RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780233|ref|YP_003064646.1| GTP-binding protein [Candidatus Liberibacter asiaticus str. psy62] (624 letters) >gnl|CDD|31410 COG1217, TypA, Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]. Length = 603 Score = 944 bits (2443), Expect = 0.0 Identities = 377/602 (62%), Positives = 454/602 (75%), Gaps = 3/602 (0%) Query: 17 MQIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTS 76 IRNIAIIAHVDHGKTTLVD LLKQSG FR+ + V+ERVMD NDLEKERGITILAK T+ Sbjct: 3 EDIRNIAIIAHVDHGKTTLVDALLKQSGTFREREEVAERVMDSNDLEKERGITILAKNTA 62 Query: 77 IVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLR 136 + +N RINIVDTPGHADFGGEVER+L MV+ V++LVDA+EGPMPQT+FV+ KAL +GL+ Sbjct: 63 VNYNGTRINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALALGLK 122 Query: 137 PIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSRDQ 196 PIVV+NK+DR DAR DEV++EVFDLF L ATD QLDFPI+Y S R G S + D Sbjct: 123 PIVVINKIDRPDARPDEVVDEVFDLFVELGATDEQLDFPIVYASARNGTASLDPEDEADD 182 Query: 197 GMVPLLNLIVDHVPPPVI-SEGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALS 255 M PL I+DHVP P + +M T L+ + ++GRI GRI GT+K NQ + + Sbjct: 183 -MAPLFETILDHVPAPKGDLDEPLQMQVTQLDYNSYVGRIGIGRIFRGTVKPNQQVALIK 241 Query: 256 PDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAGLVKATVADTFCDPSIDEPLKAQ 315 DG E GR++K+L F G++R I+EA AGDIV+IAGL + DT CDP E L A Sbjct: 242 SDGT-TENGRITKLLGFLGLERIEIEEAEAGDIVAIAGLEDINIGDTICDPDNPEALPAL 300 Query: 316 PIDPPTVTMTFGVNDSPLAGTEGDKVTSRMIRDRLFKEAEGNIALKIEESSSKDAFFVSG 375 +D PT++MTF VNDSP AG EG VTSR IRDRL KE E N+AL++EE+ S DAF VSG Sbjct: 301 SVDEPTLSMTFSVNDSPFAGKEGKFVTSRQIRDRLNKELETNVALRVEETESPDAFEVSG 360 Query: 376 RGELQLAVLIETMRREGFELAVSRPRVVIKKEGDSLLEPIEEVVIDVDEEHSGAVVQKMT 435 RGEL L++LIE MRREGFEL VSRP V+IK+ EP EEV IDV EEH GAV++K+ Sbjct: 361 RGELHLSILIENMRREGFELQVSRPEVIIKEIDGVKCEPFEEVTIDVPEEHQGAVIEKLG 420 Query: 436 LHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQLMTDTRGTAIMNRLFHSYQPHKGEIG 495 K EM ++ P G GRVRL F+ P RGLIG++++ +T TRGT IMN F Y+P KGEIG Sbjct: 421 ERKGEMKDMAPDGKGRVRLEFVIPARGLIGFRTEFLTMTRGTGIMNHSFDHYRPVKGEIG 480 Query: 496 GRSNGVLLSNEEGKVVAYALFNLEDRGSMIVEPGDKVYQGMIVGIHTRENDLDVNVLKGK 555 GR NGVL+SNE GK VAYALFNL+DRG + +EPG KVY+GMI+G H+R+NDL VNVLKGK Sbjct: 481 GRHNGVLISNETGKAVAYALFNLQDRGKLFIEPGTKVYEGMIIGEHSRDNDLTVNVLKGK 540 Query: 556 KLTNMRASGKDEAVKLVPAVKMTLEQALSWIQNDELVEVTPKSIRLRKMYLDPNERKRKG 615 KLTNMRASGKDEAV L P ++MTLE+AL +I +DELVEVTP+SIRLRK L+ NERKR Sbjct: 541 KLTNMRASGKDEAVTLTPPIRMTLERALEFIADDELVEVTPESIRLRKKILNENERKRAE 600 Query: 616 KS 617 K Sbjct: 601 KR 602 >gnl|CDD|35683 KOG0462, KOG0462, KOG0462, Elongation factor-type GTP-binding protein [Translation, ribosomal structure and biogenesis]. Length = 650 Score = 415 bits (1069), Expect = e-116 Identities = 171/612 (27%), Positives = 264/612 (43%), Gaps = 57/612 (9%) Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIV 78 IRN +IIAHVDHGK+TL D LL+ +G DN E+V+D +E+ERGITI A+ SI Sbjct: 60 IRNFSIIAHVDHGKSTLADRLLELTG-TIDNNIGQEQVLDKLQVERERGITIKAQTASIF 118 Query: 79 WNDVR---INIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGL 135 + D + +N++DTPGH DF GEV R L + +++VDA++G QT A + GL Sbjct: 119 YKDGQSYLLNLIDTPGHVDFSGEVSRSLAACDGALLVVDASQGVQAQTVANFYLAFEAGL 178 Query: 136 RPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSRD 195 I V+NK+D A + V N++F+LF A ++Y S + G Sbjct: 179 AIIPVLNKIDLPSADPERVENQLFELFDIPPA-------EVIYVSAKTGL---------- 221 Query: 196 QGMVPLLNLIVDHVPPP-VISEGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKAL 254 + LL I+ VPPP I + +M+ E D + G I R+ G ++ +++ Sbjct: 222 -NVEELLEAIIRRVPPPKGIRDAPLRMLIFDSEYDEYRGVIALVRVVDGVVRKGDKVQSA 280 Query: 255 SPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAGLVK-ATVADTFCDPSIDEPLK 313 + G EV +V ++ +D G I+ VK A + DT S+ + ++ Sbjct: 281 A-TGKSYEV-KVVGVMRPEMTPVVELDAGQVGYIICNMRNVKEAQIGDTIAHKSVTKAVE 338 Query: 314 AQPIDPPTVTMTFGVNDSPLAGTEGDKVTSRMIRDRLFKEAEGNIALKIEESSSKDAFFV 373 P PT M F V PL G+ D T R +RL E +K + + + Sbjct: 339 TLPGFEPTKPMVF-VGLFPLDGS--DYETLRDAIERLVLNDESVTVIKESSGALGQGWRL 395 Query: 374 SGRGELQLAVLIETMRRE-GFELAVSRPRVVIKKE--------------------GDSLL 412 G L + V IE + RE G EL V+ P V + L Sbjct: 396 GFLGLLHMEVFIERLEREYGAELIVTPPTVPYRVVYSNGDEILISNPALFPDPSDVKEFL 455 Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIG-YQSQLM 471 EP E I +E+ GAV++ + + E ++ RV L + P R L+G + +L Sbjct: 456 EPYVEATIITPDEYVGAVIELCSERRGEQKDMTYIDGNRVMLKYQLPLRELVGDFFDRLK 515 Query: 472 TDTRGTAIMNRLFHSYQPHKGEIGGRSNGVLLSNEEGKVVAYALFNLEDRGSMIVEPGDK 531 + T G A + YQ ++ + +G L E RG V+ Sbjct: 516 SLTSGYASFDYEDAGYQA--SDLVKLDILLNGKMVDGLSTIVHLSKAESRGREFVQKLKD 573 Query: 532 VYQGMIVGIHTRENDLDVNVLKGKKLTNMRASGKDEAVKLVPAVKMTLEQALSWIQNDEL 591 + I +H + N+ + + A KD KL L++ L + Sbjct: 574 LIPRQIFEVHIQACIGSKNIARET----ISAYRKDVLAKLYGGDVTRLKKLLKKQAEGKK 629 Query: 592 VEVTPKSIRLRK 603 T +IR+ K Sbjct: 630 RMKTVGNIRIPK 641 >gnl|CDD|133291 cd01891, TypA_BipA, TypA (tyrosine phosphorylated protein A)/BipA subfamily. 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 = 371 bits (956), Expect = e-103 Identities = 129/194 (66%), Positives = 161/194 (82%), Gaps = 1/194 (0%) Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIV 78 IRNIAIIAHVDHGKTTLVD LLKQSG FR+N+ V ERVMD NDLE+ERGITILAK T++ Sbjct: 2 IRNIAIIAHVDHGKTTLVDALLKQSGTFRENEEVEERVMDSNDLERERGITILAKNTAVT 61 Query: 79 WNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPI 138 + D +INIVDTPGHADFGGEVER+L MV+ V++LVDA+EGPMPQT+FV+ KAL++GL+PI Sbjct: 62 YKDTKINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALELGLKPI 121 Query: 139 VVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSRDQGM 198 VV+NK+DR DAR +EV++EVFDLF L AT+ QLDFP+LY S + GW S + + + + Sbjct: 122 VVINKIDRPDARPEEVVDEVFDLFIELGATEEQLDFPVLYASAKNGWASLNLEDPSED-L 180 Query: 199 VPLLNLIVDHVPPP 212 PL + I++HVP P Sbjct: 181 EPLFDTIIEHVPAP 194 >gnl|CDD|143801 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 = 185 Score = 201 bits (514), Expect = 4e-52 Identities = 72/197 (36%), Positives = 97/197 (49%), Gaps = 14/197 (7%) Query: 17 MQIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVS-ERVMDCNDLEKERGITILAKVT 75 + RNI II HVDHGKTTL D LL +G V E +D E+ERGITI Sbjct: 1 KRHRNIGIIGHVDHGKTTLTDALLYVTGAIDKRGEVKQEGELDRLKEERERGITIKIAAV 60 Query: 76 SIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGL 135 S INI+DTPGH DF E+ R + +++VDA EG MPQT+ + A ++G+ Sbjct: 61 SFETKKRHINIIDTPGHVDFTKEMIRGAAQADGAILVVDAVEGVMPQTREHLLLAKQLGV 120 Query: 136 RPIVVVNKVDR-SDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSR 194 IV +NK+DR DA DEV+ E+ P++ GS G Sbjct: 121 PIIVFINKMDRVDDAELDEVVEEISREL-LEKYGFGGETIPVIPGSALTGE--------- 170 Query: 195 DQGMVPLLNLIVDHVPP 211 G+ LL + ++P Sbjct: 171 --GIDTLLEALDLYLPS 185 >gnl|CDD|133257 cd00881, GTP_translation_factor, GTP translation factor family. This 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 = 189 Score = 187 bits (477), Expect = 8e-48 Identities = 77/200 (38%), Positives = 108/200 (54%), Gaps = 19/200 (9%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80 N+ I HVDHGKTTL + LL +G + V E +D E+ERGITI + V + W Sbjct: 1 NVGIAGHVDHGKTTLTERLLYVTGDIERDGTVEETFLDVLKEERERGITIKSGVATFEWP 60 Query: 81 DVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPIVV 140 D R+N +DTPGH DF EV R L + + +++VDA EG PQT+ + A + GL IV Sbjct: 61 DRRVNFIDTPGHEDFSSEVIRGLSVSDGAILVVDANEGVQPQTREHLRIAREGGLPIIVA 120 Query: 141 VNKVDR-SDARADEVINEVFDLFSAL-------DATDAQLDFPILYGSGRFGWMSDSSDG 192 +NK+DR + +EV+ E+ +L + + T L PI+ GS G Sbjct: 121 INKIDRVGEEDLEEVLREIKELLGLIGFISTKEEGTRNGLLVPIVPGSALTGI------- 173 Query: 193 SRDQGMVPLLNLIVDHVPPP 212 G+ LL IV+H+PPP Sbjct: 174 ----GVEELLEAIVEHLPPP 189 >gnl|CDD|30829 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis, outer membrane]. Length = 603 Score = 179 bits (456), Expect = 2e-45 Identities = 145/510 (28%), Positives = 226/510 (44%), Gaps = 72/510 (14%) Query: 18 QIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSI 77 IRN +IIAH+DHGK+TL D LL+ +G + + +V+D D+E+ERGITI A+ + Sbjct: 8 NIRNFSIIAHIDHGKSTLADRLLELTGGLSEREM-RAQVLDSMDIERERGITIKAQAVRL 66 Query: 78 VW-----NDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALK 132 + +N++DTPGH DF EV R L E +++VDA++G QT V AL+ Sbjct: 67 NYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYLALE 126 Query: 133 IGLRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDG 192 L I V+NK+D A + V E+ D+ +DA+DA L S + G Sbjct: 127 NNLEIIPVLNKIDLPAADPERVKQEIEDII-GIDASDAVL------VSAKTG-------- 171 Query: 193 SRDQGMVPLLNLIVDHVPPPVIS-EGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNI 251 G+ +L IV+ +PPP + K + D +LG +V RI GT+K I Sbjct: 172 ---IGIEDVLEAIVEKIPPPKGDPDAPLKALIFDSWYDNYLGVVVLVRIFDGTLKKGDKI 228 Query: 252 KALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAGLVK----ATVADTF--CD 305 + +S G EV V +DE AG++ I +K A V DT Sbjct: 229 RMMS-TGKEYEVDEV----GIFTPKMVKVDELKAGEVGYIIAGIKDVRDARVGDTITLAS 283 Query: 306 PSIDEPLKA-QPIDPPTVTMTFGVNDSPLAGTEGDKVTSRMIRDRLFKEAEGNIALKIE- 363 EPL + + P M F + L + D +RD L K + +L E Sbjct: 284 NPATEPLPGFKEVKP----MVF----AGLYPVDSDDY--EDLRDALEKLQLNDASLTYEP 333 Query: 364 ESSSKDAF-FVSG-RGELQLAVLIETMRRE-GFELAVSRPRV---VIKKEG--------- 408 E+S F F G G L + ++ E + RE +L + P V V +G Sbjct: 334 ETSQALGFGFRCGFLGLLHMEIIQERLEREFDLDLITTAPSVVYKVELTDGEEIEVDNPS 393 Query: 409 --------DSLLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPT 460 + + EP + I +E+ G V++ + I++ RV L + P Sbjct: 394 DLPDPNKIEEIEEPYVKATIITPQEYLGNVMELCQEKRGIQIDMEYLDQNRVMLTYELPL 453 Query: 461 RGLI-GYQSQLMTDTRGTAIMNRLFHSYQP 489 ++ + +L + ++G A + F Y+ Sbjct: 454 AEIVFDFFDKLKSISKGYASFDYEFIGYRE 483 >gnl|CDD|133285 cd01885, EF2, EF2 (for 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 = 222 Score = 150 bits (381), Expect = 1e-36 Identities = 75/227 (33%), Positives = 112/227 (49%), Gaps = 39/227 (17%) Query: 20 RNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSI-- 77 RNI IIAHVDHGKTTL D LL +G+ + R MD + E+ERGIT+ K ++I Sbjct: 1 RNICIIAHVDHGKTTLSDSLLASAGIISEKLAGKARYMDSREDEQERGITM--KSSAISL 58 Query: 78 ----------VWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVV 127 N+ IN++D+PGH DF EV L + + +V+VDA EG QT+ V+ Sbjct: 59 YFEYEEEDKADGNEYLINLIDSPGHVDFSSEVTAALRLCDGALVVVDAVEGVCVQTETVL 118 Query: 128 GKALKIGLRPIVVVNKVDR---------SDA--RADEVINEVFDLFSAL--------DAT 168 +ALK ++P++V+NK+DR +A R +I +V + D Sbjct: 119 RQALKERVKPVLVINKIDRLILELKLSPEEAYQRLARIIEQVNAIIGTYADEEFKEKDDE 178 Query: 169 DAQLDFP---ILYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPP 212 + +GS GW +R + +L ++V H+P P Sbjct: 179 KWYFSPQKGNVAFGSALHGWGFTIIKFAR---IYAVLEMVVKHLPSP 222 >gnl|CDD|30828 COG0480, FusA, Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]. Length = 697 Score = 145 bits (367), Expect = 4e-35 Identities = 64/156 (41%), Positives = 92/156 (58%), Gaps = 3/156 (1%) Query: 12 GRLGYMQIRNIAIIAHVDHGKTTLVDELLKQSGVFRD--NQRVSERVMDCNDLEKERGIT 69 + +IRNI I+AH+D GKTTL + +L +G+ MD + E+ERGIT Sbjct: 3 RLMPLERIRNIGIVAHIDAGKTTLTERILFYTGIISKIGEVHDGAATMDWMEQEQERGIT 62 Query: 70 ILAKVTSIVWND-VRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVG 128 I + T++ W RIN++DTPGH DF EVER L +++ VV+VDA EG PQT+ V Sbjct: 63 ITSAATTLFWKGDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVEGVEPQTETVWR 122 Query: 129 KALKIGLRPIVVVNKVDRSDARADEVINEVFDLFSA 164 +A K G+ I+ VNK+DR A V+ ++ + A Sbjct: 123 QADKYGVPRILFVNKMDRLGADFYLVVEQLKERLGA 158 Score = 96.8 bits (241), Expect = 2e-20 Identities = 71/309 (22%), Positives = 132/309 (42%), Gaps = 61/309 (19%) Query: 129 KALKIGLRPIVVVNKVDRSDARADEVINE----VFDLFSAL-DATDAQLDFPILYGSGRF 183 K + R ++ + + ++ + ++ AL T A P+L GS Sbjct: 203 KEIAEEAREKLLEALAEFDEELMEKYLEGEEPTEEEIKKALRKGTIAGKIVPVLCGSA-- 260 Query: 184 GWMSDSSDGSRDQGMVPLLNLIVDHVPPPV---------------------ISEGEFKMI 222 +++G+ PLL+ +VD++P P+ EG + Sbjct: 261 ---------FKNKGVQPLLDAVVDYLPSPLDVPPIKGDLDDEIEKAVLRKASDEGPLSAL 311 Query: 223 GTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDE 282 + DPF+G++ R++SGT+KS + + + RV ++L G +R+ +DE Sbjct: 312 VFKIMTDPFVGKLTFVRVYSGTLKSGSEVLNSTKG----KKERVGRLLLMHGNEREEVDE 367 Query: 283 AHAGDIVSIAGLVKATVADTFCDPSIDEPLKAQPIDPPTVTMTFGVNDSPLAGTEGDKVT 342 AGDIV++ GL AT DT CD + L++ P +++ P + +K+ Sbjct: 368 VPAGDIVALVGLKDATTGDTLCDENKPVILESMEFPEPVISVAV----EPKTKADQEKL- 422 Query: 343 SRMIRDRLFKEAEGNIA-----LKIEESSSKDAFFVSGRGELQLAVLIETMRRE-GFELA 396 EA +A ++E +SG GEL L ++++ ++RE G E+ Sbjct: 423 ---------SEALNKLAEEDPTFRVETDEETGETIISGMGELHLEIIVDRLKREFGVEVE 473 Query: 397 VSRPRVVIK 405 V +P+V + Sbjct: 474 VGKPQVAYR 482 Score = 39.4 bits (92), Expect = 0.003 Identities = 26/99 (26%), Positives = 46/99 (46%), Gaps = 2/99 (2%) Query: 393 FELAVSRP-RVVIKKEGDSLLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRP-SGTG 450 F++A S + + K LLEPI +V I EE+ G V+ + + +++ + G G Sbjct: 580 FKIAASLAFKEAMLKAKPVLLEPIMKVEITTPEEYMGDVIGDLNSRRGQILGMEQRPGGG 639 Query: 451 RVRLVFLSPTRGLIGYQSQLMTDTRGTAIMNRLFHSYQP 489 + P + GY + L + T+G A + F Y+ Sbjct: 640 LDVIKAEVPLAEMFGYATDLRSATQGRASFSMEFDHYEE 678 >gnl|CDD|133368 cd04168, TetM_like, Tet(M)-like subfamily. 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 = 140 bits (354), Expect = 1e-33 Identities = 59/147 (40%), Positives = 91/147 (61%), Gaps = 4/147 (2%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER--VMDCNDLEKERGITILAKVTSIV 78 NI I+AHVD GKTTL + LL SG R V + D +LE++RGITI + V S Sbjct: 1 NIGILAHVDAGKTTLTESLLYTSGAIRKLGSVDKGTTRTDTMELERQRGITIFSAVASFQ 60 Query: 79 WNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKI-GLRP 137 W D ++N++DTPGH DF EVER L +++ ++++ A EG QT+ ++ + L+ + Sbjct: 61 WEDTKVNLIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTR-ILWRLLRKLNIPT 119 Query: 138 IVVVNKVDRSDARADEVINEVFDLFSA 164 I+ VNK+DR+ A ++V E+ + S+ Sbjct: 120 IIFVNKIDRAGADLEKVYQEIKEKLSS 146 >gnl|CDD|133290 cd01890, LepA, LepA subfamily. LepA belongs to the GTPase family of 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 = 138 bits (349), Expect = 6e-33 Identities = 73/198 (36%), Positives = 106/198 (53%), Gaps = 24/198 (12%) Query: 20 RNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVW 79 RN +IIAH+DHGK+TL D LL+ +G + E+V+D DLE+ERGITI A+ + + Sbjct: 1 RNFSIIAHIDHGKSTLADRLLELTGTVSKREM-KEQVLDSMDLERERGITIKAQTVRLNY 59 Query: 80 -----NDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIG 134 + +N++DTPGH DF EV R L E ++LVDA +G QT AL+ Sbjct: 60 KAKDGQEYLLNLIDTPGHVDFSYEVSRSLAACEGALLLVDATQGVEAQTLANFYLALENN 119 Query: 135 LRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSR 194 L I V+NK+D A + V ++ D+ LD ++A + S + G Sbjct: 120 LEIIPVINKIDLPSADPERVKQQIEDVLG-LDPSEA------ILVSAKTG---------- 162 Query: 195 DQGMVPLLNLIVDHVPPP 212 G+ LL IV+ +PPP Sbjct: 163 -LGVEDLLEAIVERIPPP 179 >gnl|CDD|133286 cd01886, EF-G, Elongation factor G (EF-G) subfamily. 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 = 127 bits (321), Expect = 1e-29 Identities = 59/140 (42%), Positives = 81/140 (57%), Gaps = 2/140 (1%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER--VMDCNDLEKERGITILAKVTSIV 78 NI IIAH+D GKTT + +L +G V MD + E+ERGITI + T+ Sbjct: 1 NIGIIAHIDAGKTTTTERILYYTGRIHKIGEVHGGGATMDFMEQERERGITIQSAATTCF 60 Query: 79 WNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPI 138 W D RINI+DTPGH DF EVER L +++ V + DA G PQT+ V +A + + I Sbjct: 61 WKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVEPQTETVWRQADRYNVPRI 120 Query: 139 VVVNKVDRSDARADEVINEV 158 VNK+DR+ A V+ ++ Sbjct: 121 AFVNKMDRTGADFFRVVEQI 140 >gnl|CDD|35686 KOG0465, KOG0465, KOG0465, Mitochondrial elongation factor [Translation, ribosomal structure and biogenesis]. Length = 721 Score = 125 bits (315), Expect = 4e-29 Identities = 62/161 (38%), Positives = 90/161 (55%), Gaps = 5/161 (3%) Query: 18 QIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER--VMDCNDLEKERGITILAKVT 75 +IRNI I AH+D GKTTL + +L +G + V MD +LE++RGITI + T Sbjct: 38 KIRNIGISAHIDAGKTTLTERMLYYTGRIKHIGEVRGGGATMDSMELERQRGITIQSAAT 97 Query: 76 SIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGL 135 W D RINI+DTPGH DF EVER L +++ V+++DA G QT+ V + + + Sbjct: 98 YFTWRDYRINIIDTPGHVDFTFEVERALRVLDGAVLVLDAVAGVESQTETVWRQMKRYNV 157 Query: 136 RPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPI 176 I +NK+DR A +N + + L+ A + PI Sbjct: 158 PRICFINKMDRMGASPFRTLN---QIRTKLNHKPAVVQIPI 195 Score = 63.4 bits (154), Expect = 2e-10 Identities = 70/287 (24%), Positives = 122/287 (42%), Gaps = 58/287 (20%) Query: 149 ARADEVINEVF---------DLFSAL-DATDAQLDFPILYGSGRFGWMSDSSDGSRDQGM 198 A DE + E+F L +A+ AT + P+L GS +++G+ Sbjct: 248 ADVDETLAEMFLEEEEPSAQQLKAAIRRATIKRSFVPVLCGSAL-----------KNKGV 296 Query: 199 VPLLNLIVDHVPPPV---------ISEGEFKMIGTI-LEKDPFLG---RIVTG------- 238 PLL+ +VD++P P + + K+ + +KDPF+ ++ G Sbjct: 297 QPLLDAVVDYLPSPSEVENYALNKETNSKEKVTLSPSRDKDPFVALAFKLEEGRFGQLTY 356 Query: 239 -RIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAGLVKA 297 R++ GT+ I G V VGR+ ++ A D + ++E AGDI ++ G+ A Sbjct: 357 VRVYQGTLSKGDTIYN-VRTGKKVRVGRLVRMHA---NDMEDVNEVLAGDICALFGIDCA 412 Query: 298 TVADTFCDPSIDEPLKAQPID-PPTVTMTFGVNDSPLAGTEGDKVTSRMIRDRLFKEAEG 356 + DTF D + L + I P V V P+ + D + + R KE Sbjct: 413 S-GDTFTDKQ-NLALSMESIHIPEPV---ISVAIKPVNKKDADNFSKALN--RFTKE--- 462 Query: 357 NIALKIEESSSKDAFFVSGRGELQLAVLIETMRRE-GFELAVSRPRV 402 + ++ +SG GEL L + +E + RE + + +P+V Sbjct: 463 DPTFRVSLDPEMKQTVISGMGELHLEIYVERLVREYKVDAELGKPQV 509 Score = 34.5 bits (79), Expect = 0.086 Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 1/89 (1%) Query: 401 RVVIKKEGDSLLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPT 460 R K+ +LEPI V + EE G V+ + K+++ + S + + P Sbjct: 621 REAFKRAPPRILEPIMNVEVTTPEEFQGTVIGDLNKRKAQITGIDSSEDYKT-IKAEVPL 679 Query: 461 RGLIGYQSQLMTDTRGTAIMNRLFHSYQP 489 + GY S+L + T+G + Y P Sbjct: 680 NEMFGYSSELRSLTQGKGEFTMEYSRYSP 708 >gnl|CDD|58063 cd03710, BipA_TypA_C, BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. 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 = 79 Score = 122 bits (307), Expect = 3e-28 Identities = 45/79 (56%), Positives = 61/79 (77%) Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQLMT 472 EPIEE+ IDV EE+SGAV++K+ K EM+++ P G GR RL F P+RGLIG++S+ +T Sbjct: 1 EPIEELTIDVPEEYSGAVIEKLGKRKGEMVDMEPDGNGRTRLEFKIPSRGLIGFRSEFLT 60 Query: 473 DTRGTAIMNRLFHSYQPHK 491 DTRGT IMN +F Y+P+K Sbjct: 61 DTRGTGIMNHVFDGYEPYK 79 >gnl|CDD|35688 KOG0467, KOG0467, KOG0467, Translation elongation factor 2/ribosome biogenesis protein RIA1 and related proteins [Translation, ribosomal structure and biogenesis]. Length = 887 Score = 120 bits (301), Expect = 2e-27 Identities = 55/128 (42%), Positives = 79/128 (61%) Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIV 78 IRNI ++AHVDHGKT+L D L+ +GV R +D + E+ RGIT+ + S++ Sbjct: 9 IRNICLVAHVDHGKTSLADSLVASNGVISSRLAGKIRFLDTREDEQTRGITMKSSAISLL 68 Query: 79 WNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPI 138 D IN++D+PGH DF EV + + +VLVD EG QT V+ +A GL+PI Sbjct: 69 HKDYLINLIDSPGHVDFSSEVSSASRLSDGALVLVDVVEGVCSQTYAVLRQAWIEGLKPI 128 Query: 139 VVVNKVDR 146 +V+NK+DR Sbjct: 129 LVINKIDR 136 Score = 41.9 bits (98), Expect = 5e-04 Identities = 60/267 (22%), Positives = 101/267 (37%), Gaps = 29/267 (10%) Query: 220 KMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPD---GALVEVGRVSKILAFRGID 276 KM+ T L+ P + RI SGT++ Q + L PD + V + F G + Sbjct: 366 KMLATPLKYLPQSRLLAFARIFSGTLRVGQVVYVLGPDPLSPEHITECTVESLYLFMGQE 425 Query: 277 RQPIDEAHAGDIVSIAGLVKATVADTFCDPSIDEPLKAQPIDPPTVTMTFGVNDSPLAGT 336 P+DE +G++V+I G + T C P +T V P Sbjct: 426 LVPLDEVPSGNVVAIGGAGIVLKSATLCSKVPCGPNLVVNF---QITPIVRVAIEPDDPD 482 Query: 337 EGDKVTSRMIRDRLFKEAEGNIALKIEESSSKDAFFVSGRGELQLAVLIETMRR-EGFEL 395 E DK+ + +L +A+ + +++EE+ + GE+ L ++ ++ E+ Sbjct: 483 EMDKLVEGL---KLLNQADPFVKIRVEENGE---HVLVTAGEVHLERCLKDLKEFAKIEI 536 Query: 396 AVSRPRVVIKKEGDSLLEPIEEVVI---DVDEEHSGAVVQKMTLHKSEMIELRPSGTGRV 452 +VS P L P E +I D+ S K I+LR Sbjct: 537 SVSEP-----------LVPFRETIIEDSDLLANLSIGQETKCLPRGQLKIKLRVVPLSGA 585 Query: 453 RLVFLSPTRGLIGYQSQLMTDTRGTAI 479 + L LI + L ++R I Sbjct: 586 VVDLLDKNSSLIS--NILRGESRQVPI 610 >gnl|CDD|133367 cd04167, Snu114p, 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 = 119 bits (300), Expect = 2e-27 Identities = 67/217 (30%), Positives = 112/217 (51%), Gaps = 28/217 (12%) Query: 20 RNIAIIAHVDHGKTTLVDELLKQS---GVFRDNQRVSERVMDCNDLEKERGITILAKVTS 76 RN+AI H+ HGKT+L+D L++Q+ + R D E+ERGI+I + S Sbjct: 1 RNVAIAGHLHHGKTSLLDMLIEQTHDLTPSGKDGWKPLRYTDIRKDEQERGISIKSSPIS 60 Query: 77 IVWNDVR-----INIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKAL 131 +V D + NI+DTPGH +F EV L + + VV++VD EG T+ ++ A+ Sbjct: 61 LVLPDSKGKSYLFNIIDTPGHVNFMDEVAAALRLSDGVVLVVDVVEGVTSNTERLIRHAI 120 Query: 132 KIGLRPIVVVNKVDR---------SDA--RADEVINEVFDLFSALDATDAQLDFP----I 176 GL ++V+NK+DR +DA + +I+EV ++ ++ T + L P + Sbjct: 121 LEGLPIVLVINKIDRLILELKLPPNDAYFKLRHIIDEVNNIIASFSTTLSFLFSPENGNV 180 Query: 177 LYGSGRFGWM-SDSSDGSRDQGMVPLLNLIVDHVPPP 212 + S +FG+ + S L++ IV ++P P Sbjct: 181 CFASSKFGFCFTLESFAK----KYGLVDSIVSNIPSP 213 >gnl|CDD|35690 KOG0469, KOG0469, KOG0469, Elongation factor 2 [Translation, ribosomal structure and biogenesis]. Length = 842 Score = 107 bits (268), Expect = 1e-23 Identities = 64/201 (31%), Positives = 102/201 (50%), Gaps = 35/201 (17%) Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIV 78 IRN+++IAHVDHGK+TL D L++++G+ + R D E+ERGITI + S+ Sbjct: 19 IRNMSVIAHVDHGKSTLTDSLVQKAGIISAAKAGETRFTDTRKDEQERGITIKSTAISLF 78 Query: 79 W----------------NDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQ 122 + N IN++D+PGH DF EV L + + +V+VD G Q Sbjct: 79 FEMSDDDLKFIKQEGDGNGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQ 138 Query: 123 TKFVVGKALKIGLRPIVVVNKVDRSD--------------ARADEVINEVFDLFSALDAT 168 T+ V+ +A+ ++P++V+NK+DR+ R E +N + + Sbjct: 139 TETVLRQAIAERIKPVLVMNKMDRALLELQLSQEELYQTFQRIVENVNVIISTYGDGPMG 198 Query: 169 DAQLDFP----ILYGSGRFGW 185 D Q+D P + +GSG GW Sbjct: 199 DVQVD-PEKGTVGFGSGLHGW 218 Score = 28.8 bits (64), Expect = 4.2 Identities = 23/112 (20%), Positives = 41/112 (36%), Gaps = 11/112 (9%) Query: 384 LIETMRREGFELAV-SRPRVVIKKEGDSLLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMI 442 +I T RR + + + P L EP+ V I E+ G + + + + Sbjct: 705 IIPTARRVLYASVLTAGPI---------LQEPVYLVEIQCPEQAVGGIYGVLNRKRGHVF 755 Query: 443 ELRP-SGTGRVRLVFLSPTRGLIGYQSQLMTDTRGTAIMNRLFHSYQPHKGE 493 E GT + P G+ + L ++T G A +F + G+ Sbjct: 756 EEEQVPGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQMVFDHWSILPGD 807 Score = 27.6 bits (61), Expect = 9.8 Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 9/75 (12%) Query: 238 GRIHSGTIKSNQNIKALSPD-----GALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIA 292 GR+ SG + + ++ P+ + + + + + G +PI++ AG+I+ + Sbjct: 398 GRVFSGKVFTGLKVRIQGPNYVPGKKEDLYIKAIQRTVLMMGRFVEPIEDCPAGNIIGLV 457 Query: 293 G----LVKATVADTF 303 G LVK T Sbjct: 458 GVDQFLVKTGTITTS 472 >gnl|CDD|35685 KOG0464, KOG0464, KOG0464, Elongation factor G [Translation, ribosomal structure and biogenesis]. Length = 753 Score = 107 bits (267), Expect = 1e-23 Identities = 54/143 (37%), Positives = 80/143 (55%), Gaps = 2/143 (1%) Query: 18 QIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSE--RVMDCNDLEKERGITILAKVT 75 +IRNI IIAH+D GKTT + +L +G V + V D +E+ERGITI + Sbjct: 36 KIRNIGIIAHIDAGKTTTTERILYLAGAIHSAGDVDDGDTVTDFLAIERERGITIQSAAV 95 Query: 76 SIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGL 135 + W RIN++DTPGH DF EVER L +++ V + DA+ G QT V +A K + Sbjct: 96 NFDWKGHRINLIDTPGHVDFRLEVERCLRVLDGAVAVFDASAGVEAQTLTVWRQADKFKI 155 Query: 136 RPIVVVNKVDRSDARADEVINEV 158 +NK+D+ A + ++ + Sbjct: 156 PAHCFINKMDKLAANFENAVDSI 178 Score = 35.1 bits (80), Expect = 0.052 Identities = 44/176 (25%), Positives = 72/176 (40%), Gaps = 33/176 (18%) Query: 145 DRSDARADEVINEVFDLFSALDA----------TDAQLDFPILYGSGRFGWMSDSSDGSR 194 D AD+ ++E + F +DA T AQ PIL GS + Sbjct: 254 DLDADFADKFLDEFDENFDKIDAEELKSAIHELTCAQKAAPILCGSA-----------IK 302 Query: 195 DQGMVPLLNLIVDHVPPPVISEGEFKM--------IGTILEKDPFLGRIVTGRIHSGTIK 246 ++G+ PLL+ + ++P P EF + + D G + RI+SG+I Sbjct: 303 NKGIQPLLDAVTMYLPSPEERNYEFLQWYKDDLCALAFKVLHDKQRGPLSFMRIYSGSIH 362 Query: 247 SNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAGLVKATVADT 302 +N I ++ G E + K+ + + I++ AG+I AGL DT Sbjct: 363 NNLAIFNIN--GMCSE--GILKLFLPFADEHREIEQLSAGNIALTAGLKHTATGDT 414 >gnl|CDD|133369 cd04169, RF3, RF3 subfamily. 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 = 267 Score = 106 bits (266), Expect = 3e-23 Identities = 59/152 (38%), Positives = 85/152 (55%), Gaps = 18/152 (11%) Query: 20 RNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER------VMDCNDLEKERGITILAK 73 R AII+H D GKTTL ++LL G R+ V R D ++EK+RGI++ + Sbjct: 3 RTFAIISHPDAGKTTLTEKLLLFGGAIREAGAVKARKSRKHATSDWMEIEKQRGISVTSS 62 Query: 74 VTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTK--FVVGKAL 131 V + D IN++DTPGH DF + R L V+S V+++DAA+G PQT+ F V + Sbjct: 63 VMQFEYRDCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLR 122 Query: 132 KIGLRPIV-VVNKVDRSDARA-----DEVINE 157 I PI+ +NK+DR + R DE+ E Sbjct: 123 GI---PIITFINKLDR-EGRDPLELLDEIEEE 150 >gnl|CDD|58082 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 = 105 bits (263), Expect = 5e-23 Identities = 36/87 (41%), Positives = 55/87 (63%), Gaps = 1/87 (1%) Query: 219 FKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQ 278 +M+ T L+ D ++GRI GRI GT+K Q + + DG +E +++K+ F G+ R Sbjct: 1 LQMLVTTLDYDDYVGRIAIGRIFRGTVKVGQQVAVVKRDGK-IEKAKITKLFGFEGLKRV 59 Query: 279 PIDEAHAGDIVSIAGLVKATVADTFCD 305 ++EA AGDIV+IAG+ T+ DT CD Sbjct: 60 EVEEAEAGDIVAIAGIEDITIGDTICD 86 >gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily. 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 = 104 bits (262), Expect = 7e-23 Identities = 47/146 (32%), Positives = 76/146 (52%), Gaps = 2/146 (1%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSE--RVMDCNDLEKERGITILAKVTSIV 78 NIA++ H GKTTL + LL +G V + V D + E +R ++I V + Sbjct: 1 NIALVGHSGSGKTTLAEALLYATGAIDRLGSVEDGTTVSDYDPEEIKRKMSISTSVAPLE 60 Query: 79 WNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPI 138 W +IN++DTPG+ADF GE L ++ +V+V A G T+ + A + G+ I Sbjct: 61 WKGHKINLIDTPGYADFVGETRAALRAADAALVVVSAQSGVEVGTEKLWEFADEAGIPRI 120 Query: 139 VVVNKVDRSDARADEVINEVFDLFSA 164 + +NK+DR A D+ + + + F Sbjct: 121 IFINKMDRERADFDKTLAALQEAFGR 146 >gnl|CDD|33865 COG4108, PrfC, Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]. Length = 528 Score = 102 bits (255), Expect = 4e-22 Identities = 55/148 (37%), Positives = 83/148 (56%), Gaps = 12/148 (8%) Query: 20 RNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER------VMDCNDLEKERGITILAK 73 R AII+H D GKTTL ++LL G ++ V R D ++EK+RGI++ + Sbjct: 13 RTFAIISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGKHAKSDWMEIEKQRGISVTSS 72 Query: 74 VTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTK--FVVGKAL 131 V + D +N++DTPGH DF + R L V+S V+++DAA+G PQT F V + Sbjct: 73 VMQFDYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIEPQTLKLFEVCRLR 132 Query: 132 KIGLRPIV-VVNKVDRSDARADEVINEV 158 I PI +NK+DR E+++E+ Sbjct: 133 DI---PIFTFINKLDREGRDPLELLDEI 157 Score = 38.3 bits (89), Expect = 0.006 Identities = 36/137 (26%), Positives = 55/137 (40%), Gaps = 26/137 (18%) Query: 197 GMVPLLNLIVDHVPPP--------VISEGEFKMIGTILE----KDP-FLGRIVTGRIHSG 243 G+ L+ +VD P P + E K G + + DP RI R+ SG Sbjct: 263 GVDHFLDALVDWAPSPRARQADTREVEPTEDKFSGFVFKIQANMDPKHRDRIAFMRVCSG 322 Query: 244 TIKSNQNIKALSPDGALVEVGR---VSKILAFRGIDRQPIDEAHAGDIVSIAGLVKATVA 300 + + V G+ +S L F DR+ ++EA+AGDI+ + + Sbjct: 323 KFERGMKVT-------HVRTGKDVKLSDALTFMAQDRETVEEAYAGDIIGLHNHGTIQIG 375 Query: 301 DTFCDPSIDEPLKAQPI 317 DTF + E LK I Sbjct: 376 DTFTE---GEKLKFTGI 389 >gnl|CDD|35689 KOG0468, KOG0468, KOG0468, U5 snRNP-specific protein [Translation, ribosomal structure and biogenesis]. Length = 971 Score = 100 bits (251), Expect = 1e-21 Identities = 64/188 (34%), Positives = 102/188 (54%), Gaps = 21/188 (11%) Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGV-FRDNQRVSERVMDCNDLEKERGITILAKVTSI 77 IRN+ ++ H+ HGKT L+D L++Q+ F N R D E+ERG +I + ++ Sbjct: 128 IRNVGLVGHLHHGKTALMDLLVEQTHPDFSKNTEADLRYTDTLFYEQERGCSIKSTPVTL 187 Query: 78 VWNDVR-----INIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALK 132 V +D + +NI+DTPGH +F E L + + VV++VD AEG M T+ ++ A++ Sbjct: 188 VLSDSKGKSYLMNILDTPGHVNFSDETTASLRLSDGVVLVVDVAEGVMLNTERIIKHAIQ 247 Query: 133 IGLRPIVVVNKVDR---------SDA--RADEVINEVFDLFSALDATDAQLDFPIL---- 177 L +VV+NKVDR DA + +I+E+ +L S D + PIL Sbjct: 248 NRLPIVVVINKVDRLILELKLPPMDAYYKLRHIIDEINNLISTFSKDDNPVVSPILGNVC 307 Query: 178 YGSGRFGW 185 + SG+ G+ Sbjct: 308 FASGKLGF 315 Score = 40.4 bits (94), Expect = 0.002 Identities = 45/181 (24%), Positives = 74/181 (40%), Gaps = 24/181 (13%) Query: 236 VTGRIHSGTIKSNQNIKALS-----PDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVS 290 V GR++SG + + Q+++ L D + + V ++ R R P+ A AG V Sbjct: 491 VFGRVYSGQVVTGQDVRVLGENYSLEDEEDMVICEVGELWVVRARYRIPVSRAPAGLWVL 550 Query: 291 IAGLVKATV-ADTFCDPSIDEPLKAQPIDPPTVTMT---FGVNDSPLAGTEGDKVTSRMI 346 I G+ ++ V T E + I P T V PL +E K+ Sbjct: 551 IEGVDQSIVKTATIKSLEYKEDVY---IFRPLKFNTEPVVKVAVEPLNPSELPKML---- 603 Query: 347 RDRLFKEAEG--NIALKIEESSSKDAFFVSGRGELQLAVLIETMRR--EGFELAVSRPRV 402 D L K + + K+EES + G GEL + ++ +R+ E+ V+ P V Sbjct: 604 -DGLRKINKSYPLVITKVEESGEH---VILGTGELYMDCVLYDLRKSYSEIEIKVADPVV 659 Query: 403 V 403 Sbjct: 660 R 660 Score = 28.5 bits (63), Expect = 5.8 Identities = 23/113 (20%), Positives = 45/113 (39%), Gaps = 11/113 (9%) Query: 383 VLIETMRREGFE-LAVSRPRVVIKKEGDSLLEPIEEVVIDVDEEHSGAVVQKMTLHKSEM 441 +I T RR + ++ PR L+EP+ V I + AV ++ + + Sbjct: 806 QIIPTARRVAYSAFLMATPR---------LMEPVYLVEITAPADCVPAVYTVLSRRRGHV 856 Query: 442 IELRP-SGTGRVRLVFLSPTRGLIGYQSQLMTDTRGTAIMNRLFHSYQPHKGE 493 + P G+ + P G+++ L T+G A +F ++ G+ Sbjct: 857 TQDIPVPGSPLYTVKAYLPVIESFGFETDLRVHTQGQAFCLSVFDHWRIVPGD 909 >gnl|CDD|34853 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]. Length = 428 Score = 97.6 bits (243), Expect = 9e-21 Identities = 83/339 (24%), Positives = 132/339 (38%), Gaps = 55/339 (16%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER-----------------VMDCNDLE 63 N+ I HVD GK+TLV LL G ++R E+ V+D E Sbjct: 9 NLVFIGHVDAGKSTLVGRLLYDLGEI--DKRTMEKLEKEAKELGKESFKFAWVLDKTKEE 66 Query: 64 KERGITILAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEG----- 118 +ERG+TI + + I+D PGH DF + + V++VDA +G Sbjct: 67 RERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARDGEFEAG 126 Query: 119 --PMPQTKFVVGKALKIGLRPIVV-VNKVDR---SDARADEVINEVFDLFSALDATDAQL 172 QT+ A +G++ ++V VNK+D + R +E+++EV L + + Sbjct: 127 FGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLLKMVGYNPKDV 186 Query: 173 DF-PI--LYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPPVISEGEFKMIGTILEKD 229 F PI G ++ S+ LL + PP + ++ I + Sbjct: 187 PFIPISGFKGDN----LTKKSENMPWYKGPTLLEALDQLEPPERPLDKPLRL--PIQDVY 240 Query: 230 PFLGR--IVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGD 287 G + GR+ SG IK Q + P G + EV + + + I +A GD Sbjct: 241 SISGIGTVPVGRVESGVIKPGQKVT-FMPAGVVGEVKSIE-------MHHEEISQAEPGD 292 Query: 288 IVSIAGLVKATVADTFCDPSIDEPLKAQPIDPPTVTMTF 326 V G V + +PPTV+ F Sbjct: 293 NV---GFNVRGVEKNDIRRGD---VIGHSDNPPTVSPEF 325 >gnl|CDD|30399 COG0050, TufB, GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis]. Length = 394 Score = 91.8 bits (228), Expect = 4e-19 Identities = 77/291 (26%), Positives = 123/291 (42%), Gaps = 47/291 (16%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDL---EKERGITILAKVTSI 77 N+ I HVDHGKTTL + + V + D D EK RGITI Sbjct: 14 NVGTIGHVDHGKTTLTAAI---TTVLAKKGGAEAKAYDQIDNAPEEKARGITINTAHVEY 70 Query: 78 VWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRP 137 + VD PGHAD+ + ++ +++V A +GPMPQT+ + A ++G+ Sbjct: 71 ETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLARQVGVPY 130 Query: 138 IVV-VNKVDRSDAR--ADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSR 194 IVV +NKVD D + V EV +L S D PI+ GS + + Sbjct: 131 IVVFLNKVDMVDDEELLELVEMEVRELLSEYGFPGD--DTPIIRGSA-LKALEGDAKW-- 185 Query: 195 DQGMVPLLNLIVDHVPPPVISEGEFKMIGTILEKDPFL------------GRIVTGRIHS 242 + + L++ + ++P P PFL G +VTGR+ Sbjct: 186 EAKIEELMDAVDSYIPTPERD-----------IDKPFLMPVEDVFSISGRGTVVTGRVER 234 Query: 243 GTIKSNQNIKALSPDGALVEVGRVSKILAFRGID--RQPIDEAHAGDIVSI 291 G +K + ++ + + ++ G++ R+ +DE AGD V + Sbjct: 235 GILKVGEEVEIVG--------IKETQKTTVTGVEMFRKLLDEGQAGDNVGV 277 >gnl|CDD|144322 pfam00679, EFG_C, Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold. Length = 89 Score = 90.7 bits (226), Expect = 1e-18 Identities = 29/84 (34%), Positives = 47/84 (55%) Query: 411 LLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQL 470 LLEPI +V I V EE+ G V+ + + E++++ P G GRV + P L G+ ++L Sbjct: 2 LLEPIMKVEITVPEEYLGDVIGDLNKRRGEILDMEPIGGGRVVIEAEVPLAELFGFSTEL 61 Query: 471 MTDTRGTAIMNRLFHSYQPHKGEI 494 + T+G + F Y+P G+I Sbjct: 62 RSLTQGRGSFSMEFSGYEPVPGDI 85 >gnl|CDD|35681 KOG0460, KOG0460, KOG0460, Mitochondrial translation elongation factor Tu [Translation, ribosomal structure and biogenesis]. Length = 449 Score = 81.1 bits (200), Expect = 8e-16 Identities = 77/276 (27%), Positives = 125/276 (45%), Gaps = 23/276 (8%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80 N+ I HVDHGKTTL + K + +D EK RGITI A Sbjct: 56 NVGTIGHVDHGKTTLTAAITKILAEKGGAKFKKYDEIDKAPEEKARGITINAAHVEYETA 115 Query: 81 DVRINIVDTPGHADFGGEVERILC---MVESVVVLVDAAEGPMPQTKFVVGKALKIGLRP 137 D PGHAD+ ++ ++ ++ +++V A +GPMPQT+ + A ++G++ Sbjct: 116 KRHYAHTDCPGHADY---IKNMITGAAQMDGAILVVAATDGPMPQTREHLLLARQVGVKH 172 Query: 138 IVV-VNKVDR-SDARADEVIN-EVFDLFS--ALDATDAQLDFPILYGSGRFGWMSDSSDG 192 IVV +NKVD D E++ E+ +L S D + P++ GS + Sbjct: 173 IVVFINKVDLVDDPEMLELVEMEIRELLSEFGFDGDNT----PVIRGSALCALEGRQPEI 228 Query: 193 SRDQGMVPLLNLIVDHVPPPV-ISEGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNI 251 + + LL+ + ++P P + F + + P G +VTGR+ G +K + Sbjct: 229 GL-EAIEKLLDAVDSYIPTPERDLDKPFLLPIEDVFSIPGRGTVVTGRLERGVLKKGDEV 287 Query: 252 KALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGD 287 + + + L V+ I FR +DEA AGD Sbjct: 288 EIVGHNKTLKTT--VTGIEMFRKS----LDEAQAGD 317 >gnl|CDD|58061 cd01514, Elongation_Factor_C, Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p. This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain. EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome. Tet(M) and Tet(O) mediate Tc resistance. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. Yeast Snu114p is essential for cell viability and for splicing in vivo. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. The function of LepA proteins is unknown.. Length = 79 Score = 76.4 bits (188), Expect = 2e-14 Identities = 27/77 (35%), Positives = 44/77 (57%) Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQLMT 472 EPI +V I V EE+ GAV+ ++ + E++ + P GTGRV + P + G+ + L + Sbjct: 1 EPIMKVEITVPEEYLGAVIGDLSKRRGEILGMEPRGTGRVVIKAELPLAEMFGFATDLRS 60 Query: 473 DTRGTAIMNRLFHSYQP 489 T+G A + F Y+P Sbjct: 61 LTQGRASFSMEFSHYEP 77 >gnl|CDD|133283 cd01883, EF1_alpha, Eukaryotic elongation factor 1 (EF1) alpha subfamily. EF1 is responsible for the GTP-dependent binding of aminoacyl-tRNAs to the ribosomes. EF1 is composed of four subunits: the alpha chain which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This subfamily is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha interacts with the actin of the eukaryotic cytoskeleton and may thereby play a role in cellular transformation and apoptosis. EF-Tu can have no such role in bacteria. In humans, the isoform eEF1A2 is overexpressed in 2/3 of breast cancers and has been identified as a putative oncogene. This subfamily also includes Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation in yeast, and to associate with Dom34. It has been speculated that yeast Hbs1 and Dom34 proteins may function as part of a complex with a role in gene expression. Length = 219 Score = 76.4 bits (189), Expect = 2e-14 Identities = 52/179 (29%), Positives = 77/179 (43%), Gaps = 54/179 (30%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER-----------------VMDCNDLE 63 N+ +I HVD GK+T LL G ++R E+ V+D E Sbjct: 1 NLVVIGHVDAGKSTTTGHLLYLLGGV--DKRTIEKYEKEAKEMGKGSFKYAWVLDTLKEE 58 Query: 64 KERGITI---LAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESV------VVLVD 114 +ERG+TI LAK + R I+D PGH DF + M+ V++VD Sbjct: 59 RERGVTIDVGLAKFET---EKYRFTILDAPGHRDF------VPNMITGASQADVAVLVVD 109 Query: 115 AAEG-------PMPQTK---FVVGKALKIGLRPIVVVNKVDR-----SDARADEVINEV 158 A +G QT+ + + L + + IV VNK+D S+ R DE+ E+ Sbjct: 110 ARKGEFEAGFEKGGQTREHALLA-RTLGVK-QLIVAVNKMDDVTVNWSEERYDEIKKEL 166 >gnl|CDD|177010 CHL00071, tufA, elongation factor Tu. Length = 409 Score = 74.2 bits (183), Expect = 1e-13 Identities = 87/306 (28%), Positives = 130/306 (42%), Gaps = 67/306 (21%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80 NI I HVDHGKTTL + + +D EK RGITI Sbjct: 14 NIGTIGHVDHGKTTLTAAITMTLAAKGGAKAKKYDEIDSAPEEKARGITINTAHVEYETE 73 Query: 81 DVRINIVDTPGHADFGGEVERILCM------VESVVVLVDAAEGPMPQTKFVVGKALKIG 134 + VD PGHAD+ + M ++ +++V AA+GPMPQTK + A ++G Sbjct: 74 NRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVSAADGPMPQTKEHILLAKQVG 127 Query: 135 LRPIVV-VNKVDRSDARADEVIN----EVFDLFSALD-ATDAQLDFPILYGSGRFGWMSD 188 + IVV +NK D+ D +E++ EV +L S D D D PI+ GS + Sbjct: 128 VPNIVVFLNKEDQVD--DEELLELVELEVRELLSKYDFPGD---DIPIVSGSALLALEAL 182 Query: 189 SSDGSRDQGMVP-------LLNLIVDHVPPPVISEGEFKMIGTILEKD-PFL-------- 232 + + +G L++ + ++P P + D PFL Sbjct: 183 TENPKIKRGENKWVDKIYNLMDAVDSYIPTPE------------RDTDKPFLMAIEDVFS 230 Query: 233 ----GRIVTGRIHSGTIKSNQNIKALSPDGALVEVG-RVSKILAFRGID--RQPIDEAHA 285 G + TGRI GT+K ++ VG R +K G++ ++ +DE A Sbjct: 231 ITGRGTVATGRIERGTVKVGDTVEI---------VGLRETKTTTVTGLEMFQKTLDEGLA 281 Query: 286 GDIVSI 291 GD V I Sbjct: 282 GDNVGI 287 >gnl|CDD|133371 cd04171, SelB, SelB subfamily. 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 = 164 Score = 73.0 bits (180), Expect = 2e-13 Identities = 51/154 (33%), Positives = 74/154 (48%), Gaps = 30/154 (19%) Query: 27 HVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITI-LAKVTSIVWNDVRIN 85 H+DHGKTTL+ L +G+ + R+ E EK+RGITI L + + R+ Sbjct: 8 HIDHGKTTLIKAL---TGI--ETDRLPE--------EKKRGITIDLGFAYLDLPSGKRLG 54 Query: 86 IVDTPGHADFGGEVERILCMVESV-----VVLVDAA-EGPMPQTK--FVVGKALKIGLRP 137 +D PGH F I M+ V+LV AA EG MPQT+ + + L I R Sbjct: 55 FIDVPGHEKF------IKNMLAGAGGIDLVLLVVAADEGIMPQTREHLEILELLGIK-RG 107 Query: 138 IVVVNKVDR-SDARADEVINEVFDLFSALDATDA 170 +VV+ K D + + V E+ +L + DA Sbjct: 108 LVVLTKADLVDEDWLELVEEEIRELLAGTFLADA 141 >gnl|CDD|133287 cd01887, IF2_eIF5B, IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. 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 = 168 Score = 71.8 bits (177), Expect = 6e-13 Identities = 46/147 (31%), Positives = 68/147 (46%), Gaps = 33/147 (22%) Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKE-RGIT--ILA-KVTSI 77 + ++ HVDHGKTTL+D++ K N E GIT I A +V + Sbjct: 3 VTVMGHVDHGKTTLLDKIRK-----------------TNVAAGEAGGITQHIGAFEVPAE 45 Query: 78 VWNDVRINIVDTPGHADF------GGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKAL 131 V I +DTPGH F G + I +++V A +G MPQT + A Sbjct: 46 VLKIPGITFIDTPGHEAFTNMRARGASLTDI------AILVVAADDGVMPQTIEAIKLAK 99 Query: 132 KIGLRPIVVVNKVDRSDARADEVINEV 158 + IV +NK+D+ +A + V NE+ Sbjct: 100 AANVPFIVALNKIDKPNANPERVKNEL 126 >gnl|CDD|32720 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]. Length = 431 Score = 70.7 bits (173), Expect = 1e-12 Identities = 78/327 (23%), Positives = 129/327 (39%), Gaps = 46/327 (14%) Query: 27 HVDHGKTTLVDELLKQSGVFRDNQ-----RVSER------------VMDCNDLEKERGIT 69 VD GK+TL+ LL + ++Q R S+R ++D + E+E+GIT Sbjct: 14 SVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLVDGLEAEREQGIT 73 Query: 70 ILAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGK 129 I + I DTPGH + + + ++LVDA +G + QT+ Sbjct: 74 IDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTADLAILLVDARKGVLEQTRRHSFI 133 Query: 130 ALKIGLRPIVV-VNK---VDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFG- 184 A +G+R +VV VNK VD S+ + ++ + + L D + PI S G Sbjct: 134 ASLLGIRHVVVAVNKMDLVDYSEEVFEAIVADYLAFAAQLGLKDVRF-IPI---SALLGD 189 Query: 185 WMSDSSDGSRDQGMVPLLNLIVDHVPPPVISEGEFKMIGTILEKDPFLGRIVTGRIHSGT 244 + S+ LL ++ S F+ + + R G I SG+ Sbjct: 190 NVVSKSENMPWYKGPTLLEILETVEIADDRSAKAFRFPVQYVNRPNLDFRGYAGTIASGS 249 Query: 245 IKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSI--AGLVKATVADT 302 +K + L P G + RV +I+ F G + +A AG+ V++ A + + D Sbjct: 250 VKVGDEVVVL-PSG---KTSRVKRIVTFDG----ELAQASAGEAVTLVLADEIDISRGDL 301 Query: 303 FCDPSIDEPLKAQPIDPPTVTMTFGVN 329 PP V F + Sbjct: 302 IVAAD----------APPAVADAFDAD 318 >gnl|CDD|33087 COG3276, SelB, Selenocysteine-specific translation elongation factor [Translation, ribosomal structure and biogenesis]. Length = 447 Score = 70.0 bits (171), Expect = 2e-12 Identities = 77/276 (27%), Positives = 116/276 (42%), Gaps = 44/276 (15%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80 I H+DHGKTTL+ L +G D R+ E EK+RGITI Sbjct: 2 IIGTAGHIDHGKTTLLKAL---TGGVTD--RLPE--------EKKRGITIDLGFYYRKLE 48 Query: 81 DVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTK--FVVGKALKIGLRPI 138 D + +D PGH DF + L ++ +++V A EG M QT ++ L I I Sbjct: 49 DGVMGFIDVPGHPDFISNLLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGI-KNGI 107 Query: 139 VVVNKVDRSD-ARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSRDQG 197 +V+ K DR D AR ++ I ++ S +A F +G +G Sbjct: 108 IVLTKADRVDEARIEQKIKQILADLSLANAK----IFKTSAKTG--------------RG 149 Query: 198 MVPLLNLIVDHVPPPVI-SEGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSP 256 + L N ++D + + F++ +G +VTG + SG +K + LSP Sbjct: 150 IEELKNELIDLLEEIERDEQKPFRIAIDRAFTVKGVGTVVTGTVLSGEVKVGDKLY-LSP 208 Query: 257 DGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIA 292 V RV I A ++EA AG V +A Sbjct: 209 INKEV---RVRSIQAH----DVDVEEAKAGQRVGLA 237 >gnl|CDD|35679 KOG0458, KOG0458, KOG0458, Elongation factor 1 alpha [Translation, ribosomal structure and biogenesis]. Length = 603 Score = 67.3 bits (164), Expect = 1e-11 Identities = 75/304 (24%), Positives = 128/304 (42%), Gaps = 43/304 (14%) Query: 21 NIAIIAHVDHGKTTLVDELLK-----QSGVFRDNQRVSER----------VMDCNDLEKE 65 N+ ++ HVD GK+TL+ LL S +R S+ ++D E+E Sbjct: 179 NLVVLGHVDAGKSTLMGHLLYDLGEISSRSMHKLERESKNLGKSSFAYAWILDETKEERE 238 Query: 66 RGITILAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEG------- 118 RG+T+ K T + ++D PGH DF + + V++VDA+ G Sbjct: 239 RGVTMDVKTTWFESKSKIVTLIDAPGHKDFIPNMISGASQADVAVLVVDASTGEFESGFD 298 Query: 119 PMPQTKFVVGKALKIGLRP-IVVVNKVDR---SDARADEVINEVFD-LFSALDATDAQLD 173 P QT+ +G+ IV +NK+D S R +E+ N++ L + ++ + Sbjct: 299 PGGQTREHALLLRSLGISQLIVAINKMDLVSWSQDRFEEIKNKLSSFLKESCGFKESSVK 358 Query: 174 F-PI--LYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPPVISEGEFKMIGTILE--K 228 F PI L G ++ +G LL+ I P + ++ TI + Sbjct: 359 FIPISGLSGENLIKIEQENELSQWYKGPT-LLSQIDSFKIPERPIDKPLRL--TISDIYP 415 Query: 229 DPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDI 288 P G ++G+I SG I+ Q + ++ E V + + + +P A AGD Sbjct: 416 LPSSGVSISGKIESGYIQPGQKLYIMTS----REDATVKGLTS----NDEPKTWAVAGDN 467 Query: 289 VSIA 292 VS+ Sbjct: 468 VSLK 471 >gnl|CDD|30878 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]. Length = 509 Score = 66.0 bits (161), Expect = 3e-11 Identities = 74/305 (24%), Positives = 120/305 (39%), Gaps = 74/305 (24%) Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGIT--ILA-KVTSIV 78 + I+ HVDHGKTTL+D++ K + + GIT I A +V V Sbjct: 8 VTIMGHVDHGKTTLLDKIRKTNVAAGE----------------AGGITQHIGAYQVPLDV 51 Query: 79 WNDVRINIVDTPGHADF------GGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALK 132 I +DTPGH F G V I +++V A +G MPQT + A Sbjct: 52 IKIPGITFIDTPGHEAFTAMRARGASVTDI------AILVVAADDGVMPQTIEAINHAKA 105 Query: 133 IGLRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDG 192 G+ +V +NK+D+ +A D+V E+ + L + D + S + G Sbjct: 106 AGVPIVVAINKIDKPEANPDKVKQELQEY--GLVPEEWGGDVIFVPVSAKTG-------- 155 Query: 193 SRDQGMVPLLNLIVDHVPPPVISEGEFKM--------IGTILE--KDPFLGRIVTGRIHS 242 +G+ LL LI ++ ++ GT++E D LG + T + Sbjct: 156 ---EGIDELLELI-------LLLAEVLELKANPEGPARGTVIEVKLDKGLGPVATVIVQD 205 Query: 243 GTIK---------SNQNIKALSPD-GALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIA 292 GT+K ++ + D G ++ SK + G+ P A + + Sbjct: 206 GTLKKGDIIVAGGEYGRVRTMVDDLGKPIKEAGPSKPVEILGLSEVP---AAGDVFIVVK 262 Query: 293 GLVKA 297 KA Sbjct: 263 DEKKA 267 >gnl|CDD|36360 KOG1145, KOG1145, KOG1145, Mitochondrial translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]. Length = 683 Score = 65.4 bits (159), Expect = 5e-11 Identities = 45/139 (32%), Positives = 67/139 (48%), Gaps = 19/139 (13%) Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGIT--ILAKVTSIVW 79 + I+ HVDHGKTTL+D L K S + GIT I A ++ Sbjct: 156 VTIMGHVDHGKTTLLDALRKSSVAAGEAG----------------GITQHIGAFTVTLP- 198 Query: 80 NDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPIV 139 + I +DTPGHA F R + + VV++V A +G MPQT + A + +V Sbjct: 199 SGKSITFLDTPGHAAFSAMRARGANVTDIVVLVVAADDGVMPQTLEAIKHAKSANVPIVV 258 Query: 140 VVNKVDRSDARADEVINEV 158 +NK+D+ A ++V E+ Sbjct: 259 AINKIDKPGANPEKVKREL 277 >gnl|CDD|133284 cd01884, EF_Tu, 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 = 63.7 bits (156), Expect = 1e-10 Identities = 65/228 (28%), Positives = 94/228 (41%), Gaps = 72/228 (31%) Query: 21 NIAIIAHVDHGKTTLVDEL-----LKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVT 75 N+ I HVDHGKTTL + K F+ + D EK RGITI Sbjct: 4 NVGTIGHVDHGKTTLTAAITKVLAKKGGAKFKKYDEI-----DKAPEEKARGITI----- 53 Query: 76 SIVWNDVRINI--------------VDTPGHADFGGEVERILCMV------ESVVVLVDA 115 N VD PGHAD+ I M+ + +++V A Sbjct: 54 ---------NTAHVEYETANRHYAHVDCPGHADY------IKNMITGAAQMDGAILVVSA 98 Query: 116 AEGPMPQTKFVVGKALKIGLRPIVV-VNKVDRSDARADE-----VINEVFDLFSA--LDA 167 +GPMPQT+ + A ++G+ IVV +NK D D DE V EV +L S D Sbjct: 99 TDGPMPQTREHLLLARQVGVPYIVVFLNKADMVD---DEELLELVEMEVRELLSKYGFDG 155 Query: 168 TDAQLDFPILYGSGRFGWMSDSSDGSRDQGMVPLLNLI--VD-HVPPP 212 + PI+ GS + ++ + +L L+ +D ++P P Sbjct: 156 DNT----PIVRGSA-LKALEGDDP---NKWVKKILELLDALDSYIPTP 195 >gnl|CDD|133289 cd01889, SelB_euk, SelB subfamily. 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 = 63.5 bits (155), Expect = 1e-10 Identities = 42/144 (29%), Positives = 71/144 (49%), Gaps = 33/144 (22%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITI---------- 70 N+ ++ HVD GKT+L L ++ S D N +ERGIT+ Sbjct: 2 NVGVLGHVDSGKTSLAKAL---------SEIASTAAFDKNPQSQERGITLDLGFSSFYVD 52 Query: 71 ----LAKVTSIVWNDVRINIVDTPGHADFGGEVERILC---MVESVVVLVDAAEGPMPQT 123 L ++ + +++I +VD PGHA + I+ +++ ++++VDA +G QT Sbjct: 53 KPKHLRELINPGEENLQITLVDCPGHASL---IRTIIGGAQIIDLMLLVVDATKGIQTQT 109 Query: 124 K--FVVGKALKIGLRPIVVVNKVD 145 V+G+ L L IVV+NK+D Sbjct: 110 AECLVIGEILCKKL--IVVLNKID 131 >gnl|CDD|58095 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 = 61.6 bits (150), Expect = 6e-10 Identities = 26/77 (33%), Positives = 44/77 (57%), Gaps = 4/77 (5%) Query: 229 DPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDI 288 DPF+G++ R++SGT+K+ + + + RV ++L G ++ ++EA AGDI Sbjct: 11 DPFVGKLSFVRVYSGTLKAGSTLYNSTKG----KKERVGRLLRMHGKKQEEVEEAGAGDI 66 Query: 289 VSIAGLVKATVADTFCD 305 ++AGL DT CD Sbjct: 67 GAVAGLKDTATGDTLCD 83 >gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional. Length = 742 Score = 61.0 bits (148), Expect = 9e-10 Identities = 40/138 (28%), Positives = 63/138 (45%), Gaps = 22/138 (15%) Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKER-GIT--ILAKVTSIV 78 + I+ HVDHGKTTL+D++ K +KE GIT I A Sbjct: 247 VTILGHVDHGKTTLLDKIRKT-----------------QIAQKEAGGITQKIGAYEVEFE 289 Query: 79 WNDVRINIV--DTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLR 136 + D IV DTPGH F R + + ++++ A +G PQT + + Sbjct: 290 YKDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANVP 349 Query: 137 PIVVVNKVDRSDARADEV 154 IV +NK+D+++A + + Sbjct: 350 IIVAINKIDKANANTERI 367 >gnl|CDD|133366 cd04166, CysN_ATPS, 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 = 208 Score = 58.7 bits (143), Expect = 5e-09 Identities = 49/188 (26%), Positives = 79/188 (42%), Gaps = 57/188 (30%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQR---VSER------------VMDCNDLEKE 65 VD GK+TL+ LL S ++Q S+ ++D E+E Sbjct: 1 RFLTCGSVDDGKSTLIGRLLYDSKSIFEDQLAALESKSCGTGGEPLDLALLVDGLQAERE 60 Query: 66 RGITILAKVTSIVWNDV----------RINIVDTPGHADFGGEVERILCMV------ESV 109 +GITI DV + I DTPGH + MV + Sbjct: 61 QGITI----------DVAYRYFSTPKRKFIIADTPGHEQYTRN------MVTGASTADLA 104 Query: 110 VVLVDAAEGPMPQTK---FVVGKALKIGLRPIVV-VNK---VDRSDARADEVINEVFDLF 162 ++LVDA +G + QT+ +++ +L +G+R +VV VNK VD S+ +E++ + Sbjct: 105 ILLVDARKGVLEQTRRHSYIL--SL-LGIRHVVVAVNKMDLVDYSEEVFEEIVADYLAFA 161 Query: 163 SALDATDA 170 + L D Sbjct: 162 AKLGIEDI 169 >gnl|CDD|35680 KOG0459, KOG0459, KOG0459, Polypeptide release factor 3 [Translation, ribosomal structure and biogenesis]. Length = 501 Score = 57.3 bits (138), Expect = 1e-08 Identities = 69/302 (22%), Positives = 117/302 (38%), Gaps = 43/302 (14%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQR-VSER--------------VMDCNDLEKE 65 N I HVD GK+T+ +L +G+ ER +D N E++ Sbjct: 81 NAVFIGHVDAGKSTIGGNILFLTGMVDKRTLEKYEREAKEKNRESWYLSWALDTNGEERD 140 Query: 66 RGITILAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPM----- 120 +G T+ + R I+D PGH F + + V+++ A +G Sbjct: 141 KGKTVEVGRAYFETENKRFTILDAPGHKSFVPNMIGGASQADLAVLVISARKGEFETGFE 200 Query: 121 --PQTK--FVVGKALKIGLRPIVVVNKVDR-----SDARADEVINEVFDLFSALDATDAQ 171 QT+ ++ K + IV++NK+D S+ R +E E F + + Sbjct: 201 KGGQTREHAMLAKTAGVK-HLIVLINKMDDPTVNWSNERYEE-CKEKLQPFLRKLGFNPK 258 Query: 172 LDFPILYGSGRFG-WMSDSSDGSRDQGMVPLLNLIVDHVP-PPVISEGEFKMIGTILEKD 229 D + SG G + D +D P+ +D +P I G + + K Sbjct: 259 PDKHFVPVSGLTGANVKDRTDSVCPWYKGPIFLEYLDELPHLERILNGPIRC--PVANKY 316 Query: 230 PFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIV 289 +G +V G++ SG+IK Q + + P+ VE V I + D D G+ V Sbjct: 317 KDMGTVVGGKVESGSIKKGQQLVVM-PNKTNVE---VLGIYS----DDVETDRVAPGENV 368 Query: 290 SI 291 + Sbjct: 369 KL 370 >gnl|CDD|35682 KOG0461, KOG0461, KOG0461, Selenocysteine-specific elongation factor [Translation, ribosomal structure and biogenesis]. Length = 522 Score = 56.2 bits (135), Expect = 3e-08 Identities = 66/284 (23%), Positives = 115/284 (40%), Gaps = 38/284 (13%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITI---------L 71 N+ I+ HVD GKTTL L + S D + ERGIT+ L Sbjct: 9 NLGILGHVDSGKTTLARALSELG---------STAAFDKHPQSTERGITLDLGFSTMTVL 59 Query: 72 AKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKAL 131 + ++ +VD PGHA + +++ +++++D +G QT + Sbjct: 60 SPARLPQGEQLQFTLVDCPGHASLIRTIIGGAQIIDLMILVIDVQKGKQTQTAECLIIGE 119 Query: 132 KIGLRPIVVVNKVD--RSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDS 189 + + +VV+NK+D + RA ++ + L++T + PI+ S + Sbjct: 120 LLCKKLVVVINKIDVLPENQRASKIEKSAKKVRKTLESTGFDGNSPIVEVS--------A 171 Query: 190 SDGSRDQGMVPLLNLIVDH--VPPPVISEGEFKMIGTILEKDPFLGRIVTGRIHSGTIKS 247 +DG + M+ L ++ P EG F M G ++TG + G ++ Sbjct: 172 ADGYFKEEMIQELKEALESRIFEPKRDEEGPFLMAVDHCFAIKGQGTVLTGTVLRGVLRL 231 Query: 248 NQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSI 291 N I+ AL E +V + F +Q + A AGD Sbjct: 232 NTEIEF----PALNEKRKVKSLQMF----KQRVTSAAAGDRAGF 267 >gnl|CDD|145992 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 = 54.6 bits (132), Expect = 9e-08 Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 2/72 (2%) Query: 233 GRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIA 292 G + TGR+ SGT+K + + GRV+ + F G R+ + A+AG I++ Sbjct: 1 GTVATGRVESGTLKKGDKVVIGP--NGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGI 58 Query: 293 GLVKATVADTFC 304 GL DT Sbjct: 59 GLKDIKRGDTLT 70 >gnl|CDD|34854 COG5257, GCD11, Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]. Length = 415 Score = 53.3 bits (128), Expect = 2e-07 Identities = 75/334 (22%), Positives = 131/334 (39%), Gaps = 87/334 (26%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80 NI ++ HVDHGKTTL L SGV+ D R SE E +RGITI Sbjct: 12 NIGMVGHVDHGKTTLTKAL---SGVWTD--RHSE--------ELKRGITIKLGYADAKIY 58 Query: 81 DV--------------------------RINIVDTPGHADFGGEVERILCMVESVVVLVD 114 R++ VD PGH + +++ ++++ Sbjct: 59 KCPECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGHETLMATMLSGAALMDGALLVIA 118 Query: 115 AAEG-PMPQTKFVVGKALKIGLRPIVVV-NKVDR-SDARADEVINEVFDLFSALDATDAQ 171 A E P PQT+ + IG++ I++V NK+D S RA E ++ + A +A Sbjct: 119 ANEPCPQPQTREHLMALEIIGIKNIIIVQNKIDLVSRERALENYEQIKEFVKGTVAENA- 177 Query: 172 LDFPILYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPPVISEGE-FKMI-------- 222 PI+ S + D+ L+ I ++P P + +M Sbjct: 178 ---PIIPISAQHKANIDA-----------LIEAIEKYIPTPERDLDKPPRMYVARSFDVN 223 Query: 223 --GTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRV------SKILAFRG 274 GT + G ++ G + G ++ I+ + P + + G+ ++I++ + Sbjct: 224 KPGT--PPEELKGGVIGGSLVQGVLRVGDEIE-IRPGIVVEKGGKTVWEPITTEIVSLQA 280 Query: 275 IDRQPIDEAHAGDIVSIAGLVKATVADTFCDPSI 308 + ++EA G +V + T DP++ Sbjct: 281 -GGEDVEEARPGGLVGVG---------TKLDPTL 304 >gnl|CDD|133288 cd01888, eIF2_gamma, eIF2-gamma (gamma subunit of initiation factor 2). eIF2 is a heterotrimeric translation initiation factor that consists of alpha, beta, and gamma subunits. The GTP-bound gamma subunit also binds initiator methionyl-tRNA and delivers it to the 40S ribosomal subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is released from the ribosome. The gamma subunit has no intrinsic GTPase activity, but is stimulated by the GTPase activating protein (GAP) eIF5, and GDP/GTP exchange is stimulated by the guanine nucleotide exchange factor (GEF) eIF2B. eIF2B is a heteropentamer, and the epsilon chain binds eIF2. Both eIF5 and eIF2B-epsilon are known to bind strongly to eIF2-beta, but have also been shown to bind directly to eIF2-gamma. It is possible that eIF2-beta serves simply as a high-affinity docking site for eIF5 and eIF2B-epsilon, or that eIF2-beta serves a regulatory role. eIF2-gamma is found only in eukaryotes and archaea. It is closely related to SelB, the selenocysteine-specific elongation factor from eubacteria. The translational factor components of the ternary complex, IF2 in eubacteria and eIF2 in eukaryotes are not the same protein (despite their unfortunately similar names). Both factors are GTPases; however, eubacterial IF-2 is a single polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is a member of the same family as eubacterial IF2, but the two proteins are only distantly related. This family includes translation initiation, elongation, and release factors. Length = 203 Score = 52.6 bits (127), Expect = 3e-07 Identities = 47/171 (27%), Positives = 63/171 (36%), Gaps = 70/171 (40%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITI---------- 70 NI I HV HGK+TLV L SGV+ R E E ER ITI Sbjct: 2 NIGTIGHVAHGKSTLVKAL---SGVWTV--RFKE--------ELERNITIKLGYANAKIY 48 Query: 71 -----------LAKVTSIVWNDVR------------INIVDTPGHADFGGEVERIL---- 103 + ++ VD PGH IL Sbjct: 49 KCPNCGCPRPYCYRSKEDSPECECPGCGGETKLVRHVSFVDCPGH--------EILMATM 100 Query: 104 ----CMVESVVVLVDAAEG-PMPQTK--FVVGKALKI-GLRPIVVV-NKVD 145 +++ ++L+ A E P PQT AL+I GL+ I++V NK+D Sbjct: 101 LSGAAVMDGALLLIAANEPCPQPQTSEHLA---ALEIMGLKHIIIVQNKID 148 >gnl|CDD|58078 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 = 49.2 bits (117), Expect = 3e-06 Identities = 28/89 (31%), Positives = 41/89 (46%), Gaps = 8/89 (8%) Query: 219 FKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQ 278 + + + KD G + TGR+ SGT+K ++ G G+V + F+G Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGG--GVKGKVKSLKRFKG---- 54 Query: 279 PIDEAHAGDIVSIAGLVK--ATVADTFCD 305 +DEA AGDIV I K + DT D Sbjct: 55 EVDEAVAGDIVGIVLKDKDDIKIGDTLTD 83 >gnl|CDD|34855 COG5258, GTPBP1, GTPase [General function prediction only]. Length = 527 Score = 48.8 bits (116), Expect = 5e-06 Identities = 76/314 (24%), Positives = 121/314 (38%), Gaps = 56/314 (17%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80 + + HVDHGK+TLV L+ +G D + +D E ERG++ + ++ Sbjct: 119 LVGVAGHVDHGKSTLVGVLV--TGRLDDGDGATRSYLDVQKHEVERGLSADISLRVYGFD 176 Query: 81 DVR-----------------------INIVDTPGHADFGGEVERILC--MVESVVVLVDA 115 D + ++ VDT GH + R L V+ +++V A Sbjct: 177 DGKVVRLKNPLDEAEKAAVVKRADKLVSFVDTVGHEPWLRTTIRGLLGQKVDYGLLVVAA 236 Query: 116 AEGPMPQTKFVVGKALKIGLRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFP 175 +G TK +G AL + L IVVV K+D D+ V + SAL ++ Sbjct: 237 DDGVTKMTKEHLGIALAMELPVIVVVTKIDMVP---DDRFQGVVEEISALLKRVGRIPLI 293 Query: 176 ILYGSGRFGWMSDSSDGSRDQGMVP-------------LLNLIVDHVPPPVIS--EGEFK 220 + + + +G+VP LL+ +P EG F Sbjct: 294 V---KDTDDVVLAAKAMKAGRGVVPIFYTSSVTGEGLDLLDEFFLLLPKRRRWDDEGPFL 350 Query: 221 MIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSP--DGALVEVGRVSKILAFRGIDRQ 278 M + +G +V+G + SG + + L P DG EV V I + Sbjct: 351 MYIDKIYSVTGVGTVVSGSVKSGILHVGDTV-LLGPFKDGKFREV-VVKSI----EMHHY 404 Query: 279 PIDEAHAGDIVSIA 292 +D A AG I+ IA Sbjct: 405 RVDSAKAGSIIGIA 418 >gnl|CDD|31354 COG1160, COG1160, Predicted GTPases [General function prediction only]. Length = 444 Score = 48.6 bits (116), Expect = 5e-06 Identities = 41/179 (22%), Positives = 72/179 (40%), Gaps = 37/179 (20%) Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWND 81 IAII + GK++L++ +L + ERV+ + G T + + Sbjct: 181 IAIIGRPNVGKSSLINAILGE-----------ERVIVSD----IAGTTRDSIDIEFERDG 225 Query: 82 VRINIVDTPG---HADFGGEVE--------RILCMVESVVVLVDAAEGPMPQTKFVVGKA 130 + ++DT G VE + + + V++++DA EG Q + G Sbjct: 226 RKYVLIDTAGIRRKGKITESVEKYSVARTLKAIERADVVLLVIDATEGISEQDLRIAGLI 285 Query: 131 LKIGLRPIVVVNK---VDRSDARADEVINEVFDLFSALDATDAQLDF-PILYGSGRFGW 185 + G ++VVNK V+ +A +E + L LDF PI++ S G Sbjct: 286 EEAGRGIVIVVNKWDLVEEDEATMEEFKKK-------LRRKLPFLDFAPIVFISALTGQ 337 Score = 44.4 bits (105), Expect = 9e-05 Identities = 40/211 (18%), Positives = 73/211 (34%), Gaps = 47/211 (22%) Query: 17 MQIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTS 76 M +AI+ + GK+TL + L + R+ +D G+T Sbjct: 1 MSTPVVAIVGRPNVGKSTLFNRLTGR------------RIAIVSDTP---GVTRDRIYGD 45 Query: 77 IVWNDVRINIVDTPGHADFGGE---------VERILCMVESVVVLVDAAEGPMPQTKFVV 127 W ++DT G D + + + ++ +VD EG P + + Sbjct: 46 AEWLGREFILIDTGGLDDGDEDELQELIREQALIAIEEADVILFVVDGREGITPADEEIA 105 Query: 128 GKALKIGLRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMS 187 + I+VVNK+D A ++ +S G G +S Sbjct: 106 KILRRSKKPVILVVNKIDNLKAEEL-----AYEFYS--------------LGFGEPVPIS 146 Query: 188 DSSDGSRDQGMVPLLNLIVDHVPPPVISEGE 218 +G+ LL+ +++ +PP E E Sbjct: 147 ----AEHGRGIGDLLDAVLELLPPDEEEEEE 173 >gnl|CDD|133295 cd01895, EngA2, EngA2 subfamily. This 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 = 47.8 bits (115), Expect = 8e-06 Identities = 42/179 (23%), Positives = 73/179 (40%), Gaps = 37/179 (20%) Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWND 81 IAII + GK++LV+ LL + ERV+ + G T + ++ Sbjct: 5 IAIIGRPNVGKSSLVNALLGE-----------ERVIVSD----IAGTTRDSIDVPFEYDG 49 Query: 82 VRINIVDTPG-----HADFGGE------VERILCMVESVVVLVDAAEGPMPQTKFVVGKA 130 + ++DT G + G E + + + V++++DA EG Q + G Sbjct: 50 KKYTLIDTAGIRRKGKVEEGIEKYSVLRTLKAIERADVVLLVIDATEGITEQDLRIAGLI 109 Query: 131 LKIGLRPIVVVNK---VDRSDARADEVINEVFDLFSALDATDAQLDF-PILYGSGRFGW 185 L+ G ++VVNK V++ E E+ LD+ PI++ S G Sbjct: 110 LEEGKALVIVVNKWDLVEKDSKTMKEFKKEIRRKL-------PFLDYAPIVFISALTGQ 161 >gnl|CDD|145217 pfam01926, MMR_HSR1, GTPase of unknown function. Length = 106 Score = 44.6 bits (106), Expect = 8e-05 Identities = 30/121 (24%), Positives = 51/121 (42%), Gaps = 23/121 (19%) Query: 31 GKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDVRINIVDTP 90 GK+TL++ L + VS+ G T + + +I +VDTP Sbjct: 1 GKSTLINALTG-----KKRAIVSDYP----------GTTRDPNEGRVELDGKQIILVDTP 45 Query: 91 G-----HADFGGEVERILCMVES---VVVLVDAAEGPMPQTKFVVGKALKIGLRPIVVVN 142 G G R L +E ++ +VDA+EG + ++ L++G I+V+N Sbjct: 46 GIIEGASKGEGELGNRTLEAIEEADLILHVVDASEGLTEEDLEILDLLLELGKPVILVLN 105 Query: 143 K 143 K Sbjct: 106 K 106 >gnl|CDD|58091 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 = 44.4 bits (105), Expect = 1e-04 Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 5/73 (6%) Query: 235 IVTGRIHSGTIKSNQNIKALSP-----DGALVEVGRVSKILAFRGIDRQPIDEAHAGDIV 289 I GR+ SGTI+ Q ++ L P D + + ++ G R+P+DE AG+IV Sbjct: 18 IAFGRVFSGTIRKGQKVRVLGPNYSPEDEEDLSKKTIQRLYLMMGRYREPVDEVPAGNIV 77 Query: 290 SIAGLVKATVADT 302 I GL + T Sbjct: 78 LIVGLDQLKSGTT 90 >gnl|CDD|35275 KOG0052, KOG0052, KOG0052, Translation elongation factor EF-1 alpha/Tu [Translation, ribosomal structure and biogenesis]. Length = 391 Score = 43.8 bits (103), Expect = 1e-04 Identities = 48/166 (28%), Positives = 71/166 (42%), Gaps = 29/166 (17%) Query: 20 RNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER--------------VMDCNDLEKE 65 NI +I HVD GK+T K G+ + E+ V+D E+E Sbjct: 8 INIVVIGHVDSGKSTTT--GYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERE 65 Query: 66 RGITILAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPM----- 120 RGITI + + + I+D PGH DF + + V++V A G Sbjct: 66 RGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGIS 125 Query: 121 --PQTKFVVGKALKIGLR-PIVVVNKVDR-----SDARADEVINEV 158 QT+ A +G++ IV VNK+D S+AR +E+ EV Sbjct: 126 KNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARYEEIKKEV 171 >gnl|CDD|32410 COG2229, COG2229, Predicted GTPase [General function prediction only]. Length = 187 Score = 42.2 bits (99), Expect = 4e-04 Identities = 36/142 (25%), Positives = 56/142 (39%), Gaps = 8/142 (5%) Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWND 81 I +I V GKTT V L + V + S + +R T+ SI ++ Sbjct: 13 IVVIGPVGAGKTTFVRALSDKPLVITEADASSVS------GKGKRPTTVAMDFGSIELDE 66 Query: 82 V-RINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPIVV 140 +++ TPG F E + +VLVD++ + ++ P+VV Sbjct: 67 DTGVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPIPVVV 126 Query: 141 -VNKVDRSDARADEVINEVFDL 161 +NK D DA E I E L Sbjct: 127 AINKQDLFDALPPEKIREALKL 148 >gnl|CDD|58098 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 = 41.3 bits (97), Expect = 8e-04 Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 6/80 (7%) Query: 226 LEKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHA 285 LE+ F G++ RI+ G +K I + + RV +++ + + ++EA A Sbjct: 8 LEEGRF-GQLTYMRIYQGKLKKGDTIYNVRTGKKV----RVPRLVRMHSNEMEEVEEAGA 62 Query: 286 GDIVSIAGLVKATVADTFCD 305 GDI +I G+ A+ DTF D Sbjct: 63 GDICAIFGIDCAS-GDTFTD 81 >gnl|CDD|58065 cd03713, EFG_mtEFG_C, EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. 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. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2.. Length = 78 Score = 41.3 bits (97), Expect = 9e-04 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 1/77 (1%) Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQLMT 472 EPI +V + V EE+ G V+ ++ + +++ G G + P + GY + L + Sbjct: 1 EPIMKVEVTVPEEYMGDVIGDLSSRRGQILGTESRG-GWKVIKAEVPLAEMFGYSTDLRS 59 Query: 473 DTRGTAIMNRLFHSYQP 489 T+G F Y+ Sbjct: 60 LTQGRGSFTMEFSHYEE 76 >gnl|CDD|36359 KOG1144, KOG1144, KOG1144, Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]. Length = 1064 Score = 39.3 bits (91), Expect = 0.003 Identities = 35/131 (26%), Positives = 56/131 (42%), Gaps = 10/131 (7%) Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMD------CNDLEKERGITILAKVT 75 I+ HVD GKT L+D+ ++ + V + + N EK + + AK Sbjct: 478 CCILGHVDTGKTKLLDK-IRGTNVQEGEAGGITQQIGATYFPAENIREKTKELKKDAKKR 536 Query: 76 SIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGL 135 V + ++DTPGH F R + + +++VD G PQT + Sbjct: 537 LKV---PGLLVIDTPGHESFTNLRSRGSSLCDLAILVVDIMHGLEPQTIESINLLRMRKT 593 Query: 136 RPIVVVNKVDR 146 IV +NK+DR Sbjct: 594 PFIVALNKIDR 604 >gnl|CDD|133294 cd01894, EngA1, EngA1 subfamily. This 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 = 39.3 bits (93), Expect = 0.003 Identities = 34/144 (23%), Positives = 49/144 (34%), Gaps = 47/144 (32%) Query: 31 GKTTLVDELLKQ--------SGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDV 82 GK+TL + L + GV RD R+ W Sbjct: 9 GKSTLFNRLTGRRDAIVEDTPGVTRD--RIYGEA---------------------EWGGR 45 Query: 83 RINIVDTPGHADFGGEVERILCMV---------ESVVVL--VDAAEGPMPQTKFVVGKAL 131 ++DT G + E I + E+ V+L VD EG P + + Sbjct: 46 EFILIDTGG---IEPDDEGISKEIREQAELAIEEADVILFVVDGREGLTPADEEIAKYLR 102 Query: 132 KIGLRPIVVVNKVD--RSDARADE 153 K I+VVNKVD + + A E Sbjct: 103 KSKKPVILVVNKVDNIKEEDEAAE 126 >gnl|CDD|133256 cd00880, Era_like, Era (E. coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), 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 = 163 Score = 38.5 bits (90), Expect = 0.006 Identities = 29/126 (23%), Positives = 51/126 (40%), Gaps = 27/126 (21%) Query: 31 GKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVW---NDVRINIV 87 GK++L++ LL Q V VS G T VW + ++ Sbjct: 8 GKSSLLNALLGQE-VAI----VSPV----------PGTTT--DPVEYVWELGPLGPVVLI 50 Query: 88 DTPGHADFGG-------EVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPIVV 140 DTPG + GG R+L + ++ +VDA + + ++ + G ++V Sbjct: 51 DTPGIDEAGGLGREREELARRVLERADLILFVVDADLRADEEEEKLLELLRERGKPVLLV 110 Query: 141 VNKVDR 146 +NK+D Sbjct: 111 LNKIDL 116 >gnl|CDD|133363 cd04163, Era, Era subfamily. 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 = 38.2 bits (90), Expect = 0.008 Identities = 21/89 (23%), Positives = 39/89 (43%), Gaps = 16/89 (17%) Query: 87 VDTPG-HADFGGEVERILCMVES----------VVVLVDAAEGPMPQTKFVVGKALKIGL 135 VDTPG H + + MV++ V+ +VDA+E +F++ K Sbjct: 56 VDTPGIHKP---KKKLGERMVKAAWSALKDVDLVLFVVDASEPIGEGDEFILELLKKSKT 112 Query: 136 RPIVVVNKVDR--SDARADEVINEVFDLF 162 I+V+NK+D ++ ++ +L Sbjct: 113 PVILVLNKIDLVKDKEDLLPLLEKLKELG 141 >gnl|CDD|133258 cd00882, Ras_like_GTPase, 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 regulate 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 = 157 Score = 36.7 bits (85), Expect = 0.017 Identities = 21/137 (15%), Positives = 45/137 (32%), Gaps = 19/137 (13%) Query: 24 IIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDVR 83 ++ GKT+L++ + V E + I +K + V+ Sbjct: 1 VVGDSGVGKTSLLN-------RLLGGEFVPEE-------YETTIIDFYSKTIEVDGKKVK 46 Query: 84 INIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQ-----TKFVVGKALKIGLRPI 138 + I DT G F + ++++ D + + ++ + I Sbjct: 47 LQIWDTAGQERFRSLRRLYYRGADGIILVYDVTDRESFENVKEWLLLILINKEGENIPII 106 Query: 139 VVVNKVDRSDARADEVI 155 +V NK+D + R Sbjct: 107 LVGNKIDLPEERVVSEE 123 >gnl|CDD|58097 cd04090, eEF2_II_snRNP, Loc2 eEF2_C_snRNP, cd01514/C terminal domain:eEF2_C_snRNP: This family includes C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to domain II of the eukaryotic translational elongation factor EF-2. 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. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.. Length = 94 Score = 36.7 bits (85), Expect = 0.022 Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 11/65 (16%) Query: 238 GRIHSGTIKSNQNIKALSP--------DGALVEVGRVSKILAFRGIDRQPIDEAHAGDIV 289 GRI+SGTIK Q +K L D + +GR+ G + ++EA AG+ V Sbjct: 21 GRIYSGTIKKGQKVKVLGENYSLDDEEDMTICTIGRLW---ILGGRYKIEVNEAPAGNWV 77 Query: 290 SIAGL 294 I G+ Sbjct: 78 LIKGI 82 >gnl|CDD|31353 COG1159, Era, GTPase [General function prediction only]. Length = 298 Score = 36.3 bits (84), Expect = 0.027 Identities = 39/135 (28%), Positives = 60/135 (44%), Gaps = 27/135 (20%) Query: 22 IAIIAHVDHGKTTLVDELLKQ--SGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVW 79 +AII + GK+TL++ L+ Q S V Q R+ RGI Sbjct: 9 VAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRI---------RGIVTT-------- 51 Query: 80 NDVRINIVDTPG----HADFG----GEVERILCMVESVVVLVDAAEGPMPQTKFVVGKAL 131 ++ +I VDTPG G L V+ ++ +VDA EG P +F++ + Sbjct: 52 DNAQIIFVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLK 111 Query: 132 KIGLRPIVVVNKVDR 146 K I+VVNK+D+ Sbjct: 112 KTKTPVILVVNKIDK 126 >gnl|CDD|58099 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 = 36.0 bits (83), Expect = 0.036 Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 4/74 (5%) Query: 229 DPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDI 288 DP G + R++SGT+K + + R+S++L Q I AG+I Sbjct: 11 DPQRGPLTFVRVYSGTLKRGSALYNTNTGKKE----RISRLLQPFADQYQEIPSLSAGNI 66 Query: 289 VSIAGLVKATVADT 302 I GL + DT Sbjct: 67 GVITGLKQTRTGDT 80 >gnl|CDD|133259 cd01850, CDC_Septin, CDC/Septin. Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis. In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments. Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities. Length = 276 Score = 35.6 bits (83), Expect = 0.037 Identities = 13/67 (19%), Positives = 27/67 (40%), Gaps = 8/67 (11%) Query: 31 GKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDVRI--NIVD 88 GK+T ++ L + + + ++ + I + I N V++ ++D Sbjct: 16 GKSTFINTLFNTK-LIPSDYPPDPA-----EEHIDKTVEIKSSKAEIEENGVKLKLTVID 69 Query: 89 TPGHADF 95 TPG D Sbjct: 70 TPGFGDN 76 >gnl|CDD|58080 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 = 35.2 bits (81), Expect = 0.061 Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 4/71 (5%) Query: 234 RIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAG 293 RI R+ SG + +K L + R+S F DR+ +DEA+ GDI+ + Sbjct: 17 RIAFVRVCSGKFERGMKVK----HVRLGKEVRLSNPQQFFAQDRETVDEAYPGDIIGLVN 72 Query: 294 LVKATVADTFC 304 + DT Sbjct: 73 PGNFQIGDTLT 83 >gnl|CDD|30567 COG0218, COG0218, Predicted GTPase [General function prediction only]. Length = 200 Score = 34.5 bits (79), Expect = 0.087 Identities = 34/149 (22%), Positives = 63/149 (42%), Gaps = 37/149 (24%) Query: 31 GKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDVRINIVDTP 90 GK++L++ L Q + R S K G T L + +D + +VD P Sbjct: 36 GKSSLINALTNQKNL----ARTS----------KTPGRTQL--INFFEVDD-ELRLVDLP 78 Query: 91 GHADFG------GEVERILCMVES----------VVVLVDAAEGPMPQTKFVVGKALKIG 134 G +G E+ ++E VV+L+DA P + ++ L++G Sbjct: 79 G---YGYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPPKDLDREMIEFLLELG 135 Query: 135 LRPIVVVNKVDR-SDARADEVINEVFDLF 162 + IVV+ K D+ + ++ +N+V + Sbjct: 136 IPVIVVLTKADKLKKSERNKQLNKVAEEL 164 >gnl|CDD|58062 cd03709, lepA_C, lepA_C: This family represents the C-terminal region of LepA, a GTP-binding protein localized in the cytoplasmic membrane. LepA is ubiquitous in Bacteria and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but is missing from Archaea. LepA exhibits significant homology to elongation factors (EFs) Tu and G. The function(s) of the proteins in this family are unknown. The N-terminal domain of LepA is homologous to a domain of similar size found in initiation factor 2 (IF2), and in EF-Tu and EF-G (factors required for translation in Escherichia coli). Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including S. cerevisiae GUF1) originated within the bacterial LepA family. 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 = 80 Score = 34.3 bits (79), Expect = 0.090 Identities = 14/78 (17%), Positives = 33/78 (42%), Gaps = 1/78 (1%) Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLI-GYQSQLM 471 EP + I E+ GA+++ + ++ RV L + P ++ + +L Sbjct: 1 EPFVKATIITPSEYLGAIMELCQERRGVQKDMEYLDANRVMLTYELPLAEIVYDFFDKLK 60 Query: 472 TDTRGTAIMNRLFHSYQP 489 + ++G A ++ Y+ Sbjct: 61 SISKGYASLDYELIGYRE 78 >gnl|CDD|58089 cd03698, eRF3_II_like, eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils. This group also contains proteins similar to S. cerevisiae Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation and, to associate with Dom34. It has been speculated that yeast Hbs1 and Dom34 proteins may function as part of a complex with a role in gene expression.. Length = 83 Score = 33.9 bits (78), Expect = 0.14 Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 8/60 (13%) Query: 233 GRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIA 292 G +V+G++ SG+I+ + + P VEV + +D + +D A AG+ V + Sbjct: 15 GTVVSGKVESGSIQKGDTL-LVMPSKESVEVKSIY-------VDDEEVDYAVAGENVRLK 66 >gnl|CDD|58086 cd03695, CysN_NodQ_II, CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which shows no aa sequence similarity to CysN or NodQ. CysN and the N-terminal portion of NodQ show similarity to GTPases involved in translation, in particular, EF-Tu and EF-1alpha.. Length = 81 Score = 33.1 bits (76), Expect = 0.21 Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 8/58 (13%) Query: 234 RIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSI 291 R G I SG+I+ + L P G + RV I F G +DEA AG+ V++ Sbjct: 16 RGYAGTIASGSIRVGDEVVVL-PSG---KTSRVKSIETFDG----ELDEAGAGESVTL 65 >gnl|CDD|58087 cd03696, selB_II, selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.. Length = 83 Score = 32.8 bits (75), Expect = 0.28 Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 8/60 (13%) Query: 233 GRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIA 292 G +VTG + SG++K ++ L E RV I + ++EA AGD V++ Sbjct: 15 GTVVTGTVLSGSVKVGDKVEILPLG----EETRVRSIQVH----GKDVEEAKAGDRVALN 66 >gnl|CDD|144365 pfam00735, Septin, Septin. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerize to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis. Length = 280 Score = 32.3 bits (74), Expect = 0.37 Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 9/67 (13%) Query: 31 GKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDVRIN--IVD 88 GKTTL++ L + ++ + + ++ + I A I + V++N ++D Sbjct: 16 GKTTLINTLF-LTDLYPERGIPGPS------EKIKKTVEIKATTVEIEEDGVKLNLTVID 68 Query: 89 TPGHADF 95 TPG D Sbjct: 69 TPGFGDA 75 >gnl|CDD|36233 KOG1015, KOG1015, KOG1015, Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]. Length = 1567 Score = 32.0 bits (72), Expect = 0.44 Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 7/85 (8%) Query: 376 RGELQLAVLIETMRREGFELAVSRPR---VVIKKEGDSLLEPIE-EVVIDVDEEHSGAVV 431 R E Q A+ E RR+ E R + V+ ++ EPI ++V+D DEE +V Sbjct: 600 RKETQNALKEEKERRKRIEEERERQKLRNVIEIEDASPTKEPITTKLVLDEDEETKEPLV 659 Query: 432 QKMTLHKSEMIELRPSGTGRVRLVF 456 Q +H+S +I+L+P V+ ++ Sbjct: 660 Q---VHRSLVIKLKPHQVDGVQFMW 681 >gnl|CDD|58066 cd04096, eEF2_snRNP_like_C, eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor 2 (eEF-2) and a homologous domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. 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. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.. Length = 80 Score = 31.6 bits (72), Expect = 0.68 Identities = 18/78 (23%), Positives = 32/78 (41%), Gaps = 1/78 (1%) Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRP-SGTGRVRLVFLSPTRGLIGYQSQLM 471 EPI V I E+ G V ++ + ++ P GT + P G+++ L Sbjct: 1 EPIYLVEIQCPEDALGKVYSVLSKRRGHVLSEEPKEGTPLFEIKAYLPVIESFGFETDLR 60 Query: 472 TDTRGTAIMNRLFHSYQP 489 + T G A +F ++ Sbjct: 61 SATSGQAFPQLVFSHWEI 78 >gnl|CDD|58064 cd03711, Tet_C, Tet_C: C-terminus of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to the C terminal domains 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 = 78 Score = 31.7 bits (72), Expect = 0.69 Identities = 17/77 (22%), Positives = 29/77 (37%), Gaps = 1/77 (1%) Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQLMT 472 EP ++V ++ G + + + E V L P YQS+L + Sbjct: 1 EPYLRFELEVPQDALGRAMSDLAKMGAT-FEDPQIKGDEVTLEGTIPVATSQDYQSELPS 59 Query: 473 DTRGTAIMNRLFHSYQP 489 T G ++ F Y+P Sbjct: 60 YTHGEGVLETEFKGYRP 76 >gnl|CDD|146419 pfam03767, Acid_phosphat_B, HAD superfamily, subfamily IIIB (Acid phosphatase). This family proteins includes acid phosphatases and a number of vegetative storage proteins. Length = 230 Score = 31.2 bits (71), Expect = 0.82 Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 3/40 (7%) Query: 371 FFVSGRGELQLAVLIETMRREGFELAVSRPRVVIKKEGDS 410 FFVSGR E A +E +++ GF +++++ + DS Sbjct: 140 FFVSGRSEDLRAATVENLKKAGFH---GWEKLILRGKKDS 176 >gnl|CDD|35298 KOG0075, KOG0075, KOG0075, GTP-binding ADP-ribosylation factor-like protein [General function prediction only]. Length = 186 Score = 30.7 bits (69), Expect = 1.2 Identities = 25/103 (24%), Positives = 43/103 (41%), Gaps = 5/103 (4%) Query: 69 TILAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAE-----GPMPQT 123 T+ + + +V I + D G F ER V ++V +VDAA+ + Sbjct: 52 TVGFNMRKVTKGNVTIKLWDLGGQPRFRSMWERYCRGVSAIVYVVDAADPDKLEASRSEL 111 Query: 124 KFVVGKALKIGLRPIVVVNKVDRSDARADEVINEVFDLFSALD 166 ++ K G+ +V+ NK+D A + + E L S D Sbjct: 112 HDLLDKPSLTGIPLLVLGNKIDLPGALSKIALIERMGLSSITD 154 >gnl|CDD|30833 COG0486, ThdF, Predicted GTPase [General function prediction only]. Length = 454 Score = 30.9 bits (70), Expect = 1.2 Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 9/78 (11%) Query: 76 SIVWNDVRINIVDTPGHADFGGEVERI--------LCMVESVVVLVDAAEGPMPQTKFVV 127 I N + + +VDT G + VERI + + V+ ++DA++ P+ + + Sbjct: 259 DINLNGIPVRLVDTAGIRETDDVVERIGIERAKKAIEEADLVLFVLDASQ-PLDKEDLAL 317 Query: 128 GKALKIGLRPIVVVNKVD 145 + L IVV+NK D Sbjct: 318 IELLPKKKPIIVVLNKAD 335 >gnl|CDD|58093 cd03702, IF2_mtIF2_II, This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2.. Length = 95 Score = 30.8 bits (70), Expect = 1.2 Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 11/74 (14%) Query: 223 GTILEK--DPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPI 280 G ++E D G + T + +GT+K + A + G+V + G + + Sbjct: 3 GVVIESKLDKGRGPVATVLVQNGTLKVGDVLVAGT------TYGKVRAMFDENG---KRV 53 Query: 281 DEAHAGDIVSIAGL 294 EA V I GL Sbjct: 54 KEAGPSTPVEILGL 67 >gnl|CDD|58090 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 = 30.4 bits (69), Expect = 1.4 Identities = 26/81 (32%), Positives = 34/81 (41%), Gaps = 9/81 (11%) Query: 229 DPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDI 288 DP+ G I R+ GT+K I+ +S G EV V I + P DE AG + Sbjct: 11 DPYRGVIALVRVFDGTLKKGDKIRFMS-TGKEYEVEEVG-IFRP---EMTPTDELSAGQV 65 Query: 289 VSIAGLVK----ATVADTFCD 305 I +K A V DT Sbjct: 66 GYIIAGIKTVKDARVGDTITL 86 >gnl|CDD|32934 COG3120, COG3120, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 149 Score = 30.4 bits (68), Expect = 1.5 Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 4/67 (5%) Query: 562 ASGKDEAVKLVPAVKMTLEQALSWIQ---NDELVEVTPKSIRL-RKMYLDPNERKRKGKS 617 AS +EAV+ + +++ + WI + ELV ++IR RK + + + + KS Sbjct: 34 ASAAEEAVQQLLSLENEPVKVNEWIDAHMSPELVNKLKQAIRARRKRHFNAEHQHTRKKS 93 Query: 618 VNLEYNV 624 ++LEY V Sbjct: 94 IDLEYAV 100 >gnl|CDD|58067 cd04097, mtEFG1_C, 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 = 78 Score = 29.8 bits (67), Expect = 2.2 Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 1/77 (1%) Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQLMT 472 EPI +V + E G V+ + K I +G L P + GY ++L + Sbjct: 1 EPIMKVEVTAPTEFQGNVIGLLNKRKG-TIVDTDTGEDEFTLEAEVPLNDMFGYSTELRS 59 Query: 473 DTRGTAIMNRLFHSYQP 489 T+G + F Y P Sbjct: 60 MTQGKGEFSMEFSRYAP 76 >gnl|CDD|38742 KOG3534, KOG3534, KOG3534, p53 inducible protein PIR121 [General function prediction only]. Length = 1253 Score = 30.0 bits (67), Expect = 2.2 Identities = 15/53 (28%), Positives = 25/53 (47%) Query: 561 RASGKDEAVKLVPAVKMTLEQALSWIQNDELVEVTPKSIRLRKMYLDPNERKR 613 +A GKDE +K +P KM I N+++ + K ++ + P E R Sbjct: 1183 KADGKDEIIKGIPLKKMVERIRRFQILNNQIFIILNKYLKSGEGEGSPVEHVR 1235 >gnl|CDD|58096 cd04089, eRF3_II, eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils.. Length = 82 Score = 29.7 bits (67), Expect = 2.7 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 8/68 (11%) Query: 225 ILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAH 284 I++K +G +V G++ SGTIK + + P+ VEV + + + A Sbjct: 6 IIDKYKDMGTVVLGKVESGTIKKGDKL-LVMPNKTQVEVLSIY-------NEDVEVRYAR 57 Query: 285 AGDIVSIA 292 G+ V + Sbjct: 58 PGENVRLR 65 >gnl|CDD|30719 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion transport and metabolism]. Length = 653 Score = 29.4 bits (66), Expect = 3.1 Identities = 32/137 (23%), Positives = 61/137 (44%), Gaps = 26/137 (18%) Query: 17 MQIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTS 76 M+ +A++ + + GKTTL + L +G NQ+V G+T+ K Sbjct: 1 MKKLTVALVGNPNVGKTTLFNAL---TGA---NQKVGNWP----------GVTVEKKEGK 44 Query: 77 IVWNDVRINIVDTPGHADFGG--EVERILC------MVESVVVLVDAAEGPMPQTKFVVG 128 + + I IVD PG E E++ + +V +VDA + + ++ Sbjct: 45 LKYKGHEIEIVDLPGTYSLTAYSEDEKVARDFLLEGKPDLIVNVVDATN--LERNLYLTL 102 Query: 129 KALKIGLRPIVVVNKVD 145 + L++G+ I+ +N +D Sbjct: 103 QLLELGIPMILALNMID 119 >gnl|CDD|144080 pfam00350, Dynamin_N, Dynamin family. Length = 168 Score = 29.1 bits (66), Expect = 3.5 Identities = 28/142 (19%), Positives = 46/142 (32%), Gaps = 23/142 (16%) Query: 20 RNIAII-------AHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILA 72 R ++ A K D L K F D + E + D D G I + Sbjct: 33 RRPLVLRLGEEPGAIPGAVKVEYKDGLKK----FEDFSELREEIEDETDKISGTGKGISS 88 Query: 73 KVTSI---VWNDVRINIVDTPG-----HADFGGEVERILCMVESVVVLVDAAEGPMPQT- 123 + + + +VDTPG D E + +++ V A + + Sbjct: 89 EPIILEILSPLVPGLTLVDTPGLDSVAVGDQ-DLTEEYIKP-ADIILAVVDANHDLSTSE 146 Query: 124 -KFVVGKALKIGLRPIVVVNKV 144 F+ + G R I V+ K Sbjct: 147 ALFLAREVDPNGKRTIGVLTKD 168 >gnl|CDD|37866 KOG2655, KOG2655, KOG2655, Septin family protein (P-loop GTPase) [Cell cycle control, cell division, chromosome partitioning, Nuclear structure, Intracellular trafficking, secretion, and vesicular transport]. Length = 366 Score = 28.8 bits (64), Expect = 4.7 Identities = 14/67 (20%), Positives = 24/67 (35%), Gaps = 9/67 (13%) Query: 31 GKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDV--RINIVD 88 GK+T ++ L R + + + I + I N V + ++D Sbjct: 33 GKSTFINSLFLTD-------LSGNREVPGASERIKETVEIESTKVEIEENGVKLNLTVID 85 Query: 89 TPGHADF 95 TPG D Sbjct: 86 TPGFGDA 92 >gnl|CDD|35687 KOG0466, KOG0466, KOG0466, Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]. Length = 466 Score = 28.8 bits (64), Expect = 4.9 Identities = 61/271 (22%), Positives = 104/271 (38%), Gaps = 57/271 (21%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGV----FRDN-QR--------VSERVMDCNDLE---- 63 NI I HV HGK+T+V + SGV F++ +R + ++ C+D + Sbjct: 40 NIGTIGHVAHGKSTVVKAI---SGVHTVRFKNELERNITIKLGYANAKIYKCDDPKCPRP 96 Query: 64 ---------KERGITILAKVTSIVWNDVR-INIVDTPGHADFGGEVERILCMVESVVVLV 113 KE VR ++ VD PGH + ++++ ++L+ Sbjct: 97 GCYRSFGSSKEDRPPCDRPGCEGKMKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLI 156 Query: 114 DAAEG-PMPQTKFVVGKALKIGLRPIVVV-NKVDR-SDARADEVINEVFDLFSALDATDA 170 E P PQT + + L+ I+++ NK+D +++A E ++ A A Sbjct: 157 AGNESCPQPQTSEHLAAVEIMKLKHIIILQNKIDLIKESQALEQHEQIQKFIQGTVAEGA 216 Query: 171 QLDFPILYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPPV---ISEGEFKMIGTI-- 225 PI+ S + + D + IV +P PV S +I + Sbjct: 217 ----PIIPISAQLKYNIDV-----------VCEYIVKKIPVPVRDFTSPPRLIVIRSFDV 261 Query: 226 ----LEKDPFLGRIVTGRIHSGTIKSNQNIK 252 E D G + G I G +K Q I+ Sbjct: 262 NKPGSEVDDLKGGVAGGSILKGVLKVGQEIE 292 >gnl|CDD|57926 cd01855, YqeH, YqeH. YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts. Proteins of the YqeH family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases.. Length = 190 Score = 28.7 bits (64), Expect = 4.9 Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 4/64 (6%) Query: 83 RINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRP-IVVV 141 +I+ V+ P + I VV +VD + P + L G P I+V Sbjct: 12 KIDPVEIPDEDFILNLLSSISPKKALVVHVVDIFDFPG---SLIPRLRLFGGNNPVILVG 68 Query: 142 NKVD 145 NK+D Sbjct: 69 NKID 72 >gnl|CDD|144639 pfam01120, Alpha_L_fucos, Alpha-L-fucosidase. Length = 344 Score = 28.8 bits (65), Expect = 5.1 Identities = 7/16 (43%), Positives = 8/16 (50%) Query: 85 NIVDTPGHADFGGEVE 100 N VDT D GE+ Sbjct: 130 NSVDTGPKRDIVGELA 145 >gnl|CDD|36760 KOG1547, KOG1547, KOG1547, Septin CDC10 and related P-loop GTPases [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms, Cytoskeleton]. Length = 336 Score = 28.4 bits (63), Expect = 5.4 Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 11/78 (14%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80 NI ++ GK+TL++ L K VS+ N E T + +T ++ Sbjct: 48 NIMVVGQSGLGKSTLINTLFKS--------HVSDSSSSDNSAEPIPKTTEIKSITHVIEE 99 Query: 81 D---VRINIVDTPGHADF 95 +++ ++DTPG D Sbjct: 100 KGVKLKLTVIDTPGFGDQ 117 >gnl|CDD|143612 cd07304, Chorismate_synthase, Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway. Chorismate synthase (CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; 1-carboxyvinyl-3-phosphoshikimate phosphate-lyase; E.C. 4.2.3.5) catalyzes the seventh and final step in the shikimate pathway: the conversion of 5- enolpyruvylshikimate-3-phosphate (EPSP) to chorismate, a precursor for the biosynthesis of aromatic compounds. This process has an absolute requirement for reduced FMN as a co-factor which is thought to facilitate cleavage of C-O bonds by transiently donating an electron to the substrate, having no overall change its redox state. Depending on the capacity of these enzymes to regenerate the reduced form of FMN, chorismate synthases are divided into two classes: Enzymes, mostly from plants and eubacteria, that sequester CS from the cellular environment, are monofunctiona,l while those that can generate reduced FMN at the expense of NADPH, such as found in fungi and the ciliated protozoan Euglena gracilis, are bifunctional, having an additional NADPH:FMN oxidoreductase activity. Recently, bifunctionality of the Mycobacterium tuberculosis enzyme (MtCS) was determined by measurements of both chorismate synthase and NADH:FMN oxidoreductase activities. Since shikimate pathway enzymes are present in bacteria, fungi and apicomplexan parasites (such as Toxoplasma gondii, Plasmodium falciparum, and Cryptosporidium parvum) but absent in mammals, they are potentially attractive targets for the development of new therapy against infectious diseases such as tuberculosis (TB). Length = 344 Score = 28.2 bits (64), Expect = 6.6 Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 7/40 (17%) Query: 67 GITILAKVTSIVWN-DVR----INIVDT--PGHADFGGEV 99 G T + ++ N D R + PGHAD+ G + Sbjct: 65 GKTTGTPIALLIRNKDQRSWDYSMLKTLPRPGHADYTGFL 104 >gnl|CDD|58068 cd04098, eEF2_C_snRNP, eEF2_C_snRNP: This family includes a C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to the C-terminal domain of the eukaryotic translational elongation factor EF-2. 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. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.. Length = 80 Score = 28.2 bits (63), Expect = 6.6 Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 1/78 (1%) Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMI-ELRPSGTGRVRLVFLSPTRGLIGYQSQLM 471 EPI EV I + AV + ++ + +I + GT + P G+++ L Sbjct: 1 EPIYEVEITCPADAVSAVYEVLSRRRGHVIYDTPIPGTPLYEVKAFIPVIESFGFETDLR 60 Query: 472 TDTRGTAIMNRLFHSYQP 489 T+G A +F +Q Sbjct: 61 VHTQGQAFCQSVFDHWQI 78 >gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]. Length = 323 Score = 28.0 bits (62), Expect = 7.2 Identities = 32/128 (25%), Positives = 49/128 (38%), Gaps = 28/128 (21%) Query: 86 IVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPI---VVVN 142 IV+T G EV+ I M ++ +V++ G Q +K G+ I +V+N Sbjct: 148 IVETVGVGQ--SEVD-IANMADTFLVVMIPGAGDDLQ-------GIKAGIMEIADIIVIN 197 Query: 143 KVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSD--SSDGSRDQGMVP 200 K DR A +L SALD GW ++ +G+ Sbjct: 198 KADRKGAEK-----AARELRSALDLLREVWREN--------GWRPPVVTTSALEGEGIDE 244 Query: 201 LLNLIVDH 208 L + I DH Sbjct: 245 LWDAIEDH 252 >gnl|CDD|58085 cd03694, GTPBP_II, Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.. Length = 87 Score = 28.2 bits (63), Expect = 7.4 Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 10/66 (15%) Query: 230 PFLGRIVTGRIHSGTIKSNQNIK-ALSPDGALVEVGRVSKILAFRGI--DRQPIDEAHAG 286 P +G +V G + G I+ + DG+ V + I +R P+ AG Sbjct: 12 PGVGTVVGGTVSKGVIRLGDTLLLGPDQDGSFRPV-------TVKSIHRNRSPVRVVRAG 64 Query: 287 DIVSIA 292 S+A Sbjct: 65 QSASLA 70 >gnl|CDD|173942 cd08183, Fe-ADH2, Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contains different protein domain. Proteins of this family have not been characterized. Their specific function is unknown. They are mainly found in bacteria. Length = 374 Score = 27.9 bits (63), Expect = 9.1 Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 6/62 (9%) Query: 370 AFFVSGRGELQLAVLIETMRREGFELAVSRPRVVIKKEGDSLLEPIEEVVIDVDEEHSGA 429 V+G L+ A LIE +R G E+ VV+ E +E ++ V + Sbjct: 25 VLLVTGASSLRAAWLIEALRAAGIEVTH----VVVAGEPS--VELVDAAVAEARNAGCDV 78 Query: 430 VV 431 V+ Sbjct: 79 VI 80 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.318 0.138 0.390 Gapped Lambda K H 0.267 0.0783 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 7,411,369 Number of extensions: 404739 Number of successful extensions: 1197 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1061 Number of HSP's successfully gapped: 130 Length of query: 624 Length of database: 6,263,737 Length adjustment: 100 Effective length of query: 524 Effective length of database: 4,102,837 Effective search space: 2149886588 Effective search space used: 2149886588 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 60 (26.8 bits)