RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1177
(283 letters)
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 425 bits (1094), Expect = e-149
Identities = 166/242 (68%), Positives = 202/242 (83%), Gaps = 1/242 (0%)
Query: 15 TVAEGAPVIPISAQLKYNIEVLCEYITKKIPIPIRDFTSSPRLIVIRSFDVNKPGCEVDD 74
T+A+ AP+IPISAQLKYNI+V+ EYI +IPIP RD TS PR+IVIRSFDVNKPG ++++
Sbjct: 203 TIADNAPIIPISAQLKYNIDVVLEYICTQIPIPKRDLTSPPRMIVIRSFDVNKPGEDIEN 262
Query: 75 LKGGVAGGSILRGVLKVGMEIEVRPGLVSKDSEGKLTCKPIFSRIVSLFAEQNELQFAVP 134
LKGGVAGGSIL+GVLKVG EIE+RPG++SKDS G+ TC+PI +RIVSLFAE NELQ+AVP
Sbjct: 263 LKGGVAGGSILQGVLKVGDEIEIRPGIISKDSGGEFTCRPIRTRIVSLFAENNELQYAVP 322
Query: 135 GGLIGVGTKIEPTLCRADRLVGQVLGAVGALPKIFIELEISYHLLKRLLGVRMEGDKKGA 194
GGLIGVGT I+PTL RADRLVGQVLG G LP+++ E+EI Y+LL+RLLGV+ + KK
Sbjct: 323 GGLIGVGTTIDPTLTRADRLVGQVLGYPGKLPEVYAEIEIQYYLLRRLLGVKSQDGKKAT 382
Query: 195 KVQKLTRNEVLLVNIGSLSTGGRVLATKAD-LAKISLTNPVCTEVNEKIALSRRVEKHWS 253
KV KL + E L++NIGS +TGGRV+ K D +AK+ LT PVCT V EKIALSRRV+KHW
Sbjct: 383 KVAKLKKGESLMINIGSTTTGGRVVGIKDDGIAKLELTTPVCTSVGEKIALSRRVDKHWR 442
Query: 254 WI 255
I
Sbjct: 443 LI 444
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 330 bits (848), Expect = e-112
Identities = 122/244 (50%), Positives = 168/244 (68%), Gaps = 6/244 (2%)
Query: 12 LERTVAEGAPVIPISAQLKYNIEVLCEYITKKIPIPIRDFTSSPRLIVIRSFDVNKPGCE 71
++ TVAE AP+IPISAQ K NI+ L E I K IP P RD PR+ V RSFDVNKPG
Sbjct: 169 VKGTVAENAPIIPISAQHKANIDALIEAIEKYIPTPERDLDKPPRMYVARSFDVNKPGTP 228
Query: 72 VDDLKGGVAGGSILRGVLKVGMEIEVRPGLVSKDSEGKLTCKPIFSRIVSLFAEQNELQF 131
++LKGGV GGS+++GVL+VG EIE+RPG+V + GK +PI + IVSL A +++
Sbjct: 229 PEELKGGVIGGSLVQGVLRVGDEIEIRPGIVVEK-GGKTVWEPITTEIVSLQAGGEDVEE 287
Query: 132 AVPGGLIGVGTKIEPTLCRADRLVGQVLGAVGALPKIFIELEISYHLLKRLLGVRMEGDK 191
A PGGL+GVGTK++PTL +AD LVGQV+G G LP ++ + I YHLL+R++G K
Sbjct: 288 ARPGGLVGVGTKLDPTLTKADALVGQVVGKPGTLPPVWTSIRIEYHLLERVVGT-----K 342
Query: 192 KGAKVQKLTRNEVLLVNIGSLSTGGRVLATKADLAKISLTNPVCTEVNEKIALSRRVEKH 251
+ KV+ + NEVL++N+G+ +T G V + K D ++ L PVC E+ E++A+SRR+
Sbjct: 343 EELKVEPIKTNEVLMLNVGTATTVGVVTSAKKDEIEVKLKRPVCAEIGERVAISRRIGNR 402
Query: 252 WSWI 255
W I
Sbjct: 403 WRLI 406
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 268 bits (687), Expect = 3e-88
Identities = 113/241 (46%), Positives = 161/241 (66%), Gaps = 6/241 (2%)
Query: 12 LERTVAEGAPVIPISAQLKYNIEVLCEYITKKIPIPIRDFTSSPRLIVIRSFDVNKPGCE 71
++ TVAE AP+IP+SA K NI+ L E I ++IP P RD PR+ V RSFDVNKPG
Sbjct: 168 VKGTVAENAPIIPVSALHKVNIDALIEAIEEEIPTPERDLDKPPRMYVARSFDVNKPGTP 227
Query: 72 VDDLKGGVAGGSILRGVLKVGMEIEVRPGLVSKDSEGKLTCKPIFSRIVSLFAEQNELQF 131
+ LKGGV GGS+++GVLKVG EIE+RPG+ ++ GK +PI ++IVSL A +++
Sbjct: 228 PEKLKGGVIGGSLIQGVLKVGDEIEIRPGIKVEE-GGKTKWEPITTKIVSLRAGGEKVEE 286
Query: 132 AVPGGLIGVGTKIEPTLCRADRLVGQVLGAVGALPKIFIELEISYHLLKRLLGVRMEGDK 191
A PGGL+GVGTK++P+L +AD L G V G G LP ++ L I HLL+R++G K
Sbjct: 287 ARPGGLVGVGTKLDPSLTKADALAGSVAGKPGTLPPVWESLTIEVHLLERVVGT-----K 341
Query: 192 KGAKVQKLTRNEVLLVNIGSLSTGGRVLATKADLAKISLTNPVCTEVNEKIALSRRVEKH 251
+ KV+ + E L++N+G+ +T G V + + D A++ L PVC E +++A+SRRV
Sbjct: 342 EELKVEPIKTGEPLMLNVGTATTVGVVTSARKDEAEVKLKRPVCAEEGDRVAISRRVGGR 401
Query: 252 W 252
W
Sbjct: 402 W 402
>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 = 250 bits (640), Expect = 2e-81
Identities = 111/244 (45%), Positives = 157/244 (64%), Gaps = 6/244 (2%)
Query: 12 LERTVAEGAPVIPISAQLKYNIEVLCEYITKKIPIPIRDFTSSPRLIVIRSFDVNKPGCE 71
++ T+AE AP+IP+SA NI+ L E I K IP P RD P + V RSFDVNKPG
Sbjct: 163 VKGTIAENAPIIPVSALHNANIDALLEAIEKFIPTPERDLDKPPLMYVARSFDVNKPGTP 222
Query: 72 VDDLKGGVAGGSILRGVLKVGMEIEVRPGLVSKDSEGKLTCKPIFSRIVSLFAEQNELQF 131
+ LKGGV GGS+++G LKVG EIE+RPG + + GK +PI++ I SL A +++
Sbjct: 223 PEKLKGGVIGGSLIQGKLKVGDEIEIRPG-IKVEKGGKTKWEPIYTEITSLRAGGYKVEE 281
Query: 132 AVPGGLIGVGTKIEPTLCRADRLVGQVLGAVGALPKIFIELEISYHLLKRLLGVRMEGDK 191
A PGGL+GVGTK++P L +AD L GQV+G G LP ++ LE+ HLL+R++G E
Sbjct: 282 ARPGGLVGVGTKLDPALTKADALAGQVVGKPGTLPPVWESLELEVHLLERVVGTEEE--- 338
Query: 192 KGAKVQKLTRNEVLLVNIGSLSTGGRVLATKADLAKISLTNPVCTEVNEKIALSRRVEKH 251
KV+ + EVL++N+G+ +T G V + + D ++ L PVC E +++A+SRRV
Sbjct: 339 --LKVEPIKTGEVLMLNVGTATTVGVVTSARKDEIEVKLKRPVCAEEGDRVAISRRVGGR 396
Query: 252 WSWI 255
W I
Sbjct: 397 WRLI 400
>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 = 209 bits (535), Expect = 2e-69
Identities = 88/114 (77%), Positives = 102/114 (89%), Gaps = 1/114 (0%)
Query: 50 DFTSSPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILRGVLKVGMEIEVRPGLVSKDSEGK 109
DFTS PR+IVIRSFDVNKPG EVDDLKGGVAGGS+L+GVLKVG EIE+RPG+V KD EGK
Sbjct: 1 DFTSPPRMIVIRSFDVNKPGTEVDDLKGGVAGGSLLQGVLKVGDEIEIRPGIVVKD-EGK 59
Query: 110 LTCKPIFSRIVSLFAEQNELQFAVPGGLIGVGTKIEPTLCRADRLVGQVLGAVG 163
+ C+PIF++IVSL AE N+LQ AVPGGLIGVGTK++PTL +ADRLVGQV+G G
Sbjct: 60 IKCRPIFTKIVSLKAENNDLQEAVPGGLIGVGTKLDPTLTKADRLVGQVVGEPG 113
>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 (303), Expect = 1e-34
Identities = 46/84 (54%), Positives = 65/84 (77%), Gaps = 4/84 (4%)
Query: 169 FIELEISYHLLKRLLGVRMEGDKKGAKVQKLTRNEVLLVNIGSLSTGGRVLATKADLAKI 228
+ E+EI Y+LL+RL+GV+ ++ AKV+KL + EVL++NIGS +TGG V A K DLA++
Sbjct: 1 YTEIEIEYYLLERLVGVK----EEEAKVEKLKKGEVLMLNIGSATTGGVVTAVKKDLAEV 56
Query: 229 SLTNPVCTEVNEKIALSRRVEKHW 252
L PVCTE+ EK+A+SRRV+K W
Sbjct: 57 ELKRPVCTEIGEKVAISRRVDKRW 80
>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 = 69.6 bits (171), Expect = 2e-14
Identities = 28/38 (73%), Positives = 33/38 (86%)
Query: 12 LERTVAEGAPVIPISAQLKYNIEVLCEYITKKIPIPIR 49
++ T+AE AP+IPISAQLKYNI+VLCEYI KKIP P R
Sbjct: 160 VKGTIAENAPIIPISAQLKYNIDVLCEYIVKKIPTPPR 197
>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 = 44.2 bits (105), Expect = 3e-06
Identities = 24/101 (23%), Positives = 40/101 (39%), Gaps = 19/101 (18%)
Query: 55 PRLIVIRSFDVNKPGCEVDDLKGGVAGGSILRGVLKVGMEIEVRPGLVSKDSEGKLTCKP 114
R +V + F +G VA G + G LK G ++ V PG
Sbjct: 1 LRALVFKVFKDKG--------RGTVATGRVESGTLKKGDKVRVGPG-----------GGG 41
Query: 115 IFSRIVSLFAEQNELQFAVPGGLIGVGTKIEPTLCRADRLV 155
+ ++ SL + E+ AV G ++G+ K + + D L
Sbjct: 42 VKGKVKSLKRFKGEVDEAVAGDIVGIVLKDKDDIKIGDTLT 82
>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 = 43.0 bits (102), Expect = 5e-06
Identities = 21/84 (25%), Positives = 29/84 (34%), Gaps = 14/84 (16%)
Query: 77 GGVAGGSILRGVLKVGMEIEVRPGLVSKDSEGKLTCKPIFSRIVSLFAEQNELQFAVPGG 136
G VA G + G LK G ++ + P K R+ SL +L+ AV G
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGK-----------KGRVTSLEMFHGDLREAVAGA 49
Query: 137 LIGVGTKIEPTLCRADRLVGQVLG 160
G+ D G L
Sbjct: 50 NAGIILAGIGLK---DIKRGDTLT 70
>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 = 36.3 bits (85), Expect = 0.007
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 18 EGAPVIPISAQLKYNIEVLCEYITKKIP 45
E PV+P SA I+ L E + +P
Sbjct: 156 ETVPVVPGSALTGEGIDELLEALDLYLP 183
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 31.1 bits (71), Expect = 0.63
Identities = 30/90 (33%), Positives = 41/90 (45%), Gaps = 20/90 (22%)
Query: 18 EGAPVIPISAQLKY---------NIEVLCEYITKKIPIPIRDFTSSPRLIVIRSFDV-NK 67
+ PVI SA LK I L + + + IP P RD T P L+ + DV
Sbjct: 166 DDIPVIRGSA-LKALEGDPKWEDAIMELMDAVDEYIPTPERD-TDKPFLMPVE--DVFTI 221
Query: 68 PGCEVDDLKGGVAGGSILRGVLKVGMEIEV 97
G +G V G + RG +KVG E+E+
Sbjct: 222 TG------RGTVVTGRVERGTVKVGDEVEI 245
>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 = 30.8 bits (70), Expect = 0.82
Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 8/76 (10%)
Query: 22 VIPISAQLKYNIEVLCEYITKKIPIPIRDFTSSPRLIVIRSFDVNKPGCEVDDLKGGVAG 81
I SA+ IE + E I K++P P D + + ++ S D+ +G VA
Sbjct: 157 AILASAKTGIGIEEILEAIVKRVPPPKGDPDAPLKALIFDSH--------YDNYRGVVAL 208
Query: 82 GSILRGVLKVGMEIEV 97
+ G +K G +I
Sbjct: 209 VRVFEGTIKPGDKIRF 224
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 30.5 bits (70), Expect = 1.1
Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 10/66 (15%)
Query: 33 IEVLCEYITKKIPIPIRDFTSSPRLIVIRSFDV-NKPGCEVDDLKGGVAGGSILRGVLKV 91
I L + + IP P R P L+ I DV + G +G V G + RG++KV
Sbjct: 191 ILELMDAVDSYIPTPERA-IDKPFLMPIE--DVFSISG------RGTVVTGRVERGIIKV 241
Query: 92 GMEIEV 97
G E+E+
Sbjct: 242 GEEVEI 247
>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 = 30.1 bits (68), Expect = 1.1
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 10/63 (15%)
Query: 36 LCEYITKKIPIPIRDFTSSPRLIVIRS-FDVNKPGCEVDDLKGGVAGGSILRGVLKVGME 94
L + + + IP P R+ T P L+ I F + +G V G + RG++KVG E
Sbjct: 192 LMDAVDEYIPTPERE-TDKPFLMPIEDVFSITG--------RGTVVTGRVERGIVKVGEE 242
Query: 95 IEV 97
+E+
Sbjct: 243 VEI 245
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 30.4 bits (69), Expect = 1.2
Identities = 22/88 (25%), Positives = 35/88 (39%), Gaps = 8/88 (9%)
Query: 12 LERTVAEGAPVIPISAQLKYNIEVLCEYITKKIPIPIRDFTSSPRLIVIRSFDVNKPGCE 71
L A + SA+ IE L + + RD R+ + R+F V G
Sbjct: 129 LADLSLANAKIFKTSAKTGRGIEELKNELIDLLEEIERDEQKPFRIAIDRAFTVKGVGT- 187
Query: 72 VDDLKGGVAGGSILRGVLKVGMEIEVRP 99
V G++L G +KVG ++ + P
Sbjct: 188 -------VVTGTVLSGEVKVGDKLYLSP 208
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 29.8 bits (68), Expect = 1.7
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 76 KGGVAGGSILRGVLKVGMEIEV 97
+G V G + RG++KVG E+E+
Sbjct: 226 RGTVVTGRVERGIVKVGDEVEI 247
>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 = 27.5 bits (62), Expect = 2.6
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 76 KGGVAGGSILRGVLKVGMEIEV 97
+G V G I RG +KVG E+E+
Sbjct: 14 RGTVVTGRIERGTIKVGDEVEI 35
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 29.2 bits (66), Expect = 2.8
Identities = 13/63 (20%), Positives = 22/63 (34%), Gaps = 13/63 (20%)
Query: 82 GSILRGVLKVGMEIEVRPGLVSKDSEGKLTCKPIFSRIVSLFAEQNELQFAVPGGLIGVG 141
G + GV+K G ++ P V + S+ E+ A PG +G
Sbjct: 251 GRVESGVIKPGQKVTFMPAGVV-------------GEVKSIEMHHEEISQAEPGDNVGFN 297
Query: 142 TKI 144
+
Sbjct: 298 VRG 300
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 28.9 bits (66), Expect = 3.0
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 20 APVIPISAQLKYNIEVLCEYITKKIP 45
A ++PISA N++ L + I K +P
Sbjct: 146 AEIVPISALKGDNVDELLDVIAKYLP 171
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 28.8 bits (65), Expect = 3.2
Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 10/63 (15%)
Query: 36 LCEYITKKIPIPIRDFTSSPRLIVIRS-FDVNKPGCEVDDLKGGVAGGSILRGVLKVGME 94
L + + IP P RD T P L+ I F + G +G VA G I RG +KVG
Sbjct: 202 LMDAVDSYIPTPERD-TDKPFLMAIEDVFSI--TG------RGTVATGRIERGTVKVGDT 252
Query: 95 IEV 97
+E+
Sbjct: 253 VEI 255
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 29.1 bits (66), Expect = 3.4
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 24 PISAQLKYNIEVLCEYITKKIPIPIRDFTSSPRLIV-IRSFDVNK 67
IS L+ +E E IT+ + IP + I + VNK
Sbjct: 1149 SISMNLEKRLEGWNERITRILGIPWGFLIGAELSIAQSQISLVNK 1193
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 28.7 bits (65), Expect = 3.5
Identities = 25/92 (27%), Positives = 38/92 (41%), Gaps = 20/92 (21%)
Query: 65 VNKPGCEVDDLKGGVAGGSILRGVLKVGMEIEVRP-GLVSKDSEGKLTCKPIFSRIVSLF 123
VN+P + G +A G + KVG ++V P G S +RIV+
Sbjct: 253 VNRPNLDFRGYAGTLASGVV-----KVGDRVKVLPSGKESN-----------VARIVTF- 295
Query: 124 AEQNELQFAVPGGLIGVGTKIEPTLCRADRLV 155
+L+ A G I + + E + R D LV
Sbjct: 296 --DGDLEEAFAGEAITLVLEDEIDISRGDLLV 325
>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 = 28.8 bits (65), Expect = 3.6
Identities = 31/148 (20%), Positives = 56/148 (37%), Gaps = 34/148 (22%)
Query: 32 NIEVLCEYITKKIPIPIRDFTSSPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILRGVLKV 91
N+ L + I + +P P D P +++ + D D+ G +A G + RG +K
Sbjct: 178 NMAPLFDAIVRHVPAPKGD-LDEPLQMLVTNLDY-------DEYLGRIAIGRVHRGTVKK 229
Query: 92 GMEIEVRPGLVSKDSEGKLTCKPIFSRIVSLFA----EQNELQFAVPGGLIGVG----TK 143
G ++ + +G + RI L E+ E+ A G ++ V
Sbjct: 230 GQQVAL------MKRDGTIE----NGRISKLLGFEGLERVEIDEAGAGDIVAVAGLEDIN 279
Query: 144 IEPTLCRADRLVGQVLGAVGALPKIFIE 171
I T+ + ALP I ++
Sbjct: 280 IGETIADPEVPE--------ALPTITVD 299
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 27.8 bits (63), Expect = 4.2
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 18 EGAPVIPISAQLKYNIEVLCEYITKKI 44
+G V PISA ++ L + + K +
Sbjct: 144 KGKKVFPISALTGEGLDELLKKLAKLL 170
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 28.7 bits (65), Expect = 4.3
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 8/76 (10%)
Query: 22 VIPISAQLKYNIEVLCEYITKKIPIPIRDFTSSPRLIVIRSFDVNKPGCEVDDLKGGVAG 81
+ +SA+ IE + E I +KIP P D + + ++ S+ D+ G V
Sbjct: 163 AVLVSAKTGIGIEDVLEAIVEKIPPPKGDPDAPLKALIFDSW--------YDNYLGVVVL 214
Query: 82 GSILRGVLKVGMEIEV 97
I G LK G +I +
Sbjct: 215 VRIFDGTLKKGDKIRM 230
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 28.4 bits (64), Expect = 4.6
Identities = 27/94 (28%), Positives = 42/94 (44%), Gaps = 19/94 (20%)
Query: 17 AEGAPVIPISA--------QLKYNIEVLCEYITKKIPIPIRDFTSSPRLIVIRS-FDVNK 67
+ P+I SA + + IE L + + IP P RD P L+ + F +
Sbjct: 165 GDDTPIIRGSALKALEGDAKWEAKIEELMDAVDSYIPTPERD-IDKPFLMPVEDVFSI-- 221
Query: 68 PGCEVDDLKGGVAGGSILRGVLKVGMEIEVRPGL 101
+G V G + RG+LKVG E+E+ G+
Sbjct: 222 ------SGRGTVVTGRVERGILKVGEEVEI-VGI 248
>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 = 26.7 bits (60), Expect = 4.7
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 7/41 (17%)
Query: 71 EVDDLKGGVAGGSILRGVLKVGMEI-------EVRPGLVSK 104
+ DD G +A G I RG +KVG ++ ++ ++K
Sbjct: 9 DYDDYVGRIAIGRIFRGTVKVGQQVAVVKRDGKIEKAKITK 49
>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 = 26.7 bits (60), Expect = 4.9
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 8/45 (17%)
Query: 55 PRLIVIRSFDVNKPGCEVDDLKGGVAGGSILRGVLKVGMEIEVRP 99
RL + R F V G V G++L G +KVG ++E+ P
Sbjct: 1 FRLPIDRVFTVKGQGT--------VVTGTVLSGSVKVGDKVEILP 37
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 28.5 bits (65), Expect = 5.2
Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 22 VIPISAQLKYNIEVLCEYITKKIPIPIRDFTSSPRLIVIRSFDVNKPGCEVDDLKGGVAG 81
+ +SA+ IE + E I ++IP P D + + ++ S+ D+ +G V
Sbjct: 161 AVLVSAKTGIGIEEVLEAIVERIPPPKGDPDAPLKALIFDSW--------YDNYRGVVVL 212
Query: 82 GSILRGVLKVGMEI 95
++ G LK G +I
Sbjct: 213 VRVVDGTLKKGDKI 226
>gnl|CDD|238681 cd01385, MYSc_type_IX, Myosin motor domain, type IX myosins. Myosin
IX is a processive single-headed motor, which might play
a role in signalling. This catalytic (head) domain has
ATPase activity and belongs to the larger group of
P-loop NTPases. Myosins are actin-dependent molecular
motors that play important roles in muscle contraction,
cell motility, and organelle transport. The head domain
is a molecular motor, which utilizes ATP hydrolysis to
generate directed movement toward the plus end along
actin filaments. A cyclical interaction between myosin
and actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle.
Length = 692
Score = 28.3 bits (63), Expect = 5.5
Identities = 13/50 (26%), Positives = 21/50 (42%)
Query: 9 KWRLERTVAEGAPVIPISAQLKYNIEVLCEYITKKIPIPIRDFTSSPRLI 58
+W + R +SAQ + ++ L E + K P IR S+ I
Sbjct: 547 RWAVLRAAFRAMAAPSVSAQFQTSLNKLMETLGKAEPFFIRCIKSNAEKI 596
>gnl|CDD|215345 PLN02641, PLN02641, anthranilate phosphoribosyltransferase.
Length = 343
Score = 27.8 bits (62), Expect = 6.1
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 9/47 (19%)
Query: 45 PIPIRDFTSSPRLIVIRSFDVNKPGCEVDDLKGGVA--GGSILRGVL 89
P I +F+ P D P C ++DL+GG +LR VL
Sbjct: 239 PEKIEEFSFDP-------LDFGIPRCTLEDLRGGDPDYNAKVLRDVL 278
>gnl|CDD|184477 PRK14052, PRK14052, effector protein; Provisional.
Length = 387
Score = 28.0 bits (62), Expect = 6.2
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 201 RNEVLLVNIGSLSTGGRVLATKADLAKISLTNP 233
RNE+L N G LS GG+ AD + + TNP
Sbjct: 18 RNEIL--NEGKLSIGGKEYHINADTQQFTRTNP 48
>gnl|CDD|140321 PTZ00300, PTZ00300, pyruvate kinase; Provisional.
Length = 454
Score = 28.1 bits (62), Expect = 6.5
Identities = 23/65 (35%), Positives = 30/65 (46%), Gaps = 19/65 (29%)
Query: 65 VNKPGCEVD----------DLKGGVAGG------SILRGVLKVGMEIEVRPGLVSKDSEG 108
VN PGC+VD DL+ GV G S +R +VG EVR L +K +
Sbjct: 133 VNLPGCDVDLPAVSAKDCADLQFGVEQGVDMIFASFIRSAEQVG---EVRKALGAKGGDI 189
Query: 109 KLTCK 113
+ CK
Sbjct: 190 MIICK 194
>gnl|CDD|236314 PRK08624, PRK08624, hypothetical protein; Provisional.
Length = 373
Score = 27.6 bits (61), Expect = 7.3
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 10/60 (16%)
Query: 3 VKYVTQKWRLERTVAEGAPVIPISAQLKYNIEVLCEYITKKIPIPIRDFTSSPRLIVIRS 62
VK +KW + EG I Q + I+ + I+++I IP RD S LI IR
Sbjct: 151 VKIPNRKW-----LDEG---ISEKTQKYWEIKFYLDVISQRIIIPHRD--ESGELIGIRG 200
>gnl|CDD|241516 cd13362, PH_PLC_gamma, Phospholipase C-gamma (PLC-gamma) pleckstrin
homology (PH) domain. PLC-gamma (PLCgamma) is activated
by receptor and non-receptor tyrosine kinases due to the
presence of its SH2 and SH3 domains. There are two main
isoforms of PLC-gamma expressed in human specimens,
PLC-gamma1 and PLC-gamma2. PLC-gamma consists of an
N-terminal PH domain, a EF hand domain, a catalytic
domain split into X and Y halves internal to which is a
PH domain split by two SH2 domains and a single SH3
domain, and a C-terminal C2 domain. Only the first PH
domain is present in this hierarchy. PLCs (EC 3.1.4.3)
play a role in the initiation of cellular activation,
proliferation, differentiation and apoptosis. They are
central to inositol lipid signalling pathways,
facilitating intracellular Ca2+ release and protein
kinase C (PKC) activation. Specificaly, PLCs catalyze
the cleavage of phosphatidylinositol-4,5-bisphosphate
(PIP2) and result in the release of 1,2-diacylglycerol
(DAG) and inositol 1,4,5-triphosphate (IP3). These
products trigger the activation of protein kinase C
(PKC) and the release of Ca2+ from intracellular stores.
There are fourteen kinds of mammalian phospholipase C
proteins which are are classified into six isotypes
(beta, gamma, delta, epsilon, zeta, eta). PH domains
have diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 121
Score = 26.4 bits (59), Expect = 8.1
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 80 AGGSILRGVLKVGMEI-EVRPGLVSKDSE 107
GG + G + + EI E+RPG SKD E
Sbjct: 35 GGGKRIEGAIDI-REIKEIRPGKNSKDFE 62
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 27.5 bits (62), Expect = 8.1
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 20 APVIPISAQLKYNIEVLCEYITKKIP 45
++PISA N++ L E I + +P
Sbjct: 147 KEIVPISALKGDNVDTLLEIIKEYLP 172
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 27.6 bits (62), Expect = 8.5
Identities = 8/41 (19%), Positives = 16/41 (39%)
Query: 12 LERTVAEGAPVIPISAQLKYNIEVLCEYITKKIPIPIRDFT 52
L + ISA+ +++L E I + + + T
Sbjct: 323 LAELERGSPNPVFISAKTGEGLDLLRERIIELLSGLRTEVT 363
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 27.8 bits (62), Expect = 8.7
Identities = 25/98 (25%), Positives = 36/98 (36%), Gaps = 5/98 (5%)
Query: 19 GAPVIPISAQLKYNIEVLCEYITKKIPIPIRDFTSSPRLIVIRSFDVNKPGCEVDDLKGG 78
G PV+P SA IE L + I K I + + + G
Sbjct: 129 GVPVVPTSATEGRGIERLKDAIRKAIGLKELKKRAIEIVPEAYQVVEVVEGLIEIIYSIS 188
Query: 79 VAGGSILRGVL-KVGMEIEVR----PGLVSKDSEGKLT 111
G IL G+L + +EIE +V K+S L+
Sbjct: 189 KRGLEILLGLLEDLSLEIEKIERNLAEVVIKESPSNLS 226
>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 = 27.1 bits (61), Expect = 8.7
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 22 VIPISAQLKYNIEVLCEYITKKIPIP 47
I +SA+ +E L E I ++IP P
Sbjct: 154 AILVSAKTGLGVEDLLEAIVERIPPP 179
>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 = 26.9 bits (60), Expect = 9.6
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 18 EGAPVIPISAQLKYNIEVLCEYITKKIPIP 47
+ P+IPISA IE L + I + +P P
Sbjct: 154 KDVPIIPISALTGEGIEELLDAIVEHLPPP 183
>gnl|CDD|232977 TIGR00440, glnS, glutaminyl-tRNA synthetase. This protein is a
relatively rare aminoacyl-tRNA synthetase, found in the
cytosolic compartment of eukaryotes, in E. coli and a
number of other Gram-negative Bacteria, and in
Deinococcus radiodurans. In contrast, the pathway to
Gln-tRNA in mitochondria, Archaea, Gram-positive
Bacteria, and a number of other lineages is by
misacylation with Glu followed by transamidation to
correct the aminoacylation to Gln. This enzyme is a
class I tRNA synthetase (hit by the pfam model
tRNA-synt_1c) and is quite closely related to
glutamyl-tRNA synthetases [Protein synthesis, tRNA
aminoacylation].
Length = 522
Score = 27.6 bits (61), Expect = 10.0
Identities = 23/72 (31%), Positives = 28/72 (38%), Gaps = 11/72 (15%)
Query: 61 RSFDVNKPGCEVDDL----------KGGVAGGSILRGVLKVGMEIEVRPGLVSKDSEGKL 110
R F V PG D L K G S+ V + E R G DS+
Sbjct: 448 RLFKVPNPGAPDDFLSVINPESLVIKQGFMEHSLGDAVANKRFQFE-REGYFCLDSKEST 506
Query: 111 TCKPIFSRIVSL 122
T K +F+R VSL
Sbjct: 507 TEKVVFNRTVSL 518
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 0.394
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,242,203
Number of extensions: 1378922
Number of successful extensions: 1089
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1077
Number of HSP's successfully gapped: 55
Length of query: 283
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 187
Effective length of database: 6,679,618
Effective search space: 1249088566
Effective search space used: 1249088566
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: 58 (26.0 bits)