RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9646
(211 letters)
>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 = 228 bits (583), Expect = 1e-76
Identities = 81/103 (78%), Positives = 89/103 (86%)
Query: 108 VLADKKLAKVKQYADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMIT 167
VLA K AK K+Y +ID APEEKARGITIN AHVEY T NRHY+H DCPGHADYIKNMIT
Sbjct: 25 VLAKKGGAKAKKYDEIDKAPEEKARGITINTAHVEYETANRHYAHVDCPGHADYIKNMIT 84
Query: 168 GTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
G +QMDGAILVV+ATDG MPQTREHLLLA+Q+GV IVVF+NK
Sbjct: 85 GAAQMDGAILVVSATDGPMPQTREHLLLARQVGVPYIVVFLNK 127
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 221 bits (567), Expect = 2e-71
Identities = 77/103 (74%), Positives = 86/103 (83%)
Query: 108 VLADKKLAKVKQYADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMIT 167
VLA K A+ K Y ID APEEKARGITIN AHVEY TE RHY+H DCPGHADY+KNMIT
Sbjct: 35 VLAKKGGAEAKAYDQIDKAPEEKARGITINTAHVEYETEKRHYAHVDCPGHADYVKNMIT 94
Query: 168 GTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
G +QMDGAILVV+A DG MPQTREH+LLA+Q+GV IVVF+NK
Sbjct: 95 GAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFLNK 137
Score = 168 bits (427), Expect = 1e-50
Identities = 63/107 (58%), Positives = 84/107 (78%)
Query: 1 MELLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYG 60
+EL++ +D+YIP P R +DKPF +P+E +SI GRGTVVTGR+ERGI+K G E E G
Sbjct: 192 LELMDAVDSYIPTPERAIDKPFLMPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIR 251
Query: 61 RQFKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMAKP 107
KTTVTG+EMF K+LDE QAGD +GAL++G+KR++V RG ++AKP
Sbjct: 252 DTQKTTVTGVEMFRKLLDEGQAGDNVGALLRGIKREDVERGQVLAKP 298
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 219 bits (560), Expect = 2e-70
Identities = 76/103 (73%), Positives = 86/103 (83%)
Query: 108 VLADKKLAKVKQYADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMIT 167
VLA K + K Y IDNAPEEKARGITIN +HVEY T NRHY+H DCPGHADY+KNMIT
Sbjct: 35 VLAKKGGGEAKAYDQIDNAPEEKARGITINTSHVEYETANRHYAHVDCPGHADYVKNMIT 94
Query: 168 GTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
G +QMDGAILVV+A DG MPQTREH+LLA+Q+GV IVVF+NK
Sbjct: 95 GAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFLNK 137
Score = 165 bits (421), Expect = 9e-50
Identities = 63/107 (58%), Positives = 83/107 (77%)
Query: 1 MELLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYG 60
+EL++ +D+YIP+P R +DKPF +P+E +SI GRGTVVTGR+ERGIVK G E E G
Sbjct: 192 LELMDAVDSYIPEPERAIDKPFLMPIEDVFSISGRGTVVTGRVERGIVKVGDEVEIVGIK 251
Query: 61 RQFKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMAKP 107
KTTVTG+EMF K+LDE QAGD +G L++G KR++V RG ++AKP
Sbjct: 252 ETQKTTVTGVEMFRKLLDEGQAGDNVGVLLRGTKREDVERGQVLAKP 298
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 211 bits (540), Expect = 2e-67
Identities = 76/103 (73%), Positives = 87/103 (84%)
Query: 108 VLADKKLAKVKQYADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMIT 167
VLA++ L + K Y ID APEEK RGITIN AHVEY TE RHY+H DCPGHADY+KNMIT
Sbjct: 35 VLAERGLNQAKDYDSIDAAPEEKERGITINTAHVEYETEKRHYAHVDCPGHADYVKNMIT 94
Query: 168 GTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
G +QMDGAILVVAATDG MPQTREH+LLA+Q+GV +VVF+NK
Sbjct: 95 GAAQMDGAILVVAATDGPMPQTREHILLARQVGVPYLVVFLNK 137
Score = 163 bits (414), Expect = 1e-48
Identities = 64/107 (59%), Positives = 79/107 (73%)
Query: 1 MELLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYG 60
MEL++ +D YIP P RD DKPF +PVE ++I GRGTVVTGR+ERG VK G E E G
Sbjct: 190 MELMDAVDEYIPTPERDTDKPFLMPVEDVFTITGRGTVVTGRVERGTVKVGDEVEIVGIK 249
Query: 61 RQFKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMAKP 107
KT VTG+EMF K+LDE QAGD +G L++G+ RDEV RG ++AKP
Sbjct: 250 ETQKTVVTGVEMFRKLLDEGQAGDNVGVLLRGVDRDEVERGQVLAKP 296
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 212 bits (541), Expect = 2e-67
Identities = 79/103 (76%), Positives = 90/103 (87%)
Query: 108 VLADKKLAKVKQYADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMIT 167
LA K AK K+Y +ID+APEEKARGITIN AHVEY TENRHY+H DCPGHADY+KNMIT
Sbjct: 35 TLAAKGGAKAKKYDEIDSAPEEKARGITINTAHVEYETENRHYAHVDCPGHADYVKNMIT 94
Query: 168 GTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
G +QMDGAILVV+A DG MPQT+EH+LLAKQ+GV NIVVF+NK
Sbjct: 95 GAAQMDGAILVVSAADGPMPQTKEHILLAKQVGVPNIVVFLNK 137
Score = 142 bits (359), Expect = 2e-40
Identities = 54/106 (50%), Positives = 75/106 (70%)
Query: 2 ELLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGR 61
L++ +D+YIP P RD DKPF + +E +SI GRGTV TGR+ERG VK G E G
Sbjct: 201 NLMDAVDSYIPTPERDTDKPFLMAIEDVFSITGRGTVATGRIERGTVKVGDTVEIVGLRE 260
Query: 62 QFKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMAKP 107
TTVTG+EMF K LDE AGD +G L++G++++++ RG+++AKP
Sbjct: 261 TKTTTVTGLEMFQKTLDEGLAGDNVGILLRGIQKEDIERGMVLAKP 306
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 201 bits (514), Expect = 1e-63
Identities = 80/103 (77%), Positives = 88/103 (85%)
Query: 108 VLADKKLAKVKQYADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMIT 167
VLA K A+ K Y IDNAPEEKARGITIN AHVEY T NRHY+H DCPGHADY+KNMIT
Sbjct: 35 VLAKKGGAEAKAYDQIDNAPEEKARGITINTAHVEYETANRHYAHVDCPGHADYVKNMIT 94
Query: 168 GTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
G +QMDGAILVVAATDG MPQTREH+LLA+Q+GV IVVF+NK
Sbjct: 95 GAAQMDGAILVVAATDGPMPQTREHILLARQVGVPYIVVFLNK 137
Score = 152 bits (387), Expect = 1e-44
Identities = 64/107 (59%), Positives = 83/107 (77%)
Query: 1 MELLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYG 60
EL++ +D+YIP P RD+DKPF +PVE +SI GRGTVVTGR+ERGI+K G E E G
Sbjct: 190 EELMDAVDSYIPTPERDIDKPFLMPVEDVFSISGRGTVVTGRVERGILKVGEEVEIVGIK 249
Query: 61 RQFKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMAKP 107
KTTVTG+EMF K+LDE QAGD +G L++G+KR++V RG ++AKP
Sbjct: 250 ETQKTTVTGVEMFRKLLDEGQAGDNVGVLLRGVKREDVERGQVLAKP 296
>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 = 191 bits (487), Expect = 1e-59
Identities = 78/103 (75%), Positives = 88/103 (85%)
Query: 108 VLADKKLAKVKQYADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMIT 167
VLA + A + Y IDNAPEEKARGITIN AHVEY TENRHY+H DCPGHADY+KNMIT
Sbjct: 35 VLAKEGGAAARAYDQIDNAPEEKARGITINTAHVEYETENRHYAHVDCPGHADYVKNMIT 94
Query: 168 GTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
G +QMDGAILVV+ATDG MPQTREH+LLA+Q+GV IVVF+NK
Sbjct: 95 GAAQMDGAILVVSATDGPMPQTREHILLARQVGVPYIVVFLNK 137
Score = 147 bits (372), Expect = 2e-42
Identities = 62/107 (57%), Positives = 82/107 (76%)
Query: 1 MELLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYG 60
+EL++ +D YIP P R+ DKPF +P+E +SI GRGTVVTGR+ERGIVK G E E G
Sbjct: 190 LELMDAVDEYIPTPERETDKPFLMPIEDVFSITGRGTVVTGRVERGIVKVGEEVEIVGLK 249
Query: 61 RQFKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMAKP 107
KTTVTG+EMF K LDE +AGD +G L++G+KR+E+ RG+++AKP
Sbjct: 250 DTRKTTVTGVEMFRKELDEGRAGDNVGLLLRGIKREEIERGMVLAKP 296
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 186 bits (474), Expect = 3e-57
Identities = 70/103 (67%), Positives = 85/103 (82%)
Query: 108 VLADKKLAKVKQYADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMIT 167
VLA++ AK + +ID APEEKARGITI AHVEY T RHY+H DCPGHADY+KNMIT
Sbjct: 84 VLAEEGKAKAVAFDEIDKAPEEKARGITIATAHVEYETAKRHYAHVDCPGHADYVKNMIT 143
Query: 168 GTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
G +QMDG ILVV+A DG MPQT+EH+LLA+Q+GV ++VVF+NK
Sbjct: 144 GAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLVVFLNK 186
Score = 147 bits (373), Expect = 3e-42
Identities = 60/109 (55%), Positives = 82/109 (75%), Gaps = 2/109 (1%)
Query: 1 MELLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGY- 59
++L++ +D YIP+PVR LDKPF +P+E +SI GRGTV TGR+E+G +K G E E G
Sbjct: 241 LKLMDAVDEYIPEPVRVLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEIVGLR 300
Query: 60 -GRQFKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMAKP 107
G KTTVTG+EMF KILD+ QAGD +G L++G+KR++V RG ++ KP
Sbjct: 301 PGGPLKTTVTGVEMFKKILDQGQAGDNVGLLLRGLKREDVQRGQVICKP 349
>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 = 162 bits (412), Expect = 9e-51
Identities = 54/103 (52%), Positives = 64/103 (62%), Gaps = 1/103 (0%)
Query: 108 VLADKKLAKVKQYADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMIT 167
V K +D EE+ RGITI +A V + T+ R + D PGH D+ K MI
Sbjct: 26 VTGAISKESAKGARVLDKLKEERERGITIKIAAVSFETKKRLINIIDTPGHVDFTKEMIR 85
Query: 168 GTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
G SQ DGAILVV A +G MPQTREHLLLAK +GV I+VFINK
Sbjct: 86 GASQADGAILVVDAVEGVMPQTREHLLLAKTLGV-PIIVFINK 127
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 169 bits (428), Expect = 4e-50
Identities = 72/103 (69%), Positives = 85/103 (82%)
Query: 108 VLADKKLAKVKQYADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMIT 167
LA + K+Y +ID APEE+ARGITIN A VEY TENRHY+H DCPGHADY+KNMIT
Sbjct: 104 ALASMGGSAPKKYDEIDAAPEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMIT 163
Query: 168 GTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
G +QMDGAILVV+ DG MPQT+EH+LLAKQ+GV N+VVF+NK
Sbjct: 164 GAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFLNK 206
Score = 125 bits (314), Expect = 1e-33
Identities = 56/106 (52%), Positives = 75/106 (70%)
Query: 2 ELLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGR 61
EL++ +D+YIP P R D PF L VE +SI GRGTV TGR+ERG VK G + G
Sbjct: 270 ELMDAVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVERGTVKVGETVDIVGLRE 329
Query: 62 QFKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMAKP 107
TTVTG+EMF KILDEA AGD +G L++G+++ ++ RG+++AKP
Sbjct: 330 TRSTTVTGVEMFQKILDEALAGDNVGLLLRGIQKADIQRGMVLAKP 375
>gnl|CDD|239668 cd03697, EFTU_II, EFTU_II: Elongation factor Tu domain II.
Elongation factors Tu (EF-Tu) are three-domain GTPases
with an essential function in the elongation phase of
mRNA translation. The GTPase center of EF-Tu is in the
N-terminal domain (domain I), also known as the
catalytic or G-domain. The G-domain is composed of about
200 amino acid residues, arranged into a predominantly
parallel six-stranded beta-sheet core surrounded by
seven a-helices. Non-catalytic domains II and III are
beta-barrels of seven and six, respectively,
antiparallel beta-strands that share an extended
interface. Either non-catalytic domain is composed of
about 100 amino acid residues. EF-Tu proteins exist in
two principal conformations: in a compact one,
EF-Tu*GTP, with tight interfaces between all three
domains and a high affinity for aminoacyl-tRNA, and in
an open one, EF-Tu*GDP, with essentially no
G-domain-domain II interactions and a low affinity for
aminoacyl-tRNA. EF-Tu has approximately a 100-fold
higher affinity for GDP than for GTP.
Length = 87
Score = 144 bits (365), Expect = 6e-45
Identities = 53/86 (61%), Positives = 69/86 (80%)
Query: 22 FYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGRQFKTTVTGIEMFHKILDEAQ 81
F +P+E +SIPGRGTVVTGR+ERG +K G E E G+G KTTVTGIEMF K LDEA+
Sbjct: 1 FLMPIEDVFSIPGRGTVVTGRIERGTIKVGDEVEIVGFGETLKTTVTGIEMFRKTLDEAE 60
Query: 82 AGDQLGALVKGMKRDEVNRGLIMAKP 107
AGD +G L++G+KR++V RG+++AKP
Sbjct: 61 AGDNVGVLLRGVKREDVERGMVLAKP 86
>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 = 129 bits (326), Expect = 2e-37
Identities = 43/94 (45%), Positives = 59/94 (62%), Gaps = 7/94 (7%)
Query: 124 DNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATD 183
D EE+ RG+TI+V ++ TE ++ D PGH D++KNMITG SQ D A+LVV+A
Sbjct: 53 DKLKEERERGVTIDVGLAKFETEKYRFTIIDAPGHRDFVKNMITGASQADVAVLVVSARK 112
Query: 184 GA-------MPQTREHLLLAKQIGVTNIVVFINK 210
G QTREH LLA+ +GV ++V +NK
Sbjct: 113 GEFEAGFEKGGQTREHALLARTLGVKQLIVAVNK 146
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 126 bits (320), Expect = 1e-34
Identities = 47/89 (52%), Positives = 66/89 (74%), Gaps = 2/89 (2%)
Query: 124 DNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATD 183
D EE+ RG+TI++AH ++ T+ +++ DCPGH D++KNMITG SQ D A+LVVAA D
Sbjct: 60 DRLKEERERGVTIDLAHKKFETDKYYFTIVDCPGHRDFVKNMITGASQADAAVLVVAADD 119
Query: 184 --GAMPQTREHLLLAKQIGVTNIVVFINK 210
G MPQTREH+ LA+ +G+ ++V INK
Sbjct: 120 AGGVMPQTREHVFLARTLGINQLIVAINK 148
Score = 75.7 bits (187), Expect = 3e-16
Identities = 36/103 (34%), Positives = 58/103 (56%), Gaps = 10/103 (9%)
Query: 1 MELLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEF--TG 58
+E L+ + P + DKP +P++ YSI G GTV GR+E G++K G + F G
Sbjct: 209 LEALDNL----KPPEKPTDKPLRIPIQDVYSISGVGTVPVGRVETGVLKVGDKVVFMPAG 264
Query: 59 YGRQFKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRG 101
+ K+ IEM H+ L +A+ GD +G V+G+ + ++ RG
Sbjct: 265 VVGEVKS----IEMHHEELPQAEPGDNIGFNVRGVGKKDIKRG 303
>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 = 117 bits (296), Expect = 2e-33
Identities = 40/103 (38%), Positives = 54/103 (52%), Gaps = 1/103 (0%)
Query: 108 VLADKKLAKVKQYADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMIT 167
++ +D EE+ RGITI VE+ R + D PGH D+ K +
Sbjct: 22 QTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWPKRRINFIDTPGHEDFSKETVR 81
Query: 168 GTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
G +Q DGA+LVV A +G PQTREHL +A G I+V +NK
Sbjct: 82 GLAQADGALLVVDANEGVEPQTREHLNIALA-GGLPIIVAVNK 123
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 114 bits (288), Expect = 4e-30
Identities = 43/94 (45%), Positives = 61/94 (64%), Gaps = 7/94 (7%)
Query: 124 DNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATD 183
D EE+ RG+TI+VAH ++ T+ +++ D PGH D++KNMITG SQ D A+LVV A D
Sbjct: 61 DKTKEERERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARD 120
Query: 184 GA-------MPQTREHLLLAKQIGVTNIVVFINK 210
G QTREH LA+ +G+ ++V +NK
Sbjct: 121 GEFEAGFGVGGQTREHAFLARTLGIKQLIVAVNK 154
Score = 85.4 bits (212), Expect = 1e-19
Identities = 38/105 (36%), Positives = 60/105 (57%), Gaps = 3/105 (2%)
Query: 3 LLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGRQ 62
LL +D + P R LDKP LP++ YSI G GTV GR+E G++K G + F
Sbjct: 214 LLEALD-QLEPPERPLDKPLRLPIQDVYSISGIGTVPVGRVESGVIKPGQKVTF--MPAG 270
Query: 63 FKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMAKP 107
V IEM H+ + +A+ GD +G V+G++++++ RG ++
Sbjct: 271 VVGEVKSIEMHHEEISQAEPGDNVGFNVRGVEKNDIRRGDVIGHS 315
>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 = 108 bits (272), Expect = 6e-28
Identities = 47/91 (51%), Positives = 62/91 (68%), Gaps = 3/91 (3%)
Query: 123 IDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAAT 182
+D EE+ RG+TI+VAH ++ T+ + DCPGH D+IKNMITG SQ D A+LVVA
Sbjct: 60 MDRLKEERERGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVG 119
Query: 183 DGA---MPQTREHLLLAKQIGVTNIVVFINK 210
DG PQTREH LA+ +G+ ++V INK
Sbjct: 120 DGEFEVQPQTREHAFLARTLGINQLIVAINK 150
Score = 74.5 bits (183), Expect = 9e-16
Identities = 37/105 (35%), Positives = 59/105 (56%), Gaps = 3/105 (2%)
Query: 3 LLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGRQ 62
LL +D + P + DKP +P++ YSI G GTV GR+E G++K G + F G
Sbjct: 210 LLEALDA-LEPPEKPTDKPLRIPIQDVYSITGVGTVPVGRVETGVLKPGDKVVFEPAG-- 266
Query: 63 FKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMAKP 107
V IEM H+ +++A+ GD +G V+G+ + ++ RG + P
Sbjct: 267 VSGEVKSIEMHHEQIEQAEPGDNIGFNVRGVSKKDIRRGDVCGHP 311
>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 = 96.5 bits (241), Expect = 3e-25
Identities = 37/91 (40%), Positives = 57/91 (62%), Gaps = 3/91 (3%)
Query: 122 DIDNAPEEKARGITINV--AHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVV 179
+ D PEEK RGITI++ A+++ + + D PGH ++KNM+ G +D +LVV
Sbjct: 23 ETDRLPEEKKRGITIDLGFAYLDLP-DGKRLGFIDVPGHEKFVKNMLAGAGGIDAVLLVV 81
Query: 180 AATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
AA +G MPQTREHL + + +G+ +V + K
Sbjct: 82 AADEGIMPQTREHLEILELLGIKKGLVVLTK 112
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 100 bits (252), Expect = 5e-25
Identities = 47/96 (48%), Positives = 61/96 (63%), Gaps = 7/96 (7%)
Query: 123 IDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAAT 182
+D E+ RGITI++A ++ T +++ D PGH D+IKNMITGTSQ D AILVVA+T
Sbjct: 60 LDKLKAERERGITIDIALWKFETPKYYFTIIDAPGHRDFIKNMITGTSQADVAILVVAST 119
Query: 183 DGAMP-------QTREHLLLAKQIGVTNIVVFINKF 211
G QTREH LLA +GV ++V INK
Sbjct: 120 AGEFEAGISKDGQTREHALLAFTLGVKQMIVCINKM 155
Score = 75.2 bits (185), Expect = 5e-16
Identities = 43/99 (43%), Positives = 55/99 (55%), Gaps = 3/99 (3%)
Query: 3 LLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGRQ 62
LL +DT P P R +DKP LP++ Y I G GTV GR+E GI+K GM F G
Sbjct: 216 LLEALDTLEP-PKRPVDKPLRLPLQDVYKIGGIGTVPVGRVETGILKPGMVVTFAPSG-- 272
Query: 63 FKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRG 101
T V +EM H+ L EA GD +G VK + ++ RG
Sbjct: 273 VTTEVKSVEMHHEQLAEAVPGDNVGFNVKNVSVKDIKRG 311
>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 = 89.2 bits (222), Expect = 4e-22
Identities = 36/83 (43%), Positives = 53/83 (63%)
Query: 128 EEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATDGAMP 187
E+ +GITI+VA+ ++T R + D PGH Y +NM+TG S D AIL+V A G +
Sbjct: 58 AEREQGITIDVAYRYFSTPKRKFIIADTPGHEQYTRNMVTGASTADLAILLVDARKGVLE 117
Query: 188 QTREHLLLAKQIGVTNIVVFINK 210
QTR H +A +G+ ++VV +NK
Sbjct: 118 QTRRHSYIASLLGIRHVVVAVNK 140
>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 = 91.5 bits (227), Expect = 2e-21
Identities = 36/97 (37%), Positives = 50/97 (51%)
Query: 114 LAKVKQYADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMD 173
L K D PEEK RG+TI++ + + D PGH +I N I G +D
Sbjct: 16 LLKALTGIAADRLPEEKKRGMTIDLGFAYFPLPDYRLGFIDVPGHEKFISNAIAGGGGID 75
Query: 174 GAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
A+LVV A +G M QT EHL + +G+ + +V I K
Sbjct: 76 AALLVVDADEGVMTQTGEHLAVLDLLGIPHTIVVITK 112
Score = 53.7 bits (129), Expect = 1e-08
Identities = 26/105 (24%), Positives = 48/105 (45%), Gaps = 8/105 (7%)
Query: 3 LLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGRQ 62
LL +D Q KP + ++ + + G GTVVTG G VK G +
Sbjct: 164 LLESLDIKRIQ------KPLRMAIDRAFKVKGAGTVVTGTAFSGEVKVGDNLRLLPINHE 217
Query: 63 FKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMAKP 107
+ V I+ ++ ++ A AG ++ + ++ + + RGL++ P
Sbjct: 218 VR--VKAIQAQNQDVEIAYAGQRIALNLMDVEPESLKRGLLILTP 260
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 88.6 bits (220), Expect = 1e-20
Identities = 39/97 (40%), Positives = 54/97 (55%)
Query: 114 LAKVKQYADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMD 173
L K D PEEK RGITI++ E+ D PGH D+I N++ G +D
Sbjct: 16 LLKALTGGVTDRLPEEKKRGITIDLGFYYRKLEDGVMGFIDVPGHPDFISNLLAGLGGID 75
Query: 174 GAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
A+LVVAA +G M QT EHLL+ +G+ N ++ + K
Sbjct: 76 YALLVVAADEGLMAQTGEHLLILDLLGIKNGIIVLTK 112
Score = 70.5 bits (173), Expect = 2e-14
Identities = 33/108 (30%), Positives = 62/108 (57%), Gaps = 2/108 (1%)
Query: 2 ELLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGR 61
EL N++ + + RD KPF + ++ +++ G GTVVTG + G VK G + + +
Sbjct: 152 ELKNELIDLLEEIERDEQKPFRIAIDRAFTVKGVGTVVTGTVLSGEVKVGDKLYLSPINK 211
Query: 62 QFKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMAKPVL 109
+ + V I+ ++EA+AG ++G +KG++++E+ RG + KP
Sbjct: 212 EVR--VRSIQAHDVDVEEAKAGQRVGLALKGVEKEEIERGDWLLKPEP 257
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 87.7 bits (218), Expect = 2e-20
Identities = 37/83 (44%), Positives = 53/83 (63%)
Query: 128 EEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATDGAMP 187
E+ +GITI+VA+ ++TE R + D PGH Y +NM TG S D AIL+V A G +
Sbjct: 66 AEREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTADLAILLVDARKGVLE 125
Query: 188 QTREHLLLAKQIGVTNIVVFINK 210
QTR H +A +G+ ++VV +NK
Sbjct: 126 QTRRHSFIASLLGIRHVVVAVNK 148
Score = 33.4 bits (77), Expect = 0.066
Identities = 21/68 (30%), Positives = 28/68 (41%), Gaps = 8/68 (11%)
Query: 20 KPFYLPVEHTYSIPG---RGTVVTGRLERGIVKKGMECEFTGYGRQFKTTVTGIEMFHKI 76
K F PV++ P RG G + G VK G E G+ + V I F
Sbjct: 222 KAFRFPVQYVNR-PNLDFRG--YAGTIASGSVKVGDEVVVLPSGKT--SRVKRIVTFDGE 276
Query: 77 LDEAQAGD 84
L +A AG+
Sbjct: 277 LAQASAGE 284
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 84.6 bits (210), Expect = 3e-19
Identities = 47/133 (35%), Positives = 67/133 (50%), Gaps = 26/133 (19%)
Query: 84 DQLGALVKGMKRDEVNRGLIMAKPVLADKKLAKVKQYADIDNA------PEEKARGITIN 137
DQL AL +RD G Q +ID A E+ +GITI+
Sbjct: 54 DQLAAL----ERDSKKVG----------------TQGDEIDLALLVDGLAAEREQGITID 93
Query: 138 VAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATDGAMPQTREHLLLAK 197
VA+ +AT R + D PGH Y +NM+TG S D AI++V A G + QTR H +A
Sbjct: 94 VAYRYFATPKRKFIVADTPGHEQYTRNMVTGASTADLAIILVDARKGVLTQTRRHSFIAS 153
Query: 198 QIGVTNIVVFINK 210
+G+ ++V+ +NK
Sbjct: 154 LLGIRHVVLAVNK 166
>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 = 81.6 bits (202), Expect = 2e-18
Identities = 35/88 (39%), Positives = 55/88 (62%)
Query: 123 IDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAAT 182
+D E+ +GITI+VA+ ++T+ R + D PGH Y +NM TG S D A+L+V A
Sbjct: 55 VDGLQAEREQGITIDVAYRYFSTDKRKFIVADTPGHEQYTRNMATGASTADLAVLLVDAR 114
Query: 183 DGAMPQTREHLLLAKQIGVTNIVVFINK 210
G + QTR H +A +G+ ++V+ +NK
Sbjct: 115 KGVLEQTRRHSYIASLLGIRHVVLAVNK 142
>gnl|CDD|239667 cd03696, selB_II, selB_II: this subfamily represents the domain of
elongation factor SelB, homologous to domain II of
EF-Tu. SelB may function by replacing EF-Tu. 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' or 5' non-coding elements of mRNA have been found as
probable structures for directing selenocysteine
incorporation.
Length = 83
Score = 74.1 bits (183), Expect = 9e-18
Identities = 27/85 (31%), Positives = 51/85 (60%), Gaps = 2/85 (2%)
Query: 22 FYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGRQFKTTVTGIEMFHKILDEAQ 81
F LP++ +++ G+GTVVTG + G VK G + E G + + V I++ K ++EA+
Sbjct: 1 FRLPIDRVFTVKGQGTVVTGTVLSGSVKVGDKVEILPLGEETR--VRSIQVHGKDVEEAK 58
Query: 82 AGDQLGALVKGMKRDEVNRGLIMAK 106
AGD++ + G+ ++ RG +++
Sbjct: 59 AGDRVALNLTGVDAKDLERGDVLSS 83
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 79.7 bits (197), Expect = 2e-17
Identities = 37/93 (39%), Positives = 51/93 (54%), Gaps = 7/93 (7%)
Query: 122 DIDNAPEEKARGITINVAHVEYA----TENRHYSHTDCPGHADYIKNMITGTSQMDGAIL 177
+ D PEEK RG+TI++ YA + R D PGH ++ NM+ G +D A+L
Sbjct: 24 NADRLPEEKKRGMTIDLG---YAYWPQPDGRVLGFIDVPGHEKFLSNMLAGVGGIDHALL 80
Query: 178 VVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
VVA DG M QTREHL + + G + V + K
Sbjct: 81 VVACDDGVMAQTREHLAILQLTGNPMLTVALTK 113
Score = 37.7 bits (88), Expect = 0.003
Identities = 25/92 (27%), Positives = 47/92 (51%), Gaps = 3/92 (3%)
Query: 11 IPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGRQFKTTVTGI 70
+P+ F L ++ +++ G G VVTG G VK G TG + + V G+
Sbjct: 164 LPEREHAAQHRFRLAIDRAFTVKGAGLVVTGTALSGEVKVGDTLWLTGVNKPMR--VRGL 221
Query: 71 EMFHKILDEAQAGDQLGALVKG-MKRDEVNRG 101
++ ++AQAG ++ + G +++++NRG
Sbjct: 222 HAQNQPTEQAQAGQRIALNIAGDAEKEQINRG 253
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 79.6 bits (197), Expect = 2e-17
Identities = 36/82 (43%), Positives = 53/82 (64%)
Query: 129 EKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATDGAMPQ 188
E+ +GITI+VA+ ++TE R + D PGH Y +NM TG S D AIL++ A G + Q
Sbjct: 88 EREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTCDLAILLIDARKGVLDQ 147
Query: 189 TREHLLLAKQIGVTNIVVFINK 210
TR H +A +G+ ++VV +NK
Sbjct: 148 TRRHSFIATLLGIKHLVVAVNK 169
>gnl|CDD|217388 pfam03144, GTP_EFTU_D2, Elongation factor Tu domain 2. Elongation
factor Tu consists of three structural domains, this is
the second domain. This domain adopts a beta barrel
structure. This the second domain is involved in binding
to charged tRNA. This domain is also found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This domain is structurally
related to pfam03143, and in fact has weak sequence
matches to this domain.
Length = 70
Score = 71.9 bits (177), Expect = 5e-17
Identities = 28/66 (42%), Positives = 37/66 (56%)
Query: 36 GTVVTGRLERGIVKKGMECEFTGYGRQFKTTVTGIEMFHKILDEAQAGDQLGALVKGMKR 95
GTV TGR+E G +KKG + G K VT +EMFH L EA AG G ++ G+
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGIGL 60
Query: 96 DEVNRG 101
++ RG
Sbjct: 61 KDIKRG 66
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 77.1 bits (189), Expect = 1e-16
Identities = 41/95 (43%), Positives = 57/95 (60%), Gaps = 7/95 (7%)
Query: 123 IDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAAT 182
+D E+ RGITI++A ++ T + + D PGH D+IKNMITGTSQ D A+L++ +T
Sbjct: 60 LDKLKAERERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDST 119
Query: 183 DGAMP-------QTREHLLLAKQIGVTNIVVFINK 210
G QTREH LLA +GV ++ NK
Sbjct: 120 TGGFEAGISKDGQTREHALLAFTLGVKQMICCCNK 154
Score = 69.0 bits (168), Expect = 9e-14
Identities = 41/103 (39%), Positives = 56/103 (54%), Gaps = 3/103 (2%)
Query: 3 LLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGRQ 62
LL +D I +P R DKP LP++ Y I G GTV GR+E G++K GM F G
Sbjct: 216 LLEALDQ-INEPKRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFGPTG-- 272
Query: 63 FKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMA 105
T V +EM H+ L EA GD +G VK + ++ RG + +
Sbjct: 273 LTTEVKSVEMHHESLQEALPGDNVGFNVKNVAVKDLKRGYVAS 315
>gnl|CDD|239664 cd03693, EF1_alpha_II, EF1_alpha_II: this family represents the
domain II of elongation factor 1-alpha (EF-1a) that is
found in archaea and all eukaryotic lineages. EF-1A is
very abundant in the cytosol, where it is involved in
the GTP-dependent binding of aminoacyl-tRNAs to the A
site of the ribosomes in the second step of translation
from mRNAs to proteins. Both domain II of EF1A and
domain IV of IF2/eIF5B have been implicated in
recognition of the 3'-ends of tRNA. More than 61% of
eukaryotic elongation factor 1A (eEF-1A) in cells is
estimated to be associated with actin cytoskeleton. The
binding of eEF1A to actin is a noncanonical function
that may link two distinct cellular processes,
cytoskeleton organization and gene expression.
Length = 91
Score = 70.7 bits (174), Expect = 3e-16
Identities = 34/86 (39%), Positives = 49/86 (56%), Gaps = 2/86 (2%)
Query: 19 DKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGRQFKTTVTGIEMFHKILD 78
DKP LP++ Y I G GTV GR+E G++K GM F G + V +EM H+ L+
Sbjct: 2 DKPLRLPIQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGVTGE--VKSVEMHHEPLE 59
Query: 79 EAQAGDQLGALVKGMKRDEVNRGLIM 104
EA GD +G VK + + ++ RG +
Sbjct: 60 EALPGDNVGFNVKNVSKKDIKRGDVA 85
>gnl|CDD|238652 cd01342, Translation_Factor_II_like, Translation_Factor_II_like:
Elongation factor Tu (EF-Tu) domain II-like proteins.
Elongation factor Tu consists of three structural
domains, this family represents the second domain.
Domain II adopts a beta barrel structure and is involved
in binding to charged tRNA. Domain II is found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This group also includes the C2
subdomain of domain IV of IF-2 that has the same fold as
domain II of (EF-Tu). Like IF-2 from certain prokaryotes
such as Thermus thermophilus, mitochondrial IF-2 lacks
domain II, which is thought to be involved in binding
of E.coli IF-2 to 30S subunits.
Length = 83
Score = 69.3 bits (170), Expect = 7e-16
Identities = 28/85 (32%), Positives = 42/85 (49%), Gaps = 2/85 (2%)
Query: 22 FYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGRQFKTTVTGIEMFHKILDEAQ 81
V + GRGTV TGR+E G +KKG + G K V ++ F +DEA
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRFKGEVDEAV 60
Query: 82 AGDQLGALVKGMKRDEVNRGLIMAK 106
AGD +G ++K +D++ G +
Sbjct: 61 AGDIVGIVLKD--KDDIKIGDTLTD 83
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 73.0 bits (180), Expect = 3e-15
Identities = 40/110 (36%), Positives = 53/110 (48%), Gaps = 27/110 (24%)
Query: 128 EEKARGITINVAHVE--------------YATEN------------RHYSHTDCPGHADY 161
EE RGITI + + + Y TE R S D PGH
Sbjct: 39 EELKRGITIRLGYADATIRKCPDCEEPEAYTTEPKCPNCGSETELLRRVSFVDAPGHETL 98
Query: 162 IKNMITGTSQMDGAILVVAATDGA-MPQTREHLLLAKQIGVTNIVVFINK 210
+ M++G + MDGAILV+AA + PQT+EHL+ IG+ NIV+ NK
Sbjct: 99 MATMLSGAALMDGAILVIAANEPCPQPQTKEHLMALDIIGIKNIVIVQNK 148
Score = 38.3 bits (90), Expect = 0.002
Identities = 31/116 (26%), Positives = 52/116 (44%), Gaps = 27/116 (23%)
Query: 3 LLNQIDTYIPQPVRDLDKPFYLPVEHTYSI--PG------RGTVVTGRLERGIVKKGMEC 54
L+ I+ IP P RDLDKP + V ++ + PG +G V+ G L +G++K G E
Sbjct: 192 LIEAIEEEIPTPERDLDKPPRMYVARSFDVNKPGTPPEKLKGGVIGGSLIQGVLKVGDEI 251
Query: 55 EFTGYGRQFK-----------TTVTGIEMFHKILDEAQAGDQLG-------ALVKG 92
E G + + T + + + ++EA+ G +G +L K
Sbjct: 252 EIRP-GIKVEEGGKTKWEPITTKIVSLRAGGEKVEEARPGGLVGVGTKLDPSLTKA 306
>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 = 68.8 bits (169), Expect = 2e-14
Identities = 27/64 (42%), Positives = 41/64 (64%), Gaps = 1/64 (1%)
Query: 148 RHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATDGA-MPQTREHLLLAKQIGVTNIVV 206
RH S DCPGH + M++G + MDGA+L++AA + PQT EHL + +G+ +I++
Sbjct: 77 RHVSFVDCPGHEILMATMLSGAAVMDGALLLIAANEPCPQPQTSEHLAALEIMGLKHIII 136
Query: 207 FINK 210
NK
Sbjct: 137 LQNK 140
>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 = 70.9 bits (174), Expect = 2e-14
Identities = 40/114 (35%), Positives = 55/114 (48%), Gaps = 27/114 (23%)
Query: 124 DNAPEEKARGITINVAHVE--------------YATEN------------RHYSHTDCPG 157
D EE RGI+I + + + Y TE R S D PG
Sbjct: 30 DTHSEELKRGISIRLGYADAEIYKCPECDGPECYTTEPVCPNCGSETELLRRVSFVDAPG 89
Query: 158 HADYIKNMITGTSQMDGAILVVAATDGA-MPQTREHLLLAKQIGVTNIVVFINK 210
H + M++G + MDGA+LV+AA + PQTREHL+ + IG+ NIV+ NK
Sbjct: 90 HETLMATMLSGAALMDGALLVIAANEPCPQPQTREHLMALEIIGIKNIVIVQNK 143
Score = 41.6 bits (98), Expect = 1e-04
Identities = 31/103 (30%), Positives = 48/103 (46%), Gaps = 18/103 (17%)
Query: 3 LLNQIDTYIPQPVRDLDKPFYLPVEHTYSI--PG------RGTVVTGRLERGIVKKGMEC 54
LL I+ +IP P RDLDKP + V ++ + PG +G V+ G L +G +K G E
Sbjct: 187 LLEAIEKFIPTPERDLDKPPLMYVARSFDVNKPGTPPEKLKGGVIGGSLIQGKLKVGDEI 246
Query: 55 EF------TGYGRQ----FKTTVTGIEMFHKILDEAQAGDQLG 87
E G+ T +T + ++EA+ G +G
Sbjct: 247 EIRPGIKVEKGGKTKWEPIYTEITSLRAGGYKVEEARPGGLVG 289
>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 = 68.5 bits (168), Expect = 2e-14
Identities = 36/119 (30%), Positives = 58/119 (48%), Gaps = 16/119 (13%)
Query: 106 KPVLADKKLAKVKQYADIDNAPEEKARGITIN-------VAHVEYATENRHYSHT----- 153
K LA K L+++ A D P+ + RGIT++ V ++ +N +
Sbjct: 13 KTSLA-KALSEIASTAAFDKNPQSQERGITLDLGFSSFEVDKPKHLEDNENPQIENYQIT 71
Query: 154 --DCPGHADYIKNMITGTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
DCPGHA I+ +I G +D +LVV A G QT E L++ ++ ++V +NK
Sbjct: 72 LVDCPGHASLIRTIIGGAQIIDLMLLVVDAKKGIQTQTAECLVIG-ELLCKPLIVVLNK 129
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 68.9 bits (169), Expect = 9e-14
Identities = 29/64 (45%), Positives = 41/64 (64%), Gaps = 1/64 (1%)
Query: 148 RHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATDGA-MPQTREHLLLAKQIGVTNIVV 206
R S D PGH + M++G + MDGA+LV+AA + PQTREHL+ + IG+ NI++
Sbjct: 86 RRVSFVDAPGHETLMATMLSGAALMDGALLVIAANEPCPQPQTREHLMALEIIGIKNIII 145
Query: 207 FINK 210
NK
Sbjct: 146 VQNK 149
Score = 42.3 bits (100), Expect = 9e-05
Identities = 29/103 (28%), Positives = 50/103 (48%), Gaps = 18/103 (17%)
Query: 3 LLNQIDTYIPQPVRDLDKPFYLPVEHTYSI--PG------RGTVVTGRLERGIVKKGMEC 54
L+ I+ YIP P RDLDKP + V ++ + PG +G V+ G L +G+++ G E
Sbjct: 193 LIEAIEKYIPTPERDLDKPPRMYVARSFDVNKPGTPPEELKGGVIGGSLVQGVLRVGDEI 252
Query: 55 EF------TGYGRQ----FKTTVTGIEMFHKILDEAQAGDQLG 87
E G+ T + ++ + ++EA+ G +G
Sbjct: 253 EIRPGIVVEKGGKTVWEPITTEIVSLQAGGEDVEEARPGGLVG 295
>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 = 66.1 bits (162), Expect = 2e-13
Identities = 32/84 (38%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 129 EKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATDGAMPQ 188
E+ RGITI A + E+ + D PGH D+I + S +DGAILV++A +G Q
Sbjct: 45 ERQRGITIFSAVASFQWEDTKVNIIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQ 104
Query: 189 TRE--HLLLAKQIGVTNIVVFINK 210
TR LL I ++F+NK
Sbjct: 105 TRILFRLLRKLNIPT---IIFVNK 125
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 66.1 bits (162), Expect = 8e-13
Identities = 29/88 (32%), Positives = 44/88 (50%), Gaps = 2/88 (2%)
Query: 124 DNAPEEKARGITINVAHVEYATENRH-YSHTDCPGHADYIKNMITGTSQMDGAILVVAAT 182
D +E+ RGITI A + + + D PGH D+ + +DGA++VV A
Sbjct: 51 DWMEQEQERGITITSAATTLFWKGDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAV 110
Query: 183 DGAMPQTREHLLLAKQIGVTNIVVFINK 210
+G PQT A + GV ++F+NK
Sbjct: 111 EGVEPQTETVWRQADKYGVP-RILFVNK 137
Score = 32.2 bits (74), Expect = 0.20
Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 7/79 (8%)
Query: 17 DLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGRQFKTTVTGIEMFH-- 74
+ P V + P G + R+ G +K G E + K V + + H
Sbjct: 303 SDEGPLSALVFKIMTDPFVGKLTFVRVYSGTLKSGS--EVLNSTKGKKERVGRLLLMHGN 360
Query: 75 --KILDEAQAGDQLGALVK 91
+ +DE AGD + ALV
Sbjct: 361 EREEVDEVPAGD-IVALVG 378
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 64.0 bits (156), Expect = 4e-12
Identities = 34/110 (30%), Positives = 65/110 (59%), Gaps = 3/110 (2%)
Query: 1 MELLNQIDTYIPQPVRDLDK-PFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGY 59
++LL++ +P+ R D+ PF + ++ YS+ G GTVV+G ++ GI+ G +
Sbjct: 327 LDLLDEFFLLLPKRRRWDDEGPFLMYIDKIYSVTGVGTVVSGSVKSGILHVGDTVLLGPF 386
Query: 60 --GRQFKTTVTGIEMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMAKP 107
G+ + V IEM H +D A+AG +G +KG++++E+ RG++++
Sbjct: 387 KDGKFREVVVKSIEMHHYRVDSAKAGSIIGIALKGVEKEELERGMVLSAG 436
Score = 41.3 bits (97), Expect = 2e-04
Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 151 SHTDCPGHADYIKNMITG--TSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVV 206
S D GH +++ I G ++D +LVVAA DG T+EHL +A + + IVV
Sbjct: 204 SFVDTVGHEPWLRTTIRGLLGQKVDYGLLVVAADDGVTKMTKEHLGIALAMELPVIVV 261
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 63.1 bits (154), Expect = 9e-12
Identities = 25/64 (39%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 148 RHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATDGA-MPQTREHLLLAKQIGVTNIVV 206
RH S DCPGH + M+ G + MD A+L++AA + PQT EHL + + + +I++
Sbjct: 117 RHVSFVDCPGHDILMATMLNGAAVMDAALLLIAANESCPQPQTSEHLAAVEIMKLKHIII 176
Query: 207 FINK 210
NK
Sbjct: 177 LQNK 180
Score = 34.6 bits (80), Expect = 0.031
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 8/61 (13%)
Query: 3 LLNQIDTYIPQPVRDLDKPFYLPVEHTYSI--PG------RGTVVTGRLERGIVKKGMEC 54
+L I T IP P RDL P + V ++ + PG +G V G + +G++K G E
Sbjct: 224 VLEYICTQIPIPKRDLTSPPRMIVIRSFDVNKPGEDIENLKGGVAGGSILQGVLKVGDEI 283
Query: 55 E 55
E
Sbjct: 284 E 284
>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 = 60.7 bits (147), Expect = 7e-11
Identities = 42/112 (37%), Positives = 60/112 (53%), Gaps = 7/112 (6%)
Query: 103 IMAKPVLADKKLAKVKQYADIDNAPEEKARGITINVAHV----EYATENRHYSHTDCPGH 158
++A + ++LA + Y D D +E+ RGITIN A+V EY + D PGH
Sbjct: 39 LLAGAGMISEELAGQQLYLDFDE--QEQERGITINAANVSMVHEYEGNEYLINLIDTPGH 96
Query: 159 ADYIKNMITGTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
D+ ++ +DGAI+VV A +G MPQT L A + V V+FINK
Sbjct: 97 VDFGGDVTRAMRAVDGAIVVVCAVEGVMPQTETVLRQALKENVKP-VLFINK 147
>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 = 57.9 bits (141), Expect = 1e-10
Identities = 37/86 (43%), Positives = 43/86 (50%), Gaps = 5/86 (5%)
Query: 128 EEKARGIT--INVAHVEYATENRHYSHTDCPGHADYIKNMIT-GTSQMDGAILVVAATDG 184
+A GIT I V + + D PGH + NM G S D AILVVAA DG
Sbjct: 27 AGEAGGITQHIGAYQVPIDVKIPGITFIDTPGHEAF-TNMRARGASVTDIAILVVAADDG 85
Query: 185 AMPQTREHLLLAKQIGVTNIVVFINK 210
MPQT E + AK V I+V INK
Sbjct: 86 VMPQTIEAINHAKAANVP-IIVAINK 110
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 59.8 bits (146), Expect = 1e-10
Identities = 31/91 (34%), Positives = 45/91 (49%), Gaps = 9/91 (9%)
Query: 124 DNAPEEKARGITIN--VAHVEYATENRHYSHT--DCPGHADYIKNMITGTSQMDGAILVV 179
D PEE+ RGI+I E+ + + D PGH D+ + +DGA++VV
Sbjct: 36 DFMPEERERGISITSAATTCEW----KGHKINLIDTPGHVDFTGEVERALRVLDGAVVVV 91
Query: 180 AATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
A G PQT A++ GV I +F+NK
Sbjct: 92 CAVGGVEPQTETVWRQAEKYGVPRI-IFVNK 121
Score = 32.0 bits (74), Expect = 0.21
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 7/79 (8%)
Query: 17 DLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGRQFKTTVTGIEMFH-- 74
D D P V T P G + R+ G +KKG +G G++ + V + H
Sbjct: 284 DPDGPLVALVFKTMDDPFVGKLSLVRVYSGTLKKGDTLYNSGTGKKER--VGRLYRMHGK 341
Query: 75 --KILDEAQAGDQLGALVK 91
+ +DEA AGD + A+ K
Sbjct: 342 QREEVDEAVAGD-IVAVAK 359
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 59.1 bits (144), Expect = 2e-10
Identities = 43/111 (38%), Positives = 58/111 (52%), Gaps = 12/111 (10%)
Query: 104 MAKPVLADKKLAKVKQYADIDNAPEEKARGITINVAHV----EYATENRHYSHTDCPGHA 159
M LA ++LA +D EE+ARGITI A+V EY + + D PGH
Sbjct: 46 MISEELAGEQLA-------LDFDEEEQARGITIKAANVSMVHEYEGKEYLINLIDTPGHV 98
Query: 160 DYIKNMITGTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
D+ ++ +DGAI+VV A +G MPQT L A + V V+FINK
Sbjct: 99 DFGGDVTRAMRAVDGAIVVVDAVEGVMPQTETVLRQALRERVKP-VLFINK 148
Score = 28.7 bits (65), Expect = 2.5
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 33 PGRGTVVTGRLERGIVKKGMECEFTGYGRQFKTTVTGIEM--FHKILDEAQAG 83
P G V TGR+ G ++KG E G ++ + GI M + ++E AG
Sbjct: 302 PHAGEVATGRVFSGTLRKGQEVYLVGAKKKNRVQQVGIYMGPEREEVEEIPAG 354
>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 = 56.4 bits (137), Expect = 5e-10
Identities = 37/97 (38%), Positives = 53/97 (54%), Gaps = 19/97 (19%)
Query: 124 DNAPEEKARGITI---NVAHVEYATENRHYSHTDCPGHADY------IKNMITGTSQMDG 174
D+ E+ RGITI N A + Y ++ + D PGHAD+ + +M+ DG
Sbjct: 41 DSNDLERERGITILAKNTA-ITY--KDTKINIIDTPGHADFGGEVERVLSMV------DG 91
Query: 175 AILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINKF 211
+L+V A++G MPQTR L A + G+ IVV INK
Sbjct: 92 VLLLVDASEGPMPQTRFVLKKALEAGLKPIVV-INKI 127
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 56.9 bits (138), Expect = 1e-09
Identities = 38/85 (44%), Positives = 48/85 (56%), Gaps = 7/85 (8%)
Query: 129 EKARGITI---NVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATDGA 185
EK RGITI N A V Y + D PGHAD+ + S +DG +L+V A++G
Sbjct: 49 EKERGITILAKNTA-VNY--NGTRINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGP 105
Query: 186 MPQTREHLLLAKQIGVTNIVVFINK 210
MPQTR L A +G+ IVV INK
Sbjct: 106 MPQTRFVLKKALALGLKPIVV-INK 129
Score = 39.5 bits (93), Expect = 7e-04
Identities = 24/89 (26%), Positives = 37/89 (41%), Gaps = 5/89 (5%)
Query: 1 MELLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYG 60
L I ++P P DLD+P + V G + GR+ RG VK +
Sbjct: 184 APLFETILDHVPAPKGDLDEPLQMQVTQLDYNSYVGRIGIGRIFRGTVKPNQQVALIKSD 243
Query: 61 ---RQFK-TTVTGIEMFHKI-LDEAQAGD 84
+ T + G +I ++EA+AGD
Sbjct: 244 GTTENGRITKLLGFLGLERIEIEEAEAGD 272
>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 = 55.8 bits (135), Expect = 3e-09
Identities = 35/85 (41%), Positives = 48/85 (56%), Gaps = 7/85 (8%)
Query: 129 EKARGITI---NVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATDGA 185
E+ RGITI N A + Y + D PGHAD+ + +DG +L+V A++G
Sbjct: 45 ERERGITILAKNTA-IRY--NGTKINIVDTPGHADFGGEVERVLGMVDGVLLLVDASEGP 101
Query: 186 MPQTREHLLLAKQIGVTNIVVFINK 210
MPQTR L A ++G+ IVV INK
Sbjct: 102 MPQTRFVLKKALELGLKPIVV-INK 125
Score = 43.8 bits (104), Expect = 3e-05
Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 5/88 (5%)
Query: 2 ELLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGME---CEFTG 58
L + I ++P P DLD+P + V + G + GR+ RG VKKG + + G
Sbjct: 181 PLFDAIVRHVPAPKGDLDEPLQMLVTNLDYDEYLGRIAIGRVHRGTVKKGQQVALMKRDG 240
Query: 59 YGRQFK-TTVTGIEMFHKI-LDEAQAGD 84
+ + + G E ++ +DEA AGD
Sbjct: 241 TIENGRISKLLGFEGLERVEIDEAGAGD 268
>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 = 55.2 bits (133), Expect = 4e-09
Identities = 34/82 (41%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 131 ARGIT--INVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATDGAMPQ 188
A GIT I HVE + + + D PGH + G D +LVVAA DG MPQ
Sbjct: 117 AGGITQHIGAYHVEN-EDGKMITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQ 175
Query: 189 TREHLLLAKQIGVTNIVVFINK 210
T E + AK V I+V INK
Sbjct: 176 TIEAISHAKAANVP-IIVAINK 196
>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 = 54.1 bits (131), Expect = 6e-09
Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 5/89 (5%)
Query: 124 DNAPEEKARGITIN--VAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAA 181
D PEEK R ++I VA +E+ + D PG+AD++ ++ +D A++VV A
Sbjct: 40 DYDPEEKKRKMSIETSVAPLEW--NGHKINLIDTPGYADFVGETLSALRAVDAALIVVEA 97
Query: 182 TDGAMPQTREHLLLAKQIGVTNIVVFINK 210
G T + + ++FINK
Sbjct: 98 QSGVEVGTEKVWEFLDDAKLP-RIIFINK 125
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 52.2 bits (126), Expect = 4e-08
Identities = 35/90 (38%), Positives = 41/90 (45%), Gaps = 21/90 (23%)
Query: 131 ARGIT--INVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQM--------DGAILVVA 180
A GIT I VE T + D PGH + + M D +LVVA
Sbjct: 279 AGGITQHIGAYQVE--TNGGKITFLDTPGHEAF--------TAMRARGAQVTDIVVLVVA 328
Query: 181 ATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
A DG MPQT E + AK GV I+V INK
Sbjct: 329 ADDGVMPQTIEAINHAKAAGVP-IIVAINK 357
>gnl|CDD|239665 cd03694, GTPBP_II, Domain II of the GP-1 family of GTPase. This
group includes proteins similar to GTPBP1 and GTPBP2.
GTPB1 is structurally, related to elongation factor 1
alpha, a key component of protein biosynthesis
machinery. Immunohistochemical analyses on mouse tissues
revealed that GTPBP1 is expressed in some neurons and
smooth muscle cells of various organs as well as
macrophages. Immunofluorescence analyses revealed that
GTPBP1 is localized exclusively in cytoplasm and shows a
diffuse granular network forming a gradient from the
nucleus to the periphery of the cells in smooth muscle
cell lines and macrophages. No significant difference
was observed in the immune response to protein antigen
between mutant mice and wild-type mice, suggesting
normal function of antigen-presenting cells of the
mutant mice. The absence of an eminent phenotype in
GTPBP1-deficient mice may be due to functional
compensation by GTPBP2, which is similar to GTPBP1 in
structure and tissue distribution.
Length = 87
Score = 48.4 bits (116), Expect = 6e-08
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 2/82 (2%)
Query: 26 VEHTYSIPGRGTVVTGRLERGIVKKGMECEF--TGYGRQFKTTVTGIEMFHKILDEAQAG 83
++ YS+PG GTVV G + +G+++ G G TV I + +AG
Sbjct: 5 IDEIYSVPGVGTVVGGTVSKGVIRLGDTLLLGPDQDGSFRPVTVKSIHRNRSPVRVVRAG 64
Query: 84 DQLGALVKGMKRDEVNRGLIMA 105
+K + R + +G+++
Sbjct: 65 QSASLALKKIDRSLLRKGMVLV 86
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 51.4 bits (124), Expect = 7e-08
Identities = 32/58 (55%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 154 DCPGHADYIKNMIT-GTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
D PGH M G S D AILVVAA DG MPQT E + AK GV IVV INK
Sbjct: 61 DTPGHE-AFTAMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAAGVP-IVVAINK 116
>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 = 49.9 bits (120), Expect = 1e-07
Identities = 28/96 (29%), Positives = 41/96 (42%), Gaps = 10/96 (10%)
Query: 124 DNAPEEKARGITI---NVA--HVEYATENRHYSH----TDCPGHADYIKNMITGTSQMDG 174
D +E+ RGITI ++ + + D PGH D+ + DG
Sbjct: 39 DTREDEQERGITIKSSAISLYFEYEEEKMDGNDYLINLIDSPGHVDFSSEVTAALRLTDG 98
Query: 175 AILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
A++VV A +G QT L A + V V+ INK
Sbjct: 99 ALVVVDAVEGVCVQTETVLRQALEERVK-PVLVINK 133
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 49.9 bits (120), Expect = 3e-07
Identities = 30/87 (34%), Positives = 43/87 (49%), Gaps = 1/87 (1%)
Query: 124 DNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATD 183
D P+E+ RGITI A +N + D PGH D+ + +DGA++V A
Sbjct: 49 DWMPQEQERGITIESAATSCDWDNHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDAVT 108
Query: 184 GAMPQTREHLLLAKQIGVTNIVVFINK 210
G PQT A + G+ ++FINK
Sbjct: 109 GVQPQTETVWRQADRYGIP-RLIFINK 134
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 49.1 bits (117), Expect = 5e-07
Identities = 32/92 (34%), Positives = 43/92 (46%), Gaps = 9/92 (9%)
Query: 125 NAPEEKARGITINVA----HVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVA 180
+++A GIT + EY EN+ D PGH + G + D AIL++A
Sbjct: 268 QIAQKEAGGITQKIGAYEVEFEYKDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIA 327
Query: 181 ATDGAMPQTREHLLLAKQIGVTN--IVVFINK 210
A DG PQT E + I N I+V INK
Sbjct: 328 ADDGVKPQTIEAI---NYIQAANVPIIVAINK 356
>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 = 47.3 bits (113), Expect = 1e-06
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 6/93 (6%)
Query: 124 DNAPEEKARGITINVAHVEYATEN-RHYSHT----DCPGHADYIKNMITGTSQMDGAILV 178
D +E+ RGI+I + E+ + S+ D PGH +++ + DG +LV
Sbjct: 42 DTRKDEQERGISIKSNPISLVLEDSKGKSYLINIIDTPGHVNFMDEVAAALRLCDGVVLV 101
Query: 179 VAATDGAMPQTREHLLLAKQIGVTNIVVFINKF 211
V +G T + A Q G+ +V+ INK
Sbjct: 102 VDVVEGLTSVTERLIRHAIQEGLP-MVLVINKI 133
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 47.8 bits (113), Expect = 1e-06
Identities = 35/88 (39%), Positives = 45/88 (51%), Gaps = 1/88 (1%)
Query: 123 IDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAAT 182
+D+ EK RGITI + + + D PGHAD+ + S +D +LVV A
Sbjct: 43 MDSNDLEKERGITILAKNTAIKWNDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAF 102
Query: 183 DGAMPQTREHLLLAKQIGVTNIVVFINK 210
DG MPQTR A G+ IVV INK
Sbjct: 103 DGPMPQTRFVTKKAFAYGLKPIVV-INK 129
Score = 27.0 bits (59), Expect = 8.0
Identities = 24/87 (27%), Positives = 36/87 (41%), Gaps = 5/87 (5%)
Query: 3 LLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGRQ 62
L I ++P P DLD PF + + G + GR++RG VK + +
Sbjct: 186 LYQAIVDHVPAPDVDLDGPFQMQISQLDYNSYVGVIGIGRIKRGKVKPNQQVTIIDSEGK 245
Query: 63 FKTTVTGIEMFHKIL-----DEAQAGD 84
+ G + H L D A+AGD
Sbjct: 246 TRNAKVGKVLGHLGLERIETDLAEAGD 272
>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 = 46.3 bits (110), Expect = 4e-06
Identities = 29/90 (32%), Positives = 41/90 (45%), Gaps = 1/90 (1%)
Query: 121 ADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVA 180
A +D +EK RGITI A + + D PGH D+ + +DGA+ V+
Sbjct: 48 ATMDWMEQEKERGITITSAATTVFWKGHRINIIDTPGHVDFTVEVERSLRVLDGAVAVLD 107
Query: 181 ATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
A G PQ+ A + V I F+NK
Sbjct: 108 AVGGVQPQSETVWRQANRYEVPRI-AFVNK 136
>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 = 45.2 bits (108), Expect = 8e-06
Identities = 30/90 (33%), Positives = 42/90 (46%), Gaps = 1/90 (1%)
Query: 121 ADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVA 180
A +D +E+ RGITI A ++ + D PGH D+ + +DGA+ V
Sbjct: 37 ATMDWMEQERERGITIQSAATTCFWKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFD 96
Query: 181 ATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
A G PQT A + GV I F+NK
Sbjct: 97 AVAGVQPQTETVWRQADRYGVPRI-AFVNK 125
>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 = 42.5 bits (101), Expect = 3e-05
Identities = 29/87 (33%), Positives = 42/87 (48%), Gaps = 6/87 (6%)
Query: 129 EKARGITI--NVAHVEYATENRH---YSHTDCPGHADYIKNMITGTSQMDGAILVVAATD 183
E+ RGITI + Y ++ + D PGH D+ + + +GA+LVV AT
Sbjct: 43 ERERGITIKAQAVRLFYKAKDGEEYLLNLIDTPGHVDFSYEVSRSLAACEGALLVVDATQ 102
Query: 184 GAMPQTREHLLLAKQIGVTNIVVFINK 210
G QT + LA + + I V INK
Sbjct: 103 GVEAQTLANFYLALENNLEIIPV-INK 128
>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 = 41.0 bits (96), Expect = 2e-04
Identities = 25/94 (26%), Positives = 49/94 (52%), Gaps = 1/94 (1%)
Query: 118 KQYADIDNAPEEKARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAIL 177
+++A D EK RGI+I + +++ + + D PGH D+ ++ + +D ++
Sbjct: 50 QRHAKSDWMEMEKQRGISITTSVMQFPYRDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLM 109
Query: 178 VVAATDGAMPQTREHLLLAKQIGVTNIVVFINKF 211
V+ A G +TR+ L+ ++ T I F+NK
Sbjct: 110 VIDAAKGVETRTRK-LMEVTRLRDTPIFTFMNKL 142
>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 = 40.4 bits (95), Expect = 4e-04
Identities = 32/117 (27%), Positives = 53/117 (45%), Gaps = 13/117 (11%)
Query: 106 KPVLADKKLAKVKQYAD-------IDNAPEEKARGITI--NVAHVEYATENRH---YSHT 153
K LAD+ L ++ +D+ E+ RGITI + Y ++ +
Sbjct: 16 KSTLADRLLEYTGAISEREMREQVLDSMDLERERGITIKAQAVRLNYKAKDGETYVLNLI 75
Query: 154 DCPGHADYIKNMITGTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
D PGH D+ + + +GA+L+V A G QT ++ LA + + I+ INK
Sbjct: 76 DTPGHVDFSYEVSRSLAACEGALLLVDAAQGIEAQTLANVYLALENDLE-IIPVINK 131
Score = 37.7 bits (88), Expect = 0.003
Identities = 25/94 (26%), Positives = 43/94 (45%), Gaps = 2/94 (2%)
Query: 2 ELLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGR 61
E+L I +P P D D P + ++ RG V R+ G +K G + F G+
Sbjct: 170 EILEAIVKRVPPPKGDPDAPLKALIFDSHYDNYRGVVALVRVFEGTIKPGDKIRFMSTGK 229
Query: 62 QFKTTVTGIEMFH-KILDEAQAGDQLGALVKGMK 94
+++ G+ DE AG+ +G ++ G+K
Sbjct: 230 EYEVDEVGVFTPKLTKTDELSAGE-VGYIIAGIK 262
>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 = 39.1 bits (92), Expect = 8e-04
Identities = 28/85 (32%), Positives = 44/85 (51%), Gaps = 5/85 (5%)
Query: 129 EKARGITI--NVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATDGAM 186
EK RGI++ +V EY + D PGH D+ ++ + +D A++V+ A G
Sbjct: 52 EKQRGISVTSSVMQFEYK--GCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVE 109
Query: 187 PQTREHLLLAKQIGVTNIVVFINKF 211
PQTR+ + + G I+ FINK
Sbjct: 110 PQTRKLFEVCRLRG-IPIITFINKL 133
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 38.5 bits (90), Expect = 0.001
Identities = 30/97 (30%), Positives = 42/97 (43%), Gaps = 11/97 (11%)
Query: 124 DNAPEEKARGITINVA----HVEYATENRHYSH------TDCPGHADYIKNMITGTSQMD 173
D +E+ RGITI + E+ E+ D PGH D+ + D
Sbjct: 58 DTRADEQERGITIKSTGISLYYEHDLEDGDDKQPFLINLIDSPGHVDFSSEVTAALRVTD 117
Query: 174 GAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
GA++VV +G QT L A Q + V+FINK
Sbjct: 118 GALVVVDCVEGVCVQTETVLRQALQERIRP-VLFINK 153
>gnl|CDD|239666 cd03695, CysN_NodQ_II, CysN_NodQ_II: This subfamily represents the
domain II of the large subunit of ATP sulfurylase
(ATPS): CysN or the N-terminal portion of NodQ, found
mainly in proteobacteria and homologous to the domain II
of EF-Tu. Escherichia coli ATPS consists of CysN and a
smaller subunit CysD and CysN. ATPS produces
adenosine-5'-phosphosulfate (APS) from ATP and sulfate,
coupled with GTP hydrolysis. In the subsequent reaction
APS is phosphorylated by an APS kinase (CysC), to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for
use in amino acid (aa) biosynthesis. The Rhizobiaceae
group (alpha-proteobacteria) appears to carry out the
same chemistry for the sufation of a nodulation factor.
In Rhizobium meliloti, a the hererodimeric complex
comprised of NodP and NodQ appears to possess both ATPS
and APS kinase activities. The N and C termini of NodQ
correspond to CysN and CysC, respectively. Other
eubacteria, Archaea, and eukaryotes use a different ATP
sulfurylase, which shows no aa sequence similarity to
CysN or NodQ. CysN and the N-terminal portion of NodQ
show similarity to GTPases involved in translation, in
particular, EF-Tu and EF-1alpha.
Length = 81
Score = 35.6 bits (83), Expect = 0.002
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 14/90 (15%)
Query: 22 FYLPVEHTYSIPG---RGTVVTGRLERGIVKKGMECEFTGYGRQFKTTVTGIEMFHKILD 78
F PV++ P RG G + G ++ G E G+ + V IE F LD
Sbjct: 1 FRFPVQYVIR-PNADFRG--YAGTIASGSIRVGDEVVVLPSGK--TSRVKSIETFDGELD 55
Query: 79 EAQAGDQLGALVKGMKRDEVN--RGLIMAK 106
EA AG+ + ++ DE++ RG ++
Sbjct: 56 EAGAGESVTLTLE----DEIDVSRGDVIVA 81
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 38.0 bits (89), Expect = 0.002
Identities = 26/84 (30%), Positives = 43/84 (51%), Gaps = 5/84 (5%)
Query: 129 EKARGITI--NVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATDGAM 186
EK RGI++ +V +YA + + D PGH D+ ++ + +D A++V+ A G
Sbjct: 62 EKQRGISVTSSVMQFDYA--DCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIE 119
Query: 187 PQTREHLLLAKQIGVTNIVVFINK 210
PQT + + + I FINK
Sbjct: 120 PQTLKLFEVCRLRD-IPIFTFINK 142
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 37.5 bits (88), Expect = 0.003
Identities = 29/92 (31%), Positives = 45/92 (48%), Gaps = 6/92 (6%)
Query: 124 DNAPEEKARGITI---NVAHVEYATENRHY--SHTDCPGHADYIKNMITGTSQMDGAILV 178
D+ E+ RGITI V A + Y + D PGH D+ + + +GA+LV
Sbjct: 47 DSMDIERERGITIKAQAVRLNYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLV 106
Query: 179 VAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
V A+ G QT ++ LA + + I+ +NK
Sbjct: 107 VDASQGVEAQTLANVYLALENNLE-IIPVLNK 137
Score = 34.5 bits (80), Expect = 0.034
Identities = 26/94 (27%), Positives = 45/94 (47%), Gaps = 2/94 (2%)
Query: 2 ELLNQIDTYIPQPVRDLDKPFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGR 61
++L I IP P D D P + ++ G VV R+ G +KKG + G+
Sbjct: 176 DVLEAIVEKIPPPKGDPDAPLKALIFDSWYDNYLGVVVLVRIFDGTLKKGDKIRMMSTGK 235
Query: 62 QFKTTVTGIEM-FHKILDEAQAGDQLGALVKGMK 94
+++ GI +DE +AG+ +G ++ G+K
Sbjct: 236 EYEVDEVGIFTPKMVKVDELKAGE-VGYIIAGIK 268
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 37.5 bits (88), Expect = 0.003
Identities = 30/87 (34%), Positives = 41/87 (47%), Gaps = 9/87 (10%)
Query: 128 EEKARGITINVAHVEYAT----ENRHYSHTDCPGHADYIKNMITGTSQMDGAILVVAATD 183
+E+ RGITI A AT + + D PGH D+ + +DGA+ V A
Sbjct: 53 QEQERGITITSA----ATTCFWKGHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVS 108
Query: 184 GAMPQTREHLLLAKQIGVTNIVVFINK 210
G PQ+ A + GV I VF+NK
Sbjct: 109 GVEPQSETVWRQADKYGVPRI-VFVNK 134
>gnl|CDD|239669 cd03698, eRF3_II_like, eRF3_II_like: domain similar to domain II of
the eukaryotic class II release factor (eRF3). In
eukaryotes, translation termination is mediated by two
interacting release factors, eRF1 and eRF3, which act as
class I and II factors, respectively. eRF1 functions as
an omnipotent release factor, decoding all three stop
codons and triggering the release of the nascent peptide
catalyzed by the ribsome. eRF3 is a GTPase, which
enhances the termination efficiency by stimulating the
eRF1 activity in a GTP-dependent manner. Sequence
comparison of class II release factors with elongation
factors shows that eRF3 is more similar to eEF1alpha
whereas prokaryote RF3 is more similar to EF-G, implying
that their precise function may differ. Only eukaryote
RF3s are found in this group. Saccharomyces cerevisiae
eRF3 (Sup35p) is a translation termination factor which
is divided into three regions N, M and a C-terminal
eEF1a-like region essential for translation termination.
Sup35NM is a non-pathogenic prion-like protein with
the property of aggregating into polymer-like fibrils.
This group also contains proteins similar to S.
cerevisiae Hbs1, a G protein known to be important for
efficient growth and protein synthesis under conditions
of limiting translation initiation 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 = 83
Score = 34.8 bits (81), Expect = 0.004
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 3/83 (3%)
Query: 21 PFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGRQFKTTVTGIEMFHKILDEA 80
PF LP+ Y G GTVV+G++E G ++KG + V I + + +D A
Sbjct: 1 PFRLPISDKYKDQG-GTVVSGKVESGSIQKGDTL--LVMPSKESVEVKSIYVDDEEVDYA 57
Query: 81 QAGDQLGALVKGMKRDEVNRGLI 103
AG+ + +KG+ ++++ G +
Sbjct: 58 VAGENVRLKLKGIDEEDISPGDV 80
>gnl|CDD|239756 cd04089, eRF3_II, eRF3_II: domain II of the eukaryotic class II
release factor (eRF3). In eukaryotes, translation
termination is mediated by two interacting release
factors, eRF1 and eRF3, which act as class I and II
factors, respectively. eRF1 functions as an omnipotent
release factor, decoding all three stop codons and
triggering the release of the nascent peptide catalyzed
by the ribsome. eRF3 is a GTPase, which enhances the
termination efficiency by stimulating the eRF1 activity
in a GTP-dependent manner. Sequence comparison of class
II release factors with elongation factors shows that
eRF3 is more similar to eEF1alpha whereas prokaryote RF3
is more similar to EF-G, implying that their precise
function may differ. Only eukaryote RF3s are found in
this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a
translation termination factor which is divided into
three regions N, M and a C-terminal eEF1a-like region
essential for translation termination. Sup35NM is a
non-pathogenic prion-like protein with the property of
aggregating into polymer-like fibrils.
Length = 82
Score = 34.4 bits (80), Expect = 0.005
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 4/83 (4%)
Query: 21 PFYLPVEHTYSIPGRGTVVTGRLERGIVKKGMECEFTGYGRQFKTTVTGIEMFHKILDEA 80
P LP+ Y GTVV G++E G +KKG + Q + V I + A
Sbjct: 1 PLRLPIIDKYK--DMGTVVLGKVESGTIKKGDKLLVMPNKTQVE--VLSIYNEDVEVRYA 56
Query: 81 QAGDQLGALVKGMKRDEVNRGLI 103
+ G+ + +KG++ ++++ G +
Sbjct: 57 RPGENVRLRLKGIEEEDISPGFV 79
>gnl|CDD|206728 cd04165, GTPBP1_like, GTP binding protein 1 (GTPBP1)-like family
includes GTPBP2. Mammalian GTP binding protein 1
(GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1
are GTPases whose specific functions remain unknown. In
mouse, GTPBP1 is expressed in macrophages, in smooth
muscle cells of various tissues and in some neurons of
the cerebral cortex; GTPBP2 tissue distribution appears
to overlap that of GTPBP1. In human leukemia and
macrophage cell lines, expression of both GTPBP1 and
GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The
chromosomal location of both genes has been identified
in humans, with GTPBP1 located in chromosome 22q12-13.1
and GTPBP2 located in chromosome 6p21-12. Human
glioblastoma multiforme (GBM), a highly-malignant
astrocytic glioma and the most common cancer in the
central nervous system, has been linked to chromosomal
deletions and a translocation on chromosome 6. The GBM
translocation results in a fusion of GTPBP2 and PTPRZ1,
a protein involved in oligodendrocyte differentiation,
recovery, and survival. This fusion product may
contribute to the onset of GBM.
Length = 224
Score = 35.3 bits (82), Expect = 0.012
Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 154 DCPGHADYIKNMITGTS--QMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVV 206
D GH Y+K + G + D A+LVV A G + T+EHL LA + V VV
Sbjct: 90 DLAGHERYLKTTVFGMTGYAPDYAMLVVGANAGIIGMTKEHLGLALALKVPVFVV 144
>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 = 32.0 bits (73), Expect = 0.099
Identities = 18/103 (17%), Positives = 34/103 (33%), Gaps = 8/103 (7%)
Query: 117 VKQYADIDNAPEEKARGIT--INVAHVEYATENRHYSHTDCPGHADYIKNMITGTSQM-- 172
+ + G T +V E D PG ++ +++
Sbjct: 14 LNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEFGGLGREELARLLL 73
Query: 173 ---DGAILVVAATDGAMPQTREHLLLAKQIGV-TNIVVFINKF 211
D +LVV +TD + + L+L + I++ NK
Sbjct: 74 RGADLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGNKI 116
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 32.2 bits (73), Expect = 0.19
Identities = 22/57 (38%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 154 DCPGHADYIKNMITGTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
D PGH + G S D A+LVV +G PQT E + + +Q T VV NK
Sbjct: 532 DTPGHEAFTSLRKRGGSLADLAVLVVDINEGFKPQTIEAINILRQYK-TPFVVAANK 587
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 32.1 bits (74), Expect = 0.20
Identities = 20/57 (35%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 154 DCPGHADYIKNMITGTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
D PGH + G + D AILVV +G PQT E + + K+ +V NK
Sbjct: 77 DTPGHEAFTNLRKRGGALADIAILVVDINEGFQPQTIEAINILKRRKTPFVVA-ANK 132
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 31.2 bits (72), Expect = 0.44
Identities = 29/94 (30%), Positives = 43/94 (45%), Gaps = 20/94 (21%)
Query: 129 EKARGITI--NVAHVEY-ATENRHYSHT--DCPGHADYIKNMITGT-------SQMDGAI 176
E+ RGITI + Y A + Y D PGH D+ + + +GA+
Sbjct: 50 ERERGITIKAQAVRLNYKAKDGETYILNLIDTPGHVDF-------SYEVSRSLAACEGAL 102
Query: 177 LVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
LVV A+ G QT ++ LA + + I V +NK
Sbjct: 103 LVVDASQGVEAQTLANVYLALENDLEIIPV-LNK 135
Score = 30.4 bits (70), Expect = 0.62
Identities = 30/104 (28%), Positives = 48/104 (46%), Gaps = 22/104 (21%)
Query: 2 ELLNQIDTYIPQPVRDLDKP--------FYLPVEHTYSIPGRGTVVTGRLERGIVKKGME 53
E+L I IP P D D P +Y Y RG VV R+ G +KKG +
Sbjct: 174 EVLEAIVERIPPPKGDPDAPLKALIFDSWYDN----Y----RGVVVLVRVVDGTLKKGDK 225
Query: 54 CEFTGYGRQFKTTVTGI---EMFHKILDEAQAGDQLGALVKGMK 94
+ G++++ G+ +M +DE AG+ +G ++ G+K
Sbjct: 226 IKMMSTGKEYEVDEVGVFTPKM--VPVDELSAGE-VGYIIAGIK 266
>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 = 30.9 bits (70), Expect = 0.47
Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 154 DCPGHADYIKNMITGTSQMDGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVFINK 210
D PGH + G + D AIL+V +G PQT+E L + + T VV NK
Sbjct: 75 DTPGHEAFTNLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYK-TPFVVAANK 130
>gnl|CDD|239662 cd03691, BipA_TypA_II, BipA_TypA_II: domain II of BipA (also
called TypA) having homology to domain II of the
elongation factors (EFs) EF-G and EF-Tu. BipA is a
highly conserved protein with global regulatory
properties in Escherichia coli. BipA is phosphorylated
on a tyrosine residue under some cellular conditions.
Mutants show altered regulation of some pathways. BipA
functions as a translation factor that is required
specifically for the expression of the transcriptional
modulator Fis. BipA binds to ribosomes at a site that
coincides with that of EF-G and has a GTPase activity
that is sensitive to high GDP:GTP ratios and, is
stimulated by 70S ribosomes programmed with mRNA and
aminoacylated tRNAs. The growth rate-dependent
induction of BipA allows the efficient expression of
Fis, thereby modulating a range of downstream
processes, including DNA metabolism and type III
secretion.
Length = 86
Score = 28.6 bits (65), Expect = 0.78
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 9/56 (16%)
Query: 36 GTVVTGRLERGIVKKGME---CEFTGYGRQFKTTVTGIEMFH----KILDEAQAGD 84
G + GR+ RG VK G + + G + K +T + F ++EA+AGD
Sbjct: 15 GRIAIGRIFRGTVKVGQQVAVVKRDGKIEKAK--ITKLFGFEGLKRVEVEEAEAGD 68
>gnl|CDD|239670 cd03699, lepA_II, lepA_II: This subfamily represents the domain
II of LepA, a GTP-binding protein localized in the
cytoplasmic membrane. The N-terminal domain of LepA
shares regions of homology to translation factors. In
terms of interaction with the ribosome, EF-G, EF-Tu and
IF2 have all been demonstrated to interact at
overlapping sites on the ribosome. Chemical protection
studies demonstrate that they all include the
universally conserved alpha-sarcin loop as part of
their binding site. These data indicate that LepA may
bind to this location on the ribosome as well. LepA
has never been observed in archaea, and eukaryl LepA is
organellar. LepA is therefore a true bacterial GTPase,
found only in the bacterial lineage.
Length = 86
Score = 28.2 bits (64), Expect = 0.94
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 35 RGTVVTGRLERGIVKKGMECEFTGYGRQFKTTVTGI---EMFHKILDEAQAGDQLGALVK 91
RG + R+ G +KKG + F G++++ GI EM DE AG Q+G ++
Sbjct: 14 RGVIALVRVFDGTLKKGDKIRFMSTGKEYEVEEVGIFRPEM--TPTDELSAG-QVGYIIA 70
Query: 92 GMK 94
G+K
Sbjct: 71 GIK 73
>gnl|CDD|221246 pfam11824, DUF3344, Protein of unknown function (DUF3344). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and archaea. Proteins
in this family are typically between 367 to 1857 amino
acids in length.
Length = 267
Score = 29.3 bits (66), Expect = 1.2
Identities = 23/99 (23%), Positives = 31/99 (31%), Gaps = 31/99 (31%)
Query: 134 ITINVAHVEYATENRHYSHTDCPGH---------------ADYIKNM-----ITGTSQMD 173
+T N +E T+ Y D GH D I +T S D
Sbjct: 76 VTFNGQGLETLTDEAPY--VDQKGHGSYVDYDYGLWVYDVTDLISGGTNTVVVTSDSGFD 133
Query: 174 GAI----LVVAATDGAMPQTR-----EHLLLAKQIGVTN 203
G I LVV DG+ P+ L + +T
Sbjct: 134 GRIYGITLVVVYEDGSGPEIEYWINEGCDWLYYKSTITP 172
>gnl|CDD|179912 PRK04998, PRK04998, hypothetical protein; Provisional.
Length = 88
Score = 27.6 bits (62), Expect = 1.6
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 8/46 (17%)
Query: 105 AKPVLADKKLAKVKQYADIDNAPEEKARG--------ITINVAHVE 142
A+P L D+ + V+++A D P K ITI +E
Sbjct: 24 ARPELVDQVVEVVQRHAPGDYTPTVKPSSKGNYHSVSITITATSIE 69
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 29.3 bits (67), Expect = 1.8
Identities = 31/98 (31%), Positives = 41/98 (41%), Gaps = 31/98 (31%)
Query: 128 EEKARGITINVAHVEYATENRHYSHT----DCPGHADYIKNMITGTSQ-------MDGAI 176
+E+ RGITI A AT H D PGH D+ T + +DGA+
Sbjct: 55 QEQERGITITSA----ATTCFWKDHRINIIDTPGHVDF-------TIEVERSLRVLDGAV 103
Query: 177 LVVAATDGAMPQT----REHLLLAKQIGVTNIVVFINK 210
V A G PQ+ R+ A + V I F+NK
Sbjct: 104 AVFDAVGGVEPQSETVWRQ----ADKYKVPRI-AFVNK 136
>gnl|CDD|205806 pfam13629, T2SS-T3SS_pil_N, Pilus formation protein N terminal
region.
Length = 72
Score = 26.7 bits (60), Expect = 2.5
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 173 DGAILVVAATDGAMPQTREHLLLAKQIGVTNIVVF 207
+ AI V R + K+ G TN++V+
Sbjct: 28 NPAIADVTVLSP-----RTLYVTGKKPGTTNLIVW 57
>gnl|CDD|235479 PRK05458, PRK05458, guanosine 5'-monophosphate oxidoreductase;
Provisional.
Length = 326
Score = 28.0 bits (63), Expect = 3.8
Identities = 23/80 (28%), Positives = 32/80 (40%), Gaps = 25/80 (31%)
Query: 88 ALVKGMKRDEVNRGLIMAKPV-LADKKLAKVKQYADIDNAPEEKARGITINVAHVEYATE 146
+K M +GLI + V + D + V Q A PE ITI++AH
Sbjct: 76 PFIKDMH----EQGLIASISVGVKDDEYDFVDQLAAEGLTPEY----ITIDIAH------ 121
Query: 147 NRHYSHTDCPGHADYIKNMI 166
GH+D + NMI
Sbjct: 122 ----------GHSDSVINMI 131
>gnl|CDD|239659 cd03688, eIF2_gamma_II, eIF2_gamma_II: this subfamily represents
the domain II of the gamma subunit of eukaryotic
translation initiation factor 2 (eIF2-gamma) found in
Eukaryota and Archaea. eIF2 is a G protein that
delivers the methionyl initiator tRNA to the small
ribosomal subunit and releases it upon GTP hydrolysis
after the recognition of the initiation codon. eIF2 is
composed three subunits, alpha, beta and gamma. Subunit
gamma shows strongest conservation, and it confers both
tRNA binding and GTP/GDP binding.
Length = 113
Score = 26.7 bits (60), Expect = 4.4
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 18/85 (21%)
Query: 17 DLDKPFYLPVEHTYSI--PG------RGTVVTGRLERGIVKKGMECE------FTGYGRQ 62
D P + V ++ + PG +G V G L +G++K G E E G+
Sbjct: 1 DFTSPPRMIVIRSFDVNKPGTEVDDLKGGVAGGSLLQGVLKVGDEIEIRPGIVVKDEGKI 60
Query: 63 ----FKTTVTGIEMFHKILDEAQAG 83
T + ++ + L EA G
Sbjct: 61 KCRPIFTKIVSLKAENNDLQEAVPG 85
>gnl|CDD|221829 pfam12883, DUF3828, Protein of unknown function (DUF3828). This is
a family of bacterial proteins of unknown function.
Length = 120
Score = 26.5 bits (59), Expect = 5.9
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 160 DYIKNMITGTSQMDGAILVVAATDGAMPQTREHLL 194
D+I + G ++MDG VV T G P HL+
Sbjct: 67 DWISQIRVGKAKMDGGGAVVDVTFGRQPSKPHHLI 101
>gnl|CDD|99992 cd03822, GT1_ecORF704_like, This family is most closely related to
the GT1 family of glycosyltransferases. ORF704 in E.
coli has been shown to be involved in the biosynthesis
of O-specific mannose homopolysaccharides.
Length = 366
Score = 27.2 bits (61), Expect = 6.1
Identities = 12/37 (32%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 176 ILVVAATDGAMPQTR-EHLLLAKQIGVTNIVVFINKF 211
+LV T + + R E LA+++G+ + V+FIN++
Sbjct: 219 LLVAGETHPDLERYRGEAYALAERLGLADRVIFINRY 255
>gnl|CDD|225736 COG3195, COG3195, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 176
Score = 27.0 bits (60), Expect = 6.2
Identities = 21/97 (21%), Positives = 34/97 (35%), Gaps = 25/97 (25%)
Query: 57 TGYGRQFKTTVTGI-EMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMAKPVLADKKLA 115
Y + + G+ + + A ++L LI A P LA K
Sbjct: 36 RAYDLRPFASAEGLHAAMCRAVRAASEEERLA--------------LIRAHPDLAGKAAI 81
Query: 116 KVKQYADIDN----------APEEKARGITINVAHVE 142
+ A+ + +PEE AR +N A+VE
Sbjct: 82 AGELTAESTSEQASAGLDRLSPEEFARFTELNAAYVE 118
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 27.4 bits (61), Expect = 7.9
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 154 DCPGHADYIKNMITGTSQMDGAILVVAATDGAMPQT 189
D PGH D+ + DGA++VV +G QT
Sbjct: 104 DSPGHVDFSSEVTAALRITDGALVVVDCIEGVCVQT 139
>gnl|CDD|217488 pfam03313, SDH_alpha, Serine dehydratase alpha chain. L-serine
dehydratase (EC:4.2.1.13) is a found as a heterodimer of
alpha and beta chain or as a fusion of the two chains in
a single protein. This enzyme catalyzes the deamination
of serine to form pyruvate. This enzyme is part of the
gluconeogenesis pathway.
Length = 269
Score = 26.7 bits (60), Expect = 9.1
Identities = 18/120 (15%), Positives = 33/120 (27%), Gaps = 30/120 (25%)
Query: 71 EMFHKILDEAQAGDQLGALVKGMKRDEVNRGLIMAKPVLADKKLAKVKQYADIDNAPEEK 130
EM + + G ++ A + M V +GL + + +K
Sbjct: 15 EMSVGVPGTGEVGLKMAAALGAMGGS-VEKGL---------------EVLEGLTPGDLKK 58
Query: 131 ARGITINVAHVEYATENRHYSHTDCPGHADYIKNMITGTS-----QMDGAILVVAATDGA 185
AR N+ + D + + G +V A T G+
Sbjct: 59 AR---------RALAANKALAGEGLLLGNDLLNRAVAYALAASEANASGGRIVAAPTAGS 109
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.137 0.396
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,969,743
Number of extensions: 1035327
Number of successful extensions: 959
Number of sequences better than 10.0: 1
Number of HSP's gapped: 893
Number of HSP's successfully gapped: 133
Length of query: 211
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 118
Effective length of database: 6,812,680
Effective search space: 803896240
Effective search space used: 803896240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (25.7 bits)