RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 011581
(482 letters)
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 891 bits (2303), Expect = 0.0
Identities = 422/482 (87%), Positives = 449/482 (93%), Gaps = 4/482 (0%)
Query: 1 MAISASAAATVASTSPKLTHPYASASPSNSLLSTTALRTKLTPSNLSSSFLPPFATTTAV 60
MAISASAA+ S+S L +S+SPS+S S + KL LSSSFL PF+TTT
Sbjct: 1 MAISASAAS---SSSSLLLPSSSSSSPSSSTFSFKSTSGKLKSLTLSSSFLSPFSTTTT- 56
Query: 61 TVTTTRRRSLIVRAARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKY 120
+ + RRRS VRAARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMALAS+G SAPKKY
Sbjct: 57 STSQRRRRSFTVRAARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMALASMGGSAPKKY 116
Query: 121 DEIDAAPEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVS 180
DEIDAAPEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVS
Sbjct: 117 DEIDAAPEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVS 176
Query: 181 GADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDD 240
GADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELL+LVELEVRELLSSYEFPGDD
Sbjct: 177 GADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLELVELEVRELLSSYEFPGDD 236
Query: 241 VPIISGSALLALEALMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVED 300
+PIISGSALLALEALM NP+IKRG+N+WVDKIYELMD+VDSYIPIPQRQTDLPFLLAVED
Sbjct: 237 IPIISGSALLALEALMENPNIKRGDNKWVDKIYELMDAVDSYIPIPQRQTDLPFLLAVED 296
Query: 301 VFSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAMAGDNVGL 360
VFSITGRGTVATGRVERGT+KVGETVD+VGL+ETR+ TVTGVEMFQK LDEA+AGDNVGL
Sbjct: 297 VFSITGRGTVATGRVERGTVKVGETVDIVGLRETRSTTVTGVEMFQKILDEALAGDNVGL 356
Query: 361 LLRGVQKADIQRGMVLAKPGTITPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTD 420
LLRG+QKADIQRGMVLAKPG+ITPHTKF AIVYVLKKEEGGRHSPFFAGYRPQFYMRTTD
Sbjct: 357 LLRGIQKADIQRGMVLAKPGSITPHTKFEAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTD 416
Query: 421 VTGRVSSIMNDKDEESKMVMPGDRIKMVVELIMPVACEQGMRFAIREGGKTVGAGVIQSI 480
VTG+V+SIMNDKDEESKMVMPGDR+KMVVELI+PVACEQGMRFAIREGGKTVGAGVIQSI
Sbjct: 417 VTGKVTSIMNDKDEESKMVMPGDRVKMVVELIVPVACEQGMRFAIREGGKTVGAGVIQSI 476
Query: 481 IE 482
IE
Sbjct: 477 IE 478
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 853 bits (2207), Expect = 0.0
Identities = 330/408 (80%), Positives = 372/408 (91%)
Query: 75 ARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGI 134
AR KFERKKPHVNIGTIGHVDHGKTTLTAA+TM LA+ G + KKYDEID+APEE+ARGI
Sbjct: 2 AREKFERKKPHVNIGTIGHVDHGKTTLTAAITMTLAAKGGAKAKKYDEIDSAPEEKARGI 61
Query: 135 TINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHIL 194
TINTA VEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVS ADGPMPQTKEHIL
Sbjct: 62 TINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTKEHIL 121
Query: 195 LAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEA 254
LAKQVGVPN+VVFLNK+DQVDDEELL+LVELEVRELLS Y+FPGDD+PI+SGSALLALEA
Sbjct: 122 LAKQVGVPNIVVFLNKEDQVDDEELLELVELEVRELLSKYDFPGDDIPIVSGSALLALEA 181
Query: 255 LMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGR 314
L NP IKRGEN+WVDKIY LMD+VDSYIP P+R TD PFL+A+EDVFSITGRGTVATGR
Sbjct: 182 LTENPKIKRGENKWVDKIYNLMDAVDSYIPTPERDTDKPFLMAIEDVFSITGRGTVATGR 241
Query: 315 VERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAMAGDNVGLLLRGVQKADIQRGM 374
+ERGT+KVG+TV++VGL+ET+ TVTG+EMFQKTLDE +AGDNVG+LLRG+QK DI+RGM
Sbjct: 242 IERGTVKVGDTVEIVGLRETKTTTVTGLEMFQKTLDEGLAGDNVGILLRGIQKEDIERGM 301
Query: 375 VLAKPGTITPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGRVSSIMNDKDE 434
VLAKPGTITPHTKF A VY+L KEEGGRH+PFF GYRPQFY+RTTDVTG++ S D
Sbjct: 302 VLAKPGTITPHTKFEAQVYILTKEEGGRHTPFFPGYRPQFYVRTTDVTGKIESFTADDGS 361
Query: 435 ESKMVMPGDRIKMVVELIMPVACEQGMRFAIREGGKTVGAGVIQSIIE 482
+++MVMPGDRIKM VELI P+A E+GMRFAIREGG+TVGAGV+ I++
Sbjct: 362 KTEMVMPGDRIKMTVELIYPIAIEKGMRFAIREGGRTVGAGVVSKILK 409
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 811 bits (2098), Expect = 0.0
Identities = 292/408 (71%), Positives = 334/408 (81%), Gaps = 13/408 (3%)
Query: 75 ARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGI 134
A+ KFER KPHVN+GTIGHVDHGKTTLTAA+T LA G + K YD+ID APEE+ARGI
Sbjct: 2 AKEKFERTKPHVNVGTIGHVDHGKTTLTAAITKVLAKKGGAEAKAYDQIDKAPEEKARGI 61
Query: 135 TINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHIL 194
TINTA VEYETE RHYAHVDCPGHADYVKNMITGAAQMDGAILVVS ADGPMPQT+EHIL
Sbjct: 62 TINTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHIL 121
Query: 195 LAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEA 254
LA+QVGVP +VVFLNK D VDDEELL+LVE+EVRELLS Y+FPGDD PII GSAL ALE
Sbjct: 122 LARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSKYDFPGDDTPIIRGSALKALEG 181
Query: 255 LMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGR 314
+ +W KI ELMD+VDSYIP P+R D PFL+ +EDVFSI+GRGTV TGR
Sbjct: 182 --------DDDEEWEKKILELMDAVDSYIPTPERAIDKPFLMPIEDVFSISGRGTVVTGR 233
Query: 315 VERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAMAGDNVGLLLRGVQKADIQRGM 374
VERG IKVGE V++VG+++T+ TVTGVEMF+K LDE AGDNVG LLRG+++ D++RG
Sbjct: 234 VERGIIKVGEEVEIVGIRDTQKTTVTGVEMFRKLLDEGQAGDNVGALLRGIKREDVERGQ 293
Query: 375 VLAKPGTITPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGRVSSIMNDKDE 434
VLAKPG+ITPHTKF A VYVL KEEGGRH+PFF GYRPQFY RTTDVTG + E
Sbjct: 294 VLAKPGSITPHTKFEAEVYVLSKEEGGRHTPFFNGYRPQFYFRTTDVTGVIEL-----PE 348
Query: 435 ESKMVMPGDRIKMVVELIMPVACEQGMRFAIREGGKTVGAGVIQSIIE 482
+MVMPGD ++M VELI P+A E+G+RFAIREGG+TVGAGV+ IIE
Sbjct: 349 GVEMVMPGDNVEMTVELIAPIAMEEGLRFAIREGGRTVGAGVVTKIIE 396
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 794 bits (2054), Expect = 0.0
Identities = 291/408 (71%), Positives = 332/408 (81%), Gaps = 13/408 (3%)
Query: 75 ARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGI 134
A+ KFER KPHVN+GTIGHVDHGKTTLTAA+T LA G K YD+ID APEE+ARGI
Sbjct: 2 AKEKFERTKPHVNVGTIGHVDHGKTTLTAAITKVLAKKGGGEAKAYDQIDNAPEEKARGI 61
Query: 135 TINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHIL 194
TINT+ VEYET NRHYAHVDCPGHADYVKNMITGAAQMDGAILVVS ADGPMPQT+EHIL
Sbjct: 62 TINTSHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHIL 121
Query: 195 LAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEA 254
LA+QVGVP +VVFLNK D VDDEELL+LVE+EVRELLS Y+FPGDD PII GSAL ALE
Sbjct: 122 LARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSKYDFPGDDTPIIRGSALKALEG 181
Query: 255 LMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGR 314
+ +W KI ELMD+VDSYIP P+R D PFL+ +EDVFSI+GRGTV TGR
Sbjct: 182 --------DDDEEWEAKILELMDAVDSYIPEPERAIDKPFLMPIEDVFSISGRGTVVTGR 233
Query: 315 VERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAMAGDNVGLLLRGVQKADIQRGM 374
VERG +KVG+ V++VG+KET+ TVTGVEMF+K LDE AGDNVG+LLRG ++ D++RG
Sbjct: 234 VERGIVKVGDEVEIVGIKETQKTTVTGVEMFRKLLDEGQAGDNVGVLLRGTKREDVERGQ 293
Query: 375 VLAKPGTITPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGRVSSIMNDKDE 434
VLAKPG+I PHTKF A VYVL KEEGGRH+PFF GYRPQFY RTTDVTG + E
Sbjct: 294 VLAKPGSIKPHTKFEAEVYVLSKEEGGRHTPFFNGYRPQFYFRTTDVTGTIEL-----PE 348
Query: 435 ESKMVMPGDRIKMVVELIMPVACEQGMRFAIREGGKTVGAGVIQSIIE 482
+MVMPGD +KM VELI P+A E+G+RFAIREGG+TVGAGV+ IIE
Sbjct: 349 GVEMVMPGDNVKMTVELIAPIAMEEGLRFAIREGGRTVGAGVVAKIIE 396
>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 = 746 bits (1927), Expect = 0.0
Identities = 301/409 (73%), Positives = 340/409 (83%), Gaps = 15/409 (3%)
Query: 74 AARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARG 133
A+ KFER KPHVNIGTIGHVDHGKTTLTAA+T LA G +A + YD+ID APEE+ARG
Sbjct: 1 MAKEKFERTKPHVNIGTIGHVDHGKTTLTAAITTVLAKEGGAAARAYDQIDNAPEEKARG 60
Query: 134 ITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHI 193
ITINTA VEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVS DGPMPQT+EHI
Sbjct: 61 ITINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSATDGPMPQTREHI 120
Query: 194 LLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALE 253
LLA+QVGVP +VVFLNK D VDDEELL+LVE+EVRELLS Y+FPGDD PII GSAL ALE
Sbjct: 121 LLARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSEYDFPGDDTPIIRGSALKALE 180
Query: 254 ALMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATG 313
G+ +W KI ELMD+VD YIP P+R+TD PFL+ +EDVFSITGRGTV TG
Sbjct: 181 ----------GDAEWEAKILELMDAVDEYIPTPERETDKPFLMPIEDVFSITGRGTVVTG 230
Query: 314 RVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAMAGDNVGLLLRGVQKADIQRG 373
RVERG +KVGE V++VGLK+TR TVTGVEMF+K LDE AGDNVGLLLRG+++ +I+RG
Sbjct: 231 RVERGIVKVGEEVEIVGLKDTRKTTVTGVEMFRKELDEGRAGDNVGLLLRGIKREEIERG 290
Query: 374 MVLAKPGTITPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGRVSSIMNDKD 433
MVLAKPG+I PHTKF A VYVLKKEEGGRH+PFF+GYRPQFY RTTDVTG ++
Sbjct: 291 MVLAKPGSIKPHTKFEAEVYVLKKEEGGRHTPFFSGYRPQFYFRTTDVTGSITLPEG--- 347
Query: 434 EESKMVMPGDRIKMVVELIMPVACEQGMRFAIREGGKTVGAGVIQSIIE 482
+MVMPGD +KM VELI P+A EQGMRFAIREGG+TVGAGV+ IIE
Sbjct: 348 --VEMVMPGDNVKMTVELISPIALEQGMRFAIREGGRTVGAGVVSKIIE 394
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 738 bits (1908), Expect = 0.0
Identities = 284/409 (69%), Positives = 332/409 (81%), Gaps = 15/409 (3%)
Query: 74 AARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARG 133
A+ KF+R KPHVNIGTIGHVDHGKTTLTAA+T LA G + K YD IDAAPEE+ RG
Sbjct: 1 MAKEKFDRSKPHVNIGTIGHVDHGKTTLTAAITKVLAERGLNQAKDYDSIDAAPEEKERG 60
Query: 134 ITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHI 193
ITINTA VEYETE RHYAHVDCPGHADYVKNMITGAAQMDGAILVV+ DGPMPQT+EHI
Sbjct: 61 ITINTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI 120
Query: 194 LLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALE 253
LLA+QVGVP +VVFLNK D VDDEELL+LVE+EVRELLS Y+FPGDD+P+I GSAL ALE
Sbjct: 121 LLARQVGVPYLVVFLNKVDLVDDEELLELVEMEVRELLSEYDFPGDDIPVIRGSALKALE 180
Query: 254 ALMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATG 313
G+ +W D I ELMD+VD YIP P+R TD PFL+ VEDVF+ITGRGTV TG
Sbjct: 181 ----------GDPKWEDAIMELMDAVDEYIPTPERDTDKPFLMPVEDVFTITGRGTVVTG 230
Query: 314 RVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAMAGDNVGLLLRGVQKADIQRG 373
RVERGT+KVG+ V++VG+KET+ VTGVEMF+K LDE AGDNVG+LLRGV + +++RG
Sbjct: 231 RVERGTVKVGDEVEIVGIKETQKTVVTGVEMFRKLLDEGQAGDNVGVLLRGVDRDEVERG 290
Query: 374 MVLAKPGTITPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGRVSSIMNDKD 433
VLAKPG+I PHTKF A VY+L KEEGGRH+PFF YRPQFY RTTDVTG + +
Sbjct: 291 QVLAKPGSIKPHTKFKAEVYILTKEEGGRHTPFFNNYRPQFYFRTTDVTGSI-----ELP 345
Query: 434 EESKMVMPGDRIKMVVELIMPVACEQGMRFAIREGGKTVGAGVIQSIIE 482
E ++MVMPGD + + VELI P+A EQG++FAIREGG+TVGAG + I++
Sbjct: 346 EGTEMVMPGDNVTITVELIHPIAMEQGLKFAIREGGRTVGAGTVTEILD 394
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 712 bits (1840), Expect = 0.0
Identities = 295/408 (72%), Positives = 335/408 (82%), Gaps = 15/408 (3%)
Query: 75 ARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGI 134
A+ KFER KPHVN+GTIGHVDHGKTTLTAA+T LA G + K YD+ID APEE+ARGI
Sbjct: 2 AKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKKGGAEAKAYDQIDNAPEEKARGI 61
Query: 135 TINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHIL 194
TINTA VEYET NRHYAHVDCPGHADYVKNMITGAAQMDGAILVV+ DGPMPQT+EHIL
Sbjct: 62 TINTAHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHIL 121
Query: 195 LAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEA 254
LA+QVGVP +VVFLNK D VDDEELL+LVE+EVRELLS Y FPGDD PII GSAL ALE
Sbjct: 122 LARQVGVPYIVVFLNKVDMVDDEELLELVEMEVRELLSEYGFPGDDTPIIRGSALKALE- 180
Query: 255 LMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGR 314
G+ +W KI ELMD+VDSYIP P+R D PFL+ VEDVFSI+GRGTV TGR
Sbjct: 181 ---------GDAKWEAKIEELMDAVDSYIPTPERDIDKPFLMPVEDVFSISGRGTVVTGR 231
Query: 315 VERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAMAGDNVGLLLRGVQKADIQRGM 374
VERG +KVGE V++VG+KET+ TVTGVEMF+K LDE AGDNVG+LLRGV++ D++RG
Sbjct: 232 VERGILKVGEEVEIVGIKETQKTTVTGVEMFRKLLDEGQAGDNVGVLLRGVKREDVERGQ 291
Query: 375 VLAKPGTITPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGRVSSIMNDKDE 434
VLAKPG+I PHTKF A VYVL KEEGGRH+PFF GYRPQFY RTTDVTG ++ E
Sbjct: 292 VLAKPGSIKPHTKFEAEVYVLSKEEGGRHTPFFHGYRPQFYFRTTDVTGAITLP-----E 346
Query: 435 ESKMVMPGDRIKMVVELIMPVACEQGMRFAIREGGKTVGAGVIQSIIE 482
+MVMPGD +KMVVELI P+A E+G+RFAIREGG+TVGAGV+ IIE
Sbjct: 347 GVEMVMPGDNVKMVVELIHPIAMEEGLRFAIREGGRTVGAGVVTKIIE 394
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 638 bits (1647), Expect = 0.0
Identities = 277/479 (57%), Positives = 336/479 (70%), Gaps = 34/479 (7%)
Query: 6 SAAATVASTSPKLTHPYASASPSNSLLSTTALRTKLTPSNLSSSFLPPFATTTAVTVTTT 65
A+ + + + K P++S + + + S+S + +
Sbjct: 1 MASVVLRNPNSKRLLPFSSQ---------IYCACRGSAPSTSASISAADDRQS----PSP 47
Query: 66 RRRSLIVRAARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDA 125
RS+ F R KPHVN+GTIGHVDHGKTTLTAA+T LA G + +DEID
Sbjct: 48 WWRSM------ATFTRTKPHVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAVAFDEIDK 101
Query: 126 APEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGP 185
APEE+ARGITI TA VEYET RHYAHVDCPGHADYVKNMITGAAQMDG ILVVS DGP
Sbjct: 102 APEEKARGITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGP 161
Query: 186 MPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIIS 245
MPQTKEHILLA+QVGVP++VVFLNK D VDDEELL+LVE+E+RELLS Y+FPGD++PII
Sbjct: 162 MPQTKEHILLARQVGVPSLVVFLNKVDVVDDEELLELVEMELRELLSFYKFPGDEIPIIR 221
Query: 246 GSALLALEALMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSIT 305
GSAL AL+ N I + + I +LMD+VD YIP P R D PFL+ +EDVFSI
Sbjct: 222 GSALSALQG--TNDEIGK------NAILKLMDAVDEYIPEPVRVLDKPFLMPIEDVFSIQ 273
Query: 306 GRGTVATGRVERGTIKVGETVDLVGLKETRNF--TVTGVEMFQKTLDEAMAGDNVGLLLR 363
GRGTVATGRVE+GTIKVGE V++VGL+ TVTGVEMF+K LD+ AGDNVGLLLR
Sbjct: 274 GRGTVATGRVEQGTIKVGEEVEIVGLRPGGPLKTTVTGVEMFKKILDQGQAGDNVGLLLR 333
Query: 364 GVQKADIQRGMVLAKPGTITPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTG 423
G+++ D+QRG V+ KPG+I + KF A +YVL K+EGGRH+PFF+ YRPQFY+RT DVTG
Sbjct: 334 GLKREDVQRGQVICKPGSIKTYKKFEAEIYVLTKDEGGRHTPFFSNYRPQFYLRTADVTG 393
Query: 424 RVSSIMNDKDEESKMVMPGDRIKMVVELIMPVACEQGMRFAIREGGKTVGAGVIQSIIE 482
+V E KMVMPGD + V ELI PV E G RFA+REGG+TVGAGV+ ++
Sbjct: 394 KVE-----LPEGVKMVMPGDNVTAVFELISPVPLEPGQRFALREGGRTVGAGVVSKVLS 447
>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 = 411 bits (1058), Expect = e-144
Identities = 152/203 (74%), Positives = 168/203 (82%), Gaps = 8/203 (3%)
Query: 84 PHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITINTATVEY 143
PHVN+GTIGHVDHGKTTLTAA+T LA G + KKYDEID APEE+ARGITINTA VEY
Sbjct: 1 PHVNVGTIGHVDHGKTTLTAAITKVLAKKGGAKAKKYDEIDKAPEEKARGITINTAHVEY 60
Query: 144 ETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPN 203
ET NRHYAHVDCPGHADY+KNMITGAAQMDGAILVVS DGPMPQT+EH+LLA+QVGVP
Sbjct: 61 ETANRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSATDGPMPQTREHLLLARQVGVPY 120
Query: 204 MVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEALMANPSIKR 263
+VVFLNK D VDDEELL+LVE+EVRELLS Y F GDD PI+ GSAL ALE
Sbjct: 121 IVVFLNKADMVDDEELLELVEMEVRELLSKYGFDGDDTPIVRGSALKALEG--------D 172
Query: 264 GENQWVDKIYELMDSVDSYIPIP 286
N+WVDKI EL+D++DSYIP P
Sbjct: 173 DPNKWVDKILELLDALDSYIPTP 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 = 269 bits (691), Expect = 3e-89
Identities = 97/202 (48%), Positives = 125/202 (61%), Gaps = 19/202 (9%)
Query: 83 KPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITINTATVE 142
K H NIG IGHVDHGKTTLT AL ++ + K +D EER RGITI A V
Sbjct: 1 KRHRNIGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVS 60
Query: 143 YETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVP 202
+ET+ R +D PGH D+ K MI GA+Q DGAILVV +G MPQT+EH+LLAK +GVP
Sbjct: 61 FETKKRLINIIDTPGHVDFTKEMIRGASQADGAILVVDAVEGVMPQTREHLLLAKTLGVP 120
Query: 203 NMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEALMANPSIK 262
++VF+NK D+VDD EL ++VE RELL Y F G+ VP++ GSAL
Sbjct: 121 -IIVFINKIDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPGSALTG----------- 168
Query: 263 RGENQWVDKIYELMDSVDSYIP 284
+ I EL++++D Y+P
Sbjct: 169 -------EGIDELLEALDLYLP 183
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 276 bits (708), Expect = 2e-88
Identities = 153/444 (34%), Positives = 233/444 (52%), Gaps = 69/444 (15%)
Query: 81 RKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDE---------------IDA 125
++KPH+N+ IGHVDHGK+TL L ++ ++ E +D
Sbjct: 2 KEKPHLNLAVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMDR 61
Query: 126 APEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGAD-- 183
EER RG+TI+ A ++ET+ ++ VDCPGH D+VKNMITGA+Q D A+LVV+ D
Sbjct: 62 LKEERERGVTIDLAHKKFETDKYYFTIVDCPGHRDFVKNMITGASQADAAVLVVAADDAG 121
Query: 184 GPMPQTKEHILLAKQVGVPNMVVFLNKQDQVD-DEELLQLVELEVRELLSSYEFPGDDVP 242
G MPQT+EH+ LA+ +G+ ++V +NK D V+ DE+ + V+ EV +LL + DD+P
Sbjct: 122 GVMPQTREHVFLARTLGINQLIVAINKMDAVNYDEKRYEEVKEEVSKLLKMVGYKPDDIP 181
Query: 243 IISGSALLALEALMANPSIKRGENQ-WVD--KIYELMDSVDSYIPIPQRQTDLPFLLAVE 299
I SA + +K+ EN W + + E +D+ + P++ TD P + ++
Sbjct: 182 FIPVSAFE------GDNVVKKSENMPWYNGPTLLEALDN----LKPPEKPTDKPLRIPIQ 231
Query: 300 DVFSITGRGTVATGRVERGTIKVGETV-----DLVGLKETRNFTVTGVEMFQKTLDEAMA 354
DV+SI+G GTV GRVE G +KVG+ V +VG V +EM + L +A
Sbjct: 232 DVYSISGVGTVPVGRVETGVLKVGDKVVFMPAGVVG-------EVKSIEMHHEELPQAEP 284
Query: 355 GDNVGLLLRGVQKADIQRGMV---LAKPGTITPHTKFLAIVYVLKKEEGGRH-SPFFAGY 410
GDN+G +RGV K DI+RG V P T+ +F A + VL+ H S GY
Sbjct: 285 GDNIGFNVRGVGKKDIKRGDVCGHPDNPPTVA--EEFTAQIVVLQ------HPSAITVGY 336
Query: 411 RPQFYMRTTDVTGRVSSIM--------NDKDEESKMVMPGDRIKMVVELIMPVACE---- 458
P F+ T V ++ +E + + GD + ++ P+ E
Sbjct: 337 TPVFHAHTAQVACTFEELVKKLDPRTGQVAEENPQFIKTGDAAIVKIKPTKPLVIEKVKE 396
Query: 459 --QGMRFAIREGGKTVGAGVIQSI 480
Q RFAIR+ G+T+ AG++ +
Sbjct: 397 IPQLGRFAIRDMGQTIAAGMVIDV 420
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 273 bits (701), Expect = 3e-87
Identities = 146/438 (33%), Positives = 216/438 (49%), Gaps = 56/438 (12%)
Query: 83 KPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDE---------------IDAAP 127
KPH+N+ IGHVD GK+TL L L + +K ++ +D
Sbjct: 5 KPHLNLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVLDKTK 64
Query: 128 EERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADG--- 184
EER RG+TI+ A ++ET+ ++ +D PGH D+VKNMITGA+Q D A+LVV DG
Sbjct: 65 EERERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARDGEFE 124
Query: 185 ----PMPQTKEHILLAKQVGVPNMVVFLNKQDQVD-DEELLQLVELEVRELLSSYEFPGD 239
QT+EH LA+ +G+ ++V +NK D V DEE + + EV +LL +
Sbjct: 125 AGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLLKMVGYNPK 184
Query: 240 DVPIISGSALLALEALMANPSIKRGEN-QWVDKIYELMDSVDSYIPIPQRQTDLPFLLAV 298
DVP I S N K+ EN W K L++++D + P+R D P L +
Sbjct: 185 DVPFIPISGFKG-----DN-LTKKSENMPWY-KGPTLLEALD-QLEPPERPLDKPLRLPI 236
Query: 299 EDVFSITGRGTVATGRVERGTIKVGETVDLV-GLKETRNFTVTGVEMFQKTLDEAMAGDN 357
+DV+SI+G GTV GRVE G IK G+ V + V +EM + + +A GDN
Sbjct: 237 QDVYSISGIGTVPVGRVESGVIKPGQKVTFMPAGVVGE---VKSIEMHHEEISQAEPGDN 293
Query: 358 VGLLLRGVQKADIQRGMVLAKP-GTITPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYM 416
VG +RGV+K DI+RG V+ T +F A + VL +GY P +
Sbjct: 294 VGFNVRGVEKNDIRRGDVIGHSDNPPTVSPEFTAQIIVL-----WHPGIITSGYTPVLHA 348
Query: 417 RTTDVTGRVSSIM--NDKDEESKM------VMPGDRIKMVVELIMPVA------CEQGMR 462
T V R++ ++ D K+ + GD + +E P+ Q R
Sbjct: 349 HTAQVACRIAELLSKLDPRTGKKLEENPQFLKRGDAAIVKIEPEKPLCLEKVSEIPQLGR 408
Query: 463 FAIREGGKTVGAGVIQSI 480
FA+R+ G+T+ AG + +
Sbjct: 409 FALRDMGQTIAAGKVLEV 426
>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 = 228 bits (584), Expect = 5e-70
Identities = 146/436 (33%), Positives = 222/436 (50%), Gaps = 52/436 (11%)
Query: 81 RKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDE---------------IDA 125
++K H+N+ IGHVDHGK+T L ++ +K+++ +D
Sbjct: 3 KEKEHINVAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFEFAWVMDR 62
Query: 126 APEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGP 185
EER RG+TI+ A ++ET+ VDCPGH D++KNMITGA+Q D A+LVV+ DG
Sbjct: 63 LKEERERGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGDGE 122
Query: 186 ---MPQTKEHILLAKQVGVPNMVVFLNKQDQVD-DEELLQLVELEVRELLSSYEFPGDDV 241
PQT+EH LA+ +G+ ++V +NK D V+ DEE + ++ EV L+ + D V
Sbjct: 123 FEVQPQTREHAFLARTLGINQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVGYNPDTV 182
Query: 242 PIISGSALLALEALMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDV 301
P I + A + IK+ EN K L++++D+ P P++ TD P + ++DV
Sbjct: 183 PFIP------ISAWNGDNVIKKSENTPWYKGKTLLEALDALEP-PEKPTDKPLRIPIQDV 235
Query: 302 FSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAMAGDNVGLL 361
+SITG GTV GRVE G +K G+ V + V +EM + +++A GDN+G
Sbjct: 236 YSITGVGTVPVGRVETGVLKPGDKVVFEPAGVSGE--VKSIEMHHEQIEQAEPGDNIGFN 293
Query: 362 LRGVQKADIQRGMVLAKPGTITPHT---KFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRT 418
+RGV K DI+RG V P P +F A + VL+ GY P F+ T
Sbjct: 294 VRGVSKKDIRRGDVCGHPD--NPPKVAKEFTAQIVVLQHP-----GAITVGYTPVFHCHT 346
Query: 419 TDVTGRVSSIMNDKD--------EESKMVMPGDRIKMVVELIMPVACE------QGMRFA 464
+ R ++ D E + + GD + + P+ E RFA
Sbjct: 347 AQIACRFDELLKKNDPRTGQVLEENPQFLKTGDAAIVKFKPTKPMVIEAVKEIPPLGRFA 406
Query: 465 IREGGKTVGAGVIQSI 480
IR+ G+TV AG+I +
Sbjct: 407 IRDMGQTVAAGMIIDV 422
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 199 bits (508), Expect = 1e-58
Identities = 140/441 (31%), Positives = 207/441 (46%), Gaps = 55/441 (12%)
Query: 81 RKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDE---------------IDA 125
++K H+N+ IGHVD GK+T T L + +K+++ +D
Sbjct: 3 KEKTHINLVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDK 62
Query: 126 APEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGP 185
ER RGITI+ A ++ET ++ +D PGH D++KNMITG +Q D AILVV+ G
Sbjct: 63 LKAERERGITIDIALWKFETPKYYFTIIDAPGHRDFIKNMITGTSQADVAILVVASTAGE 122
Query: 186 MP-------QTKEHILLAKQVGVPNMVVFLNKQD--QVD-DEELLQLVELEVRELLSSYE 235
QT+EH LLA +GV M+V +NK D V+ +E ++ EV L
Sbjct: 123 FEAGISKDGQTREHALLAFTLGVKQMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKKVG 182
Query: 236 FPGDDVPIISGSALLALEALMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFL 295
+ + VP I + + I++ +N K L++++D+ P P+R D P
Sbjct: 183 YNPEKVPFI------PISGWQGDNMIEKSDNMPWYKGPTLLEALDTLEP-PKRPVDKPLR 235
Query: 296 LAVEDVFSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAMAG 355
L ++DV+ I G GTV GRVE G +K G V T V VEM + L EA+ G
Sbjct: 236 LPLQDVYKIGGIGTVPVGRVETGILKPGMVVTFAPSGVTTE--VKSVEMHHEQLAEAVPG 293
Query: 356 DNVGLLLRGVQKADIQRGMVL--AKPGTITPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQ 413
DNVG ++ V DI+RG V +K F A V VL G+ GY P
Sbjct: 294 DNVGFNVKNVSVKDIKRGYVASDSKNDPAKECADFTAQVIVLNHP--GQIKN---GYTPV 348
Query: 414 FYMRTTDVTGRVSSIM--NDK------DEESKMVMPGDRIKMVVELIMPVACEQGM---- 461
T + + + I D+ +E K + GD + + P+ E
Sbjct: 349 LDCHTAHIACKFAEIESKIDRRSGKVLEENPKAIKSGDAAIVKMVPTKPMCVEVFNEYPP 408
Query: 462 --RFAIREGGKTVGAGVIQSI 480
RFA+R+ +TV GVI+S+
Sbjct: 409 LGRFAVRDMKQTVAVGVIKSV 429
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 191 bits (486), Expect = 2e-55
Identities = 112/380 (29%), Positives = 178/380 (46%), Gaps = 46/380 (12%)
Query: 86 VNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITINTATVEYET 145
+ IGT GH+DHGKTTL ALT D PEE+ RGITI+ +
Sbjct: 1 MIIGTAGHIDHGKTTLLKALT-------------GGVTDRLPEEKKRGITIDLGFYYRKL 47
Query: 146 ENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMV 205
E+ +D PGH D++ N++ G +D A+LVV+ +G M QT EH+L+ +G+ N +
Sbjct: 48 EDGVMGFIDVPGHPDFISNLLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGIKNGI 107
Query: 206 VFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEALMANPSIKRGE 265
+ L K D+VD+ + Q ++++L+ + I S K G
Sbjct: 108 IVLTKADRVDEARIEQK----IKQILADLSLA--NAKIFK-------------TSAKTGR 148
Query: 266 NQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVERGTIKVGET 325
I EL + + + +R PF +A++ F++ G GTV TG V G +KVG+
Sbjct: 149 G-----IEELKNELIDLLEEIERDEQKPFRIAIDRAFTVKGVGTVVTGTVLSGEVKVGDK 203
Query: 326 VDLVGL-KETRNFTVTGVEMFQKTLDEAMAGDNVGLLLRGVQKADIQRGMVLAKPGTITP 384
+ L + KE R V ++ ++EA AG VGL L+GV+K +I+RG L KP +
Sbjct: 204 LYLSPINKEVR---VRSIQAHDVDVEEAKAGQRVGLALKGVEKEEIERGDWLLKPEPLEV 260
Query: 385 HTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGRVSSIM-NDKDEESKMVMPGD 443
T+ + + + + G ++ VTGR+ + N + K + GD
Sbjct: 261 TTRLIVELEIDPLFK----KTLKQGQPVHIHVGLRSVTGRIVPLEKNAELNLVKPIALGD 316
Query: 444 RIKMVVELIMPVACEQGMRF 463
++V+ V G R
Sbjct: 317 NDRLVLRDNSAVIKLAGARV 336
>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 = 178 bits (455), Expect = 3e-55
Identities = 66/95 (69%), Positives = 78/95 (82%), Gaps = 5/95 (5%)
Query: 383 TPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGRVSSIMNDKDEESKMVMPG 442
PHTKF A VYVL KEEGGRH+PFF+GYRPQFY+RTTDVTG ++ E ++MVMPG
Sbjct: 1 KPHTKFEAEVYVLTKEEGGRHTPFFSGYRPQFYIRTTDVTGSITLP-----EGTEMVMPG 55
Query: 443 DRIKMVVELIMPVACEQGMRFAIREGGKTVGAGVI 477
D +KM VELI P+A E+G+RFAIREGG+TVGAGVI
Sbjct: 56 DNVKMTVELIHPIALEKGLRFAIREGGRTVGAGVI 90
>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 = 180 bits (458), Expect = 2e-54
Identities = 81/203 (39%), Positives = 108/203 (53%), Gaps = 23/203 (11%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITINTATVEYETE 146
N+G IGHVDHGKTTLT +L ++ +K +D EER RGITI T VE+E
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWP 60
Query: 147 NRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVV 206
R +D PGH D+ K + G AQ DGA+LVV +G PQT+EH+ +A G ++V
Sbjct: 61 KRRINFIDTPGHEDFSKETVRGLAQADGALLVVDANEGVEPQTREHLNIALA-GGLPIIV 119
Query: 207 FLNKQDQVDDEELLQLVELEVRELLSSYEF---PGDDVPIISGSALLALEALMANPSIKR 263
+NK D+V EE V E++ELL F G DVPII SAL
Sbjct: 120 AVNKIDRV-GEEDFDEVLREIKELLKLIGFTFLKGKDVPIIPISALTG------------ 166
Query: 264 GENQWVDKIYELMDSVDSYIPIP 286
+ I EL+D++ ++P P
Sbjct: 167 ------EGIEELLDAIVEHLPPP 183
>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 = 168 bits (427), Expect = 4e-51
Identities = 63/87 (72%), Positives = 76/87 (87%)
Query: 294 FLLAVEDVFSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAM 353
FL+ +EDVFSI GRGTV TGR+ERGTIKVG+ V++VG ET TVTG+EMF+KTLDEA
Sbjct: 1 FLMPIEDVFSIPGRGTVVTGRIERGTIKVGDEVEIVGFGETLKTTVTGIEMFRKTLDEAE 60
Query: 354 AGDNVGLLLRGVQKADIQRGMVLAKPG 380
AGDNVG+LLRGV++ D++RGMVLAKPG
Sbjct: 61 AGDNVGVLLRGVKREDVERGMVLAKPG 87
>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 = 172 bits (437), Expect = 2e-47
Identities = 95/346 (27%), Positives = 162/346 (46%), Gaps = 50/346 (14%)
Query: 86 VNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAA--PEERARGITINTATVEY 143
+ I T GHVDHGKTTL ALT I A PEE+ RG+TI+ +
Sbjct: 1 MIIATAGHVDHGKTTLLKALT---------------GIAADRLPEEKKRGMTIDLGFAYF 45
Query: 144 ETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPN 203
+ +D PGH ++ N I G +D A+LVV +G M QT EH+ + +G+P+
Sbjct: 46 PLPDYRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIPH 105
Query: 204 MVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEALMANPSIKR 263
+V + K D+V++EE+ + E+ ++++L+SY F + I SA +
Sbjct: 106 TIVVITKADRVNEEEIKR-TEMFMKQILNSYIF-LKNAKIFKTSAKTG-----------Q 152
Query: 264 GENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVERGTIKVG 323
G + ++ L++S+D ++ P +A++ F + G GTV TG G +KVG
Sbjct: 153 GIGELKKELKNLLESLDI------KRIQKPLRMAIDRAFKVKGAGTVVTGTAFSGEVKVG 206
Query: 324 ETVDLVGL-KETRNFTVTGVEMFQKTLDEAMAGDNVGLLLRGVQKADIQRGMVLAKPGTI 382
+ + L+ + E R V ++ + ++ A AG + L L V+ ++RG+++ +
Sbjct: 207 DNLRLLPINHEVR---VKAIQAQNQDVEIAYAGQRIALNLMDVEPESLKRGLLI-----L 258
Query: 383 TPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGRVSSI 428
TP L +V P + TG++S +
Sbjct: 259 TPEDPKLRVVVKFIA-----EVPLLELQPYHIAHGMSVTTGKISLL 299
>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 = 156 bits (396), Expect = 6e-45
Identities = 69/188 (36%), Positives = 96/188 (51%), Gaps = 25/188 (13%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDE---------------IDAAPEERA 131
N+ IGHVD GK+TLT L L + +KY++ +D EER
Sbjct: 1 NLVVIGHVDAGKSTLTGHLLYKLGGVDKRTIEKYEKEAKEMGKESFKYAWVLDKLKEERE 60
Query: 132 RGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADG------- 184
RG+TI+ ++ETE + +D PGH D+VKNMITGA+Q D A+LVVS G
Sbjct: 61 RGVTIDVGLAKFETEKYRFTIIDAPGHRDFVKNMITGASQADVAVLVVSARKGEFEAGFE 120
Query: 185 PMPQTKEHILLAKQVGVPNMVVFLNKQDQVD---DEELLQLVELEVRELLSSYEFPGDDV 241
QT+EH LLA+ +GV ++V +NK D V +E ++ +V L + DV
Sbjct: 121 KGGQTREHALLARTLGVKQLIVAVNKMDDVTVNWSQERYDEIKKKVSPFLKKVGYNPKDV 180
Query: 242 PIISGSAL 249
P I S
Sbjct: 181 PFIPISGF 188
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 162 bits (410), Expect = 1e-44
Identities = 133/441 (30%), Positives = 200/441 (45%), Gaps = 55/441 (12%)
Query: 81 RKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDE---------------IDA 125
++K H+NI IGHVD GK+T T L L + +++++ +D
Sbjct: 3 KEKVHINIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFEKEAAEMNKRSFKYAWVLDK 62
Query: 126 APEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGP 185
ER RGITI+ A ++ET + +D PGH D++KNMITG +Q D A+L++ G
Sbjct: 63 LKAERERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGG 122
Query: 186 MP-------QTKEHILLAKQVGVPNMVVFLNKQDQVD---DEELLQLVELEVRELLSSYE 235
QT+EH LLA +GV M+ NK D + + EV L
Sbjct: 123 FEAGISKDGQTREHALLAFTLGVKQMICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVG 182
Query: 236 FPGDDVPIISGSALLALEALMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFL 295
+ D +P + + + I+R N K L++++D I P+R +D P
Sbjct: 183 YNPDKIPFV------PISGFEGDNMIERSTNLDWYKGPTLLEALDQ-INEPKRPSDKPLR 235
Query: 296 LAVEDVFSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAMAG 355
L ++DV+ I G GTV GRVE G IK G V T V VEM ++L EA+ G
Sbjct: 236 LPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFGPTGLTTE--VKSVEMHHESLQEALPG 293
Query: 356 DNVGLLLRGVQKADIQRGMVL--AKPGTITPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQ 413
DNVG ++ V D++RG V +K F + V ++ GY P
Sbjct: 294 DNVGFNVKNVAVKDLKRGYVASNSKDDPAKEAANFTSQVIIMNHP-----GQIGNGYAPV 348
Query: 414 FYMRTTDVTGRVSSIMNDKD--------EESKMVMPGDR--IKMVVELIMPVACEQGM-- 461
T+ + + + I+ D +E K + GD +KM+ M V
Sbjct: 349 LDCHTSHIAVKFAEILTKIDRRSGKELEKEPKFLKNGDAGFVKMIPTKPMVVETFSEYPP 408
Query: 462 --RFAIREGGKTVGAGVIQSI 480
RFA+R+ +TV GVI+S+
Sbjct: 409 LGRFAVRDMRQTVAVGVIKSV 429
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 161 bits (408), Expect = 1e-43
Identities = 129/447 (28%), Positives = 200/447 (44%), Gaps = 68/447 (15%)
Query: 76 RGKFERKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGIT 135
R K E HV +G GHVDHGK+TL L G+ A + Y +D E RG++
Sbjct: 108 RRKTEEAPEHVLVGVAGHVDHGKSTLVGVLVTGRLDDGDGATRSY--LDVQKHEVERGLS 165
Query: 136 INTA-----------------------TVEYETENRHYAHVDCPGHADYVKNMITG--AA 170
+ + + ++ + VD GH +++ I G
Sbjct: 166 ADISLRVYGFDDGKVVRLKNPLDEAEKAAVVKRADKLVSFVDTVGHEPWLRTTIRGLLGQ 225
Query: 171 QMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVREL 230
++D +LVV+ DG TKEH+ +A + +P +VV + K D V D+ +VE E+ L
Sbjct: 226 KVDYGLLVVAADDGVTKMTKEHLGIALAMELPVIVV-VTKIDMVPDDRFQGVVE-EISAL 283
Query: 231 LSSYEFPGDDVPIISGSALLALEALMANPSIKRGENQWVDKI----------YELMDSVD 280
L +P+I + A A + + V I +L+D
Sbjct: 284 LKRVG----RIPLIVKDTDDVVLAAKAMKA-----GRGVVPIFYTSSVTGEGLDLLDEFF 334
Query: 281 SYIPIPQRQTDL--PFLLAVEDVFSITGRGTVATGRVERGTIKVGETVDLVGLK--ETRN 336
+P +R+ D PFL+ ++ ++S+TG GTV +G V+ G + VG+TV L K + R
Sbjct: 335 LLLP-KRRRWDDEGPFLMYIDKIYSVTGVGTVVSGSVKSGILHVGDTVLLGPFKDGKFRE 393
Query: 337 FTVTGVEMFQKTLDEAMAGDNVGLLLRGVQKADIQRGMVLAKPGTITPHTKFLAIVYVLK 396
V +EM +D A AG +G+ L+GV+K +++RGMVL+ +F A V VL
Sbjct: 394 VVVKSIEMHHYRVDSAKAGSIIGIALKGVEKEELERGMVLSAGADPKAVREFDAEVLVL- 452
Query: 397 KEEGGRHSPFF-AGYRPQFYMRTTDVTGRVSSIMNDKDEESKMVMPGDRIKMVVELIM-P 454
RH AGY P F+ T I DK +MPGDR + + P
Sbjct: 453 -----RHPTTIRAGYEPVFHYETIREAVYFEEI--DKGF----LMPGDRGVVRMRFKYRP 501
Query: 455 VACEQGMRFAIREGGKTVGAGVIQSII 481
E+G +F RE G++ G G + +
Sbjct: 502 HHVEEGQKFVFRE-GRSKGVGRVIRVD 527
>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 = 153 bits (389), Expect = 6e-42
Identities = 134/451 (29%), Positives = 198/451 (43%), Gaps = 105/451 (23%)
Query: 84 PHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITI------- 136
P VNIG +GHVDHGKTTLT ALT D EE RGI+I
Sbjct: 3 PEVNIGMVGHVDHGKTTLTKALTGVW-------------TDTHSEELKRGISIRLGYADA 49
Query: 137 -----------NTATVEYETEN--------RHYAHVDCPGHADYVKNMITGAAQMDGAIL 177
T E N R + VD PGH + M++GAA MDGA+L
Sbjct: 50 EIYKCPECDGPECYTTEPVCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGALL 109
Query: 178 VVSGADG-PMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEF 236
V++ + P PQT+EH++ + +G+ N+V+ NK D V E+ L+ E E++E +
Sbjct: 110 VIAANEPCPQPQTREHLMALEIIGIKNIVIVQNKIDLVSKEKALENYE-EIKEFVKGT-- 166
Query: 237 PGDDVPIISGSALLALEALMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLL 296
++ PII SAL N L+++++ +IP P+R D P L+
Sbjct: 167 IAENAPIIPVSAL-------------HNANIDA-----LLEAIEKFIPTPERDLDKPPLM 208
Query: 297 AVEDVFSITGRGT--------VATGRVERGTIKVGETVDLV-GLKETRN---------FT 338
V F + GT V G + +G +KVG+ +++ G+K +
Sbjct: 209 YVARSFDVNKPGTPPEKLKGGVIGGSLIQGKLKVGDEIEIRPGIKVEKGGKTKWEPIYTE 268
Query: 339 VTGVEMFQKTLDEAMAGDNVGL---LLRGVQKADIQRGMVLAKPGTITP-HTKFLAIVYV 394
+T + ++EA G VG+ L + KAD G V+ KPGT+ P V++
Sbjct: 269 ITSLRAGGYKVEEARPGGLVGVGTKLDPALTKADALAGQVVGKPGTLPPVWESLELEVHL 328
Query: 395 LKK----EEGGRHSPFFAGYRPQFYMRTTDVTGRVSSIMNDKDEESKMVMPGDRIKMVVE 450
L++ EE + P G + T G V+S D+ E V+
Sbjct: 329 LERVVGTEEELKVEPIKTGEVLMLNVGTATTVGVVTSARKDEIE--------------VK 374
Query: 451 LIMPVACEQGMRFAI--REGGK--TVGAGVI 477
L PV E+G R AI R GG+ +G G+I
Sbjct: 375 LKRPVCAEEGDRVAISRRVGGRWRLIGYGII 405
>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 = 138 bits (351), Expect = 5e-40
Identities = 48/101 (47%), Positives = 60/101 (59%), Gaps = 10/101 (9%)
Query: 381 TITPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGRVSSIMNDKDEESKMVM 440
I PHTKF A VY+L +P F GYRP FY T DVTG+ + + VM
Sbjct: 1 PIKPHTKFKAQVYILNH-----PTPIFNGYRPVFYCHTADVTGKF-----ILPGKKEFVM 50
Query: 441 PGDRIKMVVELIMPVACEQGMRFAIREGGKTVGAGVIQSII 481
PGD + VELI P+A E+G RFAIREGG+TV GV+ ++
Sbjct: 51 PGDNAIVTVELIKPIAVEKGQRFAIREGGRTVAVGVVTEVL 91
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 144 bits (366), Expect = 1e-38
Identities = 129/461 (27%), Positives = 199/461 (43%), Gaps = 105/461 (22%)
Query: 76 RGKFERKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGIT 135
+ +P VNIG +GHVDHGKTTLT AL+ G D EE RGIT
Sbjct: 1 MADPKHIQPEVNIGMVGHVDHGKTTLTKALS------GVWT-------DRHSEELKRGIT 47
Query: 136 I------------------NTATVEYETEN--------RHYAHVDCPGHADYVKNMITGA 169
I T E + N R + VD PGH + M++GA
Sbjct: 48 IKLGYADAKIYKCPECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGHETLMATMLSGA 107
Query: 170 AQMDGAILVVSGADG-PMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVR 228
A MDGA+LV++ + P PQT+EH++ + +G+ N+++ NK D V E L+ E +++
Sbjct: 108 ALMDGALLVIAANEPCPQPQTREHLMALEIIGIKNIIIVQNKIDLVSRERALENYE-QIK 166
Query: 229 ELLSSYEFPGDDVPIISGSALLALEALMANPSIKRGENQWVDKIYELMDSVDSYIPIPQR 288
E + ++ PII SA AN I L+++++ YIP P+R
Sbjct: 167 EFVK--GTVAENAPIIPISAQHK-----AN-------------IDALIEAIEKYIPTPER 206
Query: 289 QTDLPFLLAVEDVFSITGRGT--------VATGRVERGTIKVGETVDLV-GLKETRN--- 336
D P + V F + GT V G + +G ++VG+ +++ G+ +
Sbjct: 207 DLDKPPRMYVARSFDVNKPGTPPEELKGGVIGGSLVQGVLRVGDEIEIRPGIVVEKGGKT 266
Query: 337 -----FT-VTGVEMFQKTLDEAMAGDNVGL---LLRGVQKADIQRGMVLAKPGTITP-HT 386
T + ++ + ++EA G VG+ L + KAD G V+ KPGT+ P T
Sbjct: 267 VWEPITTEIVSLQAGGEDVEEARPGGLVGVGTKLDPTLTKADALVGQVVGKPGTLPPVWT 326
Query: 387 KFLAIVYVLKK----EEGGRHSPFFAGYRPQFYMRTTDVTGRVSSIMNDKDEESKMVMPG 442
++L++ +E + P + T G V+S D+ E
Sbjct: 327 SIRIEYHLLERVVGTKEELKVEPIKTNEVLMLNVGTATTVGVVTSAKKDEIE-------- 378
Query: 443 DRIKMVVELIMPVACEQGMRFAI--REGG--KTVGAGVIQS 479
V+L PV E G R AI R G + +G G I+
Sbjct: 379 ------VKLKRPVCAEIGERVAISRRIGNRWRLIGYGTIKE 413
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 141 bits (359), Expect = 1e-37
Identities = 133/459 (28%), Positives = 196/459 (42%), Gaps = 111/459 (24%)
Query: 80 ERKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITI--- 136
E+ +P VNIG +GHVDHGKTTL ALT D EE RGITI
Sbjct: 4 EKVQPEVNIGMVGHVDHGKTTLVQALTGVWT-------------DRHSEELKRGITIRLG 50
Query: 137 ---------------NTATVEYETEN--------RHYAHVDCPGHADYVKNMITGAAQMD 173
T E + N R + VD PGH + M++GAA MD
Sbjct: 51 YADATIRKCPDCEEPEAYTTEPKCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMD 110
Query: 174 GAILVVSGADG-PMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLS 232
GAILV++ + P PQTKEH++ +G+ N+V+ NK D V E L+ E +++E +
Sbjct: 111 GAILVIAANEPCPQPQTKEHLMALDIIGIKNIVIVQNKIDLVSKERALENYE-QIKEFVK 169
Query: 233 SYEFPGDDVPIISGSALLALEALMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDL 292
++ PII SAL N L+++++ IP P+R D
Sbjct: 170 GTVA--ENAPIIPVSAL-------------HKVNIDA-----LIEAIEEEIPTPERDLDK 209
Query: 293 PFLLAVEDVFSITGRGT--------VATGRVERGTIKVGETVDLV-GLKETRNF------ 337
P + V F + GT V G + +G +KVG+ +++ G+K
Sbjct: 210 PPRMYVARSFDVNKPGTPPEKLKGGVIGGSLIQGVLKVGDEIEIRPGIKVEEGGKTKWEP 269
Query: 338 ---TVTGVEMFQKTLDEAMAGDNVGLLLRG------VQKADIQRGMVLAKPGTITP-HTK 387
+ + + ++EA G GL+ G + KAD G V KPGT+ P
Sbjct: 270 ITTKIVSLRAGGEKVEEARPG---GLVGVGTKLDPSLTKADALAGSVAGKPGTLPPVWES 326
Query: 388 FLAIVYVLKK----EEGGRHSPFFAGYRPQFYMRTTDVTGRVSSIMNDKDEESKMVMPGD 443
V++L++ +E + P G + T G V+S D+ E
Sbjct: 327 LTIEVHLLERVVGTKEELKVEPIKTGEPLMLNVGTATTVGVVTSARKDEAE--------- 377
Query: 444 RIKMVVELIMPVACEQGMRFAI--REGGK--TVGAGVIQ 478
V+L PV E+G R AI R GG+ +G G+I+
Sbjct: 378 -----VKLKRPVCAEEGDRVAISRRVGGRWRLIGYGIIK 411
>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 = 135 bits (341), Expect = 2e-37
Identities = 62/171 (36%), Positives = 92/171 (53%), Gaps = 19/171 (11%)
Query: 88 IGTIGHVDHGKTTLTAALT-MALASLGNSAPKKYDEIDAAPEERARGITINT--ATVEYE 144
IGT GH+DHGKTTL ALT + L PEE+ RGITI+ A ++
Sbjct: 2 IGTAGHIDHGKTTLIKALTGIETDRL--------------PEEKKRGITIDLGFAYLDLP 47
Query: 145 TENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNM 204
+ + +D PGH +VKNM+ GA +D +LVV+ +G MPQT+EH+ + + +G+
Sbjct: 48 -DGKRLGFIDVPGHEKFVKNMLAGAGGIDAVLLVVAADEGIMPQTREHLEILELLGIKKG 106
Query: 205 VVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEAL 255
+V L K D VD++ L + E E+ ELL+ + +S +E L
Sbjct: 107 LVVLTKADLVDEDRLELVEE-EILELLAGTFLADAPIFPVSSVTGEGIEEL 156
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 142 bits (360), Expect = 1e-36
Identities = 92/289 (31%), Positives = 142/289 (49%), Gaps = 41/289 (14%)
Query: 88 IGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITINTATVEY-ETE 146
I T GHVDHGKTTL A+T G +A D PEE+ RG+TI+ + + +
Sbjct: 3 IATAGHVDHGKTTLLQAIT------GVNA-------DRLPEEKKRGMTIDLGYAYWPQPD 49
Query: 147 NRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVV 206
R +D PGH ++ NM+ G +D A+LVV+ DG M QT+EH+ + + G P + V
Sbjct: 50 GRVLGFIDVPGHEKFLSNMLAGVGGIDHALLVVACDDGVMAQTREHLAILQLTGNPMLTV 109
Query: 207 FLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEALMANPSIKRGEN 266
L K D+VD+ + + V +V+ +L Y F + + +A + RG
Sbjct: 110 ALTKADRVDEARIAE-VRRQVKAVLREYGFA--EAKLFVTAA-----------TEGRG-- 153
Query: 267 QWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVERGTIKVGETV 326
I L + + +P + F LA++ F++ G G V TG G +KVG+T+
Sbjct: 154 -----IDALREHL-LQLPEREHAAQHRFRLAIDRAFTVKGAGLVVTGTALSGEVKVGDTL 207
Query: 327 DLVGL-KETRNFTVTGVEMFQKTLDEAMAGDNVGLLLRG-VQKADIQRG 373
L G+ K R V G+ + ++A AG + L + G +K I RG
Sbjct: 208 WLTGVNKPMR---VRGLHAQNQPTEQAQAGQRIALNIAGDAEKEQINRG 253
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 137 bits (348), Expect = 5e-36
Identities = 119/434 (27%), Positives = 183/434 (42%), Gaps = 60/434 (13%)
Query: 81 RKKPHVNIGTIGHVDHGKTTL--------TAALTMALASLGNSAPKK---YDEIDAA--- 126
+ K + T G VD GK+TL A LASL + +K ++ID A
Sbjct: 2 QHKSLLRFITCGSVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLV 61
Query: 127 ---PEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGAD 183
ER +GITI+ A + TE R + D PGH Y +NM TGA+ D AIL+V
Sbjct: 62 DGLEAEREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTADLAILLVDARK 121
Query: 184 GPMPQTKEHILLAKQVGVPNMVVFLNKQDQVD-DEELLQLVELEVRELLSSYEFPGDDVP 242
G + QT+ H +A +G+ ++VV +NK D VD EE+ + + + + + DV
Sbjct: 122 GVLEQTRRHSFIASLLGIRHVVVAVNKMDLVDYSEEVFEAIVADYLAFAA--QLGLKDVR 179
Query: 243 IISGSALLALEALMANPSIKRGENQWVD--KIYELMDSVDSYIPIPQRQTDLPFLLAVED 300
I SALL N K W + E++++V+ I ++ F V+
Sbjct: 180 FIPISALLG-----DNVVSKSENMPWYKGPTLLEILETVE----IADDRSAKAFRFPVQY 230
Query: 301 V--FSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAMAGDNV 358
V ++ RG G + G++KVG+ V V L + V + F L +A AG+ V
Sbjct: 231 VNRPNLDFRGY--AGTIASGSVKVGDEV--VVLPSGKTSRVKRIVTFDGELAQASAGEAV 286
Query: 359 GLLLRGVQKADIQRG-MVLAKPGTITPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMR 417
L+L + DI RG +++A F A V + +E P G +
Sbjct: 287 TLVLA--DEIDISRGDLIVAADAPPAVADAFDADVVWMDEE------PLLPGRSYDLKIA 338
Query: 418 TTDVTGRVSSIMNDKDEESKMVMPGDRIKM------VVELIMPVACEQ--------GMRF 463
T V RV I + D + + + + + P+A +
Sbjct: 339 TRTVRARVEEIKHQLDVNTLEQEGAESLPLNEIGRVRISFDKPIAFDAYAENRATGSFIL 398
Query: 464 AIREGGKTVGAGVI 477
R TVGAG+I
Sbjct: 399 IDRLTNGTVGAGMI 412
>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 = 111 bits (279), Expect = 2e-28
Identities = 63/193 (32%), Positives = 94/193 (48%), Gaps = 44/193 (22%)
Query: 86 VNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITI--------- 136
+NIGTIGHV HGKTTL AL+ G + +E+ R ITI
Sbjct: 1 INIGTIGHVAHGKTTLVKALS------GVWTVRHKEELK-------RNITIKLGYANAKI 47
Query: 137 ----------NTATVEYETEN--------RHYAHVDCPGHADYVKNMITGAAQMDGAILV 178
T E E RH + VDCPGH + M++GAA MDGA+L+
Sbjct: 48 YKCPNCGCPRPYDTPECECPGCGGETKLVRHVSFVDCPGHEILMATMLSGAAVMDGALLL 107
Query: 179 VSGADG-PMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFP 237
++ + P PQT EH+ + +G+ ++++ NK D V +E+ L+ E +++E +
Sbjct: 108 IAANEPCPQPQTSEHLAALEIMGLKHIIILQNKIDLVKEEQALENYE-QIKEFVK--GTI 164
Query: 238 GDDVPIISGSALL 250
++ PII SA L
Sbjct: 165 AENAPIIPISAQL 177
>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 = 110 bits (278), Expect = 3e-28
Identities = 61/180 (33%), Positives = 87/180 (48%), Gaps = 23/180 (12%)
Query: 90 TIGHVDHGKTTLTAAL--------TMALASLGNSAPKKYDE----------IDAAPEERA 131
T G VD GK+TL L LA+L S K +D ER
Sbjct: 4 TCGSVDDGKSTLIGRLLYDSKSIFEDQLAALERS--KSSGTQGEKLDLALLVDGLQAERE 61
Query: 132 RGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKE 191
+GITI+ A + T R + D PGH Y +NM+TGA+ D AIL+V G + QT+
Sbjct: 62 QGITIDVAYRYFSTPKRKFIIADTPGHEQYTRNMVTGASTADLAILLVDARKGVLEQTRR 121
Query: 192 HILLAKQVGVPNMVVFLNKQDQVD-DEELLQLVELEVRELLSSYEFPGDDVPIISGSALL 250
H +A +G+ ++VV +NK D VD DEE+ + ++ + +S D+ I SAL
Sbjct: 122 HSYIASLLGIRHVVVAVNKMDLVDYDEEVFEEIKADYLAFAASLGIE--DITFIPISALE 179
>gnl|CDD|233394 TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA. This
bacterial (and Arabidopsis) protein, termed TypA or
BipA, a GTP-binding protein, is phosphorylated on a
tyrosine residue under some cellular conditions. Mutants
show altered regulation of some pathways, but the
precise function is unknown [Regulatory functions,
Other, Cellular processes, Adaptations to atypical
conditions, Protein synthesis, Translation factors].
Length = 594
Score = 114 bits (287), Expect = 4e-27
Identities = 99/308 (32%), Positives = 143/308 (46%), Gaps = 54/308 (17%)
Query: 87 NIGTIGHVDHGKTTLTAAL---TMALASLGNSAPKKYDEIDAAPEERARGITI---NTAT 140
NI I HVDHGKTTL AL + + A + D D ER RGITI NTA
Sbjct: 3 NIAIIAHVDHGKTTLVDALLKQSGTFRANEAVAERVMDSNDL---ERERGITILAKNTA- 58
Query: 141 VEYETENRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVSGADGPMPQTKEHIL 194
+ Y VD PGHAD+ V M+ DG +L+V ++GPMPQT+ +
Sbjct: 59 IRY--NGTKINIVDTPGHADFGGEVERVLGMV------DGVLLLVDASEGPMPQTRFVLK 110
Query: 195 LAKQVGVPNMVVFLNKQDQVD---DEELLQLVELEVRELLSSYEFPGD--DVPIISGSAL 249
A ++G+ +VV +NK D+ DE V EV +L + + D PI+ S
Sbjct: 111 KALELGLKPIVV-INKIDRPSARPDE-----VVDEVFDLFAELGADDEQLDFPIVYASGR 164
Query: 250 LALEALMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVE--DVFSITGR 307
+L + D + L D++ ++P P+ D P + V D GR
Sbjct: 165 AGWASLDLDDP--------SDNMAPLFDAIVRHVPAPKGDLDEPLQMLVTNLDYDEYLGR 216
Query: 308 GTVATGRVERGTIKVGETVDLVGLKET-RNFTVTGVEMFQ----KTLDEAMAGDNVGLLL 362
+A GRV RGT+K G+ V L+ T N ++ + F+ +DEA AGD V +
Sbjct: 217 --IAIGRVHRGTVKKGQQVALMKRDGTIENGRISKLLGFEGLERVEIDEAGAGDIVAVA- 273
Query: 363 RGVQKADI 370
G++ +I
Sbjct: 274 -GLEDINI 280
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 113 bits (286), Expect = 6e-27
Identities = 97/306 (31%), Positives = 146/306 (47%), Gaps = 50/306 (16%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASLGN-SAPKKYDE--IDAAPEERARGITI---NTAT 140
NI I HVDHGKTTL AL L G ++ E +D+ E+ RGITI NTA
Sbjct: 7 NIAIIAHVDHGKTTLVDAL---LKQSGTFREREEVAERVMDSNDLEKERGITILAKNTA- 62
Query: 141 VEYETENRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVSGADGPMPQTKEHIL 194
V Y VD PGHAD+ V +M+ DG +L+V ++GPMPQT+ +
Sbjct: 63 VNY--NGTRINIVDTPGHADFGGEVERVLSMV------DGVLLLVDASEGPMPQTRFVLK 114
Query: 195 LAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGD--DVPIISGSALLAL 252
A +G+ +VV +NK D+ D ++V+ EV +L + D PI+ SA
Sbjct: 115 KALALGLKPIVV-INKIDR-PDARPDEVVD-EVFDLFVELGATDEQLDFPIVYASARNGT 171
Query: 253 EAL-MANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVE--DVFSITGRGT 309
+L + + D + L +++ ++P P+ D P + V D S GR
Sbjct: 172 ASLDPEDEA---------DDMAPLFETILDHVPAPKGDLDEPLQMQVTQLDYNSYVGR-- 220
Query: 310 VATGRVERGTIKVGETVDLVGL-KETRNFTVTGVEMFQ----KTLDEAMAGDNVGLLLRG 364
+ GR+ RGT+K + V L+ T N +T + F ++EA AGD V + G
Sbjct: 221 IGIGRIFRGTVKPNQQVALIKSDGTTENGRITKLLGFLGLERIEIEEAEAGDIV--AIAG 278
Query: 365 VQKADI 370
++ +I
Sbjct: 279 LEDINI 284
>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 = 105 bits (264), Expect = 2e-26
Identities = 57/179 (31%), Positives = 86/179 (48%), Gaps = 25/179 (13%)
Query: 86 VNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITI--------- 136
VN+G +GHVD GKT+L AL+ ++ +A D P+ + RGIT+
Sbjct: 1 VNVGLLGHVDSGKTSLAKALSEIAST---AA------FDKNPQSQERGITLDLGFSSFEV 51
Query: 137 -----NTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKE 191
+ EN VDCPGHA ++ +I GA +D +LVV G QT E
Sbjct: 52 DKPKHLEDNENPQIENYQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDAKKGIQTQTAE 111
Query: 192 HILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFP-GDDVPIISGSAL 249
+++ + + P ++V LNK D + +EE + +E + L + E D PII SA
Sbjct: 112 CLVIGELLCKP-LIVVLNKIDLIPEEERKRKIEKMKKRLQKTLEKTRLKDSPIIPVSAK 169
>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 = 107 bits (270), Expect = 2e-25
Identities = 120/432 (27%), Positives = 182/432 (42%), Gaps = 74/432 (17%)
Query: 90 TIGHVDHGKTTLTAALTM--------ALASLGNSAPKKY---DEIDAA------PEERAR 132
T G VD GK+TL L LA+L + K EID A ER +
Sbjct: 5 TCGSVDDGKSTLIGRLLHDTKQIYEDQLAALERDSKKHGTQGGEIDLALLVDGLQAEREQ 64
Query: 133 GITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEH 192
GITI+ A + T+ R + D PGH Y +NM TGA+ D A+L+V G + QT+ H
Sbjct: 65 GITIDVAYRYFSTDKRKFIVADTPGHEQYTRNMATGASTADLAVLLVDARKGVLEQTRRH 124
Query: 193 ILLAKQVGVPNMVVFLNKQDQVD-DEELLQLVELEVRELLSSYEFPGDDVPIISGSALLA 251
+A +G+ ++V+ +NK D VD DEE+ + ++ + F DV I SAL
Sbjct: 125 SYIASLLGIRHVVLAVNKMDLVDYDEEVFENIKKDYLAFAEQLGF--RDVTFIPLSALKG 182
Query: 252 LEALMANPSIKRGENQWVDKIYE---LMDSVDSYIPIPQRQTDLPFLLAVEDV------- 301
N + W Y L++ +++ + + + DLP V+ V
Sbjct: 183 -----DNVVSRSESMPW----YSGPTLLEILET-VEVERDAQDLPLRFPVQYVNRPNLDF 232
Query: 302 --FSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAMAGDNVG 359
++ GT+A+G V VG+ V V L R+ V + F L++A AG V
Sbjct: 233 RGYA----GTIASGSV-----HVGDEV--VVLPSGRSSRVARIVTFDGDLEQARAGQAVT 281
Query: 360 LLLRGVQKADIQRGMVLAKPGTITPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTT 419
L L + DI RG +LA + A V EE P G + T
Sbjct: 282 LTLD--DEIDISRGDLLAAADSAPEVADQFAATLVWMAEE-----PLLPGRSYDLKLGTR 334
Query: 420 DVTGRVSSI-----MNDKDEESKMVMPGDRIKMV-VELIMPVACEQ--------GMRFAI 465
V V++I +N ++ + + + I V + L P+A +
Sbjct: 335 KVRASVAAIKHKVDVNTLEKGAAKSLELNEIGRVNLSLDEPIAFDPYAENRTTGAFILID 394
Query: 466 REGGKTVGAGVI 477
R +TVGAG+I
Sbjct: 395 RLSNRTVGAGMI 406
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 107 bits (268), Expect = 4e-25
Identities = 110/450 (24%), Positives = 173/450 (38%), Gaps = 121/450 (26%)
Query: 86 VNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITIN----TATV 141
+NIGTIGHV HGK+T+ AL+ ++ E+ R ITI A +
Sbjct: 35 INIGTIGHVAHGKSTVVKALSGVKT-------VRFKR------EKVRNITIKLGYANAKI 81
Query: 142 EYETEN------------------------------RHYAHVDCPGHADYVKNMITGAAQ 171
Y+ RH + VDCPGH + M+ GAA
Sbjct: 82 -YKCPKCPRPTCYQSYGSSKPDNPPCPGCGHKMTLKRHVSFVDCPGHDILMATMLNGAAV 140
Query: 172 MDGAILVVSGADG-PMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVREL 230
MD A+L+++ + P PQT EH+ + + + ++++ NK D V + + E E+R
Sbjct: 141 MDAALLLIAANESCPQPQTSEHLAAVEIMKLKHIIILQNKIDLVKEAQAQDQYE-EIRNF 199
Query: 231 LSSYEFPGDDVPIISGSALLALEALMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQT 290
+ D+ PII SA L K I +++ + + IPIP+R
Sbjct: 200 VKGTI--ADNAPIIPISAQL-----------KY-------NIDVVLEYICTQIPIPKRDL 239
Query: 291 DLPFLLAVEDVFSI--------TGRGTVATGRVERGTIKVGETVD----LVGLKETRNFT 338
P + V F + +G VA G + +G +KVG+ ++ ++ FT
Sbjct: 240 TSPPRMIVIRSFDVNKPGEDIENLKGGVAGGSILQGVLKVGDEIEIRPGIISKDSGGEFT 299
Query: 339 VTG-----VEMF--QKTLDEAMAGDNVGLLLRGVQ------KADIQRGMVLAKPGTITPH 385
V +F L A+ G GL+ G +AD G VL PG +
Sbjct: 300 CRPIRTRIVSLFAENNELQYAVPG---GLIGVGTTIDPTLTRADRLVGQVLGYPGKLPEV 356
Query: 386 TKFLAIVYVL-------KKEEGGRH---SPFFAGYRPQFYMRTTDVTGRVSSIMNDKDEE 435
+ I Y L K ++G + + G + +T GRV I +D
Sbjct: 357 YAEIEIQYYLLRRLLGVKSQDGKKATKVAKLKKGESLMINIGSTTTGGRVVGIKDDG--- 413
Query: 436 SKMVMPGDRIKMVVELIMPVACEQGMRFAI 465
+EL PV G + A+
Sbjct: 414 ----------IAKLELTTPVCTSVGEKIAL 433
>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 = 95.9 bits (239), Expect = 3e-24
Identities = 38/98 (38%), Positives = 57/98 (58%), Gaps = 5/98 (5%)
Query: 383 TPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGRVSSIMNDKDEESKMVMPG 442
PH K A VY+L K EGGRH PF + ++PQ + T D R+ + K+ MVMPG
Sbjct: 1 KPHDKVEAQVYILSKAEGGRHKPFVSNFQPQMFSLTWDCAARID-LPPGKE----MVMPG 55
Query: 443 DRIKMVVELIMPVACEQGMRFAIREGGKTVGAGVIQSI 480
+ K+ + L P+ E+G RF +R+G +T+G G++
Sbjct: 56 EDTKVTLILRRPMVLEKGQRFTLRDGNRTIGTGLVTDT 93
>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 = 100 bits (250), Expect = 6e-24
Identities = 57/156 (36%), Positives = 87/156 (55%), Gaps = 11/156 (7%)
Query: 87 NIGTIGHVDHGKTTLTAAL---TMALASLGNSAPKKYDEIDAAPEERARGITINTATVEY 143
NIG + HVD GKTTLT +L + A+ LG S K D+ ER RGITI +A +
Sbjct: 1 NIGILAHVDAGKTTLTESLLYTSGAIRELG-SVDKGTTRTDSMELERQRGITIFSAVASF 59
Query: 144 ETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPN 203
+ E+ +D PGH D++ + + +DGAILV+S +G QT+ L +++ +P
Sbjct: 60 QWEDTKVNIIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTRILFRLLRKLNIPT 119
Query: 204 MVVFLNKQDQ--VDDEELLQLVELEVRELLSSYEFP 237
++F+NK D+ D E++ Q E++E LS P
Sbjct: 120 -IIFVNKIDRAGADLEKVYQ----EIKEKLSPDIVP 150
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 103 bits (258), Expect = 3e-23
Identities = 98/329 (29%), Positives = 144/329 (43%), Gaps = 71/329 (21%)
Query: 90 TIGHVDHGKTTLTAAL--------TMALASLGNSAPKK---YDEIDAA------PEERAR 132
T G VD GK+TL L LA+L + K DEID A ER +
Sbjct: 29 TCGSVDDGKSTLIGRLLYDSKMIFEDQLAALERDSKKVGTQGDEIDLALLVDGLAAEREQ 88
Query: 133 GITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEH 192
GITI+ A + T R + D PGH Y +NM+TGA+ D AI++V G + QT+ H
Sbjct: 89 GITIDVAYRYFATPKRKFIVADTPGHEQYTRNMVTGASTADLAIILVDARKGVLTQTRRH 148
Query: 193 ILLAKQVGVPNMVVFLNKQDQVD-DEELLQLVELEVRELLSSYEFPGDDVPIISGSALLA 251
+A +G+ ++V+ +NK D VD D+E+ + + R + DV I SAL
Sbjct: 149 SFIASLLGIRHVVLAVNKMDLVDYDQEVFDEIVADYRAFAAKLGLH--DVTFIPISAL-- 204
Query: 252 LEALMANPSIKRGEN--------QWVDKIYE---LMDSVDSYIPIPQRQTDLPFLLAVED 300
+G+N W YE L++ +++ + I + F V+
Sbjct: 205 -----------KGDNVVTRSARMPW----YEGPSLLEHLET-VEIASDRNLKDFRFPVQY 248
Query: 301 V---------FSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDE 351
V F+ GTVA+ G ++ G+ V V L + V + LDE
Sbjct: 249 VNRPNLDFRGFA----GTVAS-----GVVRPGDEV--VVLPSGKTSRVKRIVTPDGDLDE 297
Query: 352 AMAGDNVGLLLRGVQKADIQRGMVLAKPG 380
A AG V L L + DI RG +LA+
Sbjct: 298 AFAGQAVTLTLA--DEIDISRGDMLARAD 324
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 97.7 bits (244), Expect = 1e-21
Identities = 44/132 (33%), Positives = 66/132 (50%), Gaps = 10/132 (7%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASLG-NSAPKKYDEIDAA----PEERARGITINTATV 141
NIG + H+D GKTTLT + L G S + + A +E+ RGITI +A
Sbjct: 12 NIGIVAHIDAGKTTLTERI---LFYTGIISKIGEVHDGAATMDWMEQEQERGITITSAAT 68
Query: 142 EYETENRH-YAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVG 200
+ + +D PGH D+ + +DGA++VV +G PQT+ A + G
Sbjct: 69 TLFWKGDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVEGVEPQTETVWRQADKYG 128
Query: 201 VPNMVVFLNKQD 212
VP ++F+NK D
Sbjct: 129 VP-RILFVNKMD 139
Score = 34.9 bits (81), Expect = 0.11
Identities = 37/187 (19%), Positives = 65/187 (34%), Gaps = 30/187 (16%)
Query: 202 PNMVVFLNKQDQVDDEELLQLVELEVRELLSSYE---FPGDDVPIISGSAL--LALEALM 256
++ L + D+ E+ L+ E E+ + G VP++ GSA ++ L+
Sbjct: 211 EKLLEALAEFDEELMEKYLEGEEPTEEEIKKALRKGTIAGKIVPVLCGSAFKNKGVQPLL 270
Query: 257 -----------ANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSIT 305
P IK + ++K S + P V + +
Sbjct: 271 DAVVDYLPSPLDVPPIKGDLDDEIEKAVLRKASDEG-----------PLSALVFKIMTDP 319
Query: 306 GRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEM--FQKTLDEAMAGDNVGLL-L 362
G + RV GT+K G V + + ++ +DE AGD V L+ L
Sbjct: 320 FVGKLTFVRVYSGTLKSGSEVLNSTKGKKERVGRLLLMHGNEREEVDEVPAGDIVALVGL 379
Query: 363 RGVQKAD 369
+ D
Sbjct: 380 KDATTGD 386
>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 = 3e-21
Identities = 35/85 (41%), Positives = 54/85 (63%), Gaps = 2/85 (2%)
Query: 294 FLLAVEDVFSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAM 353
F L ++ VF++ G+GTV TG V G++KVG+ V+++ L E V +++ K ++EA
Sbjct: 1 FRLPIDRVFTVKGQGTVVTGTVLSGSVKVGDKVEILPLGEET--RVRSIQVHGKDVEEAK 58
Query: 354 AGDNVGLLLRGVQKADIQRGMVLAK 378
AGD V L L GV D++RG VL+
Sbjct: 59 AGDRVALNLTGVDAKDLERGDVLSS 83
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 95.8 bits (239), Expect = 4e-21
Identities = 117/447 (26%), Positives = 185/447 (41%), Gaps = 93/447 (20%)
Query: 90 TIGHVDHGKTTLTAAL---TMA-----LASLGNSAPKK---YDEIDAA------PEERAR 132
T G VD GK+TL L T LASL N + + +++D A ER +
Sbjct: 32 TCGSVDDGKSTLIGRLLHDTKQIYEDQLASLHNDSKRHGTQGEKLDLALLVDGLQAEREQ 91
Query: 133 GITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEH 192
GITI+ A + TE R + D PGH Y +NM TGA+ D AIL++ G + QT+ H
Sbjct: 92 GITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTCDLAILLIDARKGVLDQTRRH 151
Query: 193 ILLAKQVGVPNMVVFLNKQDQVD-DEELLQLVELEVRELLSSYEFPGD-DVPIISGSALL 250
+A +G+ ++VV +NK D VD EE+ + + + PG+ D+ + SAL
Sbjct: 152 SFIATLLGIKHLVVAVNKMDLVDYSEEVFERIREDYLTFAEQ--LPGNLDIRFVPLSAL- 208
Query: 251 ALEALMANPSIKRGEN--------QWVDKIYE---LMDSVDSYIPIPQRQTDLPFLLAVE 299
G+N W Y L++ +++ + I + PF V+
Sbjct: 209 ------------EGDNVVSQSESMPW----YSGPTLLEVLET-VDIQRVVDAQPFRFPVQ 251
Query: 300 DV---------FSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLD 350
V ++ GT+A+ G +KVG+ V L + V + F L+
Sbjct: 252 YVNRPNLDFRGYA----GTLAS-----GVVKVGDRV--KVLPSGKESNVARIVTFDGDLE 300
Query: 351 EAMAGDNVGLLLRGVQKADIQRGMVLAKPG-TITPHTKFLAIVYVLKKEEGGRHSPFFAG 409
EA AG+ + L+L + DI RG +L + A V V E+ P G
Sbjct: 301 EAFAGEAITLVLE--DEIDISRGDLLVAADEALQAVQHASADV-VWMAEQ-----PLQPG 352
Query: 410 YRPQFYMRTTDVTGRVSSI-----MNDKDEESKMVMPGDRIKMV-VELIMPVACEQ---- 459
+ RV +I +N + +P + I +V + P+ +
Sbjct: 353 QSYDIKIAGKKTRARVDAIRYQVDINTLTQREAENLPLNGIGLVELTFDEPLVLDPYQQN 412
Query: 460 ----GMRFAIREGGKTVGAGVIQSIIE 482
G F R TVGAG+++ +
Sbjct: 413 RVTGGFIFIDRLTNVTVGAGMVREPLA 439
>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 = 86.8 bits (216), Expect = 4e-20
Identities = 65/178 (36%), Positives = 82/178 (46%), Gaps = 30/178 (16%)
Query: 92 GHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGIT--INTATVEYETENRH 149
GHVDHGKTTL L + + AA E A GIT I V + +
Sbjct: 7 GHVDHGKTTL-------LDKIRKTN-------VAAGE--AGGITQHIGAYQVPIDVKIPG 50
Query: 150 YAHVDCPGHADYVKNMITGAAQM-DGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFL 208
+D PGH + NM A + D AILVV+ DG MPQT E I AK VP ++V +
Sbjct: 51 ITFIDTPGHEAF-TNMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAANVP-IIVAI 108
Query: 209 NKQDQV-DDEELLQLVELEVRELLSSYEFPGDDVPIISGSA--------LLALEALMA 257
NK D+ E + V+ E+ EL E G DV I+ SA LL L+A
Sbjct: 109 NKIDKPYGTEADPERVKNELSELGLVGEEWGGDVSIVPISAKTGEGIDDLLEAILLLA 166
>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 = 82.7 bits (205), Expect = 9e-20
Identities = 33/70 (47%), Positives = 43/70 (61%)
Query: 308 GTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAMAGDNVGLLLRGVQK 367
GTVATGRVE GT+K G+ V + + VT +EMF L EA+AG N G++L G+
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGIGL 60
Query: 368 ADIQRGMVLA 377
DI+RG L
Sbjct: 61 KDIKRGDTLT 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 = 82.4 bits (204), Expect = 2e-19
Identities = 34/85 (40%), Positives = 46/85 (54%), Gaps = 2/85 (2%)
Query: 294 FLLAVEDVFSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAM 353
V VF GRGTVATGRVE GT+K G+ V + V ++ F+ +DEA+
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRFKGEVDEAV 60
Query: 354 AGDNVGLLLRGVQKADIQRGMVLAK 378
AGD VG++L+ DI+ G L
Sbjct: 61 AGDIVGIVLKDKD--DIKIGDTLTD 83
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 90.7 bits (226), Expect = 3e-19
Identities = 60/170 (35%), Positives = 89/170 (52%), Gaps = 32/170 (18%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASLGNSAPK--------KYDEIDAAPEERARGITINT 138
NIG I H+DHGKTTL+ L LA G + + +DE EE+ARGITI
Sbjct: 22 NIGIIAHIDHGKTTLSDNL---LAGAGMISEELAGEQLALDFDE-----EEQARGITIKA 73
Query: 139 ATV----EYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHIL 194
A V EYE + +D PGH D+ ++ +DGAI+VV +G MPQT+ +
Sbjct: 74 ANVSMVHEYEGKEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVDAVEGVMPQTETVLR 133
Query: 195 LAKQVGV-PNMVVFLNKQD------QVDDEELLQ-LVEL--EVRELLSSY 234
A + V P V+F+NK D ++ +E+ Q L+++ +V +L+
Sbjct: 134 QALRERVKP--VLFINKVDRLIKELKLTPQEMQQRLLKIIKDVNKLIKGM 181
Score = 32.5 bits (75), Expect = 0.50
Identities = 26/89 (29%), Positives = 46/89 (51%), Gaps = 9/89 (10%)
Query: 308 GTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEM--FQKTLDEAMAGDNVGLLLRGV 365
G VATGRV GT++ G+ V LVG K+ G+ M ++ ++E AG+ + G+
Sbjct: 305 GEVATGRVFSGTLRKGQEVYLVGAKKKNRVQQVGIYMGPEREEVEEIPAGNIAAVT--GL 362
Query: 366 QKADIQRGMVLAKPGTITPHTKFLAIVYV 394
+ A + G + +TP F ++ ++
Sbjct: 363 KDA--RAGETVVSVEDMTP---FESLKHI 386
>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 = 84.6 bits (210), Expect = 1e-18
Identities = 58/173 (33%), Positives = 86/173 (49%), Gaps = 33/173 (19%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEI---DAAPEERARGITINTATV-- 141
NI I HVDHGKTTL+ +L LAS G + K + D +E+ RGITI ++ +
Sbjct: 2 NICIIAHVDHGKTTLSDSL---LASAGIISEKLAGKARYLDTREDEQERGITIKSSAISL 58
Query: 142 --EYETENRHYAH-----VDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHIL 194
EYE E +D PGH D+ + DGA++VV +G QT E +L
Sbjct: 59 YFEYEEEKMDGNDYLINLIDSPGHVDFSSEVTAALRLTDGALVVVDAVEGVCVQT-ETVL 117
Query: 195 ---LAKQVGVPNMVVFLNKQD------QVDDEE----LLQLVELEVRELLSSY 234
L ++V V+ +NK D ++ EE LL++VE +V ++ +Y
Sbjct: 118 RQALEERV---KPVLVINKIDRLILELKLSPEEAYQRLLRIVE-DVNAIIETY 166
>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 = 88.3 bits (219), Expect = 1e-18
Identities = 79/249 (31%), Positives = 106/249 (42%), Gaps = 40/249 (16%)
Query: 80 ERKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGIT--IN 137
+ P V I +GHVDHGKT+L L S+ A E A GIT I
Sbjct: 84 VERPPVVTI--MGHVDHGKTSL-------LDSIRK--------TKVAQGE-AGGITQHIG 125
Query: 138 TATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAK 197
VE E + + +D PGH + GA D +LVV+ DG MPQT E I AK
Sbjct: 126 AYHVENE-DGKMITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAK 184
Query: 198 QVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEALMA 257
VP ++V +NK D+ + V+ E+ E E G D + SAL
Sbjct: 185 AANVP-IIVAINKIDKPEAN--PDRVKQELSEYGLVPEDWGGDTIFVPVSALTG------ 235
Query: 258 NPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVER 317
G ++ +D I L V+ P Q V + GRG VAT V+
Sbjct: 236 -----DGIDELLDMIL-LQSEVEELKANPNGQAS----GVVIEAQLDKGRGPVATVLVQS 285
Query: 318 GTIKVGETV 326
GT++VG+ V
Sbjct: 286 GTLRVGDIV 294
>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 = 79.9 bits (198), Expect = 2e-18
Identities = 39/88 (44%), Positives = 50/88 (56%), Gaps = 6/88 (6%)
Query: 290 TDLPFLLAVEDVFSITGRGTVATGRVERGTIKVGETVDL--VGLKETRNFTVTGVEMFQK 347
TD P L ++DV+ I G GTV GRVE G +K G V G+ V VEM +
Sbjct: 1 TDKPLRLPIQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGVT----GEVKSVEMHHE 56
Query: 348 TLDEAMAGDNVGLLLRGVQKADIQRGMV 375
L+EA+ GDNVG ++ V K DI+RG V
Sbjct: 57 PLEEALPGDNVGFNVKNVSKKDIKRGDV 84
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 87.6 bits (218), Expect = 2e-18
Identities = 83/262 (31%), Positives = 109/262 (41%), Gaps = 63/262 (24%)
Query: 92 GHVDHGKTTLTAALTMALASLGNSAPKKYDEI---DAAPEERARGIT--INTATVEYET- 145
GHVDHGKTTL D+I + A E A GIT I V +
Sbjct: 12 GHVDHGKTTLL------------------DKIRKTNVAAGE-AGGITQHIGAYQVPLDVI 52
Query: 146 ENRHYAHVDCPGHADYVKNMIT-GAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNM 204
+ +D PGH M GA+ D AILVV+ DG MPQT E I AK GVP +
Sbjct: 53 KIPGITFIDTPGHE-AFTAMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAAGVP-I 110
Query: 205 VVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSA--------LLALEALM 256
VV +NK D+ + EL+ L+ E G DV + SA LL L L+
Sbjct: 111 VVAINKIDKPEANPDKVKQELQEYGLVP--EEWGGDVIFVPVSAKTGEGIDELLELILLL 168
Query: 257 ANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVE 316
A ++ EL + + P V +V G G VAT V+
Sbjct: 169 A-------------EVLELKANPEG-----------PARGTVIEVKLDKGLGPVATVIVQ 204
Query: 317 RGTIKVGETVDLVGLKETRNFT 338
GT+K G+ + + G + R T
Sbjct: 205 DGTLKKGDII-VAGGEYGRVRT 225
Score = 32.5 bits (75), Expect = 0.56
Identities = 23/100 (23%), Positives = 40/100 (40%), Gaps = 10/100 (10%)
Query: 272 IYELMDSVDSYI-----PIPQRQTD-LPFLLAVEDVFSITGRGTVATGRVERGTIKVGET 325
IY+L++ V++ + P + + L V VF + G +A V G IK G
Sbjct: 389 IYKLIEDVEAAMKGMLEPEKKERVIGLAE---VRAVFKLPKVGAIAGCMVTEGVIKRGAP 445
Query: 326 VDLV-GLKETRNFTVTGVEMFQKTLDEAMAGDNVGLLLRG 364
V +V V ++ F+ + E G G+ +
Sbjct: 446 VRVVRDGVVIYEGEVESLKRFKDDVKEVRKGQECGIAIEN 485
>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 = 83.0 bits (206), Expect = 2e-18
Identities = 63/178 (35%), Positives = 89/178 (50%), Gaps = 33/178 (18%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITI---NTATVEY 143
NI I HVDHGKTTL AL + + +D+ ER RGITI NTA + Y
Sbjct: 4 NIAIIAHVDHGKTTLVDALLKQSGTFRENEEVGERVMDSNDLERERGITILAKNTA-ITY 62
Query: 144 ETENRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAK 197
++ +D PGHAD+ V +M+ DG +L+V ++GPMPQT+ +L K
Sbjct: 63 --KDTKINIIDTPGHADFGGEVERVLSMV------DGVLLLVDASEGPMPQTR--FVLKK 112
Query: 198 --QVGVPNMVVFLNKQDQVD---DEELLQLVELEVRELLSSYEFPGD--DVPIISGSA 248
+ G+ +VV +NK D+ D +E V EV +L + D PI+ SA
Sbjct: 113 ALEAGLKPIVV-INKIDRPDARPEE-----VVDEVFDLFLELNATDEQLDFPIVYASA 164
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 87.1 bits (215), Expect = 4e-18
Identities = 78/276 (28%), Positives = 124/276 (44%), Gaps = 22/276 (7%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITINTATVEYETE 146
NI I HVDHGKTTL L + + A + +D+ E+ RGITI +
Sbjct: 7 NIAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNTAIKWN 66
Query: 147 NRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVV 206
+ VD PGHAD+ + + +D +LVV DGPMPQT+ A G+ +VV
Sbjct: 67 DYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPIVV 126
Query: 207 FLNKQDQVD---DEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEALMANPSIKR 263
+NK D+ D + Q+ +L V + + D PI+ SAL + L
Sbjct: 127 -INKVDRPGARPDWVVDQVFDLFVNLDATDEQL---DFPIVYASALNGIAGL-------- 174
Query: 264 GENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVERGTIKVG 323
+ + L ++ ++P P D PF + + + + G + GR++RG +K
Sbjct: 175 DHEDMAEDMTPLYQAIVDHVPAPDVDLDGPFQMQISQLDYNSYVGVIGIGRIKRGKVKPN 234
Query: 324 ETVDLVGLK-ETRN------FTVTGVEMFQKTLDEA 352
+ V ++ + +TRN G+E + L EA
Sbjct: 235 QQVTIIDSEGKTRNAKVGKVLGHLGLERIETDLAEA 270
>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 = 77.1 bits (190), Expect = 2e-17
Identities = 40/107 (37%), Positives = 55/107 (51%), Gaps = 17/107 (15%)
Query: 383 TPHTKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGRVSSIM--NDKDEESK--- 437
KF+A +YVL E P GY+P + T V GR++ ++ D E K
Sbjct: 1 QAVDKFVAEIYVLDHPE-----PLSPGYKPVLNVGTAHVPGRIAKLLSKVDGKTEEKKPP 55
Query: 438 -MVMPGDRIKMVVELIMPVACEQ------GMRFAIREGGKTVGAGVI 477
+ G+R + VEL PVA E G RFA+R+GG+TVGAG+I
Sbjct: 56 EFLKSGERGIVEVELQKPVALETFSENQEGGRFALRDGGRTVGAGLI 102
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 81.7 bits (203), Expect = 2e-16
Identities = 46/129 (35%), Positives = 65/129 (50%), Gaps = 13/129 (10%)
Query: 91 IGHVDHGKTTLTAALTMALASLGNSAPKKYDEI-------DAAPEERARGITINTATVEY 143
+GH GKTTLT A+ L G A + E+ D PEER RGI+I +A
Sbjct: 1 VGHSGAGKTTLTEAI---LFYTG--AIHRIGEVEDGTTTMDFMPEERERGISITSAATTC 55
Query: 144 ETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPN 203
E + +D PGH D+ + +DGA++VV G PQT+ A++ GVP
Sbjct: 56 EWKGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGGVEPQTETVWRQAEKYGVPR 115
Query: 204 MVVFLNKQD 212
+ +F+NK D
Sbjct: 116 I-IFVNKMD 123
>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 = 81.1 bits (200), Expect = 3e-16
Identities = 53/146 (36%), Positives = 77/146 (52%), Gaps = 5/146 (3%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITINTATV----E 142
NIG + H+DHGKTTL+ L + + +D +E+ RGITIN A V E
Sbjct: 21 NIGIVAHIDHGKTTLSDNLLAGAGMISEELAGQQLYLDFDEQEQERGITINAANVSMVHE 80
Query: 143 YETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVP 202
YE +D PGH D+ ++ +DGAI+VV +G MPQT+ + A + V
Sbjct: 81 YEGNEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVCAVEGVMPQTETVLRQALKENV- 139
Query: 203 NMVVFLNKQDQVDDEELLQLVELEVR 228
V+F+NK D++ +E L EL+ R
Sbjct: 140 KPVLFINKVDRLINELKLTPQELQER 165
Score = 30.6 bits (69), Expect = 2.4
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 293 PFLLAVEDVFSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTL--D 350
P L + + G VA GR+ GTI+ G V +V K GV M + + D
Sbjct: 289 PLALMITKIVVDKHAGEVAVGRLYSGTIRPGMEVYIVDRKAKARIQQVGVYMGPERVEVD 348
Query: 351 EAMAGDNVGLL 361
E AG+ V ++
Sbjct: 349 EIPAGNIVAVI 359
>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 = 74.9 bits (185), Expect = 5e-15
Identities = 40/129 (31%), Positives = 60/129 (46%), Gaps = 5/129 (3%)
Query: 87 NIGTIGHVDHGKTTLTAAL---TMALASLGNSAPKKYDEIDAAPEERARGITINTATVEY 143
NI +GH GKTTL AL T A+ LG D PEE+ R ++I T+
Sbjct: 1 NIALVGHSGSGKTTLAEALLYATGAIDRLG-RVEDGNTVSDYDPEEKKRKMSIETSVAPL 59
Query: 144 ETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPN 203
E +D PG+AD+V ++ +D A++VV G T++ +P
Sbjct: 60 EWNGHKINLIDTPGYADFVGETLSALRAVDAALIVVEAQSGVEVGTEKVWEFLDDAKLPR 119
Query: 204 MVVFLNKQD 212
+ +F+NK D
Sbjct: 120 I-IFINKMD 127
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 75.3 bits (185), Expect = 2e-14
Identities = 74/261 (28%), Positives = 111/261 (42%), Gaps = 49/261 (18%)
Query: 74 AARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARG 133
A + P V I +GHVDHGKTTL L + + A +E A G
Sbjct: 235 AFTENSINRPPIVTI--LGHVDHGKTTL-------LDKIRKT--------QIAQKE-AGG 276
Query: 134 ITINTAT----VEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQT 189
IT EY+ EN+ +D PGH + GA D AIL+++ DG PQT
Sbjct: 277 ITQKIGAYEVEFEYKDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQT 336
Query: 190 KEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFP----GDDVPIIS 245
E I + VP ++V +NK D+ + E +++ L+ Y G D P+I
Sbjct: 337 IEAINYIQAANVP-IIVAINKIDKANAN-----TE-RIKQQLAKYNLIPEKWGGDTPMIP 389
Query: 246 GSALLALEALMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSIT 305
SA +G N +DK+ E + + + T L + +E T
Sbjct: 390 ISAS-------------QGTN--IDKLLETILLLAEIEDLKADPTQLAQGIILEAHLDKT 434
Query: 306 GRGTVATGRVERGTIKVGETV 326
+G VAT V+ GT+ +G+ +
Sbjct: 435 -KGPVATILVQNGTLHIGDII 454
>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 = 74.7 bits (184), Expect = 3e-14
Identities = 81/300 (27%), Positives = 134/300 (44%), Gaps = 47/300 (15%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDE--IDAAPEERARGITI--NTATVE 142
N I H+DHGK+TL L L G + ++ E +D+ ER RGITI +
Sbjct: 5 NFSIIAHIDHGKSTLADRL---LEYTGAISEREMREQVLDSMDLERERGITIKAQAVRLN 61
Query: 143 YETENRH---YAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQV 199
Y+ ++ +D PGH D+ + A +GA+L+V A G QT ++ LA +
Sbjct: 62 YKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLLVDAAQGIEAQTLANVYLALEN 121
Query: 200 GVPNMVVFLNKQD--QVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEALMA 257
+ ++ +NK D D E + + +E + + + + A+LA
Sbjct: 122 DL-EIIPVINKIDLPSADPERVKKEIE--------------EVIGLDASEAILA------ 160
Query: 258 NPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVER 317
S K G I E+++++ +P P+ D P + D RG VA RV
Sbjct: 161 --SAKTGIG-----IEEILEAIVKRVPPPKGDPDAPLKALIFDSHYDNYRGVVALVRVFE 213
Query: 318 GTIKVGETVDLVGLKETRNFTVTGVEMFQKTL---DEAMAGDNVGLLLRGVQKA-DIQRG 373
GTIK G+ + + + + V V +F L DE AG+ VG ++ G++ D++ G
Sbjct: 214 GTIKPGDKIRFMSTG--KEYEVDEVGVFTPKLTKTDELSAGE-VGYIIAGIKDVSDVRVG 270
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 74.6 bits (184), Expect = 4e-14
Identities = 47/145 (32%), Positives = 73/145 (50%), Gaps = 5/145 (3%)
Query: 87 NIGTIGHVDHGKTTLTAAL---TMALASLGNSAPKKYDEIDAAPEERARGITINTATVEY 143
NIG + H+D GKTTLT + T + +G D P+E+ RGITI +A
Sbjct: 10 NIGILAHIDAGKTTLTERILFYTGKIHKMG-EVEDGTTVTDWMPQEQERGITIESAATSC 68
Query: 144 ETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPN 203
+ +N +D PGH D+ + +DGA++V G PQT+ A + G+P
Sbjct: 69 DWDNHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDAVTGVQPQTETVWRQADRYGIPR 128
Query: 204 MVVFLNKQDQVDDEELLQLVELEVR 228
+ +F+NK D+V + L ++E R
Sbjct: 129 L-IFINKMDRVGADLFKVLEDIEER 152
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 72.6 bits (179), Expect = 2e-13
Identities = 81/268 (30%), Positives = 110/268 (41%), Gaps = 89/268 (33%)
Query: 90 TI-GHVDHGKTTLTAALTMALASLGNSAPKKYDEID-------AAPEERARGIT--INTA 139
TI GHVDHGKT+L +D AA E A GIT I
Sbjct: 253 TIMGHVDHGKTSL---------------------LDAIRKTNVAAGE--AGGITQHIGAY 289
Query: 140 TVEYETENRHYAHVDCPGHADYVKNMIT-----GAAQMDGAILVVSGADGPMPQTKEHIL 194
VE T +D PGH + T GA D +LVV+ DG MPQT E I
Sbjct: 290 QVE--TNGGKITFLDTPGHEAF-----TAMRARGAQVTDIVVLVVAADDGVMPQTIEAIN 342
Query: 195 LAKQVGVPNMVVFLNKQDQVD-DEELL--QLVELEVRELLSSYEFPGDDVPIISGSALLA 251
AK GVP ++V +NK D+ + + + +L E + + + G D + SA
Sbjct: 343 HAKAAGVP-IIVAINKIDKPGANPDRVKQELSEYGL--VPEEW---GGDTIFVPVSA--- 393
Query: 252 LEALMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSI------- 304
K GE I EL++++ Q ++ L A D +
Sbjct: 394 ----------KTGEG-----IDELLEAI-------LLQAEVLELKANPDRPARGTVIEAK 431
Query: 305 --TGRGTVATGRVERGTIKVGETVDLVG 330
GRG VAT V+ GT+KVG+ V + G
Sbjct: 432 LDKGRGPVATVLVQNGTLKVGDIV-VAG 458
>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 = 65.2 bits (160), Expect = 2e-13
Identities = 32/85 (37%), Positives = 52/85 (61%), Gaps = 3/85 (3%)
Query: 293 PFLLAVEDVFSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEA 352
PF L + D + G GTV +G+VE G+I+ G+T+ ++ KE+ V + + + +D A
Sbjct: 1 PFRLPISDKYKDQG-GTVVSGKVESGSIQKGDTLLVMPSKES--VEVKSIYVDDEEVDYA 57
Query: 353 MAGDNVGLLLRGVQKADIQRGMVLA 377
+AG+NV L L+G+ + DI G VL
Sbjct: 58 VAGENVRLKLKGIDEEDISPGDVLC 82
>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 = 66.9 bits (164), Expect = 8e-13
Identities = 39/136 (28%), Positives = 63/136 (46%), Gaps = 13/136 (9%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASL-----GNSAPKKYDEIDAAPEERARGITINTATV 141
N+ GH+ HGKT+L L P +Y D +E+ RGI+I + +
Sbjct: 2 NVCIAGHLHHGKTSLLDMLIEQTHKRTPSVKLGWKPLRY--TDTRKDEQERGISIKSNPI 59
Query: 142 EYETEN-RHYAHV----DCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLA 196
E+ + +++ D PGH +++ + DG +LVV +G T+ I A
Sbjct: 60 SLVLEDSKGKSYLINIIDTPGHVNFMDEVAAALRLCDGVVLVVDVVEGLTSVTERLIRHA 119
Query: 197 KQVGVPNMVVFLNKQD 212
Q G+P MV+ +NK D
Sbjct: 120 IQEGLP-MVLVINKID 134
>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 = 66.4 bits (163), Expect = 3e-12
Identities = 43/133 (32%), Positives = 59/133 (44%), Gaps = 13/133 (9%)
Query: 87 NIGTIGHVDHGKTTLTAA---LTMALASLGNSAPKKYDEIDAA----PEERARGITINTA 139
NIG I H+D GKTT T T + +G A +ER RGITI +A
Sbjct: 1 NIGIIAHIDAGKTTTTERILYYTGRIHKIGE-----VHGGGATMDWMEQERERGITIQSA 55
Query: 140 TVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQV 199
++ +D PGH D+ + +DGA+ V G PQT+ A +
Sbjct: 56 ATTCFWKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVQPQTETVWRQADRY 115
Query: 200 GVPNMVVFLNKQD 212
GVP + F+NK D
Sbjct: 116 GVP-RIAFVNKMD 127
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 64.5 bits (158), Expect = 5e-11
Identities = 80/300 (26%), Positives = 130/300 (43%), Gaps = 47/300 (15%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDE--IDAAPEERARGITI--NTATVE 142
N I H+DHGK+TL L L G + ++ +D+ ER RGITI +
Sbjct: 11 NFSIIAHIDHGKSTLADRL---LELTGGLSEREMRAQVLDSMDIERERGITIKAQAVRLN 67
Query: 143 Y---ETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQV 199
Y + E +D PGH D+ + A +GA+LVV + G QT ++ LA +
Sbjct: 68 YKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYLALEN 127
Query: 200 GVPNMVVFLNKQD--QVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEALMA 257
+ + V LNK D D E + Q +E D + I + A+L
Sbjct: 128 NLEIIPV-LNKIDLPAADPERVKQEIE--------------DIIGIDASDAVLV------ 166
Query: 258 NPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVER 317
S K G I ++++++ IP P+ D P + D + G V R+
Sbjct: 167 --SAKTGIG-----IEDVLEAIVEKIPPPKGDPDAPLKALIFDSWYDNYLGVVVLVRIFD 219
Query: 318 GTIKVGETVDLVGLKETRNFTVTGVEMF---QKTLDEAMAGDNVGLLLRGVQK-ADIQRG 373
GT+K G+ + ++ + + V V +F +DE AG+ VG ++ G++ D + G
Sbjct: 220 GTLKKGDKIRMMSTGKE--YEVDEVGIFTPKMVKVDELKAGE-VGYIIAGIKDVRDARVG 276
>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 = 60.5 bits (147), Expect = 5e-11
Identities = 38/149 (25%), Positives = 60/149 (40%), Gaps = 26/149 (17%)
Query: 86 VNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITINTAT--VEY 143
+ I +G + GK+TL L LGN + E G T N T +E
Sbjct: 2 IKIVIVGDPNVGKSTLLNRL------LGN---------KISITEYKPGTTRNYVTTVIEE 46
Query: 144 ETENRHYAHVDCPGHADYVK------NMITGAAQM-DGAILVVSGADGPMPQTKEHILLA 196
+ + + +D G DY + + ++ D ILV+ + QTKE I A
Sbjct: 47 DGKTYKFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHA 106
Query: 197 KQVGVPNMVVFLNKQDQVDDEELLQLVEL 225
+ GVP +++ NK D D + + L
Sbjct: 107 ES-GVP-IILVGNKIDLRDAKLKTHVAFL 133
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 64.3 bits (157), Expect = 7e-11
Identities = 51/157 (32%), Positives = 82/157 (52%), Gaps = 29/157 (18%)
Query: 87 NIGTIGHVDHGKTTLTAALTMA--LASLGNSAPKKYDEIDAAPEERARGITINTATV--- 141
N+ I HVDHGK+TLT +L + S N+ ++ D +E+ RGITI + +
Sbjct: 21 NMSVIAHVDHGKSTLTDSLVCKAGIISSKNAGDARF--TDTRADEQERGITIKSTGISLY 78
Query: 142 -EYETENRHYAH------VDCPGHADYVKNMITGAAQM-DGAILVVSGADGPMPQTKEHI 193
E++ E+ +D PGH D+ + +T A ++ DGA++VV +G QT E +
Sbjct: 79 YEHDLEDGDDKQPFLINLIDSPGHVDF-SSEVTAALRVTDGALVVVDCVEGVCVQT-ETV 136
Query: 194 L---LAKQVGVPNMVVFLNKQD------QVDDEELLQ 221
L L +++ V+F+NK D Q+D EE+ Q
Sbjct: 137 LRQALQERI---RPVLFINKVDRAILELQLDPEEIYQ 170
>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 = 59.1 bits (144), Expect = 2e-10
Identities = 52/209 (24%), Positives = 88/209 (42%), Gaps = 40/209 (19%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDE--IDAAPEERARGITI--NTATVE 142
N I H+DHGK+TL L L G + ++ E +D+ ER RGITI +
Sbjct: 2 NFSIIAHIDHGKSTLADRL---LELTGTVSEREMKEQVLDSMDLERERGITIKAQAVRLF 58
Query: 143 YETENRH---YAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQV 199
Y+ ++ +D PGH D+ + A +GA+LVV G QT + LA +
Sbjct: 59 YKAKDGEEYLLNLIDTPGHVDFSYEVSRSLAACEGALLVVDATQGVEAQTLANFYLALEN 118
Query: 200 GVPNMVVFLNKQDQV--DDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEALMA 257
+ ++ +NK D D + V+ E+ ++L + ++S
Sbjct: 119 NL-EIIPVINKIDLPAADPDR----VKQEIEDVL---GLDASEAILVSA----------- 159
Query: 258 NPSIKRGENQWVDKIYELMDSVDSYIPIP 286
K G + +L++++ IP P
Sbjct: 160 ----KTGLG-----VEDLLEAIVERIPPP 179
>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 = 54.9 bits (133), Expect = 8e-10
Identities = 28/84 (33%), Positives = 42/84 (50%), Gaps = 4/84 (4%)
Query: 293 PFLLAVEDVFSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEA 352
P L + D + GTV G+VE GTIK G+ + ++ K V + + A
Sbjct: 1 PLRLPIIDKYK--DMGTVVLGKVESGTIKKGDKLLVMPNKTQ--VEVLSIYNEDVEVRYA 56
Query: 353 MAGDNVGLLLRGVQKADIQRGMVL 376
G+NV L L+G+++ DI G VL
Sbjct: 57 RPGENVRLRLKGIEEEDISPGFVL 80
>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 = 60.6 bits (147), Expect = 1e-09
Identities = 41/135 (30%), Positives = 60/135 (44%), Gaps = 13/135 (9%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEI-------DAAPEERARGITINTA 139
NIG H+D GKTT T + L G K E+ D +E+ RGITI +A
Sbjct: 12 NIGISAHIDAGKTTTTERI---LFYTGRI--HKIGEVHDGAATMDWMEQEKERGITITSA 66
Query: 140 TVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQV 199
+ +D PGH D+ + +DGA+ V+ G PQ++ A +
Sbjct: 67 ATTVFWKGHRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAVGGVQPQSETVWRQANRY 126
Query: 200 GVPNMVVFLNKQDQV 214
VP + F+NK D+
Sbjct: 127 EVPR-IAFVNKMDKT 140
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 58.6 bits (142), Expect = 5e-09
Identities = 51/163 (31%), Positives = 76/163 (46%), Gaps = 35/163 (21%)
Query: 87 NIGTIGHVDHGKTTLTAALTMA--LASLGNSAPKKYDEIDAAPEERARGITINTATVE-- 142
N+ I HVDHGK+TLT +L A + + + + D +E RGITI + +
Sbjct: 21 NMSVIAHVDHGKSTLTDSLVAAAGIIAQEVAGDVRM--TDTRADEAERGITIKSTGISLY 78
Query: 143 YETENRHYAH--------------VDCPGHADYVKNMITGAAQM-DGAILVVSGADGPMP 187
YE + +D PGH D+ + +T A ++ DGA++VV +G
Sbjct: 79 YEMTDESLKDFKGERDGNEYLINLIDSPGHVDF-SSEVTAALRITDGALVVVDCIEGVCV 137
Query: 188 QTKEHIL---LAKQVGVPNMVVFLNKQD------QVDDEELLQ 221
QT E +L L +++ P + V NK D QVD EE Q
Sbjct: 138 QT-ETVLRQALGERI-RPVLTV--NKMDRCFLELQVDGEEAYQ 176
>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 = 54.8 bits (132), Expect = 7e-09
Identities = 31/166 (18%), Positives = 58/166 (34%), Gaps = 28/166 (16%)
Query: 91 IGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITINTATVEYETENRHY 150
+G GK++L AL E+ + + E +
Sbjct: 3 VGRGGVGKSSLLNALL-------------GGEVGEVSDVPGTTRDPDVYVKELDKGKVKL 49
Query: 151 AHVDCPGHADYVKNMITGAAQM-----DGAILVVSGADGPMP--QTKEHILLAKQVGVPN 203
VD PG ++ A++ D +LVV D + ++ G+P
Sbjct: 50 VLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIP- 108
Query: 204 MVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSAL 249
+++ NK D +++ E+ +L+ LE + VP+ SA
Sbjct: 109 IILVGNKIDLLEEREVEELLRLEELAKIL-------GVPVFEVSAK 147
>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 = 52.2 bits (126), Expect = 8e-09
Identities = 24/87 (27%), Positives = 49/87 (56%), Gaps = 4/87 (4%)
Query: 294 FLLAVEDVFSITGRGTVATGRVERGTIKVGETVDLVGLKETRNF---TVTGVEMFQKTLD 350
+++++S+ G GTV G V +G I++G+T+ L+G + +F TV + + +
Sbjct: 1 AEFQIDEIYSVPGVGTVVGGTVSKGVIRLGDTL-LLGPDQDGSFRPVTVKSIHRNRSPVR 59
Query: 351 EAMAGDNVGLLLRGVQKADIQRGMVLA 377
AG + L L+ + ++ +++GMVL
Sbjct: 60 VVRAGQSASLALKKIDRSLLRKGMVLV 86
>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 = 54.5 bits (132), Expect = 8e-09
Identities = 48/205 (23%), Positives = 79/205 (38%), Gaps = 34/205 (16%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITINTATVEYETE 146
+ +G GK+TL AL LG ++ P T + Y
Sbjct: 2 LLAVVGEFSAGKSTLLNAL------LG----EEVLPTGVTPT------TAVITVLRYGLL 45
Query: 147 NRHYAHVDCPG-------HADYVKNMITGAAQMDGAILVVSGADGPMPQT-KEHILLAKQ 198
VD PG H + ++ + + D I V+S AD P+ ++ +E + +
Sbjct: 46 K-GVVLVDTPGLNSTIEHHTEITESFL---PRADAVIFVLS-ADQPLTESEREFLKEILK 100
Query: 199 VGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEALMAN 258
+ LNK D + +EEL +++E RE L E G + I SA ALEA +
Sbjct: 101 WSGKKIFFVLNKIDLLSEEELEEVLE-YSREELGVLELGGGEPRIFPVSAKEALEARLQG 159
Query: 259 PSIKRGENQWVDKIYELMDSVDSYI 283
E EL + ++ ++
Sbjct: 160 DE----ELLEQSGFEELEEHLEEFL 180
>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 = 42/143 (29%), Positives = 73/143 (51%), Gaps = 11/143 (7%)
Query: 91 IGHVDHGKTTLTAAL-------TMALASLGNSAPKKYDEIDAAPEERARGITINTATVEY 143
I H D GKTTLT L A A + +K+ D E+ RGI++ ++ +++
Sbjct: 8 ISHPDAGKTTLTEKLLLFGGAIQEAGAVKARKS-RKHATSDWMEIEKQRGISVTSSVMQF 66
Query: 144 ETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPN 203
E + +D PGH D+ ++ +D A++V+ A G PQT++ + + G+P
Sbjct: 67 EYKGCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLRGIP- 125
Query: 204 MVVFLNKQDQVDDE--ELLQLVE 224
++ F+NK D+ + ELL +E
Sbjct: 126 IITFINKLDREGRDPLELLDEIE 148
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 55.3 bits (134), Expect = 4e-08
Identities = 41/143 (28%), Positives = 71/143 (49%), Gaps = 11/143 (7%)
Query: 91 IGHVDHGKTTLTAALTM---ALASLGNSAPKKYDEIDAAPE----ERARGITINTATVEY 143
I H D GKTTLT L + A+ G +K A + E+ RGI++ ++ +++
Sbjct: 18 ISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRK-SGKHAKSDWMEIEKQRGISVTSSVMQF 76
Query: 144 ETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPN 203
+ + +D PGH D+ ++ +D A++V+ A G PQT + + + +P
Sbjct: 77 DYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIEPQTLKLFEVCRLRDIP- 135
Query: 204 MVVFLNKQDQV--DDEELLQLVE 224
+ F+NK D+ D ELL +E
Sbjct: 136 IFTFINKLDREGRDPLELLDEIE 158
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 54.8 bits (133), Expect = 6e-08
Identities = 42/144 (29%), Positives = 58/144 (40%), Gaps = 35/144 (24%)
Query: 87 NIGTIGHVDHGKTTLT------------------AALTMALASLGNSAPKKYDEIDAAPE 128
NIG + H+D GKTT T A TM D +
Sbjct: 10 NIGIMAHIDAGKTTTTERILYYTGKSHKIGEVHDGAATM----------------DWMEQ 53
Query: 129 ERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQ 188
E+ RGITI +A + +D PGH D+ + +DGA+ V G PQ
Sbjct: 54 EQERGITITSAATTCFWKGHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVSGVEPQ 113
Query: 189 TKEHILLAKQVGVPNMVVFLNKQD 212
++ A + GVP + VF+NK D
Sbjct: 114 SETVWRQADKYGVPRI-VFVNKMD 136
>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 = 53.8 bits (129), Expect = 1e-07
Identities = 40/153 (26%), Positives = 73/153 (47%), Gaps = 15/153 (9%)
Query: 87 NIGTIGHVDHGKTTLTAALTM---------ALASLGNSAPKKYDEIDAAPEERARGITIN 137
I H D GKTT+T + + A+ G+ K D ++ E+ RGI+I
Sbjct: 13 TFAIISHPDAGKTTITEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEM---EKQRGISIT 69
Query: 138 TATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAK 197
T+ +++ + +D PGH D+ ++ +D ++V+ A G +T++ + + +
Sbjct: 70 TSVMQFPYRDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLMEVTR 129
Query: 198 QVGVPNMVVFLNKQDQ--VDDEELLQLVELEVR 228
P + F+NK D+ D ELL VE E++
Sbjct: 130 LRDTP-IFTFMNKLDRDIRDPLELLDEVENELK 161
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 53.5 bits (130), Expect = 1e-07
Identities = 80/308 (25%), Positives = 125/308 (40%), Gaps = 92/308 (29%)
Query: 87 NIGTIGHVDHGKTTL-------TAALT-----------MALASLGNSAPKKYDEIDAAPE 128
N I H+DHGK+TL T L+ M L
Sbjct: 9 NFSIIAHIDHGKSTLADRLIELTGTLSEREMKAQVLDSMDL------------------- 49
Query: 129 ERARGITI--NTATVEYETEN-RHYA-H-VDCPGHADY---VKNMITGAAQMDGAILVVS 180
ER RGITI + Y+ ++ Y + +D PGH D+ V + AA +GA+LVV
Sbjct: 50 ERERGITIKAQAVRLNYKAKDGETYILNLIDTPGHVDFSYEVSRSL--AA-CEGALLVVD 106
Query: 181 GADGPMPQTKEHILLAKQVGVPNMVVFLNKQD--QVDDEELLQLVELEVRELLSSYEFPG 238
+ G QT ++ LA + + + V LNK D D E V+ E+ +++
Sbjct: 107 ASQGVEAQTLANVYLALENDLEIIPV-LNKIDLPAADPER----VKQEIEDVIG---IDA 158
Query: 239 DDVPIISGSALLALEALMANPSIKRGENQWVDKIYELMDSVDSYIPIPQRQTDLPF--LL 296
D ++S K G I E+++++ IP P+ D P L+
Sbjct: 159 SDAVLVSA---------------KTGIG-----IEEVLEAIVERIPPPKGDPDAPLKALI 198
Query: 297 --AVEDVFSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMF---QKTLDE 351
+ D + RG V RV GT+K G+ + ++ + + V V +F +DE
Sbjct: 199 FDSWYDNY----RGVVVLVRVVDGTLKKGDKIKMMSTGKE--YEVDEVGVFTPKMVPVDE 252
Query: 352 AMAGDNVG 359
AG+ VG
Sbjct: 253 LSAGE-VG 259
>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 = 45.6 bits (109), Expect = 2e-06
Identities = 24/66 (36%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 313 GRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDEAMAGDNVGLLLRGVQKADIQR 372
G + G+I+VG+ V V L + V +E F LDEA AG++V L L + D+ R
Sbjct: 20 GTIASGSIRVGDEV--VVLPSGKTSRVKSIETFDGELDEAGAGESVTLTLE--DEIDVSR 75
Query: 373 GMVLAK 378
G V+
Sbjct: 76 GDVIVA 81
>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 = 44.5 bits (106), Expect = 6e-06
Identities = 22/84 (26%), Positives = 35/84 (41%), Gaps = 14/84 (16%)
Query: 408 AGYRPQFYMRTTDVTGRVSSIMNDKD--------EESKMVMPGDRIKMVVELIMPVACE- 458
GY P T V R + I++ D E K + GD + + P+ E
Sbjct: 21 PGYTPVLDCHTAHVACRFAEILSKIDPRTGKKLEENPKFLKSGDAAIVKIVPQKPLVVET 80
Query: 459 ----QGM-RFAIREGGKTVGAGVI 477
+ RFA+R+ G+TV G++
Sbjct: 81 FSEYPPLGRFAVRDMGQTVAVGIV 104
>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 = 43.6 bits (104), Expect = 9e-06
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 7/68 (10%)
Query: 308 GTVATGRVERGTIKVGETVDLVGLKET-RNFTVTGVEMFQKT----LDEAMAGDNVGLLL 362
G +A GR+ RGT+KVG+ V +V +T + F+ ++EA AGD V +
Sbjct: 15 GRIAIGRIFRGTVKVGQQVAVVKRDGKIEKAKITKLFGFEGLKRVEVEEAEAGDIVA--I 72
Query: 363 RGVQKADI 370
G++ I
Sbjct: 73 AGIEDITI 80
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 43.2 bits (103), Expect = 3e-04
Identities = 43/156 (27%), Positives = 61/156 (39%), Gaps = 55/156 (35%)
Query: 87 NIGTIGHVDHGKTTLT------------------AALTMALASLGNSAPKKYDEIDAAPE 128
NIG + H+D GKTT T A TM D +
Sbjct: 12 NIGIMAHIDAGKTTTTERILFYTGVNHKIGEVHDGAATM----------------DWMEQ 55
Query: 129 ERARGITINTA-TVEYETENRHYAHVDCPGHADY---------VKNMITGAAQMDGAILV 178
E+ RGITI +A T + ++R +D PGH D+ V +DGA+ V
Sbjct: 56 EQERGITITSAATTCFWKDHR-INIIDTPGHVDFTIEVERSLRV---------LDGAVAV 105
Query: 179 VSGADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQV 214
G PQ++ A + VP + F+NK D+
Sbjct: 106 FDAVGGVEPQSETVWRQADKYKVPRI-AFVNKMDRT 140
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 41.3 bits (97), Expect = 4e-04
Identities = 42/183 (22%), Positives = 64/183 (34%), Gaps = 19/183 (10%)
Query: 86 VNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDA-APEERARGITINTATVEYE 144
I IG V GKTT AL + K +A A +G T +++
Sbjct: 11 TKIVVIGPVGAGKTTFVRAL----------SDKPLVITEADASSVSGKGKRPTTVAMDFG 60
Query: 145 T---ENRHYAH-VDCPGHADYVKNMITGAAQ-MDGAILVVSGADGPMPQTKEHILLAKQV 199
+ + H PG + K M ++ GAI++V + +E I
Sbjct: 61 SIELDEDTGVHLFGTPGQ-ERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSR 119
Query: 200 GVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEALMANP 259
+VV +NKQD D ++ E ELLS D A L+ L+
Sbjct: 120 NPIPVVVAINKQDLFDALPPEKIREALKLELLSVPVIEIDATE--GEGARDQLDVLLLKD 177
Query: 260 SIK 262
+
Sbjct: 178 LLG 180
>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 = 41.3 bits (97), Expect = 9e-04
Identities = 39/129 (30%), Positives = 57/129 (44%), Gaps = 9/129 (6%)
Query: 91 IGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAA--PEERARGIT---INTATVEYET 145
+GHVDHGKTTL + + A A I A P + GI + + +
Sbjct: 10 LGHVDHGKTTLLDKIRGS-AVAKREAGGITQHIGATEIPMDVIEGICGDLLKKFKIRLKI 68
Query: 146 ENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMV 205
+ +D PGH + G A D AIL+V +G PQT+E + + + P V
Sbjct: 69 PGLLF--IDTPGHEAFTNLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYKTP-FV 125
Query: 206 VFLNKQDQV 214
V NK D++
Sbjct: 126 VAANKIDRI 134
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 39.8 bits (94), Expect = 0.003
Identities = 25/62 (40%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 153 VDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFLNKQD 212
+D PGH + G A D AILVV +G PQT E I + K+ P VV NK D
Sbjct: 76 IDTPGHEAFTNLRKRGGALADIAILVVDINEGFQPQTIEAINILKRRKTP-FVVAANKID 134
Query: 213 QV 214
++
Sbjct: 135 RI 136
Score = 32.8 bits (76), Expect = 0.42
Identities = 10/10 (100%), Positives = 10/10 (100%)
Query: 92 GHVDHGKTTL 101
GHVDHGKTTL
Sbjct: 13 GHVDHGKTTL 22
>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 = 37.2 bits (87), Expect = 0.006
Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 9/81 (11%)
Query: 169 AAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVR 228
A + D +LVV P+ + + LL ++ G P ++V NK D V + E +L+
Sbjct: 74 ADRADLVLLVVDSDLTPVEEEAKLGLLRER-GKPVLLVL-NKIDLVPESEEEELLRERKL 131
Query: 229 ELLSSYEFPGDDVPIISGSAL 249
ELL D+P+I+ SAL
Sbjct: 132 ELLP-------DLPVIAVSAL 145
>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 = 38.0 bits (89), Expect = 0.006
Identities = 43/170 (25%), Positives = 67/170 (39%), Gaps = 29/170 (17%)
Query: 87 NIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGIT--INTATVEYE 144
+ +G+VD GK+TL LT L N K + E G T ++ + ++
Sbjct: 1 RVAVVGNVDAGKSTLLGVLT--QGELDNGRGKARLNLFRHKHEVESGRTSSVSNDILGFD 58
Query: 145 TE----NRHYAH------------------VDCPGHADYVKNMITG--AAQMDGAILVVS 180
++ N H +D GH Y+K + G D A+LVV
Sbjct: 59 SDGEVVNYPDNHLGELDVEICEKSSKVVTFIDLAGHERYLKTTVFGMTGYAPDYAMLVVG 118
Query: 181 GADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVREL 230
G + TKEH+ LA + VP + V + K D L + ++ R L
Sbjct: 119 ANAGIIGMTKEHLGLALALKVP-VFVVVTKIDMTPANVLQETLKDLKRLL 167
>gnl|CDD|223597 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 37.3 bits (87), Expect = 0.012
Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 2/65 (3%)
Query: 166 ITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVEL 225
+ ++DG + VV A L Q+ +++V LNK D VD EEL L E
Sbjct: 111 LADGVRLDGVVTVVDAAHFLEGLDAIAELAEDQLAFADVIV-LNKTDLVDAEELEAL-EA 168
Query: 226 EVREL 230
+R+L
Sbjct: 169 RLRKL 173
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 37.9 bits (88), Expect = 0.013
Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 153 VDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFLNKQD 212
+D PGH + G + D A+LVV +G PQT E I + +Q P VV NK D
Sbjct: 531 IDTPGHEAFTSLRKRGGSLADLAVLVVDINEGFKPQTIEAINILRQYKTP-FVVAANKID 589
Query: 213 QV 214
+
Sbjct: 590 LI 591
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 34.3 bits (79), Expect = 0.057
Identities = 37/181 (20%), Positives = 60/181 (33%), Gaps = 44/181 (24%)
Query: 89 GTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITINTATVEYETENR 148
G +G + GK+TL +ALT A +++ A + N E+
Sbjct: 1 GLVGLPNVGKSTLLSALTSA-------------KVEIASYPFTT-LEPNVGVFEFGDGVD 46
Query: 149 HYAHVDCPG-----HADYVK-NMITGAAQMDGAILVV---SGADGPMPQTKEHILLAKQV 199
+D PG I IL V S P ++ L ++V
Sbjct: 47 -IQIIDLPGLLDGASEGRGLGEQILAHLYRSDLILHVIDASEDCVGDP-LEDQKTLNEEV 104
Query: 200 GV--------PNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLA 251
P M+V NK D + L +L +++ +P++ SAL
Sbjct: 105 SGSFLFLKNKPEMIVA-NKIDMASENNLKRLKLDKLK----------RGIPVVPTSALTR 153
Query: 252 L 252
L
Sbjct: 154 L 154
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 33.4 bits (77), Expect = 0.17
Identities = 31/131 (23%), Positives = 54/131 (41%), Gaps = 22/131 (16%)
Query: 132 RGITINTATVEYETENRHYAHVDCPG---------HADYVKNMI----TGAAQMDGAILV 178
R IN +E ++ VD PG + K +I A + G +L+
Sbjct: 59 RTQLIN----FFEVDDELRL-VDLPGYGYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLL 113
Query: 179 VSGADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPG 238
+ P +E I ++G+P +VV K D++ E + + +V E L + P
Sbjct: 114 IDARHPPKDLDREMIEFLLELGIPVIVVL-TKADKLKKSERNKQLN-KVAEEL--KKPPP 169
Query: 239 DDVPIISGSAL 249
DD ++ S+L
Sbjct: 170 DDQWVVLFSSL 180
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 33.9 bits (79), Expect = 0.21
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 294 FLLAVEDVFSITGRGTVATGRVERGTIKVGETVDLV 329
+ V D V G+VE G +KVG+ V
Sbjct: 505 GVFEVTDTQKPPNGLIVHRGKVEEGELKVGDEVTAE 540
>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 = 31.4 bits (72), Expect = 0.25
Identities = 19/109 (17%), Positives = 40/109 (36%), Gaps = 19/109 (17%)
Query: 386 TKFLAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGRVS---SIMNDKDEESKMVMP- 441
T+F A + + P G + + + ++ SI++ E P
Sbjct: 4 TRFEARILTFNVD-----KPILPGTPFELFRHSLKEPATITKLVSILDKSTGEVSKKKPR 58
Query: 442 --GDRIKMVVELIM--PVA------CEQGMRFAIREGGKTVGAGVIQSI 480
+VE+ + P+ ++ R +R G+T+ AG++ I
Sbjct: 59 CLTKGQTAIVEIELERPIPLELFKDNKELGRVVLRRDGETIAAGLVTEI 107
>gnl|CDD|235306 PRK04531, PRK04531, acetylglutamate kinase; Provisional.
Length = 398
Score = 33.5 bits (77), Expect = 0.26
Identities = 31/116 (26%), Positives = 48/116 (41%), Gaps = 16/116 (13%)
Query: 238 GDDVPIISGSALLALEALMANPSIKRGENQWVDKIYELMDSV--DSYIPIPQRQTDLPFL 295
G + I+ S + LM P I G +++I EL+D + +S + I P
Sbjct: 180 GKLISSINLST--EYDHLMQQPWINGGMKLKLEQIKELLDRLPLESSVSITS-----PSD 232
Query: 296 LAVEDVFSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEMFQKTLDE 351
LA E +F+ G GT+ V RG ++ D L R + F +TL
Sbjct: 233 LAKE-LFTHKGSGTL----VRRGE-RILRATDWDELDLERLNLLIE-SSFGRTLKP 281
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 32.8 bits (76), Expect = 0.40
Identities = 44/154 (28%), Positives = 70/154 (45%), Gaps = 33/154 (21%)
Query: 91 IGHVDHGKTTLT-------AALTMALASLGNSAPK--KYD--EIDAAPEERARGITINTA 139
I H D GKTTLT A+ A G + + D E+ E+ RGI++ T+
Sbjct: 16 ISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGRHATSDWMEM-----EKQRGISV-TS 69
Query: 140 TV---EYETENRHYAHV----DCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEH 192
+V Y + D PGH D+ ++ +D A++V+ A G PQT++
Sbjct: 70 SVMQFPYRD------CLINLLDTPGHEDFSEDTYRTLTAVDSALMVIDAAKGVEPQTRKL 123
Query: 193 ILLAKQVGVPNMVVFLNKQDQVDDE--ELLQLVE 224
+ + + P + F+NK D+ E ELL +E
Sbjct: 124 MEVCRLRDTP-IFTFINKLDRDGREPLELLDEIE 156
>gnl|CDD|237730 PRK14493, PRK14493, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobB/MoaE;
Provisional.
Length = 274
Score = 32.3 bits (74), Expect = 0.44
Identities = 30/151 (19%), Positives = 51/151 (33%), Gaps = 14/151 (9%)
Query: 88 IGTIGHVDHGKTTLTAALTMALASLGNSAPKKY-DEIDAAPEER--ARGITINTATVEYE 144
+ +G+ GKTTL L L+ G K+ D P+ R V
Sbjct: 4 LSIVGYKATGKTTLVERLVDRLSGRGRVGTVKHMDTERLNPDGTDTGRHFDAGADVVYGL 63
Query: 145 TENRHYAHVDCPGHADYVKNMITGAAQMDGAILV-VSGADGPMPQTKEHILLAKQVGVPN 203
T+ A D + ++ A MD A++ + P ++L +
Sbjct: 64 TDGEWVASGRDRSLDDALDDL---APGMDYAVVEGFKDSRLPK------VVLGDMDADSD 114
Query: 204 MVVFLNKQDQVDDEELLQLVE-LEVRELLSS 233
+V +D E+L+ +E L S
Sbjct: 115 VVARAPTAADLDTEDLVAALESQPPYVTLES 145
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC protein.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 378
Score = 32.6 bits (74), Expect = 0.49
Identities = 18/86 (20%), Positives = 26/86 (30%), Gaps = 11/86 (12%)
Query: 5 ASAAATVASTSPKLTHPYASASPSNSLLSTTALRTKLTPSNLSSSFLPPFATTTAVT--- 61
+ AS + ++ ASA S +A T + S A +T V
Sbjct: 96 TPTPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGSDAASTLVVGSE 155
Query: 62 --VTTTR------RRSLIVRAARGKF 79
T R + RA R F
Sbjct: 156 RETTIEEIMEMGYEREEVERALRAAF 181
>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 = 29.8 bits (68), Expect = 0.77
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 306 GRGTVATGRVERGTIKVG 323
GRG VAT V+ GT+KVG
Sbjct: 13 GRGPVATVLVQNGTLKVG 30
>gnl|CDD|202832 pfam03960, ArsC, ArsC family. This family is related to
glutaredoxins pfam00462.
Length = 109
Score = 30.2 bits (69), Expect = 0.78
Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 10/62 (16%)
Query: 210 KQDQVDDEEL---LQLVELEVRELLSS----YEFPGDDVPIISGSALLALEALMANPS-I 261
+ EEL L ELL++ Y DV +S L+ L ++ NPS I
Sbjct: 29 LETPPSKEELKDILSKTGDGWEELLNTRGTTYRELNLDVEELSEDELIEL--MLENPSLI 86
Query: 262 KR 263
+R
Sbjct: 87 RR 88
>gnl|CDD|216645 pfam01678, DAP_epimerase, Diaminopimelate epimerase.
Diaminopimelate epimerase contains two domains of the
same alpha/beta fold, both contained in this family.
Length = 119
Score = 30.3 bits (69), Expect = 0.79
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 5/45 (11%)
Query: 196 AKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDD 240
AK G P+ VV ++ + + E L + FPG D
Sbjct: 2 AKMHGNPHDVVVVDDVEGANLLEPEL-----GPALCHRHFFPGAD 41
>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 = 32.1 bits (73), Expect = 0.85
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 7/86 (8%)
Query: 158 HADYVKNMITGAAQMDGAILVVSGADGPMP------QTKEHILLAKQVG-VPNMVVFLNK 210
HA + + A + G I VV+GAD P+P E+ L +V + V +
Sbjct: 37 HARILAIDTSEAEALPGVIAVVTGADCPVPYGVLPIAENEYPLARDKVRYRGDPVAAVAA 96
Query: 211 QDQVDDEELLQLVELEVRELLSSYEF 236
D+V E+ L L+++E EL + +
Sbjct: 97 VDEVTAEKALALIKVEYEELPAYMDP 122
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 31.0 bits (71), Expect = 0.85
Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 11/68 (16%)
Query: 173 DGAILVVSGADGP-MPQTKE--HILLAKQ--VGVPNMVVFLNKQDQVDDEELLQLVELEV 227
D I VV AD + + KE H LL ++ P +++ NKQD + E E+
Sbjct: 83 DAVIFVVDSADRDRIEEAKEELHALLNEEELADAP-LLILANKQDLPGA-----MSEAEI 136
Query: 228 RELLSSYE 235
RELL +E
Sbjct: 137 RELLGLHE 144
>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 = 30.7 bits (70), Expect = 1.1
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 3/58 (5%)
Query: 173 DGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVREL 230
DG + VV A+ Q+ +++V +NK D L+ +E ++R L
Sbjct: 116 DGVVTVVDVAE--TEGEDIPEKAPDQIAFADLIV-INKTDLAPAVADLEKLEADLRRL 170
>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 = 30.9 bits (71), Expect = 1.3
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 173 DGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELE 226
D A+LVV GP E I K+ +P +VV NK D ++ L+ +E +
Sbjct: 87 DLALLVVDAGVGPGEYELELIEELKERKIPYIVVI-NKIDLGEESAELEKLEKK 139
>gnl|CDD|180919 PRK07282, PRK07282, acetolactate synthase catalytic subunit;
Reviewed.
Length = 566
Score = 31.3 bits (71), Expect = 1.4
Identities = 14/43 (32%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 240 DVPIISGSALLALEALMANPSIKRGENQWVDKIYELMDSVDSY 282
D+P++ G A AL+ L+A P++ +W++K+ + + V SY
Sbjct: 321 DIPVV-GDAKKALQMLLAEPTVHNNTEKWIEKVTKDKNRVRSY 362
>gnl|CDD|234438 TIGR03999, thiol_BshA, N-acetyl-alpha-D-glucosaminyl L-malate
synthase BshA. Members of this protein family are BshA,
a glycosyltransferase required for bacillithiol
biosynthesis. This enzyme combines UDP-GlcNAc and
L-malate to form N-acetyl-alpha-D-glucosaminyl L-malate
synthase. Bacillithiol is a low-molecular-weight thiol,
an analog of glutathione and mycothiol, and is found
largely in the Firmicutes [Biosynthesis of cofactors,
prosthetic groups, and carriers, Glutathione and
analogs].
Length = 374
Score = 31.0 bits (71), Expect = 1.5
Identities = 28/75 (37%), Positives = 37/75 (49%), Gaps = 17/75 (22%)
Query: 183 DGPMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVP 242
DGP E L +++G+ + V+FL KQD V ELL + +L + L S E G
Sbjct: 237 DGPERSPAEQ--LVRELGLTDRVLFLGKQDDV--AELLSISDLFL--LPSEKESFG---- 286
Query: 243 IISGSALLALEALMA 257
L ALEA MA
Sbjct: 287 ------LAALEA-MA 294
>gnl|CDD|100002 cd04962, GT1_like_5, This family is most closely related to the GT1
family of glycosyltransferases. Glycosyltransferases
catalyze the transfer of sugar moieties from activated
donor molecules to specific acceptor molecules, forming
glycosidic bonds. The acceptor molecule can be a lipid,
a protein, a heterocyclic compound, or another
carbohydrate residue. This group of glycosyltransferases
is most closely related to the previously defined
glycosyltransferase family 1 (GT1). The members of this
family may transfer UDP, ADP, GDP, or CMP linked sugars.
The diverse enzymatic activities among members of this
family reflect a wide range of biological functions. The
protein structure available for this family has the GTB
topology, one of the two protein topologies observed for
nucleotide-sugar-dependent glycosyltransferases. GTB
proteins have distinct N- and C- terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two domains
includes the catalytic center and permits a high degree
of flexibility. The members of this family are found
mainly in bacteria, while some of them are also found in
Archaea and eukaryotes.
Length = 371
Score = 30.7 bits (70), Expect = 1.6
Identities = 29/76 (38%), Positives = 39/76 (51%), Gaps = 19/76 (25%)
Query: 183 DGP-MPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDV 241
DGP + LA+++G+ + V+FL KQD V EELL + +L + L S E G
Sbjct: 235 DGPERSPAER---LARELGLQDDVLFLGKQDHV--EELLSIADLFL--LPSEKESFG--- 284
Query: 242 PIISGSALLALEALMA 257
L ALEA MA
Sbjct: 285 -------LAALEA-MA 292
>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 = 30.4 bits (69), Expect = 1.7
Identities = 14/29 (48%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 88 IGTIGHVDHGKTTLTAALTMALASLGNSA 116
+ G V GKTTLTA L AL LG
Sbjct: 7 VSVRGGV--GKTTLTANLASALKLLGEPV 33
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 30.6 bits (70), Expect = 1.8
Identities = 29/98 (29%), Positives = 45/98 (45%), Gaps = 18/98 (18%)
Query: 169 AAQMDGAILVVSGADGPMPQTKEHIL-----LAKQVGVPNMVVFLNKQDQVDDEELLQLV 223
AA +D I++VS +P+ +I+ + +G+ ++V LNK D +DDE
Sbjct: 118 AANID-QIVIVSA---VLPELSLNIIDRYLVACETLGIEPLIV-LNKIDLLDDEGR---- 168
Query: 224 ELEVRELLSSYEFPGDDVPIIS---GSALLALEALMAN 258
V E L Y G V ++S G L LEA +
Sbjct: 169 -AFVNEQLDIYRNIGYRVLMVSSHTGEGLEELEAALTG 205
>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 = 29.7 bits (68), Expect = 2.0
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 204 MVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISG 246
+V LNK D +D EE + ++ ++ E G V IS
Sbjct: 117 RIVVLNKIDLLDAEERFEKLKELLK------ELKGKKVFPISA 153
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 30.4 bits (70), Expect = 2.0
Identities = 46/145 (31%), Positives = 64/145 (44%), Gaps = 36/145 (24%)
Query: 162 VKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQVDD-EELL 220
K + +D + VV + P + + K+V P ++V LNK D V D EELL
Sbjct: 75 NKAAWSSLKDVDLVLFVVDADEKIGPGDEFILEKLKKVKTPVILV-LNKIDLVKDKEELL 133
Query: 221 QLVELEVRELLSSYEFPGDDVPIISGSALLALEALMANPSIKRGENQWVDKIYELMDSVD 280
L+E E+ EL+ E VPI S +G+N VD EL+D +
Sbjct: 134 PLLE-ELSELMDFAEI----VPI----------------SALKGDN--VD---ELLDVIA 167
Query: 281 SYIPI-----PQRQ-TDLP--FLLA 297
Y+P P+ Q TD P FL A
Sbjct: 168 KYLPEGPPYYPEDQITDRPERFLAA 192
>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 = 28.6 bits (65), Expect = 2.1
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 306 GRGTVATGRVERGTIKVGETV 326
GRG VAT V+ GT+K G+ +
Sbjct: 13 GRGPVATVIVQNGTLKKGDVI 33
>gnl|CDD|223092 COG0013, AlaS, Alanyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 879
Score = 30.7 bits (70), Expect = 2.2
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 298 VEDVFSITGRGTVATGRVERGTIKVGETVDLVGLKE-----TRNFTVT 340
V DV + V G+VE G +KVG+ V +E RN T T
Sbjct: 523 VTDVQKVGNGVIVHKGKVESGELKVGDEVTAEVDEERRRRLMRNHTAT 570
>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 = 29.7 bits (68), Expect = 2.2
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 173 DGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLS 232
D + VV ++ + + L K+ P +++ LNK D V D+E L + +++EL
Sbjct: 84 DLVLFVVDASEWIGEGDEFILELLKKSKTP-VILVLNKIDLVKDKEDLLPLLEKLKEL-- 140
Query: 233 SYEFPGDDVPIIS 245
P ++ IS
Sbjct: 141 ---HPFAEIFPIS 150
>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 = 29.7 bits (68), Expect = 2.3
Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 16/87 (18%)
Query: 176 ILVVSGADGPMPQTK---EHILLAKQVGVPNMVVFLNKQDQVDDEELLQLVELEVRELLS 232
+L+V P + +++ A+ G+ V+ LNK D VDDEEL +L+E +L
Sbjct: 6 VLIVFSLKEPFFNLRLLDRYLVAAEASGIE-PVIVLNKADLVDDEELEELLE-IYEKL-- 61
Query: 233 SYEFPGDDVPIISGSAL--LALEALMA 257
P+++ SA L+ L
Sbjct: 62 -------GYPVLAVSAKTGEGLDELRE 81
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 30.5 bits (69), Expect = 2.4
Identities = 22/73 (30%), Positives = 31/73 (42%), Gaps = 16/73 (21%)
Query: 85 HVNIGTIGHVDHGKTTLTAALTMALASLGNSAPKKYDEIDAAPEERARGITINTATVEYE 144
+ IG IG+ + GKTTL LT A +GN A G+T+ ++
Sbjct: 3 KLTIGLIGNPNSGKTTLFNQLTGARQRVGNWA----------------GVTVERKEGQFS 46
Query: 145 TENRHYAHVDCPG 157
T + VD PG
Sbjct: 47 TTDHQVTLVDLPG 59
>gnl|CDD|225447 COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell
division and chromosome partitioning].
Length = 272
Score = 29.5 bits (67), Expect = 3.2
Identities = 15/29 (51%), Positives = 16/29 (55%), Gaps = 4/29 (13%)
Query: 97 GKTTLTAALTMALASLGNSAPKKYDEIDA 125
GKTT TA + ALA LG KK ID
Sbjct: 15 GKTTTTANIGTALAQLG----KKVVLIDF 39
>gnl|CDD|131023 TIGR01968, minD_bact, septum site-determining protein MinD. This
model describes the bacterial and chloroplast form of
MinD, a multifunctional cell division protein that
guides correct placement of the septum. The homologous
archaeal MinD proteins, with many archaeal genomes
having two or more forms, are described by a separate
model [Cellular processes, Cell division].
Length = 261
Score = 29.6 bits (67), Expect = 3.3
Identities = 17/29 (58%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 97 GKTTLTAALTMALASLGNSAPKKYDEIDA 125
GKTT TA L ALA LG KK IDA
Sbjct: 14 GKTTTTANLGTALARLG----KKVVLIDA 38
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 29.8 bits (68), Expect = 3.4
Identities = 30/93 (32%), Positives = 43/93 (46%), Gaps = 16/93 (17%)
Query: 169 AAQMDGAILVVSGADGPMPQTKEHIL-----LAKQVGVPNMVVFLNKQDQVDDEELLQLV 223
AA +D A+LV + + P +L LA+ G+ ++V NK D +DD E
Sbjct: 78 AANVDQAVLVFAAKE---PDFSTDLLDRFLVLAEANGIKPIIVL-NKIDLLDDLE----- 128
Query: 224 ELEVRELLSSYEFPGDDVPIISGSALLALEALM 256
E RELL+ Y G DV +S L+ L
Sbjct: 129 --EARELLALYRAIGYDVLELSAKEGEGLDELK 159
>gnl|CDD|180674 PRK06733, PRK06733, hypothetical protein; Provisional.
Length = 151
Score = 28.9 bits (65), Expect = 3.5
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 7/65 (10%)
Query: 295 LLAVEDVFSITGRGTVATGRVERGTIKVGETVDLVGLKETRNFTVTGVEM-----FQKTL 349
++A E V+SI+G + T R+E +K+ + V ++E R+ G ++ ++KT
Sbjct: 75 IIANESVYSISGAAEILTDRMEGVPLKL--ALIEVNVEEVRDVMFYGAKIATEPTYEKTY 132
Query: 350 DEAMA 354
D A
Sbjct: 133 DLRAA 137
>gnl|CDD|238993 cd02036, MinD, Bacterial cell division requires the formation of a
septum at mid-cell. The site is determined by the min
operon products MinC, MinD and MinE. MinC is a
nonspecific inhibitor of the septum protein FtsZ. MinE
is the supressor of MinC. MinD plays a pivotal role,
selecting the mid-cell over other sites through the
activation and regulation of MinC and MinE. MinD is a
membrane-associated ATPase, related to nitrogenase iron
protein. More distantly related proteins include
flagellar biosynthesis proteins and ParA chromosome
partitioning proteins. MinD is a monomer.
Length = 179
Score = 29.1 bits (66), Expect = 3.7
Identities = 12/17 (70%), Positives = 12/17 (70%)
Query: 97 GKTTLTAALTMALASLG 113
GKTT TA L ALA LG
Sbjct: 12 GKTTTTANLGTALAQLG 28
>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 = 29.5 bits (67), Expect = 4.0
Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 136 INTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSG 181
I A VE E NRH A + H+ V+N+ A M I V +G
Sbjct: 348 IELA-VELEHGNRHTAII----HSKNVENLTKMARAMQTTIFVKNG 388
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 29.2 bits (66), Expect = 4.6
Identities = 34/94 (36%), Positives = 45/94 (47%), Gaps = 18/94 (19%)
Query: 173 DGAILVVSGADGPMPQTKEHIL-----LAKQVGVPNMVVFLNKQDQVDDEELLQLVELEV 227
D AI+VVS D ++L LA+ G+ ++V LNK D +DDE E V
Sbjct: 81 DQAIIVVSLVDPDF---NTNLLDRYLVLAEAGGIEPVIV-LNKIDLLDDE------EAAV 130
Query: 228 RELLSSYEFPGDDVPIIS---GSALLALEALMAN 258
+ELL YE G V +S G L L L+A
Sbjct: 131 KELLREYEDIGYPVLFVSAKNGDGLEELAELLAG 164
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA, an
essential protein involved in cell division control.
YihA and its orthologs are small proteins that typically
contain less than 200 amino acid residues and consists
of the GTPase domain only (some of the eukaryotic
homologs contain an N-terminal extension of about 120
residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 28.6 bits (65), Expect = 4.7
Identities = 21/98 (21%), Positives = 40/98 (40%), Gaps = 14/98 (14%)
Query: 153 VDCPG---------HADYVKNMI----TGAAQMDGAILVVSGADGPMPQTKEHILLAKQV 199
VD PG + +I + G +L++ GP P E + +++
Sbjct: 50 VDLPGYGYAKVSKEVREKWGKLIEEYLENRENLKGVVLLIDARHGPTPIDLEMLEFLEEL 109
Query: 200 GVPNMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFP 237
G+P ++ L K D++ EL ++++ EL P
Sbjct: 110 GIP-FLIVLTKADKLKKSELAKVLKKIKEELNLFNILP 146
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 29.1 bits (66), Expect = 4.9
Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 5/54 (9%)
Query: 203 NMVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEALM 256
+V LNK D DEE L+ ++ + E + +IS L+ L+
Sbjct: 277 PRIVVLNKIDLPLDEEELEELKKALAE-----ALGWEVFYLISALTREGLDELL 325
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 28.3 bits (64), Expect = 5.0
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 9/62 (14%)
Query: 173 DGAILVVSGADGP-MPQTKEHI--LLAKQ--VGVPNMVVFLNKQDQ---VDDEELLQLVE 224
DG I VV +D + + K + LL ++ G P +++ NKQD + + EL++L+
Sbjct: 68 DGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAP-LLILANKQDLPGALTESELIELLG 126
Query: 225 LE 226
LE
Sbjct: 127 LE 128
>gnl|CDD|214646 smart00392, PROF, Profilin. Binds actin monomers, membrane
polyphosphoinositides and poly-L-proline.
Length = 129
Score = 28.1 bits (63), Expect = 5.6
Identities = 9/25 (36%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 160 DYVKNMITGAAQMDGAILVVSGADG 184
YV N++ G+ +D A + G DG
Sbjct: 5 AYVDNLLVGSGCVDAAAIG--GKDG 27
>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 = 27.1 bits (61), Expect = 5.8
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 11/62 (17%)
Query: 310 VATGRVERGTIKVGETVDLVG-------LKETRNFTVTGVEMF----QKTLDEAMAGDNV 358
+A GRV GTI+ G+ V ++G ++ T+ + + ++ +DE AG+ V
Sbjct: 18 IAFGRVFSGTIRKGQKVRVLGPNYSPEDEEDLSKKTIQRLYLMMGRYREPVDEVPAGNIV 77
Query: 359 GL 360
+
Sbjct: 78 LI 79
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 28.7 bits (65), Expect = 6.1
Identities = 26/99 (26%), Positives = 40/99 (40%), Gaps = 10/99 (10%)
Query: 135 TINTATVEYETENRHYAHVDCPG-----HADY---VKNMITGAAQMDGAILVVSGADGPM 186
T N T+N VD PG HA K + +D + VV +G
Sbjct: 41 TRNRIRGIVTTDNAQIIFVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADEGWG 100
Query: 187 PQTKEHILLAKQVGVPNMVVFLNKQDQV-DDEELLQLVE 224
P + + K+ P ++V +NK D+V LL+L+
Sbjct: 101 PGDEFILEQLKKTKTPVILV-VNKIDKVKPKTVLLKLIA 138
>gnl|CDD|150009 pfam09173, eIF2_C, Initiation factor eIF2 gamma, C terminal.
Members of this family, which are found in the
initiation factors eIF2 and EF-Tu, adopt a structure
consisting of a beta barrel with Greek key topology.
They are required for formation of the ternary complex
with GTP and initiator tRNA.
Length = 88
Score = 27.2 bits (61), Expect = 6.5
Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 6/40 (15%)
Query: 442 GDRIKMVVELIMPVACEQGMRFAI-REGGKT---VGAGVI 477
D + VEL PV E G + AI R K +G G I
Sbjct: 51 KDLAE--VELKRPVCTEIGEKVAISRRVDKRWRLIGWGTI 88
>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 = 27.4 bits (61), Expect = 7.0
Identities = 11/17 (64%), Positives = 11/17 (64%)
Query: 97 GKTTLTAALTMALASLG 113
GKTTL A L ALA G
Sbjct: 11 GKTTLAANLAAALAKRG 27
>gnl|CDD|239663 cd03692, mtIF2_IVc, mtIF2_IVc: this family represents the C2
subdomain of domain IV of mitochondrial translation
initiation factor 2 (mtIF2) which adopts a beta-barrel
fold displaying a high degree of structural similarity
with domain II of the translation elongation factor
EF-Tu. The C-terminal part of mtIF2 contains the entire
fMet-tRNAfmet binding site of IF-2 and is resistant to
proteolysis. This C-terminal portion consists of two
domains, IF2 C1 and IF2 C2. IF2 C2 been shown to
contain all molecular determinants necessary and
sufficient for the recognition and binding of
fMet-tRNAfMet. Like IF2 from certain prokaryotes such as
Thermus thermophilus, mtIF2lacks domain II which is
thought to be involved in binding of E.coli IF-2 to 30S
subunits.
Length = 84
Score = 26.7 bits (60), Expect = 7.6
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 297 AVEDVFSITGRGTVATGRVERGTIKVGETVDLV 329
V VF I+ G +A V G IK V ++
Sbjct: 4 EVRAVFKISKVGNIAGCYVTDGKIKRNAKVRVL 36
>gnl|CDD|238615 cd01288, FabZ, FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein
(ACP) dehydratase that primarily catalyzes the
dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP,
the third step in the elongation phase of the bacterial/
plastid, type II, fatty-acid biosynthesis pathway.
Length = 131
Score = 27.5 bits (62), Expect = 8.3
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 431 DKDEESKMVMPGDRIKMVVELIM 453
DK K V+PGD++ + VEL+
Sbjct: 80 DKARFRKPVVPGDQLILEVELLK 102
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 27.8 bits (63), Expect = 9.0
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 11/63 (17%)
Query: 169 AAQMDGAILVVSGADGPMPQTKEHI-----LLAKQVGVPN--MVVFLNKQDQVDDEELLQ 221
A+ D + VV +D P +E I +L K++G + +++ LNK D +DDEEL +
Sbjct: 118 VAEADLLLHVVDASD---PDREEQIETVEEVL-KELGADDIPIILVLNKIDLLDDEELEE 173
Query: 222 LVE 224
+
Sbjct: 174 RLR 176
>gnl|CDD|193256 pfam12780, AAA_8, P-loop containing dynein motor region D4. The
380 kDa motor unit of dynein belongs to the AAA class of
chaperone-like ATPases. The core of the 380 kDa motor
unit contains a concatenated chain of six AAA modules,
of which four correspond to the ATP binding sites with
P-loop signatures described previously, and two are
modules in which the P loop has been lost in evolution.
This particular family is the D4 ATP-binding region of
the motor.
Length = 268
Score = 28.4 bits (63), Expect = 9.4
Identities = 28/96 (29%), Positives = 46/96 (47%), Gaps = 15/96 (15%)
Query: 198 QVGVPNM-VVFLNKQDQVDDEELLQLVELEVRELLSSYEFPG----DDVPIISGSALLAL 252
+ GV N+ VFL QV DE+ L L+ +LL+S E P D+V I S +
Sbjct: 83 KAGVKNVPTVFLMTDAQVADEQFLVLIN----DLLASGEIPDLFMDDEVENIISSVRNEV 138
Query: 253 EALMANPSIKRGENQW---VDKIYELMDSVDSYIPI 285
++L N + EN W +D++ + + + P+
Sbjct: 139 KSLGLNDT---RENCWKFFIDRVRRQLKVILCFSPV 171
>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 = 28.2 bits (64), Expect = 9.6
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 19/76 (25%)
Query: 204 MVVFLNKQDQVDDEELLQLVELEVRELLSSYEFPGDDVPIISGSALLALEALMANPSIKR 263
+V+ +NK D V DE+ + + E+R L +F PI+ SAL
Sbjct: 286 LVIVVNKWDLVKDEKTREEFKKELRRKLPFLDF----APIVFISAL-------------- 327
Query: 264 GENQWVDKIYELMDSV 279
Q VDK+ + +D V
Sbjct: 328 -TGQGVDKLLDAIDEV 342
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
0.316 0.132 0.370
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,629,005
Number of extensions: 2471934
Number of successful extensions: 3042
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2843
Number of HSP's successfully gapped: 181
Length of query: 482
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 381
Effective length of database: 6,457,848
Effective search space: 2460440088
Effective search space used: 2460440088
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 (27.3 bits)