RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12559
(610 letters)
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 676 bits (1746), Expect = 0.0
Identities = 253/540 (46%), Positives = 359/540 (66%), Gaps = 11/540 (2%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
MD M ER+RGI+I SAAT WK H IN+IDTPGHVDFT EVERALRVLDGA++V+CAV
Sbjct: 35 MDFMPEERERGISITSAATTCEWKGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAV 94
Query: 61 GGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLG 120
GGV+ QT TV RQ ++Y VP I F+NK+DR GAD +RV+ Q+++K+G LQ+PIG G
Sbjct: 95 GGVEPQTETVWRQAEKYGVPRIIFVNKMDRAGADFFRVLAQLQEKLGAPVVPLQLPIGEG 154
Query: 121 SETKGIIDLIQRKAIYFEGPLGDNLRIEEIPADLKKEAESKRQELIEHVAEGDEILGEMF 180
+ G++DL+ KA ++ G EIPA+L AE R+EL+E +AE D+ L E +
Sbjct: 155 DDFTGVVDLLSMKAYRYDE--GGPSEEIEIPAELLDRAEEAREELLEALAEFDDELMEKY 212
Query: 181 LEEKSISEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLDYLPNPGEVTNYAI 240
LE + +SE++IK +R++TL + PV G+ALKNKGVQ LLDAV+DYLP+P EV
Sbjct: 213 LEGEELSEEEIKAGLRKATLAGEIVPVFCGSALKNKGVQRLLDAVVDYLPSPLEVPPVDG 272
Query: 241 ENGQEDKKVVLNPSRDGKHPFIALAFKLEAGKF-GQLTYMRCYQGKLRKGEMIYNVRTDK 299
E+G+E ++ +P P +AL FK F G+L+ +R Y G L+KG+ +YN T K
Sbjct: 273 EDGEEGAELAPDPDG----PLVALVFKTMDDPFVGKLSLVRVYSGTLKKGDTLYNSGTGK 328
Query: 300 KVRVSRLVRLHSNEMEDVEEVLAGDIFALFGV-DCASGDTFVTDKNNSISLESIYVADPV 358
K RV RL R+H + E+V+E +AGDI A+ + D A+GDT DK + I LE + +PV
Sbjct: 329 KERVGRLYRMHGKQREEVDEAVAGDIVAVAKLKDAATGDTL-CDKGDPILLEPMEFPEPV 387
Query: 359 VSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQRMER 418
+S++I+ + D + S+A+ + +EDPT D E+ +T++SGMGELHL++ +R++R
Sbjct: 388 ISLAIEPKDKGDEEKLSEALGKLAEEDPTLRVERDEETGQTILSGMGELHLDVALERLKR 447
Query: 419 EYNCPVVLGKPKVAFKETLVQPFDFDYLHKKQSGGSGQYGRVIGTLEPLPPSANTKLEFI 478
EY V G P+V ++ET+ + + HKKQSGG GQ+G V +EPLP EF+
Sbjct: 448 EYGVEVETGPPQVPYRETIRKKAEGHGRHKKQSGGHGQFGDVWLEVEPLPRGEG--FEFV 505
Query: 479 DETVGTNVPKPFLPAIIKGFKQMCEKGCLSGSRVAGVRMVLKDGDNHMVDSNEISFILAA 538
D+ VG VP+ ++PA+ KG ++ EKG L+G V V++ L DG H VDS+E++F +AA
Sbjct: 506 DKVVGGAVPRQYIPAVEKGVREALEKGVLAGYPVVDVKVTLTDGSYHSVDSSEMAFKIAA 565
Score = 100 bits (252), Expect = 4e-22
Identities = 27/74 (36%), Positives = 47/74 (63%)
Query: 537 AAHDPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIY 596
+PV+S++I+ + D + S+A+ + +EDPT D E+ +T++SGMGELHL++
Sbjct: 382 EFPEPVISLAIEPKDKGDEEKLSEALGKLAEEDPTLRVERDEETGQTILSGMGELHLDVA 441
Query: 597 AQRMEREYNCPVVL 610
+R++REY V
Sbjct: 442 LERLKREYGVEVET 455
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 656 bits (1696), Expect = 0.0
Identities = 256/551 (46%), Positives = 365/551 (66%), Gaps = 13/551 (2%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
MD ME E++RGITI SAAT WK H INIIDTPGHVDFT+EVER+LRVLDGA+ V AV
Sbjct: 48 MDWMEQEQERGITITSAATTCFWKGHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAV 107
Query: 61 GGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLG 120
GV+ Q+ TV RQ +Y VP I F+NK+DR+GAD +R + Q++ ++G NA +Q+PIG
Sbjct: 108 SGVEPQSETVWRQADKYGVPRIVFVNKMDRIGADFFRSVEQIKDRLGANAVPIQLPIGAE 167
Query: 121 SETKGIIDLIQRKAIYFEG-PLGDNLRIEEIPADLKKEAESKRQELIEHVAEGDEILGEM 179
+ KG+IDLI+ KAI ++ LG E+IPADLK++AE R++LIE VAE DE L E
Sbjct: 168 DDFKGVIDLIKMKAIIWDDETLGAKYEEEDIPADLKEKAEEYREKLIEAVAEVDEELMEK 227
Query: 180 FLEEKSISEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLDYLPNPGEVTNYA 239
+LE + I+E++IK AIR++T+ +F PVL G+A KNKGVQ LLDAV+DYLP+P +V
Sbjct: 228 YLEGEEITEEEIKAAIRKATINMEFFPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPAIK 287
Query: 240 IENGQEDKKVVLNPSRDGKHPFIALAFKLEAGKF-GQLTYMRCYQGKLRKGEMIYNVRTD 298
N ++++ S D PF ALAFK+ F G+LT+ R Y G L G + N
Sbjct: 288 GINPDTEEEIERPASDDE--PFAALAFKIMTDPFVGRLTFFRVYSGVLESGSYVLNTTKG 345
Query: 299 KKVRVSRLVRLHSNEMEDVEEVLAGDIFALFGV-DCASGDTFVTDKNNSISLESIYVADP 357
KK R+ RL+++H+N+ E+++EV AGDI A G+ D +GDT + D+ I LES+ +P
Sbjct: 346 KKERIGRLLQMHANKREEIKEVYAGDIAAAVGLKDTTTGDT-LCDEKAPIILESMEFPEP 404
Query: 358 VVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQRME 417
V+S++++ D+D A+Q+ +EDPTF D E+ +T++SGMGELHL+I RM+
Sbjct: 405 VISLAVEPKTKADQDKMGLALQKLAEEDPTFRVETDEETGQTIISGMGELHLDIIVDRMK 464
Query: 418 REYNCPVVLGKPKVAFKETLVQPFDFDYLHKKQSGGSGQYGRVIGTLEPLPPSANTKLEF 477
RE+ +G P+VA++ET+ + + + +KKQSGG GQYG V EP EF
Sbjct: 465 REFKVEANVGAPQVAYRETITKSVEAEGKYKKQSGGRGQYGDVWIEFEPNEE--GKGFEF 522
Query: 478 IDETVGTNVPKPFLPAIIKGFKQMCEKGCLSGSRVAGVRMVLKDGDNHMVDSNEISFILA 537
+++ VG +PK ++PA+ KG ++ + G L+G + V+ L DG H VDS+E++F +A
Sbjct: 523 VNKIVGGVIPKEYIPAVEKGLEEAMKNGVLAGYPMVDVKATLYDGSYHDVDSSELAFKIA 582
Query: 538 AHDPVVSMSIK 548
A SM++K
Sbjct: 583 A-----SMALK 588
Score = 85.7 bits (213), Expect = 2e-17
Identities = 28/66 (42%), Positives = 45/66 (68%)
Query: 540 DPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQR 599
+PV+S++++ D+D A+Q+ +EDPTF D E+ +T++SGMGELHL+I R
Sbjct: 403 EPVISLAVEPKTKADQDKMGLALQKLAEEDPTFRVETDEETGQTIISGMGELHLDIIVDR 462
Query: 600 MEREYN 605
M+RE+
Sbjct: 463 MKREFK 468
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 653 bits (1688), Expect = 0.0
Identities = 257/552 (46%), Positives = 366/552 (66%), Gaps = 14/552 (2%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
MD ME E++RGITI SAAT WKDH INIIDTPGHVDFT+EVER+LRVLDGA+ V AV
Sbjct: 50 MDWMEQEQERGITITSAATTCFWKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAV 109
Query: 61 GGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLG 120
GGV+ Q+ TV RQ +Y VP IAF+NK+DR GAD YRV+ Q++ ++G N +Q+PIG
Sbjct: 110 GGVEPQSETVWRQADKYKVPRIAFVNKMDRTGADFYRVVEQIKDRLGANPVPIQLPIGAE 169
Query: 121 SETKGIIDLIQRKAI-YFEGPLGDNLRIEEIPADLKKEAESKRQELIEHVAEGDEILGEM 179
+ KG++DL++ KAI + E LG EEIPADLK +AE R++LIE AE DE L E
Sbjct: 170 DDFKGVVDLVKMKAIIWNEADLGATFEYEEIPADLKDKAEEYREKLIEAAAEADEELMEK 229
Query: 180 FLEEKSISEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLDYLPNPGEVTNY- 238
+LE + ++E++IK A+R++T+ + PVL G+A KNKGVQ LLDAV+DYLP+P +V
Sbjct: 230 YLEGEELTEEEIKAALRKATIANEIVPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPAIK 289
Query: 239 AIENGQEDKKVVLNPSRDGKHPFIALAFKLEAGKF-GQLTYMRCYQGKLRKGEMIYNVRT 297
I E+++V S D PF ALAFK+ F G+LT+ R Y G L G + N
Sbjct: 290 GILPDGEEEEVERKASDDE--PFSALAFKIMTDPFVGKLTFFRVYSGVLESGSYVLNSTK 347
Query: 298 DKKVRVSRLVRLHSNEMEDVEEVLAGDIFALFGV-DCASGDTFVTDKNNSISLESIYVAD 356
KK R+ R++++H+N+ E+++EV AGDI A G+ D +GDT + D+ N I LES+ +
Sbjct: 348 GKKERIGRILQMHANKREEIKEVRAGDIAAAVGLKDTTTGDT-LCDEKNPIILESMEFPE 406
Query: 357 PVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQRM 416
PV+S++++ D++ A+Q+ +EDP+F D E+ +T+++GMGELHL+I RM
Sbjct: 407 PVISVAVEPKTKADQEKMGIALQKLAEEDPSFRVSTDEETGQTIIAGMGELHLDIIVDRM 466
Query: 417 EREYNCPVVLGKPKVAFKETLVQPFDFDYLHKKQSGGSGQYGRVIGTLEPLPPSANTKLE 476
+RE+ +GKP+VA++ET+ + + + KQSGG GQYG V+ EP P E
Sbjct: 467 KREFKVEANVGKPQVAYRETIRKKVEVEGKFVKQSGGRGQYGHVVIEFEPNEPGKG--YE 524
Query: 477 FIDETVGTNVPKPFLPAIIKGFKQMCEKGCLSGSRVAGVRMVLKDGDNHMVDSNEISFIL 536
F+++ VG +PK ++PA+ KG ++ E G L+G V V++ L DG H VDS+E++F +
Sbjct: 525 FVNKIVGGVIPKEYIPAVDKGIQEAMESGVLAGYPVVDVKVTLFDGSYHDVDSSEMAFKI 584
Query: 537 AAHDPVVSMSIK 548
A SM+ K
Sbjct: 585 AG-----SMAFK 591
Score = 81.7 bits (203), Expect = 4e-16
Identities = 25/66 (37%), Positives = 45/66 (68%)
Query: 540 DPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQR 599
+PV+S++++ D++ A+Q+ +EDP+F D E+ +T+++GMGELHL+I R
Sbjct: 406 EPVISVAVEPKTKADQEKMGIALQKLAEEDPSFRVSTDEETGQTIIAGMGELHLDIIVDR 465
Query: 600 MEREYN 605
M+RE+
Sbjct: 466 MKREFK 471
>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 = 622 bits (1606), Expect = 0.0
Identities = 264/593 (44%), Positives = 375/593 (63%), Gaps = 16/593 (2%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
MD ME E++RGITI SAAT WK H INIIDTPGHVDFTVEVER+LRVLDGA+ VL AV
Sbjct: 50 MDWMEQEKERGITITSAATTVFWKGHRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAV 109
Query: 61 GGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLG 120
GGVQ Q+ TV RQ RY+VP IAF+NK+D+ GA+ RV+NQ++Q++G NA +Q+PIG
Sbjct: 110 GGVQPQSETVWRQANRYEVPRIAFVNKMDKTGANFLRVVNQIKQRLGANAVPIQLPIGAE 169
Query: 121 SETKGIIDLIQRKAIYFEGPLGDNLRIEEIPADLKKEAESKRQELIEHVAEGDEILGEMF 180
G+IDL++ KA +F G G +EIP+DL ++A+ R+ L+E VAE DE L E +
Sbjct: 170 DNFIGVIDLVEMKAYFFNGDKGTKAIEKEIPSDLLEQAKELRENLVEAVAEFDEELMEKY 229
Query: 181 LEEKSISEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLDYLPNPGEVTNYAI 240
LE + ++ ++IK AIR+ L +F PVL G+A KNKGVQ LLDAV+DYLP+P +V
Sbjct: 230 LEGEELTIEEIKNAIRKGVLNCEFFPVLCGSAFKNKGVQLLLDAVVDYLPSPTDVPAIKG 289
Query: 241 ENGQEDKKVVLNPSRDGKHPFIALAFKLEAGKF-GQLTYMRCYQGKLRKGEMIYNVRTDK 299
+ +K++ S D PF ALAFK+ F GQLT++R Y G L+ G + N R +K
Sbjct: 290 IDPDTEKEIERKASDDE--PFSALAFKVATDPFVGQLTFVRVYSGVLKSGSYVKNSRKNK 347
Query: 300 KVRVSRLVRLHSNEMEDVEEVLAGDIFALFGVDCAS-GDTFVTDKNNSISLESIYVADPV 358
K RV RLV++H+N E+++EV AGDI A G+ + GDT K + + LE + +PV
Sbjct: 348 KERVGRLVKMHANNREEIKEVRAGDICAAIGLKDTTTGDTLCDPKID-VILERMEFPEPV 406
Query: 359 VSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQRMER 418
+S++++ D++ A+ + +EDPTF F DPE+ +T+++GMGELHL+I RM+R
Sbjct: 407 ISLAVEPKTKADQEKMGIALGKLAEEDPTFRTFTDPETGQTIIAGMGELHLDIIVDRMKR 466
Query: 419 EYNCPVVLGKPKVAFKETLVQPFDFDYLHKKQSGGSGQYGRVIGTLEPLPPSANTKLEFI 478
E+ +G P+VA++ET+ + + H KQSGG GQYG V EPL P EF+
Sbjct: 467 EFKVEANVGAPQVAYRETIRSKVEVEGKHAKQSGGRGQYGHVKIRFEPLEPKG---YEFV 523
Query: 479 DETVGTNVPKPFLPAIIKGFKQMCEKGCLSGSRVAGVRMVLKDGDNHMVDSNEISFILAA 538
+E G +P+ ++PA+ KG ++ E G L+G V ++ L DG H VDS+E++F LAA
Sbjct: 524 NEIKGGVIPREYIPAVDKGLQEAMESGPLAGYPVVDIKATLFDGSYHDVDSSEMAFKLAA 583
Query: 539 HDPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHF---FYDPESKETLVSGM 588
S++ K K + + + E P + D S+ ++ GM
Sbjct: 584 -----SLAFKEAGKKANPVLLEPIMKVEVEVPEEYMGDVMGDLSSRRGIIEGM 631
Score = 88.7 bits (220), Expect = 2e-18
Identities = 27/69 (39%), Positives = 46/69 (66%)
Query: 540 DPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQR 599
+PV+S++++ D++ A+ + +EDPTF F DPE+ +T+++GMGELHL+I R
Sbjct: 404 EPVISLAVEPKTKADQEKMGIALGKLAEEDPTFRTFTDPETGQTIIAGMGELHLDIIVDR 463
Query: 600 MEREYNCPV 608
M+RE+
Sbjct: 464 MKREFKVEA 472
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 617 bits (1593), Expect = 0.0
Identities = 261/553 (47%), Positives = 370/553 (66%), Gaps = 16/553 (2%)
Query: 1 MDSMELERQRGITIQSAATYTLWKD-HNINIIDTPGHVDFTVEVERALRVLDGAILVLCA 59
MD ME E++RGITI SAAT WK + IN+IDTPGHVDFT+EVER+LRVLDGA++V+ A
Sbjct: 50 MDWMEQEQERGITITSAATTLFWKGDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDA 109
Query: 60 VGGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGL 119
V GV+ QT TV RQ +Y VP I F+NK+DRLGAD Y V+ Q+++++G N +Q+PIG
Sbjct: 110 VEGVEPQTETVWRQADKYGVPRILFVNKMDRLGADFYLVVEQLKERLGANPVPVQLPIGA 169
Query: 120 GSETKGIIDLIQRKAIYFEGPLGDNLRIEEIPADLKKEAESKRQELIEHVAEGDEILGEM 179
E +G+IDL++ KA+ F G EIPADLK+ AE R++L+E +AE DE L E
Sbjct: 170 EEEFEGVIDLVEMKAVAFGD--GAKYEWIEIPADLKEIAEEAREKLLEALAEFDEELMEK 227
Query: 180 FLEEKSISEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLDYLPNPGEVTNY- 238
+LE + +E++IKKA+R+ T+ K PVL G+A KNKGVQ LLDAV+DYLP+P +V
Sbjct: 228 YLEGEEPTEEEIKKALRKGTIAGKIVPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPPIK 287
Query: 239 AIENGQEDKKVVLNPSRDGKHPFIALAFKLEAGKF-GQLTYMRCYQGKLRKGEMIYNVRT 297
+ + +K V+ S +G P AL FK+ F G+LT++R Y G L+ G + N
Sbjct: 288 GDLDDEIEKAVLRKASDEG--PLSALVFKIMTDPFVGKLTFVRVYSGTLKSGSEVLNSTK 345
Query: 298 DKKVRVSRLVRLHSNEMEDVEEVLAGDIFALFGVDCA-SGDTFVTDKNNSISLESIYVAD 356
KK RV RL+ +H NE E+V+EV AGDI AL G+ A +GDT + D+N + LES+ +
Sbjct: 346 GKKERVGRLLLMHGNEREEVDEVPAGDIVALVGLKDATTGDT-LCDENKPVILESMEFPE 404
Query: 357 PVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQRM 416
PV+S++++ D++ S+A+ + +EDPTF D E+ ET++SGMGELHLEI R+
Sbjct: 405 PVISVAVEPKTKADQEKLSEALNKLAEEDPTFRVETDEETGETIISGMGELHLEIIVDRL 464
Query: 417 EREYNCPVVLGKPKVAFKETLVQPFDFDYLHKKQSGGSGQYGRVIGTLEPLPPSANTKLE 476
+RE+ V +GKP+VA++ET+ + + + HKKQSGG GQYG V +EPL + E
Sbjct: 465 KREFGVEVEVGKPQVAYRETIRKKSEVEGKHKKQSGGPGQYGHVYIEIEPLED--GSGFE 522
Query: 477 FIDETVGTNVPKPFLPAIIKGFKQMCEKGCLSGSRVAGVRMVLKDGDNHMVDSNEISFIL 536
F+D+ VG VPK ++PA+ KGF++ + G L+G V V++ L DG H VDS+E++F +
Sbjct: 523 FVDKIVGGVVPKEYIPAVEKGFREALKSGPLAGYPVVDVKVTLLDGSYHEVDSSEMAFKI 582
Query: 537 AAHDPVVSMSIKA 549
AA S++ K
Sbjct: 583 AA-----SLAFKE 590
Score = 94.2 bits (235), Expect = 5e-20
Identities = 29/69 (42%), Positives = 47/69 (68%)
Query: 540 DPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQR 599
+PV+S++++ D++ S+A+ + +EDPTF D E+ ET++SGMGELHLEI R
Sbjct: 404 EPVISVAVEPKTKADQEKLSEALNKLAEEDPTFRVETDEETGETIISGMGELHLEIIVDR 463
Query: 600 MEREYNCPV 608
++RE+ V
Sbjct: 464 LKREFGVEV 472
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 536 bits (1382), Expect = 0.0
Identities = 226/542 (41%), Positives = 334/542 (61%), Gaps = 9/542 (1%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
D M E++RGITI+SAAT W +H IN+IDTPGH+DFT EVER+LRVLDGA++V AV
Sbjct: 48 TDWMPQEQERGITIESAATSCDWDNHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDAV 107
Query: 61 GGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLG 120
GVQ QT TV RQ RY +P + FINK+DR+GAD ++V+ + ++ G LQ+PIG
Sbjct: 108 TGVQPQTETVWRQADRYGIPRLIFINKMDRVGADLFKVLEDIEERFGKRPLPLQLPIGSE 167
Query: 121 SETKGIIDLIQRKAIYF-EGPLGDNLRIEEIPADLKKEAESKRQELIEHVAEGDEILGEM 179
+G++DLI ++F EG G + IP +L +E E R++LIE +AE D+ L E+
Sbjct: 168 DGFEGVVDLITEPELHFSEGDGGSTVEEGPIPEELLEEVEEAREKLIEALAEFDDELLEL 227
Query: 180 FLEEKSISEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLDYLPNPGEVTNYA 239
+LE + +S + ++ +R T + PVL G+ALKN G++ LLDAV+DYLP+P EV
Sbjct: 228 YLEGEELSAEQLRAPLREGTRSGHLVPVLFGSALKNIGIEPLLDAVVDYLPSPLEVPPPR 287
Query: 240 IENGQEDKKVVLNPSRDGKHPFIALAFKLEA-GKFGQLTYMRCYQGKLRKGEMIYNVRTD 298
K V ++P + P +AL FK++ G+LTY+R Y G LR G +YN
Sbjct: 288 GSKDN-GKPVKVDPDPEK--PLLALVFKVQYDPYAGKLTYLRVYSGTLRAGSQLYNGTGG 344
Query: 299 KKVRVSRLVRLHSNEMEDVEEVLAGDIFALFGVDCA-SGDTFVTDKNNSISLESIYVADP 357
K+ +V RL RL N+ E+V+ AGDI A+ G+ +GDT + D + + LE + +P
Sbjct: 345 KREKVGRLFRLQGNKREEVDRAKAGDIVAVAGLKELETGDT-LHDSADPVLLELLTFPEP 403
Query: 358 VVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQRME 417
VVS++++ D ++A+++ EDP+ D E+ +T++SGMGELHLE+ +R+
Sbjct: 404 VVSLAVEPERRGDEQKLAEALEKLVWEDPSLRVEEDEETGQTILSGMGELHLEVALERLR 463
Query: 418 REYNCPVVLGKPKVAFKETLVQPFDFDYLHKKQSGGSGQYGRVIGTLEPLPPSANTKLEF 477
RE+ V GKP+VA++ET+ + + Y HKKQ GG GQ+G V +EPL A F
Sbjct: 464 REFKLEVNTGKPQVAYRETIRKMAEGVYRHKKQFGGKGQFGEVHLRVEPLERGAG--FIF 521
Query: 478 IDETVGTNVPKPFLPAIIKGFKQMCEKGCLSGSRVAGVRMVLKDGDNHMVDSNEISFILA 537
+ + VG +P+ +PA+ KG ++ G L+G V +R+ + DG H VDS+E +F A
Sbjct: 522 VSKVVGGAIPEELIPAVEKGIREALASGPLAGYPVTDLRVTVLDGKYHPVDSSESAFKAA 581
Query: 538 AH 539
A
Sbjct: 582 AR 583
Score = 81.2 bits (201), Expect = 6e-16
Identities = 25/70 (35%), Positives = 44/70 (62%)
Query: 540 DPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQR 599
+PVVS++++ D ++A+++ EDP+ D E+ +T++SGMGELHLE+ +R
Sbjct: 402 EPVVSLAVEPERRGDEQKLAEALEKLVWEDPSLRVEEDEETGQTILSGMGELHLEVALER 461
Query: 600 MEREYNCPVV 609
+ RE+ V
Sbjct: 462 LRREFKLEVN 471
>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 = 430 bits (1108), Expect = e-149
Identities = 142/232 (61%), Positives = 178/232 (76%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
MD ME ER+RGITIQSAAT WKDH INIIDTPGHVDFT+EVER+LRVLDGA+ V AV
Sbjct: 39 MDWMEQERERGITIQSAATTCFWKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAV 98
Query: 61 GGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLG 120
GVQ QT TV RQ RY VP IAF+NK+DR GAD YRV+ Q+R+K+G N LQ+PIG
Sbjct: 99 AGVQPQTETVWRQADRYGVPRIAFVNKMDRTGADFYRVVEQIREKLGANPVPLQLPIGAE 158
Query: 121 SETKGIIDLIQRKAIYFEGPLGDNLRIEEIPADLKKEAESKRQELIEHVAEGDEILGEMF 180
+ +G++DLI+ KA+Y++G LG+ + +IP DL +EAE R+ELIE +AE D+ L E +
Sbjct: 159 DDFEGVVDLIEMKALYWDGELGEKIEETDIPEDLLEEAEEAREELIETLAEVDDELMEKY 218
Query: 181 LEEKSISEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLDYLPNP 232
LE + I+E++IK AIR+ T+ K PVL G+A KNKGVQ LLDAV+DYLP+P
Sbjct: 219 LEGEEITEEEIKAAIRKGTIANKIVPVLCGSAFKNKGVQPLLDAVVDYLPSP 270
>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 = 212 bits (542), Expect = 2e-64
Identities = 86/232 (37%), Positives = 135/232 (58%), Gaps = 2/232 (0%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
D E++R ++I+++ W H IN+IDTPG+ DF E ALR +D A++V+ A
Sbjct: 39 SDYDPEEKKRKMSIETSVAPLEWNGHKINLIDTPGYADFVGETLSALRAVDAALIVVEAQ 98
Query: 61 GGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLG 120
GV+ T V + +P I FINK+DR AD + + +R+ G +Q+PIG G
Sbjct: 99 SGVEVGTEKVWEFLDDAKLPRIIFINKMDRARADFDKTLAALREAFGRPVVPIQLPIGEG 158
Query: 121 SETKGIIDLIQRKAIYFEGPLGDNLRIEEIPADLKKEAESKRQELIEHVAEGDEILGEMF 180
E G++DL+ KA ++ G+ EIP +LK++ R+EL+E VAE DE L E +
Sbjct: 159 DEFTGVVDLLSEKAYRYDP--GEPSVEIEIPEELKEKVAEAREELLEAVAETDEELMEKY 216
Query: 181 LEEKSISEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLDYLPNP 232
LEE ++E++++ +RR+ PV G+AL GV+ LLDA+++ P+P
Sbjct: 217 LEEGELTEEELRAGLRRALRAGLIVPVFFGSALTGIGVRRLLDALVELAPSP 268
>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 = 201 bits (513), Expect = 1e-60
Identities = 85/229 (37%), Positives = 121/229 (52%), Gaps = 33/229 (14%)
Query: 2 DSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVG 61
DSMELERQRGITI SA W+D +NIIDTPGH+DF EVER+L VLDGAILV+ AV
Sbjct: 40 DSMELERQRGITIFSAVASFQWEDTKVNIIDTPGHMDFIAEVERSLSVLDGAILVISAVE 99
Query: 62 GVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLGS 121
GVQ+QT + R +++ ++P I F+NK+DR GAD +V ++++K+ + +Q
Sbjct: 100 GVQAQTRILFRLLRKLNIPTIIFVNKIDRAGADLEKVYQEIKEKLSPDIVPMQ------- 152
Query: 122 ETKGIIDLIQRKAIYFEGPLGDNLRIEEIPADLKKEAESKRQELIEHVAEGDEILGEMFL 181
+ L N+ D E IE VAEG++ L E +L
Sbjct: 153 ----------------KVGLYPNICDTNNIDD----------EQIETVAEGNDELLEKYL 186
Query: 182 EEKSISEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLDYLP 230
+ E ++ + PV G+ALK G+ LL+ + + P
Sbjct: 187 SGGPLEELELDNELSARIQKASLFPVYHGSALKGIGIDELLEGITNLFP 235
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 208 bits (533), Expect = 1e-58
Identities = 146/462 (31%), Positives = 227/462 (49%), Gaps = 77/462 (16%)
Query: 1 MDSMELERQRGITIQSAATYTLW-----KDHNINIIDTPGHVDFTVEVERALRVLDGAIL 55
+D E E+ RGITI+ AA ++ K++ IN+IDTPGHVDF +V RA+R +DGAI+
Sbjct: 58 LDFDEEEQARGITIK-AANVSMVHEYEGKEYLINLIDTPGHVDFGGDVTRAMRAVDGAIV 116
Query: 56 VLCAVGGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQI 115
V+ AV GV QT TV RQ R V + FINK+D R+I ++ K+ ++
Sbjct: 117 VVDAVEGVMPQTETVLRQALRERVKPVLFINKVD-------RLIKEL--KLTPQ----EM 163
Query: 116 PIGLGSETKGIIDLIQRKAIYFEGPLGDNLRIEEIPADLKKEAESKRQELIEHVAEGDEI 175
L K + LI+ A E K + ++ V +G
Sbjct: 164 QQRLLKIIKDVNKLIKGMA----------------------PEEFKEKWKVD-VEDGTVA 200
Query: 176 LGEM---------FLEEKSISEDDIKKAIR---RSTLTRKFTPVLVGTALKNKGVQTLLD 223
G +++ I DI + L K P+ + +LD
Sbjct: 201 FGSALYNWAISVPMMQKTGIKFKDIIDYYEKGKQKELAEK-APL----------HEVVLD 249
Query: 224 AVLDYLPNPGEVTNYAIEN---GQEDKKV---VLNPSRDGKHPFIALAFKLEAGKF-GQL 276
V+ +LPNP E Y I G + +V +LN +G P + + + G++
Sbjct: 250 MVVKHLPNPIEAQKYRIPKIWKGDLNSEVGKAMLNCDPNG--PLVMMVTDIIVDPHAGEV 307
Query: 277 TYMRCYQGKLRKGEMIYNVRTDKKVRVSRLVRLHSNEMEDVEEVLAGDIFALFGVDCA-S 335
R + G LRKG+ +Y V KK RV ++ E E+VEE+ AG+I A+ G+ A +
Sbjct: 308 ATGRVFSGTLRKGQEVYLVGAKKKNRVQQVGIYMGPEREEVEEIPAGNIAAVTGLKDARA 367
Query: 336 GDTFVTDKNNSISLESI-YVADPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDP 394
G+T V + ES+ ++++PVV+++I+A N KD + +++ KEDPT +
Sbjct: 368 GET-VVSVEDMTPFESLKHISEPVVTVAIEAKNPKDLPKLIEVLRQLAKEDPTLVVKINE 426
Query: 395 ESKETLVSGMGELHLEIYAQRMEREYNCPVVLGKPKVAFKET 436
E+ E L+SGMGELHLE+ R++R+Y VV +P V ++ET
Sbjct: 427 ETGEHLLSGMGELHLEVITYRIKRDYGIEVVTSEPIVVYRET 468
Score = 70.3 bits (173), Expect = 2e-12
Identities = 30/70 (42%), Positives = 46/70 (65%)
Query: 540 DPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQR 599
+PVV+++I+A N KD + +++ KEDPT + E+ E L+SGMGELHLE+ R
Sbjct: 388 EPVVTVAIEAKNPKDLPKLIEVLRQLAKEDPTLVVKINEETGEHLLSGMGELHLEVITYR 447
Query: 600 MEREYNCPVV 609
++R+Y VV
Sbjct: 448 IKRDYGIEVV 457
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 186 bits (475), Expect = 5e-52
Identities = 122/431 (28%), Positives = 202/431 (46%), Gaps = 31/431 (7%)
Query: 2 DSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVG 61
D ME+E+QRGI++ S+ + D +N++DTPGH DF+ + R L +D A++V+ A
Sbjct: 57 DWMEIEKQRGISVTSSVMQFDYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAK 116
Query: 62 GVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLGS 121
G++ QTL + + D+P FINKLDR G DP +++++ +++G A + PIG+G
Sbjct: 117 GIEPQTLKLFEVCRLRDIPIFTFINKLDREGRDPLELLDEIEEELGIQCAPITWPIGMGK 176
Query: 122 ETKGIIDLIQRKAIYFEGPLGDNLRIEEIPADLKKEAESKRQELIEHVAEGDEILGEMFL 181
+ KG+ L + +E D R +I L E L E
Sbjct: 177 DFKGVYHLYNDEVELYESGHTDQERRADIVKGLDNPELDALLG---------EDLAEQLR 227
Query: 182 EEKSISEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLDYLPNPGEVTNYAIE 241
EE + + + + L + TPV G+AL N GV LDA++D+ P+P
Sbjct: 228 EELELVQGAGNEFDLEAFLAGELTPVFFGSALGNFGVDHFLDALVDWAPSPRAR------ 281
Query: 242 NGQEDKKVVLNPSRDGKHPFIALAFKLEAGKFGQ----LTYMRCYQGKLRKGEMIYNVRT 297
Q D + V P+ D F FK++A + + +MR GK +G + +VRT
Sbjct: 282 --QADTREV-EPTED---KFSGFVFKIQANMDPKHRDRIAFMRVCSGKFERGMKVTHVRT 335
Query: 298 DKKVRVSRLVRLHSNEMEDVEEVLAGDIFALF--GVDCASGDTFVTDKNNSISLESIYVA 355
K V++S + + + E VEE AGDI L G GDTF + + I
Sbjct: 336 GKDVKLSDALTFMAQDRETVEEAYAGDIIGLHNHGT-IQIGDTFTEGEK--LKFTGIPNF 392
Query: 356 DPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQR 415
P + ++ + + K +++ +E F + + ++ +G+L E+ R
Sbjct: 393 APELFRRVRLKDPLKQKQLKKGLEQLAEEGAV-QVFKPLDGNDLILGAVGQLQFEVVQAR 451
Query: 416 MEREYNCPVVL 426
++ EYN V
Sbjct: 452 LKNEYNVEAVF 462
Score = 31.1 bits (71), Expect = 2.2
Identities = 11/66 (16%), Positives = 28/66 (42%), Gaps = 1/66 (1%)
Query: 545 MSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQRMEREY 604
++ + + K +++ +E F + + ++ +G+L E+ R++ EY
Sbjct: 398 RRVRLKDPLKQKQLKKGLEQLAEEGAV-QVFKPLDGNDLILGAVGQLQFEVVQARLKNEY 456
Query: 605 NCPVVL 610
N V
Sbjct: 457 NVEAVF 462
>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 = 187 bits (477), Expect = 3e-51
Identities = 145/459 (31%), Positives = 220/459 (47%), Gaps = 68/459 (14%)
Query: 1 MDSMELERQRGITIQSAATYTLW----KDHNINIIDTPGHVDFTVEVERALRVLDGAILV 56
+D E E++RGITI +A + ++ IN+IDTPGHVDF +V RA+R +DGAI+V
Sbjct: 57 LDFDEQEQERGITINAANVSMVHEYEGNEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVV 116
Query: 57 LCAVGGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIP 116
+CAV GV QT TV RQ + +V + FINK+DRL IN+++ P
Sbjct: 117 VCAVEGVMPQTETVLRQALKENVKPVLFINKVDRL-------INELKLT----------P 159
Query: 117 IGLGSETKGIIDLIQRKAIYFEGPLGDNLRIEEIPADLKKEAESKRQELIEHVAEGDEIL 176
L II + + L + EE R + V +G
Sbjct: 160 QELQERFIKIITEVNK--------LIKAMAPEEF-----------RDKWKVRVEDGSVAF 200
Query: 177 GEM---------FLEEKSISEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLD 227
G +++ I DI K + A K+ Q +LD V+
Sbjct: 201 GSAYYNWAISVPSMKKTGIGFKDIYKYCKEDKQKE--------LAKKSPLHQVVLDMVIR 252
Query: 228 YLPNPGEVTNYAI------ENGQEDKKVVLNPSRDGKHPFIALAFKLEAGKF-GQLTYMR 280
+LP+P E Y I + E K +LN D K P + K+ K G++ R
Sbjct: 253 HLPSPIEAQKYRIPVIWKGDLNSEVGKAMLNC--DPKGPLALMITKIVVDKHAGEVAVGR 310
Query: 281 CYQGKLRKGEMIYNVRTDKKVRVSRLVRLHSNEMEDVEEVLAGDIFALFGV-DCASGDTF 339
Y G +R G +Y V K R+ ++ E +V+E+ AG+I A+ G+ D +G+T
Sbjct: 311 LYSGTIRPGMEVYIVDRKAKARIQQVGVYMGPERVEVDEIPAGNIVAVIGLKDAVAGETI 370
Query: 340 VTDKNNSISLESI-YVADPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKE 398
T N ESI ++++PVV+++I+A N KD + +++ KEDPT H + E+ E
Sbjct: 371 CTTVENITPFESIKHISEPVVTVAIEAKNTKDLPKLIEVLRQVAKEDPTVHVEINEETGE 430
Query: 399 TLVSGMGELHLEIYAQRMEREYNCPVVLGKPKVAFKETL 437
L+SGMGELHLEI +++ +Y V P V ++ET+
Sbjct: 431 HLISGMGELHLEIIVEKIREDYGLDVETSPPIVVYRETV 469
Score = 66.5 bits (162), Expect = 2e-11
Identities = 29/69 (42%), Positives = 45/69 (65%)
Query: 540 DPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQR 599
+PVV+++I+A N KD + +++ KEDPT H + E+ E L+SGMGELHLEI ++
Sbjct: 388 EPVVTVAIEAKNTKDLPKLIEVLRQVAKEDPTVHVEINEETGEHLISGMGELHLEIIVEK 447
Query: 600 MEREYNCPV 608
+ +Y V
Sbjct: 448 IREDYGLDV 456
>gnl|CDD|239758 cd04091, mtEFG1_II_like, mtEFG1_C: C-terminus of mitochondrial
Elongation factor G1 (mtEFG1)-like proteins found in
eukaryotes. Eukaryotic cells harbor 2 protein synthesis
systems: one localized in the cytoplasm, the other in
the mitochondria. Most factors regulating mitochondrial
protein synthesis are encoded by nuclear genes,
translated in the cytoplasm, and then transported to the
mitochondria. The eukaryotic system of elongation factor
(EF) components is more complex than that in
prokaryotes, with both cytoplasmic and mitochondrial
elongation factors and multiple isoforms being expressed
in certain species. Eukaryotic EF-2 operates in the
cytosolic protein synthesis machinery of eukaryotes,
EF-Gs in protein synthesis in bacteria. Eukaryotic
mtEFG1 proteins show significant homology to bacterial
EF-Gs. Mutants in yeast mtEFG1 have impaired
mitochondrial protein synthesis, respiratory defects and
a tendency to lose mitochondrial DNA. There are two
forms of mtEFG present in mammals (designated mtEFG1s
and mtEFG2s) mtEFG2s are not present in this group.
Length = 81
Score = 162 bits (411), Expect = 5e-48
Identities = 62/81 (76%), Positives = 70/81 (86%)
Query: 261 FIALAFKLEAGKFGQLTYMRCYQGKLRKGEMIYNVRTDKKVRVSRLVRLHSNEMEDVEEV 320
F+ LAFKLE G+FGQLTYMR YQGKL+KG+ IYNVRT KKVRV RLVR+HSNEME+VEE
Sbjct: 1 FVGLAFKLEEGRFGQLTYMRIYQGKLKKGDTIYNVRTGKKVRVPRLVRMHSNEMEEVEEA 60
Query: 321 LAGDIFALFGVDCASGDTFVT 341
AGDI A+FG+DCASGDTF
Sbjct: 61 GAGDICAIFGIDCASGDTFTD 81
>gnl|CDD|238715 cd01434, EFG_mtEFG1_IV, EFG_mtEFG1_IV: domains similar to domain IV
of the bacterial translational elongation factor (EF)
EF-G. Included in this group is a domain of
mitochondrial Elongation factor G1 (mtEFG1) proteins
homologous to domain IV of EF-G. Eukaryotic cells harbor
2 protein synthesis systems: one localized in the
cytoplasm, the other in the mitochondria. Most factors
regulating mitochondrial protein synthesis are encoded
by nuclear genes, translated in the cytoplasm, and then
transported to the mitochondria. The eukaryotic system
of elongation factor (EF) components is more complex
than that in prokaryotes, with both cytoplasmic and
mitochondrial elongation factors and multiple isoforms
being expressed in certain species. During the process
of peptide synthesis and tRNA site changes, the ribosome
is moved along the mRNA a distance equal to one codon
with the addition of each amino acid. In bacteria this
translocation step is catalyzed by EF-G_GTP, which is
hydrolyzed to provide the required energy. Thus, this
action releases the uncharged tRNA from the P site and
transfers the newly formed peptidyl-tRNA from the A site
to the P site. Eukaryotic mtEFG1 proteins show
significant homology to bacterial EF-Gs. Mutants in
yeast mtEFG1 have impaired mitochondrial protein
synthesis, respiratory defects and a tendency to lose
mitochondrial DNA. There are two forms of mtEFG present
in mammals (designated mtEFG1s and mtEFG2s) mtEFG2s are
not present in this group.
Length = 116
Score = 156 bits (397), Expect = 2e-45
Identities = 50/106 (47%), Positives = 76/106 (71%), Gaps = 2/106 (1%)
Query: 433 FKETLVQPFDFDYLHKKQSGGSGQYGRVIGTLEPLPPSANTKLEFIDETVGTNVPKPFLP 492
++ET+ +P +F+Y HKKQSGG+GQYG V+ +EPLP + EF+++ VG +PK ++P
Sbjct: 1 YRETITKPAEFEYRHKKQSGGAGQYGHVVLEIEPLPR--GSGFEFVNKIVGGAIPKEYIP 58
Query: 493 AIIKGFKQMCEKGCLSGSRVAGVRMVLKDGDNHMVDSNEISFILAA 538
A+ KGF++ EKG L+G V V++ L DG H VDS+E++F +AA
Sbjct: 59 AVEKGFREALEKGPLAGYPVVDVKVTLYDGSYHDVDSSEMAFKIAA 104
>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 = 161 bits (410), Expect = 4e-43
Identities = 115/430 (26%), Positives = 195/430 (45%), Gaps = 29/430 (6%)
Query: 2 DSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVG 61
D ME+E+QRGI+I ++ ++D +N++DTPGH DF+ + R L +D ++V+ A
Sbjct: 56 DWMEMEKQRGISITTSVMQFPYRDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAK 115
Query: 62 GVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLGS 121
GV+++T + + D P F+NKLDR DP +++++ ++ N A + PIG G
Sbjct: 116 GVETRTRKLMEVTRLRDTPIFTFMNKLDRDIRDPLELLDEVENELKINCAPITWPIGCGK 175
Query: 122 ETKGIIDLIQRKAIYFEGPLGDNLRIEEIPADLKKEAESKRQELIEHVAEGDEILGEMFL 181
KG+ L++ + ++ G ++ L A A G ++ +
Sbjct: 176 LFKGVYHLLKDETYLYQSGTGGTIQAVRQVKGLNNPALD--------SAVGSDLAQQ-LR 226
Query: 182 EEKSISEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLDYLPNPGEVTNYAIE 241
+E + E + + + TPV GTAL N GV LD +L + P P E
Sbjct: 227 DELELVEGASNEFDLAAFHGGEMTPVFFGTALGNFGVDHFLDGLLQWAPKP--------E 278
Query: 242 NGQEDKKVVLNPSRDGKHPFIALAFKLEAG----KFGQLTYMRCYQGKLRKGEMIYNVRT 297
Q D + V P+ + F FK++A ++ +MR GK KG + +VRT
Sbjct: 279 ARQSDTRTV-EPTEE---KFSGFVFKIQANMDPKHRDRVAFMRVVSGKYEKGMKLKHVRT 334
Query: 298 DKKVRVSRLVRLHSNEMEDVEEVLAGDIFALFGVDCAS-GDTFVTDKNNSISLESIYVAD 356
K V +S + + + E VEE AGDI L GDTF + I I
Sbjct: 335 GKDVVISDALTFMAGDREHVEEAYAGDIIGLHNHGTIQIGDTFTQGE--KIKFTGIPNFA 392
Query: 357 PVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQRM 416
P + I+ + + K + + ++E F ++ + +V +G L ++ R+
Sbjct: 393 PELFRRIRLKDPLKQKQLLKGLVQLSEEGAV-QVFRPLDNNDLIVGAVGVLQFDVVVYRL 451
Query: 417 EREYNCPVVL 426
+ EYN
Sbjct: 452 KEEYNVEARY 461
>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 = 150 bits (381), Expect = 2e-42
Identities = 54/124 (43%), Positives = 72/124 (58%), Gaps = 3/124 (2%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
+D ++ ER+RGITI+ AA K INIIDTPGHVDFT E+ R DGAILV+ AV
Sbjct: 41 LDKLKEERERGITIKIAAVSFETKKRLINIIDTPGHVDFTKEMIRGASQADGAILVVDAV 100
Query: 61 GGVQSQTLTVNRQMKRYDVPCIAFINKLDRL-GADPYRVINQMRQKVGHNAAF--LQIPI 117
GV QT K VP I FINK+DR+ A+ V+ ++ +++ F +P+
Sbjct: 101 EGVMPQTREHLLLAKTLGVPIIVFINKIDRVDDAELEEVVEEISRELLEKYGFGGETVPV 160
Query: 118 GLGS 121
GS
Sbjct: 161 VPGS 164
Score = 38.2 bits (90), Expect = 0.005
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 205 TPVLVGTALKNKGVQTLLDAVLDYLP 230
PV+ G+AL +G+ LL+A+ YLP
Sbjct: 158 VPVVPGSALTGEGIDELLEALDLYLP 183
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 155 bits (395), Expect = 6e-41
Identities = 129/455 (28%), Positives = 207/455 (45%), Gaps = 79/455 (17%)
Query: 2 DSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVG 61
D ME+E+QRGI++ S+ ++D IN++DTPGH DF+ + R L +D A++V+ A
Sbjct: 55 DWMEMEKQRGISVTSSVMQFPYRDCLINLLDTPGHEDFSEDTYRTLTAVDSALMVIDAAK 114
Query: 62 GVQSQT---LTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIG 118
GV+ QT + V R R D P FINKLDR G +P +++++ + +G A + PIG
Sbjct: 115 GVEPQTRKLMEVCRL--R-DTPIFTFINKLDRDGREPLELLDEIEEVLGIACAPITWPIG 171
Query: 119 LGSETKGIIDLIQRKAIYFEGPLGDNLRIEEIPADLKKEAESKRQELIEHV-----AEGD 173
+G KG+ DL + ++ QE +E + E D
Sbjct: 172 MGKRFKGVYDLYNDEVELYQ-----------------PGEGHTIQE-VEIIKGLDNPELD 213
Query: 174 EILGEMFLEEKSISEDDI-----------KKAIRRSTLTRKFTPVLVGTALKNKGVQTLL 222
E+LGE E+ +++ +A L + TPV G+AL N GVQ L
Sbjct: 214 ELLGEDLAEQ---LREELELVQGASNEFDLEAF----LAGELTPVFFGSALNNFGVQEFL 266
Query: 223 DAVLDYLPNPGEVTNYAIENGQEDKKVVLNPSRDGKHPFIALAFKLEAG---------KF 273
DA +++ P P Q D++ V P+ + F FK++A F
Sbjct: 267 DAFVEWAPAPQP--------RQTDEREVE-PTEE---KFSGFVFKIQANMDPKHRDRIAF 314
Query: 274 GQLTYMRCYQGKLRKGEMIYNVRTDKKVRVSRLVRLHSNEMEDVEEVLAGDIFALF--GV 331
+R GK KG + +VRT K VR+S + + + E VEE AGDI L G
Sbjct: 315 -----VRVCSGKFEKGMKVRHVRTGKDVRISNALTFMAQDREHVEEAYAGDIIGLHNHGT 369
Query: 332 DCASGDTFVTDKNNSISLESIYVADPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFF 391
GDTF + + I P + ++ N + K + + ++E F
Sbjct: 370 -IQIGDTFTQGEK--LKFTGIPNFAPELFRRVRLKNPLKQKQLQKGLVQLSEEGAV-QVF 425
Query: 392 YDPESKETLVSGMGELHLEIYAQRMEREYNCPVVL 426
++ + ++ +G+L E+ A R++ EYN +
Sbjct: 426 RPLDNNDLILGAVGQLQFEVVAHRLKNEYNVEAIY 460
>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 = 138 bits (350), Expect = 5e-37
Identities = 78/233 (33%), Positives = 123/233 (52%), Gaps = 13/233 (5%)
Query: 2 DSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVG 61
D ME+E+QRGI++ S+ +K IN++DTPGH DF+ + R L +D A++V+ A
Sbjct: 47 DWMEIEKQRGISVTSSVMQFEYKGCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAK 106
Query: 62 GVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLGS 121
GV+ QT + + +P I FINKLDR G DP +++++ ++G + A + PIG+G
Sbjct: 107 GVEPQTRKLFEVCRLRGIPIITFINKLDREGRDPLELLDEIENELGIDCAPMTWPIGMGK 166
Query: 122 ETKGIIDLIQRKAIYFEGPLGDNLRIEEIPADL--KKEAESKRQELIEHVAEGDEILGEM 179
+ KG+ D ++ +E G ++ E L K E ++L E + E E++
Sbjct: 167 DFKGVYDRYDKEIYLYERGAGGAIKAPEETKGLDDPKLDELLGEDLAEQLREELELV--- 223
Query: 180 FLEEKSISEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLDYLPNP 232
+ + K+ L TPV G+AL N GVQ LLDA + P P
Sbjct: 224 ----EGAGPEFDKELFLAGEL----TPVFFGSALNNFGVQELLDAFVKLAPAP 268
>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 = 128 bits (325), Expect = 1e-34
Identities = 45/131 (34%), Positives = 67/131 (51%), Gaps = 5/131 (3%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
+D+++ ER+RGITI++ W IN IDTPGH DF+ E R L DGA+LV+ A
Sbjct: 37 LDTLKEERERGITIKTGVVEFEWPKRRINFIDTPGHEDFSKETVRGLAQADGALLVVDAN 96
Query: 61 GGVQSQTLTVNRQMKRYDVPCIAFINKLDRLG-ADPYRVINQMRQKVGH----NAAFLQI 115
GV+ QT +P I +NK+DR+G D V+ ++++ + +
Sbjct: 97 EGVEPQTREHLNIALAGGLPIIVAVNKIDRVGEEDFDEVLREIKELLKLIGFTFLKGKDV 156
Query: 116 PIGLGSETKGI 126
PI S G
Sbjct: 157 PIIPISALTGE 167
Score = 33.4 bits (77), Expect = 0.18
Identities = 12/30 (40%), Positives = 22/30 (73%)
Query: 203 KFTPVLVGTALKNKGVQTLLDAVLDYLPNP 232
K P++ +AL +G++ LLDA++++LP P
Sbjct: 154 KDVPIIPISALTGEGIEELLDAIVEHLPPP 183
>gnl|CDD|214887 smart00889, EFG_IV, Elongation factor G, domain IV. Translation
elongation factors are responsible for two main
processes during protein synthesis on the ribosome. EF1A
(or EF-Tu) is responsible for the selection and binding
of the cognate aminoacyl-tRNA to the A-site (acceptor
site) of the ribosome. EF2 (or EF-G) is responsible for
the translocation of the peptidyl-tRNA from the A-site
to the P-site (peptidyl-tRNA site) of the ribosome,
thereby freeing the A-site for the next aminoacyl-tRNA
to bind. Elongation factors are responsible for
achieving accuracy of translation and both EF1A and EF2
are remarkably conserved throughout evolution.
Elongation factor EF2 (EF-G) is a G-protein. It brings
about the translocation of peptidyl-tRNA and mRNA
through a ratchet-like mechanism: the binding of GTP-EF2
to the ribosome causes a counter-clockwise rotation in
the small ribosomal subunit; the hydrolysis of GTP to
GDP by EF2 and the subsequent release of EF2 causes a
clockwise rotation of the small subunit back to the
starting position. This twisting action destabilises
tRNA-ribosome interactions, freeing the tRNA to
translocate along the ribosome upon GTP-hydrolysis by
EF2. EF2 binding also affects the entry and exit channel
openings for the mRNA, widening it when bound to enable
the mRNA to translocate along the ribosome. EF2 has five
domains. This entry represents domain IV found in EF2
(or EF-G) of both prokaryotes and eukaryotes. The
EF2-GTP-ribosome complex undergoes extensive structural
rearrangement for tRNA-mRNA movement to occur. Domain
IV, which extends from the 'body' of the EF2 molecule
much like a lever arm, appears to be essential for the
structural transition to take place.
Length = 120
Score = 118 bits (298), Expect = 1e-31
Identities = 50/110 (45%), Positives = 72/110 (65%), Gaps = 3/110 (2%)
Query: 430 KVAFKETLVQPF-DFDYLHKKQSGGSGQYGRVIGTLEPLPPSANTKLEFIDETVGTNVPK 488
+VA++ET+ +P + + HKKQSGG GQY RVI +EPL + EF D VG +PK
Sbjct: 1 QVAYRETITKPVKEAEGKHKKQSGGDGQYARVILEVEPLERGSG--FEFDDTIVGGVIPK 58
Query: 489 PFLPAIIKGFKQMCEKGCLSGSRVAGVRMVLKDGDNHMVDSNEISFILAA 538
++PA+ KGF++ E+G L+G V V++ L DG H VDS+E++F AA
Sbjct: 59 EYIPAVEKGFREALEEGPLAGYPVVDVKVTLLDGSYHEVDSSEMAFKPAA 108
>gnl|CDD|239755 cd04088, EFG_mtEFG_II, EFG_mtEFG_II: this subfamily represents the
domain II of elongation factor G (EF-G) in bacteria and,
the C-terminus of mitochondrial Elongation factor G1
(mtEFG1) and G2 (mtEFG2)_like proteins found in
eukaryotes. During the process of peptide synthesis and
tRNA site changes, the ribosome is moved along the mRNA
a distance equal to one codon with the addition of each
amino acid. In bacteria this translocation step is
catalyzed by EF-G_GTP, which is hydrolyzed to provide
the required energy. Thus, this action releases the
uncharged tRNA from the P site and transfers the newly
formed peptidyl-tRNA from the A site to the P site.
Eukaryotic cells harbor 2 protein synthesis systems: one
localized in the cytoplasm, the other in the
mitochondria. Most factors regulating mitochondrial
protein synthesis are encoded by nuclear genes,
translated in the cytoplasm, and then transported to the
mitochondria. The eukaryotic system of elongation factor
(EF) components is more complex than that in
prokaryotes, with both cytoplasmic and mitochondrial
elongation factors and multiple isoforms being expressed
in certain species. mtEFG1 and mtEFG2 show significant
homology to bacterial EF-Gs. Mutants in yeast mtEFG1
have impaired mitochondrial protein synthesis,
respiratory defects and a tendency to lose mitochondrial
DNA. No clear phenotype has been found for mutants in
the yeast homologue of mtEFG2, MEF2.
Length = 83
Score = 116 bits (292), Expect = 3e-31
Identities = 37/83 (44%), Positives = 51/83 (61%), Gaps = 2/83 (2%)
Query: 261 FIALAFKLEAGKF-GQLTYMRCYQGKLRKGEMIYNVRTDKKVRVSRLVRLHSNEMEDVEE 319
F+AL FK F G+L+++R Y G L+ G +YN KK RV RL+R+H + E+VEE
Sbjct: 1 FVALVFKTIHDPFVGKLSFVRVYSGTLKAGSTLYNSTKGKKERVGRLLRMHGKKQEEVEE 60
Query: 320 VLAGDIFALFGVDC-ASGDTFVT 341
AGDI A+ G+ A+GDT
Sbjct: 61 AGAGDIGAVAGLKDTATGDTLCD 83
>gnl|CDD|202760 pfam03764, EFG_IV, Elongation factor G, domain IV. This domain is
found in elongation factor G, elongation factor 2 and
some tetracycline resistance proteins and adopts a
ribosomal protein S5 domain 2-like fold.
Length = 120
Score = 115 bits (290), Expect = 2e-30
Identities = 52/111 (46%), Positives = 70/111 (63%), Gaps = 4/111 (3%)
Query: 429 PKVAFKETLVQPFD-FDYLHKKQSGGSGQYGRVIGTLEPLPPSANTKLEFIDETVGTNVP 487
P+VA++ET+ + Y KKQSGG GQY +VI +EPLP N EF+DET G P
Sbjct: 1 PQVAYRETIGKDVKERAYKLKKQSGGDGQYAKVILRIEPLPGGGN---EFVDETKGGQYP 57
Query: 488 KPFLPAIIKGFKQMCEKGCLSGSRVAGVRMVLKDGDNHMVDSNEISFILAA 538
F PA+ KGF++ ++G L+G V V++ L DG H VDS+E +FI AA
Sbjct: 58 NEFKPAVEKGFQEAMKEGPLAGEPVRDVKVTLTDGSYHEVDSSEAAFIPAA 108
>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 = 116 bits (294), Expect = 8e-30
Identities = 48/100 (48%), Positives = 64/100 (64%), Gaps = 9/100 (9%)
Query: 1 MDSMELERQRGITIQSAA-----TYTLW----KDHNINIIDTPGHVDFTVEVERALRVLD 51
+D+ E E++RGITI+S+A Y D+ IN+ID+PGHVDF+ EV ALR+ D
Sbjct: 38 LDTREDEQERGITIKSSAISLYFEYEEEKMDGNDYLINLIDSPGHVDFSSEVTAALRLTD 97
Query: 52 GAILVLCAVGGVQSQTLTVNRQMKRYDVPCIAFINKLDRL 91
GA++V+ AV GV QT TV RQ V + INK+DRL
Sbjct: 98 GALVVVDAVEGVCVQTETVLRQALEERVKPVLVINKIDRL 137
>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 = 113 bits (285), Expect = 6e-29
Identities = 47/102 (46%), Positives = 64/102 (62%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
MDS +LER+RGITI + T +KD INIIDTPGH DF EVER L ++DG +L++ A
Sbjct: 40 MDSNDLERERGITILAKNTAITYKDTKINIIDTPGHADFGGEVERVLSMVDGVLLLVDAS 99
Query: 61 GGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQM 102
G QT V ++ + I INK+DR A P V++++
Sbjct: 100 EGPMPQTRFVLKKALEAGLKPIVVINKIDRPDARPEEVVDEV 141
>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 = 104 bits (263), Expect = 4e-26
Identities = 46/107 (42%), Positives = 68/107 (63%), Gaps = 5/107 (4%)
Query: 1 MDSMELERQRGITIQSAA-----TYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAIL 55
+DSM+LER+RGITI++ A +++ +N+IDTPGHVDF+ EV R+L +GA+L
Sbjct: 37 LDSMDLERERGITIKAQAVRLFYKAKDGEEYLLNLIDTPGHVDFSYEVSRSLAACEGALL 96
Query: 56 VLCAVGGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQM 102
V+ A GV++QTL ++ I INK+D ADP RV ++
Sbjct: 97 VVDATQGVEAQTLANFYLALENNLEIIPVINKIDLPAADPDRVKQEI 143
>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 = 110 bits (277), Expect = 2e-25
Identities = 44/101 (43%), Positives = 61/101 (60%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
MDS +LER+RGITI + T + INI+DTPGH DF EVER L ++DG +L++ A
Sbjct: 39 MDSNDLERERGITILAKNTAIRYNGTKINIVDTPGHADFGGEVERVLGMVDGVLLLVDAS 98
Query: 61 GGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQ 101
G QT V ++ + I INK+DR A P V+++
Sbjct: 99 EGPMPQTRFVLKKALELGLKPIVVINKIDRPSARPDEVVDE 139
Score = 75.0 bits (185), Expect = 4e-14
Identities = 61/238 (25%), Positives = 110/238 (46%), Gaps = 55/238 (23%)
Query: 221 LLDAVLDYLPNPGEVTNYAIENGQEDKKVVLNPSRDGKHPFIALAFKLEAGKF-GQLTYM 279
L DA++ ++P P G D+ P L L+ ++ G++
Sbjct: 182 LFDAIVRHVPAP---------KGDLDE------------PLQMLVTNLDYDEYLGRIAIG 220
Query: 280 RCYQGKLRKGEMIYNVRTD---KKVRVSRLVRLHSNEMEDVEEVLAGDIFALFGVDCAS- 335
R ++G ++KG+ + ++ D + R+S+L+ E +++E AGDI A+ G++ +
Sbjct: 221 RVHRGTVKKGQQVALMKRDGTIENGRISKLLGFEGLERVEIDEAGAGDIVAVAGLEDINI 280
Query: 336 GDTFVTDKNNSISLESIYVADPVVSMSIKAVNN--------------KDRDNFSKAVQR- 380
G+T + D +L +I V +P +SM+ +VN+ RD + ++
Sbjct: 281 GET-IADPEVPEALPTITVDEPTLSMTF-SVNDSPLAGKEGKKVTSRHIRDRLMRELETN 338
Query: 381 -FTKEDPTFHFFYDPESKET-LVSGMGELHLEIYAQRMERE-YNCPVVLGKPKVAFKE 435
+ + T ES + VSG GELHL I + M RE + V G+P+V +KE
Sbjct: 339 VALRVEDT-------ESADKFEVSGRGELHLSILIETMRREGFELQV--GRPQVIYKE 387
Score = 30.7 bits (70), Expect = 2.3
Identities = 15/28 (53%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 577 DPESKET-LVSGMGELHLEIYAQRMERE 603
D ES + VSG GELHL I + M RE
Sbjct: 345 DTESADKFEVSGRGELHLSILIETMRRE 372
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 110 bits (276), Expect = 3e-25
Identities = 43/101 (42%), Positives = 61/101 (60%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
MDS +LE++RGITI + T + INI+DTPGH DF EVER L ++DG +L++ A
Sbjct: 43 MDSNDLEKERGITILAKNTAVNYNGTRINIVDTPGHADFGGEVERVLSMVDGVLLLVDAS 102
Query: 61 GGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQ 101
G QT V ++ + I INK+DR A P V+++
Sbjct: 103 EGPMPQTRFVLKKALALGLKPIVVINKIDRPDARPDEVVDE 143
Score = 67.6 bits (166), Expect = 8e-12
Identities = 57/220 (25%), Positives = 99/220 (45%), Gaps = 37/220 (16%)
Query: 248 KVVLNPSRDGKHPFIALAFKLEAGKF-GQLTYMRCYQGKLRKGEMIYNVRTDKKV---RV 303
V P D P +L+ + G++ R ++G ++ + + +++D R+
Sbjct: 192 DHVPAPKGDLDEPLQMQVTQLDYNSYVGRIGIGRIFRGTVKPNQQVALIKSDGTTENGRI 251
Query: 304 SRLVRLHSNEMEDVEEVLAGDIFALFGVDCAS-GDTFVTDKNNSISLESIYVADPVVSMS 362
++L+ E ++EE AGDI A+ G++ + GDT + D +N +L ++ V +P +SM+
Sbjct: 252 TKLLGFLGLERIEIEEAEAGDIVAIAGLEDINIGDT-ICDPDNPEALPALSVDEPTLSMT 310
Query: 363 IKAVNNK-------DRDNFSKAVQRFTKE---------DPTFHFFYDPESKET-LVSGMG 405
+VN+ + R KE + T ES + VSG G
Sbjct: 311 F-SVNDSPFAGKEGKFVTSRQIRDRLNKELETNVALRVEET-------ESPDAFEVSGRG 362
Query: 406 ELHLEIYAQRMERE-YNCPVVLGKPKVAFKE---TLVQPF 441
ELHL I + M RE + V +P+V KE +PF
Sbjct: 363 ELHLSILIENMRREGFELQV--SRPEVIIKEIDGVKCEPF 400
Score = 30.7 bits (70), Expect = 2.7
Identities = 12/19 (63%), Positives = 13/19 (68%)
Query: 585 VSGMGELHLEIYAQRMERE 603
VSG GELHL I + M RE
Sbjct: 358 VSGRGELHLSILIENMRRE 376
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 102 bits (256), Expect = 1e-22
Identities = 48/112 (42%), Positives = 70/112 (62%), Gaps = 5/112 (4%)
Query: 1 MDSMELERQRGITIQSAA---TYTLW--KDHNINIIDTPGHVDFTVEVERALRVLDGAIL 55
+DSM+LER+RGITI++ A Y + + +N+IDTPGHVDF+ EV R+L +GA+L
Sbjct: 44 LDSMDLERERGITIKAQAVRLNYKAKDGETYILNLIDTPGHVDFSYEVSRSLAACEGALL 103
Query: 56 VLCAVGGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVG 107
V+ A GV++QTL D+ I +NK+D ADP RV ++ +G
Sbjct: 104 VVDASQGVEAQTLANVYLALENDLEIIPVLNKIDLPAADPERVKQEIEDVIG 155
Score = 52.0 bits (126), Expect = 7e-07
Identities = 48/176 (27%), Positives = 88/176 (50%), Gaps = 16/176 (9%)
Query: 274 GQLTYMRCYQGKLRKGEMIYNVRTDKKVRVSRLVRLHSNEMEDVEEVLAGDI-FALFGV- 331
G + +R G L+KG+ I + T K+ V V + + +M V+E+ AG++ + + G+
Sbjct: 208 GVVVLVRVVDGTLKKGDKIKMMSTGKEYEVDE-VGVFTPKMVPVDELSAGEVGYIIAGIK 266
Query: 332 ---DCASGDTFVTDKNNSIS--LESIYVADPVVSMSIKAVNNKDRDNFSKAVQRFTKEDP 386
D GDT +T N L P+V + V++ D ++ A+++ D
Sbjct: 267 DVRDARVGDT-ITLAKNPAEEPLPGFKEVKPMVFAGLYPVDSDDYEDLRDALEKLQLNDA 325
Query: 387 TFHFFYDPESKETLVSG-----MGELHLEIYAQRMEREYNCPVVLGKPKVAFKETL 437
+ Y+PE+ + L G +G LH+EI +R+ERE++ ++ P V ++ TL
Sbjct: 326 SL--TYEPETSQALGFGFRCGFLGLLHMEIIQERLEREFDLDLITTAPSVVYEVTL 379
Score = 35.8 bits (84), Expect = 0.068
Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 7/70 (10%)
Query: 541 PVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSG-----MGELHLEI 595
P+V + V++ D ++ A+++ D + Y+PE+ + L G +G LH+EI
Sbjct: 296 PMVFAGLYPVDSDDYEDLRDALEKLQLNDASL--TYEPETSQALGFGFRCGFLGLLHMEI 353
Query: 596 YAQRMEREYN 605
+R+ERE++
Sbjct: 354 IQERLEREFD 363
>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 = 100 bits (251), Expect = 3e-22
Identities = 48/116 (41%), Positives = 74/116 (63%), Gaps = 5/116 (4%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHN-----INIIDTPGHVDFTVEVERALRVLDGAIL 55
+DSM+LER+RGITI++ A +K + +N+IDTPGHVDF+ EV R+L +GA+L
Sbjct: 40 LDSMDLERERGITIKAQAVRLNYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALL 99
Query: 56 VLCAVGGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAA 111
++ A G+++QTL D+ I INK+D ADP RV ++ + +G +A+
Sbjct: 100 LVDAAQGIEAQTLANVYLALENDLEIIPVINKIDLPSADPERVKKEIEEVIGLDAS 155
Score = 65.8 bits (161), Expect = 3e-11
Identities = 53/230 (23%), Positives = 103/230 (44%), Gaps = 36/230 (15%)
Query: 217 GVQTLLDAVLDYLPNPGEVTNYAIENGQEDKKVVLNPSRDGKHPFIALAFKLEAGKF-GQ 275
G++ +L+A++ +P P D P AL F + G
Sbjct: 167 GIEEILEAIVKRVPPP---------------------KGDPDAPLKALIFDSHYDNYRGV 205
Query: 276 LTYMRCYQGKLRKGEMIYNVRTDKKVRVSRLVRLHSNEMEDVEEVLAGDI-FALFGV--- 331
+ +R ++G ++ G+ I + T K+ V V + + ++ +E+ AG++ + + G+
Sbjct: 206 VALVRVFEGTIKPGDKIRFMSTGKEYEVDE-VGVFTPKLTKTDELSAGEVGYIIAGIKDV 264
Query: 332 -DCASGDTFVTDKNNSIS-LESIYVADPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFH 389
D GDT KN + L P+V + ++ +D ++ A+++ D +
Sbjct: 265 SDVRVGDTITHVKNPAKEPLPGFKEVKPMVFAGLYPIDTEDYEDLRDALEKLKLNDASL- 323
Query: 390 FFYDPESKETLVSG-----MGELHLEIYAQRMEREYNCPVVLGKPKVAFK 434
Y+PES L G +G LH+EI +R+ERE+N ++ P V ++
Sbjct: 324 -TYEPESSPALGFGFRCGFLGLLHMEIIQERLEREFNLDLITTAPSVIYR 372
Score = 40.8 bits (96), Expect = 0.002
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 7/75 (9%)
Query: 541 PVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSG-----MGELHLEI 595
P+V + ++ +D ++ A+++ D + Y+PES L G +G LH+EI
Sbjct: 292 PMVFAGLYPIDTEDYEDLRDALEKLKLNDASL--TYEPESSPALGFGFRCGFLGLLHMEI 349
Query: 596 YAQRMEREYNCPVVL 610
+R+ERE+N ++
Sbjct: 350 IQERLEREFNLDLIT 364
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 100 bits (251), Expect = 4e-22
Identities = 46/112 (41%), Positives = 70/112 (62%), Gaps = 5/112 (4%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHN-----INIIDTPGHVDFTVEVERALRVLDGAIL 55
+DSM++ER+RGITI++ A +K + +N+IDTPGHVDF+ EV R+L +GA+L
Sbjct: 46 LDSMDIERERGITIKAQAVRLNYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALL 105
Query: 56 VLCAVGGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVG 107
V+ A GV++QTL ++ I +NK+D ADP RV ++ +G
Sbjct: 106 VVDASQGVEAQTLANVYLALENNLEIIPVLNKIDLPAADPERVKQEIEDIIG 157
Score = 62.2 bits (152), Expect = 5e-10
Identities = 57/230 (24%), Positives = 106/230 (46%), Gaps = 36/230 (15%)
Query: 217 GVQTLLDAVLDYLPNPGEVTNYAIENGQEDKKVVLNPSRDGKHPFIALAFKLEAGKF-GQ 275
G++ +L+A+++ +P P G D P AL F + G
Sbjct: 173 GIEDVLEAIVEKIPPP---------KGDPDA------------PLKALIFDSWYDNYLGV 211
Query: 276 LTYMRCYQGKLRKGEMIYNVRTDKKVRVSRLVRLHSNEMEDVEEVLAGDI-FALFGV--- 331
+ +R + G L+KG+ I + T K+ V V + + +M V+E+ AG++ + + G+
Sbjct: 212 VVLVRIFDGTLKKGDKIRMMSTGKEYEVDE-VGIFTPKMVKVDELKAGEVGYIIAGIKDV 270
Query: 332 -DCASGDTFVTDKNNSIS-LESIYVADPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFH 389
D GDT N + L P+V + V++ D ++ A+++ D +
Sbjct: 271 RDARVGDTITLASNPATEPLPGFKEVKPMVFAGLYPVDSDDYEDLRDALEKLQLNDASL- 329
Query: 390 FFYDPESKETLVSG-----MGELHLEIYAQRMEREYNCPVVLGKPKVAFK 434
Y+PE+ + L G +G LH+EI +R+ERE++ ++ P V +K
Sbjct: 330 -TYEPETSQALGFGFRCGFLGLLHMEIIQERLEREFDLDLITTAPSVVYK 378
Score = 38.7 bits (91), Expect = 0.008
Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 7/70 (10%)
Query: 541 PVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSG-----MGELHLEI 595
P+V + V++ D ++ A+++ D + Y+PE+ + L G +G LH+EI
Sbjct: 298 PMVFAGLYPVDSDDYEDLRDALEKLQLNDASL--TYEPETSQALGFGFRCGFLGLLHMEI 355
Query: 596 YAQRMEREYN 605
+R+ERE++
Sbjct: 356 IQERLEREFD 365
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 89.0 bits (220), Expect = 2e-18
Identities = 47/102 (46%), Positives = 65/102 (63%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
MDS +LE++RGITI + T W D+ INI+DTPGH DF EVER + ++D +LV+ A
Sbjct: 43 MDSNDLEKERGITILAKNTAIKWNDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAF 102
Query: 61 GGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQM 102
G QT V ++ Y + I INK+DR GA P V++Q+
Sbjct: 103 DGPMPQTRFVTKKAFAYGLKPIVVINKVDRPGARPDWVVDQV 144
Score = 43.5 bits (102), Expect = 3e-04
Identities = 41/168 (24%), Positives = 78/168 (46%), Gaps = 13/168 (7%)
Query: 280 RCYQGKLRKGEMIYNVRTDKKVRVSRLVRLHSN---EMEDVEEVLAGDIFALFGVDCASG 336
R +GK++ + + + ++ K R +++ ++ + E + + AGDI A+ G+ +
Sbjct: 225 RIKRGKVKPNQQVTIIDSEGKTRNAKVGKVLGHLGLERIETDLAEAGDIVAITGLGELNI 284
Query: 337 DTFVTDKNNSISLESIYVADPVVSM----SIKAVNNKDRDNFS--KAVQRFTKE---DPT 387
V D N +L ++ V +P VSM + K+ + + + R KE +
Sbjct: 285 SDTVCDTQNVEALPALSVDEPTVSMFFCVNTSPFCGKEGKFVTSRQILDRLNKELVHNVA 344
Query: 388 FHFFYDPESKETLVSGMGELHLEIYAQRMEREYNCPVVLGKPKVAFKE 435
++ VSG GELHL + + M RE + + +PKV F+E
Sbjct: 345 LRVEETEDADAFRVSGRGELHLSVLIENMRRE-GFELAVSRPKVIFRE 391
>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 = 82.7 bits (205), Expect = 5e-18
Identities = 40/96 (41%), Positives = 58/96 (60%), Gaps = 5/96 (5%)
Query: 1 MDSMELERQRGITIQS-----AATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAIL 55
D+ + E++RGI+I+S + K + INIIDTPGHV+F EV ALR+ DG +L
Sbjct: 41 TDTRKDEQERGISIKSNPISLVLEDSKGKSYLINIIDTPGHVNFMDEVAAALRLCDGVVL 100
Query: 56 VLCAVGGVQSQTLTVNRQMKRYDVPCIAFINKLDRL 91
V+ V G+ S T + R + +P + INK+DRL
Sbjct: 101 VVDVVEGLTSVTERLIRHAIQEGLPMVLVINKIDRL 136
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 86.3 bits (214), Expect = 2e-17
Identities = 44/101 (43%), Positives = 60/101 (59%), Gaps = 10/101 (9%)
Query: 1 MDSMELERQRGITIQSAAT-----YTLWKDHN-----INIIDTPGHVDFTVEVERALRVL 50
D+ E++RGITI+S + L + IN+ID+PGHVDF+ EV ALRV
Sbjct: 57 TDTRADEQERGITIKSTGISLYYEHDLEDGDDKQPFLINLIDSPGHVDFSSEVTAALRVT 116
Query: 51 DGAILVLCAVGGVQSQTLTVNRQMKRYDVPCIAFINKLDRL 91
DGA++V+ V GV QT TV RQ + + + FINK+DR
Sbjct: 117 DGALVVVDCVEGVCVQTETVLRQALQERIRPVLFINKVDRA 157
Score = 69.3 bits (170), Expect = 3e-12
Identities = 72/280 (25%), Positives = 125/280 (44%), Gaps = 49/280 (17%)
Query: 220 TLLDAVLDYLPNPGEVTNYAIEN----GQEDKKVVLNPSRDGKHPFIALAFKL----EAG 271
TLL+ ++D+LP+P E Y +EN +D+ + D P + K+ + G
Sbjct: 327 TLLEMIVDHLPSPKEAQKYRVENLYEGPMDDEAANAIRNCDPNGPLMMYISKMVPTSDKG 386
Query: 272 KFGQLTYMRCYQGKLRKGEMIYNVRTDKKVR------------------VSRLVRLHSNE 313
+F + R + G V T +KVR + R V +
Sbjct: 387 RF--YAFGRVFSGT---------VATGQKVRIQGPNYVPGKKEDLFEKNIQRTVLMMGRY 435
Query: 314 MEDVEEVLAGDIFALFGVDCA---SGDTFVTDKNNSISLESI-YVADPVVSMSIKAVNNK 369
+E +E+V G+ L GVD SG +T + ++ + Y PVV ++++ N K
Sbjct: 436 VEQIEDVPCGNTVGLVGVDQYLVKSGT--ITTSETAHNIRDMKYSVSPVVRVAVEPKNPK 493
Query: 370 DRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEIYAQRMEREY-NCPVVLGK 428
D + ++R K DP + ES E +V+G GELH+EI + +E +Y N +++
Sbjct: 494 DLPKLVEGLKRLAKSDPLVVCTTE-ESGEHIVAGCGELHVEICLKDLEDDYANIDIIVSD 552
Query: 429 PKVAFKETLVQPFDFDYLHKKQSGGSGQYGRVIGTLEPLP 468
P V+++ET+ + L K + ++ R+ EPL
Sbjct: 553 PVVSYRETVTEESSQTCLSKSPN----KHNRLYMKAEPLT 588
Score = 44.7 bits (106), Expect = 2e-04
Identities = 30/97 (30%), Positives = 50/97 (51%), Gaps = 11/97 (11%)
Query: 523 DNHMVDSNEISFILAAHD---------PVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFH 573
D ++V S I+ AH+ PVV ++++ N KD + ++R K DP
Sbjct: 454 DQYLVKSGTITTSETAHNIRDMKYSVSPVVRVAVEPKNPKDLPKLVEGLKRLAKSDPLVV 513
Query: 574 FFYDPESKETLVSGMGELHLEIYAQRMEREY-NCPVV 609
+ ES E +V+G GELH+EI + +E +Y N ++
Sbjct: 514 CTTE-ESGEHIVAGCGELHVEICLKDLEDDYANIDII 549
>gnl|CDD|239759 cd04092, mtEFG2_II_like, mtEFG2_C: C-terminus of mitochondrial
Elongation factor G2 (mtEFG2)-like proteins found in
eukaryotes. Eukaryotic cells harbor 2 protein synthesis
systems: one localized in the cytoplasm, the other in
the mitochondria. Most factors regulating mitochondrial
protein synthesis are encoded by nuclear genes,
translated in the cytoplasm, and then transported to the
mitochondria. The eukaryotic system of elongation factor
(EF) components is more complex than that in
prokaryotes, with both cytoplasmic and mitochondrial
elongation factors and multiple isoforms being expressed
in certain species. Eukaryotic EF-2 operates in the
cytosolic protein synthesis machinery of eukaryotes,
EF-Gs in protein synthesis in bacteria. Eukaryotic
mtEFG1 proteins show significant homology to bacterial
EF-Gs. No clear phenotype has been found for mutants in
the yeast homologue of mtEFG2, MEF2. There are two
forms of mtEFG present in mammals (designated mtEFG1s
and mtEFG2s) mtEFG1s are not present in this group.
Length = 83
Score = 73.1 bits (180), Expect = 5e-16
Identities = 31/83 (37%), Positives = 51/83 (61%), Gaps = 2/83 (2%)
Query: 261 FIALAFKLEAGKF-GQLTYMRCYQGKLRKGEMIYNVRTDKKVRVSRLVRLHSNEMEDVEE 319
ALAFK+ G LT++R Y G L++G +YN T KK R+SRL++ +++ +++
Sbjct: 1 LCALAFKVVHDPQRGPLTFVRVYSGTLKRGSALYNTNTGKKERISRLLQPFADQYQEIPS 60
Query: 320 VLAGDIFALFGV-DCASGDTFVT 341
+ AG+I + G+ +GDT VT
Sbjct: 61 LSAGNIGVITGLKQTRTGDTLVT 83
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 75.5 bits (186), Expect = 3e-14
Identities = 41/106 (38%), Positives = 58/106 (54%), Gaps = 16/106 (15%)
Query: 1 MDSMELERQRGITIQSAA-------------TYTLWKDHN---INIIDTPGHVDFTVEVE 44
D+ E +RGITI+S + +D N IN+ID+PGHVDF+ EV
Sbjct: 57 TDTRADEAERGITIKSTGISLYYEMTDESLKDFKGERDGNEYLINLIDSPGHVDFSSEVT 116
Query: 45 RALRVLDGAILVLCAVGGVQSQTLTVNRQMKRYDVPCIAFINKLDR 90
ALR+ DGA++V+ + GV QT TV RQ + + +NK+DR
Sbjct: 117 AALRITDGALVVVDCIEGVCVQTETVLRQALGERIRPVLTVNKMDR 162
Score = 61.3 bits (149), Expect = 1e-09
Identities = 75/274 (27%), Positives = 118/274 (43%), Gaps = 63/274 (22%)
Query: 208 LVGTALKNKGVQTLL---DAVLD----YLPNPGEVTNYAIENGQE----DKKVVLNPSRD 256
L+G AL + +QT L DA+L+ +LP+P + Y +EN E DK + D
Sbjct: 312 LMGKALMKRVMQTWLPASDALLEMIIFHLPSPAKAQRYRVENLYEGPLDDKYATAIRNCD 371
Query: 257 GKHPFIALAFKL----EAGKFGQLTYMRCYQGKLRKGEMIYNVRTDKKVR---------- 302
P + K+ + G+F + R + G V T KVR
Sbjct: 372 PNGPLMLYVSKMIPASDKGRF--FAFGRVFSGT---------VATGMKVRIMGPNYVPGE 420
Query: 303 --------VSRLVRLHSNEMEDVEEVLAGDIFALFGVDCASGDTFVTDKNNSISLESIYV 354
V R V + E VE+V G+ A+ G+D F+T KN +++ E
Sbjct: 421 KKDLYVKSVQRTVIWMGKKQESVEDVPCGNTVAMVGLD-----QFIT-KNATLTNEKEVD 474
Query: 355 ADPVVSMSI-------KAVNNKDRDNFSKAVQ---RFTKEDPTFHFFYDPESKETLVSGM 404
A P+ +M AV K+ + K V+ R K DP + ES E +++G
Sbjct: 475 AHPIKAMKFSVSPVVRVAVQCKNASDLPKLVEGLKRLAKSDPMVQCTIE-ESGEHIIAGA 533
Query: 405 GELHLEIYAQRMEREY--NCPVVLGKPKVAFKET 436
GELHLEI + ++ ++ + + P V+F+ET
Sbjct: 534 GELHLEICLKDLQDDFMGGAEIKVSDPVVSFRET 567
Score = 37.8 bits (88), Expect = 0.018
Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 541 PVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMGELHLEI 595
PVV ++++ N D + ++R K DP + ES E +++G GELHLEI
Sbjct: 487 PVVRVAVQCKNASDLPKLVEGLKRLAKSDPMVQCTIE-ESGEHIIAGAGELHLEI 540
>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 = 69.4 bits (170), Expect = 3e-12
Identities = 35/96 (36%), Positives = 49/96 (51%), Gaps = 3/96 (3%)
Query: 11 GITIQSAATYTLWKDHN--INIIDTPGHVDFTVEVERALRVLDGAILVLCAVGGVQSQTL 68
GIT Q Y + + I +DTPGH FT R +V D +LV+ A GV QT+
Sbjct: 119 GIT-QHIGAYHVENEDGKMITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQTI 177
Query: 69 TVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQ 104
K +VP I INK+D+ A+P RV ++ +
Sbjct: 178 EAISHAKAANVPIIVAINKIDKPEANPDRVKQELSE 213
>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 = 64.0 bits (157), Expect = 5e-12
Identities = 39/98 (39%), Positives = 46/98 (46%), Gaps = 5/98 (5%)
Query: 10 RGITIQSAATYTLWKDHN--INIIDTPGHVDFTVEVERALRVLDGAILVLCAVGGVQSQT 67
GIT A I IDTPGH FT R V D AILV+ A GV QT
Sbjct: 31 GGITQHIGAYQVPIDVKIPGITFIDTPGHEAFTNMRARGASVTDIAILVVAADDGVMPQT 90
Query: 68 LTVNRQMKRYDVPCIAFINKLDRL---GADPYRVINQM 102
+ K +VP I INK+D+ ADP RV N++
Sbjct: 91 IEAINHAKAANVPIIVAINKIDKPYGTEADPERVKNEL 128
>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 = 59.6 bits (145), Expect = 2e-11
Identities = 23/70 (32%), Positives = 30/70 (42%), Gaps = 3/70 (4%)
Query: 274 GQLTYMRCYQGKLRKGEMIYNV--RTDKKVRVSRLVRLHSNEMEDVEEVLAGDIFALFGV 331
G + R G L+KG+ + T KK RV+ L H + E V AG I A G+
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGIGL 60
Query: 332 DCAS-GDTFV 340
GDT
Sbjct: 61 KDIKRGDTLT 70
>gnl|CDD|238838 cd01680, EFG_like_IV, Elongation Factor G-like domain IV. This
family includes the translational elongation factor
termed EF-2 (for Archaea and Eukarya) and EF-G (for
Bacteria), ribosomal protection proteins that mediate
tetracycline resistance and, an evolutionarily conserved
U5 snRNP-specific protein (U5-116kD). In complex with
GTP, EF-G/EF-2 promotes the translocation step of
translation. During translocation the peptidyl-tRNA is
moved from the A site to the P site of the small subunit
of ribosome and the mRNA is shifted one codon relative
to the ribosome. It has been shown that EF-G/EF-2_IV
domain mimics the shape of anticodon arm of the tRNA in
the structurally homologous ternary complex of Petra,
EF-Tu (another transcriptional elongation factor) and
GTP analog. The tip portion of this domain is found in a
position that overlaps the anticodon arm of the A-site
tRNA, implying that EF-G/EF-2 displaces the A-site tRNA
to the P-site by physical interaction with the anticodon
arm.
Length = 116
Score = 58.0 bits (141), Expect = 2e-10
Identities = 32/122 (26%), Positives = 52/122 (42%), Gaps = 12/122 (9%)
Query: 433 FKETLVQP----FDFDYLHKKQSGGSGQYGRVIGTLEPLP-PSANTKLEFIDETVGTNVP 487
++ET+ + +F+ ++ GG Q+G V +EPL S +D +P
Sbjct: 1 YRETIRKSVEATGEFE----RELGGKPQFGEVTLRVEPLERGSGV---RVVDPVDEELLP 53
Query: 488 KPFLPAIIKGFKQMCEKGCLSGSRVAGVRMVLKDGDNHMVDSNEISFILAAHDPVVSMSI 547
A+ +G + C G L+G + VR+ + D H S E F AA S +
Sbjct: 54 AELKEAVEEGIRDACASGPLTGYPLTDVRVTVLDVPYHEGVSTEAGFRAAAGRAFESAAQ 113
Query: 548 KA 549
KA
Sbjct: 114 KA 115
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 62.2 bits (152), Expect = 4e-10
Identities = 36/98 (36%), Positives = 47/98 (47%), Gaps = 3/98 (3%)
Query: 11 GITIQSAATYTLW---KDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVGGVQSQT 67
GIT A K I IDTPGH FT R V D AILV+ A GV QT
Sbjct: 37 GITQHIGAYQVPLDVIKIPGITFIDTPGHEAFTAMRARGASVTDIAILVVAADDGVMPQT 96
Query: 68 LTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQK 105
+ K VP + INK+D+ A+P +V ++++
Sbjct: 97 IEAINHAKAAGVPIVVAINKIDKPEANPDKVKQELQEY 134
>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 = 57.0 bits (138), Expect = 1e-09
Identities = 26/101 (25%), Positives = 37/101 (36%), Gaps = 20/101 (19%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDF-------TVEVERALRVLDGA 53
+ + G T + N++DT G D+ VE +LRV D
Sbjct: 38 NYVTTVIEEDGKTYK------------FNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIV 85
Query: 54 ILVLCAVGGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGAD 94
ILVL ++ QT + VP I NK+D A
Sbjct: 86 ILVLDVEEILEKQTKEIIHH-AESGVPIILVGNKIDLRDAK 125
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 57.9 bits (140), Expect = 1e-08
Identities = 40/117 (34%), Positives = 58/117 (49%), Gaps = 11/117 (9%)
Query: 11 GITIQSAATYTLW--KDHNINII--DTPGHVDFTVEVERALRVLDGAILVLCAVGGVQSQ 66
GIT + A + KD N I+ DTPGH F+ R V D AIL++ A GV+ Q
Sbjct: 276 GITQKIGAYEVEFEYKDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQ 335
Query: 67 TLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLGSET 123
T+ ++ +VP I INK+D+ A+ R+ Q+ A + IP G +T
Sbjct: 336 TIEAINYIQAANVPIIVAINKIDKANANTERIKQQL-------AKYNLIPEKWGGDT 385
>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 = 49.6 bits (119), Expect = 8e-08
Identities = 24/87 (27%), Positives = 34/87 (39%), Gaps = 10/87 (11%)
Query: 261 FIALAFKLEA-GKFGQLTYMRCYQGKLRKGEMIYNVRTD--KKVRVSRLVRLHSNEMEDV 317
AL FK+ G + R G L+KG+ + K +V L R +V
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRFK----GEV 56
Query: 318 EEVLAGDIFALFGV---DCASGDTFVT 341
+E +AGDI + D GDT
Sbjct: 57 DEAVAGDIVGIVLKDKDDIKIGDTLTD 83
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 52.2 bits (126), Expect = 7e-07
Identities = 37/97 (38%), Positives = 47/97 (48%), Gaps = 12/97 (12%)
Query: 11 GITIQSAATYTL-WKDHNINIIDTPGHVDFTVEVERALR-----VLDGAILVLCAVGGVQ 64
GIT Q Y + I +DTPGH FT A+R V D +LV+ A GV
Sbjct: 281 GIT-QHIGAYQVETNGGKITFLDTPGHEAFT-----AMRARGAQVTDIVVLVVAADDGVM 334
Query: 65 SQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQ 101
QT+ K VP I INK+D+ GA+P RV +
Sbjct: 335 PQTIEAINHAKAAGVPIIVAINKIDKPGANPDRVKQE 371
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 51.2 bits (123), Expect = 1e-06
Identities = 37/131 (28%), Positives = 57/131 (43%), Gaps = 6/131 (4%)
Query: 2 DSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVG 61
D + E++RGITI Y +D + ID PGH DF + L +D A+LV+ A
Sbjct: 26 DRLPEEKKRGITIDLGFYYRKLEDGVMGFIDVPGHPDFISNLLAGLGGIDYALLVVAADE 85
Query: 62 GVQSQTLTVNRQMKRYDVPCIAF-INKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLG 120
G+ +QT + + + K DR D R I Q +++ + + I
Sbjct: 86 GLMAQTGEHLLILDLLGIKNGIIVLTKADR--VDEAR-IEQKIKQILADLSLANAKIFKT 142
Query: 121 SETK--GIIDL 129
S GI +L
Sbjct: 143 SAKTGRGIEEL 153
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 50.8 bits (122), Expect = 1e-06
Identities = 25/75 (33%), Positives = 35/75 (46%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
+D + ER+RG+TI A + +N IID PGH DF + D A+LV+ A
Sbjct: 60 LDKTKEERERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDAR 119
Query: 61 GGVQSQTLTVNRQMK 75
G V Q +
Sbjct: 120 DGEFEAGFGVGGQTR 134
>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 = 47.1 bits (112), Expect = 3e-06
Identities = 18/93 (19%), Positives = 37/93 (39%), Gaps = 7/93 (7%)
Query: 24 KDHNINIIDTPGHVDFTV-----EVERALRVLDGAILVLCAVGG--VQSQTLTVNRQMKR 76
+ ++DTPG +F LR D +LV+ + + L + R++++
Sbjct: 45 GKVKLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRK 104
Query: 77 YDVPCIAFINKLDRLGADPYRVINQMRQKVGHN 109
+P I NK+D L + ++ +
Sbjct: 105 EGIPIILVGNKIDLLEEREVEELLRLEELAKIL 137
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 48.4 bits (116), Expect = 7e-06
Identities = 37/118 (31%), Positives = 55/118 (46%), Gaps = 20/118 (16%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCA- 59
MD ++ ER+RG+TI A + I+D PGH DF + D A+LV+ A
Sbjct: 59 MDRLKEERERGVTIDLAHKKFETDKYYFTIVDCPGHRDFVKNMITGASQADAAVLVVAAD 118
Query: 60 -VGGVQSQ---------TLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVG 107
GGV Q TL +N Q+ I INK+D + D R +++++V
Sbjct: 119 DAGGVMPQTREHVFLARTLGIN-QL-------IVAINKMDAVNYDEKR-YEEVKEEVS 167
>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 = 46.8 bits (112), Expect = 7e-06
Identities = 34/88 (38%), Positives = 45/88 (51%), Gaps = 9/88 (10%)
Query: 7 ERQRGITIQSA-ATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVGGVQS 65
E+ RGITI +A Y H ++ D PGH D+ + +DGAILV+ A G
Sbjct: 46 EKARGITINTAHVEYETANRHYAHV-DCPGHADYIKNMITGAAQMDGAILVVSATDGPMP 104
Query: 66 QT---LTVNRQMKRYDVPCIA-FINKLD 89
QT L + RQ+ VP I F+NK D
Sbjct: 105 QTREHLLLARQV---GVPYIVVFLNKAD 129
Score = 28.3 bits (64), Expect = 8.0
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 10/38 (26%)
Query: 205 TPVLVGTALK-------NKGVQ---TLLDAVLDYLPNP 232
TP++ G+ALK NK V LLDA+ Y+P P
Sbjct: 158 TPIVRGSALKALEGDDPNKWVDKILELLDALDSYIPTP 195
>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 = 48.7 bits (116), Expect = 8e-06
Identities = 28/85 (32%), Positives = 39/85 (45%), Gaps = 1/85 (1%)
Query: 7 ERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVGGVQSQ 66
E++RG+TI Y D+ + ID PGH F +D A+LV+ A GV +Q
Sbjct: 31 EKKRGMTIDLGFAYFPLPDYRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVMTQ 90
Query: 67 TLTVNRQMKRYDVPC-IAFINKLDR 90
T + +P I I K DR
Sbjct: 91 TGEHLAVLDLLGIPHTIVVITKADR 115
>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 = 46.8 bits (112), Expect = 9e-06
Identities = 25/67 (37%), Positives = 34/67 (50%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
+D ++ ER++GITI A Y I DTPGH +T + D AIL++ A
Sbjct: 53 VDGLQAEREQGITIDVAYRYFSTPKRKFIIADTPGHEQYTRNMVTGASTADLAILLVDAR 112
Query: 61 GGVQSQT 67
GV QT
Sbjct: 113 KGVLEQT 119
>gnl|CDD|239662 cd03691, BipA_TypA_II, BipA_TypA_II: domain II of BipA (also called
TypA) having homology to domain II of the elongation
factors (EFs) EF-G and EF-Tu. BipA is a highly
conserved protein with global regulatory properties in
Escherichia coli. BipA is phosphorylated on a tyrosine
residue under some cellular conditions. Mutants show
altered regulation of some pathways. BipA functions as a
translation factor that is required specifically for the
expression of the transcriptional modulator Fis. BipA
binds to ribosomes at a site that coincides with that of
EF-G and has a GTPase activity that is sensitive to high
GDP:GTP ratios and, is stimulated by 70S ribosomes
programmed with mRNA and aminoacylated tRNAs. The growth
rate-dependent induction of BipA allows the efficient
expression of Fis, thereby modulating a range of
downstream processes, including DNA metabolism and type
III secretion.
Length = 86
Score = 42.9 bits (102), Expect = 2e-05
Identities = 20/67 (29%), Positives = 39/67 (58%), Gaps = 5/67 (7%)
Query: 280 RCYQGKLRKGEMIYNVRTDKKV---RVSRLVRLHSNEMEDVEEVLAGDIFALFGVDCAS- 335
R ++G ++ G+ + V+ D K+ ++++L + +VEE AGDI A+ G++ +
Sbjct: 21 RIFRGTVKVGQQVAVVKRDGKIEKAKITKLFGFEGLKRVEVEEAEAGDIVAIAGIEDITI 80
Query: 336 GDTFVTD 342
GDT + D
Sbjct: 81 GDT-ICD 86
>gnl|CDD|239660 cd03689, RF3_II, RF3_II: this subfamily represents the domain II of
bacterial Release Factor 3 (RF3). Termination of protein
synthesis by the ribosome requires two release factor
(RF) classes. The class II RF3 is a GTPase that removes
class I RFs (RF1 or RF2) from the ribosome after release
of the nascent polypeptide. RF3 in the GDP state binds
to the ribosomal class I RF complex, followed by an
exchange of GDP for GTP and release of the class I RF.
Sequence comparison of class II release factors with
elongation factors shows that prokaryotic RF3 is more
similar to EF-G whereas eukaryotic eRF3 is more similar
to eEF1A, implying that their precise function may
differ.
Length = 85
Score = 42.6 bits (101), Expect = 2e-05
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 3/67 (4%)
Query: 278 YMRCYQGKLRKGEMIYNVRTDKKVRVSRLVRLHSNEMEDVEEVLAGDIFALF--GVDCAS 335
++R GK +G + +VR K+VR+S + + + E V+E GDI L G
Sbjct: 20 FVRVCSGKFERGMKVKHVRLGKEVRLSNPQQFFAQDRETVDEAYPGDIIGLVNPGN-FQI 78
Query: 336 GDTFVTD 342
GDT
Sbjct: 79 GDTLTEG 85
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 46.5 bits (111), Expect = 2e-05
Identities = 33/88 (37%), Positives = 44/88 (50%), Gaps = 9/88 (10%)
Query: 7 ERQRGITIQSA-ATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVGGVQS 65
E+ RGITI +A Y H +D PGH D+ + +DGAILV+ A G
Sbjct: 56 EKARGITINTAHVEYETANRH-YAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMP 114
Query: 66 QT---LTVNRQMKRYDVPCI-AFINKLD 89
QT + + RQ VP I F+NK+D
Sbjct: 115 QTREHILLARQ---VGVPYIVVFLNKVD 139
>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 = 44.5 bits (106), Expect = 3e-05
Identities = 26/105 (24%), Positives = 42/105 (40%), Gaps = 4/105 (3%)
Query: 2 DSMELERQRGITIQSAATYT-LWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
D + E++RGITI Y L + ID PGH F + +D +LV+ A
Sbjct: 25 DRLPEEKKRGITIDLGFAYLDLPDGKRLGFIDVPGHEKFVKNMLAGAGGIDAVLLVVAAD 84
Query: 61 GGVQSQTLTVNRQMKRYDVP-CIAFINKLDRLGADPYRVINQMRQ 104
G+ QT ++ + + + K D D R+ +
Sbjct: 85 EGIMPQTREHLEILELLGIKKGLVVLTKADL--VDEDRLELVEEE 127
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 45.8 bits (108), Expect = 6e-05
Identities = 30/92 (32%), Positives = 46/92 (50%), Gaps = 1/92 (1%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
+D+ ER RGITI +A ++ + +D PGH D+ + +DGAILV+
Sbjct: 119 IDAAPEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGA 178
Query: 61 GGVQSQTLTVNRQMKRYDVP-CIAFINKLDRL 91
G QT K+ VP + F+NK D++
Sbjct: 179 DGPMPQTKEHILLAKQVGVPNMVVFLNKQDQV 210
>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 = 45.2 bits (107), Expect = 7e-05
Identities = 34/94 (36%), Positives = 48/94 (51%), Gaps = 9/94 (9%)
Query: 1 MDSMELERQRGITIQSA-ATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCA 59
+D+ E+ RGITI +A Y H ++ D PGH D+ + +DGAILV+ A
Sbjct: 50 IDNAPEEKARGITINTAHVEYETENRHYAHV-DCPGHADYVKNMITGAAQMDGAILVVSA 108
Query: 60 VGGVQSQT---LTVNRQMKRYDVPCI-AFINKLD 89
G QT + + RQ+ VP I F+NK D
Sbjct: 109 TDGPMPQTREHILLARQV---GVPYIVVFLNKCD 139
>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 = 43.6 bits (104), Expect = 9e-05
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDF 39
+D ++ ER+RG+TI + + IID PGH DF
Sbjct: 52 LDKLKEERERGVTIDVGLAKFETEKYRFTIIDAPGHRDF 90
>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 = 44.5 bits (105), Expect = 1e-04
Identities = 39/131 (29%), Positives = 58/131 (44%), Gaps = 34/131 (25%)
Query: 1 MDSMELERQRGITIQSAATYTLWK----DHNINIIDTPGHVDFTVEVERALRVLDGAILV 56
MD ++ ER+RG+TI A WK + + I+D PGH DF + D A+LV
Sbjct: 60 MDRLKEERERGVTIDVA----HWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLV 115
Query: 57 LCAVGG---VQSQ---------TLTVNRQMKRYDVPCIAFINKLDRLGADPYR------V 98
+ G VQ Q TL +N+ I INK+D + D
Sbjct: 116 VAVGDGEFEVQPQTREHAFLARTLGINQ--------LIVAINKMDSVNYDEEEFEAIKKE 167
Query: 99 INQMRQKVGHN 109
++ + +KVG+N
Sbjct: 168 VSNLIKKVGYN 178
>gnl|CDD|239661 cd03690, Tet_II, Tet_II: This subfamily represents domain II of
ribosomal protection proteins Tet(M) and Tet(O). This
domain has homology to domain II of the elongation
factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the
release of tetracycline (Tc) from the ribosome in a
GTP-dependent manner thereby mediating Tc resistance.
Tcs are broad-spectrum antibiotics. Typical Tcs bind to
the ribosome and inhibit the elongation phase of protein
synthesis, by inhibiting the occupation of site A by
aminoacyl-tRNA.
Length = 85
Score = 40.3 bits (95), Expect = 1e-04
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 260 PFIALAFKLEAGKFGQ-LTYMRCYQGKLRKGEMIYNVRTDKKVRVSRLVRLHSNEMEDVE 318
FK+E G+ L Y+R Y G LR + + V ++K++++ L ++ E+ +
Sbjct: 3 ELSGTVFKIERDDKGERLAYLRLYSGTLRLRDSVR-VNREEKIKITELRVFNNGEVVTAD 61
Query: 319 EVLAGDIFALFGVD 332
V AGDI L G+
Sbjct: 62 TVTAGDIAILTGLK 75
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 44.2 bits (105), Expect = 2e-04
Identities = 33/88 (37%), Positives = 48/88 (54%), Gaps = 9/88 (10%)
Query: 7 ERQRGITIQSA-ATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVGGVQS 65
E++RGITI +A Y K H ++ D PGH D+ + +DGAILV+ A G
Sbjct: 56 EKERGITINTAHVEYETEKRHYAHV-DCPGHADYVKNMITGAAQMDGAILVVAATDGPMP 114
Query: 66 QT---LTVNRQMKRYDVPCI-AFINKLD 89
QT + + RQ+ VP + F+NK+D
Sbjct: 115 QTREHILLARQV---GVPYLVVFLNKVD 139
>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 = 44.4 bits (105), Expect = 2e-04
Identities = 22/62 (35%), Positives = 32/62 (51%)
Query: 30 IIDTPGHVDFTVEVERALRVLDGAILVLCAVGGVQSQTLTVNRQMKRYDVPCIAFINKLD 89
IDTPGH FT +R + D AIL++ G + QT ++ Y P + NK+D
Sbjct: 73 FIDTPGHEAFTNLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYKTPFVVAANKID 132
Query: 90 RL 91
R+
Sbjct: 133 RI 134
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 43.7 bits (103), Expect = 2e-04
Identities = 30/85 (35%), Positives = 43/85 (50%), Gaps = 3/85 (3%)
Query: 7 ERQRGITIQSA-ATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVGGVQS 65
E+ RGITI +A Y K H ++ D PGH D+ + +DG ILV+ A G
Sbjct: 105 EKARGITIATAHVEYETAKRHYAHV-DCPGHADYVKNMITGAAQMDGGILVVSAPDGPMP 163
Query: 66 QTLTVNRQMKRYDVPCIA-FINKLD 89
QT ++ VP + F+NK+D
Sbjct: 164 QTKEHILLARQVGVPSLVVFLNKVD 188
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 41.1 bits (97), Expect = 3e-04
Identities = 23/117 (19%), Positives = 46/117 (39%), Gaps = 13/117 (11%)
Query: 27 NINIIDTPGHVDFTVE----VERALRVL---DGAILVLCAVGGVQSQTLTVNRQMKRYDV 79
+ +IDTPG + VE A +V D +LV+ + + + ++
Sbjct: 47 PVVLIDTPGLDEEGGLGRERVEEARQVADRADLVLLVVDSDLTPVEEEAKLGL-LRERGK 105
Query: 80 PCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLGSETKGI-IDLIQRKAI 135
P + +NK+D + + + R+ +P+ S G ID +++K
Sbjct: 106 PVLLVLNKIDLVPESEEEELLRERKL----ELLPDLPVIAVSALPGEGIDELRKKIA 158
>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 = 42.7 bits (101), Expect = 4e-04
Identities = 23/67 (34%), Positives = 34/67 (50%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
+D ++ ER++GITI A Y + DTPGH +T + D A+L++ A
Sbjct: 55 VDGLQAEREQGITIDVAYRYFSTDKRKFIVADTPGHEQYTRNMATGASTADLAVLLVDAR 114
Query: 61 GGVQSQT 67
GV QT
Sbjct: 115 KGVLEQT 121
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 42.6 bits (101), Expect = 4e-04
Identities = 34/95 (35%), Positives = 49/95 (51%), Gaps = 9/95 (9%)
Query: 2 DSMELERQRGITIQSA-ATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAV 60
DS E+ RGITI +A Y H ++ D PGH D+ + +DGAILV+ A
Sbjct: 51 DSAPEEKARGITINTAHVEYETENRHYAHV-DCPGHADYVKNMITGAAQMDGAILVVSAA 109
Query: 61 GGVQSQT---LTVNRQMKRYDVPCI-AFINKLDRL 91
G QT + + +Q+ VP I F+NK D++
Sbjct: 110 DGPMPQTKEHILLAKQV---GVPNIVVFLNKEDQV 141
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 42.4 bits (100), Expect = 5e-04
Identities = 26/66 (39%), Positives = 34/66 (51%), Gaps = 8/66 (12%)
Query: 1 MDSMELERQRGITIQSAATYTLWK----DHNINIIDTPGHVDFTVEVERALRVLDGAILV 56
+D ++ ER+RGITI A LWK + IID PGH DF + D AILV
Sbjct: 60 LDKLKAERERGITIDIA----LWKFETPKYYFTIIDAPGHRDFIKNMITGTSQADVAILV 115
Query: 57 LCAVGG 62
+ + G
Sbjct: 116 VASTAG 121
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 42.1 bits (100), Expect = 6e-04
Identities = 32/88 (36%), Positives = 45/88 (51%), Gaps = 9/88 (10%)
Query: 7 ERQRGITIQSA-ATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVGGVQS 65
E+ RGITI ++ Y H ++ D PGH D+ + +DGAILV+ A G
Sbjct: 56 EKARGITINTSHVEYETANRHYAHV-DCPGHADYVKNMITGAAQMDGAILVVSAADGPMP 114
Query: 66 QT---LTVNRQMKRYDVPCI-AFINKLD 89
QT + + RQ+ VP I F+NK D
Sbjct: 115 QTREHILLARQV---GVPYIVVFLNKCD 139
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 41.9 bits (99), Expect = 7e-04
Identities = 26/66 (39%), Positives = 34/66 (51%)
Query: 2 DSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVG 61
D +E ER++GITI A Y + I DTPGH +T + D AIL++ A
Sbjct: 62 DGLEAEREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTADLAILLVDARK 121
Query: 62 GVQSQT 67
GV QT
Sbjct: 122 GVLEQT 127
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 42.1 bits (100), Expect = 7e-04
Identities = 25/61 (40%), Positives = 33/61 (54%)
Query: 31 IDTPGHVDFTVEVERALRVLDGAILVLCAVGGVQSQTLTVNRQMKRYDVPCIAFINKLDR 90
IDTPGH FT +R + D AILV+ G Q QT+ +KR P + NK+DR
Sbjct: 76 IDTPGHEAFTNLRKRGGALADIAILVVDINEGFQPQTIEAINILKRRKTPFVVAANKIDR 135
Query: 91 L 91
+
Sbjct: 136 I 136
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 41.7 bits (99), Expect = 8e-04
Identities = 34/88 (38%), Positives = 46/88 (52%), Gaps = 9/88 (10%)
Query: 7 ERQRGITIQSA-ATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVGGVQS 65
E+ RGITI +A Y K H ++ D PGH D+ + +DGAILV+ A G
Sbjct: 56 EKARGITINTAHVEYETEKRHYAHV-DCPGHADYVKNMITGAAQMDGAILVVSAADGPMP 114
Query: 66 QT---LTVNRQMKRYDVPCI-AFINKLD 89
QT + + RQ+ VP I F+NK D
Sbjct: 115 QTREHILLARQV---GVPYIVVFLNKCD 139
>gnl|CDD|238842 cd01693, mtEFG2_like_IV, mtEF-G2 domain IV. This subfamily is a
part the of mitochondrial transcriptional elongation
factor, mtEF-G2. Mitochondrial translation is crucial
for maintaining mitochondrial function and mutations in
this system lead to a breakdown in the respiratory
chain-oxidative phosphorylation system and to impaired
maintenance of mitochondrial DNA. In complex with GTP,
EF-G promotes the translocation step of translation.
During translocation the peptidyl-tRNA is moved from the
A site to the P site of the small subunit of ribosome
and the mRNA is shifted one codon relative to the
ribosome.
Length = 120
Score = 39.3 bits (92), Expect = 9e-04
Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 1/90 (1%)
Query: 431 VAFKETLVQPFDFDYLHKKQSGGSGQYGRVIGTLEPLPPSANTKLEF-IDETVGTNVPKP 489
+A++ET+++P +K G V + P S++ + + + K
Sbjct: 1 IAYRETILEPARATDTLEKVIGDKKHSVTVTMEVRPNQASSSPVELIELANSAIEVLLKR 60
Query: 490 FLPAIIKGFKQMCEKGCLSGSRVAGVRMVL 519
A+ G +G L G V V + L
Sbjct: 61 IQEAVENGVHSALLQGPLLGFPVQDVAITL 90
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 41.4 bits (97), Expect = 0.001
Identities = 21/62 (33%), Positives = 33/62 (53%)
Query: 30 IIDTPGHVDFTVEVERALRVLDGAILVLCAVGGVQSQTLTVNRQMKRYDVPCIAFINKLD 89
IDTPGH FT +R + D A+LV+ G + QT+ +++Y P + NK+D
Sbjct: 530 FIDTPGHEAFTSLRKRGGSLADLAVLVVDINEGFKPQTIEAINILRQYKTPFVVAANKID 589
Query: 90 RL 91
+
Sbjct: 590 LI 591
>gnl|CDD|239671 cd03700, eEF2_snRNP_like_II, EF2_snRNP_like_II: this subfamily
represents domain II of elongation factor (EF) EF-2
found eukaryotes and archaea and, the C-terminal portion
of the spliceosomal human 116kD U5 small nuclear
ribonucleoprotein (snRNP) protein (U5-116 kD) and, its
yeast counterpart Snu114p. During the process of peptide
synthesis and tRNA site changes, the ribosome is moved
along the mRNA a distance equal to one codon with the
addition of each amino acid. This translocation step is
catalyzed by EF-2_GTP, which is hydrolyzed to provide
the required energy. Thus, this action releases the
uncharged tRNA from the P site and transfers the newly
formed peptidyl-tRNA from the A site to the P site.
Yeast Snu114p is essential for cell viability and for
splicing in vivo. U5-116 kD binds GTP. Experiments
suggest that GTP binding and probably GTP hydrolysis is
important for the function of the U5-116 kD/Snu114p.
Length = 93
Score = 36.4 bits (85), Expect = 0.004
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 9/62 (14%)
Query: 280 RCYQGKLRKGEMIY---------NVRTDKKVRVSRLVRLHSNEMEDVEEVLAGDIFALFG 330
R + G +RKG+ + + K + RL + E V+EV AG+I + G
Sbjct: 22 RVFSGTIRKGQKVRVLGPNYSPEDEEDLSKKTIQRLYLMMGRYREPVDEVPAGNIVLIVG 81
Query: 331 VD 332
+D
Sbjct: 82 LD 83
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 37.8 bits (88), Expect = 0.006
Identities = 26/106 (24%), Positives = 40/106 (37%), Gaps = 10/106 (9%)
Query: 3 SMELERQRGITI-QSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAI-LVLCAV 60
S+ + +R T+ + L +D +++ TPG F E R GAI LV +
Sbjct: 44 SVSGKGKRPTTVAMDFGSIELDEDTGVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSR 103
Query: 61 GGVQSQTLTVNRQMK----RYDVPCIAFINKLDRLGADPYRVINQM 102
T + R +P + INK D A P I +
Sbjct: 104 P----ITFHAEEIIDFLTSRNPIPVVVAINKQDLFDALPPEKIREA 145
>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 = 37.7 bits (88), Expect = 0.007
Identities = 30/132 (22%), Positives = 54/132 (40%), Gaps = 24/132 (18%)
Query: 7 ERQRGITI------------QSAATYTLWKDHNINI--IDTPGHVDFTVEVERALRVLDG 52
++RGIT+ + + N I +D PGH + +++D
Sbjct: 35 SQERGITLDLGFSSFEVDKPKHLEDNENPQIENYQITLVDCPGHASLIRTIIGGAQIIDL 94
Query: 53 AILVLCAVGGVQSQT---LTVNRQMKRYDVPCIAFINKLDRLGADPYRV-INQMR---QK 105
+LV+ A G+Q+QT L + + + P I +NK+D + + + I +M+ QK
Sbjct: 95 MLLVVDAKKGIQTQTAECLVIGELLCK---PLIVVLNKIDLIPEEERKRKIEKMKKRLQK 151
Query: 106 VGHNAAFLQIPI 117
PI
Sbjct: 152 TLEKTRLKDSPI 163
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 38.1 bits (88), Expect = 0.010
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 1 MDSMELERQRGITIQSAATYTLWKDHNI----NIIDTPGHVDFTVEVERALRVLDGAILV 56
+D ++ ER+RGITI A LWK +ID PGH DF + D A+L+
Sbjct: 60 LDKLKAERERGITIDIA----LWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLI 115
Query: 57 LCAVGG 62
+ + G
Sbjct: 116 IDSTTG 121
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 38.3 bits (90), Expect = 0.011
Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 9/82 (10%)
Query: 23 WKDHNINIIDTPGHVDFTVE------VERALRVLDGA---ILVLCAVGGVQSQTLTVNRQ 73
W +IDT G D + E+AL ++ A + V+ G+ + +
Sbjct: 48 WLGREFILIDTGGLDDGDEDELQELIREQALIAIEEADVILFVVDGREGITPADEEIAKI 107
Query: 74 MKRYDVPCIAFINKLDRLGADP 95
++R P I +NK+D L A+
Sbjct: 108 LRRSKKPVILVVNKIDNLKAEE 129
>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 = 37.0 bits (87), Expect = 0.012
Identities = 29/119 (24%), Positives = 46/119 (38%), Gaps = 13/119 (10%)
Query: 11 GITIQSAATYTLWKDHNINIIDTPG-----HVDFTVE---VERALRVLDGA---ILVLCA 59
G T S + +IDT G V +E V R L+ ++ A +LVL A
Sbjct: 35 GTTRDSIDVPFEYDGQKYTLIDTAGIRKKGKVTEGIEKYSVLRTLKAIERADVVLLVLDA 94
Query: 60 VGGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQ-IPI 117
G+ Q L + + I +NK D + D + + +++ FL PI
Sbjct: 95 SEGITEQDLRIAGLILEEGKALIIVVNKWDLVEKDEKT-MKEFEKELRRKLPFLDYAPI 152
Score = 29.3 bits (67), Expect = 4.2
Identities = 12/47 (25%), Positives = 25/47 (53%)
Query: 181 LEEKSISEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLD 227
+E+ + + +K +RR + P++ +AL +GV L DA+ +
Sbjct: 126 VEKDEKTMKEFEKELRRKLPFLDYAPIVFISALTGQGVDKLFDAIKE 172
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 37.5 bits (88), Expect = 0.018
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 30 IIDTPGHVDFTVE-----VERALRVL---DGAILVLCAVGGVQSQTLTVNRQMKRYDVPC 81
+IDT G +D E VE+ VL D A+LV+ A G L + ++K +P
Sbjct: 59 LIDTAG-LDDEGELGELRVEKTREVLDKTDLALLVVDAGVGPGEYELELIEELKERKIPY 117
Query: 82 IAFINKLDRLGADP 95
I INK+D
Sbjct: 118 IVVINKIDLGEESA 131
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 35.7 bits (83), Expect = 0.070
Identities = 25/66 (37%), Positives = 34/66 (51%)
Query: 2 DSMELERQRGITIQSAATYTLWKDHNINIIDTPGHVDFTVEVERALRVLDGAILVLCAVG 61
D ++ ER++GITI A Y + I DTPGH +T + D AIL++ A
Sbjct: 83 DGLQAEREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTCDLAILLIDARK 142
Query: 62 GVQSQT 67
GV QT
Sbjct: 143 GVLDQT 148
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 35.7 bits (83), Expect = 0.082
Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 1 MDSMELERQRGITIQSAATY--TLWKDHNINII-DTPGHVDFTVEVERALRVLDGAILVL 57
+D + ER++GITI A Y T I+ DTPGH +T + D AI+++
Sbjct: 79 VDGLAAEREQGITIDVAYRYFAT---PKRKFIVADTPGHEQYTRNMVTGASTADLAIILV 135
Query: 58 CAVGGVQSQT 67
A GV +QT
Sbjct: 136 DARKGVLTQT 145
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 33.4 bits (77), Expect = 0.085
Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 10/79 (12%)
Query: 19 TYTLWKDHNINIIDTPG---------HVDFTVEVERALRVLDGAILVLCAVGGVQSQTLT 69
L I ++DTPG V+ A+R D +LV+ A G+
Sbjct: 39 LGVLGLGRQIILVDTPGLIEGASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEE 98
Query: 70 VNRQM-KRYDVPCIAFINK 87
+ ++ K P I +NK
Sbjct: 99 ILEELEKLPKKPIILVLNK 117
>gnl|CDD|201536 pfam00984, UDPG_MGDP_dh, UDP-glucose/GDP-mannose dehydrogenase
family, central domain. The UDP-glucose/GDP-mannose
dehydrogenaseses are a small group of enzymes which
possesses the ability to catalyze the NAD-dependent
2-fold oxidation of an alcohol to an acid without the
release of an aldehyde intermediate.
Length = 96
Score = 32.6 bits (75), Expect = 0.12
Identities = 13/44 (29%), Positives = 17/44 (38%), Gaps = 4/44 (9%)
Query: 81 CIAFINKL----DRLGADPYRVINQMRQKVGHNAAFLQIPIGLG 120
I+FIN+L + +GAD V FL G G
Sbjct: 18 KISFINELANICEAVGADVSEVARAAGLDPRIGRKFLNPGPGFG 61
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 34.7 bits (81), Expect = 0.14
Identities = 30/119 (25%), Positives = 44/119 (36%), Gaps = 14/119 (11%)
Query: 11 GITIQSAATYTLWKDHNINIIDTPG-----HVDFTVE---VERALRVLDGA---ILVLCA 59
G T S +IDT G V VE V R L+ ++ A +LVL A
Sbjct: 205 GTTRDSIDIPFERNGKKYTLIDTAGIRRKGKVTEGVEKYSVLRTLKAIERADVVLLVLDA 264
Query: 60 VGGVQSQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFL-QIPI 117
G+ Q L + + +NK D L D + ++++ FL PI
Sbjct: 265 TEGITEQDLRIAGLALEAGKALVIVVNKWD-LVKDEKT-REEFKKELRRKLPFLDFAPI 321
Score = 30.5 bits (70), Expect = 3.1
Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 8/80 (10%)
Query: 23 WKDHNINIIDTPGHVDFTVE--------VERALRVLDGAILVLCAVGGVQSQTLTVNRQM 74
W +IDT G + E A+ D + V+ G+ + + + +
Sbjct: 44 WGGREFILIDTGGIEEDDDGLDKQIREQAEIAIEEADVILFVVDGREGLTPEDEEIAKWL 103
Query: 75 KRYDVPCIAFINKLDRLGAD 94
++ P I NK+D D
Sbjct: 104 RKSGKPVILVANKIDGKKED 123
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 33.4 bits (77), Expect = 0.31
Identities = 32/137 (23%), Positives = 54/137 (39%), Gaps = 22/137 (16%)
Query: 28 INIIDTPGHVDFTVE----VER----ALRVLDGAILVLCAVGGVQSQTLTVNRQMK---- 75
I +IDTPG +D +E +ER ALR L G IL L ++ ++ Q+
Sbjct: 217 IQVIDTPGLLDRPLEERNEIERQAILALRHLAGVILFL--FDPSETCGYSLEEQISLLEE 274
Query: 76 ---RYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLGSETKGIIDLIQR 132
+ P + INK+D AD ++ V + P+ + + +D ++
Sbjct: 275 IKELFKAPIVVVINKIDI--ADEEKLEEI-EASV--LEEGGEEPLKISATKGCGLDKLRE 329
Query: 133 KAIYFEGPLGDNLRIEE 149
+ R EE
Sbjct: 330 EVRKTALEPLLEERSEE 346
>gnl|CDD|132364 TIGR03321, alt_F1F0_F0_B, alternate F1F0 ATPase, F0 subunit B. A
small number of taxonomically diverse prokaryotic
species, including Methanosarcina barkeri, have what
appears to be a second ATP synthase, in addition to the
normal F1F0 ATPase in bacteria and A1A0 ATPase in
archaea. These enzymes use ion gradients to synthesize
ATP, CC and in principle may run in either direction.
This model represents the F0 subunit B of this apparent
second ATP synthase.
Length = 246
Score = 33.1 bits (76), Expect = 0.36
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 6/75 (8%)
Query: 155 KKEAESKRQELIEHV-AEGDEILG---EMFLEEKSISEDDIKKAIRRSTL--TRKFTPVL 208
K+EA+++RQ L++ E DEI E E++ D++++ RK L
Sbjct: 81 KEEAQAERQRLLDEAREEADEIREKWQEALRREQAALSDELRRRTGAEVFAIARKVLTDL 140
Query: 209 VGTALKNKGVQTLLD 223
T L+ + V +
Sbjct: 141 ADTDLEERMVDVFVQ 155
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 33.5 bits (77), Expect = 0.38
Identities = 33/111 (29%), Positives = 51/111 (45%), Gaps = 23/111 (20%)
Query: 7 ERQRGITIQSAATYTLWKDHN---INIIDTPGHVDFTVEVERALRVLDGAILVLCAVGGV 63
E++RG+TI Y W + + ID PGH F + + +D A+LV+ GV
Sbjct: 31 EKKRGMTIDLG--YAYWPQPDGRVLGFIDVPGHEKFLSNMLAGVGGIDHALLVVACDDGV 88
Query: 64 QSQT--------LTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKV 106
+QT LT N + +A + K DR D R I ++R++V
Sbjct: 89 MAQTREHLAILQLTGNPMLT------VA-LTKADR--VDEAR-IAEVRRQV 129
>gnl|CDD|206681 cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.
This EngA1 subfamily CD represents the first 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 = 157
Score = 31.6 bits (73), Expect = 0.60
Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 8/82 (9%)
Query: 23 WKDHNINIIDTPGHVDFTVE--------VERALRVLDGAILVLCAVGGVQSQTLTVNRQM 74
W +IDT G E A+ D + V+ G+ + + +
Sbjct: 42 WGGREFILIDTGGIEPDDEGISKEIREQAEIAIEEADVILFVVDGREGLTPADEEIAKYL 101
Query: 75 KRYDVPCIAFINKLDRLGADPY 96
++ P I +NK+D + +
Sbjct: 102 RKSKKPVILVVNKIDNIKEEEE 123
>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 = 32.8 bits (75), Expect = 0.63
Identities = 40/198 (20%), Positives = 74/198 (37%), Gaps = 19/198 (9%)
Query: 11 GITIQSAATYTLWKDHNINIIDTPGHVDFTV-----EVERALRVLDGAILVLCAVGGVQ- 64
G+T++ ++ +I I+D PG T EV R + + LV+ V
Sbjct: 26 GVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTFSLEEEVARDYLLNEKPDLVVNVVDASNL 85
Query: 65 SQTLTVNRQMKRYDVPCIAFINKLDRLGADPYRVINQMRQKVGHNAAFLQIPIGLGSETK 124
+ L + Q+ +P I +N +D R+ + ++ L +P+ S T+
Sbjct: 86 ERNLYLTLQLLELGIPMILALNLVDEAEKKGIRIDEEKLEER------LGVPVVPTSATE 139
Query: 125 GI-IDLIQRKAIYFEGPLGDNLRIEEIPADLKKEAESKRQELIEHVAEGDEILGEMFLE- 182
G I+ ++ G R EI EA E++E + E + + LE
Sbjct: 140 GRGIERLKDAIRKAIGLKELKKRAIEI----VPEAYQVV-EVVEGLIEIIYSISKRGLEI 194
Query: 183 EKSISEDDIKKAIRRSTL 200
+ ED + +
Sbjct: 195 LLGLLEDLSLEIEKIERN 212
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 31.0 bits (71), Expect = 0.93
Identities = 23/93 (24%), Positives = 37/93 (39%), Gaps = 13/93 (13%)
Query: 28 INIIDTPGHVDFTVE----VER----ALRVLDGAILVLCAVGG-----VQSQTLTVNRQM 74
+IDTPG +D +E +E AL L A+L ++ Q
Sbjct: 49 WQVIDTPGILDRPLEERNTIEMQAITALAHLRAAVLFFIDPSETCGYSIEEQLSLFKEIK 108
Query: 75 KRYDVPCIAFINKLDRLGADPYRVINQMRQKVG 107
++ P I +NK+D L + I + +K G
Sbjct: 109 PLFNKPVIVVLNKIDLLTEEDLSEIEKELEKEG 141
>gnl|CDD|223783 COG0711, AtpF, F0F1-type ATP synthase, subunit b [Energy production
and conversion].
Length = 161
Score = 30.7 bits (70), Expect = 1.2
Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 2/81 (2%)
Query: 148 EEIPADLKKEAESKRQELIEHVAEGDEILGEMFLEEKSISEDDIKKAIRRST--LTRKFT 205
EI KKEAE +E+ E E + E E ++ + +R L
Sbjct: 75 SEIIEQAKKEAEQIAEEIKAEAEEELERIKEAAEAEIEAEKERALEELRAEVAELAVAIA 134
Query: 206 PVLVGTALKNKGVQTLLDAVL 226
L+G + + L+DA +
Sbjct: 135 EKLLGKKVDEAAQKDLIDAFI 155
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 31.4 bits (72), Expect = 1.3
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 126 IIDLIQ-RKAIYFEGPLGDNL---RIEEIPADLKKEAESKRQELIEHVAEGD 173
IID IQ R A++ PL R+ I + E E I +V+EGD
Sbjct: 145 IIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGD 196
>gnl|CDD|218214 pfam04695, Pex14_N, Peroxisomal membrane anchor protein (Pex14p)
conserved region. Family of peroxisomal membrane anchor
proteins which bind the PTS1 (peroxisomal targeting
signal) receptor and are required for the import of
PTS1-containing proteins into peroxisomes. Loss of
functional Pex14p results in defects in both the PTS1
and PTS2-dependent import pathways. Deletion analysis of
this conserved region implicates it in selective
peroxisome degradation. In the majority of members this
region is situated at the N-terminus of the protein.
Length = 79
Score = 28.8 bits (65), Expect = 1.5
Identities = 8/19 (42%), Positives = 16/19 (84%)
Query: 180 FLEEKSISEDDIKKAIRRS 198
FLE K ++E++I +A++R+
Sbjct: 29 FLESKGLTEEEIDEALKRA 47
>gnl|CDD|235966 PRK07207, PRK07207, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 965
Score = 31.5 bits (72), Expect = 1.6
Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 17/45 (37%)
Query: 136 YFEGPLGDNLRIEEIPADLKK--------------EAESKRQELI 166
YF+G L RI+ IPADLK EA S+RQ+ I
Sbjct: 831 YFDGSLQ---RIDRIPADLKALYATAFEVDPRWLVEAASRRQKWI 872
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 30.8 bits (71), Expect = 2.2
Identities = 10/44 (22%), Positives = 22/44 (50%)
Query: 186 ISEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLDYL 229
+ E++ ++ L PV + +A+ +G+ LL A+ + L
Sbjct: 284 LDEEEEREKRAALELAALGGPVFLISAVTGEGLDELLRALWELL 327
>gnl|CDD|227244 COG4907, COG4907, Predicted membrane protein [Function unknown].
Length = 595
Score = 31.1 bits (70), Expect = 2.3
Identities = 21/137 (15%), Positives = 43/137 (31%), Gaps = 25/137 (18%)
Query: 346 SISLESIYVADPVVSMSIKAVNNKDRDNFSKAVQRFTKEDPTFHFFYDPESKETLVSGMG 405
++ S Y V+ S+ D + E TF F Y + + +
Sbjct: 81 ENNVISPYREVDPVNYSVTDEG--DGVYRIGLYSKNYNEVRTFKFVYTLPEAIKVYNDVA 138
Query: 406 ELHLEIYAQRMEREYNCPVVLGKPKVAFKETLVQPFDFDYLHKKQSGGSGQYGRVIGTLE 465
+ + ++ Q + + + K T+ P + DY + K L
Sbjct: 139 QFNRKLVGQDWQ----------QGISSVKVTIELPVENDYDNSK-------------VLV 175
Query: 466 PLPPSANTKLEFIDETV 482
P +++ I+ V
Sbjct: 176 FGHPPLTGEVDKIENNV 192
>gnl|CDD|239670 cd03699, lepA_II, lepA_II: This subfamily represents the domain II
of LepA, a GTP-binding protein localized in the
cytoplasmic membrane. The N-terminal domain of LepA
shares regions of homology to translation factors. In
terms of interaction with the ribosome, EF-G, EF-Tu and
IF2 have all been demonstrated to interact at
overlapping sites on the ribosome. Chemical protection
studies demonstrate that they all include the
universally conserved alpha-sarcin loop as part of their
binding site. These data indicate that LepA may bind to
this location on the ribosome as well. LepA has never
been observed in archaea, and eukaryl LepA is
organellar. LepA is therefore a true bacterial GTPase,
found only in the bacterial lineage.
Length = 86
Score = 28.6 bits (65), Expect = 2.3
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 274 GQLTYMRCYQGKLRKGEMIYNVRTDKKVRVSRLVRLHSNEMEDVEEVLAGDI-FALFGV- 331
G + +R + G L+KG+ I + T K+ V + EM +E+ AG + + + G+
Sbjct: 15 GVIALVRVFDGTLKKGDKIRFMSTGKEYEVEEVGIFRP-EMTPTDELSAGQVGYIIAGIK 73
Query: 332 ---DCASGDTF 339
D GDT
Sbjct: 74 TVKDARVGDTI 84
>gnl|CDD|188935 cd09536, SAM_Ste50_fungal, SAM domain of Ste50 fungal subfamily.
SAM (sterile alpha motif) domain of Ste50 fungal
subfamily is a protein-protein interaction domain.
Proteins of this subfamily have SAM domain at the
N-terminus and Ras-associated UBQ superfamily domain at
the C-terminus. They participate in regulation of mating
pheromone response, invasive growth and high osmolarity
growth response, and contribute to cell wall integrity
in vegetative cells. Ste50 of S.cerevisiae acts as an
adaptor protein between G protein and MAP triple kinase
Ste11. Ste50 proteins are able to form homooligomers,
binding each other via their SAM domains, as well as
heterodimers and heterogeneous complexes with SAM domain
or SAM homodimers of MAPKKK Ste11 protein kinase.
Length = 74
Score = 28.2 bits (63), Expect = 2.5
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 163 QELIEHVAEGDEILGEMFLEE-KSISEDDIKKAIRRSTLTRKF 204
L E+ G +L E+ LE+ K + ++D+ AIR L K
Sbjct: 29 DRLRENNITGS-LLSELTLEDCKELCDNDLSLAIRLKLLINKL 70
>gnl|CDD|212166 cd11652, SSH-N, N-terminal domain conserved in slingshot (SSH)
phosphatases. This domain or region conserved in
Bilateria is found N-terminal to the DEK_C-like and
catalytic domains of slingshot phosphatases. Slingshot
is a cofilin-specific phosphatase. Dephosphorylation
reactivates cofilin, which in turn depolymerizes actin
and is thus required for actin filament reorganization.
Slingshot is a member of the dual-specificity protein
phosphatase family. This N-terminal SSH region may be
involved in P-cofilin binding (the model C-terminus plus
the DEK_C-like domain, which are characterized as the
"B" domain in some of the literature), and may be
required for the F-actin mediated activation of
slingshot (the N-terminal region of this model,
sometimes referred to as the "A" domain).
Length = 233
Score = 30.0 bits (68), Expect = 2.7
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 6/40 (15%)
Query: 302 RVSRLVRLHSNEMEDVEEVLAGDIFALFGVDCASGDTFVT 341
R LV + + +D EE + L GVD ++ T
Sbjct: 101 RTRYLVVVSTLGRQDTEESI------LLGVDFPPKESSCT 134
>gnl|CDD|237248 PRK12890, PRK12890, allantoate amidohydrolase; Reviewed.
Length = 414
Score = 30.3 bits (69), Expect = 3.4
Identities = 24/98 (24%), Positives = 40/98 (40%), Gaps = 16/98 (16%)
Query: 26 HNINIIDTPGHVDFTVEV--------ERALRVLDGAILVLCAVGGVQSQTLTVNRQMK-R 76
+ IN++ PG V FT+++ E A L + + A GV+ + ++R
Sbjct: 275 NAINVV--PGRVVFTLDLRSPDDAVLEAAEAALLAELEAIAAARGVRIELERLSRSEPVP 332
Query: 77 YDVPCIAFINK-LDRLGADPYRVINQMRQKVGHNAAFL 113
D + + RLG R M GH+AA +
Sbjct: 333 CDPALVDAVEAAAARLGYPSRR----MPSGAGHDAAAI 366
>gnl|CDD|106966 PHA00657, PHA00657, crystallin beta/gamma motif-containing protein.
Length = 2052
Score = 30.1 bits (67), Expect = 4.2
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 413 AQRMEREYNCPV--VLGKPKVAFKETLVQPFDFDYLHK 448
AQR+ R N P+ VL +PK A ++ + DFD L K
Sbjct: 60 AQRVARRANLPIETVLNQPKEAKRQDTIGAIDFDTLGK 97
>gnl|CDD|215445 PLN02831, PLN02831, Bifunctional GTP cyclohydrolase II/
3,4-dihydroxy-2-butanone-4-phosphate synthase.
Length = 450
Score = 29.7 bits (67), Expect = 5.8
Identities = 21/55 (38%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 281 CYQGKLRKGEMIYNVRTDKKVRVSRLVRLHSNEMEDVEEVLAGDIFALFGVDCAS 335
CY+ KL E I V+ D LVR+HS E L GDIF DC +
Sbjct: 260 CYRSKLDGIEHIAFVKGDIGDGQDVLVRVHS-------ECLTGDIFGSARCDCGN 307
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 29.2 bits (67), Expect = 6.9
Identities = 20/67 (29%), Positives = 27/67 (40%), Gaps = 11/67 (16%)
Query: 11 GITIQSAATYTLWKDHNINIIDTPG-----HVDFTVE---VERALRVLDGA---ILVLCA 59
G T S T +IDT G V VE V R L+ ++ A +LV+ A
Sbjct: 206 GTTRDSIDTPFERDGQKYTLIDTAGIRRKGKVTEGVEKYSVIRTLKAIERADVVLLVIDA 265
Query: 60 VGGVQSQ 66
G+ Q
Sbjct: 266 TEGITEQ 272
>gnl|CDD|233829 TIGR02349, DnaJ_bact, chaperone protein DnaJ. This model
represents bacterial forms of DnaJ, part of the
DnaK-DnaJ-GrpE chaperone system. The three components
typically are encoded by consecutive genes. DnaJ
homologs occur in many genomes, typically not near DnaK
and GrpE-like genes; most such genes are not included by
this family. Eukaryotic (mitochondrial and chloroplast)
forms are not included in the scope of this family.
Length = 354
Score = 29.1 bits (66), Expect = 7.0
Identities = 15/33 (45%), Positives = 20/33 (60%), Gaps = 6/33 (18%)
Query: 174 EILGEMFLEEKSISEDDIKKAIRRSTLTRKFTP 206
EILG K SE++IKKA R+ L +K+ P
Sbjct: 4 EILGV----SKDASEEEIKKAYRK--LAKKYHP 30
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 28.2 bits (64), Expect = 7.7
Identities = 10/43 (23%), Positives = 22/43 (51%)
Query: 187 SEDDIKKAIRRSTLTRKFTPVLVGTALKNKGVQTLLDAVLDYL 229
++D+ + + F + +ALK + V LL+ +++YL
Sbjct: 126 DKEDLLPLLEKLKELHPFAEIFPISALKGENVDELLEYIVEYL 168
>gnl|CDD|129596 TIGR00505, ribA, GTP cyclohydrolase II. Several members of the
family are bifunctional, involving both ribA and ribB
function. In these cases, ribA tends to be on the
C-terminal end of the protein and ribB tends to be on
the N-terminal. The function of archaeal members of the
family has not been demonstrated and is assigned
tentatively [Biosynthesis of cofactors, prosthetic
groups, and carriers, Riboflavin, FMN, and FAD].
Length = 191
Score = 28.2 bits (63), Expect = 8.6
Identities = 18/69 (26%), Positives = 26/69 (37%), Gaps = 10/69 (14%)
Query: 271 GKFGQLTYMRCYQGKLRKGEMIYNVRTDKKVRVSRLVRLHSNEMEDVEEVLAGDIFALFG 330
+G YM ++ + + V+ D LVR+HS E L GD AL
Sbjct: 10 TPYGDF-YMVGFEEPATGKDHVALVKGDISAHTDVLVRIHS-------ECLTGD--ALHS 59
Query: 331 VDCASGDTF 339
+ C G
Sbjct: 60 LRCDCGFQL 68
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 28.8 bits (65), Expect = 9.1
Identities = 13/72 (18%), Positives = 30/72 (41%), Gaps = 11/72 (15%)
Query: 181 LEEKSISEDDIKKAIRRSTLTRK----FTPVLVGTALKNKGVQTLLDAVLDYLPNPGEVT 236
+ + +++ A+ + PV+ +AL+ +G+ L DA+ D+
Sbjct: 201 RKGAEKAARELRSALDLLREVWRENGWRPPVVTTSALEGEGIDELWDAIEDHR------- 253
Query: 237 NYAIENGQEDKK 248
+ E+G +K
Sbjct: 254 KFLTESGLFTEK 265
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 28.5 bits (65), Expect = 9.6
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 212 ALKNKGVQTLLDAVLDYLP 230
ALK V LLD + YLP
Sbjct: 153 ALKGDNVDELLDVIAKYLP 171
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
0.319 0.137 0.393
Gapped
Lambda K H
0.267 0.0810 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,656,582
Number of extensions: 3198261
Number of successful extensions: 3680
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3541
Number of HSP's successfully gapped: 180
Length of query: 610
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 507
Effective length of database: 6,369,140
Effective search space: 3229153980
Effective search space used: 3229153980
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 62 (27.5 bits)