L +
Sbjct: 106 TIVVITKADRVNEEEIKRTEMFMKQILNSYIFLKNAKIFKTSAKTGQGIGELKKELKNLL 165
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 45.0 bits (107), Expect = 1e-05
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 22 PEIAFAGRSNVGKSSMLNALTRQWGV-VRTSDKPGLT---QTINFFKLGTKLCLVDLPG- 76
+A G NVGK+++ NALT G + + PG+T + G ++ +VDLPG
Sbjct: 4 LTVALVGNPNVGKTTLFNALT---GANQKVGNWPGVTVEKKEGKLKYKGHEIEIVDLPGT 60
Query: 77 YGFAYAKEEVKDAWEELVKE 96
Y E+ K A + L++
Sbjct: 61 YSLTAYSEDEKVARDFLLEG 80
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 44.7 bits (106), Expect = 1e-05
Identities = 40/175 (22%), Positives = 74/175 (42%), Gaps = 21/175 (12%)
Query: 24 IAFAGRSNVGKSSMLNALT-RQWGVVRTSDKPGLTQTINF--FKLGTK-LCLVDLPGYGF 79
I AG + GK+++L ALT + K G+T + F KL + +D+PG+
Sbjct: 3 IGTAGHIDHGKTTLLKALTGGVTDRLPEEKKRGITIDLGFYYRKLEDGVMGFIDVPGH-- 60
Query: 80 AYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKYQ-VV 138
+ + ++ + L++ G+ + E + +++ K +V
Sbjct: 61 -----------PDFISNLLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGIKNGIIV 109
Query: 139 LTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIA 193
LTK D V D AR +I++ L + + S+K+G GI L+ L +
Sbjct: 110 LTKADRV---DEARIEQKIKQILADLSLANAKIFKTSAKTGRGIEELKNELIDLL 161
>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 = 42.9 bits (102), Expect = 4e-05
Identities = 18/46 (39%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 31 NVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPG 76
NVGKS+++N L + V + ++PG+T+ + KL L L+D PG
Sbjct: 128 NVGKSTLINRLAGK-KVAKVGNRPGVTKGQQWIKLSDGLELLDTPG 172
>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 = 42.1 bits (100), Expect = 4e-05
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 8/57 (14%)
Query: 24 IAFAGRSNVGKSSMLNALTRQ----WGVVRTSDKPGLTQTINFFKLGTKLCLVDLPG 76
+A G + GKS++LNAL + GV T+ T+ + L + LVD PG
Sbjct: 3 LAVVGEFSAGKSTLLNALLGEEVLPTGVTPTTAVI----TVLRYGLLKGVVLVDTPG 55
>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 = 40.9 bits (97), Expect = 8e-05
Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 11/68 (16%)
Query: 25 AFAGRSNVGKSSMLNALT--RQWGVVRTSDKPGLT--QTINFFKLGTKLC-LVDLPG-YG 78
A G NVGK+++ NALT RQ + + PG+T + FKLG K +VDLPG Y
Sbjct: 1 ALVGNPNVGKTTLFNALTGARQ----KVGNWPGVTVEKKEGEFKLGGKEIEIVDLPGTYS 56
Query: 79 F-AYAKEE 85
Y+++E
Sbjct: 57 LTPYSEDE 64
>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 = 39.7 bits (93), Expect = 2e-04
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 6/56 (10%)
Query: 25 AFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINF----FKLGTKLCLVDLPG 76
G NVGKS++L+ALT V + P T N F G + ++DLPG
Sbjct: 1 GLVGLPNVGKSTLLSALTS--AKVEIASYPFTTLEPNVGVFEFGDGVDIQIIDLPG 54
>gnl|CDD|206753 cd04178, Nucleostemin_like, A circularly permuted subfamily of the
Ras GTPases. Nucleostemin (NS) is a nucleolar protein
that functions as a regulator of cell growth and
proliferation in stem cells and in several types of
cancer cells, but is not expressed in the differentiated
cells of most mammalian adult tissues. NS shuttles
between the nucleolus and nucleoplasm bidirectionally at
a rate that is fast and independent of cell type.
Lowering GTP levels decreases the nucleolar retention of
NS, and expression of NS is abruptly down-regulated
during differentiation prior to terminal cell division.
Found only in eukaryotes, NS consists of an N-terminal
basic domain, a coiled-coil domain, a GTP-binding
domain, an intermediate domain, and a C-terminal acidic
domain. Experimental evidence indicates that NS uses its
GTP-binding property as a molecular switch to control
the transition between the nucleolus and nucleoplasm,
and this process involves interaction between the basic,
GTP-binding, and intermediate domains of the protein.
Length = 171
Score = 39.9 bits (94), Expect = 2e-04
Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 31 NVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGY 77
NVGKSS++N+L R PG+T+++ L + L+D PG
Sbjct: 126 NVGKSSVINSLKRS-RACNVGATPGVTKSMQEVHLDKHVKLLDSPGV 171
>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 = 38.9 bits (91), Expect = 4e-04
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPG 76
+ G NVGKSS +NAL ++ ++ PG T+ KL ++ L D PG
Sbjct: 94 VGVVGLPNVGKSSFINALLNKFK-LKVGSIPGTTKLQQDVKLDKEIYLYDTPG 145
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 39.4 bits (93), Expect = 5e-04
Identities = 19/46 (41%), Positives = 31/46 (67%), Gaps = 1/46 (2%)
Query: 31 NVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPG 76
NVGKS+++N L + + +T ++PG+T+ + KLG L L+D PG
Sbjct: 131 NVGKSTLINRLAGK-KIAKTGNRPGVTKAQQWIKLGKGLELLDTPG 175
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 38.3 bits (90), Expect = 6e-04
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 10/82 (12%)
Query: 24 IAFAGRSNVGKSSMLNALT---RQW-GVVRTSDKPG--LTQTINFFKLGTKLCLVDLPG- 76
AG+S VGKS++LNAL G + G T + F L L+D PG
Sbjct: 38 SVLAGQSGVGKSTLLNALLPELDLRTGEISEKLGRGRHTTTHVELFPLPGGGLLIDTPGF 97
Query: 77 --YGFAY-AKEEVKDAWEELVK 95
G + EE+ + + E +
Sbjct: 98 RELGLWHLDPEELAEYFPEFRE 119
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 39.4 bits (92), Expect = 7e-04
Identities = 19/42 (45%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 4 LEFFAAAKVSSSFPAPD-LPEIAFAGRSNVGKSSMLNALTRQ 44
L+ A+ +S F P L +A GR NVGKSS+LN LT +
Sbjct: 432 LDSLKVAEKTSGFLTPSGLRRVALVGRPNVGKSSLLNQLTHE 473
Score = 34.0 bits (78), Expect = 0.038
Identities = 34/125 (27%), Positives = 60/125 (48%), Gaps = 13/125 (10%)
Query: 24 IAFAGRSNVGKSSMLNA-LTRQWGVVRTSDKPGLTQ---TINFFKLGTKLCLVDLPGYGF 79
+A GR NVGKS+++N L R+ VV D PG+T+ + + GT LVD G+
Sbjct: 278 VAIVGRPNVGKSTLVNRILGRREAVVE--DTPGVTRDRVSYDAEWAGTDFKLVDTGGW-- 333
Query: 80 AYAKEEVKDAWEELVKEYVSTRVSLKR-VCLLIDTKWGVKPRDHELISLMERSQTKYQVV 138
+ +V+ + + VSL V ++D + G+ D ++ ++ R+ +
Sbjct: 334 ---EADVEGIDSAIASQ-AQIAVSLADAVVFVVDGQVGLTSTDERIVRMLRRAGKPVVLA 389
Query: 139 LTKTD 143
+ K D
Sbjct: 390 VNKID 394
>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 = 9e-04
Identities = 29/132 (21%), Positives = 54/132 (40%), Gaps = 14/132 (10%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLT----QTINFFKLGTKLCLVDLPGYGF 79
+A GR NVGKS++LN L Q + TS K T I +++ +D PG+
Sbjct: 3 VAILGRPNVGKSTLLNQLHGQ-KISITSPKAQTTRNRISGI-HTTGASQIIFIDTPGF-- 58
Query: 80 AYAKEEVKDAWEELVKEYVSTRVSLKRVCLLID-TKWGVKPRDHELISLMERSQTKYQVV 138
E+ ++KE S + + ++D +W +++ ++ + +
Sbjct: 59 ---HEKKHSLNRLMMKEARSAIGGVDLILFVVDSDQW--NGDGEFVLTKLQNLKRPVVLT 113
Query: 139 LTKTDTVFPIDV 150
K D F +
Sbjct: 114 RNKLDNKFKDKL 125
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 38.4 bits (90), Expect = 0.001
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 10/79 (12%)
Query: 25 AFAGRSNVGKSSMLNAL----TRQWGVVRTSDKPG--LTQTINFFKLGTKLCLVDLPGY- 77
G+S VGKS+++NAL ++ G + G T + F L ++D PG+
Sbjct: 168 VLLGQSGVGKSTLINALLPELNQKTGEISEKLGRGRHTTTHVELFPLPGGGWIIDTPGFR 227
Query: 78 --GFAYA-KEEVKDAWEEL 93
G A+ E++ A+ E
Sbjct: 228 SLGLAHLEPEDLVQAFPEF 246
>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 = 37.3 bits (87), Expect = 0.002
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPG 76
+ F G NVGKSS++N L R V + + PG T+ + L ++ L+D PG
Sbjct: 105 VGFIGYPNVGKSSVINTL-RSKKVCKVAPIPGETKVWQYITLMKRIYLIDCPG 156
>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 = 37.1 bits (87), Expect = 0.002
Identities = 41/186 (22%), Positives = 61/186 (32%), Gaps = 41/186 (22%)
Query: 24 IAFAGRSNVGKSSMLNALT--------RQWGVVRTSDKP------GLTQTINFFKLGTKL 69
I G + GK+++ +AL R DK G+T I TK
Sbjct: 6 IGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVSFETKK 65
Query: 70 C---LVDLPGYGFAYAKEEVKDAWEELVKE-YVSTRVSLKRVCLLIDTKWGVKPRDHELI 125
++D PG+ + KE L++D GV P+ E +
Sbjct: 66 RLINIIDTPGH-------------VDFTKEMIRGASQ-ADGAILVVDAVEGVMPQTREHL 111
Query: 126 SLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEE------SLKANNSLVQPVMMVSSKSG 179
L + V + K D V D A +EE PV+ S+ +G
Sbjct: 112 LLAKTLGVPIIVFINKIDRV---DDAELEEVVEEISRELLEKYGFGGETVPVVPGSALTG 168
Query: 180 AGIRSL 185
GI L
Sbjct: 169 EGIDEL 174
>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 = 36.6 bits (85), Expect = 0.004
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 27 AGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGFAYAKEEV 86
A R +G S+M + LT +R K L + I+ + LG + V+ A EEV
Sbjct: 95 ALRGVIGDSTMDDILTEGRSQIREDTKERLNEIIDNYDLGITVTDVNFQS---ARPPEEV 151
Query: 87 KDAWEELVK 95
K+A+++++
Sbjct: 152 KEAFDDVII 160
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 36.3 bits (84), Expect = 0.005
Identities = 28/92 (30%), Positives = 35/92 (38%), Gaps = 10/92 (10%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKL---GTKLCLVDLPGYGFA 80
+ G + GKSS++NAL Q V S T +L G L L D PG G
Sbjct: 42 VLLMGATGAGKSSLINALF-QGEVKEVSKVGVGTDITTRLRLSYDGENLVLWDTPGLG-- 98
Query: 81 YAKEEVKDAWEELVKEYVSTRVSLKRVCLLID 112
+ KD E + Y L V LI
Sbjct: 99 ----DGKDKDAEHRQLYRDYLPKLDLVLWLIK 126
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 36.5 bits (85), Expect = 0.005
Identities = 21/43 (48%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 4 LEFFAAAKVS-SSFPA--PDLPEIAFAGRSNVGKSSMLNALTR 43
LEF A+ PA PDLP I AG NVGKSS++ LT
Sbjct: 148 LEFLRKARDHLKKLPAIDPDLPTIVVAGYPNVGKSSLVRKLTT 190
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 35.2 bits (82), Expect = 0.014
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 26 FAGRSNVGKSSMLNAL 41
F G+S VGKSS++NAL
Sbjct: 210 FVGQSGVGKSSLINAL 225
Score = 33.7 bits (78), Expect = 0.040
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 137 VVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLS-KIARF 195
+VL K D +D RA + E L ++ V+MVSS +G G+ L L+ +I+ F
Sbjct: 155 IVLNKIDL---LDDEGRA-FVNEQLDIYRNIGYRVLMVSSHTGEGLEELEAALTGRISIF 210
Query: 196 A 196
Sbjct: 211 V 211
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 34.9 bits (81), Expect = 0.019
Identities = 21/51 (41%), Positives = 31/51 (60%), Gaps = 4/51 (7%)
Query: 8 AAAKVSSSFPAPDLPEIAFAGRSNVGKSSMLN-ALTRQWGVVRTSDKPGLT 57
A++ ++ P LP +A GR NVGKS+++N L R+ VV D PG+T
Sbjct: 26 DLAELEAAEGGP-LPVVAVVGRPNVGKSTLVNRILGRREAVVE--DVPGVT 73
Score = 34.6 bits (80), Expect = 0.025
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 11 KVSSSFPAPDLP-EIAFAGRSNVGKSSMLNALTRQWGVV 48
+V A P +A G+ NVGKSS+LN L + V
Sbjct: 200 EVPRVGSASGGPRRVALVGKPNVGKSSLLNKLAGEERSV 238
>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 = 35.1 bits (81), Expect = 0.020
Identities = 24/63 (38%), Positives = 33/63 (52%), Gaps = 7/63 (11%)
Query: 28 GRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTK---LCLVDLPG-YGF-AYA 82
G NVGKS++ NALT + PG+T KLG + + +VDLPG Y ++
Sbjct: 1 GNPNVGKSTLFNALTG--ANQTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTFS 58
Query: 83 KEE 85
EE
Sbjct: 59 LEE 61
>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 = 34.3 bits (80), Expect = 0.023
Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 10/82 (12%)
Query: 24 IAFAGRSNVGKSSMLNALT---RQW-GVVRTSDKPGL--TQTINFFKLGTKLCLVDLPG- 76
G+S VGKS++LNAL G + G T F L ++D PG
Sbjct: 88 SVLVGQSGVGKSTLLNALLPELVLATGEISEKLGRGRHTTTHRELFPLPGGGLIIDTPGF 147
Query: 77 --YGFAY-AKEEVKDAWEELVK 95
G + EE+ + + E +
Sbjct: 148 RELGLLHIDPEELAEYFPEFEE 169
Score = 33.9 bits (79), Expect = 0.028
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 137 VVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSK 191
+VL K D V ++ E L PV+ VS+K+G G+ LR +L
Sbjct: 38 IVLNKADLVDDEELEELLEIYE-------KLGYPVLAVSAKTGEGLDELRELLKG 85
>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 = 0.029
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 20 DLPEIAFAGRSNVGKSSMLNALTR 43
+P +A G +N GKS++ NALT
Sbjct: 40 GVPTVALVGYTNAGKSTLFNALTG 63
>gnl|CDD|236865 PRK11160, PRK11160, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 574
Score = 33.3 bits (77), Expect = 0.079
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 4/35 (11%)
Query: 24 IAFAGRSNVGKSSMLNALTRQW----GVVRTSDKP 54
+A GR+ GKS++L LTR W G + + +P
Sbjct: 369 VALLGRTGCGKSTLLQLLTRAWDPQQGEILLNGQP 403
>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 = 33.0 bits (76), Expect = 0.081
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 24 IAFAGRSNVGKSSMLNALT 42
I G+ NVGKS+ NA T
Sbjct: 1 IGLVGKPNVGKSTFFNAAT 19
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 32.5 bits (75), Expect = 0.10
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 22 PEIAFAGRSNVGKSSMLNALTR 43
+I G NVGKS++ NALT+
Sbjct: 3 LKIGIVGLPNVGKSTLFNALTK 24
>gnl|CDD|218401 pfam05049, IIGP, Interferon-inducible GTPase (IIGP).
Interferon-inducible GTPase (IIGP) is thought to play a
role in in intracellular defence. IIGP is predominantly
associated with the Golgi apparatus and also localises
to the endoplasmic reticulum and exerts a distinct role
in IFN-induced intracellular membrane trafficking or
processing.
Length = 375
Score = 32.5 bits (74), Expect = 0.11
Identities = 23/65 (35%), Positives = 29/65 (44%), Gaps = 13/65 (20%)
Query: 23 EIAFAGRSNVGKSSMLNAL---------TRQWGVVRTSDKPGLTQTINFFKLGTKLCLVD 73
+IA G S GKSS +NAL + GVV T+ K +F + L D
Sbjct: 37 KIAVTGDSGNGKSSFINALRGIGHEEDGSAPTGVVETTMKRTPYSHPHF----PNVVLWD 92
Query: 74 LPGYG 78
LPG G
Sbjct: 93 LPGLG 97
>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 = 32.3 bits (74), Expect = 0.11
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 22 PEIAFAGRSNVGKSSMLNAL-TRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYG 78
P + G S+ GK+++ L T + TS +P + + G KL LVD+PG+
Sbjct: 1 PTVLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKGKKLTLVDVPGHE 58
>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 = 0.13
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 12/70 (17%)
Query: 126 SLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSL 185
L E+ + VVL K D + ++ +++E+L +PV +S+ +G G+ L
Sbjct: 270 ELAEKPRI---VVLNKIDLLDEEELEELLKELKEALG------KPVFPISALTGEGLDEL 320
Query: 186 RTVLSKIARF 195
L +A
Sbjct: 321 ---LYALAEL 327
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 32.1 bits (74), Expect = 0.13
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 26 FAGRSNVGKSSMLNAL 41
AG+S VGKS++LNAL
Sbjct: 169 LAGQSGVGKSTLLNAL 184
>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 = 32.1 bits (74), Expect = 0.15
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 20 DLPEIAFAGRSNVGKSSMLNALTR 43
D+P +A G +N GKS++ NALT
Sbjct: 188 DVPTVALVGYTNAGKSTLFNALTG 211
>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 = 31.7 bits (73), Expect = 0.16
Identities = 39/174 (22%), Positives = 65/174 (37%), Gaps = 43/174 (24%)
Query: 27 AGRSNVGKSSMLNAL------TRQWGVVRTSDKPGLTQTI--------NFFKLGTKLCLV 72
G S +GKS+ +N L ++ + N KL KL ++
Sbjct: 10 VGESGLGKSTFINTLFGTKLYPSKYPPAPGEHITKTVEIKISKAELEENGVKL--KLTVI 67
Query: 73 DLPGYGFAYAKEEVKDAWEELVK-------EYVSTRVSLKRVCLLIDTK----------- 114
D PG+G D W+ +V Y+ + R + DT+
Sbjct: 68 DTPGFGDNINNS---DCWKPIVDYIDDQFESYLREESRINRNRRIPDTRVHCCLYFIPPT 124
Query: 115 -WGVKPRDHELISLMERSQTKYQV--VLTKTDTVFPIDVARRAMQIEESLKANN 165
G+KP D I M++ K + V+ K DT+ P ++ +I E ++ NN
Sbjct: 125 GHGLKPLD---IEFMKKLSKKVNIIPVIAKADTLTPEELTEFKKRIMEDIEENN 175
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 31.6 bits (72), Expect = 0.16
Identities = 25/95 (26%), Positives = 41/95 (43%), Gaps = 16/95 (16%)
Query: 22 PEIAFAGRSNVGKSSMLNALTRQWGVVR---TSDKPGLTQTINFFKLGTKLCLVDLPGYG 78
P + AG + GK+S+ LT G V+ TS +P K G L+D PG+
Sbjct: 4 PAVIIAGLCDSGKTSLFTLLTT--GTVKKTVTSQEPSAAYKYMLHK-GFSFTLIDFPGH- 59
Query: 79 FAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDT 113
VK + + E + SL+ + ++D+
Sbjct: 60 -------VKLRQK--LLETIKDSSSLRGIVFVVDS 85
>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 = 31.6 bits (72), Expect = 0.17
Identities = 25/70 (35%), Positives = 32/70 (45%), Gaps = 12/70 (17%)
Query: 26 FAGRSNVGKSSMLNALTRQWG--VVRTSDKPGL-----TQTINFFKLGTKLCLVDLPGY- 77
FAG+S VGKSS++NAL V S K GL T F G + D PG+
Sbjct: 125 FAGQSGVGKSSLINALDPSVKQQVNDISSKLGLGKHTTTHVELFHFHGGLIA--DTPGFN 182
Query: 78 --GFAYAKEE 85
G + + E
Sbjct: 183 EFGLWHLEPE 192
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 31.9 bits (73), Expect = 0.17
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 20 DLPEIAFAGRSNVGKSSMLNALT 42
+P +A G +N GKS++ NALT
Sbjct: 191 GIPLVALVGYTNAGKSTLFNALT 213
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 31.5 bits (72), Expect = 0.23
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 9/66 (13%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGV-VRTSDKPGLTQTINFFKL---GTKLCLVDLPG--Y 77
+A G +VGKS++LN LT +D P T L G ++ L+DLPG
Sbjct: 66 VALVGFPSVGKSTLLNKLT---NTKSEVADYPFTTLEPVPGMLEYKGAQIQLLDLPGIIE 122
Query: 78 GFAYAK 83
G + +
Sbjct: 123 GASSGR 128
>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 = 31.4 bits (72), Expect = 0.25
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGV-VRTSDKPGLTQTINFFKL---GTKLCLVDLPG 76
+A G +VGKS++L+ LT + T T + G K+ L+DLPG
Sbjct: 3 VALVGFPSVGKSTLLSKLT---NTKSEVAAYEFTTLTCVPGVMEYKGAKIQLLDLPG 56
>gnl|CDD|178633 PLN03084, PLN03084, alpha/beta hydrolase fold protein; Provisional.
Length = 383
Score = 31.4 bits (71), Expect = 0.26
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 74 LPGYGFAYAKEEVKDAWEELVKEYVSTRVSL 104
PGYGF Y +E + E L+ E S +VSL
Sbjct: 171 QPGYGFNYTLDEYVSSLESLIDELKSDKVSL 201
>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 = 31.0 bits (71), Expect = 0.26
Identities = 12/17 (70%), Positives = 14/17 (82%)
Query: 27 AGRSNVGKSSMLNALTR 43
AG NVGKSS++N LTR
Sbjct: 6 AGYPNVGKSSLVNKLTR 22
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 31.4 bits (72), Expect = 0.27
Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 24 IAFAGRSNVGKSSMLNALTRQ----WGVVRTSDKPG--LTQTINFFKLGTKLCLVDLPG 76
+A G S VGKS+++NAL + G VR D G T L + L+D PG
Sbjct: 198 VALLGSSGVGKSTLVNALLGEEVQKTGAVREDDSKGRHTTTHRELHPLPSGGLLIDTPG 256
Score = 26.8 bits (60), Expect = 8.3
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 7/55 (12%)
Query: 137 VVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSK 191
+VLTK D + ++ A V PV+ VS+ G G+ L LS
Sbjct: 147 IVLTKADLCEDAEEKIAEVE------ALAPGV-PVLAVSALDGEGLDVLAAWLSG 194
>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 = 30.5 bits (70), Expect = 0.29
Identities = 19/83 (22%), Positives = 32/83 (38%), Gaps = 6/83 (7%)
Query: 116 GVKPRDHELISLMERSQTKYQVVLTKTD-----TVFPIDVARRAMQIEESLKANNSLVQP 170
GV P+ E I+ + + V + K D P V ++ + V
Sbjct: 85 GVMPQTIEAINHAKAANVPIIVAINKIDKPYGTEADPERVKNELSELGLVGEEWGGDVSI 144
Query: 171 VMMVSSKSGAGIRSLRTVLSKIA 193
V +S+K+G GI L + +A
Sbjct: 145 VP-ISAKTGEGIDDLLEAILLLA 166
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 31.2 bits (71), Expect = 0.35
Identities = 21/59 (35%), Positives = 26/59 (44%), Gaps = 11/59 (18%)
Query: 24 IAFAGRSNVGKSSMLNALT--RQ----WGVVRTSDKPGLTQTINFFKLGTKLCLVDLPG 76
I G N GK+++ N LT RQ W V K G F ++ LVDLPG
Sbjct: 6 IGLIGNPNSGKTTLFNQLTGARQRVGNWAGVTVERKEG-----QFSTTDHQVTLVDLPG 59
>gnl|CDD|215595 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 30.9 bits (70), Expect = 0.42
Identities = 12/17 (70%), Positives = 13/17 (76%)
Query: 27 AGRSNVGKSSMLNALTR 43
GR+ GKSSMLNAL R
Sbjct: 1271 VGRTGAGKSSMLNALFR 1287
>gnl|CDD|237728 PRK14490, PRK14490, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobB/MobA;
Provisional.
Length = 369
Score = 30.8 bits (70), Expect = 0.45
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 23 EIAFAGRSNVGKSSMLNALTRQ 44
EIAF G S GK++++ AL R+
Sbjct: 7 EIAFCGYSGSGKTTLITALVRR 28
>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 = 0.50
Identities = 27/125 (21%), Positives = 52/125 (41%), Gaps = 17/125 (13%)
Query: 70 CLVDLPGYGFAYAKEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLME 129
LVD PG+ L++ + + + L++D K G++ + E + + E
Sbjct: 71 TLVDCPGHA-------------SLIRTIIGGAQIIDLMLLVVDAKKGIQTQTAECLVIGE 117
Query: 130 RSQTKYQVVLTKTDTVFPIDVARRAMQ----IEESLKANNSLVQPVMMVSSKSGAGIRSL 185
VVL K D + + R+ + ++++L+ P++ VS+K G G L
Sbjct: 118 LLCKPLIVVLNKIDLIPEEERKRKIEKMKKRLQKTLEKTRLKDSPIIPVSAKPGEGEAEL 177
Query: 186 RTVLS 190
L
Sbjct: 178 GGELK 182
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 30.5 bits (70), Expect = 0.56
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 23 EIAFAGRSNVGKSSMLNALT 42
I G+ NVGKS+ NA T
Sbjct: 3 TIGLVGKPNVGKSTFFNAAT 22
>gnl|CDD|206690 cd04104, p47_IIGP_like, p47 GTPase family includes IGTP,
TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. The p47
GTPase family consists of several highly homologous
proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI,
LRG-47, and IIGP1. They are found in higher eukaryotes
where they play a role in immune resistance against
intracellular pathogens. p47 proteins exist at low
resting levels in mouse cells, but are strongly induced
by Type II interferon (IFN-gamma). ITGP is critical for
resistance to Toxoplasma gondii infection and in
involved in inhibition of Coxsackievirus-B3-induced
apoptosis. TGTP was shown to limit vesicular stomatitis
virus (VSV) infection of fibroblasts in vitro. IRG-47
is involved in resistance to T. gondii infection.
LRG-47 has been implicated in resistance to T. gondii,
Listeria monocytogenes, Leishmania, and mycobacterial
infections. IIGP1 has been shown to localize to the ER
and to the Golgi membranes in IFN-induced cells and
inflamed tissues. In macrophages, IIGP1 interacts with
hook3, a microtubule binding protein that participates
in the organization of the cis-Golgi compartment.
Length = 197
Score = 30.0 bits (68), Expect = 0.58
Identities = 23/65 (35%), Positives = 26/65 (40%), Gaps = 13/65 (20%)
Query: 23 EIAFAGRSNVGKSSMLNAL---------TRQWGVVRTSDKPGLTQTINFFKLGTKLCLVD 73
IA G S GKSS +NAL GVV T+ K F + L D
Sbjct: 3 NIAVTGESGAGKSSFINALRGIGHEEEGAAPTGVVETTMKRTPYPHPKF----PNVTLWD 58
Query: 74 LPGYG 78
LPG G
Sbjct: 59 LPGIG 63
>gnl|CDD|206738 cd08771, DLP_1, Dynamin_like protein family includes dynamins and
Mx proteins. The dynamin family of large
mechanochemical GTPases includes the classical dynamins
and dynamin-like proteins (DLPs) that are found
throughout the Eukarya. 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 interferon-induced Mx proteins that inhibit a
wide range of viruses by blocking an early stage of the
replication cycle. Dynamin oligomerizes into helical
structures around the neck of budding vesicles in a GTP
hydrolysis-dependent manner.
Length = 278
Score = 30.3 bits (69), Expect = 0.59
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 20 DLPEIAFAGRSNVGKSSMLNALT 42
DLP+I G + GKSS+L AL
Sbjct: 2 DLPQIVVVGDQSSGKSSVLEALV 24
>gnl|CDD|213214 cd03247, ABCC_cytochrome_bd, ATP-binding cassette domain of
CydCD, subfamily C. The CYD subfamily implicated in
cytochrome bd biogenesis. The CydC and CydD proteins
are important for the formation of cytochrome bd
terminal oxidase of E. coli and it has been proposed
that they were necessary for biosynthesis of the
cytochrome bd quinol oxidase and for periplasmic c-type
cytochromes. CydCD were proposed to determine a
heterooligomeric complex important for heme export into
the periplasm or to be involved in the maintenance of
the proper redox state of the periplasmic space. In
Bacillus subtilis, the absence of CydCD does not affect
the presence of halo-cytochrome c in the membrane and
this observation suggests that CydCD proteins are not
involved in the export of heme in this organism.
Length = 178
Score = 29.6 bits (67), Expect = 0.63
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 24 IAFAGRSNVGKSSMLNALTRQW 45
IA GRS GKS++L LT
Sbjct: 31 IALLGRSGSGKSTLLQLLTGDL 52
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 29.8 bits (68), Expect = 0.80
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 137 VVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSL 185
+V K D + + RA I E+L PV ++S+ SG G++ L
Sbjct: 280 LVFNKIDLLDEEEAEERAKAIVEALGW----EGPVYLISAASGLGVKEL 324
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 29.5 bits (66), Expect = 0.83
Identities = 16/73 (21%), Positives = 22/73 (30%), Gaps = 11/73 (15%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINF----FKLGTKLCLVDLPGYGF 79
I G VGK+++LN L ++ KL L D G
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDE-FPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQ-- 64
Query: 80 AYAKEEVKDAWEE 92
EE + E
Sbjct: 65 ----EEYRSLRPE 73
>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 = 29.3 bits (67), Expect = 0.92
Identities = 14/61 (22%), Positives = 21/61 (34%), Gaps = 28/61 (45%)
Query: 31 NVGKSSMLNALTR---------------QWGVVRTSDKPGLTQTINFFKLGTKLCLVDLP 75
N GKS++L+A++ GVVR D + D+P
Sbjct: 10 NAGKSTLLSAISNAKPKIADYPFTTLVPNLGVVRVDDGRSFV-------------IADIP 56
Query: 76 G 76
G
Sbjct: 57 G 57
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 30.0 bits (68), Expect = 0.93
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 137 VVLTKTDTVFPIDVARRA---MQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIA 193
V LTK D V D AR A Q++ L+ + + ++ G GI +LR L ++
Sbjct: 109 VALTKADRV---DEARIAEVRRQVKAVLREYGFAEAKLFVTAATEGRGIDALREHLLQLP 165
>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 = 29.7 bits (68), Expect = 0.93
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 31 NVGKSSMLNALTR 43
NVGKS++ NALT+
Sbjct: 8 NVGKSTLFNALTK 20
>gnl|CDD|185364 PRK15467, PRK15467, ethanolamine utilization protein EutP;
Provisional.
Length = 158
Score = 29.2 bits (65), Expect = 1.0
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 10/63 (15%)
Query: 21 LPEIAFAGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGFA 80
+ IAF G GK+++ NAL + + R TQ + F G +D PG F+
Sbjct: 1 MKRIAFVGAVGAGKTTLFNALQGNYTLARK------TQAVEFNDKGD----IDTPGEYFS 50
Query: 81 YAK 83
+ +
Sbjct: 51 HPR 53
>gnl|CDD|236799 PRK10930, PRK10930, FtsH protease regulator HflK; Provisional.
Length = 419
Score = 29.4 bits (66), Expect = 1.1
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 27 AGRSNVGKSSMLNALTRQWGVVRTSDKPGLTQTINFFKLGTKLCLVDLPGYGFAYAKEEV 86
A R +GK +M LT V+R+ + L +TI + +G L V+ A EEV
Sbjct: 191 ALRGVIGKYTMDRILTEGRTVIRSDTQRELEETIRPYDMGITLLDVNFQA---ARPPEEV 247
Query: 87 KDAWEELV 94
K A+++ +
Sbjct: 248 KAAFDDAI 255
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 29.4 bits (67), Expect = 1.1
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 4/34 (11%)
Query: 28 GRSNVGKSSMLNALTRQWG----VVRTSDKPGLT 57
G +NVGKS+++N + ++ V+ TS PG T
Sbjct: 167 GVTNVGKSTLINRIIKEITGEKDVITTSRFPGTT 200
>gnl|CDD|215640 PLN03232, PLN03232, ABC transporter C family member; Provisional.
Length = 1495
Score = 29.6 bits (66), Expect = 1.4
Identities = 14/29 (48%), Positives = 17/29 (58%)
Query: 15 SFPAPDLPEIAFAGRSNVGKSSMLNALTR 43
SF ++ GR+ GKSSMLNAL R
Sbjct: 1256 SFFVSPSEKVGVVGRTGAGKSSMLNALFR 1284
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 29.3 bits (67), Expect = 1.4
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 31 NVGKSSMLNALTR 43
NVGKS++ NALT+
Sbjct: 12 NVGKSTLFNALTK 24
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 28.8 bits (65), Expect = 1.9
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 4/35 (11%)
Query: 24 IAFAGRSNVGKSSMLNALTRQW----GVVRTSDKP 54
+A GRS GKS++L L W G + +
Sbjct: 367 VAILGRSGSGKSTLLQLLAGAWDPQQGSITLNGVE 401
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2;
Reviewed.
Length = 337
Score = 28.4 bits (64), Expect = 2.2
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 19 PDLPEIAFAGRSNVGKSSMLNALTRQ 44
P+LP + G GK++ + AL R+
Sbjct: 34 PNLPHLLVQGPPGSGKTAAVRALARE 59
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 28.5 bits (65), Expect = 2.2
Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 8/61 (13%)
Query: 137 VVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLSKIARFA 196
+VL K D + + R + L A PV ++S+ +G G+ L L +
Sbjct: 276 LVLNKIDLL--DEEEEREKRAALELAALG---GPVFLISAVTGEGLDEL---LRALWELL 327
Query: 197 K 197
+
Sbjct: 328 E 328
>gnl|CDD|233405 TIGR01418, PEP_synth, phosphoenolpyruvate synthase. Also called
pyruvate,water dikinase and PEP synthase. The member
from Methanococcus jannaschii contains a large intein.
This enzyme generates phosphoenolpyruvate (PEP) from
pyruvate, hydrolyzing ATP to AMP and releasing inorganic
phosphate in the process. The enzyme shows extensive
homology to other enzymes that use PEP as substrate or
product. This enzyme may provide PEP for
gluconeogenesis, for PTS-type carbohydrate transport
systems, or for other processes [Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 782
Score = 28.9 bits (65), Expect = 2.2
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 12 VSSSFPAPDLPEIAFAGRS----NV-GKSSMLNALTRQWG 46
V SS A DLP+ +FAG+ NV G+ +L + + W
Sbjct: 120 VRSSATAEDLPDASFAGQQETYLNVTGEEEVLEHVKKCWA 159
>gnl|CDD|239390 cd03116, MobB, Molybdenum is an essential trace element in the
form of molybdenum cofactor (Moco) which is associated
with the metabolism of nitrogen, carbon and sulfur by
redox active enzymes. In E. coli, the synthesis of Moco
involves genes from several loci: moa, mob, mod, moe
and mog. The mob locus contains mobA and mobB genes.
MobB catalyzes the attachment of the guanine
dinucleotide to molybdopterin.
Length = 159
Score = 28.0 bits (63), Expect = 2.4
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 22 PEIAFAGRSNVGKSSMLNALTRQ 44
I F G S GK+++L L
Sbjct: 2 KVIGFVGYSGSGKTTLLEKLIPA 24
>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 = 2.4
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 72 VDLPGYGFAYAKEEVKDAWEELVKEY 97
+ P Y F Y EE K W+++ K
Sbjct: 44 ENGPFYVFKYKDEEAKKIWKKINKRA 69
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 28.7 bits (65), Expect = 2.6
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 15 SFPAPDLPEIAFAGRSNVGKSSMLNAL 41
+F P IA G S GK+S+LNAL
Sbjct: 370 NFTLPAGQRIALVGPSGAGKTSLLNAL 396
>gnl|CDD|183016 PRK11176, PRK11176, lipid transporter ATP-binding/permease protein;
Provisional.
Length = 582
Score = 28.1 bits (63), Expect = 3.2
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 15 SFPAPDLPEIAFAGRSNVGKSSMLNALTR 43
+F P +A GRS GKS++ N LTR
Sbjct: 363 NFKIPAGKTVALVGRSGSGKSTIANLLTR 391
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 28.1 bits (63), Expect = 3.2
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 20 DLPEIAFAGRSNVGKSSMLNALT 42
D+P ++ G +N GKS++ N +T
Sbjct: 196 DVPTVSLVGYTNAGKSTLFNRIT 218
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 27.6 bits (62), Expect = 3.5
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 24 IAFAGRSNVGKSSMLNAL 41
IA G + GKSS+LNAL
Sbjct: 1 IAVVGDQSAGKSSVLNAL 18
>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 = 28.1 bits (63), Expect = 3.7
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 90 WEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTKYQVVLTKTDT 144
W L K+ R LK++ +T+W V P D + + + +R + + +L T T
Sbjct: 150 WLHLSKKQQKER--LKKLEKDPETRWRVTPEDWKQLKVYDRYRKLAERMLRYTST 202
>gnl|CDD|143438 cd07120, ALDH_PsfA-ACA09737, Pseudomonas putida aldehyde
dehydrogenase PsfA (ACA09737)-like. Included in this CD
is the aldehyde dehydrogenase (PsfA, locus ACA09737) of
Pseudomonas putida involved in furoic acid metabolism.
Transcription of psfA was induced in response to
2-furoic acid, furfuryl alcohol, and furfural.
Length = 455
Score = 28.1 bits (63), Expect = 3.7
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 8 AAAKVSSSFPAPDLPEIAFAGRSNVGKSSMLNA 40
AA V+S PD+ I+F G + G++ M A
Sbjct: 189 AAHLVAS----PDVDVISFTGSTATGRAIMAAA 217
>gnl|CDD|227321 COG4988, CydD, ABC-type transport system involved in cytochrome bd
biosynthesis, ATPase and permease components [Energy
production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 559
Score = 28.0 bits (63), Expect = 3.9
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 7 FAAAKVSSSFPAPDLPEIAFAGRSNVGKSSMLNAL 41
A + ++ + A L A G S GKS++LN L
Sbjct: 335 PALSDLNLTIKAGQL--TALVGASGAGKSTLLNLL 367
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 27.7 bits (62), Expect = 4.0
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 26 FAGRSNVGKSSMLNALT 42
AG S VGKSS++N L
Sbjct: 177 VAGPSGVGKSSLINRLI 193
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 27.9 bits (63), Expect = 4.2
Identities = 24/72 (33%), Positives = 32/72 (44%), Gaps = 9/72 (12%)
Query: 121 DHELISLMERSQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGA 180
D L L ER + VVL K D P D A + L+A PV VS+ S
Sbjct: 276 DLGLGDLAERPRL---VVLNKIDV--P-DARELAEFVRPELEARG---WPVFEVSAASRE 326
Query: 181 GIRSLRTVLSKI 192
G+R L L+++
Sbjct: 327 GLRELSFALAEL 338
>gnl|CDD|226469 COG3960, COG3960, Glyoxylate carboligase [General function
prediction only].
Length = 592
Score = 27.5 bits (61), Expect = 4.7
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 115 WGVKPRDHELISLMERSQTKYQ---VVLTKTDTVFPI 148
WG P DH L++ M QT ++ L +D VF I
Sbjct: 241 WGCIPDDHPLMAGMVGLQTSHRYGNATLLASDMVFGI 277
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 27.6 bits (62), Expect = 4.9
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 28 GRSNVGKSSMLNALTRQ 44
G NVGKS+ NAL +Q
Sbjct: 28 GLPNVGKSTTFNALCKQ 44
>gnl|CDD|197491 smart00053, DYNc, Dynamin, GTPase. Large GTPases that mediate
vesicle trafficking. Dynamin participates in the
endocytic uptake of receptors, associated ligands, and
plasma membrane following an exocytic event.
Length = 240
Score = 27.2 bits (60), Expect = 5.0
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 20 DLPEIAFAGRSNVGKSSMLNALT 42
DLP+IA G + GKSS+L
Sbjct: 25 DLPQIAVVGGQSAGKSSVLENFV 47
>gnl|CDD|239161 cd02760, MopB_Phenylacetyl-CoA-OR, The MopB_Phenylacetyl-CoA-OR CD
contains the phenylacetyl-CoA:acceptor oxidoreductase,
large subunit (PadB2), and other related proteins. The
phenylacetyl-CoA:acceptor oxidoreductase has been
characterized as a membrane-bound molybdenum-iron-sulfur
enzyme involved in anaerobic metabolism of phenylalanine
in the denitrifying bacterium Thauera aromatica. Members
of this CD belong to the molybdopterin_binding (MopB)
superfamily of proteins.
Length = 760
Score = 27.6 bits (61), Expect = 5.2
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 15 SFPAPDLPEIAFAGRSNVGKS 35
F P LP++ F R+N S
Sbjct: 507 KFELPTLPDVWFNYRTNPAIS 527
>gnl|CDD|213211 cd03244, ABCC_MRP_domain2, ATP-binding cassette domain 2 of
multidrug resistance-associated protein. The ABC
subfamily C is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resistance lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 221
Score = 27.1 bits (61), Expect = 5.9
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 24 IAFAGRSNVGKSSMLNALTR 43
+ GR+ GKSS+L AL R
Sbjct: 33 VGIVGRTGSGKSSLLLALFR 52
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 27.4 bits (62), Expect = 6.3
Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 23/49 (46%)
Query: 31 NVGKSSMLNALTR---------------QWGVVRTS--------DKPGL 56
NVGKS++L+ ++ GVV T D PGL
Sbjct: 168 NVGKSTLLSVVSNAKPKIANYHFTTLVPNLGVVETDDGRSFVMADIPGL 216
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They
belong to the subfamily C of the ATP-binding cassette
(ABC) superfamily of transport proteins. The ABCC
subfamily contains transporters with a diverse
functional spectrum that includes ion transport, cell
surface receptor, and toxin secretion activities. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains, each composed of six
transmembrane (TM) helices, and two nucleotide-binding
domains (NBD). ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 171
Score = 26.6 bits (60), Expect = 6.6
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 24 IAFAGRSNVGKSSMLNALTR 43
+A G S GKS++L L R
Sbjct: 31 VAIVGPSGSGKSTLLKLLLR 50
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 26.1 bits (57), Expect = 6.9
Identities = 18/112 (16%), Positives = 34/112 (30%), Gaps = 4/112 (3%)
Query: 24 IAFAGRSNVGKSSMLNALTRQWGVVRTS-DKPGLTQTINFFKLGTKLCLVDLPGYGFAYA 82
I G GKS++ L + G+ S D + + G +
Sbjct: 2 ILITGPPGSGKSTLAKKLAEKLGIPVISLDDLLREEGLAELDDGELDDIDIDLELLEEIL 61
Query: 83 KEEVKDAWEELVKEYVSTRVSLKRVCLLIDTKWGVKPRDHELISLMERSQTK 134
E K W + + L+ L++ + P L++R +
Sbjct: 62 DELAKQEWVIDGVRESTLELRLEEADLVV---FLDLPLPACRFRLLKRRLQR 110
>gnl|CDD|150287 pfam09570, RE_SinI, SinI restriction endonuclease. This family
includes the SinI (recognises and cleaves G^GWCC)
restriction endonuclease.
Length = 221
Score = 26.8 bits (59), Expect = 6.9
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 29 RSNVGKSSMLNALTRQWGVVRTSDKPGLTQTI 60
R +VG +N L + + R D P QTI
Sbjct: 46 RPSVGNDEGINILAQNFFDGRKPDFPAPPQTI 77
>gnl|CDD|218872 pfam06048, DUF927, Domain of unknown function (DUF927). Family of
bacterial proteins of unknown function. The C-terminal
half of this family contains a P-loop motif.
Length = 284
Score = 26.9 bits (60), Expect = 7.2
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 7/42 (16%)
Query: 12 VSSSFPAPDLPEIA-------FAGRSNVGKSSMLNALTRQWG 46
VS++ AP L + F G S+ GK++ L WG
Sbjct: 175 VSAALAAPLLKLLGAEGGGFHFVGDSSTGKTTALKLAASVWG 216
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 26.7 bits (60), Expect = 7.8
Identities = 15/59 (25%), Positives = 22/59 (37%), Gaps = 23/59 (38%)
Query: 21 LPEIAFAGRSNVGKSSMLNALTR---------------QWGVVRTSDK--------PGL 56
L ++ G N GKS++L+A++ GVVR PGL
Sbjct: 159 LADVGLVGLPNAGKSTLLSAVSAAKPKIADYPFTTLVPNLGVVRVDGGESFVVADIPGL 217
>gnl|CDD|112128 pfam03299, TF_AP-2, Transcription factor AP-2.
Length = 207
Score = 26.3 bits (58), Expect = 8.8
Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 12/62 (19%)
Query: 131 SQTKYQVVLTKTDTVFPIDVARRAMQIEESLKANNSLVQPVMMVSSKSGAGIRSLRTVLS 190
S +KY+V + +R + E L N SL+ V+ +KS G R LR L
Sbjct: 15 STSKYKVT---------VAEVQRRLSPPECL--NASLLGGVLR-RAKSKNGGRLLREKLD 62
Query: 191 KI 192
KI
Sbjct: 63 KI 64
>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 = 26.4 bits (59), Expect = 9.5
Identities = 8/29 (27%), Positives = 11/29 (37%)
Query: 73 DLPGYGFAYAKEEVKDAWEELVKEYVSTR 101
DL G +K+ W LV +Y
Sbjct: 137 DLSGLNAGTVLSVIKNDWTNLVDKYKILD 165
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
0.319 0.132 0.374
Gapped
Lambda K H
0.267 0.0608 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,650,327
Number of extensions: 867730
Number of successful extensions: 1266
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1219
Number of HSP's successfully gapped: 155
Length of query: 198
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 106
Effective length of database: 6,857,034
Effective search space: 726845604
Effective search space used: 726845604
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: 56 (25.6 bits)