RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13961
(459 letters)
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 860 bits (2225), Expect = 0.0
Identities = 347/440 (78%), Positives = 384/440 (87%), Gaps = 12/440 (2%)
Query: 1 MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL 60
MGKEKTHIN+VVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEA EMGKGSFKYAWVL
Sbjct: 1 MGKEKTHINLVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVL 60
Query: 61 DKLKAERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT 120
DKLKAERERGITIDIALWKFET K+Y TIIDAPGHRDFIKNMITGTSQAD A+L+VA+
Sbjct: 61 DKLKAERERGITIDIALWKFETPKYYFTIIDAPGHRDFIKNMITGTSQADVAILVVASTA 120
Query: 121 GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKK 180
GEFEAGISK+GQTREHALLAFTLGVKQ+IV +NKMD YS+ R++EIKKEVS Y+KK
Sbjct: 121 GEFEAGISKDGQTREHALLAFTLGVKQMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKK 180
Query: 181 IGYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPSR 240
+GYNP V F+PISGW GDNM+E SD MPW+K G L+EALD + PP R
Sbjct: 181 VGYNPEKVPFIPISGWQGDNMIEKSDNMPWYK------------GPTLLEALDTLEPPKR 228
Query: 241 PTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQ 300
P +KPLRLPLQDVYKIGGIGTVPVGRVETG++KPGM+VTFAP+ +TTEVKSVEMHHE L
Sbjct: 229 PVDKPLRLPLQDVYKIGGIGTVPVGRVETGILKPGMVVTFAPSGVTTEVKSVEMHHEQLA 288
Query: 301 EAVPGDNVGFNVKNVSVKELRRGFVAGDSKASPPKATQDFTAQVIVLNHPGQISNGYTPV 360
EAVPGDNVGFNVKNVSVK+++RG+VA DSK P K DFTAQVIVLNHPGQI NGYTPV
Sbjct: 289 EAVPGDNVGFNVKNVSVKDIKRGYVASDSKNDPAKECADFTAQVIVLNHPGQIKNGYTPV 348
Query: 361 LDCHTAHIACKFAEIKEKCDRRTGKTTEENPKALKSGDAAIIVLVPSKPMCVESFSEFPP 420
LDCHTAHIACKFAEI+ K DRR+GK EENPKA+KSGDAAI+ +VP+KPMCVE F+E+PP
Sbjct: 349 LDCHTAHIACKFAEIESKIDRRSGKVLEENPKAIKSGDAAIVKMVPTKPMCVEVFNEYPP 408
Query: 421 LGRFAVRDMRQTVAVGVIKV 440
LGRFAVRDM+QTVAVGVIK
Sbjct: 409 LGRFAVRDMKQTVAVGVIKS 428
>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 = 685 bits (1768), Expect = 0.0
Identities = 277/439 (63%), Positives = 336/439 (76%), Gaps = 19/439 (4%)
Query: 1 MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL 60
M KEK HIN+ IGHVD GKSTT GHL+YKCG ID++TIEKFEKEAQE GK SF++AWV+
Sbjct: 1 MAKEKEHINVAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFEFAWVM 60
Query: 61 DKLKAERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT 120
D+LK ERERG+TID+A WKFET K+ VTI+D PGHRDFIKNMITG SQAD AVL+VA G
Sbjct: 61 DRLKEERERGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGD 120
Query: 121 GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKK 180
GEFE QTREHA LA TLG+ QLIV +NKMDS Y E FE IKKEVS IKK
Sbjct: 121 GEFE----VQPQTREHAFLARTLGINQLIVAINKMDSVN--YDEEEFEAIKKEVSNLIKK 174
Query: 181 IGYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPSR 240
+GYNP TV F+PIS W+GDN+++ S+ PW+K GK L+EALDA+ PP +
Sbjct: 175 VGYNPDTVPFIPISAWNGDNVIKKSENTPWYK------------GKTLLEALDALEPPEK 222
Query: 241 PTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQ 300
PT+KPLR+P+QDVY I G+GTVPVGRVETGV+KPG V F PA ++ EVKS+EMHHE ++
Sbjct: 223 PTDKPLRIPIQDVYSITGVGTVPVGRVETGVLKPGDKVVFEPAGVSGEVKSIEMHHEQIE 282
Query: 301 EAVPGDNVGFNVKNVSVKELRRGFVAGDSKASPPKATQDFTAQVIVLNHPGQISNGYTPV 360
+A PGDN+GFNV+ VS K++RRG V G +PPK ++FTAQ++VL HPG I+ GYTPV
Sbjct: 283 QAEPGDNIGFNVRGVSKKDIRRGDVCGHPD-NPPKVAKEFTAQIVVLQHPGAITVGYTPV 341
Query: 361 LDCHTAHIACKFAEIKEKCDRRTGKTTEENPKALKSGDAAIIVLVPSKPMCVESFSEFPP 420
CHTA IAC+F E+ +K D RTG+ EENP+ LK+GDAAI+ P+KPM +E+ E PP
Sbjct: 342 FHCHTAQIACRFDELLKKNDPRTGQVLEENPQFLKTGDAAIVKFKPTKPMVIEAVKEIPP 401
Query: 421 LGRFAVRDMRQTVAVGVIK 439
LGRFA+RDM QTVA G+I
Sbjct: 402 LGRFAIRDMGQTVAAGMII 420
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 679 bits (1754), Expect = 0.0
Identities = 328/439 (74%), Positives = 372/439 (84%), Gaps = 12/439 (2%)
Query: 1 MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL 60
MGKEK HINIVVIGHVDSGKSTTTGHLIYK GGIDKR IE+FEKEA EM K SFKYAWVL
Sbjct: 1 MGKEKVHINIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFEKEAAEMNKRSFKYAWVL 60
Query: 61 DKLKAERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT 120
DKLKAERERGITIDIALWKFET+K+Y T+IDAPGHRDFIKNMITGTSQADCAVLI+ + T
Sbjct: 61 DKLKAERERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTT 120
Query: 121 GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKK 180
G FEAGISK+GQTREHALLAFTLGVKQ+I NKMD+T P YS+AR++EI KEVS Y+KK
Sbjct: 121 GGFEAGISKDGQTREHALLAFTLGVKQMICCCNKMDATTPKYSKARYDEIVKEVSSYLKK 180
Query: 181 IGYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPSR 240
+GYNP + FVPISG+ GDNM+E S + W+K G L+EALD I P R
Sbjct: 181 VGYNPDKIPFVPISGFEGDNMIERSTNLDWYK------------GPTLLEALDQINEPKR 228
Query: 241 PTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQ 300
P++KPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGM+VTF P LTTEVKSVEMHHE+LQ
Sbjct: 229 PSDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFGPTGLTTEVKSVEMHHESLQ 288
Query: 301 EAVPGDNVGFNVKNVSVKELRRGFVAGDSKASPPKATQDFTAQVIVLNHPGQISNGYTPV 360
EA+PGDNVGFNVKNV+VK+L+RG+VA +SK P K +FT+QVI++NHPGQI NGY PV
Sbjct: 289 EALPGDNVGFNVKNVAVKDLKRGYVASNSKDDPAKEAANFTSQVIIMNHPGQIGNGYAPV 348
Query: 361 LDCHTAHIACKFAEIKEKCDRRTGKTTEENPKALKSGDAAIIVLVPSKPMCVESFSEFPP 420
LDCHT+HIA KFAEI K DRR+GK E+ PK LK+GDA + ++P+KPM VE+FSE+PP
Sbjct: 349 LDCHTSHIAVKFAEILTKIDRRSGKELEKEPKFLKNGDAGFVKMIPTKPMVVETFSEYPP 408
Query: 421 LGRFAVRDMRQTVAVGVIK 439
LGRFAVRDMRQTVAVGVIK
Sbjct: 409 LGRFAVRDMRQTVAVGVIK 427
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 653 bits (1688), Expect = 0.0
Identities = 271/439 (61%), Positives = 323/439 (73%), Gaps = 15/439 (3%)
Query: 1 MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL 60
M EK H+N+V IGHVD+GKST G L+Y G IDKRT+EK EKEA+E+GK SFK+AWVL
Sbjct: 1 MASEKPHLNLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVL 60
Query: 61 DKLKAERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT 120
DK K ERERG+TID+A KFET K+ TIIDAPGHRDF+KNMITG SQAD AVL+V A
Sbjct: 61 DKTKEERERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARD 120
Query: 121 GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKK 180
GEFEAG GQTREHA LA TLG+KQLIV VNKMD + E RFEEI EVS +K
Sbjct: 121 GEFEAGFGVGGQTREHAFLARTLGIKQLIVAVNKMD--LVSWDEERFEEIVSEVSKLLKM 178
Query: 181 IGYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPSR 240
+GYNP V F+PISG+ GDN+ + S+ MPW+K G L+EALD + PP R
Sbjct: 179 VGYNPKDVPFIPISGFKGDNLTKKSENMPWYK------------GPTLLEALDQLEPPER 226
Query: 241 PTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQ 300
P +KPLRLP+QDVY I GIGTVPVGRVE+GVIKPG VTF PA + EVKS+EMHHE +
Sbjct: 227 PLDKPLRLPIQDVYSISGIGTVPVGRVESGVIKPGQKVTFMPAGVVGEVKSIEMHHEEIS 286
Query: 301 EAVPGDNVGFNVKNVSVKELRRGFVAGDSKASPPKATQDFTAQVIVLNHPGQISNGYTPV 360
+A PGDNVGFNV+ V ++RRG V G S +PP + +FTAQ+IVL HPG I++GYTPV
Sbjct: 287 QAEPGDNVGFNVRGVEKNDIRRGDVIGHSD-NPPTVSPEFTAQIIVLWHPGIITSGYTPV 345
Query: 361 LDCHTAHIACKFAEIKEKCDRRTGKTTEENPKALKSGDAAIIVLVPSKPMCVESFSEFPP 420
L HTA +AC+ AE+ K D RTGK EENP+ LK GDAAI+ + P KP+C+E SE P
Sbjct: 346 LHAHTAQVACRIAELLSKLDPRTGKKLEENPQFLKRGDAAIVKIEPEKPLCLEKVSEIPQ 405
Query: 421 LGRFAVRDMRQTVAVGVIK 439
LGRFA+RDM QT+A G +
Sbjct: 406 LGRFALRDMGQTIAAGKVL 424
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 653 bits (1686), Expect = 0.0
Identities = 241/440 (54%), Positives = 312/440 (70%), Gaps = 21/440 (4%)
Query: 3 KEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDK 62
KEK H+N+ VIGHVD GKST G L+Y+ G ID+ IE+ +EA+E GK SFK+AWV+D+
Sbjct: 2 KEKPHLNLAVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMDR 61
Query: 63 LKAERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGE 122
LK ERERG+TID+A KFET K+Y TI+D PGHRDF+KNMITG SQAD AVL+VAA
Sbjct: 62 LKEERERGVTIDLAHKKFETDKYYFTIVDCPGHRDFVKNMITGASQADAAVLVVAA---- 117
Query: 123 FEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIG 182
+ QTREH LA TLG+ QLIV +NKMD+ Y E R+EE+K+EVS +K +G
Sbjct: 118 -DDAGGVMPQTREHVFLARTLGINQLIVAINKMDAVN--YDEKRYEEVKEEVSKLLKMVG 174
Query: 183 YNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPSRPT 242
Y P + F+P+S + GDN+++ S+ MPW+ G L+EALD + PP +PT
Sbjct: 175 YKPDDIPFIPVSAFEGDNVVKKSENMPWYN------------GPTLLEALDNLKPPEKPT 222
Query: 243 EKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQEA 302
+KPLR+P+QDVY I G+GTVPVGRVETGV+K G V F PA + EVKS+EMHHE L +A
Sbjct: 223 DKPLRIPIQDVYSISGVGTVPVGRVETGVLKVGDKVVFMPAGVVGEVKSIEMHHEELPQA 282
Query: 303 VPGDNVGFNVKNVSVKELRRGFVAGDSKASPPKATQDFTAQVIVLNHPGQISNGYTPVLD 362
PGDN+GFNV+ V K+++RG V G +PP ++FTAQ++VL HP I+ GYTPV
Sbjct: 283 EPGDNIGFNVRGVGKKDIKRGDVCG-HPDNPPTVAEEFTAQIVVLQHPSAITVGYTPVFH 341
Query: 363 CHTAHIACKFAEIKEKCDRRTGKTTEENPKALKSGDAAIIVLVPSKPMCVESFSEFPPLG 422
HTA +AC F E+ +K D RTG+ EENP+ +K+GDAAI+ + P+KP+ +E E P LG
Sbjct: 342 AHTAQVACTFEELVKKLDPRTGQVAEENPQFIKTGDAAIVKIKPTKPLVIEKVKEIPQLG 401
Query: 423 RFAVRDMRQTVAVG-VIKVN 441
RFA+RDM QT+A G VI V
Sbjct: 402 RFAIRDMGQTIAAGMVIDVK 421
>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 = 452 bits (1166), Expect = e-161
Identities = 155/230 (67%), Positives = 184/230 (80%), Gaps = 12/230 (5%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERE 68
N+VVIGHVD+GKST TGHL+YK GG+DKRTIEK+EKEA+EMGK SFKYAWVLDKLK ERE
Sbjct: 1 NLVVIGHVDAGKSTLTGHLLYKLGGVDKRTIEKYEKEAKEMGKESFKYAWVLDKLKEERE 60
Query: 69 RGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGIS 128
RG+TID+ L KFET K+ TIIDAPGHRDF+KNMITG SQAD AVL+V+A GEFEAG
Sbjct: 61 RGVTIDVGLAKFETEKYRFTIIDAPGHRDFVKNMITGASQADVAVLVVSARKGEFEAGFE 120
Query: 129 KNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNPATV 188
K GQTREHALLA TLGVKQLIV VNKMD +S+ R++EIKK+VS ++KK+GYNP V
Sbjct: 121 KGGQTREHALLARTLGVKQLIVAVNKMDDVTVNWSQERYDEIKKKVSPFLKKVGYNPKDV 180
Query: 189 AFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPP 238
F+PISG+ GDN++E S+ MPW+KG L+EALD++ PP
Sbjct: 181 PFIPISGFTGDNLIEKSENMPWYKGP------------TLLEALDSLEPP 218
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 255 bits (654), Expect = 1e-80
Identities = 136/454 (29%), Positives = 214/454 (47%), Gaps = 49/454 (10%)
Query: 5 KTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGK--GSFKYAWVLDK 62
K+ + + G VD GKST G L+Y I + + E++++ G A ++D
Sbjct: 4 KSLLRFITCGSVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLVDG 63
Query: 63 LKAERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGE 122
L+AERE+GITID+A F T K I D PGH + +NM TG S AD A+L+V A G
Sbjct: 64 LEAEREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTADLAILLVDARKGV 123
Query: 123 FEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIG 182
E QTR H+ +A LG++ ++V VNKMD + YSE FE I + + ++G
Sbjct: 124 LE-------QTRRHSFIASLLGIRHVVVAVNKMDLVD--YSEEVFEAIVADYLAFAAQLG 174
Query: 183 YNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPSRPT 242
V F+PIS GDN++ S+ MPW+K G L+E L+ + +
Sbjct: 175 LKD--VRFIPISALLGDNVVSKSENMPWYK------------GPTLLEILETVEIADDRS 220
Query: 243 EKPLRLPLQDVYKIG----GIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEA 298
K R P+Q V + G G + +G +K G V P+ T+ VK +
Sbjct: 221 AKAFRFPVQYVNRPNLDFRGYA----GTIASGSVKVGDEVVVLPSGKTSRVKRIVTFDGE 276
Query: 299 LQEAVPGDNVGFNVKN-VSVKELRRG--FVAGDSKASPPKATQDFTAQVIVLNHPGQISN 355
L +A G+ V + + + + RG VA D +PP F A V+ ++ +
Sbjct: 277 LAQASAGEAVTLVLADEIDIS---RGDLIVAAD---APPAVADAFDADVVWMD-EEPLLP 329
Query: 356 GYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPKALKSGDAAIIVLVPSKPMCVESF 415
G + L T + + EIK + D T + +E ++L + + + KP+ +++
Sbjct: 330 GRSYDLKIATRTVRARVEEIKHQLDVNTLE--QEGAESLPLNEIGRVRISFDKPIAFDAY 387
Query: 416 SEFPPLGRFAV--RDMRQTVAVGVI--KVNNNHG 445
+E G F + R TV G+I ++ N G
Sbjct: 388 AENRATGSFILIDRLTNGTVGAGMILASLSANTG 421
>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 = 235 bits (602), Expect = 4e-76
Identities = 93/201 (46%), Positives = 112/201 (55%), Gaps = 28/201 (13%)
Query: 5 KTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLK 64
K H NI +IGHVD GK+T T L+Y G I K S K A VLDKLK
Sbjct: 1 KRHRNIGIIGHVDHGKTTLTDALLYVTGAISK---------------ESAKGARVLDKLK 45
Query: 65 AERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFE 124
ERERGITI IA FET K + IID PGH DF K MI G SQAD A+L+V A G
Sbjct: 46 EERERGITIKIAAVSFETKKRLINIIDTPGHVDFTKEMIRGASQADGAILVVDAVEG--- 102
Query: 125 AGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSG-YIKKIGY 183
QTREH LLA TLGV +IV +NK+D +A EE+ +E+S ++K G+
Sbjct: 103 ----VMPQTREHLLLAKTLGVP-IIVFINKIDRV----DDAELEEVVEEISRELLEKYGF 153
Query: 184 NPATVAFVPISGWHGDNMLEV 204
TV VP S G+ + E+
Sbjct: 154 GGETVPVVPGSALTGEGIDEL 174
>gnl|CDD|239676 cd03705, EF1_alpha_III, Domain III of EF-1. Eukaryotic elongation
factor 1 (EF-1) is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to ribosomes. EF-1 is
composed of four subunits: the alpha chain, which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This family is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea (aEF-1
alpha) and eukaryotes (eEF-1 alpha).
Length = 104
Score = 204 bits (521), Expect = 4e-65
Identities = 78/104 (75%), Positives = 88/104 (84%)
Query: 335 KATQDFTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPKAL 394
K + FTAQVIVLNHPGQI GYTPVLDCHTAH+AC+FAEI K D RTGK EENPK L
Sbjct: 1 KVAESFTAQVIVLNHPGQIKPGYTPVLDCHTAHVACRFAEILSKIDPRTGKKLEENPKFL 60
Query: 395 KSGDAAIIVLVPSKPMCVESFSEFPPLGRFAVRDMRQTVAVGVI 438
KSGDAAI+ +VP KP+ VE+FSE+PPLGRFAVRDM QTVAVG++
Sbjct: 61 KSGDAAIVKIVPQKPLVVETFSEYPPLGRFAVRDMGQTVAVGIV 104
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 208 bits (532), Expect = 7e-63
Identities = 140/452 (30%), Positives = 206/452 (45%), Gaps = 77/452 (17%)
Query: 1 MGKE-----KTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFK 55
M KE K H+N+ IGHVD GK+T T + + G K
Sbjct: 1 MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAI---------------TTVLAKKGGAEAK 45
Query: 56 YAWVLDKLKAERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLI 115
+D E+ RGITI+ A ++ET+ + +D PGH D++KNMITG +Q D A+L+
Sbjct: 46 AYDQIDNAPEEKARGITINTAHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILV 105
Query: 116 VAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVS 175
VAA G QTREH LLA +GV ++V +NK+D + E E ++ EV
Sbjct: 106 VAATDGPMP-------QTREHILLARQVGVPYIVVFLNKVDMVD---DEELLELVEMEVR 155
Query: 176 GYIKKIGYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADG-KCLIEALDA 234
+ + G+ P D P +G A++ EG A + E +DA
Sbjct: 156 ELLSEYGF-PG-------------------DDTPIIRGSALKALEGDAKWEAKIEELMDA 195
Query: 235 ----ILPPSRPTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPG---MLVTFAPANLTT 287
I P R +KP +P++DV+ I G GTV GRVE G++K G +V TT
Sbjct: 196 VDSYIPTPERDIDKPFLMPVEDVFSISGRGTVVTGRVERGILKVGEEVEIVGIKETQKTT 255
Query: 288 EVKSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGFVAGDSKASPPKATQDFTAQVIVL 347
V VEM + L E GDNVG ++ V +++ RG V K K F A+V VL
Sbjct: 256 -VTGVEMFRKLLDEGQAGDNVGVLLRGVKREDVERGQVLA--KPGSIKPHTKFEAEVYVL 312
Query: 348 NHPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTE-ENPKALKSGDAAIIVLVP 406
+ + +TP + + ++ TG T E + + GD +V+
Sbjct: 313 SK--EEGGRHTPFFHGYRPQFYFRTTDV-------TGAITLPEGVEMVMPGDNVKMVVEL 363
Query: 407 SKPMCVESFSEFPPLGRFAVRDMRQTVAVGVI 438
P+ +E RFA+R+ +TV GV+
Sbjct: 364 IHPIAME------EGLRFAIREGGRTVGAGVV 389
>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 = 206 bits (525), Expect = 8e-62
Identities = 131/437 (29%), Positives = 205/437 (46%), Gaps = 49/437 (11%)
Query: 14 GHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGK--GSFKYAWVLDKLKAERERGI 71
G VD GKST G L++ I + + E+++++ G G A ++D L+AERE+GI
Sbjct: 7 GSVDDGKSTLIGRLLHDTKQIYEDQLAALERDSKKHGTQGGEIDLALLVDGLQAEREQGI 66
Query: 72 TIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGISKNG 131
TID+A F T K + D PGH + +NM TG S AD AVL+V A G E
Sbjct: 67 TIDVAYRYFSTDKRKFIVADTPGHEQYTRNMATGASTADLAVLLVDARKGVLE------- 119
Query: 132 QTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNPATVAFV 191
QTR H+ +A LG++ +++ VNKMD + Y E FE IKK+ + +++G V F+
Sbjct: 120 QTRRHSYIASLLGIRHVVLAVNKMDLVD--YDEEVFENIKKDYLAFAEQLG--FRDVTFI 175
Query: 192 PISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPSRPTEKPLRLPLQ 251
P+S GDN++ S+ MPW+ G L+E L+ + + PLR P+Q
Sbjct: 176 PLSALKGDNVVSRSESMPWYS------------GPTLLEILETVEVERDAQDLPLRFPVQ 223
Query: 252 DVYKI-----GGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQEAVPGD 306
V + G GT+ G V G V P+ ++ V + L++A G
Sbjct: 224 YVNRPNLDFRGYAGTIASGSV-----HVGDEVVVLPSGRSSRVARIVTFDGDLEQARAGQ 278
Query: 307 NVGFNVKNVSVKELRRG--FVAGDSKASPPKATQDFTAQVIVL-NHPGQISNGYTPVLDC 363
V + + ++ RG A D S P+ F A ++ + P + G + L
Sbjct: 279 AVTLTLDDEI--DISRGDLLAAAD---SAPEVADQFAATLVWMAEEP--LLPGRSYDLKL 331
Query: 364 HTAHIACKFAEIKEKCDRRTGKTTEENPKALKSGDAAIIVLVPSKPMCVESFSEFPPLGR 423
T + A IK K D T + K+L+ + + L +P+ + ++E G
Sbjct: 332 GTRKVRASVAAIKHKVDVNTLEKGAA--KSLELNEIGRVNLSLDEPIAFDPYAENRTTGA 389
Query: 424 FAV--RDMRQTVAVGVI 438
F + R +TV G+I
Sbjct: 390 FILIDRLSNRTVGAGMI 406
>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 = 198 bits (506), Expect = 2e-61
Identities = 86/234 (36%), Positives = 122/234 (52%), Gaps = 28/234 (11%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGI--DK-RTIEKFEKEAQEMGKGSFKYAWVLDKLKA 65
+ G VD GKST G L+Y I D+ +E+ + + K A ++D L+A
Sbjct: 1 RFITCGSVDDGKSTLIGRLLYDSKSIFEDQLAALERSKSSGTQGEK--LDLALLVDGLQA 58
Query: 66 ERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEA 125
ERE+GITID+A F T K I D PGH + +NM+TG S AD A+L+V A G E
Sbjct: 59 EREQGITIDVAYRYFSTPKRKFIIADTPGHEQYTRNMVTGASTADLAILLVDARKGVLE- 117
Query: 126 GISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNP 185
QTR H+ +A LG++ ++V VNKMD + Y E FEEIK + + +G
Sbjct: 118 ------QTRRHSYIASLLGIRHVVVAVNKMDLVD--YDEEVFEEIKADYLAFAASLGIED 169
Query: 186 ATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPS 239
+ F+PIS GDN++ S+ MPW+K G L+E L+ + S
Sbjct: 170 --ITFIPISALEGDNVVSRSENMPWYK------------GPTLLEHLETVEIAS 209
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 203 bits (518), Expect = 1e-58
Identities = 131/443 (29%), Positives = 200/443 (45%), Gaps = 61/443 (13%)
Query: 14 GHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMG--KGSFKYAWVLDKLKAERERGI 71
G VD GKST G L+Y I + + E++++++G A ++D L AERE+GI
Sbjct: 31 GSVDDGKSTLIGRLLYDSKMIFEDQLAALERDSKKVGTQGDEIDLALLVDGLAAEREQGI 90
Query: 72 TIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGISKNG 131
TID+A F T K + D PGH + +NM+TG S AD A+++V A G
Sbjct: 91 TIDVAYRYFATPKRKFIVADTPGHEQYTRNMVTGASTADLAIILVDARKGVLT------- 143
Query: 132 QTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNPATVAFV 191
QTR H+ +A LG++ +++ VNKMD + Y + F+EI + + K+G V F+
Sbjct: 144 QTRRHSFIASLLGIRHVVLAVNKMDLVD--YDQEVFDEIVADYRAFAAKLGL--HDVTFI 199
Query: 192 PISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPSRPTEKPLRLPLQ 251
PIS GDN++ S +MPW++G + L+E L+ + S K R P+Q
Sbjct: 200 PISALKGDNVVTRSARMPWYEGPS------------LLEHLETVEIASDRNLKDFRFPVQ 247
Query: 252 DVYKI-----GGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQEAVPGD 306
V + G GT V +GV++PG V P+ T+ VK + L EA G
Sbjct: 248 YVNRPNLDFRGFAGT-----VASGVVRPGDEVVVLPSGKTSRVKRIVTPDGDLDEAFAGQ 302
Query: 307 NVGFNVKN---VSVKELRRG--FVAGDSKASPPKATQDFTAQVIVLN----HPGQISNGY 357
V + + +S RG D + P+ F A V+ + PG Y
Sbjct: 303 AVTLTLADEIDIS-----RGDMLARAD---NRPEVADQFDATVVWMAEEPLLPG---RPY 351
Query: 358 TPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPKALKSGDAAIIVLVPSKPMCVESFSE 417
+L T + A IK + D T K L+ + L P+ + ++
Sbjct: 352 --LLKHGTRTVPASVAAIKYRVDVNT--LERLAAKTLELNEIGRCNLSTDAPIAFDPYAR 407
Query: 418 FPPLGRFAV--RDMRQTVAVGVI 438
G F + R TV G+I
Sbjct: 408 NRTTGSFILIDRLTNATVGAGMI 430
>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 = 181 bits (463), Expect = 1e-56
Identities = 74/89 (83%), Positives = 84/89 (94%)
Query: 242 TEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQE 301
T+KPLRLP+QDVYKIGGIGTVPVGRVETGV+KPGM+VTFAPA +T EVKSVEMHHE L+E
Sbjct: 1 TDKPLRLPIQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGVTGEVKSVEMHHEPLEE 60
Query: 302 AVPGDNVGFNVKNVSVKELRRGFVAGDSK 330
A+PGDNVGFNVKNVS K+++RG VAGDSK
Sbjct: 61 ALPGDNVGFNVKNVSKKDIKRGDVAGDSK 89
>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 = 183 bits (467), Expect = 4e-56
Identities = 77/198 (38%), Positives = 101/198 (51%), Gaps = 30/198 (15%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERE 68
N+ VIGHVD GK+T TG L+Y+ G ID+R K LD LK ERE
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKE---------------TFLDTLKEERE 45
Query: 69 RGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGIS 128
RGITI + +FE K + ID PGH DF K + G +QAD A+L+V A G
Sbjct: 46 RGITIKTGVVEFEWPKRRINFIDTPGHEDFSKETVRGLAQADGALLVVDANEGV------ 99
Query: 129 KNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGY---NP 185
QTREH +A G +IV VNK+D E F+E+ +E+ +K IG+
Sbjct: 100 -EPQTREHLNIAL-AGGLPIIVAVNKIDRV----GEEDFDEVLREIKELLKLIGFTFLKG 153
Query: 186 ATVAFVPISGWHGDNMLE 203
V +PIS G+ + E
Sbjct: 154 KDVPIIPISALTGEGIEE 171
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 186 bits (474), Expect = 1e-53
Identities = 110/349 (31%), Positives = 167/349 (47%), Gaps = 57/349 (16%)
Query: 14 GHVDSGKSTTTGHLIYKCGGIDKRTI-----EKFEKEAQEMGKGSFK--YAWVLDKLKAE 66
G VD GKST G L++ D + I +++ G K A ++D L+AE
Sbjct: 34 GSVDDGKSTLIGRLLH-----DTKQIYEDQLASLHNDSKRHGTQGEKLDLALLVDGLQAE 88
Query: 67 RERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAG 126
RE+GITID+A F T K I D PGH + +NM TG S D A+L++ A G +
Sbjct: 89 REQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTCDLAILLIDARKGVLD-- 146
Query: 127 ISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNPA 186
QTR H+ +A LG+K L+V VNKMD + YSE FE I+++ + +++ N
Sbjct: 147 -----QTRRHSFIATLLGIKHLVVAVNKMDLVD--YSEEVFERIREDYLTFAEQLPGNL- 198
Query: 187 TVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPSRPTEKPL 246
+ FVP+S GDN++ S+ MPW+ G L+E L+ + +P
Sbjct: 199 DIRFVPLSALEGDNVVSQSESMPWYS------------GPTLLEVLETVDIQRVVDAQPF 246
Query: 247 RLPLQDVYKI-----GGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQE 301
R P+Q V + G GT + +GV+K G V P+ + V + L+E
Sbjct: 247 RFPVQYVNRPNLDFRGYAGT-----LASGVVKVGDRVKVLPSGKESNVARIVTFDGDLEE 301
Query: 302 AVPGDNVGFNVKN---VSVKELRRG--FVAGDSKASPPKATQDFTAQVI 345
A G+ + +++ +S RG VA D +A Q +A V+
Sbjct: 302 AFAGEAITLVLEDEIDIS-----RGDLLVAADEA---LQAVQHASADVV 342
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 182 bits (464), Expect = 6e-53
Identities = 118/362 (32%), Positives = 173/362 (47%), Gaps = 63/362 (17%)
Query: 1 MGKE-----KTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFK 55
M KE K H+N+ IGHVD GK+T T + K + G G K
Sbjct: 1 MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAIT---------------KVLAKKGGGEAK 45
Query: 56 YAWVLDKLKAERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLI 115
+D E+ RGITI+ + ++ET+ + +D PGH D++KNMITG +Q D A+L+
Sbjct: 46 AYDQIDNAPEEKARGITINTSHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILV 105
Query: 116 VAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVS 175
V+A G QTREH LLA +GV ++V +NK D + E ++ EV
Sbjct: 106 VSAADGPMP-------QTREHILLARQVGVPYIVVFLNKCDMVDDE---ELLELVEMEVR 155
Query: 176 GYIKKIGYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKC------LI 229
+ K + GD+ P +G A++ EG D + L+
Sbjct: 156 ELLSKYDFP-------------GDD-------TPIIRGSALKALEGDDDEEWEAKILELM 195
Query: 230 EALDAILP-PSRPTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPG---MLVTFAPANL 285
+A+D+ +P P R +KP +P++DV+ I G GTV GRVE G++K G +V
Sbjct: 196 DAVDSYIPEPERAIDKPFLMPIEDVFSISGRGTVVTGRVERGIVKVGDEVEIVGIKE-TQ 254
Query: 286 TTEVKSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGFVAGDSKASPPKATQDFTAQVI 345
T V VEM + L E GDNVG ++ +++ RG V +K K F A+V
Sbjct: 255 KTTVTGVEMFRKLLDEGQAGDNVGVLLRGTKREDVERGQVL--AKPGSIKPHTKFEAEVY 312
Query: 346 VL 347
VL
Sbjct: 313 VL 314
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 182 bits (464), Expect = 7e-53
Identities = 124/363 (34%), Positives = 178/363 (49%), Gaps = 65/363 (17%)
Query: 1 MGKE-----KTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFK 55
M KE K H+N+ IGHVD GK+T T I K +K EA+
Sbjct: 1 MAKEKFERTKPHVNVGTIGHVDHGKTTLTA-------AITKVLAKKGGAEAK-------A 46
Query: 56 YAWVLDKLKAERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLI 115
Y + DK E+ RGITI+ A ++ET K + +D PGH D++KNMITG +Q D A+L+
Sbjct: 47 YDQI-DKAPEEKARGITINTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILV 105
Query: 116 VAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTE-PPYSEARFEEIKKEV 174
V+A G QTREH LLA +GV ++V +NK D + E E+++ +
Sbjct: 106 VSAADGPMP-------QTREHILLARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELL 158
Query: 175 SGYIKKIGYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKC------L 228
S Y + GD+ P +G A++ EG D + L
Sbjct: 159 SKY-----------------DFPGDD-------TPIIRGSALKALEGDDDEEWEKKILEL 194
Query: 229 IEALDAILP-PSRPTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPG---MLVTFAPAN 284
++A+D+ +P P R +KP +P++DV+ I G GTV GRVE G+IK G +V
Sbjct: 195 MDAVDSYIPTPERAIDKPFLMPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIRDTQ 254
Query: 285 LTTEVKSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGFVAGDSKASPPKATQDFTAQV 344
TT V VEM + L E GDNVG ++ + +++ RG V +K F A+V
Sbjct: 255 KTT-VTGVEMFRKLLDEGQAGDNVGALLRGIKREDVERGQVL--AKPGSITPHTKFEAEV 311
Query: 345 IVL 347
VL
Sbjct: 312 YVL 314
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 180 bits (460), Expect = 3e-52
Identities = 132/448 (29%), Positives = 201/448 (44%), Gaps = 63/448 (14%)
Query: 3 KEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDK 62
++K H+NI IGHVD GK+T T + +K+++ +D
Sbjct: 8 RKKPHVNIGTIGHVDHGKTTLTAAITMTLAAKGGAKAKKYDE---------------IDS 52
Query: 63 LKAERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGE 122
E+ RGITI+ A ++ET + +D PGH D++KNMITG +Q D A+L+V+A G
Sbjct: 53 APEEKARGITINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGP 112
Query: 123 FEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIG 182
QT+EH LLA +GV ++V +NK D + E E ++ EV + K
Sbjct: 113 MP-------QTKEHILLAKQVGVPNIVVFLNKEDQVD---DEELLELVELEVRELLSKYD 162
Query: 183 YNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKC--LIEALDAILP-PS 239
+ + V S LE + P I+R E K K L++A+D+ +P P
Sbjct: 163 FPGDDIPIVSGSALLA---LEALTENP-----KIKRGENKWVDKIYNLMDAVDSYIPTPE 214
Query: 240 RPTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPG---MLVTFAPANLTTEVKSVEMHH 296
R T+KP + ++DV+ I G GTV GR+E G +K G +V TT V +EM
Sbjct: 215 RDTDKPFLMAIEDVFSITGRGTVATGRIERGTVKVGDTVEIVGLRETKTTT-VTGLEMFQ 273
Query: 297 EALQEAVPGDNVGFNVKNVSVKELRRGFVAGDSKASPPKATQDFTAQVIVLN------HP 350
+ L E + GDNVG ++ + +++ RG V P F AQV +L H
Sbjct: 274 KTLDEGLAGDNVGILLRGIQKEDIERGMVLAKPGTITPHTK--FEAQVYILTKEEGGRHT 331
Query: 351 GQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPKALKSGDAAIIVLVPSKPM 410
GY P T + K + + GD + + P+
Sbjct: 332 P-FFPGYRPQFYVRTTDVTGKIESFTA--------DDGSKTEMVMPGDRIKMTVELIYPI 382
Query: 411 CVESFSEFPPLGRFAVRDMRQTVAVGVI 438
+E RFA+R+ +TV GV+
Sbjct: 383 AIEKGM------RFAIREGGRTVGAGVV 404
>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 = 178 bits (454), Expect = 1e-51
Identities = 139/452 (30%), Positives = 206/452 (45%), Gaps = 86/452 (19%)
Query: 3 KEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDK 62
+ K H+NI IGHVD GK+T T + + G + + +D
Sbjct: 8 RTKPHVNIGTIGHVDHGKTTLTAAIT---------------TVLAKEGGAAARAYDQIDN 52
Query: 63 LKAERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGE 122
E+ RGITI+ A ++ET + +D PGH D++KNMITG +Q D A+L+V+A G
Sbjct: 53 APEEKARGITINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSATDGP 112
Query: 123 FEAGISKNGQTREHALLAFTLGVKQLIVGVNKMD-STEPPYSEARFEEIKKEVSGYIKKI 181
QTREH LLA +GV ++V +NK D + E E+++ +S Y
Sbjct: 113 MP-------QTREHILLARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSEY---- 161
Query: 182 GYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKC----LIEALDAILP 237
+ GD+ P +G A++ EG A+ + L++A+D +P
Sbjct: 162 -------------DFPGDD-------TPIIRGSALKALEGDAEWEAKILELMDAVDEYIP 201
Query: 238 -PSRPTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPG---MLVTFAPANLTTEVKSVE 293
P R T+KP +P++DV+ I G GTV GRVE G++K G +V TT V VE
Sbjct: 202 TPERETDKPFLMPIEDVFSITGRGTVVTGRVERGIVKVGEEVEIVGLKDTRKTT-VTGVE 260
Query: 294 MHHEALQEAVPGDNVGFNVKNVSVKELRRGFVAGDSKASPPKATQDFTAQVIVLN----- 348
M + L E GDNVG ++ + +E+ RG V +K K F A+V VL
Sbjct: 261 MFRKELDEGRAGDNVGLLLRGIKREEIERGMVL--AKPGSIKPHTKFEAEVYVLKKEEGG 318
Query: 349 -HPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTE-ENPKALKSGDAAIIVLVP 406
H S GY P T + TG T E + + GD + +
Sbjct: 319 RHTPFFS-GYRPQFYFRTTDV--------------TGSITLPEGVEMVMPGDNVKMTVEL 363
Query: 407 SKPMCVESFSEFPPLGRFAVRDMRQTVAVGVI 438
P+ +E RFA+R+ +TV GV+
Sbjct: 364 ISPIALEQGM------RFAIREGGRTVGAGVV 389
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 180 bits (457), Expect = 2e-51
Identities = 144/454 (31%), Positives = 212/454 (46%), Gaps = 86/454 (18%)
Query: 3 KEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDK 62
+ K H+N+ IGHVD GK+T T I K E + +F +DK
Sbjct: 57 RTKPHVNVGTIGHVDHGKTTLTA------------AITKVLAEEGKAKAVAFDE---IDK 101
Query: 63 LKAERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGE 122
E+ RGITI A ++ET+K + +D PGH D++KNMITG +Q D +L+V+A G
Sbjct: 102 APEEKARGITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGP 161
Query: 123 FEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIG 182
QT+EH LLA +GV L+V +NK+D + E+ + V ++++
Sbjct: 162 MP-------QTKEHILLARQVGVPSLVVFLNKVDVVDDE-------ELLELVEMELREL- 206
Query: 183 YNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKAD--GKC----LIEALDAIL 236
++F G D++P +G A+ +G D GK L++A+D +
Sbjct: 207 -----LSFYKFPG----------DEIPIIRGSALSALQGTNDEIGKNAILKLMDAVDEYI 251
Query: 237 P-PSRPTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPG---MLVTFAP-ANLTTEVKS 291
P P R +KP +P++DV+ I G GTV GRVE G IK G +V P L T V
Sbjct: 252 PEPVRVLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEIVGLRPGGPLKTTVTG 311
Query: 292 VEMHHEALQEAVPGDNVGFNVKNVSVKELRRGFVAGDSKASPPKATQDFTAQVIVLN--- 348
VEM + L + GDNVG ++ + ++++RG V K K + F A++ VL
Sbjct: 312 VEMFKKILDQGQAGDNVGLLLRGLKREDVQRGQVI--CKPGSIKTYKKFEAEIYVLTKDE 369
Query: 349 ---HPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTT-EENPKALKSGDAAIIVL 404
H SN Y P TA + TGK E K + GD V
Sbjct: 370 GGRHTPFFSN-YRPQFYLRTADV--------------TGKVELPEGVKMVMPGDNVTAVF 414
Query: 405 VPSKPMCVESFSEFPPLGRFAVRDMRQTVAVGVI 438
P+ +E P RFA+R+ +TV GV+
Sbjct: 415 ELISPVPLE------PGQRFALREGGRTVGAGVV 442
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 175 bits (445), Expect = 3e-50
Identities = 145/458 (31%), Positives = 207/458 (45%), Gaps = 89/458 (19%)
Query: 1 MGKE-----KTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFK 55
M KE K H+NI IGHVD GK+T T I K E+ +A+
Sbjct: 1 MAKEKFDRSKPHVNIGTIGHVDHGKTTLTA-------AITKVLAERGLNQAK-------D 46
Query: 56 YAWVLDKLKAERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLI 115
Y + D E+ERGITI+ A ++ET K + +D PGH D++KNMITG +Q D A+L+
Sbjct: 47 YDSI-DAAPEEKERGITINTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILV 105
Query: 116 VAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVS 175
VAA G QTREH LLA +GV L+V +NK+D + E E ++ EV
Sbjct: 106 VAATDGPMP-------QTREHILLARQVGVPYLVVFLNKVDLVD---DEELLELVEMEVR 155
Query: 176 GYIKKIGYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADG----KCLIEA 231
+ + + GD+ +P +G A++ EG L++A
Sbjct: 156 ELLSEYDFP-------------GDD-------IPVIRGSALKALEGDPKWEDAIMELMDA 195
Query: 232 LDAILP-PSRPTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPG---MLVTFAPANLTT 287
+D +P P R T+KP +P++DV+ I G GTV GRVE G +K G +V T
Sbjct: 196 VDEYIPTPERDTDKPFLMPVEDVFTITGRGTVVTGRVERGTVKVGDEVEIVGIKET-QKT 254
Query: 288 EVKSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGFVAGDSKASPPKATQDFTAQVIVL 347
V VEM + L E GDNVG ++ V E+ RG V +K K F A+V +L
Sbjct: 255 VVTGVEMFRKLLDEGQAGDNVGVLLRGVDRDEVERGQVL--AKPGSIKPHTKFKAEVYIL 312
Query: 348 N------HPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTT-EENPKALKSGDAA 400
H +N Y P T + TG E + + GD
Sbjct: 313 TKEEGGRHTPFFNN-YRPQFYFRTTDV--------------TGSIELPEGTEMVMPGDNV 357
Query: 401 IIVLVPSKPMCVESFSEFPPLGRFAVRDMRQTVAVGVI 438
I + P+ +E +FA+R+ +TV G +
Sbjct: 358 TITVELIHPIAMEQGL------KFAIREGGRTVGAGTV 389
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 176 bits (447), Expect = 8e-50
Identities = 141/447 (31%), Positives = 205/447 (45%), Gaps = 59/447 (13%)
Query: 3 KEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDK 62
++K H+NI IGHVD GK+T T L + +K+++ +D
Sbjct: 77 RKKPHVNIGTIGHVDHGKTTLTAALTMALASMGGSAPKKYDE---------------IDA 121
Query: 63 LKAERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGE 122
ER RGITI+ A ++ET + +D PGH D++KNMITG +Q D A+L+V+ G
Sbjct: 122 APEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGP 181
Query: 123 FEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIG 182
QT+EH LLA +GV ++V +NK D + E E ++ EV +
Sbjct: 182 MP-------QTKEHILLAKQVGVPNMVVFLNKQDQVD---DEELLELVELEVRELLSSYE 231
Query: 183 YNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKC--LIEALDAILP-PS 239
+ +PI LE + P I+R + K K L++A+D+ +P P
Sbjct: 232 FPGDD---IPIISGSALLALEALMENP-----NIKRGDNKWVDKIYELMDAVDSYIPIPQ 283
Query: 240 RPTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLT--TEVKSVEMHHE 297
R T+ P L ++DV+ I G GTV GRVE G +K G V T T V VEM +
Sbjct: 284 RQTDLPFLLAVEDVFSITGRGTVATGRVERGTVKVGETVDIVGLRETRSTTVTGVEMFQK 343
Query: 298 ALQEAVPGDNVGFNVKNVSVKELRRGFVAGDSKASPPKATQDFTAQVIVLNHP--GQIS- 354
L EA+ GDNVG ++ + +++RG V + P F A V VL G+ S
Sbjct: 344 ILDEALAGDNVGLLLRGIQKADIQRGMVLAKPGSITPHTK--FEAIVYVLKKEEGGRHSP 401
Query: 355 --NGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPKALKSGDAAIIVLVPSKPMCV 412
GY P T + K I D E K + GD +V+ P+
Sbjct: 402 FFAGYRPQFYMRTTDVTGKVTSIMNDKD--------EESKMVMPGDRVKMVVELIVPVAC 453
Query: 413 ESFSEFPPLGRFAVRDMRQTVAVGVIK 439
E RFA+R+ +TV GVI+
Sbjct: 454 EQGM------RFAIREGGKTVGAGVIQ 474
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 150 bits (381), Expect = 1e-40
Identities = 88/370 (23%), Positives = 145/370 (39%), Gaps = 70/370 (18%)
Query: 8 INIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAER 67
+ I GH+D GK+T L V D+L E+
Sbjct: 1 MIIGTAGHIDHGKTTLLKALTGG----------------------------VTDRLPEEK 32
Query: 68 ERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGI 127
+RGITID+ + + + ID PGH DFI N++ G D A+L+VAA G
Sbjct: 33 KRGITIDLGFYYRKLEDGVMGFIDVPGHPDFISNLLAGLGGIDYALLVVAADEG------ 86
Query: 128 SKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNPAT 187
QT EH L+ LG+K I+ + K D + E + ++I ++S KI
Sbjct: 87 -LMAQTGEHLLILDLLGIKNGIIVLTKADRVDEARIEQKIKQILADLSLANAKI------ 139
Query: 188 VAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPSRPTEKPLR 247
S G + E+ +++ D + R +KP R
Sbjct: 140 ---FKTSAKTGRGIEELKNELI-----------------------DLLEEIERDEQKPFR 173
Query: 248 LPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQEAVPGDN 307
+ + + + G+GTV G V +G +K G + +P N V+S++ H ++EA G
Sbjct: 174 IAIDRAFTVKGVGTVVTGTVLSGEVKVGDKLYLSPINKEVRVRSIQAHDVDVEEAKAGQR 233
Query: 308 VGFNVKNVSVKELRRGFVAGDSKASPPKATQDFTAQVIVLNHPGQISNGYTPVLDCH-TA 366
VG +K V +E+ RG K P + T ++ + + PV
Sbjct: 234 VGLALKGVEKEEIERGDWL--LKPEPLEVTTRLIVELEIDPLFKKTLKQGQPVHIHVGLR 291
Query: 367 HIACKFAEIK 376
+ + ++
Sbjct: 292 SVTGRIVPLE 301
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 147 bits (373), Expect = 5e-39
Identities = 115/436 (26%), Positives = 185/436 (42%), Gaps = 91/436 (20%)
Query: 5 KTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLK 64
H+ + V GHVD GKST G L+ G +D G G+ + LD K
Sbjct: 115 PEHVLVGVAGHVDHGKSTLVGVLV--TGRLDD-------------GDGATRSY--LDVQK 157
Query: 65 AERERGITIDIALWKF-----------------------ETSKFYVTIIDAPGHRDFIKN 101
E ERG++ DI+L + + + V+ +D GH +++
Sbjct: 158 HEVERGLSADISLRVYGFDDGKVVRLKNPLDEAEKAAVVKRADKLVSFVDTVGHEPWLRT 217
Query: 102 MITG--TSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTE 159
I G + D +L+VAA + G++K T+EH +A + + +IV V K+D
Sbjct: 218 TIRGLLGQKVDYGLLVVAA-----DDGVTK--MTKEHLGIALAMELP-VIVVVTKIDM-- 267
Query: 160 PPYSEARFEEIKKEVSGYIKKIGYNPATVAFVPISGWHGDNMLEVSDKM-----PWFKGW 214
+ RF+ + +E+S +K++G P + + + + K P F
Sbjct: 268 --VPDDRFQGVVEEISALLKRVGRIP-----LIVKDTDDVVLAAKAMKAGRGVVPIFYTS 320
Query: 215 AIERKEGKADGKCLIEALDAILPPSRPT--EKPLRLPLQDVYKIGGIGTVPVGRVETGVI 272
++ +G L++ +LP R E P + + +Y + G+GTV G V++G++
Sbjct: 321 SV-----TGEGLDLLDEFFLLLPKRRRWDDEGPFLMYIDKIYSVTGVGTVVSGSVKSGIL 375
Query: 273 KPGMLVTFAPANL----TTEVKSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGFVAGD 328
G V P VKS+EMHH + A G +G +K V +EL RG V
Sbjct: 376 HVGDTVLLGPFKDGKFREVVVKSIEMHHYRVDSAKAGSIIGIALKGVEKEELERGMVL-- 433
Query: 329 SKASPPKATQDFTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTE 388
S + PKA ++F A+V+VL HP I GY PV T R E
Sbjct: 434 SAGADPKAVREFDAEVLVLRHPTTIRAGYEPVFHYETI--------------REAVYFEE 479
Query: 389 ENPKALKSGDAAIIVL 404
+ L GD ++ +
Sbjct: 480 IDKGFLMPGDRGVVRM 495
>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 = 131 bits (331), Expect = 3e-37
Identities = 42/107 (39%), Positives = 53/107 (49%), Gaps = 19/107 (17%)
Query: 333 PPKATQDFTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPK 392
P K F AQV +LNHP I NGY PV CHTA + KF GK +
Sbjct: 1 PIKPHTKFKAQVYILNHPTPIFNGYRPVFYCHTADVTGKFI--------LPGKK-----E 47
Query: 393 ALKSGDAAIIVLVPSKPMCVESFSEFPPLGRFAVRDMRQTVAVGVIK 439
+ GD AI+ + KP+ VE RFA+R+ +TVAVGV+
Sbjct: 48 FVMPGDNAIVTVELIKPIAVEKGQ------RFAIREGGRTVAVGVVT 88
>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 = 125 bits (315), Expect = 1e-33
Identities = 74/233 (31%), Positives = 108/233 (46%), Gaps = 39/233 (16%)
Query: 6 THINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKA 65
H+N+ IGHVD GK+T T + +K+++ DK
Sbjct: 1 PHVNVGTIGHVDHGKTTLTAAITKVLAKKGGAKAKKYDEI---------------DKAPE 45
Query: 66 ERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEA 125
E+ RGITI+ A ++ET+ + +D PGH D+IKNMITG +Q D A+L+V+A G
Sbjct: 46 EKARGITINTAHVEYETANRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSATDGPMP- 104
Query: 126 GISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNP 185
QTREH LLA +GV ++V +NK D + E E ++ EV + K G++
Sbjct: 105 ------QTREHLLLARQVGVPYIVVFLNKADMVD---DEELLELVEMEVRELLSKYGFDG 155
Query: 186 ATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPP 238
V S LE D W I L++ALD+ +P
Sbjct: 156 DDTPIVRGSAL---KALEGDDPNKWVD--KILE---------LLDALDSYIPT 194
>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 = 128 bits (322), Expect = 6e-32
Identities = 85/350 (24%), Positives = 138/350 (39%), Gaps = 64/350 (18%)
Query: 8 INIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAER 67
+ I GHVD GK+T L+ GI D+L E+
Sbjct: 1 MIIATAGHVDHGKTT----LLKALTGIAA------------------------DRLPEEK 32
Query: 68 ERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGI 127
+RG+TID+ F + + ID PGH FI N I G D A+L+V A G
Sbjct: 33 KRGMTIDLGFAYFPLPDYRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVMT--- 89
Query: 128 SKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNPAT 187
QT EH + LG+ IV + K D E + + + + +
Sbjct: 90 ----QTGEHLAVLDLLGIPHTIVVITKADRVN----EEEIKRTEMFMKQILNSYIFLKNA 141
Query: 188 VAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPSRPTEKPLR 247
F S G + E+ ++ K L+E+LD + +KPLR
Sbjct: 142 KIFK-TSAKTGQGIGELKKEL-----------------KNLLESLDI-----KRIQKPLR 178
Query: 248 LPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQEAVPGDN 307
+ + +K+ G GTV G +G +K G + P N VK+++ ++ ++ A G
Sbjct: 179 MAIDRAFKVKGAGTVVTGTAFSGEVKVGDNLRLLPINHEVRVKAIQAQNQDVEIAYAGQR 238
Query: 308 VGFNVKNVSVKELRRGFVAGDSKASPPKATQDFTAQVIVLNHPGQISNGY 357
+ N+ +V + L+RG + + + F A+V +L Q +
Sbjct: 239 IALNLMDVEPESLKRGLLILTPEDPKLRVVVKFIAEVPLL--ELQPYHIA 286
>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 = 115 bits (290), Expect = 2e-31
Identities = 42/104 (40%), Positives = 65/104 (62%), Gaps = 2/104 (1%)
Query: 335 KATQDFTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPKAL 394
+A F A++ VL+HP +S GY PVL+ TAH+ + A++ K D +T ++ P+ L
Sbjct: 1 QAVDKFVAEIYVLDHPEPLSPGYKPVLNVGTAHVPGRIAKLLSKVDGKT--EEKKPPEFL 58
Query: 395 KSGDAAIIVLVPSKPMCVESFSEFPPLGRFAVRDMRQTVAVGVI 438
KSG+ I+ + KP+ +E+FSE GRFA+RD +TV G+I
Sbjct: 59 KSGERGIVEVELQKPVALETFSENQEGGRFALRDGGRTVGAGLI 102
>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 = 99.6 bits (249), Expect = 1e-24
Identities = 56/184 (30%), Positives = 81/184 (44%), Gaps = 42/184 (22%)
Query: 10 IVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERER 69
I GH+D GK+T LI GI+ D+L E++R
Sbjct: 2 IGTAGHIDHGKTT----LIKALTGIET------------------------DRLPEEKKR 33
Query: 70 GITIDI--ALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGI 127
GITID+ A K + ID PGH F+KNM+ G D +L+VAA + GI
Sbjct: 34 GITIDLGFAYLDLPDGK-RLGFIDVPGHEKFVKNMLAGAGGIDAVLLVVAA-----DEGI 87
Query: 128 SKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNPAT 187
QTREH + LG+K+ +V + K D + E R E +++E+ + A
Sbjct: 88 MP--QTREHLEILELLGIKKGLVVLTKADLVD----EDRLELVEEEILELLAGTFLADAP 141
Query: 188 VAFV 191
+ V
Sbjct: 142 IFPV 145
>gnl|CDD|239675 cd03704, eRF3c_III, This family represents eEF1alpha-like
C-terminal region of eRF3 homologous to the domain III
of EF-Tu. eRF3 is a GTPase, which enhances the
termination efficiency by stimulating the eRF1 activity
in a GTP-dependent manner. The C-terminal region is
responsible for translation termination activity and is
essential for viability. 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 = 108
Score = 90.4 bits (225), Expect = 4e-22
Identities = 39/108 (36%), Positives = 63/108 (58%), Gaps = 2/108 (1%)
Query: 335 KATQDFTAQVIVLNHPGQI-SNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPKA 393
+F AQ+ +L I + GY+ VL HTA ++ D++TGK +++ P+
Sbjct: 1 HVVTEFEAQIAILELKRSIITAGYSAVLHIHTAVEEVTIKKLIALIDKKTGKKSKKRPRF 60
Query: 394 LKSGDAAIIVLVPSKPMCVESFSEFPPLGRFAVRDMRQTVAVG-VIKV 440
+KSG I L + P+C+E F +FP LGRF +RD +T+A+G V+K+
Sbjct: 61 VKSGMKVIARLETTGPICLEKFEDFPQLGRFTLRDEGKTIAIGKVLKL 108
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 90.7 bits (226), Expect = 2e-19
Identities = 89/334 (26%), Positives = 137/334 (41%), Gaps = 82/334 (24%)
Query: 1 MGKEKTHI-NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWV 59
+ +I N +I H+D GKST L+ GG+ +R E AQ V
Sbjct: 2 TFTPQKNIRNFSIIAHIDHGKSTLADRLLELTGGLSER-----EMRAQ-----------V 45
Query: 60 LDKLKAERERGITID---IAL-WKFETSKFYV-TIIDAPGHRDFIKNMITGTSQADC--A 112
LD + ERERGITI + L +K + + YV +ID PGH DF + S A C A
Sbjct: 46 LDSMDIERERGITIKAQAVRLNYKAKDGETYVLNLIDTPGHVDFSYEV--SRSLAACEGA 103
Query: 113 VLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGV-NKMD--STEPPYSEARFEE 169
+L+V A G EA QT + LA ++ I+ V NK+D + +P + E+
Sbjct: 104 LLVVDASQG-VEA------QTLANVYLALENNLE--IIPVLNKIDLPAADPERVKQEIED 154
Query: 170 IKKEVSGYIKKIGYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLI 229
I IG + + V +S G + +V +
Sbjct: 155 I----------IGIDASDA--VLVSAKTGIGIEDV------------------------L 178
Query: 230 EAL-DAILPPSRPTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTE 288
EA+ + I PP + PL+ + D + +G V + R+ G +K G + E
Sbjct: 179 EAIVEKIPPPKGDPDAPLKALIFDSWYDNYLGVVVLVRIFDGTLKKGDKIRMMSTGKEYE 238
Query: 289 VKSVEM---HHEALQEAVPGDNVGF---NVKNVS 316
V V + + E G+ VG+ +K+V
Sbjct: 239 VDEVGIFTPKMVKVDELKAGE-VGYIIAGIKDVR 271
>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 = 89.7 bits (223), Expect = 2e-19
Identities = 90/377 (23%), Positives = 145/377 (38%), Gaps = 114/377 (30%)
Query: 8 INIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAER 67
+NI ++GHVD GK+T T G+ W D E
Sbjct: 5 VNIGMVGHVDHGKTTLT----KALTGV-----------------------WT-DTHSEEL 36
Query: 68 ERGITI-----DIALWKFETSKFY---------------------VTIIDAPGHRDFIKN 101
+RGI+I D ++K V+ +DAPGH +
Sbjct: 37 KRGISIRLGYADAEIYKCPECDGPECYTTEPVCPNCGSETELLRRVSFVDAPGHETLMAT 96
Query: 102 MITGTSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPP 161
M++G + D A+L++AA + QTREH + +G+K +++ NK+D
Sbjct: 97 MLSGAALMDGALLVIAANEPCPQP------QTREHLMALEIIGIKNIVIVQNKIDLVSKE 150
Query: 162 YSEARFEEIKKEVSGYIKKIGYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEG 221
+ +EEIK+ V G I +P+S H N+ A
Sbjct: 151 KALENYEEIKEFVKGTI------AENAPIIPVSALHNANI------------DA------ 186
Query: 222 KADGKCLIEALDAILP-PSRPTEKPLRLPLQ---DVYK--------IGGI--GTVPVGRV 267
L+EA++ +P P R +KP + + DV K GG+ G++ G++
Sbjct: 187 ------LLEAIEKFIPTPERDLDKPPLMYVARSFDVNKPGTPPEKLKGGVIGGSLIQGKL 240
Query: 268 ETG---VIKPGMLVTFAPA----NLTTEVKSVEMHHEALQEAVPGDNVGFNVK---NVSV 317
+ G I+PG+ V + TE+ S+ ++EA PG VG K ++
Sbjct: 241 KVGDEIEIRPGIKVEKGGKTKWEPIYTEITSLRAGGYKVEEARPGGLVGVGTKLDPALTK 300
Query: 318 KELRRGFVAGDSKASPP 334
+ G V G PP
Sbjct: 301 ADALAGQVVGKPGTLPP 317
>gnl|CDD|217388 pfam03144, GTP_EFTU_D2, Elongation factor Tu domain 2. Elongation
factor Tu consists of three structural domains, this is
the second domain. This domain adopts a beta barrel
structure. This the second domain is involved in binding
to charged tRNA. This domain is also found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This domain is structurally
related to pfam03143, and in fact has weak sequence
matches to this domain.
Length = 70
Score = 78.1 bits (193), Expect = 4e-18
Identities = 27/70 (38%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 260 GTVPVGRVETGVIKPGMLVTFAPA--NLTTEVKSVEMHHEALQEAVPGDNVGFNVKNVSV 317
GTV GRVE+G +K G V P V S+EM H L+EAV G N G + + +
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGIGL 60
Query: 318 KELRRGFVAG 327
K+++RG
Sbjct: 61 KDIKRGDTLT 70
>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 = 77.9 bits (193), Expect = 7e-18
Identities = 31/80 (38%), Positives = 45/80 (56%)
Query: 246 LRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQEAVPG 305
RLP+ V+ + G GTV G V +G +K G V P T V+S+++H + ++EA G
Sbjct: 1 FRLPIDRVFTVKGQGTVVTGTVLSGSVKVGDKVEILPLGEETRVRSIQVHGKDVEEAKAG 60
Query: 306 DNVGFNVKNVSVKELRRGFV 325
D V N+ V K+L RG V
Sbjct: 61 DRVALNLTGVDAKDLERGDV 80
>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 = 84.7 bits (210), Expect = 1e-17
Identities = 92/323 (28%), Positives = 135/323 (41%), Gaps = 77/323 (23%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERE 68
N +I H+D GKST L+ G I +R E Q VLD + ERE
Sbjct: 5 NFSIIAHIDHGKSTLADRLLEYTGAISER-----EMREQ-----------VLDSMDLERE 48
Query: 69 RGITID---IAL-WKFETSKFYV-TIIDAPGHRDFIKNMITGTSQADC--AVLIVAAGTG 121
RGITI + L +K + + YV +ID PGH DF + S A C A+L+V A G
Sbjct: 49 RGITIKAQAVRLNYKAKDGETYVLNLIDTPGHVDF--SYEVSRSLAACEGALLLVDAAQG 106
Query: 122 EFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMD--STEPPYSEARFEEIKKEVSGYIK 179
EA QT + LA ++ + V +NK+D S +P E +KKE+ +
Sbjct: 107 -IEA------QTLANVYLALENDLEIIPV-INKIDLPSADP-------ERVKKEI---EE 148
Query: 180 KIGYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPS 239
IG + + + S G + E+ + AI ++ + PP
Sbjct: 149 VIGLDASEA--ILASAKTGIGIEEILE--------AIVKR---------------VPPPK 183
Query: 240 RPTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHH--- 296
+ PL+ + D + G V + RV G IKPG + F EV V +
Sbjct: 184 GDPDAPLKALIFDSHYDNYRGVVALVRVFEGTIKPGDKIRFMSTGKEYEVDEVGVFTPKL 243
Query: 297 EALQEAVPGDNVGF---NVKNVS 316
E G+ VG+ +K+VS
Sbjct: 244 TKTDELSAGE-VGYIIAGIKDVS 265
>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 = 79.5 bits (197), Expect = 2e-17
Identities = 55/173 (31%), Positives = 81/173 (46%), Gaps = 38/173 (21%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERE 68
N +I H+D GKST L+ G + +R E + Q VLD + ERE
Sbjct: 2 NFSIIAHIDHGKSTLADRLLELTGTVSER-----EMKEQ-----------VLDSMDLERE 45
Query: 69 RGITID---IAL-WKFETSKFYV-TIIDAPGHRDFIKNMITGTSQADC--AVLIVAAGTG 121
RGITI + L +K + + Y+ +ID PGH DF + S A C A+L+V A G
Sbjct: 46 RGITIKAQAVRLFYKAKDGEEYLLNLIDTPGHVDF--SYEVSRSLAACEGALLVVDATQG 103
Query: 122 EFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEV 174
EA QT + LA ++ + V +NK+D A + +K+E+
Sbjct: 104 -VEA------QTLANFYLALENNLEIIPV-INKID-----LPAADPDRVKQEI 143
>gnl|CDD|239760 cd04093, HBS1_C, HBS1_C: this family represents the C-terminal
domain of Hsp70 subfamily B suppressor 1 (HBS1) which is
homologous to the domain III of EF-1alpha. This group
contains proteins similar to yeast Hbs1, a G protein
known to be important for efficient growth and protein
synthesis under conditions of limiting translation
initiation and, to associate with Dom34. It has been
speculated that yeast Hbs1 and Dom34 proteins may
function as part of a complex with a role in gene
expression.
Length = 107
Score = 77.3 bits (191), Expect = 2e-17
Identities = 25/105 (23%), Positives = 50/105 (47%)
Query: 335 KATQDFTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPKAL 394
++ F A+++ N I G L H+ ++ D+ TG+ +++ P+ L
Sbjct: 1 PSSTRFEARILTFNVDKPILPGTPFELFRHSLKEPATITKLVSILDKSTGEVSKKKPRCL 60
Query: 395 KSGDAAIIVLVPSKPMCVESFSEFPPLGRFAVRDMRQTVAVGVIK 439
G AI+ + +P+ +E F + LGR +R +T+A G++
Sbjct: 61 TKGQTAIVEIELERPIPLELFKDNKELGRVVLRRDGETIAAGLVT 105
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 82.6 bits (205), Expect = 4e-17
Identities = 89/354 (25%), Positives = 143/354 (40%), Gaps = 121/354 (34%)
Query: 8 INIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAER 67
+NI ++GHVD GK+T L+ G+ W D+ E
Sbjct: 10 VNIGMVGHVDHGKTT----LVQALTGV-----------------------WT-DRHSEEL 41
Query: 68 ERGITI-----DIALWKFETSKFY---------------------VTIIDAPGHRDFIKN 101
+RGITI D + K + V+ +DAPGH +
Sbjct: 42 KRGITIRLGYADATIRKCPDCEEPEAYTTEPKCPNCGSETELLRRVSFVDAPGHETLMAT 101
Query: 102 MITGTSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFT-LGVKQLIVGVNKMDSTEP 160
M++G + D A+L++AA + QT+EH L+A +G+K +++ NK+D
Sbjct: 102 MLSGAALMDGAILVIAANEPCPQP------QTKEH-LMALDIIGIKNIVIVQNKIDLVSK 154
Query: 161 PYSEARFEEIKKEVSGYIKKIGYNPATVA----FVPISGWHGDNMLEVSDKMPWFKGWAI 216
+ +E+IK+ V G TVA +P+S H N+
Sbjct: 155 ERALENYEQIKEFVKG----------TVAENAPIIPVSALHKVNI--------------- 189
Query: 217 ERKEGKADGKCLIEALDAILP-PSRPTEKPLRLPLQ---DVYK--------IGGI--GTV 262
LIEA++ +P P R +KP R+ + DV K GG+ G++
Sbjct: 190 ---------DALIEAIEEEIPTPERDLDKPPRMYVARSFDVNKPGTPPEKLKGGVIGGSL 240
Query: 263 PVGRVETG---VIKPGMLVTFAPAN----LTTEVKSVEMHHEALQEAVPGDNVG 309
G ++ G I+PG+ V +TT++ S+ E ++EA PG VG
Sbjct: 241 IQGVLKVGDEIEIRPGIKVEEGGKTKWEPITTKIVSLRAGGEKVEEARPGGLVG 294
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 82.7 bits (205), Expect = 9e-17
Identities = 48/157 (30%), Positives = 71/157 (45%), Gaps = 23/157 (14%)
Query: 1 MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL 60
M E+ NI ++ H+D+GK+T T +++ G I K +G+ A +
Sbjct: 5 MPLERI-RNIGIVAHIDAGKTTLTERILFYTGIISK------------IGEVHDGAA-TM 50
Query: 61 DKLKAERERGITIDIALWKFETSKFY-VTIIDAPGHRDFIKNMITGTSQADCAVLIVAAG 119
D ++ E+ERGITI A Y + +ID PGH DF + D AV++V A
Sbjct: 51 DWMEQEQERGITITSAATTLFWKGDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAV 110
Query: 120 TGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMD 156
G QT A GV +++ VNKMD
Sbjct: 111 EGVEP-------QTETVWRQADKYGVPRILF-VNKMD 139
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 81.2 bits (201), Expect = 1e-16
Identities = 89/349 (25%), Positives = 137/349 (39%), Gaps = 111/349 (31%)
Query: 8 INIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAER 67
+NI ++GHVD GK+T T L G+ W D+ E
Sbjct: 11 VNIGMVGHVDHGKTTLTKAL----SGV-----------------------WT-DRHSEEL 42
Query: 68 ERGITI-----DIALWKFETSKFY---------------------VTIIDAPGHRDFIKN 101
+RGITI D ++K V+ +DAPGH +
Sbjct: 43 KRGITIKLGYADAKIYKCPECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGHETLMAT 102
Query: 102 MITGTSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPP 161
M++G + D A+L++AA QTREH + +G+K +I+ NK+D
Sbjct: 103 MLSGAALMDGALLVIAANEP------CPQPQTREHLMALEIIGIKNIIIVQNKIDLVSRE 156
Query: 162 YSEARFEEIKKEVSGYIKKIGYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEG 221
+ +E+IK+ V G + +PIS H N+
Sbjct: 157 RALENYEQIKEFVKGTV------AENAPIIPISAQHKANI-------------------- 190
Query: 222 KADGKCLIEAL-DAILPPSRPTEKPLRLPLQ---DVYK--------IGGI--GTVPVGRV 267
LIEA+ I P R +KP R+ + DV K GG+ G++ G +
Sbjct: 191 ----DALIEAIEKYIPTPERDLDKPPRMYVARSFDVNKPGTPPEELKGGVIGGSLVQGVL 246
Query: 268 ETG---VIKPGMLVT----FAPANLTTEVKSVEMHHEALQEAVPGDNVG 309
G I+PG++V +TTE+ S++ E ++EA PG VG
Sbjct: 247 RVGDEIEIRPGIVVEKGGKTVWEPITTEIVSLQAGGEDVEEARPGGLVG 295
>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 = 73.3 bits (181), Expect = 3e-16
Identities = 34/81 (41%), Positives = 47/81 (58%), Gaps = 4/81 (4%)
Query: 248 LPLQDVYKIGGIGTVPVGRVETGVIKPGM---LVTFAPANLTTEVKSVEMHHEALQEAVP 304
+P++DV+ I G GTV GR+E G IK G +V F L T V +EM + L EA
Sbjct: 3 MPIEDVFSIPGRGTVVTGRIERGTIKVGDEVEIVGFGE-TLKTTVTGIEMFRKTLDEAEA 61
Query: 305 GDNVGFNVKNVSVKELRRGFV 325
GDNVG ++ V +++ RG V
Sbjct: 62 GDNVGVLLRGVKREDVERGMV 82
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 79.7 bits (198), Expect = 6e-16
Identities = 94/343 (27%), Positives = 136/343 (39%), Gaps = 112/343 (32%)
Query: 7 HI-NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKA 65
+I N +I H+D GKST LI G + +R E +AQ VLD +
Sbjct: 6 NIRNFSIIAHIDHGKSTLADRLIELTGTLSER-----EMKAQ-----------VLDSMDL 49
Query: 66 ERERGITID---IAL-WKFETSKFYV-TIIDAPGHRDFIKNMITGT-----SQADC--AV 113
ERERGITI + L +K + + Y+ +ID PGH DF + S A C A+
Sbjct: 50 ERERGITIKAQAVRLNYKAKDGETYILNLIDTPGHVDF-------SYEVSRSLAACEGAL 102
Query: 114 LIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGV-NKMD--STEPPYSEARFEEI 170
L+V A G EA QT + LA ++ I+ V NK+D + +P E +
Sbjct: 103 LVVDASQG-VEA------QTLANVYLALENDLE--IIPVLNKIDLPAADP-------ERV 146
Query: 171 KKEVSGYIKKIGYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIE 230
K+E+ IG + + V +S G + EV
Sbjct: 147 KQEI---EDVIGIDASDA--VLVSAKTGIGIEEV-------------------------- 175
Query: 231 ALDAI---LPPSRPTEKPLRLPLQ--------DVYKIGGIGTVPVGRVETGVIKPGMLVT 279
L+AI +PP P P PL+ D Y+ G V + RV G +K G +
Sbjct: 176 -LEAIVERIPP--PKGDP-DAPLKALIFDSWYDNYR----GVVVLVRVVDGTLKKGDKIK 227
Query: 280 FAPANLTTEVKSV---EMHHEALQEAVPGDNVGF---NVKNVS 316
EV V + E G+ VG+ +K+V
Sbjct: 228 MMSTGKEYEVDEVGVFTPKMVPVDELSAGE-VGYIIAGIKDVR 269
>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 = 72.0 bits (177), Expect = 7e-16
Identities = 30/85 (35%), Positives = 44/85 (51%), Gaps = 4/85 (4%)
Query: 246 LRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPA--NLTTEVKSVEMHHEALQEAV 303
LR + V+K G GTV GRVE+G +K G V P + +VKS++ + EAV
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRFKGEVDEAV 60
Query: 304 PGDNVGFNVKNVSVKELRRGFVAGD 328
GD VG +K+ +++ G D
Sbjct: 61 AGDIVGIVLKD--KDDIKIGDTLTD 83
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 78.6 bits (194), Expect = 2e-15
Identities = 79/322 (24%), Positives = 124/322 (38%), Gaps = 79/322 (24%)
Query: 10 IVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERER 69
I GHVD GK+T L+ G++ D+L E++R
Sbjct: 3 IATAGHVDHGKTT----LLQAITGVNA------------------------DRLPEEKKR 34
Query: 70 GITIDI--ALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGI 127
G+TID+ A W + + ID PGH F+ NM+ G D A+L+VA G
Sbjct: 35 GMTIDLGYAYWPQPDGRV-LGFIDVPGHEKFLSNMLAGVGGIDHALLVVACDDGVM---- 89
Query: 128 SKNGQTREH-ALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNPA 186
QTREH A+L T G L V + K D + EAR E++++V A
Sbjct: 90 ---AQTREHLAILQLT-GNPMLTVALTKADRVD----EARIAEVRRQVK----------A 131
Query: 187 TVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPSRPTEKPL 246
+ G+ + + A E G I+AL L E
Sbjct: 132 VLR---EYGFAEAKLFVTA---------ATE-GRG-------IDALREHLLQLPEREHAA 171
Query: 247 ----RLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQEA 302
RL + + + G G V G +G +K G + N V+ + ++ ++A
Sbjct: 172 QHRFRLAIDRAFTVKGAGLVVTGTALSGEVKVGDTLWLTGVNKPMRVRGLHAQNQPTEQA 231
Query: 303 VPGDNVGFNVK-NVSVKELRRG 323
G + N+ + +++ RG
Sbjct: 232 QAGQRIALNIAGDAEKEQINRG 253
>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 = 71.0 bits (175), Expect = 2e-15
Identities = 31/82 (37%), Positives = 47/82 (57%), Gaps = 1/82 (1%)
Query: 245 PLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQEAVP 304
P RLP+ D YK G GTV G+VE+G I+ G + P+ + EVKS+ + E + AV
Sbjct: 1 PFRLPISDKYKDQG-GTVVSGKVESGSIQKGDTLLVMPSKESVEVKSIYVDDEEVDYAVA 59
Query: 305 GDNVGFNVKNVSVKELRRGFVA 326
G+NV +K + +++ G V
Sbjct: 60 GENVRLKLKGIDEEDISPGDVL 81
>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 = 74.2 bits (183), Expect = 4e-15
Identities = 53/158 (33%), Positives = 74/158 (46%), Gaps = 41/158 (25%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWV------LDK 62
NI ++ HVD+GK+T T L+Y G I + GS V D
Sbjct: 1 NIGILAHVDAGKTTLTESLLYTSGAIREL--------------GS-----VDKGTTRTDS 41
Query: 63 LKAERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGE 122
++ ER+RGITI A+ F+ V IID PGH DFI + S D A+L+++A G
Sbjct: 42 MELERQRGITIFSAVASFQWEDTKVNIIDTPGHMDFIAEVERSLSVLDGAILVISAVEG- 100
Query: 123 FEAGISKNGQTREHALLAFTLGVKQL----IVGVNKMD 156
QTR +L L ++L I+ VNK+D
Sbjct: 101 ------VQAQTR---ILFRLL--RKLNIPTIIFVNKID 127
>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 = 76.6 bits (189), Expect = 6e-15
Identities = 84/312 (26%), Positives = 126/312 (40%), Gaps = 58/312 (18%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERE 68
NI +I HVD GK+T L+ + G E V+D ERE
Sbjct: 3 NIAIIAHVDHGKTTLVDALLKQSGTFRANEAV------AER---------VMDSNDLERE 47
Query: 69 RGITIDIALWKFETSKFY----VTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFE 124
RGITI L K T+ Y + I+D PGH DF + D +L+V A G
Sbjct: 48 RGITI---LAK-NTAIRYNGTKINIVDTPGHADFGGEVERVLGMVDGVLLLVDASEGPMP 103
Query: 125 AGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYN 184
QTR A LG+K ++V +NK+D AR +E+ EV ++G +
Sbjct: 104 -------QTRFVLKKALELGLKPIVV-INKIDR-----PSARPDEVVDEVFDLFAELGAD 150
Query: 185 PATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAIL----PPSR 240
+ F PI + S + GWA + + DAI+ P
Sbjct: 151 DEQLDF-PI--------VYASGR----AGWA--SLDLDDPSDNMAPLFDAIVRHVPAPKG 195
Query: 241 PTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTE-VKSVE-MHHEA 298
++PL++ + ++ +G + +GRV G +K G V + T E + + + E
Sbjct: 196 DLDEPLQMLVTNLDYDEYLGRIAIGRVHRGTVKKGQQVALMKRDGTIENGRISKLLGFEG 255
Query: 299 LQEAVPGDNVGF 310
L E V D G
Sbjct: 256 L-ERVEIDEAGA 266
>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 = 68.5 bits (168), Expect = 2e-13
Identities = 50/201 (24%), Positives = 82/201 (40%), Gaps = 48/201 (23%)
Query: 8 INIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAER 67
+N+ ++GHVDSGK++ + K E A DK +
Sbjct: 1 VNVGLLGHVDSGKTS-----------LAKALSEIASTAA-------------FDKNPQSQ 36
Query: 68 ERGITIDIALWKF--------------ETSKFYVTIIDAPGHRDFIKNMITGTSQADCAV 113
ERGIT+D+ F + + +T++D PGH I+ +I G D +
Sbjct: 37 ERGITLDLGFSSFEVDKPKHLEDNENPQIENYQITLVDCPGHASLIRTIIGGAQIIDLML 96
Query: 114 LIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKE 173
L+V A G QT E ++ L K LIV +NK+D + + E++KK
Sbjct: 97 LVVDAKKG-------IQTQTAECLVIGELLC-KPLIVVLNKIDLIPEEERKRKIEKMKKR 148
Query: 174 VSGYIKKIGYNPATVAFVPIS 194
+ ++K +P+S
Sbjct: 149 LQKTLEKT--RLKDSPIIPVS 167
>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 = 68.4 bits (168), Expect = 2e-13
Identities = 54/230 (23%), Positives = 83/230 (36%), Gaps = 85/230 (36%)
Query: 8 INIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAER 67
INI IGHV GK+T L G+ W + K E
Sbjct: 1 INIGTIGHVAHGKTTLVKAL----SGV-----------------------WT-VRHKEEL 32
Query: 68 ERGITI-----DIALWKFETSKFY----------------------VTIIDAPGHRDFIK 100
+R ITI + ++K V+ +D PGH +
Sbjct: 33 KRNITIKLGYANAKIYKCPNCGCPRPYDTPECECPGCGGETKLVRHVSFVDCPGHEILMA 92
Query: 101 NMITGTSQADCAVLIVAAGTGEFEAGISKN-----GQTREHALLAFTLGVKQLIVGVNKM 155
M++G + D A+L++AA N QT EH +G+K +I+ NK+
Sbjct: 93 TMLSGAAVMDGALLLIAA-----------NEPCPQPQTSEHLAALEIMGLKHIIILQNKI 141
Query: 156 DSTEPPYSEARFEEIKKEVSGYIKKIGYNPATVA----FVPISGWHGDNM 201
D + + +E+IK+ V G T+A +PIS N+
Sbjct: 142 DLVKEEQALENYEQIKEFVKG----------TIAENAPIIPISAQLKYNI 181
>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 = 66.8 bits (164), Expect = 7e-13
Identities = 59/176 (33%), Positives = 79/176 (44%), Gaps = 48/176 (27%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERE 68
NI +I HVD GK+T L+ + G +E +E+G+ V+D ERE
Sbjct: 4 NIAIIAHVDHGKTTLVDALLKQSGT---------FRENEEVGER------VMDSNDLERE 48
Query: 69 RGITIDIALWKFETSKFY----VTIIDAPGHRDF------IKNMITGTSQADCAVLIVAA 118
RGITI L K T+ Y + IID PGH DF + +M D +L+V A
Sbjct: 49 RGITI---LAK-NTAITYKDTKINIIDTPGHADFGGEVERVLSM------VDGVLLLVDA 98
Query: 119 GTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEV 174
G QTR A G+K IV +NK+D +AR EE+ EV
Sbjct: 99 SEGPMP-------QTRFVLKKALEAGLK-PIVVINKIDR-----PDARPEEVVDEV 141
>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 = 65.7 bits (161), Expect = 3e-12
Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 26/120 (21%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERE 68
NI +I HVD GK+T + L+ G I ++ G +Y LD + E+E
Sbjct: 2 NICIIAHVDHGKTTLSDSLLASAGIISEKLA------------GKARY---LDTREDEQE 46
Query: 69 RGITID---IALWKFETSK-------FYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAA 118
RGITI I+L FE + + + +ID+PGH DF + D A+++V A
Sbjct: 47 RGITIKSSAISL-YFEYEEEKMDGNDYLINLIDSPGHVDFSSEVTAALRLTDGALVVVDA 105
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 68.6 bits (167), Expect = 3e-12
Identities = 68/274 (24%), Positives = 114/274 (41%), Gaps = 45/274 (16%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERE 68
NI +I HVD GK+T L+ + G D R E QE V+D E+E
Sbjct: 7 NIAIIAHVDHGKTTLVDKLLQQSGTFDSRA------ETQER---------VMDSNDLEKE 51
Query: 69 RGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGIS 128
RGITI + + + + I+D PGH DF + S D +L+V A G
Sbjct: 52 RGITILAKNTAIKWNDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMP---- 107
Query: 129 KNGQTREHALLAFTLGVKQLIVGVNKMD--STEPPYSEARFEEIKKEVSGYIKKIGYNPA 186
QTR AF G+K ++V +NK+D P + + ++ + +++ +
Sbjct: 108 ---QTRFVTKKAFAYGLKPIVV-INKVDRPGARPDWVVDQVFDLFVNLDATDEQLDFPIV 163
Query: 187 -TVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPSRPTEKP 245
A I+G ++M E D P ++ +D + P + P
Sbjct: 164 YASALNGIAGLDHEDMAE--DMTPLYQA-----------------IVDHVPAPDVDLDGP 204
Query: 246 LRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVT 279
++ + + +G + +GR++ G +KP VT
Sbjct: 205 FQMQISQLDYNSYVGVIGIGRIKRGKVKPNQQVT 238
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 68.4 bits (168), Expect = 3e-12
Identities = 93/333 (27%), Positives = 137/333 (41%), Gaps = 79/333 (23%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERE 68
NI +I HVD GK+T L+ + G +R +E E V+D E+E
Sbjct: 7 NIAIIAHVDHGKTTLVDALLKQSGTFRER------EEVAER---------VMDSNDLEKE 51
Query: 69 RGITIDIALWKFETSKFY----VTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFE 124
RGITI L K T+ Y + I+D PGH DF + S D +L+V A G
Sbjct: 52 RGITI---LAK-NTAVNYNGTRINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMP 107
Query: 125 AGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYN 184
QTR A LG+K IV +NK+D +AR +E+ EV ++G
Sbjct: 108 -------QTRFVLKKALALGLKP-IVVINKIDR-----PDARPDEVVDEVFDLFVELGAT 154
Query: 185 PATVAFVPI------SGWHGDNMLEVSDKM-PWFKGWAIERKEGKADGKCLIEALDAILP 237
+ F PI +G + + +D M P F+ I LD +
Sbjct: 155 DEQLDF-PIVYASARNGTASLDPEDEADDMAPLFE--TI---------------LDHVPA 196
Query: 238 PSRPTEKPLRLPLQ----DVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVE 293
P ++PL++ + + Y +G IG GR+ G +KP V ++ TTE +
Sbjct: 197 PKGDLDEPLQMQVTQLDYNSY-VGRIGI---GRIFRGTVKPNQQVALIKSDGTTENGRIT 252
Query: 294 --MHHEALQ-----EAVPGDNV---GFNVKNVS 316
+ L+ EA GD V G N+
Sbjct: 253 KLLGFLGLERIEIEEAEAGDIVAIAGLEDINIG 285
>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 = 61.8 bits (151), Expect = 3e-12
Identities = 31/81 (38%), Positives = 46/81 (56%), Gaps = 2/81 (2%)
Query: 245 PLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQEAVP 304
PLRLP+ D YK +GTV +G+VE+G IK G + P EV S+ ++ A P
Sbjct: 1 PLRLPIIDKYK--DMGTVVLGKVESGTIKKGDKLLVMPNKTQVEVLSIYNEDVEVRYARP 58
Query: 305 GDNVGFNVKNVSVKELRRGFV 325
G+NV +K + +++ GFV
Sbjct: 59 GENVRLRLKGIEEEDISPGFV 79
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 66.5 bits (163), Expect = 1e-11
Identities = 45/153 (29%), Positives = 66/153 (43%), Gaps = 31/153 (20%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKR-TIEKFEKEAQEMGKGSFKYAWVLDKLKAER 67
NI ++ H+D+GK+T T +++ G I K +E D + E+
Sbjct: 10 NIGILAHIDAGKTTLTERILFYTGKIHKMGEVEDGTTVT--------------DWMPQEQ 55
Query: 68 ERGITIDIAL----WKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEF 123
ERGITI+ A W + +ID PGH DF + D AV++ A TG
Sbjct: 56 ERGITIESAATSCDWD----NHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDAVTG-V 110
Query: 124 EAGISKNGQTREHALLAFTLGVKQLIVGVNKMD 156
+ QT A G+ +LI +NKMD
Sbjct: 111 QP------QTETVWRQADRYGIPRLIF-INKMD 136
Score = 29.9 bits (68), Expect = 3.7
Identities = 26/125 (20%), Positives = 45/125 (36%), Gaps = 27/125 (21%)
Query: 228 LIEALDAILP---------PSRPTEKPLRLPLQD-------VYKI---GGIGTVPVGRVE 268
L++A+ LP S+ KP+++ V+K+ G + RV
Sbjct: 269 LLDAVVDYLPSPLEVPPPRGSKDNGKPVKVDPDPEKPLLALVFKVQYDPYAGKLTYLRVY 328
Query: 269 TGVIKPGMLVTFAPANLTTEV-KSVEMH---HEALQEAVPGDNVGFNVKNVSVKELRRGF 324
+G ++ G + +V + + E + A GD V +KEL G
Sbjct: 329 SGTLRAGSQLYNGTGGKREKVGRLFRLQGNKREEVDRAKAGDIVAV----AGLKELETGD 384
Query: 325 VAGDS 329
DS
Sbjct: 385 TLHDS 389
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 66.3 bits (163), Expect = 1e-11
Identities = 51/194 (26%), Positives = 75/194 (38%), Gaps = 44/194 (22%)
Query: 13 IGHVDSGKSTTTGHLIYKCGGIDKR-TIEKFEKEAQEMGKGSFKYAWVLDKLKAERERGI 71
+GH +GK+T T +++ G I + +E + +D + ERERGI
Sbjct: 1 VGHSGAGKTTLTEAILFYTGAIHRIGEVE--DGTT------------TMDFMPEERERGI 46
Query: 72 TIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGISKNG 131
+I A E + +ID PGH DF + D AV++V A G
Sbjct: 47 SITSAATTCEWKGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGG-------VEP 99
Query: 132 QTREHALLAFT--LGVKQLIVGVNKMDSTEPPYSEARFEEIK---KEVSGYIKKIGYNPA 186
QT + GV ++I VNKMD A F + +E G P
Sbjct: 100 QTE--TVWRQAEKYGVPRIIF-VNKMDRA-----GADFFRVLAQLQEKLG-------APV 144
Query: 187 TVAFVPISGWHGDN 200
+PI GD+
Sbjct: 145 VPLQLPI--GEGDD 156
>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 = 63.7 bits (156), Expect = 3e-11
Identities = 34/90 (37%), Positives = 44/90 (48%), Gaps = 13/90 (14%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERE 68
NI +I H+D+GK+TTT ++Y G I K E A +D ++ ERE
Sbjct: 1 NIGIIAHIDAGKTTTTERILYYTGRIHKIG-EVHGGGA------------TMDWMEQERE 47
Query: 69 RGITIDIALWKFETSKFYVTIIDAPGHRDF 98
RGITI A + IID PGH DF
Sbjct: 48 RGITIQSAATTCFWKDHRINIIDTPGHVDF 77
>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 = 62.6 bits (153), Expect = 6e-11
Identities = 38/149 (25%), Positives = 68/149 (45%), Gaps = 23/149 (15%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKR-TIEKFEKEAQEMGKGSFKYAWVLDKLKAER 67
NI ++GH SGK+T L+Y G ID+ +E G+ V D E+
Sbjct: 1 NIALVGHSGSGKTTLAEALLYATGAIDRLGRVED----------GNT----VSDYDPEEK 46
Query: 68 ERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGI 127
+R ++I+ ++ E + + +ID PG+ DF+ ++ D A+++V A +G
Sbjct: 47 KRKMSIETSVAPLEWNGHKINLIDTPGYADFVGETLSALRAVDAALIVVEAQSG------ 100
Query: 128 SKNGQTREHALLAFTLGVKQLIVGVNKMD 156
T + + ++I +NKMD
Sbjct: 101 -VEVGTEKVWEFLDDAKLPRIIF-INKMD 127
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G [Protein synthesis, Translation factors].
Length = 689
Score = 61.7 bits (150), Expect = 4e-10
Identities = 48/152 (31%), Positives = 68/152 (44%), Gaps = 25/152 (16%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERE 68
NI + H+D+GK+TTT +++ G I K E+ G A +D ++ E+E
Sbjct: 12 NIGISAHIDAGKTTTTERILFYTGRIHK---------IGEVHDG----AATMDWMEQEKE 58
Query: 69 RGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGIS 128
RGITI A + IID PGH DF + D AV ++ A G+
Sbjct: 59 RGITITSAATTVFWKGHRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDA-----VGGVQ 113
Query: 129 KNGQT--REHALLAFTLGVKQLIVGVNKMDST 158
+T R+ A V + I VNKMD T
Sbjct: 114 PQSETVWRQ----ANRYEVPR-IAFVNKMDKT 140
>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 = 56.7 bits (138), Expect = 1e-09
Identities = 60/207 (28%), Positives = 83/207 (40%), Gaps = 69/207 (33%)
Query: 10 IVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLK----A 65
+ V+GHVD GK+T +LDK++ A
Sbjct: 3 VTVMGHVDHGKTT------------------------------------LLDKIRKTNVA 26
Query: 66 ERE-RGITIDIALWKFETSKFY--VTIIDAPGHRDFIKNMIT-GTSQADCAVLIVAAGTG 121
E GIT I ++ +T ID PGH F NM G S D A+L+VAA G
Sbjct: 27 AGEAGGITQHIGAYQVPIDVKIPGITFIDTPGHEAF-TNMRARGASVTDIAILVVAADDG 85
Query: 122 EFEAGISKNGQTRE---HALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYI 178
QT E HA A +IV +NK+D +P +EA E +K E+S
Sbjct: 86 -VMP------QTIEAINHAKAANV----PIIVAINKID--KPYGTEADPERVKNELS--- 129
Query: 179 KKIGYNP----ATVAFVPISGWHGDNM 201
++G V+ VPIS G+ +
Sbjct: 130 -ELGLVGEEWGGDVSIVPISAKTGEGI 155
>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
Snu114p subfamily. Snu114p is one of several proteins
that make up the U5 small nuclear ribonucleoprotein
(snRNP) particle. U5 is a component of the spliceosome,
which catalyzes the splicing of pre-mRNA to remove
introns. Snu114p is homologous to EF-2, but typically
contains an additional N-terminal domain not found in
Ef-2. This protein is part of the GTP translation factor
family and the Ras superfamily, characterized by five
G-box motifs.
Length = 213
Score = 57.7 bits (140), Expect = 1e-09
Identities = 56/218 (25%), Positives = 87/218 (39%), Gaps = 44/218 (20%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERE 68
N+ + GH+ GK++ LI + KRT +Y D K E+E
Sbjct: 2 NVCIAGHLHHGKTSLLDMLIEQ---THKRTPSVKLGWKPL------RY---TDTRKDEQE 49
Query: 69 RGITID---IALWKFETSK---FYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGE 122
RGI+I I+L E SK + + IID PGH +F+ + D VL+V
Sbjct: 50 RGISIKSNPISL-VLEDSKGKSYLINIIDTPGHVNFMDEVAAALRLCDGVVLVVDVVE-- 106
Query: 123 FEAGISKNGQT--REHALLAFTLGVKQLIVGVNKMDS--TE---PPYSEARFE--EIKKE 173
G++ + R A G+ ++V +NK+D E PP +A ++ E
Sbjct: 107 ---GLTSVTERLIRH----AIQEGLPMVLV-INKIDRLILELKLPPT-DAYYKLRHTIDE 157
Query: 174 VSGYIKKIGYNPATVAFVPISGWHGDNMLEVSDKMPWF 211
++ YI P G N+L S K +
Sbjct: 158 INNYIASFS-TTEGFLVSPELG----NVLFASSKFGFC 190
>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 = 57.3 bits (139), Expect = 2e-09
Identities = 53/203 (26%), Positives = 77/203 (37%), Gaps = 59/203 (29%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERE 68
+ V+G+VD+GKST G L G +D G+G + L + K E E
Sbjct: 1 RVAVVGNVDAGKSTLLGVL--TQGELDN-------------GRGKARLN--LFRHKHEVE 43
Query: 69 RGIT--------------------IDIALWK----FETSKFYVTIIDAPGHRDFIKNMIT 104
G T + E S VT ID GH ++K +
Sbjct: 44 SGRTSSVSNDILGFDSDGEVVNYPDNHLGELDVEICEKSSKVVTFIDLAGHERYLKTTVF 103
Query: 105 GTS--QADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPY 162
G + D A+L+V A G G T+EH LA L V +V V K+D T
Sbjct: 104 GMTGYAPDYAMLVVGANAGI-------IGMTKEHLGLALALKVPVFVV-VTKIDMT---- 151
Query: 163 SEARFEEIKKEVSGYIKKIGYNP 185
+E K+ +K++ +P
Sbjct: 152 PANVLQETLKD----LKRLLKSP 170
>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 = 52.9 bits (128), Expect = 4e-09
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 246 LRLPLQDVYKIG----GIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSVEMHHEALQE 301
R P+Q V + G G + +G I+ G V P+ T+ VKS+E L E
Sbjct: 1 FRFPVQYVIRPNADFRGY----AGTIASGSIRVGDEVVVLPSGKTSRVKSIETFDGELDE 56
Query: 302 AVPGDNVGF 310
A G++V
Sbjct: 57 AGAGESVTL 65
>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 = 56.5 bits (137), Expect = 6e-09
Identities = 33/111 (29%), Positives = 59/111 (53%), Gaps = 11/111 (9%)
Query: 12 VIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEM-GKGSFKYAWVLDKLKAERERG 70
+I H D+GK+T T L+ G I +EA + + S K+A D ++ E++RG
Sbjct: 7 IISHPDAGKTTLTEKLLLFGGAI---------QEAGAVKARKSRKHA-TSDWMEIEKQRG 56
Query: 71 ITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTG 121
I++ ++ +FE + ++D PGH DF ++ + D AV+++ A G
Sbjct: 57 ISVTSSVMQFEYKGCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKG 107
>gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. This translation
releasing factor, RF-3 (prfC) was originally described
as stop codon-independent, in contrast to peptide chain
release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and
RF-2 are closely related to each other, while RF-3 is
similar to elongation factors EF-Tu and EF-G; RF-1 is
active at UAA and UAG and RF-2 is active at UAA and UGA.
More recently, RF-3 was shown to be active primarily at
UGA stop codons in E. coli. All bacteria and organelles
have RF-1. The Mycoplasmas and organelles, which
translate UGA as Trp rather than as a stop codon, lack
RF-2. RF-3, in contrast, seems to be rare among bacteria
and is found so far only in Escherichia coli and some
other gamma subdivision Proteobacteria, in Synechocystis
PCC6803, and in Staphylococcus aureus [Protein
synthesis, Translation factors].
Length = 527
Score = 56.5 bits (136), Expect = 1e-08
Identities = 31/113 (27%), Positives = 56/113 (49%), Gaps = 9/113 (7%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERE 68
+I H D+GK+T T ++ G I K G+GS ++A D ++ E++
Sbjct: 13 TFAIISHPDAGKTTITEKVLLYGGAIQTAGAVK--------GRGSQRHA-KSDWMEMEKQ 63
Query: 69 RGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTG 121
RGI+I ++ +F V ++D PGH DF ++ + D ++++ A G
Sbjct: 64 RGISITTSVMQFPYRDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKG 116
>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 = 50.7 bits (122), Expect = 3e-08
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 4/78 (5%)
Query: 252 DVYKIGGIGTVPVGRVETGVIKPGMLVTFAPAN----LTTEVKSVEMHHEALQEAVPGDN 307
++Y + G+GTV G V GVI+ G + P VKS+ + ++ G +
Sbjct: 7 EIYSVPGVGTVVGGTVSKGVIRLGDTLLLGPDQDGSFRPVTVKSIHRNRSPVRVVRAGQS 66
Query: 308 VGFNVKNVSVKELRRGFV 325
+K + LR+G V
Sbjct: 67 ASLALKKIDRSLLRKGMV 84
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 55.3 bits (134), Expect = 4e-08
Identities = 34/111 (30%), Positives = 61/111 (54%), Gaps = 11/111 (9%)
Query: 12 VIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEM-GKGSFKYAWVLDKLKAERERG 70
+I H D+GK+T T L+ G I +EA + G+ S K+A D ++ E++RG
Sbjct: 17 IISHPDAGKTTLTEKLLLFGGAI---------QEAGTVKGRKSGKHA-KSDWMEIEKQRG 66
Query: 71 ITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTG 121
I++ ++ +F+ + V ++D PGH DF ++ + D AV+++ A G
Sbjct: 67 ISVTSSVMQFDYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKG 117
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 53.9 bits (130), Expect = 1e-07
Identities = 78/346 (22%), Positives = 134/346 (38%), Gaps = 105/346 (30%)
Query: 8 INIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAER 67
INI IGHV GKST ++ G+ +T+ + K E+
Sbjct: 35 INIGTIGHVAHGKST----VVKALSGV--KTV----------------------RFKREK 66
Query: 68 ERGITIDIA-----LWKFE----------------------------TSKFYVTIIDAPG 94
R ITI + ++K T K +V+ +D PG
Sbjct: 67 VRNITIKLGYANAKIYKCPKCPRPTCYQSYGSSKPDNPPCPGCGHKMTLKRHVSFVDCPG 126
Query: 95 HRDFIKNMITGTSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNK 154
H + M+ G + D A+L++AA QT EH + +K +I+ NK
Sbjct: 127 HDILMATMLNGAAVMDAALLLIAANES------CPQPQTSEHLAAVEIMKLKHIIILQNK 180
Query: 155 MDSTEPPYSEARFEEIKKEVSGYIKKIGYNPATVAFVPISGWHGDNMLEVSD----KMPW 210
+D + ++ ++EEI+ V G I +PIS N+ V + ++P
Sbjct: 181 IDLVKEAQAQDQYEEIRNFVKGTIAD------NAPIIPISAQLKYNIDVVLEYICTQIP- 233
Query: 211 FKGWAIERKEGKADGK-CLIEALDAILPPSRPTEKPLRLPLQDVYKIGGI--GTVPVGRV 267
I +++ + + +I + D ++P E L GG+ G++ G +
Sbjct: 234 -----IPKRDLTSPPRMIVIRSFDV----NKPGEDIENL-------KGGVAGGSILQGVL 277
Query: 268 ETG---VIKPGMLVTFAPANLT-----TEVKSVEMHHEALQEAVPG 305
+ G I+PG++ + T T + S+ + LQ AVPG
Sbjct: 278 KVGDEIEIRPGIISKDSGGEFTCRPIRTRIVSLFAENNELQYAVPG 323
>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 = 53.7 bits (129), Expect = 1e-07
Identities = 95/412 (23%), Positives = 154/412 (37%), Gaps = 112/412 (27%)
Query: 1 MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL 60
M K K NI ++ H+D GK+T + +L+ G I + E Q++ L
Sbjct: 13 MWKPKFIRNIGIVAHIDHGKTTLSDNLLAGAGMISE------ELAGQQL---------YL 57
Query: 61 DKLKAERERGITIDIA----LWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIV 116
D + E+ERGITI+ A + ++E +++ + +ID PGH DF ++ D A+++V
Sbjct: 58 DFDEQEQERGITINAANVSMVHEYEGNEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVV 117
Query: 117 AAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMD------STEPPYSEARFEEI 170
A G QT A VK ++ +NK+D P + RF +I
Sbjct: 118 CAVEGVMP-------QTETVLRQALKENVKPVLF-INKVDRLINELKLTPQELQERFIKI 169
Query: 171 KKEVSGYIK-----------KIGYNPATVAF----------VPISGWHG----------- 198
EV+ IK K+ +VAF VP G
Sbjct: 170 ITEVNKLIKAMAPEEFRDKWKVRVEDGSVAFGSAYYNWAISVPSMKKTGIGFKDIYKYCK 229
Query: 199 -DNMLEVSDKMPWFKG-----------------------WA--IERKEGKADGKCLIEAL 232
D E++ K P + W + + GKA C
Sbjct: 230 EDKQKELAKKSPLHQVVLDMVIRHLPSPIEAQKYRIPVIWKGDLNSEVGKAMLNC----- 284
Query: 233 DAILPPSRPTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPANLTTEVKSV 292
+ PL L + + G V VGR+ +G I+PGM V ++ V
Sbjct: 285 --------DPKGPLALMITKIVVDKHAGEVAVGRLYSGTIRPGMEVYIVDRKAKARIQQV 336
Query: 293 EMHHEALQEAVPGDNV--GFNVKNVSVKELRRGFVAGDSKASPPKATQDFTA 342
++ E V D + G V + +K+ VAG++ + + F +
Sbjct: 337 GVYMGP--ERVEVDEIPAGNIVAVIGLKDA----VAGETICTTVENITPFES 382
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 53.1 bits (128), Expect = 2e-07
Identities = 39/108 (36%), Positives = 46/108 (42%), Gaps = 25/108 (23%)
Query: 1 MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL 60
M N+ VI HVD GKST T L+ K G I K A G F
Sbjct: 13 MDNPDQIRNMSVIAHVDHGKSTLTDSLVCKAGIIS-------SKNA---GDARF-----T 57
Query: 61 DKLKAERERGITID---IAL---WKFETSK----FYVTIIDAPGHRDF 98
D E+ERGITI I+L E F + +ID+PGH DF
Sbjct: 58 DTRADEQERGITIKSTGISLYYEHDLEDGDDKQPFLINLIDSPGHVDF 105
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 52.6 bits (127), Expect = 3e-07
Identities = 31/101 (30%), Positives = 48/101 (47%), Gaps = 20/101 (19%)
Query: 3 KEKTHI-NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLD 61
K I NI +I H+D GK+T + +L+ G I + G+ LD
Sbjct: 15 KNPEQIRNIGIIAHIDHGKTTLSDNLLAGAGMISEEL----------AGE-----QLALD 59
Query: 62 KLKAERERGITIDIA----LWKFETSKFYVTIIDAPGHRDF 98
+ E+ RGITI A + ++E ++ + +ID PGH DF
Sbjct: 60 FDEEEQARGITIKAANVSMVHEYEGKEYLINLIDTPGHVDF 100
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 51.8 bits (125), Expect = 5e-07
Identities = 34/95 (35%), Positives = 47/95 (49%), Gaps = 23/95 (24%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTI-EKFEKEAQEMGKGSFKYAWVLDKLKAER 67
NI ++ H+D+GK+TTT ++Y G K I E + A +D ++ E+
Sbjct: 10 NIGIMAHIDAGKTTTTERILYYTGKSHK--IGEVHDGAAT------------MDWMEQEQ 55
Query: 68 ERGITIDIA----LWKFETSKFYVTIIDAPGHRDF 98
ERGITI A WK + IID PGH DF
Sbjct: 56 ERGITITSAATTCFWK----GHRINIIDTPGHVDF 86
>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 = 50.1 bits (120), Expect = 2e-06
Identities = 57/205 (27%), Positives = 81/205 (39%), Gaps = 59/205 (28%)
Query: 10 IVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERER 69
+ ++GHVD GK++ +D +I K + E G
Sbjct: 90 VTIMGHVDHGKTSL----------LD--SIRKTKVAQGEAG------------------- 118
Query: 70 GITIDIALWKFETS-KFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGIS 128
GIT I + E +T +D PGH F G D VL+VAA + G+
Sbjct: 119 GITQHIGAYHVENEDGKMITFLDTPGHEAFTSMRARGAKVTDIVVLVVAA-----DDGVM 173
Query: 129 KNGQTRE---HALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNP 185
QT E HA A +IV +NK+D EA + +K+E+S Y G P
Sbjct: 174 P--QTIEAISHAKAANV----PIIVAINKIDK-----PEANPDRVKQELSEY----GLVP 218
Query: 186 ----ATVAFVPISGWHGDNMLEVSD 206
FVP+S GD + E+ D
Sbjct: 219 EDWGGDTIFVPVSALTGDGIDELLD 243
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 50.1 bits (120), Expect = 2e-06
Identities = 36/114 (31%), Positives = 51/114 (44%), Gaps = 31/114 (27%)
Query: 1 MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL 60
M K+ N+ VI HVD GKST T L+ G I AQE+ +
Sbjct: 13 MDKKHNIRNMSVIAHVDHGKSTLTDSLVAAAGII-----------AQEVAGD----VRMT 57
Query: 61 DKLKAERERGITID---IALW-------------KFETSKFYVTIIDAPGHRDF 98
D E ERGITI I+L+ + + +++ + +ID+PGH DF
Sbjct: 58 DTRADEAERGITIKSTGISLYYEMTDESLKDFKGERDGNEYLINLIDSPGHVDF 111
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 48.3 bits (116), Expect = 6e-06
Identities = 61/237 (25%), Positives = 89/237 (37%), Gaps = 74/237 (31%)
Query: 10 IVVI-GHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERE 68
+V I GHVD GK+T + ++T + A
Sbjct: 7 VVTIMGHVDHGKTTLLDKI--------RKT-----------------------NVAAGEA 35
Query: 69 RGITIDIALWKFETSKFYV---TIIDAPGHRDFIKNMIT-GTSQADCAVLIVAAGTGEFE 124
GIT I ++ + T ID PGH F M G S D A+L+VAA G
Sbjct: 36 GGITQHIGAYQVPLDVIKIPGITFIDTPGHEAF-TAMRARGASVTDIAILVVAADDG-VM 93
Query: 125 AGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYN 184
QT E A GV ++V +NK+D EA +++K+E+ + G
Sbjct: 94 P------QTIEAINHAKAAGV-PIVVAINKIDKP-----EANPDKVKQELQ----EYGLV 137
Query: 185 PA----TVAFVPISGWHGDNM---------------LEVSDKMPWFKGWAIERKEGK 222
P V FVP+S G+ + L+ + + P +G IE K K
Sbjct: 138 PEEWGGDVIFVPVSAKTGEGIDELLELILLLAEVLELKANPEGP-ARGTVIEVKLDK 193
Score = 29.8 bits (68), Expect = 3.7
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 252 DVYKIGGIGTVPVG-RVETGVIKPG--MLVTFAPANLTT-EVKSVEMHHEALQEAVPGDN 307
V+K+ +G + G V GVIK G + V + EV+S++ + ++E G
Sbjct: 420 AVFKLPKVGAI-AGCMVTEGVIKRGAPVRVVRDGVVIYEGEVESLKRFKDDVKEVRKGQE 478
Query: 308 VGFNVKN 314
G ++N
Sbjct: 479 CGIAIEN 485
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 46.3 bits (111), Expect = 3e-05
Identities = 33/97 (34%), Positives = 48/97 (49%), Gaps = 27/97 (27%)
Query: 9 NIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGK---GSFKYAWVLDKLKA 65
NI ++ H+D+GK+TTT +++ G K +G+ G A +D ++
Sbjct: 12 NIGIMAHIDAGKTTTTERILFYTGVNHK------------IGEVHDG----AATMDWMEQ 55
Query: 66 ERERGITIDIA----LWKFETSKFYVTIIDAPGHRDF 98
E+ERGITI A WK + IID PGH DF
Sbjct: 56 EQERGITITSAATTCFWK----DHRINIIDTPGHVDF 88
>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 = 43.2 bits (102), Expect = 5e-05
Identities = 36/205 (17%), Positives = 63/205 (30%), Gaps = 53/205 (25%)
Query: 11 VVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERERG 70
VV+G GKS+ L+ + + G
Sbjct: 1 VVVGRGGVGKSSLLNALLGG------------------------------EVGEVSDVPG 30
Query: 71 ITIDIAL--WKFETSKFYVTIIDAPGHRDFIKNMITGT-----SQADCAVLIVAAGTGEF 123
T D + + + K + ++D PG +F AD +L+V + E
Sbjct: 31 TTRDPDVYVKELDKGKVKLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRES 90
Query: 124 EAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGY 183
E G+ ++VG NK+D E E + + KI
Sbjct: 91 EEDA-----KLLILRRLRKEGIPIILVG-NKIDLLEER------EVEELLRLEELAKILG 138
Query: 184 NPATVAFVPISGWHGDNMLEVSDKM 208
P +S G+ + E+ +K+
Sbjct: 139 VP----VFEVSAKTGEGVDELFEKL 159
>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 = 40.8 bits (96), Expect = 3e-04
Identities = 39/204 (19%), Positives = 63/204 (30%), Gaps = 48/204 (23%)
Query: 8 INIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAER 67
I IV++G + GKST L+ + E + G+ +
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGN---------KISITEYKP---GTTRNYVTT----VIE 45
Query: 68 ERGITIDIALWKFETSKFYVTIIDAPGHRDF---IKNMITGTSQADCAVLIVAAGTGEFE 124
E G T L D G D+ + + IV E
Sbjct: 46 EDGKTYKFNLL------------DTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLD-VE 92
Query: 125 AGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYN 184
+ K + H GV ++VG NK+D R ++K V+ K+
Sbjct: 93 EILEKQTKEIIHHA---ESGVPIILVG-NKIDL--------RDAKLKTHVAFLFAKLNGE 140
Query: 185 PATVAFVPISGWHGDNMLEVSDKM 208
P +P+S G N+ +
Sbjct: 141 P----IIPLSAETGKNIDSAFKIV 160
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 42.5 bits (100), Expect = 4e-04
Identities = 51/199 (25%), Positives = 78/199 (39%), Gaps = 54/199 (27%)
Query: 10 IVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERER 69
+ ++GHVD GK+T +DK I K + +E G
Sbjct: 247 VTILGHVDHGKTTL----------LDK--IRKTQIAQKEAG------------------- 275
Query: 70 GITIDIA----LWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEA 125
GIT I ++++ + +D PGH F G + D A+LI+AA G
Sbjct: 276 GITQKIGAYEVEFEYKDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDG---- 331
Query: 126 GISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGY---IKKIG 182
QT E A+ +IV +NK+D A E IK++++ Y +K G
Sbjct: 332 ---VKPQTIE-AINYIQAANVPIIVAINKIDKA-----NANTERIKQQLAKYNLIPEKWG 382
Query: 183 YNPATVAFVPISGWHGDNM 201
+PIS G N+
Sbjct: 383 ---GDTPMIPISASQGTNI 398
>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 = 36.8 bits (86), Expect = 0.002
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 335 KATQDFTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKT 386
KA +F A+++VL+HP IS GY + + + I + RTG
Sbjct: 1 KACWEFEAEILVLHHPTTISPGYQATVHIGSIRQTARIVSIDKDVL-RTGDR 51
>gnl|CDD|241351 cd13197, FERM_C_CCM1, Cerebral cavernous malformation 1 FERM domain
C-lobe. CCM1 (also called KRIT-1/Krev interaction
trapped 1;ankyrin repeat-containing protein Krit1; CAM),
a Rap1-binding protein, is expressed in endothelial
cells where it is present in cell-cell junctions and
associated with junctional proteins. Together with
CCM2/MGC4607 and CCM3/PDCD10, KRIT1 constitutes a set of
proteins, mutations of which are found in cerebral
cavernous malformations which are characterized by
cerebral hemorrhages and vascular malformations in the
central nervous system. KRIT-1 possesses four ankyrin
repeats, a FERM domain, and multiple NPXY sequences, one
of which is essential for integrin cytoplasmic
domain-associated protein-1alpha (ICAP1alpha) binding
and all of which mediate binding of CCM2. KRIT-1
localization is mediated by its FERM domain. The FERM
domain has a cloverleaf tripart structure (FERM_N,
FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe,
C-lobe/F1, F2, F3). The C-lobe/F3 within the FERM domain
is part of the PH domain family. The FERM domain is
found in the cytoskeletal-associated proteins such as
ezrin, moesin, radixin, 4.1R, and merlin. These proteins
provide a link between the membrane and cytoskeleton and
are involved in signal transduction pathways. The FERM
domain is also found in protein tyrosine phosphatases
(PTPs) , the tyrosine kinases FAK and JAK, in addition
to other proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 122
Score = 36.0 bits (83), Expect = 0.008
Identities = 4/31 (12%), Positives = 8/31 (25%)
Query: 399 AAIIVLVPSKPMCVESFSEFPPLGRFAVRDM 429
A ++ L M ++ M
Sbjct: 63 ALLLSLKYGCFMWQLGDADTCFQIHSLENKM 93
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 37.4 bits (88), Expect = 0.016
Identities = 27/91 (29%), Positives = 48/91 (52%), Gaps = 17/91 (18%)
Query: 12 VIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEM-GKGSFKYA---WVLDKLKAER 67
+I H D+GK+T T L+ G I +EA + G+ S ++A W ++ E+
Sbjct: 15 IISHPDAGKTTLTEKLLLFGGAI---------QEAGTVKGRKSGRHATSDW----MEMEK 61
Query: 68 ERGITIDIALWKFETSKFYVTIIDAPGHRDF 98
+RGI++ ++ +F + ++D PGH DF
Sbjct: 62 QRGISVTSSVMQFPYRDCLINLLDTPGHEDF 92
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 36.4 bits (85), Expect = 0.029
Identities = 49/152 (32%), Positives = 65/152 (42%), Gaps = 42/152 (27%)
Query: 60 LDKLK----AERE-RGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMIT-----GTSQA 109
LD ++ A E GIT I ++ ET+ +T +D PGH F T G
Sbjct: 266 LDAIRKTNVAAGEAGGITQHIGAYQVETNGGKITFLDTPGHEAF-----TAMRARGAQVT 320
Query: 110 DCAVLIVAAGTGEFEAGISKNGQTRE---HALLAFTLGVKQLIVGVNKMDSTEPPYSEAR 166
D VL+VAA G QT E HA A GV +IV +NK+D A
Sbjct: 321 DIVVLVVAADDGVMP-------QTIEAINHAKAA---GVP-IIVAINKIDK-----PGAN 364
Query: 167 FEEIKKEVSGYIKKIGYNPA----TVAFVPIS 194
+ +K+E+S Y G P FVP+S
Sbjct: 365 PDRVKQELSEY----GLVPEEWGGDTIFVPVS 392
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 33.6 bits (77), Expect = 0.13
Identities = 31/150 (20%), Positives = 46/150 (30%), Gaps = 33/150 (22%)
Query: 10 IVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERER 69
IVVIG V +GK+T L DK + + GKG +D E
Sbjct: 13 IVVIGPVGAGKTTFVRAL------SDKPLVITEADASSVSGKGKRPTTVAMDFGSIE--- 63
Query: 70 GITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGISK 129
V + PG F + A A+++V S
Sbjct: 64 ------LDEDTG-----VHLFGTPGQERFKFMWEILSRGAVGAIVLVD----------SS 102
Query: 130 NGQTREH-ALLAFTLGVKQ--LIVGVNKMD 156
T ++ F ++V +NK D
Sbjct: 103 RPITFHAEEIIDFLTSRNPIPVVVAINKQD 132
>gnl|CDD|239762 cd04095, CysN_NoDQ_III, TCysN_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 = 103
Score = 31.7 bits (73), Expect = 0.17
Identities = 25/106 (23%), Positives = 42/106 (39%), Gaps = 7/106 (6%)
Query: 336 ATQDFTAQVIVLN-HPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPKAL 394
+ F A ++ ++ P + Y +L T + IK + D T + E L
Sbjct: 2 VSDQFAATLVWMDEEPLRPGRKY--LLKLGTRTVRATVTAIKYRVDVNTLE--HEAADTL 57
Query: 395 KSGDAAIIVLVPSKPMCVESFSEFPPLGRFAV--RDMRQTVAVGVI 438
+ D + L SKP+ + + E G F + R TV G+I
Sbjct: 58 ELNDIGRVELSLSKPLAFDPYRENRATGSFILIDRLTNATVGAGMI 103
>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 = 34.0 bits (78), Expect = 0.19
Identities = 50/226 (22%), Positives = 83/226 (36%), Gaps = 56/226 (24%)
Query: 10 IVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEA----QEMGKGSFKYAWVLDKLKA 65
+ V+GHVD GK+T I + K +EA Q +G + V++ +
Sbjct: 7 VSVLGHVDHGKTTLLDK-------IRGSAVAK--REAGGITQHIG-ATEIPMDVIEGICG 56
Query: 66 ERERGITIDIALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEA 125
+ + I + + + ID PGH F G + AD A+LIV +
Sbjct: 57 DLLKKFKIRLKIPG-------LLFIDTPGHEAFTNLRKRGGALADLAILIV-----DINE 104
Query: 126 GISKNGQTREHALLAFTLGVKQLIVGVNKMD-------STEPPYSEA----------RFE 168
G QT+E AL + +V NK+D P+ E+ +
Sbjct: 105 GFKP--QTQE-ALNILRMYKTPFVVAANKIDRIPGWRSHEGRPFMESFSKQEIQVQQNLD 161
Query: 169 EIKKEVSGYIKKIGYNP----------ATVAFVPISGWHGDNMLEV 204
+ + + G+ TVA +PIS G+ + E+
Sbjct: 162 TKVYNLVIKLHEEGFEAERFDRVTDFTKTVAIIPISAITGEGIPEL 207
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor of
a mutation in RCC1. Biochemical analysis revealed that
Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 32.9 bits (76), Expect = 0.21
Identities = 35/136 (25%), Positives = 59/136 (43%), Gaps = 16/136 (11%)
Query: 70 GITIDI--ALWKFETSKFYVTIIDAPGHRDFIKNMITGTSQAD-----CAVLI--VAAGT 120
G TID+ + +F + + D PG DF++N T Q + VLI +
Sbjct: 32 GATIDVEQSHVRFL-GNLTLNLWDCPGQDDFMEN--YLTRQKEHIFSNVGVLIYVFDVES 88
Query: 121 GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKK 180
E+E ++ + E AL ++ K + V ++KMD + FE+ K+E+ I+
Sbjct: 89 REYEEDLATLVKIIE-ALYQYSPNAK-VFVLIHKMDLLSEDERKEIFEDRKEEIIEEIED 146
Query: 181 IGYNPATVAFVPISGW 196
G + F S W
Sbjct: 147 FGIED--LTFFLTSIW 160
>gnl|CDD|227056 COG4712, COG4712, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 234
Score = 32.3 bits (73), Expect = 0.44
Identities = 36/167 (21%), Positives = 54/167 (32%), Gaps = 19/167 (11%)
Query: 131 GQTREHAL----LAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKK------ 180
G REH L L T+ V + V K D E +EA K + S +K+
Sbjct: 56 GWEREHQLVNGNLFCTVRVYDEDMWVTKQDVGEESNTEA----EKGQASDSMKRAAVQFG 111
Query: 181 IGYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKADGKCLIEALDAILPPSR 240
IG + F+ W D + E ++P WA K + + I L+ + R
Sbjct: 112 IGRYLYDLPFIWAGLWP-DEVTENKKRVPLLPKWAFPVKSINYNQEREINQLEIVDNNVR 170
Query: 241 ---PTEKPLRL-PLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPA 283
T+ + V + T G V A
Sbjct: 171 YKLGTDISTDIDKATVVIPLDKKATGKPNSNTYKCAVCGKSVPEKVA 217
>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 = 29.2 bits (66), Expect = 1.0
Identities = 21/110 (19%), Positives = 39/110 (35%), Gaps = 26/110 (23%)
Query: 335 KATQDFTAQVIVLN------HPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTE 388
K AQV +L+ H + + P + T A + K
Sbjct: 1 KPHDKVEAQVYILSKAEGGRHKP-FVSNFQPQMFSLTWDCAARIDLPPGK---------- 49
Query: 389 ENPKALKSGDAAIIVLVPSKPMCVESFSEFPPLGRFAVRDMRQTVAVGVI 438
+ + G+ + L+ +PM +E RF +RD +T+ G++
Sbjct: 50 ---EMVMPGEDTKVTLILRRPMVLE------KGQRFTLRDGNRTIGTGLV 90
>gnl|CDD|182795 PRK10870, PRK10870, transcriptional repressor MprA; Provisional.
Length = 176
Score = 30.5 bits (69), Expect = 1.3
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 9/35 (25%)
Query: 212 KGWAIERKEGKADGKCL--------IEALDAILPP 238
+GW IER+E D +CL E L +LPP
Sbjct: 98 RGW-IERRESDNDRRCLHLQLTEKGHEFLREVLPP 131
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 31.4 bits (71), Expect = 1.4
Identities = 26/81 (32%), Positives = 34/81 (41%), Gaps = 23/81 (28%)
Query: 59 VLDKLK----AERERG----------ITID---------IALWKFETSKFYVTIIDAPGH 95
+LDK++ A++E G I ID + L K E + ID PGH
Sbjct: 477 LLDKIRKTRVAKKEAGGITQHIGATEIPIDVIKKICGPLLKLLKAEIKIPGLLFIDTPGH 536
Query: 96 RDFIKNMITGTSQADCAVLIV 116
F G S AD AVL+V
Sbjct: 537 EAFTSLRKRGGSLADLAVLVV 557
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 31.2 bits (71), Expect = 1.4
Identities = 36/172 (20%), Positives = 62/172 (36%), Gaps = 52/172 (30%)
Query: 70 GITIDIALWKFETSKFYVTIIDAPG-------------HRDFIKNMITGTSQADCAVLIV 116
G+T++ K + I+D PG RD++ N + D V +V
Sbjct: 26 GVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTFSLEEEVARDYLLN-----EKPDLVVNVV 80
Query: 117 AAGTGEFEAGISKNGQTREHALLAFTLGV----KQLIVGVNKMDSTEPPYSEARFEEIKK 172
A + + +N L TL + +I+ +N +D EA + I+
Sbjct: 81 DA------SNLERN--------LYLTLQLLELGIPMILALNLVD-------EAEKKGIRI 119
Query: 173 EVSGYIKKIGYNPATVAFVPISGWHGDNMLEVSDKMPWFKGWAIERKEGKAD 224
+ +++G V VP S G + + D + AI KE K
Sbjct: 120 DEEKLEERLG-----VPVVPTSATEGRGIERLKDAI----RKAIGLKELKKR 162
>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 = 1.8
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 146 KQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNPATVAFVPIS---GWHGDNML 202
K LI+ VNK D E E +E +KE+ + + Y P V IS G D +
Sbjct: 114 KALIIVVNKWDLVEK--DEKTMKEFEKELRRKLPFLDYAP----IVFISALTGQGVDKLF 167
Query: 203 EVSDK 207
+ +
Sbjct: 168 DAIKE 172
>gnl|CDD|238941 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety
of proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion.
Length = 99
Score = 28.5 bits (64), Expect = 2.4
Identities = 10/30 (33%), Positives = 13/30 (43%)
Query: 10 IVVIGHVDSGKSTTTGHLIYKCGGIDKRTI 39
IVV G GK+T +L KR +
Sbjct: 2 IVVTGKGGVGKTTLAANLAAALAKRGKRVL 31
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 29.1 bits (66), Expect = 2.8
Identities = 20/110 (18%), Positives = 38/110 (34%), Gaps = 25/110 (22%)
Query: 10 IVVIGHVDSGKST-----------------TTGHLIYKCGGIDKRTIEKFEKEAQ-EMGK 51
I V+G +GKS+ TT + G + I K + K
Sbjct: 1 IAVVGDQSAGKSSVLNALLGRDILPRGPGPTTRRPLVLRLGEEPGAIPGAVKVEYKDGLK 60
Query: 52 GSFKYAWVLDKLKAERER----GITIDIALWKFETSKFY---VTIIDAPG 94
++ + ++++ E ++ G I E +T++D PG
Sbjct: 61 KFEDFSELREEIEDETDKISGTGKGISSEPIILEILSPLVPGLTLVDTPG 110
>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 = 29.7 bits (68), Expect = 3.6
Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 10/66 (15%)
Query: 146 KQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNPATVAFVPISGWHG---DNML 202
K L++ VNK D + E EE KKE+ + + + P V IS G D +L
Sbjct: 284 KALVIVVNKWDLVK---DEKTREEFKKELRRKLPFLDFAP----IVFISALTGQGVDKLL 336
Query: 203 EVSDKM 208
+ D++
Sbjct: 337 DAIDEV 342
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 28.9 bits (66), Expect = 5.6
Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 16/63 (25%)
Query: 146 KQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNPATVAFVPISGWHGDNMLEVS 205
Q++V NKMD P +E EE K++ K+ PIS G + E+
Sbjct: 276 PQIVV-ANKMDL---PEAEENLEEFKEK---LGPKV---------FPISALTGQGLDELL 319
Query: 206 DKM 208
+
Sbjct: 320 YAV 322
>gnl|CDD|236700 PRK10489, PRK10489, enterobactin exporter EntS; Provisional.
Length = 417
Score = 28.8 bits (65), Expect = 6.6
Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 6/56 (10%)
Query: 228 LIEALDAILPPSRPTEKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMLVTFAPA 283
+ L A+ PP +P E PLR L G + V G+ G L+T A A
Sbjct: 192 PLLRLPALPPPPQPREHPLRSLL------AGFRFLLASPVVGGIALLGGLLTMASA 241
>gnl|CDD|217326 pfam03029, ATP_bind_1, Conserved hypothetical ATP binding protein.
Members of this family are found in a range of archaea
and eukaryotes and have hypothesised ATP binding
activity.
Length = 235
Score = 28.5 bits (64), Expect = 7.1
Identities = 51/267 (19%), Positives = 79/267 (29%), Gaps = 76/267 (28%)
Query: 12 VIGHVDSGKSTTTG-----------------------HLIYKCGGIDKRTIEKFEKEAQE 48
V+G SGK+T G +L Y+ ID I + A
Sbjct: 1 VVGPAGSGKTTFVGALSEILPLLGRSVYVVNLDPAAENLPYEA-DID---IRELITVADV 56
Query: 49 M------GKGSFKYAWVLDKLKAERERGITIDIALWKFETSKFYVTIIDAPG------HR 96
M G+ A +D L IT+D L + E Y + D PG H
Sbjct: 57 MEDDGLGPNGALTVA--MDFL------RITLDWLLEELEYEDDYY-LFDTPGQIELFTHW 107
Query: 97 DFIKNMITG--TSQADCAVLIVAAGTGEFEAGISKNGQTR-EHALLA----FTLGVKQLI 149
+ + + S AV +V + + L A LG+ +
Sbjct: 108 ESLARGVEALEASLRLGAVYLV-------DTRRLTDPSDFFSGLLYALSIMLRLGLPF-V 159
Query: 150 VGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNPATVAFVPISGWHGDNMLEVSDKMP 209
V +NK D ++ F + + L++ +P
Sbjct: 160 VALNKFDLLSLEFALKWFTDPDDLQLLLELDPSKLNEAIR----------EALDLFYLVP 209
Query: 210 WFKGWAIERKEGKADGKCLIEALDAIL 236
F A E E D L+ +D L
Sbjct: 210 RFLPDARETGESMED---LLTLIDEAL 233
>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 = 27.9 bits (63), Expect = 8.5
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 9 NIVVIGHVDSGKST 22
+ V+G +GKST
Sbjct: 2 LLAVVGEFSAGKST 15
>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 = 26.7 bits (60), Expect = 8.6
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 286 TTEVKSVEMHHEALQEAVPGDNVGFNVK 313
TT+V E + +PGDNV V+
Sbjct: 36 TTDVTGSITLPEGTEMVMPGDNVKMTVE 63
>gnl|CDD|133009 cd02516, CDP-ME_synthetase, CDP-ME synthetase is involved in
mevalonate-independent isoprenoid production.
4-diphosphocytidyl-2-methyl-D-erythritol synthase
(CDP-ME), also called 2C-methyl-d-erythritol
4-phosphate cytidylyltransferase catalyzes the third
step in the alternative (non-mevalonate) pathway of
Isopentenyl diphosphate (IPP) biosynthesis: the
formation of 4-diphosphocytidyl-2C-methyl-D-erythritol
from CTP and 2C-methyl-D-erythritol 4-phosphate. This
mevalonate independent pathway that utilizes pyruvate
and glyceraldehydes 3-phosphate as starting materials
for production of IPP occurs in a variety of bacteria,
archaea and plant cells, but is absent in mammals. Thus,
CDP-ME synthetase is an attractive targets for the
structure-based design of selective antibacterial,
herbicidal and antimalarial drugs.
Length = 218
Score = 27.9 bits (63), Expect = 9.2
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 9/53 (16%)
Query: 111 CAVLIVAAGTGE-FEAGISK-----NGQTR-EHALLAFT--LGVKQLIVGVNK 154
A +I+AAG+G A I K G+ EH L AF + +++V V
Sbjct: 1 VAAIILAAGSGSRMGADIPKQFLELGGKPVLEHTLEAFLAHPAIDEIVVVVPP 53
>gnl|CDD|215463 PLN02858, PLN02858, fructose-bisphosphate aldolase.
Length = 1378
Score = 28.7 bits (64), Expect = 9.7
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 325 VAGDSKASPPKATQDFTAQVIVLNHPGQISN 355
+ G SP +A +D A V+VL+HP Q+ +
Sbjct: 46 LGGHRCDSPAEAAKDAAALVVVLSHPDQVDD 76
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 27.9 bits (63), Expect = 10.0
Identities = 27/129 (20%), Positives = 47/129 (36%), Gaps = 30/129 (23%)
Query: 90 IDAPG-HR------DFIKNMITGT-SQADCAVLIVAA--GTGEFEAGISKNGQTREHALL 139
+D PG H+ + + D + +V A G G + E L
Sbjct: 59 VDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADEGWGPGD----------EFILE 108
Query: 140 AFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSGYIKKIGYNPATVAFVPISGWHGD 199
+I+ VNK+D +P + K++ + K+I VPIS GD
Sbjct: 109 QLKKTKTPVILVVNKIDKVKPKTVLLKLIAFLKKLLPF-KEI---------VPISALKGD 158
Query: 200 NMLEVSDKM 208
N+ + + +
Sbjct: 159 NVDTLLEII 167
>gnl|CDD|234670 PRK00155, ispD, 2-C-methyl-D-erythritol 4-phosphate
cytidylyltransferase; Reviewed.
Length = 227
Score = 27.8 bits (63), Expect = 10.0
Identities = 17/61 (27%), Positives = 23/61 (37%), Gaps = 9/61 (14%)
Query: 108 QADCAVLIVAAGTGE-FEAGISK-----NGQT-REHALLAFTL--GVKQLIVGVNKMDST 158
+I AAG G A K G+ EH L AF + ++IV V D
Sbjct: 1 MMMVYAIIPAAGKGSRMGADRPKQYLPLGGKPILEHTLEAFLAHPRIDEIIVVVPPDDRP 60
Query: 159 E 159
+
Sbjct: 61 D 61
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.135 0.401
Gapped
Lambda K H
0.267 0.0787 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,749,345
Number of extensions: 2338837
Number of successful extensions: 2523
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2329
Number of HSP's successfully gapped: 136
Length of query: 459
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 359
Effective length of database: 6,502,202
Effective search space: 2334290518
Effective search space used: 2334290518
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 61 (27.2 bits)