RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15224
(502 letters)
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 649 bits (1678), Expect = 0.0
Identities = 234/291 (80%), Positives = 257/291 (88%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
MITGAAQMDGAILV SAADGPMPQTREHILLARQVGVPYIVVFLNK DMVDDEELLELVE
Sbjct: 92 MITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFLNKCDMVDDEELLELVE 151
Query: 61 IEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDG 120
+E+RELL+KY+FPG+D PII+GSA ALEGD E+ IL L A+D+YIPTP RAID
Sbjct: 152 MEVRELLSKYDFPGDDTPIIRGSALKALEGDDDEEWEKKILELMDAVDSYIPTPERAIDK 211
Query: 121 AFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQG 180
FL+P+EDVFSISGRGTVVTGRVERGI++VGEE+EI+GI+DT KTT TGVEMFRKLLD+G
Sbjct: 212 PFLMPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIRDTQKTTVTGVEMFRKLLDEG 271
Query: 181 QAGDNIGLLLRGTKREDVERGQVLAKPGSIKPHKHFTGEIYALSKDEGGRHTPFFSNYRP 240
QAGDN+G LLRG KREDVERGQVLAKPGSI PH F E+Y LSK+EGGRHTPFF+ YRP
Sbjct: 272 QAGDNVGALLRGIKREDVERGQVLAKPGSITPHTKFEAEVYVLSKEEGGRHTPFFNGYRP 331
Query: 241 QFYFRTTDVTGSIELPKNKEMVMPGDNVLITVRLINPIAMEEGLRFAIREG 291
QFYFRTTDVTG IELP+ EMVMPGDNV +TV LI PIAMEEGLRFAIREG
Sbjct: 332 QFYFRTTDVTGVIELPEGVEMVMPGDNVEMTVELIAPIAMEEGLRFAIREG 382
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 644 bits (1664), Expect = 0.0
Identities = 235/291 (80%), Positives = 259/291 (89%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
MITGAAQMDGAILV SAADGPMPQTREHILLARQVGVPYIVVFLNK DMVDDEELLELVE
Sbjct: 92 MITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFLNKCDMVDDEELLELVE 151
Query: 61 IEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDG 120
+E+RELL+KY+FPG+D PII+GSA ALEGD E IL L A+D+YIP P RAID
Sbjct: 152 MEVRELLSKYDFPGDDTPIIRGSALKALEGDDDEEWEAKILELMDAVDSYIPEPERAIDK 211
Query: 121 AFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQG 180
FL+P+EDVFSISGRGTVVTGRVERGIV+VG+E+EI+GIK+T KTT TGVEMFRKLLD+G
Sbjct: 212 PFLMPIEDVFSISGRGTVVTGRVERGIVKVGDEVEIVGIKETQKTTVTGVEMFRKLLDEG 271
Query: 181 QAGDNIGLLLRGTKREDVERGQVLAKPGSIKPHKHFTGEIYALSKDEGGRHTPFFSNYRP 240
QAGDN+G+LLRGTKREDVERGQVLAKPGSIKPH F E+Y LSK+EGGRHTPFF+ YRP
Sbjct: 272 QAGDNVGVLLRGTKREDVERGQVLAKPGSIKPHTKFEAEVYVLSKEEGGRHTPFFNGYRP 331
Query: 241 QFYFRTTDVTGSIELPKNKEMVMPGDNVLITVRLINPIAMEEGLRFAIREG 291
QFYFRTTDVTG+IELP+ EMVMPGDNV +TV LI PIAMEEGLRFAIREG
Sbjct: 332 QFYFRTTDVTGTIELPEGVEMVMPGDNVKMTVELIAPIAMEEGLRFAIREG 382
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 587 bits (1516), Expect = 0.0
Identities = 222/291 (76%), Positives = 257/291 (88%), Gaps = 2/291 (0%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
MITGAAQMDGAILV +A DGPMPQTREHILLARQVGVPY+VVFLNK D+VDDEELLELVE
Sbjct: 92 MITGAAQMDGAILVVAATDGPMPQTREHILLARQVGVPYLVVFLNKVDLVDDEELLELVE 151
Query: 61 IEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDG 120
+E+RELL++Y+FPG+DIP+I+GSA ALEGD P E +I+ L A+D YIPTP R D
Sbjct: 152 MEVRELLSEYDFPGDDIPVIRGSALKALEGD--PKWEDAIMELMDAVDEYIPTPERDTDK 209
Query: 121 AFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQG 180
FL+PVEDVF+I+GRGTVVTGRVERG V+VG+E+EI+GIK+T KT TGVEMFRKLLD+G
Sbjct: 210 PFLMPVEDVFTITGRGTVVTGRVERGTVKVGDEVEIVGIKETQKTVVTGVEMFRKLLDEG 269
Query: 181 QAGDNIGLLLRGTKREDVERGQVLAKPGSIKPHKHFTGEIYALSKDEGGRHTPFFSNYRP 240
QAGDN+G+LLRG R++VERGQVLAKPGSIKPH F E+Y L+K+EGGRHTPFF+NYRP
Sbjct: 270 QAGDNVGVLLRGVDRDEVERGQVLAKPGSIKPHTKFKAEVYILTKEEGGRHTPFFNNYRP 329
Query: 241 QFYFRTTDVTGSIELPKNKEMVMPGDNVLITVRLINPIAMEEGLRFAIREG 291
QFYFRTTDVTGSIELP+ EMVMPGDNV ITV LI+PIAME+GL+FAIREG
Sbjct: 330 QFYFRTTDVTGSIELPEGTEMVMPGDNVTITVELIHPIAMEQGLKFAIREG 380
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 553 bits (1428), Expect = 0.0
Identities = 229/291 (78%), Positives = 253/291 (86%), Gaps = 2/291 (0%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
MITGAAQMDGAILV +A DGPMPQTREHILLARQVGVPYIVVFLNK DMVDDEELLELVE
Sbjct: 92 MITGAAQMDGAILVVAATDGPMPQTREHILLARQVGVPYIVVFLNKVDMVDDEELLELVE 151
Query: 61 IEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDG 120
+E+RELL++Y FPG+D PII+GSA ALEGD E I L A+D+YIPTP R ID
Sbjct: 152 MEVRELLSEYGFPGDDTPIIRGSALKALEGD--AKWEAKIEELMDAVDSYIPTPERDIDK 209
Query: 121 AFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQG 180
FL+PVEDVFSISGRGTVVTGRVERGI++VGEE+EI+GIK+T KTT TGVEMFRKLLD+G
Sbjct: 210 PFLMPVEDVFSISGRGTVVTGRVERGILKVGEEVEIVGIKETQKTTVTGVEMFRKLLDEG 269
Query: 181 QAGDNIGLLLRGTKREDVERGQVLAKPGSIKPHKHFTGEIYALSKDEGGRHTPFFSNYRP 240
QAGDN+G+LLRG KREDVERGQVLAKPGSIKPH F E+Y LSK+EGGRHTPFF YRP
Sbjct: 270 QAGDNVGVLLRGVKREDVERGQVLAKPGSIKPHTKFEAEVYVLSKEEGGRHTPFFHGYRP 329
Query: 241 QFYFRTTDVTGSIELPKNKEMVMPGDNVLITVRLINPIAMEEGLRFAIREG 291
QFYFRTTDVTG+I LP+ EMVMPGDNV + V LI+PIAMEEGLRFAIREG
Sbjct: 330 QFYFRTTDVTGAITLPEGVEMVMPGDNVKMVVELIHPIAMEEGLRFAIREG 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 = 532 bits (1371), Expect = 0.0
Identities = 224/291 (76%), Positives = 252/291 (86%), Gaps = 2/291 (0%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
MITGAAQMDGAILV SA DGPMPQTREHILLARQVGVPYIVVFLNK DMVDDEELLELVE
Sbjct: 92 MITGAAQMDGAILVVSATDGPMPQTREHILLARQVGVPYIVVFLNKCDMVDDEELLELVE 151
Query: 61 IEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDG 120
+E+RELL++Y+FPG+D PII+GSA ALEGD E IL L A+D YIPTP R D
Sbjct: 152 MEVRELLSEYDFPGDDTPIIRGSALKALEGD--AEWEAKILELMDAVDEYIPTPERETDK 209
Query: 121 AFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQG 180
FL+P+EDVFSI+GRGTVVTGRVERGIV+VGEE+EI+G+KDT KTT TGVEMFRK LD+G
Sbjct: 210 PFLMPIEDVFSITGRGTVVTGRVERGIVKVGEEVEIVGLKDTRKTTVTGVEMFRKELDEG 269
Query: 181 QAGDNIGLLLRGTKREDVERGQVLAKPGSIKPHKHFTGEIYALSKDEGGRHTPFFSNYRP 240
+AGDN+GLLLRG KRE++ERG VLAKPGSIKPH F E+Y L K+EGGRHTPFFS YRP
Sbjct: 270 RAGDNVGLLLRGIKREEIERGMVLAKPGSIKPHTKFEAEVYVLKKEEGGRHTPFFSGYRP 329
Query: 241 QFYFRTTDVTGSIELPKNKEMVMPGDNVLITVRLINPIAMEEGLRFAIREG 291
QFYFRTTDVTGSI LP+ EMVMPGDNV +TV LI+PIA+E+G+RFAIREG
Sbjct: 330 QFYFRTTDVTGSITLPEGVEMVMPGDNVKMTVELISPIALEQGMRFAIREG 380
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 508 bits (1310), Expect = e-178
Identities = 203/293 (69%), Positives = 243/293 (82%), Gaps = 2/293 (0%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
MITGAAQMDG ILV SA DGPMPQT+EHILLARQVGVP +VVFLNK D+VDDEELLELVE
Sbjct: 141 MITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLVVFLNKVDVVDDEELLELVE 200
Query: 61 IEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDG 120
+E+RELL+ Y+FPG++IPII+GSA AL+G +G+ +IL L A+D YIP P R +D
Sbjct: 201 MELRELLSFYKFPGDEIPIIRGSALSALQGTNDEIGKNAILKLMDAVDEYIPEPVRVLDK 260
Query: 121 AFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKD--TVKTTCTGVEMFRKLLD 178
FL+P+EDVFSI GRGTV TGRVE+G ++VGEE+EI+G++ +KTT TGVEMF+K+LD
Sbjct: 261 PFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEIVGLRPGGPLKTTVTGVEMFKKILD 320
Query: 179 QGQAGDNIGLLLRGTKREDVERGQVLAKPGSIKPHKHFTGEIYALSKDEGGRHTPFFSNY 238
QGQAGDN+GLLLRG KREDV+RGQV+ KPGSIK +K F EIY L+KDEGGRHTPFFSNY
Sbjct: 321 QGQAGDNVGLLLRGLKREDVQRGQVICKPGSIKTYKKFEAEIYVLTKDEGGRHTPFFSNY 380
Query: 239 RPQFYFRTTDVTGSIELPKNKEMVMPGDNVLITVRLINPIAMEEGLRFAIREG 291
RPQFY RT DVTG +ELP+ +MVMPGDNV LI+P+ +E G RFA+REG
Sbjct: 381 RPQFYLRTADVTGKVELPEGVKMVMPGDNVTAVFELISPVPLEPGQRFALREG 433
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 498 bits (1284), Expect = e-175
Identities = 199/304 (65%), Positives = 239/304 (78%), Gaps = 13/304 (4%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
MITGAAQMDGAILV SAADGPMPQT+EHILLA+QVGVP IVVFLNK D VDDEELLELVE
Sbjct: 92 MITGAAQMDGAILVVSAADGPMPQTKEHILLAKQVGVPNIVVFLNKEDQVDDEELLELVE 151
Query: 61 IEIRELLNKYEFPGNDIPIIKGSAKLALE----GDTGPLGEQS----ILSLSKALDTYIP 112
+E+RELL+KY+FPG+DIPI+ GSA LALE GE I +L A+D+YIP
Sbjct: 152 LEVRELLSKYDFPGDDIPIVSGSALLALEALTENPKIKRGENKWVDKIYNLMDAVDSYIP 211
Query: 113 TPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEM 172
TP R D FL+ +EDVFSI+GRGTV TGR+ERG V+VG+ +EI+G+++T TT TG+EM
Sbjct: 212 TPERDTDKPFLMAIEDVFSITGRGTVATGRIERGTVKVGDTVEIVGLRETKTTTVTGLEM 271
Query: 173 FRKLLDQGQAGDNIGLLLRGTKREDVERGQVLAKPGSIKPHKHFTGEIYALSKDEGGRHT 232
F+K LD+G AGDN+G+LLRG ++ED+ERG VLAKPG+I PH F ++Y L+K+EGGRHT
Sbjct: 272 FQKTLDEGLAGDNVGILLRGIQKEDIERGMVLAKPGTITPHTKFEAQVYILTKEEGGRHT 331
Query: 233 PFFSNYRPQFYFRTTDVTGSIEL-----PKNKEMVMPGDNVLITVRLINPIAMEEGLRFA 287
PFF YRPQFY RTTDVTG IE EMVMPGD + +TV LI PIA+E+G+RFA
Sbjct: 332 PFFPGYRPQFYVRTTDVTGKIESFTADDGSKTEMVMPGDRIKMTVELIYPIAIEKGMRFA 391
Query: 288 IREG 291
IREG
Sbjct: 392 IREG 395
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 416 bits (1070), Expect = e-142
Identities = 198/304 (65%), Positives = 234/304 (76%), Gaps = 13/304 (4%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
MITGAAQMDGAILV S ADGPMPQT+EHILLA+QVGVP +VVFLNK D VDDEELLELVE
Sbjct: 161 MITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLELVE 220
Query: 61 IEIRELLNKYEFPGNDIPIIKGSAKLALEGDTG----PLGEQS----ILSLSKALDTYIP 112
+E+RELL+ YEFPG+DIPII GSA LALE G+ I L A+D+YIP
Sbjct: 221 LEVRELLSSYEFPGDDIPIISGSALLALEALMENPNIKRGDNKWVDKIYELMDAVDSYIP 280
Query: 113 TPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEM 172
P R D FLL VEDVFSI+GRGTV TGRVERG V+VGE ++I+G+++T TT TGVEM
Sbjct: 281 IPQRQTDLPFLLAVEDVFSITGRGTVATGRVERGTVKVGETVDIVGLRETRSTTVTGVEM 340
Query: 173 FRKLLDQGQAGDNIGLLLRGTKREDVERGQVLAKPGSIKPHKHFTGEIYALSKDEGGRHT 232
F+K+LD+ AGDN+GLLLRG ++ D++RG VLAKPGSI PH F +Y L K+EGGRH+
Sbjct: 341 FQKILDEALAGDNVGLLLRGIQKADIQRGMVLAKPGSITPHTKFEAIVYVLKKEEGGRHS 400
Query: 233 PFFSNYRPQFYFRTTDVTG---SIELPKNKE--MVMPGDNVLITVRLINPIAMEEGLRFA 287
PFF+ YRPQFY RTTDVTG SI K++E MVMPGD V + V LI P+A E+G+RFA
Sbjct: 401 PFFAGYRPQFYMRTTDVTGKVTSIMNDKDEESKMVMPGDRVKMVVELIVPVACEQGMRFA 460
Query: 288 IREG 291
IREG
Sbjct: 461 IREG 464
>gnl|CDD|180161 PRK05609, nusG, transcription antitermination protein NusG;
Validated.
Length = 181
Score = 282 bits (725), Expect = 4e-94
Identities = 106/178 (59%), Positives = 146/178 (82%)
Query: 325 NNKKRWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKR 384
+ KKRWYV+ +YSG EK V+ L RI LGM+ G +LVPTEE+V+VK +K ++++
Sbjct: 3 SMKKRWYVVQTYSGYEKKVKENLENRIETLGMEDLIGEVLVPTEEVVEVKNGKKKKVERK 62
Query: 385 FFPGYVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILKQIKKGVEKPR 444
FFPGYVL++M MTDESWHLV+NT VTGF+G ++PTP+S KE+E+ILKQ+++GVEKP+
Sbjct: 63 FFPGYVLVKMVMTDESWHLVRNTPGVTGFVGSTGSKPTPLSEKEVEKILKQLQEGVEKPK 122
Query: 445 PKILYQLDELVRIKDGPFTDFSGNIEEVNYEKSRVRVSVTIFGRATPVELEFNQVEKI 502
PK+ +++ E+VR+ DGPF DF+G +EEV+YEKS+++V V+IFGR TPVELEF+QVEKI
Sbjct: 123 PKVDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVSIFGRETPVELEFSQVEKI 180
>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 = 235 bits (601), Expect = 3e-75
Identities = 88/114 (77%), Positives = 96/114 (84%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
MITGAAQMDGAILV SA DGPMPQTREH+LLARQVGVPYIVVFLNKADMVDDEELLELVE
Sbjct: 82 MITGAAQMDGAILVVSATDGPMPQTREHLLLARQVGVPYIVVFLNKADMVDDEELLELVE 141
Query: 61 IEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTP 114
+E+RELL+KY F G+D PI++GSA ALEGD IL L ALD+YIPTP
Sbjct: 142 MEVRELLSKYGFDGDDTPIVRGSALKALEGDDPNKWVDKILELLDALDSYIPTP 195
>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 = 229 bits (586), Expect = 2e-73
Identities = 90/172 (52%), Positives = 130/172 (75%)
Query: 330 WYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPGY 389
WYV+ +YSG EK V++ L E I LGM ++VPTEE+V++KK +K V++++ FPGY
Sbjct: 1 WYVVQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGY 60
Query: 390 VLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILKQIKKGVEKPRPKILY 449
VL++M++TD SWHLVKNT VTGF+G +E++ IL +++G +KP+PKI +
Sbjct: 61 VLVKMDLTDVSWHLVKNTPGVTGFVGSGGKPKALSEDEEVKNILNALEEGKDKPKPKIDF 120
Query: 450 QLDELVRIKDGPFTDFSGNIEEVNYEKSRVRVSVTIFGRATPVELEFNQVEK 501
++ E VR+ DGPF +F+G +EEV+YEKS+++VSV+IFGR TPVELEF+QVEK
Sbjct: 121 EVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPVELEFSQVEK 172
>gnl|CDD|223328 COG0250, NusG, Transcription antiterminator [Transcription].
Length = 178
Score = 217 bits (556), Expect = 8e-69
Identities = 89/177 (50%), Positives = 128/177 (72%)
Query: 326 NKKRWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRF 385
KRWYV+ +YSG EK V+ L + LGM+ +LVPTEE+V+VK +K +++++
Sbjct: 1 LMKRWYVVQTYSGQEKKVKENLERKAELLGMEDLIFEVLVPTEEVVEVKGKRKVIVERKL 60
Query: 386 FPGYVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILKQIKKGVEKPRP 445
FPGYVL+EM+MTDE+WHLV+NT VTGF+G +P P+S +EIE IL +++ V +P
Sbjct: 61 FPGYVLVEMDMTDEAWHLVRNTPGVTGFVGSGGAKPVPLSEEEIEHILGFLEEEVAPKKP 120
Query: 446 KILYQLDELVRIKDGPFTDFSGNIEEVNYEKSRVRVSVTIFGRATPVELEFNQVEKI 502
K+ ++ ++VRI DGPF F +EEV+ EK +++V V+IFGR TPVELEF+QVEK+
Sbjct: 121 KVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIFGRPTPVELEFDQVEKL 177
>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 (423), Expect = 2e-50
Identities = 61/81 (75%), Positives = 69/81 (85%)
Query: 211 KPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVLI 270
KPH F E+Y L+K+EGGRHTPFFS YRPQFY RTTDVTGSI LP+ EMVMPGDNV +
Sbjct: 1 KPHTKFEAEVYVLTKEEGGRHTPFFSGYRPQFYIRTTDVTGSITLPEGTEMVMPGDNVKM 60
Query: 271 TVRLINPIAMEEGLRFAIREG 291
TV LI+PIA+E+GLRFAIREG
Sbjct: 61 TVELIHPIALEKGLRFAIREG 81
>gnl|CDD|239668 cd03697, EFTU_II, EFTU_II: Elongation factor Tu domain II.
Elongation factors Tu (EF-Tu) are three-domain GTPases
with an essential function in the elongation phase of
mRNA translation. The GTPase center of EF-Tu is in the
N-terminal domain (domain I), also known as the
catalytic or G-domain. The G-domain is composed of about
200 amino acid residues, arranged into a predominantly
parallel six-stranded beta-sheet core surrounded by
seven a-helices. Non-catalytic domains II and III are
beta-barrels of seven and six, respectively,
antiparallel beta-strands that share an extended
interface. Either non-catalytic domain is composed of
about 100 amino acid residues. EF-Tu proteins exist in
two principal conformations: in a compact one,
EF-Tu*GTP, with tight interfaces between all three
domains and a high affinity for aminoacyl-tRNA, and in
an open one, EF-Tu*GDP, with essentially no
G-domain-domain II interactions and a low affinity for
aminoacyl-tRNA. EF-Tu has approximately a 100-fold
higher affinity for GDP than for GTP.
Length = 87
Score = 165 bits (421), Expect = 4e-50
Identities = 63/87 (72%), Positives = 78/87 (89%)
Query: 122 FLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQ 181
FL+P+EDVFSI GRGTVVTGR+ERG ++VG+E+EI+G +T+KTT TG+EMFRK LD+ +
Sbjct: 1 FLMPIEDVFSIPGRGTVVTGRIERGTIKVGDEVEIVGFGETLKTTVTGIEMFRKTLDEAE 60
Query: 182 AGDNIGLLLRGTKREDVERGQVLAKPG 208
AGDN+G+LLRG KREDVERG VLAKPG
Sbjct: 61 AGDNVGVLLRGVKREDVERGMVLAKPG 87
>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 = 157 bits (400), Expect = 1e-46
Identities = 54/108 (50%), Positives = 79/108 (73%), Gaps = 1/108 (0%)
Query: 329 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPG 388
+WYV+H+YSG E V+ L +RI G++ G +LVPTEE+V+VK +K V +++ FPG
Sbjct: 1 KWYVVHTYSGYENKVKENLEKRIESEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKLFPG 60
Query: 389 YVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILKQI 436
YVL+EM+M D++WHLV+NT VTGF+G +P P+S +E+E IL Q+
Sbjct: 61 YVLVEMDMNDDTWHLVRNTPGVTGFVGSG-GKPVPLSEEEVERILGQV 107
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 161 bits (410), Expect = 2e-44
Identities = 101/332 (30%), Positives = 153/332 (46%), Gaps = 62/332 (18%)
Query: 1 MITGAAQMDGAILVCSAADG-------PMPQTREHILLARQVGVPYIVVFLNKADMVD-D 52
MITGA+Q D A+LV A DG QTREH LAR +G+ ++V +NK D+V D
Sbjct: 102 MITGASQADVAVLVVDARDGEFEAGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWD 161
Query: 53 EELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGD------------TGPLGEQSI 100
EE E + E+ +LL + D+P I S +GD GP
Sbjct: 162 EERFEEIVSEVSKLLKMVGYNPKDVPFIPISG---FKGDNLTKKSENMPWYKGP------ 212
Query: 101 LSLSKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIK 160
+L +ALD + P R +D LP++DV+SISG GTV GRVE G+++ G+++ +
Sbjct: 213 -TLLEALD-QLEPPERPLDKPLRLPIQDVYSISGIGTVPVGRVESGVIKPGQKVTFMPAG 270
Query: 161 DTVKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERGQVLAKPGSIKPHKH---FT 217
V +EM + + Q + GDN+G +RG ++ D+ RG V+ P FT
Sbjct: 271 --VVGEVKSIEMHHEEISQAEPGDNVGFNVRGVEKNDIRRGDVIGHS--DNPPTVSPEFT 326
Query: 218 GEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSI-------------ELPKNKEMVMP 264
+I L S Y P + T V I +L +N + +
Sbjct: 327 AQIIVL-----WHPGIITSGYTPVLHAHTAQVACRIAELLSKLDPRTGKKLEENPQFLKR 381
Query: 265 GDNVLITVRLINPIAMEEGL------RFAIRE 290
GD ++ + P+ +E+ RFA+R+
Sbjct: 382 GDAAIVKIEPEKPLCLEKVSEIPQLGRFALRD 413
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 161 bits (409), Expect = 2e-44
Identities = 111/330 (33%), Positives = 169/330 (51%), Gaps = 65/330 (19%)
Query: 1 MITGAAQMDGAILVCSAAD--GPMPQTREHILLARQVGVPYIVVFLNKADMVD-DEELLE 57
MITGA+Q D A+LV +A D G MPQTREH+ LAR +G+ ++V +NK D V+ DE+ E
Sbjct: 101 MITGASQADAAVLVVAADDAGGVMPQTREHVFLARTLGINQLIVAINKMDAVNYDEKRYE 160
Query: 58 LVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGD------------TGPLGEQSILSLSK 105
V+ E+ +LL + +DIP I SA EGD GP +L +
Sbjct: 161 EVKEEVSKLLKMVGYKPDDIPFIPVSA---FEGDNVVKKSENMPWYNGP-------TLLE 210
Query: 106 ALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEEL--EIIGIKDTV 163
ALD + P + D +P++DV+SISG GTV GRVE G+++VG+++ G+ V
Sbjct: 211 ALDN-LKPPEKPTDKPLRIPIQDVYSISGVGTVPVGRVETGVLKVGDKVVFMPAGVVGEV 269
Query: 164 KTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERGQV---LAKPGSIKPHKHFTGEI 220
K+ +EM + L Q + GDNIG +RG ++D++RG V P ++ + FT +I
Sbjct: 270 KS----IEMHHEELPQAEPGDNIGFNVRGVGKKDIKRGDVCGHPDNPPTVA--EEFTAQI 323
Query: 221 YALSKDEGGRH-TPFFSNYRPQFYFRTTDVTGSIE-------------LPKNKEMVMPGD 266
L +H + Y P F+ T V + E +N + + GD
Sbjct: 324 VVL------QHPSAITVGYTPVFHAHTAQVACTFEELVKKLDPRTGQVAEENPQFIKTGD 377
Query: 267 NVLITVRLINPIAMEE-------GLRFAIR 289
++ ++ P+ +E+ G RFAIR
Sbjct: 378 AAIVKIKPTKPLVIEKVKEIPQLG-RFAIR 406
>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 = 140 bits (356), Expect = 2e-39
Identities = 59/113 (52%), Positives = 73/113 (64%), Gaps = 11/113 (9%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
MI GA+Q DGAILV A +G MPQTREH+LLA+ +GVP I+VF+NK D VDD EL E+VE
Sbjct: 83 MIRGASQADGAILVVDAVEGVMPQTREHLLLAKTLGVP-IIVFINKIDRVDDAELEEVVE 141
Query: 61 IEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPT 113
RELL KY F G +P++ GSA I L +ALD Y+P+
Sbjct: 142 EISRELLEKYGFGGETVPVVPGSALTGE----------GIDELLEALDLYLPS 184
>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 = 138 bits (348), Expect = 6e-36
Identities = 105/328 (32%), Positives = 158/328 (48%), Gaps = 58/328 (17%)
Query: 1 MITGAAQMDGAILVCSAADGP---MPQTREHILLARQVGVPYIVVFLNKADMVD-DEELL 56
MITGA+Q D A+LV + DG PQTREH LAR +G+ ++V +NK D V+ DEE
Sbjct: 102 MITGASQADAAVLVVAVGDGEFEVQPQTREHAFLARTLGINQLIVAINKMDSVNYDEEEF 161
Query: 57 ELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGDT------------GPLGEQSILSLS 104
E ++ E+ L+ K + + +P I SA GD G +L
Sbjct: 162 EAIKKEVSNLIKKVGYNPDTVPFIPISA---WNGDNVIKKSENTPWYKGK-------TLL 211
Query: 105 KALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEEL--EIIGIKDT 162
+ALD P P + D +P++DV+SI+G GTV GRVE G+++ G+++ E G+
Sbjct: 212 EALDALEP-PEKPTDKPLRIPIQDVYSITGVGTVPVGRVETGVLKPGDKVVFEPAGVSGE 270
Query: 163 VKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERGQVLAKPGS-IKPHKHFTGEIY 221
VK+ +EM + ++Q + GDNIG +RG ++D+ RG V P + K K FT +I
Sbjct: 271 VKS----IEMHHEQIEQAEPGDNIGFNVRGVSKKDIRRGDVCGHPDNPPKVAKEFTAQIV 326
Query: 222 ALSKDEGGRHTPFFSNYRPQFYFRTTDVTGS-IELPK------------NKEMVMPGDNV 268
L Y P F+ T + EL K N + + GD
Sbjct: 327 VLQHP-----GAITVGYTPVFHCHTAQIACRFDELLKKNDPRTGQVLEENPQFLKTGDAA 381
Query: 269 LITVRLINPIAMEEGL------RFAIRE 290
++ + P+ +E RFAIR+
Sbjct: 382 IVKFKPTKPMVIEAVKEIPPLGRFAIRD 409
>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 = 128 bits (323), Expect = 7e-36
Identities = 46/83 (55%), Positives = 54/83 (65%), Gaps = 5/83 (6%)
Query: 209 SIKPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNV 268
IKPH F ++Y L+ TP F+ YRP FY T DVTG LP KE VMPGDN
Sbjct: 1 PIKPHTKFKAQVYILNH-----PTPIFNGYRPVFYCHTADVTGKFILPGKKEFVMPGDNA 55
Query: 269 LITVRLINPIAMEEGLRFAIREG 291
++TV LI PIA+E+G RFAIREG
Sbjct: 56 IVTVELIKPIAVEKGQRFAIREG 78
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 133 bits (336), Expect = 5e-34
Identities = 77/292 (26%), Positives = 131/292 (44%), Gaps = 28/292 (9%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
++ G +D A+LV +A +G M QT EH+L+ +G+ ++ L KAD VD+ +E
Sbjct: 67 LLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGIKNGIIVLTKADRVDEAR----IE 122
Query: 61 IEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDG 120
+I+++L + I K SAK + I L L + R
Sbjct: 123 QKIKQILADLSLA--NAKIFKTSAKT----------GRGIEELKNELIDLLEEIERDEQK 170
Query: 121 AFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQG 180
F + ++ F++ G GTVVTG V G V+VG++L + I V+ ++ +++
Sbjct: 171 PFRIAIDRAFTVKGVGTVVTGTVLSGEVKVGDKLYLSPINKEVRV--RSIQAHDVDVEEA 228
Query: 181 QAGDNIGLLLRGTKREDVERGQVLAKPGSIKPHKHFTGEIYALSKDEGGRHTPFFSNYRP 240
+AG +GL L+G ++E++ERG L KP ++ E+ +
Sbjct: 229 KAGQRVGLALKGVEKEEIERGDWLLKPEPLEVTTRLIVELEIDPLFK----KTLKQGQPV 284
Query: 241 QFYFRTTDVTGSIE-LPKNKEMVM-----PGDNVLITVRLINPIAMEEGLRF 286
+ VTG I L KN E+ + GDN + +R + + G R
Sbjct: 285 HIHVGLRSVTGRIVPLEKNAELNLVKPIALGDNDRLVLRDNSAVIKLAGARV 336
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 127 bits (322), Expect = 7e-32
Identities = 91/300 (30%), Positives = 147/300 (49%), Gaps = 25/300 (8%)
Query: 7 QMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIREL 66
++D +LV +A DG T+EH+ +A + +P IVV + K DMV D+ +VE EI L
Sbjct: 226 KVDYGLLVVAADDGVTKMTKEHLGIALAMELPVIVV-VTKIDMVPDDRFQGVVE-EISAL 283
Query: 67 L---NKYEFPGNDIPIIKGSAKLALEGDT-GPLGEQSILSLSKALDTYI-------PTPN 115
L + D + +AK G P+ S ++ + LD
Sbjct: 284 LKRVGRIPLIVKDTDDVVLAAKAMKAGRGVVPIFYTSSVTG-EGLDLLDEFFLLLPKRRR 342
Query: 116 RAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDT--VKTTCTGVEMF 173
+G FL+ ++ ++S++G GTVV+G V+ GI+ VG+ + + KD + +EM
Sbjct: 343 WDDEGPFLMYIDKIYSVTGVGTVVSGSVKSGILHVGDTVLLGPFKDGKFREVVVKSIEMH 402
Query: 174 RKLLDQGQAGDNIGLLLRGTKREDVERGQVLAKPGSIKPHKHFTGEIYALSKDEGGRH-T 232
+D +AG IG+ L+G ++E++ERG VL+ K + F E+ L RH T
Sbjct: 403 HYRVDSAKAGSIIGIALKGVEKEELERGMVLSAGADPKAVREFDAEVLVL------RHPT 456
Query: 233 PFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVLITVRL-INPIAMEEGLRFAIREG 291
+ Y P F++ T E +K +MPGD ++ +R P +EEG +F REG
Sbjct: 457 TIRAGYEPVFHYETIREAVYFE-EIDKGFLMPGDRGVVRMRFKYRPHHVEEGQKFVFREG 515
>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 = 117 bits (296), Expect = 7e-32
Identities = 43/107 (40%), Positives = 68/107 (63%), Gaps = 1/107 (0%)
Query: 329 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPG 388
WY + + SG EK V L + LG++ K ILVPTEE+ ++++ +K V++++ FPG
Sbjct: 1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPG 60
Query: 389 YVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILKQ 435
Y+ +E ++ DE W ++ T V GF+GG +PTP+ EIE+ILK
Sbjct: 61 YIFVEADLEDEVWTAIRGTPGVRGFVGGG-GKPTPVPDDEIEKILKP 106
>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 = 119 bits (299), Expect = 1e-28
Identities = 77/310 (24%), Positives = 133/310 (42%), Gaps = 32/310 (10%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
I G +D A+LV A +G M QT EH+ + +G+P+ +V + KAD V++EE+ E
Sbjct: 67 AIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIPHTIVVITKADRVNEEEIKR-TE 125
Query: 61 IEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDG 120
+ ++++LN Y F N I K SAK G ++ + +L ++LD + I
Sbjct: 126 MFMKQILNSYIFLKN-AKIFKTSAK---TGQGIGELKKELKNLLESLD------IKRIQK 175
Query: 121 AFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQG 180
+ ++ F + G GTVVTG G V+VG+ L ++ I V+ ++ + ++
Sbjct: 176 PLRMAIDRAFKVKGAGTVVTGTAFSGEVKVGDNLRLLPINHEVRV--KAIQAQNQDVEIA 233
Query: 181 QAGDNIGLLLRGTKREDVERGQVLAKPGSIKPHKHFTGEIYALSKDEGGRHTPFFSNYRP 240
AG I L L + E ++RG ++ P P + A P
Sbjct: 234 YAGQRIALNLMDVEPESLKRGLLILTPED--PKLRVVVKFIA--------EVPLLELQPY 283
Query: 241 QFYFRTTDVTGSIELPKNK--EMVMP-------GDNVLITVRLINPIAMEEGLRFAIREG 291
+ TG I L + + GD +++ N +A L +R
Sbjct: 284 HIAHGMSVTTGKISLLDKGIALLTLDAPLILAKGDKLVLRDSSGNFLAGARVLEPPVRVK 343
Query: 292 VQQFIQDNLL 301
+ FI + +
Sbjct: 344 RKAFIAELIK 353
>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 = 102 bits (256), Expect = 2e-26
Identities = 39/81 (48%), Positives = 54/81 (66%)
Query: 211 KPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVLI 270
KPH ++Y LSK EGGRH PF SN++PQ + T D I+LP KEMVMPG++ +
Sbjct: 1 KPHDKVEAQVYILSKAEGGRHKPFVSNFQPQMFSLTWDCAARIDLPPGKEMVMPGEDTKV 60
Query: 271 TVRLINPIAMEEGLRFAIREG 291
T+ L P+ +E+G RF +R+G
Sbjct: 61 TLILRRPMVLEKGQRFTLRDG 81
>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 = 108 bits (271), Expect = 1e-25
Identities = 97/327 (29%), Positives = 149/327 (45%), Gaps = 73/327 (22%)
Query: 1 MITGAAQMDGAILVCSAADG-PMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELV 59
M++GAA MDGA+LV +A + P PQTREH++ +G+ IV+ NK D+V E+ LE
Sbjct: 97 MLSGAALMDGALLVIAANEPCPQPQTREHLMALEIIGIKNIVIVQNKIDLVSKEKALENY 156
Query: 60 EIEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAID 119
E EI+E + + PII SA L +I +L +A++ +IPTP R +D
Sbjct: 157 E-EIKEFVKGT--IAENAPIIPVSA----------LHNANIDALLEAIEKFIPTPERDLD 203
Query: 120 GAFLLPVEDVFSISGRGT--------VVTGRVERGIVRVGEELEII-GIKDT-------- 162
L+ V F ++ GT V+ G + +G ++VG+E+EI GIK
Sbjct: 204 KPPLMYVARSFDVNKPGTPPEKLKGGVIGGSLIQGKLKVGDEIEIRPGIKVEKGGKTKWE 263
Query: 163 -VKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTK------REDVERGQVLAKPGSIKPHKH 215
+ T T + +++ + G GL+ GTK + D GQV+ KPG++ P
Sbjct: 264 PIYTEITSLRAGGYKVEEARPG---GLVGVGTKLDPALTKADALAGQVVGKPGTLPPVWE 320
Query: 216 -FTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVLIT--- 271
E++ L + G T+ +E K E++M T
Sbjct: 321 SLELEVHLLERVVG------------------TEEELKVEPIKTGEVLMLNVGTATTVGV 362
Query: 272 ----------VRLINPIAMEEGLRFAI 288
V+L P+ EEG R AI
Sbjct: 363 VTSARKDEIEVKLKRPVCAEEGDRVAI 389
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 103 bits (260), Expect = 1e-23
Identities = 69/233 (29%), Positives = 110/233 (47%), Gaps = 22/233 (9%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
M+ G +D A+LV + DG M QTREH+ + + G P + V L KAD VD+ + E V
Sbjct: 68 MLAGVGGIDHALLVVACDDGVMAQTREHLAILQLTGNPMLTVALTKADRVDEARIAE-VR 126
Query: 61 IEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDG 120
+++ +L +Y F + + + A EG + I +L + L +P A
Sbjct: 127 RQVKAVLREYGFA--EAKLFVTA---ATEG-------RGIDALREHLLQ-LPEREHAAQH 173
Query: 121 AFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQG 180
F L ++ F++ G G VVTG G V+VG+ L + G+ ++ G+ + +Q
Sbjct: 174 RFRLAIDRAFTVKGAGLVVTGTALSGEVKVGDTLWLTGVNKPMRV--RGLHAQNQPTEQA 231
Query: 181 QAGDNIGLLLRG-TKREDVERGQ-VLAKPGSIKPHKHFTGEIYALSKDEGGRH 231
QAG I L + G ++E + RG +LA P + FT I L
Sbjct: 232 QAGQRIALNIAGDAEKEQINRGDWLLADA----PPEPFTRVIVELQTHTPLTQ 280
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 102 bits (257), Expect = 1e-23
Identities = 75/220 (34%), Positives = 110/220 (50%), Gaps = 25/220 (11%)
Query: 1 MITGAAQMDGAILVCSAADGPMP-------QTREHILLARQVGVPYIVVFLNKADMVD-- 51
MITG +Q D AILV ++ G QTREH LLA +GV ++V +NK D
Sbjct: 102 MITGTSQADVAILVVASTAGEFEAGISKDGQTREHALLAFTLGVKQMIVCINKMDDKTVN 161
Query: 52 -DEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSI-------LSL 103
+E + ++ E+ L K + +P I S +GD + E+S +L
Sbjct: 162 YSQERYDEIKKEVSAYLKKVGYNPEKVPFIPISG---WQGDN--MIEKSDNMPWYKGPTL 216
Query: 104 SKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTV 163
+ALDT P P R +D LP++DV+ I G GTV GRVE GI++ G + + V
Sbjct: 217 LEALDTLEP-PKRPVDKPLRLPLQDVYKIGGIGTVPVGRVETGILKPG--MVVTFAPSGV 273
Query: 164 KTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERGQV 203
T VEM + L + GDN+G ++ +D++RG V
Sbjct: 274 TTEVKSVEMHHEQLAEAVPGDNVGFNVKNVSVKDIKRGYV 313
>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 = 94.3 bits (235), Expect = 2e-22
Identities = 44/117 (37%), Positives = 58/117 (49%), Gaps = 15/117 (12%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
+ G AQ DGA+LV A +G PQTREH+ +A G I+V +NK D V EE + V
Sbjct: 79 TVRGLAQADGALLVVDANEGVEPQTREHLNIALA-GGLPIIVAVNKIDRV-GEEDFDEVL 136
Query: 61 IEIRELLNKYEF---PGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTP 114
EI+ELL F G D+PII SA + L A+ ++P P
Sbjct: 137 REIKELLKLIGFTFLKGKDVPIIPISALTGEGIEE----------LLDAIVEHLPPP 183
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 94.9 bits (237), Expect = 5e-21
Identities = 95/331 (28%), Positives = 147/331 (44%), Gaps = 81/331 (24%)
Query: 1 MITGAAQMDGAILVCSAADG-PMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELV 59
M++GAA MDGAILV +A + P PQT+EH++ +G+ IV+ NK D+V E LE
Sbjct: 102 MLSGAALMDGAILVIAANEPCPQPQTKEHLMALDIIGIKNIVIVQNKIDLVSKERALENY 161
Query: 60 EIEIRELLNKYEFPGN---DIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNR 116
E +I+E + G + PII SA L + +I +L +A++ IPTP R
Sbjct: 162 E-QIKEFVK-----GTVAENAPIIPVSA----------LHKVNIDALIEAIEEEIPTPER 205
Query: 117 AIDGAFLLPVEDVFSISGRGT--------VVTGRVERGIVRVGEELEII-GIKDTVK--- 164
+D + V F ++ GT V+ G + +G+++VG+E+EI GIK
Sbjct: 206 DLDKPPRMYVARSFDVNKPGTPPEKLKGGVIGGSLIQGVLKVGDEIEIRPGIKVEEGGKT 265
Query: 165 ------TTCTGVEMFRKLLDQGQAGDNIGLLLRGTK------REDVERGQVLAKPGSIKP 212
T + + +++ + G GL+ GTK + D G V KPG++ P
Sbjct: 266 KWEPITTKIVSLRAGGEKVEEARPG---GLVGVGTKLDPSLTKADALAGSVAGKPGTLPP 322
Query: 213 -HKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVM-------- 263
+ T E++ L + G T +E K E +M
Sbjct: 323 VWESLTIEVHLLERVVG------------------TKEELKVEPIKTGEPLMLNVGTATT 364
Query: 264 PG------DNVLITVRLINPIAMEEGLRFAI 288
G + V+L P+ EEG R AI
Sbjct: 365 VGVVTSARKDE-AEVKLKRPVCAEEGDRVAI 394
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 93.9 bits (234), Expect = 1e-20
Identities = 97/318 (30%), Positives = 148/318 (46%), Gaps = 55/318 (17%)
Query: 1 MITGAAQMDGAILVCSAADG-PMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELV 59
M++GAA MDGA+LV +A + P PQTREH++ +G+ I++ NK D+V E LE
Sbjct: 103 MLSGAALMDGALLVIAANEPCPQPQTREHLMALEIIGIKNIIIVQNKIDLVSRERALENY 162
Query: 60 EIEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAID 119
E +I+E + K N PII SA+ + +I +L +A++ YIPTP R +D
Sbjct: 163 E-QIKEFV-KGTVAEN-APIIPISAQH----------KANIDALIEAIEKYIPTPERDLD 209
Query: 120 GAFLLPVEDVFSISGRGT--------VVTGRVERGIVRVGEELEI---IGIKDTVKTTCT 168
+ V F ++ GT V+ G + +G++RVG+E+EI I ++ KT
Sbjct: 210 KPPRMYVARSFDVNKPGTPPEELKGGVIGGSLVQGVLRVGDEIEIRPGIVVEKGGKTVWE 269
Query: 169 GVEMFRKLLDQGQAGDNI-------GLLLRGTK------REDVERGQVLAKPGSIKPHKH 215
+ +++ QAG GL+ GTK + D GQV+ KPG++ P
Sbjct: 270 PI--TTEIVSL-QAGGEDVEEARPGGLVGVGTKLDPTLTKADALVGQVVGKPGTLPPVWT 326
Query: 216 -FTGEIYALSK----DEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVLI 270
E + L + E + P +N T G + K E I
Sbjct: 327 SIRIEYHLLERVVGTKEELKVEPIKTNEVLMLNVGTATTVGVVTSAKKDE---------I 377
Query: 271 TVRLINPIAMEEGLRFAI 288
V+L P+ E G R AI
Sbjct: 378 EVKLKRPVCAEIGERVAI 395
>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 = 84.1 bits (209), Expect = 5e-20
Identities = 32/85 (37%), Positives = 56/85 (65%), Gaps = 2/85 (2%)
Query: 122 FLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQ 181
F LP++ VF++ G+GTVVTG V G V+VG+++EI+ + + + +++ K +++ +
Sbjct: 1 FRLPIDRVFTVKGQGTVVTGTVLSGSVKVGDKVEILPLGEETRV--RSIQVHGKDVEEAK 58
Query: 182 AGDNIGLLLRGTKREDVERGQVLAK 206
AGD + L L G +D+ERG VL+
Sbjct: 59 AGDRVALNLTGVDAKDLERGDVLSS 83
>gnl|CDD|216991 pfam02357, NusG, Transcription termination factor nusG.
Length = 90
Score = 83.1 bits (206), Expect = 1e-19
Identities = 35/99 (35%), Positives = 59/99 (59%), Gaps = 12/99 (12%)
Query: 328 KRWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKN-QKSVIKKRFF 386
K+WYV+ + SG EK V L +++ +P EE+V+V+KN +K +++ F
Sbjct: 1 KKWYVLRTKSGQEKKVAENL---------ERQGIESFLPPEEVVEVRKNGRKKKVERPLF 51
Query: 387 PGYVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPIS 425
PGYV + M++ DE+W +++T VTGF+G +P P+
Sbjct: 52 PGYVFVRMDLNDETWA-IRSTPGVTGFVGFGG-KPAPVP 88
>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 = 79.8 bits (198), Expect = 6e-19
Identities = 28/56 (50%), Positives = 42/56 (75%)
Query: 446 KILYQLDELVRIKDGPFTDFSGNIEEVNYEKSRVRVSVTIFGRATPVELEFNQVEK 501
++ +++ + VRI GPF F G +EE++ EK +V+V V +FGR TPVEL+F+QVEK
Sbjct: 1 EVDFEVGDTVRIISGPFAGFEGKVEEIDEEKGKVKVLVEMFGRETPVELDFDQVEK 56
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 86.6 bits (215), Expect = 3e-18
Identities = 63/243 (25%), Positives = 107/243 (44%), Gaps = 37/243 (15%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVD-DEELLELV 59
M TGA+ D AIL+ A G + QTR H +A +G+ ++VV +NK D+VD EE+ E +
Sbjct: 103 MATGASTADLAILLVDARKGVLEQTRRHSFIASLLGIRHVVVAVNKMDLVDYSEEVFEAI 162
Query: 60 EIEIRELLNKYEFPGNDIPIIKGSAKLALEGD------------TGPLGEQSILSLSKAL 107
+ + D+ I S AL GD GP ++L + L
Sbjct: 163 VADYLAFAAQ--LGLKDVRFIPIS---ALLGDNVVSKSENMPWYKGP----TLLEI---L 210
Query: 108 DTYIPTPNRAIDGAFLLPVEDV--FSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKT 165
+T + + AF PV+ V ++ RG G + G V+VG+ E++ + +
Sbjct: 211 ET-VEIADDRSAKAFRFPVQYVNRPNLDFRG--YAGTIASGSVKVGD--EVVVLPSGKTS 265
Query: 166 TCTGVEMFRKLLDQGQAGDNIGLLLRGTKRE-DVERGQVLAKPGSI-KPHKHFTGEIYAL 223
+ F L Q AG+ + L+L E D+ RG ++ + F ++ +
Sbjct: 266 RVKRIVTFDGELAQASAGEAVTLVL---ADEIDISRGDLIVAADAPPAVADAFDADVVWM 322
Query: 224 SKD 226
++
Sbjct: 323 DEE 325
>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 = 77.3 bits (191), Expect = 9e-18
Identities = 27/70 (38%), Positives = 39/70 (55%)
Query: 136 GTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKR 195
GTV TGRVE G ++ G+++ I K T +EMF L + AG N G++L G
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGIGL 60
Query: 196 EDVERGQVLA 205
+D++RG L
Sbjct: 61 KDIKRGDTLT 70
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 85.1 bits (210), Expect = 9e-18
Identities = 88/326 (26%), Positives = 142/326 (43%), Gaps = 41/326 (12%)
Query: 1 MITGAAQMDGAILVCSAADGPMP-------QTREHILLARQVGVPYIVVFLNKADMVD-- 51
MITG +Q D A+L+ + G QTREH LLA +GV ++ NK D
Sbjct: 102 MITGTSQADCAVLIIDSTTGGFEAGISKDGQTREHALLAFTLGVKQMICCCNKMDATTPK 161
Query: 52 -DEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSI-------LSL 103
+ + + E+ L K + + IP + S EGD + E+S +L
Sbjct: 162 YSKARYDEIVKEVSSYLKKVGYNPDKIPFVPISG---FEGDN--MIERSTNLDWYKGPTL 216
Query: 104 SKALDTYIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTV 163
+ALD I P R D LP++DV+ I G GTV GRVE G+++ G + + +
Sbjct: 217 LEALDQ-INEPKRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPG--MVVTFGPTGL 273
Query: 164 KTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERGQVL--AKPGSIKPHKHFTGEIY 221
T VEM + L + GDN+G ++ +D++RG V +K K +FT ++
Sbjct: 274 TTEVKSVEMHHESLQEALPGDNVGFNVKNVAVKDLKRGYVASNSKDDPAKEAANFTSQVI 333
Query: 222 ALSK--DEGGRHTPFFSNYRPQFYFRTTDVTGSI------ELPKNKEMVMPGDNVLITVR 273
++ G + P + + ++ I EL K + + GD + +
Sbjct: 334 IMNHPGQIGNGYAPVLDCHTSHIAVKFAEILTKIDRRSGKELEKEPKFLKNGDAGFVKMI 393
Query: 274 LINPIAMEEGL------RFAIREGVQ 293
P+ +E RFA+R+ Q
Sbjct: 394 PTKPMVVETFSEYPPLGRFAVRDMRQ 419
>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 = 75.8 bits (187), Expect = 4e-17
Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 2/85 (2%)
Query: 122 FLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQ 181
V VF GRGTV TGRVE G ++ G+++ + VK ++ F+ +D+
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRFKGEVDEAV 60
Query: 182 AGDNIGLLLRGTKREDVERGQVLAK 206
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 = 74.7 bits (184), Expect = 1e-16
Identities = 33/104 (31%), Positives = 58/104 (55%), Gaps = 6/104 (5%)
Query: 330 WYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPGY 389
WYV+ +G E+ V+ KL+E+ + + VP +E+ + K+ + + K FPGY
Sbjct: 2 WYVLFVKTGREEKVE-KLLEKRFEANDIE----AFVPKKEVPERKRGKIEEVIKPLFPGY 56
Query: 390 VLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEIL 433
V +E +++ E + L++ V G +G P+P+S +EIE IL
Sbjct: 57 VFVETDLSPELYELIREVPGVIGILGNG-EEPSPVSDEEIEMIL 99
>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 = 76.9 bits (190), Expect = 2e-16
Identities = 38/85 (44%), Positives = 51/85 (60%), Gaps = 3/85 (3%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
M+ GA +D +LV +A +G MPQTREH+ + +G+ +V L KAD+V DE+ LELVE
Sbjct: 67 MLAGAGGIDAVLLVVAADEGIMPQTREHLEILELLGIKKGLVVLTKADLV-DEDRLELVE 125
Query: 61 IEIRELLNKYEFPGNDIPIIKGSAK 85
EI ELL D PI S+
Sbjct: 126 EEILELLAGTFLA--DAPIFPVSSV 148
>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 = 76.8 bits (190), Expect = 5e-16
Identities = 38/101 (37%), Positives = 52/101 (51%), Gaps = 13/101 (12%)
Query: 1 MITGAAQMDGAILVCSAADG-------PMPQTREHILLARQVGVPYIVVFLNKADMVD-- 51
MITGA+Q D A+LV SA G QTREH LLAR +GV ++V +NK D V
Sbjct: 94 MITGASQADVAVLVVSARKGEFEAGFEKGGQTREHALLARTLGVKQLIVAVNKMDDVTVN 153
Query: 52 -DEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGD 91
+E + ++ ++ L K + D+P I S GD
Sbjct: 154 WSQERYDEIKKKVSPFLKKVGYNPKDVPFIPIS---GFTGD 191
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 77.3 bits (191), Expect = 4e-15
Identities = 68/228 (29%), Positives = 107/228 (46%), Gaps = 41/228 (17%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVD-DEELLELV 59
M TGA+ D AIL+ A G + QTR H +A +G+ ++VV +NK D+VD EE+ E +
Sbjct: 124 MATGASTCDLAILLIDARKGVLDQTRRHSFIATLLGIKHLVVAVNKMDLVDYSEEVFERI 183
Query: 60 EIEIRELLNKYEFPGN-DIPIIKGSAKLALEGD------------TGPLGEQSILSLSKA 106
+ + PGN DI + S ALEGD +GP +L +
Sbjct: 184 REDYLTFAEQ--LPGNLDIRFVPLS---ALEGDNVVSQSESMPWYSGP-------TLLEV 231
Query: 107 LDTYIPTPNRAIDGAFLLPVEDVF--SISGRGTVVTGRVERGIVRVGEELEII--GIKDT 162
L+T + F PV+ V ++ RG G + G+V+VG+ ++++ G +
Sbjct: 232 LET-VDIQRVVDAQPFRFPVQYVNRPNLDFRG--YAGTLASGVVKVGDRVKVLPSGKESN 288
Query: 163 VKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKRE-DVERGQVLAKPGS 209
V T F L++ AG+ I L+L + E D+ RG +L
Sbjct: 289 VARIVT----FDGDLEEAFAGEAITLVL---EDEIDISRGDLLVAADE 329
>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 = 69.1 bits (170), Expect = 1e-14
Identities = 31/88 (35%), Positives = 50/88 (56%), Gaps = 6/88 (6%)
Query: 118 IDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEII--GIKDTVKTTCTGVEMFRK 175
D LP++DV+ I G GTV GRVE G+++ G + G+ VK+ VEM +
Sbjct: 1 TDKPLRLPIQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGVTGEVKS----VEMHHE 56
Query: 176 LLDQGQAGDNIGLLLRGTKREDVERGQV 203
L++ GDN+G ++ ++D++RG V
Sbjct: 57 PLEEALPGDNVGFNVKNVSKKDIKRGDV 84
>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 = 68.4 bits (168), Expect = 3e-13
Identities = 36/92 (39%), Positives = 51/92 (55%), Gaps = 6/92 (6%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVD-DEELLELV 59
M+TGA+ D AIL+ A G + QTR H +A +G+ ++VV +NK D+VD DEE+ E +
Sbjct: 95 MVTGASTADLAILLVDARKGVLEQTRRHSYIASLLGIRHVVVAVNKMDLVDYDEEVFEEI 154
Query: 60 EIEIRELLNKYEFPGNDIPIIKGSAKLALEGD 91
+ + DI I S ALEGD
Sbjct: 155 KADYLAFAASLGIE--DITFIPIS---ALEGD 181
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 70.8 bits (174), Expect = 4e-13
Identities = 67/239 (28%), Positives = 110/239 (46%), Gaps = 44/239 (18%)
Query: 1 MITGAAQMDGAILVCSAADG-PMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELV 59
M+ GAA MD A+L+ +A + P PQT EH+ + + +I++ NK D+V + + +
Sbjct: 134 MLNGAAVMDAALLLIAANESCPQPQTSEHLAAVEIMKLKHIIILQNKIDLVKEAQAQDQY 193
Query: 60 EIEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAID 119
E EIR + ++ PII SA+L D + + + T IP P R +
Sbjct: 194 E-EIRNFVKGTI--ADNAPIIPISAQLKYNIDV----------VLEYICTQIPIPKRDLT 240
Query: 120 GAFLL----------PVEDVFSISGRGTVVTGRVERGIVRVGEELEII-GI--KDTVKTT 166
+ P ED+ ++ +G V G + +G+++VG+E+EI GI KD+
Sbjct: 241 SPPRMIVIRSFDVNKPGEDIENL--KGGVAGGSILQGVLKVGDEIEIRPGIISKDS-GGE 297
Query: 167 CTGVEMFRKLLDQGQAGDNI-------GLLLRGTK------REDVERGQVLAKPGSIKP 212
T + +++ A +N GL+ GT R D GQVL PG +
Sbjct: 298 FTCRPIRTRIVSL-FAENNELQYAVPGGLIGVGTTIDPTLTRADRLVGQVLGYPGKLPE 355
>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 = 66.9 bits (163), Expect = 2e-12
Identities = 44/205 (21%), Positives = 87/205 (42%), Gaps = 35/205 (17%)
Query: 329 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVK-------------K 375
+WY+ + +G E V + ++ LG++ + E ++ K K
Sbjct: 1 QWYIATTINGNEDEVIENIKAKVRALGLENYISDFKILKEREIEEKVFEPKNGQAPRSMK 60
Query: 376 NQKS---------------VIKKRFFPGYVLIEMEMTDESWHLVKNTKKVTGFIG--GKS 418
N + + +K + GY+ I+M MT+++W L++NT+ VTG +G GK
Sbjct: 61 NTATTKWETLDETKYKKTKISEKNKYNGYIYIKMIMTEDAWFLIRNTENVTGLVGSSGKG 120
Query: 419 NRPTPISSKEIEEILKQIKKGVE-KPRPKILYQLDELVRIKDGPFTDFSGNIEEVNYEKS 477
+P PIS+ + ++ KG+ + ++L +V +++ F + I + K
Sbjct: 121 AKPIPISADADKL---KMLKGISENTKKRVLVTNTAIVEMEENKFDEKCQYILKHKQVKP 177
Query: 478 RVRVSVTIFG-RATPVELEFNQVEK 501
V+ G + EF V+
Sbjct: 178 EAIAQVSESGEIIDEIVEEFQLVDN 202
>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 = 65.4 bits (160), Expect = 2e-12
Identities = 41/117 (35%), Positives = 65/117 (55%), Gaps = 14/117 (11%)
Query: 1 MITGAAQMDGAILVCSAADG-PMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELV 59
M++GAA MDGA+L+ +A + P PQT EH+ +G+ +I++ NK D+V +E+ LE
Sbjct: 94 MLSGAAVMDGALLLIAANEPCPQPQTSEHLAALEIMGLKHIIILQNKIDLVKEEQALENY 153
Query: 60 EIEIRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNR 116
E +I+E + + PII SA+L + +I L + + IPTP R
Sbjct: 154 E-QIKEFVK--GTIAENAPIIPISAQL----------KYNIDVLCEYIVKKIPTPPR 197
>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 = 64.4 bits (157), Expect = 3e-12
Identities = 41/173 (23%), Positives = 74/173 (42%), Gaps = 16/173 (9%)
Query: 330 WYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPGY 389
WY+++ E+ Q L ER +P + + + ++ + + FP Y
Sbjct: 1 WYLLYCKPRQEQRAQEHL-ERQAV--------ECYLPMITVEKIVRGKRQAVSEPLFPNY 51
Query: 390 VLIEMEMTDESWHLVKNTKKVTGFI--GGKSNRPTPISSKEIEEILKQIKKGVEKPRPKI 447
+ IE + +SW +++T+ V+ F+ GG P P+ I ++ +Q + P
Sbjct: 52 LFIEFDPEVDSWTTIRSTRGVSRFVRFGGH---PAPVPDDLIHQL-RQYEPKDSVPPATT 107
Query: 448 LYQLDELVRIKDGPFTDFSGNIEEVNYEKSRVRVSVTIFGRATPVELEFNQVE 500
L + VRI DG F F E + EK R + + + G+ V + VE
Sbjct: 108 LPYKGDKVRITDGAFAGFEAIFLEPDGEK-RSMLLLNMIGKQIKVSVPNTSVE 159
>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 = 67.4 bits (165), Expect = 4e-12
Identities = 68/230 (29%), Positives = 105/230 (45%), Gaps = 40/230 (17%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVD-DEELLELV 59
M TGA+ D A+L+ A G + QTR H +A +G+ ++V+ +NK D+VD DEE+ E +
Sbjct: 97 MATGASTADLAVLLVDARKGVLEQTRRHSYIASLLGIRHVVLAVNKMDLVDYDEEVFENI 156
Query: 60 EIEIRELLNKYEFPGNDIPIIKGSAKLALEGD------------TGPLGEQSILSLSKAL 107
+ + + F D+ I S AL+GD +GP +L + L
Sbjct: 157 KKDYLAFAEQLGF--RDVTFIPLS---ALKGDNVVSRSESMPWYSGP-------TLLEIL 204
Query: 108 DTYIPTPNRAIDGAFLLPVEDVF--SISGRGTVVTGRVERGIVRVGEELEII--GIKDTV 163
+T + A D PV+ V ++ RG G + G V VG+E+ ++ G V
Sbjct: 205 ET-VEVERDAQDLPLRFPVQYVNRPNLDFRG--YAGTIASGSVHVGDEVVVLPSGRSSRV 261
Query: 164 KTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKRE-DVERGQVLAKPGSIKP 212
T F L+Q +AG + L L E D+ RG +LA S
Sbjct: 262 ARIVT----FDGDLEQARAGQAVTLTL---DDEIDISRGDLLAAADSAPE 304
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 67.3 bits (165), Expect = 7e-12
Identities = 66/228 (28%), Positives = 102/228 (44%), Gaps = 44/228 (19%)
Query: 1 MITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVD-DEELLELV 59
M+TGA+ D AI++ A G + QTR H +A +G+ ++V+ +NK D+VD D+E+ + +
Sbjct: 121 MVTGASTADLAIILVDARKGVLTQTRRHSFIASLLGIRHVVLAVNKMDLVDYDQEVFDEI 180
Query: 60 EIEIRELLNKYEFPGNDIPIIKGSAKLALEGD------------TGPLGEQSILSLSKAL 107
+ R K D+ I S AL+GD GP SL + L
Sbjct: 181 VADYRAFAAKLGLH--DVTFIPIS---ALKGDNVVTRSARMPWYEGP-------SLLEHL 228
Query: 108 DT-YIPTPNRAIDGAFLLPVEDV------FSISGRGTVVTGRVERGIVRVGEELEIIGIK 160
+T I + D F PV+ V F RG G V G+VR G+E+ ++
Sbjct: 229 ETVEIASDRNLKD--FRFPVQYVNRPNLDF----RG--FAGTVASGVVRPGDEVVVLPSG 280
Query: 161 DTVKTTCTGVEMFRKLLDQGQAGDNIGLLLRGTKREDVERGQVLAKPG 208
T + + LD+ AG + L L D+ RG +LA+
Sbjct: 281 KT--SRVKRIVTPDGDLDEAFAGQAVTLTLA--DEIDISRGDMLARAD 324
>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 = 62.9 bits (154), Expect = 1e-11
Identities = 37/83 (44%), Positives = 46/83 (55%), Gaps = 2/83 (2%)
Query: 4 GAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKAD-MVDDEELLELVEIE 62
GA+ D AILV +A DG MPQT E I A+ VP I+V +NK D E E V+ E
Sbjct: 69 GASVTDIAILVVAADDGVMPQTIEAINHAKAANVP-IIVAINKIDKPYGTEADPERVKNE 127
Query: 63 IRELLNKYEFPGNDIPIIKGSAK 85
+ EL E G D+ I+ SAK
Sbjct: 128 LSELGLVGEEWGGDVSIVPISAK 150
>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 = 62.7 bits (153), Expect = 2e-10
Identities = 48/186 (25%), Positives = 85/186 (45%), Gaps = 16/186 (8%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLN 68
DG +L+ A++GPMPQTR + A ++G+ IVV +NK D E+V+ E+ +L
Sbjct: 89 DGVLLLVDASEGPMPQTRFVLKKALELGLKPIVV-INKIDR-PSARPDEVVD-EVFDLF- 144
Query: 69 KYEFPGN----DIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFLL 124
E + D PI+ S + ++ L A+ ++P P +D +
Sbjct: 145 -AELGADDEQLDFPIVYASGRAGWASLDLDDPSDNMAPLFDAIVRHVPAPKGDLDEPLQM 203
Query: 125 PVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMF------RKLLD 178
V ++ G + GRV RG V+ G+++ ++ +D ++ R +D
Sbjct: 204 LVTNLDYDEYLGRIAIGRVHRGTVKKGQQVALMK-RDGTIENGRISKLLGFEGLERVEID 262
Query: 179 QGQAGD 184
+ AGD
Sbjct: 263 EAGAGD 268
>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 = 56.3 bits (136), Expect = 5e-10
Identities = 28/98 (28%), Positives = 38/98 (38%), Gaps = 22/98 (22%)
Query: 211 KPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELP-----------KNK 259
+ F EIY L E P Y+P T V G I K
Sbjct: 1 QAVDKFVAEIYVLDHPE-----PLSPGYKPVLNVGTAHVPGRIAKLLSKVDGKTEEKKPP 55
Query: 260 EMVMPGDNVLITVRLINPIAME------EGLRFAIREG 291
E + G+ ++ V L P+A+E EG RFA+R+G
Sbjct: 56 EFLKSGERGIVEVELQKPVALETFSENQEGGRFALRDG 93
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 60.7 bits (148), Expect = 8e-10
Identities = 47/188 (25%), Positives = 85/188 (45%), Gaps = 20/188 (10%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDD------EELLELVEIE 62
DG +L+ A++GPMPQTR + A +G+ IVV +NK D D +E+ +L +E
Sbjct: 93 DGVLLLVDASEGPMPQTRFVLKKALALGLKPIVV-INKIDRPDARPDEVVDEVFDLF-VE 150
Query: 63 IRELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDGAF 122
+ + +FP G+A L E + + L + + ++P P +D
Sbjct: 151 LGATDEQLDFPIVYASARNGTASLDPEDEADDMA-----PLFETILDHVPAPKGDLDEPL 205
Query: 123 LLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMF------RKL 176
+ V + S G + GR+ RG V+ +++ +I D ++ R
Sbjct: 206 QMQVTQLDYNSYVGRIGIGRIFRGTVKPNQQVALIK-SDGTTENGRITKLLGFLGLERIE 264
Query: 177 LDQGQAGD 184
+++ +AGD
Sbjct: 265 IEEAEAGD 272
>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 = 53.3 bits (129), Expect = 2e-08
Identities = 35/110 (31%), Positives = 52/110 (47%), Gaps = 7/110 (6%)
Query: 7 QMDGAILVCSAADGPMPQT-REHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRE 65
+ D I V SA D P+ ++ RE + + I LNK D++ +EEL E++E RE
Sbjct: 73 RADAVIFVLSA-DQPLTESEREFLKEILKWSGKKIFFVLNKIDLLSEEELEEVLE-YSRE 130
Query: 66 LLNKYEFPGNDIPIIKGSAKLALEG----DTGPLGEQSILSLSKALDTYI 111
L E G + I SAK ALE D L + L + L+ ++
Sbjct: 131 ELGVLELGGGEPRIFPVSAKEALEARLQGDEELLEQSGFEELEEHLEEFL 180
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 56.0 bits (136), Expect = 2e-08
Identities = 51/156 (32%), Positives = 70/156 (44%), Gaps = 25/156 (16%)
Query: 4 GAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEI 63
GA+ D AILV +A DG MPQT E I A+ GVP IVV +NK D + + V+ E
Sbjct: 75 GASVTDIAILVVAADDGVMPQTIEAINHAKAAGVP-IVVAINKIDKPEAN--PDKVKQE- 130
Query: 64 RELLNKYEFP----GNDIPIIKGSAKLALEGDTG---PLGEQSILSLSKALDTYIPTPNR 116
L +Y G D+ + SAK TG + IL L++ L+
Sbjct: 131 ---LQEYGLVPEEWGGDVIFVPVSAK------TGEGIDELLELILLLAEVLELKANPEGP 181
Query: 117 AIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRVGE 152
A G + D G G V T V+ G ++ G+
Sbjct: 182 AR-GTVIEVKLD----KGLGPVATVIVQDGTLKKGD 212
>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 = 48.7 bits (117), Expect = 2e-07
Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 3/84 (3%)
Query: 122 FLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEMFRKLLDQGQ 181
F LP+ D + GTVV+G+VE G ++ G+ L ++ K++V + + + +D
Sbjct: 2 FRLPISDKYK-DQGGTVVSGKVESGSIQKGDTLLVMPSKESV--EVKSIYVDDEEVDYAV 58
Query: 182 AGDNIGLLLRGTKREDVERGQVLA 205
AG+N+ L L+G ED+ G VL
Sbjct: 59 AGENVRLKLKGIDEEDISPGDVLC 82
>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 = 50.8 bits (122), Expect = 2e-07
Identities = 32/88 (36%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 2 ITGAAQ-MDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
I G AQ +D +LV A G QT E +++ + P IVV LNK D++ +EE +E
Sbjct: 85 IIGGAQIIDLMLLVVDAKKGIQTQTAECLVIGELLCKPLIVV-LNKIDLIPEEERKRKIE 143
Query: 61 I---EIRELLNKYEFPGNDIPIIKGSAK 85
+++ L K D PII SAK
Sbjct: 144 KMKKRLQKTLEKTRLK--DSPIIPVSAK 169
>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 = 48.4 bits (116), Expect = 2e-07
Identities = 23/87 (26%), Positives = 43/87 (49%), Gaps = 4/87 (4%)
Query: 122 FLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDT---VKTTCTGVEMFRKLLD 178
+++++S+ G GTVV G V +G++R+G+ L ++G T + R +
Sbjct: 1 AEFQIDEIYSVPGVGTVVGGTVSKGVIRLGDTL-LLGPDQDGSFRPVTVKSIHRNRSPVR 59
Query: 179 QGQAGDNIGLLLRGTKREDVERGQVLA 205
+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 = 47.9 bits (115), Expect = 2e-07
Identities = 29/90 (32%), Positives = 44/90 (48%), Gaps = 14/90 (15%)
Query: 122 FLLPVEDV--FSISGRGTVVTGRVERGIVRVGEELEII--GIKDTVKTTCTGVEMFRKLL 177
F PV+ V + RG G + G +RVG+E+ ++ G VK +E F L
Sbjct: 1 FRFPVQYVIRPNADFRG--YAGTIASGSIRVGDEVVVLPSGKTSRVK----SIETFDGEL 54
Query: 178 DQGQAGDNIGLLLRGTKRE-DVERGQVLAK 206
D+ AG+++ L L + E DV RG V+
Sbjct: 55 DEAGAGESVTLTL---EDEIDVSRGDVIVA 81
>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 = 48.9 bits (117), Expect = 2e-07
Identities = 31/115 (26%), Positives = 50/115 (43%), Gaps = 16/115 (13%)
Query: 330 WYVIHSYSGMEKNVQRKLIERINKLGMQKKFGR---ILVPTEEIVDVKKNQK-SVIKKRF 385
WY++ +G E E + + + R + VP+ + KN SV +K
Sbjct: 2 WYMLRVPAGRENQAA----EALERALATEFPDREFEVWVPSIPVDRKLKNGSISVKEKPL 57
Query: 386 FPGYVLIEMEMTDESWHLVKNTKKVTGFIGGKS--------NRPTPISSKEIEEI 432
FPGYVL+ + E + +++ V GF+G K P P+ +EIE I
Sbjct: 58 FPGYVLLRCVLNKEVYDFIRDNDSVYGFVGSKVGKTGKRQIEIPRPVPVEEIEAI 112
>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 = 52.1 bits (125), Expect = 5e-07
Identities = 49/150 (32%), Positives = 69/150 (46%), Gaps = 13/150 (8%)
Query: 4 GAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEI 63
GA D +LV +A DG MPQT E I A+ VP I+V +NK D + + V+ E+
Sbjct: 155 GAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVP-IIVAINKIDKPEAN--PDRVKQEL 211
Query: 64 REL-LNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDGAF 122
E L ++ G+ I + SA +G L IL S+ + PN G
Sbjct: 212 SEYGLVPEDWGGDTI-FVPVSALTG-DGIDELL--DMILLQSEVEE-LKANPNGQASGV- 265
Query: 123 LLPVEDVFSISGRGTVVTGRVERGIVRVGE 152
V + GRG V T V+ G +RVG+
Sbjct: 266 ---VIEAQLDKGRGPVATVLVQSGTLRVGD 292
>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 = 46.9 bits (112), Expect = 8e-07
Identities = 30/104 (28%), Positives = 51/104 (49%), Gaps = 11/104 (10%)
Query: 329 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPG 388
WY +++ S EK K+ +R+ K G++ +P E++ K++K IK FPG
Sbjct: 1 SWYALYTRSRHEK----KVADRLAKKGIE-----SFLPLYEVLSRWKDRKKKIKVPLFPG 51
Query: 389 YVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEI 432
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 = 45.8 bits (109), Expect = 2e-06
Identities = 30/110 (27%), Positives = 49/110 (44%), Gaps = 15/110 (13%)
Query: 329 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRF--F 386
WYV+ +G EK V +E + KL +P E K++Q ++++ F
Sbjct: 1 MWYVVQVRTGREKAV----LELLEKLVGPDVLQECFIPQYERK--KRSQGVWRERKYTLF 54
Query: 387 PGYVLIEMEMTDES-WHLVKNTKKVTGFIG--GKSNRPTPISSKEIEEIL 433
PGYV + + DE + L K+V GF G P++ +E + I
Sbjct: 55 PGYVFVVTDDIDELYYEL----KRVPGFTRLLGNDGSFFPLTPEEADFIR 100
>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 = 48.0 bits (115), Expect = 2e-06
Identities = 33/108 (30%), Positives = 53/108 (49%), Gaps = 5/108 (4%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLN 68
DG +L+ A++GPMPQTR + A + G+ IVV +NK D D E+V+ E+ +L
Sbjct: 90 DGVLLLVDASEGPMPQTRFVLKKALEAGLKPIVV-INKIDR-PDARPEEVVD-EVFDLFL 146
Query: 69 KYEFPGN--DIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTP 114
+ D PI+ SAK + + L + + ++P P
Sbjct: 147 ELNATDEQLDFPIVYASAKNGWASLNLDDPSEDLDPLFETIIEHVPAP 194
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 48.6 bits (115), Expect = 6e-06
Identities = 49/190 (25%), Positives = 86/190 (45%), Gaps = 10/190 (5%)
Query: 6 AQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRE 65
+ +D +LV A DGPMPQTR A G+ IVV +NK D + V ++ +
Sbjct: 90 SMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPIVV-INKVDRPGARP--DWVVDQVFD 146
Query: 66 LLNKYEFPGN--DIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFL 123
L + D PI+ SA + G + + L +A+ ++P P+ +DG F
Sbjct: 147 LFVNLDATDEQLDFPIVYASALNGIAGLDHEDMAEDMTPLYQAIVDHVPAPDVDLDGPFQ 206
Query: 124 LPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKT-----TCTGVEMFRKLLD 178
+ + + S G + GR++RG V+ +++ II + + + + R D
Sbjct: 207 MQISQLDYNSYVGVIGIGRIKRGKVKPNQQVTIIDSEGKTRNAKVGKVLGHLGLERIETD 266
Query: 179 QGQAGDNIGL 188
+AGD + +
Sbjct: 267 LAEAGDIVAI 276
>gnl|CDD|239756 cd04089, eRF3_II, eRF3_II: domain II of the eukaryotic class II
release factor (eRF3). In eukaryotes, translation
termination is mediated by two interacting release
factors, eRF1 and eRF3, which act as class I and II
factors, respectively. eRF1 functions as an omnipotent
release factor, decoding all three stop codons and
triggering the release of the nascent peptide catalyzed
by the ribsome. eRF3 is a GTPase, which enhances the
termination efficiency by stimulating the eRF1 activity
in a GTP-dependent manner. Sequence comparison of class
II release factors with elongation factors shows that
eRF3 is more similar to eEF1alpha whereas prokaryote RF3
is more similar to EF-G, implying that their precise
function may differ. Only eukaryote RF3s are found in
this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a
translation termination factor which is divided into
three regions N, M and a C-terminal eEF1a-like region
essential for translation termination. Sup35NM is a
non-pathogenic prion-like protein with the property of
aggregating into polymer-like fibrils.
Length = 82
Score = 43.7 bits (104), Expect = 9e-06
Identities = 27/86 (31%), Positives = 44/86 (51%), Gaps = 10/86 (11%)
Query: 122 FLLPVEDVFSISGRGTVVTGRVERGIVRVGEELEIIGIKDTVKTT---CTGVEMFRKLLD 178
LP+ D + GTVV G+VE G ++ G++L ++ K V+ VE+
Sbjct: 2 LRLPIIDKYK--DMGTVVLGKVESGTIKKGDKLLVMPNKTQVEVLSIYNEDVEV-----R 54
Query: 179 QGQAGDNIGLLLRGTKREDVERGQVL 204
+ G+N+ L L+G + ED+ G VL
Sbjct: 55 YARPGENVRLRLKGIEEEDISPGFVL 80
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 45.2 bits (108), Expect = 6e-05
Identities = 21/40 (52%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKAD 48
D +LV +A DG MPQT E I A+ GVP I+V +NK D
Sbjct: 321 DIVVLVVAADDGVMPQTIEAINHAKAAGVP-IIVAINKID 359
>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 = 42.6 bits (101), Expect = 2e-04
Identities = 30/87 (34%), Positives = 44/87 (50%), Gaps = 10/87 (11%)
Query: 8 MDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADM--VDDEELLELVEIEIRE 65
+DGAILV SA +G QTR L R++ +P I +F+NK D D E++ + EI+E
Sbjct: 88 LDGAILVISAVEGVQAQTRILFRLLRKLNIPTI-IFVNKIDRAGADLEKVYQ----EIKE 142
Query: 66 LLNKYEFPGND---IPIIKGSAKLALE 89
L+ P P I + + E
Sbjct: 143 KLSPDIVPMQKVGLYPNICDTNNIDDE 169
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 43.0 bits (102), Expect = 3e-04
Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 4/76 (5%)
Query: 8 MDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELL 67
+DGA++V A G PQT A + G+P ++F+NK D V +L +++E +I E
Sbjct: 97 LDGAVVVFDAVTGVQPQTETVWRQADRYGIP-RLIFINKMDRVGA-DLFKVLE-DIEERF 153
Query: 68 NKYEFPGNDIPIIKGS 83
K P +PI
Sbjct: 154 GKRPLPLQ-LPIGSED 168
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 41.1 bits (97), Expect = 3e-04
Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 9/81 (11%)
Query: 5 AAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIR 64
A + D +LV + P+ + + LL R+ G P ++V NK D+V + E EL+
Sbjct: 74 ADRADLVLLVVDSDLTPVEEEAKLGLL-RERGKPVLLVL-NKIDLVPESEEEELLRERKL 131
Query: 65 ELLNKYEFPGNDIPIIKGSAK 85
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 = 39.5 bits (93), Expect = 4e-04
Identities = 20/104 (19%), Positives = 49/104 (47%), Gaps = 10/104 (9%)
Query: 329 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPG 388
WY++++ E+ L ER F + +P + ++ +++V+ + FPG
Sbjct: 1 AWYLLYTKPRQEERAAENL-ERQG-------F-EVFLPMIRVEKRRRGKRTVVTEPLFPG 51
Query: 389 YVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEI 432
Y+ + ++ ++W +++T+ V+ + P P+ IE +
Sbjct: 52 YLFVRLDPEVQNWRPIRSTRGVSRLVRF-GGEPAPVPDALIEAL 94
>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 = 40.5 bits (95), Expect = 5e-04
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 10/79 (12%)
Query: 9 DGAILVCSAADGPMP--QTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIREL 66
D +LV + D + R+ G+P I+V NK D++++ E+ EL+ +E
Sbjct: 77 DLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILV-GNKIDLLEEREVEELLRLEELAK 135
Query: 67 LNKYEFPGNDIPIIKGSAK 85
+ +P+ + SAK
Sbjct: 136 I-------LGVPVFEVSAK 147
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 41.1 bits (97), Expect = 0.001
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 4/74 (5%)
Query: 6 AQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRE 65
+DGA++V A +G PQT A + GVP ++F+NK D + + LV +++E
Sbjct: 98 RVLDGAVVVVDAVEGVEPQTETVWRQADKYGVP-RILFVNKMDRLGAD--FYLVVEQLKE 154
Query: 66 LLNKYEFPGNDIPI 79
L P +PI
Sbjct: 155 RLGANPVPVQ-LPI 167
>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 = 0.002
Identities = 28/80 (35%), Positives = 41/80 (51%), Gaps = 15/80 (18%)
Query: 9 DGAILVCSAADGPMPQTR---EHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRE 65
D ++V S + P R +++ A G+ V+ LNKAD+VDDEEL EL+EI +
Sbjct: 4 DQVLIVFSLKE-PFFNLRLLDRYLVAAEASGIE-PVIVLNKADLVDDEELEELLEI-YEK 60
Query: 66 LLNKYEFPGNDIPIIKGSAK 85
L P++ SAK
Sbjct: 61 L---------GYPVLAVSAK 71
>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 = 37.9 bits (89), Expect = 0.005
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 10 GAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNK 69
G +L+ A GP P E + ++G+P+++V L KAD + E L V +I+E LN
Sbjct: 84 GVVLLIDARHGPTPIDLEMLEFLEELGIPFLIV-LTKADKLKKSE-LAKVLKKIKEELNL 141
Query: 70 YEFPGNDIPIIKGSAK 85
+ P+I S+K
Sbjct: 142 FN---ILPPVILFSSK 154
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 39.0 bits (92), Expect = 0.005
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKAD 48
DGA++V A G PQT A + GVP I +F+NK D
Sbjct: 85 DGAVVVVCAVGGVEPQTETVWRQAEKYGVPRI-IFVNKMD 123
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 38.3 bits (90), Expect = 0.008
Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 18/76 (23%)
Query: 8 MDGAILVCSAADGPMPQTREHILLARQV---GV-PYIVVFLNKAD------MVDDEELLE 57
+DGAI+V A +G MPQT E +L RQ V P V+F+NK D + +E+ +
Sbjct: 111 VDGAIVVVDAVEGVMPQT-ETVL--RQALRERVKP--VLFINKVDRLIKELKLTPQEMQQ 165
Query: 58 -LVEI--EIRELLNKY 70
L++I ++ +L+
Sbjct: 166 RLLKIIKDVNKLIKGM 181
Score = 34.1 bits (79), Expect = 0.20
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 3/53 (5%)
Query: 136 GTVVTGRVERGIVRVGEELEIIGIKDTVKTTCTGVEM--FRKLLDQGQAGDNI 186
G V TGRV G +R G+E+ ++G K + G+ M R+ +++ AG NI
Sbjct: 305 GEVATGRVFSGTLRKGQEVYLVGAKKKNRVQQVGIYMGPEREEVEEIPAG-NI 356
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 36.8 bits (86), Expect = 0.010
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 2/69 (2%)
Query: 2 ITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEI 61
+ A + G +L+ A P RE I ++G+P IVV KAD + E + +
Sbjct: 101 LEKRANLKGVVLLIDARHPPKDLDREMIEFLLELGIPVIVVL-TKADKLKKSERNKQLN- 158
Query: 62 EIRELLNKY 70
++ E L K
Sbjct: 159 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 = 0.014
Identities = 17/36 (47%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 38 PYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFP 73
P IVV LNK D++D EE E ++ ++EL K FP
Sbjct: 116 PRIVV-LNKIDLLDAEERFEKLKELLKELKGKKVFP 150
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 37.1 bits (86), Expect = 0.019
Identities = 31/85 (36%), Positives = 40/85 (47%), Gaps = 11/85 (12%)
Query: 4 GAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEI 63
GA D AIL+ +A DG PQT E I + VP I+V +NK D + I
Sbjct: 315 GANVTDIAILIIAADDGVKPQTIEAINYIQAANVP-IIVAINKIDKANAN------TERI 367
Query: 64 RELLNKYEFP----GNDIPIIKGSA 84
++ L KY G D P+I SA
Sbjct: 368 KQQLAKYNLIPEKWGGDTPMIPISA 392
>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 = 36.4 bits (85), Expect = 0.024
Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLN 68
D A++V AA G PQTR+ + R G+P I+ F+NK D + + LEL++ EI L
Sbjct: 96 DSAVMVIDAAKGVEPQTRKLFEVCRLRGIP-IITFINKLDR-EGRDPLELLD-EIENELG 152
>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 = 33.7 bits (78), Expect = 0.030
Identities = 22/104 (21%), Positives = 41/104 (39%), Gaps = 11/104 (10%)
Query: 329 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPG 388
WY ++++ EK K+ E + K G+ +P + V +K ++ FP
Sbjct: 1 PWYALYTFPRREK----KVAEYLEKKGI-----ECFLPMQYEVRQWSGRKKRVEVPLFPN 51
Query: 389 YVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEI 432
V + + + V T V F+ + P I K++E
Sbjct: 52 LVFVHITREELD--EVLETPGVVRFVRYRGKEPAIIPDKQMESF 93
>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 = 0.044
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
D A+LV A GP E I ++ +PYIVV NK D+ ++ LE +E
Sbjct: 87 DLALLVVDAGVGPGEYELELIEELKERKIPYIVVI-NKIDLGEESAELEKLE 137
>gnl|CDD|181467 PRK08559, nusG, transcription antitermination protein NusG;
Validated.
Length = 153
Score = 34.5 bits (80), Expect = 0.046
Identities = 33/153 (21%), Positives = 56/153 (36%), Gaps = 32/153 (20%)
Query: 331 YVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPGYV 390
+ + + +G E+NV L R K + IL P E +K GYV
Sbjct: 9 FAVKTTAGQERNVALMLAMRAKKENLPIY--AILAPPE------------LK-----GYV 49
Query: 391 LIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILKQIKKGVEKPRPKILYQ 450
L+E E ++ V G + G+ + EE+ +K + I +
Sbjct: 50 LVEAESKGAVEEAIRGIPHVRGVVPGEIS---------FEEVEHFLKP--KPIVEGI--K 96
Query: 451 LDELVRIKDGPFTDFSGNIEEVNYEKSRVRVSV 483
++V + GPF + V+ K V V +
Sbjct: 97 EGDIVELIAGPFKGEKARVVRVDESKEEVTVEL 129
>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 = 35.3 bits (82), Expect = 0.047
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKAD 48
D A++V A G T + +P ++F+NK D
Sbjct: 89 DAALIVVEAQSGVEVGTEKVWEFLDDAKLP-RIIFINKMD 127
>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 = 0.056
Identities = 32/106 (30%), Positives = 43/106 (40%), Gaps = 25/106 (23%)
Query: 329 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPG 388
R Y + + +G E+NV L R K + ILVP E +K G
Sbjct: 1 RIYAVKTTAGQERNVADLLAMRAEKENLDVY--SILVPEE------------LK-----G 41
Query: 389 YVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILK 434
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 = 32.7 bits (75), Expect = 0.082
Identities = 22/107 (20%), Positives = 45/107 (42%), Gaps = 11/107 (10%)
Query: 329 RWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPG 388
WY + + G E+ + L R G++ +P ++ +K +++ FPG
Sbjct: 1 SWYALRTNPGCEQRAEEALEAR----GVE-----AFLPMLTEERKRRRKKFDVERPLFPG 51
Query: 389 YVLIEM-EMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILK 434
YV + + ++ V G +G RP P+ +E+ ++ K
Sbjct: 52 YVFARLDRSKGQDTSTIRACDGVLGVVGF-DGRPAPVPEQEMRDLRK 97
>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 = 0.086
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 452 DELVRIKDGPFTDFSGNIEEVNYEKSRVRV 481
++VR+ GPF G + EV+ K+RV V
Sbjct: 2 GDVVRVISGPFKGKKGKVVEVDDSKARVHV 31
>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 = 34.2 bits (79), Expect = 0.090
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVE 60
D A+LV A G + T+EH+ LA + VP VV + K DM L E ++
Sbjct: 111 DYAMLVVGANAGIIGMTKEHLGLALALKVPVFVV-VTKIDMTPANVLQETLK 161
>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 = 32.5 bits (75), Expect = 0.12
Identities = 29/90 (32%), Positives = 47/90 (52%), Gaps = 19/90 (21%)
Query: 135 RGTVVTGRVERGIVRVGEELEI---IGIKDTVKTTCTGVEMFRKLLDQGQAGDNI----- 186
+G V G + +G+++VG+E+EI I +KD K C + F K++ +A +N
Sbjct: 27 KGGVAGGSLLQGVLKVGDEIEIRPGIVVKDEGKIKCRPI--FTKIVSL-KAENNDLQEAV 83
Query: 187 --GLLLRGTK------REDVERGQVLAKPG 208
GL+ GTK + D GQV+ +PG
Sbjct: 84 PGGLIGVGTKLDPTLTKADRLVGQVVGEPG 113
>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 = 33.7 bits (78), Expect = 0.12
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 8 MDGAILVCSAADGPMPQTREHILLARQVGVPYI--VVFLNKAD 48
DGA++V A +G QT +L RQ + V+ +NK D
Sbjct: 96 TDGALVVVDAVEGVCVQT--ETVL-RQALEERVKPVLVINKID 135
>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 = 34.3 bits (80), Expect = 0.12
Identities = 34/115 (29%), Positives = 51/115 (44%), Gaps = 14/115 (12%)
Query: 11 AILVCSAADGPMPQTREHIL-LARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNK 69
+LV A +G Q I LA + G ++V NK D+V DE+ E + E+R L
Sbjct: 258 VLLVLDATEGITEQD-LRIAGLALEAGKALVIVV-NKWDLVKDEKTREEFKKELRRKLPF 315
Query: 70 YEFPGNDIPIIKGSAKLALEG-DTGPLGEQSILSLSKALDTYIPTP--NRAIDGA 121
+F PI+ S AL G L +I + + + I T NR ++ A
Sbjct: 316 LDF----APIVFIS---ALTGQGVDKL-LDAIDEVYENANRRISTSKLNRVLEEA 362
>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 = 33.5 bits (77), Expect = 0.13
Identities = 25/77 (32%), Positives = 33/77 (42%), Gaps = 11/77 (14%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLN 68
D ILV + QT+E I A GVP I++ NK D+ D L+ + LN
Sbjct: 83 DIVILVLDVEEILEKQTKEIIHHAES-GVP-IILVGNKIDLRD--AKLKTHVAFLFAKLN 138
Query: 69 KYEFPGNDIPIIKGSAK 85
PII SA+
Sbjct: 139 G-------EPIIPLSAE 148
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 34.4 bits (80), Expect = 0.17
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 4 GAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKAD 48
G A D AILV +G PQT E I + ++ P++V NK D
Sbjct: 91 GGALADIAILVVDINEGFQPQTIEAINILKRRKTPFVVA-ANKID 134
>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 = 0.28
Identities = 15/54 (27%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 136 GTVVTGRVERGIVRVGEELEIIGIKDTV-KTTCTGVEMFRKL----LDQGQAGD 184
G + GR+ RG V+VG+++ ++ + K T + F L +++ +AGD
Sbjct: 15 GRIAIGRIFRGTVKVGQQVAVVKRDGKIEKAKITKLFGFEGLKRVEVEEAEAGD 68
>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 = 33.1 bits (76), Expect = 0.33
Identities = 41/153 (26%), Positives = 70/153 (45%), Gaps = 18/153 (11%)
Query: 6 AQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRE 65
A +GA+L+ AA G QT ++ LA + + I V +NK D+ + E V+ EI E
Sbjct: 92 AACEGALLLVDAAQGIEAQTLANVYLALENDLEIIPV-INKIDLPSAD--PERVKKEIEE 148
Query: 66 LLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLP 125
++ ++ + SAK TG +G + IL +A+ +P P D
Sbjct: 149 VIG---LDASEAILA--SAK------TG-IGIEEIL---EAIVKRVPPPKGDPDAPLKAL 193
Query: 126 VEDVFSISGRGTVVTGRVERGIVRVGEELEIIG 158
+ D + RG V RV G ++ G+++ +
Sbjct: 194 IFDSHYDNYRGVVALVRVFEGTIKPGDKIRFMS 226
>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 = 32.8 bits (76), Expect = 0.34
Identities = 18/32 (56%), Positives = 25/32 (78%), Gaps = 2/32 (6%)
Query: 38 PYIVVFLNKADMVDDEELLELVEIEIRELLNK 69
P IVV LNK D++D+EEL EL++ E++E L K
Sbjct: 275 PRIVV-LNKIDLLDEEELEELLK-ELKEALGK 304
>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 = 0.47
Identities = 26/128 (20%), Positives = 40/128 (31%), Gaps = 14/128 (10%)
Query: 213 HKHFTGEIYALSKDEG----GRHTPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDN- 267
HK +I+ K+ G + F V G PK GD+
Sbjct: 96 HKEIVQKIFQKLKENGYIYEKEIKQLYCPECEMFLP-DRYVEG--TCPKCGSEDARGDHC 152
Query: 268 -----VLITVRLINPIAMEEGLRFAIREGVQQFIQDNLLTKEIVNSNKINIDKGKEYIER 322
L LINP G + +R+ F + + KE+ + N + G
Sbjct: 153 EVCGRHLEPTELINPRCKICGAKPELRDSEHYFFRLSAFEKELEEWIRKNPESGS-PASN 211
Query: 323 SINNKKRW 330
N + W
Sbjct: 212 VKNKAQNW 219
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 32.3 bits (75), Expect = 0.48
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 38 PYIVVFLNKADMVDDEELLELVEIEIRELLNK 69
P I+V LNK D++D+EE E L
Sbjct: 273 PRILV-LNKIDLLDEEEEREKRAALELAALGG 303
>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 = 32.6 bits (74), Expect = 0.53
Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 8 MDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELL 67
+DGAI+V A +G MPQT + A + V V+F+NK D + +E L+L E++E
Sbjct: 110 VDGAIVVVCAVEGVMPQTETVLRQALKENVK-PVLFINKVDRLINE--LKLTPQELQERF 166
Query: 68 NK 69
K
Sbjct: 167 IK 168
>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 = 31.0 bits (70), Expect = 0.57
Identities = 41/178 (23%), Positives = 65/178 (36%), Gaps = 44/178 (24%)
Query: 331 YVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRFFPGYV 390
+ + + G EKNV R + + K G+ + IL P GY+
Sbjct: 1 FAVKTSVGQEKNVARLMARKARKSGL--EVYSILAPES-----------------LKGYI 41
Query: 391 LIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTPISSKEIEEILK------QIKKGVEKPR 444
L+E E + + + V G + G+ I +EIE L IKKG
Sbjct: 42 LVEAETKIDMRNPIIGVPHVRGVVEGE------IDFEEIERFLTPKKIIESIKKG----- 90
Query: 445 PKILYQLDELVRIKDGPFTDFSGNIEEVNYEKSRVRVSVTIFGRATPVELEFNQVEKI 502
++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 = 30.3 bits (69), Expect = 0.64
Identities = 25/111 (22%), Positives = 46/111 (41%), Gaps = 16/111 (14%)
Query: 328 KRWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKK--RF 385
KRWY++ SG + +I + +LG+ + P + + KS +K
Sbjct: 1 KRWYLLRCKSGKI----QSVIFSLERLGV-----EVFCPMIRTRRKRTDCKSYREKIEPL 51
Query: 386 FPGYVLIEMEMTDESWHLVKNTKKVTGFI--GGKSNRPTPISSKEIEEILK 434
FPGY+ + + + V+GF+ GG+ P P+ I ++
Sbjct: 52 FPGYLFVRFDPEVVHTSKITLASGVSGFVRFGGE---PCPVPDAVIRALML 99
>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 = 31.5 bits (72), Expect = 0.72
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKAD 48
DG +LV +G T I A Q G+P ++V +NK D
Sbjct: 96 DGVVLVVDVVEGLTSVTERLIRHAIQEGLPMVLV-INKID 134
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 31.7 bits (73), Expect = 0.74
Identities = 26/72 (36%), Positives = 35/72 (48%), Gaps = 16/72 (22%)
Query: 5 AAQMDGAILVCSAADGPMPQTREHIL-----LARQVGVPYIVVFLNKADMVDDEELLELV 59
AA +D A+LV +A + P +L LA G+ I+V NK D++DD E
Sbjct: 78 AANVDQAVLVFAAKE---PDFSTDLLDRFLVLAEANGIKPIIVL-NKIDLLDDLE----- 128
Query: 60 EIEIRELLNKYE 71
E RELL Y
Sbjct: 129 --EARELLALYR 138
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 31.8 bits (73), Expect = 0.87
Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMV--DDEELLELVEIEI 63
D A++V AA G PQT + + R +P I F+NK D D ELL+ +E E+
Sbjct: 106 DSAVMVIDAAKGIEPQTLKLFEVCRLRDIP-IFTFINKLDREGRDPLELLDEIEEEL 161
>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 = 1.0
Identities = 25/91 (27%), Positives = 37/91 (40%), Gaps = 5/91 (5%)
Query: 201 GQVLAKPGSIKPHKHFTGEIYALSKDEGGRHTPFFSNYRPQFYFRTTDVTGSIELPKNKE 260
G VLA PGS+ P + + L P R + T++V + L E
Sbjct: 1 GDVLADPGSLLPTRRLDVRLTVLLSAP----RPLKHRQRVHLHHGTSEVLARVVLLDRDE 56
Query: 261 MVMPGDNVLITVRLINPIAMEEGLRFAIREG 291
+ PG+ L +RL P+ G RF +R
Sbjct: 57 LA-PGEEALAQLRLEEPLVALRGDRFILRSY 86
>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 = 30.5 bits (70), Expect = 1.0
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 11 AILVCSAADGPMPQTREHIL-LARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNK 69
+L A + + E IL L ++ P I+V LNK D+V D+E L + +++EL
Sbjct: 85 LVLFVVDASEWIGEGDEFILELLKKSKTPVILV-LNKIDLVKDKEDLLPLLEKLKELHPF 143
Query: 70 YEFPGNDIPIIKGSAK 85
E PI SA
Sbjct: 144 AEI----FPI---SAL 152
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 31.7 bits (73), Expect = 1.1
Identities = 18/40 (45%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKAD 48
DGA+ V A G PQ+ A + GVP I VF+NK D
Sbjct: 98 DGAVAVFDAVSGVEPQSETVWRQADKYGVPRI-VFVNKMD 136
>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: 452 DELVRIKDGPFTDFSGNIEEVNYE 475
+ VR+ GPF G + EV+ E
Sbjct: 5 GDTVRVIAGPFKGKVGKVLEVDGE 28
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 30.8 bits (71), Expect = 1.3
Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 10/78 (12%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDD-EELLELVEIEIRELL 67
D + V A + P + ++V P I+V LNK D+V D EELL L+E E+ EL+
Sbjct: 86 DLVLFVVDADEKIGPGDEFILEKLKKVKTPVILV-LNKIDLVKDKEELLPLLE-ELSELM 143
Query: 68 NKYEFPGNDIPIIKGSAK 85
+ E +PI SA
Sbjct: 144 DFAEI----VPI---SAL 154
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 31.4 bits (72), Expect = 1.4
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 38 PYIVVFLNKADMVDDEELLELVEIEIRE 65
P +VV LNK D+ D EL E V E+
Sbjct: 286 PRLVV-LNKIDVPDARELAEFVRPELEA 312
>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 = 29.1 bits (66), Expect = 1.4
Identities = 19/63 (30%), Positives = 21/63 (33%), Gaps = 23/63 (36%)
Query: 195 REDVERGQ----VLAKPGS-IKPHKHFTG-EIYALS---KDEGGR--------------H 231
R E + V PGS PH+H G EI L DE G H
Sbjct: 17 RFGGEVARATSLVRYAPGSRFPPHRHPGGEEILVLEGVFSDEHGDYPAGSYLRNPPGSSH 76
Query: 232 TPF 234
PF
Sbjct: 77 APF 79
>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 = 1.5
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 41 VVFLNKADMVDDEELLELVEIEIREL 66
++ +NK D+ LE +E ++R L
Sbjct: 145 LIVINKTDLAPAVADLEKLEADLRRL 170
>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 = 1.5
Identities = 21/79 (26%), Positives = 31/79 (39%), Gaps = 9/79 (11%)
Query: 216 FTGEIYALSKDEGGRH-TPFFSNYRPQFYFRTTDVTGSIELPKNKEMVMPGDNVLITVRL 274
F EI L H T Y+ + + T I +K+++ GD L+ R
Sbjct: 6 FEAEILVLH------HPTTISPGYQATVHIGSIRQTARIV-SIDKDVLRTGDRALVRFRF 58
Query: 275 IN-PIAMEEGLRFAIREGV 292
+ P + EG R REG
Sbjct: 59 LYHPEYLREGQRLIFREGR 77
>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 = 30.9 bits (70), Expect = 1.6
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 4 GAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMV 50
G A D AIL+ +G PQT+E + + R P++V NK D +
Sbjct: 89 GGALADLAILIVDINEGFKPQTQEALNILRMYKTPFVVA-ANKIDRI 134
>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 = 28.7 bits (65), Expect = 1.7
Identities = 19/50 (38%), Positives = 23/50 (46%), Gaps = 9/50 (18%)
Query: 309 NKINIDKGKEYIERSINNKKRW--YVIHSYSGMEKNVQRKLIERINKLGM 356
NKIN GK Y+ SIN KR Y+ SY + R L K G+
Sbjct: 8 NKIN---GKIYVGSSINLYKRLRSYLNPSYLKKNSPILRAL----LKYGL 50
>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 = 1.7
Identities = 19/63 (30%), Positives = 24/63 (38%), Gaps = 18/63 (28%)
Query: 139 VTGRVERGIVRVGEELEIIGIKDTV------------------KTTCTGVEMFRKLLDQG 180
V VE I V E L G+ TV +TC GVE+ +KL G
Sbjct: 20 VKEAVEEAIEIVAERLAEAGLNVTVNANFEGFNTSLYRSRGCRSSTCEGVELLKKLSVTG 79
Query: 181 QAG 183
+ G
Sbjct: 80 RLG 82
>gnl|CDD|223597 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 30.7 bits (70), Expect = 1.7
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 2 ITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEI 61
+ ++DG + V AA L Q+ ++V LNK D+VD EEL L
Sbjct: 111 LADGVRLDGVVTVVDAAHFLEGLDAIAELAEDQLAFADVIV-LNKTDLVDAEELEALEAR 169
Query: 62 EIREL 66
+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 = 30.1 bits (69), Expect = 1.9
Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 11/63 (17%)
Query: 5 AAQMDGAILVCSAADGPMPQTREHILLARQV-------GVPYIVVFLNKADMVDDEELLE 57
A+ D + V A+D P E I +V +P I+V NK D++DDEEL E
Sbjct: 118 VAEADLLLHVVDASD---PDREEQIETVEEVLKELGADDIPIILVL-NKIDLLDDEELEE 173
Query: 58 LVE 60
+
Sbjct: 174 RLR 176
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 30.6 bits (70), Expect = 2.1
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 6/40 (15%)
Query: 32 ARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYE 71
+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 = 29.3 bits (66), Expect = 2.2
Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 326 NKKRWYVIHSYSGMEKNVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRF 385
+ +R +++ G+++ + ++I+R K G + ++L PT EI +++ K K F
Sbjct: 1 SSERTFIMVKPDGVQRGLVGEIIKRFEKKGYKLVALKMLQPTPEI--AEEHYKEHKGKPF 58
Query: 386 FPGYV 390
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 = 2.4
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 5/47 (10%)
Query: 40 IVVFLNKADMVD-DEELLELVEIEIRELLNKYEFPGNDIPIIKGSAK 85
+++ +NK D+V+ DE+ ++ E E+R L ++ PI+ SA
Sbjct: 116 LIIVVNKWDLVEKDEKTMKEFEKELRRKLPFLDY----APIVFISAL 158
>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 = 30.5 bits (69), Expect = 2.4
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 8 MDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKAD 48
+DGA+ V A G PQ+ A + VP I F+NK D
Sbjct: 99 LDGAVAVLDAVGGVQPQSETVWRQANRYEVPRI-AFVNKMD 138
>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 = 29.9 bits (68), Expect = 2.9
Identities = 13/85 (15%), Positives = 26/85 (30%), Gaps = 20/85 (23%)
Query: 294 QFIQDNLLTKEIVNSNKINIDKGKEYIERSINNKKRWYVIHSYSGMEKNVQRKLIERINK 353
+ Q + I Y E K + +E+ KL+E + K
Sbjct: 116 ELAQG----LNKSTGRNVGI-----YPE----TKHPTFHKQEGPDIEE----KLLEVLKK 158
Query: 354 LGMQKKFGRILVPT---EEIVDVKK 375
G K + + + E + ++
Sbjct: 159 YGYTGKNDPVFIQSFEPESLKRLRN 183
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 29.8 bits (68), Expect = 3.1
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 38 PYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPG 74
P IVV LNK D+ DEE LE ++ + E L F
Sbjct: 277 PRIVV-LNKIDLPLDEEELEELKKALAEALGWEVFYL 312
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 29.8 bits (68), Expect = 3.7
Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 16/88 (18%)
Query: 40 IVVFLNKADMVD-DEELLELVEIEIRELLNKYEFPGNDIPIIKGSAKLALEGDTG-PLGE 97
IV+ +NK D+V+ DE +E + ++R L +F PI+ SA TG L +
Sbjct: 292 IVIVVNKWDLVEEDEATMEEFKKKLRRKLPFLDF----APIVFISAL------TGQGLDK 341
Query: 98 --QSILSLSKALDTYIPTP--NRAIDGA 121
++I + + I T NR ++ A
Sbjct: 342 LFEAIKEIYECATRRISTSLLNRVLEDA 369
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 29.9 bits (67), Expect = 3.7
Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 4 GAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMV 50
G + D A+LV +G PQT E I + RQ P+ VV NK D++
Sbjct: 546 GGSLADLAVLVVDINEGFKPQTIEAINILRQYKTPF-VVAANKIDLI 591
>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 = 29.0 bits (66), Expect = 3.8
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 2/63 (3%)
Query: 10 GAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNK 69
G +L+ E I R+ G+P ++V L KAD + EL + ++ +I++ L K
Sbjct: 103 GVVLLMDIRHPLKELDLEMIEWLRERGIPVLIV-LTKADKLKKSELNKQLK-KIKKALKK 160
Query: 70 YEF 72
Sbjct: 161 DAD 163
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 29.8 bits (68), Expect = 3.8
Identities = 40/144 (27%), Positives = 68/144 (47%), Gaps = 18/144 (12%)
Query: 10 GAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNK 69
GA+LV A+ G QT ++ LA + + I V LNK D+ + E V+ EI +++
Sbjct: 102 GALLVVDASQGVEAQTLANVYLALENNLEIIPV-LNKIDLPAAD--PERVKQEIEDII-- 156
Query: 70 YEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFLLPVEDV 129
+D ++ SAK TG +G + +L +A+ IP P D + D
Sbjct: 157 -GIDASDAVLV--SAK------TG-IGIEDVL---EAIVEKIPPPKGDPDAPLKALIFDS 203
Query: 130 FSISGRGTVVTGRVERGIVRVGEE 153
+ + G VV R+ G ++ G++
Sbjct: 204 WYDNYLGVVVLVRIFDGTLKKGDK 227
>gnl|CDD|240370 PTZ00342, PTZ00342, acyl-CoA synthetase; Provisional.
Length = 746
Score = 29.7 bits (67), Expect = 4.6
Identities = 18/94 (19%), Positives = 36/94 (38%), Gaps = 9/94 (9%)
Query: 296 IQDNLLTKEIVNSNKINIDKGKEYIERSINNKKRWYVIHSYSGMEKNVQRKL-------I 348
I D L+ + +N NK + G N K + S +++ +
Sbjct: 206 ILDTLIKSKEININKEEKNNGSNVNNNGNKNNKEEQKGNDLSNELEDISLGPLEYDKEKL 265
Query: 349 ERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIK 382
E+I L ++K ++ + D+ KN+ + K
Sbjct: 266 EKIKDL--KEKAKKLGISIILFDDMTKNKTTNYK 297
>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 = 29.1 bits (66), Expect = 4.9
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 6/46 (13%)
Query: 30 LLARQVGVPYIVVFLNKAD--MVDDEELLELVEIEIRELLNKYEFP 73
LLA + G Y+ F+ + D D EL+ EIR + + Y F
Sbjct: 116 LLAAKAGATYVSPFVGRIDDLGGDGMELIR----EIRTIFDNYGFD 157
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 29.1 bits (66), Expect = 5.4
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 5 AAQMDGAILVCSAADGPMPQTRE-HILLARQVGV-PYIVVFLNKADMVDD-EELLELVE 60
AA +D +VCS + E ++ LA + G P V+ L KAD+ +D EE + VE
Sbjct: 110 AANVDTVFIVCSLNHDFNLRRIERYLALAWESGAEP--VIVLTKADLCEDAEEKIAEVE 166
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 29.1 bits (66), Expect = 5.6
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 8/47 (17%)
Query: 38 PYIVVFLNKADMVDDEELLELVEIEIRELLNKYEFPGNDIPIIKGSA 84
P +VF NK D++D+EE E + I E L G + P+ SA
Sbjct: 277 PRWLVF-NKIDLLDEEEAEERAK-AIVEAL------GWEGPVYLISA 315
>gnl|CDD|237498 PRK13768, PRK13768, GTPase; Provisional.
Length = 253
Score = 28.7 bits (65), Expect = 6.1
Identities = 12/27 (44%), Positives = 19/27 (70%), Gaps = 1/27 (3%)
Query: 36 GVPYIVVFLNKADMVDDEELLELVEIE 62
G+P I V LNKAD++ +EEL +++
Sbjct: 162 GLPQIPV-LNKADLLSEEELERILKWL 187
>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 = 6.2
Identities = 16/90 (17%), Positives = 34/90 (37%), Gaps = 4/90 (4%)
Query: 298 DNLLTKEIVNSNKINIDKGK---EYIERSINN-KKRWYVIHSYSGMEKNVQRKLIERINK 353
D E + + ID+ + + ++ K+ W + HSY ++ + LI K
Sbjct: 30 DITSLSEDIKPATVIIDEDTLRVTWPDGHVSKFKEDWLIRHSYEPKKEKNVKALILPNRK 89
Query: 354 LGMQKKFGRILVPTEEIVDVKKNQKSVIKK 383
+ +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 = 6.7
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 342 NVQRKLIERINKLGMQKKFGRILVPTEEIVDVKKNQKSVIKKRF 385
V KL+ER N + GR+ V TE I+D K+ K+V+ + F
Sbjct: 59 TVVSKLMERYNI--DYDQIGRLEVGTETIIDKSKSVKTVLMQLF 100
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 28.9 bits (66), Expect = 6.7
Identities = 26/60 (43%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLN 68
D A++V AA G PQTR+ + + R P I F+NK D D E LEL++ EI E+L
Sbjct: 104 DSALMVIDAAKGVEPQTRKLMEVCRLRDTP-IFTFINKLDR-DGREPLELLD-EIEEVLG 160
>gnl|CDD|181611 PRK09014, rfaH, transcriptional activator RfaH; Provisional.
Length = 162
Score = 28.3 bits (64), Expect = 6.7
Identities = 24/101 (23%), Positives = 46/101 (45%), Gaps = 11/101 (10%)
Query: 364 LVPTEEIVDVKKNQKSVIKKRFFPGYVLIEMEMTDESWHLVKNTKKVTGFIGGKSNRPTP 423
++ E+IV K+ + S + FP Y+ +E + +++T+ V+ F+ +P
Sbjct: 32 MITLEKIVRGKRTEVS---EPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVR-FGAQPAI 87
Query: 424 ISSKEIEEILKQ--IKKGVEKPRPKILYQLDELVRIKDGPF 462
+ S I + L +K V+ PK + V I +G F
Sbjct: 88 VPSDVIYQ-LSVYKPEKIVDPETPKP----GDKVIITEGAF 123
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 28.8 bits (65), Expect = 6.8
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 40 IVVFLNKADMVDDEELLELV----EIEIRELLNKYEFPGNDIPIIKGS-AKLALEG 90
IVV +NK D+ D+E+L E+ E E L G + ++ K ALE
Sbjct: 283 IVVVINKIDIADEEKLEEIEASVLEEGGEEPLKISATKGCGLDKLREEVRKTALEP 338
>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 = 6.9
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 39 YIVVFLNKADMVDDEELLELVEIEIRELLNKYE 71
+ +K D EE ++ V ++EL ++YE
Sbjct: 69 LLEFCFSKLYGDDAEEYIKEVRDTLKELFDEYE 101
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 28.2 bits (63), Expect = 7.2
Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 8/77 (10%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLN 68
GAI++ ++ E I +VV +NK D+ D L +IRE L
Sbjct: 93 VGAIVLVDSSRPITFHAEEIIDFLTSRNPIPVVVAINKQDLFD-----ALPPEKIREAL- 146
Query: 69 KYEFPGNDIPIIKGSAK 85
+ +P+I+ A
Sbjct: 147 --KLELLSVPVIEIDAT 161
>gnl|CDD|233421 TIGR01453, grpIintron_endo, group I intron endonuclease. This
model represents one subfamily of endonucleases
containing the endo/excinuclease amino terminal domain,
pfam01541 at its amino end. A distinct subfamily
includes excinuclease abc subunit c (uvrC). Members of
pfam01541 are often termed GIY-YIG endonucleases after
conserved motifs near the amino end. This subfamily in
This model is found in open reading frames of group I
introns in both phage and mitochondria. The closely
related endonucleases of phage T4: segA, segB, segC,
segD and segE, score below the trusted cutoff for the
family.
Length = 214
Score = 28.5 bits (64), Expect = 7.2
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 2/42 (4%)
Query: 311 INIDKGKEYIERSINNKKRW--YVIHSYSGMEKNVQRKLIER 350
N GK Y+ S+N +KR ++ G +Q+ L +
Sbjct: 8 TNNINGKIYVGSSVNLEKRLKEHLKLLKKGNRIKLQKALNKY 49
>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 = 27.5 bits (62), Expect = 7.4
Identities = 22/75 (29%), Positives = 29/75 (38%), Gaps = 19/75 (25%)
Query: 5 AAQMDGAILVCSAADGP-----MPQTREHILLA----RQVGVPYIVVFLNKADMVDDEEL 55
A M G + V +A D P P + +LA R VG P V + EE
Sbjct: 38 ARAMPGVVAVLTAKDVPGLNDFGPLGPDEPVLADDKVRYVGQPVAAVV------AETEEA 91
Query: 56 ----LELVEIEIREL 66
E V++E EL
Sbjct: 92 ARDAAEAVKVEYEEL 106
>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 = 27.3 bits (61), Expect = 7.6
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 137 TVVTGRVERGIVRVGEE----LEIIGIKDTVKTTCTGVEMFRKLLDQG 180
+V G + G ++V E LE G++ V T V+ + +L +G
Sbjct: 61 VIVIGTGQSGALKVPPETVEKLEKRGVEVLVLPTEEAVKRYNELAGKG 108
>gnl|CDD|130264 TIGR01196, edd, 6-phosphogluconate dehydratase. A close homolog,
designated MocB (mannityl opine catabolism), is found in
a mannopine catabolism region of a plasmid of
Agrobacterium tumefaciens. However, it is not essential
for mannopine catabolism, branches within the cluster of
6-phosphogluconate dehydratases (with a short branch
length) in a tree rooted by the presence of other
dehydyatases. It may represent an authentic
6-phosphogluconate dehydratase, redundant with the
chromosomal copy shown to exist in plasmid-cured
strains. This model includes mocB above the trusted
cutoff, although the designation is somewhat tenuous
[Energy metabolism, Entner-Doudoroff].
Length = 601
Score = 28.6 bits (64), Expect = 8.0
Identities = 11/41 (26%), Positives = 23/41 (56%)
Query: 110 YIPTPNRAIDGAFLLPVEDVFSISGRGTVVTGRVERGIVRV 150
+ P ++D L PV+D FS +G ++ G + R ++++
Sbjct: 393 WREAPEHSLDTDILRPVDDPFSANGGLKLLKGNLGRAVIKI 433
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 28.0 bits (63), Expect = 8.1
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 11/81 (13%)
Query: 9 DGAILVCSAADGP-MPQTRE--HILLARQ--VGVPYIVVFLNKADMVDDEELLELVEIEI 63
D I V +AD + + +E H LL + P +++ NK D+ + E EI
Sbjct: 83 DAVIFVVDSADRDRIEEAKEELHALLNEEELADAP-LLILANKQDLPGA-----MSEAEI 136
Query: 64 RELLNKYEFPGNDIPIIKGSA 84
RELL +E I SA
Sbjct: 137 RELLGLHELKDRPWEIQGCSA 157
>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 = 28.2 bits (64), Expect = 8.4
Identities = 19/44 (43%), Positives = 23/44 (52%), Gaps = 9/44 (20%)
Query: 9 DGAILVCSAADGPMPQT----REHILLARQVGVPYIVVFLNKAD 48
DGA+ V A G PQT R+ A + GVP I F+NK D
Sbjct: 89 DGAVAVFDAVAGVQPQTETVWRQ----ADRYGVPRI-AFVNKMD 127
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 28.7 bits (65), Expect = 8.5
Identities = 30/119 (25%), Positives = 42/119 (35%), Gaps = 25/119 (21%)
Query: 5 AAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIR 64
+ D + V A+ + I L + P IVV LNKAD+V EL
Sbjct: 294 IEEADLVLFVLDASQPLDKEDLALIELLPK-KKPIIVV-LNKADLVSKIELESEKLA--- 348
Query: 65 ELLNKYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTPNRAIDGAFL 123
N II SAK TG + + +L +A+ +G FL
Sbjct: 349 ----------NGDAIISISAK------TG----EGLDALREAIKQLFGKGLGNQEGLFL 387
>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 = 28.5 bits (64), Expect = 9.1
Identities = 17/81 (20%), Positives = 28/81 (34%), Gaps = 16/81 (19%)
Query: 2 ITGAAQMDGAILVCSAADGPMPQTREHILLARQVGVPYIVV-----------FLNKADMV 50
+ A + ++ CS A + + E + G+PY + AD+
Sbjct: 236 VQTAHRAKLNMVQCSKAMINLARKME-----EKYGIPYFEGSFYGIEDTSKALRDIADLF 290
Query: 51 DDEELLELVEIEIRELLNKYE 71
D ELL+ E I K
Sbjct: 291 GDPELLKRTEELIAREEAKIR 311
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 28.6 bits (65), Expect = 9.3
Identities = 18/41 (43%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 32 ARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLNKYEF 72
RQ G+P V AD+V DEELLE + RELL +
Sbjct: 626 TRQSGLPEFKV----ADLVRDEELLEEARKDARELLERDPE 662
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4). LepA
(also known as elongation factor 4, EF4) belongs to the
GTPase family and exhibits significant homology to the
translation factors EF-G and EF-Tu, indicating its
possible involvement in translation and association with
the ribosome. LepA is ubiquitous in bacteria and
eukaryota (e.g. yeast GUF1p), but is missing from
archaea. This pattern of phyletic distribution suggests
that LepA evolved through a duplication of the EF-G gene
in bacteria, followed by early transfer into the
eukaryotic lineage, most likely from the
promitochondrial endosymbiont. Yeast GUF1p is not
essential and mutant cells did not reveal any marked
phenotype.
Length = 179
Score = 27.9 bits (63), Expect = 9.9
Identities = 32/106 (30%), Positives = 50/106 (47%), Gaps = 18/106 (16%)
Query: 9 DGAILVCSAADGPMPQTREHILLARQVGVPYIVVFLNKADMVDDEELLELVEIEIRELLN 68
+GA+LV A G QT + LA + + I V +NK D+ + + V+ EI ++L
Sbjct: 92 EGALLVVDATQGVEAQTLANFYLALENNLEIIPV-INKIDLPAAD--PDRVKQEIEDVL- 147
Query: 69 KYEFPGNDIPIIKGSAKLALEGDTGPLGEQSILSLSKALDTYIPTP 114
++ I SAK TG LG + +L +A+ IP P
Sbjct: 148 --GLDASE--AILVSAK------TG-LGVEDLL---EAIVERIPPP 179
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
0.318 0.138 0.390
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: 26,747,290
Number of extensions: 2798261
Number of successful extensions: 3717
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3606
Number of HSP's successfully gapped: 199
Length of query: 502
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 401
Effective length of database: 6,457,848
Effective search space: 2589597048
Effective search space used: 2589597048
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 61 (27.1 bits)