RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18211
(127 letters)
>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 = 86.9 bits (216), Expect = 2e-22
Identities = 32/51 (62%), Positives = 39/51 (76%)
Query: 33 GDVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLK 83
GDVY+VG TNVGKSTL NA L+S+ K++A L+ R T SP PGTTL L+K
Sbjct: 126 GDVYVVGATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPGTTLGLIK 176
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 59.1 bits (144), Expect = 2e-11
Identities = 26/52 (50%), Positives = 33/52 (63%), Gaps = 7/52 (13%)
Query: 34 DVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEI 85
DVY+VG TNVGKSTL N ++ D+I TTS +PGTTL+ + EI
Sbjct: 162 DVYVVGVTNVGKSTLINRIIKE---ITGEKDVI---TTSRFPGTTLDKI-EI 206
>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 = 56.5 bits (137), Expect = 1e-10
Identities = 24/50 (48%), Positives = 33/50 (66%), Gaps = 6/50 (12%)
Query: 34 DVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLK 83
DVY+VG TNVGKS+L N L+ + + TTSP+PGTTL+L++
Sbjct: 156 DVYVVGVTNVGKSSLINKLLK------QNNGDKDVITTSPFPGTTLDLIE 199
>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 = 50.4 bits (121), Expect = 4e-09
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 11/54 (20%)
Query: 34 DVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEIIK 87
V LVG NVGKSTL NA + + S +PGTT + + ++
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAI-----------VSDYPGTTRDPILGVLG 43
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 46.6 bits (112), Expect = 4e-07
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 11/55 (20%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEIIKIQTV 91
+ G NVGKS+L NA L + RA + GTT ++++E I + +
Sbjct: 220 IAGRPNVGKSSLLNALLGEE-----------RAIVTDIAGTTRDVIEEHINLDGI 263
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 46.4 bits (111), Expect = 6e-07
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 11/55 (20%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEIIKIQTV 91
++G NVGKS+L NA L D RA + GTT ++++E I + +
Sbjct: 222 IIGRPNVGKSSLLNALLGRD-----------RAIVTDIAGTTRDVIEEDINLNGI 265
>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 = 6e-07
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 11/52 (21%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEIIKI 88
+ G NVGKS+L NA D RA S GTT ++++E I +
Sbjct: 8 IAGKPNVGKSSLLNALAGRD-----------RAIVSDIAGTTRDVIEEEIDL 48
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 45.1 bits (107), Expect = 2e-06
Identities = 21/56 (37%), Positives = 24/56 (42%), Gaps = 13/56 (23%)
Query: 34 DVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEIIKIQ 89
V +VG NVGKSTL N L A TS PGTT + IK+
Sbjct: 134 RVGVVGYPNVGKSTLINRLLGK-----------KVAKTSNRPGTTKG--IQWIKLD 176
>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 = 41.3 bits (98), Expect = 2e-05
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 11/44 (25%)
Query: 35 VYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTT 78
+ ++G NVGKS+L NA L + R S GTT
Sbjct: 5 IAIIGRPNVGKSSLLNALLGEE-----------RVIVSDIAGTT 37
>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 = 40.9 bits (97), Expect = 4e-05
Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 11/42 (26%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTT 78
++G NVGKSTL NA L + R S GTT
Sbjct: 177 IIGRPNVGKSTLVNALLGEE-----------RVIVSDIAGTT 207
Score = 36.7 bits (86), Expect = 0.002
Identities = 17/44 (38%), Positives = 18/44 (40%), Gaps = 11/44 (25%)
Query: 35 VYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTT 78
V +VG NVGKSTLFN A S PG T
Sbjct: 2 VAIVGRPNVGKSTLFNRLTGK-----------RDAIVSDTPGVT 34
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane
protein. The N terminus contains a P-loop motif
suggesting that iron transport may be ATP dependent.
Length = 159
Score = 39.4 bits (93), Expect = 9e-05
Identities = 18/42 (42%), Positives = 20/42 (47%), Gaps = 12/42 (28%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTT 78
LVG NVGK+TLFNA L +R WPG T
Sbjct: 2 LVGNPNVGKTTLFNA-----LTG-------ARQKVGNWPGVT 31
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 40.0 bits (95), Expect = 1e-04
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 11/42 (26%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTT 78
++G NVGKS+L NA L + R S GTT
Sbjct: 178 IIGRPNVGKSSLINALLGEE-----------RVIVSDIAGTT 208
Score = 34.6 bits (81), Expect = 0.008
Identities = 11/14 (78%), Positives = 12/14 (85%)
Query: 37 LVGCTNVGKSTLFN 50
+VG NVGKSTLFN
Sbjct: 6 IVGRPNVGKSTLFN 19
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 40.0 bits (94), Expect = 1e-04
Identities = 18/46 (39%), Positives = 21/46 (45%), Gaps = 12/46 (26%)
Query: 34 DVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTL 79
V LVG NVGK+TLFNA L + WPG T+
Sbjct: 5 TVALVGNPNVGKTTLFNA-----LTG-------ANQKVGNWPGVTV 38
>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 = 38.6 bits (91), Expect = 3e-04
Identities = 15/22 (68%), Positives = 16/22 (72%)
Query: 35 VYLVGCTNVGKSTLFNAFLQSD 56
V LVG TN GKSTLFNA +D
Sbjct: 192 VALVGYTNAGKSTLFNALTGAD 213
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 38.3 bits (90), Expect = 4e-04
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 11/55 (20%)
Query: 32 AGDVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEII 86
+G V ++G NVGKSTL NA + + + SP P TT N ++ I+
Sbjct: 6 SGFVAIIGRPNVGKSTLLNALVGQKI-----------SIVSPKPQTTRNRIRGIV 49
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 37.9 bits (89), Expect = 5e-04
Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 11/49 (22%)
Query: 30 SSAGDVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTT 78
+ + ++G NVGKS+L NA L + R S GTT
Sbjct: 176 TDPIKIAIIGRPNVGKSSLINAILGEE-----------RVIVSDIAGTT 213
Score = 36.8 bits (86), Expect = 0.002
Identities = 17/57 (29%), Positives = 21/57 (36%), Gaps = 11/57 (19%)
Query: 35 VYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEIIKIQTV 91
V +VG NVGKSTLFN A S PG T + + +
Sbjct: 6 VAIVGRPNVGKSTLFNRLTGR-----------RIAIVSDTPGVTRDRIYGDAEWLGR 51
>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 = 37.5 bits (88), Expect = 5e-04
Identities = 18/44 (40%), Positives = 21/44 (47%), Gaps = 12/44 (27%)
Query: 35 VYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTT 78
+ LVG NVGK+TLFNA L +R WPG T
Sbjct: 3 IALVGNPNVGKTTLFNA-----LTG-------ARQHVGNWPGVT 34
>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 = 36.6 bits (86), Expect = 8e-04
Identities = 16/42 (38%), Positives = 17/42 (40%), Gaps = 11/42 (26%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTT 78
+VG NVGKSTLFN A S PG T
Sbjct: 2 IVGRPNVGKSTLFNRLTGR-----------RDAIVSDTPGVT 32
>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 = 36.8 bits (86), Expect = 9e-04
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 11/44 (25%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLN 80
+ G NVGKS+L NA L + SP PGTT +
Sbjct: 2 IFGRPNVGKSSLLNALLGQN-----------VGIVSPIPGTTRD 34
>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 = 37.1 bits (87), Expect = 0.001
Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 11/42 (26%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTT 78
+ G N GKS+L NA D+ A S PGTT
Sbjct: 11 IFGRRNAGKSSLINALTGQDI-----------AIVSDVPGTT 41
>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 = 36.7 bits (86), Expect = 0.001
Identities = 15/23 (65%), Positives = 17/23 (73%)
Query: 35 VYLVGCTNVGKSTLFNAFLQSDL 57
V LVG TN GKSTLFNA +D+
Sbjct: 44 VALVGYTNAGKSTLFNALTGADV 66
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 37.1 bits (86), Expect = 0.001
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 11/54 (20%)
Query: 35 VYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEIIKI 88
+ +VG NVGKS+L NA L+ D RA S GTT ++++ ++
Sbjct: 206 LAIVGSPNVGKSSLLNALLKQD-----------RAIVSDIKGTTRDVVEGDFEL 248
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 35.6 bits (83), Expect = 0.004
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 37 LVGCTNVGKSTLFNA 51
+VG NVGKSTLFNA
Sbjct: 7 IVGLPNVGKSTLFNA 21
>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 = 34.7 bits (81), Expect = 0.005
Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 11/55 (20%)
Query: 32 AGDVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEII 86
+G V ++G NVGKSTL NA + KI + SP P TT N ++ I
Sbjct: 3 SGFVAIIGRPNVGKSTLLNALVG---QKI--------SIVSPKPQTTRNRIRGIY 46
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 34.8 bits (81), Expect = 0.006
Identities = 22/64 (34%), Positives = 30/64 (46%), Gaps = 12/64 (18%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEIIKIQTVCKVKE 96
LVG NVGKST FNA +D + +P TT++ + ++ C KE
Sbjct: 6 LVGKPNVGKSTFFNAATLAD------------VEIANYPFTTIDPNVGVAYVRVECPCKE 53
Query: 97 LGKK 100
LG K
Sbjct: 54 LGVK 57
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 34.5 bits (80), Expect = 0.007
Identities = 14/26 (53%), Positives = 16/26 (61%), Gaps = 5/26 (19%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKA 62
+VG NVGKST FNA LCK +
Sbjct: 26 IVGLPNVGKSTTFNA-----LCKQQV 46
>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 = 33.9 bits (78), Expect = 0.009
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTS 72
L+G T GKS+L NA +++ + D R TT
Sbjct: 2 LMGKTGAGKSSLCNALFGTEVAAV--GDR--RPTTR 33
>gnl|CDD|222997 PHA03132, PHA03132, thymidine kinase; Provisional.
Length = 580
Score = 34.4 bits (79), Expect = 0.010
Identities = 23/80 (28%), Positives = 31/80 (38%), Gaps = 16/80 (20%)
Query: 35 VYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSP-----WPGTTLNLLKEIIKIQ 89
++L G VGK+TL N + I L P W N LKEI K+
Sbjct: 260 LFLEGVMGVGKTTLLNH-----MRGI----LGDNVLVFPEPMRYWTEVYSNCLKEIYKLV 310
Query: 90 TVCKVKEL--GKKILLSQVK 107
K + K+L Q+K
Sbjct: 311 KPGKHGKTSTSAKLLACQMK 330
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 34.3 bits (80), Expect = 0.010
Identities = 12/14 (85%), Positives = 12/14 (85%)
Query: 38 VGCTNVGKSTLFNA 51
VG NVGKSTLFNA
Sbjct: 8 VGLPNVGKSTLFNA 21
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 33.9 bits (79), Expect = 0.011
Identities = 20/47 (42%), Positives = 24/47 (51%), Gaps = 11/47 (23%)
Query: 32 AGDVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTT 78
+G V +VG NVGKSTL NA + KI + SP P TT
Sbjct: 5 SGFVAIVGRPNVGKSTLLNALVGQ---KI--------SIVSPKPQTT 40
>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 = 33.6 bits (77), Expect = 0.011
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 11/42 (26%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTT 78
+VG VGKS+L NA L ++ + S PGTT
Sbjct: 2 VVGRGGVGKSSLLNALLGGEVGE-----------VSDVPGTT 32
>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 = 34.0 bits (79), Expect = 0.012
Identities = 12/14 (85%), Positives = 12/14 (85%)
Query: 38 VGCTNVGKSTLFNA 51
VG NVGKSTLFNA
Sbjct: 4 VGLPNVGKSTLFNA 17
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 33.7 bits (78), Expect = 0.017
Identities = 20/55 (36%), Positives = 24/55 (43%), Gaps = 16/55 (29%)
Query: 27 LVLSSAGDVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRA--TTSPWPGTTL 79
L L DV LVG N GKSTL +A +S A + +P TTL
Sbjct: 154 LELKLLADVGLVGLPNAGKSTLLSA--------------VSAAKPKIADYPFTTL 194
>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 = 32.8 bits (76), Expect = 0.019
Identities = 19/49 (38%), Positives = 22/49 (44%), Gaps = 16/49 (32%)
Query: 34 DVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATT--SPWPGTTLN 80
DV LVG N GKSTL +A IS A + +P TTL
Sbjct: 2 DVGLVGLPNAGKSTLLSA--------------ISNAKPKIADYPFTTLV 36
>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 = 33.4 bits (77), Expect = 0.022
Identities = 21/64 (32%), Positives = 29/64 (45%), Gaps = 12/64 (18%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEIIKIQTVCKVKE 96
LVG NVGKST FNA +D + +P TT++ + ++ C KE
Sbjct: 3 LVGKPNVGKSTFFNAATLAD------------VEIANYPFTTIDPNVGVGYVRVECPCKE 50
Query: 97 LGKK 100
LG
Sbjct: 51 LGVS 54
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 33.4 bits (77), Expect = 0.022
Identities = 15/22 (68%), Positives = 16/22 (72%)
Query: 35 VYLVGCTNVGKSTLFNAFLQSD 56
V LVG TN GKSTLFNA +D
Sbjct: 195 VALVGYTNAGKSTLFNALTGAD 216
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 33.0 bits (76), Expect = 0.028
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 28 VLSSAGDVYLVGCTNVGKSTLFNAFLQSDLCK---IKASDLISRATT 71
LS V L+G + VGKSTL NA L ++ K ++ D R TT
Sbjct: 191 WLSGGKTVALLGSSGVGKSTLVNALLGEEVQKTGAVREDDSKGRHTT 237
>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 = 32.7 bits (75), Expect = 0.029
Identities = 18/54 (33%), Positives = 23/54 (42%), Gaps = 11/54 (20%)
Query: 33 GDVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEII 86
G V ++G NVGKSTL N + + TSP TT N + I
Sbjct: 1 GFVAILGRPNVGKSTLLNQLHGQKI-----------SITSPKAQTTRNRISGIH 43
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 32.8 bits (75), Expect = 0.030
Identities = 13/16 (81%), Positives = 13/16 (81%)
Query: 35 VYLVGCTNVGKSTLFN 50
V LVG TN GKSTLFN
Sbjct: 200 VSLVGYTNAGKSTLFN 215
>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 = 32.3 bits (74), Expect = 0.032
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 11/52 (21%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEIIKI 88
+VG NVGKSTL N L + + T PGTT N + +I+
Sbjct: 6 IVGDPNVGKSTLLNRLLGNK-----------ISITEYKPGTTRNYVTTVIEE 46
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 32.1 bits (73), Expect = 0.058
Identities = 26/89 (29%), Positives = 36/89 (40%), Gaps = 17/89 (19%)
Query: 6 ALEGR------EVILVARPEPNIVSADLVLSSAGDVYLVGCTNVGKSTLFNAFLQSDLCK 59
A+ GR + L + S L S V LVG NVGKS+L N +
Sbjct: 418 AMHGRGVGDLLDEALDSLKVAEKTSGFLTPSGLRRVALVGRPNVGKSSLLNQLTHEE--- 474
Query: 60 IKASDLISRATTSPWPGTTLNLLKEIIKI 88
RA + GTT + + EI++I
Sbjct: 475 --------RAVVNDLAGTTRDPVDEIVEI 495
Score = 30.9 bits (70), Expect = 0.17
Identities = 18/53 (33%), Positives = 21/53 (39%), Gaps = 14/53 (26%)
Query: 4 WPALEGREVI---LVARPEPNIVSADLVLSSAGDVYLVGCTNVGKSTLFNAFL 53
LEG + A P+ G V +VG NVGKSTL N L
Sbjct: 255 EDLLEGSGFVAGDEKAGPKA-----------VGVVAIVGRPNVGKSTLVNRIL 296
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 31.7 bits (72), Expect = 0.064
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 34 DVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPW 74
+V L+G T GKS+L NA Q ++ ++ + + TT
Sbjct: 41 NVLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLR 81
>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 = 31.2 bits (72), Expect = 0.095
Identities = 20/52 (38%), Positives = 24/52 (46%), Gaps = 18/52 (34%)
Query: 34 DVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATT--SPWPGTTL--NL 81
DV LVG N GKSTL +A +S A + +P TTL NL
Sbjct: 159 DVGLVGLPNAGKSTLISA--------------VSAAKPKIADYPFTTLVPNL 196
>gnl|CDD|215595 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 31.2 bits (71), Expect = 0.14
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 5/53 (9%)
Query: 4 WP---ALEGREVILVARPE--PNIVSADLVLSSAGDVYLVGCTNVGKSTLFNA 51
WP +++ +V+L RPE P + +S + V +VG T GKS++ NA
Sbjct: 1232 WPSSGSIKFEDVVLRYRPELPPVLHGLSFEISPSEKVGIVGRTGAGKSSMLNA 1284
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 31.1 bits (71), Expect = 0.14
Identities = 30/99 (30%), Positives = 42/99 (42%), Gaps = 29/99 (29%)
Query: 2 ELWP--ALEGR------EVILVARPEPNIVSADLVLSSAGD----VYLVGCTNVGKSTLF 49
E P AL GR + +L A PE V SA V LVG NVGKS+L
Sbjct: 175 EPHPVSALHGRGVGDLLDAVLAALPE---VPRV---GSASGGPRRVALVGKPNVGKSSLL 228
Query: 50 NAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEIIKI 88
N K+ + R+ GTT++ + +I++
Sbjct: 229 N--------KLAGEE---RSVVDDVAGTTVDPVDSLIEL 256
Score = 28.8 bits (65), Expect = 0.67
Identities = 12/19 (63%), Positives = 13/19 (68%)
Query: 35 VYLVGCTNVGKSTLFNAFL 53
V +VG NVGKSTL N L
Sbjct: 41 VAVVGRPNVGKSTLVNRIL 59
>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 = 30.4 bits (69), Expect = 0.15
Identities = 14/48 (29%), Positives = 19/48 (39%)
Query: 17 RPEPNIVSADLVLSSAGDVYLVGCTNVGKSTLFNAFLQSDLCKIKASD 64
+ E L V +VG NVGKS+ NA L K+ +
Sbjct: 76 KAEITKQKLKLKYKKGIRVGVVGLPNVGKSSFINALLNKFKLKVGSIP 123
>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 = 30.9 bits (70), Expect = 0.18
Identities = 16/40 (40%), Positives = 17/40 (42%), Gaps = 12/40 (30%)
Query: 39 GCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTT 78
G NVGKSTLFNA + T WPG T
Sbjct: 1 GNPNVGKSTLFNALTG------------ANQTVGNWPGVT 28
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 30.5 bits (70), Expect = 0.20
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 34 DVYLVGCTNVGKSTLFNA 51
DV LVG NVGKSTL +
Sbjct: 160 DVGLVGFPNVGKSTLLSV 177
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 29.9 bits (68), Expect = 0.26
Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 10/44 (22%)
Query: 35 VYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTT 78
+ G +NVGKS+L NA L K + A TS PG T
Sbjct: 27 IAFAGRSNVGKSSLINA-----LTNQK-----NLARTSKTPGRT 60
>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 = 29.4 bits (67), Expect = 0.35
Identities = 16/54 (29%), Positives = 20/54 (37%), Gaps = 13/54 (24%)
Query: 35 VYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEIIKI 88
+VG NVGKSTL N A PG T ++ I+I
Sbjct: 118 AMVVGIPNVGKSTLINRLRG-----------KKVAKVGNKPGVTRG--QQWIRI 158
>gnl|CDD|185375 PRK15478, cbiH, cobalt-precorrin-3B C(17)-methyltransferase;
Provisional.
Length = 241
Score = 29.1 bits (65), Expect = 0.48
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 14/79 (17%)
Query: 6 ALEGREVILVARPEPNIVS-ADLVLSSAG------DVYLV-GCT-NVGKSTLFNAFLQSD 56
A G V L++ + I A LVL +V L+ G T ++ ++L A L D
Sbjct: 67 AQAGHNVALISSGDAGIYGMAGLVLELVSKQKLDVEVRLIPGMTASIAAASLLGAPLMHD 126
Query: 57 LCKIKASDLISRATTSPWP 75
C I SDL+ +PWP
Sbjct: 127 FCHISLSDLL-----TPWP 140
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 29.3 bits (67), Expect = 0.50
Identities = 20/52 (38%), Positives = 24/52 (46%), Gaps = 18/52 (34%)
Query: 34 DVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATT--SPWPGTTL--NL 81
DV LVG N GKSTL +A +S A + +P TTL NL
Sbjct: 160 DVGLVGLPNAGKSTLISA--------------VSAAKPKIADYPFTTLHPNL 197
>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 = 28.9 bits (65), Expect = 0.55
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 16/47 (34%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATT--SPWPGTTLNL 81
LVG NVGKSTL +A ++ A + +P TTL
Sbjct: 2 LVGLPNVGKSTLLSA--------------LTSAKVEIASYPFTTLEP 34
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 28.8 bits (64), Expect = 0.63
Identities = 12/57 (21%), Positives = 23/57 (40%), Gaps = 5/57 (8%)
Query: 35 VYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPGTTLNLLKEIIKIQTV 91
+ ++G VGK+TL N + + + + P T+ + IK+Q
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEF-----PEGYPPTIGNLDPAKTIEPYRRNIKLQLW 59
>gnl|CDD|233424 TIGR01466, cobJ_cbiH, precorrin-3B C17-methyltransferase. This
model represents precorrin-3B C17-methyltransferase, one
of two methyltransferases commonly referred to as
precorrin-3 methylase (the other is precorrin-4
C11-methyltransferase, EC 2.1.1.133). This enzyme
participates in the pathway toward the biosynthesis of
cobalamin and related products. Members of this family
may appear as fusion proteins with other enzymes of
cobalamin biosynthesis [Biosynthesis of cofactors,
prosthetic groups, and carriers, Heme, porphyrin, and
cobalamin].
Length = 239
Score = 28.4 bits (64), Expect = 0.83
Identities = 27/79 (34%), Positives = 37/79 (46%), Gaps = 14/79 (17%)
Query: 6 ALEGREVILVARPEPNIVS-ADLVL------SSAGDVYLV-GCTNVGK-STLFNAFLQSD 56
A EGR V LV+ +P I A LV + D+ ++ G T ++L A L D
Sbjct: 66 AAEGRTVALVSSGDPGIYGMAALVFEALEKKGAEVDIEVIPGITAASAAASLLGAPLGHD 125
Query: 57 LCKIKASDLISRATTSPWP 75
C I SDL+ +PWP
Sbjct: 126 FCVISLSDLL-----TPWP 139
>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 = 28.2 bits (64), Expect = 0.93
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 37 LVGCTNVGKSTLFNA 51
G +NVGKS+L NA
Sbjct: 4 FAGRSNVGKSSLINA 18
>gnl|CDD|213256 cd03289, ABCC_CFTR2, ATP-binding cassette domain 2 of
CFTR,subfamily C. The cystic fibrosis transmembrane
regulator (CFTR), the product of the gene mutated in
patients with cystic fibrosis, has adapted the ABC
transporter structural motif to form a tightly
regulated anion channel at the apical surface of many
epithelia. Use of the term assembly of a functional ion
channel implies the coming together of subunits or at
least smaller not-yet functional components of the
active whole. In fact, on the basis of current
knowledge only the CFTR polypeptide itself is required
to form an ATP- and protein kinase A-dependent
low-conductance chloride channel of the type present in
the apical membrane of many epithelial cells. CFTR
displays the typical organization (IM-ABC)2 and carries
a characteristic hydrophilic R-domain that separates
IM1-ABC1 from IM2-ABC2.
Length = 275
Score = 28.3 bits (63), Expect = 0.97
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 29 LSSAGDVYLVGCTNVGKSTLFNAFLQ 54
+S V L+G T GKSTL +AFL+
Sbjct: 27 ISPGQRVGLLGRTGSGKSTLLSAFLR 52
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 28.3 bits (64), Expect = 1.0
Identities = 18/52 (34%), Positives = 22/52 (42%), Gaps = 18/52 (34%)
Query: 34 DVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRAT--TSPWPGTTL--NL 81
DV L+G N GKST A +S A + +P TTL NL
Sbjct: 161 DVGLLGLPNAGKSTFIRA--------------VSAAKPKVADYPFTTLVPNL 198
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction
only].
Length = 365
Score = 28.4 bits (64), Expect = 1.1
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 30 SSAGDVYLVGCTNVGKSTLFNA 51
S V LVG +VGKSTL N
Sbjct: 61 SGDATVALVGFPSVGKSTLLNK 82
>gnl|CDD|217282 pfam02911, Formyl_trans_C, Formyl transferase, C-terminal domain.
Length = 100
Score = 27.2 bits (61), Expect = 1.2
Identities = 11/50 (22%), Positives = 25/50 (50%), Gaps = 6/50 (12%)
Query: 59 KIKASDLISRATTSPWPGTTLNLLKEIIKIQT---VCKVKEL---GKKIL 102
KI ++++ ++ + PGT +++ K + + + EL GKK +
Sbjct: 41 KILKAEVVEDSSGAASPGTIVSVDKGGLLVACGDGALLILELQPEGKKAM 90
>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 = 27.5 bits (62), Expect = 1.4
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 38 VGCTNVGKSTLFNAFLQSDL 57
VG + GKSTL NA L ++
Sbjct: 6 VGEFSAGKSTLLNALLGEEV 25
>gnl|CDD|201420 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are
polypeptides of 30-65kDa with three characteristic
GTPase motifs (G-1, G-3 and G-4) that are similar to
those of the Ras family. The G-4 motif is strictly
conserved with a unique septin consensus of AKAD. Most
septins are thought to have at least one coiled-coil
region, which in some cases is necessary for
intermolecular interactions that allow septins to
polymerise to form rod-shaped complexes. In turn, these
are arranged into tandem arrays to form filaments. They
are multifunctional proteins, with roles in
cytokinesis, sporulation, germ cell development,
exocytosis and apoptosis.
Length = 280
Score = 27.6 bits (62), Expect = 1.7
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 37 LVGCTNVGKSTLFNAFLQSDL 57
+VG + +GK+TL N +DL
Sbjct: 9 VVGESGLGKTTLINTLFLTDL 29
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 27.5 bits (62), Expect = 1.8
Identities = 24/66 (36%), Positives = 29/66 (43%), Gaps = 24/66 (36%)
Query: 24 SADLVLS--SAGDVYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSP----WPGT 77
DLVL S DV LVG + GKS+L +A +S A P +P T
Sbjct: 149 ERDLVLELKSVADVGLVGFPSAGKSSLISA--------------LSAA--KPKIADYPFT 192
Query: 78 TL--NL 81
TL NL
Sbjct: 193 TLVPNL 198
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 27.2 bits (61), Expect = 2.0
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 35 VYLVGCTNVGKSTLF 49
+ VG +NVGKSTL
Sbjct: 12 IVFVGRSNVGKSTLV 26
>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 = 27.3 bits (61), Expect = 2.1
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 11/42 (26%)
Query: 35 VYLVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPG 76
V +VG VGKS++ NA A+TSP PG
Sbjct: 102 VGVVGYPKVGKSSIINALKGR-----------HSASTSPIPG 132
>gnl|CDD|223272 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 27.1 bits (61), Expect = 2.3
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRATTSPWPG 76
L G + VGKSTL A L+ D K++ S +S T P PG
Sbjct: 9 LSGPSGVGKSTLVKALLEDD--KLRFS--VSATTRKPRPG 44
>gnl|CDD|226237 COG3714, COG3714, Predicted membrane protein [Function unknown].
Length = 212
Score = 27.0 bits (60), Expect = 2.5
Identities = 20/76 (26%), Positives = 26/76 (34%), Gaps = 19/76 (25%)
Query: 16 ARPEPNIVSADLVLSSAGDV---------YLVGCTNVGKSTLFNAFLQSDLCKIKASDLI 66
++ A L LS+ GD ++ G AFL + L I A L
Sbjct: 49 LSGRRWLIVAGLALSALGDALLLLPGRLAFVAG---------LIAFLLAHLLYIGAL-LR 98
Query: 67 SRATTSPWPGTTLNLL 82
S T S W LL
Sbjct: 99 SARTLSLWWPLPAALL 114
>gnl|CDD|238982 cd02024, NRK1, Nicotinamide riboside kinase (NRK) is an enzyme
involved in the metabolism of nicotinamide adenine
dinucleotide (NAD+). This enzyme catalyzes the
phosphorylation of nicotinamide riboside (NR) to form
nicotinamide mononucleotide (NMN). It defines the NR
salvage pathway of NAD+ biosynthesis in addition to the
pathways through nicotinic acid mononucleotide (NaMN).
This enzyme can also phosphorylate the anticancer drug
tiazofurin, which is an analog of nicotinamide
riboside.
Length = 187
Score = 26.9 bits (60), Expect = 2.6
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 39 GCTNVGKSTLFNAFLQ 54
G TN GK+TL +
Sbjct: 6 GVTNSGKTTLAKLLQR 21
>gnl|CDD|131259 TIGR02204, MsbA_rel, ABC transporter, permease/ATP-binding protein.
This protein is related to a Proteobacterial ATP
transporter that exports lipid A and to eukaryotic
P-glycoproteins.
Length = 576
Score = 27.0 bits (60), Expect = 3.5
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 16 ARPE-PNIVSADLVLSSAGDVYLVGCTNVGKSTLFNAFLQ 54
ARP+ P + +L + V LVG + GKSTLF L+
Sbjct: 349 ARPDQPALDGLNLTVRPGETVALVGPSGAGKSTLFQLLLR 388
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with
duplicated ATPase domains [General function prediction
only].
Length = 530
Score = 26.8 bits (60), Expect = 3.7
Identities = 9/21 (42%), Positives = 10/21 (47%), Gaps = 1/21 (4%)
Query: 32 AGDVY-LVGCTNVGKSTLFNA 51
G+ LVG GKSTL
Sbjct: 28 PGERIGLVGRNGAGKSTLLKI 48
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family
are found in a variety of single stranded RNA viruses.
Length = 105
Score = 26.0 bits (58), Expect = 3.7
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 3/43 (6%)
Query: 35 VYLVGCTNVGKSTLFNAF---LQSDLCKIKASDLISRATTSPW 74
++L G GKSTL L L K + SR +
Sbjct: 1 IWLYGPPGCGKSTLAKYLARALLKHLGLPKKDSVYSRNPDDDF 43
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 26.4 bits (59), Expect = 4.0
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 37 LVGCTNVGKSTLFNAFLQSD 56
L G + VGKSTL NA L
Sbjct: 40 LAGQSGVGKSTLLNALLPEL 59
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 26.3 bits (59), Expect = 4.1
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 37 LVGCTNVGKSTLFNA 51
L G + VGKSTL NA
Sbjct: 169 LAGQSGVGKSTLLNA 183
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 26.5 bits (59), Expect = 4.4
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 37 LVGCTNVGKSTLFNAFL 53
L+G + VGKSTL NA L
Sbjct: 169 LLGQSGVGKSTLINALL 185
>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 = 26.0 bits (58), Expect = 5.8
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIK 61
+VG + +GKST N + L K
Sbjct: 9 VVGESGLGKSTFINTLFGTKLYPSK 33
>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 = 25.7 bits (57), Expect = 6.2
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 37 LVGCTNVGKSTLFNA 51
LVG NVGKS+L NA
Sbjct: 87 LVGYPNVGKSSLINA 101
>gnl|CDD|235631 PRK05866, PRK05866, short chain dehydrogenase; Provisional.
Length = 293
Score = 25.9 bits (57), Expect = 6.2
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 6 ALEGREVILVARPEPNIVS-ADLVLSSAGDVYLVGC 40
A G V+ VAR E + + AD + + GD V C
Sbjct: 61 ARRGATVVAVARREDLLDAVADRITRAGGDAMAVPC 96
>gnl|CDD|215640 PLN03232, PLN03232, ABC transporter C family member; Provisional.
Length = 1495
Score = 26.1 bits (57), Expect = 6.7
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 5/56 (8%)
Query: 4 WPA---LEGREVILVARPE--PNIVSADLVLSSAGDVYLVGCTNVGKSTLFNAFLQ 54
WP+ ++ +V L RP P + +S + V +VG T GKS++ NA +
Sbjct: 1229 WPSRGSIKFEDVHLRYRPGLPPVLHGLSFFVSPSEKVGVVGRTGAGKSSMLNALFR 1284
>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 = 26.0 bits (58), Expect = 6.8
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 35 VYLVGCTNVGKSTLFNA 51
V LVG +VGKSTL +
Sbjct: 3 VALVGFPSVGKSTLLSK 19
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase
fold. The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons,
ATPase subunits of proteases, helicases, or
nucleic-acid stimulated ATPases. The AAA+ proteins
contain several distinct features in addition to the
conserved alpha-beta-alpha core domain structure and
the Walker A and B motifs of the P-loop NTPases.
Length = 151
Score = 25.6 bits (56), Expect = 7.2
Identities = 11/41 (26%), Positives = 15/41 (36%), Gaps = 6/41 (14%)
Query: 35 VYLVGCTNVGKSTLFNAFLQS------DLCKIKASDLISRA 69
+ L G GK+TL A + ASDL+
Sbjct: 22 LLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGL 62
>gnl|CDD|214863 smart00859, Semialdhyde_dh, Semialdehyde dehydrogenase, NAD
binding domain. The semialdehyde dehydrogenase family
is found in N-acetyl-glutamine semialdehyde
dehydrogenase (AgrC), which is involved in arginine
biosynthesis, and aspartate-semialdehyde dehydrogenase,
an enzyme involved in the biosynthesis of various amino
acids from aspartate. This family is also found in
yeast and fungal Arg5,6 protein, which is cleaved into
the enzymes N-acety-gamma-glutamyl-phosphate reductase
and acetylglutamate kinase. These are also involved in
arginine biosynthesis. All proteins in this entry
contain a NAD binding region of semialdehyde
dehydrogenase.
Length = 123
Score = 25.2 bits (56), Expect = 7.4
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 2 ELWPALEGREVILVARPEPNIVSADLVLSSAGD 34
E P L+G V+ + P+ ++ D+V +
Sbjct: 43 EAGPHLKGEVVLELDPPDFEELAVDIVFLALPH 75
>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 = 25.4 bits (57), Expect = 7.6
Identities = 12/17 (70%), Positives = 13/17 (76%)
Query: 37 LVGCTNVGKSTLFNAFL 53
LVG + VGKSTL NA L
Sbjct: 90 LVGQSGVGKSTLLNALL 106
>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 = 25.6 bits (57), Expect = 7.9
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 16/48 (33%)
Query: 37 LVGCTNVGKSTLFNAFLQSDLCKIKASDLISRAT--TSPWPGTTLNLL 82
+ G NVGKS+L N ++RA +P+P TT +L
Sbjct: 5 IAGYPNVGKSSLVNK--------------LTRAKPEVAPYPFTTKSLF 38
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 25.0 bits (55), Expect = 9.4
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 35 VYLVGCTNVGKSTL 48
V +VG + GK+TL
Sbjct: 3 VLVVGPKDSGKTTL 16
>gnl|CDD|146762 pfam04294, VanW, VanW like protein. Family members include
vancomycin resistance protein W (VanW). Genes encoding
members of this family have been found in vancomycin
resistance gene clusters vanB and vanG. The function of
VanW is unknown.
Length = 132
Score = 25.1 bits (56), Expect = 9.6
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 46 STLFNAFLQSDL 57
+TL+NA L + L
Sbjct: 64 TTLYNAVLHAGL 75
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 25.1 bits (56), Expect = 9.8
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 37 LVGCTNVGKSTLFNAFLQ 54
G +NVGKS+L NA
Sbjct: 29 FAGRSNVGKSSLINALTN 46
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.133 0.378
Gapped
Lambda K H
0.267 0.0807 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,970,346
Number of extensions: 493039
Number of successful extensions: 810
Number of sequences better than 10.0: 1
Number of HSP's gapped: 795
Number of HSP's successfully gapped: 126
Length of query: 127
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 42
Effective length of database: 7,167,512
Effective search space: 301035504
Effective search space used: 301035504
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.0 bits)