RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8869
(593 letters)
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 867 bits (2244), Expect = 0.0
Identities = 312/382 (81%), Positives = 341/382 (89%)
Query: 1 MAKSKFERTKPHINVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARG 60
MAK KFERTKPH+NVGTIGHVDHGKTTLTAAI VL+KK G EAK+YDQID APEEKARG
Sbjct: 1 MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAITKVLAKKGGAEAKAYDQIDKAPEEKARG 60
Query: 61 ITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHI 120
ITINTAH+EYET+ RHYAHVDCPGHADY+KNMITGAAQMDGAILV SAADGPMPQTREHI
Sbjct: 61 ITINTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHI 120
Query: 121 LLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALE 180
LLARQVGVPYIVVFLNK DMVDDEELLELVE+E+RELL+KY+FPG+D PII+GSA ALE
Sbjct: 121 LLARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSKYDFPGDDTPIIRGSALKALE 180
Query: 181 GDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVR 240
GD E+ IL L A+D+YIPTP RAID FL+P+EDVFSISGRGTVVTGRVERGI++
Sbjct: 181 GDDDEEWEKKILELMDAVDSYIPTPERAIDKPFLMPIEDVFSISGRGTVVTGRVERGIIK 240
Query: 241 VGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERGQVLAKPGS 300
VGEE+EI+GI+DT KTT TGVEMFRKLLD+GQAGDN+G LLRG KREDVERGQVLAKPGS
Sbjct: 241 VGEEVEIVGIRDTQKTTVTGVEMFRKLLDEGQAGDNVGALLRGIKREDVERGQVLAKPGS 300
Query: 301 IKPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVL 360
I PH F E+Y LSK+EGGRHTPFF+ YRPQFYFRTTDVTG IELP+ EMVMPGDNV
Sbjct: 301 ITPHTKFEAEVYVLSKEEGGRHTPFFNGYRPQFYFRTTDVTGVIELPEGVEMVMPGDNVE 360
Query: 361 ITVRLINPIAMEEGLRFAIREG 382
+TV LI PIAMEEGLRFAIREG
Sbjct: 361 MTVELIAPIAMEEGLRFAIREG 382
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 858 bits (2220), Expect = 0.0
Identities = 313/382 (81%), Positives = 343/382 (89%)
Query: 1 MAKSKFERTKPHINVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARG 60
MAK KFERTKPH+NVGTIGHVDHGKTTLTAAI VL+KK GGEAK+YDQID APEEKARG
Sbjct: 1 MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAITKVLAKKGGGEAKAYDQIDNAPEEKARG 60
Query: 61 ITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHI 120
ITINT+H+EYET RHYAHVDCPGHADY+KNMITGAAQMDGAILV SAADGPMPQTREHI
Sbjct: 61 ITINTSHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHI 120
Query: 121 LLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALE 180
LLARQVGVPYIVVFLNK DMVDDEELLELVE+E+RELL+KY+FPG+D PII+GSA ALE
Sbjct: 121 LLARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSKYDFPGDDTPIIRGSALKALE 180
Query: 181 GDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVR 240
GD E IL L A+D+YIP P RAID FL+P+EDVFSISGRGTVVTGRVERGIV+
Sbjct: 181 GDDDEEWEAKILELMDAVDSYIPEPERAIDKPFLMPIEDVFSISGRGTVVTGRVERGIVK 240
Query: 241 VGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERGQVLAKPGS 300
VG+E+EI+GIK+T KTT TGVEMFRKLLD+GQAGDN+G+LLRGTKREDVERGQVLAKPGS
Sbjct: 241 VGDEVEIVGIKETQKTTVTGVEMFRKLLDEGQAGDNVGVLLRGTKREDVERGQVLAKPGS 300
Query: 301 IKPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVL 360
IKPH F E+Y LSK+EGGRHTPFF+ YRPQFYFRTTDVTG+IELP+ EMVMPGDNV
Sbjct: 301 IKPHTKFEAEVYVLSKEEGGRHTPFFNGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNVK 360
Query: 361 ITVRLINPIAMEEGLRFAIREG 382
+TV LI PIAMEEGLRFAIREG
Sbjct: 361 MTVELIAPIAMEEGLRFAIREG 382
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 790 bits (2043), Expect = 0.0
Identities = 292/382 (76%), Positives = 338/382 (88%), Gaps = 2/382 (0%)
Query: 1 MAKSKFERTKPHINVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARG 60
MAK KF+R+KPH+N+GTIGHVDHGKTTLTAAI VL+++ +AK YD IDAAPEEK RG
Sbjct: 1 MAKEKFDRSKPHVNIGTIGHVDHGKTTLTAAITKVLAERGLNQAKDYDSIDAAPEEKERG 60
Query: 61 ITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHI 120
ITINTAH+EYET+ RHYAHVDCPGHADY+KNMITGAAQMDGAILV +A DGPMPQTREHI
Sbjct: 61 ITINTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI 120
Query: 121 LLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALE 180
LLARQVGVPY+VVFLNK D+VDDEELLELVE+E+RELL++Y+FPG+DIP+I+GSA ALE
Sbjct: 121 LLARQVGVPYLVVFLNKVDLVDDEELLELVEMEVRELLSEYDFPGDDIPVIRGSALKALE 180
Query: 181 GDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVR 240
GD P E +I+ L A+D YIPTP R D FL+PVEDVF+I+GRGTVVTGRVERG V+
Sbjct: 181 GD--PKWEDAIMELMDAVDEYIPTPERDTDKPFLMPVEDVFTITGRGTVVTGRVERGTVK 238
Query: 241 VGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERGQVLAKPGS 300
VG+E+EI+GIK+T KT TGVEMFRKLLD+GQAGDN+G+LLRG R++VERGQVLAKPGS
Sbjct: 239 VGDEVEIVGIKETQKTVVTGVEMFRKLLDEGQAGDNVGVLLRGVDRDEVERGQVLAKPGS 298
Query: 301 IKPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVL 360
IKPH F E+Y L+K+EGGRHTPFF+NYRPQFYFRTTDVTGSIELP+ EMVMPGDNV
Sbjct: 299 IKPHTKFKAEVYILTKEEGGRHTPFFNNYRPQFYFRTTDVTGSIELPEGTEMVMPGDNVT 358
Query: 361 ITVRLINPIAMEEGLRFAIREG 382
ITV LI+PIAME+GL+FAIREG
Sbjct: 359 ITVELIHPIAMEQGLKFAIREG 380
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 750 bits (1939), Expect = 0.0
Identities = 308/382 (80%), Positives = 337/382 (88%), Gaps = 2/382 (0%)
Query: 1 MAKSKFERTKPHINVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARG 60
MAK KFERTKPH+NVGTIGHVDHGKTTLTAAI TVL+KK G EAK+YDQID APEEKARG
Sbjct: 1 MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKKGGAEAKAYDQIDNAPEEKARG 60
Query: 61 ITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHI 120
ITINTAH+EYET RHYAHVDCPGHADY+KNMITGAAQMDGAILV +A DGPMPQTREHI
Sbjct: 61 ITINTAHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI 120
Query: 121 LLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALE 180
LLARQVGVPYIVVFLNK DMVDDEELLELVE+E+RELL++Y FPG+D PII+GSA ALE
Sbjct: 121 LLARQVGVPYIVVFLNKVDMVDDEELLELVEMEVRELLSEYGFPGDDTPIIRGSALKALE 180
Query: 181 GDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVR 240
GD E I L A+D+YIPTP R ID FL+PVEDVFSISGRGTVVTGRVERGI++
Sbjct: 181 GD--AKWEAKIEELMDAVDSYIPTPERDIDKPFLMPVEDVFSISGRGTVVTGRVERGILK 238
Query: 241 VGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERGQVLAKPGS 300
VGEE+EI+GIK+T KTT TGVEMFRKLLD+GQAGDN+G+LLRG KREDVERGQVLAKPGS
Sbjct: 239 VGEEVEIVGIKETQKTTVTGVEMFRKLLDEGQAGDNVGVLLRGVKREDVERGQVLAKPGS 298
Query: 301 IKPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVL 360
IKPH F E+Y LSK+EGGRHTPFF YRPQFYFRTTDVTG+I LP+ EMVMPGDNV
Sbjct: 299 IKPHTKFEAEVYVLSKEEGGRHTPFFHGYRPQFYFRTTDVTGAITLPEGVEMVMPGDNVK 358
Query: 361 ITVRLINPIAMEEGLRFAIREG 382
+ V LI+PIAMEEGLRFAIREG
Sbjct: 359 MVVELIHPIAMEEGLRFAIREG 380
>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 = 714 bits (1844), Expect = 0.0
Identities = 299/382 (78%), Positives = 336/382 (87%), Gaps = 2/382 (0%)
Query: 1 MAKSKFERTKPHINVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARG 60
MAK KFERTKPH+N+GTIGHVDHGKTTLTAAI TVL+K+ G A++YDQID APEEKARG
Sbjct: 1 MAKEKFERTKPHVNIGTIGHVDHGKTTLTAAITTVLAKEGGAAARAYDQIDNAPEEKARG 60
Query: 61 ITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHI 120
ITINTAH+EYET+ RHYAHVDCPGHADY+KNMITGAAQMDGAILV SA DGPMPQTREHI
Sbjct: 61 ITINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSATDGPMPQTREHI 120
Query: 121 LLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALE 180
LLARQVGVPYIVVFLNK DMVDDEELLELVE+E+RELL++Y+FPG+D PII+GSA ALE
Sbjct: 121 LLARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSEYDFPGDDTPIIRGSALKALE 180
Query: 181 GDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVR 240
GD E IL L A+D YIPTP R D FL+P+EDVFSI+GRGTVVTGRVERGIV+
Sbjct: 181 GD--AEWEAKILELMDAVDEYIPTPERETDKPFLMPIEDVFSITGRGTVVTGRVERGIVK 238
Query: 241 VGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERGQVLAKPGS 300
VGEE+EI+G+KDT KTT TGVEMFRK LD+G+AGDN+GLLLRG KRE++ERG VLAKPGS
Sbjct: 239 VGEEVEIVGLKDTRKTTVTGVEMFRKELDEGRAGDNVGLLLRGIKREEIERGMVLAKPGS 298
Query: 301 IKPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVL 360
IKPH F E+Y L K+EGGRHTPFFS YRPQFYFRTTDVTGSI LP+ EMVMPGDNV
Sbjct: 299 IKPHTKFEAEVYVLKKEEGGRHTPFFSGYRPQFYFRTTDVTGSITLPEGVEMVMPGDNVK 358
Query: 361 ITVRLINPIAMEEGLRFAIREG 382
+TV LI+PIA+E+G+RFAIREG
Sbjct: 359 MTVELISPIALEQGMRFAIREG 380
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 694 bits (1793), Expect = 0.0
Identities = 270/395 (68%), Positives = 320/395 (81%), Gaps = 13/395 (3%)
Query: 1 MAKSKFERTKPHINVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARG 60
MA+ KFER KPH+N+GTIGHVDHGKTTLTAAI L+ K G +AK YD+ID+APEEKARG
Sbjct: 1 MAREKFERKKPHVNIGTIGHVDHGKTTLTAAITMTLAAKGGAKAKKYDEIDSAPEEKARG 60
Query: 61 ITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHI 120
ITINTAH+EYET+ RHYAHVDCPGHADY+KNMITGAAQMDGAILV SAADGPMPQT+EHI
Sbjct: 61 ITINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTKEHI 120
Query: 121 LLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALE 180
LLA+QVGVP IVVFLNK D VDDEELLELVE+E+RELL+KY+FPG+DIPI+ GSA LALE
Sbjct: 121 LLAKQVGVPNIVVFLNKEDQVDDEELLELVELEVRELLSKYDFPGDDIPIVSGSALLALE 180
Query: 181 ----GDTGPLGEQS----ILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTG 232
GE I +L A+D+YIPTP R D FL+ +EDVFSI+GRGTV TG
Sbjct: 181 ALTENPKIKRGENKWVDKIYNLMDAVDSYIPTPERDTDKPFLMAIEDVFSITGRGTVATG 240
Query: 233 RVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERG 292
R+ERG V+VG+ +EI+G+++T TT TG+EMF+K LD+G AGDN+G+LLRG ++ED+ERG
Sbjct: 241 RIERGTVKVGDTVEIVGLRETKTTTVTGLEMFQKTLDEGLAGDNVGILLRGIQKEDIERG 300
Query: 293 QVLAKPGSIKPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIEL-----P 347
VLAKPG+I PH F ++Y L+K+EGGRHTPFF YRPQFY RTTDVTG IE
Sbjct: 301 MVLAKPGTITPHTKFEAQVYILTKEEGGRHTPFFPGYRPQFYVRTTDVTGKIESFTADDG 360
Query: 348 KNKEMVMPGDNVLITVRLINPIAMEEGLRFAIREG 382
EMVMPGD + +TV LI PIA+E+G+RFAIREG
Sbjct: 361 SKTEMVMPGDRIKMTVELIYPIAIEKGMRFAIREG 395
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 674 bits (1740), Expect = 0.0
Identities = 268/383 (69%), Positives = 320/383 (83%), Gaps = 2/383 (0%)
Query: 2 AKSKFERTKPHINVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGI 61
+ + F RTKPH+NVGTIGHVDHGKTTLTAAI VL+++ +A ++D+ID APEEKARGI
Sbjct: 51 SMATFTRTKPHVNVGTIGHVDHGKTTLTAAITKVLAEEGKAKAVAFDEIDKAPEEKARGI 110
Query: 62 TINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHIL 121
TI TAH+EYET RHYAHVDCPGHADY+KNMITGAAQMDG ILV SA DGPMPQT+EHIL
Sbjct: 111 TIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHIL 170
Query: 122 LARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEG 181
LARQVGVP +VVFLNK D+VDDEELLELVE+E+RELL+ Y+FPG++IPII+GSA AL+G
Sbjct: 171 LARQVGVPSLVVFLNKVDVVDDEELLELVEMELRELLSFYKFPGDEIPIIRGSALSALQG 230
Query: 182 DTGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRV 241
+G+ +IL L A+D YIP P R +D FL+P+EDVFSI GRGTV TGRVE+G ++V
Sbjct: 231 TNDEIGKNAILKLMDAVDEYIPEPVRVLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKV 290
Query: 242 GEELEIIGIKD--TVKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERGQVLAKPG 299
GEE+EI+G++ +KTT TGVEMF+K+LDQGQAGDN+GLLLRG KREDV+RGQV+ KPG
Sbjct: 291 GEEVEIVGLRPGGPLKTTVTGVEMFKKILDQGQAGDNVGLLLRGLKREDVQRGQVICKPG 350
Query: 300 SIKPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNV 359
SIK +K F EIY L+KDEGGRHTPFFSNYRPQFY RT DVTG +ELP+ +MVMPGDNV
Sbjct: 351 SIKTYKKFEAEIYVLTKDEGGRHTPFFSNYRPQFYLRTADVTGKVELPEGVKMVMPGDNV 410
Query: 360 LITVRLINPIAMEEGLRFAIREG 382
LI+P+ +E G RFA+REG
Sbjct: 411 TAVFELISPVPLEPGQRFALREG 433
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 575 bits (1482), Expect = 0.0
Identities = 264/394 (67%), Positives = 310/394 (78%), Gaps = 13/394 (3%)
Query: 2 AKSKFERTKPHINVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGI 61
A+ KFER KPH+N+GTIGHVDHGKTTLTAA+ L+ G K YD+IDAAPEE+ARGI
Sbjct: 71 ARGKFERKKPHVNIGTIGHVDHGKTTLTAALTMALASMGGSAPKKYDEIDAAPEERARGI 130
Query: 62 TINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHIL 121
TINTA +EYET+ RHYAHVDCPGHADY+KNMITGAAQMDGAILV S ADGPMPQT+EHIL
Sbjct: 131 TINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHIL 190
Query: 122 LARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEG 181
LA+QVGVP +VVFLNK D VDDEELLELVE+E+RELL+ YEFPG+DIPII GSA LALE
Sbjct: 191 LAKQVGVPNMVVFLNKQDQVDDEELLELVELEVRELLSSYEFPGDDIPIISGSALLALEA 250
Query: 182 DTG----PLGEQS----ILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGR 233
G+ I L A+D+YIP P R D FLL VEDVFSI+GRGTV TGR
Sbjct: 251 LMENPNIKRGDNKWVDKIYELMDAVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGR 310
Query: 234 VERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERGQ 293
VERG V+VGE ++I+G+++T TT TGVEMF+K+LD+ AGDN+GLLLRG ++ D++RG
Sbjct: 311 VERGTVKVGETVDIVGLRETRSTTVTGVEMFQKILDEALAGDNVGLLLRGIQKADIQRGM 370
Query: 294 VLAKPGSIKPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTG---SIELPKNK 350
VLAKPGSI PH F +Y L K+EGGRH+PFF+ YRPQFY RTTDVTG SI K++
Sbjct: 371 VLAKPGSITPHTKFEAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGKVTSIMNDKDE 430
Query: 351 E--MVMPGDNVLITVRLINPIAMEEGLRFAIREG 382
E MVMPGD V + V LI P+A E+G+RFAIREG
Sbjct: 431 ESKMVMPGDRVKMVVELIVPVACEQGMRFAIREG 464
>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 = 416 bits (1073), Expect = e-145
Identities = 156/195 (80%), Positives = 169/195 (86%)
Query: 11 PHINVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIEY 70
PH+NVGTIGHVDHGKTTLTAAI VL+KK G +AK YD+ID APEEKARGITINTAH+EY
Sbjct: 1 PHVNVGTIGHVDHGKTTLTAAITKVLAKKGGAKAKKYDEIDKAPEEKARGITINTAHVEY 60
Query: 71 ETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPY 130
ET RHYAHVDCPGHADYIKNMITGAAQMDGAILV SA DGPMPQTREH+LLARQVGVPY
Sbjct: 61 ETANRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSATDGPMPQTREHLLLARQVGVPY 120
Query: 131 IVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQS 190
IVVFLNKADMVDDEELLELVE+E+RELL+KY F G+D PI++GSA ALEGD
Sbjct: 121 IVVFLNKADMVDDEELLELVEMEVRELLSKYGFDGDDTPIVRGSALKALEGDDPNKWVDK 180
Query: 191 ILSLSKALDTYIPTP 205
IL L ALD+YIPTP
Sbjct: 181 ILELLDALDSYIPTP 195
>gnl|CDD|180161 PRK05609, nusG, transcription antitermination protein NusG;
Validated.
Length = 181
Score = 286 bits (734), Expect = 3e-94
Identities = 106/178 (59%), Positives = 146/178 (82%)
Query: 416 NNKKRWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKR 475
+ KKRWYV+ +YSG EK V+ L RI LGM+ G +LVPTEE+V+VK +K ++++
Sbjct: 3 SMKKRWYVVQTYSGYEKKVKENLENRIETLGMEDLIGEVLVPTEEVVEVKNGKKKKVERK 62
Query: 476 FFPGYVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILKQIKKGVEKPR 535
FFPGYVL++M MTDESWHLV+NT VTGF+G ++PTP+S KE+E+ILKQ+++GVEKP+
Sbjct: 63 FFPGYVLVKMVMTDESWHLVRNTPGVTGFVGSTGSKPTPLSEKEVEKILKQLQEGVEKPK 122
Query: 536 PKILYQLDELVRIKDGPFTDFSGNIEEVNYEKSRVRVSVTIFGRATPVELEFNQVEKI 593
PK+ +++ E+VR+ DGPF DF+G +EEV+YEKS+++V V+IFGR TPVELEF+QVEKI
Sbjct: 123 PKVDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVSIFGRETPVELEFSQVEKI 180
>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 = 7e-88
Identities = 98/195 (50%), Positives = 120/195 (61%), Gaps = 11/195 (5%)
Query: 10 KPHINVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIE 69
K H N+G IGHVDHGKTTLT A+ V AK +D EE+ RGITI A +
Sbjct: 1 KRHRNIGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVS 60
Query: 70 YETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVP 129
+ETK R +D PGH D+ K MI GA+Q DGAILV A +G MPQTREH+LLA+ +GVP
Sbjct: 61 FETKKRLINIIDTPGHVDFTKEMIRGASQADGAILVVDAVEGVMPQTREHLLLAKTLGVP 120
Query: 130 YIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQ 189
I+VF+NK D VDD EL E+VE RELL KY F G +P++ GSA
Sbjct: 121 -IIVFINKIDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPGSALTGE---------- 169
Query: 190 SILSLSKALDTYIPT 204
I L +ALD Y+P+
Sbjct: 170 GIDELLEALDLYLPS 184
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 246 bits (630), Expect = 2e-75
Identities = 151/429 (35%), Positives = 227/429 (52%), Gaps = 80/429 (18%)
Query: 8 RTKPHINVGTIGHVDHGKTTL-------TAAIATVLSKKFGGEAKSYDQ--------IDA 52
+ KPH+N+ IGHVDHGK+TL T AI + ++ EAK + +D
Sbjct: 2 KEKPHLNLAVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMDR 61
Query: 53 APEEKARGITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAAD-- 110
EE+ RG+TI+ AH ++ET ++ VDCPGH D++KNMITGA+Q D A+LV +A D
Sbjct: 62 LKEERERGVTIDLAHKKFETDKYYFTIVDCPGHRDFVKNMITGASQADAAVLVVAADDAG 121
Query: 111 GPMPQTREHILLARQVGVPYIVVFLNKADMVD-DEELLELVEIEIRELLNKYEFPGNDIP 169
G MPQTREH+ LAR +G+ ++V +NK D V+ DE+ E V+ E+ +LL + +DIP
Sbjct: 122 GVMPQTREHVFLARTLGINQLIVAINKMDAVNYDEKRYEEVKEEVSKLLKMVGYKPDDIP 181
Query: 170 IIKGSAKLALEGD------------TGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLPV 217
I S A EGD GP +L +ALD + P + D +P+
Sbjct: 182 FIPVS---AFEGDNVVKKSENMPWYNGP-------TLLEALDN-LKPPEKPTDKPLRIPI 230
Query: 218 EDVFSISGRGTVVTGRVERGIVRVGEEL--EIIGIKDTVKTTCTGVEMFRKLLDQGQAGD 275
+DV+SISG GTV GRVE G+++VG+++ G+ VK+ +EM + L Q + GD
Sbjct: 231 QDVYSISGVGTVPVGRVETGVLKVGDKVVFMPAGVVGEVKS----IEMHHEELPQAEPGD 286
Query: 276 NIGLLLRGTKREDVERGQV---LAKPGSIKPHKHFTGEIYALSKDEGGRH-TPFFSNYRP 331
NIG +RG ++D++RG V P ++ + FT +I L +H + Y P
Sbjct: 287 NIGFNVRGVGKKDIKRGDVCGHPDNPPTVA--EEFTAQIVVL------QHPSAITVGYTP 338
Query: 332 QFYFRTTDVTGSIE-------------LPKNKEMVMPGDNVLITVRLINPIAMEE----- 373
F+ T V + E +N + + GD ++ ++ P+ +E+
Sbjct: 339 VFHAHTAQVACTFEELVKKLDPRTGQVAEENPQFIKTGDAAIVKIKPTKPLVIEKVKEIP 398
Query: 374 --GLRFAIR 380
G RFAIR
Sbjct: 399 QLG-RFAIR 406
>gnl|CDD|233188 TIGR00922, nusG, transcription termination/antitermination factor
NusG. NusG proteins are transcription factors which are
aparrently universal in prokaryotes (archaea and
eukaryotes have homologs that may have related
functions). The essential components of these factors
include an N-terminal RNP-like (ribonucleoprotein)
domain and a C-terminal KOW motif (pfam00467) believed
to be a nucleic acid binding domain. In E. coli, NusA
has been shown to interact with RNA polymerase and
termination factor Rho. This model covers a wide variety
of bacterial species but excludes mycoplasmas which are
covered by a separate model (TIGR01956).The function of
all of these NusG proteins is likely to be the same at
the level of interaction with RNA and other protein
factors to affect termination; however different species
may utilize NusG towards different processes and in
combination with different suites of affector
proteins.In E. coli, NusG promotes rho-dependent
termination. It is an essential gene. In Streptomyces
virginiae and related species, an additional N-terminal
sequence is also present and is suggested to play a role
in butyrolactone-mediated autoregulation. In Thermotoga
maritima, NusG has a long insert, fails to substitute
for E. coli NusG (with or without the long insert), is a
large 0.7 % of total cellular protein, and has a
general, sequence non-specific DNA and RNA binding
activity that blocks ethidium staining, yet permits
transcription.Archaeal proteins once termed NusG share
the KOW domain but are actually a ribosomal protein
corresponding to L24p in bacterial and L26e in
eukaryotes (TIGR00405) [Transcription, Transcription
factors].
Length = 172
Score = 232 bits (593), Expect = 1e-73
Identities = 90/172 (52%), Positives = 130/172 (75%)
Query: 421 WYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPGY 480
WYV+ +YSG EK V++ L E I LGM ++VPTEE+V++KK +K V++++ FPGY
Sbjct: 1 WYVVQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGY 60
Query: 481 VLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILKQIKKGVEKPRPKILY 540
VL++M++TD SWHLVKNT VTGF+G +E++ IL +++G +KP+PKI +
Sbjct: 61 VLVKMDLTDVSWHLVKNTPGVTGFVGSGGKPKALSEDEEVKNILNALEEGKDKPKPKIDF 120
Query: 541 QLDELVRIKDGPFTDFSGNIEEVNYEKSRVRVSVTIFGRATPVELEFNQVEK 592
++ E VR+ DGPF +F+G +EEV+YEKS+++VSV+IFGR TPVELEF+QVEK
Sbjct: 121 EVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPVELEFSQVEK 172
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 234 bits (599), Expect = 6e-71
Identities = 135/429 (31%), Positives = 206/429 (48%), Gaps = 77/429 (17%)
Query: 10 KPHINVGTIGHVDHGKTTLTAAI--------------ATVLSKKFGGEAKSYDQI-DAAP 54
KPH+N+ IGHVD GK+TL + +K+ G E+ + + D
Sbjct: 5 KPHLNLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVLDKTK 64
Query: 55 EEKARGITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADG--- 111
EE+ RG+TI+ AH ++ET ++ +D PGH D++KNMITGA+Q D A+LV A DG
Sbjct: 65 EERERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARDGEFE 124
Query: 112 ----PMPQTREHILLARQVGVPYIVVFLNKADMVD-DEELLELVEIEIRELLNKYEFPGN 166
QTREH LAR +G+ ++V +NK D+V DEE E + E+ +LL +
Sbjct: 125 AGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLLKMVGYNPK 184
Query: 167 DIPIIKGSAKLALEGD------------TGPLGEQSILSLSKALDTYIPTPNRAIDGAFL 214
D+P I S +GD GP +L +ALD + P R +D
Sbjct: 185 DVPFIPIS---GFKGDNLTKKSENMPWYKGP-------TLLEALD-QLEPPERPLDKPLR 233
Query: 215 LPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQAG 274
LP++DV+SISG GTV GRVE G+++ G+++ + V +EM + + Q + G
Sbjct: 234 LPIQDVYSISGIGTVPVGRVESGVIKPGQKVTFMPAG--VVGEVKSIEMHHEEISQAEPG 291
Query: 275 DNIGLLLRGTKREDVERGQVLAKPGSIKPHKH---FTGEIYALSKDEGGRHTPFFSNYRP 331
DN+G +RG ++ D+ RG V+ P FT +I L S Y P
Sbjct: 292 DNVGFNVRGVEKNDIRRGDVIGHS--DNPPTVSPEFTAQIIVL-----WHPGIITSGYTP 344
Query: 332 QFYFRTTDVTGSI-------------ELPKNKEMVMPGDNVLITVRLINPIAMEEGL--- 375
+ T V I +L +N + + GD ++ + P+ +E+
Sbjct: 345 VLHAHTAQVACRIAELLSKLDPRTGKKLEENPQFLKRGDAAIVKIEPEKPLCLEKVSEIP 404
Query: 376 ---RFAIRE 381
RFA+R+
Sbjct: 405 QLGRFALRD 413
>gnl|CDD|223328 COG0250, NusG, Transcription antiterminator [Transcription].
Length = 178
Score = 221 bits (565), Expect = 3e-69
Identities = 89/177 (50%), Positives = 128/177 (72%)
Query: 417 NKKRWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRF 476
KRWYV+ +YSG EK V+ L + LGM+ +LVPTEE+V+VK +K +++++
Sbjct: 1 LMKRWYVVQTYSGQEKKVKENLERKAELLGMEDLIFEVLVPTEEVVEVKGKRKVIVERKL 60
Query: 477 FPGYVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILKQIKKGVEKPRP 536
FPGYVL+EM+MTDE+WHLV+NT VTGF+G +P P+S +EIE IL +++ V +P
Sbjct: 61 FPGYVLVEMDMTDEAWHLVRNTPGVTGFVGSGGAKPVPLSEEEIEHILGFLEEEVAPKKP 120
Query: 537 KILYQLDELVRIKDGPFTDFSGNIEEVNYEKSRVRVSVTIFGRATPVELEFNQVEKI 593
K+ ++ ++VRI DGPF F +EEV+ EK +++V V+IFGR TPVELEF+QVEK+
Sbjct: 121 KVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIFGRPTPVELEFDQVEKL 177
>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 = 212 bits (540), Expect = 2e-62
Identities = 149/434 (34%), Positives = 213/434 (49%), Gaps = 78/434 (17%)
Query: 1 MAKSKFERTKPHINVGTIGHVDHGKTTLTA-------AIATVLSKKFGGEAKSYDQ---- 49
MAK K HINV IGHVDHGK+T AI +KF EA+ +
Sbjct: 1 MAKEK-----EHINVAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFE 55
Query: 50 ----IDAAPEEKARGITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILV 105
+D EE+ RG+TI+ AH ++ET VDCPGH D+IKNMITGA+Q D A+LV
Sbjct: 56 FAWVMDRLKEERERGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLV 115
Query: 106 CSAADGP---MPQTREHILLARQVGVPYIVVFLNKADMVD-DEELLELVEIEIRELLNKY 161
+ DG PQTREH LAR +G+ ++V +NK D V+ DEE E ++ E+ L+ K
Sbjct: 116 VAVGDGEFEVQPQTREHAFLARTLGINQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKV 175
Query: 162 EFPGNDIPIIKGSAKLALEGDT------------GPLGEQSILSLSKALDTYIPTPNRAI 209
+ + +P I S A GD G +L +ALD P P +
Sbjct: 176 GYNPDTVPFIPIS---AWNGDNVIKKSENTPWYKGK-------TLLEALDALEP-PEKPT 224
Query: 210 DGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEEL--EIIGIKDTVKTTCTGVEMFRKL 267
D +P++DV+SI+G GTV GRVE G+++ G+++ E G+ VK+ +EM +
Sbjct: 225 DKPLRIPIQDVYSITGVGTVPVGRVETGVLKPGDKVVFEPAGVSGEVKS----IEMHHEQ 280
Query: 268 LDQGQAGDNIGLLLRGTKREDVERGQVLAKPGS-IKPHKHFTGEIYALSKDEGGRHTPFF 326
++Q + GDNIG +RG ++D+ RG V P + K K FT +I L
Sbjct: 281 IEQAEPGDNIGFNVRGVSKKDIRRGDVCGHPDNPPKVAKEFTAQIVVLQHP-----GAIT 335
Query: 327 SNYRPQFYFRTTDVTGS-IELPK------------NKEMVMPGDNVLITVRLINPIAMEE 373
Y P F+ T + EL K N + + GD ++ + P+ +E
Sbjct: 336 VGYTPVFHCHTAQIACRFDELLKKNDPRTGQVLEENPQFLKTGDAAIVKFKPTKPMVIEA 395
Query: 374 GL------RFAIRE 381
RFAIR+
Sbjct: 396 VKEIPPLGRFAIRD 409
>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 = 188 bits (479), Expect = 1e-56
Identities = 77/195 (39%), Positives = 100/195 (51%), Gaps = 15/195 (7%)
Query: 14 NVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIEYETK 73
NVG IGHVDHGKTTLT ++ + +D EE+ RGITI T +E+E
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWP 60
Query: 74 ARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVV 133
R +D PGH D+ K + G AQ DGA+LV A +G PQTREH+ +A G I+V
Sbjct: 61 KRRINFIDTPGHEDFSKETVRGLAQADGALLVVDANEGVEPQTREHLNIALA-GGLPIIV 119
Query: 134 FLNKADMVDDEELLELVEIEIRELLNKYEF---PGNDIPIIKGSAKLALEGDTGPLGEQS 190
+NK D V EE + V EI+ELL F G D+PII SA +
Sbjct: 120 AVNKIDRV-GEEDFDEVLREIKELLKLIGFTFLKGKDVPIIPISALTGEGIEE------- 171
Query: 191 ILSLSKALDTYIPTP 205
L A+ ++P P
Sbjct: 172 ---LLDAIVEHLPPP 183
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 186 bits (473), Expect = 1e-52
Identities = 107/373 (28%), Positives = 173/373 (46%), Gaps = 45/373 (12%)
Query: 13 INVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINT--AHIEY 70
+ +GT GH+DHGKTTL A+ ++ D PEEK RGITI+ + +
Sbjct: 1 MIIGTAGHIDHGKTTLLKALTGGVT-------------DRLPEEKKRGITIDLGFYYRKL 47
Query: 71 ETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPY 130
E + +D PGH D+I N++ G +D A+LV +A +G M QT EH+L+ +G+
Sbjct: 48 EDGVMGF--IDVPGHPDFISNLLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGIKN 105
Query: 131 IVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQS 190
++ L KAD VD+ +E +I+++L + I K SAK +
Sbjct: 106 GIIVLTKADRVDEAR----IEQKIKQILADLSLA--NAKIFKTSAKT----------GRG 149
Query: 191 ILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGI 250
I L L + R F + ++ F++ G GTVVTG V G V+VG++L + I
Sbjct: 150 IEELKNELIDLLEEIERDEQKPFRIAIDRAFTVKGVGTVVTGTVLSGEVKVGDKLYLSPI 209
Query: 251 KDTVKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERGQVLAKPGSIKPHKHFTGE 310
V+ ++ +++ +AG +GL L+G ++E++ERG L KP ++ E
Sbjct: 210 NKEVRV--RSIQAHDVDVEEAKAGQRVGLALKGVEKEEIERGDWLLKPEPLEVTTRLIVE 267
Query: 311 IYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIE-LPKNKEMVM-----PGDNVLITVR 364
+ + + VTG I L KN E+ + GDN + +R
Sbjct: 268 LEIDPLFK----KTLKQGQPVHIHVGLRSVTGRIVPLEKNAELNLVKPIALGDNDRLVLR 323
Query: 365 LINPIAMEEGLRF 377
+ + G R
Sbjct: 324 DNSAVIKLAGARV 336
>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 = 167 bits (426), Expect = 3e-50
Identities = 63/87 (72%), Positives = 78/87 (89%)
Query: 213 FLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQ 272
FL+P+EDVFSI GRGTVVTGR+ERG ++VG+E+EI+G +T+KTT TG+EMFRK LD+ +
Sbjct: 1 FLMPIEDVFSIPGRGTVVTGRIERGTIKVGDEVEIVGFGETLKTTVTGIEMFRKTLDEAE 60
Query: 273 AGDNIGLLLRGTKREDVERGQVLAKPG 299
AGDN+G+LLRG KREDVERG VLAKPG
Sbjct: 61 AGDNVGVLLRGVKREDVERGMVLAKPG 87
>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 = 166 bits (424), Expect = 8e-50
Identities = 61/81 (75%), Positives = 69/81 (85%)
Query: 302 KPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVLI 361
KPH F E+Y L+K+EGGRHTPFFS YRPQFY RTTDVTGSI LP+ EMVMPGDNV +
Sbjct: 1 KPHTKFEAEVYVLTKEEGGRHTPFFSGYRPQFYIRTTDVTGSITLPEGTEMVMPGDNVKM 60
Query: 362 TVRLINPIAMEEGLRFAIREG 382
TV LI+PIA+E+GLRFAIREG
Sbjct: 61 TVELIHPIALEKGLRFAIREG 81
>gnl|CDD|193580 cd09891, NGN_Bact_1, Bacterial N-Utilization Substance G (NusG)
N-terminal (NGN) domain, subgroup 1. The N-Utilization
Substance G (NusG) protein is involved in transcription
elongation and termination in bacteria. NusG is
essential in Escherichia coli and associates with RNA
polymerase elongation and Rho-termination. Homologs of
the NusG gene exist in all bacteria. The NusG N-terminal
domain (NGN) is similar in all NusG homologs, but its
C-terminal domain and the linker that separates these
two domains are different. The domain organization of
NusG suggests that the common properties of NusG and its
homologs are due to their similar NGN domains.
Length = 107
Score = 159 bits (405), Expect = 7e-47
Identities = 54/108 (50%), Positives = 79/108 (73%), Gaps = 1/108 (0%)
Query: 420 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPG 479
+WYV+H+YSG E V+ L +RI G++ G +LVPTEE+V+VK +K V +++ FPG
Sbjct: 1 KWYVVHTYSGYENKVKENLEKRIESEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKLFPG 60
Query: 480 YVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILKQI 527
YVL+EM+M D++WHLV+NT VTGF+G +P P+S +E+E IL Q+
Sbjct: 61 YVLVEMDMNDDTWHLVRNTPGVTGFVGSG-GKPVPLSEEEVERILGQV 107
>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 = 170 bits (433), Expect = 5e-46
Identities = 104/389 (26%), Positives = 170/389 (43%), Gaps = 45/389 (11%)
Query: 13 INVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIEYET 72
+ + T GHVDHGKTTL A+ + + D PEEK RG+TI+ +
Sbjct: 1 MIIATAGHVDHGKTTLLKALTGIAA-------------DRLPEEKKRGMTIDLGFAYFPL 47
Query: 73 KARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIV 132
+D PGH +I N I G +D A+LV A +G M QT EH+ + +G+P+ +
Sbjct: 48 PDYRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIPHTI 107
Query: 133 VFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSIL 192
V + KAD V++EE+ E+ ++++LN Y F N I K SAK G ++ +
Sbjct: 108 VVITKADRVNEEEIKR-TEMFMKQILNSYIFLKN-AKIFKTSAK---TGQGIGELKKELK 162
Query: 193 SLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKD 252
+L ++LD + I + ++ F + G GTVVTG G V+VG+ L ++ I
Sbjct: 163 NLLESLD------IKRIQKPLRMAIDRAFKVKGAGTVVTGTAFSGEVKVGDNLRLLPINH 216
Query: 253 TVKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERGQVLAKPGSIKPHKHFTGEIY 312
V+ ++ + ++ AG I L L + E ++RG ++ P P +
Sbjct: 217 EVRV--KAIQAQNQDVEIAYAGQRIALNLMDVEPESLKRGLLILTPED--PKLRVVVKFI 272
Query: 313 ALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNK--EMVMP-------GDNVLITV 363
A P + TG I L + + GD +++
Sbjct: 273 A--------EVPLLELQPYHIAHGMSVTTGKISLLDKGIALLTLDAPLILAKGDKLVLRD 324
Query: 364 RLINPIAMEEGLRFAIREGVQQFIQDNLL 392
N +A L +R + FI + +
Sbjct: 325 SSGNFLAGARVLEPPVRVKRKAFIAELIK 353
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 162 bits (413), Expect = 4e-44
Identities = 110/317 (34%), Positives = 159/317 (50%), Gaps = 40/317 (12%)
Query: 10 KPHINVGTIGHVDHGKTTLTAAIATVLS-------KKFGGEAKSYDQ--------IDAAP 54
K HIN+ IGHVD GK+T T + +KF EA + +D
Sbjct: 5 KTHINLVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLK 64
Query: 55 EEKARGITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMP 114
E+ RGITI+ A ++ET ++ +D PGH D+IKNMITG +Q D AILV ++ G
Sbjct: 65 AERERGITIDIALWKFETPKYYFTIIDAPGHRDFIKNMITGTSQADVAILVVASTAGEFE 124
Query: 115 -------QTREHILLARQVGVPYIVVFLNKADMVD---DEELLELVEIEIRELLNKYEFP 164
QTREH LLA +GV ++V +NK D +E + ++ E+ L K +
Sbjct: 125 AGISKDGQTREHALLAFTLGVKQMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKKVGYN 184
Query: 165 GNDIPIIKGSAKLALEGDTGPLGEQSI-------LSLSKALDTYIPTPNRAIDGAFLLPV 217
+P I S +GD + E+S +L +ALDT P P R +D LP+
Sbjct: 185 PEKVPFIPIS---GWQGDN--MIEKSDNMPWYKGPTLLEALDTLEP-PKRPVDKPLRLPL 238
Query: 218 EDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQAGDNI 277
+DV+ I G GTV GRVE GI++ G + + V T VEM + L + GDN+
Sbjct: 239 QDVYKIGGIGTVPVGRVETGILKPG--MVVTFAPSGVTTEVKSVEMHHEQLAEAVPGDNV 296
Query: 278 GLLLRGTKREDVERGQV 294
G ++ +D++RG V
Sbjct: 297 GFNVKNVSVKDIKRGYV 313
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 161 bits (409), Expect = 5e-43
Identities = 120/418 (28%), Positives = 191/418 (45%), Gaps = 52/418 (12%)
Query: 5 KFERTKPHINVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGIT-- 62
K E H+ VG GHVDHGK+TL + T G +SY +D E RG++
Sbjct: 110 KTEEAPEHVLVGVAGHVDHGKSTLVGVLVTGRLDDGDGATRSY--LDVQKHEVERGLSAD 167
Query: 63 INTAHIEY---------------------ETKARHYAHVDCPGHADYIKNMITG--AAQM 99
I+ + + + + VD GH +++ I G ++
Sbjct: 168 ISLRVYGFDDGKVVRLKNPLDEAEKAAVVKRADKLVSFVDTVGHEPWLRTTIRGLLGQKV 227
Query: 100 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELL- 158
D +LV +A DG T+EH+ +A + +P IVV + K DMV D+ +VE EI LL
Sbjct: 228 DYGLLVVAADDGVTKMTKEHLGIALAMELPVIVV-VTKIDMVPDDRFQGVVE-EISALLK 285
Query: 159 --NKYEFPGNDIPIIKGSAKLALEGDT-GPLGEQSILSLSKALDTYI-------PTPNRA 208
+ D + +AK G P+ S ++ + LD
Sbjct: 286 RVGRIPLIVKDTDDVVLAAKAMKAGRGVVPIFYTSSVTG-EGLDLLDEFFLLLPKRRRWD 344
Query: 209 IDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDT--VKTTCTGVEMFRK 266
+G FL+ ++ ++S++G GTVV+G V+ GI+ VG+ + + KD + +EM
Sbjct: 345 DEGPFLMYIDKIYSVTGVGTVVSGSVKSGILHVGDTVLLGPFKDGKFREVVVKSIEMHHY 404
Query: 267 LLDQGQAGDNIGLLLRGTKREDVERGQVLAKPGSIKPHKHFTGEIYALSKDEGGRH-TPF 325
+D +AG IG+ L+G ++E++ERG VL+ K + F E+ L RH T
Sbjct: 405 RVDSAKAGSIIGIALKGVEKEELERGMVLSAGADPKAVREFDAEVLVL------RHPTTI 458
Query: 326 FSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVLITVRL-INPIAMEEGLRFAIREG 382
+ Y P F++ T E +K +MPGD ++ +R P +EEG +F REG
Sbjct: 459 RAGYEPVFHYETIREAVYFE-EIDKGFLMPGDRGVVRMRFKYRPHHVEEGQKFVFREG 515
>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 = 145 bits (369), Expect = 3e-40
Identities = 70/194 (36%), Positives = 101/194 (52%), Gaps = 28/194 (14%)
Query: 14 NVGTIGHVDHGKTTLTAAIATVLS-------KKFGGEAKSYDQ--------IDAAPEEKA 58
N+ IGHVD GK+TLT + L +K+ EAK + +D EE+
Sbjct: 1 NLVVIGHVDAGKSTLTGHLLYKLGGVDKRTIEKYEKEAKEMGKESFKYAWVLDKLKEERE 60
Query: 59 RGITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADG------- 111
RG+TI+ ++ET+ + +D PGH D++KNMITGA+Q D A+LV SA G
Sbjct: 61 RGVTIDVGLAKFETEKYRFTIIDAPGHRDFVKNMITGASQADVAVLVVSARKGEFEAGFE 120
Query: 112 PMPQTREHILLARQVGVPYIVVFLNKADMVD---DEELLELVEIEIRELLNKYEFPGNDI 168
QTREH LLAR +GV ++V +NK D V +E + ++ ++ L K + D+
Sbjct: 121 KGGQTREHALLARTLGVKQLIVAVNKMDDVTVNWSQERYDEIKKKVSPFLKKVGYNPKDV 180
Query: 169 PIIKGSAKLALEGD 182
P I S GD
Sbjct: 181 PFIPIS---GFTGD 191
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 153 bits (389), Expect = 8e-40
Identities = 98/309 (31%), Positives = 147/309 (47%), Gaps = 36/309 (11%)
Query: 17 TIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIEY-ETKAR 75
T GHVDHGKTTL AI V D PEEK RG+TI+ + + + R
Sbjct: 5 TAGHVDHGKTTLLQAITGV-------------NADRLPEEKKRGMTIDLGYAYWPQPDGR 51
Query: 76 HYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFL 135
+D PGH ++ NM+ G +D A+LV + DG M QTREH+ + + G P + V L
Sbjct: 52 VLGFIDVPGHEKFLSNMLAGVGGIDHALLVVACDDGVMAQTREHLAILQLTGNPMLTVAL 111
Query: 136 NKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLS 195
KAD VD+ + E V +++ +L +Y F + + + A EG + I +L
Sbjct: 112 TKADRVDEARIAE-VRRQVKAVLREYGFA--EAKLFVTA---ATEG-------RGIDALR 158
Query: 196 KALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVK 255
+ L +P A F L ++ F++ G G VVTG G V+VG+ L + G+ ++
Sbjct: 159 EHLLQ-LPEREHAAQHRFRLAIDRAFTVKGAGLVVTGTALSGEVKVGDTLWLTGVNKPMR 217
Query: 256 TTCTGVEMFRKLLDQGQAGDNIGLLLRG-TKREDVERGQ-VLAKPGSIKPHKHFTGEIYA 313
G+ + +Q QAG I L + G ++E + RG +LA P + FT I
Sbjct: 218 V--RGLHAQNQPTEQAQAGQRIALNIAGDAEKEQINRGDWLLADA----PPEPFTRVIVE 271
Query: 314 LSKDEGGRH 322
L
Sbjct: 272 LQTHTPLTQ 280
>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 = 147 bits (373), Expect = 6e-39
Identities = 127/434 (29%), Positives = 189/434 (43%), Gaps = 112/434 (25%)
Query: 11 PHINVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIEY 70
P +N+G +GHVDHGKTTLT A+ V + D EE RGI+I + +
Sbjct: 3 PEVNIGMVGHVDHGKTTLTKALTGVWT-------------DTHSEELKRGISIRLGYADA 49
Query: 71 ETKA--------------------------RHYAHVDCPGHADYIKNMITGAAQMDGAIL 104
E R + VD PGH + M++GAA MDGA+L
Sbjct: 50 EIYKCPECDGPECYTTEPVCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGALL 109
Query: 105 VCSAADG-PMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEF 163
V +A + P PQTREH++ +G+ IV+ NK D+V E+ LE E EI+E +
Sbjct: 110 VIAANEPCPQPQTREHLMALEIIGIKNIVIVQNKIDLVSKEKALENYE-EIKEFVKGT-- 166
Query: 164 PGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSI 223
+ PII SA L +I +L +A++ +IPTP R +D L+ V F +
Sbjct: 167 IAENAPIIPVSA----------LHNANIDALLEAIEKFIPTPERDLDKPPLMYVARSFDV 216
Query: 224 SGRGT--------VVTGRVERGIVRVGEELEII-GIKDT---------VKTTCTGVEMFR 265
+ GT V+ G + +G ++VG+E+EI GIK + T T +
Sbjct: 217 NKPGTPPEKLKGGVIGGSLIQGKLKVGDEIEIRPGIKVEKGGKTKWEPIYTEITSLRAGG 276
Query: 266 KLLDQGQAGDNIGLLLRGTK------REDVERGQVLAKPGSIKPHKH-FTGEIYALSKDE 318
+++ + G GL+ GTK + D GQV+ KPG++ P E++ L +
Sbjct: 277 YKVEEARPG---GLVGVGTKLDPALTKADALAGQVVGKPGTLPPVWESLELEVHLLERVV 333
Query: 319 GGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVLIT-------------VRL 365
G T+ +E K E++M T V+L
Sbjct: 334 G------------------TEEELKVEPIKTGEVLMLNVGTATTVGVVTSARKDEIEVKL 375
Query: 366 INPIAMEEGLRFAI 379
P+ EEG R AI
Sbjct: 376 KRPVCAEEGDRVAI 389
>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 (342), Expect = 4e-37
Identities = 69/164 (42%), Positives = 93/164 (56%), Gaps = 19/164 (11%)
Query: 15 VGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINT--AHIEYET 72
+GT GH+DHGKTTL A+ G E D PEEK RGITI+ A+++
Sbjct: 2 IGTAGHIDHGKTTLIKALT-------GIET------DRLPEEKKRGITIDLGFAYLDLP- 47
Query: 73 KARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIV 132
+ +D PGH ++KNM+ GA +D +LV +A +G MPQTREH+ + +G+ +
Sbjct: 48 DGKRLGFIDVPGHEKFVKNMLAGAGGIDAVLLVVAADEGIMPQTREHLEILELLGIKKGL 107
Query: 133 VFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAK 176
V L KAD+V DE+ LELVE EI ELL D PI S+
Sbjct: 108 VVLTKADLV-DEDRLELVEEEILELLAGTFLA--DAPIFPVSSV 148
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 141 bits (358), Expect = 9e-37
Identities = 128/432 (29%), Positives = 194/432 (44%), Gaps = 94/432 (21%)
Query: 4 SKFERTKPHINVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITI 63
+ + +P +N+G +GHVDHGKTTLT A++ V + + EE RGITI
Sbjct: 2 ADPKHIQPEVNIGMVGHVDHGKTTLTKALSGVWTDRHS-------------EELKRGITI 48
Query: 64 NTAHIE--------------YETKA------------RHYAHVDCPGHADYIKNMITGAA 97
+ + Y T+ R + VD PGH + M++GAA
Sbjct: 49 KLGYADAKIYKCPECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGHETLMATMLSGAA 108
Query: 98 QMDGAILVCSAADG-PMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRE 156
MDGA+LV +A + P PQTREH++ +G+ I++ NK D+V E LE E +I+E
Sbjct: 109 LMDGALLVIAANEPCPQPQTREHLMALEIIGIKNIIIVQNKIDLVSRERALENYE-QIKE 167
Query: 157 LLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLP 216
+ K N PII SA+ + +I +L +A++ YIPTP R +D +
Sbjct: 168 FV-KGTVAEN-APIIPISAQH----------KANIDALIEAIEKYIPTPERDLDKPPRMY 215
Query: 217 VEDVFSISGRGT--------VVTGRVERGIVRVGEELEI---IGIKDTVKTTCTGVEMFR 265
V F ++ GT V+ G + +G++RVG+E+EI I ++ KT +
Sbjct: 216 VARSFDVNKPGTPPEELKGGVIGGSLVQGVLRVGDEIEIRPGIVVEKGGKTVWEPI--TT 273
Query: 266 KLLDQGQAGDNI-------GLLLRGTK------REDVERGQVLAKPGSIKPHKH-FTGEI 311
+++ QAG GL+ GTK + D GQV+ KPG++ P E
Sbjct: 274 EIVSL-QAGGEDVEEARPGGLVGVGTKLDPTLTKADALVGQVVGKPGTLPPVWTSIRIEY 332
Query: 312 YALSK----DEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVLITVRLIN 367
+ L + E + P +N T G + K E I V+L
Sbjct: 333 HLLERVVGTKEELKVEPIKTNEVLMLNVGTATTVGVVTSAKKDE---------IEVKLKR 383
Query: 368 PIAMEEGLRFAI 379
P+ E G R AI
Sbjct: 384 PVCAEIGERVAI 395
>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 = 127 bits (322), Expect = 2e-35
Identities = 46/83 (55%), Positives = 54/83 (65%), Gaps = 5/83 (6%)
Query: 300 SIKPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNV 359
IKPH F ++Y L+ TP F+ YRP FY T DVTG LP KE VMPGDN
Sbjct: 1 PIKPHTKFKAQVYILNH-----PTPIFNGYRPVFYCHTADVTGKFILPGKKEFVMPGDNA 55
Query: 360 LITVRLINPIAMEEGLRFAIREG 382
++TV LI PIA+E+G RFAIREG
Sbjct: 56 IVTVELIKPIAVEKGQRFAIREG 78
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 137 bits (347), Expect = 4e-35
Identities = 92/342 (26%), Positives = 153/342 (44%), Gaps = 54/342 (15%)
Query: 10 KPHINVGTIGHVDHGKTTL------------TAAIATV--LSKKFGGEAKSYD---QIDA 52
K + T G VD GK+TL +A++ SK+ G + + D +D
Sbjct: 4 KSLLRFITCGSVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLVDG 63
Query: 53 APEEKARGITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGP 112
E+ +GITI+ A+ + T+ R + D PGH Y +NM TGA+ D AIL+ A G
Sbjct: 64 LEAEREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTADLAILLVDARKGV 123
Query: 113 MPQTREHILLARQVGVPYIVVFLNKADMVD-DEELLELVEIEIRELLNKYEFPGNDIPII 171
+ QTR H +A +G+ ++VV +NK D+VD EE+ E + + + D+ I
Sbjct: 124 LEQTRRHSFIASLLGIRHVVVAVNKMDLVDYSEEVFEAIVADYLAFAAQ--LGLKDVRFI 181
Query: 172 KGSAKLALEGD------------TGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVED 219
S AL GD GP ++L + L+T + + AF PV+
Sbjct: 182 PIS---ALLGDNVVSKSENMPWYKGP----TLLEI---LET-VEIADDRSAKAFRFPVQY 230
Query: 220 V--FSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQAGDNI 277
V ++ RG G + G V+VG+ E++ + + + F L Q AG+ +
Sbjct: 231 VNRPNLDFRG--YAGTIASGSVKVGD--EVVVLPSGKTSRVKRIVTFDGELAQASAGEAV 286
Query: 278 GLLLRGTKRE-DVERGQVLAKPGSI-KPHKHFTGEIYALSKD 317
L+L E D+ RG ++ + F ++ + ++
Sbjct: 287 TLVL---ADEIDISRGDLIVAADAPPAVADAFDADVVWMDEE 325
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 137 bits (345), Expect = 5e-35
Identities = 125/432 (28%), Positives = 194/432 (44%), Gaps = 61/432 (14%)
Query: 1 MAKSKFERTKPHINVGTIGHVDHGKTTLTAAIATVLS-------KKFGGEAKSYDQ---- 49
M K K HIN+ IGHVD GK+T T + L ++F EA ++
Sbjct: 1 MGKEKV-----HINIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFEKEAAEMNKRSFK 55
Query: 50 ----IDAAPEEKARGITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILV 105
+D E+ RGITI+ A ++ET + +D PGH D+IKNMITG +Q D A+L+
Sbjct: 56 YAWVLDKLKAERERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLI 115
Query: 106 CSAADGPMP-------QTREHILLARQVGVPYIVVFLNKADMVD---DEELLELVEIEIR 155
+ G QTREH LLA +GV ++ NK D + + + E+
Sbjct: 116 IDSTTGGFEAGISKDGQTREHALLAFTLGVKQMICCCNKMDATTPKYSKARYDEIVKEVS 175
Query: 156 ELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSI-------LSLSKALDTYIPTPNRA 208
L K + + IP + S EGD + E+S +L +ALD I P R
Sbjct: 176 SYLKKVGYNPDKIPFVPIS---GFEGDN--MIERSTNLDWYKGPTLLEALDQ-INEPKRP 229
Query: 209 IDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLL 268
D LP++DV+ I G GTV GRVE G+++ G + + + T VEM + L
Sbjct: 230 SDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPG--MVVTFGPTGLTTEVKSVEMHHESL 287
Query: 269 DQGQAGDNIGLLLRGTKREDVERGQVL--AKPGSIKPHKHFTGEIYALSK--DEGGRHTP 324
+ GDN+G ++ +D++RG V +K K +FT ++ ++ G + P
Sbjct: 288 QEALPGDNVGFNVKNVAVKDLKRGYVASNSKDDPAKEAANFTSQVIIMNHPGQIGNGYAP 347
Query: 325 FFSNYRPQFYFRTTDVTGSI------ELPKNKEMVMPGDNVLITVRLINPIAMEEGL--- 375
+ + ++ I EL K + + GD + + P+ +E
Sbjct: 348 VLDCHTSHIAVKFAEILTKIDRRSGKELEKEPKFLKNGDAGFVKMIPTKPMVVETFSEYP 407
Query: 376 ---RFAIREGVQ 384
RFA+R+ Q
Sbjct: 408 PLGRFAVRDMRQ 419
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 134 bits (340), Expect = 2e-34
Identities = 127/442 (28%), Positives = 191/442 (43%), Gaps = 120/442 (27%)
Query: 7 ERTKPHINVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTA 66
E+ +P +N+G +GHVDHGKTTL A+ V + D EE RGITI
Sbjct: 4 EKVQPEVNIGMVGHVDHGKTTLVQALTGVWT-------------DRHSEELKRGITIRLG 50
Query: 67 HIE--------------YETKA------------RHYAHVDCPGHADYIKNMITGAAQMD 100
+ + Y T+ R + VD PGH + M++GAA MD
Sbjct: 51 YADATIRKCPDCEEPEAYTTEPKCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMD 110
Query: 101 GAILVCSAADG-PMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLN 159
GAILV +A + P PQT+EH++ +G+ IV+ NK D+V E LE E +I+E +
Sbjct: 111 GAILVIAANEPCPQPQTKEHLMALDIIGIKNIVIVQNKIDLVSKERALENYE-QIKEFVK 169
Query: 160 KYEFPGN---DIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLP 216
G + PII SA L + +I +L +A++ IPTP R +D +
Sbjct: 170 -----GTVAENAPIIPVSA----------LHKVNIDALIEAIEEEIPTPERDLDKPPRMY 214
Query: 217 VEDVFSISGRGT--------VVTGRVERGIVRVGEELEII-GIKDTVK---------TTC 258
V F ++ GT V+ G + +G+++VG+E+EI GIK T
Sbjct: 215 VARSFDVNKPGTPPEKLKGGVIGGSLIQGVLKVGDEIEIRPGIKVEEGGKTKWEPITTKI 274
Query: 259 TGVEMFRKLLDQGQAGDNIGLLLRGTK------REDVERGQVLAKPGSIKP-HKHFTGEI 311
+ + +++ + G GL+ GTK + D G V KPG++ P + T E+
Sbjct: 275 VSLRAGGEKVEEARPG---GLVGVGTKLDPSLTKADALAGSVAGKPGTLPPVWESLTIEV 331
Query: 312 YALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVM--------PG------D 357
+ L + G T +E K E +M G
Sbjct: 332 HLLERVVG------------------TKEELKVEPIKTGEPLMLNVGTATTVGVVTSARK 373
Query: 358 NVLITVRLINPIAMEEGLRFAI 379
+ V+L P+ EEG R AI
Sbjct: 374 DE-AEVKLKRPVCAEEGDRVAI 394
>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 = 123 bits (312), Expect = 1e-32
Identities = 65/183 (35%), Positives = 93/183 (50%), Gaps = 22/183 (12%)
Query: 17 TIGHVDHGKTTL-------TAAI------ATVLSKKFGGEAKSYDQ---IDAAPEEKARG 60
T G VD GK+TL + +I A SK G + + D +D E+ +G
Sbjct: 4 TCGSVDDGKSTLIGRLLYDSKSIFEDQLAALERSKSSGTQGEKLDLALLVDGLQAEREQG 63
Query: 61 ITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHI 120
ITI+ A+ + T R + D PGH Y +NM+TGA+ D AIL+ A G + QTR H
Sbjct: 64 ITIDVAYRYFSTPKRKFIIADTPGHEQYTRNMVTGASTADLAILLVDARKGVLEQTRRHS 123
Query: 121 LLARQVGVPYIVVFLNKADMVD-DEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLAL 179
+A +G+ ++VV +NK D+VD DEE+ E ++ + DI I S AL
Sbjct: 124 YIASLLGIRHVVVAVNKMDLVDYDEEVFEEIKADYLAFAASLGIE--DITFIPIS---AL 178
Query: 180 EGD 182
EGD
Sbjct: 179 EGD 181
>gnl|CDD|197850 smart00738, NGN, In Spt5p, this domain may confer affinity for
Spt4p. It possesses a RNP-like fold. In Spt5p, this
domain may confer affinity for Spt4p.Spt4p.
Length = 106
Score = 119 bits (299), Expect = 5e-32
Identities = 43/107 (40%), Positives = 68/107 (63%), Gaps = 1/107 (0%)
Query: 420 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPG 479
WY + + SG EK V L + LG++ K ILVPTEE+ ++++ +K V++++ FPG
Sbjct: 1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPG 60
Query: 480 YVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILKQ 526
Y+ +E ++ DE W ++ T V GF+GG +PTP+ EIE+ILK
Sbjct: 61 YIFVEADLEDEVWTAIRGTPGVRGFVGGG-GKPTPVPDDEIEKILKP 106
>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 = 116 bits (292), Expect = 7e-30
Identities = 72/223 (32%), Positives = 105/223 (47%), Gaps = 54/223 (24%)
Query: 13 INVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITI--------- 63
IN+GTIGHV HGKTTL A++ V + + E K R ITI
Sbjct: 1 INIGTIGHVAHGKTTLVKALSGVWTVRHKEELK-------------RNITIKLGYANAKI 47
Query: 64 --------NTAHIEYETKA----------RHYAHVDCPGHADYIKNMITGAAQMDGAILV 105
+ E + RH + VDCPGH + M++GAA MDGA+L+
Sbjct: 48 YKCPNCGCPRPYDTPECECPGCGGETKLVRHVSFVDCPGHEILMATMLSGAAVMDGALLL 107
Query: 106 CSAADG-PMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFP 164
+A + P PQT EH+ +G+ +I++ NK D+V +E+ LE E +I+E +
Sbjct: 108 IAANEPCPQPQTSEHLAALEIMGLKHIIILQNKIDLVKEEQALENYE-QIKEFVK--GTI 164
Query: 165 GNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNR 207
+ PII SA+L + +I L + + IPTP R
Sbjct: 165 AENAPIIPISAQL----------KYNIDVLCEYIVKKIPTPPR 197
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 117 bits (294), Expect = 4e-28
Identities = 98/354 (27%), Positives = 151/354 (42%), Gaps = 96/354 (27%)
Query: 13 INVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIEYE- 71
IN+GTIGHV HGK+T+ A++ V + +F EK R ITI + Y
Sbjct: 35 INIGTIGHVAHGKSTVVKALSGVKTVRF-------------KREKVRNITI---KLGYAN 78
Query: 72 -----------------------------------TKARHYAHVDCPGHADYIKNMITGA 96
T RH + VDCPGH + M+ GA
Sbjct: 79 AKIYKCPKCPRPTCYQSYGSSKPDNPPCPGCGHKMTLKRHVSFVDCPGHDILMATMLNGA 138
Query: 97 AQMDGAILVCSAADG-PMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIR 155
A MD A+L+ +A + P PQT EH+ + + +I++ NK D+V + + + E EIR
Sbjct: 139 AVMDAALLLIAANESCPQPQTSEHLAAVEIMKLKHIIILQNKIDLVKEAQAQDQYE-EIR 197
Query: 156 ELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFLL 215
+ ++ PII SA+L D + + + T IP P R + +
Sbjct: 198 NFVKGTI--ADNAPIIPISAQLKYNIDV----------VLEYICTQIPIPKRDLTSPPRM 245
Query: 216 ----------PVEDVFSISGRGTVVTGRVERGIVRVGEELEII-GI--KDTVKTTCTGVE 262
P ED+ ++ +G V G + +G+++VG+E+EI GI KD+ T
Sbjct: 246 IVIRSFDVNKPGEDIENL--KGGVAGGSILQGVLKVGDEIEIRPGIISKDS-GGEFTCRP 302
Query: 263 MFRKLLDQGQAGDNI-------GLLLRGTK------REDVERGQVLAKPGSIKP 303
+ +++ A +N GL+ GT R D GQVL PG +
Sbjct: 303 IRTRIVSL-FAENNELQYAVPGGLIGVGTTIDPTLTRADRLVGQVLGYPGKLPE 355
>gnl|CDD|206676 cd01889, SelB_euk, SelB, the dedicated elongation factor for
delivery of selenocysteinyl-tRNA to the ribosome. SelB
is an elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains eukaryotic SelBs and some from archaea.
Length = 192
Score = 107 bits (269), Expect = 6e-27
Identities = 59/181 (32%), Positives = 86/181 (47%), Gaps = 29/181 (16%)
Query: 13 INVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIEYET 72
+NVG +GHVD GKT+L A++ + S D P+ + RGIT++ +E
Sbjct: 1 VNVGLLGHVDSGKTSLAKALSEIASTA---------AFDKNPQSQERGITLDLGFSSFEV 51
Query: 73 KARHYAH--------------VDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTRE 118
+ VDCPGHA I+ +I GA +D +LV A G QT E
Sbjct: 52 DKPKHLEDNENPQIENYQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDAKKGIQTQTAE 111
Query: 119 HILLARQVGVPYIVVFLNKADMVDDEELLELVEI---EIRELLNKYEFPGNDIPIIKGSA 175
+++ + P IVV LNK D++ +EE +E +++ L K D PII SA
Sbjct: 112 CLVIGELLCKPLIVV-LNKIDLIPEEERKRKIEKMKKRLQKTLEKTRLK--DSPIIPVSA 168
Query: 176 K 176
K
Sbjct: 169 K 169
>gnl|CDD|239677 cd03706, mtEFTU_III, Domain III of mitochondrial EF-TU (mtEF-TU).
mtEF-TU is highly conserved and is 55-60% identical to
bacterial EF-TU. The overall structure is similar to
that observed in the Escherichia coli and Thermus
aquaticus EF-TU. However, compared with that observed in
prokaryotic EF-TU the nucleotide-binding domain (domain
I) of EF-TUmt is in a different orientation relative to
the rest of the structure. Furthermore, domain III is
followed by a short 11-amino acid extension that forms
one helical turn. This extension seems to be specific to
the mitochondrial factors and has not been observed in
any of the prokaryotic factors.
Length = 93
Score = 103 bits (258), Expect = 1e-26
Identities = 39/81 (48%), Positives = 54/81 (66%)
Query: 302 KPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVLI 361
KPH ++Y LSK EGGRH PF SN++PQ + T D I+LP KEMVMPG++ +
Sbjct: 1 KPHDKVEAQVYILSKAEGGRHKPFVSNFQPQMFSLTWDCAARIDLPPGKEMVMPGEDTKV 60
Query: 362 TVRLINPIAMEEGLRFAIREG 382
T+ L P+ +E+G RF +R+G
Sbjct: 61 TLILRRPMVLEKGQRFTLRDG 81
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 109 bits (275), Expect = 2e-25
Identities = 100/323 (30%), Positives = 152/323 (47%), Gaps = 64/323 (19%)
Query: 17 TIGHVDHGKTTL-------TAAI-----ATVL--SKKFG--GEAKSY----DQIDAAPEE 56
T G VD GK+TL T I A++ SK+ G GE D + A E
Sbjct: 32 TCGSVDDGKSTLIGRLLHDTKQIYEDQLASLHNDSKRHGTQGEKLDLALLVDGLQA---E 88
Query: 57 KARGITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQT 116
+ +GITI+ A+ + T+ R + D PGH Y +NM TGA+ D AIL+ A G + QT
Sbjct: 89 REQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTCDLAILLIDARKGVLDQT 148
Query: 117 REHILLARQVGVPYIVVFLNKADMVD-DEELLELVEIEIRELLNKYEFPGN-DIPIIKGS 174
R H +A +G+ ++VV +NK D+VD EE+ E + + + PGN DI + S
Sbjct: 149 RRHSFIATLLGIKHLVVAVNKMDLVDYSEEVFERIREDYLTFAEQ--LPGNLDIRFVPLS 206
Query: 175 AKLALEGD------------TGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVEDVF- 221
ALEGD +GP +L + L+T + F PV+ V
Sbjct: 207 ---ALEGDNVVSQSESMPWYSGP-------TLLEVLET-VDIQRVVDAQPFRFPVQYVNR 255
Query: 222 -SISGRGTVVTGRVERGIVRVGEELEII--GIKDTVKTTCTGVEMFRKLLDQGQAGDNIG 278
++ RG G + G+V+VG+ ++++ G + V T F L++ AG+ I
Sbjct: 256 PNLDFRG--YAGTLASGVVKVGDRVKVLPSGKESNVARIVT----FDGDLEEAFAGEAIT 309
Query: 279 LLLRGTKRE-DVERGQVLAKPGS 300
L+L + E D+ RG +L
Sbjct: 310 LVL---EDEIDISRGDLLVAADE 329
>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 (269), Expect = 4e-25
Identities = 97/322 (30%), Positives = 144/322 (44%), Gaps = 57/322 (17%)
Query: 17 TIGHVDHGKTTLT--------------AAIATVLSKKFGGEAKSYD---QIDAAPEEKAR 59
T G VD GK+TL A SKK G + D +D E+ +
Sbjct: 5 TCGSVDDGKSTLIGRLLHDTKQIYEDQLAALERDSKKHGTQGGEIDLALLVDGLQAEREQ 64
Query: 60 GITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREH 119
GITI+ A+ + T R + D PGH Y +NM TGA+ D A+L+ A G + QTR H
Sbjct: 65 GITIDVAYRYFSTDKRKFIVADTPGHEQYTRNMATGASTADLAVLLVDARKGVLEQTRRH 124
Query: 120 ILLARQVGVPYIVVFLNKADMVD-DEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLA 178
+A +G+ ++V+ +NK D+VD DEE+ E ++ + + F D+ I S A
Sbjct: 125 SYIASLLGIRHVVLAVNKMDLVDYDEEVFENIKKDYLAFAEQLGF--RDVTFIPLS---A 179
Query: 179 LEGD------------TGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVEDVF--SIS 224
L+GD +GP +L + L+T + A D PV+ V ++
Sbjct: 180 LKGDNVVSRSESMPWYSGP-------TLLEILET-VEVERDAQDLPLRFPVQYVNRPNLD 231
Query: 225 GRGTVVTGRVERGIVRVGEELEII--GIKDTVKTTCTGVEMFRKLLDQGQAGDNIGLLLR 282
RG G + G V VG+E+ ++ G V T F L+Q +AG + L L
Sbjct: 232 FRG--YAGTIASGSVHVGDEVVVLPSGRSSRVARIVT----FDGDLEQARAGQAVTLTL- 284
Query: 283 GTKRE-DVERGQVLAKPGSIKP 303
E D+ RG +LA S
Sbjct: 285 --DDEIDISRGDLLAAADSAPE 304
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 106 bits (268), Expect = 3e-24
Identities = 98/324 (30%), Positives = 145/324 (44%), Gaps = 69/324 (21%)
Query: 17 TIGHVDHGKTTLT---------------AAIATVLSKKFGGEAKSYDQIDAA------PE 55
T G VD GK+TL AA+ SKK G + D+ID A
Sbjct: 29 TCGSVDDGKSTLIGRLLYDSKMIFEDQLAALERD-SKKVGTQG---DEIDLALLVDGLAA 84
Query: 56 EKARGITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQ 115
E+ +GITI+ A+ + T R + D PGH Y +NM+TGA+ D AI++ A G + Q
Sbjct: 85 EREQGITIDVAYRYFATPKRKFIVADTPGHEQYTRNMVTGASTADLAIILVDARKGVLTQ 144
Query: 116 TREHILLARQVGVPYIVVFLNKADMVD-DEELLELVEIEIRELLNKYEFPGNDIPIIKGS 174
TR H +A +G+ ++V+ +NK D+VD D+E+ + + + R K D+ I S
Sbjct: 145 TRRHSFIASLLGIRHVVLAVNKMDLVDYDQEVFDEIVADYRAFAAKLGLH--DVTFIPIS 202
Query: 175 AKLALEGD------------TGPLGEQSILSLSKALDT-YIPTPNRAIDGAFLLPVEDV- 220
AL+GD GP SL + L+T I + D F PV+ V
Sbjct: 203 ---ALKGDNVVTRSARMPWYEGP-------SLLEHLETVEIASDRNLKD--FRFPVQYVN 250
Query: 221 -----FSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQAGD 275
F RG G V G+VR G+E+ ++ T + + LD+ AG
Sbjct: 251 RPNLDF----RG--FAGTVASGVVRPGDEVVVLPSGKT--SRVKRIVTPDGDLDEAFAGQ 302
Query: 276 NIGLLLRGTKREDVERGQVLAKPG 299
+ L L D+ RG +LA+
Sbjct: 303 AVTLTLA--DEIDISRGDMLARAD 324
>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 = 102 bits (256), Expect = 7e-23
Identities = 82/286 (28%), Positives = 130/286 (45%), Gaps = 44/286 (15%)
Query: 14 NVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQI-----DAAPEEKARGITI---NT 65
N+ I HVDHGKTTL A+ K G ++ + + D+ E+ RGITI NT
Sbjct: 3 NIAIIAHVDHGKTTLVDALL-----KQSGTFRANEAVAERVMDSNDLERERGITILAKNT 57
Query: 66 AHIEYETKARHYAHVDCPGHADY------IKNMITGAAQMDGAILVCSAADGPMPQTREH 119
A I Y VD PGHAD+ + M+ DG +L+ A++GPMPQTR
Sbjct: 58 A-IRY--NGTKINIVDTPGHADFGGEVERVLGMV------DGVLLLVDASEGPMPQTRFV 108
Query: 120 ILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGN----DIPIIKGSA 175
+ A ++G+ IVV +NK D E+V+ E+ +L E + D PI+ S
Sbjct: 109 LKKALELGLKPIVV-INKIDR-PSARPDEVVD-EVFDLF--AELGADDEQLDFPIVYASG 163
Query: 176 KLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVE 235
+ ++ L A+ ++P P +D + V ++ G + GRV
Sbjct: 164 RAGWASLDLDDPSDNMAPLFDAIVRHVPAPKGDLDEPLQMLVTNLDYDEYLGRIAIGRVH 223
Query: 236 RGIVRVGEELEIIGIKDTVKTTCTGVEMF------RKLLDQGQAGD 275
RG V+ G+++ ++ +D ++ R +D+ AGD
Sbjct: 224 RGTVKKGQQVALMK-RDGTIENGRISKLLGFEGLERVEIDEAGAGD 268
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 100 bits (250), Expect = 4e-22
Identities = 85/291 (29%), Positives = 131/291 (45%), Gaps = 54/291 (18%)
Query: 14 NVGTIGHVDHGKTTLTAAIATVLSKKFG----GEAKSYDQIDAAPEEKARGITI---NTA 66
N+ I HVDHGKTTL A L K+ G E + +D+ EK RGITI NTA
Sbjct: 7 NIAIIAHVDHGKTTLVDA----LLKQSGTFREREEVAERVMDSNDLEKERGITILAKNTA 62
Query: 67 HIEYETKARHYAHVDCPGHADY------IKNMITGAAQMDGAILVCSAADGPMPQTREHI 120
+ Y VD PGHAD+ + +M+ DG +L+ A++GPMPQTR +
Sbjct: 63 -VNY--NGTRINIVDTPGHADFGGEVERVLSMV------DGVLLLVDASEGPMPQTRFVL 113
Query: 121 LLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELL-----NKYEFPGNDIPIIKGS- 174
A +G+ IVV +NK D D E+V+ E+ +L + D PI+ S
Sbjct: 114 KKALALGLKPIVV-INKIDR-PDARPDEVVD-EVFDLFVELGATDEQL---DFPIVYASA 167
Query: 175 ----AKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVV 230
A L E + + L + + ++P P +D + V + S G +
Sbjct: 168 RNGTASLDPEDEADDMA-----PLFETILDHVPAPKGDLDEPLQMQVTQLDYNSYVGRIG 222
Query: 231 TGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMF------RKLLDQGQAGD 275
GR+ RG V+ +++ +I D ++ R +++ +AGD
Sbjct: 223 IGRIFRGTVKPNQQVALIK-SDGTTENGRITKLLGFLGLERIEIEEAEAGD 272
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 96.2 bits (240), Expect = 8e-21
Identities = 52/160 (32%), Positives = 78/160 (48%), Gaps = 7/160 (4%)
Query: 14 NVGTIGHVDHGKTTLTAAI--ATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIEYE 71
N+G + H+D GKTTLT I T + K G +D +E+ RGITI +A
Sbjct: 12 NIGIVAHIDAGKTTLTERILFYTGIISKIGEVHDGAATMDWMEQEQERGITITSAATTLF 71
Query: 72 TKARH-YAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPY 130
K + +D PGH D+ + +DGA++V A +G PQT A + GVP
Sbjct: 72 WKGDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVEGVEPQTETVWRQADKYGVP- 130
Query: 131 IVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPI 170
++F+NK D + + LV +++E L P +PI
Sbjct: 131 RILFVNKMDRLGAD--FYLVVEQLKERLGANPVPVQ-LPI 167
>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 = 84.5 bits (210), Expect = 5e-20
Identities = 32/85 (37%), Positives = 56/85 (65%), Gaps = 2/85 (2%)
Query: 213 FLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQ 272
F LP++ VF++ G+GTVVTG V G V+VG+++EI+ + + + +++ K +++ +
Sbjct: 1 FRLPIDRVFTVKGQGTVVTGTVLSGSVKVGDKVEILPLGEETRV--RSIQVHGKDVEEAK 58
Query: 273 AGDNIGLLLRGTKREDVERGQVLAK 297
AGD + L L G +D+ERG VL+
Sbjct: 59 AGDRVALNLTGVDAKDLERGDVLSS 83
>gnl|CDD|216991 pfam02357, NusG, Transcription termination factor nusG.
Length = 90
Score = 84.7 bits (210), Expect = 5e-20
Identities = 35/99 (35%), Positives = 59/99 (59%), Gaps = 12/99 (12%)
Query: 419 KRWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKN-QKSVIKKRFF 477
K+WYV+ + SG EK V L +++ +P EE+V+V+KN +K +++ F
Sbjct: 1 KKWYVLRTKSGQEKKVAENL---------ERQGIESFLPPEEVVEVRKNGRKKKVERPLF 51
Query: 478 PGYVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPIS 516
PGYV + M++ DE+W +++T VTGF+G +P P+
Sbjct: 52 PGYVFVRMDLNDETWA-IRSTPGVTGFVGFGG-KPAPVP 88
>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 = 86.5 bits (215), Expect = 1e-19
Identities = 67/208 (32%), Positives = 100/208 (48%), Gaps = 33/208 (15%)
Query: 14 NVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQI-----DAAPEEKARGITI---NT 65
N+ I HVDHGKTTL A+ K G + +++ D+ E+ RGITI NT
Sbjct: 4 NIAIIAHVDHGKTTLVDALL-----KQSGTFRENEEVGERVMDSNDLERERGITILAKNT 58
Query: 66 AHIEYETKARHYAHVDCPGHADY------IKNMITGAAQMDGAILVCSAADGPMPQTREH 119
A I Y K +D PGHAD+ + +M+ DG +L+ A++GPMPQTR
Sbjct: 59 A-ITY--KDTKINIIDTPGHADFGGEVERVLSMV------DGVLLLVDASEGPMPQTRFV 109
Query: 120 ILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGN--DIPIIKGSAKL 177
+ A + G+ IVV +NK D D E+V+ E+ +L + D PI+ SAK
Sbjct: 110 LKKALEAGLKPIVV-INKIDR-PDARPEEVVD-EVFDLFLELNATDEQLDFPIVYASAKN 166
Query: 178 ALEGDTGPLGEQSILSLSKALDTYIPTP 205
+ + L + + ++P P
Sbjct: 167 GWASLNLDDPSEDLDPLFETIIEHVPAP 194
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 85.6 bits (213), Expect = 2e-19
Identities = 63/164 (38%), Positives = 76/164 (46%), Gaps = 26/164 (15%)
Query: 19 GHVDHGKTTLTAAI--ATVLSKKFGGEAKSYDQIDAAPEEKARGIT--INTAHIEYETKA 74
GHVDHGKTTL I V AA E A GIT I + + K
Sbjct: 7 GHVDHGKTTLLDKIRKTNV----------------AAGE--AGGITQHIGAYQVPIDVKI 48
Query: 75 RHYAHVDCPGHADYIKNMITGAAQM-DGAILVCSAADGPMPQTREHILLARQVGVPYIVV 133
+D PGH + NM A + D AILV +A DG MPQT E I A+ VP I+V
Sbjct: 49 PGITFIDTPGHEAF-TNMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAANVP-IIV 106
Query: 134 FLNKAD-MVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAK 176
+NK D E E V+ E+ EL E G D+ I+ SAK
Sbjct: 107 AINKIDKPYGTEADPERVKNELSELGLVGEEWGGDVSIVPISAK 150
>gnl|CDD|240515 cd06091, KOW_NusG, NusG contains an NGN domain at its N-terminus
and KOW motif at its C-terminus. KOW_NusG motif is one
of the two domains of N-Utilization Substance G (NusG) a
transcription elongation and Rho-termination factor in
bacteria and archaea. KOW domain is known as an
RNA-binding motif that is shared so far among some
families of ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. The eukaryotic ortholog of NusG
is Spt5 with multiple KOW motifs at its C-terminus.
Length = 56
Score = 81.0 bits (201), Expect = 3e-19
Identities = 28/56 (50%), Positives = 42/56 (75%)
Query: 537 KILYQLDELVRIKDGPFTDFSGNIEEVNYEKSRVRVSVTIFGRATPVELEFNQVEK 592
++ +++ + VRI GPF F G +EE++ EK +V+V V +FGR TPVEL+F+QVEK
Sbjct: 1 EVDFEVGDTVRIISGPFAGFEGKVEEIDEEKGKVKVLVEMFGRETPVELDFDQVEK 56
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 89.5 bits (223), Expect = 1e-18
Identities = 61/168 (36%), Positives = 93/168 (55%), Gaps = 28/168 (16%)
Query: 14 NVGTIGHVDHGKTTLT---AAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHI-- 68
N+G I H+DHGKTTL+ A A ++S++ GE + +D EE+ARGITI A++
Sbjct: 22 NIGIIAHIDHGKTTLSDNLLAGAGMISEELAGEQLA---LDFDEEEQARGITIKAANVSM 78
Query: 69 --EYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQV 126
EYE K +D PGH D+ ++ +DGAI+V A +G MPQT E +L RQ
Sbjct: 79 VHEYEGKEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVDAVEGVMPQT-ETVL--RQA 135
Query: 127 ---GV-PYIVVFLNKAD------MVDDEELLE-LVEI--EIRELLNKY 161
V P V+F+NK D + +E+ + L++I ++ +L+
Sbjct: 136 LRERVKP--VLFINKVDRLIKELKLTPQEMQQRLLKIIKDVNKLIKGM 181
Score = 34.1 bits (79), Expect = 0.22
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 3/53 (5%)
Query: 227 GTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEM--FRKLLDQGQAGDNI 277
G V TGRV G +R G+E+ ++G K + G+ M R+ +++ AG NI
Sbjct: 305 GEVATGRVFSGTLRKGQEVYLVGAKKKNRVQQVGIYMGPEREEVEEIPAG-NI 356
>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 = 82.7 bits (205), Expect = 5e-18
Identities = 46/140 (32%), Positives = 70/140 (50%), Gaps = 20/140 (14%)
Query: 14 NVGTIGHVDHGKTTLT---AAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHI-- 68
N+ I HVDHGKTTL+ A A ++S+K G+A+ +D +E+ RGITI ++ I
Sbjct: 2 NICIIAHVDHGKTTLSDSLLASAGIISEKLAGKARY---LDTREDEQERGITIKSSAISL 58
Query: 69 EYETKARHYAH-------VDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHIL 121
+E + +D PGH D+ + DGA++V A +G QT +
Sbjct: 59 YFEYEEEKMDGNDYLINLIDSPGHVDFSSEVTAALRLTDGALVVVDAVEGVCVQT--ETV 116
Query: 122 LARQVGVPYI--VVFLNKAD 139
L RQ + V+ +NK D
Sbjct: 117 L-RQALEERVKPVLVINKID 135
>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 = 78.1 bits (193), Expect = 5e-18
Identities = 27/70 (38%), Positives = 39/70 (55%)
Query: 227 GTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKR 286
GTV TGRVE G ++ G+++ I K T +EMF L + AG N G++L G
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGIGL 60
Query: 287 EDVERGQVLA 296
+D++RG L
Sbjct: 61 KDIKRGDTLT 70
>gnl|CDD|206731 cd04168, TetM_like, Tet(M)-like family includes Tet(M), Tet(O),
Tet(W), and OtrA, containing tetracycline resistant
proteins. Tet(M), Tet(O), Tet(W), and OtrA are
tetracycline resistance genes found in Gram-positive and
Gram-negative bacteria. Tetracyclines inhibit protein
synthesis by preventing aminoacyl-tRNA from binding to
the ribosomal acceptor site. This subfamily contains
tetracycline resistance proteins that function through
ribosomal protection and are typically found on mobile
genetic elements, such as transposons or plasmids, and
are often conjugative. Ribosomal protection proteins are
homologous to the elongation factors EF-Tu and EF-G.
EF-G and Tet(M) compete for binding on the ribosomes.
Tet(M) has a higher affinity than EF-G, suggesting these
two proteins may have overlapping binding sites and that
Tet(M) must be released before EF-G can bind. Tet(M) and
Tet(O) have been shown to have ribosome-dependent GTPase
activity. These proteins are part of the GTP translation
factor family, which includes EF-G, EF-Tu, EF2, LepA,
and SelB.
Length = 237
Score = 82.3 bits (204), Expect = 1e-17
Identities = 57/174 (32%), Positives = 89/174 (51%), Gaps = 12/174 (6%)
Query: 14 NVGTIGHVDHGKTTLTAAI--ATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIEYE 71
N+G + HVD GKTTLT ++ + ++ G K + D+ E+ RGITI +A ++
Sbjct: 1 NIGILAHVDAGKTTLTESLLYTSGAIRELGSVDKGTTRTDSMELERQRGITIFSAVASFQ 60
Query: 72 TKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYI 131
+ +D PGH D+I + + +DGAILV SA +G QTR L R++ +P I
Sbjct: 61 WEDTKVNIIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTRILFRLLRKLNIPTI 120
Query: 132 VVFLNKADM--VDDEELLELVEIEIRELLNKYEFPGND---IPIIKGSAKLALE 180
+F+NK D D E++ + EI+E L+ P P I + + E
Sbjct: 121 -IFVNKIDRAGADLEKVYQ----EIKEKLSPDIVPMQKVGLYPNICDTNNIDDE 169
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 85.2 bits (212), Expect = 2e-17
Identities = 47/128 (36%), Positives = 61/128 (47%), Gaps = 11/128 (8%)
Query: 18 IGHVDHGKTTLTAAI--ATVLSKKFG----GEAKSYDQIDAAPEEKARGITINTAHIEYE 71
+GH GKTTLT AI T + G G D PEE+ RGI+I +A E
Sbjct: 1 VGHSGAGKTTLTEAILFYTGAIHRIGEVEDGTTTM----DFMPEERERGISITSAATTCE 56
Query: 72 TKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYI 131
K +D PGH D+ + +DGA++V A G PQT A + GVP I
Sbjct: 57 WKGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGGVEPQTETVWRQAEKYGVPRI 116
Query: 132 VVFLNKAD 139
+F+NK D
Sbjct: 117 -IFVNKMD 123
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 85.1 bits (210), Expect = 2e-17
Identities = 78/274 (28%), Positives = 127/274 (46%), Gaps = 12/274 (4%)
Query: 14 NVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQI-DAAPEEKARGITINTAHIEYET 72
N+ I HVDHGKTTL + S F A++ +++ D+ EK RGITI + +
Sbjct: 7 NIAIIAHVDHGKTTLVDKLLQ-QSGTFDSRAETQERVMDSNDLEKERGITILAKNTAIKW 65
Query: 73 KARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIV 132
VD PGHAD+ + + +D +LV A DGPMPQTR A G+ IV
Sbjct: 66 NDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPIV 125
Query: 133 VFLNKADMVDDEELLELVEIEIRELLNKYEFPGN--DIPIIKGSAKLALEGDTGPLGEQS 190
V +NK D + V ++ +L + D PI+ SA + G +
Sbjct: 126 V-INKVDRPGARP--DWVVDQVFDLFVNLDATDEQLDFPIVYASALNGIAGLDHEDMAED 182
Query: 191 ILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGI 250
+ L +A+ ++P P+ +DG F + + + S G + GR++RG V+ +++ II
Sbjct: 183 MTPLYQAIVDHVPAPDVDLDGPFQMQISQLDYNSYVGVIGIGRIKRGKVKPNQQVTIIDS 242
Query: 251 KDTVKT-----TCTGVEMFRKLLDQGQAGDNIGL 279
+ + + + R D +AGD + +
Sbjct: 243 EGKTRNAKVGKVLGHLGLERIETDLAEAGDIVAI 276
>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 = 76.6 bits (189), Expect = 3e-17
Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 2/85 (2%)
Query: 213 FLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQ 272
V VF GRGTV TGRVE G ++ G+++ + VK ++ F+ +D+
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRFKGEVDEAV 60
Query: 273 AGDNIGLLLRGTKREDVERGQVLAK 297
AGD +G++L+ ++D++ G L
Sbjct: 61 AGDIVGIVLKD--KDDIKIGDTLTD 83
>gnl|CDD|193574 cd08000, NGN, N-Utilization Substance G (NusG) N-terminal (NGN)
domain Superfamily. The N-Utilization Substance G
(NusG) and its eukaryotic homolog Spt5 are involved in
transcription elongation and termination. NusG contains
an NGN domain at its N-terminus and Kyrpides Ouzounis
and Woese (KOW) repeats at its C-terminus in bacteria
and archaea. The eukaryotic ortholog, Spt5, is a large
protein composed of an acidic N-terminus, an NGN domain,
and multiple KOW motifs at its C-terminus. Spt5 forms a
Spt4-Spt5 complex that is an essential RNA Polymerase II
elongation factor. NusG was originally discovered as an
N-dependent antitermination enhancing activity in
Escherichia coli and has a variety of functions, such as
being involved in RNA polymerase elongation and
Rho-termination in bacteria. Orthologs of the NusG gene
exist in all bacteria, but its functions and
requirements are different. The diverse activities
suggest that, after diverging from a common ancestor,
NusG proteins became specialized in different bacteria.
Length = 99
Score = 76.2 bits (188), Expect = 5e-17
Identities = 33/104 (31%), Positives = 58/104 (55%), Gaps = 6/104 (5%)
Query: 421 WYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPGY 480
WYV+ +G E+ V+ KL+E+ + + VP +E+ + K+ + + K FPGY
Sbjct: 2 WYVLFVKTGREEKVE-KLLEKRFEANDIE----AFVPKKEVPERKRGKIEEVIKPLFPGY 56
Query: 481 VLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEIL 524
V +E +++ E + L++ V G +G P+P+S +EIE IL
Sbjct: 57 VFVETDLSPELYELIREVPGVIGILGNG-EEPSPVSDEEIEMIL 99
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 81.9 bits (203), Expect = 3e-16
Identities = 53/165 (32%), Positives = 80/165 (48%), Gaps = 10/165 (6%)
Query: 14 NVGTIGHVDHGKTTLTAAI---ATVLSKKFGGEAKSYDQI-DAAPEEKARGITINTAHIE 69
N+G + H+D GKTTLT I + K GE + + D P+E+ RGITI +A
Sbjct: 10 NIGILAHIDAGKTTLTERILFYTGKIHKM--GEVEDGTTVTDWMPQEQERGITIESAATS 67
Query: 70 YETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVP 129
+ +D PGH D+ + +DGA++V A G PQT A + G+P
Sbjct: 68 CDWDNHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDAVTGVQPQTETVWRQADRYGIP 127
Query: 130 YIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGS 174
++F+NK D V +L +++E +I E K P +PI
Sbjct: 128 -RLIFINKMDRVGA-DLFKVLE-DIEERFGKRPLPLQ-LPIGSED 168
>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 = 78.4 bits (194), Expect = 4e-16
Identities = 38/130 (29%), Positives = 61/130 (46%), Gaps = 7/130 (5%)
Query: 14 NVGTIGHVDHGKTTLTAAI--ATVLSKKFGGEAKSYDQIDAAPEEKARGITINT--AHIE 69
N+ +GH GKTTL A+ AT + G D PEEK R ++I T A +E
Sbjct: 1 NIALVGHSGSGKTTLAEALLYATGAIDRLGRVEDGNTVSDYDPEEKKRKMSIETSVAPLE 60
Query: 70 YETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVP 129
+ + +D PG+AD++ ++ +D A++V A G T + +P
Sbjct: 61 WNGH-KINL-IDTPGYADFVGETLSALRAVDAALIVVEAQSGVEVGTEKVWEFLDDAKLP 118
Query: 130 YIVVFLNKAD 139
++F+NK D
Sbjct: 119 -RIIFINKMD 127
>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 = 79.9 bits (197), Expect = 1e-15
Identities = 60/167 (35%), Positives = 90/167 (53%), Gaps = 18/167 (10%)
Query: 1 MAKSKFERTKPHINVGTIGHVDHGKTTLT---AAIATVLSKKFGGEAKSYDQIDAAPEEK 57
M K KF R N+G + H+DHGKTTL+ A A ++S++ G+ +D +E+
Sbjct: 13 MWKPKFIR-----NIGIVAHIDHGKTTLSDNLLAGAGMISEELAGQQLY---LDFDEQEQ 64
Query: 58 ARGITINTAHI----EYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPM 113
RGITIN A++ EYE +D PGH D+ ++ +DGAI+V A +G M
Sbjct: 65 ERGITINAANVSMVHEYEGNEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVCAVEGVM 124
Query: 114 PQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNK 160
PQT + A + V V+F+NK D + +E L+L E++E K
Sbjct: 125 PQTETVLRQALKENVK-PVLFINKVDRLINE--LKLTPQELQERFIK 168
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 78.4 bits (194), Expect = 3e-15
Identities = 77/240 (32%), Positives = 99/240 (41%), Gaps = 54/240 (22%)
Query: 19 GHVDHGKTTLTAAI--ATVLSKKFGGEAKSYDQ-IDA----APEEKARGITINTAHIEYE 71
GHVDHGKTTL I V + + GG Q I A K GIT
Sbjct: 12 GHVDHGKTTLLDKIRKTNVAAGEAGG----ITQHIGAYQVPLDVIKIPGITF-------- 59
Query: 72 TKARHYAHVDCPGHADYIKNMIT-GAAQMDGAILVCSAADGPMPQTREHILLARQVGVPY 130
+D PGH M GA+ D AILV +A DG MPQT E I A+ GVP
Sbjct: 60 --------IDTPGHE-AFTAMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAAGVP- 109
Query: 131 IVVFLNKADMVDDEELLELVEIEIRELLNKYEFP----GNDIPIIKGSAKLALEGDTG-- 184
IVV +NK D + + V+ E L +Y G D+ + SAK TG
Sbjct: 110 IVVAINKIDKPEAN--PDKVKQE----LQEYGLVPEEWGGDVIFVPVSAK------TGEG 157
Query: 185 -PLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGE 243
+ IL L++ L+ A G + D G G V T V+ G ++ G+
Sbjct: 158 IDELLELILLLAEVLELKANPEGPAR-GTVIEVKLD----KGLGPVATVIVQDGTLKKGD 212
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 77.5 bits (191), Expect = 6e-15
Identities = 73/234 (31%), Positives = 101/234 (43%), Gaps = 36/234 (15%)
Query: 15 VGTIGHVDHGKTTLTAAI--ATVLSKKFGGEAKSYDQIDAAPEEKARGIT--INTAHIEY 70
V +GHVDHGKT+L +I V + GG IT I H+E
Sbjct: 90 VTIMGHVDHGKTSLLDSIRKTKVAQGEAGG------------------ITQHIGAYHVEN 131
Query: 71 ETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPY 130
E + +D PGH + GA D +LV +A DG MPQT E I A+ VP
Sbjct: 132 EDG-KMITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVP- 189
Query: 131 IVVFLNKADMVDDEELLELVEIEIREL-LNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQ 189
I+V +NK D + + V+ E+ E L ++ G+ I + SA +G L
Sbjct: 190 IIVAINKIDKPEAN--PDRVKQELSEYGLVPEDWGGDTI-FVPVSALTG-DGIDELL--D 243
Query: 190 SILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGE 243
IL S+ + PN G V + GRG V T V+ G +RVG+
Sbjct: 244 MILLQSEVEE-LKANPNGQASGV----VIEAQLDKGRGPVATVLVQSGTLRVGD 292
>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 = 69.5 bits (171), Expect = 1e-14
Identities = 31/88 (35%), Positives = 50/88 (56%), Gaps = 6/88 (6%)
Query: 209 IDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEII--GIKDTVKTTCTGVEMFRK 266
D LP++DV+ I G GTV GRVE G+++ G + G+ VK+ VEM +
Sbjct: 1 TDKPLRLPIQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGVTGEVKS----VEMHHE 56
Query: 267 LLDQGQAGDNIGLLLRGTKREDVERGQV 294
L++ GDN+G ++ ++D++RG V
Sbjct: 57 PLEEALPGDNVGFNVKNVSKKDIKRGDV 84
>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 = 68.0 bits (167), Expect = 1e-12
Identities = 50/152 (32%), Positives = 76/152 (50%), Gaps = 17/152 (11%)
Query: 18 IGHVDHGKTTLTAAIA----------TVLSKKFGGEAKSYDQIDAAPEEKARGITINTAH 67
I H D GKTTLT + V ++K A S D EK RGI++ ++
Sbjct: 8 ISHPDAGKTTLTEKLLLFGGAIQEAGAVKARKSRKHATS----DWMEIEKQRGISVTSSV 63
Query: 68 IEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVG 127
+++E K +D PGH D+ ++ +D A++V AA G PQTR+ + R G
Sbjct: 64 MQFEYKGCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLRG 123
Query: 128 VPYIVVFLNKADMVDDEELLELVEIEIRELLN 159
+P I+ F+NK D + + LEL++ EI L
Sbjct: 124 IP-IITFINKLDR-EGRDPLELLD-EIENELG 152
>gnl|CDD|233655 TIGR01956, NusG_myco, NusG family protein. This model represents a
family of Mycoplasma proteins orthologous to the
bacterial transcription termination/antitermination
factor NusG. These sequences from Mycoplasma are notably
diverged (long branches in a Neighbor-joining
phylogenetic tree) from the bacterial species. And
although NusA and ribosomal protein S10 (NusE) appear to
be present, NusB may be absent in Mycoplasmas calling
into question whether these species have a functional
Nus system including this family as a member.
Length = 258
Score = 67.7 bits (165), Expect = 1e-12
Identities = 44/205 (21%), Positives = 87/205 (42%), Gaps = 35/205 (17%)
Query: 420 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVK-------------K 466
+WY+ + +G E V + ++ LG++ + E ++ K K
Sbjct: 1 QWYIATTINGNEDEVIENIKAKVRALGLENYISDFKILKEREIEEKVFEPKNGQAPRSMK 60
Query: 467 NQKS---------------VIKKRFFPGYVLIEMEMTDESWHLVKNTKKVTGFIG--GKS 509
N + + +K + GY+ I+M MT+++W L++NT+ VTG +G GK
Sbjct: 61 NTATTKWETLDETKYKKTKISEKNKYNGYIYIKMIMTEDAWFLIRNTENVTGLVGSSGKG 120
Query: 510 NRPTPISSKEIEEILKQIKKGVE-KPRPKILYQLDELVRIKDGPFTDFSGNIEEVNYEKS 568
+P PIS+ + ++ KG+ + ++L +V +++ F + I + K
Sbjct: 121 AKPIPISADADKL---KMLKGISENTKKRVLVTNTAIVEMEENKFDEKCQYILKHKQVKP 177
Query: 569 RVRVSVTIFG-RATPVELEFNQVEK 592
V+ G + EF V+
Sbjct: 178 EAIAQVSESGEIIDEIVEEFQLVDN 202
>gnl|CDD|131010 TIGR01955, RfaH, transcriptional activator RfaH. This model
represents the transcriptional activator protein, RfaH.
This protein is most closely related to the
transcriptional termination/antitermination protein NusG
(TIGR00922) and contains the KOW motif (pfam00467). This
protein appears to be limited to the gamma
proteobacteria. In E. coli, this gene appears to control
the expression of haemolysin, sex factor and
lipopolysaccharide genes [Transcription, Transcription
factors].
Length = 159
Score = 65.6 bits (160), Expect = 2e-12
Identities = 41/173 (23%), Positives = 74/173 (42%), Gaps = 16/173 (9%)
Query: 421 WYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPGY 480
WY+++ E+ Q L ER +P + + + ++ + + FP Y
Sbjct: 1 WYLLYCKPRQEQRAQEHL-ERQAV--------ECYLPMITVEKIVRGKRQAVSEPLFPNY 51
Query: 481 VLIEMEMTDESWHLVKNTKKVTGFI--GGKSNRPTPISSKEIEEILKQIKKGVEKPRPKI 538
+ IE + +SW +++T+ V+ F+ GG P P+ I ++ +Q + P
Sbjct: 52 LFIEFDPEVDSWTTIRSTRGVSRFVRFGGH---PAPVPDDLIHQL-RQYEPKDSVPPATT 107
Query: 539 LYQLDELVRIKDGPFTDFSGNIEEVNYEKSRVRVSVTIFGRATPVELEFNQVE 591
L + VRI DG F F E + EK R + + + G+ V + VE
Sbjct: 108 LPYKGDKVRITDGAFAGFEAIFLEPDGEK-RSMLLLNMIGKQIKVSVPNTSVE 159
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 67.4 bits (165), Expect = 1e-11
Identities = 51/152 (33%), Positives = 79/152 (51%), Gaps = 27/152 (17%)
Query: 14 NVGTIGHVDHGKTTLTAAI---ATVLSKKFGGEAKSYDQIDAAPEEKARGITINTA---- 66
N+ I HVDHGK+TLT ++ A ++S K G+A+ D +E+ RGITI +
Sbjct: 21 NMSVIAHVDHGKSTLTDSLVCKAGIISSKNAGDARF---TDTRADEQERGITIKSTGISL 77
Query: 67 HIEYETKARHYAH------VDCPGHADYIKNMITGAAQM-DGAILVCSAADGPMPQTREH 119
+ E++ + +D PGH D+ + +T A ++ DGA++V +G QT E
Sbjct: 78 YYEHDLEDGDDKQPFLINLIDSPGHVDF-SSEVTAALRVTDGALVVVDCVEGVCVQT-ET 135
Query: 120 ILLARQVGVPYI--VVFLNKADMVDDEELLEL 149
+L RQ I V+F+NK D +LEL
Sbjct: 136 VL--RQALQERIRPVLFINKVDRA----ILEL 161
>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 = 65.2 bits (160), Expect = 1e-11
Identities = 49/136 (36%), Positives = 63/136 (46%), Gaps = 19/136 (13%)
Query: 14 NVGTIGHVDHGKTTLTAAIA--TVLSKKFG----GEAKSYDQIDAAPEEKARGITINTAH 67
N+G I H+D GKTT T I T K G G A +D +E+ RGITI +A
Sbjct: 1 NIGIIAHIDAGKTTTTERILYYTGRIHKIGEVHGGGAT----MDWMEQERERGITIQSAA 56
Query: 68 IEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQT----REHILLA 123
K +D PGH D+ + +DGA+ V A G PQT R+ A
Sbjct: 57 TTCFWKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVQPQTETVWRQ----A 112
Query: 124 RQVGVPYIVVFLNKAD 139
+ GVP I F+NK D
Sbjct: 113 DRYGVPRI-AFVNKMD 127
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G [Protein synthesis, Translation factors].
Length = 689
Score = 65.6 bits (160), Expect = 3e-11
Identities = 44/128 (34%), Positives = 57/128 (44%), Gaps = 3/128 (2%)
Query: 14 NVGTIGHVDHGKTTLTAAIA--TVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIEYE 71
N+G H+D GKTT T I T K G +D +EK RGITI +A
Sbjct: 12 NIGISAHIDAGKTTTTERILFYTGRIHKIGEVHDGAATMDWMEQEKERGITITSAATTVF 71
Query: 72 TKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYI 131
K +D PGH D+ + +DGA+ V A G PQ+ A + VP I
Sbjct: 72 WKGHRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAVGGVQPQSETVWRQANRYEVPRI 131
Query: 132 VVFLNKAD 139
F+NK D
Sbjct: 132 -AFVNKMD 138
>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 = 61.1 bits (149), Expect = 1e-10
Identities = 39/136 (28%), Positives = 61/136 (44%), Gaps = 13/136 (9%)
Query: 14 NVGTIGHVDHGKTTLT-----AAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHI 68
NV GH+ HGKT+L S K G + Y D +E+ RGI+I + I
Sbjct: 2 NVCIAGHLHHGKTSLLDMLIEQTHKRTPSVKLGWKPLRY--TDTRKDEQERGISIKSNPI 59
Query: 69 -EYETKARHYAHV----DCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLA 123
++ +++ D PGH +++ + DG +LV +G T I A
Sbjct: 60 SLVLEDSKGKSYLINIIDTPGHVNFMDEVAAALRLCDGVVLVVDVVEGLTSVTERLIRHA 119
Query: 124 RQVGVPYIVVFLNKAD 139
Q G+P ++V +NK D
Sbjct: 120 IQEGLPMVLV-INKID 134
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 64.1 bits (157), Expect = 1e-10
Identities = 50/134 (37%), Positives = 61/134 (45%), Gaps = 38/134 (28%)
Query: 17 TI-GHVDHGKTTLTAAI--ATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHI---EY 70
TI GHVDHGKT+L AI V + + GG I T HI +
Sbjct: 253 TIMGHVDHGKTSLLDAIRKTNVAAGEAGG--------------------I-TQHIGAYQV 291
Query: 71 ETKARHYAHVDCPGHADYIKNMIT-----GAAQMDGAILVCSAADGPMPQTREHILLARQ 125
ET +D PGH + T GA D +LV +A DG MPQT E I A+
Sbjct: 292 ETNGGKITFLDTPGHEAF-----TAMRARGAQVTDIVVLVVAADDGVMPQTIEAINHAKA 346
Query: 126 VGVPYIVVFLNKAD 139
GVP I+V +NK D
Sbjct: 347 AGVP-IIVAINKID 359
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 63.0 bits (154), Expect = 2e-10
Identities = 51/149 (34%), Positives = 74/149 (49%), Gaps = 17/149 (11%)
Query: 18 IGHVDHGKTTLT-------AAIA---TVLSKKFGGEAKSYDQIDAAPEEKARGITINTAH 67
I H D GKTTLT AI TV +K G AKS D EK RGI++ ++
Sbjct: 18 ISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGKHAKS----DWMEIEKQRGISVTSSV 73
Query: 68 IEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVG 127
++++ +D PGH D+ ++ +D A++V AA G PQT + + R
Sbjct: 74 MQFDYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIEPQTLKLFEVCRLRD 133
Query: 128 VPYIVVFLNKADMV--DDEELLELVEIEI 154
+P I F+NK D D ELL+ +E E+
Sbjct: 134 IP-IFTFINKLDREGRDPLELLDEIEEEL 161
>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 = 56.7 bits (137), Expect = 5e-10
Identities = 28/98 (28%), Positives = 38/98 (38%), Gaps = 22/98 (22%)
Query: 302 KPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELP-----------KNK 350
+ F EIY L E P Y+P T V G I K
Sbjct: 1 QAVDKFVAEIYVLDHPE-----PLSPGYKPVLNVGTAHVPGRIAKLLSKVDGKTEEKKPP 55
Query: 351 EMVMPGDNVLITVRLINPIAME------EGLRFAIREG 382
E + G+ ++ V L P+A+E EG RFA+R+G
Sbjct: 56 EFLKSGERGIVEVELQKPVALETFSENQEGGRFALRDG 93
>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 = 61.8 bits (150), Expect = 5e-10
Identities = 47/151 (31%), Positives = 72/151 (47%), Gaps = 11/151 (7%)
Query: 14 NVGTIGHVDHGKTTLT-------AAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTA 66
I H D GKTT+T AI T + K G + D EK RGI+I T+
Sbjct: 13 TFAIISHPDAGKTTITEKVLLYGGAIQTAGAVKGRGSQRHAKS-DWMEMEKQRGISITTS 71
Query: 67 HIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQV 126
+++ + +D PGH D+ ++ +D ++V AA G +TR+ + + R
Sbjct: 72 VMQFPYRDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLMEVTRLR 131
Query: 127 GVPYIVVFLNKAD--MVDDEELLELVEIEIR 155
P I F+NK D + D ELL+ VE E++
Sbjct: 132 DTP-IFTFMNKLDRDIRDPLELLDEVENELK 161
>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 = 61.6 bits (150), Expect = 7e-10
Identities = 65/245 (26%), Positives = 108/245 (44%), Gaps = 32/245 (13%)
Query: 14 NVGTIGHVDHGKTTLTAAI----ATVLSKKFGGEAKSYDQIDAAPEEKARGITI--NTAH 67
N I H+DHGK+TL + + ++ + D +D E+ RGITI
Sbjct: 5 NFSIIAHIDHGKSTLADRLLEYTGAISEREM--REQVLDSMDL---ERERGITIKAQAVR 59
Query: 68 IEYETKARH---YAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLAR 124
+ Y+ K +D PGH D+ + A +GA+L+ AA G QT ++ LA
Sbjct: 60 LNYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLLVDAAQGIEAQTLANVYLAL 119
Query: 125 QVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGDTG 184
+ + I V +NK D+ + E V+ EI E++ ++ + SAK TG
Sbjct: 120 ENDLEIIPV-INKIDLPSAD--PERVKKEIEEVIG---LDASEAILA--SAK------TG 165
Query: 185 PLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEE 244
+G + IL +A+ +P P D + D + RG V RV G ++ G++
Sbjct: 166 -IGIEEIL---EAIVKRVPPPKGDPDAPLKALIFDSHYDNYRGVVALVRVFEGTIKPGDK 221
Query: 245 LEIIG 249
+ +
Sbjct: 222 IRFMS 226
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 61.0 bits (148), Expect = 1e-09
Identities = 55/169 (32%), Positives = 72/169 (42%), Gaps = 31/169 (18%)
Query: 15 VGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTA----HIEY 70
V +GHVDHGKTTL I + A +E A GIT EY
Sbjct: 247 VTILGHVDHGKTTLLDKIR---------------KTQIAQKE-AGGITQKIGAYEVEFEY 290
Query: 71 ETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPY 130
+ + + +D PGH + GA D AIL+ +A DG PQT E I + VP
Sbjct: 291 KDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANVP- 349
Query: 131 IVVFLNKADMVDDEELLELVEIEIRELLNKYEFP----GNDIPIIKGSA 175
I+V +NK D + I++ L KY G D P+I SA
Sbjct: 350 IIVAINKIDKANAN------TERIKQQLAKYNLIPEKWGGDTPMIPISA 392
>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 = 57.5 bits (140), Expect = 1e-09
Identities = 60/200 (30%), Positives = 92/200 (46%), Gaps = 30/200 (15%)
Query: 14 NVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSY--DQI-DAAPEEKARGITI--NTAHI 68
N I H+DHGK+TL A L + G ++ +Q+ D+ E+ RGITI +
Sbjct: 2 NFSIIAHIDHGKSTL----ADRLLELTGTVSEREMKEQVLDSMDLERERGITIKAQAVRL 57
Query: 69 EYETKARH---YAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQ 125
Y+ K +D PGH D+ + A +GA+LV A G QT + LA +
Sbjct: 58 FYKAKDGEEYLLNLIDTPGHVDFSYEVSRSLAACEGALLVVDATQGVEAQTLANFYLALE 117
Query: 126 VGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGP 185
+ I V +NK D+ + + V+ EI ++L ++ I SAK TG
Sbjct: 118 NNLEIIPV-INKIDLPAAD--PDRVKQEIEDVL---GLDASE--AILVSAK------TG- 162
Query: 186 LGEQSILSLSKALDTYIPTP 205
LG + +L +A+ IP P
Sbjct: 163 LGVEDLL---EAIVERIPPP 179
>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 = 57.2 bits (139), Expect = 1e-09
Identities = 54/206 (26%), Positives = 82/206 (39%), Gaps = 44/206 (21%)
Query: 14 NVGTIGHVDHGKTTLTAAI--ATVLSKKFGGEAKSYDQIDAAPEEKARGITINTA---HI 68
+ +G GK+TL A+ VL P G+T TA +
Sbjct: 2 LLAVVGEFSAGKSTLLNALLGEEVL-----------------PT----GVTPTTAVITVL 40
Query: 69 EYETKARHYAHVDCPG-------HADYIKNMITGAAQMDGAILVCSAADGPMPQT-REHI 120
Y + VD PG H + ++ + + D I V SA D P+ ++ RE +
Sbjct: 41 RYGLL-KGVVLVDTPGLNSTIEHHTEITESFL---PRADAVIFVLSA-DQPLTESEREFL 95
Query: 121 LLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALE 180
+ I LNK D++ +EEL E++E RE L E G + I SAK ALE
Sbjct: 96 KEILKWSGKKIFFVLNKIDLLSEEELEEVLE-YSREELGVLELGGGEPRIFPVSAKEALE 154
Query: 181 G----DTGPLGEQSILSLSKALDTYI 202
D L + L + L+ ++
Sbjct: 155 ARLQGDEELLEQSGFEELEEHLEEFL 180
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 59.5 bits (145), Expect = 3e-09
Identities = 48/132 (36%), Positives = 63/132 (47%), Gaps = 11/132 (8%)
Query: 14 NVGTIGHVDHGKTTLTAAIA--TVLSKKFG----GEAKSYDQIDAAPEEKARGITINTAH 67
N+G + H+D GKTT T I T S K G G A +D +E+ RGITI +A
Sbjct: 10 NIGIMAHIDAGKTTTTERILYYTGKSHKIGEVHDGAA----TMDWMEQEQERGITITSAA 65
Query: 68 IEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVG 127
K +D PGH D+ + +DGA+ V A G PQ+ A + G
Sbjct: 66 TTCFWKGHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVSGVEPQSETVWRQADKYG 125
Query: 128 VPYIVVFLNKAD 139
VP I VF+NK D
Sbjct: 126 VPRI-VFVNKMD 136
>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 = 54.3 bits (131), Expect = 1e-08
Identities = 44/173 (25%), Positives = 64/173 (36%), Gaps = 35/173 (20%)
Query: 13 INVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGIT--INTAHIEY 70
I + +G + GK+TL + K E K G T T IE
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGN--KISITEYKP-------------GTTRNYVTTVIEE 46
Query: 71 ETKARHYAHVDCPGHADYIK------NMITGAAQM-DGAILVCSAADGPMPQTREHILLA 123
+ K + +D G DY + + ++ D ILV + QT+E I A
Sbjct: 47 DGKTYKFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHA 106
Query: 124 RQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAK 176
GVP I++ NK D+ D L+ + LN PII SA+
Sbjct: 107 ES-GVP-IILVGNKIDLRD--AKLKTHVAFLFAKLNG-------EPIIPLSAE 148
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 56.8 bits (138), Expect = 2e-08
Identities = 71/241 (29%), Positives = 113/241 (46%), Gaps = 34/241 (14%)
Query: 14 NVGTIGHVDHGKTTLTAAIATVLSKKFGG--EAKSYDQI-DAAPEEKARGITI--NTAHI 68
N I H+DHGK+TL A L + GG E + Q+ D+ E+ RGITI +
Sbjct: 11 NFSIIAHIDHGKSTL----ADRLLELTGGLSEREMRAQVLDSMDIERERGITIKAQAVRL 66
Query: 69 EYETKARH----YAH-VDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLA 123
Y KA+ + +D PGH D+ + A +GA+LV A+ G QT ++ LA
Sbjct: 67 NY--KAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYLA 124
Query: 124 RQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGDT 183
+ + I V LNK D+ + E V+ EI +++ +D ++ SAK T
Sbjct: 125 LENNLEIIPV-LNKIDLPAAD--PERVKQEIEDII---GIDASDAVLV--SAK------T 170
Query: 184 GPLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGE 243
G +G + +L +A+ IP P D + D + + G VV R+ G ++ G+
Sbjct: 171 G-IGIEDVL---EAIVEKIPPPKGDPDAPLKALIFDSWYDNYLGVVVLVRIFDGTLKKGD 226
Query: 244 E 244
+
Sbjct: 227 K 227
>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 = 53.2 bits (128), Expect = 3e-08
Identities = 31/166 (18%), Positives = 61/166 (36%), Gaps = 28/166 (16%)
Query: 18 IGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIEYETKARHY 77
+G GK++L A+ ++ + + E +
Sbjct: 3 VGRGGVGKSSLLNALL-------------GGEVGEVSDVPGTTRDPDVYVKELDKGKVKL 49
Query: 78 AHVDCPGHADYIKNMITGAAQM-----DGAILVCSAADGPMP--QTREHILLARQVGVPY 130
VD PG ++ A++ D +LV + D + R+ G+P
Sbjct: 50 VLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIPI 109
Query: 131 IVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAK 176
I+V NK D++++ E+ EL+ +E + +P+ + SAK
Sbjct: 110 ILV-GNKIDLLEEREVEELLRLEELAKI-------LGVPVFEVSAK 147
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 56.7 bits (137), Expect = 3e-08
Identities = 51/161 (31%), Positives = 74/161 (45%), Gaps = 35/161 (21%)
Query: 14 NVGTIGHVDHGKTTLT---AAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIE- 69
N+ I HVDHGK+TLT A A +++++ G+ + D +E RGITI + I
Sbjct: 21 NMSVIAHVDHGKSTLTDSLVAAAGIIAQEVAGDVR---MTDTRADEAERGITIKSTGISL 77
Query: 70 -YETKARHYAH--------------VDCPGHADYIKNMITGAAQM-DGAILVCSAADGPM 113
YE +D PGH D+ + +T A ++ DGA++V +G
Sbjct: 78 YYEMTDESLKDFKGERDGNEYLINLIDSPGHVDF-SSEVTAALRITDGALVVVDCIEGVC 136
Query: 114 PQTREHILLARQVGVPYI--VVFLNKAD------MVDDEEL 146
QT E +L RQ I V+ +NK D VD EE
Sbjct: 137 VQT-ETVL--RQALGERIRPVLTVNKMDRCFLELQVDGEEA 174
>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 = 49.4 bits (119), Expect = 1e-07
Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 3/84 (3%)
Query: 213 FLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQ 272
F LP+ D + GTVV+G+VE G ++ G+ L ++ K++V + + + +D
Sbjct: 2 FRLPISDKYK-DQGGTVVSGKVESGSIQKGDTLLVMPSKESV--EVKSIYVDDEEVDYAV 58
Query: 273 AGDNIGLLLRGTKREDVERGQVLA 296
AG+N+ L L+G ED+ G VL
Sbjct: 59 AGENVRLKLKGIDEEDISPGDVLC 82
>gnl|CDD|193579 cd09890, NGN_plant, Plant N-Utilization Substance G (NusG)
N-terminal (NGN) domain. The N-Utilization Substance G
(NusG) protein and its eukaryotic homolog, Spt5, are
involved in transcription elongation and termination.
NusG contains a NGN domain at its N-terminus and
Kyrpides Ouzounis and Woese (KOW) repeats at its
C-terminus in bacteria and archaea. The eukaryotic
ortholog, Spt5, is a large protein comprising an acidic
N-terminus, an NGN domain, and multiple KOW motifs at
its C-terminus. Spt5 forms an Spt4-Spt5 complex that is
an essential RNA polymerase II elongation factor. The
bacterial infected plants contain bacterial DNA, such as
NGN sequences, that can be used to clone the DNA of
uncultured organisms.
Length = 113
Score = 49.7 bits (119), Expect = 2e-07
Identities = 31/115 (26%), Positives = 50/115 (43%), Gaps = 16/115 (13%)
Query: 421 WYVIHSYSGMEKNVQRKLIERINKLGMQKKFGR---ILVPTEEIVDVKKNQK-SVIKKRF 476
WY++ +G E E + + + R + VP+ + KN SV +K
Sbjct: 2 WYMLRVPAGRENQAA----EALERALATEFPDREFEVWVPSIPVDRKLKNGSISVKEKPL 57
Query: 477 FPGYVLIEMEMTDESWHLVKNTKKVTGFIGGKS--------NRPTPISSKEIEEI 523
FPGYVL+ + E + +++ V GF+G K P P+ +EIE I
Sbjct: 58 FPGYVLLRCVLNKEVYDFIRDNDSVYGFVGSKVGKTGKRQIEIPRPVPVEEIEAI 112
>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 = 48.8 bits (117), Expect = 2e-07
Identities = 23/87 (26%), Positives = 43/87 (49%), Gaps = 4/87 (4%)
Query: 213 FLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDT---VKTTCTGVEMFRKLLD 269
+++++S+ G GTVV G V +G++R+G+ L ++G T + R +
Sbjct: 1 AEFQIDEIYSVPGVGTVVGGTVSKGVIRLGDTL-LLGPDQDGSFRPVTVKSIHRNRSPVR 59
Query: 270 QGQAGDNIGLLLRGTKREDVERGQVLA 296
+AG + L L+ R + +G VL
Sbjct: 60 VVRAGQSASLALKKIDRSLLRKGMVLV 86
>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 = 48.3 bits (116), Expect = 2e-07
Identities = 29/90 (32%), Positives = 44/90 (48%), Gaps = 14/90 (15%)
Query: 213 FLLPVEDV--FSISGRGTVVTGRVERGIVRVGEELEII--GIKDTVKTTCTGVEMFRKLL 268
F PV+ V + RG G + G +RVG+E+ ++ G VK +E F L
Sbjct: 1 FRFPVQYVIRPNADFRG--YAGTIASGSIRVGDEVVVLPSGKTSRVK----SIETFDGEL 54
Query: 269 DQGQAGDNIGLLLRGTKRE-DVERGQVLAK 297
D+ AG+++ L L + E DV RG V+
Sbjct: 55 DEAGAGESVTLTL---EDEIDVSRGDVIVA 81
>gnl|CDD|193582 cd09893, NGN_SP_TaA, N-Utilization Substance G (NusG) N-terminal
domain in the NusG Specialized Paralog (SP), TaA. The
N-Utilization Substance G (NusG) protein is involved in
transcription elongation and termination. NusG is
essential in Escherichia coli and is associated with RNA
polymerase elongation and Rho-termination in bacteria.
Paralogs of eubacterial NusG, NusG SP (Specialized
Paralog of NusG), are more diverse and often found as
the first ORF in operons encoding secreted proteins and
LPS biosynthesis genes. NusG SP family members are
operon-specific transcriptional antiterminationn
factors. TaA is a NusG SP factor that is required for
synthesis of a polyketide antibiotic TA in Myxococcus
xanthus. Orthologs of the NusG gene exist in all
bacteria, but its functions and requirements are
different. The NusG N-terminal (NGN) domain is quite
similar in all NusG orthologs, but its C-terminal
domains and the linker that separate these two domains
are different. The domain organization of NusG and its
orthologs suggest that the common properties of NusG and
its orthologs and paralogs are due to their similar NGN
domains.
Length = 95
Score = 47.3 bits (113), Expect = 7e-07
Identities = 30/104 (28%), Positives = 51/104 (49%), Gaps = 11/104 (10%)
Query: 420 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPG 479
WY +++ S EK K+ +R+ K G++ +P E++ K++K IK FPG
Sbjct: 1 SWYALYTRSRHEK----KVADRLAKKGIE-----SFLPLYEVLSRWKDRKKKIKVPLFPG 51
Query: 480 YVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEI 523
Y+ + ++ E ++K V I G S P PI +EI +
Sbjct: 52 YLFVRFQLDPERLRILKTPGVVR--IVGNSGGPIPIPDEEIASL 93
>gnl|CDD|193578 cd09889, NGN_Bact_2, Bacterial N-Utilization Substance G (NusG)
N-terminal (NGN) domain, subgroup 2. The N-Utilization
Substance G (NusG) protein is involved in transcription
elongation and termination. NusG is essential in
Escherichia coli and associates with RNA polymerase
elongation and Rho-termination. Paralogs of eubacterial
NusG, NusG SP (Specialized Paralog of NusG), are more
diverse and often found as the first ORF in operons
encoding secreted proteins and LPS biosynthesis genes.
NusG SP family members are operon-specific
transcriptional antitermination factors. The NusG
N-terminal domain (NGN) is quite similar in all NusG
orthologs, but its C-terminal domain and the linker that
separates these two domains are different. The domain
organization of NusG and its orthologs suggests that the
common properties of NusG and its orthologs and paralogs
are due to their similar NGN domains.
Length = 100
Score = 46.9 bits (112), Expect = 9e-07
Identities = 30/110 (27%), Positives = 49/110 (44%), Gaps = 15/110 (13%)
Query: 420 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRF--F 477
WYV+ +G EK V +E + KL +P E K++Q ++++ F
Sbjct: 1 MWYVVQVRTGREKAV----LELLEKLVGPDVLQECFIPQYERK--KRSQGVWRERKYTLF 54
Query: 478 PGYVLIEMEMTDES-WHLVKNTKKVTGFIG--GKSNRPTPISSKEIEEIL 524
PGYV + + DE + L K+V GF G P++ +E + I
Sbjct: 55 PGYVFVVTDDIDELYYEL----KRVPGFTRLLGNDGSFFPLTPEEADFIR 100
>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 = 44.1 bits (105), Expect = 6e-06
Identities = 27/86 (31%), Positives = 44/86 (51%), Gaps = 10/86 (11%)
Query: 213 FLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTT---CTGVEMFRKLLD 269
LP+ D + GTVV G+VE G ++ G++L ++ K V+ VE+
Sbjct: 2 LRLPIIDKYK--DMGTVVLGKVESGTIKKGDKLLVMPNKTQVEVLSIYNEDVEV-----R 54
Query: 270 QGQAGDNIGLLLRGTKREDVERGQVL 295
+ G+N+ L L+G + ED+ G VL
Sbjct: 55 YARPGENVRLRLKGIEEEDISPGFVL 80
>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 = 48.3 bits (115), Expect = 1e-05
Identities = 39/129 (30%), Positives = 58/129 (44%), Gaps = 3/129 (2%)
Query: 15 VGTIGHVDHGKTTLTAAI-ATVLSKKFGGEAKSYDQIDAAPEEKARGITINT-AHIEYET 72
V +GHVDHGKTTL I + ++K+ G + P + GI + +
Sbjct: 7 VSVLGHVDHGKTTLLDKIRGSAVAKREAGGITQHIGATEIPMDVIEGICGDLLKKFKIRL 66
Query: 73 KARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIV 132
K +D PGH + G A D AIL+ +G PQT+E + + R P++V
Sbjct: 67 KIPGLLFIDTPGHEAFTNLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYKTPFVV 126
Query: 133 VFLNKADMV 141
NK D +
Sbjct: 127 A-ANKIDRI 134
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 47.8 bits (115), Expect = 1e-05
Identities = 55/157 (35%), Positives = 77/157 (49%), Gaps = 27/157 (17%)
Query: 18 IGHVDHGKTTLT-------AAIA---TVLSKKFGGEAKSYDQIDAAPEEKARGITINTAH 67
I H D GKTTLT AI TV +K G A S D EK RGI++ ++
Sbjct: 16 ISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGRHATS----DWMEMEKQRGISVTSSV 71
Query: 68 IEYETKARHYAH-----VDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILL 122
+++ Y +D PGH D+ ++ +D A++V AA G PQTR+ + +
Sbjct: 72 MQFP-----YRDCLINLLDTPGHEDFSEDTYRTLTAVDSALMVIDAAKGVEPQTRKLMEV 126
Query: 123 ARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLN 159
R P I F+NK D D E LEL++ EI E+L
Sbjct: 127 CRLRDTP-IFTFINKLDR-DGREPLELLD-EIEEVLG 160
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 44.7 bits (107), Expect = 1e-04
Identities = 46/140 (32%), Positives = 66/140 (47%), Gaps = 27/140 (19%)
Query: 14 NVGTIGHVDHGKTTLTAAIA--TVLSKKFG----GEAKSYDQIDAAPEEKARGITINTAH 67
N+G + H+D GKTT T I T ++ K G G A +D +E+ RGITI +A
Sbjct: 12 NIGIMAHIDAGKTTTTERILFYTGVNHKIGEVHDGAA----TMDWMEQEQERGITITSAA 67
Query: 68 IEYETKARHYAHVDCPGHADYI----KNMITGAAQMDGAILVCSAADGPMPQT----REH 119
K +D PGH D+ +++ +DGA+ V A G PQ+ R+
Sbjct: 68 TTCFWKDHRINIIDTPGHVDFTIEVERSL----RVLDGAVAVFDAVGGVEPQSETVWRQ- 122
Query: 120 ILLARQVGVPYIVVFLNKAD 139
A + VP I F+NK D
Sbjct: 123 ---ADKYKVPRI-AFVNKMD 138
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 41.5 bits (98), Expect = 3e-04
Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 9/81 (11%)
Query: 96 AAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIR 155
A + D +LV + P+ + + LL R+ G P ++V NK D+V + E EL+
Sbjct: 74 ADRADLVLLVVDSDLTPVEEEAKLGLL-RERGKPVLLVL-NKIDLVPESEEEELLRERKL 131
Query: 156 ELLNKYEFPGNDIPIIKGSAK 176
ELL D+P+I SA
Sbjct: 132 ELL-------PDLPVIAVSAL 145
>gnl|CDD|193581 cd09892, NGN_SP_RfaH, N-Utilization Substance G (NusG) N-terminal
domain in the NusG Specialized Paralog (SP), RfaH. RfaH
is an operon-specific virulence regulator, thought to
have arisen from an early duplication of N-Utilization
Substance G (NusG). Paralogs of eubacterial NusG, NusG
SP (Specialized Paralog of NusG), are more diverse and
often found as the first ORF in operons encoding
secreted proteins and LPS biosynthesis genes. NusG SP
family members are operon-specific transcriptional
antitermination factors. NusG is essential in
Escherichia coli and is associated with RNA polymerase
elongation and Rho-termination in bacteria. In contrast,
RfaH is a non-essential protein that controls expression
of operons containing an ops (operon polarity
suppressor) element in their transcribed DNA. RfaH and
NusG are different in their response to Rho-dependent
terminators and regulatory targets. The NusG N-terminal
(NGN) domain is quite similar in all NusG orthologs, but
its C-terminal domains and the linker that separate
these two domains are different. The domain organization
of NusG and its homologs suggest that the common
properties of NusG and RfaH are due to their similar NGN
domains.
Length = 96
Score = 39.9 bits (94), Expect = 3e-04
Identities = 20/104 (19%), Positives = 49/104 (47%), Gaps = 10/104 (9%)
Query: 420 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPG 479
WY++++ E+ L ER F + +P + ++ +++V+ + FPG
Sbjct: 1 AWYLLYTKPRQEERAAENL-ERQG-------F-EVFLPMIRVEKRRRGKRTVVTEPLFPG 51
Query: 480 YVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEI 523
Y+ + ++ ++W +++T+ V+ + P P+ IE +
Sbjct: 52 YLFVRLDPEVQNWRPIRSTRGVSRLVRF-GGEPAPVPDALIEAL 94
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 42.5 bits (101), Expect = 6e-04
Identities = 44/129 (34%), Positives = 56/129 (43%), Gaps = 15/129 (11%)
Query: 19 GHVDHGKTTLTAAI--ATVLSKKFGGEAKSYDQIDAAPE------EKARGITINTAHIEY 70
GHVDHGKTTL I V +K EA Q A E EK G I+
Sbjct: 13 GHVDHGKTTLLDKIRGTAVAAK----EAGGITQHIGATEVPIDVIEKIAGPLKKPLPIKL 68
Query: 71 ETKARHYAHVDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPY 130
+ + +D PGH + G A D AILV +G PQT E I + ++ P+
Sbjct: 69 KIPGLLF--IDTPGHEAFTNLRKRGGALADIAILVVDINEGFQPQTIEAINILKRRKTPF 126
Query: 131 IVVFLNKAD 139
+V NK D
Sbjct: 127 VVA-ANKID 134
>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 = 40.2 bits (95), Expect = 9e-04
Identities = 30/110 (27%), Positives = 48/110 (43%), Gaps = 18/110 (16%)
Query: 80 VDCPG---------HADYIKNMI----TGAAQMDGAILVCSAADGPMPQTREHILLARQV 126
VD PG + +I + G +L+ A GP P E + ++
Sbjct: 50 VDLPGYGYAKVSKEVREKWGKLIEEYLENRENLKGVVLLIDARHGPTPIDLEMLEFLEEL 109
Query: 127 GVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAK 176
G+P+++V L KAD + E L V +I+E LN + P+I S+K
Sbjct: 110 GIPFLIV-LTKADKLKKSE-LAKVLKKIKEELNLFN---ILPPVILFSSK 154
>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 = 40.7 bits (96), Expect = 0.001
Identities = 26/74 (35%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 80 VDCPGHADYIKNMITG--AAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNK 137
+D GH Y+K + G D A+LV A G + T+EH+ LA + VP VV + K
Sbjct: 89 IDLAGHERYLKTTVFGMTGYAPDYAMLVVGANAGIIGMTKEHLGLALALKVPVFVV-VTK 147
Query: 138 ADMVDDEELLELVE 151
DM L E ++
Sbjct: 148 IDMTPANVLQETLK 161
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 39.8 bits (93), Expect = 0.001
Identities = 37/165 (22%), Positives = 60/165 (36%), Gaps = 25/165 (15%)
Query: 18 IGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDA-APEEKARGITINTAHIEYET---K 73
IG V GKTT A++ K +A A +G T +++ +
Sbjct: 16 IGPVGAGKTTFVRALSD----------KPLVITEADASSVSGKGKRPTTVAMDFGSIELD 65
Query: 74 ARHYAH-VDCPGHADYIKNMITGAAQ-MDGAILVCSAADGPMPQTREHILLARQVGVPYI 131
H PG + K M ++ GAI++ ++ E I +
Sbjct: 66 EDTGVHLFGTPGQ-ERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPIPV 124
Query: 132 VVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAK 176
VV +NK D+ D L +IRE L + +P+I+ A
Sbjct: 125 VVAINKQDLFD-----ALPPEKIREAL---KLELLSVPVIEIDAT 161
>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 = 39.3 bits (93), Expect = 0.003
Identities = 28/80 (35%), Positives = 41/80 (51%), Gaps = 15/80 (18%)
Query: 100 DGAILVCSAADGPMPQTR---EHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRE 156
D ++V S + P R +++ A G+ V+ LNKAD+VDDEEL EL+EI +
Sbjct: 4 DQVLIVFSLKE-PFFNLRLLDRYLVAAEASGIE-PVIVLNKADLVDDEELEELLEI-YEK 60
Query: 157 LLNKYEFPGNDIPIIKGSAK 176
L P++ SAK
Sbjct: 61 L---------GYPVLAVSAK 71
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 40.4 bits (96), Expect = 0.003
Identities = 74/248 (29%), Positives = 116/248 (46%), Gaps = 54/248 (21%)
Query: 18 IGHVDHGKTTLTAAI--AT-VLSKKFGGEAKSYDQI-DAAPEEKARGITI--NTAHIEYE 71
I H+DHGK+TL + T LS++ E K Q+ D+ E+ RGITI + Y+
Sbjct: 13 IAHIDHGKSTLADRLIELTGTLSER---EMK--AQVLDSMDLERERGITIKAQAVRLNYK 67
Query: 72 TK-ARHYA-H-VDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGV 128
K Y + +D PGH D+ + A +GA+LV A+ G QT ++ LA + +
Sbjct: 68 AKDGETYILNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYLALENDL 127
Query: 129 PYIVVFLNKADM--VDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPL 186
I V LNK D+ D E V+ EI +++ +D ++ SAK TG +
Sbjct: 128 EIIPV-LNKIDLPAADPER----VKQEIEDVIG---IDASDAVLV--SAK------TG-I 170
Query: 187 GEQSILSLSKALDTYIPTPN-------RA--IDGAFLLPVEDVFSISGRGTVVTGRVERG 237
G + +L +A+ IP P +A D + D + RG VV RV G
Sbjct: 171 GIEEVL---EAIVERIPPPKGDPDAPLKALIFDSWY-----DNY----RGVVVLVRVVDG 218
Query: 238 IVRVGEEL 245
++ G+++
Sbjct: 219 TLKKGDKI 226
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 38.8 bits (91), Expect = 0.004
Identities = 26/95 (27%), Positives = 39/95 (41%), Gaps = 15/95 (15%)
Query: 80 VDCPG---------HADYIKNMI----TGAAQMDGAILVCSAADGPMPQTREHILLARQV 126
VD PG + K +I A + G +L+ A P RE I ++
Sbjct: 75 VDLPGYGYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPPKDLDREMIEFLLEL 134
Query: 127 GVPYIVVFLNKADMVDDEELLELVEIEIRELLNKY 161
G+P IVV KAD + E + + ++ E L K
Sbjct: 135 GIPVIVVL-TKADKLKKSERNKQLN-KVAEELKKP 167
>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 = 36.2 bits (85), Expect = 0.015
Identities = 17/36 (47%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 129 PYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFP 164
P IVV LNK D++D EE E ++ ++EL K FP
Sbjct: 116 PRIVV-LNKIDLLDAEERFEKLKELLKELKGKKVFP 150
>gnl|CDD|193584 cd09895, NGN_SP_UpxY, N-Utilization Substance G (NusG) N-terminal
domain in the NusG Specialized Paralog (SP), UpxY. The
N-Utilization Substance G (NusG) proteins are involved
in transcription elongation and termination. NusG is
essential in Escherichia coli and is associated with RNA
polymerase elongation and Rho-termination. Paralogs of
eubacterial NusG, NusG SP (Specialized Paralog of NusG),
are more diverse and often found as the first ORF in
operons encoding secreted proteins and LPS
(lipopolysaccharide) biosynthesis genes. NusG SP family
members are operon-specific transcriptional
antitermination factors. UpxY proteins, UpxY proteins,
where the x is replaced by the letter designation of the
specific polysaccharide (UpaY to UphY), are a family of
NusG SP factors that act specifically in transcriptional
antitermination of operons from which they are encoded.
UpxYs are necessary and specific for transcription
regulation of the polysaccharide biosynthesis operon.
Orthologs of the NusG gene exist in all bacteria, but
their functions and requirements are different. The NusG
N-terminal (NGN) domain is similar in all NusG
orthologs, but its C-terminal domain and the linker that
separate these two domains are different. The domain
organization of NusG and its orthologs suggests that the
common properties of NusG and its orthologs and paralogs
are due to their similar NGN domains.
Length = 95
Score = 34.5 bits (80), Expect = 0.026
Identities = 22/104 (21%), Positives = 41/104 (39%), Gaps = 11/104 (10%)
Query: 420 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPG 479
WY ++++ EK K+ E + K G+ +P + V +K ++ FP
Sbjct: 1 PWYALYTFPRREK----KVAEYLEKKGI-----ECFLPMQYEVRQWSGRKKRVEVPLFPN 51
Query: 480 YVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEI 523
V + + + V T V F+ + P I K++E
Sbjct: 52 LVFVHITREELD--EVLETPGVVRFVRYRGKEPAIIPDKQMESF 93
>gnl|CDD|181467 PRK08559, nusG, transcription antitermination protein NusG;
Validated.
Length = 153
Score = 35.2 bits (82), Expect = 0.034
Identities = 33/153 (21%), Positives = 56/153 (36%), Gaps = 32/153 (20%)
Query: 422 YVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPGYV 481
+ + + +G E+NV L R K + IL P E +K GYV
Sbjct: 9 FAVKTTAGQERNVALMLAMRAKKENLPIY--AILAPPE------------LK-----GYV 49
Query: 482 LIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILKQIKKGVEKPRPKILYQ 541
L+E E ++ V G + G+ + EE+ +K + I +
Sbjct: 50 LVEAESKGAVEEAIRGIPHVRGVVPGEIS---------FEEVEHFLKP--KPIVEGI--K 96
Query: 542 LDELVRIKDGPFTDFSGNIEEVNYEKSRVRVSV 574
++V + GPF + V+ K V V +
Sbjct: 97 EGDIVELIAGPFKGEKARVVRVDESKEEVTVEL 129
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme ethanolamine
ammonia lyase. The function of this gene is unknown,
although the presence of an N-terminal GxxGxGK motif
implies a GTP-binding site [Energy metabolism, Amino
acids and amines].
Length = 142
Score = 34.7 bits (80), Expect = 0.039
Identities = 34/145 (23%), Positives = 50/145 (34%), Gaps = 40/145 (27%)
Query: 18 IGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIEYETKARHY 77
IG V GKTTLT + GE Y + A +EY A
Sbjct: 6 IGSVGCGKTTLT--------QALQGEEILYKKTQA---------------VEYNDGA--- 39
Query: 78 AHVDCPG----HADYIKNMITGAAQMDGAILVCSAADG--PMPQTREHILLARQVGVPYI 131
+D PG + +I AA D LV SA D P I + +G+
Sbjct: 40 --IDTPGEYVENRRLYSALIVTAADADVIALVQSATDPESRFPPGFASIFVKPVIGL--- 94
Query: 132 VVFLNKADMVDDEELLELVEIEIRE 156
+ K D+ + + +E + +
Sbjct: 95 ---VTKIDLAEADVDIERAKELLET 116
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 36.0 bits (84), Expect = 0.049
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 100 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 151
D A+LV A GP E I ++ +PYIVV NK D+ ++ LE +E
Sbjct: 87 DLALLVVDAGVGPGEYELELIEELKERKIPYIVVI-NKIDLGEESAELEKLE 137
>gnl|CDD|193576 cd09887, NGN_Arch, Archaeal N-Utilization Substance G (NusG)
N-terminal (NGN) domain. The N-Utilization Substance G
(NusG) protein and its eukaryotic homolog, Spt5, are
involved in transcription elongation and termination.
Transcription in archaea has a eukaryotic-type
transcription apparatus, but contains bacterial-type
transcription factors. NusG is one of the few archaeal
transcription factors that has orthologs in both
bacteria and eukaryotes. Archaeal NusG is similar to
bacterial NusG, composed of an NGN domain and a Kyrpides
Ouzounis and Woese (KOW) repeat. The eukaryotic
ortholog, Spt5, is a large protein composed of an acidic
N-terminus, an NGN domain, and multiple KOW motifs at
its C-terminus. NusG was originally discovered as a
N-dependent antitermination enhancing activity in
Escherichia coli and has a variety of functions, such as
being involved in RNA polymerase elongation and
Rho-termination in bacteria. Archaeal NusG forms a
complex with DNA-directed RNA polymerase subunit E
(rpoE) that is similar to the Spt5-Spt4 complex in
eukaryotes.
Length = 82
Score = 32.9 bits (76), Expect = 0.058
Identities = 32/106 (30%), Positives = 43/106 (40%), Gaps = 25/106 (23%)
Query: 420 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPG 479
R Y + + +G E+NV L R K + ILVP E +K G
Sbjct: 1 RIYAVKTTAGQERNVADLLAMRAEKENLDVY--SILVPEE------------LK-----G 41
Query: 480 YVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILK 525
YV +E E D L++ V G + G IS +EIE LK
Sbjct: 42 YVFVEAEDPDRVEELIRGIPHVRGVVPG------EISLEEIEHFLK 81
>gnl|CDD|193575 cd09886, NGN_SP, N-Utilization Substance G (NusG) N-terminal domain
in the NusG Specialized Paralog (SP). The N-Utilization
Substance G (NusG) protein is involved in transcription
elongation and termination. NusG is essential in
Escherichia coli and is associated with RNA polymerase
elongation and Rho-termination in bacteria. Paralogs of
eubacterial NusG, NusG SP (Specialized Paralog of NusG),
are more diverse and often found as the first ORF in
operons encoding secreted proteins and LPS biosynthesis
genes. NusG SP family members are operon-specific
transcriptional antitermination factors. The NusG
N-terminal (NGN) domain is quite similar in all NusG
orthologs, but its C-terminal domains and the linker
that separate these two domains are different. The
domain organization of NusG and its orthologs suggest
that the common properties of NusG and its orthologs and
paralogs are due to their similar NGN domains.
Length = 97
Score = 33.5 bits (77), Expect = 0.058
Identities = 22/107 (20%), Positives = 45/107 (42%), Gaps = 11/107 (10%)
Query: 420 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPG 479
WY + + G E+ + L R G++ +P ++ +K +++ FPG
Sbjct: 1 SWYALRTNPGCEQRAEEALEAR----GVE-----AFLPMLTEERKRRRKKFDVERPLFPG 51
Query: 480 YVLIEM-EMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILK 525
YV + + ++ V G +G RP P+ +E+ ++ K
Sbjct: 52 YVFARLDRSKGQDTSTIRACDGVLGVVGF-DGRPAPVPEQEMRDLRK 97
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 36.0 bits (83), Expect = 0.067
Identities = 23/62 (37%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 80 VDCPGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKAD 139
+D PGH + G + D A+LV +G PQT E I + RQ P+ VV NK D
Sbjct: 531 IDTPGHEAFTSLRKRGGSLADLAVLVVDINEGFKPQTIEAINILRQYKTPF-VVAANKID 589
Query: 140 MV 141
++
Sbjct: 590 LI 591
>gnl|CDD|239659 cd03688, eIF2_gamma_II, eIF2_gamma_II: this subfamily represents
the domain II of the gamma subunit of eukaryotic
translation initiation factor 2 (eIF2-gamma) found in
Eukaryota and Archaea. eIF2 is a G protein that delivers
the methionyl initiator tRNA to the small ribosomal
subunit and releases it upon GTP hydrolysis after the
recognition of the initiation codon. eIF2 is composed
three subunits, alpha, beta and gamma. Subunit gamma
shows strongest conservation, and it confers both tRNA
binding and GTP/GDP binding.
Length = 113
Score = 33.3 bits (77), Expect = 0.082
Identities = 29/90 (32%), Positives = 47/90 (52%), Gaps = 19/90 (21%)
Query: 226 RGTVVTGRVERGIVRVGEELEI---IGIKDTVKTTCTGVEMFRKLLDQGQAGDNI----- 277
+G V G + +G+++VG+E+EI I +KD K C + F K++ +A +N
Sbjct: 27 KGGVAGGSLLQGVLKVGDEIEIRPGIVVKDEGKIKCRPI--FTKIVSL-KAENNDLQEAV 83
Query: 278 --GLLLRGTK------REDVERGQVLAKPG 299
GL+ GTK + D GQV+ +PG
Sbjct: 84 PGGLIGVGTKLDPTLTKADRLVGQVVGEPG 113
>gnl|CDD|144165 pfam00467, KOW, KOW motif. This family has been extended to
coincide with ref. The KOW (Kyprides, Ouzounis, Woese)
motif is found in a variety of ribosomal proteins and
NusG.
Length = 32
Score = 30.9 bits (71), Expect = 0.087
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 543 DELVRIKDGPFTDFSGNIEEVNYEKSRVRV 572
++VR+ GPF G + EV+ K+RV V
Sbjct: 2 GDVVRVISGPFKGKKGKVVEVDDSKARVHV 31
>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 = 34.7 bits (81), Expect = 0.12
Identities = 34/115 (29%), Positives = 51/115 (44%), Gaps = 14/115 (12%)
Query: 102 AILVCSAADGPMPQTREHIL-LARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNK 160
+LV A +G Q I LA + G ++V NK D+V DE+ E + E+R L
Sbjct: 258 VLLVLDATEGITEQD-LRIAGLALEAGKALVIVV-NKWDLVKDEKTREEFKKELRRKLPF 315
Query: 161 YEFPGNDIPIIKGSAKLALEG-DTGPLGEQSILSLSKALDTYIPTP--NRAIDGA 212
+F PI+ S AL G L +I + + + I T NR ++ A
Sbjct: 316 LDF----APIVFIS---ALTGQGVDKL-LDAIDEVYENANRRISTSKLNRVLEEA 362
>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 = 33.1 bits (76), Expect = 0.18
Identities = 34/176 (19%), Positives = 58/176 (32%), Gaps = 42/176 (23%)
Query: 16 GTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIEYETKAR 75
G +G + GK+TL +A+ + +++ A + N E+
Sbjct: 1 GLVGLPNVGKSTLLSALTSA-------------KVEIASYPFTT-LEPNVGVFEFGDGVD 46
Query: 76 HYAHVDCPGHAD------YIKNMITGAAQMDGAIL-VCSAA-DGPMPQTREHILLARQVG 127
+D PG D + I IL V A+ D + L +V
Sbjct: 47 -IQIIDLPGLLDGASEGRGLGEQILAHLYRSDLILHVIDASEDCVGDPLEDQKTLNEEVS 105
Query: 128 V--------PYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSA 175
P ++V NK DM + L L +++ IP++ SA
Sbjct: 106 GSFLFLKNKPEMIVA-NKIDMASENNLKRLKLDKLK----------RGIPVVPTSA 150
>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 = 30.9 bits (71), Expect = 0.29
Identities = 15/54 (27%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 227 GTVVTGRVERGIVRVGEELEIIGIKDTV-KTTCTGVEMFRKL----LDQGQAGD 275
G + GR+ RG V+VG+++ ++ + K T + F L +++ +AGD
Sbjct: 15 GRIAIGRIFRGTVKVGQQVAVVKRDGKIEKAKITKLFGFEGLKRVEVEEAEAGD 68
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 33.2 bits (77), Expect = 0.38
Identities = 18/32 (56%), Positives = 25/32 (78%), Gaps = 2/32 (6%)
Query: 129 PYIVVFLNKADMVDDEELLELVEIEIRELLNK 160
P IVV LNK D++D+EEL EL++ E++E L K
Sbjct: 275 PRIVV-LNKIDLLDEEELEELLK-ELKEALGK 304
>gnl|CDD|129499 TIGR00405, L26e_arch, ribosomal protein L24p/L26e, archaeal. This
protein contains a KOW domain, shared by bacterial NusG
and the L24p/L26e family of ribosomal proteins. Although
called archaeal NusG in several publications, it is the
only close homolog of eukaryotic L26e in archaeal
genomes, shares an operon with L11 in many genomes, and
has been sequenced from purified ribosomes. It is here
designated as a ribosomal protein for these reasons
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 145
Score = 31.8 bits (72), Expect = 0.47
Identities = 41/178 (23%), Positives = 65/178 (36%), Gaps = 44/178 (24%)
Query: 422 YVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPGYV 481
+ + + G EKNV R + + K G+ + IL P GY+
Sbjct: 1 FAVKTSVGQEKNVARLMARKARKSGL--EVYSILAPES-----------------LKGYI 41
Query: 482 LIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILK------QIKKGVEKPR 535
L+E E + + + V G + G+ I +EIE L IKKG
Sbjct: 42 LVEAETKIDMRNPIIGVPHVRGVVEGE------IDFEEIERFLTPKKIIESIKKG----- 90
Query: 536 PKILYQLDELVRIKDGPFTDFSGNIEEVNYEKSRVRVSVTIFGRATPVELEFNQVEKI 593
++V I GPF + V+ K V + + PV ++ +QV I
Sbjct: 91 --------DIVEIISGPFKGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRII 140
>gnl|CDD|193583 cd09894, NGN_SP_AnfA1, N-Utilization Substance G (NusG) N-terminal
domain in the NusG Specialized Paralog (SP), AnFA1.
Regulation of the afp, antifeeding prophage, gene
cluster is mediated by AnFA1, a RfaH-like
transcriptional antiterminator. RfaH is an
operon-specific virulence regulator, thought to arisen
from an early duplication of N-Utilization Substance G
(NusG). NusG is essential in Escherichia coli and is
associated with RNA polymerase elongation and
Rho-termination in bacteria. Paralogs of eubacterial
NusG, NusG SP (Specialized Paralog of NusG), are more
diverse and often found as the first ORF in operons
encoding secreted proteins and LPS biosynthesis genes.
NusG SP family members are operon-specific
transcriptional antitermination factors. Orthologs of
the NusG gene exist in all bacteria, but their functions
and requirements are different. The NusG N-terminal
domain (NGN) is similar in all NusG orthologs, but its
C-terminal domain and the linker that separate these two
domains are different. The domain organization of NusG
and its orthologs suggests that the common properties of
NusG and its orthologs and paralogs are due to their
similar NGN domains.
Length = 99
Score = 30.7 bits (70), Expect = 0.50
Identities = 25/111 (22%), Positives = 46/111 (41%), Gaps = 16/111 (14%)
Query: 419 KRWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKK--RF 476
KRWY++ SG + +I + +LG+ + P + + KS +K
Sbjct: 1 KRWYLLRCKSGKI----QSVIFSLERLGV-----EVFCPMIRTRRKRTDCKSYREKIEPL 51
Query: 477 FPGYVLIEMEMTDESWHLVKNTKKVTGFI--GGKSNRPTPISSKEIEEILK 525
FPGY+ + + + V+GF+ GG+ P P+ I ++
Sbjct: 52 FPGYLFVRFDPEVVHTSKITLASGVSGFVRFGGE---PCPVPDAVIRALML 99
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 32.3 bits (75), Expect = 0.57
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 129 PYIVVFLNKADMVDDEELLELVEIEIRELLNK 160
P I+V LNK D++D+EE E L
Sbjct: 273 PRILV-LNKIDLLDEEEEREKRAALELAALGG 303
>gnl|CDD|232957 TIGR00398, metG, methionyl-tRNA synthetase. The methionyl-tRNA
synthetase (metG) is a class I amino acyl-tRNA ligase.
This model appears to recognize the methionyl-tRNA
synthetase of every species, including eukaryotic
cytosolic and mitochondrial forms. The UPGMA difference
tree calculated after search and alignment according to
This model shows an unusual deep split between two
families of MetG. One family contains forms from the
Archaea, yeast cytosol, spirochetes, and E. coli, among
others. The other family includes forms from yeast
mitochondrion, Synechocystis sp., Bacillus subtilis, the
Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori.
The E. coli enzyme is homodimeric, although monomeric
forms can be prepared that are fully active. Activity of
this enzyme in bacteria includes aminoacylation of
fMet-tRNA with Met; subsequent formylation of the Met to
fMet is catalyzed by a separate enzyme. Note that the
protein from Aquifex aeolicus is split into an alpha
(large) and beta (small) subunit; this model does not
include the C-terminal region corresponding to the beta
chain [Protein synthesis, tRNA aminoacylation].
Length = 530
Score = 32.7 bits (75), Expect = 0.57
Identities = 26/128 (20%), Positives = 40/128 (31%), Gaps = 14/128 (10%)
Query: 304 HKHFTGEIYALSKDEG----GRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDN- 358
HK +I+ K+ G + F V G PK GD+
Sbjct: 96 HKEIVQKIFQKLKENGYIYEKEIKQLYCPECEMFLP-DRYVEG--TCPKCGSEDARGDHC 152
Query: 359 -----VLITVRLINPIAMEEGLRFAIREGVQQFIQDNLLTKEIVNSNKINIDKGKEYIER 413
L LINP G + +R+ F + + KE+ + N + G
Sbjct: 153 EVCGRHLEPTELINPRCKICGAKPELRDSEHYFFRLSAFEKELEEWIRKNPESGS-PASN 211
Query: 414 SINNKKRW 421
N + W
Sbjct: 212 VKNKAQNW 219
>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 = 0.99
Identities = 29/112 (25%), Positives = 44/112 (39%), Gaps = 23/112 (20%)
Query: 73 KARHYAHVDCPG------------HADYIKNMITGAAQMDGAILVCSAADGPMP------ 114
KA++ A + PG HA + + A + G I V + AD P+P
Sbjct: 13 KAKYTADLAAPGALVGRILRSPHAHARILAIDTSEAEALPGVIAVVTGADCPVPYGVLPI 72
Query: 115 QTREHILL---ARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEF 163
E+ L R G P V + D V E+ L L+++E EL +
Sbjct: 73 AENEYPLARDKVRYRGDP--VAAVAAVDEVTAEKALALIKVEYEELPAYMDP 122
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 31.7 bits (73), Expect = 0.99
Identities = 26/72 (36%), Positives = 35/72 (48%), Gaps = 16/72 (22%)
Query: 96 AAQMDGAILVCSAADGPMPQTREHIL-----LARQVGVPYIVVFLNKADMVDDEELLELV 150
AA +D A+LV +A + P +L LA G+ I+V NK D++DD E
Sbjct: 78 AANVDQAVLVFAAKE---PDFSTDLLDRFLVLAEANGIKPIIVL-NKIDLLDDLE----- 128
Query: 151 EIEIRELLNKYE 162
E RELL Y
Sbjct: 129 --EARELLALYR 138
>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 = 30.9 bits (71), Expect = 1.1
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 102 AILVCSAADGPMPQTREHIL-LARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNK 160
+L A + + E IL L ++ P I+V LNK D+V D+E L + +++EL
Sbjct: 85 LVLFVVDASEWIGEGDEFILELLKKSKTPVILV-LNKIDLVKDKEDLLPLLEKLKELHPF 143
Query: 161 YEFPGNDIPIIKGSAK 176
E PI SA
Sbjct: 144 AEI----FPI---SAL 152
>gnl|CDD|128978 smart00739, KOW, KOW (Kyprides, Ouzounis, Woese) motif. Motif in
ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Length = 28
Score = 27.7 bits (63), Expect = 1.1
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 543 DELVRIKDGPFTDFSGNIEEVNYE 566
+ VR+ GPF G + EV+ E
Sbjct: 5 GDTVRVIAGPFKGKVGKVLEVDGE 28
>gnl|CDD|239761 cd04094, selB_III, This family represents the domain of elongation
factor SelB, homologous to domain III of EF-Tu. SelB may
function by replacing EF-Tu. In prokaryotes, the
incorporation of selenocysteine as the 21st amino acid,
encoded by TGA, requires several elements: SelC is the
tRNA itself, SelD acts as a donor of reduced selenium,
SelA modifies a serine residue on SelC into
selenocysteine, and SelB is a selenocysteine-specific
translation elongation factor. 3' or 5' non-coding
elements of mRNA have been found as probable structures
for directing selenocysteine incorporation.
Length = 97
Score = 29.5 bits (67), Expect = 1.2
Identities = 25/91 (27%), Positives = 37/91 (40%), Gaps = 5/91 (5%)
Query: 292 GQVLAKPGSIKPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKE 351
G VLA PGS+ P + + L P R + T++V + L E
Sbjct: 1 GDVLADPGSLLPTRRLDVRLTVLLSAP----RPLKHRQRVHLHHGTSEVLARVVLLDRDE 56
Query: 352 MVMPGDNVLITVRLINPIAMEEGLRFAIREG 382
+ PG+ L +RL P+ G RF +R
Sbjct: 57 LA-PGEEALAQLRLEEPLVALRGDRFILRSY 86
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 31.8 bits (73), Expect = 1.2
Identities = 53/218 (24%), Positives = 87/218 (39%), Gaps = 43/218 (19%)
Query: 12 HINVGTIGHVDHGKTTLTAAIATVLSKKFGGEAKSYDQIDAAPEEKARGITINTAHIEYE 71
I + IG + GK++L AI GE +++ + G T ++ IE+E
Sbjct: 178 PIKIAIIGRPNVGKSSLINAIL--------GE----ERVIVSDIA---GTTRDSIDIEFE 222
Query: 72 TKARHYAHVDCPG---------HADYIKNMITGAA--QMDGAILVCSAADGPMPQTREHI 120
R Y +D G + T A + D +LV A +G Q
Sbjct: 223 RDGRKYVLIDTAGIRRKGKITESVEKYSVARTLKAIERADVVLLVIDATEGISEQDLRIA 282
Query: 121 LLARQVGVPYIVVFLNKADMVD-DEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLAL 179
L + G ++V NK D+V+ DE +E + ++R L +F PI+ SA
Sbjct: 283 GLIEEAGRGIVIVV-NKWDLVEEDEATMEEFKKKLRRKLPFLDF----APIVFISAL--- 334
Query: 180 EGDTG-PLGE--QSILSLSKALDTYIPTP--NRAIDGA 212
TG L + ++I + + I T NR ++ A
Sbjct: 335 ---TGQGLDKLFEAIKEIYECATRRISTSLLNRVLEDA 369
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 31.2 bits (72), Expect = 1.3
Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 10/78 (12%)
Query: 100 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDD-EELLELVEIEIRELL 158
D + V A + P + ++V P I+V LNK D+V D EELL L+E E+ EL+
Sbjct: 86 DLVLFVVDADEKIGPGDEFILEKLKKVKTPVILV-LNKIDLVKDKEELLPLLE-ELSELM 143
Query: 159 NKYEFPGNDIPIIKGSAK 176
+ E +PI SA
Sbjct: 144 DFAEI----VPI---SAL 154
>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 = 30.3 bits (69), Expect = 1.6
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 132 VVFLNKADMVDDEELLELVEIEIREL 157
++ +NK D+ LE +E ++R L
Sbjct: 145 LIVINKTDLAPAVADLEKLEADLRRL 170
>gnl|CDD|198392 cd10445, GIY-YIG_bI1_like, Catalytic GIY-YIG domain of putative
intron-encoded endonuclease bI1 and similar proteins.
The prototype of this family is a putative
intron-encoded mitochondrial DNA endonuclease bI1 found
in mitochondrion Ustilago maydis. This protein may arise
from proteolytic cleavage of an in-frame translation of
COB exon 1 plus intron 1, containing the bI1 open
reading frame. It contains an N-terminal truncated
non-functional cytochrome b region and a C-terminal
intron-encoded endonuclease bI1 region. The bI1 region
shows high sequence similarity to endonucleases of group
I introns of fungi and phage and might be involved in
intron homing. Many uncharacterized bI1 homologs
existing in fungi and chlorophyta in this family do not
contain the cytochrome b region, but have a standalone
bI1-like region, which contains a GIY-YIG domain and a
minor-groove binding alpha-helix nuclease-associated
modular domain (NUMOD). This family also includes a
Yarrowia lipolytica mobile group-II intron COX1-i1, also
called intron alpha, encoding protein with reverse
transcriptase activity. The group-II intron COX1-i1 may
be involv ed both in the generation of the circular
multimeric DNA molecules (senDNA alpha) which amplify
during the senescence syndrome and in the generation of
the site-specific deletion which accumulates in the
premature-death syndrome.
Length = 88
Score = 29.1 bits (66), Expect = 1.6
Identities = 19/50 (38%), Positives = 23/50 (46%), Gaps = 9/50 (18%)
Query: 400 NKINIDKGKEYIERSINNKKRW--YVIHSYSGMEKNVQRKLIERINKLGM 447
NKIN GK Y+ SIN KR Y+ SY + R L K G+
Sbjct: 8 NKIN---GKIYVGSSINLYKRLRSYLNPSYLKKNSPILRAL----LKYGL 50
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 31.0 bits (71), Expect = 1.8
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 129 PYIVVFLNKADMVDDEELLELVEIEIRE 156
P +VV LNK D+ D EL E V E+
Sbjct: 286 PRLVV-LNKIDVPDARELAEFVRPELEA 312
>gnl|CDD|107364 cd06369, PBP1_GC_C_enterotoxin_receptor, Ligand-binding domain of
the membrane guanylyl cyclase C. Ligand-binding domain
of the membrane guanylyl cyclase C (GC-C or StaR). StaR
is a key receptor for the STa (Escherichia coli Heat
Stable enterotoxin), a potent stimulant of intestinal
chloride and bicarbonate secretion that cause acute
secretory diarrhea. The catalytic domain of the
STa/guanylin receptor type membrane GC is highly similar
to those of the natriuretic peptide receptor (NPR) type
and sensory organ-specific type membrane GCs (GC-D, GC-E
and GC-F). The GC-C receptor is mainly expressed in the
intestine of most vertebrates, but is also found in the
kidney and other organs. Moreover, GC-C is activated by
guanylin and uroguanylin, endogenous peptide ligands
synthesized in the intestine and kidney. Consequently,
the receptor activation results in increased cGMP levels
and phosphorylation of the CFTR chloride channel and
secretion.
Length = 380
Score = 30.8 bits (70), Expect = 1.8
Identities = 19/63 (30%), Positives = 24/63 (38%), Gaps = 18/63 (28%)
Query: 230 VTGRVERGIVRVGEELEIIGIKDTV------------------KTTCTGVEMFRKLLDQG 271
V VE I V E L G+ TV +TC GVE+ +KL G
Sbjct: 20 VKEAVEEAIEIVAERLAEAGLNVTVNANFEGFNTSLYRSRGCRSSTCEGVELLKKLSVTG 79
Query: 272 QAG 274
+ G
Sbjct: 80 RLG 82
>gnl|CDD|239679 cd03708, GTPBP_III, Domain III of the GP-1 family of GTPase. This
group includes proteins similar to GTPBP1 and GTPBP2.
GTPB1 is structurally, related to elongation factor 1
alpha, a key component of protein biosynthesis
machinery. Immunohistochemical analyses on mouse tissues
revealed that GTPBP1 is expressed in some neurons and
smooth muscle cells of various organs as well as
macrophages. Immunofluorescence analyses revealed that
GTPBP1 is localized exclusively in cytoplasm and shows a
diffuse granular network forming a gradient from the
nucleus to the periphery of the cells in smooth muscle
cell lines and macrophages. No significant difference
was observed in the immune response to protein antigen
between mutant mice and wild-type mice, suggesting
normal function of antigen-presenting cells of the
mutant mice. The absence of an eminent phenotype in
GTPBP1-deficient mice may be due to functional
compensation by GTPBP2, which is similar to GTPBP1 in
structure and tissue distribution.
Length = 87
Score = 28.7 bits (65), Expect = 1.9
Identities = 21/79 (26%), Positives = 31/79 (39%), Gaps = 9/79 (11%)
Query: 307 FTGEIYALSKDEGGRH-TPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVLITVRL 365
F EI L H T Y+ + + T I +K+++ GD L+ R
Sbjct: 6 FEAEILVLH------HPTTISPGYQATVHIGSIRQTARIV-SIDKDVLRTGDRALVRFRF 58
Query: 366 IN-PIAMEEGLRFAIREGV 383
+ P + EG R REG
Sbjct: 59 LYHPEYLREGQRLIFREGR 77
>gnl|CDD|223597 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 30.7 bits (70), Expect = 1.9
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 93 ITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEI 152
+ ++DG + V AA L Q+ ++V LNK D+VD EEL L
Sbjct: 111 LADGVRLDGVVTVVDAAHFLEGLDAIAELAEDQLAFADVIV-LNKTDLVDAEELEALEAR 169
Query: 153 EIREL 157
+R+L
Sbjct: 170 -LRKL 173
>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 = 30.5 bits (70), Expect = 2.0
Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 11/63 (17%)
Query: 96 AAQMDGAILVCSAADGPMPQTREHILLARQV-------GVPYIVVFLNKADMVDDEELLE 148
A+ D + V A+D P E I +V +P I+V NK D++DDEEL E
Sbjct: 118 VAEADLLLHVVDASD---PDREEQIETVEEVLKELGADDIPIILVL-NKIDLLDDEELEE 173
Query: 149 LVE 151
+
Sbjct: 174 RLR 176
>gnl|CDD|193446 pfam12973, Cupin_7, ChrR Cupin-like domain. Members of this family
are part of the cupin superfamily. This family includes
the transcriptional activator ChrR.
Length = 91
Score = 28.7 bits (65), Expect = 2.3
Identities = 19/63 (30%), Positives = 21/63 (33%), Gaps = 23/63 (36%)
Query: 286 REDVERGQ----VLAKPGS-IKPHKHFTG-EIYALS---KDEGGR--------------H 322
R E + V PGS PH+H G EI L DE G H
Sbjct: 17 RFGGEVARATSLVRYAPGSRFPPHRHPGGEEILVLEGVFSDEHGDYPAGSYLRNPPGSSH 76
Query: 323 TPF 325
PF
Sbjct: 77 APF 79
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 30.6 bits (70), Expect = 2.5
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 6/40 (15%)
Query: 123 ARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYE 162
+G+ ++V LNK D++DDE + E L+ Y
Sbjct: 146 CETLGIEPLIV-LNKIDLLDDEGR-----AFVNEQLDIYR 179
>gnl|CDD|173387 PTZ00093, PTZ00093, nucleoside diphosphate kinase, cytosolic;
Provisional.
Length = 149
Score = 29.7 bits (67), Expect = 2.5
Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 417 NKKRWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRF 476
+ +R +++ G+++ + ++I+R K G + ++L PT EI +++ K K F
Sbjct: 1 SSERTFIMVKPDGVQRGLVGEIIKRFEKKGYKLVALKMLQPTPEI--AEEHYKEHKGKPF 58
Query: 477 FPGYV 481
FPG V
Sbjct: 59 FPGLV 63
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 29.7 bits (68), Expect = 2.6
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 5/47 (10%)
Query: 131 IVVFLNKADMVD-DEELLELVEIEIRELLNKYEFPGNDIPIIKGSAK 176
+++ +NK D+V+ DE+ ++ E E+R L ++ PI+ SA
Sbjct: 116 LIIVVNKWDLVEKDEKTMKEFEKELRRKLPFLDY----APIVFISAL 158
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 30.2 bits (69), Expect = 3.5
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 129 PYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPG 165
P IVV LNK D+ DEE LE ++ + E L F
Sbjct: 277 PRIVV-LNKIDLPLDEEELEELKKALAEALGWEVFYL 312
>gnl|CDD|213835 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members commonly
are called EngB based on homology to EngA, one of
several other GTPases of ribosome biogenesis. Cutoffs as
set find essentially all bacterial members, but also
identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about 80
percent of bacterial genomes [Protein synthesis, Other].
Length = 178
Score = 29.4 bits (67), Expect = 4.0
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 2/63 (3%)
Query: 101 GAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNK 160
G +L+ E I R+ G+P ++V L KAD + EL + ++ +I++ L K
Sbjct: 103 GVVLLMDIRHPLKELDLEMIEWLRERGIPVLIV-LTKADKLKKSELNKQLK-KIKKALKK 160
Query: 161 YEF 163
Sbjct: 161 DAD 163
>gnl|CDD|176502 cd08559, GDPD_periplasmic_GlpQ_like, Periplasmic
glycerophosphodiester phosphodiesterase domain (GlpQ)
and similar proteins. This subfamily corresponds to the
glycerophosphodiester phosphodiesterase domain (GDPD)
present in bacterial and eukaryotic
glycerophosphodiester phosphodiesterase (GP-GDE, EC
3.1.4.46) similar to Escherichia coli periplasmic
phosphodiesterase GlpQ. GP-GDEs are involved in glycerol
metabolism and catalyze the degradation of
glycerophosphodiesters to produce
sn-glycerol-3-phosphate (G3P) and the corresponding
alcohols, which are major sources of carbon and
phosphate. In E. coli, there are two major G3P uptake
systems: Glp and Ugp, which contain genes coding for two
different GP-GDEs. GlpQ gene from the glp operon codes
for a periplasmic phosphodiesterase GlpQ. GlpQ is a
dimeric enzyme that hydrolyzes periplasmic
glycerophosphodiesters, such as glycerophosphocholine
(GPC), glycerophosphoethanolanmine (GPE),
glycerophosphoglycerol (GPG), glycerophosphoinositol
(GPI), and glycerophosphoserine (GPS), to the
corresponding alcohols and G3P, which is subsequently
transported into the cell through the GlpT transport
system. Ca2+ is required for GlpQ enzymatic activity.
This subfamily also includes some GP-GDEs in higher
plants and their eukaryotic homologs, which show very
high sequence similarities with bacterial periplasmic
GP-GDEs.
Length = 296
Score = 29.5 bits (67), Expect = 4.6
Identities = 13/85 (15%), Positives = 26/85 (30%), Gaps = 20/85 (23%)
Query: 385 QFIQDNLLTKEIVNSNKINIDKGKEYIERSINNKKRWYVIHSYSGMEKNVQRKLIERINK 444
+ Q + I Y E K + +E+ KL+E + K
Sbjct: 116 ELAQG----LNKSTGRNVGI-----YPE----TKHPTFHKQEGPDIEE----KLLEVLKK 158
Query: 445 LGMQKKFGRILVPT---EEIVDVKK 466
G K + + + E + ++
Sbjct: 159 YGYTGKNDPVFIQSFEPESLKRLRN 183
>gnl|CDD|214971 smart01008, Ald_Xan_dh_C, Aldehyde oxidase and xanthine
dehydrogenase, a/b hammerhead domain. Aldehyde oxidase
catalyses the conversion of an aldehyde in the presence
of oxygen and water to an acid and hydrogen peroxide.
The enzyme is a homodimer, and requires FAD, molybdenum
and two 2FE-2S clusters as cofactors. Xanthine
dehydrogenase catalyses the hydrogenation of xanthine to
urate, and also requires FAD, molybdenum and two 2FE-2S
clusters as cofactors. This activity is often found in a
bifunctional enzyme with xanthine oxidase activity too.
The enzyme can be converted from the dehydrogenase form
to the oxidase form irreversibly by proteolysis or
reversibly through oxidation of sulphydryl groups.
Length = 107
Score = 27.9 bits (63), Expect = 5.2
Identities = 26/87 (29%), Positives = 36/87 (41%), Gaps = 21/87 (24%)
Query: 85 HADYIKNM-ITGAAQMDGAILVCSAADGP-----MPQTREHILLA----RQVGVPYIVVF 134
HA IK++ + A M G + V +A D P P + +LA R VG P V
Sbjct: 27 HAR-IKSIDTSAARAMPGVVAVLTAKDVPGLNDFGPLGPDEPVLADDKVRYVGQPVAAVV 85
Query: 135 LNKADMVDDEEL----LELVEIEIREL 157
+ EE E V++E EL
Sbjct: 86 ------AETEEAARDAAEAVKVEYEEL 106
>gnl|CDD|240370 PTZ00342, PTZ00342, acyl-CoA synthetase; Provisional.
Length = 746
Score = 29.7 bits (67), Expect = 5.2
Identities = 18/94 (19%), Positives = 36/94 (38%), Gaps = 9/94 (9%)
Query: 387 IQDNLLTKEIVNSNKINIDKGKEYIERSINNKKRWYVIHSYSGMEKNVQRKL-------I 439
I D L+ + +N NK + G N K + S +++ +
Sbjct: 206 ILDTLIKSKEININKEEKNNGSNVNNNGNKNNKEEQKGNDLSNELEDISLGPLEYDKEKL 265
Query: 440 ERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIK 473
E+I L ++K ++ + D+ KN+ + K
Sbjct: 266 EKIKDL--KEKAKKLGISIILFDDMTKNKTTNYK 297
>gnl|CDD|237498 PRK13768, PRK13768, GTPase; Provisional.
Length = 253
Score = 29.1 bits (66), Expect = 5.6
Identities = 12/27 (44%), Positives = 19/27 (70%), Gaps = 1/27 (3%)
Query: 127 GVPYIVVFLNKADMVDDEELLELVEIE 153
G+P I V LNKAD++ +EEL +++
Sbjct: 162 GLPQIPV-LNKADLLSEEELERILKWL 187
>gnl|CDD|181611 PRK09014, rfaH, transcriptional activator RfaH; Provisional.
Length = 162
Score = 28.7 bits (65), Expect = 6.0
Identities = 24/101 (23%), Positives = 46/101 (45%), Gaps = 11/101 (10%)
Query: 455 LVPTEEIVDVKKNQKSVIKKRFFPGYVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTP 514
++ E+IV K+ + S + FP Y+ +E + +++T+ V+ F+ +P
Sbjct: 32 MITLEKIVRGKRTEVS---EPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVR-FGAQPAI 87
Query: 515 ISSKEIEEILKQ--IKKGVEKPRPKILYQLDELVRIKDGPF 553
+ S I + L +K V+ PK + V I +G F
Sbjct: 88 VPSDVIYQ-LSVYKPEKIVDPETPKP----GDKVIITEGAF 123
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 29.1 bits (66), Expect = 6.5
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 8/47 (17%)
Query: 129 PYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSA 175
P +VF NK D++D+EE E + I E L G + P+ SA
Sbjct: 277 PRWLVF-NKIDLLDEEEAEERAK-AIVEAL------GWEGPVYLISA 315
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 29.2 bits (66), Expect = 6.9
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 131 IVVFLNKADMVDDEELLELV----EIEIRELLNKYEFPGNDIPIIKGS-AKLALEG 181
IVV +NK D+ D+E+L E+ E E L G + ++ K ALE
Sbjct: 283 IVVVINKIDIADEEKLEEIEASVLEEGGEEPLKISATKGCGLDKLREEVRKTALEP 338
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 29.1 bits (66), Expect = 7.0
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 96 AAQMDGAILVCSAADGPMPQTRE-HILLARQVGV-PYIVVFLNKADMVDD-EELLELVE 151
AA +D +VCS + E ++ LA + G P V+ L KAD+ +D EE + VE
Sbjct: 110 AANVDTVFIVCSLNHDFNLRRIERYLALAWESGAEP--VIVLTKADLCEDAEEKIAEVE 166
>gnl|CDD|188643 cd00956, Transaldolase_FSA, Transaldolase-like fructose-6-phosphate
aldolases (FSA) found in bacteria and archaea.
Transaldolase-like fructose-6-phosphate aldolases (FSA)
found in bacteria and archaea, which are member of the
MipB/TalC subfamily of class I aldolases. FSA catalyze
an aldol cleavage of fructose 6-phosphate and do not
utilize fructose, fructose 1-phosphate, fructose
1,6-phosphate, or dihydroxyacetone phosphate. The
enzymes belong to the transaldolase family that serves
in transfer reactions in the pentose phosphate cycle,
and are more distantly related to fructose
1,6-bisphosphate aldolase.
Length = 211
Score = 28.7 bits (65), Expect = 7.0
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 6/46 (13%)
Query: 121 LLARQVGVPYIVVFLNKAD--MVDDEELLELVEIEIRELLNKYEFP 164
LLA + G Y+ F+ + D D EL+ EIR + + Y F
Sbjct: 116 LLAAKAGATYVSPFVGRIDDLGGDGMELIR----EIRTIFDNYGFD 157
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 28.3 bits (64), Expect = 7.0
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 11/81 (13%)
Query: 100 DGAILVCSAADGP-MPQTRE--HILLARQ--VGVPYIVVFLNKADMVDDEELLELVEIEI 154
D I V +AD + + +E H LL + P +++ NK D+ + E EI
Sbjct: 83 DAVIFVVDSADRDRIEEAKEELHALLNEEELADAP-LLILANKQDLPGA-----MSEAEI 136
Query: 155 RELLNKYEFPGNDIPIIKGSA 175
RELL +E I SA
Sbjct: 137 RELLGLHELKDRPWEIQGCSA 157
>gnl|CDD|188126 TIGR01283, nifE, nitrogenase molybdenum-iron cofactor biosynthesis
protein NifE. This protein is part of the NifEN complex
involved in biosynthesis of the molybdenum-iron cofactor
used by the homologous NifDK complex of nitrogenase. In
a few species, the protein is found as a NifEN fusion
protein [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other, Central intermediary metabolism,
Nitrogen fixation].
Length = 453
Score = 28.9 bits (65), Expect = 7.9
Identities = 19/91 (20%), Positives = 32/91 (35%), Gaps = 18/91 (19%)
Query: 83 PGHADYIKNMITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVV--------- 133
G + Y + + A + ++ CS A + + E + G+PY
Sbjct: 228 TGDSRYAE--VQTAHRAKLNMVQCSKAMINLARKME-----EKYGIPYFEGSFYGIEDTS 280
Query: 134 --FLNKADMVDDEELLELVEIEIRELLNKYE 162
+ AD+ D ELL+ E I K
Sbjct: 281 KALRDIADLFGDPELLKRTEELIAREEAKIR 311
>gnl|CDD|237731 PRK14494, PRK14494, putative molybdopterin-guanine dinucleotide
biosynthesis protein MobB/FeS domain-containing protein
protein; Provisional.
Length = 229
Score = 28.4 bits (64), Expect = 8.3
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 15 VGTIGHVDHGKTTLTAAIATVLSKK 39
+G IG D GKTTL I L ++
Sbjct: 4 IGVIGFKDSGKTTLIEKILKNLKER 28
>gnl|CDD|206540 pfam14372, DUF4413, Domain of unknown function (DUF4413). This
domain is part of an RNase-H fold section of longer
proteins some of which are transposable elements
possibly of the Pong type, since some members are
putative Tam3 transposases.
Length = 101
Score = 27.1 bits (61), Expect = 8.3
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 130 YIVVFLNKADMVDDEELLELVEIEIRELLNKYE 162
+ +K D EE ++ V ++EL ++YE
Sbjct: 69 LLEFCFSKLYGDDAEEYIKEVRDTLKELFDEYE 101
>gnl|CDD|233855 TIGR02410, carnitine_TMLD, trimethyllysine dioxygenase. Members of
this family with known function act as trimethyllysine
dioxygenase, an enzyme in the pathway for carnitine
biosynthesis from lysine. This enzyme is homologous to
gamma-butyrobetaine,2-oxoglutarate dioxygenase, which
catalyzes the last step in carnitine biosynthesis.
Members of this family appear to be eukaryotic only.
Length = 362
Score = 29.0 bits (65), Expect = 8.5
Identities = 16/90 (17%), Positives = 34/90 (37%), Gaps = 4/90 (4%)
Query: 389 DNLLTKEIVNSNKINIDKGK---EYIERSINN-KKRWYVIHSYSGMEKNVQRKLIERINK 444
D E + + ID+ + + ++ K+ W + HSY ++ + LI K
Sbjct: 30 DITSLSEDIKPATVIIDEDTLRVTWPDGHVSKFKEDWLIRHSYEPKKEKNVKALILPNRK 89
Query: 445 LGMQKKFGRILVPTEEIVDVKKNQKSVIKK 474
+ +F + P+ + S +K
Sbjct: 90 IYWLAEFNELKDPSVHFKTTYDHTDSTLKS 119
>gnl|CDD|233591 TIGR01833, HMG-CoA-S_euk, 3-hydroxy-3-methylglutaryl-CoA-synthase,
eukaryotic clade. Hydroxymethylglutaryl(HMG)-CoA
synthase is the first step of isopentenyl pyrophosphate
(IPP) biosynthesis via the mevalonate pathway. This
pathway is found mainly in eukaryotes, but also in
archaea and some bacteria. This model is specific for
eukaryotes.
Length = 457
Score = 29.0 bits (65), Expect = 8.7
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 433 NVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRF 476
V KL+ER N + GR+ V TE I+D K+ K+V+ + F
Sbjct: 59 TVVSKLMERYNI--DYDQIGRLEVGTETIIDKSKSVKTVLMQLF 100
>gnl|CDD|223841 COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 451
Score = 28.8 bits (65), Expect = 8.7
Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 1 MAKSKFERTKPHINVGTIGHVDHGKTTLTAAIATVLSKKF 40
+AK+ ++ + + G GKTT +A +LS K
Sbjct: 93 LAKAYRQKFNAKV-IAITGSN--GKTTTKEMLAAILSTKG 129
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 29.1 bits (66), Expect = 8.7
Identities = 30/119 (25%), Positives = 42/119 (35%), Gaps = 25/119 (21%)
Query: 96 AAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIR 155
+ D + V A+ + I L + P IVV LNKAD+V EL
Sbjct: 294 IEEADLVLFVLDASQPLDKEDLALIELLPK-KKPIIVV-LNKADLVSKIELESEKLA--- 348
Query: 156 ELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFL 214
N II SAK TG + + +L +A+ +G FL
Sbjct: 349 ----------NGDAIISISAK------TG----EGLDALREAIKQLFGKGLGNQEGLFL 387
>gnl|CDD|240162 cd05126, Mth938, Mth938 domain. Mth938 is a hypothetical protein
encoded by the Methanobacterium thermoautotrophicum
(Mth) genome. This protein crystallizes as a dimer,
although it is monomeric in solution, with one disulfide
bond in each monomer. The function of the protein has
not been determined.
Length = 117
Score = 27.7 bits (62), Expect = 8.8
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 228 TVVTGRVERGIVRVGEE----LEIIGIKDTVKTTCTGVEMFRKLLDQG 271
+V G + G ++V E LE G++ V T V+ + +L +G
Sbjct: 61 VIVIGTGQSGALKVPPETVEKLEKRGVEVLVLPTEEAVKRYNELAGKG 108
>gnl|CDD|223563 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 265
Score = 28.5 bits (64), Expect = 9.0
Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 5/64 (7%)
Query: 80 VDC-PGHADYIKNMITGAAQM-DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNK 137
+D PG D T ++ DG ++V + + ++ I + + G+P + V N
Sbjct: 172 IDTPPGTGDAD---ATVLQRIPDGVVIVTTPGKTALEDVKKAIDMLEKAGIPVLGVVENM 228
Query: 138 ADMV 141
+ +
Sbjct: 229 SYFI 232
>gnl|CDD|226978 COG4631, XdhB, Xanthine dehydrogenase, molybdopterin-binding
subunit B [Nucleotide transport and metabolism].
Length = 781
Score = 29.0 bits (65), Expect = 9.3
Identities = 20/96 (20%), Positives = 35/96 (36%), Gaps = 11/96 (11%)
Query: 45 KSYDQIDAAPEEKARGITINTAHIEYETKARHYAHVDCPGHADYIKNMITGAAQMDGAIL 104
I P + RG + +E+ +H G A YI ++ A + GA+
Sbjct: 2 MMQHSIADLPTAEIRGGV--GTSLRHESAHKHVT-----GTAVYIDDIPEPAGTLHGALG 54
Query: 105 VCSAADGPMPQTREHILLARQVGVPYIVVFLNKADM 140
+ A + + L+ P +V L AD+
Sbjct: 55 LSERAHARI----TRMDLSAVRAAPGVVDVLTAADV 86
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.137 0.388
Gapped
Lambda K H
0.267 0.0825 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,303,474
Number of extensions: 3256567
Number of successful extensions: 4451
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4244
Number of HSP's successfully gapped: 219
Length of query: 593
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 491
Effective length of database: 6,413,494
Effective search space: 3149025554
Effective search space used: 3149025554
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: 62 (27.5 bits)