RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 013007
(451 letters)
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 879 bits (2273), Expect = 0.0
Identities = 395/451 (87%), Positives = 412/451 (91%), Gaps = 4/451 (0%)
Query: 1 MASVVLRNPNSKRIVPFSSQIYSCCRGSLSISDAFSANETSATRCGPSVNPWWRSMATFT 60
MASVVLRNPNSKR++PFSSQIY CRGS + A SA S +PWWRSMATFT
Sbjct: 1 MASVVLRNPNSKRLLPFSSQIYCACRGSAPSTSASI----SAADDRQSPSPWWRSMATFT 56
Query: 61 RTKLHVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAH 120
RTK HVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKA+AFDEIDKAPEEK RGITIATAH
Sbjct: 57 RTKPHVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAVAFDEIDKAPEEKARGITIATAH 116
Query: 121 VEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVG 180
VEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVG
Sbjct: 117 VEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVG 176
Query: 181 VPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIG 240
VPSLV FLNKVD+V+DEELLELVEMELRELLSFYKFPGDEIPIIRGSA SALQG N+EIG
Sbjct: 177 VPSLVVFLNKVDVVDDEELLELVEMELRELLSFYKFPGDEIPIIRGSALSALQGTNDEIG 236
Query: 241 KKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEV 300
K AILKLMDAVDEYIP+P R LDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVE+
Sbjct: 237 KNAILKLMDAVDEYIPEPVRVLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEI 296
Query: 301 LGLTQGPSLKTTVTGVEMFKKILDRGEAGDNVGLLLRGLKREDVQRGQVIAKPGSVKTYK 360
+GL G LKTTVTGVEMFKKILD+G+AGDNVGLLLRGLKREDVQRGQVI KPGS+KTYK
Sbjct: 297 VGLRPGGPLKTTVTGVEMFKKILDQGQAGDNVGLLLRGLKREDVQRGQVICKPGSIKTYK 356
Query: 361 KFEAEIYVLTKDEGGRHTAFFSNYRPQIYLRTADVTGKVELLGDVKMVMPGDNVNAAFEL 420
KFEAEIYVLTKDEGGRHT FFSNYRPQ YLRTADVTGKVEL VKMVMPGDNV A FEL
Sbjct: 357 KFEAEIYVLTKDEGGRHTPFFSNYRPQFYLRTADVTGKVELPEGVKMVMPGDNVTAVFEL 416
Query: 421 ISPLPLQQGQRFALREGGRTVGAGVVSKVIS 451
ISP+PL+ GQRFALREGGRTVGAGVVSKV+S
Sbjct: 417 ISPVPLEPGQRFALREGGRTVGAGVVSKVLS 447
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 812 bits (2099), Expect = 0.0
Identities = 296/394 (75%), Positives = 340/394 (86%), Gaps = 2/394 (0%)
Query: 57 ATFTRTKLHVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITI 116
F RTK HVNVGTIGHVDHGKTTLTAAITKVLA++G A+A A+D+IDKAPEEK RGITI
Sbjct: 4 EKFERTKPHVNVGTIGHVDHGKTTLTAAITKVLAKKGGAEAKAYDQIDKAPEEKARGITI 63
Query: 117 ATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLA 176
TAHVEYET KRHYAHVDCPGHADYVKNMITGAAQMDG ILVVSA DGPMPQT+EHILLA
Sbjct: 64 NTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLA 123
Query: 177 RQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKN 236
RQVGVP +V FLNK D+V+DEELLELVEME+RELLS Y FPGD+ PIIRGSA AL+G +
Sbjct: 124 RQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSKYDFPGDDTPIIRGSALKALEGDD 183
Query: 237 EEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGE 296
+E +K IL+LMDAVD YIP PER +DKPFLMPIEDVFSI GRGTV TGRVE+G IKVGE
Sbjct: 184 DEEWEKKILELMDAVDSYIPTPERAIDKPFLMPIEDVFSISGRGTVVTGRVERGIIKVGE 243
Query: 297 EVEVLGLTQGPSLKTTVTGVEMFKKILDRGEAGDNVGLLLRGLKREDVQRGQVIAKPGSV 356
EVE++G+ + KTTVTGVEMF+K+LD G+AGDNVG LLRG+KREDV+RGQV+AKPGS+
Sbjct: 244 EVEIVGIR--DTQKTTVTGVEMFRKLLDEGQAGDNVGALLRGIKREDVERGQVLAKPGSI 301
Query: 357 KTYKKFEAEIYVLTKDEGGRHTAFFSNYRPQIYLRTADVTGKVELLGDVKMVMPGDNVNA 416
+ KFEAE+YVL+K+EGGRHT FF+ YRPQ Y RT DVTG +EL V+MVMPGDNV
Sbjct: 302 TPHTKFEAEVYVLSKEEGGRHTPFFNGYRPQFYFRTTDVTGVIELPEGVEMVMPGDNVEM 361
Query: 417 AFELISPLPLQQGQRFALREGGRTVGAGVVSKVI 450
ELI+P+ +++G RFA+REGGRTVGAGVV+K+I
Sbjct: 362 TVELIAPIAMEEGLRFAIREGGRTVGAGVVTKII 395
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 800 bits (2070), Expect = 0.0
Identities = 293/397 (73%), Positives = 341/397 (85%), Gaps = 4/397 (1%)
Query: 56 MA--TFTRTKLHVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRG 113
MA F RTK HVNVGTIGHVDHGKTTLTAAITKVLA++G +A A+D+ID APEEK RG
Sbjct: 1 MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAITKVLAKKGGGEAKAYDQIDNAPEEKARG 60
Query: 114 ITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHI 173
ITI T+HVEYETA RHYAHVDCPGHADYVKNMITGAAQMDG ILVVSA DGPMPQT+EHI
Sbjct: 61 ITINTSHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHI 120
Query: 174 LLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQ 233
LLARQVGVP +V FLNK D+V+DEELLELVEME+RELLS Y FPGD+ PIIRGSA AL+
Sbjct: 121 LLARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSKYDFPGDDTPIIRGSALKALE 180
Query: 234 GKNEEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIK 293
G ++E + IL+LMDAVD YIP+PER +DKPFLMPIEDVFSI GRGTV TGRVE+G +K
Sbjct: 181 GDDDEEWEAKILELMDAVDSYIPEPERAIDKPFLMPIEDVFSISGRGTVVTGRVERGIVK 240
Query: 294 VGEEVEVLGLTQGPSLKTTVTGVEMFKKILDRGEAGDNVGLLLRGLKREDVQRGQVIAKP 353
VG+EVE++G+ + KTTVTGVEMF+K+LD G+AGDNVG+LLRG KREDV+RGQV+AKP
Sbjct: 241 VGDEVEIVGI--KETQKTTVTGVEMFRKLLDEGQAGDNVGVLLRGTKREDVERGQVLAKP 298
Query: 354 GSVKTYKKFEAEIYVLTKDEGGRHTAFFSNYRPQIYLRTADVTGKVELLGDVKMVMPGDN 413
GS+K + KFEAE+YVL+K+EGGRHT FF+ YRPQ Y RT DVTG +EL V+MVMPGDN
Sbjct: 299 GSIKPHTKFEAEVYVLSKEEGGRHTPFFNGYRPQFYFRTTDVTGTIELPEGVEMVMPGDN 358
Query: 414 VNAAFELISPLPLQQGQRFALREGGRTVGAGVVSKVI 450
V ELI+P+ +++G RFA+REGGRTVGAGVV+K+I
Sbjct: 359 VKMTVELIAPIAMEEGLRFAIREGGRTVGAGVVAKII 395
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 749 bits (1935), Expect = 0.0
Identities = 283/394 (71%), Positives = 334/394 (84%), Gaps = 4/394 (1%)
Query: 57 ATFTRTKLHVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITI 116
F R+K HVN+GTIGHVDHGKTTLTAAITKVLAE G +A +D ID APEEK+RGITI
Sbjct: 4 EKFDRSKPHVNIGTIGHVDHGKTTLTAAITKVLAERGLNQAKDYDSIDAAPEEKERGITI 63
Query: 117 ATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLA 176
TAHVEYET KRHYAHVDCPGHADYVKNMITGAAQMDG ILVV+A DGPMPQT+EHILLA
Sbjct: 64 NTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLA 123
Query: 177 RQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKN 236
RQVGVP LV FLNKVDLV+DEELLELVEME+RELLS Y FPGD+IP+IRGSA AL+G
Sbjct: 124 RQVGVPYLVVFLNKVDLVDDEELLELVEMEVRELLSEYDFPGDDIPVIRGSALKALEGDP 183
Query: 237 EEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGE 296
+ AI++LMDAVDEYIP PER DKPFLMP+EDVF+I GRGTV TGRVE+GT+KVG+
Sbjct: 184 KWE--DAIMELMDAVDEYIPTPERDTDKPFLMPVEDVFTITGRGTVVTGRVERGTVKVGD 241
Query: 297 EVEVLGLTQGPSLKTTVTGVEMFKKILDRGEAGDNVGLLLRGLKREDVQRGQVIAKPGSV 356
EVE++G+ + KT VTGVEMF+K+LD G+AGDNVG+LLRG+ R++V+RGQV+AKPGS+
Sbjct: 242 EVEIVGI--KETQKTVVTGVEMFRKLLDEGQAGDNVGVLLRGVDRDEVERGQVLAKPGSI 299
Query: 357 KTYKKFEAEIYVLTKDEGGRHTAFFSNYRPQIYLRTADVTGKVELLGDVKMVMPGDNVNA 416
K + KF+AE+Y+LTK+EGGRHT FF+NYRPQ Y RT DVTG +EL +MVMPGDNV
Sbjct: 300 KPHTKFKAEVYILTKEEGGRHTPFFNNYRPQFYFRTTDVTGSIELPEGTEMVMPGDNVTI 359
Query: 417 AFELISPLPLQQGQRFALREGGRTVGAGVVSKVI 450
ELI P+ ++QG +FA+REGGRTVGAG V++++
Sbjct: 360 TVELIHPIAMEQGLKFAIREGGRTVGAGTVTEIL 393
>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 = 723 bits (1867), Expect = 0.0
Identities = 296/398 (74%), Positives = 332/398 (83%), Gaps = 4/398 (1%)
Query: 54 RSMATFTRTKLHVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRG 113
+ F RTK HVN+GTIGHVDHGKTTLTAAIT VLA+EG A A A+D+ID APEEK RG
Sbjct: 1 MAKEKFERTKPHVNIGTIGHVDHGKTTLTAAITTVLAKEGGAAARAYDQIDNAPEEKARG 60
Query: 114 ITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHI 173
ITI TAHVEYET RHYAHVDCPGHADYVKNMITGAAQMDG ILVVSA DGPMPQT+EHI
Sbjct: 61 ITINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSATDGPMPQTREHI 120
Query: 174 LLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQ 233
LLARQVGVP +V FLNK D+V+DEELLELVEME+RELLS Y FPGD+ PIIRGSA AL+
Sbjct: 121 LLARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSEYDFPGDDTPIIRGSALKALE 180
Query: 234 GKNEEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIK 293
G E + IL+LMDAVDEYIP PER+ DKPFLMPIEDVFSI GRGTV TGRVE+G +K
Sbjct: 181 GDAE--WEAKILELMDAVDEYIPTPERETDKPFLMPIEDVFSITGRGTVVTGRVERGIVK 238
Query: 294 VGEEVEVLGLTQGPSLKTTVTGVEMFKKILDRGEAGDNVGLLLRGLKREDVQRGQVIAKP 353
VGEEVE++GL + KTTVTGVEMF+K LD G AGDNVGLLLRG+KRE+++RG V+AKP
Sbjct: 239 VGEEVEIVGLK--DTRKTTVTGVEMFRKELDEGRAGDNVGLLLRGIKREEIERGMVLAKP 296
Query: 354 GSVKTYKKFEAEIYVLTKDEGGRHTAFFSNYRPQIYLRTADVTGKVELLGDVKMVMPGDN 413
GS+K + KFEAE+YVL K+EGGRHT FFS YRPQ Y RT DVTG + L V+MVMPGDN
Sbjct: 297 GSIKPHTKFEAEVYVLKKEEGGRHTPFFSGYRPQFYFRTTDVTGSITLPEGVEMVMPGDN 356
Query: 414 VNAAFELISPLPLQQGQRFALREGGRTVGAGVVSKVIS 451
V ELISP+ L+QG RFA+REGGRTVGAGVVSK+I
Sbjct: 357 VKMTVELISPIALEQGMRFAIREGGRTVGAGVVSKIIE 394
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 706 bits (1824), Expect = 0.0
Identities = 289/394 (73%), Positives = 334/394 (84%), Gaps = 4/394 (1%)
Query: 57 ATFTRTKLHVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITI 116
F RTK HVNVGTIGHVDHGKTTLTAAIT VLA++G A+A A+D+ID APEEK RGITI
Sbjct: 4 EKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKKGGAEAKAYDQIDNAPEEKARGITI 63
Query: 117 ATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLA 176
TAHVEYETA RHYAHVDCPGHADYVKNMITGAAQMDG ILVV+A DGPMPQT+EHILLA
Sbjct: 64 NTAHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLA 123
Query: 177 RQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKN 236
RQVGVP +V FLNKVD+V+DEELLELVEME+RELLS Y FPGD+ PIIRGSA AL+G
Sbjct: 124 RQVGVPYIVVFLNKVDMVDDEELLELVEMEVRELLSEYGFPGDDTPIIRGSALKALEGDA 183
Query: 237 EEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGE 296
+ + I +LMDAVD YIP PER +DKPFLMP+EDVFSI GRGTV TGRVE+G +KVGE
Sbjct: 184 K--WEAKIEELMDAVDSYIPTPERDIDKPFLMPVEDVFSISGRGTVVTGRVERGILKVGE 241
Query: 297 EVEVLGLTQGPSLKTTVTGVEMFKKILDRGEAGDNVGLLLRGLKREDVQRGQVIAKPGSV 356
EVE++G+ + KTTVTGVEMF+K+LD G+AGDNVG+LLRG+KREDV+RGQV+AKPGS+
Sbjct: 242 EVEIVGI--KETQKTTVTGVEMFRKLLDEGQAGDNVGVLLRGVKREDVERGQVLAKPGSI 299
Query: 357 KTYKKFEAEIYVLTKDEGGRHTAFFSNYRPQIYLRTADVTGKVELLGDVKMVMPGDNVNA 416
K + KFEAE+YVL+K+EGGRHT FF YRPQ Y RT DVTG + L V+MVMPGDNV
Sbjct: 300 KPHTKFEAEVYVLSKEEGGRHTPFFHGYRPQFYFRTTDVTGAITLPEGVEMVMPGDNVKM 359
Query: 417 AFELISPLPLQQGQRFALREGGRTVGAGVVSKVI 450
ELI P+ +++G RFA+REGGRTVGAGVV+K+I
Sbjct: 360 VVELIHPIAMEEGLRFAIREGGRTVGAGVVTKII 393
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 694 bits (1794), Expect = 0.0
Identities = 274/409 (66%), Positives = 324/409 (79%), Gaps = 15/409 (3%)
Query: 55 SMATFTRTKLHVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGI 114
+ F R K HVN+GTIGHVDHGKTTLTAAIT LA +G AKA +DEID APEEK RGI
Sbjct: 2 AREKFERKKPHVNIGTIGHVDHGKTTLTAAITMTLAAKGGAKAKKYDEIDSAPEEKARGI 61
Query: 115 TIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHIL 174
TI TAHVEYET RHYAHVDCPGHADYVKNMITGAAQMDG ILVVSA DGPMPQTKEHIL
Sbjct: 62 TINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTKEHIL 121
Query: 175 LARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQG 234
LA+QVGVP++V FLNK D V+DEELLELVE+E+RELLS Y FPGD+IPI+ GSA AL+
Sbjct: 122 LAKQVGVPNIVVFLNKEDQVDDEELLELVELEVRELLSKYDFPGDDIPIVSGSALLALEA 181
Query: 235 --KNEEIGK------KAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGR 286
+N +I + I LMDAVD YIP PER DKPFLM IEDVFSI GRGTVATGR
Sbjct: 182 LTENPKIKRGENKWVDKIYNLMDAVDSYIPTPERDTDKPFLMAIEDVFSITGRGTVATGR 241
Query: 287 VEQGTIKVGEEVEVLGLTQGPSLKTTVTGVEMFKKILDRGEAGDNVGLLLRGLKREDVQR 346
+E+GT+KVG+ VE++GL + TTVTG+EMF+K LD G AGDNVG+LLRG+++ED++R
Sbjct: 242 IERGTVKVGDTVEIVGL--RETKTTTVTGLEMFQKTLDEGLAGDNVGILLRGIQKEDIER 299
Query: 347 GQVIAKPGSVKTYKKFEAEIYVLTKDEGGRHTAFFSNYRPQIYLRTADVTGKVELL---- 402
G V+AKPG++ + KFEA++Y+LTK+EGGRHT FF YRPQ Y+RT DVTGK+E
Sbjct: 300 GMVLAKPGTITPHTKFEAQVYILTKEEGGRHTPFFPGYRPQFYVRTTDVTGKIESFTADD 359
Query: 403 -GDVKMVMPGDNVNAAFELISPLPLQQGQRFALREGGRTVGAGVVSKVI 450
+MVMPGD + ELI P+ +++G RFA+REGGRTVGAGVVSK++
Sbjct: 360 GSKTEMVMPGDRIKMTVELIYPIAIEKGMRFAIREGGRTVGAGVVSKIL 408
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 571 bits (1472), Expect = 0.0
Identities = 271/411 (65%), Positives = 319/411 (77%), Gaps = 19/411 (4%)
Query: 55 SMATFTRTKLHVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGI 114
+ F R K HVN+GTIGHVDHGKTTLTAA+T LA G + +DEID APEE+ RGI
Sbjct: 71 ARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMALASMGGSAPKKYDEIDAAPEERARGI 130
Query: 115 TIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHIL 174
TI TA VEYET RHYAHVDCPGHADYVKNMITGAAQMDG ILVVS DGPMPQTKEHIL
Sbjct: 131 TINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHIL 190
Query: 175 LARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQ- 233
LA+QVGVP++V FLNK D V+DEELLELVE+E+RELLS Y+FPGD+IPII GSA AL+
Sbjct: 191 LAKQVGVPNMVVFLNKQDQVDDEELLELVELEVRELLSSYEFPGDDIPIISGSALLALEA 250
Query: 234 ---------GKNEEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVAT 284
G N+ + K I +LMDAVD YIP P+RQ D PFL+ +EDVFSI GRGTVAT
Sbjct: 251 LMENPNIKRGDNKWVDK--IYELMDAVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVAT 308
Query: 285 GRVEQGTIKVGEEVEVLGLTQGPSLKTTVTGVEMFKKILDRGEAGDNVGLLLRGLKREDV 344
GRVE+GT+KVGE V+++GL + S TTVTGVEMF+KILD AGDNVGLLLRG+++ D+
Sbjct: 309 GRVERGTVKVGETVDIVGLRETRS--TTVTGVEMFQKILDEALAGDNVGLLLRGIQKADI 366
Query: 345 QRGQVIAKPGSVKTYKKFEAEIYVLTKDEGGRHTAFFSNYRPQIYLRTADVTGKV-ELLG 403
QRG V+AKPGS+ + KFEA +YVL K+EGGRH+ FF+ YRPQ Y+RT DVTGKV ++
Sbjct: 367 QRGMVLAKPGSITPHTKFEAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGKVTSIMN 426
Query: 404 D----VKMVMPGDNVNAAFELISPLPLQQGQRFALREGGRTVGAGVVSKVI 450
D KMVMPGD V ELI P+ +QG RFA+REGG+TVGAGV+ +I
Sbjct: 427 DKDEESKMVMPGDRVKMVVELIVPVACEQGMRFAIREGGKTVGAGVIQSII 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 = 420 bits (1082), Expect = e-148
Identities = 150/194 (77%), Positives = 167/194 (86%)
Query: 65 HVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHVEYE 124
HVNVGTIGHVDHGKTTLTAAITKVLA++G AKA +DEIDKAPEEK RGITI TAHVEYE
Sbjct: 2 HVNVGTIGHVDHGKTTLTAAITKVLAKKGGAKAKKYDEIDKAPEEKARGITINTAHVEYE 61
Query: 125 TAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSL 184
TA RHYAHVDCPGHADY+KNMITGAAQMDG ILVVSA DGPMPQT+EH+LLARQVGVP +
Sbjct: 62 TANRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSATDGPMPQTREHLLLARQVGVPYI 121
Query: 185 VCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKAI 244
V FLNK D+V+DEELLELVEME+RELLS Y F GD+ PI+RGSA AL+G + I
Sbjct: 122 VVFLNKADMVDDEELLELVEMEVRELLSKYGFDGDDTPIVRGSALKALEGDDPNKWVDKI 181
Query: 245 LKLMDAVDEYIPDP 258
L+L+DA+D YIP 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 = 275 bits (707), Expect = 7e-92
Identities = 96/195 (49%), Positives = 126/195 (64%), Gaps = 11/195 (5%)
Query: 63 KLHVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHVE 122
K H N+G IGHVDHGKTTLT A+ V K A +DK EE++RGITI A V
Sbjct: 1 KRHRNIGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVS 60
Query: 123 YETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVP 182
+ET KR +D PGH D+ K MI GA+Q DG ILVV A +G MPQT+EH+LLA+ +GVP
Sbjct: 61 FETKKRLINIIDTPGHVDFTKEMIRGASQADGAILVVDAVEGVMPQTREHLLLAKTLGVP 120
Query: 183 SLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKK 242
++ F+NK+D V+D EL E+VE RELL Y F G+ +P++ G SAL G+
Sbjct: 121 -IIVFINKIDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPG---SALTGEG------ 170
Query: 243 AILKLMDAVDEYIPD 257
I +L++A+D Y+P
Sbjct: 171 -IDELLEALDLYLPS 184
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 275 bits (705), Expect = 2e-88
Identities = 158/438 (36%), Positives = 223/438 (50%), Gaps = 67/438 (15%)
Query: 63 KLHVNVGTIGHVDHGKTTL-------TAAITK-------VLAEEGKAKAIAFDEI-DKAP 107
K H+N+ IGHVD GK+TL I K A+E ++ F + DK
Sbjct: 5 KPHLNLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVLDKTK 64
Query: 108 EEKKRGITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDG--- 164
EE++RG+TI AH ++ET K ++ +D PGH D+VKNMITGA+Q D +LVV A DG
Sbjct: 65 EERERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARDGEFE 124
Query: 165 ----PMPQTKEHILLARQVGVPSLVCFLNKVDLVE-DEELLELVEMELRELLSFYKFPGD 219
QT+EH LAR +G+ L+ +NK+DLV DEE E + E+ +LL +
Sbjct: 125 AGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLLKMVGYNPK 184
Query: 220 EIPIIRGSATSALQGKN-EEIGKKA----ILKLMDAVDEYIPDPERQLDKPFLMPIEDVF 274
++P I S +G N + + L++A+D+ + PER LDKP +PI+DV+
Sbjct: 185 DVPFI---PISGFKGDNLTKKSENMPWYKGPTLLEALDQ-LEPPERPLDKPLRLPIQDVY 240
Query: 275 SIQGRGTVATGRVEQGTIKVGEEVEVLGLTQGPSLKTTVTGVEMFKKILDRGEAGDNVGL 334
SI G GTV GRVE G IK G++V + G + V +EM + + + E GDNVG
Sbjct: 241 SISGIGTVPVGRVESGVIKPGQKVTF--MPAG--VVGEVKSIEMHHEEISQAEPGDNVGF 296
Query: 335 LLRGLKREDVQRGQVIAKPGSVKTY-KKFEAEIYVLTKDEGGRHTAFFSNYRPQIYLRTA 393
+RG+++ D++RG VI + T +F A+I VL S Y P ++ TA
Sbjct: 297 NVRGVEKNDIRRGDVIGHSDNPPTVSPEFTAQIIVL-----WHPGIITSGYTPVLHAHTA 351
Query: 394 DV--------------TGKV--ELLGDVKMVMPGDNVNAAFELISPLPL------QQGQR 431
V TGK E +K GD E PL L Q R
Sbjct: 352 QVACRIAELLSKLDPRTGKKLEENPQFLK---RGDAAIVKIEPEKPLCLEKVSEIPQLGR 408
Query: 432 FALREGGRTVGAGVVSKV 449
FALR+ G+T+ AG V +V
Sbjct: 409 FALRDMGQTIAAGKVLEV 426
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 270 bits (693), Expect = 2e-86
Identities = 168/440 (38%), Positives = 238/440 (54%), Gaps = 72/440 (16%)
Query: 61 RTKLHVNVGTIGHVDHGKTTLT-----------AAITKVLAEEGKAKAIAFDE----IDK 105
+ K H+N+ IGHVDHGK+TL I + L EE K K + +D+
Sbjct: 2 KEKPHLNLAVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMDR 61
Query: 106 APEEKKRGITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPD-- 163
EE++RG+TI AH ++ET K ++ VDCPGH D+VKNMITGA+Q D +LVV+A D
Sbjct: 62 LKEERERGVTIDLAHKKFETDKYYFTIVDCPGHRDFVKNMITGASQADAAVLVVAADDAG 121
Query: 164 GPMPQTKEHILLARQVGVPSLVCFLNKVDLVE-DEELLELVEMELRELLSFYKFPGDEIP 222
G MPQT+EH+ LAR +G+ L+ +NK+D V DE+ E V+ E+ +LL + D+IP
Sbjct: 122 GVMPQTREHVFLARTLGINQLIVAINKMDAVNYDEKRYEEVKEEVSKLLKMVGYKPDDIP 181
Query: 223 IIRGSATSALQGKNEEIGKKAI-------LKLMDAVDEYIPDPERQLDKPFLMPIEDVFS 275
I SA +G N + KK+ L++A+D + PE+ DKP +PI+DV+S
Sbjct: 182 FI---PVSAFEGDN--VVKKSENMPWYNGPTLLEALDN-LKPPEKPTDKPLRIPIQDVYS 235
Query: 276 IQGRGTVATGRVEQGTIKVGEEVEVLGLTQGPSLKT-TVTGVEMFKKILDRGEAGDNVGL 334
I G GTV GRVE G +KVG++V + P+ V +EM + L + E GDN+G
Sbjct: 236 ISGVGTVPVGRVETGVLKVGDKVVFM-----PAGVVGEVKSIEMHHEELPQAEPGDNIGF 290
Query: 335 LLRGLKREDVQRGQVIAKPGSVKTY-KKFEAEIYVLTKDEGGRH-TAFFSNYRPQIYLRT 392
+RG+ ++D++RG V P + T ++F A+I VL +H +A Y P + T
Sbjct: 291 NVRGVGKKDIKRGDVCGHPDNPPTVAEEFTAQIVVL------QHPSAITVGYTPVFHAHT 344
Query: 393 ADVTGKVELL--------GDVKMVMP-----GDNVNAAFELISPL-PL---------QQG 429
A V E L G V P GD AA I P PL Q G
Sbjct: 345 AQVACTFEELVKKLDPRTGQVAEENPQFIKTGD---AAIVKIKPTKPLVIEKVKEIPQLG 401
Query: 430 QRFALREGGRTVGAGVVSKV 449
RFA+R+ G+T+ AG+V V
Sbjct: 402 -RFAIRDMGQTIAAGMVIDV 420
>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 = 232 bits (592), Expect = 1e-71
Identities = 156/436 (35%), Positives = 226/436 (51%), Gaps = 63/436 (14%)
Query: 61 RTKLHVNVGTIGHVDHGKTTLT---------------AAITKVLAEEGKAKAIAFDEIDK 105
+ K H+NV IGHVDHGK+T K E+GKA +D+
Sbjct: 3 KEKEHINVAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFEFAWVMDR 62
Query: 106 APEEKKRGITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGP 165
EE++RG+TI AH ++ET K VDCPGH D++KNMITGA+Q D +LVV+ DG
Sbjct: 63 LKEERERGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGDGE 122
Query: 166 ---MPQTKEHILLARQVGVPSLVCFLNKVDLVE-DEELLELVEMELRELLSFYKFPGDEI 221
PQT+EH LAR +G+ L+ +NK+D V DEE E ++ E+ L+ + D +
Sbjct: 123 FEVQPQTREHAFLARTLGINQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVGYNPDTV 182
Query: 222 PIIRGSATSALQGKN--EEIGKKAILK---LMDAVDEYIPDPERQLDKPFLMPIEDVFSI 276
P I SA G N ++ K L++A+D P PE+ DKP +PI+DV+SI
Sbjct: 183 PFI---PISAWNGDNVIKKSENTPWYKGKTLLEALDALEP-PEKPTDKPLRIPIQDVYSI 238
Query: 277 QGRGTVATGRVEQGTIKVGEEV--EVLGLTQGPSLKTTVTGVEMFKKILDRGEAGDNVGL 334
G GTV GRVE G +K G++V E G++ V +EM + +++ E GDN+G
Sbjct: 239 TGVGTVPVGRVETGVLKPGDKVVFEPAGVS------GEVKSIEMHHEQIEQAEPGDNIGF 292
Query: 335 LLRGLKREDVQRGQVIAKPGS-VKTYKKFEAEIYVLTKDEGGRH-TAFFSNYRPQIYLRT 392
+RG+ ++D++RG V P + K K+F A+I VL +H A Y P + T
Sbjct: 293 NVRGVSKKDIRRGDVCGHPDNPPKVAKEFTAQIVVL------QHPGAITVGYTPVFHCHT 346
Query: 393 ADVTGK-VELL-------GDVKMVMP-----GDNVNAAFELISPLPLQ------QGQRFA 433
A + + ELL G V P GD F+ P+ ++ RFA
Sbjct: 347 AQIACRFDELLKKNDPRTGQVLEENPQFLKTGDAAIVKFKPTKPMVIEAVKEIPPLGRFA 406
Query: 434 LREGGRTVGAGVVSKV 449
+R+ G+TV AG++ V
Sbjct: 407 IRDMGQTVAAGMIIDV 422
>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 = 193 bits (492), Expect = 7e-60
Identities = 79/195 (40%), Positives = 109/195 (55%), Gaps = 15/195 (7%)
Query: 67 NVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHVEYETA 126
NVG IGHVDHGKTTLT ++ + +D EE++RGITI T VE+E
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWP 60
Query: 127 KRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLVC 186
KR +D PGH D+ K + G AQ DG +LVV A +G PQT+EH+ +A G+P +V
Sbjct: 61 KRRINFIDTPGHEDFSKETVRGLAQADGALLVVDANEGVEPQTREHLNIALAGGLPIIVA 120
Query: 187 FLNKVDLVEDEELLELVEMELRELLS---FYKFPGDEIPIIRGSATSALQGKNEEIGKKA 243
+NK+D V EE + V E++ELL F G ++PII SA +
Sbjct: 121 -VNKIDRV-GEEDFDEVLREIKELLKLIGFTFLKGKDVPIIPISALTGE----------G 168
Query: 244 ILKLMDAVDEYIPDP 258
I +L+DA+ E++P P
Sbjct: 169 IEELLDAIVEHLPPP 183
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 193 bits (492), Expect = 1e-56
Identities = 106/393 (26%), Positives = 183/393 (46%), Gaps = 63/393 (16%)
Query: 66 VNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHVEYET 125
+ +GT GH+DHGKTTL A+T + D+ PEEKKRGITI +
Sbjct: 1 MIIGTAGHIDHGKTTLLKALTGGVT-------------DRLPEEKKRGITIDLGFYYRKL 47
Query: 126 AKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLV 185
+D PGH D++ N++ G +D +LVV+A +G M QT EH+L+ +G+ + +
Sbjct: 48 EDGVMGFIDVPGHPDFISNLLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGIKNGI 107
Query: 186 CFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKAIL 245
L K D V++ +E +++++L+ I + SA + G+ E K ++
Sbjct: 108 IVLTKADRVDEAR----IEQKIKQILADLSLA--NAKIFKTSAKT---GRGIEELKNELI 158
Query: 246 KLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQ 305
L++ + ER KPF + I+ F+++G GTV TG V G +KVG+++ + + +
Sbjct: 159 DLLE-------EIERDEQKPFRIAIDRAFTVKGVGTVVTGTVLSGEVKVGDKLYLSPINK 211
Query: 306 GPSLKTTVTGVEMFKKILDRGEAGDNVGLLLRGLKREDVQRGQVIAKPGS--VKTYKKFE 363
+ V ++ ++ +AG VGL L+G+++E+++RG + KP V T E
Sbjct: 212 ----EVRVRSIQAHDVDVEEAKAGQRVGLALKGVEKEEIERGDWLLKPEPLEVTTRLIVE 267
Query: 364 AEIYVLTKDEGGRHTAFFSNYRP----QIYLRTADVTGKVELL-GDVKMVM-----PGDN 413
EI F + I++ VTG++ L + ++ + GDN
Sbjct: 268 LEI----------DPLFKKTLKQGQPVHIHVGLRSVTGRIVPLEKNAELNLVKPIALGDN 317
Query: 414 VNAAFELISPLPLQQGQRFALREGGRTVGAGVV 446
L L+ G R + +
Sbjct: 318 DR--------LVLRDNSAVIKLAGARVLSLNLP 342
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 189 bits (483), Expect = 2e-55
Identities = 145/444 (32%), Positives = 208/444 (46%), Gaps = 76/444 (17%)
Query: 63 KLHVNVGTIGHVDHGKTTLTAAIT---------------KVLAEEGKAKAIAFDEIDKAP 107
K H+N+ IGHVD GK+T T + K AE GK +DK
Sbjct: 5 KTHINLVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLK 64
Query: 108 EEKKRGITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMP 167
E++RGITI A ++ET K ++ +D PGH D++KNMITG +Q D ILVV++ G
Sbjct: 65 AERERGITIDIALWKFETPKYYFTIIDAPGHRDFIKNMITGTSQADVAILVVASTAGEFE 124
Query: 168 -------QTKEHILLARQVGVPSLVCFLNKVDLVE---DEELLELVEMELRELLSFYKFP 217
QT+EH LLA +GV ++ +NK+D +E + ++ E+ L +
Sbjct: 125 AGISKDGQTREHALLAFTLGVKQMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKKVGYN 184
Query: 218 GDEIPIIRGSATSALQGKN--EEIGKKAILK---LMDAVDEYIPDPERQLDKPFLMPIED 272
+++P I S QG N E+ K L++A+D P P+R +DKP +P++D
Sbjct: 185 PEKVPFI---PISGWQGDNMIEKSDNMPWYKGPTLLEALDTLEP-PKRPVDKPLRLPLQD 240
Query: 273 VFSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQGPSLKTT-VTGVEMFKKILDRGEAGDN 331
V+ I G GTV GRVE G +K G V T PS TT V VEM + L GDN
Sbjct: 241 VYKIGGIGTVPVGRVETGILKPGMVV-----TFAPSGVTTEVKSVEMHHEQLAEAVPGDN 295
Query: 332 VGLLLRGLKREDVQRGQVI--AKPGSVKTYKKFEAEIYVLTKDEGGRHTAFFSN-YRPQI 388
VG ++ + +D++RG V +K K F A++ VL H N Y P +
Sbjct: 296 VGFNVKNVSVKDIKRGYVASDSKNDPAKECADFTAQVIVLN------HPGQIKNGYTPVL 349
Query: 389 YLRTADV--------------TGKVELLGDVKMVMPGDNVNAAFELISPL---------P 425
TA + +GKV L + K + GD P+ P
Sbjct: 350 DCHTAHIACKFAEIESKIDRRSGKV-LEENPKAIKSGDAAIVKMVPTKPMCVEVFNEYPP 408
Query: 426 LQQGQRFALREGGRTVGAGVVSKV 449
L RFA+R+ +TV GV+ V
Sbjct: 409 L---GRFAVRDMKQTVAVGVIKSV 429
>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 = 191 bits (487), Expect = 7e-55
Identities = 111/381 (29%), Positives = 176/381 (46%), Gaps = 51/381 (13%)
Query: 66 VNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHVEYET 125
+ + T GHVDHGKTTL A+T + A D+ PEEKKRG+TI +
Sbjct: 1 MIIATAGHVDHGKTTLLKALTGIAA-------------DRLPEEKKRGMTIDLGFAYFPL 47
Query: 126 AKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLV 185
+D PGH ++ N I G +D +LVV A +G M QT EH+ + +G+P +
Sbjct: 48 PDYRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIPHTI 107
Query: 186 CFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKAIL 245
+ K D V +EE ++ EM ++++L+ Y F + TSA G+ KK +
Sbjct: 108 VVITKADRV-NEEEIKRTEMFMKQILNSYIFLKNAKIFK----TSAKTGQGIGELKKELK 162
Query: 246 KLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQ 305
L++++D +++ KP M I+ F ++G GTV TG G +KVG+ + +L +
Sbjct: 163 NLLESLD------IKRIQKPLRMAIDRAFKVKGAGTVVTGTAFSGEVKVGDNLRLLPINH 216
Query: 306 GPSLKTTVTGVEMFKKILDRGEAGDNVGLLLRGLKREDVQRGQVIAKPGSVKT--YKKFE 363
+ V ++ + ++ AG + L L ++ E ++RG +I P K KF
Sbjct: 217 ----EVRVKAIQAQNQDVEIAYAGQRIALNLMDVEPESLKRGLLILTPEDPKLRVVVKFI 272
Query: 364 AEIYVLTKDEGGRHTAFFSNYRPQIYLRTADVTGKVELLGDVKMVMPGDNVNAAFELISP 423
AE+ +L I + TGK+ LL D A L +P
Sbjct: 273 AEVPLL------------ELQPYHIAHGMSVTTGKISLL---------DKGIALLTLDAP 311
Query: 424 LPLQQGQRFALREGGRTVGAG 444
L L +G + LR+ AG
Sbjct: 312 LILAKGDKLVLRDSSGNFLAG 332
>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 = 175 bits (445), Expect = 4e-54
Identities = 60/90 (66%), Positives = 71/90 (78%)
Query: 357 KTYKKFEAEIYVLTKDEGGRHTAFFSNYRPQIYLRTADVTGKVELLGDVKMVMPGDNVNA 416
K + KFEAE+YVLTK+EGGRHT FFS YRPQ Y+RT DVTG + L +MVMPGDNV
Sbjct: 1 KPHTKFEAEVYVLTKEEGGRHTPFFSGYRPQFYIRTTDVTGSITLPEGTEMVMPGDNVKM 60
Query: 417 AFELISPLPLQQGQRFALREGGRTVGAGVV 446
ELI P+ L++G RFA+REGGRTVGAGV+
Sbjct: 61 TVELIHPIALEKGLRFAIREGGRTVGAGVI 90
>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 = 165 bits (421), Expect = 1e-50
Identities = 67/89 (75%), Positives = 79/89 (88%), Gaps = 2/89 (2%)
Query: 266 FLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQGPSLKTTVTGVEMFKKILDR 325
FLMPIEDVFSI GRGTV TGR+E+GTIKVG+EVE++G G +LKTTVTG+EMF+K LD
Sbjct: 1 FLMPIEDVFSIPGRGTVVTGRIERGTIKVGDEVEIVGF--GETLKTTVTGIEMFRKTLDE 58
Query: 326 GEAGDNVGLLLRGLKREDVQRGQVIAKPG 354
EAGDNVG+LLRG+KREDV+RG V+AKPG
Sbjct: 59 AEAGDNVGVLLRGVKREDVERGMVLAKPG 87
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 165 bits (419), Expect = 2e-45
Identities = 121/435 (27%), Positives = 200/435 (45%), Gaps = 73/435 (16%)
Query: 65 HVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHVEY- 123
HV VG GHVDHGK+TL + ++G ++ +D E +RG++ + Y
Sbjct: 117 HVLVGVAGHVDHGKSTLVGVLVTGRLDDGDGATRSY--LDVQKHEVERGLSADISLRVYG 174
Query: 124 ----------------------ETAKRHYAHVDCPGHADYVKNMITG--AAQMDGGILVV 159
+ A + + VD GH +++ I G ++D G+LVV
Sbjct: 175 FDDGKVVRLKNPLDEAEKAAVVKRADKLVSFVDTVGHEPWLRTTIRGLLGQKVDYGLLVV 234
Query: 160 SAPDGPMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFY-KFP- 217
+A DG TKEH+ +A + +P +V + K+D+V D+ +VE E+ LL + P
Sbjct: 235 AADDGVTKMTKEHLGIALAMELPVIVV-VTKIDMVPDDRFQGVVE-EISALLKRVGRIPL 292
Query: 218 -----------------GDEI-PIIRGSATSALQGKNEEIGKKAILKLMDAVDEYIPDPE 259
G + PI TS++ G+ ++ + L L
Sbjct: 293 IVKDTDDVVLAAKAMKAGRGVVPIFY---TSSVTGEGLDLLDEFFLLL---------PKR 340
Query: 260 RQLD--KPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQGPSLKTTVTGVE 317
R+ D PFLM I+ ++S+ G GTV +G V+ G + VG+ V + G + V +E
Sbjct: 341 RRWDDEGPFLMYIDKIYSVTGVGTVVSGSVKSGILHVGDTVLLGPFKDGKFREVVVKSIE 400
Query: 318 MFKKILDRGEAGDNVGLLLRGLKREDVQRGQVIAKPGSVKTYKKFEAEIYVLTKDEGGRH 377
M +D +AG +G+ L+G+++E+++RG V++ K ++F+AE+ VL RH
Sbjct: 401 MHHYRVDSAKAGSIIGIALKGVEKEELERGMVLSAGADPKAVREFDAEVLVL------RH 454
Query: 378 -TAFFSNYRPQIYLRTADVTGKVELLGDVKMVMPGDNVNAAFEL-ISPLPLQQGQRFALR 435
T + Y P + T E + D +MPGD P +++GQ+F R
Sbjct: 455 PTTIRAGYEPVFHYETIREAVYFEEI-DKGFLMPGDRGVVRMRFKYRPHHVEEGQKFVFR 513
Query: 436 EGGRTVGAGVVSKVI 450
E GR+ G G V +V
Sbjct: 514 E-GRSKGVGRVIRVD 527
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 162 bits (411), Expect = 4e-45
Identities = 136/442 (30%), Positives = 214/442 (48%), Gaps = 68/442 (15%)
Query: 61 RTKLHVNVGTIGHVDHGKTTLTA-------AITKVLAEEGKAKAIAFDE--------IDK 105
+ K+H+N+ IGHVD GK+T T I K + E + +A ++ +DK
Sbjct: 3 KEKVHINIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFEKEAAEMNKRSFKYAWVLDK 62
Query: 106 APEEKKRGITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGP 165
E++RGITI A ++ET K + +D PGH D++KNMITG +Q D +L++ + G
Sbjct: 63 LKAERERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGG 122
Query: 166 MP-------QTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPG 218
QT+EH LLA +GV ++C NK+D + + ++E+ S+ K G
Sbjct: 123 FEAGISKDGQTREHALLAFTLGVKQMICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVG 182
Query: 219 ---DEIPIIRGSATSALQGKNEEIGKKAILK------LMDAVDEYIPDPERQLDKPFLMP 269
D+IP + S +G N I + L L++A+D+ I +P+R DKP +P
Sbjct: 183 YNPDKIPFV---PISGFEGDN-MIERSTNLDWYKGPTLLEALDQ-INEPKRPSDKPLRLP 237
Query: 270 IEDVFSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQGPS-LKTTVTGVEMFKKILDRGEA 328
++DV+ I G GTV GRVE G IK G + +T GP+ L T V VEM + L
Sbjct: 238 LQDVYKIGGIGTVPVGRVETGVIKPG-----MVVTFGPTGLTTEVKSVEMHHESLQEALP 292
Query: 329 GDNVGLLLRGLKREDVQRGQVI--AKPGSVKTYKKFEAEIYVLTK--DEGGRHTAFFSNY 384
GDNVG ++ + +D++RG V +K K F +++ ++ G + +
Sbjct: 293 GDNVGFNVKNVAVKDLKRGYVASNSKDDPAKEAANFTSQVIIMNHPGQIGNGYAPVLDCH 352
Query: 385 RPQIYLRTADVTGKVEL-----------------LGDVKMVMPGDNVNAAFELISPLPLQ 427
I ++ A++ K++ G VKM+ V F PL
Sbjct: 353 TSHIAVKFAEILTKIDRRSGKELEKEPKFLKNGDAGFVKMIPTKPMVVETFSEYPPL--- 409
Query: 428 QGQRFALREGGRTVGAGVVSKV 449
RFA+R+ +TV GV+ V
Sbjct: 410 --GRFAVRDMRQTVAVGVIKSV 429
>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 = 159 bits (405), Expect = 2e-44
Identities = 113/354 (31%), Positives = 169/354 (47%), Gaps = 75/354 (21%)
Query: 66 VNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHVEYET 125
VN+G +GHVDHGKTTLT A+T V D EE KRGI+I + + E
Sbjct: 5 VNIGMVGHVDHGKTTLTKALTGVW-------------TDTHSEELKRGISIRLGYADAEI 51
Query: 126 AK--------------------------RHYAHVDCPGHADYVKNMITGAAQMDGGILVV 159
K R + VD PGH + M++GAA MDG +LV+
Sbjct: 52 YKCPECDGPECYTTEPVCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGALLVI 111
Query: 160 SAPDG-PMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYK-FP 217
+A + P PQT+EH++ +G+ ++V NK+DLV E+ LE E+ F K
Sbjct: 112 AANEPCPQPQTREHLMALEIIGIKNIVIVQNKIDLVSKEKALE----NYEEIKEFVKGTI 167
Query: 218 GDEIPIIRGSATSALQGKNEEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQ 277
+ PII SAL N + L++A++++IP PER LDKP LM + F +
Sbjct: 168 AENAPII---PVSALHNANIDA-------LLEAIEKFIPTPERDLDKPPLMYVARSFDVN 217
Query: 278 GRGT--------VATGRVEQGTIKVGEEVEVL--------GLTQGPSLKTTVTGVEMFKK 321
GT V G + QG +KVG+E+E+ G T+ + T +T +
Sbjct: 218 KPGTPPEKLKGGVIGGSLIQGKLKVGDEIEIRPGIKVEKGGKTKWEPIYTEITSLRAGGY 277
Query: 322 ILDRGEAGDNVGL---LLRGLKREDVQRGQVIAKPGSV-KTYKKFEAEIYVLTK 371
++ G VG+ L L + D GQV+ KPG++ ++ E E+++L +
Sbjct: 278 KVEEARPGGLVGVGTKLDPALTKADALAGQVVGKPGTLPPVWESLELEVHLLER 331
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 157 bits (399), Expect = 2e-43
Identities = 114/358 (31%), Positives = 164/358 (45%), Gaps = 87/358 (24%)
Query: 66 VNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITI----ATAHV 121
VN+G +GHVDHGKTTL A+T V D+ EE KRGITI A A +
Sbjct: 10 VNIGMVGHVDHGKTTLVQALTGVWT-------------DRHSEELKRGITIRLGYADATI 56
Query: 122 ---------EYETAK-------------RHYAHVDCPGHADYVKNMITGAAQMDGGILVV 159
E T + R + VD PGH + M++GAA MDG ILV+
Sbjct: 57 RKCPDCEEPEAYTTEPKCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGAILVI 116
Query: 160 SAPDG-PMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPG 218
+A + P PQTKEH++ +G+ ++V NK+DLV E LE ++ F K
Sbjct: 117 AANEPCPQPQTKEHLMALDIIGIKNIVIVQNKIDLVSKERALE----NYEQIKEFVKGTV 172
Query: 219 DE----IPIIRGSATSALQGKNEEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVF 274
E IP+ SAL N I L++A++E IP PER LDKP M + F
Sbjct: 173 AENAPIIPV------SALHKVN-------IDALIEAIEEEIPTPERDLDKPPRMYVARSF 219
Query: 275 SIQGRGT--------VATGRVEQGTIKVGEEVEVL--------GLTQGPSLKTTVTGVEM 318
+ GT V G + QG +KVG+E+E+ G T+ + T + +
Sbjct: 220 DVNKPGTPPEKLKGGVIGGSLIQGVLKVGDEIEIRPGIKVEEGGKTKWEPITTKIVSLRA 279
Query: 319 FKKILDRGEAGDNVGLLLRG------LKREDVQRGQVIAKPGSV-KTYKKFEAEIYVL 369
+ ++ G GL+ G L + D G V KPG++ ++ E+++L
Sbjct: 280 GGEKVEEARPG---GLVGVGTKLDPSLTKADALAGSVAGKPGTLPPVWESLTIEVHLL 334
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 155 bits (395), Expect = 5e-43
Identities = 108/352 (30%), Positives = 163/352 (46%), Gaps = 75/352 (21%)
Query: 66 VNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHVE--- 122
VN+G +GHVDHGKTTLT A++ V D+ EE KRGITI + +
Sbjct: 11 VNIGMVGHVDHGKTTLTKALSGV-------------WTDRHSEELKRGITIKLGYADAKI 57
Query: 123 -----------YETAK------------RHYAHVDCPGHADYVKNMITGAAQMDGGILVV 159
Y T R + VD PGH + M++GAA MDG +LV+
Sbjct: 58 YKCPECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGHETLMATMLSGAALMDGALLVI 117
Query: 160 SAPDG-PMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFP- 217
+A + P PQT+EH++ +G+ +++ NK+DLV E LE ++ F K
Sbjct: 118 AANEPCPQPQTREHLMALEIIGIKNIIIVQNKIDLVSRERALE----NYEQIKEFVKGTV 173
Query: 218 GDEIPIIRGSATSALQGKNEEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQ 277
+ PII SA N I L++A+++YIP PER LDKP M + F +
Sbjct: 174 AENAPII---PISAQHKAN-------IDALIEAIEKYIPTPERDLDKPPRMYVARSFDVN 223
Query: 278 GRGT--------VATGRVEQGTIKVGEEVEVL--------GLTQGPSLKTTVTGVEMFKK 321
GT V G + QG ++VG+E+E+ G T + T + ++ +
Sbjct: 224 KPGTPPEELKGGVIGGSLVQGVLRVGDEIEIRPGIVVEKGGKTVWEPITTEIVSLQAGGE 283
Query: 322 ILDRGEAGDNVGL---LLRGLKREDVQRGQVIAKPGSV-KTYKKFEAEIYVL 369
++ G VG+ L L + D GQV+ KPG++ + E ++L
Sbjct: 284 DVEEARPGGLVGVGTKLDPTLTKADALVGQVVGKPGTLPPVWTSIRIEYHLL 335
>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 = 148 bits (376), Expect = 3e-42
Identities = 70/196 (35%), Positives = 98/196 (50%), Gaps = 30/196 (15%)
Query: 67 NVGTIGHVDHGKTTLT---------------AAITKVLAEEGKAK-AIAFDEIDKAPEEK 110
N+ IGHVD GK+TLT K E GK A+ +DK EE+
Sbjct: 1 NLVVIGHVDAGKSTLTGHLLYKLGGVDKRTIEKYEKEAKEMGKESFKYAW-VLDKLKEER 59
Query: 111 KRGITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDG------ 164
+RG+TI ++ET K + +D PGH D+VKNMITGA+Q D +LVVSA G
Sbjct: 60 ERGVTIDVGLAKFETEKYRFTIIDAPGHRDFVKNMITGASQADVAVLVVSARKGEFEAGF 119
Query: 165 -PMPQTKEHILLARQVGVPSLVCFLNKVDLVE---DEELLELVEMELRELLSFYKFPGDE 220
QT+EH LLAR +GV L+ +NK+D V +E + ++ ++ L + +
Sbjct: 120 EKGGQTREHALLARTLGVKQLIVAVNKMDDVTVNWSQERYDEIKKKVSPFLKKVGYNPKD 179
Query: 221 IPIIRGSATSALQGKN 236
+P I S G N
Sbjct: 180 VPFI---PISGFTGDN 192
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 150 bits (382), Expect = 6e-41
Identities = 101/333 (30%), Positives = 158/333 (47%), Gaps = 60/333 (18%)
Query: 70 TIGHVDHGKTTLTAAI---TKVLAEE--------GKAKAIAFDEIDKA------PEEKKR 112
T G VD GK+TL + TK + E+ K K ++ID A E+++
Sbjct: 11 TCGSVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLVDGLEAEREQ 70
Query: 113 GITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEH 172
GITI A+ + T KR + D PGH Y +NM TGA+ D IL+V A G + QT+ H
Sbjct: 71 GITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTADLAILLVDARKGVLEQTRRH 130
Query: 173 ILLARQVGVPSLVCFLNKVDLVE-DEELLELVEMELRELLSFYKFPGDE---IPIIRGSA 228
+A +G+ +V +NK+DLV+ EE+ E + + + + + IPI
Sbjct: 131 SFIASLLGIRHVVVAVNKMDLVDYSEEVFEAIVADYLAFAA--QLGLKDVRFIPI----- 183
Query: 229 TSALQGKNEEIGKK----------AILKLMDAVDEYIPDPERQLDKPFLMPIEDV--FSI 276
SAL G N + K +L++++ V+ +R K F P++ V ++
Sbjct: 184 -SALLGDN--VVSKSENMPWYKGPTLLEILETVE---IADDRSA-KAFRFPVQYVNRPNL 236
Query: 277 QGRGTVATGRVEQGTIKVGEEVEVLGLTQGPSLKTT-VTGVEMFKKILDRGEAGDNVGLL 335
RG G + G++KVG+EV VL PS KT+ V + F L + AG+ V L+
Sbjct: 237 DFRGY--AGTIASGSVKVGDEVVVL-----PSGKTSRVKRIVTFDGELAQASAGEAVTLV 289
Query: 336 LRGLKRE-DVQRGQVIAKPGS-VKTYKKFEAEI 366
L E D+ RG +I + F+A++
Sbjct: 290 ---LADEIDISRGDLIVAADAPPAVADAFDADV 319
>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 = 140 bits (355), Expect = 8e-41
Identities = 47/96 (48%), Positives = 63/96 (65%), Gaps = 5/96 (5%)
Query: 355 SVKTYKKFEAEIYVLTKDEGGRHTAFFSNYRPQIYLRTADVTGKVELLGDVKMVMPGDNV 414
+K + KF+A++Y+L T F+ YRP Y TADVTGK L G + VMPGDN
Sbjct: 1 PIKPHTKFKAQVYILNH-----PTPIFNGYRPVFYCHTADVTGKFILPGKKEFVMPGDNA 55
Query: 415 NAAFELISPLPLQQGQRFALREGGRTVGAGVVSKVI 450
ELI P+ +++GQRFA+REGGRTV GVV++V+
Sbjct: 56 IVTVELIKPIAVEKGQRFAIREGGRTVAVGVVTEVL 91
>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 = 141 bits (359), Expect = 2e-40
Identities = 73/188 (38%), Positives = 104/188 (55%), Gaps = 22/188 (11%)
Query: 68 VGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITI--ATAHVEYET 125
+GT GH+DHGKTTL A+T + E D+ PEEKKRGITI A+++
Sbjct: 2 IGTAGHIDHGKTTLIKALTGI-------------ETDRLPEEKKRGITIDLGFAYLDLPD 48
Query: 126 AKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLV 185
KR +D PGH +VKNM+ GA +D +LVV+A +G MPQT+EH+ + +G+ +
Sbjct: 49 GKR-LGFIDVPGHEKFVKNMLAGAGGIDAVLLVVAADEGIMPQTREHLEILELLGIKKGL 107
Query: 186 CFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKAIL 245
L K DLV DE+ LELVE E+ ELL+ I S++ G+ E K +
Sbjct: 108 VVLTKADLV-DEDRLELVEEEILELLAGTFLADAPIFP-----VSSVTGEGIEELKNYLD 161
Query: 246 KLMDAVDE 253
+L + +
Sbjct: 162 ELAEPQSK 169
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 148 bits (375), Expect = 6e-39
Identities = 115/391 (29%), Positives = 176/391 (45%), Gaps = 69/391 (17%)
Query: 70 TIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHVEY-ETAKR 128
T GHVDHGKTTL AIT V A D+ PEEKKRG+TI + + + R
Sbjct: 5 TAGHVDHGKTTLLQAITGVNA-------------DRLPEEKKRGMTIDLGYAYWPQPDGR 51
Query: 129 HYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLVCFL 188
+D PGH ++ NM+ G +D +LVV+ DG M QT+EH+ + + G P L L
Sbjct: 52 VLGFIDVPGHEKFLSNMLAGVGGIDHALLVVACDDGVMAQTREHLAILQLTGNPMLTVAL 111
Query: 189 NKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKAILKLM 248
K D V++ + E V +++ +L Y F E + T+A +G+ + ++ +L+L
Sbjct: 112 TKADRVDEARIAE-VRRQVKAVLREYGFA--EAKLF---VTAATEGRGIDALREHLLQL- 164
Query: 249 DAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQGPS 308
P+ E F + I+ F+++G G V TG G +KVG + L LT G +
Sbjct: 165 -------PEREHAAQHRFRLAIDRAFTVKGAGLVVTGTALSGEVKVG---DTLWLT-GVN 213
Query: 309 LKTTVTGVEMFKKILDRGEAGDNVGLLLRG-LKREDVQRG-----QVIAKPGSVKTYKKF 362
V G+ + ++ +AG + L + G ++E + RG +P F
Sbjct: 214 KPMRVRGLHAQNQPTEQAQAGQRIALNIAGDAEKEQINRGDWLLADAPPEP--------F 265
Query: 363 EAEIYVLTKDEGGRHTAFFSNYRP-QIYLRTADVTGKVELLGDVKMVMPGDNVNAAFELI 421
I L ++P I+ + VTG+V LL + EL+
Sbjct: 266 TRVIVELQTHTPLTQ------WQPLHIHHAASHVTGRVSLL-----------EDNLAELV 308
Query: 422 --SPLPLQQGQRFALRE-GGRTV--GAGVVS 447
+PL L R LR+ R GA VV
Sbjct: 309 LDTPLWLADNDRLVLRDISARNTLAGARVVM 339
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 127 bits (320), Expect = 4e-32
Identities = 117/444 (26%), Positives = 181/444 (40%), Gaps = 120/444 (27%)
Query: 66 VNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHVEYET 125
+N+GTIGHV HGK+T+ A++ V K + F EK R ITI + Y
Sbjct: 35 INIGTIGHVAHGKSTVVKALSGV-------KTVRFKR------EKVRNITI---KLGYAN 78
Query: 126 AK------------------------------------RHYAHVDCPGHADYVKNMITGA 149
AK RH + VDCPGH + M+ GA
Sbjct: 79 AKIYKCPKCPRPTCYQSYGSSKPDNPPCPGCGHKMTLKRHVSFVDCPGHDILMATMLNGA 138
Query: 150 AQMDGGILVVSAPDG-PMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELR 208
A MD +L+++A + P PQT EH+ + + ++ NK+DLV++ + + +
Sbjct: 139 AVMDAALLLIAANESCPQPQTSEHLAAVEIMKLKHIIILQNKIDLVKEAQAQD----QYE 194
Query: 209 ELLSFYKFP-GDEIPIIRGSATSALQGKNEEIGKKAILKLMDAVDEY----IPDPERQLD 263
E+ +F K D PII SA N +D V EY IP P+R L
Sbjct: 195 EIRNFVKGTIADNAPII---PISAQLKYN-----------IDVVLEYICTQIPIPKRDLT 240
Query: 264 KPFLM----------PIEDVFSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQGPSLKTTV 313
P M P ED+ ++ +G VA G + QG +KVG+E+E+
Sbjct: 241 SPPRMIVIRSFDVNKPGEDIENL--KGGVAGGSILQGVLKVGDEIEIRPGIISKDSGGEF 298
Query: 314 TGVEMFKKILDRGEAGDN------------VGLLLR-GLKREDVQRGQVIAKPGSV-KTY 359
T + +I+ A +N VG + L R D GQV+ PG + + Y
Sbjct: 299 TCRPIRTRIV-SLFAENNELQYAVPGGLIGVGTTIDPTLTRADRLVGQVLGYPGKLPEVY 357
Query: 360 KKFEAEIYVL-----TKDEGGRHTAFFSNYRP----QIYLRTADVTGKVELLGDVKMVMP 410
+ E + Y+L K + G+ + + I + + G+V + D +
Sbjct: 358 AEIEIQYYLLRRLLGVKSQDGKKATKVAKLKKGESLMINIGSTTTGGRVVGIKDDGI--- 414
Query: 411 GDNVNAAFELISPLPLQQGQRFAL 434
A EL +P+ G++ AL
Sbjct: 415 -----AKLELTTPVCTSVGEKIAL 433
>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 = 1e-31
Identities = 70/224 (31%), Positives = 99/224 (44%), Gaps = 56/224 (25%)
Query: 66 VNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITI--------- 116
+N+GTIGHV HGKTTL A++ V + EE KR ITI
Sbjct: 1 INIGTIGHVAHGKTTLVKALSGVWT-------------VRHKEELKRNITIKLGYANAKI 47
Query: 117 ----------ATAHVEYE--------TAKRHYAHVDCPGHADYVKNMITGAAQMDGGILV 158
E E RH + VDCPGH + M++GAA MDG +L+
Sbjct: 48 YKCPNCGCPRPYDTPECECPGCGGETKLVRHVSFVDCPGHEILMATMLSGAAVMDGALLL 107
Query: 159 VSAPDG-PMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYK-F 216
++A + P PQT EH+ +G+ ++ NK+DLV++E+ LE ++ F K
Sbjct: 108 IAANEPCPQPQTSEHLAALEIMGLKHIIILQNKIDLVKEEQALE----NYEQIKEFVKGT 163
Query: 217 PGDEIPIIRGSATSALQGKNEEIGKKAILKLMDAVDEYIPDPER 260
+ PII SA N I L + + + IP P R
Sbjct: 164 IAENAPII---PISAQLKYN-------IDVLCEYIVKKIPTPPR 197
>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 = 111 bits (281), Expect = 1e-28
Identities = 61/185 (32%), Positives = 94/185 (50%), Gaps = 24/185 (12%)
Query: 70 TIGHVDHGKTTLTAAI---TKVLAE-------EGKAKAIAFDEIDKA------PEEKKRG 113
T G VD GK+TL + +K + E K+ +++D A E+++G
Sbjct: 4 TCGSVDDGKSTLIGRLLYDSKSIFEDQLAALERSKSSGTQGEKLDLALLVDGLQAEREQG 63
Query: 114 ITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHI 173
ITI A+ + T KR + D PGH Y +NM+TGA+ D IL+V A G + QT+ H
Sbjct: 64 ITIDVAYRYFSTPKRKFIIADTPGHEQYTRNMVTGASTADLAILLVDARKGVLEQTRRHS 123
Query: 174 LLARQVGVPSLVCFLNKVDLVE-DEELLELVEMELRELLSFYKFPG-DEIPIIRGSATSA 231
+A +G+ +V +NK+DLV+ DEE+ E ++ + + IPI SA
Sbjct: 124 YIASLLGIRHVVVAVNKMDLVDYDEEVFEEIKADYLAFAASLGIEDITFIPI------SA 177
Query: 232 LQGKN 236
L+G N
Sbjct: 178 LEGDN 182
>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 = 117 bits (294), Expect = 3e-28
Identities = 92/307 (29%), Positives = 147/307 (47%), Gaps = 42/307 (13%)
Query: 67 NVGTIGHVDHGKTTLTAAI---TKVLAEEGKAKAIAFDEIDKAPEEKKRGITIA---TAH 120
N+ I HVDHGKTTL A+ + D D E++RGITI TA
Sbjct: 3 NIAIIAHVDHGKTTLVDALLKQSGTFRANEAVAERVMDSNDL---ERERGITILAKNTA- 58
Query: 121 VEYETAKRHYAHVDCPGHADY------VKNMITGAAQMDGGILVVSAPDGPMPQTKEHIL 174
+ Y K + VD PGHAD+ V M+ DG +L+V A +GPMPQT+ +
Sbjct: 59 IRYNGTKINI--VDTPGHADFGGEVERVLGMV------DGVLLLVDASEGPMPQTRFVLK 110
Query: 175 LARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDE----IPIIRGSATS 230
A ++G+ +V +NK+D + V E+ +L F + D+ PI+ S +
Sbjct: 111 KALELGLKPIVV-INKID--RPSARPDEVVDEVFDL--FAELGADDEQLDFPIVYASGRA 165
Query: 231 ALQGKNEEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQG 290
+ + + L DA+ ++P P+ LD+P M + ++ + G +A GRV +G
Sbjct: 166 GWASLDLDDPSDNMAPLFDAIVRHVPAPKGDLDEPLQMLVTNLDYDEYLGRIAIGRVHRG 225
Query: 291 TIKVGEEVEVLGLTQGPSLKTTVTGVEMFKKI----LDRGEAGDNVGLLLRGLKREDVQR 346
T+K G++V ++ G ++ + F+ + +D AGD V + GL ED+
Sbjct: 226 TVKKGQQVALMKR-DGTIENGRISKLLGFEGLERVEIDEAGAGDIVAVA--GL--EDINI 280
Query: 347 GQVIAKP 353
G+ IA P
Sbjct: 281 GETIADP 287
>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 = 105 bits (265), Expect = 6e-28
Identities = 39/89 (43%), Positives = 60/89 (67%)
Query: 361 KFEAEIYVLTKDEGGRHTAFFSNYRPQIYLRTADVTGKVELLGDVKMVMPGDNVNAAFEL 420
K EA++Y+L+K EGGRH F SN++PQ++ T D +++L +MVMPG++ L
Sbjct: 5 KVEAQVYILSKAEGGRHKPFVSNFQPQMFSLTWDCAARIDLPPGKEMVMPGEDTKVTLIL 64
Query: 421 ISPLPLQQGQRFALREGGRTVGAGVVSKV 449
P+ L++GQRF LR+G RT+G G+V+
Sbjct: 65 RRPMVLEKGQRFTLRDGNRTIGTGLVTDT 93
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 114 bits (288), Expect = 2e-27
Identities = 91/298 (30%), Positives = 141/298 (47%), Gaps = 62/298 (20%)
Query: 67 NVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPE--------EKKRGITI-- 116
N+ I HVDHGKTTL + +L + G F E ++ E EK+RGITI
Sbjct: 7 NIAIIAHVDHGKTTL---VDALLKQSG-----TFREREEVAERVMDSNDLEKERGITILA 58
Query: 117 -ATAHVEYETAKRHYAHVDCPGHADY------VKNMITGAAQMDGGILVVSAPDGPMPQT 169
TA V Y + + VD PGHAD+ V +M+ DG +L+V A +GPMPQT
Sbjct: 59 KNTA-VNYNGTRINI--VDTPGHADFGGEVERVLSMV------DGVLLLVDASEGPMPQT 109
Query: 170 KEHILLARQVGVPSLVCFLNKVD-------LVEDEELLELVEMELR-ELLSFYKFPGDEI 221
+ + A +G+ +V +NK+D V DE VE+ E L F
Sbjct: 110 RFVLKKALALGLKPIVV-INKIDRPDARPDEVVDEVFDLFVELGATDEQLDF-------- 160
Query: 222 PIIRGSATSALQGKNEEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIE--DVFSIQGR 279
PI+ SA + + E + L + + +++P P+ LD+P M + D S GR
Sbjct: 161 PIVYASARNGTASLDPEDEADDMAPLFETILDHVPAPKGDLDEPLQMQVTQLDYNSYVGR 220
Query: 280 GTVATGRVEQGTIKVGEEVEVLGLTQGPSLK----TTVTGVEMFKKI-LDRGEAGDNV 332
+ GR+ +GT+K ++V ++ + + T + G ++I ++ EAGD V
Sbjct: 221 --IGIGRIFRGTVKPNQQVALIKS--DGTTENGRITKLLGFLGLERIEIEEAEAGDIV 274
>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 = 107 bits (268), Expect = 4e-27
Identities = 62/180 (34%), Positives = 91/180 (50%), Gaps = 25/180 (13%)
Query: 66 VNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITI--------- 116
VNVG +GHVD GKT+L A++++ A AFD K P+ ++RGIT+
Sbjct: 1 VNVGLLGHVDSGKTSLAKALSEI------ASTAAFD---KNPQSQERGITLDLGFSSFEV 51
Query: 117 -ATAHVEYETAKRH----YAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKE 171
H+E + VDCPGHA ++ +I GA +D +LVV A G QT E
Sbjct: 52 DKPKHLEDNENPQIENYQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDAKKGIQTQTAE 111
Query: 172 HILLARQVGVPSLVCFLNKVDLVEDEELLELVE-MELRELLSFYKFPGDEIPIIRGSATS 230
+++ + P L+ LNK+DL+ +EE +E M+ R + K + PII SA
Sbjct: 112 CLVIGELLCKP-LIVVLNKIDLIPEEERKRKIEKMKKRLQKTLEKTRLKDSPIIPVSAKP 170
>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 = 108 bits (273), Expect = 5e-26
Identities = 99/332 (29%), Positives = 156/332 (46%), Gaps = 58/332 (17%)
Query: 70 TIGHVDHGKTTLTAAI---TKVLAEE--------GKAKAIAFDEIDKA------PEEKKR 112
T G VD GK+TL + TK + E+ K EID A E+++
Sbjct: 5 TCGSVDDGKSTLIGRLLHDTKQIYEDQLAALERDSKKHGTQGGEIDLALLVDGLQAEREQ 64
Query: 113 GITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEH 172
GITI A+ + T KR + D PGH Y +NM TGA+ D +L+V A G + QT+ H
Sbjct: 65 GITIDVAYRYFSTDKRKFIVADTPGHEQYTRNMATGASTADLAVLLVDARKGVLEQTRRH 124
Query: 173 ILLARQVGVPSLVCFLNKVDLVE-DEELLELVEMELRELLSFYKF-PGDEIPIIRGSATS 230
+A +G+ +V +NK+DLV+ DEE+ E ++ + F IP+ S
Sbjct: 125 SYIASLLGIRHVVLAVNKMDLVDYDEEVFENIKKDYLAFAEQLGFRDVTFIPL------S 178
Query: 231 ALQGKNEEIGKKA--------ILKLMDAVDEYIPDPERQLDKPFLMPIEDV----FSIQG 278
AL+G N ++ +L++++ V+ + + D P P++ V +G
Sbjct: 179 ALKGDNVVSRSESMPWYSGPTLLEILETVE--VERDAQ--DLPLRFPVQYVNRPNLDFRG 234
Query: 279 -RGTVATGRVEQGTIKVGEEVEVLGLTQGPSLKTT-VTGVEMFKKILDRGEAGDNVGLLL 336
GT+A+G V VG+EV VL PS +++ V + F L++ AG V L
Sbjct: 235 YAGTIASGSV-----HVGDEVVVL-----PSGRSSRVARIVTFDGDLEQARAGQAVTLT- 283
Query: 337 RGLKRE-DVQRGQVIAKPGSV-KTYKKFEAEI 366
L E D+ RG ++A S + +F A +
Sbjct: 284 --LDDEIDISRGDLLAAADSAPEVADQFAATL 313
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 106 bits (268), Expect = 9e-25
Identities = 99/328 (30%), Positives = 149/328 (45%), Gaps = 75/328 (22%)
Query: 70 TIGHVDHGKTTLT---------------AAITKVLAEEGKAKAIAFDEIDKA------PE 108
T G VD GK+TL AA+ + + G DEID A
Sbjct: 29 TCGSVDDGKSTLIGRLLYDSKMIFEDQLAALERDSKKVGTQG----DEIDLALLVDGLAA 84
Query: 109 EKKRGITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQ 168
E+++GITI A+ + T KR + D PGH Y +NM+TGA+ D I++V A G + Q
Sbjct: 85 EREQGITIDVAYRYFATPKRKFIVADTPGHEQYTRNMVTGASTADLAIILVDARKGVLTQ 144
Query: 169 TKEHILLARQVGVPSLVCFLNKVDLVE-DEELLELVEMELREL-----LSFYKFPGDEIP 222
T+ H +A +G+ +V +NK+DLV+ D+E+ + + + R L F IP
Sbjct: 145 TRRHSFIASLLGIRHVVLAVNKMDLVDYDQEVFDEIVADYRAFAAKLGLHDVTF----IP 200
Query: 223 IIRGSATSALQGKNEEIGKKAIL------KLMDAVDEYIPDPERQLDKPFLMPIEDV--- 273
I SAL+G N + + A + L++ ++ +R L K F P++ V
Sbjct: 201 I------SALKGDN-VVTRSARMPWYEGPSLLEHLETVEIASDRNL-KDFRFPVQYVNRP 252
Query: 274 ------FSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQGPSLKT-TVTGVEMFKKILDRG 326
F+ GTVA+ G ++ G+EV VL PS KT V + LD
Sbjct: 253 NLDFRGFA----GTVAS-----GVVRPGDEVVVL-----PSGKTSRVKRIVTPDGDLDEA 298
Query: 327 EAGDNVGLLLRGLKREDVQRGQVIAKPG 354
AG V L L D+ RG ++A+
Sbjct: 299 FAGQAVTLTLA--DEIDISRGDMLARAD 324
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 103 bits (260), Expect = 4e-24
Identities = 93/320 (29%), Positives = 148/320 (46%), Gaps = 56/320 (17%)
Query: 70 TIGHVDHGKTTL-------TAAI----TKVLAEEGKAKAIAFDEIDKA------PEEKKR 112
T G VD GK+TL T I L + K +++D A E+++
Sbjct: 32 TCGSVDDGKSTLIGRLLHDTKQIYEDQLASLHNDSKRHGTQGEKLDLALLVDGLQAEREQ 91
Query: 113 GITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEH 172
GITI A+ + T KR + D PGH Y +NM TGA+ D IL++ A G + QT+ H
Sbjct: 92 GITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTCDLAILLIDARKGVLDQTRRH 151
Query: 173 ILLARQVGVPSLVCFLNKVDLVE-DEELLELVEMELRELLSFYKFPGDE----IPIIRGS 227
+A +G+ LV +NK+DLV+ EE+ E + + + PG+ +P+
Sbjct: 152 SFIATLLGIKHLVVAVNKMDLVDYSEEVFERIREDYLTFAE--QLPGNLDIRFVPL---- 205
Query: 228 ATSALQGKNEEIGKKAI-----LKLMDAVDEYIPDPERQLDKPFLMPIEDV----FSIQG 278
SAL+G N +++ L++ V E + +PF P++ V +G
Sbjct: 206 --SALEGDNVVSQSESMPWYSGPTLLE-VLETVDIQRVVDAQPFRFPVQYVNRPNLDFRG 262
Query: 279 -RGTVATGRVEQGTIKVGEEVEVLGLTQGPSLKT-TVTGVEMFKKILDRGEAGDNVGLLL 336
GT+A+ G +KVG+ V+VL PS K V + F L+ AG+ + L+
Sbjct: 263 YAGTLAS-----GVVKVGDRVKVL-----PSGKESNVARIVTFDGDLEEAFAGEAITLV- 311
Query: 337 RGLKRE-DVQRGQVIAKPGS 355
L+ E D+ RG ++
Sbjct: 312 --LEDEIDISRGDLLVAADE 329
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 100 bits (249), Expect = 2e-22
Identities = 85/282 (30%), Positives = 135/282 (47%), Gaps = 26/282 (9%)
Query: 67 NVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDE---IDKAPEEKKRGITIATAHVEY 123
N+ I HVDHGKTTL + K+L + G + A + +D EK+RGITI +
Sbjct: 7 NIAIIAHVDHGKTTL---VDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNTAI 63
Query: 124 ETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPS 183
+ VD PGHAD+ + + +D +LVV A DGPMPQT+ A G+
Sbjct: 64 KWNDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKP 123
Query: 184 LVCFLNKVD-------LVEDEELLELVEMELR-ELLSFYKFPGDEIPIIRGSATSALQGK 235
+V +NKVD V D+ V ++ E L F PI+ SA + + G
Sbjct: 124 IVV-INKVDRPGARPDWVVDQVFDLFVNLDATDEQLDF--------PIVYASALNGIAGL 174
Query: 236 NEEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVG 295
+ E + + L A+ +++P P+ LD PF M I + G + GR+++G +K
Sbjct: 175 DHEDMAEDMTPLYQAIVDHVPAPDVDLDGPFQMQISQLDYNSYVGVIGIGRIKRGKVKPN 234
Query: 296 EEVEVL---GLTQGPSLKTTVTGVEMFKKILDRGEAGDNVGL 334
++V ++ G T+ + + + + + D EAGD V +
Sbjct: 235 QQVTIIDSEGKTRNAKVGKVLGHLGLERIETDLAEAGDIVAI 276
>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 = 87.5 bits (218), Expect = 2e-21
Identities = 34/87 (39%), Positives = 58/87 (66%), Gaps = 4/87 (4%)
Query: 266 FLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQGPSLKTTVTGVEMFKKILDR 325
F +PI+ VF+++G+GTV TG V G++KVG++VE+L L +T V +++ K ++
Sbjct: 1 FRLPIDRVFTVKGQGTVVTGTVLSGSVKVGDKVEILPL----GEETRVRSIQVHGKDVEE 56
Query: 326 GEAGDNVGLLLRGLKREDVQRGQVIAK 352
+AGD V L L G+ +D++RG V++
Sbjct: 57 AKAGDRVALNLTGVDAKDLERGDVLSS 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 = 95.6 bits (238), Expect = 5e-21
Identities = 85/243 (34%), Positives = 113/243 (46%), Gaps = 34/243 (13%)
Query: 68 VGTI-GHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGIT--IATAHVEYE 124
V TI GHVDHGKT+L +I K +G+A GIT I HVE E
Sbjct: 89 VVTIMGHVDHGKTSLLDSIRKTKVAQGEAG----------------GITQHIGAYHVENE 132
Query: 125 TAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSL 184
K +D PGH + GA D +LVV+A DG MPQT E I A+ VP +
Sbjct: 133 DGKM-ITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVP-I 190
Query: 185 VCFLNKVDLVEDEELLELVEMELREL-LSFYKFPGDEIPIIRGSATSALQGKNEEIGKKA 243
+ +NK+D E + V+ EL E L + GD I + SAL G +
Sbjct: 191 IVAINKIDKPEAN--PDRVKQELSEYGLVPEDWGGDTIFVP----VSALTGDGIDELLDM 244
Query: 244 ILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEVLGL 303
IL L V+E +P Q + + +GRG VAT V+ GT++VG+ V V+G
Sbjct: 245 IL-LQSEVEELKANPNGQASGVVI----EAQLDKGRGPVATVLVQSGTLRVGDIV-VVGA 298
Query: 304 TQG 306
G
Sbjct: 299 AYG 301
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 94.6 bits (236), Expect = 1e-20
Identities = 52/162 (32%), Positives = 84/162 (51%), Gaps = 10/162 (6%)
Query: 56 MATFTRTKLHVNVGTIGHVDHGKTTLTAAI---TKVLAEEGKAKAIAFDEIDKAPEEKKR 112
MA + N+G + H+D GKTTLT I T ++++ G+ A +D +E++R
Sbjct: 1 MARLMPLERIRNIGIVAHIDAGKTTLTERILFYTGIISKIGEVHDGA-ATMDWMEQEQER 59
Query: 113 GITI--ATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTK 170
GITI A + ++ R +D PGH D+ + +DG ++VV A +G PQT+
Sbjct: 60 GITITSAATTLFWKGDYRINL-IDTPGHVDFTIEVERSLRVLDGAVVVVDAVEGVEPQTE 118
Query: 171 EHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLS 212
A + GVP + F+NK+D + + LV +L+E L
Sbjct: 119 TVWRQADKYGVP-RILFVNKMDRLGAD--FYLVVEQLKERLG 157
Score = 45.7 bits (109), Expect = 4e-05
Identities = 48/197 (24%), Positives = 73/197 (37%), Gaps = 45/197 (22%)
Query: 196 DEELLELV-------EMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKAILKLM 248
DEEL+E E E+++ L G +P++ GSA KN K + L+
Sbjct: 221 DEELMEKYLEGEEPTEEEIKKALRKGTIAGKIVPVLCGSAF-----KN-----KGVQPLL 270
Query: 249 DAVDEYIPDP-ERQL-------------------DKPFLMPIEDVFSIQGRGTVATGRVE 288
DAV +Y+P P + + P + + + G + RV
Sbjct: 271 DAVVDYLPSPLDVPPIKGDLDDEIEKAVLRKASDEGPLSALVFKIMTDPFVGKLTFVRVY 330
Query: 289 QGTIKVGEEVEVLGLTQGPSLKTTVTGVEMFKKI--LDRGEAGDNVGLLLRGLKREDVQR 346
GT+K G EVL T+G + + + +D AGD V L GLK D
Sbjct: 331 SGTLKSGS--EVLNSTKGKKERVGRLLLMHGNEREEVDEVPAGDIVA--LVGLK--DATT 384
Query: 347 GQVIAKPGSVKTYKKFE 363
G + + E
Sbjct: 385 GDTLCDENKPVILESME 401
>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 = 88.8 bits (221), Expect = 2e-20
Identities = 66/210 (31%), Positives = 103/210 (49%), Gaps = 37/210 (17%)
Query: 67 NVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAH--VEYE 124
N+ I HVDHGKTTL A+ K + + + +D E++RGITI + + Y+
Sbjct: 4 NIAIIAHVDHGKTTLVDALLKQSGTFRENEEVGERVMDSNDLERERGITILAKNTAITYK 63
Query: 125 TAKRHYAHVDCPGHADY------VKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQ 178
K + +D PGHAD+ V +M+ DG +L+V A +GPMPQT+ + A +
Sbjct: 64 DTKINI--IDTPGHADFGGEVERVLSMV------DGVLLLVDASEGPMPQTRFVLKKALE 115
Query: 179 VGVPSLVCFLNKVD-------LVEDE--EL-LELVEMELRELLSFYKFPGDEIPIIRGSA 228
G+ +V +NK+D V DE +L LEL + E L F PI+ SA
Sbjct: 116 AGLKPIVV-INKIDRPDARPEEVVDEVFDLFLELNATD--EQLDF--------PIVYASA 164
Query: 229 TSALQGKNEEIGKKAILKLMDAVDEYIPDP 258
+ N + + + L + + E++P P
Sbjct: 165 KNGWASLNLDDPSEDLDPLFETIIEHVPAP 194
>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 = 83.4 bits (207), Expect = 8e-20
Identities = 37/89 (41%), Positives = 51/89 (57%), Gaps = 6/89 (6%)
Query: 263 DKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQGPSLKTT-VTGVEMFKK 321
DKP +PI+DV+ I G GTV GRVE G +K G V T P+ T V VEM +
Sbjct: 2 DKPLRLPIQDVYKIGGIGTVPVGRVETGVLKPGMVV-----TFAPAGVTGEVKSVEMHHE 56
Query: 322 ILDRGEAGDNVGLLLRGLKREDVQRGQVI 350
L+ GDNVG ++ + ++D++RG V
Sbjct: 57 PLEEALPGDNVGFNVKNVSKKDIKRGDVA 85
>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 = 85.6 bits (213), Expect = 1e-19
Identities = 60/171 (35%), Positives = 75/171 (43%), Gaps = 29/171 (16%)
Query: 72 GHVDHGKTTLTAAI--TKVLAEEGKAKAIAFDEIDKAPEEKKRGIT--IATAHVEYETAK 127
GHVDHGKTTL I T V A E GIT I V +
Sbjct: 7 GHVDHGKTTLLDKIRKTNVAAGE------------------AGGITQHIGAYQVPIDVKI 48
Query: 128 RHYAHVDCPGHADYVKNMITGAAQM-DGGILVVSAPDGPMPQTKEHILLARQVGVPSLVC 186
+D PGH + NM A + D ILVV+A DG MPQT E I A+ VP +V
Sbjct: 49 PGITFIDTPGHEAF-TNMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAANVPIIV- 106
Query: 187 FLNKVDLVED-EELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKN 236
+NK+D E E V+ EL EL + G ++ I+ SA G+
Sbjct: 107 AINKIDKPYGTEADPERVKNELSELGLVGEEWGGDVSIVP---ISAKTGEG 154
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 91.5 bits (228), Expect = 1e-19
Identities = 95/318 (29%), Positives = 148/318 (46%), Gaps = 94/318 (29%)
Query: 67 NVGTIGHVDHGKTTLT-----AA--ITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATA 119
N+G I H+DHGKTTL+ A I++ LA G+ A+ FDE EE+ RGITI A
Sbjct: 22 NIGIIAHIDHGKTTLSDNLLAGAGMISEELA--GEQLALDFDE-----EEQARGITIKAA 74
Query: 120 HV----EYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILL 175
+V EYE + +D PGH D+ ++ +DG I+VV A +G MPQT E +L
Sbjct: 75 NVSMVHEYEGKEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVDAVEGVMPQT-ETVL- 132
Query: 176 ARQV---GV-PSLVCFLNKVDL------VEDEELLE-LVEM--ELRELLSFYKFPGDE-- 220
RQ V P L F+NKVD + +E+ + L+++ ++ +L+ +
Sbjct: 133 -RQALRERVKPVL--FINKVDRLIKELKLTPQEMQQRLLKIIKDVNKLIKGMAPEEFKEK 189
Query: 221 --IPIIRGSAT--SAL-------------------------QGKNEEIGKKAILK--LMD 249
+ + G+ SAL +GK +E+ +KA L ++D
Sbjct: 190 WKVDVEDGTVAFGSALYNWAISVPMMQKTGIKFKDIIDYYEKGKQKELAEKAPLHEVVLD 249
Query: 250 AVDEYIPDP-ERQL------------------------DKPFLMPIEDVFSIQGRGTVAT 284
V +++P+P E Q + P +M + D+ G VAT
Sbjct: 250 MVVKHLPNPIEAQKYRIPKIWKGDLNSEVGKAMLNCDPNGPLVMMVTDIIVDPHAGEVAT 309
Query: 285 GRVEQGTIKVGEEVEVLG 302
GRV GT++ G+EV ++G
Sbjct: 310 GRVFSGTLRKGQEVYLVG 327
>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 = 88.4 bits (219), Expect = 1e-18
Identities = 104/382 (27%), Positives = 161/382 (42%), Gaps = 104/382 (27%)
Query: 67 NVGTIGHVDHGKTTLT-------AAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATA 119
N+G + H+DHGKTTL+ I++ LA G+ + FDE +E++RGITI A
Sbjct: 21 NIGIVAHIDHGKTTLSDNLLAGAGMISEELA--GQQLYLDFDE-----QEQERGITINAA 73
Query: 120 HV----EYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILL 175
+V EYE + +D PGH D+ ++ +DG I+VV A +G MPQT+ +
Sbjct: 74 NVSMVHEYEGNEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVCAVEGVMPQTETVLRQ 133
Query: 176 ARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIR---------- 225
A + V V F+NKVD + +E L+L EL+E F K + +I+
Sbjct: 134 ALKENVKP-VLFINKVDRLINE--LKLTPQELQE--RFIKIITEVNKLIKAMAPEEFRDK 188
Query: 226 -------GSAT--SAL-------------------------QGKNEEIGKKAILK--LMD 249
GS SA + K +E+ KK+ L ++D
Sbjct: 189 WKVRVEDGSVAFGSAYYNWAISVPSMKKTGIGFKDIYKYCKEDKQKELAKKSPLHQVVLD 248
Query: 250 AVDEYIPDP-ERQLDK------------------------PFLMPIEDVFSIQGRGTVAT 284
V ++P P E Q + P + I + + G VA
Sbjct: 249 MVIRHLPSPIEAQKYRIPVIWKGDLNSEVGKAMLNCDPKGPLALMITKIVVDKHAGEVAV 308
Query: 285 GRVEQGTIKVGEEVEVLGLTQGPSLKTTVTGVEMFKKIL--DRGEAGDNVGLLLRGLKRE 342
GR+ GTI+ G EV ++ ++ GV M + + D AG+ V ++ GLK
Sbjct: 309 GRLYSGTIRPGMEVYIVDRKAKARIQQ--VGVYMGPERVEVDEIPAGNIVAVI--GLK-- 362
Query: 343 DVQRGQVIAKPGSVKTYKKFEA 364
D G+ I + FE+
Sbjct: 363 DAVAGETICTTV--ENITPFES 382
>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 = 79.2 bits (196), Expect = 1e-18
Identities = 31/72 (43%), Positives = 43/72 (59%), Gaps = 2/72 (2%)
Query: 280 GTVATGRVEQGTIKVGEEVEVLGLTQGPSLKTTVTGVEMFKKILDRGEAGDNVGLLLRGL 339
GTVATGRVE GT+K G++V + G K VT +EMF L AG N G++L G+
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTG--KKGRVTSLEMFHGDLREAVAGANAGIILAGI 58
Query: 340 KREDVQRGQVIA 351
+D++RG +
Sbjct: 59 GLKDIKRGDTLT 70
>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 = 79.7 bits (197), Expect = 2e-18
Identities = 33/87 (37%), Positives = 49/87 (56%), Gaps = 4/87 (4%)
Query: 266 FLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQGPSLKTTVTGVEMFKKILDR 325
+ VF +GRGTVATGRVE GT+K G++V V G +K V ++ FK +D
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGG--VKGKVKSLKRFKGEVDE 58
Query: 326 GEAGDNVGLLLRGLKREDVQRGQVIAK 352
AGD VG++L+ +D++ G +
Sbjct: 59 AVAGDIVGIVLKDK--DDIKIGDTLTD 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 = 83.0 bits (206), Expect = 3e-18
Identities = 66/228 (28%), Positives = 108/228 (47%), Gaps = 47/228 (20%)
Query: 67 NVGTIGHVDHGKTTLTAA-------ITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATA 119
N+ I HVDHGKTTL+ + I++ LA GKA+ + E +E++RGITI ++
Sbjct: 2 NICIIAHVDHGKTTLSDSLLASAGIISEKLA--GKARYLDTRE-----DEQERGITIKSS 54
Query: 120 HV----EYETAKRHYAH-----VDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTK 170
+ EYE K +D PGH D+ + DG ++VV A +G QT
Sbjct: 55 AISLYFEYEEEKMDGNDYLINLIDSPGHVDFSSEVTAALRLTDGALVVVDAVEGVCVQT- 113
Query: 171 EHILLARQVGVPSL--VCFLNKVD-LVED---------EELLELVEMELRELLSFY---K 215
+L RQ + V +NK+D L+ + + LL +VE ++ ++ Y +
Sbjct: 114 -ETVL-RQALEERVKPVLVINKIDRLILELKLSPEEAYQRLLRIVE-DVNAIIETYAPEE 170
Query: 216 FPGDEIPI--IRGSA--TSALQGKNEEIGK-KAILKLMDAVDEYIPDP 258
F ++ +G+ SAL G I K I +++ V +++P P
Sbjct: 171 FKQEKWKFSPQKGNVAFGSALDGWGFTIIKFADIYAVLEMVVKHLPSP 218
>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 = 82.3 bits (204), Expect = 7e-18
Identities = 53/155 (34%), Positives = 85/155 (54%), Gaps = 19/155 (12%)
Query: 67 NVGTIGHVDHGKTTLTAAI---TKVLAEEGKA-KAIAF---DEIDKAPEEKKRGITIATA 119
N+G + HVD GKTTLT ++ + + E G K E+ E++RGITI +A
Sbjct: 1 NIGILAHVDAGKTTLTESLLYTSGAIRELGSVDKGTTRTDSMEL-----ERQRGITIFSA 55
Query: 120 HVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHIL--LAR 177
++ +D PGH D++ + + +DG ILV+SA +G QT+ IL L R
Sbjct: 56 VASFQWEDTKVNIIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTR--ILFRLLR 113
Query: 178 QVGVPSLVCFLNKVDLVEDEELLELVEMELRELLS 212
++ +P+++ F+NK+D + LE V E++E LS
Sbjct: 114 KLNIPTII-FVNKIDRAGAD--LEKVYQEIKEKLS 145
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 84.1 bits (209), Expect = 2e-17
Identities = 80/252 (31%), Positives = 106/252 (42%), Gaps = 57/252 (22%)
Query: 72 GHVDHGKTTLTAAI--TKVLA-EEGKAKAIAFDEIDKAPEEKKRGIT--IATAHVEYETA 126
GHVDHGKTTL I T V A E G GIT I V +
Sbjct: 12 GHVDHGKTTLLDKIRKTNVAAGEAG-------------------GITQHIGAYQVPLDVI 52
Query: 127 KRH-YAHVDCPGHADYVKNMIT-GAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSL 184
K +D PGH M GA+ D ILVV+A DG MPQT E I A+ GVP +
Sbjct: 53 KIPGITFIDTPGHE-AFTAMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAAGVPIV 111
Query: 185 VCFLNKVDLVEDEELLELVEMELRELLSFYKFP---GDEIPIIRGSATSALQGKNEEIGK 241
V +NK+D E + +EL + P G ++ + SA G+
Sbjct: 112 V-AINKIDKPEAN-----PDKVKQELQEYGLVPEEWGGDVIFV---PVSAKTGEG----- 157
Query: 242 KAILKLMDA------VDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVG 295
I +L++ V E +PE P + +V +G G VAT V+ GT+K G
Sbjct: 158 --IDELLELILLLAEVLELKANPEG----PARGTVIEVKLDKGLGPVATVIVQDGTLKKG 211
Query: 296 EEVEVLGLTQGP 307
+ + V G G
Sbjct: 212 DII-VAGGEYGR 222
Score = 29.1 bits (66), Expect = 5.2
Identities = 25/116 (21%), Positives = 49/116 (42%), Gaps = 18/116 (15%)
Query: 244 ILKLMDAVDEYI-----PDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEV 298
I KL++ V+ + P+ + ++ L + VF + G +A V +G IK G V
Sbjct: 389 IYKLIEDVEAAMKGMLEPEKKERVIG--LAEVRAVFKLPKVGAIAGCMVTEGVIKRGAPV 446
Query: 299 EVLG----LTQGPSLKTTVTGVEMFKKILDRGEAGDNVGLLLRGLKREDVQRGQVI 350
V+ + +G V ++ FK + G G+ + D++ G ++
Sbjct: 447 RVVRDGVVIYEG-----EVESLKRFKDDVKEVRKGQECGIAIEN--YRDIKEGDIL 495
>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 = 75.1 bits (185), Expect = 8e-17
Identities = 36/107 (33%), Positives = 50/107 (46%), Gaps = 22/107 (20%)
Query: 357 KTYKKFEAEIYVLTKDEGGRHTAFFSNYRPQIYLRTADVTGKVELL-----------GDV 405
+ KF AEIYVL E Y+P + + TA V G++ L
Sbjct: 1 QAVDKFVAEIYVLDHPEP-----LSPGYKPVLNVGTAHVPGRIAKLLSKVDGKTEEKKPP 55
Query: 406 KMVMPGDNVNAAFELISPLPL------QQGQRFALREGGRTVGAGVV 446
+ + G+ EL P+ L Q+G RFALR+GGRTVGAG++
Sbjct: 56 EFLKSGERGIVEVELQKPVALETFSENQEGGRFALRDGGRTVGAGLI 102
>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 = 80.4 bits (199), Expect = 3e-16
Identities = 86/296 (29%), Positives = 133/296 (44%), Gaps = 39/296 (13%)
Query: 67 NVGTIGHVDHGKTTLTAAI---TKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHV-- 121
N I H+DHGK+TL + T + E + + D +D E++RGITI V
Sbjct: 5 NFSIIAHIDHGKSTLADRLLEYTGAI-SEREMREQVLDSMDL---ERERGITIKAQAVRL 60
Query: 122 EY-----ETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLA 176
Y ET + +D PGH D+ + A +G +L+V A G QT ++ LA
Sbjct: 61 NYKAKDGETYVLNL--IDTPGHVDFSYEVSRSLAACEGALLLVDAAQGIEAQTLANVYLA 118
Query: 177 RQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKN 236
+ + ++ +NK+DL + E V+ E+ E++ D I SA +
Sbjct: 119 LENDL-EIIPVINKIDLPSAD--PERVKKEIEEVIGL-----DASEAILASAKTG----- 165
Query: 237 EEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGE 296
IG + IL +A+ + +P P+ D P I D RG VA RV +GTIK G+
Sbjct: 166 --IGIEEIL---EAIVKRVPPPKGDPDAPLKALIFDSHYDNYRGVVALVRVFEGTIKPGD 220
Query: 297 EVEVLGLTQGPSLKTTVTGVEMFKKILDRG-EAGDNVGLLLRGLKR-EDVQRGQVI 350
++ + G + GV K AG+ VG ++ G+K DV+ G I
Sbjct: 221 KIRFMS--TGKEYEVDEVGVFTPKLTKTDELSAGE-VGYIIAGIKDVSDVRVGDTI 273
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 79.6 bits (197), Expect = 8e-16
Identities = 47/149 (31%), Positives = 73/149 (48%), Gaps = 17/149 (11%)
Query: 67 NVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKA-------PEEKKRGITI--A 117
N+G + H+D GKTTLT I L GK + E++ P+E++RGITI A
Sbjct: 10 NIGILAHIDAGKTTLTERI---LFYTGKIHKMG--EVEDGTTVTDWMPQEQERGITIESA 64
Query: 118 TAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLAR 177
+++ +D PGH D+ + +DG ++V A G PQT+ A
Sbjct: 65 ATSCDWD--NHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDAVTGVQPQTETVWRQAD 122
Query: 178 QVGVPSLVCFLNKVDLVEDEELLELVEME 206
+ G+P L F+NK+D V + L ++E
Sbjct: 123 RYGIPRL-IFINKMDRVGADLFKVLEDIE 150
Score = 31.8 bits (73), Expect = 0.76
Identities = 44/191 (23%), Positives = 76/191 (39%), Gaps = 51/191 (26%)
Query: 133 VDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQT-KEHILLARQVGVPSLVCFLNKV 191
VD + + G + ++ +GP+P+ E + AR+ + +L F +++
Sbjct: 174 VDLITEPELHFSEGDGGSTVE---------EGPIPEELLEEVEEAREKLIEALAEFDDEL 224
Query: 192 --DLVEDEELL-ELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKAILKLM 248
+E EEL E + LRE G +P++ SAL+ I L+
Sbjct: 225 LELYLEGEELSAEQLRAPLREGTR----SGHLVPVL---FGSALKNI-------GIEPLL 270
Query: 249 DAVDEYIPDPERQLDKPFLMPIED------------------VFSIQ---GRGTVATGRV 287
DAV +Y+P P L+ P +D VF +Q G + RV
Sbjct: 271 DAVVDYLPSP---LEVPPPRGSKDNGKPVKVDPDPEKPLLALVFKVQYDPYAGKLTYLRV 327
Query: 288 EQGTIKVGEEV 298
GT++ G ++
Sbjct: 328 YSGTLRAGSQL 338
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 79.1 bits (196), Expect = 1e-15
Identities = 90/272 (33%), Positives = 115/272 (42%), Gaps = 97/272 (35%)
Query: 70 TI-GHVDHGKTTLTAAI--TKVLA-EEGKAKAIAFDEIDKAPEEKKRGIT--IATAHVEY 123
TI GHVDHGKT+L AI T V A E G GIT I VE
Sbjct: 253 TIMGHVDHGKTSLLDAIRKTNVAAGEAG-------------------GITQHIGAYQVE- 292
Query: 124 ETAKRHYAHVDCPGHADYVKNMIT-----GAAQMDGGILVVSAPDGPMPQTKEHILLARQ 178
T +D PGH + T GA D +LVV+A DG MPQT E I A+
Sbjct: 293 -TNGGKITFLDTPGHEAF-----TAMRARGAQVTDIVVLVVAADDGVMPQTIEAINHAKA 346
Query: 179 VGVPSLVCFLNKVDLVE-DEELL--ELVEMELRELLSFYKFP----GD--EIPIIRGSAT 229
GVP ++ +NK+D + + + EL E L P GD +P+
Sbjct: 347 AGVP-IIVAINKIDKPGANPDRVKQELSEYGL--------VPEEWGGDTIFVPV------ 391
Query: 230 SALQGKNEEIGKKAILKLMDA------VDEYIPDPER---------QLDKPFLMPIEDVF 274
SA G+ I +L++A V E +P+R +LDK
Sbjct: 392 SAKTGEG-------IDELLEAILLQAEVLELKANPDRPARGTVIEAKLDK---------- 434
Query: 275 SIQGRGTVATGRVEQGTIKVGEEVEVLGLTQG 306
GRG VAT V+ GT+KVG+ V V G T G
Sbjct: 435 ---GRGPVATVLVQNGTLKVGDIV-VAGTTYG 462
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 77.1 bits (191), Expect = 4e-15
Identities = 46/129 (35%), Positives = 64/129 (49%), Gaps = 13/129 (10%)
Query: 71 IGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEI-------DKAPEEKKRGITIATAHVEY 123
+GH GKTTLT AI L G I E+ D PEE++RGI+I +A
Sbjct: 1 VGHSGAGKTTLTEAI---LFYTGAIHRIG--EVEDGTTTMDFMPEERERGISITSAATTC 55
Query: 124 ETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPS 183
E +D PGH D+ + +DG ++VV A G PQT+ A + GVP
Sbjct: 56 EWKGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGGVEPQTETVWRQAEKYGVPR 115
Query: 184 LVCFLNKVD 192
++ F+NK+D
Sbjct: 116 II-FVNKMD 123
Score = 32.8 bits (76), Expect = 0.40
Identities = 36/133 (27%), Positives = 54/133 (40%), Gaps = 44/133 (33%)
Query: 195 EDEELLE--LVEMEL----------RELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKK 242
D+EL+E L EL + L+ G+ +P+ GSA KN K
Sbjct: 204 FDDELMEKYLEGEELSEEEIKAGLRKATLA-----GEIVPVFCGSAL-----KN-----K 248
Query: 243 AILKLMDAVDEYIPDP--------ERQLDKPFLMPIED------VFSI---QGRGTVATG 285
+ +L+DAV +Y+P P E + L P D VF G ++
Sbjct: 249 GVQRLLDAVVDYLPSPLEVPPVDGEDGEEGAELAPDPDGPLVALVFKTMDDPFVGKLSLV 308
Query: 286 RVEQGTIKVGEEV 298
RV GT+K G+ +
Sbjct: 309 RVYSGTLKKGDTL 321
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 74.9 bits (184), Expect = 3e-14
Identities = 76/252 (30%), Positives = 107/252 (42%), Gaps = 50/252 (19%)
Query: 68 VGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGIT--IATAHVE--Y 123
V +GHVDHGKTTL I K IA E GIT I VE Y
Sbjct: 247 VTILGHVDHGKTTLLDKIRK--------TQIAQKEAG--------GITQKIGAYEVEFEY 290
Query: 124 ETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPS 183
+ + +D PGH + GA D IL+++A DG PQT E I + VP
Sbjct: 291 KDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANVPI 350
Query: 184 LVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKA 243
+V +NK+D + E ++ +L + + G + P+I SA QG N + +
Sbjct: 351 IVA-INKID--KANANTERIKQQLAKYNLIPEKWGGDTPMI---PISASQGTNIDKLLET 404
Query: 244 ILKLMDAVDEYIPDP---------ERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKV 294
IL L + D DP E LDK +G VAT V+ GT+ +
Sbjct: 405 ILLLAEIED-LKADPTQLAQGIILEAHLDKT-------------KGPVATILVQNGTLHI 450
Query: 295 GEEVEVLGLTQG 306
G+ + V+G +
Sbjct: 451 GDII-VIGTSYA 461
>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 = 68.4 bits (168), Expect = 6e-13
Identities = 43/156 (27%), Positives = 72/156 (46%), Gaps = 21/156 (13%)
Query: 67 NVGTIGHVDHGKTTLTAAI---TKVLA-----EEGKAKAIAFDEIDKAPEEKKRGITIAT 118
N+ +GH GKTTL A+ T + E+G + D PEEKKR ++I T
Sbjct: 1 NIALVGHSGSGKTTLAEALLYATGAIDRLGRVEDGNTVS------DYDPEEKKRKMSIET 54
Query: 119 --AHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLA 176
A +E+ + +D PG+AD+V ++ +D ++VV A G T++
Sbjct: 55 SVAPLEWNG-HKINL-IDTPGYADFVGETLSALRAVDAALIVVEAQSGVEVGTEKVWEFL 112
Query: 177 RQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLS 212
+P ++ F+NK+D + + + LRE
Sbjct: 113 DDAKLPRII-FINKMDR-ARADFDKTLA-ALREAFG 145
>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 = 61.8 bits (151), Expect = 3e-12
Identities = 32/88 (36%), Positives = 50/88 (56%), Gaps = 7/88 (7%)
Query: 265 PFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQGPS-LKTTVTGVEMFKKIL 323
PF +PI D + QG GTV +G+VE G+I+ G+ + V+ PS V + + + +
Sbjct: 1 PFRLPISDKYKDQG-GTVVSGKVESGSIQKGDTLLVM-----PSKESVEVKSIYVDDEEV 54
Query: 324 DRGEAGDNVGLLLRGLKREDVQRGQVIA 351
D AG+NV L L+G+ ED+ G V+
Sbjct: 55 DYAVAGENVRLKLKGIDEEDISPGDVLC 82
>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 = 64.1 bits (157), Expect = 5e-12
Identities = 52/200 (26%), Positives = 89/200 (44%), Gaps = 30/200 (15%)
Query: 67 NVGTIGHVDHGKTTLTAAI---TKVLAEEGKAKAIAFDEIDKAPEEKKRGITI----ATA 119
N I H+DHGK+TL + T ++E + + +D E++RGITI
Sbjct: 2 NFSIIAHIDHGKSTLADRLLELTGTVSEREMKEQV----LDSMDLERERGITIKAQAVRL 57
Query: 120 HVEYETAKRHYAH-VDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQ 178
+ + + + + +D PGH D+ + A +G +LVV A G QT + LA +
Sbjct: 58 FYKAKDGEEYLLNLIDTPGHVDFSYEVSRSLAACEGALLVVDATQGVEAQTLANFYLALE 117
Query: 179 VGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEE 238
+ ++ +NK+DL + + V+ E+ ++L D I SA G
Sbjct: 118 NNL-EIIPVINKIDLPAAD--PDRVKQEIEDVLGL-----DASEAIL---VSAKTGLG-- 164
Query: 239 IGKKAILKLMDAVDEYIPDP 258
+ L++A+ E IP P
Sbjct: 165 -----VEDLLEAIVERIPPP 179
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 66.1 bits (162), Expect = 1e-11
Identities = 81/305 (26%), Positives = 138/305 (45%), Gaps = 39/305 (12%)
Query: 58 TFTRTKLHVNVGTIGHVDHGKTTLTAAI---TKVLAEEGKAKAIAFDEIDKAPEEKKRGI 114
TFT K N I H+DHGK+TL + T L+E + +D E++RGI
Sbjct: 2 TFTPQKNIRNFSIIAHIDHGKSTLADRLLELTGGLSEREMRAQV----LDSMDIERERGI 57
Query: 115 TI----ATAHVEYETAKRHYAH-VDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQT 169
TI + + + + + + +D PGH D+ + A +G +LVV A G QT
Sbjct: 58 TIKAQAVRLNYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQT 117
Query: 170 KEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSAT 229
++ LA + + ++ LNK+DL + E V+ E+ +++ D + SA
Sbjct: 118 LANVYLALENNL-EIIPVLNKIDLPAAD--PERVKQEIEDIIGI-----DASDAVLVSAK 169
Query: 230 SALQGKNEEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQ 289
+ G I +++A+ E IP P+ D P I D + G V R+
Sbjct: 170 T---GIG-------IEDVLEAIVEKIPPPKGDPDAPLKALIFDSWYDNYLGVVVLVRIFD 219
Query: 290 GTIKVGEEVEVLGLTQGPSLKTTVTGVEMF---KKILDRGEAGDNVGLLLRGLKR-EDVQ 345
GT+K G+++ ++ + + V V +F +D +AG+ VG ++ G+K D +
Sbjct: 220 GTLKKGDKIRMMSTGK----EYEVDEVGIFTPKMVKVDELKAGE-VGYIIAGIKDVRDAR 274
Query: 346 RGQVI 350
G I
Sbjct: 275 VGDTI 279
>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 = 62.1 bits (152), Expect = 7e-11
Identities = 43/134 (32%), Positives = 61/134 (45%), Gaps = 15/134 (11%)
Query: 67 NVGTIGHVDHGKTTLTAAI------TKVLAE--EGKAKAIAFDEIDKAPEEKKRGITIAT 118
N+G I H+D GKTT T I + E G A +D +E++RGITI +
Sbjct: 1 NIGIIAHIDAGKTTTTERILYYTGRIHKIGEVHGGGAT------MDWMEQERERGITIQS 54
Query: 119 AHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQ 178
A +D PGH D+ + +DG + V A G PQT+ A +
Sbjct: 55 AATTCFWKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVQPQTETVWRQADR 114
Query: 179 VGVPSLVCFLNKVD 192
GVP + F+NK+D
Sbjct: 115 YGVPR-IAFVNKMD 127
>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 = 59.9 bits (146), Expect = 1e-10
Identities = 47/202 (23%), Positives = 83/202 (41%), Gaps = 40/202 (19%)
Query: 67 NVGTIGHVDHGKTTLTAAI--TKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATA---HV 121
+ +G GK+TL A+ +VL G+T TA +
Sbjct: 2 LLAVVGEFSAGKSTLLNALLGEEVLPT---------------------GVTPTTAVITVL 40
Query: 122 EYETAKRHYAHVDCPG-------HADYVKNMITGAAQMDGGILVVSAPDGPMPQT-KEHI 173
Y + VD PG H + ++ + + D I V+SA D P+ ++ +E +
Sbjct: 41 RYGL-LKGVVLVDTPGLNSTIEHHTEITESFL---PRADAVIFVLSA-DQPLTESEREFL 95
Query: 174 LLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQ 233
+ + LNK+DL+ +EEL E++E RE L + G E I SA AL+
Sbjct: 96 KEILKWSGKKIFFVLNKIDLLSEEELEEVLE-YSREELGVLELGGGEPRIFPVSAKEALE 154
Query: 234 GKNEEIGKKAILKLMDAVDEYI 255
+ + + + ++E++
Sbjct: 155 ARLQGDEELLEQSGFEELEEHL 176
>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 = 58.9 bits (143), Expect = 2e-10
Identities = 45/190 (23%), Positives = 69/190 (36%), Gaps = 38/190 (20%)
Query: 66 VNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGIT--IATAHVEY 123
+ + +G + GK+TL + + E K G T T +E
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGN---------------KISITEYKPGTTRNYVTTVIEE 46
Query: 124 ETAKRHYAHVDCPGHADYVK------NMITGAAQM-DGGILVVSAPDGPMPQTKEHILLA 176
+ + +D G DY + + ++ D ILV+ + QTKE I A
Sbjct: 47 DGKTYKFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHA 106
Query: 177 RQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKN 236
GVP ++ NK+DL D +L L L+ PII SA GKN
Sbjct: 107 ES-GVPIIL-VGNKIDLR-DAKLKT-HVAFLFAKLNG-------EPIIP---LSAETGKN 152
Query: 237 EEIGKKAILK 246
+ K +
Sbjct: 153 IDSAFKIVEA 162
>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 = 61.7 bits (150), Expect = 4e-10
Identities = 44/142 (30%), Positives = 63/142 (44%), Gaps = 9/142 (6%)
Query: 56 MATFTRTKLHVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAI-----AFDEIDKAPEEK 110
MA T N+G H+D GKTT T I L G+ I +D +EK
Sbjct: 1 MARTTDLNRFRNIGISAHIDAGKTTTTERI---LFYTGRIHKIGEVHDGAATMDWMEQEK 57
Query: 111 KRGITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTK 170
+RGITI +A +D PGH D+ + +DG + V+ A G PQ++
Sbjct: 58 ERGITITSAATTVFWKGHRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAVGGVQPQSE 117
Query: 171 EHILLARQVGVPSLVCFLNKVD 192
A + VP + F+NK+D
Sbjct: 118 TVWRQANRYEVPRIA-FVNKMD 138
>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 = 54.4 bits (132), Expect = 1e-09
Identities = 35/91 (38%), Positives = 47/91 (51%), Gaps = 14/91 (15%)
Query: 266 FLMPIEDV--FSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQGPSLKTT-VTGVEMFKKI 322
F P++ V + RG G + G+I+VG+EV VL PS KT+ V +E F
Sbjct: 1 FRFPVQYVIRPNADFRG--YAGTIASGSIRVGDEVVVL-----PSGKTSRVKSIETFDGE 53
Query: 323 LDRGEAGDNVGLLLRGLKRE-DVQRGQVIAK 352
LD AG++V L L+ E DV RG VI
Sbjct: 54 LDEAGAGESVTLT---LEDEIDVSRGDVIVA 81
>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 = 54.1 bits (131), Expect = 1e-09
Identities = 28/87 (32%), Positives = 45/87 (51%), Gaps = 8/87 (9%)
Query: 265 PFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQGPS-LKTTVTGVEMFKKIL 323
P +PI D + GTV G+VE GTIK G+++ V+ P+ + V + +
Sbjct: 1 PLRLPIIDKYK--DMGTVVLGKVESGTIKKGDKLLVM-----PNKTQVEVLSIYNEDVEV 53
Query: 324 DRGEAGDNVGLLLRGLKREDVQRGQVI 350
G+NV L L+G++ ED+ G V+
Sbjct: 54 RYARPGENVRLRLKGIEEEDISPGFVL 80
>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 = 57.3 bits (139), Expect = 1e-09
Identities = 36/134 (26%), Positives = 60/134 (44%), Gaps = 9/134 (6%)
Query: 67 NVGTIGHVDHGKTTLT---AAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHVEY 123
NV GH+ HGKT+L T K D +E++RGI+I + +
Sbjct: 2 NVCIAGHLHHGKTSLLDMLIEQTHKRTPSVKLGWKPLRYTDTRKDEQERGISIKSNPISL 61
Query: 124 ETA-KRHYAHV----DCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQ 178
+ +++ D PGH +++ + DG +LVV +G T+ I A Q
Sbjct: 62 VLEDSKGKSYLINIIDTPGHVNFMDEVAAALRLCDGVVLVVDVVEGLTSVTERLIRHAIQ 121
Query: 179 VGVPSLVCFLNKVD 192
G+P ++ +NK+D
Sbjct: 122 EGLPMVLV-INKID 134
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 59.3 bits (144), Expect = 2e-09
Identities = 51/155 (32%), Positives = 74/155 (47%), Gaps = 33/155 (21%)
Query: 67 NVGTIGHVDHGKTTLT------AAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAH 120
N+ I HVDHGK+TLT A I G A+ D +E++RGITI +
Sbjct: 21 NMSVIAHVDHGKSTLTDSLVCKAGIIS-SKNAGDARF-----TDTRADEQERGITIKSTG 74
Query: 121 V--------EYETAKRHYA--HVDCPGHADYVKNMITGAAQM-DGGILVVSAPDGPMPQT 169
+ E K+ + +D PGH D+ + +T A ++ DG ++VV +G QT
Sbjct: 75 ISLYYEHDLEDGDDKQPFLINLIDSPGHVDF-SSEVTAALRVTDGALVVVDCVEGVCVQT 133
Query: 170 KEHILLARQVGVPSL--VCFLNKVDLVEDEELLEL 202
E +L RQ + V F+NKVD +LEL
Sbjct: 134 -ETVL--RQALQERIRPVLFINKVDRA----ILEL 161
>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 = 52.6 bits (127), Expect = 5e-09
Identities = 24/87 (27%), Positives = 45/87 (51%), Gaps = 2/87 (2%)
Query: 266 FLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEVLGLTQ-GPSLKTTVTGVEMFKKILD 324
I++++S+ G GTV G V +G I++G+ + +LG Q G TV + + +
Sbjct: 1 AEFQIDEIYSVPGVGTVVGGTVSKGVIRLGDTL-LLGPDQDGSFRPVTVKSIHRNRSPVR 59
Query: 325 RGEAGDNVGLLLRGLKREDVQRGQVIA 351
AG + L L+ + R +++G V+
Sbjct: 60 VVRAGQSASLALKKIDRSLLRKGMVLV 86
>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 = 55.7 bits (135), Expect = 1e-08
Identities = 46/150 (30%), Positives = 77/150 (51%), Gaps = 19/150 (12%)
Query: 71 IGHVDHGKTTLTAAI---TKVLAEEG--KAKAIA------FDEIDKAPEEKKRGITIATA 119
I H D GKTTLT + + E G KA+ + EI EK+RGI++ ++
Sbjct: 8 ISHPDAGKTTLTEKLLLFGGAIQEAGAVKARKSRKHATSDWMEI-----EKQRGISVTSS 62
Query: 120 HVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQV 179
+++E +D PGH D+ ++ +D ++V+ A G PQT++ + R
Sbjct: 63 VMQFEYKGCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLR 122
Query: 180 GVPSLVCFLNKVDLVEDE--ELLELVEMEL 207
G+P ++ F+NK+D + ELL+ +E EL
Sbjct: 123 GIP-IITFINKLDREGRDPLELLDEIENEL 151
>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 = 54.5 bits (131), Expect = 6e-08
Identities = 43/151 (28%), Positives = 73/151 (48%), Gaps = 11/151 (7%)
Query: 67 NVGTIGHVDHGKTTLT-------AAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATA 119
I H D GKTT+T AI A +G+ + D EK+RGI+I T+
Sbjct: 13 TFAIISHPDAGKTTITEKVLLYGGAIQTAGAVKGRGSQ-RHAKSDWMEMEKQRGISITTS 71
Query: 120 HVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQV 179
+++ +D PGH D+ ++ +D ++V+ A G +T++ + + R
Sbjct: 72 VMQFPYRDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLMEVTRLR 131
Query: 180 GVPSLVCFLNKVD--LVEDEELLELVEMELR 208
P + F+NK+D + + ELL+ VE EL+
Sbjct: 132 DTP-IFTFMNKLDRDIRDPLELLDEVENELK 161
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 53.0 bits (128), Expect = 2e-07
Identities = 43/145 (29%), Positives = 72/145 (49%), Gaps = 9/145 (6%)
Query: 71 IGHVDHGKTTLTAAI---TKVLAEEGKAKAIA---FDEIDKAPEEKKRGITIATAHVEYE 124
I H D GKTTLT + + E G K + D EK+RGI++ ++ ++++
Sbjct: 18 ISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGKHAKSDWMEIEKQRGISVTSSVMQFD 77
Query: 125 TAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSL 184
A +D PGH D+ ++ +D ++V+ A G PQT + + R +P +
Sbjct: 78 YADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIEPQTLKLFEVCRLRDIP-I 136
Query: 185 VCFLNKVDLVEDE--ELLELVEMEL 207
F+NK+D + ELL+ +E EL
Sbjct: 137 FTFINKLDREGRDPLELLDEIEEEL 161
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 52.5 bits (127), Expect = 3e-07
Identities = 43/133 (32%), Positives = 63/133 (47%), Gaps = 13/133 (9%)
Query: 67 NVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEI-------DKAPEEKKRGITIATA 119
N+G + H+D GKTT T I L GK+ I E+ D +E++RGITI +A
Sbjct: 10 NIGIMAHIDAGKTTTTERI---LYYTGKSHKIG--EVHDGAATMDWMEQEQERGITITSA 64
Query: 120 HVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQV 179
+D PGH D+ + +DG + V A G PQ++ A +
Sbjct: 65 ATTCFWKGHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVSGVEPQSETVWRQADKY 124
Query: 180 GVPSLVCFLNKVD 192
GVP + F+NK+D
Sbjct: 125 GVPR-IVFVNKMD 136
>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 = 49.8 bits (119), Expect = 3e-07
Identities = 36/188 (19%), Positives = 71/188 (37%), Gaps = 41/188 (21%)
Query: 71 IGHVDHGKTTLTAAITK-----VLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHVEYET 125
+G GK++L A+ V G + D K ++ K + +
Sbjct: 3 VGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDP--DVYVKELDKGKVKLVL--------- 51
Query: 126 AKRHYAHVDCPGHADYVKNMITGAAQM-----DGGILVVSAPDGPMP--QTKEHILLARQ 178
VD PG ++ A++ D +LVV + D + R+
Sbjct: 52 -------VDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRK 104
Query: 179 VGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEE 238
G+P ++ NK+DL+E+ E+ EL+ +E + +P+ SA G+ +
Sbjct: 105 EGIPIIL-VGNKIDLLEEREVEELLRLEELAKIL-------GVPVF---EVSAKTGEGVD 153
Query: 239 IGKKAILK 246
+ +++
Sbjct: 154 ELFEKLIE 161
>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 = 3e-07
Identities = 43/149 (28%), Positives = 62/149 (41%), Gaps = 13/149 (8%)
Query: 68 VGTIGHVDHGKTTLTAAI--TKVLAEE--GKAKAIAFDEIDKAPEEKKRGITIATAHVEY 123
V +GHVDHGKTTL I + V E G + I EI E G + +
Sbjct: 7 VSVLGHVDHGKTTLLDKIRGSAVAKREAGGITQHIGATEIPMDVIEGICGDLLKKFKIRL 66
Query: 124 ETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPS 183
+ + +D PGH + G A D IL+V +G PQT+E + + R P
Sbjct: 67 KIPGLLF--IDTPGHEAFTNLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYKTPF 124
Query: 184 LVCFLNKVDLV------EDEELLELVEME 206
+V NK+D + E +E +
Sbjct: 125 VVA-ANKIDRIPGWRSHEGRPFMESFSKQ 152
>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 = 47.3 bits (113), Expect = 5e-06
Identities = 41/165 (24%), Positives = 69/165 (41%), Gaps = 29/165 (17%)
Query: 67 NVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGIT--IATAHVEYE 124
V +G+VD GK+TL +T+ + G+ KA + + E + G T ++ + ++
Sbjct: 1 RVAVVGNVDAGKSTLLGVLTQGELDNGRGKARLN--LFRHKHEVESGRTSSVSNDILGFD 58
Query: 125 TAKR----HYAH------------------VDCPGHADYVKNMITG--AAQMDGGILVVS 160
+ H +D GH Y+K + G D +LVV
Sbjct: 59 SDGEVVNYPDNHLGELDVEICEKSSKVVTFIDLAGHERYLKTTVFGMTGYAPDYAMLVVG 118
Query: 161 APDGPMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEM 205
A G + TKEH+ LA + VP V + K+D+ L E ++
Sbjct: 119 ANAGIIGMTKEHLGLALALKVPVFVV-VTKIDMTPANVLQETLKD 162
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 48.1 bits (116), Expect = 7e-06
Identities = 77/245 (31%), Positives = 116/245 (47%), Gaps = 48/245 (19%)
Query: 71 IGHVDHGKTTLTAA-----ITKVLAEEGKAKAIAFDEIDKAPEEKKRGITI--ATAHVEY 123
I H+DHGK+TL A +T L+E + KA D +D E++RGITI + Y
Sbjct: 13 IAHIDHGKSTL--ADRLIELTGTLSER-EMKAQVLDSMDL---ERERGITIKAQAVRLNY 66
Query: 124 ETAK--RHYA-H-VDCPGHADY---VKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLA 176
AK Y + +D PGH D+ V + A +G +LVV A G QT ++ LA
Sbjct: 67 -KAKDGETYILNLIDTPGHVDFSYEVSRSL---AACEGALLVVDASQGVEAQTLANVYLA 122
Query: 177 RQVG---VPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQ 233
+ +P V LNK+DL + E V+ E+ +++ + ++ SA
Sbjct: 123 LENDLEIIP--V--LNKIDLPAAD--PERVKQEIEDVIG---IDASDAVLV-----SAKT 168
Query: 234 GKNEEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIK 293
G IG + +L +A+ E IP P+ D P I D + RG V RV GT+K
Sbjct: 169 G----IGIEEVL---EAIVERIPPPKGDPDAPLKALIFDSWYDNYRGVVVLVRVVDGTLK 221
Query: 294 VGEEV 298
G+++
Sbjct: 222 KGDKI 226
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 46.2 bits (111), Expect = 2e-05
Identities = 44/136 (32%), Positives = 70/136 (51%), Gaps = 28/136 (20%)
Query: 142 VKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLVCFLNKVDLVED-EELL 200
K + +D + VV A + P + + ++V P ++ LNK+DLV+D EELL
Sbjct: 75 NKAAWSSLKDVDLVLFVVDADEKIGPGDEFILEKLKKVKTPVILV-LNKIDLVKDKEELL 133
Query: 201 ELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKAILKLMDAVDEYIPD--- 257
L+E EL EL+ F + +PI SAL+G N + +L+D + +Y+P+
Sbjct: 134 PLLE-ELSELMDFAEI----VPI------SALKGDN-------VDELLDVIAKYLPEGPP 175
Query: 258 --PERQL-DKP--FLM 268
PE Q+ D+P FL
Sbjct: 176 YYPEDQITDRPERFLA 191
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 47.0 bits (112), Expect = 2e-05
Identities = 45/152 (29%), Positives = 68/152 (44%), Gaps = 37/152 (24%)
Query: 67 NVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFDE------IDKAPEEKKRGITIATAH 120
N+ I HVDHGK+TLT ++ A IA + D +E +RGITI +
Sbjct: 21 NMSVIAHVDHGKSTLTDSLV------AAAGIIAQEVAGDVRMTDTRADEAERGITIKSTG 74
Query: 121 VE--YETAKRHYAH--------------VDCPGHADYVKNMITGAAQM-DGGILVVSAPD 163
+ YE +D PGH D+ + +T A ++ DG ++VV +
Sbjct: 75 ISLYYEMTDESLKDFKGERDGNEYLINLIDSPGHVDF-SSEVTAALRITDGALVVVDCIE 133
Query: 164 GPMPQTKEHIL---LARQVGVPSLVCFLNKVD 192
G QT E +L L ++ P L +NK+D
Sbjct: 134 GVCVQT-ETVLRQALGERI-RPVLT--VNKMD 161
>gnl|CDD|239679 cd03708, GTPBP_III, Domain III 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 = 42.2 bits (100), Expect = 2e-05
Identities = 30/95 (31%), Positives = 44/95 (46%), Gaps = 10/95 (10%)
Query: 357 KTYKKFEAEIYVLTKDEGGRH-TAFFSNYRPQIYLRTADVTGKVELLGDVKMVMPGDNVN 415
K +FEAEI VL H T Y+ +++ + T ++ + + GD
Sbjct: 1 KACWEFEAEILVLH------HPTTISPGYQATVHIGSIRQTARIVSIDKDVLR-TGDRAL 53
Query: 416 AAFELI-SPLPLQQGQRFALREGGRTVGAGVVSKV 449
F + P L++GQR RE GRT G G V+KV
Sbjct: 54 VRFRFLYHPEYLREGQRLIFRE-GRTKGVGEVTKV 87
>gnl|CDD|239761 cd04094, selB_III, This family represents the domain of elongation
factor SelB, homologous to domain III 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 = 97
Score = 42.2 bits (100), Expect = 3e-05
Identities = 32/103 (31%), Positives = 48/103 (46%), Gaps = 9/103 (8%)
Query: 347 GQVIAKPGSVKTYKKFEAEIYVLTKDEGG-RHTAFFSNYRPQIYLRTADVTGKVELLGDV 405
G V+A PGS+ ++ + + VL +H R ++ T++V +V LL D
Sbjct: 1 GDVLADPGSLLPTRRLDVRLTVLLSAPRPLKHRQ-----RVHLHHGTSEVLARVVLL-DR 54
Query: 406 KMVMPGDNVNAAFELISPLPLQQGQRFALREGG--RTVGAGVV 446
+ PG+ A L PL +G RF LR RT+G G V
Sbjct: 55 DELAPGEEALAQLRLEEPLVALRGDRFILRSYSPLRTLGGGRV 97
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 42.8 bits (102), Expect = 8e-05
Identities = 27/93 (29%), Positives = 48/93 (51%), Gaps = 11/93 (11%)
Query: 156 ILVVSAPDGPMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYK 215
+ VV A + + + L ++ P ++ LNK+DLV+D+E L + +L+EL F
Sbjct: 87 LFVVDASEWIGEGDEFILELLKKSKTPVILV-LNKIDLVKDKEDLLPLLEKLKELHPF-- 143
Query: 216 FPGDEIPIIRGSATSALQGKNEEIGKKAILKLM 248
EI I SAL+G+N + + I++ +
Sbjct: 144 ---AEIFPI-----SALKGENVDELLEYIVEYL 168
>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 = 41.8 bits (99), Expect = 1e-04
Identities = 33/100 (33%), Positives = 52/100 (52%), Gaps = 14/100 (14%)
Query: 149 AAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELR 208
A + D +LVV + D + + + L R+ G P L+ NK+DLV + E EL+
Sbjct: 74 ADRADLVLLVVDS-DLTPVEEEAKLGLLRERGKPVLLVL-NKIDLVPESEEEELLRERKL 131
Query: 209 ELLSFYKFPGDEIPIIRGSATSALQGKN-EEIGKKAILKL 247
ELL ++P+I A SAL G+ +E+ +K I +L
Sbjct: 132 ELLP-------DLPVI---AVSALPGEGIDEL-RKKIAEL 160
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 43.6 bits (104), Expect = 2e-04
Identities = 41/140 (29%), Positives = 54/140 (38%), Gaps = 33/140 (23%)
Query: 72 GHVDHGKTTLTAAI--TKVLAEEGKA---------------KAIAFDEIDKAPEEKKRGI 114
GHVDHGKTTL I T V A+E + IA P + +
Sbjct: 13 GHVDHGKTTLLDKIRGTAVAAKEAGGITQHIGATEVPIDVIEKIAGPLKKPLPIK----L 68
Query: 115 TIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHIL 174
I +D PGH + G A D ILVV +G PQT E I
Sbjct: 69 KIPGLLF-----------IDTPGHEAFTNLRKRGGALADIAILVVDINEGFQPQTIEAIN 117
Query: 175 LARQVGVPSLVCFLNKVDLV 194
+ ++ P +V NK+D +
Sbjct: 118 ILKRRKTPFVVA-ANKIDRI 136
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 42.0 bits (100), Expect = 5e-04
Identities = 35/99 (35%), Positives = 49/99 (49%), Gaps = 17/99 (17%)
Query: 156 ILVVSAPDGPMPQTKEHIL-LARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFY 214
+LV+ A +G Q I LA + G ++ NK DLV+DE+ E + ELR L F
Sbjct: 259 LLVLDATEGITEQDL-RIAGLALEAGKALVIVV-NKWDLVKDEKTREEFKKELRRKLPFL 316
Query: 215 KFPGDEIPIIRGSATSALQGKNEEIGKKAILKLMDAVDE 253
F PI+ SAL G+ + KL+DA+DE
Sbjct: 317 DF----APIVF---ISALTGQG-------VDKLLDAIDE 341
Score = 36.3 bits (85), Expect = 0.030
Identities = 27/111 (24%), Positives = 47/111 (42%), Gaps = 25/111 (22%)
Query: 156 ILVVSAPDGPMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYK 215
+ VV +G P+ +E R+ G P ++ NK+D +++ FY
Sbjct: 83 LFVVDGREGLTPEDEEIAKWLRKSGKPVILV-ANKIDGKKEDA----------VAAEFYS 131
Query: 216 FP-GDEIPIIRGSATSALQGKNEEIGKKAILKLMDAVDEYIPDPERQLDKP 265
G+ IPI SA G+ I L+DA+ E +P+ E + ++
Sbjct: 132 LGFGEPIPI------SAEHGRG-------IGDLLDAILELLPEEEEEEEEE 169
>gnl|CDD|237731 PRK14494, PRK14494, putative molybdopterin-guanine dinucleotide
biosynthesis protein MobB/FeS domain-containing protein
protein; Provisional.
Length = 229
Score = 40.7 bits (96), Expect = 6e-04
Identities = 19/42 (45%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 68 VGTIGHVDHGKTTLTAAITKVLAEEGKAKAIA---FDEIDKA 106
+G IG D GKTTL I K L E G A A E DK
Sbjct: 4 IGVIGFKDSGKTTLIEKILKNLKERGYRVATAKHTHHEFDKP 45
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 39.3 bits (93), Expect = 0.001
Identities = 33/100 (33%), Positives = 47/100 (47%), Gaps = 18/100 (18%)
Query: 156 ILVVSAPDGPMPQTKEHIL-LARQVGVPSLVCFLNKVDLVE-DEELLELVEMELRELLSF 213
+LV+ A +G Q I L + G ++ NK DLVE DE+ ++ E ELR L F
Sbjct: 89 LLVLDASEGITEQDL-RIAGLILEEGKALIIVV-NKWDLVEKDEKTMKEFEKELRRKLPF 146
Query: 214 YKFPGDEIPIIRGSATSALQGKNEEIGKKAILKLMDAVDE 253
+ PI+ SAL G+ + KL DA+ E
Sbjct: 147 LDY----APIVF---ISALTGQG-------VDKLFDAIKE 172
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 40.5 bits (96), Expect = 0.002
Identities = 48/149 (32%), Positives = 68/149 (45%), Gaps = 45/149 (30%)
Query: 67 NVGTIGHVDHGKTTLTAAI---TKV---LAE--EGKAKAIAFDEIDKAPEEKKRGITIAT 118
N+G + H+D GKTT T I T V + E +G A +D +E++RGITI +
Sbjct: 12 NIGIMAHIDAGKTTTTERILFYTGVNHKIGEVHDGAAT------MDWMEQEQERGITITS 65
Query: 119 AHVEYETA--KRHYAHV-DCPGHADY---------VKNMITGAAQMDGGILVVSAPDGPM 166
A T K H ++ D PGH D+ V +DG + V A G
Sbjct: 66 AAT---TCFWKDHRINIIDTPGHVDFTIEVERSLRV---------LDGAVAVFDAVGGVE 113
Query: 167 PQTKEHILLARQV---GVPSLVCFLNKVD 192
PQ+ E + RQ VP + F+NK+D
Sbjct: 114 PQS-ETVW--RQADKYKVPRI-AFVNKMD 138
>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 = 36.7 bits (86), Expect = 0.003
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 280 GTVATGRVEQGTIKVGEEVEVLGLTQGPSLKTTVTGVEMF----KKILDRGEAGDNVGL 334
G +A GR+ +GT+KVG++V V+ G K +T + F + ++ EAGD V +
Sbjct: 15 GRIAIGRIFRGTVKVGQQVAVVKRD-GKIEKAKITKLFGFEGLKRVEVEEAEAGDIVAI 72
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 39.1 bits (92), Expect = 0.003
Identities = 33/121 (27%), Positives = 60/121 (49%), Gaps = 26/121 (21%)
Query: 156 ILVVSAPDGPMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYK 215
+ VV A +G P + + ++ P ++ +NK+D V+ + +L + L++LL F +
Sbjct: 90 LFVVDADEGWGPGDEFILEQLKKTKTPVILV-VNKIDKVKPKTVLLKLIAFLKKLLPFKE 148
Query: 216 FPGDEIPIIRGSATSALQGKNEEIGKKAILKLMDAVDEYIPD-----PERQL-DKP--FL 267
+PI SAL+G N + L++ + EY+P+ PE Q+ D+P FL
Sbjct: 149 I----VPI------SALKGDN-------VDTLLEIIKEYLPEGPWYYPEDQITDRPERFL 191
Query: 268 M 268
Sbjct: 192 A 192
>gnl|CDD|239676 cd03705, EF1_alpha_III, Domain III of EF-1. Eukaryotic elongation
factor 1 (EF-1) is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to ribosomes. EF-1 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 family is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea (aEF-1
alpha) and eukaryotes (eEF-1 alpha).
Length = 104
Score = 36.8 bits (86), Expect = 0.003
Identities = 29/113 (25%), Positives = 41/113 (36%), Gaps = 32/113 (28%)
Query: 357 KTYKKFEAEIYVLTKDEGGRHTAFFSN-YRPQIYLRTADVTGKV-ELLGDV--------- 405
K + F A++ VL H Y P + TA V + E+L +
Sbjct: 1 KVAESFTAQVIVL------NHPGQIKPGYTPVLDCHTAHVACRFAEILSKIDPRTGKKLE 54
Query: 406 ---KMVMPGDNVNAAFELISPL---------PLQQGQRFALREGGRTVGAGVV 446
K + GD PL PL RFA+R+ G+TV G+V
Sbjct: 55 ENPKFLKSGDAAIVKIVPQKPLVVETFSEYPPLG---RFAVRDMGQTVAVGIV 104
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 39.3 bits (93), Expect = 0.003
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 15/66 (22%)
Query: 188 LNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKAILKL 247
+NK DLV+++ + E + ELR L F + PI+ SAL G+ + KL
Sbjct: 291 VNKWDLVDEKTMEEFKK-ELRRRLPFLDY----APIV---FISALTGQG-------VDKL 335
Query: 248 MDAVDE 253
++A+DE
Sbjct: 336 LEAIDE 341
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 39.5 bits (92), Expect = 0.004
Identities = 23/62 (37%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 133 VDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLVCFLNKVD 192
+D PGH + G + D +LVV +G PQT E I + RQ P +V NK+D
Sbjct: 531 IDTPGHEAFTSLRKRGGSLADLAVLVVDINEGFKPQTIEAINILRQYKTPFVVA-ANKID 589
Query: 193 LV 194
L+
Sbjct: 590 LI 591
>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 = 37.8 bits (89), Expect = 0.005
Identities = 26/95 (27%), Positives = 46/95 (48%), Gaps = 20/95 (21%)
Query: 156 ILVVSAPDGPMPQTK---EHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLS 212
+L+V + P + +++ A G+ ++ NK DLV+DEEL EL+E +L
Sbjct: 6 VLIVFSLKEPFFNLRLLDRYLVAAEASGIEPVIVL-NKADLVDDEELEELLE-IYEKL-- 61
Query: 213 FYKFPGDEIPIIRGSATSALQGKN-EEIGKKAILK 246
P++ A SA G+ +E+ + +LK
Sbjct: 62 -------GYPVL---AVSAKTGEGLDEL--RELLK 84
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 37.6 bits (88), Expect = 0.006
Identities = 30/131 (22%), Positives = 53/131 (40%), Gaps = 20/131 (15%)
Query: 133 VDCPG---------HADYVKNMI----TGAAQMDGGILVVSAPDGPMPQTKEHILLARQV 179
VD PG + K +I A + G +L++ A P +E I ++
Sbjct: 75 VDLPGYGYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPPKDLDREMIEFLLEL 134
Query: 180 GVPSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEI 239
G+P +V K D ++ E + + EL K P D+ ++ S+L+ K +
Sbjct: 135 GIPVIVVL-TKADKLKKSERNKQLNKVAEELK---KPPPDDQWVV---LFSSLKKKGIDE 187
Query: 240 GKKAILKLMDA 250
K IL+ +
Sbjct: 188 LKAKILEWLKE 198
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 38.3 bits (90), Expect = 0.007
Identities = 35/127 (27%), Positives = 56/127 (44%), Gaps = 25/127 (19%)
Query: 153 DGGILVVSAPDGPMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLS 212
D + VV +G P +E + R+ P ++ +NK+D ++ EEL E S
Sbjct: 85 DVILFVVDGREGITPADEEIAKILRRSKKPVILV-VNKIDNLKAEELAY-------EFYS 136
Query: 213 FYKFPGDEIPIIRGSATSALQGKNEEIGKKAILKLMDAVDEYIPDPERQLDKPFLMPIED 272
G+ +PI SA G+ I L+DAV E +P E + ++ PI+
Sbjct: 137 LGF--GEPVPI------SAEHGRG-------IGDLLDAVLELLPPDEEEEEEEETDPIK- 180
Query: 273 VFSIQGR 279
+I GR
Sbjct: 181 -IAIIGR 186
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 35.1 bits (82), Expect = 0.033
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 11/63 (17%)
Query: 185 VCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKAI 244
+ LNK+DL++ EE E ++ L+EL PI SAL G+ + K +
Sbjct: 118 IVVLNKIDLLDAEERFEKLKELLKELKG-----KKVFPI------SALTGEGLDELLKKL 166
Query: 245 LKL 247
KL
Sbjct: 167 AKL 169
>gnl|CDD|239760 cd04093, HBS1_C, HBS1_C: this family represents the C-terminal
domain of Hsp70 subfamily B suppressor 1 (HBS1) which is
homologous to the domain III of EF-1alpha. This group
contains proteins similar to yeast 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 = 107
Score = 33.7 bits (78), Expect = 0.034
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 6/38 (15%)
Query: 418 FELISPLPLQ------QGQRFALREGGRTVGAGVVSKV 449
EL P+PL+ + R LR G T+ AG+V+++
Sbjct: 70 IELERPIPLELFKDNKELGRVVLRRDGETIAAGLVTEI 107
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 36.0 bits (84), Expect = 0.040
Identities = 28/95 (29%), Positives = 44/95 (46%), Gaps = 16/95 (16%)
Query: 153 DGGILVVSAPDGPMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELLS 212
D +LVV A GP E I ++ +P + +NK+DL E+ LE +E +
Sbjct: 87 DLALLVVDAGVGPGEYELELIEELKERKIP-YIVVINKIDLGEESAELEKLEKKF----- 140
Query: 213 FYKFPGDEIPIIRGSATSALQGKNEEIGKKAILKL 247
+P I SAL G+ + K+AI++L
Sbjct: 141 -------GLPPI---FVSALTGEGIDELKEAIIEL 165
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 35.9 bits (84), Expect = 0.046
Identities = 46/158 (29%), Positives = 74/158 (46%), Gaps = 35/158 (22%)
Query: 71 IGHVDHGKTTLTAAITKVL--------AEEGKA-KAIAF---D--EIDKAPEEKKRGITI 116
I H D GKTTLT K+L A K K+ D E+ EK+RGI++
Sbjct: 16 ISHPDAGKTTLT---EKLLLFGGAIQEAGTVKGRKSGRHATSDWMEM-----EKQRGISV 67
Query: 117 ATAHVEYETAKRHYAH-----VDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKE 171
++ +++ Y +D PGH D+ ++ +D ++V+ A G PQT++
Sbjct: 68 TSSVMQFP-----YRDCLINLLDTPGHEDFSEDTYRTLTAVDSALMVIDAAKGVEPQTRK 122
Query: 172 HILLARQVGVPSLVCFLNKVDLVEDE--ELLELVEMEL 207
+ + R P + F+NK+D E ELL+ +E L
Sbjct: 123 LMEVCRLRDTP-IFTFINKLDRDGREPLELLDEIEEVL 159
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 35.6 bits (83), Expect = 0.049
Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 10/81 (12%)
Query: 188 LNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKAILKL 247
NK+DL+++EE E + + L G E P+ SA G + ++
Sbjct: 282 FNKIDLLDEEEAEERAKAIVEAL-------GWEGPVYL---ISAASGLGVKELCWDLMTF 331
Query: 248 MDAVDEYIPDPERQLDKPFLM 268
++ + +K M
Sbjct: 332 IEENPREEAEEAEAPEKVEFM 352
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme ethanolamine
ammonia lyase. The function of this gene is unknown,
although the presence of an N-terminal GxxGxGK motif
implies a GTP-binding site [Energy metabolism, Amino
acids and amines].
Length = 142
Score = 33.6 bits (77), Expect = 0.078
Identities = 33/145 (22%), Positives = 50/145 (34%), Gaps = 40/145 (27%)
Query: 71 IGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHVEYETAKRHY 130
IG V GKTTLT A+ K +A+ +++
Sbjct: 6 IGSVGCGKTTLTQALQGEEILYKKTQAVEYNDGA-------------------------- 39
Query: 131 AHVDCPG----HADYVKNMITGAAQMDGGILVVSAPDG--PMPQTKEHILLARQVGVPSL 184
+D PG + +I AA D LV SA D P I + +G+
Sbjct: 40 --IDTPGEYVENRRLYSALIVTAADADVIALVQSATDPESRFPPGFASIFVKPVIGL--- 94
Query: 185 VCFLNKVDLVEDEELLELVEMELRE 209
+ K+DL E + +E + L
Sbjct: 95 ---VTKIDLAEADVDIERAKELLET 116
>gnl|CDD|217066 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This
domain is found in HypB, a hydrogenase expression /
formation protein, and UreG a urease accessory protein.
Both these proteins contain a P-loop nucleotide binding
motif. HypB has GTPase activity and is a guanine
nucleotide binding protein. It is not known whether UreG
binds GTP or some other nucleotide. Both enzymes are
involved in nickel binding. HypB can store nickel and is
required for nickel dependent hydrogenase expression.
UreG is required for functional incorporation of the
urease nickel metallocenter. GTP hydrolysis may required
by these proteins for nickel incorporation into other
nickel proteins. This family of domains also contains
P47K, a Pseudomonas chlororaphis protein needed for
nitrile hydratase expression, and the cobW gene product,
which may be involved in cobalamin biosynthesis in
Pseudomonas denitrificans.
Length = 178
Score = 33.4 bits (77), Expect = 0.13
Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 3/58 (5%)
Query: 153 DGGILVVSAPDGPMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELREL 210
DG + VV + Q+ L+ +NK DL LE +E +LR L
Sbjct: 116 DGVVTVVDVAE--TEGEDIPEKAPDQIAFADLI-VINKTDLAPAVADLEKLEADLRRL 170
>gnl|CDD|239671 cd03700, eEF2_snRNP_like_II, EF2_snRNP_like_II: this subfamily
represents domain II of elongation factor (EF) EF-2
found eukaryotes and archaea and, the C-terminal portion
of the spliceosomal human 116kD U5 small nuclear
ribonucleoprotein (snRNP) protein (U5-116 kD) and, its
yeast counterpart Snu114p. 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. This translocation step is
catalyzed by EF-2_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.
Yeast Snu114p is essential for cell viability and for
splicing in vivo. U5-116 kD binds GTP. Experiments
suggest that GTP binding and probably GTP hydrolysis is
important for the function of the U5-116 kD/Snu114p.
Length = 93
Score = 31.8 bits (73), Expect = 0.14
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 282 VATGRVEQGTIKVGEEVEVLG 302
+A GRV GTI+ G++V VLG
Sbjct: 18 IAFGRVFSGTIRKGQKVRVLG 38
>gnl|CDD|223597 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 33.8 bits (78), Expect = 0.16
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Query: 146 ITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEM 205
+ ++DG + VV A L Q+ ++ LNK DLV+ EEL L
Sbjct: 111 LADGVRLDGVVTVVDAAHFLEGLDAIAELAEDQLAFADVI-VLNKTDLVDAEELEALEAR 169
Query: 206 ELREL 210
LR+L
Sbjct: 170 -LRKL 173
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 32.0 bits (73), Expect = 0.33
Identities = 39/164 (23%), Positives = 62/164 (37%), Gaps = 23/164 (14%)
Query: 71 IGHVDHGKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHVEYETAK--- 127
IG V GKTT A++ K I + + KR T+A +++ + +
Sbjct: 16 IGPVGAGKTTFVRALSD------KPLVITEADASSVSGKGKRPTTVA---MDFGSIELDE 66
Query: 128 RHYAH-VDCPGHADYVKNMITGAAQ-MDGGILVVSAPDGPMPQTKEHILLARQVGVPSLV 185
H PG + K M ++ G I++V + +E I +V
Sbjct: 67 DTGVHLFGTPGQ-ERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPIPVV 125
Query: 186 CFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSAT 229
+NK DL D E ++RE L K +P+I AT
Sbjct: 126 VAINKQDL-FDALPPE----KIREAL---KLELLSVPVIEIDAT 161
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 32.5 bits (75), Expect = 0.35
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 16/72 (22%)
Query: 149 AAQMDGGILVVSAPDGPMPQTKEHIL-----LARQVGVPSLVCFLNKVDLVEDEELLELV 203
AA +D +LV +A + P +L LA G+ ++ NK+DL++D E
Sbjct: 78 AANVDQAVLVFAAKE---PDFSTDLLDRFLVLAEANGIKPIIVL-NKIDLLDDLE----- 128
Query: 204 EMELRELLSFYK 215
E RELL+ Y+
Sbjct: 129 --EARELLALYR 138
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 32.0 bits (74), Expect = 0.73
Identities = 19/38 (50%), Positives = 21/38 (55%), Gaps = 6/38 (15%)
Query: 176 ARQVGVPSLVCFLNKV-DLVEDEELLELVEMELRELLS 212
RQ G+P KV DLV DEELLE + RELL
Sbjct: 626 TRQSGLPEF-----KVADLVRDEELLEEARKDARELLE 658
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 31.6 bits (73), Expect = 0.85
Identities = 33/117 (28%), Positives = 49/117 (41%), Gaps = 26/117 (22%)
Query: 188 LNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKAILKL 247
NK+DL E EE LE E +E K PI SAL G+ + A+ +L
Sbjct: 281 ANKMDLPEAEENLE----EFKE-----KLGPKVFPI------SALTGQGLDELLYAVAEL 325
Query: 248 MDAVDEYIPDPERQLDKPF--LMPIEDVFSIQGRGTVATGRVEQGTIKV-GEEVEVL 301
++ E+ + E ++ + E F+I R E G V GE++E L
Sbjct: 326 LEETPEFPLEEEEVEEEVYYKFEEEEKDFTIT--------RDEDGVFVVSGEKIERL 374
>gnl|CDD|223455 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
expression and maturation of urease and hydrogenase
[Posttranslational modification, protein turnover,
chaperones / Transcription].
Length = 202
Score = 30.6 bits (70), Expect = 0.99
Identities = 19/70 (27%), Positives = 25/70 (35%), Gaps = 10/70 (14%)
Query: 54 RSMATFTRTKLHVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFD--------EIDK 105
+A R L + VG G GKT L + L +E K I D + K
Sbjct: 4 DRLAEKNRPMLRIGVG--GPPGSGKTALIEKTLRALKDEYKIAVITGDIYTKEDADRLRK 61
Query: 106 APEEKKRGIT 115
P E G+
Sbjct: 62 LPGEPIIGVE 71
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 31.4 bits (72), Expect = 1.1
Identities = 24/93 (25%), Positives = 39/93 (41%), Gaps = 14/93 (15%)
Query: 182 PSLVCFLNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGK 241
P +V LNK+DL DEE LE ++ L E + +I SAL + +
Sbjct: 277 PRIVV-LNKIDLPLDEEELEELKKALAE-----ALGWEVFYLI-----SALTREGLDELL 325
Query: 242 KAILKLMDAV---DEYIPDPERQLDKPFLMPIE 271
+A+ +L++ E E ++ L E
Sbjct: 326 RALAELLEETKAEAEAAEAEELPVEVEVLYDDE 358
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 31.4 bits (72), Expect = 1.1
Identities = 24/119 (20%), Positives = 38/119 (31%), Gaps = 22/119 (18%)
Query: 149 AAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELR 208
+ D + V+ A + I L + P +V LNK DLV EL
Sbjct: 294 IEEADLVLFVLDASQPLDKEDLALIELLPK-KKPIIV-VLNKADLVSKIELESE------ 345
Query: 209 ELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKAILKLM----DAVDEYIPDPERQLD 263
+ II SA G+ + ++AI +L + R +
Sbjct: 346 -------KLANGDAIIS---ISAKTGEGLDALREAIKQLFGKGLGNQEGLFLSNLRHIQ 394
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 30.9 bits (71), Expect = 1.2
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 12/62 (19%)
Query: 188 LNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKAILKL 247
LNK+DL+++EEL EL++ EL+E L P+ SAL G+ + A+ +L
Sbjct: 280 LNKIDLLDEEELEELLK-ELKEAL--------GKPVF---PISALTGEGLDELLYALAEL 327
Query: 248 MD 249
++
Sbjct: 328 LE 329
>gnl|CDD|239672 cd03701, IF2_IF5B_II, IF2_IF5B_II: This family represents the
domain II of prokaryotic Initiation Factor 2 (IF2) and
its archeal and eukaryotic homologue aeIF5B. IF2, the
largest initiation factor is an essential GTP binding
protein. In E. coli three natural forms of IF2 exist in
the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption
of the eIF5B gene (FUN12) in yeast causes a severe
slow-growth phenotype, associated with a defect in
translation. eIF5B has a function analogous to
prokaryotic IF2 in mediating the joining of the 60S
ribosomal subunit. The eIF5B consists of three
N-terminal domains (I, II, II) connected by a long
helix to domain IV. Domain I is a G domain, domain II
and IV are beta-barrels and domain III has a novel
alpha-beta-alpha sandwich fold. The G domain and the
beta-barrel domain II display a similar structure and
arrangement to the homologous domains in EF1A, eEF1A and
aeIF2gamma.
Length = 95
Score = 29.0 bits (66), Expect = 1.4
Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 278 GRGTVATGRVEQGTIKVGEEVEVLGLTQGP 307
GRG VAT V+ GT+K G+ + V G T G
Sbjct: 13 GRGPVATVIVQNGTLKKGDVI-VAGGTYGK 41
>gnl|CDD|189762 pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.
cryoelectron microscopy indicates that VP5 is a trimer
implying that there are 360 copies of VP5 per virion.
Length = 507
Score = 30.8 bits (70), Expect = 1.7
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 7/46 (15%)
Query: 223 IIRGSATSALQGKN--EEIGKKAILKLMDAVDEYIPDP----ERQL 262
+++GS SAL G++ E + + IL ++ A DE PDP E+ L
Sbjct: 45 VVQGSVHSALTGESYGESVKQAVILNVLGAGDE-PPDPLSPGEQGL 89
>gnl|CDD|218489 pfam05192, MutS_III, MutS domain III. This domain is found in
proteins of the MutS family (DNA mismatch repair
proteins) and is found associated with pfam00488,
pfam05188, pfam01624 and pfam05190. The MutS family of
proteins is named after the Salmonella typhimurium MutS
protein involved in mismatch repair; other members of
the family included the eukaryotic MSH 1,2,3, 4,5 and 6
proteins. These have various roles in DNA repair and
recombination. Human MSH has been implicated in
non-polyposis colorectal carcinoma (HNPCC) and is a
mismatch binding protein. The aligned region corresponds
with domain III, which is central to the structure of
Thermus aquaticus MutS as characterized in.
Length = 290
Score = 30.5 bits (69), Expect = 1.7
Identities = 22/116 (18%), Positives = 45/116 (38%), Gaps = 12/116 (10%)
Query: 241 KKAILKLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEV 300
I +DAV+E + D +L + L I D+ + R+ G + + +
Sbjct: 48 LDEINARLDAVEELLEDLREEL-REALKGIPDLERL-------LSRLALGRASPRDLLAL 99
Query: 301 L-GLTQGPSLKTTVTGVEMFKKILDRGEAGDNVGLLLRGLKRE---DVQRGQVIAK 352
L P+L+ + + + D+ + + LL R + + ++ G VI
Sbjct: 100 RSSLEALPALRKLLASAPLLADLADQLPLPELLELLERAIDEDPPLSLRDGGVIKD 155
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 30.8 bits (71), Expect = 1.7
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 270 IEDVFSIQGRGTVATGRVEQGTIKVGEEVE 299
+ D V G+VE+G +KVG+EV
Sbjct: 509 VTDTQKPPNGLIVHRGKVEEGELKVGDEVT 538
>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional.
Length = 213
Score = 29.9 bits (68), Expect = 1.9
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 3/59 (5%)
Query: 73 HVDHGKTTLTAAITKVLA---EEGKAKAIAFDEIDKAPEEKKRGITIATAHVEYETAKR 128
HV+H + L A KV A E+ K A E +KAP +++ A A++
Sbjct: 95 HVEHARKQLEEAKAKVQAQRAEQQAKKREAAGEKEKAPRRERKPKPKAPRKKRKPRAQK 153
>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 = 28.6 bits (65), Expect = 2.1
Identities = 29/116 (25%), Positives = 45/116 (38%), Gaps = 25/116 (21%)
Query: 261 QLDKPFLMPIEDVFSIQGRGT--------VATGRVEQGTIKVGEEVEV--------LGLT 304
P M + F + GT VA G + QG +KVG+E+E+ G
Sbjct: 1 DFTSPPRMIVIRSFDVNKPGTEVDDLKGGVAGGSLLQGVLKVGDEIEIRPGIVVKDEGKI 60
Query: 305 QGPSLKTTVTGVEMFKKILDRGEAGDNVGLLLRGLK------REDVQRGQVIAKPG 354
+ + T + ++ L G GL+ G K + D GQV+ +PG
Sbjct: 61 KCRPIFTKIVSLKAENNDLQEAVPG---GLIGVGTKLDPTLTKADRLVGQVVGEPG 113
>gnl|CDD|238991 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible oxidation
of CO to CO2. CODH contains a nickel-iron-sulfur cluster
(C-center) and an iron-sulfur cluster (B-center). CO
oxidation occurs at the C-center. Three accessory
proteins encoded by cooCTJ genes are involved in nickel
incorporation into a nickel site. CooC functions as a
nickel insertase that mobilizes nickel to apoCODH using
energy released from ATP hydrolysis. CooC is a homodimer
and has NTPase activities. Mutation at the P-loop
abolishs its function.
Length = 116
Score = 28.7 bits (65), Expect = 2.2
Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 77 GKTTLTAAITKVLAEEGKAKAIAFD 101
GKTT+ A + + LAE+GK +A D
Sbjct: 11 GKTTIAALLARYLAEKGK-PVLAID 34
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 30.0 bits (69), Expect = 2.5
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 11/66 (16%)
Query: 188 LNKVDLVEDEELLELVEMELRELLSFYKFPGDEIPIIRGSATSALQGKNEEIGKKAILKL 247
LNK+DL+++EE E R L G I SA+ G+ + +A+ +L
Sbjct: 278 LNKIDLLDEEEER-----EKRAALELAALGGPVFLI------SAVTGEGLDELLRALWEL 326
Query: 248 MDAVDE 253
++
Sbjct: 327 LEEARR 332
>gnl|CDD|239757 cd04090, eEF2_II_snRNP, Loc2 eEF2_C_snRNP, cd01514/C terminal
domain:eEF2_C_snRNP: This family includes C-terminal
portion of the spliceosomal human 116kD U5 small nuclear
ribonucleoprotein (snRNP) protein (U5-116 kD) and, its
yeast counterpart Snu114p. This domain is homologous to
domain II of the eukaryotic translational elongation
factor EF-2. Yeast Snu114p is essential for cell
viability and for splicing in vivo. U5-116 kD binds GTP.
Experiments suggest that GTP binding and probably GTP
hydrolysis is important for the function of the U5-116
kD/Snu114p. In complex with GTP, EF-2 promotes the
translocation step of translation. During translocation
the peptidyl-tRNA is moved from the A site to the P
site, the uncharged tRNA from the P site to the E-site
and, the mRNA is shifted one codon relative to the
ribosome.
Length = 94
Score = 27.9 bits (63), Expect = 2.8
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 285 GRVEQGTIKVGEEVEVLG 302
GR+ GTIK G++V+VLG
Sbjct: 21 GRIYSGTIKKGQKVKVLG 38
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 29.9 bits (68), Expect = 3.1
Identities = 24/104 (23%), Positives = 45/104 (43%), Gaps = 21/104 (20%)
Query: 156 ILVVSAPDGPMPQTKEH----ILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRELL 211
+ VV A D P K +L ++ LNK+DL+EDEE+L +E
Sbjct: 276 LHVVDASD-PEILEKLEAVEDVLAEIGADEIPIILVLNKIDLLEDEEILAELE------- 327
Query: 212 SFYKFPGDEIPIIRGSATSALQGKNEEIGKKAILKLMDAVDEYI 255
+ + + I SA G+ ++ ++ I++L+ + +
Sbjct: 328 ---RGSPNPVFI------SAKTGEGLDLLRERIIELLSGLRTEV 362
>gnl|CDD|223331 COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and
metabolism].
Length = 272
Score = 29.5 bits (67), Expect = 3.1
Identities = 20/85 (23%), Positives = 28/85 (32%), Gaps = 22/85 (25%)
Query: 166 MPQTKEHILLARQVGVPSLVCFLNKVDLVEDEELLELVEM-ELREL------LSFYKFPG 218
+ A +G P LV F VD VE L EL + E EL + F +
Sbjct: 140 GLGEETVTFYAVSMGNPHLVIF---VDDVETANLEELGPLLESHELFPEGVNVGFVQVLS 196
Query: 219 DEIPIIR------------GSATSA 231
+ +R G+ A
Sbjct: 197 RDAIRLRVYERGAGETLACGTGACA 221
>gnl|CDD|150037 pfam09221, Bacteriocin_IId, Bacteriocin class IId cyclical
uberolysin-like. Members of this family are
membrane-interacting peptides, produced by Enterococci
that display a broad anti-microbial spectrum against
Gram-positive and Gram-negative bacteria. They adopt a
helical structure, with five alpha helices forming a
Saposin-like fold. The structure has been found to be
cyclical. It should be pointed out that one reference
implies that both circularin A and gassericin A are
class V or IIc-type bacteriocins; however we find that
these two proteins fall into different Pfam families
families, this one and BacteriocIIc_cy, pfam12173.
Length = 69
Score = 27.5 bits (61), Expect = 3.1
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 68 VGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAF 100
G + G + A + K+LA++GKA AIA+
Sbjct: 37 GGVSALLAIGWSAFKATVKKILAKKGKAAAIAW 69
>gnl|CDD|239673 cd03702, IF2_mtIF2_II, This family represents the domain II of
bacterial Initiation Factor 2 (IF2) and its eukaryotic
mitochondrial homologue mtIF2. IF2, the largest
initiation factor is an essential GTP binding protein.
In E. coli three natural forms of IF2 exist in the cell,
IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is
structurally and functionally related to eukaryotic
mitochondrial mtIF-2.
Length = 95
Score = 27.8 bits (63), Expect = 3.2
Identities = 17/29 (58%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 278 GRGTVATGRVEQGTIKVGEEVEVLGLTQG 306
GRG VAT V+ GT+KVG +V V G T G
Sbjct: 13 GRGPVATVLVQNGTLKVG-DVLVAGTTYG 40
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 29.9 bits (68), Expect = 3.3
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 6/41 (14%)
Query: 173 ILLARQVGVPSLVCFLNKV-DLVEDEELLELVEMELRELLS 212
+L RQ G+P +V DLV D ++LE + +LLS
Sbjct: 625 LLGTRQSGLPEF-----RVADLVRDYDILEEARKDAAKLLS 660
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 29.8 bits (68), Expect = 3.4
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 188 LNKVDLVEDEELLELVEMELRE 209
LNK+D+ + EL E V EL
Sbjct: 291 LNKIDVPDARELAEFVRPELEA 312
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 29.2 bits (65), Expect = 3.5
Identities = 43/212 (20%), Positives = 69/212 (32%), Gaps = 37/212 (17%)
Query: 77 GKTTLTAAITKVLAEEGKAKAIAFDEIDKAPEEKKRGITIATAHVEYETAKRHY--AHVD 134
GKTTL + D+ PE I E +R+ D
Sbjct: 17 GKTTLLNRLVG----------------DEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWD 60
Query: 135 CPGHADYV---KNMITGAAQMDGGILVVSAPDGP-----MPQTKEHILLARQVGVPSLVC 186
G +Y GA +G ++V + + E + VP L+
Sbjct: 61 TAGQEEYRSLRPEYYRGA---NGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLV 117
Query: 187 FLNKVDLV-EDEELLELVEMELRE--LLSFYKFPGD-EIPIIRGSATSALQGKNEEIG-- 240
NK+DL E E++ RE LL E+ TSA +
Sbjct: 118 G-NKIDLFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNEL 176
Query: 241 -KKAILKLMDAVDEYIPDPERQLDKPFLMPIE 271
K+ + KL++ +++ + E + PIE
Sbjct: 177 FKELLRKLLEEIEKLVLKNELRQLDRLNNPIE 208
>gnl|CDD|132238 TIGR03194, 4hydrxCoA_A, 4-hydroxybenzoyl-CoA reductase, alpha
subunit. This model represents the largest chain,
alpha, of the enzyme 4-hydroxybenzoyl-CoA reductase. In
species capable of degrading various aromatic compounds
by way of benzoyl-CoA, this enzyme can convert
4-hydroxybenzoyl-CoA to benzoyl-CoA.
Length = 746
Score = 29.8 bits (67), Expect = 3.6
Identities = 25/88 (28%), Positives = 38/88 (43%), Gaps = 11/88 (12%)
Query: 138 HADYVKNMITGAAQMDGGILVVSAPDGPMP------QTKEHILL---ARQVGVPSLVCFL 188
HA + + A + G I VV+ D P+P E+ L R G P V +
Sbjct: 37 HARILAIDTSEAEALPGVIAVVTGADCPVPYGVLPIAENEYPLARDKVRYRGDP--VAAV 94
Query: 189 NKVDLVEDEELLELVEMELRELLSFYKF 216
VD V E+ L L+++E EL ++
Sbjct: 95 AAVDEVTAEKALALIKVEYEELPAYMDP 122
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 29.4 bits (67), Expect = 3.9
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 15/72 (20%)
Query: 149 AAQMDGGILVVSAPDGPMPQTKEHIL-----LARQVGVPSLVCFLNKVDLVEDEELLELV 203
AA +D I++VSA +P+ +I+ +G+ L+ LNK+DL++DE
Sbjct: 118 AANIDQ-IVIVSAV---LPELSLNIIDRYLVACETLGIEPLI-VLNKIDLLDDEGRA--- 169
Query: 204 EMELRELLSFYK 215
+ E L Y+
Sbjct: 170 --FVNEQLDIYR 179
>gnl|CDD|234188 TIGR03371, cellulose_yhjQ, cellulose synthase operon protein YhjQ.
Members of this family are the YhjQ protein, found
immediately upsteam of bacterial cellulose synthase
(bcs) genes in a broad range of bacteria, including both
copies of the bcs locus in Klebsiella pneumoniae. In
several species it is seen clearly as part of the bcs
operon. It is identified as a probable component of the
bacterial cellulose metabolic process not only by gene
location, but also by partial phylogenetic profiling, or
Haft-Selengut algorithm (PMID:16930487), based on a
bacterial cellulose biosynthesis genome property
profile. Cellulose plays an important role in biofilm
formation and structural integrity in some bacteria.
Mutants in yhjQ in Escherichia coli, show altered
morphology an growth, but the function of YhjQ has not
yet been determined [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 246
Score = 29.2 bits (66), Expect = 4.1
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 68 VGTIGHVDHGKTTLTAAITKVLAEEGKAKAIAFD 101
V G V GKTTLTA + L G+ +A D
Sbjct: 7 VSVRGGV--GKTTLTANLASALKLLGEP-VLAID 37
>gnl|CDD|221957 pfam13175, AAA_15, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 320
Score = 29.3 bits (66), Expect = 4.6
Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 71 IGHVDHGKTTLTAAITKVLAEEGKAKAIAFD--EIDKAPEEKKRGITIATAHVEYETAKR 128
IG GKTT+ A+ + ++ +I+ + +IDK KK + +E + +
Sbjct: 28 IGENGSGKTTILEALDNLKEKKKIYISISDNKADIDKENLNKKSKKIKISIIIELSSNEI 87
>gnl|CDD|240394 PTZ00386, PTZ00386, formyl tetrahydrofolate synthetase;
Provisional.
Length = 625
Score = 29.0 bits (65), Expect = 6.8
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 172 HILLARQVGVPSLVCFLNKVDLVEDEELLELVEMELRE 209
HI R+ GVP +V LNK D EL + E+ L+E
Sbjct: 429 HIQNIRKFGVPVVVA-LNKFSTDTDAELELVKELALQE 465
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 28.4 bits (64), Expect = 6.8
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 15/68 (22%)
Query: 156 ILVVSAPDGPMPQTKEHIL-----LARQVGVPSLVCFLNKVDLVEDEELLELVEMELREL 210
I+VVS D ++L LA G+ ++ LNK+DL++DE E ++EL
Sbjct: 84 IIVVSLVDPDF---NTNLLDRYLVLAEAGGIEPVIV-LNKIDLLDDE------EAAVKEL 133
Query: 211 LSFYKFPG 218
L Y+ G
Sbjct: 134 LREYEDIG 141
>gnl|CDD|238941 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety of
proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion.
Length = 99
Score = 27.0 bits (60), Expect = 7.7
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 77 GKTTLTAAITKVLAEEGKAKAIAFDEI 103
GKTTL A + LA+ GK + + D+
Sbjct: 11 GKTTLAANLAAALAKRGK-RVLLIDDY 36
>gnl|CDD|143439 cd07121, ALDH_EutE, Ethanolamine utilization protein EutE-like.
Coenzyme A acylating aldehyde dehydrogenase (ACDH), an
NAD+ and CoA-dependent acetaldehyde dehydrogenase,
acetylating (EC=1.2.1.10), converts acetaldehyde into
acetyl-CoA. This CD is limited to such monofunctional
enzymes as the Ethanolamine utilization protein, EutE,
in Salmonella typhimurium. Mutations in eutE abolish
the ability to utilize ethanolamine as a carbon source.
Length = 429
Score = 28.4 bits (64), Expect = 8.2
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 116 IATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAP 162
I A VE E RH A + H+ V+N+ A M I V + P
Sbjct: 348 IELA-VELEHGNRHTAII----HSKNVENLTKMARAMQTTIFVKNGP 389
>gnl|CDD|180831 PRK07088, PRK07088, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 764
Score = 28.6 bits (64), Expect = 8.6
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 7/45 (15%)
Query: 184 LVCFLNKVDL--VEDEELLELVEMELREL-----LSFYKFPGDEI 221
+ C LN + L V+DEEL E++ ++R L L++Y P EI
Sbjct: 494 VTCNLNSIVLGNVDDEELEEVIPTQIRMLDNVISLNYYPVPEAEI 538
>gnl|CDD|130264 TIGR01196, edd, 6-phosphogluconate dehydratase. A close homolog,
designated MocB (mannityl opine catabolism), is found in
a mannopine catabolism region of a plasmid of
Agrobacterium tumefaciens. However, it is not essential
for mannopine catabolism, branches within the cluster of
6-phosphogluconate dehydratases (with a short branch
length) in a tree rooted by the presence of other
dehydyatases. It may represent an authentic
6-phosphogluconate dehydratase, redundant with the
chromosomal copy shown to exist in plasmid-cured
strains. This model includes mocB above the trusted
cutoff, although the designation is somewhat tenuous
[Energy metabolism, Entner-Doudoroff].
Length = 601
Score = 28.6 bits (64), Expect = 8.6
Identities = 14/49 (28%), Positives = 22/49 (44%)
Query: 246 KLMDAVDEYIPDPERQLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKV 294
L + + PE LD L P++D FS G + G + + IK+
Sbjct: 385 FLENGQLVWREAPEHSLDTDILRPVDDPFSANGGLKLLKGNLGRAVIKI 433
>gnl|CDD|226376 COG3858, COG3858, Predicted glycosyl hydrolase [General function
prediction only].
Length = 423
Score = 28.2 bits (63), Expect = 9.4
Identities = 10/41 (24%), Positives = 13/41 (31%), Gaps = 2/41 (4%)
Query: 14 IVPFSSQIYSCCRGSLSISDA--FSANETSATRCGPSVNPW 52
+VP S Y G S A + SA + P
Sbjct: 44 VVPPSGHFYDVGPGDTLTSIARTVGVTQDSAAIMNFVICPG 84
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 27.6 bits (62), Expect = 9.5
Identities = 25/83 (30%), Positives = 35/83 (42%), Gaps = 11/83 (13%)
Query: 153 DGGILVVSAPDGP-MPQTKE--HILLARQ--VGVPSLVCFLNKVDLVEDEELLELVEMEL 207
D I VV + D + + KE H LL + P L+ NK DL + E E+
Sbjct: 83 DAVIFVVDSADRDRIEEAKEELHALLNEEELADAPLLI-LANKQDLPGA-----MSEAEI 136
Query: 208 RELLSFYKFPGDEIPIIRGSATS 230
RELL ++ I SA +
Sbjct: 137 RELLGLHELKDRPWEIQGCSAVT 159
>gnl|CDD|239390 cd03116, MobB, Molybdenum is an essential trace element in the
form of molybdenum cofactor (Moco) which is associated
with the metabolism of nitrogen, carbon and sulfur by
redox active enzymes. In E. coli, the synthesis of Moco
involves genes from several loci: moa, mob, mod, moe
and mog. The mob locus contains mobA and mobB genes.
MobB catalyzes the attachment of the guanine
dinucleotide to molybdopterin.
Length = 159
Score = 27.6 bits (62), Expect = 9.8
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 68 VGTIGHVDHGKTTLTAAITKVLAEEGK 94
+G +G+ GKTTL + L+ G
Sbjct: 4 IGFVGYSGSGKTTLLEKLIPALSARGL 30
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.135 0.386
Gapped
Lambda K H
0.267 0.0764 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,327,040
Number of extensions: 2354813
Number of successful extensions: 2854
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2637
Number of HSP's successfully gapped: 193
Length of query: 451
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 351
Effective length of database: 6,502,202
Effective search space: 2282272902
Effective search space used: 2282272902
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 61 (27.2 bits)