RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6316
(259 letters)
>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 = 218 bits (558), Expect = 2e-72
Identities = 76/175 (43%), Positives = 101/175 (57%), Gaps = 25/175 (14%)
Query: 26 IVCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGATNVPADAIRENTKHVRGPGGEV 85
+V V+GHVD GKT +LDK+R+TNV GEAGGITQ IGA VP D
Sbjct: 2 VVTVMGHVDHGKTTLLDKIRKTNVAAGEAGGITQHIGAYQVPID---------------- 45
Query: 86 GGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSK 145
++IPG+ IDTPGHE+F+N+R RG+S+ DIAILVV G+ PQTIE+IN K+
Sbjct: 46 -----VKIPGITFIDTPGHEAFTNMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAA 100
Query: 146 KTPFVVALNKIDRLYNWNTMNRRDVRDIIKSQESSVQTHKTVE----SARKGQEI 196
P +VA+NKID+ Y R ++ + + V SA+ G+ I
Sbjct: 101 NVPIIVAINKIDKPYGTEADPERVKNELSELGLVGEEWGGDVSIVPISAKTGEGI 155
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 230 bits (589), Expect = 5e-72
Identities = 92/161 (57%), Positives = 108/161 (67%), Gaps = 5/161 (3%)
Query: 23 RAAIVCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGATNVPADAIRENTKHVRGPG 82
R IV VLGHVD GKT +LDK+R T V EAGGITQ IGAT VP D I + ++ P
Sbjct: 5 RQPIVVVLGHVDHGKTTLLDKIRGTAVAAKEAGGITQHIGATEVPIDVIEKIAGPLKKPL 64
Query: 83 GEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINIL 142
P L+IPGLL IDTPGHE+F+NLR RG +L DIAILVVDI G +PQTIE+INIL
Sbjct: 65 -----PIKLKIPGLLFIDTPGHEAFTNLRKRGGALADIAILVVDINEGFQPQTIEAINIL 119
Query: 143 KSKKTPFVVALNKIDRLYNWNTMNRRDVRDIIKSQESSVQT 183
K +KTPFVVA NKIDR+ W + + I+ Q VQ
Sbjct: 120 KRRKTPFVVAANKIDRIPGWKSTEDAPFLESIEKQSQRVQQ 160
Score = 30.9 bits (71), Expect = 0.67
Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 10/64 (15%)
Query: 185 KTVESARKGQEICIKIEPIPGEAPKMFGRHFDENDFLVSKIS----RQSIDACKDYFRDD 240
+ V+ A+ G E+ I I+ GR E D L I + KD DD
Sbjct: 519 ENVKEAKAGMEVAISID------GPTVGRQIKEGDILYVDIPEEHAKILEQELKDELSDD 572
Query: 241 LQKT 244
++
Sbjct: 573 EKEA 576
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 197 bits (504), Expect = 4e-60
Identities = 70/136 (51%), Positives = 88/136 (64%), Gaps = 20/136 (14%)
Query: 23 RAAIVCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGATNVPADAIRENTKHVRGPG 82
R +V ++GHVD GKT +LDK+R+TNV GEAGGITQ IGA VP D I
Sbjct: 4 RPPVVTIMGHVDHGKTTLLDKIRKTNVAAGEAGGITQHIGAYQVPLDVI----------- 52
Query: 83 GEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINIL 142
+IPG+ IDTPGHE+F+ +R RG+S+ DIAILVV G+ PQTIE+IN
Sbjct: 53 ---------KIPGITFIDTPGHEAFTAMRARGASVTDIAILVVAADDGVMPQTIEAINHA 103
Query: 143 KSKKTPFVVALNKIDR 158
K+ P VVA+NKID+
Sbjct: 104 KAAGVPIVVAINKIDK 119
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This
model describes archaeal and eukaryotic orthologs of
bacterial IF-2. Like IF-2, it helps convey the initiator
tRNA to the ribosome, although the initiator is
N-formyl-Met in bacteria and Met here. This protein is
not closely related to the subunits of eIF-2 of
eukaryotes, which is also involved in the initiation of
translation. The aIF-2 of Methanococcus jannaschii
contains a large intein interrupting a region of very
strongly conserved sequence very near the amino end; the
alignment generated by This model does not correctly
align the sequences from Methanococcus jannaschii and
Pyrococcus horikoshii in this region [Protein synthesis,
Translation factors].
Length = 590
Score = 183 bits (466), Expect = 4e-54
Identities = 84/161 (52%), Positives = 104/161 (64%), Gaps = 5/161 (3%)
Query: 22 MRAAIVCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGATNVPADAIRENTKHVRGP 81
+R+ IV VLGHVD GKT +LDK+R + V EAGGITQ IGAT +P D I +
Sbjct: 2 LRSPIVSVLGHVDHGKTTLLDKIRGSAVAKREAGGITQHIGATEIPMDVIEGICGDLLKK 61
Query: 82 GGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINI 141
L+IPGLL IDTPGHE+F+NLR RG +L D+AIL+VDI G +PQT E++NI
Sbjct: 62 F-----KIRLKIPGLLFIDTPGHEAFTNLRKRGGALADLAILIVDINEGFKPQTQEALNI 116
Query: 142 LKSKKTPFVVALNKIDRLYNWNTMNRRDVRDIIKSQESSVQ 182
L+ KTPFVVA NKIDR+ W + R + QE VQ
Sbjct: 117 LRMYKTPFVVAANKIDRIPGWRSHEGRPFMESFSKQEIQVQ 157
Score = 29.4 bits (66), Expect = 2.1
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 6/65 (9%)
Query: 185 KTVESARKGQEICIKIEPIPGEAPKMFGRHFDENDFLVSKISRQSIDACKDYFRDDLQKT 244
+ V+SA GQE+ I I+ + ++GR E D L + K+ DDL
Sbjct: 517 ENVKSASAGQEVAIAIKDV------VYGRTIHEGDTLYVDVPENHYHILKEQLSDDLTDE 570
Query: 245 DWQLM 249
+ M
Sbjct: 571 EKDAM 575
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 160 bits (407), Expect = 8e-45
Identities = 72/132 (54%), Positives = 90/132 (68%), Gaps = 17/132 (12%)
Query: 38 TKILDKLRRTNVQDGEAGGITQQIGATNVPADAIRENTKHVRGPGGEVGGP------GPL 91
T +LDK+R+T V EAGGITQ IGAT +P D I++ + GP +
Sbjct: 475 TTLLDKIRKTRVAKKEAGGITQHIGATEIPIDVIKK-----------ICGPLLKLLKAEI 523
Query: 92 EIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPFVV 151
+IPGLL IDTPGHE+F++LR RG SL D+A+LVVDI G +PQTIE+INIL+ KTPFVV
Sbjct: 524 KIPGLLFIDTPGHEAFTSLRKRGGSLADLAVLVVDINEGFKPQTIEAINILRQYKTPFVV 583
Query: 152 ALNKIDRLYNWN 163
A NKID + WN
Sbjct: 584 AANKIDLIPGWN 595
Score = 35.6 bits (82), Expect = 0.022
Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 6/73 (8%)
Query: 185 KTVESARKGQEICIKIEPIPGEAPKMFGRHFDENDFLVSKISRQSIDACKDYFRDDLQKT 244
+ V+ A+ G+ + I IE + GRH DE + L + + + D L+
Sbjct: 975 ENVKEAKAGKAVAIAIEGA------ILGRHVDEGETLYVDVPESHVRELYHKYMDRLRDD 1028
Query: 245 DWQLMVDLKKVFQ 257
+ + + ++ Q
Sbjct: 1029 EKEALKMYMELKQ 1041
Score = 30.6 bits (69), Expect = 0.96
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 22 MRAAIVCVLGHVDTGK 37
+R IV VLGHVD GK
Sbjct: 8 LRCPIVAVLGHVDHGK 23
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 146 bits (370), Expect = 6e-40
Identities = 64/157 (40%), Positives = 87/157 (55%), Gaps = 35/157 (22%)
Query: 7 KRREKIEENPEDENFMRAAIVCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGATNV 66
K +E++ E++ R +V ++GHVD GKT +LD +R+TNV GEAGGITQ IGA V
Sbjct: 232 KLVSLLEDDDEEDLVPRPPVVTIMGHVDHGKTSLLDAIRKTNVAAGEAGGITQHIGAYQV 291
Query: 67 PADAIRENTKHVRGPGGEVGGPGPLEIPGLLI--IDTPGHESFSNLRNRGSSLCDIAILV 124
E G I +DTPGHE+F+ +R RG+ + DI +LV
Sbjct: 292 -------------------------ETNGGKITFLDTPGHEAFTAMRARGAQVTDIVVLV 326
Query: 125 V----DIMHGLEPQTIESINILKSKKTPFVVALNKID 157
V +M PQTIE+IN K+ P +VA+NKID
Sbjct: 327 VAADDGVM----PQTIEAINHAKAAGVPIIVAINKID 359
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 137 bits (346), Expect = 8e-37
Identities = 64/153 (41%), Positives = 94/153 (61%), Gaps = 20/153 (13%)
Query: 7 KRREKIEENPEDENFM-RAAIVCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGATN 65
K + EN + R IV +LGHVD GKT +LDK+R+T + EAGGITQ+IGA
Sbjct: 226 KTSNLDNTSAFTENSINRPPIVTILGHVDHGKTTLLDKIRKTQIAQKEAGGITQKIGAYE 285
Query: 66 VPADAIRENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVV 125
V + EN K ++ +DTPGHE+FS++R+RG+++ DIAIL++
Sbjct: 286 VEFEYKDENQK-------------------IVFLDTPGHEAFSSMRSRGANVTDIAILII 326
Query: 126 DIMHGLEPQTIESINILKSKKTPFVVALNKIDR 158
G++PQTIE+IN +++ P +VA+NKID+
Sbjct: 327 AADDGVKPQTIEAINYIQAANVPIIVAINKIDK 359
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 129 bits (326), Expect = 2e-34
Identities = 61/149 (40%), Positives = 88/149 (59%), Gaps = 22/149 (14%)
Query: 10 EKIEENPEDENFMRAAIVCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGATNVPAD 69
E+ +E+ D R +V ++GHVD GKT +LD +R+T V GEAGGITQ IGA +V
Sbjct: 73 EEQDEDSGDLLVERPPVVTIMGHVDHGKTSLLDSIRKTKVAQGEAGGITQHIGAYHV--- 129
Query: 70 AIRENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMH 129
E+ K + +DTPGHE+F+++R RG+ + DI +LVV
Sbjct: 130 -ENEDGKMI------------------TFLDTPGHEAFTSMRARGAKVTDIVVLVVAADD 170
Query: 130 GLEPQTIESINILKSKKTPFVVALNKIDR 158
G+ PQTIE+I+ K+ P +VA+NKID+
Sbjct: 171 GVMPQTIEAISHAKAANVPIIVAINKIDK 199
>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 = 117 bits (295), Expect = 1e-32
Identities = 45/151 (29%), Positives = 66/151 (43%), Gaps = 39/151 (25%)
Query: 26 IVCVLGHVDTGKTKILDKLRR----------------TNVQDGEAGGITQQIGATNVPAD 69
+ ++GHVD GKT + D L +++ GIT +I A +
Sbjct: 5 NIGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVSFE-- 62
Query: 70 AIRENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMH 129
+ + IIDTPGH F+ RG+S D AILVVD +
Sbjct: 63 ---TKKRLI------------------NIIDTPGHVDFTKEMIRGASQADGAILVVDAVE 101
Query: 130 GLEPQTIESINILKSKKTPFVVALNKIDRLY 160
G+ PQT E + + K+ P +V +NKIDR+
Sbjct: 102 GVMPQTREHLLLAKTLGVPIIVFINKIDRVD 132
>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 = 93.5 bits (233), Expect = 2e-23
Identities = 49/150 (32%), Positives = 64/150 (42%), Gaps = 39/150 (26%)
Query: 26 IVCVLGHVDTGKTKILDKL--------RRTNVQDGE--------AGGITQQIGATNVPAD 69
V V+GHVD GKT + L RR ++ GIT + G
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEW- 59
Query: 70 AIRENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMH 129
+ + IDTPGHE FS RG + D A+LVVD
Sbjct: 60 ----PKRRIN------------------FIDTPGHEDFSKETVRGLAQADGALLVVDANE 97
Query: 130 GLEPQTIESINILKSKKTPFVVALNKIDRL 159
G+EPQT E +NI + P +VA+NKIDR+
Sbjct: 98 GVEPQTREHLNIALAGGLPIIVAVNKIDRV 127
>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 = 60.8 bits (148), Expect = 1e-11
Identities = 33/139 (23%), Positives = 55/139 (39%), Gaps = 30/139 (21%)
Query: 27 VCVLGHVDTGKTKILDKLRRTNVQDGEAG-GITQQIGATNVPADAIRENTKHVRGPGGEV 85
+ ++G + GK+ +L++L + E G T+ N I E+ K +
Sbjct: 4 IVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTR-----NYVTTVIEEDGKTYK------ 52
Query: 86 GGPGPLEIPGLLIIDTPGHESFSNLR-------NRGSSLCDIAILVVDIMHGLEPQTIES 138
++DT G E + +R + DI ILV+D+ LE QT +
Sbjct: 53 ----------FNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQT-KE 101
Query: 139 INILKSKKTPFVVALNKID 157
I P ++ NKID
Sbjct: 102 IIHHAESGVPIILVGNKID 120
>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 = 60.8 bits (148), Expect = 3e-11
Identities = 53/194 (27%), Positives = 83/194 (42%), Gaps = 38/194 (19%)
Query: 27 VCVLGHVDTGKTKI------------LDKLRRTNVQDGEAGGITQQIG--ATNVPADAIR 72
V +LGHVD+GKT + DK ++ + GIT +G + V
Sbjct: 3 VGLLGHVDSGKTSLAKALSEIASTAAFDKNPQSQER-----GITLDLGFSSFEVDKPKHL 57
Query: 73 ENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLE 132
E+ ++ P E +I ++D PGH S G+ + D+ +LVVD G++
Sbjct: 58 EDNEN---PQIE-----NYQI---TLVDCPGHASLIRTIIGGAQIIDLMLLVVDAKKGIQ 106
Query: 133 PQTIESINILKSKKTPFVVALNKIDRLYNWNTMNRRDVRDIIKSQESSVQTHKTVESARK 192
QT E + I + P +V LNKID + R+ + +K + KT+E R
Sbjct: 107 TQTAECLVIGELLCKPLIVVLNKIDLI---PEEERKRKIEKMKK-----RLQKTLEKTRL 158
Query: 193 GQEICIKIEPIPGE 206
I + PGE
Sbjct: 159 KDSPIIPVSAKPGE 172
>gnl|CDD|206732 cd04169, RF3, Release Factor 3 (RF3) protein involved in the
terminal step of translocation in bacteria. Peptide
chain release factor 3 (RF3) is a protein involved in
the termination step of translation in bacteria.
Termination occurs when class I release factors (RF1 or
RF2) recognize the stop codon at the A-site of the
ribosome and activate the release of the nascent
polypeptide. The class II release factor RF3 then
initiates the release of the class I RF from the
ribosome. RF3 binds to the RF/ribosome complex in the
inactive (GDP-bound) state. GDP/GTP exchange occurs,
followed by the release of the class I RF. Subsequent
hydrolysis of GTP to GDP triggers the release of RF3
from the ribosome. RF3 also enhances the efficiency of
class I RFs at less preferred stop codons and at stop
codons in weak contexts.
Length = 268
Score = 58.4 bits (142), Expect = 4e-10
Identities = 23/61 (37%), Positives = 37/61 (60%)
Query: 98 IIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKID 157
++DTPGHE FS R + D A++V+D G+EPQT + + + + P + +NK+D
Sbjct: 75 LLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLRGIPIITFINKLD 134
Query: 158 R 158
R
Sbjct: 135 R 135
>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 = 59.1 bits (143), Expect = 5e-10
Identities = 54/177 (30%), Positives = 74/177 (41%), Gaps = 30/177 (16%)
Query: 26 IVCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGATNVPADAIRENTKHVRGPGGEV 85
I+ GHVD GKT +L L T + AD + E K RG ++
Sbjct: 2 IIATAGHVDHGKTTLLKAL-------------------TGIAADRLPEEKK--RGMTIDL 40
Query: 86 G-GPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDI--AILVVDIMHGLEPQTIESINIL 142
G PL L ID PGHE F + N + I A+LVVD G+ QT E + +L
Sbjct: 41 GFAYFPLPDYRLGFIDVPGHEKF--ISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVL 98
Query: 143 KSKKTPF-VVALNKIDRLYNWNTMNR--RDVRDIIKSQESSVQTHKTVESARKGQEI 196
P +V + K DR+ N + R ++ I+ S SA+ GQ I
Sbjct: 99 DLLGIPHTIVVITKADRV-NEEEIKRTEMFMKQILNSYIFLKNAKIFKTSAKTGQGI 154
>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 = 55.7 bits (135), Expect = 1e-09
Identities = 37/142 (26%), Positives = 55/142 (38%), Gaps = 36/142 (25%)
Query: 26 IVCVLGHVDTGKTKILDKLRRTNVQDGE------AGGITQQIGATNVPADAIRENTKHVR 79
I+ GH+D GKT ++ + + + GIT +G +
Sbjct: 1 IIGTAGHIDHGKTTLI---KALTGIETDRLPEEKKRGITIDLGFAYLDL----------- 46
Query: 80 GPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLC--DIAILVVDIMHGLEPQTIE 137
P G+ G ID PGHE F ++N + D +LVV G+ PQT E
Sbjct: 47 -PDGKRLG----------FIDVPGHEKF--VKNMLAGAGGIDAVLLVVAADEGIMPQTRE 93
Query: 138 SINILKSKKTP-FVVALNKIDR 158
+ IL+ +V L K D
Sbjct: 94 HLEILELLGIKKGLVVLTKADL 115
>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 = 55.5 bits (134), Expect = 1e-09
Identities = 36/177 (20%), Positives = 64/177 (36%), Gaps = 33/177 (18%)
Query: 28 CVLGHVDTGKTKILDKLRRTNV-QDGEAGGITQQIGATNVPADAIRENTKHVRGPGGEVG 86
V+G GK+ +L+ L V + + G T + G+V
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTT------------RDPDVYVKELDKGKVK 48
Query: 87 GPGPLEIPGLLIIDTPGHESFSNLRNRGSSL-----CDIAILVVDIMHG--LEPQTIESI 139
L+++DTPG + F L + D+ +LVVD E + +
Sbjct: 49 ---------LVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLIL 99
Query: 140 NILKSKKTPFVVALNKIDRLYNWNTMNRRDVRDIIKSQESSVQTHKTVESARKGQEI 196
L+ + P ++ NKID L +R ++ V + SA+ G+ +
Sbjct: 100 RRLRKEGIPIILVGNKIDLLEERE--VEELLRLEELAKILGVPVFEV--SAKTGEGV 152
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4). LepA
(also known as elongation factor 4, EF4) belongs to the
GTPase family and exhibits significant homology to the
translation factors EF-G and EF-Tu, indicating its
possible involvement in translation and association with
the ribosome. LepA is ubiquitous in bacteria and
eukaryota (e.g. yeast GUF1p), but is missing from
archaea. This pattern of phyletic distribution suggests
that LepA evolved through a duplication of the EF-G gene
in bacteria, followed by early transfer into the
eukaryotic lineage, most likely from the
promitochondrial endosymbiont. Yeast GUF1p is not
essential and mutant cells did not reveal any marked
phenotype.
Length = 179
Score = 54.1 bits (131), Expect = 4e-09
Identities = 39/145 (26%), Positives = 58/145 (40%), Gaps = 33/145 (22%)
Query: 28 CVLGHVDTGKTKILDK-LRRTNVQDGEAG--------------GITQQIGATNVPADAIR 72
++ H+D GK+ + D+ L T GIT + A A+R
Sbjct: 4 SIIAHIDHGKSTLADRLLELTGTVSEREMKEQVLDSMDLERERGIT-------IKAQAVR 56
Query: 73 ENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLE 132
K G L +IDTPGH FS +R + C+ A+LVVD G+E
Sbjct: 57 LFYKAKDGEEYL-----------LNLIDTPGHVDFSYEVSRSLAACEGALLVVDATQGVE 105
Query: 133 PQTIESINILKSKKTPFVVALNKID 157
QT+ + + + +NKID
Sbjct: 106 AQTLANFYLALENNLEIIPVINKID 130
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 56.5 bits (137), Expect = 4e-09
Identities = 38/148 (25%), Positives = 60/148 (40%), Gaps = 41/148 (27%)
Query: 29 VLGHVDTGKTKILDKL--------RRTNVQDGEA----------GGITQQIGATNVPADA 70
+L H+D GKT + +++ + V+DG GIT + AT+ D
Sbjct: 13 ILAHIDAGKTTLTERILFYTGKIHKMGEVEDGTTVTDWMPQEQERGITIESAATSCDWDN 72
Query: 71 IRENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHG 130
R N +IDTPGH F+ R + D A++V D + G
Sbjct: 73 HRIN-----------------------LIDTPGHIDFTGEVERSLRVLDGAVVVFDAVTG 109
Query: 131 LEPQTIESINILKSKKTPFVVALNKIDR 158
++PQT P ++ +NK+DR
Sbjct: 110 VQPQTETVWRQADRYGIPRLIFINKMDR 137
>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
Snu114p subfamily. Snu114p is one of several proteins
that make up the U5 small nuclear ribonucleoprotein
(snRNP) particle. U5 is a component of the spliceosome,
which catalyzes the splicing of pre-mRNA to remove
introns. Snu114p is homologous to EF-2, but typically
contains an additional N-terminal domain not found in
Ef-2. This protein is part of the GTP translation factor
family and the Ras superfamily, characterized by five
G-box motifs.
Length = 213
Score = 54.2 bits (131), Expect = 7e-09
Identities = 27/62 (43%), Positives = 35/62 (56%)
Query: 98 IIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKID 157
IIDTPGH +F + LCD +LVVD++ GL T I + P V+ +NKID
Sbjct: 75 IIDTPGHVNFMDEVAAALRLCDGVVLVVDVVEGLTSVTERLIRHAIQEGLPMVLVINKID 134
Query: 158 RL 159
RL
Sbjct: 135 RL 136
>gnl|CDD|206672 cd01885, EF2, Elongation Factor 2 (EF2) in archaea and eukarya.
Translocation requires hydrolysis of a molecule of GTP
and is mediated by EF-G in bacteria and by eEF2 in
eukaryotes. The eukaryotic elongation factor eEF2 is a
GTPase involved in the translocation of the
peptidyl-tRNA from the A site to the P site on the
ribosome. The 95-kDa protein is highly conserved, with
60% amino acid sequence identity between the human and
yeast proteins. Two major mechanisms are known to
regulate protein elongation and both involve eEF2.
First, eEF2 can be modulated by reversible
phosphorylation. Increased levels of phosphorylated eEF2
reduce elongation rates presumably because
phosphorylated eEF2 fails to bind the ribosomes.
Treatment of mammalian cells with agents that raise the
cytoplasmic Ca2+ and cAMP levels reduce elongation rates
by activating the kinase responsible for phosphorylating
eEF2. In contrast, treatment of cells with insulin
increases elongation rates by promoting eEF2
dephosphorylation. Second, the protein can be
post-translationally modified by ADP-ribosylation.
Various bacterial toxins perform this reaction after
modification of a specific histidine residue to
diphthamide, but there is evidence for endogenous ADP
ribosylase activity. Similar to the bacterial toxins, it
is presumed that modification by the endogenous enzyme
also inhibits eEF2 activity.
Length = 218
Score = 54.2 bits (131), Expect = 8e-09
Identities = 42/150 (28%), Positives = 69/150 (46%), Gaps = 32/150 (21%)
Query: 27 VCVLGHVDTGKTKILD---------------KLRRTNVQDGE-AGGITQQIGATNVPADA 70
+C++ HVD GKT + D K R + ++ E GIT I ++ +
Sbjct: 3 ICIIAHVDHGKTTLSDSLLASAGIISEKLAGKARYLDTREDEQERGIT--IKSSAI---- 56
Query: 71 IRENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHG 130
+ + ++ G L + +ID+PGH FS+ L D A++VVD + G
Sbjct: 57 ----SLYFEYEEEKMDGNDYL----INLIDSPGHVDFSSEVTAALRLTDGALVVVDAVEG 108
Query: 131 LEPQTIESI-NILKSKKTPFVVALNKIDRL 159
+ QT + L+ + P V+ +NKIDRL
Sbjct: 109 VCVQTETVLRQALEERVKP-VLVINKIDRL 137
>gnl|CDD|206729 cd04166, CysN_ATPS, CysN, together with protein CysD, forms the ATP
sulfurylase (ATPS) complex. CysN_ATPS subfamily. CysN,
together with protein CysD, form the ATP sulfurylase
(ATPS) complex in some bacteria and lower eukaryotes.
ATPS catalyzes the production of ATP sulfurylase (APS)
and pyrophosphate (PPi) from ATP and sulfate. CysD,
which catalyzes ATP hydrolysis, is a member of the ATP
pyrophosphatase (ATP PPase) family. CysN hydrolysis of
GTP is required for CysD hydrolysis of ATP; however,
CysN hydrolysis of GTP is not dependent on CysD
hydrolysis of ATP. CysN is an example of lateral gene
transfer followed by acquisition of new function. In
many organisms, an ATPS exists which is not
GTP-dependent and shares no sequence or structural
similarity to CysN.
Length = 209
Score = 53.7 bits (130), Expect = 9e-09
Identities = 29/67 (43%), Positives = 38/67 (56%), Gaps = 13/67 (19%)
Query: 98 IIDTPGHESFSNLRN--RGSSLCDIAILVVDIMHGLEPQT-----IESINILKSKKTPFV 150
I DTPGHE + RN G+S D+AIL+VD G+ QT I S +L + V
Sbjct: 82 IADTPGHEQY--TRNMVTGASTADLAILLVDARKGVLEQTRRHSYIAS--LLGIRH--VV 135
Query: 151 VALNKID 157
VA+NK+D
Sbjct: 136 VAVNKMD 142
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 53.5 bits (129), Expect = 3e-08
Identities = 29/67 (43%), Positives = 38/67 (56%), Gaps = 13/67 (19%)
Query: 98 IIDTPGHESFSNLRN--RGSSLCDIAILVVDIMHGLEPQT-----IESINILKSKKTPFV 150
I DTPGHE + RN G+S D+AIL+VD G+ QT I S +L + V
Sbjct: 90 IADTPGHEQY--TRNMATGASTADLAILLVDARKGVLEQTRRHSFIAS--LLGIRH--VV 143
Query: 151 VALNKID 157
VA+NK+D
Sbjct: 144 VAVNKMD 150
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 52.6 bits (127), Expect = 6e-08
Identities = 38/151 (25%), Positives = 61/151 (40%), Gaps = 40/151 (26%)
Query: 27 VCVLGHVDTGKTKILDKL--------RRTNVQDGEA----------GGITQQIGATNVPA 68
+ ++ H+D GKT + +++ + V DG A GIT AT +
Sbjct: 13 IGIVAHIDAGKTTLTERILFYTGIISKIGEVHDGAATMDWMEQEQERGITITSAATTLFW 72
Query: 69 DAIRENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIM 128
+ + +IDTPGH F+ R + D A++VVD +
Sbjct: 73 ----KGDYRIN------------------LIDTPGHVDFTIEVERSLRVLDGAVVVVDAV 110
Query: 129 HGLEPQTIESINILKSKKTPFVVALNKIDRL 159
G+EPQT P ++ +NK+DRL
Sbjct: 111 EGVEPQTETVWRQADKYGVPRILFVNKMDRL 141
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 52.6 bits (127), Expect = 7e-08
Identities = 23/61 (37%), Positives = 37/61 (60%)
Query: 98 IIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKID 157
++DTPGHE FS R + D A++V+D G+EPQT++ + + + P +NK+D
Sbjct: 85 LLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIEPQTLKLFEVCRLRDIPIFTFINKLD 144
Query: 158 R 158
R
Sbjct: 145 R 145
>gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. This translation
releasing factor, RF-3 (prfC) was originally described
as stop codon-independent, in contrast to peptide chain
release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and
RF-2 are closely related to each other, while RF-3 is
similar to elongation factors EF-Tu and EF-G; RF-1 is
active at UAA and UAG and RF-2 is active at UAA and UGA.
More recently, RF-3 was shown to be active primarily at
UGA stop codons in E. coli. All bacteria and organelles
have RF-1. The Mycoplasmas and organelles, which
translate UGA as Trp rather than as a stop codon, lack
RF-2. RF-3, in contrast, seems to be rare among bacteria
and is found so far only in Escherichia coli and some
other gamma subdivision Proteobacteria, in Synechocystis
PCC6803, and in Staphylococcus aureus [Protein
synthesis, Translation factors].
Length = 527
Score = 51.8 bits (124), Expect = 1e-07
Identities = 35/131 (26%), Positives = 61/131 (46%), Gaps = 3/131 (2%)
Query: 29 VLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGATNVPADAIR-ENTKHVRGPGGEVGG 87
++ H D GKT I +K+ AG + + + +D + E + + +
Sbjct: 16 IISHPDAGKTTITEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEMEKQRGISITTSVMQF 75
Query: 88 PGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKT 147
P + LL DTPGHE FS R + D ++V+D G+E +T + + + + + T
Sbjct: 76 PYRDCLVNLL--DTPGHEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLMEVTRLRDT 133
Query: 148 PFVVALNKIDR 158
P +NK+DR
Sbjct: 134 PIFTFMNKLDR 144
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 51.5 bits (124), Expect = 1e-07
Identities = 28/67 (41%), Positives = 40/67 (59%), Gaps = 13/67 (19%)
Query: 98 IIDTPGHESFSNLRN--RGSSLCDIAILVVDIMHGLEPQT-----IESINILKSKKTPFV 150
I DTPGHE ++ RN G+S CD+AIL++D G+ QT I ++ +K V
Sbjct: 111 IADTPGHEQYT--RNMATGASTCDLAILLIDARKGVLDQTRRHSFIATLLGIKH----LV 164
Query: 151 VALNKID 157
VA+NK+D
Sbjct: 165 VAVNKMD 171
>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 = 50.6 bits (122), Expect = 3e-07
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 10/78 (12%)
Query: 90 PLEIPGL---LIIDTPGHE---SFSNLRNRGS----SLCDIAILVVDIMHGLEPQTIESI 139
+E+ L ++IDT G + LR + D+A+LVVD G +E I
Sbjct: 48 AMELLPLGPVVLIDTAGLDDEGELGELRVEKTREVLDKTDLALLVVDAGVGPGEYELELI 107
Query: 140 NILKSKKTPFVVALNKID 157
LK +K P++V +NKID
Sbjct: 108 EELKERKIPYIVVINKID 125
>gnl|CDD|213679 TIGR02034, CysN, sulfate adenylyltransferase, large subunit.
Metabolic assimilation of sulfur from inorganic sulfate,
requires sulfate activation by coupling to a nucleoside,
for the production of high-energy nucleoside
phosphosulfates. This pathway appears to be similar in
all prokaryotic organisms. Activation is first achieved
through sulfation of sulfate with ATP by sulfate
adenylyltransferase (ATP sulfurylase) to produce
5'-phosphosulfate (APS), coupled by GTP hydrolysis.
Subsequently, APS is phosphorylated by an APS kinase to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In
Escherichia coli, ATP sulfurylase is a heterodimer
composed of two subunits encoded by cysD and cysN, with
APS kinase encoded by cysC. These genes are located in a
unidirectionally transcribed gene cluster, and have been
shown to be required for the synthesis of
sulfur-containing amino acids. Homologous to this E.coli
activation pathway are nodPQH gene products found among
members of the Rhizobiaceae family. These gene products
have been shown to exhibit ATP sulfurase and APS kinase
activity, yet are involved in Nod factor sulfation, and
sulfation of other macromolecules. With members of the
Rhizobiaceae family, nodQ often appears as a fusion of
cysN (large subunit of ATP sulfurase) and cysC (APS
kinase) [Central intermediary metabolism, Sulfur
metabolism].
Length = 406
Score = 50.4 bits (121), Expect = 3e-07
Identities = 25/65 (38%), Positives = 38/65 (58%), Gaps = 7/65 (10%)
Query: 97 LIIDTPGHESFSNLRN--RGSSLCDIAILVVDIMHGLEPQTIE--SINILKSKKTPFVVA 152
++ DTPGHE ++ RN G+S D+A+L+VD G+ QT I L + V+A
Sbjct: 83 IVADTPGHEQYT--RNMATGASTADLAVLLVDARKGVLEQTRRHSYIASLLGIRH-VVLA 139
Query: 153 LNKID 157
+NK+D
Sbjct: 140 VNKMD 144
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 50.4 bits (121), Expect = 3e-07
Identities = 37/143 (25%), Positives = 60/143 (41%), Gaps = 12/143 (8%)
Query: 25 AIVCVLGHVDTGKTKILDKLR--RTNVQDGEAG-GITQQIGATNVP---ADAIRENTKHV 78
+ ++GHVD GKT + L T+ E GI+ ++G + +
Sbjct: 5 VNIGMVGHVDHGKTTLTKALTGVWTDTHSEELKRGISIRLGYADAEIYKCPECDGPECYT 64
Query: 79 RGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGL-EPQTIE 137
P G + + +D PGHE+ G++L D A+LV+ +PQT E
Sbjct: 65 TEPVCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGALLVIAANEPCPQPQTRE 124
Query: 138 ---SINILKSKKTPFVVALNKID 157
++ I+ K V+ NKID
Sbjct: 125 HLMALEIIGIKN--IVIVQNKID 145
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 50.5 bits (121), Expect = 3e-07
Identities = 44/177 (24%), Positives = 60/177 (33%), Gaps = 34/177 (19%)
Query: 26 IVCVLGHVDTGKTKILDKLRRTNVQDG---EAG--GITQQIGATNVPADAIRENTKHVRG 80
I+ GH+D GKT +L L T E GIT +G +
Sbjct: 2 IIGTAGHIDHGKTTLLKAL--TGGVTDRLPEEKKRGITIDLGFYYRKLEDGV-------- 51
Query: 81 PGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESIN 140
+ ID PGH F + G D A+LVV GL QT E +
Sbjct: 52 ---------------MGFIDVPGHPDFISNLLAGLGGIDYALLVVAADEGLMAQTGEHLL 96
Query: 141 ILKSKKTP-FVVALNKIDRLYNWNTMNRRDVRDIIKSQESSVQTHKTVESARKGQEI 196
IL ++ L K DR+ + I + S SA+ G+ I
Sbjct: 97 ILDLLGIKNGIIVLTKADRV---DEARIEQKIKQILADLSLANAKIFKTSAKTGRGI 150
>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 = 48.6 bits (117), Expect = 3e-07
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 96 LLIIDTPG-HESFSNLRNR-----GSSL--CDIAILVVDIMHGLEPQTIESINILKSKKT 147
++ +DTPG H+ L R S+L D+ + VVD + + +LK KT
Sbjct: 53 IIFVDTPGIHKPKKKLGERMVKAAWSALKDVDLVLFVVDASEWIGEGDEFILELLKKSKT 112
Query: 148 PFVVALNKIDRLYN 161
P ++ LNKID + +
Sbjct: 113 PVILVLNKIDLVKD 126
>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 = 48.3 bits (116), Expect = 5e-07
Identities = 29/120 (24%), Positives = 46/120 (38%), Gaps = 22/120 (18%)
Query: 94 PGLLIIDTPG----------HESFSN-----LRNRGSSLCDIAILVVDIMHGLEPQTIES 138
++D PG E + L NR +L +L++D HG P +E
Sbjct: 45 DKFRLVDLPGYGYAKVSKEVREKWGKLIEEYLENR-ENLK-GVVLLIDARHGPTPIDLEM 102
Query: 139 INILKSKKTPFVVALNKIDRLYNWNTMNRRDVRDIIKSQESSVQTHKTVE--SARKGQEI 196
+ L+ PF++ L K D+L V IK + + V S++KG I
Sbjct: 103 LEFLEELGIPFLIVLTKADKL---KKSELAKVLKKIKEELNLFNILPPVILFSSKKGTGI 159
>gnl|CDD|206678 cd01891, TypA_BipA, Tyrosine phosphorylated protein A (TypA)/BipA
family belongs to ribosome-binding GTPases. BipA is a
protein belonging to the ribosome-binding family of
GTPases and is widely distributed in bacteria and
plants. BipA was originally described as a protein that
is induced in Salmonella typhimurium after exposure to
bactericidal/permeability-inducing protein (a cationic
antimicrobial protein produced by neutrophils), and has
since been identified in E. coli as well. The properties
thus far described for BipA are related to its role in
the process of pathogenesis by enteropathogenic E. coli.
It appears to be involved in the regulation of several
processes important for infection, including
rearrangements of the cytoskeleton of the host,
bacterial resistance to host defense peptides,
flagellum-mediated cell motility, and expression of K5
capsular genes. It has been proposed that BipA may
utilize a novel mechanism to regulate the expression of
target genes. In addition, BipA from enteropathogenic E.
coli has been shown to be phosphorylated on a tyrosine
residue, while BipA from Salmonella and from E. coli K12
strains is not phosphorylated under the conditions
assayed. The phosphorylation apparently modifies the
rate of nucleotide hydrolysis, with the phosphorylated
form showing greatly increased GTPase activity.
Length = 194
Score = 47.6 bits (114), Expect = 9e-07
Identities = 46/151 (30%), Positives = 59/151 (39%), Gaps = 45/151 (29%)
Query: 27 VCVLGHVDTGKTKILDKL------RRTNVQDGE----------AGGITQQIGATNVPADA 70
+ ++ HVD GKT ++D L R N + GE GIT I A N A
Sbjct: 5 IAIIAHVDHGKTTLVDALLKQSGTFRENEEVGERVMDSNDLERERGIT--ILAKNT---A 59
Query: 71 IRENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHG 130
I + IIDTPGH F R S+ D +L+VD G
Sbjct: 60 ITYKDTKIN------------------IIDTPGHADFGGEVERVLSMVDGVLLLVDASEG 101
Query: 131 LEPQTIESINILK---SKKTPFVVALNKIDR 158
PQT +LK +V +NKIDR
Sbjct: 102 PMPQT---RFVLKKALEAGLKPIVVINKIDR 129
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 48.6 bits (117), Expect = 1e-06
Identities = 24/61 (39%), Positives = 38/61 (62%)
Query: 98 IIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKID 157
++DTPGHE FS R + D A++V+D G+EPQT + + + + + TP +NK+D
Sbjct: 83 LLDTPGHEDFSEDTYRTLTAVDSALMVIDAAKGVEPQTRKLMEVCRLRDTPIFTFINKLD 142
Query: 158 R 158
R
Sbjct: 143 R 143
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 48.1 bits (116), Expect = 1e-06
Identities = 26/70 (37%), Positives = 35/70 (50%), Gaps = 10/70 (14%)
Query: 99 IDTPG-HESFSNLRNRG------SSL--CDIAILVVDIMHGLEPQTIESINILKSKKTPF 149
+DTPG H+ L NR SSL D+ + VVD + P + LK KTP
Sbjct: 58 VDTPGIHKPKRAL-NRAMNKAAWSSLKDVDLVLFVVDADEKIGPGDEFILEKLKKVKTPV 116
Query: 150 VVALNKIDRL 159
++ LNKID +
Sbjct: 117 ILVLNKIDLV 126
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 48.1 bits (115), Expect = 2e-06
Identities = 51/147 (34%), Positives = 59/147 (40%), Gaps = 46/147 (31%)
Query: 26 IVCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGATNVPADAIRENTKHVRG----- 80
I+ GHVD GKT +L Q I T V AD + E K RG
Sbjct: 2 IIATAGHVDHGKTTLL-----------------QAI--TGVNADRLPEEKK--RGMTIDL 40
Query: 81 -------PGGEVGGPGPLEIPGLLIIDTPGHESF-SNLRNRGSSLCDIAILVVDIMHGLE 132
P G V G ID PGHE F SN+ G D A+LVV G+
Sbjct: 41 GYAYWPQPDGRVLG----------FIDVPGHEKFLSNMLA-GVGGIDHALLVVACDDGVM 89
Query: 133 PQTIESINILKSKKTP-FVVALNKIDR 158
QT E + IL+ P VAL K DR
Sbjct: 90 AQTREHLAILQLTGNPMLTVALTKADR 116
>gnl|CDD|233394 TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA. This
bacterial (and Arabidopsis) protein, termed TypA or
BipA, a GTP-binding protein, is phosphorylated on a
tyrosine residue under some cellular conditions. Mutants
show altered regulation of some pathways, but the
precise function is unknown [Regulatory functions,
Other, Cellular processes, Adaptations to atypical
conditions, Protein synthesis, Translation factors].
Length = 594
Score = 47.7 bits (114), Expect = 2e-06
Identities = 38/140 (27%), Positives = 60/140 (42%), Gaps = 23/140 (16%)
Query: 27 VCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGATNVPADAIRE--------NTKHV 78
+ ++ HVD GKT ++D L + + + +++ +N D RE NT +
Sbjct: 4 IAIIAHVDHGKTTLVDALLKQSGTFRANEAVAERVMDSN---DLERERGITILAKNTA-I 59
Query: 79 RGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIES 138
R G ++ I+DTPGH F R + D +L+VD G PQT
Sbjct: 60 RYNGTKIN-----------IVDTPGHADFGGEVERVLGMVDGVLLLVDASEGPMPQTRFV 108
Query: 139 INILKSKKTPFVVALNKIDR 158
+ +V +NKIDR
Sbjct: 109 LKKALELGLKPIVVINKIDR 128
>gnl|CDD|130460 TIGR01393, lepA, GTP-binding protein LepA. LepA (GUF1 in
Saccaromyces) is a GTP-binding membrane protein related
to EF-G and EF-Tu. Two types of phylogenetic tree,
rooted by other GTP-binding proteins, suggest that
eukaryotic homologs (including GUF1 of yeast) originated
within the bacterial LepA family. The function is
unknown [Unknown function, General].
Length = 595
Score = 47.3 bits (113), Expect = 3e-06
Identities = 38/139 (27%), Positives = 64/139 (46%), Gaps = 21/139 (15%)
Query: 28 CVLGHVDTGKTKILDK-LRRTNVQDG--------EAGGITQQIGATNVPADAIRENTKHV 78
++ H+D GK+ + D+ L T ++ + ++ G T + A A+R N K
Sbjct: 7 SIIAHIDHGKSTLADRLLEYTGAISEREMREQVLDSMDLERERGIT-IKAQAVRLNYKAK 65
Query: 79 RGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIES 138
G L +IDTPGH FS +R + C+ A+L+VD G+E QT+ +
Sbjct: 66 DGETYV-----------LNLIDTPGHVDFSYEVSRSLAACEGALLLVDAAQGIEAQTLAN 114
Query: 139 INILKSKKTPFVVALNKID 157
+ + + +NKID
Sbjct: 115 VYLALENDLEIIPVINKID 133
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 47.2 bits (113), Expect = 4e-06
Identities = 44/150 (29%), Positives = 59/150 (39%), Gaps = 43/150 (28%)
Query: 27 VCVLGHVDTGKTKILDKLRR-----------------TNVQDGEAGGITQQIGATNVPAD 69
+ ++ HVD GKT ++D L + +N + E G IT I A N
Sbjct: 8 IAIIAHVDHGKTTLVDALLKQSGTFREREEVAERVMDSNDLEKERG-IT--ILAKNT--- 61
Query: 70 AIRENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMH 129
A+ N + I+DTPGH F R S+ D +L+VD
Sbjct: 62 AVNYNGTRIN------------------IVDTPGHADFGGEVERVLSMVDGVLLLVDASE 103
Query: 130 GLEPQT-IESINILKSKKTPFVVALNKIDR 158
G PQT L P VV +NKIDR
Sbjct: 104 GPMPQTRFVLKKALALGLKPIVV-INKIDR 132
>gnl|CDD|129581 TIGR00490, aEF-2, translation elongation factor aEF-2. This model
represents archaeal elongation factor 2, a protein more
similar to eukaryotic EF-2 than to bacterial EF-G, both
in sequence similarity and in sharing with eukaryotes
the property of having a diphthamide (modified His)
residue at a conserved position. The diphthamide can be
ADP-ribosylated by diphtheria toxin in the presence of
NAD [Protein synthesis, Translation factors].
Length = 720
Score = 46.8 bits (111), Expect = 5e-06
Identities = 50/160 (31%), Positives = 72/160 (45%), Gaps = 15/160 (9%)
Query: 7 KRREKIEENPEDENFMRAAIVCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGATNV 66
K +KI+E F+R + H+D GKT + D L AG I++++ +
Sbjct: 4 KMIDKIKELMWKPKFIRNIGIV--AHIDHGKTTLSDNLL------AGAGMISEELAGQQL 55
Query: 67 PAD-AIRENTKHVRGPGGEVGGPGPLEIPGLLI--IDTPGHESFSNLRNRGSSLCDIAIL 123
D +E + + V E LI IDTPGH F R D AI+
Sbjct: 56 YLDFDEQEQERGITINAANVSMVHEYEGNEYLINLIDTPGHVDFGGDVTRAMRAVDGAIV 115
Query: 124 VVDIMHGLEPQTIESI--NILKSKKTPFVVALNKIDRLYN 161
VV + G+ PQT E++ LK P V+ +NK+DRL N
Sbjct: 116 VVCAVEGVMPQT-ETVLRQALKENVKP-VLFINKVDRLIN 153
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 46.4 bits (111), Expect = 6e-06
Identities = 37/147 (25%), Positives = 63/147 (42%), Gaps = 20/147 (13%)
Query: 99 IDTPG-HESFSNL-----RNRGSSL--CDIAILVVDIMHGLEPQTIESINILKSKKTPFV 150
+DTPG H+ L + S+L D+ + VVD G P + LK KTP +
Sbjct: 59 VDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLKKTKTPVI 118
Query: 151 VALNKIDRLYNWNTMNRRDVRDIIKSQESSVQTHKTVE-SARKGQEI---CIKIEPIPGE 206
+ +NKID++ + + +I + + + V SA KG + I+ E
Sbjct: 119 LVVNKIDKVK-----PKTVLLKLIAFLKKLLPFKEIVPISALKGDNVDTLLEIIKEYLPE 173
Query: 207 APKMFGRHF--DEND-FLVSKISRQSI 230
P + D + FL ++I R+ +
Sbjct: 174 GPWYYPEDQITDRPERFLAAEIIREKL 200
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 46.7 bits (112), Expect = 6e-06
Identities = 37/152 (24%), Positives = 55/152 (36%), Gaps = 51/152 (33%)
Query: 30 LGHVDTGKTKILDKL--------RRTNVQDGEAG----------GITQQIGATNVPADAI 71
+GH GKT + + + R V+DG GI+ AT
Sbjct: 1 VGHSGAGKTTLTEAILFYTGAIHRIGEVEDGTTTMDFMPEERERGISITSAATTCEWKGH 60
Query: 72 RENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESF-----SNLRNRGSSLCDIAILVVD 126
+ N +IDTPGH F LR + D A++VV
Sbjct: 61 KIN-----------------------LIDTPGHVDFTGEVERALR-----VLDGAVVVVC 92
Query: 127 IMHGLEPQTIESINILKSKKTPFVVALNKIDR 158
+ G+EPQT + P ++ +NK+DR
Sbjct: 93 AVGGVEPQTETVWRQAEKYGVPRIIFVNKMDR 124
>gnl|CDD|206731 cd04168, TetM_like, Tet(M)-like family includes Tet(M), Tet(O),
Tet(W), and OtrA, containing tetracycline resistant
proteins. Tet(M), Tet(O), Tet(W), and OtrA are
tetracycline resistance genes found in Gram-positive and
Gram-negative bacteria. Tetracyclines inhibit protein
synthesis by preventing aminoacyl-tRNA from binding to
the ribosomal acceptor site. This subfamily contains
tetracycline resistance proteins that function through
ribosomal protection and are typically found on mobile
genetic elements, such as transposons or plasmids, and
are often conjugative. Ribosomal protection proteins are
homologous to the elongation factors EF-Tu and EF-G.
EF-G and Tet(M) compete for binding on the ribosomes.
Tet(M) has a higher affinity than EF-G, suggesting these
two proteins may have overlapping binding sites and that
Tet(M) must be released before EF-G can bind. Tet(M) and
Tet(O) have been shown to have ribosome-dependent GTPase
activity. These proteins are part of the GTP translation
factor family, which includes EF-G, EF-Tu, EF2, LepA,
and SelB.
Length = 237
Score = 45.7 bits (109), Expect = 7e-06
Identities = 25/62 (40%), Positives = 35/62 (56%)
Query: 98 IIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKID 157
IIDTPGH F R S+ D AILV+ + G++ QT +L+ P ++ +NKID
Sbjct: 68 IIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTRILFRLLRKLNIPTIIFVNKID 127
Query: 158 RL 159
R
Sbjct: 128 RA 129
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 45.4 bits (108), Expect = 1e-05
Identities = 37/153 (24%), Positives = 61/153 (39%), Gaps = 32/153 (20%)
Query: 25 AIVCVLGHVDTGKTKIL------------DKLRRTNVQDGEAGGITQQIGATNVP----A 68
+ ++GHVD GKT + ++L+R GIT ++G +
Sbjct: 11 VNIGMVGHVDHGKTTLTKALSGVWTDRHSEELKR---------GITIKLGYADAKIYKCP 61
Query: 69 DAIRENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDI- 127
+ R G L + +D PGHE+ G++L D A+LV+
Sbjct: 62 ECYRPECYTTEPKCPNCGAETELV-RRVSFVDAPGHETLMATMLSGAALMDGALLVIAAN 120
Query: 128 MHGLEPQTIE---SINILKSKKTPFVVALNKID 157
+PQT E ++ I+ K ++ NKID
Sbjct: 121 EPCPQPQTREHLMALEIIGIKN--IIIVQNKID 151
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G [Protein synthesis, Translation factors].
Length = 689
Score = 45.6 bits (108), Expect = 2e-05
Identities = 20/61 (32%), Positives = 33/61 (54%)
Query: 98 IIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKID 157
IIDTPGH F+ R + D A+ V+D + G++PQ+ + P + +NK+D
Sbjct: 79 IIDTPGHVDFTVEVERSLRVLDGAVAVLDAVGGVQPQSETVWRQANRYEVPRIAFVNKMD 138
Query: 158 R 158
+
Sbjct: 139 K 139
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 44.9 bits (107), Expect = 2e-05
Identities = 28/92 (30%), Positives = 46/92 (50%), Gaps = 30/92 (32%)
Query: 98 IIDTPGHESFSNLRN--RGSSLCDIAILVVDIMHGLEPQT-----------IESINILKS 144
+ DTPGHE ++ RN G+S D+AI++VD G+ QT I +
Sbjct: 108 VADTPGHEQYT--RNMVTGASTADLAIILVDARKGVLTQTRRHSFIASLLGIRHV----- 160
Query: 145 KKTPFVVALNKIDRLYNWNTMNRRDVRDIIKS 176
V+A+NK+D L +++ ++V D I +
Sbjct: 161 -----VLAVNKMD-LVDYD----QEVFDEIVA 182
>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 = 42.2 bits (100), Expect = 4e-05
Identities = 26/109 (23%), Positives = 43/109 (39%), Gaps = 12/109 (11%)
Query: 95 GLLIIDTPG-HESFSNLRNRGSSL------CDIAILVVDIMHGLEPQTIESINILKSKKT 147
+++IDTPG E R R D+ +LVVD + + +L+ +
Sbjct: 47 PVVLIDTPGLDEEGGLGRERVEEARQVADRADLVLLVVDSDLTPVEEE-AKLGLLRERGK 105
Query: 148 PFVVALNKIDRLYNWNTMNRRDVRDIIKSQESSVQTHKTVESARKGQEI 196
P ++ LNKID L + +R+ + SA G+ I
Sbjct: 106 PVLLVLNKID-LVP-ESEEEELLRERKLELLPDLPVIAV--SALPGEGI 150
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 43.1 bits (102), Expect = 7e-05
Identities = 39/176 (22%), Positives = 63/176 (35%), Gaps = 65/176 (36%)
Query: 27 VCVLGHVDTGKT---------------KILDKLRRTNVQDGEAG---------------- 55
+ +GHVD GK+ + ++KL + + G+
Sbjct: 10 LVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVLDKTKEERER 69
Query: 56 GITQQIGATNVPADAIRENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESF-SNLRNRG 114
G+T + + D IID PGH F N+ G
Sbjct: 70 GVTIDVAHSKFETDKYN-----------------------FTIIDAPGHRDFVKNMIT-G 105
Query: 115 SSLCDIAILVVD-------IMHGLEPQTIESINILKS-KKTPFVVALNKIDRLYNW 162
+S D+A+LVVD G+ QT E + ++ +VA+NK+D L +W
Sbjct: 106 ASQADVAVLVVDARDGEFEAGFGVGGQTREHAFLARTLGIKQLIVAVNKMD-LVSW 160
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 43.3 bits (103), Expect = 7e-05
Identities = 24/60 (40%), Positives = 35/60 (58%)
Query: 98 IIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKID 157
+IDTPGH FS +R + C+ A+LVVD G+E QT+ ++ + + LNKID
Sbjct: 80 LIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYLALENNLEIIPVLNKID 139
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 43.2 bits (101), Expect = 8e-05
Identities = 39/143 (27%), Positives = 61/143 (42%), Gaps = 29/143 (20%)
Query: 27 VCVLGHVDTGKTKILDKL--------RRTNVQDG--EAGGITQQIGATNVPAD-AIRENT 75
+ ++ HVD GKT ++DKL R Q+ ++ + ++ G T + + AI+ N
Sbjct: 8 IAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNTAIKWND 67
Query: 76 KHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQT 135
+ I+DTPGH F R S+ D +LVVD G PQT
Sbjct: 68 YRIN------------------IVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQT 109
Query: 136 IESINILKSKKTPFVVALNKIDR 158
+ +V +NK+DR
Sbjct: 110 RFVTKKAFAYGLKPIVVINKVDR 132
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This model
models orthologs of translation elongation factor EF-Tu
in bacteria, mitochondria, and chloroplasts, one of
several GTP-binding translation factors found by the
more general pfam model GTP_EFTU. The eukaryotic
conterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this model. EF-Tu is one
of the most abundant proteins in bacteria, as well as
one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation
[Protein synthesis, Translation factors].
Length = 394
Score = 42.5 bits (100), Expect = 1e-04
Identities = 47/154 (30%), Positives = 61/154 (39%), Gaps = 22/154 (14%)
Query: 9 REKIEENPEDENFMRAAIVCVLGHVDTGKTKILDKLRRTNVQDGEAGGIT-QQI-GATNV 66
+EK E N + +GHVD GKT + + ++G A QI A
Sbjct: 3 KEKFERTKPHVN------IGTIGHVDHGKTTLTAAITTVLAKEGGAAARAYDQIDNAPEE 56
Query: 67 PADAIRENTKHVRGPGGEVGGPGPLEIPG--LLIIDTPGHESFSNLRNRGSSLCDIAILV 124
A I NT HV E +D PGH + G++ D AILV
Sbjct: 57 KARGITINTAHVE-----------YETENRHYAHVDCPGHADYVKNMITGAAQMDGAILV 105
Query: 125 VDIMHGLEPQTIESINILKSKKTPF-VVALNKID 157
V G PQT E I + + P+ VV LNK D
Sbjct: 106 VSATDGPMPQTREHILLARQVGVPYIVVFLNKCD 139
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 42.2 bits (100), Expect = 1e-04
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 9/72 (12%)
Query: 95 GLLIIDTPGHESFSNL----RNRGSSL-----CDIAILVVDIMHGLEPQTIESINILKSK 145
++IDT G + R +L D+ + VVD G+ P E IL+
Sbjct: 52 EFILIDTGGLDDGDEDELQELIREQALIAIEEADVILFVVDGREGITPADEEIAKILRRS 111
Query: 146 KTPFVVALNKID 157
K P ++ +NKID
Sbjct: 112 KKPVILVVNKID 123
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 40.7 bits (95), Expect = 3e-04
Identities = 43/225 (19%), Positives = 82/225 (36%), Gaps = 36/225 (16%)
Query: 21 FMRAAIVCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGATNVPADAIRENTKHVRG 80
FM+ + VLG GKT +L++L V D G IG PA I ++++
Sbjct: 2 FMKEFKIVVLGDGGVGKTTLLNRL----VGDEFPEGYPPTIG-NLDPAKTIEPYRRNIK- 55
Query: 81 PGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIM---HGLE--PQT 135
L + DT G E + +LR + ++V D E +
Sbjct: 56 ---------------LQLWDTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEW 100
Query: 136 IESINILKSKKTPFVVALNKIDRLYNWNTMNRRDVRDIIKSQESSVQTHKTVESARKGQE 195
+E + L P ++ NKID + + + I +Q + + V + +
Sbjct: 101 LEELRELAPDDVPILLVGNKIDLF------DEQSSSEEILNQLNR-EVVLLVLAPKAVLP 153
Query: 196 ICIKIEPIPGEAPKMFGRHFDENDFLVSKISRQSIDACKDYFRDD 240
+ A + G + +E L ++ R+ ++ + +
Sbjct: 154 EVANPALLETSAKSLTGPNVNE---LFKELLRKLLEEIEKLVLKN 195
>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 = 41.3 bits (98), Expect = 3e-04
Identities = 22/94 (23%), Positives = 40/94 (42%), Gaps = 17/94 (18%)
Query: 97 LIIDTPG----------HESFSNLRNRGS-SLCDIAILVVDIMHGLEPQ--TIESINILK 143
+IDT G E +S LR + D+ +LV+D G+ Q I + L+
Sbjct: 223 TLIDTAGIRRKGKVTEGVEKYSVLRTLKAIERADVVLLVLDATEGITEQDLRIAGL-ALE 281
Query: 144 SKKTPFVVALNKIDRLYNWNTMNRRDVRDIIKSQ 177
+ K V+ +NK D + + T + ++ +
Sbjct: 282 AGK-ALVIVVNKWDLVKDEKTREE--FKKELRRK 312
Score = 37.8 bits (89), Expect = 0.004
Identities = 14/40 (35%), Positives = 20/40 (50%)
Query: 118 CDIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKID 157
D+ + VVD GL P+ E L+ P ++ NKID
Sbjct: 79 ADVILFVVDGREGLTPEDEEIAKWLRKSGKPVILVANKID 118
>gnl|CDD|206671 cd01884, EF_Tu, Elongation Factor Tu (EF-Tu) GTP-binding proteins.
EF-Tu subfamily. This subfamily includes orthologs of
translation elongation factor EF-Tu in bacteria,
mitochondria, and chloroplasts. It is one of several
GTP-binding translation factors found in the larger
family of GTP-binding elongation factors. The eukaryotic
counterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this family. EF-Tu is
one of the most abundant proteins in bacteria, as well
as, one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation.
Length = 195
Score = 40.3 bits (95), Expect = 3e-04
Identities = 42/142 (29%), Positives = 53/142 (37%), Gaps = 36/142 (25%)
Query: 31 GHVDTGKT-------KILDKLRRTNVQDGEAGGITQQI-GATNVPADAIRENTKHV---- 78
GHVD GKT K+L K + + +I A A I NT HV
Sbjct: 9 GHVDHGKTTLTAAITKVLAKKGGAKAKKYD------EIDKAPEEKARGITINTAHVEYET 62
Query: 79 --RGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTI 136
R +D PGH + G++ D AILVV G PQT
Sbjct: 63 ANRHYAH---------------VDCPGHADYIKNMITGAAQMDGAILVVSATDGPMPQTR 107
Query: 137 ESINILKSKKTP-FVVALNKID 157
E + + + P VV LNK D
Sbjct: 108 EHLLLARQVGVPYIVVFLNKAD 129
>gnl|CDD|206673 cd01886, EF-G, Elongation factor G (EF-G) family involved in both
the elongation and ribosome recycling phases of protein
synthesis. Translocation is mediated by EF-G (also
called translocase). The structure of EF-G closely
resembles that of the complex between EF-Tu and tRNA.
This is an example of molecular mimicry; a protein
domain evolved so that it mimics the shape of a tRNA
molecule. EF-G in the GTP form binds to the ribosome,
primarily through the interaction of its EF-Tu-like
domain with the 50S subunit. The binding of EF-G to the
ribosome in this manner stimulates the GTPase activity
of EF-G. On GTP hydrolysis, EF-G undergoes a
conformational change that forces its arm deeper into
the A site on the 30S subunit. To accommodate this
domain, the peptidyl-tRNA in the A site moves to the P
site, carrying the mRNA and the deacylated tRNA with it.
The ribosome may be prepared for these rearrangements by
the initial binding of EF-G as well. The dissociation of
EF-G leaves the ribosome ready to accept the next
aminoacyl-tRNA into the A site. This group contains both
eukaryotic and bacterial members.
Length = 270
Score = 40.6 bits (96), Expect = 4e-04
Identities = 40/146 (27%), Positives = 54/146 (36%), Gaps = 41/146 (28%)
Query: 32 HVDTGKT----KIL---DKLRRT-NVQDGEAG----------GITQQIGATNVPADAIRE 73
H+D GKT +IL ++ + V G A GIT Q AT R
Sbjct: 7 HIDAGKTTTTERILYYTGRIHKIGEVHGGGATMDWMEQERERGITIQSAATTCFWKDHRI 66
Query: 74 NTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEP 133
N IIDTPGH F+ R + D A+ V D + G++P
Sbjct: 67 N-----------------------IIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVQP 103
Query: 134 QTIESINILKSKKTPFVVALNKIDRL 159
QT P + +NK+DR
Sbjct: 104 QTETVWRQADRYGVPRIAFVNKMDRT 129
>gnl|CDD|129574 TIGR00483, EF-1_alpha, translation elongation factor EF-1 alpha.
This model represents the counterpart of bacterial EF-Tu
for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1
alpha). The trusted cutoff is set fairly high so that
incomplete sequences will score between suggested and
trusted cutoff levels [Protein synthesis, Translation
factors].
Length = 426
Score = 41.0 bits (96), Expect = 4e-04
Identities = 40/155 (25%), Positives = 65/155 (41%), Gaps = 25/155 (16%)
Query: 27 VCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQI-----------GATNVPADAIRENT 75
V +GHVD GK+ + L + G I +Q G + + +
Sbjct: 10 VAFIGHVDHGKSTTVGHLLY------KCGAIDEQTIEKFEKEAQEKGKASFEFAWVMDRL 63
Query: 76 KHVRGPGGEVG-GPGPLEIPG--LLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHG-- 130
K R G + E + I+D PGH F G+S D A+LVV + G
Sbjct: 64 KEERERGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGDGEF 123
Query: 131 -LEPQTIESINILKSKK-TPFVVALNKIDRLYNWN 163
++PQT E + ++ +VA+NK+D + N++
Sbjct: 124 EVQPQTREHAFLARTLGINQLIVAINKMDSV-NYD 157
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 40.6 bits (96), Expect = 5e-04
Identities = 27/65 (41%), Positives = 37/65 (56%), Gaps = 4/65 (6%)
Query: 99 IDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESI--NILKSKKTPFVVALNKI 156
IDTPGH F R D AI+VVD + G+ PQT E++ L+ + P V+ +NK+
Sbjct: 92 IDTPGHVDFGGDVTRAMRAVDGAIVVVDAVEGVMPQT-ETVLRQALRERVKP-VLFINKV 149
Query: 157 DRLYN 161
DRL
Sbjct: 150 DRLIK 154
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 40.3 bits (95), Expect = 6e-04
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 5/64 (7%)
Query: 98 IIDTPGHESFSNLRNRGSSLCDIAILVV---DIMHGLEPQTIESINILKSKKTP-FVVAL 153
I+D PGH F G+S D A+LVV D G+ PQT E + + ++ +VA+
Sbjct: 88 IVDCPGHRDFVKNMITGASQADAAVLVVAADDAG-GVMPQTREHVFLARTLGINQLIVAI 146
Query: 154 NKID 157
NK+D
Sbjct: 147 NKMD 150
>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 = 39.0 bits (92), Expect = 6e-04
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 8/69 (11%)
Query: 97 LIIDTPGHESFSNL---RNRGSSL-----CDIAILVVDIMHGLEPQTIESINILKSKKTP 148
++IDT G E R + D+ + VVD GL P E L+ K P
Sbjct: 48 ILIDTGGIEPDDEGISKEIREQAEIAIEEADVILFVVDGREGLTPADEEIAKYLRKSKKP 107
Query: 149 FVVALNKID 157
++ +NKID
Sbjct: 108 VILVVNKID 116
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 39.5 bits (93), Expect = 7e-04
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 110 LRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKIDRL 159
L R ++L +L++D H + E I L P +V L K D+L
Sbjct: 101 LEKR-ANLK-GVVLLIDARHPPKDLDREMIEFLLELGIPVIVVLTKADKL 148
>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 = 39.0 bits (92), Expect = 7e-04
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 110 LRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKIDRL 159
L R +L + +L++DI H L+ +E I L+ + P ++ L K D+L
Sbjct: 95 LEKR-ENLKGV-VLLMDIRHPLKELDLEMIEWLRERGIPVLIVLTKADKL 142
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 39.9 bits (94), Expect = 8e-04
Identities = 25/62 (40%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 99 IDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTP-FVVALNKID 157
+D PGH + G++ D AILVV G PQT E I + K P VV LNK D
Sbjct: 80 VDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTKEHILLAKQVGVPNIVVFLNKED 139
Query: 158 RL 159
++
Sbjct: 140 QV 141
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 39.5 bits (93), Expect = 9e-04
Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 10/66 (15%)
Query: 98 IIDTPG-----HESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPFVVA 152
+IDTPG E+ S LR D A++VV+ G+E T + L K P ++
Sbjct: 68 LIDTPGYADFVGETLSALR-----AVDAALIVVEAQSGVEVGTEKVWEFLDDAKLPRIIF 122
Query: 153 LNKIDR 158
+NK+DR
Sbjct: 123 INKMDR 128
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 39.8 bits (93), Expect = 9e-04
Identities = 41/140 (29%), Positives = 57/140 (40%), Gaps = 24/140 (17%)
Query: 27 VCVLGHVDTGKTKILDKLRRTNVQDGEAGGIT-QQIG-ATNVPADAIRENTKHV------ 78
V +GHVD GKT + + + ++G+A + +I A A I T HV
Sbjct: 64 VGTIGHVDHGKTTLTAAITKVLAEEGKAKAVAFDEIDKAPEEKARGITIATAHVEYETAK 123
Query: 79 RGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIES 138
R +D PGH + G++ D ILVV G PQT E
Sbjct: 124 RHYAH---------------VDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEH 168
Query: 139 INILKSKKTP-FVVALNKID 157
I + + P VV LNK+D
Sbjct: 169 ILLARQVGVPSLVVFLNKVD 188
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 39.0 bits (91), Expect = 9e-04
Identities = 36/142 (25%), Positives = 55/142 (38%), Gaps = 19/142 (13%)
Query: 20 NFMRAAIVCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGATNVPADAIRENTKHVR 79
N M + V+G V GKT + L + + T A ++ K
Sbjct: 6 NKMIETKIVVIGPVGAGKTTFVRAL------------SDKPLVITEADASSVSGKGKRPT 53
Query: 80 GPGGEVGGPGPLEI---PGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTI 136
+ G +E+ G+ + TPG E F + S AI++VD +
Sbjct: 54 TVAMD---FGSIELDEDTGVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAE 110
Query: 137 ESINILKSKKT-PFVVALNKID 157
E I+ L S+ P VVA+NK D
Sbjct: 111 EIIDFLTSRNPIPVVVAINKQD 132
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 39.8 bits (94), Expect = 0.001
Identities = 40/152 (26%), Positives = 63/152 (41%), Gaps = 30/152 (19%)
Query: 25 AIVCVLGHVDTGKTKI--------LDK----LRRTNVQDGEAGGITQQIGATNVP---AD 69
+ ++GHVD GKT + D+ L+R GIT ++G +
Sbjct: 10 VNIGMVGHVDHGKTTLVQALTGVWTDRHSEELKR---------GITIRLGYADATIRKCP 60
Query: 70 AIRENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDI-M 128
E + P G + + +D PGHE+ G++L D AILV+
Sbjct: 61 DCEEPEAYTTEPKCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGAILVIAANE 120
Query: 129 HGLEPQTIE---SINILKSKKTPFVVALNKID 157
+PQT E +++I+ K V+ NKID
Sbjct: 121 PCPQPQTKEHLMALDIIGIKN--IVIVQNKID 150
>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 = 37.3 bits (87), Expect = 0.001
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 10/70 (14%)
Query: 96 LLIIDTPG--HESFSNLRNRGSSL-------CDIAILVVDIMHGLEPQTIESINIL-KSK 145
++++DTPG + G + D+ +LVVD GL E + L K
Sbjct: 48 IILVDTPGLIEGASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEELEKLP 107
Query: 146 KTPFVVALNK 155
K P ++ LNK
Sbjct: 108 KKPIILVLNK 117
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 37.9 bits (88), Expect = 0.002
Identities = 22/70 (31%), Positives = 30/70 (42%), Gaps = 11/70 (15%)
Query: 98 IIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKS--------KKTPF 149
I+DT G SF +R D LV + +P++ E + L+ K P
Sbjct: 51 ILDTSGSYSFPAMRKLSIQNGDAFALVYSVD---DPESFEEVKRLREEILEVKEDKFVPI 107
Query: 150 VVALNKIDRL 159
VV NKID L
Sbjct: 108 VVVGNKIDSL 117
>gnl|CDD|206670 cd01883, EF1_alpha, Elongation Factor 1-alpha (EF1-alpha) protein
family. EF1 is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to the ribosomes. EF1 is
composed of four subunits: the alpha chain which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This subfamily is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea
(aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha
interacts with the actin of the eukaryotic cytoskeleton
and may thereby play a role in cellular transformation
and apoptosis. EF-Tu can have no such role in bacteria.
In humans, the isoform eEF1A2 is overexpressed in 2/3 of
breast cancers and has been identified as a putative
oncogene. This subfamily also includes Hbs1, a G protein
known to be important for efficient growth and protein
synthesis under conditions of limiting translation
initiation in yeast, and to associate with Dom34. It has
been speculated that yeast Hbs1 and Dom34 proteins may
function as part of a complex with a role in gene
expression.
Length = 219
Score = 37.5 bits (88), Expect = 0.003
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 14/71 (19%)
Query: 98 IIDTPGHESF-SNLRNRGSSLCDIAILVVDIMHG-------LEPQTIESINILKS---KK 146
IID PGH F N+ G+S D+A+LVV G QT E + ++ K+
Sbjct: 81 IIDAPGHRDFVKNMIT-GASQADVAVLVVSARKGEFEAGFEKGGQTREHALLARTLGVKQ 139
Query: 147 TPFVVALNKID 157
+VA+NK+D
Sbjct: 140 --LIVAVNKMD 148
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 37.7 bits (89), Expect = 0.004
Identities = 26/61 (42%), Positives = 35/61 (57%), Gaps = 4/61 (6%)
Query: 99 IDTPGHESFSNLRNRGSSL--CDIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKI 156
IDTPGH FS +R SL C+ A+LVVD G+E QT+ ++ + + LNKI
Sbjct: 79 IDTPGHVDFSYEVSR--SLAACEGALLVVDASQGVEAQTLANVYLALENDLEIIPVLNKI 136
Query: 157 D 157
D
Sbjct: 137 D 137
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 37.7 bits (87), Expect = 0.005
Identities = 29/83 (34%), Positives = 42/83 (50%), Gaps = 3/83 (3%)
Query: 99 IDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTP-FVVALNKID 157
+D PGH + G++ D AILVV G PQT E I + K P VV LNK D
Sbjct: 149 VDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFLNKQD 208
Query: 158 RLYNWNTMN--RRDVRDIIKSQE 178
++ + + +VR+++ S E
Sbjct: 209 QVDDEELLELVELEVRELLSSYE 231
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 37.2 bits (87), Expect = 0.006
Identities = 24/60 (40%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 99 IDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPF-VVALNKID 157
+D PGH + G++ D AILVV G PQT E I + + P+ VV LNK+D
Sbjct: 80 VDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLARQVGVPYLVVFLNKVD 139
>gnl|CDD|206675 cd01888, eIF2_gamma, Gamma subunit of initiation factor 2 (eIF2
gamma). eIF2 is a heterotrimeric translation initiation
factor that consists of alpha, beta, and gamma subunits.
The GTP-bound gamma subunit also binds initiator
methionyl-tRNA and delivers it to the 40S ribosomal
subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is
released from the ribosome. The gamma subunit has no
intrinsic GTPase activity, but is stimulated by the
GTPase activating protein (GAP) eIF5, and GDP/GTP
exchange is stimulated by the guanine nucleotide
exchange factor (GEF) eIF2B. eIF2B is a heteropentamer,
and the epsilon chain binds eIF2. Both eIF5 and
eIF2B-epsilon are known to bind strongly to eIF2-beta,
but have also been shown to bind directly to eIF2-gamma.
It is possible that eIF2-beta serves simply as a
high-affinity docking site for eIF5 and eIF2B-epsilon,
or that eIF2-beta serves a regulatory role. eIF2-gamma
is found only in eukaryotes and archaea. It is closely
related to SelB, the selenocysteine-specific elongation
factor from eubacteria. The translational factor
components of the ternary complex, IF2 in eubacteria and
eIF2 in eukaryotes are not the same protein (despite
their unfortunately similar names). Both factors are
GTPases; however, eubacterial IF-2 is a single
polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is
a member of the same family as eubacterial IF2, but the
two proteins are only distantly related. This family
includes translation initiation, elongation, and release
factors.
Length = 197
Score = 36.5 bits (85), Expect = 0.006
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 12/67 (17%)
Query: 98 IIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLE----PQTIE---SINILKSKKTPFV 150
+D PGHE G+++ D A+L++ E PQT E ++ I+ K +
Sbjct: 81 FVDCPGHEILMATMLSGAAVMDGALLLIA---ANEPCPQPQTSEHLAALEIMGLKH--II 135
Query: 151 VALNKID 157
+ NKID
Sbjct: 136 ILQNKID 142
>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 = 36.7 bits (85), Expect = 0.008
Identities = 38/182 (20%), Positives = 66/182 (36%), Gaps = 37/182 (20%)
Query: 89 GPLEIPGLLI--IDTPG-------------HESFSNLRNRGSSLCDIAILVVDIMHGLEP 133
G E+ G+LI +DT G +SF ++ D+ I V+D L
Sbjct: 244 GDFELNGILIKLLDTAGIREHADFVERLGIEKSFKAIKQ-----ADLVIYVLDASQPLTK 298
Query: 134 QTIESINILKSKKTPFVVALNKIDRLYNWNTMNRRDVRDIIKSQESS-VQTHKTVESARK 192
I L K PF++ LNKID + ++ SS V + + +
Sbjct: 299 DD-FLIIDLNKSKKPFILVLNKIDL-----------KINSLEFFVSSKVLNSSNLSAKQL 346
Query: 193 GQEICIKIEPIPGEAPKMFGRHFDENDFLVSKISRQSIDACKDY--FRDDLQKTDWQLMV 250
+ + + + + + + E D + + I K + L K D QL +
Sbjct: 347 KIKALVDL--LTQKINAFYSKERVELDDYLISSWQAMILLEKAIAQLQQFLSKLDRQLFL 404
Query: 251 DL 252
D+
Sbjct: 405 DM 406
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 36.7 bits (86), Expect = 0.009
Identities = 25/62 (40%), Positives = 36/62 (58%), Gaps = 2/62 (3%)
Query: 98 IIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSK-KTPFVVALNKI 156
IIDTPGH F+ R + D A+ V D + G+EPQ+ E++ K P +V +NK+
Sbjct: 77 IIDTPGHVDFTIEVERSLRVLDGAVAVFDAVSGVEPQS-ETVWRQADKYGVPRIVFVNKM 135
Query: 157 DR 158
DR
Sbjct: 136 DR 137
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 36.5 bits (85), Expect = 0.011
Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 99 IDTPGHESFSNLRN--RGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPF-VVALNK 155
+D PGH + ++N G++ D AILVV G PQT E I + + P+ VV LNK
Sbjct: 80 VDCPGHADY--VKNMITGAAQMDGAILVVAATDGPMPQTREHILLARQVGVPYIVVFLNK 137
Query: 156 ID 157
+D
Sbjct: 138 VD 139
>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 = 35.1 bits (82), Expect = 0.015
Identities = 28/122 (22%), Positives = 48/122 (39%), Gaps = 17/122 (13%)
Query: 90 PLEIPG--LLIIDTPG----------HESFSNLRNRGS-SLCDIAILVVDIMHGLEPQTI 136
P E G +IDT G E +S LR + D+ +LV+D G+ Q +
Sbjct: 44 PFEYDGQKYTLIDTAGIRKKGKVTEGIEKYSVLRTLKAIERADVVLLVLDASEGITEQDL 103
Query: 137 ESIN-ILKSKKTPFVVALNKIDRLYNWNTMNRRDVRDIIKSQESSVQTHKTVE-SARKGQ 194
IL+ K ++ +NK D + ++ ++ + + V SA GQ
Sbjct: 104 RIAGLILEEGK-ALIIVVNKWDLVEKDEK-TMKEFEKELRRKLPFLDYAPIVFISALTGQ 161
Query: 195 EI 196
+
Sbjct: 162 GV 163
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 35.8 bits (83), Expect = 0.018
Identities = 41/149 (27%), Positives = 66/149 (44%), Gaps = 33/149 (22%)
Query: 29 VLGHVDTGKTKILDKL---------------RRTNV-QDGEAGGITQQIGATNVPADAIR 72
V+ HVD GK+ + D L R T+ D + GIT I +T +
Sbjct: 24 VIAHVDHGKSTLTDSLVCKAGIISSKNAGDARFTDTRADEQERGIT--IKSTGI------ 75
Query: 73 ENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLE 132
+ + + P I +ID+PGH FS+ + D A++VVD + G+
Sbjct: 76 --SLYYEHDLEDGDDKQPFLIN---LIDSPGHVDFSSEVTAALRVTDGALVVVDCVEGVC 130
Query: 133 PQTIESI--NILKSKKTPFVVALNKIDRL 159
QT E++ L+ + P V+ +NK+DR
Sbjct: 131 VQT-ETVLRQALQERIRP-VLFINKVDRA 157
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 35.9 bits (83), Expect = 0.022
Identities = 46/150 (30%), Positives = 71/150 (47%), Gaps = 31/150 (20%)
Query: 29 VLGHVDTGKTKILDKL---------------RRTNVQDGEAG-GITQQIGATNVPA--DA 70
V+ HVD GK+ + D L R T+ + EA GIT I +T + +
Sbjct: 24 VIAHVDHGKSTLTDSLVAAAGIIAQEVAGDVRMTDTRADEAERGIT--IKSTGISLYYEM 81
Query: 71 IRENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHG 130
E+ K +G E G L + +ID+PGH FS+ + D A++VVD + G
Sbjct: 82 TDESLKDFKG---ERDGNEYL----INLIDSPGHVDFSSEVTAALRITDGALVVVDCIEG 134
Query: 131 LEPQTIESI--NILKSKKTPFVVALNKIDR 158
+ QT E++ L + P V+ +NK+DR
Sbjct: 135 VCVQT-ETVLRQALGERIRP-VLTVNKMDR 162
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 34.4 bits (80), Expect = 0.023
Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 16/72 (22%)
Query: 96 LLIIDTPGHESFSNLRN---RGSSLCDIAILVVDIMHGLEPQTIESI----NILK---SK 145
L I DT G E F ++ + RG AILV D+ + ++ E++ N LK
Sbjct: 51 LQIWDTAGQERFRSITSSYYRG---AHGAILVYDVTN---RESFENLDKWLNELKEYAPP 104
Query: 146 KTPFVVALNKID 157
P ++ NK D
Sbjct: 105 NIPIILVGNKSD 116
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 35.0 bits (82), Expect = 0.027
Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 26/95 (27%)
Query: 97 LIIDTPG-------HES---FSNLRNRGSSL-----CDIAILVVDIMHGLEPQ--TIESI 139
+IDT G E +S +R +L D+ +LV+D G+ Q I +
Sbjct: 224 TLIDTAGIRRKGKVTEGVEKYSVIR----TLKAIERADVVLLVIDATEGITEQDLRIAGL 279
Query: 140 NILKSKKTPFVVALNKIDRLYNWNTMN--RRDVRD 172
L++ + V+ +NK D + TM ++++R
Sbjct: 280 -ALEAGR-ALVIVVNKWDLVDE-KTMEEFKKELRR 311
Score = 33.9 bits (79), Expect = 0.080
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 118 CDIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKID 157
D+ + VVD GL P E IL+ P ++ +NK+D
Sbjct: 81 ADVILFVVDGRAGLTPADEEIAKILRKSNKPVILVVNKVD 120
>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 = 34.7 bits (80), Expect = 0.035
Identities = 33/147 (22%), Positives = 54/147 (36%), Gaps = 22/147 (14%)
Query: 99 IDTPG----HESFSNLRNRG--SSL--CDIAILVVDIMHGLEPQTIESINILKSKKTPFV 150
IDTPG S + L + S++ D+ + VVD + L++ K P V
Sbjct: 53 IDTPGFHEKKHSLNRLMMKEARSAIGGVDLILFVVDSDQWN-GDGEFVLTKLQNLKRPVV 111
Query: 151 VALNKIDRLYNWNTMNRRDVRDIIKSQESSVQTHKTVE-SARKG---QEICIKIEPIPGE 206
+ NK+D + + +I V SA G + IE E
Sbjct: 112 LTRNKLDN------KFKDKLLPLIDKYAILEDFKDIVPISALTGDNTSFLAAFIEVHLPE 165
Query: 207 APKMFGRHF---DENDFLVSKISRQSI 230
P + + + F +S+I R+ I
Sbjct: 166 GPFRYPEDYVTDQPDRFKISEIIREKI 192
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 35.1 bits (81), Expect = 0.035
Identities = 39/158 (24%), Positives = 62/158 (39%), Gaps = 36/158 (22%)
Query: 26 IVCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGATNVPADAIRENTKHVRGPGGEV 85
+V V GHVD GK+ ++ L + DG+ GAT D + + RG ++
Sbjct: 119 LVGVAGHVDHGKSTLVGVLVTGRLDDGD--------GATRSYLD--VQKHEVERGLSADI 168
Query: 86 ---------GGPGPLEIPG---------------LLIIDTPGHESF--SNLRNRGSSLCD 119
G L+ P + +DT GHE + + +R D
Sbjct: 169 SLRVYGFDDGKVVRLKNPLDEAEKAAVVKRADKLVSFVDTVGHEPWLRTTIRGLLGQKVD 228
Query: 120 IAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKID 157
+LVV G+ T E + I + + P +V + KID
Sbjct: 229 YGLLVVAADDGVTKMTKEHLGIALAMELPVIVVVTKID 266
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 34.8 bits (81), Expect = 0.040
Identities = 33/136 (24%), Positives = 52/136 (38%), Gaps = 15/136 (11%)
Query: 118 CDIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKIDRLYNWNTMNRRDVRDIIKSQ 177
D+ + V+D L+ + + I +L KK VV LNK D V I
Sbjct: 297 ADLVLFVLDASQPLDKEDLALIELLPKKKPIIVV-LNKADL-----------VSKIELES 344
Query: 178 ESSVQTHKTVE-SARKGQEICIKIEPIPGEAPKMFGRHFDENDFLVSKISRQSIDACKDY 236
E + SA+ G+ + E I K G E FL + Q ++ ++
Sbjct: 345 EKLANGDAIISISAKTGEGLDALREAIKQLFGKGLGN--QEGLFLSNLRHIQLLEQAAEH 402
Query: 237 FRDDLQKTDWQLMVDL 252
D LQ+ + +DL
Sbjct: 403 LEDALQQLELGQPLDL 418
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 34.0 bits (78), Expect = 0.061
Identities = 25/70 (35%), Positives = 32/70 (45%), Gaps = 12/70 (17%)
Query: 98 IIDTPGHESFSNLRNRGSSLCDIAILVVDIMHG-------LEPQTIESI---NILKSKKT 147
IID PGH F G+S D+AILVV G + QT E L K+
Sbjct: 89 IIDAPGHRDFIKNMITGTSQADVAILVVASTAGEFEAGISKDGQTREHALLAFTLGVKQ- 147
Query: 148 PFVVALNKID 157
+V +NK+D
Sbjct: 148 -MIVCINKMD 156
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 33.6 bits (78), Expect = 0.062
Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 7/86 (8%)
Query: 110 LRNRGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKIDRL-YNWNTMNRR 168
LR R +L +L++D H L+ ++ I LK P ++ L K D+L +
Sbjct: 101 LRTR-ENLK-GVVLLIDSRHPLKELDLQMIEWLKEYGIPVLIVLTKADKLKKGERKKQLK 158
Query: 169 DVRDIIKSQESSVQTHKTVESARKGQ 194
VR +K + V S+ K Q
Sbjct: 159 KVRKALKFGDDEVILF----SSLKKQ 180
>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 = 33.3 bits (77), Expect = 0.064
Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 9/72 (12%)
Query: 95 GLLIIDTPGHESFSNLRNRGS----SLCDIAILVVDIMHGL---EPQTIESINILKSKKT 147
G++++DTPG S + D I V+ L E + ++ I S K
Sbjct: 47 GVVLVDTPGLNSTIEHHTEITESFLPRADAVIFVLSADQPLTESEREFLKEIL-KWSGKK 105
Query: 148 PFVVALNKIDRL 159
F V LNKID L
Sbjct: 106 IFFV-LNKIDLL 116
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 33.6 bits (78), Expect = 0.083
Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 99 IDTPGHESFSNLRN--RGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPF-VVALNK 155
+D PGH + ++N G++ D AILVV G PQT E I + + P+ VV LNK
Sbjct: 80 VDCPGHADY--VKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFLNK 137
Query: 156 ID 157
D
Sbjct: 138 CD 139
>gnl|CDD|217326 pfam03029, ATP_bind_1, Conserved hypothetical ATP binding protein.
Members of this family are found in a range of archaea
and eukaryotes and have hypothesised ATP binding
activity.
Length = 235
Score = 33.1 bits (76), Expect = 0.084
Identities = 18/75 (24%), Positives = 27/75 (36%), Gaps = 13/75 (17%)
Query: 96 LLIIDTPGHESFSNLRNRGSSLCD--------IAILVVDIMHGLEPQT-IESI----NIL 142
+ DTPG + + A+ +VD +P + +I+
Sbjct: 92 YYLFDTPGQIELFTHWESLARGVEALEASLRLGAVYLVDTRRLTDPSDFFSGLLYALSIM 151
Query: 143 KSKKTPFVVALNKID 157
PFVVALNK D
Sbjct: 152 LRLGLPFVVALNKFD 166
>gnl|CDD|206697 cd04116, Rab9, Rab GTPase family 9 (Rab9). Rab9 is found in late
endosomes, together with mannose 6-phosphate receptors
(MPRs) and the tail-interacting protein of 47 kD
(TIP47). Rab9 is a key mediator of vesicular transport
from late endosomes to the trans-Golgi network (TGN) by
redirecting the MPRs. Rab9 has been identified as a key
component for the replication of several viruses,
including HIV1, Ebola, Marburg, and measles, making it a
potential target for inhibiting a variety of viruses.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 32.9 bits (75), Expect = 0.092
Identities = 28/79 (35%), Positives = 35/79 (44%), Gaps = 12/79 (15%)
Query: 91 LEIPG----LLIIDTPGHESFSNLRN---RGSSLCDIAILVVDI--MHGLEPQTIESIN- 140
LE+ G L I DT G E F +LR RGS C + V D L E I
Sbjct: 47 LEVDGHFVTLQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYY 106
Query: 141 --ILKSKKTPFVVALNKID 157
+ + + PFV+ NKID
Sbjct: 107 ADVKEPESFPFVILGNKID 125
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 160
Score = 32.5 bits (75), Expect = 0.098
Identities = 21/65 (32%), Positives = 28/65 (43%), Gaps = 5/65 (7%)
Query: 98 IIDTPGHESFSNLRNRGSSLCDIAILVVDI--MHGLE--PQTIESI-NILKSKKTPFVVA 152
I+DT G E FS +R++ D ILV I E E I + + P V+
Sbjct: 51 ILDTAGQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLV 110
Query: 153 LNKID 157
NK D
Sbjct: 111 GNKCD 115
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 32.9 bits (76), Expect = 0.14
Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 99 IDTPGHESFSNLRN--RGSSLCDIAILVVDIMHGLEPQTIESINILKSKKTPF-VVALNK 155
+D PGH + ++N G++ D AILVV G PQT E I + + P+ VV LNK
Sbjct: 80 VDCPGHADY--VKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFLNK 137
Query: 156 ID 157
D
Sbjct: 138 CD 139
>gnl|CDD|227510 COG5183, SSM4, Protein involved in mRNA turnover and stability [RNA
processing and modification].
Length = 1175
Score = 33.0 bits (75), Expect = 0.16
Identities = 27/142 (19%), Positives = 45/142 (31%), Gaps = 18/142 (12%)
Query: 6 NKRREKIEENPEDENFMRAAIVCVLGHVDTGKTKILDKLRRTNVQDGEAGGITQQIGA-T 64
N+ EK E D++ MR +L + IL+ + R + Q Q A
Sbjct: 197 NQIFEKFGERLSDKDLMRRLRRRMLMNPR----AILESISRESAQLERNTARQQGEHARE 252
Query: 65 NVPADAIRENTKHVRGPGGEVGGPGPLEIPGLLIIDTPGHESFSNLRNRGSSLCDIAILV 124
N + N V P +P D + N+R S+ + L
Sbjct: 253 NGRDLSSDSNN--------NVINPVSDNVPSR---DMNDSRNVENVRPVRSNDHMNSFLF 301
Query: 125 VDIMHGLEPQT--IESINILKS 144
I+ + T +I+
Sbjct: 302 RPIVDSISGMTLPDSFSSIIYG 323
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 32.5 bits (74), Expect = 0.21
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 114 GSSLCDIAILVVDIMHGLEPQTIESI-NILKSKKTPFVVALNKID 157
SL D + VVD GL T E I +L+ P V+A+NKID
Sbjct: 351 AVSLADAVVFVVDGQVGLT-STDERIVRMLRRAGKPVVLAVNKID 394
>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 = 30.9 bits (71), Expect = 0.33
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 118 CDIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKIDRL 159
D+ +LVVD GL+ + + + K P +V LNK D L
Sbjct: 83 ADLVLLVVDASEGLDEE--DLEILELPAKKPVIVVLNKSDLL 122
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7 is
a small Rab GTPase that regulates vesicular traffic from
early to late endosomal stages of the endocytic pathway.
The yeast Ypt7 and mammalian Rab7 are both involved in
transport to the vacuole/lysosome, whereas Ypt7 is also
required for homotypic vacuole fusion. Mammalian Rab7 is
an essential participant in the autophagic pathway for
sequestration and targeting of cytoplasmic components to
the lytic compartment. Mammalian Rab7 is also proposed
to function as a tumor suppressor. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 172
Score = 30.7 bits (70), Expect = 0.45
Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 20/76 (26%)
Query: 96 LLIIDTPGHESFSNLRN---RGSSLCDIAILVVDIMHGLEPQTIESINILKSK------- 145
L I DT G E F +L RG+ C +LV D+ + P++ ES++ + +
Sbjct: 51 LQIWDTAGQERFQSLGVAFYRGADCC---VLVYDVTN---PKSFESLDSWRDEFLIQASP 104
Query: 146 ----KTPFVVALNKID 157
PFVV NKID
Sbjct: 105 RDPENFPFVVLGNKID 120
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 31.2 bits (72), Expect = 0.51
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 10/43 (23%)
Query: 98 IIDTPGHESFS-----NLRNRGSSLCDIAILVVDIMHGLEPQT 135
IIDTPGH F+ +LR + D A+ V D + G+EPQ+
Sbjct: 79 IIDTPGHVDFTIEVERSLR-----VLDGAVAVFDAVGGVEPQS 116
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 30.0 bits (68), Expect = 0.90
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 119 DIAILVVDIMHGLEPQTIESINILKSKKTPFVVA-LNKIDRLYNWNTMNRR 168
D+ +L++D +G E +T E +NIL+ P V+ L +D+ N T+ +
Sbjct: 105 DLVLLLIDGSYGFEMETFEFLNILQVHGFPKVMGVLTHLDKFKNNKTLRKT 155
>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 = 29.8 bits (68), Expect = 0.91
Identities = 23/118 (19%), Positives = 42/118 (35%), Gaps = 31/118 (26%)
Query: 98 IIDTPG---HE----------SFSNLRNRGSSLCDIAILVVDI----MHGLEPQTIESIN 140
+IDTPG + + L + L + +D + +E Q ++
Sbjct: 51 VIDTPGILDRPLEERNTIEMQAITALAH----LRAAVLFFIDPSETCGYSIEEQ----LS 102
Query: 141 ILKSKK----TPFVVALNKIDRLYNWNTMNRRDVRDII--KSQESSVQTHKTVESARK 192
+ K K P +V LNKID L + + + + S T + V+ +
Sbjct: 103 LFKEIKPLFNKPVIVVLNKIDLLTEEDLSEIEKELEKEGEEVIKISTLTEEGVDELKN 160
>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 = 29.7 bits (68), Expect = 0.99
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 119 DIAILVVDIMHGLEPQTIESIN-ILKS---KKTPFVVALNKIDRL 159
D+ + VVD + IE++ +LK P ++ LNKID L
Sbjct: 122 DLLLHVVDASDPDREEQIETVEEVLKELGADDIPIILVLNKIDLL 166
>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 = 1.1
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 13/50 (26%)
Query: 118 CDIAILVVDIMHGLEPQTIESINILK----------SKKTPFVVALNKID 157
+ + V+D+ +P +E ++ ++K P +V LNKID
Sbjct: 79 TRVLLHVIDLSGEDDP--VEDYETIRNELEAYNPGLAEK-PRIVVLNKID 125
>gnl|CDD|223683 COG0610, COG0610, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 962
Score = 30.5 bits (69), Expect = 1.1
Identities = 14/67 (20%), Positives = 22/67 (32%), Gaps = 5/67 (7%)
Query: 119 DIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKIDRLYNWNTMNRRDVRDIIKSQE 178
AI + DI LE + INI + L + + + IIK
Sbjct: 793 SKAIDLDDIDFELELIGKQEINIDY-----ILELLQTFNDKNGAYESLKELIERIIKEWI 847
Query: 179 SSVQTHK 185
++ K
Sbjct: 848 EDLRQKK 854
>gnl|CDD|215692 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac,
Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
pfam00063. As regards Rab GTPases, these are important
regulators of vesicle formation, motility and fusion.
They share a fold in common with all Ras GTPases: this
is a six-stranded beta-sheet surrounded by five
alpha-helices.
Length = 162
Score = 29.0 bits (66), Expect = 1.7
Identities = 22/72 (30%), Positives = 28/72 (38%), Gaps = 16/72 (22%)
Query: 96 LLIIDTPGHESFSNLRN---RGSSLCDIAILVVDIMHGLEPQT-------IESINILKSK 145
L I DT G E F LR RG+ +LV DI + +E I +
Sbjct: 50 LQIWDTAGQERFRALRPLYYRGA---QGFLLVYDIT---SRDSFENVKKWLEEILRHADE 103
Query: 146 KTPFVVALNKID 157
P V+ NK D
Sbjct: 104 NVPIVLVGNKCD 115
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 29.3 bits (65), Expect = 2.1
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 98 IIDTPGHESFSNLRNRGSSLCDIAILVVDIMHG 130
+ID PGH F G+S D A+L++D G
Sbjct: 89 VIDAPGHRDFIKNMITGTSQADCAVLIIDSTTG 121
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 28.9 bits (66), Expect = 3.0
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 119 DIAILVVDIMHGLEPQTIESINILKSKKTPFVVALNKID 157
D+ +LV+D L + E + + K P +V LNK D
Sbjct: 296 DLVLLVLDASEPLTEEDDE--ILEELKDKPVIVVLNKAD 332
>gnl|CDD|221513 pfam12296, HsbA, Hydrophobic surface binding protein A. This
protein is found in eukaryotes. Proteins in this family
are typically between 171 to 275 amino acids in length.
Although the HsbA amino acid sequence suggests that HsbA
may be hydrophilic, HsbA adsorbed to hydrophobic PBSA
(Polybutylene succinate-co-adipate) surfaces in the
presence of NaCl or CaCl2. When HsbA was adsorbed on the
hydrophobic PBSA surfaces, it promoted PBSA degradation
via the CutL1 polyesterase. CutL1 interacts directly
with HsbA attached to the hydrophobic QCM electrode
surface. These results suggest that when HsbA is
adsorbed onto the PBSA surface, it recruits CutL1, and
that when CutL1 is accumulated on the PBSA surface, it
stimulates PBSA degradation.
Length = 124
Score = 27.6 bits (62), Expect = 3.1
Identities = 8/32 (25%), Positives = 19/32 (59%)
Query: 121 AILVVDIMHGLEPQTIESINILKSKKTPFVVA 152
++ ++ + L PQ +++++ L +KK F A
Sbjct: 66 SLALLAAVQTLTPQILDALDALIAKKPLFDAA 97
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 28.4 bits (64), Expect = 4.6
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 119 DIAILVVDIMHGLEPQTIE-SINILK---SKKTPFVVALNKIDRL 159
D+ + VVD + +E ++L + + P ++ LNKID L
Sbjct: 273 DLLLHVVDASDPEILEKLEAVEDVLAEIGADEIPIILVLNKIDLL 317
>gnl|CDD|219204 pfam06856, DUF1251, Protein of unknown function (DUF1251). This
family consists of the N-terminal region of several
hypothetical Nucleopolyhedrovirus proteins of unknown
function.
Length = 120
Score = 26.9 bits (60), Expect = 6.6
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 6/38 (15%)
Query: 144 SKKTPFVVA-LNKIDRLYNWNTMNRRDVRDIIKSQESS 180
K PFVV L + N VRD+ K+ ES
Sbjct: 70 GKTVPFVVGPLKSLR-----NDHGGLKVRDMAKAMESQ 102
>gnl|CDD|215955 pfam00503, G-alpha, G-protein alpha subunit. G proteins couple
receptors of extracellular signals to intracellular
signaling pathways. The G protein alpha subunit binds
guanyl nucleotide and is a weak GTPase. A set of
residues that are unique to G-alpha as compared to its
ancestor the Arf-like family form a ring of residues
centered on the nucleotide binding site. A Ggamma is
found fused to an inactive Galpha in the Dictyostelium
protein gbqA.
Length = 329
Score = 27.2 bits (61), Expect = 8.0
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 7/32 (21%)
Query: 135 TIESINILKS-------KKTPFVVALNKIDRL 159
ES+N+ + K TP ++ LNK D
Sbjct: 217 LEESLNLFEEICNSPWFKNTPIILFLNKKDLF 248
>gnl|CDD|234450 TIGR04056, OMP_RagA_SusC, TonB-linked outer membrane protein,
SusC/RagA family. This model describes a distinctive
clade among the TonB-linked outer membrane proteins
(OMP). Members of this family are restricted to the
Bacteriodetes lineage (except for Gemmatimonas
aurantiaca T-27 from the novel phylum Gemmatimonadetes)
and occur in high copy numbers, with over 100 members
from Bacteroides thetaiotaomicron VPI-5482 alone.
Published descriptions of members of this family are
available for RagA from Porphyromonas gingivalis, SusC
from Bacteroides thetaiotaomicron, and OmpW from
Bacteroides caccae. Members form pairs with members of
the SusD/RagB family (pfam07980). Transporter complexes
including these outer membrane proteins are likely to
import large degradation products of proteins (e.g.
RagA) or carbohydrates (e.g. SusC) as nutrients, rather
than siderophores [Transport and binding proteins,
Unknown substrate].
Length = 982
Score = 27.5 bits (62), Expect = 8.3
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 10/61 (16%)
Query: 93 IPGLLIIDT---PGHESFSNLRNRGSSLCDIAILVV-------DIMHGLEPQTIESINIL 142
+ G++I + PG ++ +R S + + L V + + L P+ IESI++L
Sbjct: 122 VAGVIITQSSGEPGGDASIWIRGISSFGGNNSPLYVIDGVPRDNGLSDLNPEDIESISVL 181
Query: 143 K 143
K
Sbjct: 182 K 182
>gnl|CDD|238266 cd00477, FTHFS, Formyltetrahydrofolate synthetase (FTHFS) catalyzes
the ATP-dependent activation of formate ion via its
addition to the N10 position of tetrahydrofolate. FTHFS
is a highly expressed key enzyme in both the
Wood-Ljungdahl pathway of autotrophic CO2 fixation
(acetogenesis) and the glycine synthase/reductase
pathways of purinolysis. The key physiological role of
this enzyme in acetogens is to catalyze the formylation
of tetrahydrofolate, an initial step in the reduction of
carbon dioxide and other one-carbon precursors to
acetate. In purinolytic organisms, the enzymatic
reaction is reversed, liberating formate from
10-formyltetrahydrofolate with concurrent production of
ATP.
Length = 524
Score = 27.5 bits (62), Expect = 9.0
Identities = 40/156 (25%), Positives = 54/156 (34%), Gaps = 44/156 (28%)
Query: 103 GHESFSNLRNRGSSLC-DIAILVVDI----MHGLEPQTIES------------------I 139
G E F N++ R S L D +LV + MHG P+ I
Sbjct: 290 GAEKFFNIKCRYSGLKPDAVVLVATVRALKMHGGVPKVTLGLEENLEALEKGFANLRKHI 349
Query: 140 NILKSKKTPFVVALNKIDRLYNWNTMNRRD-VRDIIKSQ--ESSVQTH------KTVESA 190
+K P VVA+NK ++ +T VR + + +V H VE A
Sbjct: 350 ENIKKFGVPVVVAINK----FSTDTDAELALVRKLAEEAGAFVAVSEHWAEGGKGAVELA 405
Query: 191 RKGQEICIKIEPIPGEAPKMFGRHFDENDFLVSKIS 226
E C E P F +D D L KI
Sbjct: 406 EAVIEAC--------EQPSEFKFLYDLEDPLEDKIE 433
>gnl|CDD|133338 cd04138, H_N_K_Ras_like, Ras GTPase family containing H-Ras,N-Ras
and K-Ras4A/4B. H-Ras/N-Ras/K-Ras subfamily. H-Ras,
N-Ras, and K-Ras4A/4B are the prototypical members of
the Ras family. These isoforms generate distinct signal
outputs despite interacting with a common set of
activators and effectors, and are strongly associated
with oncogenic progression in tumor initiation. Mutated
versions of Ras that are insensitive to GAP stimulation
(and are therefore constitutively active) are found in a
significant fraction of human cancers. Many Ras guanine
nucleotide exchange factors (GEFs) have been identified.
They are sequestered in the cytosol until activation by
growth factors triggers recruitment to the plasma
membrane or Golgi, where the GEF colocalizes with Ras.
Active (GTP-bound) Ras interacts with several effector
proteins that stimulate a variety of diverse cytoplasmic
signaling activities. Some are known to positively
mediate the oncogenic properties of Ras, including Raf,
phosphatidylinositol 3-kinase (PI3K), RalGEFs, and
Tiam1. Others are proposed to play negative regulatory
roles in oncogenesis, including RASSF and NORE/MST1.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 162
Score = 26.6 bits (59), Expect = 9.9
Identities = 32/112 (28%), Positives = 52/112 (46%), Gaps = 18/112 (16%)
Query: 92 EIPGLLIIDTPGHESFSNLRNRGSSLCDIAILVVDIMHGLEPQTIESIN-----ILKSKK 146
E L I+DT G E +S +R++ + + V I ++ E I+ I + K
Sbjct: 47 ETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAIN---SRKSFEDIHTYREQIKRVKD 103
Query: 147 T---PFVVALNKIDRLYNWNTMNRRDVRDIIKSQ-----ESSVQTHKTVESA 190
+ P V+ NK D L T++ R +D+ KS E+S +T + VE A
Sbjct: 104 SDDVPMVLVGNKCD-LAAR-TVSTRQGQDLAKSYGIPYIETSAKTRQGVEEA 153
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
0.318 0.137 0.398
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,297,543
Number of extensions: 1260556
Number of successful extensions: 1441
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1349
Number of HSP's successfully gapped: 151
Length of query: 259
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 164
Effective length of database: 6,723,972
Effective search space: 1102731408
Effective search space used: 1102731408
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 (21.7 bits)
S2: 58 (26.1 bits)