RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13818
(207 letters)
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 171 bits (436), Expect = 2e-51
Identities = 74/141 (52%), Positives = 91/141 (64%), Gaps = 25/141 (17%)
Query: 1 VGTKIEPTLCRADRLVGQVLGAVGALPKIFIELEISYHLLKRLLGVRMEGDKKGAKLEIS 60
VGT I+PTL RADRLVGQVLG G LP+++ E +EI
Sbjct: 328 VGTTIDPTLTRADRLVGQVLGYPGKLPEVYAE------------------------IEIQ 363
Query: 61 YHLLKRLLGVRMEGDKKGAKVQKLTRNEVLLVNIGSLSTGGRVLATKAD-LAKISLTNPV 119
Y+LL+RLLGV+ + KK KV KL + E L++NIGS +TGGRV+ K D +AK+ LT PV
Sbjct: 364 YYLLRRLLGVKSQDGKKATKVAKLKKGESLMINIGSTTTGGRVVGIKDDGIAKLELTTPV 423
Query: 120 CTEVNEKIALSRRVEKHWSLI 140
CT V EKIALSRRV+KHW LI
Sbjct: 424 CTSVGEKIALSRRVDKHWRLI 444
Score = 109 bits (275), Expect = 3e-28
Identities = 42/52 (80%), Positives = 47/52 (90%)
Query: 156 GNESCPQPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVKFVQ 207
NESCPQPQTSEHLAA+EIMKLKHIIILQNKIDLVKE QA +Q+E+I FV+
Sbjct: 150 ANESCPQPQTSEHLAAVEIMKLKHIIILQNKIDLVKEAQAQDQYEEIRNFVK 201
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 135 bits (342), Expect = 4e-38
Identities = 52/140 (37%), Positives = 78/140 (55%), Gaps = 29/140 (20%)
Query: 1 VGTKIEPTLCRADRLVGQVLGAVGALPKIFIELEISYHLLKRLLGVRMEGDKKGAKLEIS 60
VGTK++PTL +AD LVGQV+G G LP ++ + I YHLL+R++G
Sbjct: 296 VGTKLDPTLTKADALVGQVVGKPGTLPPVWTSIRIEYHLLERVVGT-------------- 341
Query: 61 YHLLKRLLGVRMEGDKKGAKVQKLTRNEVLLVNIGSLSTGGRVLATKADLAKISLTNPVC 120
K+ KV+ + NEVL++N+G+ +T G V + K D ++ L PVC
Sbjct: 342 ---------------KEELKVEPIKTNEVLMLNVGTATTVGVVTSAKKDEIEVKLKRPVC 386
Query: 121 TEVNEKIALSRRVEKHWSLI 140
E+ E++A+SRR+ W LI
Sbjct: 387 AEIGERVAISRRIGNRWRLI 406
Score = 94.3 bits (235), Expect = 8e-23
Identities = 32/52 (61%), Positives = 41/52 (78%)
Query: 156 GNESCPQPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVKFVQ 207
NE CPQPQT EHL A+EI+ +K+III+QNKIDLV +A E +EQI +FV+
Sbjct: 119 ANEPCPQPQTREHLMALEIIGIKNIIIVQNKIDLVSRERALENYEQIKEFVK 170
>gnl|CDD|150009 pfam09173, eIF2_C, Initiation factor eIF2 gamma, C terminal.
Members of this family, which are found in the
initiation factors eIF2 and EF-Tu, adopt a structure
consisting of a beta barrel with Greek key topology.
They are required for formation of the ternary complex
with GTP and initiator tRNA.
Length = 88
Score = 120 bits (304), Expect = 8e-36
Identities = 47/85 (55%), Positives = 66/85 (77%), Gaps = 4/85 (4%)
Query: 56 KLEISYHLLKRLLGVRMEGDKKGAKVQKLTRNEVLLVNIGSLSTGGRVLATKADLAKISL 115
++EI Y+LL+RL+GV+ ++ AKV+KL + EVL++NIGS +TGG V A K DLA++ L
Sbjct: 3 EIEIEYYLLERLVGVK----EEEAKVEKLKKGEVLMLNIGSATTGGVVTAVKKDLAEVEL 58
Query: 116 TNPVCTEVNEKIALSRRVEKHWSLI 140
PVCTE+ EK+A+SRRV+K W LI
Sbjct: 59 KRPVCTEIGEKVAISRRVDKRWRLI 83
>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 = 107 bits (269), Expect = 3e-29
Identities = 41/52 (78%), Positives = 45/52 (86%)
Query: 156 GNESCPQPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVKFVQ 207
NE CPQPQTSEHLAA+EIM LKHIIILQNKIDLVKE QA E +EQI +FV+
Sbjct: 110 ANEPCPQPQTSEHLAALEIMGLKHIIILQNKIDLVKEEQALENYEQIKEFVK 161
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 103 bits (258), Expect = 6e-26
Identities = 47/140 (33%), Positives = 72/140 (51%), Gaps = 29/140 (20%)
Query: 1 VGTKIEPTLCRADRLVGQVLGAVGALPKIFIELEISYHLLKRLLGVRMEGDKKGAKLEIS 60
VGTK++P+L +AD L G V G G LP ++ L I HLL+R++G
Sbjct: 295 VGTKLDPSLTKADALAGSVAGKPGTLPPVWESLTIEVHLLERVVGT-------------- 340
Query: 61 YHLLKRLLGVRMEGDKKGAKVQKLTRNEVLLVNIGSLSTGGRVLATKADLAKISLTNPVC 120
K+ KV+ + E L++N+G+ +T G V + + D A++ L PVC
Sbjct: 341 ---------------KEELKVEPIKTGEPLMLNVGTATTVGVVTSARKDEAEVKLKRPVC 385
Query: 121 TEVNEKIALSRRVEKHWSLI 140
E +++A+SRRV W LI
Sbjct: 386 AEEGDRVAISRRVGGRWRLI 405
Score = 83.7 bits (208), Expect = 4e-19
Identities = 30/50 (60%), Positives = 41/50 (82%)
Query: 157 NESCPQPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVKFV 206
NE CPQPQT EHL A++I+ +K+I+I+QNKIDLV + +A E +EQI +FV
Sbjct: 119 NEPCPQPQTKEHLMALDIIGIKNIVIVQNKIDLVSKERALENYEQIKEFV 168
>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 = 96.7 bits (241), Expect = 1e-23
Identities = 48/140 (34%), Positives = 73/140 (52%), Gaps = 29/140 (20%)
Query: 1 VGTKIEPTLCRADRLVGQVLGAVGALPKIFIELEISYHLLKRLLGVRMEGDKKGAKLEIS 60
VGTK++P L +AD L GQV+G G LP ++ LE+ HLL+R++G E
Sbjct: 290 VGTKLDPALTKADALAGQVVGKPGTLPPVWESLELEVHLLERVVGTEEE----------- 338
Query: 61 YHLLKRLLGVRMEGDKKGAKVQKLTRNEVLLVNIGSLSTGGRVLATKADLAKISLTNPVC 120
KV+ + EVL++N+G+ +T G V + + D ++ L PVC
Sbjct: 339 ------------------LKVEPIKTGEVLMLNVGTATTVGVVTSARKDEIEVKLKRPVC 380
Query: 121 TEVNEKIALSRRVEKHWSLI 140
E +++A+SRRV W LI
Sbjct: 381 AEEGDRVAISRRVGGRWRLI 400
Score = 79.3 bits (196), Expect = 1e-17
Identities = 30/50 (60%), Positives = 41/50 (82%)
Query: 157 NESCPQPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVKFV 206
NE CPQPQT EHL A+EI+ +K+I+I+QNKIDLV + +A E +E+I +FV
Sbjct: 114 NEPCPQPQTREHLMALEIIGIKNIVIVQNKIDLVSKEKALENYEEIKEFV 163
>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 = 51.0 bits (123), Expect = 9e-09
Identities = 17/24 (70%), Positives = 21/24 (87%)
Query: 1 VGTKIEPTLCRADRLVGQVLGAVG 24
VGTK++PTL +ADRLVGQV+G G
Sbjct: 90 VGTKLDPTLTKADRLVGQVVGEPG 113
>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 = 46.4 bits (111), Expect = 1e-06
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 162 QPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVKFVQ 207
PQT EHL +E++ +K +++ K DLV E + E+I++ +
Sbjct: 88 MPQTREHLEILELLGIKKGLVVLTKADLVDEDRLELVEEEILELLA 133
>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 = 43.6 bits (104), Expect = 1e-05
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 161 PQPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIV 203
PQT EHL + + + II+ NKID V + + E E+I
Sbjct: 103 VMPQTREHLLLAKTLGVP-IIVFINKIDRVDDAELEEVVEEIS 144
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 38.1 bits (89), Expect = 0.002
Identities = 14/45 (31%), Positives = 26/45 (57%)
Query: 161 PQPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVKF 205
QT EHL ++++ +K+ II+ K D V E + ++ +QI+
Sbjct: 87 LMAQTGEHLLILDLLGIKNGIIVLTKADRVDEARIEQKIKQILAD 131
>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 = 38.3 bits (89), Expect = 0.002
Identities = 12/47 (25%), Positives = 23/47 (48%)
Query: 161 PQPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVKFVQ 207
QT EHLA ++++ + H I++ K D V E + + + +
Sbjct: 87 VMTQTGEHLAVLDLLGIPHTIVVITKADRVNEEEIKRTEMFMKQILN 133
>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 = 36.1 bits (84), Expect = 0.005
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 161 PQPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVKFVQ 207
+PQT EHL L II+ NKID V E +E +I + ++
Sbjct: 99 VEPQTREHLNIALAGGLP-IIVAVNKIDRVGEEDFDEVLREIKELLK 144
>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 = 34.3 bits (79), Expect = 0.021
Identities = 17/47 (36%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 161 PQPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVKFVQ 207
Q QT+E L E++ I++L NKIDL+ E + + E++ K +Q
Sbjct: 105 IQTQTAECLVIGELLCKPLIVVL-NKIDLIPEEERKRKIEKMKKRLQ 150
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 34.9 bits (81), Expect = 0.024
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 160 CPQPQTSEHLAAIEIMKLKHIIILQNKIDLVK--EGQANEQHEQIVKFVQ 207
PQT EH+ + + +I+ NK+D V E + E E++ K ++
Sbjct: 122 GVMPQTREHVFLARTLGINQLIVAINKMDAVNYDEKRYEEVKEEVSKLLK 171
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 33.8 bits (78), Expect = 0.051
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 161 PQPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVKFVQ 207
QT EH + +K +I+ NK+DLV + E+ E+IV V
Sbjct: 129 VGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDE--ERFEEIVSEVS 173
>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 = 32.8 bits (76), Expect = 0.085
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 162 QPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVK 204
QT EH + +K +I+ NK+D V + E++++I K
Sbjct: 122 GGQTREHALLARTLGVKQLIVAVNKMDDVTVNWSQERYDEIKK 164
>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 = 32.2 bits (74), Expect = 0.11
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 161 PQPQTSEHLAAIEIMKLKHIIILQNKIDLV 190
P PQT EHL + + +I++ NK D+V
Sbjct: 102 PMPQTREHLLLARQVGVPYIVVFLNKADMV 131
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 32.7 bits (75), Expect = 0.11
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 162 QPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVK 204
QT H ++ ++H+++ NK+DLV + E E IV
Sbjct: 124 LEQTRRHSFIASLLGIRHVVVAVNKMDLVDYSE--EVFEAIVA 164
>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 = 31.8 bits (73), Expect = 0.14
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 162 QPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVK 204
QT H ++ ++H+++ NK+DLV + E E+I
Sbjct: 116 LEQTRRHSYIASLLGIRHVVVAVNKMDLVDYDE--EVFEEIKA 156
>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 = 32.1 bits (73), Expect = 0.17
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 162 QPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVKFV 206
QPQT EH + + +I+ NK+D V + E+ E I K V
Sbjct: 126 QPQTREHAFLARTLGINQLIVAINKMDSVNYDE--EEFEAIKKEV 168
>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 = 31.2 bits (71), Expect = 0.39
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 164 QTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIVK 204
QT H ++ ++H+++ NK+DLV + E E I K
Sbjct: 120 QTRRHSYIASLLGIRHVVLAVNKMDLVDYDE--EVFENIKK 158
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 30.3 bits (69), Expect = 0.74
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 161 PQPQTSEHLAAIEIMKLKHIIILQNKIDLV 190
P PQT EH+ + + + +I++ NK D V
Sbjct: 112 PMPQTKEHILLAKQVGVPNIVVFLNKEDQV 141
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 29.6 bits (67), Expect = 1.1
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 161 PQPQTSEHLAAIEIMKLKHIIILQNKIDLV 190
P PQT EH+ + + +I++ NK+D+V
Sbjct: 112 PMPQTREHILLARQVGVPYIVVFLNKVDMV 141
>gnl|CDD|173004 PRK14538, PRK14538, putative bifunctional signaling protein/50S
ribosomal protein L9; Provisional.
Length = 838
Score = 29.4 bits (66), Expect = 1.4
Identities = 39/154 (25%), Positives = 63/154 (40%), Gaps = 23/154 (14%)
Query: 53 KGAKLEISYHLLKRLLGVRMEGDKKGAKVQKLT-------RNEVLLVNIGS----LSTGG 101
KG ++ LK LL + E +K ++ LT ++E++ VN G +
Sbjct: 663 KGTNIKTVTQTLKHLLKLEYEKGEKNMEIILLTDIKNKGKKHEIIKVNNGYGNFLIQNKK 722
Query: 102 RVLATKADLAKISLTNPVCTEVNEKIALSRRVEKHWSLIEG---TVTTKVLSTRKRTGNE 158
+LA K +LAKI + E +K ++K S I+ T+ ++ K G
Sbjct: 723 ALLADKENLAKIKKKKIL--EQEKKRNHELLMKKLKSEIDNKKITLDIQLGPKGKIYG-- 778
Query: 159 SCPQPQTSEHLAAIEIMKLKHIIILQNKIDLVKE 192
Q E E K+ +I I + KI L E
Sbjct: 779 KITLKQIVE-----EFHKIHNITIDRKKISLENE 807
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 28.6 bits (65), Expect = 1.4
Identities = 9/40 (22%), Positives = 19/40 (47%)
Query: 162 QPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQ 201
+ E L +E+ K +I++ NK DL+ + + +
Sbjct: 94 EGLDEEDLEILELPAKKPVIVVLNKSDLLSDAEGISELNG 133
>gnl|CDD|206750 cd01857, HSR1_MMR1, A circularly permuted subfamily of the Ras
GTPases. Human HSR1 is localized to the human MHC class
I region and is highly homologous to a putative
GTP-binding protein, MMR1 from mouse. These proteins
represent a new subfamily of GTP-binding proteins that
has only eukaryote members. This subfamily shows a
circular permutation of the GTPase signature motifs so
that the C-terminal strands 5, 6, and 7 (strand 6
contains the G4 box with sequence NKXD) are relocated to
the N-terminus.
Length = 140
Score = 28.4 bits (64), Expect = 1.6
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 173 EIMKLKHIIILQNKIDLVKEGQ 194
E+ K ++L NK DLV E Q
Sbjct: 38 EVDPSKENVLLLNKADLVTEEQ 59
>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 = 28.6 bits (64), Expect = 2.5
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 161 PQPQTSEHLAAIEIMKLKHIIILQNKIDLVKE 192
P PQT EH+ + + +I++ NK D+V +
Sbjct: 112 PMPQTREHILLARQVGVPYIVVFLNKCDMVDD 143
>gnl|CDD|188522 TIGR04007, wcaI, colanic acid biosynthesis glycosyl transferase
WcaI. This gene is one of the glycosyl transferases
involved in the biosynthesis of colanic acid, an
exopolysaccharide expressed in Enterobacteraceae
species.
Length = 407
Score = 28.4 bits (63), Expect = 3.2
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 45 GVRMEGDKKGAK--LEISYHLLKRLLGVRMEGDKKGAKVQKLTR--NEVLLVNIGSLSTG 100
G+R+ GA+ L I + + +LG+ M G KG KV +L L N+ ++ST
Sbjct: 121 GMRLLAKLSGARTVLHIQDYEVDAMLGLGMAGKGKGGKVARLASAFERSGLHNVDNVSTI 180
Query: 101 GRVLATKA 108
R + KA
Sbjct: 181 SRSMMNKA 188
>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 = 27.4 bits (62), Expect = 3.9
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 162 QPQTSEHLAAIEIMKLKH--IIILQNKIDLVKEGQANEQ 198
PQT E AI K + II+ NKID +A+ +
Sbjct: 87 MPQTIE---AINHAKAANVPIIVAINKIDKPYGTEADPE 122
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 28.0 bits (63), Expect = 4.0
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 161 PQPQTSEHLAAIEIMKLKHIIILQNKIDLV 190
P PQT EH+ + + ++++ NK+DLV
Sbjct: 112 PMPQTREHILLARQVGVPYLVVFLNKVDLV 141
>gnl|CDD|232972 TIGR00432, arcsn_tRNA_tgt, tRNA-guanine transglycosylase,
archaeosine-15-forming. This tRNA-guanine
transglycosylase (tgt) differs from the tgt of E. coli
and other Bacteria in the site of action and the
modification that results. It exchanges
7-cyano-7-deazaguanine (preQ0) with guanine at position
15 of archaeal tRNA; this nucleotide is subsequently
converted to archaeosine, found exclusively in the
Archaea. This enzyme from Haloferax volcanii has been
purified, characterized, and partially sequenced and is
the basis for identifying this family. In contrast,
bacterial tgt catalyzes the exchange of preQ0 or preQ1
for the guanine base at position 34; this nucleotide is
subsequently modified to queuosine. Archeoglobus
fulgidus has both enzymes, while some other Archaea have
just this one [Protein synthesis, tRNA and rRNA base
modification].
Length = 540
Score = 27.6 bits (61), Expect = 5.4
Identities = 16/52 (30%), Positives = 28/52 (53%)
Query: 131 RRVEKHWSLIEGTVTTKVLSTRKRTGNESCPQPQTSEHLAAIEIMKLKHIII 182
R+V+ +W LIE K S TG ES +P+ H+ I+ ++L+ ++
Sbjct: 241 RQVKHYWDLIEKFDPRKKKSAFFYTGIESLYRPEVRRHVKRIKNVELEEEVL 292
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 26.6 bits (60), Expect = 7.3
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 169 LAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQI 202
L A E ++ +I+L NK DLV + + E E
Sbjct: 26 LVAAEASGIEPVIVL-NKADLVDDEELEELLEIY 58
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 27.1 bits (61), Expect = 7.9
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 161 PQPQTSEHLAAIEIMKLKHIIILQNKIDLV 190
P PQT EH+ + + +I++ NK D+V
Sbjct: 112 PMPQTREHILLARQVGVPYIVVFLNKCDMV 141
>gnl|CDD|184477 PRK14052, PRK14052, effector protein; Provisional.
Length = 387
Score = 26.8 bits (59), Expect = 8.9
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 86 RNEVLLVNIGSLSTGGRVLATKADLAKISLTNP 118
RNE+L N G LS GG+ AD + + TNP
Sbjct: 18 RNEIL--NEGKLSIGGKEYHINADTQQFTRTNP 48
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 26.6 bits (60), Expect = 9.3
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 162 QPQTSEHLAAIEIMKLKHIIILQNKIDLVKE 192
+P T E +E +K K +I++ NK DL E
Sbjct: 306 EPLTEEDDEILEELKDKPVIVVLNKADLTGE 336
>gnl|CDD|237377 PRK13405, bchH, magnesium chelatase subunit H; Provisional.
Length = 1209
Score = 26.9 bits (60), Expect = 9.6
Identities = 14/47 (29%), Positives = 18/47 (38%), Gaps = 5/47 (10%)
Query: 40 LKRLLGVRMEGDKKGAKLEISYHLLKRLLGVRMEGDKKGAKVQKLTR 86
L R+ M G G LLK+L G + EG G + R
Sbjct: 112 LTRMGKFDMSGPASGP-----LALLKKLRGKKKEGGSSGEGQMAMLR 153
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 26.8 bits (60), Expect = 9.9
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 162 QPQTSEHLAAIEIMKLKHIIILQNKIDLVKEGQANEQHEQIV 203
QT H ++ ++H+++ NK+DLV E ++IV
Sbjct: 142 LTQTRRHSFIASLLGIRHVVLAVNKMDLV--DYDQEVFDEIV 181
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
0.317 0.135 0.371
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,124,621
Number of extensions: 937212
Number of successful extensions: 825
Number of sequences better than 10.0: 1
Number of HSP's gapped: 812
Number of HSP's successfully gapped: 68
Length of query: 207
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 115
Effective length of database: 6,857,034
Effective search space: 788558910
Effective search space used: 788558910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (25.8 bits)