RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3124
(463 letters)
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 538 bits (1389), Expect = 0.0
Identities = 201/385 (52%), Positives = 283/385 (73%), Gaps = 2/385 (0%)
Query: 45 HCNVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYS 104
H NVGTIGHVDHGKTTLTAAITKV AK G ++ +DQID+APEEKARGITIN AHVEY
Sbjct: 12 HVNVGTIGHVDHGKTTLTAAITKVLAKKGGAEAKAYDQIDKAPEEKARGITINTAHVEYE 71
Query: 105 TNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNV 164
T RHYAH DCPGHADY+KNMI+GA+QMDGAI+VV+A++G MPQTREH+LL++Q+G+ +
Sbjct: 72 TEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYI 131
Query: 165 VVYVNKADLV-DREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSI 223
VV++NK D+V D E++ELVE+EVR++L+ Y + GD+TP + GSAL AL+GD E E I
Sbjct: 132 VVFLNKCDMVDDEELLELVEMEVRELLSKYDFPGDDTPIIRGSALKALEGDDDEEWEKKI 191
Query: 224 HRLLDALDKHIPNPVRDITSPFILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFN 283
L+DA+D +IP P R I PF++PI++ + GRG+V G +++G IK +E E++G
Sbjct: 192 LELMDAVDSYIPTPERAIDKPFLMPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIR 251
Query: 284 SKFTCTISEIQVFQKKVSEARAGDNVGVLLRNVKLKQIERGMLLAKADTLQMHNRYEAEI 343
T++ +++F+K + E +AGDNVG LLR +K + +ERG +LAK ++ H ++EAE+
Sbjct: 252 DTQKTTVTGVEMFRKLLDEGQAGDNVGALLRGIKREDVERGQVLAKPGSITPHTKFEAEV 311
Query: 344 YLLSKAEGGRYKPITSKYIQQMFSRTWNVQVRLDLPGEDDGMLMPGEHGTVTMTLLYKMY 403
Y+LSK EGGR+ P + Y Q + RT +V ++LP E M+MPG++ +T+ L+ +
Sbjct: 312 YVLSKEEGGRHTPFFNGYRPQFYFRTTDVTGVIELP-EGVEMVMPGDNVEMTVELIAPIA 370
Query: 404 LSKGQTFTIRENNKLVATGIVTKVL 428
+ +G F IRE + V G+VTK++
Sbjct: 371 MEEGLRFAIREGGRTVGAGVVTKII 395
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 537 bits (1387), Expect = 0.0
Identities = 200/385 (51%), Positives = 281/385 (72%), Gaps = 2/385 (0%)
Query: 45 HCNVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYS 104
H NVGTIGHVDHGKTTLTAAITKV AK G + +DQID APEEKARGITIN +HVEY
Sbjct: 12 HVNVGTIGHVDHGKTTLTAAITKVLAKKGGGEAKAYDQIDNAPEEKARGITINTSHVEYE 71
Query: 105 TNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNV 164
T RHYAH DCPGHADY+KNMI+GA+QMDGAI+VV+A++G MPQTREH+LL++Q+G+ +
Sbjct: 72 TANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYI 131
Query: 165 VVYVNKADLV-DREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSI 223
VV++NK D+V D E++ELVE+EVR++L+ Y + GD+TP + GSAL AL+GD E E I
Sbjct: 132 VVFLNKCDMVDDEELLELVEMEVRELLSKYDFPGDDTPIIRGSALKALEGDDDEEWEAKI 191
Query: 224 HRLLDALDKHIPNPVRDITSPFILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFN 283
L+DA+D +IP P R I PF++PI++ + GRG+V G +++G +K DE E++G
Sbjct: 192 LELMDAVDSYIPEPERAIDKPFLMPIEDVFSISGRGTVVTGRVERGIVKVGDEVEIVGIK 251
Query: 284 SKFTCTISEIQVFQKKVSEARAGDNVGVLLRNVKLKQIERGMLLAKADTLQMHNRYEAEI 343
T++ +++F+K + E +AGDNVGVLLR K + +ERG +LAK +++ H ++EAE+
Sbjct: 252 ETQKTTVTGVEMFRKLLDEGQAGDNVGVLLRGTKREDVERGQVLAKPGSIKPHTKFEAEV 311
Query: 344 YLLSKAEGGRYKPITSKYIQQMFSRTWNVQVRLDLPGEDDGMLMPGEHGTVTMTLLYKMY 403
Y+LSK EGGR+ P + Y Q + RT +V ++LP E M+MPG++ +T+ L+ +
Sbjct: 312 YVLSKEEGGRHTPFFNGYRPQFYFRTTDVTGTIELP-EGVEMVMPGDNVKMTVELIAPIA 370
Query: 404 LSKGQTFTIRENNKLVATGIVTKVL 428
+ +G F IRE + V G+V K++
Sbjct: 371 MEEGLRFAIREGGRTVGAGVVAKII 395
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 524 bits (1352), Expect = 0.0
Identities = 196/385 (50%), Positives = 282/385 (73%), Gaps = 4/385 (1%)
Query: 45 HCNVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYS 104
H N+GTIGHVDHGKTTLTAAITKV A+ G ++ +D ID APEEK RGITIN AHVEY
Sbjct: 12 HVNIGTIGHVDHGKTTLTAAITKVLAERGLNQAKDYDSIDAAPEEKERGITINTAHVEYE 71
Query: 105 TNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNV 164
T RHYAH DCPGHADY+KNMI+GA+QMDGAI+VVAA++G MPQTREH+LL++Q+G+ +
Sbjct: 72 TEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLARQVGVPYL 131
Query: 165 VVYVNKADLVDR-EIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSI 223
VV++NK DLVD E++ELVE+EVR++L+ Y + GD+ P + GSAL AL+GD E +I
Sbjct: 132 VVFLNKVDLVDDEELLELVEMEVRELLSEYDFPGDDIPVIRGSALKALEGDPKW--EDAI 189
Query: 224 HRLLDALDKHIPNPVRDITSPFILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFN 283
L+DA+D++IP P RD PF++P+++ + GRG+V G +++GT+K DE E++G
Sbjct: 190 MELMDAVDEYIPTPERDTDKPFLMPVEDVFTITGRGTVVTGRVERGTVKVGDEVEIVGIK 249
Query: 284 SKFTCTISEIQVFQKKVSEARAGDNVGVLLRNVKLKQIERGMLLAKADTLQMHNRYEAEI 343
++ +++F+K + E +AGDNVGVLLR V ++ERG +LAK +++ H +++AE+
Sbjct: 250 ETQKTVVTGVEMFRKLLDEGQAGDNVGVLLRGVDRDEVERGQVLAKPGSIKPHTKFKAEV 309
Query: 344 YLLSKAEGGRYKPITSKYIQQMFSRTWNVQVRLDLPGEDDGMLMPGEHGTVTMTLLYKMY 403
Y+L+K EGGR+ P + Y Q + RT +V ++LP E M+MPG++ T+T+ L++ +
Sbjct: 310 YILTKEEGGRHTPFFNNYRPQFYFRTTDVTGSIELP-EGTEMVMPGDNVTITVELIHPIA 368
Query: 404 LSKGQTFTIRENNKLVATGIVTKVL 428
+ +G F IRE + V G VT++L
Sbjct: 369 MEQGLKFAIREGGRTVGAGTVTEIL 393
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 509 bits (1312), Expect = e-180
Identities = 201/385 (52%), Positives = 283/385 (73%), Gaps = 4/385 (1%)
Query: 45 HCNVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYS 104
H NVGTIGHVDHGKTTLTAAIT V AK G ++ +DQID APEEKARGITIN AHVEY
Sbjct: 12 HVNVGTIGHVDHGKTTLTAAITTVLAKKGGAEAKAYDQIDNAPEEKARGITINTAHVEYE 71
Query: 105 TNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNV 164
T RHYAH DCPGHADY+KNMI+GA+QMDGAI+VVAA++G MPQTREH+LL++Q+G+ +
Sbjct: 72 TANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLARQVGVPYI 131
Query: 165 VVYVNKADLV-DREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSI 223
VV++NK D+V D E++ELVE+EVR++L+ YG+ GD+TP + GSAL AL+GD+ E I
Sbjct: 132 VVFLNKVDMVDDEELLELVEMEVRELLSEYGFPGDDTPIIRGSALKALEGDAK--WEAKI 189
Query: 224 HRLLDALDKHIPNPVRDITSPFILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFN 283
L+DA+D +IP P RDI PF++P+++ + GRG+V G +++G +K +E E++G
Sbjct: 190 EELMDAVDSYIPTPERDIDKPFLMPVEDVFSISGRGTVVTGRVERGILKVGEEVEIVGIK 249
Query: 284 SKFTCTISEIQVFQKKVSEARAGDNVGVLLRNVKLKQIERGMLLAKADTLQMHNRYEAEI 343
T++ +++F+K + E +AGDNVGVLLR VK + +ERG +LAK +++ H ++EAE+
Sbjct: 250 ETQKTTVTGVEMFRKLLDEGQAGDNVGVLLRGVKREDVERGQVLAKPGSIKPHTKFEAEV 309
Query: 344 YLLSKAEGGRYKPITSKYIQQMFSRTWNVQVRLDLPGEDDGMLMPGEHGTVTMTLLYKMY 403
Y+LSK EGGR+ P Y Q + RT +V + LP E M+MPG++ + + L++ +
Sbjct: 310 YVLSKEEGGRHTPFFHGYRPQFYFRTTDVTGAITLP-EGVEMVMPGDNVKMVVELIHPIA 368
Query: 404 LSKGQTFTIRENNKLVATGIVTKVL 428
+ +G F IRE + V G+VTK++
Sbjct: 369 MEEGLRFAIREGGRTVGAGVVTKII 393
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 504 bits (1299), Expect = e-178
Identities = 202/397 (50%), Positives = 280/397 (70%), Gaps = 13/397 (3%)
Query: 45 HCNVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYS 104
H N+GTIGHVDHGKTTLTAAIT A G +K +D+ID APEEKARGITIN AHVEY
Sbjct: 12 HVNIGTIGHVDHGKTTLTAAITMTLAAKGGAKAKKYDEIDSAPEEKARGITINTAHVEYE 71
Query: 105 TNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNV 164
T RHYAH DCPGHADY+KNMI+GA+QMDGAI+VV+A++G MPQT+EH+LL+KQ+G+ N+
Sbjct: 72 TENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTKEHILLAKQVGVPNI 131
Query: 165 VVYVNKADLV-DREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLAL----QGDSSELG 219
VV++NK D V D E++ELVELEVR++L+ Y + GD+ P V GSALLAL + + G
Sbjct: 132 VVFLNKEDQVDDEELLELVELEVRELLSKYDFPGDDIPIVSGSALLALEALTENPKIKRG 191
Query: 220 EPS----IHRLLDALDKHIPNPVRDITSPFILPIDNAIGVPGRGSVCIGTIKQGTIKRND 275
E I+ L+DA+D +IP P RD PF++ I++ + GRG+V G I++GT+K D
Sbjct: 192 ENKWVDKIYNLMDAVDSYIPTPERDTDKPFLMAIEDVFSITGRGTVATGRIERGTVKVGD 251
Query: 276 EAELLGFNSKFTCTISEIQVFQKKVSEARAGDNVGVLLRNVKLKQIERGMLLAKADTLQM 335
E++G T T++ +++FQK + E AGDNVG+LLR ++ + IERGM+LAK T+
Sbjct: 252 TVEIVGLRETKTTTVTGLEMFQKTLDEGLAGDNVGILLRGIQKEDIERGMVLAKPGTITP 311
Query: 336 HNRYEAEIYLLSKAEGGRYKPITSKYIQQMFSRTWNVQVRLDLPGEDDG----MLMPGEH 391
H ++EA++Y+L+K EGGR+ P Y Q + RT +V +++ DDG M+MPG+
Sbjct: 312 HTKFEAQVYILTKEEGGRHTPFFPGYRPQFYVRTTDVTGKIESFTADDGSKTEMVMPGDR 371
Query: 392 GTVTMTLLYKMYLSKGQTFTIRENNKLVATGIVTKVL 428
+T+ L+Y + + KG F IRE + V G+V+K+L
Sbjct: 372 IKMTVELIYPIAIEKGMRFAIREGGRTVGAGVVSKIL 408
>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 = 486 bits (1252), Expect = e-171
Identities = 199/385 (51%), Positives = 284/385 (73%), Gaps = 4/385 (1%)
Query: 45 HCNVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYS 104
H N+GTIGHVDHGKTTLTAAIT V AK G + +DQID APEEKARGITIN AHVEY
Sbjct: 12 HVNIGTIGHVDHGKTTLTAAITTVLAKEGGAAARAYDQIDNAPEEKARGITINTAHVEYE 71
Query: 105 TNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNV 164
T RHYAH DCPGHADY+KNMI+GA+QMDGAI+VV+A++G MPQTREH+LL++Q+G+ +
Sbjct: 72 TENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSATDGPMPQTREHILLARQVGVPYI 131
Query: 165 VVYVNKADLV-DREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSI 223
VV++NK D+V D E++ELVE+EVR++L+ Y + GD+TP + GSAL AL+GD+ E I
Sbjct: 132 VVFLNKCDMVDDEELLELVEMEVRELLSEYDFPGDDTPIIRGSALKALEGDAE--WEAKI 189
Query: 224 HRLLDALDKHIPNPVRDITSPFILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFN 283
L+DA+D++IP P R+ PF++PI++ + GRG+V G +++G +K +E E++G
Sbjct: 190 LELMDAVDEYIPTPERETDKPFLMPIEDVFSITGRGTVVTGRVERGIVKVGEEVEIVGLK 249
Query: 284 SKFTCTISEIQVFQKKVSEARAGDNVGVLLRNVKLKQIERGMLLAKADTLQMHNRYEAEI 343
T++ +++F+K++ E RAGDNVG+LLR +K ++IERGM+LAK +++ H ++EAE+
Sbjct: 250 DTRKTTVTGVEMFRKELDEGRAGDNVGLLLRGIKREEIERGMVLAKPGSIKPHTKFEAEV 309
Query: 344 YLLSKAEGGRYKPITSKYIQQMFSRTWNVQVRLDLPGEDDGMLMPGEHGTVTMTLLYKMY 403
Y+L K EGGR+ P S Y Q + RT +V + LP E M+MPG++ +T+ L+ +
Sbjct: 310 YVLKKEEGGRHTPFFSGYRPQFYFRTTDVTGSITLP-EGVEMVMPGDNVKMTVELISPIA 368
Query: 404 LSKGQTFTIRENNKLVATGIVTKVL 428
L +G F IRE + V G+V+K++
Sbjct: 369 LEQGMRFAIREGGRTVGAGVVSKII 393
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 488 bits (1257), Expect = e-171
Identities = 197/388 (50%), Positives = 288/388 (74%), Gaps = 4/388 (1%)
Query: 45 HCNVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYS 104
H NVGTIGHVDHGKTTLTAAITKV A+ GK+K + FD+ID+APEEKARGITI AHVEY
Sbjct: 61 HVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAVAFDEIDKAPEEKARGITIATAHVEYE 120
Query: 105 TNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNV 164
T RHYAH DCPGHADY+KNMI+GA+QMDG I+VV+A +G MPQT+EH+LL++Q+G+ ++
Sbjct: 121 TAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSL 180
Query: 165 VVYVNKADLV-DREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSI 223
VV++NK D+V D E++ELVE+E+R++L+ Y + GD P + GSAL ALQG + E+G+ +I
Sbjct: 181 VVFLNKVDVVDDEELLELVEMELRELLSFYKFPGDEIPIIRGSALSALQGTNDEIGKNAI 240
Query: 224 HRLLDALDKHIPNPVRDITSPFILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFN 283
+L+DA+D++IP PVR + PF++PI++ + GRG+V G ++QGTIK +E E++G
Sbjct: 241 LKLMDAVDEYIPEPVRVLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEIVGLR 300
Query: 284 SKFT--CTISEIQVFQKKVSEARAGDNVGVLLRNVKLKQIERGMLLAKADTLQMHNRYEA 341
T++ +++F+K + + +AGDNVG+LLR +K + ++RG ++ K +++ + ++EA
Sbjct: 301 PGGPLKTTVTGVEMFKKILDQGQAGDNVGLLLRGLKREDVQRGQVICKPGSIKTYKKFEA 360
Query: 342 EIYLLSKAEGGRYKPITSKYIQQMFSRTWNVQVRLDLPGEDDGMLMPGEHGTVTMTLLYK 401
EIY+L+K EGGR+ P S Y Q + RT +V +++LP E M+MPG++ T L+
Sbjct: 361 EIYVLTKDEGGRHTPFFSNYRPQFYLRTADVTGKVELP-EGVKMVMPGDNVTAVFELISP 419
Query: 402 MYLSKGQTFTIRENNKLVATGIVTKVLG 429
+ L GQ F +RE + V G+V+KVL
Sbjct: 420 VPLEPGQRFALREGGRTVGAGVVSKVLS 447
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 408 bits (1050), Expect = e-139
Identities = 184/400 (46%), Positives = 272/400 (68%), Gaps = 19/400 (4%)
Query: 45 HCNVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYS 104
H N+GTIGHVDHGKTTLTAA+T A +G S +D+ID APEE+ARGITIN A VEY
Sbjct: 81 HVNIGTIGHVDHGKTTLTAALTMALASMGGSAPKKYDEIDAAPEERARGITINTATVEYE 140
Query: 105 TNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNV 164
T RHYAH DCPGHADY+KNMI+GA+QMDGAI+VV+ ++G MPQT+EH+LL+KQ+G+ N+
Sbjct: 141 TENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNM 200
Query: 165 VVYVNKADLV-DREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSI 223
VV++NK D V D E++ELVELEVR++L++Y + GD+ P + GSALLAL+ + + P+I
Sbjct: 201 VVFLNKQDQVDDEELLELVELEVRELLSSYEFPGDDIPIISGSALLALE---ALMENPNI 257
Query: 224 HR-----------LLDALDKHIPNPVRDITSPFILPIDNAIGVPGRGSVCIGTIKQGTIK 272
R L+DA+D +IP P R PF+L +++ + GRG+V G +++GT+K
Sbjct: 258 KRGDNKWVDKIYELMDAVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVERGTVK 317
Query: 273 RNDEAELLGFNSKFTCTISEIQVFQKKVSEARAGDNVGVLLRNVKLKQIERGMLLAKADT 332
+ +++G + T++ +++FQK + EA AGDNVG+LLR ++ I+RGM+LAK +
Sbjct: 318 VGETVDIVGLRETRSTTVTGVEMFQKILDEALAGDNVGLLLRGIQKADIQRGMVLAKPGS 377
Query: 333 LQMHNRYEAEIYLLSKAEGGRYKPITSKYIQQMFSRTWNVQVR----LDLPGEDDGMLMP 388
+ H ++EA +Y+L K EGGR+ P + Y Q + RT +V + ++ E+ M+MP
Sbjct: 378 ITPHTKFEAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGKVTSIMNDKDEESKMVMP 437
Query: 389 GEHGTVTMTLLYKMYLSKGQTFTIRENNKLVATGIVTKVL 428
G+ + + L+ + +G F IRE K V G++ ++
Sbjct: 438 GDRVKMVVELIVPVACEQGMRFAIREGGKTVGAGVIQSII 477
>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 = 377 bits (971), Expect = e-131
Identities = 133/194 (68%), Positives = 161/194 (82%), Gaps = 1/194 (0%)
Query: 45 HCNVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYS 104
H NVGTIGHVDHGKTTLTAAITKV AK G +K +D+ID+APEEKARGITIN AHVEY
Sbjct: 2 HVNVGTIGHVDHGKTTLTAAITKVLAKKGGAKAKKYDEIDKAPEEKARGITINTAHVEYE 61
Query: 105 TNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNV 164
T RHYAH DCPGHADYIKNMI+GA+QMDGAI+VV+A++G MPQTREHLLL++Q+G+ +
Sbjct: 62 TANRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSATDGPMPQTREHLLLARQVGVPYI 121
Query: 165 VVYVNKADLV-DREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSI 223
VV++NKAD+V D E++ELVE+EVR++L+ YG+DGD+TP V GSAL AL+GD I
Sbjct: 122 VVFLNKADMVDDEELLELVEMEVRELLSKYGFDGDDTPIVRGSALKALEGDDPNKWVDKI 181
Query: 224 HRLLDALDKHIPNP 237
LLDALD +IP P
Sbjct: 182 LELLDALDSYIPTP 195
>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 = 254 bits (651), Expect = 3e-83
Identities = 93/192 (48%), Positives = 117/192 (60%), Gaps = 12/192 (6%)
Query: 45 HCNVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYS 104
H N+G IGHVDHGKTTLT A+ V I K +D+ EE+ RGITI IA V +
Sbjct: 3 HRNIGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVSFE 62
Query: 105 TNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNV 164
T R D PGH D+ K MI GASQ DGAI+VV A EG MPQTREHLLL+K +G+ +
Sbjct: 63 TKKRLINIIDTPGHVDFTKEMIRGASQADGAILVVDAVEGVMPQTREHLLLAKTLGV-PI 121
Query: 165 VVYVNKADLVDR-EIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSI 223
+V++NK D VD E+ E+VE R++L YG+ G+ P V GSAL I
Sbjct: 122 IVFINKIDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPGSALTGE----------GI 171
Query: 224 HRLLDALDKHIP 235
LL+ALD ++P
Sbjct: 172 DELLEALDLYLP 183
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 205 bits (523), Expect = 3e-61
Identities = 110/314 (35%), Positives = 174/314 (55%), Gaps = 36/314 (11%)
Query: 45 HCNVGTIGHVDHGKTTL-------TAAI--------TKVAAKIGKSKFITFDQIDRAPEE 89
H N+ IGHVDHGK+TL T AI + A + GK F +DR EE
Sbjct: 6 HLNLAVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMDRLKEE 65
Query: 90 KARGITINIAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASE--GQMP 147
+ RG+TI++AH ++ T+ ++ DCPGH D++KNMI+GASQ D A++VVAA + G MP
Sbjct: 66 RERGVTIDLAHKKFETDKYYFTIVDCPGHRDFVKNMITGASQADAAVLVVAADDAGGVMP 125
Query: 148 QTREHLLLSKQIGIDNVVVYVNKADLVD---REIMELVELEVRDVLTAYGYDGDNTPFVF 204
QTREH+ L++ +GI+ ++V +NK D V+ + E+ E EV +L GY D+ PF+
Sbjct: 126 QTREHVFLARTLGINQLIVAINKMDAVNYDEKRYEEVKE-EVSKLLKMVGYKPDDIPFIP 184
Query: 205 GSALLALQGDSSELGEPSIHR-------LLDALDKHIPNPVRDITSPFILPIDNAIGVPG 257
S A +GD+ + + S + LL+ALD + P + P +PI + + G
Sbjct: 185 VS---AFEGDN--VVKKSENMPWYNGPTLLEALDN-LKPPEKPTDKPLRIPIQDVYSISG 238
Query: 258 RGSVCIGTIKQGTIKRNDEAELLGFNSKFTCTISEIQVFQKKVSEARAGDNVGVLLRNVK 317
G+V +G ++ G +K D+ + + + I++ +++ +A GDN+G +R V
Sbjct: 239 VGTVPVGRVETGVLKVGDKVVFM--PAGVVGEVKSIEMHHEELPQAEPGDNIGFNVRGVG 296
Query: 318 LKQIERGMLLAKAD 331
K I+RG + D
Sbjct: 297 KKDIKRGDVCGHPD 310
>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 = 194 bits (496), Expect = 2e-60
Identities = 74/194 (38%), Positives = 103/194 (53%), Gaps = 14/194 (7%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYSTN 106
NVG IGHVDHGKTTLT ++ I + +D EE+ RGITI VE+
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWP 60
Query: 107 TRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNVVV 166
R D PGH D+ K + G +Q DGA++VV A+EG PQTREHL ++ G+ ++V
Sbjct: 61 KRRINFIDTPGHEDFSKETVRGLAQADGALLVVDANEGVEPQTREHLNIALAGGL-PIIV 119
Query: 167 YVNKADLVDREIMELVELEVRDVLTAYGY---DGDNTPFVFGSALLALQGDSSELGEPSI 223
VNK D V E + V E++++L G+ G + P + SAL +
Sbjct: 120 AVNKIDRVGEEDFDEVLREIKELLKLIGFTFLKGKDVPIIPISALTGEGIEE-------- 171
Query: 224 HRLLDALDKHIPNP 237
LLDA+ +H+P P
Sbjct: 172 --LLDAIVEHLPPP 183
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 201 bits (513), Expect = 9e-60
Identities = 132/442 (29%), Positives = 209/442 (47%), Gaps = 67/442 (15%)
Query: 39 SKSSLVHCNVGTIGHVDHGKTTLTAAI---------------TKVAAKIGKSKFITFDQI 83
S H N+ IGHVD GK+TL + K A ++GK F F +
Sbjct: 1 MASEKPHLNLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESF-KFAWV 59
Query: 84 -DRAPEEKARGITINIAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAAS 142
D+ EE+ RG+TI++AH ++ T+ ++ D PGH D++KNMI+GASQ D A++VV A
Sbjct: 60 LDKTKEERERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDAR 119
Query: 143 EGQ-------MPQTREHLLLSKQIGIDNVVVYVNKADLV--DREIMELVELEVRDVLTAY 193
+G+ QTREH L++ +GI ++V VNK DLV D E E + EV +L
Sbjct: 120 DGEFEAGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLLKMV 179
Query: 194 GYDGDNTPFVFGSALLALQGDS----SELGE----PSIHRLLDALDKHIPNPVRDITSPF 245
GY+ + PF+ S +GD+ SE P+ LL+ALD+ + P R + P
Sbjct: 180 GYNPKDVPFIPIS---GFKGDNLTKKSENMPWYKGPT---LLEALDQ-LEPPERPLDKPL 232
Query: 246 ILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFNSKFTCTISEIQVFQKKVSEARA 305
LPI + + G G+V +G ++ G IK + + + + I++ +++S+A
Sbjct: 233 RLPIQDVYSISGIGTVPVGRVESGVIKPGQKVTFM--PAGVVGEVKSIEMHHEEISQAEP 290
Query: 306 GDNVGVLLRNVKLKQIERGMLLAKAD-TLQMHNRYEAEIYLLSKAEGGRYKPITSKYIQQ 364
GDNVG +R V+ I RG ++ +D + + A+I +L ITS Y
Sbjct: 291 GDNVGFNVRGVEKNDIRRGDVIGHSDNPPTVSPEFTAQIIVL-----WHPGIITSGYTPV 345
Query: 365 MFSRTWNVQVRLD------------LPGEDDGMLMPGEHGTVTMTLLYKMYLSKGQ---- 408
+ + T V R+ E+ L G+ V + + L K
Sbjct: 346 LHAHTAQVACRIAELLSKLDPRTGKKLEENPQFLKRGDAAIVKIEPEKPLCLEKVSEIPQ 405
Query: 409 --TFTIRENNKLVATGIVTKVL 428
F +R+ + +A G V +V
Sbjct: 406 LGRFALRDMGQTIAAGKVLEVK 427
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 185 bits (472), Expect = 1e-53
Identities = 106/341 (31%), Positives = 155/341 (45%), Gaps = 35/341 (10%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYSTN 106
+GT GH+DHGKTTL A+T DR PEEK RGITI++
Sbjct: 2 IIGTAGHIDHGKTTLLKALTGGVT-------------DRLPEEKKRGITIDLGFYYRKLE 48
Query: 107 TRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNVVV 166
D PGH D+I N+++G +D A++VVAA EG M QT EHLL+ +GI N ++
Sbjct: 49 DGVMGFIDVPGHPDFISNLLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGIKNGII 108
Query: 167 YVNKADLVDREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSIHRL 226
+ KAD VD +E ++ L+ A + S++ G I L
Sbjct: 109 VLTKADRVDEARIEQKIKQILADLSL--------------ANAKIFKTSAKTGR-GIEEL 153
Query: 227 LDALDKHIPNPVRDITSPFILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFNSKF 286
+ L + RD PF + ID A V G G+V GT+ G +K D+ L N
Sbjct: 154 KNELIDLLEEIERDEQKPFRIAIDRAFTVKGVGTVVTGTVLSGEVKVGDKLYLSPINK-- 211
Query: 287 TCTISEIQVFQKKVSEARAGDNVGVLLRNVKLKQIERGMLLAKADTLQMHNRYEAEIYLL 346
+ IQ V EA+AG VG+ L+ V+ ++IERG L K + L++ R E+ +
Sbjct: 212 EVRVRSIQAHDVDVEEAKAGQRVGLALKGVEKEEIERGDWLLKPEPLEVTTRLIVELEID 271
Query: 347 SKAEGGRYKPITSKYIQQMFSRTWNVQVRLD-LPGEDDGML 386
+ K + + +V R+ L + L
Sbjct: 272 PLFK----KTLKQGQPVHIHVGLRSVTGRIVPLEKNAELNL 308
>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 = 182 bits (464), Expect = 9e-53
Identities = 108/316 (34%), Positives = 168/316 (53%), Gaps = 39/316 (12%)
Query: 45 HCNVGTIGHVDHGKTTLT---------------AAITKVAAKIGKSKFITFDQIDRAPEE 89
H NV IGHVDHGK+T K A + GK+ F +DR EE
Sbjct: 7 HINVAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFEFAWVMDRLKEE 66
Query: 90 KARGITINIAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQ---M 146
+ RG+TI++AH ++ T+ DCPGH D+IKNMI+GASQ D A++VVA +G+
Sbjct: 67 RERGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGDGEFEVQ 126
Query: 147 PQTREHLLLSKQIGIDNVVVYVNKADLV--DREIMELVELEVRDVLTAYGYDGDNTPFVF 204
PQTREH L++ +GI+ ++V +NK D V D E E ++ EV +++ GY+ D PF+
Sbjct: 127 PQTREHAFLARTLGINQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVGYNPDTVPFI- 185
Query: 205 GSALLALQGDSSELGEPSIH-------RLLDALDKHIPNPVRDITSPFILPIDNAIGVPG 257
+ A GD+ + + S + LL+ALD + P + P +PI + + G
Sbjct: 186 --PISAWNGDN--VIKKSENTPWYKGKTLLEALDA-LEPPEKPTDKPLRIPIQDVYSITG 240
Query: 258 RGSVCIGTIKQGTIKRNDEA--ELLGFNSKFTCTISEIQVFQKKVSEARAGDNVGVLLRN 315
G+V +G ++ G +K D+ E G + + + I++ +++ +A GDN+G +R
Sbjct: 241 VGTVPVGRVETGVLKPGDKVVFEPAGVSGE----VKSIEMHHEQIEQAEPGDNIGFNVRG 296
Query: 316 VKLKQIERGMLLAKAD 331
V K I RG + D
Sbjct: 297 VSKKDIRRGDVCGHPD 312
>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 = 180 bits (458), Expect = 2e-50
Identities = 92/283 (32%), Positives = 140/283 (49%), Gaps = 25/283 (8%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYSTN 106
+ T GHVDHGKTTL A+T +AA DR PEEK RG+TI++ +
Sbjct: 2 IIATAGHVDHGKTTLLKALTGIAA-------------DRLPEEKKRGMTIDLGFAYFPLP 48
Query: 107 TRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNVVV 166
D PGH +I N I+G +D A++VV A EG M QT EHL + +GI + +V
Sbjct: 49 DYRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIPHTIV 108
Query: 167 YVNKADLVDREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSIHRL 226
+ KAD V+ E ++ E+ ++ +L +Y + + F A G + + L
Sbjct: 109 VITKADRVNEEEIKRTEMFMKQILNSYIFLKNAKIFKTS----AKTGQGIGELKKELKNL 164
Query: 227 LDALDKHIPNPVRDITSPFILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFNSKF 286
L++LD ++ I P + ID A V G G+V GT G +K D LL N +
Sbjct: 165 LESLD------IKRIQKPLRMAIDRAFKVKGAGTVVTGTAFSGEVKVGDNLRLLPINHEV 218
Query: 287 TCTISEIQVFQKKVSEARAGDNVGVLLRNVKLKQIERGMLLAK 329
+ IQ + V A AG + + L +V+ + ++RG+L+
Sbjct: 219 --RVKAIQAQNQDVEIAYAGQRIALNLMDVEPESLKRGLLILT 259
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 170 bits (433), Expect = 5e-48
Identities = 107/320 (33%), Positives = 165/320 (51%), Gaps = 51/320 (15%)
Query: 44 VHCNVGTIGHVDHGKTTLTAAIT---------------KVAAKIGKSKFITFDQIDRAPE 88
H N+ IGHVD GK+T T + K AA++GK F +D+
Sbjct: 6 THINLVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKA 65
Query: 89 EKARGITINIAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMP- 147
E+ RGITI+IA ++ T ++ D PGH D+IKNMI+G SQ D AI+VVA++ G+
Sbjct: 66 ERERGITIDIALWKFETPKYYFTIIDAPGHRDFIKNMITGTSQADVAILVVASTAGEFEA 125
Query: 148 ------QTREHLLLSKQIGIDNVVVYVNKADLV------DR--EIMELVELEVRDVLTAY 193
QTREH LL+ +G+ ++V +NK D +R EI + EV L
Sbjct: 126 GISKDGQTREHALLAFTLGVKQMIVCINKMDDKTVNYSQERYDEIKK----EVSAYLKKV 181
Query: 194 GYDGDNTPFVFGSALLALQGDSSELGEPSIH-------RLLDALDKHIPNPVRDITSPFI 246
GY+ + PF+ + QGD+ + E S + LL+ALD P P R + P
Sbjct: 182 GYNPEKVPFI---PISGWQGDN--MIEKSDNMPWYKGPTLLEALDTLEP-PKRPVDKPLR 235
Query: 247 LPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFN-SKFTCTISEIQVFQKKVSEARA 305
LP+ + + G G+V +G ++ G +K ++ F S T + +++ ++++EA
Sbjct: 236 LPLQDVYKIGGIGTVPVGRVETGILKPGM---VVTFAPSGVTTEVKSVEMHHEQLAEAVP 292
Query: 306 GDNVGVLLRNVKLKQIERGM 325
GDNVG ++NV +K I+RG
Sbjct: 293 GDNVGFNVKNVSVKDIKRGY 312
>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 = 157 bits (399), Expect = 2e-45
Identities = 65/188 (34%), Positives = 100/188 (53%), Gaps = 26/188 (13%)
Query: 47 NVGTIGHVDHGKTTLT---------------AAITKVAAKIGKSKFITFDQIDRAPEEKA 91
N+ IGHVD GK+TLT K A ++GK F +D+ EE+
Sbjct: 1 NLVVIGHVDAGKSTLTGHLLYKLGGVDKRTIEKYEKEAKEMGKESFKYAWVLDKLKEERE 60
Query: 92 RGITINIAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQ------ 145
RG+TI++ ++ T + D PGH D++KNMI+GASQ D A++VV+A +G+
Sbjct: 61 RGVTIDVGLAKFETEKYRFTIIDAPGHRDFVKNMITGASQADVAVLVVSARKGEFEAGFE 120
Query: 146 -MPQTREHLLLSKQIGIDNVVVYVNKADLV----DREIMELVELEVRDVLTAYGYDGDNT 200
QTREH LL++ +G+ ++V VNK D V +E + ++ +V L GY+ +
Sbjct: 121 KGGQTREHALLARTLGVKQLIVAVNKMDDVTVNWSQERYDEIKKKVSPFLKKVGYNPKDV 180
Query: 201 PFVFGSAL 208
PF+ S
Sbjct: 181 PFIPISGF 188
>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 = 158 bits (401), Expect = 1e-43
Identities = 104/318 (32%), Positives = 147/318 (46%), Gaps = 86/318 (27%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVE---- 102
N+G +GHVDHGKTTLT A+T V D EE RGI+I + + +
Sbjct: 6 NIGMVGHVDHGKTTLTKALTGV-------------WTDTHSEELKRGISIRLGYADAEIY 52
Query: 103 ----------YSTN------------TRHYAHTDCPGHADYIKNMISGASQMDGAIVVVA 140
Y+T R + D PGH + M+SGA+ MDGA++V+A
Sbjct: 53 KCPECDGPECYTTEPVCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGALLVIA 112
Query: 141 ASEG-QMPQTREHLLLSKQIGIDNVVVYVNKADLVDRE--------IMELVELEVRDVLT 191
A+E PQTREHL+ + IGI N+V+ NK DLV +E I E V+
Sbjct: 113 ANEPCPQPQTREHLMALEIIGIKNIVIVQNKIDLVSKEKALENYEEIKEFVK-------- 164
Query: 192 AYGYDGDNTPFVFGSALLALQGDSSELGEPSIHRLLDALDKHIPNPVRDITSPFILPIDN 251
G +N P + SAL +I LL+A++K IP P RD+ P ++ +
Sbjct: 165 --GTIAENAPIIPVSALHNA----------NIDALLEAIEKFIPTPERDLDKPPLMYVAR 212
Query: 252 AIGV--PG------RGSVCIGTIKQGTIKRNDEAELL-------GFNSKF---TCTISEI 293
+ V PG +G V G++ QG +K DE E+ G +K+ I+ +
Sbjct: 213 SFDVNKPGTPPEKLKGGVIGGSLIQGKLKVGDEIEIRPGIKVEKGGKTKWEPIYTEITSL 272
Query: 294 QVFQKKVSEARAGDNVGV 311
+ KV EAR G VGV
Sbjct: 273 RAGGYKVEEARPGGLVGV 290
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 157 bits (399), Expect = 2e-43
Identities = 102/318 (32%), Positives = 146/318 (45%), Gaps = 86/318 (27%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVE---- 102
N+G +GHVDHGKTTLT A++ V DR EE RGITI + + +
Sbjct: 12 NIGMVGHVDHGKTTLTKALSGV-------------WTDRHSEELKRGITIKLGYADAKIY 58
Query: 103 ----------YSTN------------TRHYAHTDCPGHADYIKNMISGASQMDGAIVVVA 140
Y+T R + D PGH + M+SGA+ MDGA++V+A
Sbjct: 59 KCPECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGHETLMATMLSGAALMDGALLVIA 118
Query: 141 ASEG-QMPQTREHLLLSKQIGIDNVVVYVNKADLVDRE--------IMELVELEVRDVLT 191
A+E PQTREHL+ + IGI N+++ NK DLV RE I E V+
Sbjct: 119 ANEPCPQPQTREHLMALEIIGIKNIIIVQNKIDLVSRERALENYEQIKEFVK-------- 170
Query: 192 AYGYDGDNTPFVFGSALLALQGDSSELGEPSIHRLLDALDKHIPNPVRDITSPFILPIDN 251
G +N P + SA + +I L++A++K+IP P RD+ P + +
Sbjct: 171 --GTVAENAPIIPISAQH----------KANIDALIEAIEKYIPTPERDLDKPPRMYVAR 218
Query: 252 AIGV--PG------RGSVCIGTIKQGTIKRNDEAELL-GFNSK---------FTCTISEI 293
+ V PG +G V G++ QG ++ DE E+ G + T I +
Sbjct: 219 SFDVNKPGTPPEELKGGVIGGSLVQGVLRVGDEIEIRPGIVVEKGGKTVWEPITTEIVSL 278
Query: 294 QVFQKKVSEARAGDNVGV 311
Q + V EAR G VGV
Sbjct: 279 QAGGEDVEEARPGGLVGV 296
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 155 bits (395), Expect = 7e-43
Identities = 104/318 (32%), Positives = 147/318 (46%), Gaps = 86/318 (27%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVE---- 102
N+G +GHVDHGKTTL A+T V DR EE RGITI + + +
Sbjct: 11 NIGMVGHVDHGKTTLVQALTGVWT-------------DRHSEELKRGITIRLGYADATIR 57
Query: 103 ----------YSTNT------------RHYAHTDCPGHADYIKNMISGASQMDGAIVVVA 140
Y+T R + D PGH + M+SGA+ MDGAI+V+A
Sbjct: 58 KCPDCEEPEAYTTEPKCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGAILVIA 117
Query: 141 ASEG-QMPQTREHLLLSKQIGIDNVVVYVNKADLVDRE--------IMELVELEVRDVLT 191
A+E PQT+EHL+ IGI N+V+ NK DLV +E I E V+
Sbjct: 118 ANEPCPQPQTKEHLMALDIIGIKNIVIVQNKIDLVSKERALENYEQIKEFVK-------- 169
Query: 192 AYGYDGDNTPFVFGSALLALQGDSSELGEPSIHRLLDALDKHIPNPVRDITSPFILPIDN 251
G +N P + SA L + +I L++A+++ IP P RD+ P + +
Sbjct: 170 --GTVAENAPIIPVSA----------LHKVNIDALIEAIEEEIPTPERDLDKPPRMYVAR 217
Query: 252 AIGV--PG------RGSVCIGTIKQGTIKRNDEAELL-------GFNSKF---TCTISEI 293
+ V PG +G V G++ QG +K DE E+ G +K+ T I +
Sbjct: 218 SFDVNKPGTPPEKLKGGVIGGSLIQGVLKVGDEIEIRPGIKVEEGGKTKWEPITTKIVSL 277
Query: 294 QVFQKKVSEARAGDNVGV 311
+ +KV EAR G VGV
Sbjct: 278 RAGGEKVEEARPGGLVGV 295
>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 = 144 bits (366), Expect = 2e-41
Identities = 72/195 (36%), Positives = 104/195 (53%), Gaps = 29/195 (14%)
Query: 48 VGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINI--AHVEYST 105
+GT GH+DHGKTTL A+T + DR PEEK RGITI++ A+++
Sbjct: 2 IGTAGHIDHGKTTLIKALTGIET-------------DRLPEEKKRGITIDLGFAYLDLPD 48
Query: 106 NTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNVV 165
R D PGH ++KNM++GA +D ++VVAA EG MPQTREHL + + +GI +
Sbjct: 49 GKR-LGFIDVPGHEKFVKNMLAGAGGIDAVLLVVAADEGIMPQTREHLEILELLGIKKGL 107
Query: 166 VYVNKADLVDREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSIHR 225
V + KADLVD + +ELVE E+ ++L + P S++ I
Sbjct: 108 VVLTKADLVDEDRLELVEEEILELLAGTFL--ADAPIFPVSSVTGE----------GIEE 155
Query: 226 LLDALDKHIPNPVRD 240
L + LD+ + P
Sbjct: 156 LKNYLDE-LAEPQSK 169
>gnl|CDD|239677 cd03706, mtEFTU_III, Domain III of mitochondrial EF-TU (mtEF-TU).
mtEF-TU is highly conserved and is 55-60% identical to
bacterial EF-TU. The overall structure is similar to
that observed in the Escherichia coli and Thermus
aquaticus EF-TU. However, compared with that observed in
prokaryotic EF-TU the nucleotide-binding domain (domain
I) of EF-TUmt is in a different orientation relative to
the rest of the structure. Furthermore, domain III is
followed by a short 11-amino acid extension that forms
one helical turn. This extension seems to be specific to
the mitochondrial factors and has not been observed in
any of the prokaryotic factors.
Length = 93
Score = 137 bits (346), Expect = 2e-39
Identities = 46/94 (48%), Positives = 64/94 (68%), Gaps = 1/94 (1%)
Query: 334 QMHNRYEAEIYLLSKAEGGRYKPITSKYIQQMFSRTWNVQVRLDLPGEDDGMLMPGEHGT 393
+ H++ EA++Y+LSKAEGGR+KP S + QMFS TW+ R+DLP + M+MPGE
Sbjct: 1 KPHDKVEAQVYILSKAEGGRHKPFVSNFQPQMFSLTWDCAARIDLPPGKE-MVMPGEDTK 59
Query: 394 VTMTLLYKMYLSKGQTFTIRENNKLVATGIVTKV 427
VT+ L M L KGQ FT+R+ N+ + TG+VT
Sbjct: 60 VTLILRRPMVLEKGQRFTLRDGNRTIGTGLVTDT 93
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 144 bits (363), Expect = 4e-38
Identities = 119/432 (27%), Positives = 200/432 (46%), Gaps = 56/432 (12%)
Query: 44 VHCNVGTIGHVDHGKTTLTAAIT---------------KVAAKIGKSKFITFDQIDRAPE 88
VH N+ IGHVD GK+T T + K AA++ K F +D+
Sbjct: 6 VHINIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFEKEAAEMNKRSFKYAWVLDKLKA 65
Query: 89 EKARGITINIAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMP- 147
E+ RGITI+IA ++ T + D PGH D+IKNMI+G SQ D A++++ ++ G
Sbjct: 66 ERERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGGFEA 125
Query: 148 ------QTREHLLLSKQIGIDNVVVYVNKADLV----DREIMELVELEVRDVLTAYGYDG 197
QTREH LL+ +G+ ++ NK D + + + EV L GY+
Sbjct: 126 GISKDGQTREHALLAFTLGVKQMICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVGYNP 185
Query: 198 DNTPFVFGSALLALQGD-----SSELGEPSIHRLLDALDKHIPNPVRDITSPFILPIDNA 252
D PFV + +GD S+ L LL+ALD+ I P R P LP+ +
Sbjct: 186 DKIPFV---PISGFEGDNMIERSTNLDWYKGPTLLEALDQ-INEPKRPSDKPLRLPLQDV 241
Query: 253 IGVPGRGSVCIGTIKQGTIKRNDEAELLGFN-SKFTCTISEIQVFQKKVSEARAGDNVGV 311
+ G G+V +G ++ G IK ++ F + T + +++ + + EA GDNVG
Sbjct: 242 YKIGGIGTVPVGRVETGVIK---PGMVVTFGPTGLTTEVKSVEMHHESLQEALPGDNVGF 298
Query: 312 LLRNVKLKQIERGMLL--AKADTLQMHNRYEAEIYLLSKAE--GGRYKPITSKYIQQMFS 367
++NV +K ++RG + +K D + + +++ +++ G Y P+ + +
Sbjct: 299 NVKNVAVKDLKRGYVASNSKDDPAKEAANFTSQVIIMNHPGQIGNGYAPVLDCHTSHIAV 358
Query: 368 RTWNVQVRLDLPG-----EDDGMLMPGEHGTVTMTLLYKM-------YLSKGQTFTIREN 415
+ + ++D ++ L G+ G V M M Y G+ F +R+
Sbjct: 359 KFAEILTKIDRRSGKELEKEPKFLKNGDAGFVKMIPTKPMVVETFSEYPPLGR-FAVRDM 417
Query: 416 NKLVATGIVTKV 427
+ VA G++ V
Sbjct: 418 RQTVAVGVIKSV 429
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 137 bits (346), Expect = 2e-35
Identities = 113/435 (25%), Positives = 185/435 (42%), Gaps = 61/435 (14%)
Query: 38 SSKSSLVHCNVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITIN 97
++ + H VG GHVDHGK+TL + G ++ +D E RG++ +
Sbjct: 110 KTEEAPEHVLVGVAGHVDHGKSTLVGVLVTGRLDDGDGATRSY--LDVQKHEVERGLSAD 167
Query: 98 IAHVEY-----------------------STNTRHYAHTDCPGHADYIKNMISG--ASQM 132
I+ Y + + D GH +++ I G ++
Sbjct: 168 ISLRVYGFDDGKVVRLKNPLDEAEKAAVVKRADKLVSFVDTVGHEPWLRTTIRGLLGQKV 227
Query: 133 DGAIVVVAASEGQMPQTREHLLLSKQIGIDNVVVYVNKADLVDREIMELVELEVRDVLTA 192
D ++VVAA +G T+EHL ++ + + V+V V K D+V + + V E+ +L
Sbjct: 228 DYGLLVVAADDGVTKMTKEHLGIALAMELP-VIVVVTKIDMVPDDRFQGVVEEISALLKR 286
Query: 193 YGYDGDNTPFVF---GSALLALQGDSSELGEPSIHRL-------LDALDKHIPN-PVR-- 239
G P + +LA + + G I LD LD+ P R
Sbjct: 287 VG----RIPLIVKDTDDVVLAAKAMKAGRGVVPIFYTSSVTGEGLDLLDEFFLLLPKRRR 342
Query: 240 -DITSPFILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFNS--KF-TCTISEIQV 295
D PF++ ID V G G+V G++K G + D LLG KF + I++
Sbjct: 343 WDDEGPFLMYIDKIYSVTGVGTVVSGSVKSGILHVGDTV-LLGPFKDGKFREVVVKSIEM 401
Query: 296 FQKKVSEARAGDNVGVLLRNVKLKQIERGMLLAKADTLQMHNRYEAEIYLLSKAEGGRYK 355
+V A+AG +G+ L+ V+ +++ERGM+L+ + ++AE+ +L
Sbjct: 402 HHYRVDSAKAGSIIGIALKGVEKEELERGMVLSAGADPKAVREFDAEVLVLRHP-----T 456
Query: 356 PITSKYIQQMFSRTWNVQVRLDLPGEDDGMLMPGEHGTVTMTLLYK-MYLSKGQTFTIRE 414
I + Y T V + D G LMPG+ G V M Y+ ++ +GQ F RE
Sbjct: 457 TIRAGYEPVFHYETIREAVYFE--EIDKGFLMPGDRGVVRMRFKYRPHHVEEGQKFVFRE 514
Query: 415 N-NKLVATGIVTKVL 428
+K V G V +V
Sbjct: 515 GRSKGV--GRVIRVD 527
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 132 bits (334), Expect = 4e-34
Identities = 100/344 (29%), Positives = 161/344 (46%), Gaps = 62/344 (18%)
Query: 37 ASSKSSLVHCNVGTIGHVDHGKTTLT---------------AAITKVAAKIGKSKFITFD 81
KS L T G VD GK+TL A++ + + + G +
Sbjct: 1 QQHKSLL---RFITCGSVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGT----QGE 53
Query: 82 QIDRA------PEEKARGITINIAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGA 135
+ID A E+ +GITI++A+ +ST R + D PGH Y +NM +GAS D A
Sbjct: 54 KIDLALLVDGLEAEREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTADLA 113
Query: 136 IVVVAASEGQMPQTREHLLLSKQIGIDNVVVYVNKADLVD--REIMELVELEVRDVLTAY 193
I++V A +G + QTR H ++ +GI +VVV VNK DLVD E+ E + +
Sbjct: 114 ILLVDARKGVLEQTRRHSFIASLLGIRHVVVAVNKMDLVDYSEEVFEAIVADYLAFAAQL 173
Query: 194 GYDGDNTPFVFGSALLALQGD----SSEL-----GEPSIHRLLDALDKHIPNPVRDITS- 243
G + F+ SALL GD SE G P++ +L+ ++ D ++
Sbjct: 174 G--LKDVRFIPISALL---GDNVVSKSENMPWYKG-PTLLEILETVEI-----ADDRSAK 222
Query: 244 PFILPID--NAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFNSKFTCTISEIQVFQKKVS 301
F P+ N + RG GTI G++K DE +L S T + I F +++
Sbjct: 223 AFRFPVQYVNRPNLDFRGYA--GTIASGSVKVGDEVVVL--PSGKTSRVKRIVTFDGELA 278
Query: 302 EARAGDNVGVLL-RNVKLKQIERG-MLLAKADTLQMHNRYEAEI 343
+A AG+ V ++L + I RG +++A + + ++A++
Sbjct: 279 QASAGEAVTLVLADEI---DISRGDLIVAADAPPAVADAFDADV 319
>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 = 122 bits (309), Expect = 4e-34
Identities = 44/86 (51%), Positives = 63/86 (73%)
Query: 245 FILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFNSKFTCTISEIQVFQKKVSEAR 304
F++PI++ +PGRG+V G I++GTIK DE E++GF T++ I++F+K + EA
Sbjct: 1 FLMPIEDVFSIPGRGTVVTGRIERGTIKVGDEVEIVGFGETLKTTVTGIEMFRKTLDEAE 60
Query: 305 AGDNVGVLLRNVKLKQIERGMLLAKA 330
AGDNVGVLLR VK + +ERGM+LAK
Sbjct: 61 AGDNVGVLLRGVKREDVERGMVLAKP 86
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 130 bits (328), Expect = 1e-32
Identities = 82/235 (34%), Positives = 111/235 (47%), Gaps = 27/235 (11%)
Query: 50 TIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEY-STNTR 108
T GHVDHGKTTL AIT V A DR PEEK RG+TI++ + + + R
Sbjct: 5 TAGHVDHGKTTLLQAITGVNA-------------DRLPEEKKRGMTIDLGYAYWPQPDGR 51
Query: 109 HYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNVVVYV 168
D PGH ++ NM++G +D A++VVA +G M QTREHL + + G + V +
Sbjct: 52 VLGFIDVPGHEKFLSNMLAGVGGIDHALLVVACDDGVMAQTREHLAILQLTGNPMLTVAL 111
Query: 169 NKADLVDREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSIHRLLD 228
KAD VD + V +V+ VL YG+ + FV + + G ++ L
Sbjct: 112 TKADRVDEARIAEVRRQVKAVLREYGFA-EAKLFVTAA--------TEGRGIDALREHLL 162
Query: 229 ALDKHIPNPVRDITSPFILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFN 283
L + F L ID A V G G V GT G +K D L G N
Sbjct: 163 QLPEREHAAQHR----FRLAIDRAFTVKGAGLVVTGTALSGEVKVGDTLWLTGVN 213
>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 = 119 bits (300), Expect = 2e-31
Identities = 69/229 (30%), Positives = 96/229 (41%), Gaps = 69/229 (30%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIA------- 99
N+GTIGHV HGKTTL A++ V R EE R ITI +
Sbjct: 2 NIGTIGHVAHGKTTLVKALSGV-------------WTVRHKEELKRNITIKLGYANAKIY 48
Query: 100 ----------------HVEYSTNT----RHYAHTDCPGHADYIKNMISGASQMDGAIVVV 139
RH + DCPGH + M+SGA+ MDGA++++
Sbjct: 49 KCPNCGCPRPYDTPECECPGCGGETKLVRHVSFVDCPGHEILMATMLSGAAVMDGALLLI 108
Query: 140 AASEG-QMPQTREHLLLSKQIGIDNVVVYVNKADLVDRE--------IMELVELEVRDVL 190
AA+E PQT EHL + +G+ ++++ NK DLV E I E V+
Sbjct: 109 AANEPCPQPQTSEHLAALEIMGLKHIIILQNKIDLVKEEQALENYEQIKEFVK------- 161
Query: 191 TAYGYDGDNTPFVFGSALLALQGDSSELGEPSIHRLLDALDKHIPNPVR 239
G +N P + SA L + +I L + + K IP P R
Sbjct: 162 ---GTIAENAPIIPISAQL----------KYNIDVLCEYIVKKIPTPPR 197
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 122 bits (309), Expect = 5e-30
Identities = 89/292 (30%), Positives = 133/292 (45%), Gaps = 49/292 (16%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPE--------EKARGITINI 98
N+ I HVDHGKTTL A+ K + TF + + E EK RGITI
Sbjct: 7 NIAIIAHVDHGKTTLVDALLKQSG--------TFREREEVAERVMDSNDLEKERGITI-- 56
Query: 99 AHVEYSTNTR-HYAHT-----DCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREH 152
+ NT +Y T D PGHAD+ + S +DG +++V ASEG MPQTR
Sbjct: 57 ----LAKNTAVNYNGTRINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTR-- 110
Query: 153 LLLSKQIGID-NVVVYVNKADLVDREIMELVELEVRDVLTAYGYDGD--NTPFVFGSALL 209
+L K + + +V +NK D D E+V+ EV D+ G + + P V+ SA
Sbjct: 111 FVLKKALALGLKPIVVINKIDRPDARPDEVVD-EVFDLFVELGATDEQLDFPIVYASARN 169
Query: 210 ALQGDSSELGEPSIHRLLDALDKHIPNPVRDITSPF-----ILPIDNAIGVPGRGSVCIG 264
E + L + + H+P P D+ P L ++ +G G IG
Sbjct: 170 GTASLDPEDEADDMAPLFETILDHVPAPKGDLDEPLQMQVTQLDYNSYVGRIG-----IG 224
Query: 265 TIKQGTIKRNDEAELLGFN-SKFTCTISEIQVFQ----KKVSEARAGDNVGV 311
I +GT+K N + L+ + + I+++ F ++ EA AGD V +
Sbjct: 225 RIFRGTVKPNQQVALIKSDGTTENGRITKLLGFLGLERIEIEEAEAGDIVAI 276
>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 = 114 bits (287), Expect = 2e-29
Identities = 66/198 (33%), Positives = 100/198 (50%), Gaps = 36/198 (18%)
Query: 50 TIGHVDHGKTTL-------TAAIT--KVAA-KIGKSKFITFDQIDRA------PEEKARG 93
T G VD GK+TL + +I ++AA + KS +++D A E+ +G
Sbjct: 4 TCGSVDDGKSTLIGRLLYDSKSIFEDQLAALERSKSSGTQGEKLDLALLVDGLQAEREQG 63
Query: 94 ITINIAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHL 153
ITI++A+ +ST R + D PGH Y +NM++GAS D AI++V A +G + QTR H
Sbjct: 64 ITIDVAYRYFSTPKRKFIIADTPGHEQYTRNMVTGASTADLAILLVDARKGVLEQTRRHS 123
Query: 154 LLSKQIGIDNVVVYVNKADLVD--REIMELVELEVRDVLTAYGY-----------DGDN- 199
++ +GI +VVV VNK DLVD E+ E ++ + + G +GDN
Sbjct: 124 YIASLLGIRHVVVAVNKMDLVDYDEEVFEEIKADYLAFAASLGIEDITFIPISALEGDNV 183
Query: 200 ------TPFVFGSALLAL 211
P+ G LL
Sbjct: 184 VSRSENMPWYKGPTLLEH 201
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 115 bits (291), Expect = 4e-28
Identities = 86/291 (29%), Positives = 130/291 (44%), Gaps = 73/291 (25%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVE---- 102
N+GTIGHV HGK+T+ A++ V + R EK R ITI + +
Sbjct: 36 NIGTIGHVAHGKSTVVKALSGV-------------KTVRFKREKVRNITIKLGYANAKIY 82
Query: 103 -------------YSTNT----------------RHYAHTDCPGHADYIKNMISGASQMD 133
Y ++ RH + DCPGH + M++GA+ MD
Sbjct: 83 KCPKCPRPTCYQSYGSSKPDNPPCPGCGHKMTLKRHVSFVDCPGHDILMATMLNGAAVMD 142
Query: 134 GAIVVVAASEG-QMPQTREHLLLSKQIGIDNVVVYVNKADLVDREIMELVELEVRDVLTA 192
A++++AA+E PQT EHL + + + ++++ NK DLV + E+R+ +
Sbjct: 143 AALLLIAANESCPQPQTSEHLAAVEIMKLKHIIILQNKIDLVKEAQAQDQYEEIRNFVK- 201
Query: 193 YGYDGDNTPFVFGSALLALQGDSSELGEPSIHRLLDALDKHIPNPVRDITSPFILPIDNA 252
G DN P + SA L +I +L+ + IP P RD+TSP + + +
Sbjct: 202 -GTIADNAPIIPISAQLKY----------NIDVVLEYICTQIPIPKRDLTSPPRMIVIRS 250
Query: 253 IGV--PG------RGSVCIGTIKQGTIKRNDEAELL-GFNSK-----FTCT 289
V PG +G V G+I QG +K DE E+ G SK FTC
Sbjct: 251 FDVNKPGEDIENLKGGVAGGSILQGVLKVGDEIEIRPGIISKDSGGEFTCR 301
>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 = 114 bits (288), Expect = 2e-27
Identities = 91/290 (31%), Positives = 137/290 (47%), Gaps = 45/290 (15%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPE--------EKARGITINI 98
N+ I HVDHGKTTL A+ K + TF + E E+ RGITI
Sbjct: 3 NIAIIAHVDHGKTTLVDALLKQSG--------TFRANEAVAERVMDSNDLERERGITI-- 52
Query: 99 AHVEYSTNTR-HYAHT-----DCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREH 152
+ NT Y T D PGHAD+ + +DG +++V ASEG MPQTR
Sbjct: 53 ----LAKNTAIRYNGTKINIVDTPGHADFGGEVERVLGMVDGVLLLVDASEGPMPQTR-- 106
Query: 153 LLLSKQIGID-NVVVYVNKADLVDREIMELVELEVRDVLTAYGYDGD--NTPFVFGSALL 209
+L K + + +V +NK D E+V+ EV D+ G D + + P V+ S
Sbjct: 107 FVLKKALELGLKPIVVINKIDRPSARPDEVVD-EVFDLFAELGADDEQLDFPIVYAS--- 162
Query: 210 ALQG-DSSELGEPS--IHRLLDALDKHIPNPVRDITSPFILPIDNAIGVPGRGSVCIGTI 266
G S +L +PS + L DA+ +H+P P D+ P + + N G + IG +
Sbjct: 163 GRAGWASLDLDDPSDNMAPLFDAIVRHVPAPKGDLDEPLQMLVTNLDYDEYLGRIAIGRV 222
Query: 267 KQGTIKRNDEAELLGFN-SKFTCTISEIQVFQ----KKVSEARAGDNVGV 311
+GT+K+ + L+ + + IS++ F+ ++ EA AGD V V
Sbjct: 223 HRGTVKKGQQVALMKRDGTIENGRISKLLGFEGLERVEIDEAGAGDIVAV 272
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 113 bits (284), Expect = 9e-27
Identities = 95/340 (27%), Positives = 155/340 (45%), Gaps = 77/340 (22%)
Query: 50 TIGHVDHGKTTLT---------------AAITKVAAKIGKSKFITFDQIDRA------PE 88
T G VD GK+TL AA+ + + K+G D+ID A
Sbjct: 29 TCGSVDDGKSTLIGRLLYDSKMIFEDQLAALERDSKKVGT----QGDEIDLALLVDGLAA 84
Query: 89 EKARGITINIAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQ 148
E+ +GITI++A+ ++T R + D PGH Y +NM++GAS D AI++V A +G + Q
Sbjct: 85 EREQGITIDVAYRYFATPKRKFIVADTPGHEQYTRNMVTGASTADLAIILVDARKGVLTQ 144
Query: 149 TREHLLLSKQIGIDNVVVYVNKADLVD--REIMELV---------ELEVRDV----LTAY 193
TR H ++ +GI +VV+ VNK DLVD +E+ + + +L + DV ++A
Sbjct: 145 TRRHSFIASLLGIRHVVLAVNKMDLVDYDQEVFDEIVADYRAFAAKLGLHDVTFIPISAL 204
Query: 194 GYD-----GDNTPFVFGSALLALQGDSSELGEPSIHRLLDALDKHIPNPVRDITSPFILP 248
D P+ G +LL L+ + I + F P
Sbjct: 205 KGDNVVTRSARMPWYEGPSLLE---------------HLETV--EIASDRNLK--DFRFP 245
Query: 249 ID--NAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFNSKFTCTISEIQVFQKKVSEARAG 306
+ N + RG GT+ G ++ DE +L S T + I + EA AG
Sbjct: 246 VQYVNRPNLDFRGFA--GTVASGVVRPGDEVVVL--PSGKTSRVKRIVTPDGDLDEAFAG 301
Query: 307 DNVGVLLRNVKLKQIE--RGMLLAKADTL-QMHNRYEAEI 343
V + L + +I+ RG +LA+AD ++ ++++A +
Sbjct: 302 QAVTLTLAD----EIDISRGDMLARADNRPEVADQFDATV 337
>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 = 110 bits (278), Expect = 1e-26
Identities = 98/319 (30%), Positives = 149/319 (46%), Gaps = 60/319 (18%)
Query: 50 TIGHVDHGKTTLT---------------AAITKVAAKIGKSKFITFDQIDRA------PE 88
T G VD GK+TL AA+ + + K G +ID A
Sbjct: 5 TCGSVDDGKSTLIGRLLHDTKQIYEDQLAALERDSKKHGT----QGGEIDLALLVDGLQA 60
Query: 89 EKARGITINIAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQ 148
E+ +GITI++A+ +ST+ R + D PGH Y +NM +GAS D A+++V A +G + Q
Sbjct: 61 EREQGITIDVAYRYFSTDKRKFIVADTPGHEQYTRNMATGASTADLAVLLVDARKGVLEQ 120
Query: 149 TREHLLLSKQIGIDNVVVYVNKADLV--DREIMELVELEVRDVLTAYGYDGDNTPFVFGS 206
TR H ++ +GI +VV+ VNK DLV D E+ E ++ + G F
Sbjct: 121 TRRHSYIASLLGIRHVVLAVNKMDLVDYDEEVFENIKKDYLAFAEQLG----FRDVTF-I 175
Query: 207 ALLALQGDSSELGEPSIH-------RLLDALDK-HIPNPVRDITSPFILPID--NAIGVP 256
L AL+GD+ + S LL+ L+ + +D P P+ N +
Sbjct: 176 PLSALKGDN--VVSRSESMPWYSGPTLLEILETVEVERDAQD--LPLRFPVQYVNRPNLD 231
Query: 257 GRGSVCIGTIKQGTIKRNDEAELL--GFNSKFTCTISEIQVFQKKVSEARAGDNVGVLLR 314
RG GTI G++ DE +L G +S+ ++ I F + +ARAG V + L
Sbjct: 232 FRGYA--GTIASGSVHVGDEVVVLPSGRSSR----VARIVTFDGDLEQARAGQAVTLTLD 285
Query: 315 NVKLKQIE--RGMLLAKAD 331
+ +I+ RG LLA AD
Sbjct: 286 D----EIDISRGDLLAAAD 300
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 107 bits (270), Expect = 3e-25
Identities = 100/331 (30%), Positives = 149/331 (45%), Gaps = 58/331 (17%)
Query: 50 TIGHVDHGKTTLT---------------AAITKVAAKIGKSKFITFDQIDRA------PE 88
T G VD GK+TL A++ + + G +++D A
Sbjct: 32 TCGSVDDGKSTLIGRLLHDTKQIYEDQLASLHNDSKRHGT----QGEKLDLALLVDGLQA 87
Query: 89 EKARGITINIAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQ 148
E+ +GITI++A+ +ST R + D PGH Y +NM +GAS D AI+++ A +G + Q
Sbjct: 88 EREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTCDLAILLIDARKGVLDQ 147
Query: 149 TREHLLLSKQIGIDNVVVYVNKADLVD--REIMELVELEVRDVLTAYGYDGDNTPFVFGS 206
TR H ++ +GI ++VV VNK DLVD E+ E + + + D FV
Sbjct: 148 TRRHSFIATLLGIKHLVVAVNKMDLVDYSEEVFERIREDYLTFAEQLPGNLDIR-FV--- 203
Query: 207 ALLALQGDS----SEL-----GEPSIHRLLDALDK-HIPNPVRDITSPFILPID--NAIG 254
L AL+GD+ SE G LL+ L+ I V PF P+ N
Sbjct: 204 PLSALEGDNVVSQSESMPWYSGPT----LLEVLETVDIQRVVD--AQPFRFPVQYVNRPN 257
Query: 255 VPGRGSVCIGTIKQGTIKRNDEAELLGFNSKFTCTISEIQVFQKKVSEARAGDNVG-VLL 313
+ RG GT+ G +K D ++L S ++ I F + EA AG+ + VL
Sbjct: 258 LDFRGYA--GTLASGVVKVGDRVKVL--PSGKESNVARIVTFDGDLEEAFAGEAITLVLE 313
Query: 314 RNVKLKQIERGMLLAKAD-TLQMHNRYEAEI 343
+ I RG LL AD LQ A++
Sbjct: 314 DEI---DISRGDLLVAADEALQAVQHASADV 341
>gnl|CDD|239678 cd03707, EFTU_III, Domain III of elongation factor (EF) Tu. Ef-Tu
consists of three structural domains, designated I, II
and III. Domain III adopts a beta barrel structure.
Domain III is involved in binding to both charged tRNA
and binding to elongation factor Ts (EF-Ts). EF-Ts is
the guanine-nucleotide-exchange factor for EF-Tu. EF-Tu
and EF-G participate in the elongation phase during
protein biosynthesis on the ribosome. Their functional
cycles depend on GTP binding and its hydrolysis. The
EF-Tu complexed with GTP and aminoacyl-tRNA delivers
tRNA to the ribosome, whereas EF-G stimulates
translocation, a process in which tRNA and mRNA
movements occur in the ribosome. Crystallographic
studies revealed structural similarities ("molecular
mimicry") between tertiary structures of EF-G and the
EF-Tu-aminoacyl-tRNA ternary complex. Domains III, IV,
and V of EF-G mimic the tRNA structure in the EF-Tu
ternary complex; domains III, IV and V can be related to
the acceptor stem, anticodon helix and T stem of tRNA
respectively.
Length = 90
Score = 98.0 bits (245), Expect = 6e-25
Identities = 36/91 (39%), Positives = 57/91 (62%), Gaps = 1/91 (1%)
Query: 334 QMHNRYEAEIYLLSKAEGGRYKPITSKYIQQMFSRTWNVQVRLDLPGEDDGMLMPGEHGT 393
+ H ++EAE+Y+L+K EGGR+ P S Y Q + RT +V + LP E M+MPG++
Sbjct: 1 KPHTKFEAEVYVLTKEEGGRHTPFFSGYRPQFYIRTTDVTGSITLP-EGTEMVMPGDNVK 59
Query: 394 VTMTLLYKMYLSKGQTFTIRENNKLVATGIV 424
+T+ L++ + L KG F IRE + V G++
Sbjct: 60 MTVELIHPIALEKGLRFAIREGGRTVGAGVI 90
>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 = 100 bits (252), Expect = 7e-25
Identities = 64/209 (30%), Positives = 98/209 (46%), Gaps = 34/209 (16%)
Query: 46 CNVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQI-DRAPEEKARGITINIAHVEYS 104
N+ I HVDHGKTTL A+ K + + +++ D E+ RGITI +
Sbjct: 3 RNIAIIAHVDHGKTTLVDALLK-QSGTFRENEEVGERVMDSNDLERERGITI------LA 55
Query: 105 TNTR-HYAHT-----DCPGHADY------IKNMISGASQMDGAIVVVAASEGQMPQTREH 152
NT Y T D PGHAD+ + +M+ DG +++V ASEG MPQTR
Sbjct: 56 KNTAITYKDTKINIIDTPGHADFGGEVERVLSMV------DGVLLLVDASEGPMPQTR-- 107
Query: 153 LLLSK--QIGIDNVVVYVNKADLVDREIMELVELEVRDVLTAYGYDGD--NTPFVFGSAL 208
+L K + G+ +V +NK D D E+V+ EV D+ + + P V+ SA
Sbjct: 108 FVLKKALEAGL-KPIVVINKIDRPDARPEEVVD-EVFDLFLELNATDEQLDFPIVYASAK 165
Query: 209 LALQGDSSELGEPSIHRLLDALDKHIPNP 237
+ + + L + + +H+P P
Sbjct: 166 NGWASLNLDDPSEDLDPLFETIIEHVPAP 194
>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 = 100 bits (251), Expect = 9e-25
Identities = 52/158 (32%), Positives = 86/158 (54%), Gaps = 24/158 (15%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINI-------- 98
NVG +GHVD GKT+L A++++A+ + F D+ P+ + RGIT+++
Sbjct: 2 NVGLLGHVDSGKTSLAKALSEIAST---AAF------DKNPQSQERGITLDLGFSSFEVD 52
Query: 99 --AHVEYSTNTRH--YAHT--DCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREH 152
H+E + N + Y T DCPGHA I+ +I GA +D ++VV A +G QT E
Sbjct: 53 KPKHLEDNENPQIENYQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDAKKGIQTQTAEC 112
Query: 153 LLLSKQIGIDNVVVYVNKADLVDREIMELVELEVRDVL 190
L++ + + +VV +NK DL+ E + +++ L
Sbjct: 113 LVIGELLCKPLIVV-LNKIDLIPEEERKRKIEKMKKRL 149
>gnl|CDD|217387 pfam03143, GTP_EFTU_D3, Elongation factor Tu C-terminal domain.
Elongation factor Tu consists of three structural
domains, this is the third domain. This domain adopts a
beta barrel structure. This the third domain is involved
in binding to both charged tRNA and binding to EF-Ts
pfam00889.
Length = 91
Score = 87.2 bits (217), Expect = 4e-21
Identities = 32/93 (34%), Positives = 55/93 (59%), Gaps = 6/93 (6%)
Query: 336 HNRYEAEIYLLSKAEGGRYKPITSKYIQQMFSRTWNVQVRLDLPGEDDGMLMPGEHGTVT 395
H +++A++Y+L+ PI + Y + T +V + LPG+ + +MPG++ VT
Sbjct: 5 HTKFKAQVYILNH-----PTPIFNGYRPVFYCHTADVTGKFILPGKKE-FVMPGDNAIVT 58
Query: 396 MTLLYKMYLSKGQTFTIRENNKLVATGIVTKVL 428
+ L+ + + KGQ F IRE + VA G+VT+VL
Sbjct: 59 VELIKPIAVEKGQRFAIREGGRTVAVGVVTEVL 91
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 95.0 bits (237), Expect = 1e-20
Identities = 48/153 (31%), Positives = 71/153 (46%), Gaps = 13/153 (8%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFIT--FDQIDRAPEEKARGITINIAHV-EY 103
N+G + H+D GKTTLT I I K + +D +E+ RGITI A +
Sbjct: 12 NIGIVAHIDAGKTTLTERILFYTGIISKIGEVHDGAATMDWMEQEQERGITITSAATTLF 71
Query: 104 STNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDN 163
D PGH D+ + +DGA+VVV A EG PQT + +Q
Sbjct: 72 WKGDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVEGVEPQTE---TVWRQADKYG 128
Query: 164 V--VVYVNKADLVDREIMEL--VELEVRDVLTA 192
V +++VNK +DR + V ++++ L A
Sbjct: 129 VPRILFVNK---MDRLGADFYLVVEQLKERLGA 158
Score = 43.8 bits (104), Expect = 2e-04
Identities = 42/192 (21%), Positives = 66/192 (34%), Gaps = 57/192 (29%)
Query: 175 DREIMELV-------ELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSIHRLL 227
D E+ME E E++ L G P + GSA + LL
Sbjct: 221 DEELMEKYLEGEEPTEEEIKKALRKGTIAGKIVPVLCGSAF----------KNKGVQPLL 270
Query: 228 DALDKHIPNPVRDITSPFILPIDNAIGV----------------------PGRGSVCIGT 265
DA+ ++P+P+ D+ P +D+ I P G +
Sbjct: 271 DAVVDYLPSPL-DVP-PIKGDLDDEIEKAVLRKASDEGPLSALVFKIMTDPFVGKLTFVR 328
Query: 266 IKQGTIKRNDEAELLGFNSKFTCTISEIQVF----QKKVSEARAGDNVGVLLRNVKLKQI 321
+ GT+K E+L + + + +++V E AGD V + V LK
Sbjct: 329 VYSGTLKSGS--EVLNSTKGKKERVGRLLLMHGNEREEVDEVPAGDIVAL----VGLKDA 382
Query: 322 ERGMLLAKADTL 333
G DTL
Sbjct: 383 TTG------DTL 388
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 94.5 bits (236), Expect = 1e-20
Identities = 95/328 (28%), Positives = 137/328 (41%), Gaps = 107/328 (32%)
Query: 47 NVGTIGHVDHGKTTLT-----AA--ITKVAAKIGKSKFITFDQIDRAPEEKARGITINIA 99
N+G I H+DHGKTTL+ A I++ A G+ + FD EE+ARGITI A
Sbjct: 22 NIGIIAHIDHGKTTLSDNLLAGAGMISEELA--GEQLALDFD-----EEEQARGITIKAA 74
Query: 100 HV---------EYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTR 150
+V EY N D PGH D+ ++ +DGAIVVV A EG MPQT
Sbjct: 75 NVSMVHEYEGKEYLINL-----IDTPGHVDFGGDVTRAMRAVDGAIVVVDAVEGVMPQT- 128
Query: 151 EHLLLSKQIGIDNV--VVYVNKADLVDREIMEL-------------VELEVRDVLTAYG- 194
E +L +Q + V V+++NK VDR I EL + +V ++
Sbjct: 129 ETVL--RQALRERVKPVLFINK---VDRLIKELKLTPQEMQQRLLKIIKDVNKLIKGMAP 183
Query: 195 --------YDGDNTPFVFGSAL----------------------LALQGDSSELGEPS-I 223
D ++ FGSAL +G EL E + +
Sbjct: 184 EEFKEKWKVDVEDGTVAFGSALYNWAISVPMMQKTGIKFKDIIDYYEKGKQKELAEKAPL 243
Query: 224 HR-LLDALDKHIPNPVR------------DITS-------------PFILPIDNAIGVPG 257
H +LD + KH+PNP+ D+ S P ++ + + I P
Sbjct: 244 HEVVLDMVVKHLPNPIEAQKYRIPKIWKGDLNSEVGKAMLNCDPNGPLVMMVTDIIVDPH 303
Query: 258 RGSVCIGTIKQGTIKRNDEAELLGFNSK 285
G V G + GT+++ E L+G K
Sbjct: 304 AGEVATGRVFSGTLRKGQEVYLVGAKKK 331
>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 = 93.0 bits (231), Expect = 5e-20
Identities = 96/352 (27%), Positives = 147/352 (41%), Gaps = 99/352 (28%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKI-----GKSKFITFDQIDRAPEEKARGITINIAHV 101
N+G + H+DHGKTTL+ + A I G+ ++ FD+ +E+ RGITIN A+V
Sbjct: 21 NIGIVAHIDHGKTTLSDNLLAGAGMISEELAGQQLYLDFDE-----QEQERGITINAANV 75
Query: 102 ----EYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSK 157
EY N D PGH D+ ++ +DGAIVVV A EG MPQT L +
Sbjct: 76 SMVHEYEGNEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVCAVEGVMPQTETVL---R 132
Query: 158 QIGIDNV--VVYVNKADLVDREIMEL----VELEVRDV------------------LTAY 193
Q +NV V+++NK VDR I EL EL+ R + +
Sbjct: 133 QALKENVKPVLFINK---VDRLINELKLTPQELQERFIKIITEVNKLIKAMAPEEFRDKW 189
Query: 194 GYDGDNTPFVFGSAL----------------------LALQGDSSELGEPS-IHR-LLDA 229
++ FGSA + EL + S +H+ +LD
Sbjct: 190 KVRVEDGSVAFGSAYYNWAISVPSMKKTGIGFKDIYKYCKEDKQKELAKKSPLHQVVLDM 249
Query: 230 LDKHIPNPVR------------DITS-------------PFILPIDNAIGVPGRGSVCIG 264
+ +H+P+P+ D+ S P L I + G V +G
Sbjct: 250 VIRHLPSPIEAQKYRIPVIWKGDLNSEVGKAMLNCDPKGPLALMITKIVVDKHAGEVAVG 309
Query: 265 TIKQGTIKRNDEAELLGFNSKFTCTISEIQVF----QKKVSEARAGDNVGVL 312
+ GTI+ E ++ +K I ++ V+ + +V E AG+ V V+
Sbjct: 310 RLYSGTIRPGMEVYIVDRKAK--ARIQQVGVYMGPERVEVDEIPAGNIVAVI 359
>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 = 82.1 bits (204), Expect = 2e-19
Identities = 34/85 (40%), Positives = 47/85 (55%), Gaps = 2/85 (2%)
Query: 245 FILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFNSKFTCTISEIQVFQKKVSEAR 304
F LPID V G+G+V GT+ G++K D+ E+L + IQV K V EA+
Sbjct: 1 FRLPIDRVFTVKGQGTVVTGTVLSGSVKVGDKVEILP--LGEETRVRSIQVHGKDVEEAK 58
Query: 305 AGDNVGVLLRNVKLKQIERGMLLAK 329
AGD V + L V K +ERG +L+
Sbjct: 59 AGDRVALNLTGVDAKDLERGDVLSS 83
>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 = 83.4 bits (207), Expect = 2e-18
Identities = 51/152 (33%), Positives = 74/152 (48%), Gaps = 29/152 (19%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKI------GKSKFITFDQIDRAPEEKARGITI---N 97
N+ I HVDHGKTTL+ ++ +A I GK++++ +E+ RGITI
Sbjct: 2 NICIIAHVDHGKTTLSDSLL-ASAGIISEKLAGKARYLDTR-----EDEQERGITIKSSA 55
Query: 98 IA-HVEYSTNTRHYAH-----TDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTRE 151
I+ + EY D PGH D+ + + DGA+VVV A EG QT
Sbjct: 56 ISLYFEYEEEKMDGNDYLINLIDSPGHVDFSSEVTAALRLTDGALVVVDAVEGVCVQTET 115
Query: 152 HLLLSKQIGIDNV--VVYVNKADLVDREIMEL 181
L +Q + V V+ +NK +DR I+EL
Sbjct: 116 VL---RQALEERVKPVLVINK---IDRLILEL 141
>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 = 87.0 bits (216), Expect = 3e-18
Identities = 78/305 (25%), Positives = 137/305 (44%), Gaps = 44/305 (14%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQI-DRAPEEKARGITIN-----IAH 100
N I H+DHGK+TL + + I + + +Q+ D E+ RGITI + +
Sbjct: 5 NFSIIAHIDHGKSTLADRLLEYTGAISEREMR--EQVLDSMDLERERGITIKAQAVRLNY 62
Query: 101 VEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIG 160
T D PGH D+ + + +GA+++V A++G QT ++ L+
Sbjct: 63 KAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLLVDAAQGIEAQTLANVYLA---- 118
Query: 161 IDN---VVVYVNKADLVDREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSE 217
++N ++ +NK DL + E V+ E+ +V+ G D A+LA S++
Sbjct: 119 LENDLEIIPVINKIDLPSADP-ERVKKEIEEVI---GLDA-------SEAILA----SAK 163
Query: 218 LGEPSIHRLLDALDKHIPNPVRDITSPFILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEA 277
G I +L+A+ K +P P D +P I ++ RG V + + +GTIK D+
Sbjct: 164 TGI-GIEEILEAIVKRVPPPKGDPDAPLKALIFDSHYDNYRGVVALVRVFEGTIKPGDKI 222
Query: 278 ELLGFNSKFTCTISEIQVF---QKKVSEARAGDNVGVLLRNVK-LKQIERGMLLAKADTL 333
+ ++ + E+ VF K E AG+ VG ++ +K + + G DT+
Sbjct: 223 RFMSTGKEY--EVDEVGVFTPKLTKTDELSAGE-VGYIIAGIKDVSDVRVG------DTI 273
Query: 334 QMHNR 338
Sbjct: 274 THVKN 278
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 86.3 bits (213), Expect = 6e-18
Identities = 75/252 (29%), Positives = 110/252 (43%), Gaps = 26/252 (10%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYSTN 106
N+ I HVDHGKTTL + + + +D EK RGITI + N
Sbjct: 7 NIAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNTAIKWN 66
Query: 107 TRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNVVV 166
D PGHAD+ + S +D ++VV A +G MPQTR + G+ +VV
Sbjct: 67 DYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPIVV 126
Query: 167 YVNKAD--------LVDREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSEL 218
+NK D +VD+ V L+ D + P V+ SAL + G E
Sbjct: 127 -INKVDRPGARPDWVVDQVFDLFVNLDATDEQLDF-------PIVYASALNGIAGLDHED 178
Query: 219 GEPSIHRLLDALDKHIPNPVRDITSPFILPI-----DNAIGVPGRGSVCIGTIKQGTIKR 273
+ L A+ H+P P D+ PF + I ++ +GV G IG IK+G +K
Sbjct: 179 MAEDMTPLYQAIVDHVPAPDVDLDGPFQMQISQLDYNSYVGVIG-----IGRIKRGKVKP 233
Query: 274 NDEAELLGFNSK 285
N + ++ K
Sbjct: 234 NQQVTIIDSEGK 245
>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 = 80.6 bits (200), Expect = 7e-18
Identities = 56/166 (33%), Positives = 72/166 (43%), Gaps = 31/166 (18%)
Query: 52 GHVDHGKTTLTAAI--TKVAAKIGKSKFITFDQIDRAPEEKARGITINIA--HVEYSTNT 107
GHVDHGKTTL I T VAA +A GIT +I V
Sbjct: 7 GHVDHGKTTLLDKIRKTNVAAG------------------EAGGITQHIGAYQVPIDVKI 48
Query: 108 RHYAHTDCPGHADYIKNMIS-GASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNVVV 166
D PGH + NM + GAS D AI+VVAA +G MPQT E + +K + ++V
Sbjct: 49 PGITFIDTPGHEAF-TNMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAANVP-IIV 106
Query: 167 YVNKADLVDREIMELVELEVRDVLTAYGYDGDN----TPFVFGSAL 208
+NK D E V++ L+ G G+ V SA
Sbjct: 107 AINKIDKP-YGTEADPE-RVKNELSELGLVGEEWGGDVSIVPISAK 150
>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 = 76.9 bits (190), Expect = 6e-16
Identities = 48/157 (30%), Positives = 80/157 (50%), Gaps = 22/157 (14%)
Query: 47 NVGTIGHVDHGKTTLTAAI---TKVAAKIG----KSKFITFDQIDRAPEEKARGITINIA 99
N+G + HVD GKTTLT ++ + ++G + ++ E+ RGITI A
Sbjct: 1 NIGILAHVDAGKTTLTESLLYTSGAIRELGSVDKGTTRTDSMEL-----ERQRGITIFSA 55
Query: 100 HVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTRE--HLLLSK 157
+ D PGH D+I + S +DGAI+V++A EG QTR LL +
Sbjct: 56 VASFQWEDTKVNIIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTRILFRLL--R 113
Query: 158 QIGIDNVVVYVNKADLVDREIMELVEL--EVRDVLTA 192
++ I +++VNK +DR +L ++ E+++ L+
Sbjct: 114 KLNIP-TIIFVNK---IDRAGADLEKVYQEIKEKLSP 146
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 79.1 bits (196), Expect = 1e-15
Identities = 86/257 (33%), Positives = 106/257 (41%), Gaps = 87/257 (33%)
Query: 50 TI-GHVDHGKTTLTAAI--TKVAAKIGKSKFITFDQIDRAPEEKARGITINIA--HVEYS 104
TI GHVDHGKT+L AI T VAA +A GIT +I VE
Sbjct: 253 TIMGHVDHGKTSLLDAIRKTNVAAG------------------EAGGITQHIGAYQVE-- 292
Query: 105 TNTRHYAHTDCPGHADYIKNMIS-GASQMDGAIVVVAASEGQMPQTRE---HLLLSKQIG 160
TN D PGH + M + GA D ++VVAA +G MPQT E H +K G
Sbjct: 293 TNGGKITFLDTPGHEAFTA-MRARGAQVTDIVVLVVAADDGVMPQTIEAINH---AKAAG 348
Query: 161 IDNVVVYVNKADL----VDREIMELVELEVRDVLTAYGYDGDNTPFVFGSA--------L 208
+ ++V +NK D DR EL E + V +G GD T FV SA L
Sbjct: 349 VP-IIVAINKIDKPGANPDRVKQELSEYGL--VPEEWG--GD-TIFVPVSAKTGEGIDEL 402
Query: 209 L---ALQGDSSELGEPSIHRLLDALDKHIPNPVRDITSPFILPIDNAIGV-------PGR 258
L LQ +E+ E L A NP R A G GR
Sbjct: 403 LEAILLQ---AEVLE------LKA------NPDRP-----------ARGTVIEAKLDKGR 436
Query: 259 GSVCIGTIKQGTIKRND 275
G V ++ GT+K D
Sbjct: 437 GPVATVLVQNGTLKVGD 453
>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 = 71.2 bits (175), Expect = 2e-15
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 2/85 (2%)
Query: 245 FILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFNSKFTCTISEIQVFQKKVSEAR 304
+ GRG+V G ++ GT+K+ D+ + + ++ F+ +V EA
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRFKGEVDEAV 60
Query: 305 AGDNVGVLLRNVKLKQIERGMLLAK 329
AGD VG++L++ I+ G L
Sbjct: 61 AGDIVGIVLKDK--DDIKIGDTLTD 83
>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 = 77.9 bits (192), Expect = 2e-15
Identities = 79/244 (32%), Positives = 106/244 (43%), Gaps = 56/244 (22%)
Query: 48 VGTI-GHVDHGKTTLTAAI--TKVAAKIGKSKFITFDQIDRAPEEKARGITINIA--HVE 102
V TI GHVDHGKT+L +I TKVA +A GIT +I HVE
Sbjct: 89 VVTIMGHVDHGKTSLLDSIRKTKVAQG------------------EAGGITQHIGAYHVE 130
Query: 103 YSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGID 162
+ D PGH + GA D ++VVAA +G MPQT E + +K +
Sbjct: 131 NEDG-KMITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVP 189
Query: 163 NVVVYVNKADL----VDREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSEL 218
++V +NK D DR EL E + V +G D T FV S AL GD
Sbjct: 190 -IIVAINKIDKPEANPDRVKQELSEYGL--VPEDWGGD---TIFVPVS---ALTGD---- 236
Query: 219 GEPSIHRLLDALDKHIPNPVRDITSPFILPIDNAIGV-------PGRGSVCIGTIKQGTI 271
I LLD + + + V ++ + P A GV GRG V ++ GT+
Sbjct: 237 ---GIDELLDMI--LLQSEVEELKA---NPNGQASGVVIEAQLDKGRGPVATVLVQSGTL 288
Query: 272 KRND 275
+ D
Sbjct: 289 RVGD 292
Score = 28.6 bits (64), Expect = 8.4
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 255 VPGRGSVCIGTIKQGTIKRNDEAELLGFNSK-FTCTISEIQVFQKKVSEARAGDNVGVLL 313
VP G++ + +G IKR + ++ F I ++ F+ V E G G+ +
Sbjct: 503 VPKIGNIAGCYVTEGVIKRGNPLRVIRDGVVIFEGEIDSLKRFKDDVKEVSNGYECGIGI 562
Query: 314 RN 315
+N
Sbjct: 563 KN 564
>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 = 68.8 bits (169), Expect = 7e-15
Identities = 21/70 (30%), Positives = 39/70 (55%)
Query: 259 GSVCIGTIKQGTIKRNDEAELLGFNSKFTCTISEIQVFQKKVSEARAGDNVGVLLRNVKL 318
G+V G ++ GT+K+ D+ + + ++ +++F + EA AG N G++L + L
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGIGL 60
Query: 319 KQIERGMLLA 328
K I+RG L
Sbjct: 61 KDIKRGDTLT 70
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 75.3 bits (186), Expect = 1e-14
Identities = 76/245 (31%), Positives = 97/245 (39%), Gaps = 65/245 (26%)
Query: 52 GHVDHGKTTLTAAI--TKVAAKIGKSKFITFDQIDRAPEEKARGITINIA--HVEYSTNT 107
GHVDHGKTTL I T VAA +A GIT +I V
Sbjct: 12 GHVDHGKTTLLDKIRKTNVAAG------------------EAGGITQHIGAYQVPLDVIK 53
Query: 108 RH-YAHTDCPGHADYIKNMIS-GASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNVV 165
D PGH M + GAS D AI+VVAA +G MPQT E + +K G+ +V
Sbjct: 54 IPGITFIDTPGHE-AFTAMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAAGVP-IV 111
Query: 166 VYVNKADLV----DREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEP 221
V +NK D D+ EL E L + GD FV SA GE
Sbjct: 112 VAINKIDKPEANPDKVKQELQEYG----LVPEEWGGD-VIFVPVSAK---------TGE- 156
Query: 222 SIHRLLDAL----DKHIPNPVRDITSPFILPIDNAIGV-------PGRGSVCIGTIKQGT 270
I LL+ + + V ++ P A G G G V ++ GT
Sbjct: 157 GIDELLELILLLAE------VLELK---ANPEGPARGTVIEVKLDKGLGPVATVIVQDGT 207
Query: 271 IKRND 275
+K+ D
Sbjct: 208 LKKGD 212
Score = 30.2 bits (69), Expect = 2.7
Identities = 22/82 (26%), Positives = 32/82 (39%), Gaps = 18/82 (21%)
Query: 238 VRDITSPFILPIDNAI-GVPGRGSVCIGTIKQGT---IKRNDEAELLGFNSKFTCTISEI 293
VR + F LP AI G V G IK+G + R+ G + +
Sbjct: 418 VRAV---FKLPKVGAIAGCM----VTEGVIKRGAPVRVVRDGVVIYEG-------EVESL 463
Query: 294 QVFQKKVSEARAGDNVGVLLRN 315
+ F+ V E R G G+ + N
Sbjct: 464 KRFKDDVKEVRKGQECGIAIEN 485
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 74.1 bits (183), Expect = 4e-14
Identities = 74/287 (25%), Positives = 131/287 (45%), Gaps = 45/287 (15%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQI-DRAPEEKARGITI--NIAHVEY 103
N I H+DHGK+TL + ++ + + + Q+ D E+ RGITI + Y
Sbjct: 11 NFSIIAHIDHGKSTLADRLLELTGGLSEREMR--AQVLDSMDIERERGITIKAQAVRLNY 68
Query: 104 ---STNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIG 160
T D PGH D+ + + +GA++VV AS+G QT ++ L+
Sbjct: 69 KAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYLA---- 124
Query: 161 IDN---VVVYVNKADL----VDREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQG 213
++N ++ +NK DL +R V+ E+ D++ G D + V
Sbjct: 125 LENNLEIIPVLNKIDLPAADPER-----VKQEIEDII---GIDASDAVLV---------- 166
Query: 214 DSSELGEPSIHRLLDALDKHIPNPVRDITSPFILPIDNAIGVPGRGSVCIGTIKQGTIKR 273
S++ G I +L+A+ + IP P D +P I ++ G V + I GT+K+
Sbjct: 167 -SAKTGI-GIEDVLEAIVEKIPPPKGDPDAPLKALIFDSWYDNYLGVVVLVRIFDGTLKK 224
Query: 274 NDEAELLGFNSKFTCTISEIQVF---QKKVSEARAGDNVGVLLRNVK 317
D+ ++ ++ + E+ +F KV E +AG+ VG ++ +K
Sbjct: 225 GDKIRMMSTGKEY--EVDEVGIFTPKMVKVDELKAGE-VGYIIAGIK 268
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 73.6 bits (182), Expect = 7e-14
Identities = 44/132 (33%), Positives = 65/132 (49%), Gaps = 19/132 (14%)
Query: 51 IGHVDHGKTTLTAAI---TKVAAKIGKSKFITFDQ---IDRAPEEKARGITIN--IAHVE 102
+GH GKTTLT AI T +IG+ + D +D PEE+ RGI+I E
Sbjct: 1 VGHSGAGKTTLTEAILFYTGAIHRIGEVE----DGTTTMDFMPEERERGISITSAATTCE 56
Query: 103 YSTNTRHYAHT--DCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIG 160
+ + + D PGH D+ + +DGA+VVV A G PQT +++ G
Sbjct: 57 W----KGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGGVEPQTETVWRQAEKYG 112
Query: 161 IDNVVVYVNKAD 172
+ +++VNK D
Sbjct: 113 VP-RIIFVNKMD 123
Score = 41.6 bits (99), Expect = 8e-04
Identities = 46/191 (24%), Positives = 73/191 (38%), Gaps = 46/191 (24%)
Query: 172 DLVDR--EIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSIHRLLDA 229
+L+++ E EL E E++ L G+ P GSAL G + RLLDA
Sbjct: 207 ELMEKYLEGEELSEEEIKAGLRKATLAGEIVPVFCGSAL-------KNKG---VQRLLDA 256
Query: 230 LDKHIPNPVRDITSPFILPIDNAIGV--------------------PGRGSVCIGTIKQG 269
+ ++P+P + P + D G P G + + + G
Sbjct: 257 VVDYLPSP---LEVPPVDGEDGEEGAELAPDPDGPLVALVFKTMDDPFVGKLSLVRVYSG 313
Query: 270 TIKRNDEAELLGFNSKFTCTISEIQVF----QKKVSEARAGDNVGVLLRNVKLKQIERGM 325
T+K+ D L + + + +++V EA AGD V V KLK G
Sbjct: 314 TLKKGDT--LYNSGTGKKERVGRLYRMHGKQREEVDEAVAGDIVAV----AKLKDAATGD 367
Query: 326 LL-AKADTLQM 335
L K D + +
Sbjct: 368 TLCDKGDPILL 378
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 71.2 bits (175), Expect = 4e-13
Identities = 54/159 (33%), Positives = 75/159 (47%), Gaps = 42/159 (26%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKI-----GKSKFITFDQIDRAPEEKARGITINIAHV 101
N+ I HVDHGK+TLT ++ A I G ++F D +E+ RGITI
Sbjct: 21 NMSVIAHVDHGKSTLTDSLVCKAGIISSKNAGDARF-----TDTRADEQERGITIK---- 71
Query: 102 EYSTN-TRHYAHT---------------DCPGHADYIKNMISGASQMDGAIVVVAASEGQ 145
ST + +Y H D PGH D+ + + DGA+VVV EG
Sbjct: 72 --STGISLYYEHDLEDGDDKQPFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVEGV 129
Query: 146 MPQTREHLL---LSKQIGIDNVVVYVNKADLVDREIMEL 181
QT E +L L ++I V+++NK VDR I+EL
Sbjct: 130 CVQT-ETVLRQALQERI---RPVLFINK---VDRAILEL 161
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 70.8 bits (174), Expect = 6e-13
Identities = 48/156 (30%), Positives = 75/156 (48%), Gaps = 20/156 (12%)
Query: 47 NVGTIGHVDHGKTTLTAAI---TKVAAKIG---KSKFITFDQIDRAPEEKARGITINIAH 100
N+G + H+D GKTTLT I T K+G +T D P+E+ RGITI A
Sbjct: 10 NIGILAHIDAGKTTLTERILFYTGKIHKMGEVEDGTTVT----DWMPQEQERGITIESA- 64
Query: 101 VEYSTNTRHYAH----TDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLS 156
+T+ H D PGH D+ + +DGA+VV A G PQT +
Sbjct: 65 ---ATSCDWDNHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDAVTGVQPQTETVWRQA 121
Query: 157 KQIGIDNVVVYVNKADLVDREIMELVELEVRDVLTA 192
+ GI ++++NK D V ++ +++E ++ +
Sbjct: 122 DRYGIP-RLIFINKMDRVGADLFKVLE-DIEERFGK 155
>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 = 66.8 bits (164), Expect = 2e-12
Identities = 34/135 (25%), Positives = 61/135 (45%), Gaps = 17/135 (12%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDR-------APEEKARGITIN-- 97
N+ +GH GKTTL A+ I + +++ PEEK R ++I
Sbjct: 1 NIALVGHSGSGKTTLAEALLYATGAIDR-----LGRVEDGNTVSDYDPEEKKRKMSIETS 55
Query: 98 IAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSK 157
+A +E++ + D PG+AD++ +S +D A++VV A G T +
Sbjct: 56 VAPLEWN-GHKINL-IDTPGYADFVGETLSALRAVDAALIVVEAQSGVEVGTEKVWEFLD 113
Query: 158 QIGIDNVVVYVNKAD 172
+ ++++NK D
Sbjct: 114 DAKLP-RIIFINKMD 127
Score = 29.1 bits (66), Expect = 4.8
Identities = 25/70 (35%), Positives = 32/70 (45%), Gaps = 17/70 (24%)
Query: 175 DREIME-------LVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSIHRLL 227
D E+ME L E E+R L G P FGSAL + +G + RLL
Sbjct: 209 DEELMEKYLEEGELTEEELRAGLRRALRAGLIVPVFFGSAL-------TGIG---VRRLL 258
Query: 228 DALDKHIPNP 237
DAL + P+P
Sbjct: 259 DALVELAPSP 268
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 62.2 bits (151), Expect = 3e-10
Identities = 43/131 (32%), Positives = 58/131 (44%), Gaps = 25/131 (19%)
Query: 48 VGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIA----HVEY 103
V +GHVDHGKTTL I K + +++A GIT I EY
Sbjct: 247 VTILGHVDHGKTTLLDKIRK----------------TQIAQKEAGGITQKIGAYEVEFEY 290
Query: 104 STNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDN 163
+ D PGH + GA+ D AI+++AA +G PQT E + I N
Sbjct: 291 KDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAI---NYIQAAN 347
Query: 164 V--VVYVNKAD 172
V +V +NK D
Sbjct: 348 VPIIVAINKID 358
>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 = 58.3 bits (142), Expect = 5e-10
Identities = 54/200 (27%), Positives = 90/200 (45%), Gaps = 31/200 (15%)
Query: 47 NVGTIGHVDHGKTTLTAAI---TKVAAKIGKSKFITFDQI-DRAPEEKARGITINIAHV- 101
N I H+DHGK+TL + T ++ +Q+ D E+ RGITI V
Sbjct: 2 NFSIIAHIDHGKSTLADRLLELTGTVSEREMK-----EQVLDSMDLERERGITIKAQAVR 56
Query: 102 ---EYSTNTRHYAH-TDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSK 157
+ + + D PGH D+ + + +GA++VV A++G QT + L+
Sbjct: 57 LFYKAKDGEEYLLNLIDTPGHVDFSYEVSRSLAACEGALLVVDATQGVEAQTLANFYLAL 116
Query: 158 QIGIDNVVVYVNKADLVDREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSE 217
+ ++ + V +NK DL + + V+ E+ DVL G D V S++
Sbjct: 117 ENNLEIIPV-INKIDLPAADP-DRVKQEIEDVL---GLDASEAILV-----------SAK 160
Query: 218 LGEPSIHRLLDALDKHIPNP 237
G + LL+A+ + IP P
Sbjct: 161 TGL-GVEDLLEAIVERIPPP 179
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 61.2 bits (150), Expect = 5e-10
Identities = 81/296 (27%), Positives = 131/296 (44%), Gaps = 71/296 (23%)
Query: 51 IGHVDHGKTTL-------TAAITKVAAKIGKSKFITFDQI-DRAPEEKARGITINIAHVE 102
I H+DHGK+TL T +++ K Q+ D E+ RGITI A
Sbjct: 13 IAHIDHGKSTLADRLIELTGTLSEREMK---------AQVLDSMDLERERGITIK-AQ-- 60
Query: 103 YSTNTRHYAHTDCPGHADYIKNMI--------------SGASQMDGAIVVVAASEGQMPQ 148
+Y D G YI N+I S A+ +GA++VV AS+G Q
Sbjct: 61 --AVRLNYKAKD--GE-TYILNLIDTPGHVDFSYEVSRSLAA-CEGALLVVDASQGVEAQ 114
Query: 149 TREHLLLSKQIGIDN---VVVYVNKADLVDREIMELVELEVRDVLTAYGYDGDNTPFVFG 205
T ++ L+ ++N ++ +NK DL + E V+ E+ DV+ G D + V
Sbjct: 115 TLANVYLA----LENDLEIIPVLNKIDLPAADP-ERVKQEIEDVI---GIDASDAVLV-- 164
Query: 206 SALLALQGDSSELGEPSIHRLLDALDKHIPNPVRDITSPF-ILPIDNAIGVPGRGSVCIG 264
SA + +G I +L+A+ + IP P D +P L D + RG V +
Sbjct: 165 SA-------KTGIG---IEEVLEAIVERIPPPKGDPDAPLKALIFD-SWYDNYRGVVVLV 213
Query: 265 TIKQGTIKRNDEAELLGFNSKFTCTISEIQVF---QKKVSEARAGDNVGVLLRNVK 317
+ GT+K+ D+ +++ ++ E+ VF V E AG+ VG ++ +K
Sbjct: 214 RVVDGTLKKGDKIKMMSTGKEYEVD--EVGVFTPKMVPVDELSAGE-VGYIIAGIK 266
>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 = 58.0 bits (141), Expect = 8e-10
Identities = 41/147 (27%), Positives = 66/147 (44%), Gaps = 20/147 (13%)
Query: 47 NVGTIGHVDHGKTTL-------TAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIA 99
NV GH+ HGKT+L T T K T D +E+ RGI+I
Sbjct: 2 NVCIAGHLHHGKTSLLDMLIEQTHKRTPSVKLGWKPLRYT----DTRKDEQERGISIKSN 57
Query: 100 HV-EYSTNTRHYAHT----DCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLL 154
+ +++ ++ D PGH +++ + + DG ++VV EG T +
Sbjct: 58 PISLVLEDSKGKSYLINIIDTPGHVNFMDEVAAALRLCDGVVLVVDVVEGLTSVTERLIR 117
Query: 155 LSKQIGIDNVVVYVNKADLVDREIMEL 181
+ Q G+ V+V +NK +DR I+EL
Sbjct: 118 HAIQEGLPMVLV-INK---IDRLILEL 140
>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 = 59.0 bits (144), Expect = 1e-09
Identities = 46/137 (33%), Positives = 60/137 (43%), Gaps = 21/137 (15%)
Query: 47 NVGTIGHVDHGKTTLTAAI---TKVAAKIG--KSKFITFDQIDRAPEEKARGITINIAHV 101
N+G I H+D GKTT T I T KIG T D + +E+ RGITI A
Sbjct: 1 NIGIIAHIDAGKTTTTERILYYTGRIHKIGEVHGGGATMDWM---EQERERGITIQSA-- 55
Query: 102 EYSTNTRHYAHT----DCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSK 157
+T H D PGH D+ + +DGA+ V A G PQT + +
Sbjct: 56 --ATTCFWKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVQPQT---ETVWR 110
Query: 158 QIGIDNV--VVYVNKAD 172
Q V + +VNK D
Sbjct: 111 QADRYGVPRIAFVNKMD 127
>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 = 58.7 bits (142), Expect = 4e-09
Identities = 42/134 (31%), Positives = 61/134 (45%), Gaps = 15/134 (11%)
Query: 47 NVGTIGHVDHGKTTLTAAI---TKVAAKIGKSKFITFD---QIDRAPEEKARGITINIA- 99
N+G H+D GKTT T I T KIG+ D +D +EK RGITI A
Sbjct: 12 NIGISAHIDAGKTTTTERILFYTGRIHKIGE----VHDGAATMDWMEQEKERGITITSAA 67
Query: 100 -HVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQ 158
V + + + D PGH D+ + +DGA+ V+ A G PQ+ + +
Sbjct: 68 TTVFWKGHRINI--IDTPGHVDFTVEVERSLRVLDGAVAVLDAVGGVQPQSETVWRQANR 125
Query: 159 IGIDNVVVYVNKAD 172
+ + +VNK D
Sbjct: 126 YEVPR-IAFVNKMD 138
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 53.9 bits (130), Expect = 1e-08
Identities = 31/140 (22%), Positives = 49/140 (35%), Gaps = 28/140 (20%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSK-FITFDQIDRAPEEKARGITINIAHVEYST 105
+ +G + GK+TL + I + K T + + EE + N+
Sbjct: 3 KIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNL------- 55
Query: 106 NTRHYAHTDCPGHADY-------IKNMISGASQMDGAIVVVAASEGQMPQTRE--HLLLS 156
D G DY + + S D I+V+ E QT+E H S
Sbjct: 56 -------LDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAES 108
Query: 157 KQIGIDNVVVYVNKADLVDR 176
+ I ++ NK DL D
Sbjct: 109 G-VPI---ILVGNKIDLRDA 124
>gnl|CDD|238771 cd01513, Translation_factor_III, Domain III of Elongation factor
(EF) Tu (EF-TU) and EF-G. Elongation factors (EF) EF-Tu
and EF-G participate in the elongation phase during
protein biosynthesis on the ribosome. Their functional
cycles depend on GTP binding and its hydrolysis. The
EF-Tu complexed with GTP and aminoacyl-tRNA delivers
tRNA to the ribosome, whereas EF-G stimulates
translocation, a process in which tRNA and mRNA
movements occur in the ribosome. Experimental data
showed that: (1) intrinsic GTPase activity of EF-G is
influenced by excision of its domain III; (2) that EF-G
lacking domain III has a 1,000-fold decreased GTPase
activity on the ribosome and, a slightly decreased
affinity for GTP; and (3) EF-G lacking domain III does
not stimulate translocation, despite the physical
presence of domain IV which is also very important for
translocation. These findings indicate an essential
contribution of domain III to activation of GTP
hydrolysis. Domains III and V of EF-G have the same fold
(although they are not completely superimposable), the
double split beta-alpha-beta fold. This fold is observed
in a large number of ribonucleotide binding proteins and
is also referred to as the ribonucleoprotein (RNP) or
RNA recognition (RRM) motif. This domain III is found
in several elongation factors, as well as in peptide
chain release factors and in GT-1 family of GTPase
(GTPBP1).
Length = 102
Score = 51.6 bits (124), Expect = 2e-08
Identities = 26/107 (24%), Positives = 45/107 (42%), Gaps = 21/107 (19%)
Query: 334 QMHNRYEAEIYLLSKAEGGRYKPITSKYIQQMFSRTWNVQVRLD-LPGEDDG-------- 384
Q +++ AEIY+L +P++ Y + T +V R+ L + DG
Sbjct: 1 QAVDKFVAEIYVL-----DHPEPLSPGYKPVLNVGTAHVPGRIAKLLSKVDGKTEEKKPP 55
Query: 385 -MLMPGEHGTVTMTLLYKMYL------SKGQTFTIRENNKLVATGIV 424
L GE G V + L + L +G F +R+ + V G++
Sbjct: 56 EFLKSGERGIVEVELQKPVALETFSENQEGGRFALRDGGRTVGAGLI 102
>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 = 49.5 bits (119), Expect = 7e-08
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 2/82 (2%)
Query: 244 PFILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFNSKFTCTISEIQVFQKKVSEA 303
P LPI + + G G+V +G ++ G +K E+ + + EA
Sbjct: 4 PLRLPIQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGVTGEVKSVEMH--HEPLEEA 61
Query: 304 RAGDNVGVLLRNVKLKQIERGM 325
GDNVG ++NV K I+RG
Sbjct: 62 LPGDNVGFNVKNVSKKDIKRGD 83
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 54.3 bits (131), Expect = 9e-08
Identities = 48/154 (31%), Positives = 68/154 (44%), Gaps = 26/154 (16%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITI---------- 96
N+ I HVDHGK+TLT ++ A I + D +E RGITI
Sbjct: 21 NMSVIAHVDHGKSTLTDSLVAAAGIIAQEVAGDVRMTDTRADEAERGITIKSTGISLYYE 80
Query: 97 ----NIAHVEYSTNTRHYAHT--DCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTR 150
++ + + Y D PGH D+ + + DGA+VVV EG QT
Sbjct: 81 MTDESLKDFKGERDGNEYLINLIDSPGHVDFSSEVTAALRITDGALVVVDCIEGVCVQT- 139
Query: 151 EHLL---LSKQIGIDNVVVYVNKADLVDREIMEL 181
E +L L ++I V+ VNK +DR +EL
Sbjct: 140 ETVLRQALGERI---RPVLTVNK---MDRCFLEL 167
>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 = 52.1 bits (125), Expect = 4e-07
Identities = 43/139 (30%), Positives = 61/139 (43%), Gaps = 23/139 (16%)
Query: 48 VGTIGHVDHGKTTLTAAI--TKVAAK--------IGKSKFITFDQIDRAPEE--KARGIT 95
V +GHVDHGKTTL I + VA + IG + I D I+ + K I
Sbjct: 7 VSVLGHVDHGKTTLLDKIRGSAVAKREAGGITQHIGAT-EIPMDVIEGICGDLLKKFKIR 65
Query: 96 INIAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLL 155
+ I + + D PGH + G + D AI++V +EG PQT+E L +
Sbjct: 66 LKIPGLLF---------IDTPGHEAFTNLRKRGGALADLAILIVDINEGFKPQTQEALNI 116
Query: 156 SKQIGIDNVVVYVNKADLV 174
+ VV NK D +
Sbjct: 117 LRMYKTP-FVVAANKIDRI 134
>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 = 50.7 bits (122), Expect = 6e-07
Identities = 45/150 (30%), Positives = 77/150 (51%), Gaps = 16/150 (10%)
Query: 51 IGHVDHGKTTLT-------AAIT---KVAAKIGKSKFITFDQIDRAPEEKARGITINIAH 100
I H D GKTTLT AI V A+ K T D ++ EK RGI++ +
Sbjct: 8 ISHPDAGKTTLTEKLLLFGGAIQEAGAVKAR-KSRKHATSDWMEI---EKQRGISVTSSV 63
Query: 101 VEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIG 160
+++ D PGH D+ ++ + +D A++V+ A++G PQTR+ + + G
Sbjct: 64 MQFEYKGCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLRG 123
Query: 161 IDNVVVYVNKADLVDREIMELVELEVRDVL 190
I ++ ++NK D R+ +EL++ E+ + L
Sbjct: 124 IP-IITFINKLDREGRDPLELLD-EIENEL 151
Score = 28.3 bits (64), Expect = 7.1
Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 15/83 (18%)
Query: 159 IGIDNVVVYVNKADLVDREIMELVELEVRDVLTAYGYD----GDNTPFVFGSALLALQGD 214
G+D+ + + + ++ E +EL V + + G+ TP FGSAL
Sbjct: 197 KGLDDPKLDELLGEDLAEQLREELEL-VEGAGPEFDKELFLAGELTPVFFGSAL------ 249
Query: 215 SSELGEPSIHRLLDALDKHIPNP 237
+ G + LLDA K P P
Sbjct: 250 -NNFG---VQELLDAFVKLAPAP 268
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 51.5 bits (124), Expect = 6e-07
Identities = 41/150 (27%), Positives = 72/150 (48%), Gaps = 16/150 (10%)
Query: 51 IGHVDHGKTTLT-------AAIT---KVAAKIGKSKFITFDQIDRAPEEKARGITINIAH 100
I H D GKTTLT AI V + K D ++ EK RGI++ +
Sbjct: 18 ISHPDAGKTTLTEKLLLFGGAIQEAGTVKGR-KSGKHAKSDWMEI---EKQRGISVTSSV 73
Query: 101 VEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIG 160
+++ D PGH D+ ++ + +D A++V+ A++G PQT + + +
Sbjct: 74 MQFDYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIEPQTLKLFEVCRLRD 133
Query: 161 IDNVVVYVNKADLVDREIMELVELEVRDVL 190
I + ++NK D R+ +EL++ E+ + L
Sbjct: 134 IP-IFTFINKLDREGRDPLELLD-EIEEEL 161
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 51.0 bits (123), Expect = 1e-06
Identities = 44/138 (31%), Positives = 59/138 (42%), Gaps = 23/138 (16%)
Query: 47 NVGTIGHVDHGKTTLTAAI---TKVAAKIGKSKFITFD---QIDRAPEEKARGITINIAH 100
N+G + H+D GKTT T I T + KIG+ D +D +E+ RGITI A
Sbjct: 10 NIGIMAHIDAGKTTTTERILYYTGKSHKIGE----VHDGAATMDWMEQEQERGITITSAA 65
Query: 101 VEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQT----REHLLLS 156
D PGH D+ + +DGA+ V A G PQ+ R
Sbjct: 66 TTCFWKGHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVSGVEPQSETVWR------ 119
Query: 157 KQIGIDNV--VVYVNKAD 172
Q V +V+VNK D
Sbjct: 120 -QADKYGVPRIVFVNKMD 136
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 50.2 bits (121), Expect = 2e-06
Identities = 46/136 (33%), Positives = 62/136 (45%), Gaps = 25/136 (18%)
Query: 52 GHVDHGKTTLTAAI--TKVAAK--------IGKSKFITFDQIDRAPEE--KARGITINIA 99
GHVDHGKTTL I T VAAK IG + + D I++ K I + I
Sbjct: 13 GHVDHGKTTLLDKIRGTAVAAKEAGGITQHIGAT-EVPIDVIEKIAGPLKKPLPIKLKIP 71
Query: 100 HVEYSTNTRHYAHTDCPGHADYIKNMIS-GASQMDGAIVVVAASEGQMPQTREHLLLSKQ 158
+ + D PGH + N+ G + D AI+VV +EG PQT E + + K+
Sbjct: 72 GLLF---------IDTPGHEAF-TNLRKRGGALADIAILVVDINEGFQPQTIEAINILKR 121
Query: 159 IGIDNVVVYVNKADLV 174
VV NK D +
Sbjct: 122 RKTPFVVA-ANKIDRI 136
Score = 30.5 bits (70), Expect = 1.9
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 269 GTIKRNDEAELLGFNSKFTCTISEIQVFQKKVSEARAGDNVGVLLRNVKL-KQIERG 324
GTIK L+ + K TI +IQ + V EA+AG V + + + +QI+ G
Sbjct: 492 GTIKPGVP--LIKEDGKRVGTIKQIQDQGENVKEAKAGMEVAISIDGPTVGRQIKEG 546
>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 = 44.8 bits (107), Expect = 3e-06
Identities = 26/86 (30%), Positives = 44/86 (51%), Gaps = 5/86 (5%)
Query: 244 PFILPIDNAIGVPGRGSVCI-GTIKQGTIKRNDEAELLGFNSKFTCTISEIQVFQKKVSE 302
PF LPI + +G + G ++ G+I++ D LL SK + + I V ++V
Sbjct: 1 PFRLPISDKY--KDQGGTVVSGKVESGSIQKGDT--LLVMPSKESVEVKSIYVDDEEVDY 56
Query: 303 ARAGDNVGVLLRNVKLKQIERGMLLA 328
A AG+NV + L+ + + I G +L
Sbjct: 57 AVAGENVRLKLKGIDEEDISPGDVLC 82
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 46.8 bits (112), Expect = 4e-06
Identities = 44/210 (20%), Positives = 70/210 (33%), Gaps = 57/210 (27%)
Query: 47 NVGTIGHVDHGKTTL-----------------TAAITKVAAKIGKSKFITFDQIDRAPEE 89
+ +G GK+TL TA IT + + G K + +D
Sbjct: 2 LLAVVGEFSAGKSTLLNALLGEEVLPTGVTPTTAVITVL--RYGLLKGVVL--VD----- 52
Query: 90 KARGIT--INIAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMP 147
T +N ST H T+ ++ + D I V++A + P
Sbjct: 53 -----TPGLN------STIEHHTEITE-----SFLP-------RADAVIFVLSADQ---P 86
Query: 148 QT---REHLLLSKQIGIDNVVVYVNKADLVDREIMELVELEVRDVLTAYGYDGDNTPFVF 204
T RE L + + +NK DL+ E +E V R+ L G
Sbjct: 87 LTESEREFLKEILKWSGKKIFFVLNKIDLLSEEELEEVLEYSREELGVLELGGGEPRIFP 146
Query: 205 GSALLALQGDSSELGEPSIHRLLDALDKHI 234
SA AL+ E + L++H+
Sbjct: 147 VSAKEALEARLQGDEELLEQSGFEELEEHL 176
>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 = 48.7 bits (116), Expect = 4e-06
Identities = 40/153 (26%), Positives = 73/153 (47%), Gaps = 14/153 (9%)
Query: 47 NVGTIGHVDHGKTTLT-------AAITKVAAKIGK--SKFITFDQIDRAPEEKARGITIN 97
I H D GKTT+T AI A G+ + D ++ EK RGI+I
Sbjct: 13 TFAIISHPDAGKTTITEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEM---EKQRGISIT 69
Query: 98 IAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSK 157
+ +++ D PGH D+ ++ + +D ++V+ A++G +TR+ L+
Sbjct: 70 TSVMQFPYRDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRK-LMEVT 128
Query: 158 QIGIDNVVVYVNKADLVDREIMELVELEVRDVL 190
++ + ++NK D R+ +EL++ EV + L
Sbjct: 129 RLRDTPIFTFMNKLDRDIRDPLELLD-EVENEL 160
>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 = 43.7 bits (104), Expect = 6e-06
Identities = 24/84 (28%), Positives = 43/84 (51%), Gaps = 4/84 (4%)
Query: 244 PFILPIDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFNSKFTCTISEIQVFQKKVSEA 303
P LPI + G+V +G ++ GTIK+ D+ ++ +K + I +V A
Sbjct: 1 PLRLPIIDK--YKDMGTVVLGKVESGTIKKGDKLLVM--PNKTQVEVLSIYNEDVEVRYA 56
Query: 304 RAGDNVGVLLRNVKLKQIERGMLL 327
R G+NV + L+ ++ + I G +L
Sbjct: 57 RPGENVRLRLKGIEEEDISPGFVL 80
>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 = 43.4 bits (103), Expect = 1e-05
Identities = 26/83 (31%), Positives = 40/83 (48%), Gaps = 4/83 (4%)
Query: 249 IDNAIGVPGRGSVCIGTIKQGTIKRNDEAELLGFNS--KF-TCTISEIQVFQKKVSEARA 305
ID VPG G+V GT+ +G I+ D LLG + F T+ I + V RA
Sbjct: 5 IDEIYSVPGVGTVVGGTVSKGVIRLGDTL-LLGPDQDGSFRPVTVKSIHRNRSPVRVVRA 63
Query: 306 GDNVGVLLRNVKLKQIERGMLLA 328
G + + L+ + + +GM+L
Sbjct: 64 GQSASLALKKIDRSLLRKGMVLV 86
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 47.4 bits (114), Expect = 1e-05
Identities = 40/116 (34%), Positives = 52/116 (44%), Gaps = 24/116 (20%)
Query: 47 NVGTIGHVDHGKTTLTAAI---TKVAAKIGKSKFITFD---QIDRAPEEKARGITINIAH 100
N+G + H+D GKTT T I T V KIG+ D +D +E+ RGITI A
Sbjct: 12 NIGIMAHIDAGKTTTTERILFYTGVNHKIGE----VHDGAATMDWMEQEQERGITITSA- 66
Query: 101 VEYSTNTRHYAHT----DCPGHADYIKNMISGASQM---DGAIVVVAASEGQMPQT 149
+T H D PGH D+ I + DGA+ V A G PQ+
Sbjct: 67 ---ATTCFWKDHRINIIDTPGHVDF---TIEVERSLRVLDGAVAVFDAVGGVEPQS 116
>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 = 41.7 bits (98), Expect = 2e-04
Identities = 27/169 (15%), Positives = 56/169 (33%), Gaps = 35/169 (20%)
Query: 51 IGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGIT--INIAHVEYSTNTR 108
+G GK++L A+ +G G T ++ E
Sbjct: 3 VGRGGVGKSSLLNAL------LGGEVGEV---------SDVPGTTRDPDVYVKELDKGKV 47
Query: 109 HYAHTDCPGHADY--------IKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIG 160
D PG ++ + ++ GA D ++VV +++ + + + L+L +
Sbjct: 48 KLVLVDTPGLDEFGGLGREELARLLLRGA---DLILLVVDSTDRESEEDAKLLILRRLRK 104
Query: 161 ID-NVVVYVNKADLVDREIMELVELEVRDVLTAYGYDGDNTPFVFGSAL 208
+++ NK DL++ +E + P SA
Sbjct: 105 EGIPIILVGNKIDLLEEREVEELLRLEELAKIL------GVPVFEVSAK 147
>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 = 41.5 bits (98), Expect = 4e-04
Identities = 40/160 (25%), Positives = 65/160 (40%), Gaps = 29/160 (18%)
Query: 47 NVGTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAH------ 100
V +G+VD GK+TL +T+ G+ K + R E G T ++++
Sbjct: 1 RVAVVGNVDAGKSTLLGVLTQGELDNGRGKARLN--LFRHKHEVESGRTSSVSNDILGFD 58
Query: 101 -----VEYSTNTRHYAHT-------------DCPGHADYIKNMISG--ASQMDGAIVVVA 140
V Y N D GH Y+K + G D A++VV
Sbjct: 59 SDGEVVNYPDNHLGELDVEICEKSSKVVTFIDLAGHERYLKTTVFGMTGYAPDYAMLVVG 118
Query: 141 ASEGQMPQTREHLLLSKQIGIDNVVVYVNKADLVDREIME 180
A+ G + T+EHL L+ + + V V V K D+ +++
Sbjct: 119 ANAGIIGMTKEHLGLALALKVP-VFVVVTKIDMTPANVLQ 157
>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 = 37.5 bits (88), Expect = 0.001
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 264 GTIKQGTIKRNDEAELLGFNSKFTCTISEIQVFQKKVSEARAGDNVGVLL-RNVKLKQIE 322
GTI G+I+ DE +L S T + I+ F ++ EA AG++V + L + +
Sbjct: 20 GTIASGSIRVGDEVVVL--PSGKTSRVKSIETFDGELDEAGAGESVTLTLEDEI---DVS 74
Query: 323 RGMLLAK 329
RG ++
Sbjct: 75 RGDVIVA 81
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 39.0 bits (92), Expect = 0.004
Identities = 46/174 (26%), Positives = 72/174 (41%), Gaps = 64/174 (36%)
Query: 51 IGHVDHGKTTLT-------AAITK---VAAKIGKSKFITFDQIDRAPEEKARGI------ 94
I H D GKTTLT AI + V + + T D ++ EK RGI
Sbjct: 16 ISHPDAGKTTLTEKLLLFGGAIQEAGTVKGR-KSGRHATSDWMEM---EKQRGISVTSSV 71
Query: 95 --------TINIAHVEYSTNTRHYAHTDCPGHADYIKNMISGASQ--------MDGAIVV 138
IN+ D PGH D+ S+ +D A++V
Sbjct: 72 MQFPYRDCLINL--------------LDTPGHEDF--------SEDTYRTLTAVDSALMV 109
Query: 139 VAASEGQMPQTREHLLLSKQIGIDNVVVYVNKADLVDREIMELVEL--EVRDVL 190
+ A++G PQTR+ + + + + ++NK +DR+ E +EL E+ +VL
Sbjct: 110 IDAAKGVEPQTRKLMEVCRLRDTP-IFTFINK---LDRDGREPLELLDEIEEVL 159
>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 = 33.2 bits (77), Expect = 0.040
Identities = 14/63 (22%), Positives = 29/63 (46%), Gaps = 6/63 (9%)
Query: 258 RGSVCIGTIKQGTIKRNDEAELLGFNSKFTCTISEIQVF---QKKVSEARAGDNVGVLLR 314
RG + + + GT+K+ D+ + ++ + E+ +F E AG VG ++
Sbjct: 14 RGVIALVRVFDGTLKKGDKIRFMSTGKEY--EVEEVGIFRPEMTPTDELSAGQ-VGYIIA 70
Query: 315 NVK 317
+K
Sbjct: 71 GIK 73
>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 = 33.6 bits (78), Expect = 0.045
Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 10/64 (15%)
Query: 258 RGSVCIGTIKQGTIKRNDEAELL-GFNS----KFTCT-----ISEIQVFQKKVSEARAGD 307
+G V G++ QG +K DE E+ G K C I ++ + EA G
Sbjct: 27 KGGVAGGSLLQGVLKVGDEIEIRPGIVVKDEGKIKCRPIFTKIVSLKAENNDLQEAVPGG 86
Query: 308 NVGV 311
+GV
Sbjct: 87 LIGV 90
>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 = 32.8 bits (76), Expect = 0.046
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 5/58 (8%)
Query: 259 GSVCIGTIKQGTIKRNDEAELLGFNSKFT-CTISEIQVF----QKKVSEARAGDNVGV 311
G + IG I +GT+K + ++ + K I+++ F + +V EA AGD V +
Sbjct: 15 GRIAIGRIFRGTVKVGQQVAVVKRDGKIEKAKITKLFGFEGLKRVEVEEAEAGDIVAI 72
>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 = 34.7 bits (81), Expect = 0.052
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 13/69 (18%)
Query: 133 DGAIVVVAASEGQMPQTREHLL-----LSKQIGIDNVVVYVNKADLVDREIMELVELEVR 187
D ++V + E P LL ++ GI+ V+ +NKADLVD E +E E+
Sbjct: 4 DQVLIVFSLKE---PFFNLRLLDRYLVAAEASGIE-PVIVLNKADLVDDEELE----ELL 55
Query: 188 DVLTAYGYD 196
++ GY
Sbjct: 56 EIYEKLGYP 64
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 33.7 bits (78), Expect = 0.11
Identities = 32/145 (22%), Positives = 53/145 (36%), Gaps = 47/145 (32%)
Query: 57 GKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYSTNTRHYAHTDCP 116
GK+TL +T ++GK P G+T H ++ + TD P
Sbjct: 21 GKSTLVRELTGKKVRVGKR-----------P-----GVTRKPNHYDWGD----FILTDLP 60
Query: 117 G----------HADYIKNMI-----SGASQMDGAIVVVAA-----------SEGQMPQTR 150
G + IK+ I A ++ A++VV G++P
Sbjct: 61 GFGFMSGVPKEVQEKIKDEIVRYIEDNADRILAAVLVVDGKSFIEIIERWEGRGEIPIDV 120
Query: 151 EHLLLSKQIGIDNVVVYVNKADLVD 175
E +++GI +V VNK D +
Sbjct: 121 EMFDFLRELGIPPIVA-VNKMDKIK 144
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 34.9 bits (80), Expect = 0.11
Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 114 DCPGHADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNVVVYVNKADL 173
D PGH + G S D A++VV +EG PQT E + + +Q VV NK DL
Sbjct: 532 DTPGHEAFTSLRKRGGSLADLAVLVVDINEGFKPQTIEAINILRQYKTP-FVVAANKIDL 590
Query: 174 V 174
+
Sbjct: 591 I 591
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 32.5 bits (75), Expect = 0.41
Identities = 25/77 (32%), Positives = 35/77 (45%), Gaps = 20/77 (25%)
Query: 129 ASQMDGAIVVVAASEGQMPQTREHLL---L----SKQIGIDNVVVYVNKADLVDR--EIM 179
A+ +D A++V AA E P LL L + I ++ +NK DL+D E
Sbjct: 78 AANVDQAVLVFAAKE---PDFSTDLLDRFLVLAEANGI---KPIIVLNKIDLLDDLEEAR 131
Query: 180 ELVELEVRDVLTAYGYD 196
EL+ L A GYD
Sbjct: 132 ELLAL-----YRAIGYD 143
>gnl|CDD|223597 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 32.3 bits (74), Expect = 0.49
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 132 MDGAIVVVAASEGQMPQTREHLLLSKQIGIDNVVVYVNKADLVDREIMELVELEVRD 188
+DG + VV A+ L Q+ +V+V +NK DLVD E +E +E +R
Sbjct: 117 LDGVVTVVDAAHFLEGLDAIAELAEDQLAFADVIV-LNKTDLVDAEELEALEARLRK 172
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 31.6 bits (72), Expect = 0.53
Identities = 30/156 (19%), Positives = 55/156 (35%), Gaps = 31/156 (19%)
Query: 49 GTIGHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYSTNTR 108
G +G + GK+TL +A+T +I F T + N+ E+
Sbjct: 1 GLVGLPNVGKSTLLSALTSAKVEIASYPFTT--------------LEPNVGVFEFGDGVD 46
Query: 109 HYAHTDCPGHAD------YIKNMISGASQMDGAIV-VVAASE---GQMPQTREHL---LL 155
D PG D + I I+ V+ ASE G + ++ L +
Sbjct: 47 -IQIIDLPGLLDGASEGRGLGEQILAHLYRSDLILHVIDASEDCVGDPLEDQKTLNEEVS 105
Query: 156 SKQIGIDN--VVVYVNKADLVDRE-IMELVELEVRD 188
+ + N ++ NK D+ + L +++
Sbjct: 106 GSFLFLKNKPEMIVANKIDMASENNLKRLKLDKLKR 141
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 31.9 bits (74), Expect = 0.62
Identities = 26/69 (37%), Positives = 36/69 (52%), Gaps = 14/69 (20%)
Query: 164 VVVYVNKADLVDREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELGEPSI 223
+V+ VNK DLVD + ME + E+R L Y P VF SAL QG +
Sbjct: 287 LVIVVNKWDLVDEKTMEEFKKELRRRLPFLDY----APIVFISALTG-QG---------V 332
Query: 224 HRLLDALDK 232
+LL+A+D+
Sbjct: 333 DKLLEAIDE 341
>gnl|CDD|232978 TIGR00443, hisZ_biosyn_reg, ATP phosphoribosyltransferase,
regulatory subunit. Apparant second copies of
histidyl-tRNA synthetase, found in Bacillus subtilis,
Synechocystis sp., Aquifex aeolicus, and others, are in
fact a regulatory subunit of ATP
phosphoribosyltransferase, and usually encoded by a gene
adjacent to that encoding the catalytic subunit [Amino
acid biosynthesis, Histidine family].
Length = 313
Score = 31.4 bits (72), Expect = 0.88
Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 18/79 (22%)
Query: 179 MELVELEVRDVLTAYGYDGDNTPFV-FGSALLALQGDSSE--------LGE--------- 220
E +E +++DV ++GY TP + + L A G +E LG
Sbjct: 11 KEEIERQLQDVFRSWGYQEIITPTLEYLDTLSAGSGILNEDLFKLFDQLGRVLGLRPDMT 70
Query: 221 PSIHRLLDALDKHIPNPVR 239
I RL+ + P P+R
Sbjct: 71 APIARLVSTRLRDRPLPLR 89
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 31.5 bits (72), Expect = 0.89
Identities = 19/75 (25%), Positives = 26/75 (34%), Gaps = 18/75 (24%)
Query: 160 GIDNVVVYVNKADLVDREIMELVELEVRDVLTAYGYDGDNTPFVFGSALLALQGDSSELG 219
GI+ V+V +NK DL+D E + EL GY V S
Sbjct: 110 GIEPVIV-LNKIDLLDDEEAAVKELL--REYEDIGYP------VLF---------VSAKN 151
Query: 220 EPSIHRLLDALDKHI 234
+ L + L I
Sbjct: 152 GDGLEELAELLAGKI 166
>gnl|CDD|237731 PRK14494, PRK14494, putative molybdopterin-guanine dinucleotide
biosynthesis protein MobB/FeS domain-containing protein
protein; Provisional.
Length = 229
Score = 31.1 bits (71), Expect = 0.94
Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 48 VGTIGHVDHGKTTLTAAITKVAAKIGKSKFI---TFDQIDRA 86
+G IG D GKTTL I K + G T + D+
Sbjct: 4 IGVIGFKDSGKTTLIEKILKNLKERGYRVATAKHTHHEFDKP 45
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 31.1 bits (71), Expect = 1.3
Identities = 34/147 (23%), Positives = 55/147 (37%), Gaps = 28/147 (19%)
Query: 52 GHVDHGKTTLTAAITKVAAKIGKSKFITFDQIDRAPEEKARGITINIAHVEYSTNTRHYA 111
G+ + GK++L +T ++ F T +GI ++ H E
Sbjct: 175 GYPNVGKSSLVRKLTTAKPEVAPYPFTT------------KGI--HVGHFERGYLR--IQ 218
Query: 112 HTDCPGHADY-------I-KNMISGASQMDGAIV-VVAASE--GQMPQTREHLLLSKQIG 160
D PG D I + I + G I+ + SE G + + LL +
Sbjct: 219 VIDTPGLLDRPLEERNEIERQAILALRHLAGVILFLFDPSETCGYSLEEQISLLEEIKEL 278
Query: 161 IDNVVVYV-NKADLVDREIMELVELEV 186
+V V NK D+ D E +E +E V
Sbjct: 279 FKAPIVVVINKIDIADEEKLEEIEASV 305
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 29.9 bits (68), Expect = 1.6
Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 8/80 (10%)
Query: 129 ASQMDGAIVVVAASEGQMPQTREHLLLSKQIGIDNVVVYVNKADLVDREIMELVELEVRD 188
A + D ++VV + + + + LL ++ G ++V NK DLV E EL
Sbjct: 74 ADRADLVLLVVDSDLTPVEEEAKLGLLRER-GKPVLLVL-NKIDLVPES--EEEELLRER 129
Query: 189 VLTAYGYDGDNTPFVFGSAL 208
L P + SAL
Sbjct: 130 KLELLPDL----PVIAVSAL 145
>gnl|CDD|168322 PRK05973, PRK05973, replicative DNA helicase; Provisional.
Length = 237
Score = 30.0 bits (68), Expect = 2.3
Identities = 27/109 (24%), Positives = 43/109 (39%), Gaps = 12/109 (11%)
Query: 56 HGKTTLTAAITKVAAKIG-KSKFITFDQIDRAPEEKARGITINIAHVEYSTNTRHYAHTD 114
HGKT L + A K G F T + ++ ++ R + + A D
Sbjct: 75 HGKTLLGLELAVEAMKSGRTGVFFTLEYTEQDVRDRLRALGADRAQ------FADLFEFD 128
Query: 115 CPGH--ADYIKNMISGASQMDGAIVVVAASEGQMPQTREHLLLSKQIGI 161
ADYI ++ A + G +VV+ + + Q RE LS Q+
Sbjct: 129 TSDAICADYIIARLASAPR--GTLVVIDYLQ-LLDQRREKPDLSVQVRA 174
>gnl|CDD|235479 PRK05458, PRK05458, guanosine 5'-monophosphate oxidoreductase;
Provisional.
Length = 326
Score = 29.9 bits (68), Expect = 2.7
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 26/54 (48%)
Query: 79 TFDQIDR------APEEKARGITINIAHVEYSTNTRHYAHTDCPGHADYIKNMI 126
+D +D+ PE ITI+IAH GH+D + NMI
Sbjct: 98 EYDFVDQLAAEGLTPEY----ITIDIAH----------------GHSDSVINMI 131
>gnl|CDD|200219 TIGR02927, SucB_Actino, 2-oxoglutarate dehydrogenase, E2 component,
dihydrolipoamide succinyltransferase. This model
represents an Actinobacterial clade of E2 enzyme, a
component of the 2-oxoglutarate dehydrogenase complex
involved in the TCA cycle. These proteins have multiple
domains including the catalytic domain (pfam00198), one
or two biotin domains (pfam00364) and an E3-component
binding domain (pfam02817).
Length = 579
Score = 30.0 bits (67), Expect = 3.4
Identities = 15/52 (28%), Positives = 24/52 (46%)
Query: 206 SALLALQGDSSELGEPSIHRLLDALDKHIPNPVRDITSPFILPIDNAIGVPG 257
++ L GD+ E EP + D +D IP+P + P D+ + V G
Sbjct: 20 TSWLKAVGDTVEADEPLLEVSTDKVDTEIPSPAAGVLLEIRAPEDDTVEVGG 71
>gnl|CDD|239663 cd03692, mtIF2_IVc, mtIF2_IVc: this family represents the C2
subdomain of domain IV of mitochondrial translation
initiation factor 2 (mtIF2) which adopts a beta-barrel
fold displaying a high degree of structural similarity
with domain II of the translation elongation factor
EF-Tu. The C-terminal part of mtIF2 contains the entire
fMet-tRNAfmet binding site of IF-2 and is resistant to
proteolysis. This C-terminal portion consists of two
domains, IF2 C1 and IF2 C2. IF2 C2 been shown to
contain all molecular determinants necessary and
sufficient for the recognition and binding of
fMet-tRNAfMet. Like IF2 from certain prokaryotes such as
Thermus thermophilus, mtIF2lacks domain II which is
thought to be involved in binding of E.coli IF-2 to 30S
subunits.
Length = 84
Score = 27.5 bits (62), Expect = 3.6
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 6/59 (10%)
Query: 263 IGTI-----KQGTIKRNDEAELL-GFNSKFTCTISEIQVFQKKVSEARAGDNVGVLLRN 315
+G I G IKRN + +L + IS ++ F+ V E + G G+ L N
Sbjct: 14 VGNIAGCYVTDGKIKRNAKVRVLRNGEVIYEGKISSLKRFKDDVKEVKKGYECGITLEN 72
>gnl|CDD|240661 cd12185, HGDH_LDH_like, Putative Lactate dehydrogenase and
(R)-2-Hydroxyglutarate Dehydrogenase-like proteins,
NAD-binding and catalytic domains. This group contains
various putative dehydrogenases related to D-lactate
dehydrogenase (LDH), (R)-2-hydroxyglutarate
dehydrogenase (HGDH), and related enzymes, members of
the 2-hydroxyacid dehydrogenases family. LDH catalyzes
the interconversion of pyruvate and lactate, and HGDH
catalyzes the NAD-dependent reduction of 2-oxoglutarate
to (R)-2-hydroxyglutarate. Despite often low sequence
identity within this 2-hydroxyacid dehydrogenase family,
these proteins typically have a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD+ binding domain
is inserted within the linear sequence of the mostly
N-terminal catalytic domain, which has a similar domain
structure to the internal NAD binding domain.
Structurally, these domains are connected by extended
alpha helices and create a cleft in which NAD is bound,
primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 322
Score = 29.5 bits (67), Expect = 3.8
Identities = 15/55 (27%), Positives = 30/55 (54%), Gaps = 9/55 (16%)
Query: 57 GKTTLTAAITKVAAKIGKSKFIT-----FDQIDRAPEEKARGITINIAHVEYSTN 106
GK+ ++A + + + G K+I+ +D ID + A+ + I +++V YS N
Sbjct: 52 GKSKISAELLEKLKEAG-VKYISTRSIGYDHIDL---DAAKELGIKVSNVTYSPN 102
>gnl|CDD|238250 cd00443, ADA_AMPD, Adenosine/AMP deaminase. Adenosine deaminases
(ADAs) are present in pro- and eukaryotic organisms and
catalyze the zinc dependent irreversible deamination of
adenosine nucleosides to inosine nucleosides and
ammonia. The eukaryotic AMP deaminase catalyzes a
similar reaction leading to the hydrolytic removal of an
amino group at the 6 position of the adenine nucleotide
ring, a branch point in the adenylate catabolic pathway.
Length = 305
Score = 29.2 bits (66), Expect = 3.9
Identities = 14/75 (18%), Positives = 26/75 (34%), Gaps = 8/75 (10%)
Query: 65 ITKVAAKIGKSKFITFDQIDRAPEEKARGITI--------NIAHVEYSTNTRHYAHTDCP 116
+ ++ K KF+ + + E AR + N+ ++E T R
Sbjct: 19 LLELIKKEFFEKFLLVHNLLQKGEALARALKEVIEEFAEDNVQYLELRTTPRLLETEKGL 78
Query: 117 GHADYIKNMISGASQ 131
Y +I G S+
Sbjct: 79 TKEQYWLLVIEGISE 93
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted subfamily
of the Ras GTPases. This family represents archaeal
GTPase typified by the protein MJ1464 from Methanococcus
jannaschii. The members of this family show a circular
permutation of the GTPase signature motifs so that
C-terminal strands 5, 6, and 7 (strands 6 contain the
NKxD motif) are relocated to the N terminus.
Length = 157
Score = 28.1 bits (63), Expect = 5.6
Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 9/45 (20%)
Query: 163 NVVVYVNKADLVDREIMELVELEVRDVLTAYGYDGDNTPFVFGSA 207
+++ +NKADLV RE++E + ++V + G P V+ SA
Sbjct: 42 KLIIVLNKADLVPREVLE----KWKEVFESEGL-----PVVYVSA 77
>gnl|CDD|234848 PRK00854, rocD, ornithine--oxo-acid transaminase; Reviewed.
Length = 401
Score = 29.0 bits (65), Expect = 5.9
Identities = 25/96 (26%), Positives = 44/96 (45%), Gaps = 21/96 (21%)
Query: 298 KKVSEARAGDNVGVLLRNVKLKQIERGMLLAKADTLQMHNRYEAEIYLLSKAEGGRYKPI 357
+V E +NV ++L ++ G LLA+ H EA++ L+ KA G + P+
Sbjct: 211 TRVRELCTANNVTLILDEIQTGLGRTGKLLAEE-----HEGIEADVTLIGKALSGGFYPV 265
Query: 358 TSKYIQQMFSRTWNVQVRLDLPGEDDGMLMPGEHGT 393
++ + S + E G+L PG+HG+
Sbjct: 266 SA-----VLSNS-----------EVLGVLKPGQHGS 285
>gnl|CDD|221829 pfam12883, DUF3828, Protein of unknown function (DUF3828). This is
a family of bacterial proteins of unknown function.
Length = 120
Score = 27.7 bits (62), Expect = 6.9
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 120 DYIKNMISGASQMDGAIVVVAASEGQMPQTREHLL--LSKQIG---IDNVV 165
D+I + G ++MDG VV + G+ P HL+ L ++ G I V
Sbjct: 67 DWISQIRVGKAKMDGGGAVVDVTFGRQPSKPHHLIVFLVRENGKWKIYRVR 117
>gnl|CDD|239755 cd04088, EFG_mtEFG_II, EFG_mtEFG_II: this subfamily represents the
domain II of elongation factor G (EF-G) in bacteria and,
the C-terminus of mitochondrial Elongation factor G1
(mtEFG1) and G2 (mtEFG2)_like proteins found in
eukaryotes. During the process of peptide synthesis and
tRNA site changes, the ribosome is moved along the mRNA
a distance equal to one codon with the addition of each
amino acid. In bacteria this translocation step is
catalyzed by EF-G_GTP, which is hydrolyzed to provide
the required energy. Thus, this action releases the
uncharged tRNA from the P site and transfers the newly
formed peptidyl-tRNA from the A site to the P site.
Eukaryotic cells harbor 2 protein synthesis systems: one
localized in the cytoplasm, the other in the
mitochondria. Most factors regulating mitochondrial
protein synthesis are encoded by nuclear genes,
translated in the cytoplasm, and then transported to the
mitochondria. The eukaryotic system of elongation factor
(EF) components is more complex than that in
prokaryotes, with both cytoplasmic and mitochondrial
elongation factors and multiple isoforms being expressed
in certain species. mtEFG1 and mtEFG2 show significant
homology to bacterial EF-Gs. Mutants in yeast mtEFG1
have impaired mitochondrial protein synthesis,
respiratory defects and a tendency to lose mitochondrial
DNA. No clear phenotype has been found for mutants in
the yeast homologue of mtEFG2, MEF2.
Length = 83
Score = 26.7 bits (60), Expect = 7.0
Identities = 18/72 (25%), Positives = 24/72 (33%), Gaps = 16/72 (22%)
Query: 266 IKQGTIKRNDEAELLGFNSKFTCTISEIQVF----QKKVSEARAGDNVGVLLRNVKLKQI 321
+ GT+K L + + Q++V EA AGD V LK
Sbjct: 22 VYSGTLKAGST--LYNSTKGKKERVGRLLRMHGKKQEEVEEAGAGDIGAV----AGLKDT 75
Query: 322 ERGMLLAKADTL 333
G DTL
Sbjct: 76 ATG------DTL 81
>gnl|CDD|238223 cd00381, IMPDH, IMPDH: The catalytic domain of the inosine
monophosphate dehydrogenase. IMPDH catalyzes the
NAD-dependent oxidation of inosine 5'-monophosphate
(IMP) to xanthosine 5' monophosphate (XMP). It is a
rate-limiting step in the de novo synthesis of the
guanine nucleotides. There is often a CBS domain
inserted in the middle of this domain, which is proposed
to play a regulatory role. IMPDH is a key enzyme in the
regulation of cell proliferation and differentiation. It
has been identified as an attractive target for
developing chemotherapeutic agents.
Length = 325
Score = 28.6 bits (65), Expect = 7.0
Identities = 18/76 (23%), Positives = 26/76 (34%), Gaps = 23/76 (30%)
Query: 68 VAAKIGKSKFITFDQIDRAP---EEKARGITINIAHVEYSTNTRHYAHTDCPGHADYIKN 124
V A +G D +RA E I I+ AH GH+ Y+
Sbjct: 85 VGAAVG----TREDDKERAEALVEAGVDVIVIDSAH----------------GHSVYVIE 124
Query: 125 MISGASQMDGAIVVVA 140
MI + + V+A
Sbjct: 125 MIKFIKKKYPNVDVIA 140
>gnl|CDD|227434 COG5103, CDC39, Cell division control protein, negative regulator
of transcription [Cell division and chromosome
partitioning / Transcription].
Length = 2005
Score = 29.2 bits (65), Expect = 7.0
Identities = 22/113 (19%), Positives = 38/113 (33%), Gaps = 15/113 (13%)
Query: 141 ASEGQMPQTREHLLLSKQIGIDNVVVYV----------NKADLVDREIMELVELEVRDVL 190
+ E Q P+TRE + + I+++V ++ D +I +L+ V
Sbjct: 3 SQEQQTPETREKSSSTSESKIESIVKAQILFLLSTLREDQYDTKLEQIRQLINKNAPRV- 61
Query: 191 TAYGYDGDNTPFVFGSALLALQGDSSELGEPSIHRLLDALDKHIPNPVRDITS 243
Y + G++ S G + LLD L D S
Sbjct: 62 ----YHHFLRRLIQGNSYRIFGTGKSSDGLATYKLLLDELKSLTKKRFSDAIS 110
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 28.4 bits (64), Expect = 8.7
Identities = 13/44 (29%), Positives = 25/44 (56%), Gaps = 5/44 (11%)
Query: 153 LLLSKQIGIDNVVVYVNKADLVDREIMELVELEVRDVLTAYGYD 196
L+ ++ G++ +V+ +NKADLV + + +D L +GY
Sbjct: 113 LVKAESTGLE-IVLCLNKADLVSPTEQQ----QWQDRLQQWGYQ 151
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 0.135 0.393
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: 23,288,960
Number of extensions: 2276334
Number of successful extensions: 2429
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2224
Number of HSP's successfully gapped: 139
Length of query: 463
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 363
Effective length of database: 6,502,202
Effective search space: 2360299326
Effective search space used: 2360299326
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: 61 (27.3 bits)