RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780321|ref|YP_003064734.1| GTP-binding protein LepA [Candidatus Liberibacter asiaticus str. psy62] (606 letters) >gnl|CDD|30829 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis, outer membrane]. Length = 603 Score = 1013 bits (2622), Expect = 0.0 Identities = 393/605 (64%), Positives = 492/605 (81%), Gaps = 3/605 (0%) Query: 3 KKPTPLSRIRNFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIK 62 TP IRNFSI+AHIDHGKSTLADR ++ GL+EREM +QVLD+MDIERERGITIK Sbjct: 1 MTFTPQKNIRNFSIIAHIDHGKSTLADRLLELTGGLSEREMRAQVLDSMDIERERGITIK 60 Query: 63 AQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLAN 122 AQ VRLNY + D + Y LNLIDTPGHVDF+YEVSRSL+ACEG+LLVVDA+QGVEAQTLAN Sbjct: 61 AQAVRLNYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLAN 120 Query: 123 VYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLER 182 VY A++NN EII VLNK DLP+ADP+RVK++IE+ IGI DA+LVSAKTG GI +LE Sbjct: 121 VYLALENNLEIIPVLNKIDLPAADPERVKQEIEDIIGIDASDAVLVSAKTGIGIEDVLEA 180 Query: 183 IVQQLPSPTSPEGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQ 242 IV+++P P +APLKAL+ DSWY++YLGV+VLVRI +G L KG IR+M T +Y+ Sbjct: 181 IVEKIPPPKGDP--DAPLKALIFDSWYDNYLGVVVLVRIFDGTLKKGDKIRMMSTGKEYE 238 Query: 243 VERIGILTPKMIDIEALYPGEIGVMIASIKEVSHTRVGDTITDDSSPTTSALPGFKPIQP 302 V+ +GI TPKM+ ++ L GE+G +IA IK+V RVGDTIT S+P T LPGFK ++P Sbjct: 239 VDEVGIFTPKMVKVDELKAGEVGYIIAGIKDVRDARVGDTITLASNPATEPLPGFKEVKP 298 Query: 303 VVFCGLFPVDATQFENLRTAINKLRLNDASFSFELENSTALGFGFRCGFLGLLHLEIIQE 362 +VF GL+PVD+ +E+LR A+ KL+LNDAS ++E E S ALGFGFRCGFLGLLH+EIIQE Sbjct: 299 MVFAGLYPVDSDDYEDLRDALEKLQLNDASLTYEPETSQALGFGFRCGFLGLLHMEIIQE 358 Query: 363 RLEREFSLNLIGTSPSVVYELYMHDGSMQKLSNPIDMPEVTKIAELREPWIQVTIITPNE 422 RLEREF L+LI T+PSVVY++ + DG ++ NP D+P+ KI E+ EP+++ TIITP E Sbjct: 359 RLEREFDLDLITTAPSVVYKVELTDGEEIEVDNPSDLPDPNKIEEIEEPYVKATIITPQE 418 Query: 423 YLGSILKLCQERRGIQIDMSHLD-NRAMIVYELPLNEVIFDFYDRLKSVSKGYASFDYNV 481 YLG++++LCQE+RGIQIDM +LD NR M+ YELPL E++FDF+D+LKS+SKGYASFDY Sbjct: 419 YLGNVMELCQEKRGIQIDMEYLDQNRVMLTYELPLAEIVFDFFDKLKSISKGYASFDYEF 478 Query: 482 IDYRDSDLVKLTILVNNETIDALSILVHRSVSEKRGRGICEKLKNLIPQQMFQIAIQAAI 541 I YR+SDLVK+ ILVN E +DALS +VHR + +RGR + EKLK LIP+Q F+I IQAAI Sbjct: 479 IGYRESDLVKVDILVNGEKVDALSFIVHRDNAYERGRELVEKLKELIPRQQFEIPIQAAI 538 Query: 542 GGRIIARETVKARRKDVTAKCYGGDITRKRKLLEKQKEGKKRMRRFGRVDIPQSAFISIL 601 G +IIARET+KA RKDV AKCYGGDI+RKRKLLEKQKEGKKRM++ G V+IPQ AF+++L Sbjct: 539 GSKIIARETIKALRKDVLAKCYGGDISRKRKLLEKQKEGKKRMKQIGNVEIPQEAFLAVL 598 Query: 602 KTDNE 606 K D++ Sbjct: 599 KMDDD 603 >gnl|CDD|35683 KOG0462, KOG0462, KOG0462, Elongation factor-type GTP-binding protein [Translation, ribosomal structure and biogenesis]. Length = 650 Score = 714 bits (1843), Expect = 0.0 Identities = 305/599 (50%), Positives = 420/599 (70%), Gaps = 6/599 (1%) Query: 7 PLSRIRNFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTV 66 P+ IRNFSI+AH+DHGKSTLADR ++ + QVLD + +ERERGITIKAQT Sbjct: 56 PVENIRNFSIIAHVDHGKSTLADRLLELTGTIDNNIGQEQVLDKLQVERERGITIKAQTA 115 Query: 67 RLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQA 126 + Y D + Y LNLIDTPGHVDF+ EVSRSL+AC+G+LLVVDA+QGV+AQT+AN Y A Sbjct: 116 SIFYK--DGQSYLLNLIDTPGHVDFSGEVSRSLAACDGALLVVDASQGVQAQTVANFYLA 173 Query: 127 IDNNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQ 186 + II VLNK DLPSADP+RV+ Q+ E I + + VSAKTG + LLE I+++ Sbjct: 174 FEAGLAIIPVLNKIDLPSADPERVENQLFELFDIPPAEVIYVSAKTGLNVEELLEAIIRR 233 Query: 187 LPSPTSPEGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERI 246 +P P +APL+ L+ DS Y+ Y GV+ LVR+++G + KG ++ T Y+V+ + Sbjct: 234 VPPPKGIR--DAPLRMLIFDSEYDEYRGVIALVRVVDGVVRKGDKVQSAATGKSYEVKVV 291 Query: 247 GILTPKMIDIEALYPGEIGVMIASIKEVSHTRVGDTITDDSSPT-TSALPGFKPIQPVVF 305 G++ P+M + L G++G +I +++ V ++GDTI S LPGF+P +P+VF Sbjct: 292 GVMRPEMTPVVELDAGQVGYIICNMRNVKEAQIGDTIAHKSVTKAVETLPGFEPTKPMVF 351 Query: 306 CGLFPVDATQFENLRTAINKLRLNDASFSFELENSTALGFGFRCGFLGLLHLEIIQERLE 365 GLFP+D + +E LR AI +L LND S + E+S ALG G+R GFLGLLH+E+ ERLE Sbjct: 352 VGLFPLDGSDYETLRDAIERLVLNDESVTVIKESSGALGQGWRLGFLGLLHMEVFIERLE 411 Query: 366 REFSLNLIGTSPSVVYELYMHDGSMQKLSNPIDMPEVTKIAELREPWIQVTIITPNEYLG 425 RE+ LI T P+V Y + +G +SNP P+ + + E EP+++ TIITP+EY+G Sbjct: 412 REYGAELIVTPPTVPYRVVYSNGDEILISNPALFPDPSDVKEFLEPYVEATIITPDEYVG 471 Query: 426 SILKLCQERRGIQIDMSHLD-NRAMIVYELPLNEVIFDFYDRLKSVSKGYASFDYNVIDY 484 ++++LC ERRG Q DM+++D NR M+ Y+LPL E++ DF+DRLKS++ GYASFDY Y Sbjct: 472 AVIELCSERRGEQKDMTYIDGNRVMLKYQLPLRELVGDFFDRLKSLTSGYASFDYEDAGY 531 Query: 485 RDSDLVKLTILVNNETIDALSILVHRSVSEKRGRGICEKLKNLIPQQMFQIAIQAAIGGR 544 + SDLVKL IL+N + +D LS +VH S +E RGR +KLK+LIP+Q+F++ IQA IG + Sbjct: 532 QASDLVKLDILLNGKMVDGLSTIVHLSKAESRGREFVQKLKDLIPRQIFEVHIQACIGSK 591 Query: 545 IIARETVKARRKDVTAKCYGGDITRKRKLLEKQKEGKKRMRRFGRVDIPQSAFISILKT 603 IARET+ A RKDV AK YGGD+TR +KLL+KQ EGKKRM+ G + IP+ AFI++LK Sbjct: 592 NIARETISAYRKDVLAKLYGGDVTRLKKLLKKQAEGKKRMKTVGNIRIPKEAFINVLKR 650 >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 = 357 bits (919), Expect = 4e-99 Identities = 125/179 (69%), Positives = 154/179 (86%) Query: 12 RNFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYT 71 RNFSI+AHIDHGKSTLADR ++ +++REM QVLD+MD+ERERGITIKAQTVRLNY Sbjct: 1 RNFSIIAHIDHGKSTLADRLLELTGTVSKREMKEQVLDSMDLERERGITIKAQTVRLNYK 60 Query: 72 STDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNH 131 + D ++Y LNLIDTPGHVDF+YEVSRSL+ACEG+LL+VDATQGVEAQTLAN Y A++NN Sbjct: 61 AKDGQEYLLNLIDTPGHVDFSYEVSRSLAACEGALLLVDATQGVEAQTLANFYLALENNL 120 Query: 132 EIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQLPSP 190 EII V+NK DLPSADP+RVK+QIE+ +G+ +A+LVSAKTG G+ LLE IV+++P P Sbjct: 121 EIIPVINKIDLPSADPERVKQQIEDVLGLDPSEAILVSAKTGLGVEDLLEAIVERIPPP 179 >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 = 199 bits (509), Expect = 2e-51 Identities = 73/189 (38%), Positives = 97/189 (51%), Gaps = 14/189 (7%) Query: 10 RIRNFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQ--VLDNMDIERERGITIKAQTVR 67 R RN I+ H+DHGK+TL D + + +R Q LD + ERERGITIK V Sbjct: 2 RHRNIGIIGHVDHGKTTLTDALLYVTGAIDKRGEVKQEGELDRLKEERERGITIKIAAVS 61 Query: 68 LNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAI 127 K +N+IDTPGHVDFT E+ R + +G++LVVDA +GV QT ++ A Sbjct: 62 FET-----KKRHINIIDTPGHVDFTKEMIRGAAQADGAILVVDAVEGVMPQTREHLLLAK 116 Query: 128 DNNHEIITVLNKADLPS-ADPDRVKKQIEETIGISTEDA------LLVSAKTGEGIPLLL 180 II +NK D A+ D V ++I + + SA TGEGI LL Sbjct: 117 QLGVPIIVFINKMDRVDDAELDEVVEEISRELLEKYGFGGETIPVIPGSALTGEGIDTLL 176 Query: 181 ERIVQQLPS 189 E + LPS Sbjct: 177 EALDLYLPS 185 >gnl|CDD|31410 COG1217, TypA, Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]. Length = 603 Score = 198 bits (506), Expect = 3e-51 Identities = 147/507 (28%), Positives = 239/507 (47%), Gaps = 68/507 (13%) Query: 11 IRNFSIVAHIDHGKSTLADRFIQHCRGLTERE-MSSQVLDNMDIERERGITIKAQTVRLN 69 IRN +I+AH+DHGK+TL D ++ ERE ++ +V+D+ D+E+ERGITI A+ +N Sbjct: 5 IRNIAIIAHVDHGKTTLVDALLKQSGTFREREEVAERVMDSNDLEKERGITILAKNTAVN 64 Query: 70 YTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDN 129 Y ++N++DTPGH DF EV R LS +G LL+VDA++G QT + +A+ Sbjct: 65 Y-----NGTRINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALAL 119 Query: 130 NHEIITVLNKADLPSADPDRVKKQIEE---TIGISTED----ALLVSAKTG--------- 173 + I V+NK D P A PD V ++ + +G + E + SA+ G Sbjct: 120 GLKPIVVINKIDRPDARPDEVVDEVFDLFVELGATDEQLDFPIVYASARNGTASLDPEDE 179 Query: 174 -EGIPLLLERIVQQLPSPTSPEGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTKGQSI 232 + + L E I+ +P+P + PL+ + YNSY+G + + RI G + Q + Sbjct: 180 ADDMAPLFETILDHVPAPK--GDLDEPLQMQVTQLDYNSYVGRIGIGRIFRGTVKPNQQV 237 Query: 233 RLMGTNAKYQVERI----GILTPKMIDIEALYPGEIGVMIASIKEVSHTRVGDTITDDSS 288 L+ ++ + RI G L + I+IE G+I V IA +++++ +GDTI D + Sbjct: 238 ALIKSDGTTENGRITKLLGFLGLERIEIEEAEAGDI-VAIAGLEDIN---IGDTICDPDN 293 Query: 289 PTTSALPGFKPIQPVVFCGLFPVDATQFENLRTAINKLRLNDASFSFELENSTALGF--- 345 P ALP + F V+ + F R + ELE + AL Sbjct: 294 P--EALP-ALSVDEPTLSMTFSVNDSPFAGKEGKFVTSRQIRDRLNKELETNVALRVEET 350 Query: 346 ----GFRCGFLGLLHLEIIQERLERE-FSLNLIGTSPSVVYELYMHDGSMQKLSNPIDMP 400 F G LHL I+ E + RE F L + + P V+ + Sbjct: 351 ESPDAFEVSGRGELHLSILIENMRREGFELQV--SRPEVIIK------------------ 390 Query: 401 EVTKIAELREPWIQVTIITPNEYLGSILKLCQERRGIQIDM-SHLDNRAMIVYELPLNEV 459 EP+ +VTI P E+ G++++ ER+G DM R + + +P + Sbjct: 391 --EIDGVKCEPFEEVTIDVPEEHQGAVIEKLGERKGEMKDMAPDGKGRVRLEFVIPARGL 448 Query: 460 IFDFYDRLKSVSKGYASFDYNVIDYRD 486 I F ++++G +++ YR Sbjct: 449 I-GFRTEFLTMTRGTGIMNHSFDHYRP 474 >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 = 161 bits (410), Expect = 4e-40 Identities = 71/194 (36%), Positives = 102/194 (52%), Gaps = 21/194 (10%) Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTER-EMSSQVLDNMDIERERGITIKAQTVRLNYT 71 N I H+DHGK+TL +R + + + LD + ERERGITIK+ + Sbjct: 1 NVGIAGHVDHGKTTLTERLLYVTGDIERDGTVEETFLDVLKEERERGITIKSGVATFEW- 59 Query: 72 STDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNH 131 D ++N IDTPGH DF+ EV R LS +G++LVVDA +GV+ QT ++ A + Sbjct: 60 ----PDRRVNFIDTPGHEDFSSEVIRGLSVSDGAILVVDANEGVQPQTREHLRIAREGGL 115 Query: 132 EIITVLNKADLPS-ADPDRVKKQIEETIG-----ISTEDA---------LLVSAKTGEGI 176 II +NK D D + V ++I+E +G + E+ + SA TG G+ Sbjct: 116 PIIVAINKIDRVGEEDLEEVLREIKELLGLIGFISTKEEGTRNGLLVPIVPGSALTGIGV 175 Query: 177 PLLLERIVQQLPSP 190 LLE IV+ LP P Sbjct: 176 EELLEAIVEHLPPP 189 >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 = 151 bits (385), Expect = 3e-37 Identities = 75/202 (37%), Positives = 114/202 (56%), Gaps = 29/202 (14%) Query: 10 RIRNFSIVAHIDHGKSTLADRFIQHCRGLTERE-MSSQVLDNMDIERERGITIKAQTVRL 68 IRN +I+AH+DHGK+TL D ++ E E + +V+D+ D+ERERGITI A+ + Sbjct: 1 DIRNIAIIAHVDHGKTTLVDALLKQSGTFRENEEVEERVMDSNDLERERGITILAKNTAV 60 Query: 69 NYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAID 128 Y KD ++N++DTPGH DF EV R LS +G LL+VDA++G QT + +A++ Sbjct: 61 TY-----KDTKINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALE 115 Query: 129 NNHEIITVLNKADLPSADPDRVKKQIEETIGI-----STEDAL-----LVSAKTG----- 173 + I V+NK D P A P+ V ++E + +TE+ L SAK G Sbjct: 116 LGLKPIVVINKIDRPDARPEEV---VDEVFDLFIELGATEEQLDFPVLYASAKNGWASLN 172 Query: 174 -----EGIPLLLERIVQQLPSP 190 E + L + I++ +P+P Sbjct: 173 LEDPSEDLEPLFDTIIEHVPAP 194 >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 = 149 bits (378), Expect = 2e-36 Identities = 69/223 (30%), Positives = 112/223 (50%), Gaps = 45/223 (20%) Query: 12 RNFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQV--LDNMDIERERGITIKAQTVRLN 69 RN I+AH+DHGK+TL+D + G+ +++ + +D+ + E+ERGIT+K+ + L Sbjct: 1 RNICIIAHVDHGKTTLSDSLLASA-GIISEKLAGKARYMDSREDEQERGITMKSSAISLY 59 Query: 70 Y-----TSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVY 124 + D +Y +NLID+PGHVDF+ EV+ +L C+G+L+VVDA +GV QT + Sbjct: 60 FEYEEEDKADGNEYLINLIDSPGHVDFSSEVTAALRLCDGALVVVDAVEGVCVQTETVLR 119 Query: 125 QAIDNNHEIITVLNKAD-------LPSAD--------------------PDRVKKQIEET 157 QA+ + + V+NK D L + + K++ +E Sbjct: 120 QALKERVKPVLVINKIDRLILELKLSPEEAYQRLARIIEQVNAIIGTYADEEFKEKDDEK 179 Query: 158 IGISTEDA--LLVSAKTGEGIPL--------LLERIVQQLPSP 190 S + SA G G + +LE +V+ LPSP Sbjct: 180 WYFSPQKGNVAFGSALHGWGFTIIKFARIYAVLEMVVKHLPSP 222 >gnl|CDD|30828 COG0480, FusA, Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]. Length = 697 Score = 146 bits (370), Expect = 1e-35 Identities = 70/162 (43%), Positives = 94/162 (58%), Gaps = 9/162 (5%) Query: 3 KKPTPLSRIRNFSIVAHIDHGKSTLADRFIQHCRGLT----EREMSSQVLDNMDIERERG 58 + PL RIRN IVAHID GK+TL +R + + G+ E + +D M+ E+ERG Sbjct: 2 ARLMPLERIRNIGIVAHIDAGKTTLTERILFYT-GIISKIGEVHDGAATMDWMEQEQERG 60 Query: 59 ITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQ 118 ITI + L + DY++NLIDTPGHVDFT EV RSL +G+++VVDA +GVE Q Sbjct: 61 ITITSAATTLFWK----GDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVEGVEPQ 116 Query: 119 TLANVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGI 160 T QA I +NK D AD V +Q++E +G Sbjct: 117 TETVWRQADKYGVPRILFVNKMDRLGADFYLVVEQLKERLGA 158 Score = 100 bits (251), Expect = 9e-22 Identities = 68/254 (26%), Positives = 110/254 (43%), Gaps = 29/254 (11%) Query: 148 DRVKKQIE-ETIGISTEDALLVSAKTGEGIPLLLERIVQQLPSPT--------------- 191 + +KK + TI L SA +G+ LL+ +V LPSP Sbjct: 237 EEIKKALRKGTIAGKIVPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPPIKGDLDDEIEK 296 Query: 192 ---SPEGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGI 248 PL AL+ + ++G + VR+ +G L G + K +V R+ + Sbjct: 297 AVLRKASDEGPLSALVFKIMTDPFVGKLTFVRVYSGTLKSGSEVLNSTKGKKERVGRLLL 356 Query: 249 L-TPKMIDIEALYPGEIGVMIASIKEVSHTRVGDTITDDSSPTTSALPGFKPIQPVVFCG 307 + + +++ + G+I V + +K+ GDT+ D++ P L + +PV+ Sbjct: 357 MHGNEREEVDEVPAGDI-VALVGLKD---ATTGDTLCDENKPV--ILESMEFPEPVISVA 410 Query: 308 LFPVDATQFENLRTAINKLRLNDASFSFELENSTALGFGFRCGFLGLLHLEIIQERLERE 367 + P E L A+NKL D +F E + T G G G LHLEII +RL+RE Sbjct: 411 VEPKTKADQEKLSEALNKLAEEDPTFRVETDEET--GETIISGM-GELHLEIIVDRLKRE 467 Query: 368 FSLNLIGTSPSVVY 381 F + + P V Y Sbjct: 468 FGVEVEVGKPQVAY 481 Score = 47.2 bits (112), Expect = 1e-05 Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 3/72 (4%) Query: 408 LREPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLDNRAMIVY--ELPLNEVIFDFYD 465 L EP ++V I TP EY+G ++ RRG + M + V E+PL E +F + Sbjct: 599 LLEPIMKVEITTPEEYMGDVIGDLNSRRGQILGMEQRPGGGLDVIKAEVPLAE-MFGYAT 657 Query: 466 RLKSVSKGYASF 477 L+S ++G ASF Sbjct: 658 DLRSATQGRASF 669 >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 = 139 bits (353), Expect = 2e-33 Identities = 52/80 (65%), Positives = 70/80 (87%), Gaps = 1/80 (1%) Query: 410 EPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLD-NRAMIVYELPLNEVIFDFYDRLK 468 EP+++ TIITP+EYLG+I++LCQERRG+Q DM +LD NR M+ YELPL E+++DF+D+LK Sbjct: 1 EPFVKATIITPSEYLGAIMELCQERRGVQKDMEYLDANRVMLTYELPLAEIVYDFFDKLK 60 Query: 469 SVSKGYASFDYNVIDYRDSD 488 S+SKGYAS DY +I YR+SD Sbjct: 61 SISKGYASLDYELIGYRESD 80 >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 = 130 bits (329), Expect = 1e-30 Identities = 64/150 (42%), Positives = 87/150 (58%), Gaps = 14/150 (9%) Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTER--EMSS--QVLDNMDIERERGITIKAQTVRL 68 N I+AHID GK+T +R I + G + E+ +D M+ ERERGITI++ Sbjct: 1 NIGIIAHIDAGKTTTTER-ILYYTGRIHKIGEVHGGGATMDFMEQERERGITIQSAA--- 56 Query: 69 NYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAID 128 T+ KD+++N+IDTPGHVDFT EV RSL +G++ V DA GVE QT QA Sbjct: 57 --TTCFWKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVEPQTETVWRQA-- 112 Query: 129 NNHEI--ITVLNKADLPSADPDRVKKQIEE 156 + + + I +NK D AD RV +QI E Sbjct: 113 DRYNVPRIAFVNKMDRTGADFFRVVEQIRE 142 >gnl|CDD|35686 KOG0465, KOG0465, KOG0465, Mitochondrial elongation factor [Translation, ribosomal structure and biogenesis]. Length = 721 Score = 126 bits (317), Expect = 2e-29 Identities = 66/154 (42%), Positives = 91/154 (59%), Gaps = 14/154 (9%) Query: 7 PLSRIRNFSIVAHIDHGKSTLADR------FIQHCRGLTEREMSSQVLDNMDIERERGIT 60 PL++IRN I AHID GK+TL +R I+H + E +D+M++ER+RGIT Sbjct: 35 PLNKIRNIGISAHIDAGKTTLTERMLYYTGRIKH---IGEVRGGGATMDSMELERQRGIT 91 Query: 61 IKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTL 120 I++ T +DY++N+IDTPGHVDFT+EV R+L +G++LV+DA GVE+QT Sbjct: 92 IQSAA-----TYFTWRDYRINIIDTPGHVDFTFEVERALRVLDGAVLVLDAVAGVESQTE 146 Query: 121 ANVYQAIDNNHEIITVLNKADLPSADPDRVKKQI 154 Q N I +NK D A P R QI Sbjct: 147 TVWRQMKRYNVPRICFINKMDRMGASPFRTLNQI 180 Score = 78.8 bits (194), Expect = 4e-15 Identities = 70/259 (27%), Positives = 105/259 (40%), Gaps = 35/259 (13%) Query: 146 DPDRVKKQIEE-TIGISTEDALLVSAKTGEGIPLLLERIVQQLPSPT------------- 191 ++K I TI S L SA +G+ LL+ +V LPSP+ Sbjct: 265 SAQQLKAAIRRATIKRSFVPVLCGSALKNKGVQPLLDAVVDYLPSPSEVENYALNKETNS 324 Query: 192 ------SPEGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVER 245 SP P AL + G + VR+ G L+KG +I + T K +V R Sbjct: 325 KEKVTLSPSRDKDPFVALAFKLEEGRF-GQLTYVRVYQGTLSKGDTIYNVRTGKKVRVGR 383 Query: 246 IGIL-TPKMIDIEALYPGEIGVMIASIKEVSHTRVGDTITDDSSPTTSALPGFKPIQPVV 304 + + M D+ + G+I + GDT TD + S P +PV+ Sbjct: 384 LVRMHANDMEDVNEVLAGDICALFGI-----DCASGDTFTDKQNLALSMESIHIP-EPVI 437 Query: 305 FCGLFPVDATQFENLRTAINKLRLNDASF--SFELENSTALGFGFRCGFLGLLHLEIIQE 362 + PV+ +N A+N+ D +F S + E + G +G LHLEI E Sbjct: 438 SVAIKPVNKKDADNFSKALNRFTKEDPTFRVSLDPEMKQTVISG-----MGELHLEIYVE 492 Query: 363 RLEREFSLNLIGTSPSVVY 381 RL RE+ ++ P V Y Sbjct: 493 RLVREYKVDAELGKPQVAY 511 Score = 46.4 bits (110), Expect = 2e-05 Identities = 22/95 (23%), Positives = 46/95 (48%), Gaps = 6/95 (6%) Query: 410 EPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLDNRAMIVYELPLNEVIFDFYDRLKS 469 EP + V + TP E+ G+++ +R+ + ++ I E+PLNE +F + L+S Sbjct: 633 EPIMNVEVTTPEEFQGTVIGDLNKRKAQITGIDSSEDYKTIKAEVPLNE-MFGYSSELRS 691 Query: 470 VSKGYASFDYNVIDYRDSDLVKLTILVNNETIDAL 504 +++G F ++Y S + V ++ + Sbjct: 692 LTQGKGEFT---MEY--SRYSPVPPDVQDQLVHKY 721 >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 = 119 bits (300), Expect = 2e-27 Identities = 43/86 (50%), Positives = 57/86 (66%) Query: 200 LKALLIDSWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGILTPKMIDIEAL 259 L+AL+ DSWY+ Y GV+ LVR+ +G L KG IR M T +Y+VE +GI P+M + L Sbjct: 1 LRALIFDSWYDPYRGVIALVRVFDGTLKKGDKIRFMSTGKEYEVEEVGIFRPEMTPTDEL 60 Query: 260 YPGEIGVMIASIKEVSHTRVGDTITD 285 G++G +IA IK V RVGDTIT Sbjct: 61 SAGQVGYIIAGIKTVKDARVGDTITL 86 >gnl|CDD|35685 KOG0464, KOG0464, KOG0464, Elongation factor G [Translation, ribosomal structure and biogenesis]. Length = 753 Score = 118 bits (296), Expect = 5e-27 Identities = 62/159 (38%), Positives = 86/159 (54%), Gaps = 8/159 (5%) Query: 5 PTPLSRIRNFSIVAHIDHGKSTLADRFIQHC---RGLTEREMSSQVLDNMDIERERGITI 61 +++IRN I+AHID GK+T +R + + + V D + IERERGITI Sbjct: 31 NPAIAKIRNIGIIAHIDAGKTTTTERILYLAGAIHSAGDVDDGDTVTDFLAIERERGITI 90 Query: 62 KAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLA 121 ++ V D K +++NLIDTPGHVDF EV R L +G++ V DA+ GVEAQTL Sbjct: 91 QSAAVNF-----DWKGHRINLIDTPGHVDFRLEVERCLRVLDGAVAVFDASAGVEAQTLT 145 Query: 122 NVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGI 160 QA +NK D +A+ + IEE +G Sbjct: 146 VWRQADKFKIPAHCFINKMDKLAANFENAVDSIEEKLGA 184 Score = 62.1 bits (150), Expect = 4e-10 Identities = 72/344 (20%), Positives = 121/344 (35%), Gaps = 57/344 (16%) Query: 69 NYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAID 128 N S D KD++ + P E++ L+ + +L A + D Sbjct: 215 NCNSNDGKDFE----NKPLLEKNDPELAEELAEAKNALCEQLADLDADFADK--FLDEFD 268 Query: 129 NNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLV-SAKTGEGIPLLLERIVQQL 187 N + I D + +K I E +L SA +GI LL+ + L Sbjct: 269 ENFDKI-----------DAEELKSAIHELTCAQKAAPILCGSAIKNKGIQPLLDAVTMYL 317 Query: 188 PSPTSP-----EGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQ 242 PSP + L AL ++ G + +RI +G + +I + Sbjct: 318 PSPEERNYEFLQWYKDDLCALAFKVLHDKQRGPLSFMRIYSGSIHNNLAIFNINGMCSEG 377 Query: 243 VERIGILTP---KMIDIEALYPGEIGVMIASIKEVSHTRVGDTITDDSSPTTSA------ 293 + ++ P + +IE L G I + + HT GDTI + +A Sbjct: 378 ILKL--FLPFADEHREIEQLSAGNIALTAG----LKHTATGDTIVASKASAEAAAQKAAG 431 Query: 294 ----------------LPGFKPIQPVVFCGLFPVDATQFENLRTAINKLRLNDASFSFEL 337 G + V FC + P + + A+ L+ D S Sbjct: 432 EGEKKHLQNKDAERLLFAGIEIPDAVFFCCIEPPSLRKLNDFEHALECLQREDPSLKIRF 491 Query: 338 ENSTALGFGFRCGFLGLLHLEIIQERLEREFSLNLIGTSPSVVY 381 + + G CG +G LH+E I +R++RE+ L+ V Y Sbjct: 492 DPDS--GQTILCG-MGELHIEAIHDRIKREYGLDTFIGKLQVAY 532 >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 = 115 bits (291), Expect = 3e-26 Identities = 55/152 (36%), Positives = 90/152 (59%), Gaps = 18/152 (11%) Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTER----EMSSQVLDNMDIERERGITIKAQTVRL 68 N I+AH+D GK+TL + + + + + +++ D M++ER+RGITI + Sbjct: 1 NIGILAHVDAGKTTLTESLLYTSGAIRKLGSVDKGTTR-TDTMELERQRGITIFSAVASF 59 Query: 69 NYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQT--LANVYQA 126 + +D ++NLIDTPGH+DF EV RSLS +G++LV+ A +GV+AQT L + + Sbjct: 60 QW-----EDTKVNLIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTRILWRLLRK 114 Query: 127 IDNNHEIITVL--NKADLPSADPDRVKKQIEE 156 I T++ NK D AD ++V ++I+E Sbjct: 115 ----LNIPTIIFVNKIDRAGADLEKVYQEIKE 142 >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 = 114 bits (287), Expect = 8e-26 Identities = 53/146 (36%), Positives = 75/146 (51%), Gaps = 11/146 (7%) Query: 12 RNFSIVAHIDHGKSTLADRFIQHCRGLTER----EMSSQVLDNMDIERERGITIKAQTVR 67 RN +I H+ HGK++L D I+ LT + D E+ERGI+IK+ + Sbjct: 1 RNVAIAGHLHHGKTSLLDMLIEQTHDLTPSGKDGWKPLRYTDIRKDEQERGISIKSSPIS 60 Query: 68 LNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAI 127 L + K Y N+IDTPGHV+F EV+ +L +G +LVVD +GV + T + AI Sbjct: 61 LVLPDSKGKSYLFNIIDTPGHVNFMDEVAAALRLSDGVVLVVDVVEGVTSNTERLIRHAI 120 Query: 128 DNNHEIITVLNKAD-------LPSAD 146 I+ V+NK D LP D Sbjct: 121 LEGLPIVLVINKIDRLILELKLPPND 146 >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 = 113 bits (285), Expect = 1e-25 Identities = 55/137 (40%), Positives = 83/137 (60%), Gaps = 8/137 (5%) Query: 7 PLSRIRNFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQV--LDNMDIERERGITIKAQ 64 IRN +VAH+DHGK++LAD + G+ ++ ++ LD + E+ RGIT+K+ Sbjct: 5 GSEGIRNICLVAHVDHGKTSLADSLVA-SNGVISSRLAGKIRFLDTREDEQTRGITMKSS 63 Query: 65 TVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVY 124 + S KDY +NLID+PGHVDF+ EVS + +G+L++VD +GV +QT A + Sbjct: 64 AI-----SLLHKDYLINLIDSPGHVDFSSEVSSASRLSDGALVLVDVVEGVCSQTYAVLR 118 Query: 125 QAIDNNHEIITVLNKAD 141 QA + I V+NK D Sbjct: 119 QAWIEGLKPILVINKID 135 >gnl|CDD|35689 KOG0468, KOG0468, KOG0468, U5 snRNP-specific protein [Translation, ribosomal structure and biogenesis]. Length = 971 Score = 109 bits (274), Expect = 2e-24 Identities = 61/178 (34%), Positives = 89/178 (50%), Gaps = 14/178 (7%) Query: 10 RIRNFSIVAHIDHGKSTLADRFIQ--HCRGLTEREMSSQVLDNMDIERERGITIKAQTVR 67 RIRN +V H+ HGK+ L D ++ H E + D + E+ERG +IK+ V Sbjct: 127 RIRNVGLVGHLHHGKTALMDLLVEQTHPDFSKNTEADLRYTDTLFYEQERGCSIKSTPVT 186 Query: 68 LNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAI 127 L + + K Y +N++DTPGHV+F+ E + SL +G +LVVD +GV T + AI Sbjct: 187 LVLSDSKGKSYLMNILDTPGHVNFSDETTASLRLSDGVVLVVDVAEGVMLNTERIIKHAI 246 Query: 128 DNNHEIITVLNKAD-------LPSADPDRVKKQIEETIG-----ISTEDALLVSAKTG 173 N I+ V+NK D LP D + I + I S +D +VS G Sbjct: 247 QNRLPIVVVINKVDRLILELKLPPMDAYYKLRHIIDEINNLISTFSKDDNPVVSPILG 304 Score = 30.8 bits (69), Expect = 1.1 Identities = 21/121 (17%), Positives = 46/121 (38%), Gaps = 15/121 (12%) Query: 217 VLVRIINGQLTKGQSIRLMGTN---------AKYQVERIGILTPKM-IDIEALYPGEIGV 266 V R+ +GQ+ GQ +R++G N +V + ++ + I + G + Sbjct: 491 VFGRVYSGQVVTGQDVRVLGENYSLEDEEDMVICEVGELWVVRARYRIPVSRAPAGLWVL 550 Query: 267 MIASIKEVSHTRVGDTITDDSSPTTSAL-PGFKPI-QPVVFCGLFPVDATQFENLRTAIN 324 + + + T TI + K +PVV + P++ ++ + + Sbjct: 551 IEGVDQSIVKTA---TIKSLEYKEDVYIFRPLKFNTEPVVKVAVEPLNPSELPKMLDGLR 607 Query: 325 K 325 K Sbjct: 608 K 608 >gnl|CDD|34853 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]. Length = 428 Score = 108 bits (272), Expect = 4e-24 Identities = 84/328 (25%), Positives = 138/328 (42%), Gaps = 61/328 (18%) Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTEREMS----------------SQVLDNMDIERE 56 N + H+D GKSTL R + + +R M + VLD ERE Sbjct: 9 NLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVLDKTKEERE 68 Query: 57 RGITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQG-- 114 RG+TI + ++ + Y +ID PGH DF + S + ++LVVDA G Sbjct: 69 RGVTID-----VAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARDGEF 123 Query: 115 -----VEAQTLANVYQAIDNN-HEIITVLNKADLPSADPDR---VKKQIE---ETIGIST 162 V QT + + A ++I +NK DL S D +R + ++ + +G + Sbjct: 124 EAGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLLKMVGYNP 183 Query: 163 EDALL--VSAKTGEGI------------PLLLERIVQQLPSPTSPEGANAPLKALLIDSW 208 +D +S G+ + P LLE + QL P P + PL+ + D + Sbjct: 184 KDVPFIPISGFKGDNLTKKSENMPWYKGPTLLEAL-DQLEPPERP--LDKPLRLPIQDVY 240 Query: 209 YNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGILTPKMID--IEALYPGE-IG 265 S +G + + R+ +G + GQ + M +V+ I +M I PG+ +G Sbjct: 241 SISGIGTVPVGRVESGVIKPGQKVTFMPAGVVGEVKSI-----EMHHEEISQAEPGDNVG 295 Query: 266 VMIASIKEVSHTRVGDTITDDSSPTTSA 293 + + E + R GD I +P T + Sbjct: 296 FNVRGV-EKNDIRRGDVIGHSDNPPTVS 322 >gnl|CDD|33865 COG4108, PrfC, Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]. Length = 528 Score = 107 bits (269), Expect = 8e-24 Identities = 54/162 (33%), Positives = 91/162 (56%), Gaps = 12/162 (7%) Query: 8 LSRIRNFSIVAHIDHGKSTLADRF------IQHCRGLTEREMSSQ-VLDNMDIERERGIT 60 ++R R F+I++H D GK+TL ++ IQ + R+ D M+IE++RGI+ Sbjct: 9 VARRRTFAIISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGKHAKSDWMEIEKQRGIS 68 Query: 61 IKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTL 120 + + ++ +Y D +NL+DTPGH DF+ + R+L+A + +++V+DA +G+E QTL Sbjct: 69 VTSSVMQFDY-----ADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIEPQTL 123 Query: 121 ANVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGIST 162 + I T +NK D DP + +IEE +GI Sbjct: 124 KLFEVCRLRDIPIFTFINKLDREGRDPLELLDEIEEELGIQC 165 Score = 41.4 bits (97), Expect = 8e-04 Identities = 33/160 (20%), Positives = 67/160 (41%), Gaps = 20/160 (12%) Query: 219 VRIINGQLTKGQSIRLMGTNAKYQVER-IGILTPKMIDIEALYPGEIGVMIASIKEVSH- 276 +R+ +G+ +G + + T ++ + + +E Y G+I I +H Sbjct: 317 MRVCSGKFERGMKVTHVRTGKDVKLSDALTFMAQDRETVEEAYAGDI------IGLHNHG 370 Query: 277 -TRVGDTITDDSSPTTSALPGFKPIQPVVFCGLFPVDATQFENLRTAINKLRLNDAS--F 333 ++GDT T+ + +P F P +F + D + + L+ + +L A F Sbjct: 371 TIQIGDTFTEGEKLKFTGIPNFA---PELFRRVRLKDPLKQKQLKKGLEQLAEEGAVQVF 427 Query: 334 SFELENSTALGFGFRCGFLGLLHLEIIQERLEREFSLNLI 373 N L G +G L E++Q RL+ E+++ + Sbjct: 428 KPLDGNDLIL------GAVGQLQFEVVQARLKNEYNVEAV 461 >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 = 2e-23 Identities = 59/169 (34%), Positives = 90/169 (53%), Gaps = 30/169 (17%) Query: 10 RIRNFSIVAHIDHGKSTLADRF------IQ-----HCRGLTEREMSSQVLDNMDIERERG 58 R R F+I++H D GK+TL ++ I+ R + S D M+IE++RG Sbjct: 1 RRRTFAIISHPDAGKTTLTEKLLLFGGAIREAGAVKARKSRKHATS----DWMEIEKQRG 56 Query: 59 ITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDF---TYEVSRSLSACEGSLLVVDATQGV 115 I++ + ++ Y +D +NL+DTPGH DF TY R+L+A + +++V+DA +GV Sbjct: 57 ISVTSSVMQFEY-----RDCVINLLDTPGHEDFSEDTY---RTLTAVDSAVMVIDAAKGV 108 Query: 116 EAQT--LANVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGIST 162 E QT L V IIT +NK D DP + +IEE +GI Sbjct: 109 EPQTRKLFEV--CRLRGIPIITFINKLDREGRDPLELLDEIEEELGIDC 155 >gnl|CDD|35690 KOG0469, KOG0469, KOG0469, Elongation factor 2 [Translation, ribosomal structure and biogenesis]. Length = 842 Score = 104 bits (261), Expect = 7e-23 Identities = 55/143 (38%), Positives = 81/143 (56%), Gaps = 12/143 (8%) Query: 11 IRNFSIVAHIDHGKSTLADRFIQHCRGLT-EREMSSQVLDNMDIERERGITIKAQTVRLN 69 IRN S++AH+DHGKSTL D +Q ++ + ++ D E+ERGITIK+ + L Sbjct: 19 IRNMSVIAHVDHGKSTLTDSLVQKAGIISAAKAGETRFTDTRKDEQERGITIKSTAISLF 78 Query: 70 YT-----------STDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQ 118 + D + +NLID+PGHVDF+ EV+ +L +G+L+VVD GV Q Sbjct: 79 FEMSDDDLKFIKQEGDGNGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQ 138 Query: 119 TLANVYQAIDNNHEIITVLNKAD 141 T + QAI + + V+NK D Sbjct: 139 TETVLRQAIAERIKPVLVMNKMD 161 Score = 36.9 bits (85), Expect = 0.017 Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 3/70 (4%) Query: 408 LREPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLDNRAMIVYE--LPLNEVIFDFYD 465 L+EP V I P + +G I + +RG + + M V + LP+NE F F Sbjct: 724 LQEPVYLVEIQCPEQAVGGIYGVLNRKRGHVFEEEQVPGTPMFVVKAYLPVNES-FGFTA 782 Query: 466 RLKSVSKGYA 475 L+S + G A Sbjct: 783 DLRSNTGGQA 792 >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 = 101 bits (254), Expect = 6e-22 Identities = 64/177 (36%), Positives = 84/177 (47%), Gaps = 29/177 (16%) Query: 19 HIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGIT--IKAQTVRLNYTSTDAK 76 H+DHGK+TL D+ I+ + E GIT I A V K Sbjct: 8 HVDHGKTTLLDK-IRKTN-VAAGE-------------AGGITQHIGAFEVPAEV----LK 48 Query: 77 DYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNHEIITV 136 + IDTPGH FT +R S + ++LVV A GV QT+ + A N I Sbjct: 49 IPGITFIDTPGHEAFTNMRARGASLTDIAILVVAADDGVMPQTIEAIKLAKAANVPFIVA 108 Query: 137 LNKADLPSADPDRVKKQIEETIGISTEDALL-------VSAKTGEGIPLLLERIVQQ 186 LNK D P+A+P+RVK ++ E +G+ ED SAKTGEGI LLE I+ Sbjct: 109 LNKIDKPNANPERVKNELSE-LGLQGEDEWGGDVQIVPTSAKTGEGIDDLLEAILLL 164 >gnl|CDD|30878 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]. Length = 509 Score = 95.6 bits (238), Expect = 3e-20 Identities = 75/234 (32%), Positives = 110/234 (47%), Gaps = 28/234 (11%) Query: 15 SIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGIT--IKAQTVRLNYTS 72 +I+ H+DHGK+TL D+ I+ + E GIT I A V L+ Sbjct: 9 TIMGHVDHGKTTLLDK-IRKTN-VAAGE-------------AGGITQHIGAYQVPLD--- 50 Query: 73 TDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNHE 132 K + IDTPGH FT +R S + ++LVV A GV QT+ + A Sbjct: 51 -VIKIPGITFIDTPGHEAFTAMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAAGVP 109 Query: 133 IITVLNKADLPSADPDRVKKQIEETIGISTEDA------LLVSAKTGEGIPLLLERIVQQ 186 I+ +NK D P A+PD+VK++++E G+ E+ + VSAKTGEGI LLE I+ Sbjct: 110 IVVAINKIDKPEANPDKVKQELQE-YGLVPEEWGGDVIFVPVSAKTGEGIDELLELILLL 168 Query: 187 LPSPTSPEGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAK 240 P + +I+ + LG + V + +G L KG I G + Sbjct: 169 AEVLELKANPEGPARGTVIEVKLDKGLGPVATVIVQDGTLKKGDIIVAGGEYGR 222 >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 = 91.5 bits (228), Expect = 6e-19 Identities = 31/90 (34%), Positives = 45/90 (50%), Gaps = 2/90 (2%) Query: 407 ELREPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLDN-RAMIVYELPLNEVIFDFYD 465 L EP ++V I P EYLG ++ +RRG +DM + R +I E+PL E +F F Sbjct: 1 VLLEPIMKVEITVPEEYLGDVIGDLNKRRGEILDMEPIGGGRVVIEAEVPLAE-LFGFST 59 Query: 466 RLKSVSKGYASFDYNVIDYRDSDLVKLTIL 495 L+S+++G SF Y L L Sbjct: 60 ELRSLTQGRGSFSMEFSGYEPVPGDILDRL 89 >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 = 89.9 bits (224), Expect = 2e-18 Identities = 49/153 (32%), Positives = 76/153 (49%), Gaps = 14/153 (9%) Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTER----EMSSQVLDNMDIERERGITIKAQTVRL 68 N ++V H GK+TLA+ + + G +R E + V D E +R ++I L Sbjct: 1 NIALVGHSGSGKTTLAEA-LLYATGAIDRLGSVEDGTTVSDYDPEEIKRKMSISTSVAPL 59 Query: 69 NYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAID 128 + K +++NLIDTPG+ DF E +L A + +L+VV A GVE T +++ D Sbjct: 60 EW-----KGHKINLIDTPGYADFVGETRAALRAADAALVVVSAQSGVEVGT-EKLWEFAD 113 Query: 129 NNHEI--ITVLNKADLPSADPDRVKKQIEETIG 159 I I +NK D AD D+ ++E G Sbjct: 114 -EAGIPRIIFINKMDRERADFDKTLAALQEAFG 145 Score = 30.6 bits (70), Expect = 1.2 Identities = 12/25 (48%), Positives = 15/25 (60%) Query: 166 LLVSAKTGEGIPLLLERIVQQLPSP 190 L SA T G+ LL+ +V LPSP Sbjct: 244 LCGSALTNIGVRELLDALVHLLPSP 268 >gnl|CDD|33087 COG3276, SelB, Selenocysteine-specific translation elongation factor [Translation, ribosomal structure and biogenesis]. Length = 447 Score = 89.6 bits (222), Expect = 2e-18 Identities = 75/279 (26%), Positives = 126/279 (45%), Gaps = 34/279 (12%) Query: 18 AHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAKD 77 HIDHGK+TL + V D + E++RGITI L + +D Sbjct: 7 GHIDHGKTTLLKAL------------TGGVTDRLPEEKKRGITID-----LGFYYRKLED 49 Query: 78 YQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAID--NNHEIIT 135 + ID PGH DF + L + +LLVV A +G+ AQT ++ +D I Sbjct: 50 GVMGFIDVPGHPDFISNLLAGLGGIDYALLVVAADEGLMAQTGEHL-LILDLLGIKNGII 108 Query: 136 VLNKADLPSADPDRVKKQIEETI-GISTEDALL--VSAKTGEGIPLLLERIVQQLPSPTS 192 VL KAD D R++++I++ + +S +A + SAKTG GI L ++ L Sbjct: 109 VLTKADR--VDEARIEQKIKQILADLSLANAKIFKTSAKTGRGIEELKNELIDLLEEIER 166 Query: 193 PEGANAPLKALLIDSWYN-SYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGILTP 251 E P + + ID + +G +V +++G++ G + L N + +V I Sbjct: 167 DE--QKPFR-IAIDRAFTVKGVGTVVTGTVLSGEVKVGDKLYLSPINKEVRVRSIQAHD- 222 Query: 252 KMIDIEALYPGE-IGVMIASIKEVSHTRVGDTITDDSSP 289 +D+E G+ +G+ + +++ R GD + Sbjct: 223 --VDVEEAKAGQRVGLALKGVEKEEIER-GDWLLKPEPL 258 >gnl|CDD|36360 KOG1145, KOG1145, KOG1145, Mitochondrial translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]. Length = 683 Score = 87.3 bits (216), Expect = 1e-17 Identities = 69/225 (30%), Positives = 99/225 (44%), Gaps = 32/225 (14%) Query: 15 SIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERG-IT--IKAQTVRLNYT 71 +I+ H+DHGK+TL D S V E G IT I A TV L Sbjct: 157 TIMGHVDHGKTTLLDAL-----------RKSSV-----AAGEAGGITQHIGAFTVTLP-- 198 Query: 72 STDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNH 131 + +DTPGH F+ +R + + +LVV A GV QTL + A N Sbjct: 199 ----SGKSITFLDTPGHAAFSAMRARGANVTDIVVLVVAADDGVMPQTLEAIKHAKSANV 254 Query: 132 EIITVLNKADLPSADPDRVKKQIEETIGISTED------ALLVSAKTGEGIPLLLERIVQ 185 I+ +NK D P A+P++VK+++ GI ED + +SA TGE + LL E I+ Sbjct: 255 PIVVAINKIDKPGANPEKVKRELLS-QGIVVEDLGGDVQVIPISALTGENLDLLEEAILL 313 Query: 186 QLPSPTSPEGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTKGQ 230 P + +I+S + G + V + G L KG Sbjct: 314 LAEVMDLKADPKGPAEGWVIESSVDKGRGPVATVIVKRGTLKKGS 358 >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 = 86.8 bits (215), Expect = 2e-17 Identities = 29/80 (36%), Positives = 42/80 (52%), Gaps = 2/80 (2%) Query: 410 EPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLD-NRAMIVYELPLNEVIFDFYDRLK 468 EP ++V I P EYLG+++ +RRG + M R +I ELPL E +F F L+ Sbjct: 1 EPIMKVEITVPEEYLGAVIGDLSKRRGEILGMEPRGTGRVVIKAELPLAE-MFGFATDLR 59 Query: 469 SVSKGYASFDYNVIDYRDSD 488 S+++G ASF Y Sbjct: 60 SLTQGRASFSMEFSHYEPVP 79 >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 = 84.2 bits (209), Expect = 1e-16 Identities = 58/176 (32%), Positives = 77/176 (43%), Gaps = 29/176 (16%) Query: 19 HIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAKDY 78 HIDHGK+TL + LT E D + E++RGITI L + D Sbjct: 8 HIDHGKTTLI-------KALTGIE-----TDRLPEEKKRGITID-----LGFAYLDLPSG 50 Query: 79 Q-LNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTL--ANVYQAIDNNHEIIT 135 + L ID PGH F + + LLVV A +G+ QT + + + + Sbjct: 51 KRLGFIDVPGHEKFIKNMLAGAGGIDLVLLVVAADEGIMPQTREHLEILELLGIKR-GLV 109 Query: 136 VLNKADLPSADPDRVKKQIEETI----GISTEDA--LLVSAKTGEGIPLLLERIVQ 185 VL KADL D D ++ EE G DA VSA TGEGI L E + + Sbjct: 110 VLTKADL--VDEDWLELVEEEIRELLAGTFLADAPIFPVSAVTGEGIEELKEYLDE 163 >gnl|CDD|32720 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]. Length = 431 Score = 74.1 bits (182), Expect = 1e-13 Identities = 74/327 (22%), Positives = 132/327 (40%), Gaps = 68/327 (20%) Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQ------------------VLDNMDIE 54 F +D GKSTL R + + + E +++S ++D ++ E Sbjct: 8 RFITCGSVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLVDGLEAE 67 Query: 55 RERGITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQG 114 RE+GITI V Y ST+ + + + DTPGH +T ++ S + ++L+VDA +G Sbjct: 68 REQGITID---VAYRYFSTEKRKFII--ADTPGHEQYTRNMATGASTADLAILLVDARKG 122 Query: 115 VEAQTLANVYQA--IDNNHEIITVLNKADLPSADPDRVKKQIEE------TIGISTEDAL 166 V QT + + A + H ++ V NK DL + + + + +G+ + Sbjct: 123 VLEQTRRHSFIASLLGIRHVVVAV-NKMDLVDYSEEVFEAIVADYLAFAAQLGLKDVRFI 181 Query: 167 LVSAKTGEGI------------PLLLERIVQQLPSPTSPEGA--------NAPLKALLID 206 +SA G+ + P LLE + + A N P + Sbjct: 182 PISALLGDNVVSKSENMPWYKGPTLLEILETVEIADDRSAKAFRFPVQYVNRP------N 235 Query: 207 SWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGILTPKMIDIEALYPGEIGV 266 + Y G I +G + G + ++ + +V+R I+T ++ GE V Sbjct: 236 LDFRGYAG-----TIASGSVKVGDEVVVLPSGKTSRVKR--IVTFDG-ELAQASAGE-AV 286 Query: 267 MIASIKEVSHTRVGDTITDDSSPTTSA 293 + E+ +R GD I +P A Sbjct: 287 TLVLADEIDISR-GDLIVAADAPPAVA 312 >gnl|CDD|35679 KOG0458, KOG0458, KOG0458, Elongation factor 1 alpha [Translation, ribosomal structure and biogenesis]. Length = 603 Score = 72.0 bits (176), Expect = 5e-13 Identities = 73/295 (24%), Positives = 118/295 (40%), Gaps = 63/295 (21%) Query: 2 QKKPTPLSRIRNFSIVAHIDHGKSTLADRFI-------QHCRGLTEREMSSQ-------- 46 Q P N ++ H+D GKSTL + ERE + Sbjct: 171 QSDPKDHL---NLVVLGHVDAGKSTLMGHLLYDLGEISSRSMHKLERESKNLGKSSFAYA 227 Query: 47 -VLDNMDIERERGITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGS 105 +LD ERERG+T+ +T T ++K + LID PGH DF + S + + Sbjct: 228 WILDETKEERERGVTMDVKT-----TWFESKSKIVTLIDAPGHKDFIPNMISGASQADVA 282 Query: 106 LLVVDATQGV-------EAQT--LANVYQAIDNNHEIITVLNKADLPSADPDR------- 149 +LVVDA+ G QT A + +++ ++I +NK DL S DR Sbjct: 283 VLVVDASTGEFESGFDPGGQTREHALLLRSL-GISQLIVAINKMDLVSWSQDRFEEIKNK 341 Query: 150 VKKQIEETIGISTEDALLV--SAKTGEGI---------------PLLLERIVQQLPSPTS 192 + ++E+ G + S +GE + P LL Q+ S Sbjct: 342 LSSFLKESCGFKESSVKFIPISGLSGENLIKIEQENELSQWYKGPTLLS----QIDSFKI 397 Query: 193 PEGA-NAPLKALLIDSWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERI 246 PE + PL+ + D + GV + +I +G + GQ + +M + V+ + Sbjct: 398 PERPIDKPLRLTISDIYPLPSSGVSISGKIESGYIQPGQKLYIMTSREDATVKGL 452 >gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional. Length = 742 Score = 70.6 bits (173), Expect = 1e-12 Identities = 51/176 (28%), Positives = 83/176 (47%), Gaps = 25/176 (14%) Query: 15 SIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGIT--IKAQTVRLNYTS 72 +I+ H+DHGK+TL D+ + + + GIT I A V Y Sbjct: 248 TILGHVDHGKTTLLDKIRK---------------TQIAQKEAGGITQKIGAYEVEFEYKD 292 Query: 73 TDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNHE 132 + K + +DTPGH F+ SR + + ++L++ A GV+ QT+ + N Sbjct: 293 ENQK---IVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANVP 349 Query: 133 IITVLNKADLPSADPDRVKKQIEETIGISTE---DALLV--SAKTGEGIPLLLERI 183 II +NK D +A+ +R+K+Q+ + I + D ++ SA G I LLE I Sbjct: 350 IIVAINKIDKANANTERIKQQLAKYNLIPEKWGGDTPMIPISASQGTNIDKLLETI 405 >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 = 70.6 bits (174), Expect = 1e-12 Identities = 51/202 (25%), Positives = 85/202 (42%), Gaps = 47/202 (23%) Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTEREMS----------------SQVLDNMDIERE 56 N ++ H+D GKST + G+ +R + + VLD + ERE Sbjct: 1 NLVVIGHVDAGKSTTTGHLLYLLGGVDKRTIEKYEKEAKEMGKGSFKYAWVLDTLKEERE 60 Query: 57 RGITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQG-- 114 RG+TI V L T+ + ++D PGH DF + S + ++LVVDA +G Sbjct: 61 RGVTI---DVGLAKFETEKYRF--TILDAPGHRDFVPNMITGASQADVAVLVVDARKGEF 115 Query: 115 -----VEAQT-----LANVYQAIDNNHEIITVLNKADLPSA--DPDR---VKKQIEE--- 156 QT LA + ++I +NK D + +R +KK++ Sbjct: 116 EAGFEKGGQTREHALLAR-TLGVK---QLIVAVNKMDDVTVNWSEERYDEIKKELSPFLK 171 Query: 157 TIGISTEDALLV--SAKTGEGI 176 +G + +D + S TG+ + Sbjct: 172 KVGYNPKDVPFIPISGLTGDNL 193 >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 = 68.7 bits (169), Expect = 4e-12 Identities = 48/196 (24%), Positives = 77/196 (39%), Gaps = 46/196 (23%) Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTEREMS----------------SQVLDNMDIERE 56 F +D GKSTL R + + + E +++ + ++D + ERE Sbjct: 1 RFLTCGSVDDGKSTLIGRLLYDSKSIFEDQLAALESKSCGTGGEPLDLALLVDGLQAERE 60 Query: 57 RGITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVE 116 +GITI V Y ST + + + DTPGH +T + S + ++L+VDA +GV Sbjct: 61 QGITID---VAYRYFSTPKRKFI--IADTPGHEQYTRNMVTGASTADLAILLVDARKGVL 115 Query: 117 AQTLANVYQAIDNNHEIITVL----------NKADLPSADPDR---VKKQIEE---TIGI 160 QT H I L NK DL + + +GI Sbjct: 116 EQT---------RRHSYILSLLGIRHVVVAVNKMDLVDYSEEVFEEIVADYLAFAAKLGI 166 Query: 161 STEDALLVSAKTGEGI 176 + +SA G+ + Sbjct: 167 EDITFIPISALDGDNV 182 >gnl|CDD|30399 COG0050, TufB, GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis]. Length = 394 Score = 68.0 bits (166), Expect = 6e-12 Identities = 66/247 (26%), Positives = 106/247 (42%), Gaps = 36/247 (14%) Query: 13 NFSIVAHIDHGKSTL--ADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNY 70 N + H+DHGK+TL A + +G E + Q+ DN E+ RGITI T + Y Sbjct: 14 NVGTIGHVDHGKTTLTAAITTVLAKKGGAEAKAYDQI-DNAPEEKARGITI--NTAHVEY 70 Query: 71 TSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQT-----LANVYQ 125 T + Y +D PGH D+ + + +G++LVV AT G QT LA Sbjct: 71 -ETANRHYAH--VDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLARQVG 127 Query: 126 AIDNNHEIITVLNKADLPSADPDRVK------KQIEETIGISTED----------ALLVS 169 I+ LNK D+ D + ++ +++ G +D AL Sbjct: 128 V----PYIVVFLNKVDMVD-DEELLELVEMEVRELLSEYGFPGDDTPIIRGSALKALEGD 182 Query: 170 AKTGEGIPLLLERIVQQLPSPTSPEGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTKG 229 AK I L++ + +P+P + P + D + S G +V R+ G L G Sbjct: 183 AKWEAKIEELMDAVDSYIPTPERDI--DKPFLMPVEDVFSISGRGTVVTGRVERGILKVG 240 Query: 230 QSIRLMG 236 + + ++G Sbjct: 241 EEVEIVG 247 >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 = 50/203 (24%), Positives = 90/203 (44%), Gaps = 35/203 (17%) Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITI---------KA 63 N ++ H+D GK++LA + L+E S+ D +ERGIT+ Sbjct: 2 NVGVLGHVDSGKTSLA-------KALSEI-ASTAAFDKNPQSQERGITLDLGFSSFYVDK 53 Query: 64 QTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQT---- 119 + ++ Q+ L+D PGH + + LLVVDAT+G++ QT Sbjct: 54 PKHLRELINPGEENLQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDATKGIQTQTAECL 113 Query: 120 -LANVYQAIDNNHEIITVLNKADLPSADP-----DRVKKQIEETI-GISTEDALL--VSA 170 + + ++I VLNK DL + +++KK++++T+ +++ + VSA Sbjct: 114 VIGEIL-----CKKLIVVLNKIDLIPEEERERKIEKMKKKLQKTLEKTRFKNSPIIPVSA 168 Query: 171 KTGEGIPLLLERIVQQLPSPTSP 193 K G G L + + + P Sbjct: 169 KPGGGEAELGKDLNNLIVLPLIL 191 >gnl|CDD|35681 KOG0460, KOG0460, KOG0460, Mitochondrial translation elongation factor Tu [Translation, ribosomal structure and biogenesis]. Length = 449 Score = 63.4 bits (154), Expect = 2e-10 Identities = 74/284 (26%), Positives = 118/284 (41%), Gaps = 36/284 (12%) Query: 13 NFSIVAHIDHGKSTL--ADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNY 70 N + H+DHGK+TL A I +G + + ++ D E+ RGITI A V Sbjct: 56 NVGTIGHVDHGKTTLTAAITKILAEKGGAKFKKYDEI-DKAPEEKARGITINAAHVEY-- 112 Query: 71 TSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQA---- 126 T + Y D PGH D+ + + +G++LVV AT G QT ++ A Sbjct: 113 -ETAKRHYAH--TDCPGHADYIKNMITGAAQMDGAILVVAATDGPMPQTREHLLLARQVG 169 Query: 127 IDNNHEIITVLNKADLPSADPDR---VKKQIEE----------TIGISTEDALLV----S 169 + + I+ +NK DL DP+ V+ +I E + AL Sbjct: 170 VKH---IVVFINKVDL-VDDPEMLELVEMEIRELLSEFGFDGDNTPVIRGSALCALEGRQ 225 Query: 170 AKTG-EGIPLLLERIVQQLPSPTSPEGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTK 228 + G E I LL+ + +P+P + P + D + G +V R+ G L K Sbjct: 226 PEIGLEAIEKLLDAVDSYIPTPERDL--DKPFLLPIEDVFSIPGRGTVVTGRLERGVLKK 283 Query: 229 GQSIRLMGTNAKYQVERIGILTPKMIDIEALYPGEIGVMIASIK 272 G + ++G N + GI + EA +G ++ IK Sbjct: 284 GDEVEIVGHNKTLKTTVTGIEMFRKSLDEAQAGDNLGALLRGIK 327 >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 = 62.9 bits (153), Expect = 2e-10 Identities = 41/175 (23%), Positives = 61/175 (34%), Gaps = 23/175 (13%) Query: 16 IVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDA 75 +V GK++L +R + E E + ++D E D Sbjct: 1 VVGDSGVGKTSLLNRLLGGEFVPEEYE--TTIIDFYSKTIE----------------VDG 42 Query: 76 KDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNHE--- 132 K +L + DT G F +G +LV D T + + I N E Sbjct: 43 KKVKLQIWDTAGQERFRSLRRLYYRGADGIILVYDVTDRESFENVKEWLLLILINKEGEN 102 Query: 133 --IITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQ 185 II V NK DLP ++ E+ SAKTGE + L E + + Sbjct: 103 IPIILVGNKIDLPEERVVSEEELAEQLAKELGVPYFETSAKTGENVEELFEELAE 157 >gnl|CDD|36359 KOG1144, KOG1144, KOG1144, Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]. Length = 1064 Score = 60.8 bits (147), Expect = 1e-09 Identities = 71/282 (25%), Positives = 111/282 (39%), Gaps = 54/282 (19%) Query: 16 IVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDA 75 I+ H+D GK+ L D+ R + Q + I ++ G T T Sbjct: 480 ILGHVDTGKTKLLDKI---------RGTNVQEGEAGGITQQIGATYFPAENIREKTKELK 530 Query: 76 KDYQLNL-------IDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAID 128 KD + L IDTPGH FT SR S C+ ++LVVD G+E QT+ ++ Sbjct: 531 KDAKKRLKVPGLLVIDTPGHESFTNLRSRGSSLCDLAILVVDIMHGLEPQTIESINLLRM 590 Query: 129 NNHEIITVLNKAD-------LPSAD-PDRVKKQIEETI-----------------GISTE 163 I LNK D P+A + +KKQ ++ G++ E Sbjct: 591 RKTPFIVALNKIDRLYGWKSCPNAPIVEALKKQKKDVQNEFKERLNNIIVEFAEQGLNAE 650 Query: 164 ------------DALLVSAKTGEGIPLLLERIVQQLPSPTSPEGANA-PLKALLIDSWYN 210 + SA +GEGIP LL +VQ + A ++ +++ Sbjct: 651 LYYKNKEMGETVSIVPTSAISGEGIPDLLLLLVQLTQKTMVEKLAYVDEVQCTVLEVKVI 710 Query: 211 SYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGILTPK 252 G + V ++NG+L +G I + G +LTP+ Sbjct: 711 EGHGTTIDVILVNGELHEGDQIVVCGLQGPIVTTIRALLTPQ 752 >gnl|CDD|35682 KOG0461, KOG0461, KOG0461, Selenocysteine-specific elongation factor [Translation, ribosomal structure and biogenesis]. Length = 522 Score = 60.4 bits (146), Expect = 1e-09 Identities = 69/307 (22%), Positives = 115/307 (37%), Gaps = 31/307 (10%) Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITI----KAQTVRL 68 N I+ H+D GK+TLA R L+E S+ D ERGIT+ TV Sbjct: 9 NLGILGHVDSGKTTLA-------RALSELG-STAAFDKHPQSTERGITLDLGFSTMTVLS 60 Query: 69 NYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAID 128 + Q L+D PGH + + +LV+D +G + QT + Sbjct: 61 PARLPQGEQLQFTLVDCPGHASLIRTIIGGAQIIDLMILVIDVQKGKQTQTAECLIIGEL 120 Query: 129 NNHEIITVLNKADL-----PSADPDRVKKQIEETIGISTEDA----LLVSAKTG----EG 175 +++ V+NK D+ ++ ++ K++ +T+ + D + VSA G E Sbjct: 121 LCKKLVVVINKIDVLPENQRASKIEKSAKKVRKTLESTGFDGNSPIVEVSAADGYFKEEM 180 Query: 176 IPLLLERIVQQLPSPT-SPEGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTKGQSIRL 234 I L E + ++ P EG P + + G ++ ++ G L I Sbjct: 181 IQELKEALESRIFEPKRDEEG---PFLMAVDHCFAIKGQGTVLTGTVLRGVLRLNTEIEF 237 Query: 235 MGTNAKYQVERIGILTPKMIDIEALYPGEIGVMIASIKEVSHTRVGDTITDDSSPTTSAL 294 N K +V+ + + K A G + E R T + L Sbjct: 238 PALNEKRKVKSLQMF--KQRVTSAAAGDRAGFCVTQFDEKLLERGICGPPGTLKSTKAVL 295 Query: 295 PGFKPIQ 301 +PIQ Sbjct: 296 ATVEPIQ 302 >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 = 60.0 bits (146), Expect = 2e-09 Identities = 33/140 (23%), Positives = 51/140 (36%), Gaps = 13/140 (9%) Query: 57 RGITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVD-------FTYEVSRSLSACEGSLLVV 109 G T + LIDTPG + R L + L VV Sbjct: 28 PGTTTDPVEYVW----ELGPLGPVVLIDTPGIDEAGGLGREREELARRVLERADLILFVV 83 Query: 110 DATQGVEAQTLANVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETI--GISTEDALL 167 DA + + + + ++ VLNK DL + + ++ I + + Sbjct: 84 DADLRADEEEEKLLELLRERGKPVLLVLNKIDLLPEEEEEELLELRLLILLLLLGLPVIA 143 Query: 168 VSAKTGEGIPLLLERIVQQL 187 VSA TGEGI L E +++ L Sbjct: 144 VSALTGEGIDELREALIEAL 163 >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 = 59.4 bits (145), Expect = 3e-09 Identities = 49/179 (27%), Positives = 76/179 (42%), Gaps = 36/179 (20%) Query: 23 GKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAKDYQLNL 82 GKS+L + + ER + S DI G T + V Y + L Sbjct: 14 GKSSLVNALLG-----EERVIVS------DIA---GTTRDSIDVPFEY-----DGKKYTL 54 Query: 83 IDTPG---------HVDFTYEVSRSLSACEGS---LLVVDATQGVEAQTLANVYQAIDNN 130 IDT G ++ Y V R+L A E + LLV+DAT+G+ Q L ++ Sbjct: 55 IDTAGIRRKGKVEEGIEK-YSVLRTLKAIERADVVLLVIDATEGITEQDLRIAGLILEEG 113 Query: 131 HEIITVLNKADLPSADPDR---VKKQIEETIG-ISTEDALLVSAKTGEGIPLLLERIVQ 185 ++ V+NK DL D KK+I + + + +SA TG+G+ L + I + Sbjct: 114 KALVIVVNKWDLVEKDSKTMKEFKKEIRRKLPFLDYAPIVFISALTGQGVDKLFDAIDE 172 >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 = 56.7 bits (137), Expect = 2e-08 Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 1/68 (1%) Query: 410 EPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLDNRAMIVYELPLNEVIFDFYDRLKS 469 EP ++V + P EY+G ++ RRG + +I E+PL E +F + L+S Sbjct: 1 EPIMKVEVTVPEEYMGDVIGDLSSRRGQILGTESRGGWKVIKAEVPLAE-MFGYSTDLRS 59 Query: 470 VSKGYASF 477 +++G SF Sbjct: 60 LTQGRGSF 67 >gnl|CDD|35680 KOG0459, KOG0459, KOG0459, Polypeptide release factor 3 [Translation, ribosomal structure and biogenesis]. Length = 501 Score = 55.8 bits (134), Expect = 4e-08 Identities = 67/330 (20%), Positives = 134/330 (40%), Gaps = 65/330 (19%) Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTEREMS----------------SQVLDNMDIERE 56 N + H+D GKST+ + + +R + S LD ER+ Sbjct: 81 NAVFIGHVDAGKSTIGGNILFLTGMVDKRTLEKYEREAKEKNRESWYLSWALDTNGEERD 140 Query: 57 RGITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDAT---- 112 +G T++ Y T+ K + ++D PGH F + S + ++LV+ A Sbjct: 141 KGKTVEVGRA---YFETENKRF--TILDAPGHKSFVPNMIGGASQADLAVLVISARKGEF 195 Query: 113 -----QGVEAQTLANVYQAIDNNHEIITVLNKADLPSADPDRVK-KQIEETIG------- 159 +G + + A + + H +I ++NK D P+ + + ++ +E + Sbjct: 196 ETGFEKGGQTREHAMLAKTAGVKH-LIVLINKMDDPTVNWSNERYEECKEKLQPFLRKLG 254 Query: 160 --ISTEDALL-VSAKTGEGI-------------PLLLERIVQQLPSPTSPEGANAPLKAL 203 + + VS TG + P+ LE + +LP N P++ Sbjct: 255 FNPKPDKHFVPVSGLTGANVKDRTDSVCPWYKGPIFLE-YLDELPHL--ERILNGPIRCP 311 Query: 204 LIDSWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGILTPKMIDIEALYPGE 263 + + + + +G +V ++ +G + KGQ + +M K VE +GI + ++ + + PGE Sbjct: 312 VANKYKD--MGTVVGGKVESGSIKKGQQLVVMPN--KTNVEVLGIYSDD-VETDRVAPGE 366 Query: 264 -IGVMIASIKEVSHTRVGDTITDDSSPTTS 292 + + + I E G + ++P S Sbjct: 367 NVKLRLKGI-EEEDISPGFILCSPNNPCKS 395 >gnl|CDD|31354 COG1160, COG1160, Predicted GTPases [General function prediction only]. Length = 444 Score = 55.6 bits (134), Expect = 4e-08 Identities = 50/188 (26%), Positives = 83/188 (44%), Gaps = 36/188 (19%) Query: 14 FSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTST 73 +I+ + GKS+L + + R + +++ D++DIE ER Sbjct: 181 IAIIGRPNVGKSSLINAILGEERVIVS-DIAGTTRDSIDIEFER---------------- 223 Query: 74 DAKDYQLNLIDTPG---------HVDFTYEVSRSLSACEGS---LLVVDATQGVEAQTLA 121 + LIDT G V+ Y V+R+L A E + LLV+DAT+G+ Q L Sbjct: 224 --DGRKYVLIDTAGIRRKGKITESVEK-YSVARTLKAIERADVVLLVIDATEGISEQDLR 280 Query: 122 NVYQAIDNNHEIITVLNKADL---PSADPDRVKKQIEETIG-ISTEDALLVSAKTGEGIP 177 + I+ V+NK DL A + KK++ + + + +SA TG+G+ Sbjct: 281 IAGLIEEAGRGIVIVVNKWDLVEEDEATMEEFKKKLRRKLPFLDFAPIVFISALTGQGLD 340 Query: 178 LLLERIVQ 185 L E I + Sbjct: 341 KLFEAIKE 348 Score = 46.3 bits (110), Expect = 2e-05 Identities = 41/194 (21%), Positives = 68/194 (35%), Gaps = 35/194 (18%) Query: 23 GKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAKDYQLNL 82 GKSTL +R + D + R+R Y + + L Sbjct: 15 GKSTLFNRLTGRRIAIVS--------DTPGVTRDR-----------IYGDAEWLGREFIL 55 Query: 83 IDTPGHVDFTYE---------VSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNHEI 133 IDT G D + ++ + L VVD +G+ + + Sbjct: 56 IDTGGLDDGDEDELQELIREQALIAIEEADVILFVVDGREGITPADEEIAKILRRSKKPV 115 Query: 134 ITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQLPSP--T 191 I V+NK D A+ E + + + +SA+ G GI LL+ +++ LP Sbjct: 116 ILVVNKIDNLKAEEL-----AYEFYSLGFGEPVPISAEHGRGIGDLLDAVLELLPPDEEE 170 Query: 192 SPEGANAPLKALLI 205 E P+K +I Sbjct: 171 EEEEETDPIKIAII 184 >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 = 54.5 bits (132), Expect = 8e-08 Identities = 42/136 (30%), Positives = 65/136 (47%), Gaps = 16/136 (11%) Query: 19 HIDHGKSTL--ADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAK 76 H+DHGK+TL A + +G + + ++ D E+ RGITI V Y T + Sbjct: 10 HVDHGKTTLTAAITKVLAKKGGAKFKKYDEI-DKAPEEKARGITINTAHVE--Y-ETANR 65 Query: 77 DYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQA----IDNNHE 132 Y +D PGH D+ + + +G++LVV AT G QT ++ A + Sbjct: 66 HYA--HVDCPGHADYIKNMITGAAQMDGAILVVSATDGPMPQTREHLLLARQVGVPY--- 120 Query: 133 IITVLNKADLPSADPD 148 I+ LNKAD+ D + Sbjct: 121 IVVFLNKADM-VDDEE 135 >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 = 54.4 bits (132), Expect = 9e-08 Identities = 39/141 (27%), Positives = 59/141 (41%), Gaps = 21/141 (14%) Query: 62 KAQTVRLN----YTSTDAKDYQLNLIDTPG-----HVDFTYEVSRSLSACEGS---LLVV 109 K QT R YT D Q+ +DTPG V + SA + L VV Sbjct: 34 KPQTTRNRIRGIYTD---DDAQIIFVDTPGIHKPKKKLGERMVKAAWSALKDVDLVLFVV 90 Query: 110 DATQGV--EAQTLANVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEE-TIGISTEDAL 166 DA++ + + + + + +I VLNK DL D + + +E+ + Sbjct: 91 DASEPIGEGDEFILELLKKSKTP--VILVLNKIDL-VKDKEDLLPLLEKLKELGPFAEIF 147 Query: 167 LVSAKTGEGIPLLLERIVQQL 187 +SA GE + LLE IV+ L Sbjct: 148 PISALKGENVDELLEEIVKYL 168 >gnl|CDD|30833 COG0486, ThdF, Predicted GTPase [General function prediction only]. Length = 454 Score = 53.6 bits (129), Expect = 1e-07 Identities = 39/120 (32%), Positives = 55/120 (45%), Gaps = 15/120 (12%) Query: 78 YQLNLIDTPG---HVDFTYE--VSRSLSACEGS---LLVVDATQGVEAQTLANVYQAIDN 129 + L+DT G D + R+ A E + L V+DA+Q ++ + LA + + + Sbjct: 265 IPVRLVDTAGIRETDDVVERIGIERAKKAIEEADLVLFVLDASQPLDKEDLA-LIELLPK 323 Query: 130 NHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQLPS 189 II VLNKADL S +K IS +SAKTGEG+ L E I Q Sbjct: 324 KKPIIVVLNKADLVSKIELESEKLANGDAIIS------ISAKTGEGLDALREAIKQLFGK 377 >gnl|CDD|133364 cd04164, trmE, TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance. Length = 157 Score = 53.6 bits (130), Expect = 1e-07 Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 13/94 (13%) Query: 95 VSRSLSACEGS---LLVVDATQGVEAQTLANVYQAIDNNHEIITVLNKADLPSADPDRVK 151 + R+ A E + L V+DA++G++ + L + + II VLNK+DL Sbjct: 71 IERAREAIEEADLVLFVIDASRGLDEEDLEI--LELPADKPIIVVLNKSDLLPDSELLSL 128 Query: 152 KQIEETIGISTEDALLVSAKTGEGIPLLLERIVQ 185 + I IS AKTGEG+ L E +++ Sbjct: 129 LAGKPIIAIS--------AKTGEGLDELKEALLE 154 >gnl|CDD|31353 COG1159, Era, GTPase [General function prediction only]. Length = 298 Score = 53.3 bits (128), Expect = 2e-07 Identities = 35/138 (25%), Positives = 51/138 (36%), Gaps = 13/138 (9%) Query: 62 KAQTVRLNYTS-TDAKDYQLNLIDTPG-HVD-------FTYEVSRSLSACEGSLLVVDAT 112 K QT R + Q+ +DTPG H +L + L VVDA Sbjct: 37 KPQTTRNRIRGIVTTDNAQIIFVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDAD 96 Query: 113 QGVEAQTLANVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLV--SA 170 +G + Q +I V+NK D P V ++ + +V SA Sbjct: 97 EGWGPGDEFILEQLKKTKTPVILVVNKIDK--VKPKTVLLKLIAFLKKLLPFKEIVPISA 154 Query: 171 KTGEGIPLLLERIVQQLP 188 G+ + LLE I + LP Sbjct: 155 LKGDNVDTLLEIIKEYLP 172 >gnl|CDD|133279 cd01878, HflX, HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms. Length = 204 Score = 52.4 bits (127), Expect = 4e-07 Identities = 29/86 (33%), Positives = 45/86 (52%), Gaps = 10/86 (11%) Query: 106 LLVVDATQGVEAQTLANVYQ---AIDNNHE-IITVLNKADLPSADPDRVKKQIEETIGIS 161 L VVDA+ + + V + + +I VLNK DL D + +++++E Sbjct: 125 LHVVDASDPDYEEQIETVEKVLKELGAEDIPMILVLNKIDL--LDDEELEERLEAGR--- 179 Query: 162 TEDALLVSAKTGEGIPLLLERIVQQL 187 DA+ +SAKTGEG+ LLE I + L Sbjct: 180 -PDAVFISAKTGEGLDELLEAIEELL 204 >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 = 51.5 bits (123), Expect = 6e-07 Identities = 18/86 (20%), Positives = 41/86 (47%), Gaps = 3/86 (3%) Query: 200 LKALLIDSWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGILTPKMIDIEAL 259 L+AL+ + + G + R+ +G L KG +R+ + + + +++ Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRF-KGEVDEA 59 Query: 260 YPGEIGVMIASIKEVSHTRVGDTITD 285 G+I ++ +K+ ++GDT+TD Sbjct: 60 VAGDIVGIV--LKDKDDIKIGDTLTD 83 >gnl|CDD|35275 KOG0052, KOG0052, KOG0052, Translation elongation factor EF-1 alpha/Tu [Translation, ribosomal structure and biogenesis]. Length = 391 Score = 49.6 bits (118), Expect = 3e-06 Identities = 34/119 (28%), Positives = 51/119 (42%), Gaps = 24/119 (20%) Query: 12 RNFSIVAHIDHGKSTLADRFIQHCRGLTEREMS----------------SQVLDNMDIER 55 N ++ H+D GKST C G+ +R + + VLD + ER Sbjct: 8 INIVVIGHVDSGKST---TTGYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAER 64 Query: 56 ERGITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQG 114 ERGITI + + Y + +ID PGH DF + S + ++L+V A G Sbjct: 65 ERGITIDIALWKF-----ETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTG 118 >gnl|CDD|34854 COG5257, GCD11, Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]. Length = 415 Score = 49.1 bits (117), Expect = 3e-06 Identities = 57/228 (25%), Positives = 94/228 (41%), Gaps = 62/228 (27%) Query: 1 MQKKPTPLSRIRNFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGIT 60 M + N +V H+DHGK+TL + +S D E +RGIT Sbjct: 1 MADPKHIQPEV-NIGMVGHVDHGKTTLT------------KALSGVWTDRHSEELKRGIT 47 Query: 61 IKAQTVRLNYTSTDAKDYQ----------------------------LNLIDTPGHVDFT 92 IK L Y DAK Y+ ++ +D PGH Sbjct: 48 IK-----LGYA--DAKIYKCPECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGHETLM 100 Query: 93 YEVSRSLSACEGSLLVVDATQGV-EAQTLAN--VYQAIDNNHEIITVLNKADLPSADP-- 147 + + +G+LLV+ A + + QT + + I + II V NK DL S + Sbjct: 101 ATMLSGAALMDGALLVIAANEPCPQPQTREHLMALEIIGIKN-IIIVQNKIDLVSRERAL 159 Query: 148 ---DRVKKQIEETIGISTEDALL--VSAKTGEGIPLLLERIVQQLPSP 190 +++K+ ++ T+ E+A + +SA+ I L+E I + +P+P Sbjct: 160 ENYEQIKEFVKGTV---AENAPIIPISAQHKANIDALIEAIEKYIPTP 204 >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 = 47.4 bits (113), Expect = 1e-05 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 5/75 (6%) Query: 212 YLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGILTPK-MIDIEALYPGEIGVMIAS 270 ++G + VR+ +G L G ++ K +V R+ + K ++E G+IG + Sbjct: 13 FVGKLSFVRVYSGTLKAGSTLYNSTKGKKERVGRLLRMHGKKQEEVEEAGAGDIGAVAG- 71 Query: 271 IKEVSHTRVGDTITD 285 + T GDT+ D Sbjct: 72 ---LKDTATGDTLCD 83 >gnl|CDD|32443 COG2262, HflX, GTPases [General function prediction only]. Length = 411 Score = 47.2 bits (112), Expect = 1e-05 Identities = 32/108 (29%), Positives = 48/108 (44%), Gaps = 10/108 (9%) Query: 105 SLLVVDATQ-GVEAQ--TLANVYQAIDNNHE-IITVLNKADLPSADPDRVKKQIEETIGI 160 L VVDA+ + + + +V I + II VLNK DL + I + Sbjct: 275 LLHVVDASDPEILEKLEAVEDVLAEIGADEIPIILVLNKIDLLEDEE------ILAELER 328 Query: 161 STEDALLVSAKTGEGIPLLLERIVQQLPSPTSPEGANAPLKALLIDSW 208 + + + +SAKTGEG+ LL ERI++ L + P SW Sbjct: 329 GSPNPVFISAKTGEGLDLLRERIIELLSGLRTEVTLELPYTDAGRLSW 376 >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 = 44.9 bits (107), Expect = 7e-05 Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 1/71 (1%) Query: 214 GVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGILTPKMIDIEALYPGEIGVMIASIKE 273 G + R+ +G L KG + + N + R+ L D+ G +I + Sbjct: 1 GTVATGRVESGTLKKGDKVVIGP-NGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGIG 59 Query: 274 VSHTRVGDTIT 284 + + GDT+T Sbjct: 60 LKDIKRGDTLT 70 >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 = 44.3 bits (105), Expect = 1e-04 Identities = 24/81 (29%), Positives = 44/81 (54%), Gaps = 8/81 (9%) Query: 209 YNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGILTP----KMIDIEALYPGEI 264 Y+ Y+G + + RI G + GQ + ++ + K + +I L K +++E G+I Sbjct: 10 YDDYVGRIAIGRIFRGTVKVGQQVAVVKRDGKIEKAKITKLFGFEGLKRVEVEEAEAGDI 69 Query: 265 GVMIASIKEVSHTRVGDTITD 285 V IA I++++ +GDTI D Sbjct: 70 -VAIAGIEDIT---IGDTICD 86 >gnl|CDD|30719 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion transport and metabolism]. Length = 653 Score = 43.7 bits (103), Expect = 2e-04 Identities = 35/147 (23%), Positives = 67/147 (45%), Gaps = 23/147 (15%) Query: 58 GITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTY-----EVSRSL---SACEGSLLVV 109 G+T++ + +L Y K +++ ++D PG T +V+R + + VV Sbjct: 35 GVTVEKKEGKLKY-----KGHEIEIVDLPGTYSLTAYSEDEKVARDFLLEGKPDLIVNVV 89 Query: 110 DATQGVEAQTLANVYQAIDNNHEIITVLNKADLPSADPDRVK---KQIEETIGISTEDAL 166 DAT +E + L Q ++ +I LN D A ++ +++ + +G+ + Sbjct: 90 DATN-LE-RNLYLTLQLLELGIPMILALNMIDE--AKKRGIRIDIEKLSKLLGVP---VV 142 Query: 167 LVSAKTGEGIPLLLERIVQQLPSPTSP 193 AK GEG+ L I++ S T+P Sbjct: 143 PTVAKRGEGLEELKRAIIELAESKTTP 169 >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 = 43.7 bits (103), Expect = 2e-04 Identities = 19/68 (27%), Positives = 40/68 (58%), Gaps = 1/68 (1%) Query: 410 EPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLDNRAMIVYELPLNEVIFDFYDRLKS 469 EP ++V + P E+ G+++ L +R+G +D ++ + E+PLN+ +F + L+S Sbjct: 1 EPIMKVEVTAPTEFQGNVIGLLNKRKGTIVDTDTGEDEFTLEAEVPLND-MFGYSTELRS 59 Query: 470 VSKGYASF 477 +++G F Sbjct: 60 MTQGKGEF 67 >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 = 43.4 bits (103), Expect = 2e-04 Identities = 61/225 (27%), Positives = 95/225 (42%), Gaps = 72/225 (32%) Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIK---AQTV--- 66 N + H+ HGKSTL ++ G+ E ER ITIK A Sbjct: 2 NIGTIGHVAHGKSTL----VKALSGVWTVRFKE--------ELERNITIKLGYANAKIYK 49 Query: 67 --------RLNYTSTDAKD----------YQL----NLIDTPGHVDFTYEV--SRSLS-A 101 Y S + +L + +D PGH E+ + LS A Sbjct: 50 CPNCGCPRPYCYRSKEDSPECECPGCGGETKLVRHVSFVDCPGH-----EILMATMLSGA 104 Query: 102 C--EGSLLVVDATQGV-EAQT---LANVYQAIDN---NHEIITVLNKADLPSADP----- 147 +G+LL++ A + + QT LA A++ H II V NK DL + Sbjct: 105 AVMDGALLLIAANEPCPQPQTSEHLA----ALEIMGLKH-IIIVQNKIDLVKEEQALENY 159 Query: 148 DRVKKQIEETIGISTEDALL--VSAKTGEGIPLLLERIVQQLPSP 190 +++KK ++ TI E+A + +SA+ I +LLE IV+++P+P Sbjct: 160 EQIKKFVKGTI---AENAPIIPISAQLKYNIDVLLEYIVKKIPTP 201 >gnl|CDD|145217 pfam01926, MMR_HSR1, GTPase of unknown function. Length = 106 Score = 43.0 bits (102), Expect = 2e-04 Identities = 24/90 (26%), Positives = 38/90 (42%), Gaps = 13/90 (14%) Query: 58 GITIKAQTVRLNYTSTDAKDYQLNLIDTPG-----HVDFTYEVSRSLSA---CEGSLLVV 109 G T R+ Q+ L+DTPG +R+L A + L VV Sbjct: 22 GTTRDPNEGRVEL-----DGKQIILVDTPGIIEGASKGEGELGNRTLEAIEEADLILHVV 76 Query: 110 DATQGVEAQTLANVYQAIDNNHEIITVLNK 139 DA++G+ + L + ++ +I VLNK Sbjct: 77 DASEGLTEEDLEILDLLLELGKPVILVLNK 106 >gnl|CDD|32410 COG2229, COG2229, Predicted GTPase [General function prediction only]. Length = 187 Score = 43.0 bits (101), Expect = 2e-04 Identities = 26/135 (19%), Positives = 61/135 (45%), Gaps = 6/135 (4%) Query: 65 TVRLNYTSTDAKD-YQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGV--EAQTLA 121 TV +++ S + + ++L TPG F + G++++VD+++ + A+ + Sbjct: 54 TVAMDFGSIELDEDTGVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEII 113 Query: 122 NVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLE 181 + N ++ +NK DL A P ++ + + + + + + A GEG L+ Sbjct: 114 DFLT-SRNPIPVVVAINKQDLFDALPPEKIREALK-LELLSVPVIEIDATEGEGARDQLD 171 Query: 182 RIV-QQLPSPTSPEG 195 ++ + L + E Sbjct: 172 VLLLKDLLGSANEEA 186 >gnl|CDD|34855 COG5258, GTPBP1, GTPase [General function prediction only]. Length = 527 Score = 43.0 bits (101), Expect = 3e-04 Identities = 69/317 (21%), Positives = 123/317 (38%), Gaps = 67/317 (21%) Query: 13 NFSIVAHIDHGKSTL-------------------ADRFIQHC-RGLTEREMSSQVL--DN 50 + H+DHGKSTL D RGL+ ++S +V D+ Sbjct: 119 LVGVAGHVDHGKSTLVGVLVTGRLDDGDGATRSYLDVQKHEVERGLSA-DISLRVYGFDD 177 Query: 51 MDIERERGITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSL--SACEGSLLV 108 + R + +A+ + D ++ +DT GH + R L + LLV Sbjct: 178 GKVVRLKNPLDEAEKAAV----VKRADKLVSFVDTVGHEPWLRTTIRGLLGQKVDYGLLV 233 Query: 109 VDATQGVEAQTLANVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGI-------- 160 V A GV T ++ A+ +I V+ K D+ DR + +EE + Sbjct: 234 VAADDGVTKMTKEHLGIALAMELPVIVVVTKIDM--VPDDRFQGVVEEISALLKRVGRIP 291 Query: 161 ----STEDALL----------------VSAKTGEGIPLLLERIVQQLPSPTSPEGANAPL 200 T+D +L S+ TGEG+ LL E LP + L Sbjct: 292 LIVKDTDDVVLAAKAMKAGRGVVPIFYTSSVTGEGLDLLDE-FFLLLPKRRRWDDEGPFL 350 Query: 201 KALLIDSWYN-SYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGILTPKM--IDIE 257 + ID Y+ + +G +V + +G L G ++ L+G + + + + +M ++ Sbjct: 351 --MYIDKIYSVTGVGTVVSGSVKSGILHVGDTV-LLGPFKDGKFREVVVKSIEMHHYRVD 407 Query: 258 ALYPGEI-GVMIASIKE 273 + G I G+ + +++ Sbjct: 408 SAKAGSIIGIALKGVEK 424 >gnl|CDD|177010 CHL00071, tufA, elongation factor Tu. Length = 409 Score = 41.5 bits (98), Expect = 7e-04 Identities = 40/135 (29%), Positives = 62/135 (45%), Gaps = 13/135 (9%) Query: 13 NFSIVAHIDHGKSTL-ADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYT 71 N + H+DHGK+TL A + + +D+ E+ RGITI T + Y Sbjct: 14 NIGTIGHVDHGKTTLTAAITMTLAAKGGAKAKKYDEIDSAPEEKARGITIN--TAHVEY- 70 Query: 72 STDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQA----I 127 T+ + Y +D PGH D+ + + +G++LVV A G QT ++ A + Sbjct: 71 ETENRHYA--HVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTKEHILLAKQVGV 128 Query: 128 DNNHEIITVLNKADL 142 N I+ LNK D Sbjct: 129 PN---IVVFLNKEDQ 140 >gnl|CDD|30882 COG0536, Obg, Predicted GTPase [General function prediction only]. Length = 369 Score = 41.3 bits (97), Expect = 8e-04 Identities = 30/104 (28%), Positives = 45/104 (43%), Gaps = 15/104 (14%) Query: 97 RSLSACEGSLLVVDATQGVEAQTLANVYQAIDN----------NHEIITVLNKADLPSAD 146 R + L V+D + ++ + YQ I N I VLNK DLP + Sbjct: 233 RHIERTRVLLHVIDLS-PIDGRDPIEDYQTIRNELEKYSPKLAEKPRIVVLNKIDLPLDE 291 Query: 147 P--DRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQLP 188 + +KK + E +G E L+SA T EG+ LL + + L Sbjct: 292 EELEELKKALAEALGW--EVFYLISALTREGLDELLRALAELLE 333 >gnl|CDD|31297 COG1100, COG1100, GTPase SAR1 and related small G proteins [General function prediction only]. Length = 219 Score = 41.1 bits (95), Expect = 9e-04 Identities = 30/173 (17%), Positives = 51/173 (29%), Gaps = 23/173 (13%) Query: 23 GKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAKDYQLNL 82 GK+TL +R + + TI ++ +L L Sbjct: 17 GKTTLLNRLVGD-----------------EFPEGYPPTIGNLDPAKTIE-PYRRNIKLQL 58 Query: 83 IDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAI-----DNNHEIITVL 137 DT G ++ G L+V D+T + L + ++ I+ V Sbjct: 59 WDTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVG 118 Query: 138 NKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQLPSP 190 NK DL + + + + P LLE + L P Sbjct: 119 NKIDLFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGP 171 >gnl|CDD|133323 cd04123, Rab21, Rab21 subfamily. The localization and function of Rab21 are not clearly defined, with conflicting data reported. Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker. More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound Rab21, together with two novel LIM domain proteins, LimF and ChLim, has been shown to regulate phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 162 Score = 41.1 bits (97), Expect = 0.001 Identities = 36/132 (27%), Positives = 53/132 (40%), Gaps = 31/132 (23%) Query: 73 TDAKDYQLNLIDTPGHVDFTYEVSRSLSA-----CEGSLLVVDATQGVEAQTLANV---- 123 K L + DT G E +L +G++LV D T +A + V Sbjct: 44 IGGKRIDLAIWDTAGQ-----ERYHALGPIYYRDADGAILVYDIT---DADSFQKVKKWI 95 Query: 124 ---YQAIDNNHEIITVLNKADLPSADPDRV--KKQIEE---TIGISTEDALLVSAKTGEG 175 Q NN ++ V NK DL RV K + EE ++G SAKTG+G Sbjct: 96 KELKQMRGNNISLVIVGNKIDLER---QRVVSKSEAEEYAKSVGAKH---FETSAKTGKG 149 Query: 176 IPLLLERIVQQL 187 I L + +++ Sbjct: 150 IEELFLSLAKRM 161 >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 = 41.0 bits (96), Expect = 0.001 Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 6/76 (7%) Query: 211 SYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGIL-TPKMIDIEALYPGEIGVMIA 269 G + +RI G+L KG +I + T K +V R+ + + +M ++E G+I I Sbjct: 11 GRFGQLTYMRIYQGKLKKGDTIYNVRTGKKVRVPRLVRMHSNEMEEVEEAGAGDI-CAIF 69 Query: 270 SIKEVSHTRVGDTITD 285 I S GDT TD Sbjct: 70 GIDCAS----GDTFTD 81 >gnl|CDD|145523 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent. Length = 188 Score = 40.9 bits (97), Expect = 0.001 Identities = 40/160 (25%), Positives = 65/160 (40%), Gaps = 47/160 (29%) Query: 58 GITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSAC------------EGS 105 G+T++ + Y K Y++ ++D PG TY SLS E Sbjct: 31 GVTVEKKEGTFKY-----KGYEIEIVDLPG----TY----SLSPYSEEEKVARDYLLEEK 77 Query: 106 ----LLVVDATQGVEAQTLA-NVY---QAIDNNHEIITVLNKADLPSADPDRVK---KQI 154 + VVDAT L N+Y Q ++ ++ LN D A+ +K K++ Sbjct: 78 PDVIINVVDATN------LERNLYLTLQLLELGIPVVVALNMMDE--AEKKGIKIDIKKL 129 Query: 155 EETIGISTEDALLVSAKTGEGIPLLLERIVQQLPSPTSPE 194 E +G+ + SA+ GEGI L + I++ P Sbjct: 130 SELLGVP---VVPTSARKGEGIDELKDAIIEVAEGKVKPP 166 >gnl|CDD|133298 cd01898, Obg, Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans. The E. coli homolog, ObgE is believed to function in ribosomal biogenesis. Members of the subfamily contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain. Length = 170 Score = 40.5 bits (96), Expect = 0.001 Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 1/55 (1%) Query: 133 IITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQL 187 I VLNK DL + + + E + + +SA TGEG+ LL ++ + L Sbjct: 117 RIVVLNKIDLLDEE-ELFELLKELLKELWGKPVFPISALTGEGLDELLRKLAELL 170 >gnl|CDD|133280 cd01879, FeoB, Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent. Length = 158 Score = 40.5 bits (96), Expect = 0.001 Identities = 34/155 (21%), Positives = 50/155 (32%), Gaps = 56/155 (36%) Query: 65 TVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSA------------CEGS----LLV 108 TV ++ ++D PG TY SLS + V Sbjct: 30 TVEKKEGRFKLGGKEIEIVDLPG----TY----SLSPYSEDEKVARDFLLGEKPDLIVNV 81 Query: 109 VDATQGVEAQTLA-NVY---QAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGISTED 164 VDAT L N+Y Q ++ ++ LN D +K+ GI + Sbjct: 82 VDATN------LERNLYLTLQLLELGLPVVVALNMIDE-------AEKR-----GIKIDL 123 Query: 165 ALL----------VSAKTGEGIPLLLERIVQQLPS 189 L SA+ GEGI L + I + Sbjct: 124 DKLSELLGVPVVPTSARKGEGIDELKDAIAELAEK 158 >gnl|CDD|133281 cd01881, Obg_like, The Obg-like subfamily consists of five well-delimited, ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210, and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and Ygr210) are characterized by a distinct glycine-rich motif immediately following the Walker B motif (G3 box). Obg/CgtA is an essential gene that is involved in the initiation of sporulation and DNA replication in the bacteria Caulobacter and Bacillus, but its exact molecular role is unknown. Furthermore, several OBG family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. Nog1 is a nucleolar protein that might function in ribosome assembly. The DRG and Nog1 subfamilies are ubiquitous in archaea and eukaryotes, the Ygr210 subfamily is present in archaea and fungi, and the Obg and YyaF/YchF subfamilies are ubiquitous in bacteria and eukaryotes. The Obg/Nog1 and DRG subfamilies appear to form one major branch of the Obg family and the Ygr210 and YchF subfamilies form another branch. No GEFs, GAPs, or GDIs for Obg have been identified. Length = 176 Score = 40.2 bits (95), Expect = 0.002 Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 1/55 (1%) Query: 133 IITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQL 187 +I VLNK DL A+ + ++ + E + + +SAKT EG+ L+ I + L Sbjct: 123 VIYVLNKIDLDDAE-ELEEELVRELALEEGAEVVPISAKTEEGLDELIRAIYELL 176 >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 = 40.2 bits (94), Expect = 0.002 Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 8/84 (9%) Query: 106 LLVVDATQGVEAQTLANVYQAIDNNHEIITVLNKADL--PSADPDRVKKQIEE----TIG 159 + VVD + + N+ +I V NK DL + R+K + +G Sbjct: 39 VHVVDIFD-FPGSLIPRLR-LFGGNNPVILVGNKIDLLPKDKNLVRIKNWLRAKAAAGLG 96 Query: 160 ISTEDALLVSAKTGEGIPLLLERI 183 + +D +L+SAK G G+ L+ I Sbjct: 97 LKPKDVILISAKKGWGVEELINAI 120 >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 = 40.2 bits (94), Expect = 0.002 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 5/72 (6%) Query: 214 GVMVLVRIINGQLTKGQSIRLMGTNAKYQVERI-GILTPKMIDIEALYPGEIGVMIASIK 272 G + VR+ +G L +G ++ T K ++ R+ + +I +L G IGV I Sbjct: 15 GPLTFVRVYSGTLKRGSALYNTNTGKKERISRLLQPFADQYQEIPSLSAGNIGV----IT 70 Query: 273 EVSHTRVGDTIT 284 + TR GDT+ Sbjct: 71 GLKQTRTGDTLV 82 >gnl|CDD|133250 cd00154, Rab, Rab family. Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members, several have been found to possess 60 or more Rabs; for many of these Rab isoforms, homologous proteins are not found in other organisms. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Since crystal structures often lack C-terminal residues, the lipid modification site is not available for annotation in many of the CDs in the hierarchy, but is included where possible. Length = 159 Score = 39.0 bits (92), Expect = 0.004 Identities = 38/151 (25%), Positives = 60/151 (39%), Gaps = 48/151 (31%) Query: 58 GITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSA-----CEGSLLVVDAT 112 G+ K++T+ + D K +L + DT G E RS++ G++LV D T Sbjct: 34 GVDFKSKTIEI-----DGKTVKLQIWDTAGQ-----ERFRSITPSYYRGAHGAILVYDIT 83 Query: 113 QGVEAQTLANVY----QAIDNNHE---IITVLNKADLPSADPDRVKKQIEETIGISTEDA 165 ++ N+ + + E II V NK DL R +STE+A Sbjct: 84 N---RESFENLDKWLKELKEYAPENIPIILVGNKIDLED---QRQ---------VSTEEA 128 Query: 166 -----------LLVSAKTGEGIPLLLERIVQ 185 SAKTGE + L + + + Sbjct: 129 QQFAKENGLLFFETSAKTGENVEELFQSLAE 159 >gnl|CDD|35616 KOG0395, KOG0395, KOG0395, Ras-related GTPase [General function prediction only]. Length = 196 Score = 38.8 bits (90), Expect = 0.005 Identities = 34/190 (17%), Positives = 65/190 (34%), Gaps = 35/190 (18%) Query: 23 GKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAKDYQLNL 82 GKS L +F+ ++ + +T+ D + L + Sbjct: 15 GKSALTIQFLTG-------RFVEDYDPTIEDSYRKELTV------------DGEVCMLEI 55 Query: 83 IDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAID-----NNHEIITVL 137 +DT G +F+ + +G LLV T + + + I ++ II V Sbjct: 56 LDTAGQEEFSAMRDLYIRNGDGFLLVYSITDRSSFEEAKQLREQILRVKGRDDVPIILVG 115 Query: 138 NKADLPSADPDRVKKQIEETIGISTEDALL-----VSAKTGEGIPLLLERIVQQLPSPTS 192 NK DL ++Q+ E G + + SAK + + +V+++ P Sbjct: 116 NKCDLER------ERQVSEEEGKALARSWGCAFIETSAKLNYNVDEVFYELVREIRLPRE 169 Query: 193 PEGANAPLKA 202 L + Sbjct: 170 GSLKGRKLSS 179 >gnl|CDD|30567 COG0218, COG0218, Predicted GTPase [General function prediction only]. Length = 200 Score = 37.9 bits (88), Expect = 0.008 Identities = 29/140 (20%), Positives = 57/140 (40%), Gaps = 20/140 (14%) Query: 65 TVRLNYTSTDAKDYQLNLIDTPGH-------------VDFTYEVSRSLSACEGSLLVVDA 111 T +N+ D + L L+D PG+ E + +G +L++DA Sbjct: 60 TQLINFFEVDDE---LRLVDLPGYGYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDA 116 Query: 112 TQGVEAQTLANVYQAIDNNHEIITVLNKAD-LPSADPDRVKKQIEETIGISTEDA---LL 167 + + ++ +I VL KAD L ++ ++ ++ E + D +L Sbjct: 117 RHPPKDLDREMIEFLLELGIPVIVVLTKADKLKKSERNKQLNKVAEELKKPPPDDQWVVL 176 Query: 168 VSAKTGEGIPLLLERIVQQL 187 S+ +GI L +I++ L Sbjct: 177 FSSLKKKGIDELKAKILEWL 196 >gnl|CDD|57925 cd01854, YjeQ_engC, YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.. Length = 287 Score = 36.7 bits (85), Expect = 0.019 Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 3/56 (5%) Query: 132 EIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQL 187 E + VL KADL + + ++ +G L VSAKTGEG+ L E + + Sbjct: 111 EPVIVLTKADLLDDEEEELELVEALALGY---PVLAVSAKTGEGLDELREYLKGKT 163 >gnl|CDD|35303 KOG0080, KOG0080, KOG0080, GTPase Rab18, small G protein superfamily [General function prediction only]. Length = 209 Score = 36.5 bits (84), Expect = 0.019 Identities = 36/141 (25%), Positives = 60/141 (42%), Gaps = 13/141 (9%) Query: 67 RLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQA 126 ++ D K +L + DT G F +G +LV D T L + Sbjct: 49 KVKVMQVDGKRLKLAIWDTAGQERFRTLTPSYYRGAQGIILVYDVTSRDTFVKLDIWLKE 108 Query: 127 ID---NNHEIITVL--NKADLPSADPDRVKKQIEETIGISTEDALL---VSAKTGEGIPL 178 +D N +II +L NK D + +RV + EE + + + L SAKT E + Sbjct: 109 LDLYSTNPDIIKMLVGNKID---KESERVVDR-EEGLKFARKHRCLFIECSAKTRENVQC 164 Query: 179 LLERIVQQ-LPSPTSPEGANA 198 E +V++ + +P+ E N+ Sbjct: 165 CFEELVEKIIETPSLWEEGNS 185 >gnl|CDD|36702 KOG1489, KOG1489, KOG1489, Predicted GTP-binding protein (ODN superfamily) [General function prediction only]. Length = 366 Score = 36.5 bits (84), Expect = 0.020 Identities = 31/125 (24%), Positives = 52/125 (41%), Gaps = 19/125 (15%) Query: 79 QLNLIDTPG-----HVD--FTYEVSRSLSACEGSLLVVDATQGVEAQTLANV-------- 123 Q+ + D PG H++ Y+ R + C+G L VVD + + Sbjct: 245 QITVADIPGIIEGAHMNKGLGYKFLRHIERCKGLLFVVDLSGKQLRNPWQQLQLLIEELE 304 Query: 124 -YQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLER 182 Y+ + + V NK DLP A+ + + + + VSAK+GEG+ LL Sbjct: 305 LYEKGLADRPALIVANKIDLPEAEKNLLSSLAKRL---QNPHVVPVSAKSGEGLEELLNG 361 Query: 183 IVQQL 187 + + L Sbjct: 362 LRELL 366 >gnl|CDD|133360 cd04160, Arfrp1, Arfrp1 subfamily. Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development. Length = 167 Score = 36.5 bits (85), Expect = 0.021 Identities = 33/129 (25%), Positives = 51/129 (39%), Gaps = 25/129 (19%) Query: 65 TVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSL-----SACEGSLLVVDATQGVEAQT 119 TV LN + + + +L D G RSL + C + V+D+T + + Sbjct: 37 TVGLNIGTIEVGNARLKFWDLGGQESL-----RSLWDKYYAECHAIIYVIDST---DRER 88 Query: 120 LANVYQAIDN--NHEI-----ITVL-NKADLPSA----DPDRVKKQIEETIGISTEDALL 167 A++ +E + +L NK DLP A + V + E IG L Sbjct: 89 FEESKSALEKVLRNEALEGVPLLILANKQDLPDALSVEEIKEVFQDKAEEIGRRDCLVLP 148 Query: 168 VSAKTGEGI 176 VSA G G+ Sbjct: 149 VSALEGTGV 157 >gnl|CDD|133278 cd01876, YihA_EngB, The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be involved in organellar targeting). Homologs of yihA are found in most Gram-positive and Gram-negative pathogenic bacteria, with the exception of Mycobacterium tuberculosis. The broad-spectrum nature of YihA and its essentiality for cell viability in bacteria make it an attractive antibacterial target. Length = 170 Score = 36.3 bits (85), Expect = 0.026 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 3/87 (3%) Query: 104 GSLLVVDATQGVEAQTLANVYQAIDNNHEIITVLNKAD-LPSADPDRVKKQIEETIG--I 160 G +L++D+ G L + + + VL KAD L ++ + K+I++ + Sbjct: 84 GVVLLIDSRHGPTEIDLEMLDWLEELGIPFLVVLTKADKLKKSELAKALKEIKKELKLFE 143 Query: 161 STEDALLVSAKTGEGIPLLLERIVQQL 187 +L S+ G+GI L I + L Sbjct: 144 IDPPIILFSSLKGQGIDELRALIEKWL 170 >gnl|CDD|35687 KOG0466, KOG0466, KOG0466, Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]. Length = 466 Score = 36.1 bits (83), Expect = 0.033 Identities = 51/215 (23%), Positives = 90/215 (41%), Gaps = 31/215 (14%) Query: 79 QLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDAT----QGVEAQTLANVYQAIDNNHEII 134 ++ +D PGH + + + +LL++ Q ++ LA V + + H II Sbjct: 126 HVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAV-EIMKLKH-II 183 Query: 135 TVLNKADLPSADPDRVK-KQIEETI-GISTEDALLV--SAKTGEGIPLLLERIVQQLPSP 190 + NK DL + +QI++ I G E A ++ SA+ I ++ E IV+++P P Sbjct: 184 ILQNKIDLIKESQALEQHEQIQKFIQGTVAEGAPIIPISAQLKYNIDVVCEYIVKKIPVP 243 Query: 191 TSPEGANAPLKALLIDSW--------YNSYLGVMVLVRIINGQLTKGQSIRL------MG 236 +P + ++I S+ + G + I+ G L GQ I + Sbjct: 244 --VRDFTSPPRLIVIRSFDVNKPGSEVDDLKGGVAGGSILKGVLKVGQEIEIRPGIVTKD 301 Query: 237 TNAKYQ----VERIGILTPKMIDIEALYPGE-IGV 266 N + RI L + D++ PG IGV Sbjct: 302 ENGNIKCRPIFSRIVSLFAEQNDLQFAVPGGLIGV 336 >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 = 35.5 bits (82), Expect = 0.041 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 2/77 (2%) Query: 410 EPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLDN-RAMIVYELPLNEVIFDFYDRLK 468 EP ++TI P EY G++++ +R+G +DM N R + +++P +I F Sbjct: 1 EPIEELTIDVPEEYSGAVIEKLGKRKGEMVDMEPDGNGRTRLEFKIPSRGLI-GFRSEFL 59 Query: 469 SVSKGYASFDYNVIDYR 485 + ++G ++ Y Sbjct: 60 TDTRGTGIMNHVFDGYE 76 >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 = 35.5 bits (83), Expect = 0.044 Identities = 42/178 (23%), Positives = 70/178 (39%), Gaps = 42/178 (23%) Query: 23 GKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVR-LNYTSTDAKDYQLN 81 GKSTL +R + E D G+T R Y + + Sbjct: 9 GKSTLFNRLTGRRDAIVE-----------DTP---GVT------RDRIYGEAEWGGREFI 48 Query: 82 LIDTPGHVDFTYEVSR-----SLSACEGS---LLVVDATQGVEA--QTLANVYQAIDNNH 131 LIDT G +S+ + A E + L VVD +G+ + +A + + Sbjct: 49 LIDTGGIEPDDEGISKEIREQAELAIEEADVILFVVDGREGLTPADEEIAKYLRK--SKK 106 Query: 132 EIITVLNKADLPSADPDRVKKQIEE--TIGISTEDALLVSAKTGEGIPLLLERIVQQL 187 +I V+NK D + + E ++G + + +SA+ G GI LL+ I++ L Sbjct: 107 PVILVVNKVDNIKEEDE-----AAEFYSLGF--GEPIPISAEHGRGIGDLLDAILELL 157 >gnl|CDD|133263 cd01860, Rab5_related, Rab5-related subfamily. This subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 163 Score = 35.2 bits (82), Expect = 0.048 Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 9/65 (13%) Query: 129 NNHEIITVL--NKADLPSA---DPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERI 183 + II L NKADL S + ++ +E + E SAKTGE + L I Sbjct: 103 ASPNIIIALVGNKADLESKRQVSTEEAQEYADENGLLFFE----TSAKTGENVNELFTEI 158 Query: 184 VQQLP 188 ++LP Sbjct: 159 AKKLP 163 >gnl|CDD|31281 COG1084, COG1084, Predicted GTPase [General function prediction only]. Length = 346 Score = 34.9 bits (80), Expect = 0.063 Identities = 29/128 (22%), Positives = 54/128 (42%), Gaps = 23/128 (17%) Query: 74 DAKDYQLNLIDTPGHVDFTYE-----------VSRSLSACEGSLLVVDATQ----GVEAQ 118 + ++ +IDTPG +D E R L+ L + D ++ +E Q Sbjct: 211 ERGYLRIQVIDTPGLLDRPLEERNEIERQAILALRHLAGV--ILFLFDPSETCGYSLEEQ 268 Query: 119 T--LANVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGI 176 L + + I+ V+NK D+ AD +++++ + E+ L +SA G G+ Sbjct: 269 ISLLEEIKELFKAP--IVVVINKIDI--ADEEKLEEIEASVLEEGGEEPLKISATKGCGL 324 Query: 177 PLLLERIV 184 L E + Sbjct: 325 DKLREEVR 332 >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 = 35.1 bits (81), Expect = 0.064 Identities = 20/70 (28%), Positives = 29/70 (41%), Gaps = 3/70 (4%) Query: 410 EPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLD--NRAMIVYELPLNEVIFDFYDRL 467 EP V I P + LG + + +RRG + + I LP+ E F F L Sbjct: 1 EPIYLVEIQCPEDALGKVYSVLSKRRGHVLSEEPKEGTPLFEIKAYLPVIE-SFGFETDL 59 Query: 468 KSVSKGYASF 477 +S + G A Sbjct: 60 RSATSGQAFP 69 >gnl|CDD|133309 cd04109, Rab28, Rab28 subfamily. First identified in maize, Rab28 has been shown to be a late embryogenesis-abundant (Lea) protein that is regulated by the plant hormone abcisic acid (ABA). In Arabidopsis, Rab28 is expressed during embryo development and is generally restricted to provascular tissues in mature embryos. Unlike maize Rab28, it is not ABA-inducible. Characterization of the human Rab28 homolog revealed two isoforms, which differ by a 95-base pair insertion, producing an alternative sequence for the 30 amino acids at the C-terminus. The two human isoforms are presumbly the result of alternative splicing. Since they differ at the C-terminus but not in the GTP-binding region, they are predicted to be targeted to different cellular locations. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Length = 215 Score = 35.0 bits (81), Expect = 0.065 Identities = 30/139 (21%), Positives = 53/139 (38%), Gaps = 21/139 (15%) Query: 69 NYTSTDAKDYQLNLIDTPGHVDFTYEV-------------SRSLSACEGSLLVVDATQGV 115 +Y T D+ + PG+++ T +V + + LV D T Sbjct: 28 SYKQTIGLDFFSKRVTLPGNLNVTLQVWDIGGQSIGGKMLDKYIYGAHAVFLVYDVTNSQ 87 Query: 116 EAQTLANVYQAIDNNHE-------IITVLNKADLPSADPDRVKKQIEETIGISTEDALLV 168 + L + Y + + ++ V NK DL + K E + LV Sbjct: 88 SFENLEDWYSMVRKVLKSSETQPLVVLVGNKTDLEHNRTVKDDKHARFAQANGME-SCLV 146 Query: 169 SAKTGEGIPLLLERIVQQL 187 SAKTG+ + LL +++ +L Sbjct: 147 SAKTGDRVNLLFQQLAAEL 165 >gnl|CDD|133252 cd00876, Ras, Ras family. The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 160 Score = 34.0 bits (79), Expect = 0.11 Identities = 27/130 (20%), Positives = 50/130 (38%), Gaps = 28/130 (21%) Query: 74 DAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAI-----D 128 D + Y L+++DT G +F+ + +G +LV T + + + I D Sbjct: 43 DGETYTLDILDTAGQEEFSAMRDLYIRQGDGFILVYSITDRESFEEIKGYREQILRVKDD 102 Query: 129 NNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDA-----------LLVSAKTGEGIP 177 + I+ V NK DL E +S E+ + SAK I Sbjct: 103 EDIPIVLVGNKCDL------------ENERQVSKEEGKALAKEWGCPFIETSAKDNINID 150 Query: 178 LLLERIVQQL 187 + + +V+++ Sbjct: 151 EVFKLLVREI 160 >gnl|CDD|133296 cd01896, DRG, The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding. Length = 233 Score = 33.7 bits (78), Expect = 0.16 Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 10/55 (18%) Query: 134 ITVLNKADLPSADP-DRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQL 187 + V NK DL S + D + +Q +++++SA+ G + L ERI +L Sbjct: 180 LYVYNKIDLISIEELDLLARQP---------NSVVISAEKGLNLDELKERIWDKL 225 >gnl|CDD|31356 COG1162, COG1162, Predicted GTPases [General function prediction only]. Length = 301 Score = 33.7 bits (77), Expect = 0.16 Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 1/53 (1%) Query: 129 NNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLE 181 E + VLNK DL D + K++ L VSAK G+G+ L E Sbjct: 109 GGIEPVIVLNKIDLLD-DEEAAVKELLREYEDIGYPVLFVSAKNGDGLEELAE 160 >gnl|CDD|133339 cd04139, RalA_RalB, RalA/RalB subfamily. The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (>80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exocyst and for localizing the exocyst to the leading edge of migrating cells. In human cancer cells, RalA is required to support anchorage-independent proliferation and RalB is required to suppress apoptosis. RalA has been shown to localize to the plasma membrane while RalB is localized to the intracellular vesicles. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 164 Score = 33.5 bits (77), Expect = 0.17 Identities = 32/124 (25%), Positives = 47/124 (37%), Gaps = 13/124 (10%) Query: 74 DAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAI-----D 128 D +D QLN++DT G D+ + EG LLV T A + I D Sbjct: 44 DGEDVQLNILDTAGQEDYAAIRDNYHRSGEGFLLVFSITDMESFTATAEFREQILRVKDD 103 Query: 129 NNHEIITVLNKADL--PSADPDRVKKQIEETIGISTEDALLVSAKTGEG---IPLLLERI 183 +N ++ V NK DL + G+ + SAKT + L R Sbjct: 104 DNVPLLLVGNKCDLEDKRQVSSEEAANLARQWGVPY---VETSAKTRQNVEKAFYDLVRE 160 Query: 184 VQQL 187 ++Q Sbjct: 161 IRQR 164 >gnl|CDD|57930 cd01859, MJ1464, MJ1464. This family represents archaeal GTPase typified by the protein MJ1464 from Methanococcus jannaschii. The members of this family show a circular permutation of the GTPase signature motifs so that C-terminal strands 5, 6, and 7 (strands 6 contain the NKxD motif) are relocated to the N terminus.. Length = 156 Score = 33.3 bits (76), Expect = 0.20 Identities = 25/99 (25%), Positives = 41/99 (41%), Gaps = 3/99 (3%) Query: 95 VSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNHEIITVLNKADLPSADPDRVKKQI 154 V R + + L V+DA ++ ++ +++ VLNKADL + K I Sbjct: 6 VRRIIKESDVVLEVLDARDPELTRSRKLERYVLELGKKLLIVLNKADLVPKEVLEKWKSI 65 Query: 155 EETIGISTEDALLVSAKTGEGIPLLLERIVQQLPSPTSP 193 +E+ GI + VSAK G +L I + Sbjct: 66 KESEGIPV---VYVSAKERLGTKILRRTIKELAKIDGKE 101 >gnl|CDD|133297 cd01897, NOG, NOG1 is a nucleolar GTP-binding protein present in eukaryotes ranging from trypanosomes to humans. NOG1 is functionally linked to ribosome biogenesis and found in association with the nuclear pore complexes and identified in many preribosomal complexes. Thus, defects in NOG1 can lead to defects in 60S biogenesis. The S. cerevisiae NOG1 gene is essential for cell viability, and mutations in the predicted G motifs abrogate function. It is a member of the ODN family of GTP-binding proteins that also includes the bacterial Obg and DRG proteins. Length = 168 Score = 32.9 bits (76), Expect = 0.24 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 3/55 (5%) Query: 133 IITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQL 187 +I VLNK DL + + + EE + E+ L +S T EG+ + + + L Sbjct: 116 VIVVLNKIDL--LTFEDLSEIEEEEE-LEGEEVLKISTLTEEGVDEVKNKACELL 167 >gnl|CDD|133354 cd04154, Arl2, Arl2 subfamily. Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis. Length = 173 Score = 33.0 bits (76), Expect = 0.25 Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 2/56 (3%) Query: 132 EIITVLNKADLPSA-DPDRVKKQIEETIGISTEDALL-VSAKTGEGIPLLLERIVQ 185 ++ + NK DLP A + +++ +E S + SA TGEG+ ++ +V Sbjct: 117 TLLILANKQDLPGALSEEEIREALELDKISSHHWRIQPCSAVTGEGLLQGIDWLVD 172 >gnl|CDD|143853 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices. Length = 162 Score = 32.9 bits (76), Expect = 0.27 Identities = 38/141 (26%), Positives = 53/141 (37%), Gaps = 36/141 (25%) Query: 69 NYTST---DAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANV-- 123 YT T D K +L + DT G F +G LLV D T + NV Sbjct: 36 FYTKTIEVDGKTVKLQIWDTAGQERFRALRPLYYRGAQGFLLVYDITS---RDSFENVKK 92 Query: 124 -YQAI----DNNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDA-----------LL 167 + I D+N I+ V NK DL RV +STE+ + Sbjct: 93 WLEEILRHADDNVPIVLVGNKCDLED---QRV---------VSTEEGEALAKELGLPFME 140 Query: 168 VSAKTGEGIPLLLERIVQQLP 188 SAKT E + E + +++ Sbjct: 141 TSAKTNENVEEAFEELAREIL 161 >gnl|CDD|35307 KOG0084, KOG0084, KOG0084, GTPase Rab1/YPT1, small G protein superfamily, and related GTP-binding proteins [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport]. Length = 205 Score = 32.9 bits (75), Expect = 0.29 Identities = 42/192 (21%), Positives = 65/192 (33%), Gaps = 42/192 (21%) Query: 23 GKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAKDYQLNL 82 GK+ L RF TE +S+ G+ K +TV L D K +L + Sbjct: 21 GKTCLLLRF--KDDTFTESYISTI-----------GVDFKIRTVEL-----DGKTIKLQI 62 Query: 83 IDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAI-------DNNHEIIT 135 DT G F S G + V D T + ++ NV + I N + Sbjct: 63 WDTAGQERFRTITSSYYRGAHGIIFVYDIT---KQESFNNVKRWIQEIDRYASENVPKLL 119 Query: 136 VLNKADLPSA---DPDRVKKQIEETIGISTEDALLVSAKTGEGIP--------LLLERIV 184 V NK DL + ++ +E + L SAK + L +R Sbjct: 120 VGNKCDLTEKRVVSTEEAQEFADE---LGIPIFLETSAKDSTNVEDAFLTLAKELKQRKG 176 Query: 185 QQLPSPTSPEGA 196 + T+ + Sbjct: 177 LHVKWSTASLES 188 >gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems. Length = 267 Score = 31.6 bits (72), Expect = 0.58 Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 9/59 (15%) Query: 134 ITVLNKADLPSADPDRVKKQIEETIGISTED-------ALLVSAKTGEGIPLLLERIVQ 185 I V+NKADLP A +R +++ + + T L SA TGEGI L + I + Sbjct: 171 IYVVNKADLPGA--ERTARELRSALHLLTPKEAGWRPPVLTTSAVTGEGIDELWDAIEE 227 >gnl|CDD|133325 cd04125, RabA_like, RabA-like subfamily. RabA was first identified in D. discoideum, where its expression levels were compared to other Rabs in growing and developing cells. The RabA mRNA levels were below the level of detection by Northern blot analysis, suggesting a very low level of expression. The function of RabA remains unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Length = 188 Score = 31.6 bits (72), Expect = 0.62 Identities = 44/183 (24%), Positives = 70/183 (38%), Gaps = 37/183 (20%) Query: 23 GKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAKDYQLNL 82 GKS+L RF TE E S + G+ K +TV + + K +L + Sbjct: 12 GKSSLLKRF-------TEDEFSESTKSTI------GVDFKIKTVYI-----ENKIIKLQI 53 Query: 83 IDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNHE----IITVLN 138 DT G F + G LLV D T + L I+ + V N Sbjct: 54 WDTNGQERFRSLNNSYYRGAHGYLLVYDVTDQESFENLKFWINEINRYARENVIKVIVAN 113 Query: 139 KADLPS---ADPDRVKKQIEETIGISTEDALLVSAKTGEGI--------PLLLERIVQQL 187 K+DL + D + + K +++ I + SAK + L+++R+ +Q Sbjct: 114 KSDLVNNKVVDSN-IAKSFCDSLNIPFFE---TSAKQSINVEEAFILLVKLIIKRLEEQE 169 Query: 188 PSP 190 SP Sbjct: 170 LSP 172 >gnl|CDD|35315 KOG0092, KOG0092, KOG0092, GTPase Rab5/YPT51 and related small G protein superfamily GTPases [Intracellular trafficking, secretion, and vesicular transport]. Length = 200 Score = 31.4 bits (71), Expect = 0.66 Identities = 48/200 (24%), Positives = 73/200 (36%), Gaps = 31/200 (15%) Query: 9 SRIRNFSIVAHIDH--GKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTV 66 R F +V D GKS+L RF++ Q +N IE G +TV Sbjct: 1 MATREFKVVLLGDSGVGKSSLVLRFVK-----------DQFHEN--IEPTIGAAFLTKTV 47 Query: 67 RLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQA 126 + D + + DT G + +++V D T + N + Sbjct: 48 TV-----DDNTIKFEIWDTAGQERYHSLAPMYYRGANAAIVVYDITDEESFEKAKNWVKE 102 Query: 127 IDNN--HEIITVL--NKADLPSADPDRVKKQIEETIGISTEDALL---VSAKTGEGIPLL 179 + I+ L NKADL + V + EE + LL SAKTGE + + Sbjct: 103 LQRQASPNIVIALVGNKADL--LERREV--EFEEAQAYAESQGLLFFETSAKTGENVNEI 158 Query: 180 LERIVQQLPSPTSPEGANAP 199 + I ++LP E P Sbjct: 159 FQAIAEKLPCSDPQERQGLP 178 >gnl|CDD|144677 pfam01171, ATP_bind_3, PP-loop family. This family of proteins belongs to the PP-loop superfamily. Length = 182 Score = 31.4 bits (72), Expect = 0.66 Identities = 11/49 (22%), Positives = 23/49 (46%) Query: 16 IVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQ 64 AH+DHG +DR Q + L + + +D+ ++ G+ ++ Sbjct: 31 TAAHVDHGLREESDREAQFVKELCRQLNIPLEVLRVDVAKKSGLNLEEA 79 >gnl|CDD|133305 cd04105, SR_beta, Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are synthesized with an N-terminal hydrophobic signal sequence that binds SRP54, a component of the SRP. SRP directs targeting of the ribosome-nascent chain complex (RNC) to the ER membrane via interaction with the SR, which is localized to the ER membrane. The RNC is then transferred to the protein-conducting channel, or translocon, which facilitates polypeptide translation across the ER membrane or integration into the ER membrane. SR-beta is found only in eukaryotes; it is believed to control the release of the signal sequence from SRP54 upon binding of the ribosome to the translocon. High expression of SR-beta has been observed in human colon cancer, suggesting it may play a role in the development of this type of cancer. Length = 203 Score = 31.5 bits (72), Expect = 0.77 Identities = 24/99 (24%), Positives = 44/99 (44%), Gaps = 18/99 (18%) Query: 76 KDYQLNLIDTPGHVDFTYEVSRSL-SACEGSLLVVD-ATQGVEAQTLA-----------N 122 K + L+D PGH ++ +L ++ +G + VVD AT + +A Sbjct: 46 KGKKFRLVDVPGHPKLRDKLLETLKNSAKGIVFVVDSATFQKNLKDVAEFLYDILTDLEK 105 Query: 123 VYQAIDNNHEIITVLNKADLPSA-DPDRVKKQIEETIGI 160 V I ++ NK DL +A ++K+Q+E+ + Sbjct: 106 VKNKIP----VLIACNKQDLFTAKPAKKIKEQLEKELNT 140 >gnl|CDD|133266 cd01863, Rab18, Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 161 Score = 31.5 bits (72), Expect = 0.80 Identities = 32/133 (24%), Positives = 60/133 (45%), Gaps = 23/133 (17%) Query: 67 RLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSA-----CEGSLLVVDATQGVEAQTLA 121 ++ + D K +L + DT G F R+L++ +G +LV D T+ L Sbjct: 38 KVKTLTVDGKKVKLAIWDTAGQERF-----RTLTSSYYRGAQGVILVYDVTRRDTFTNLE 92 Query: 122 NVYQAID---NNHEIITVL--NKADLPSADPDRVKKQIEETIGISTEDALL---VSAKTG 173 ++ N++I+ +L NK D + + R EE + + + +L SAKT Sbjct: 93 TWLNELETYSTNNDIVKMLVGNKIDKENREVTR-----EEGLKFARKHNMLFIETSAKTR 147 Query: 174 EGIPLLLERIVQQ 186 +G+ E +V++ Sbjct: 148 DGVQQAFEELVEK 160 >gnl|CDD|145920 pfam03029, ATP_bind_1, Conserved hypothetical ATP binding protein. Members of this family are found in a range of archaea and eukaryotes and have hypothesized ATP binding activity. Length = 234 Score = 30.8 bits (70), Expect = 1.1 Identities = 47/222 (21%), Positives = 77/222 (34%), Gaps = 62/222 (27%) Query: 23 GKSTLADRFIQHCRGLTEREMSSQVLD----------NMDIE---------RERGITIK- 62 GK+T + L R + LD ++DI + G+ Sbjct: 8 GKTTFVGALSEILP-LRGRSVYVVNLDPAAENLPYEADIDIRELITVADVMEDYGLGPNG 66 Query: 63 AQTVRLNYTSTD--------AKDYQLNLIDTPG------HVDFTYEVSRSLSACE-GSLL 107 A TV +++ + L DTPG H D +L A G++ Sbjct: 67 ALTVAMDFGRITLDWLLEELEYEDDYYLFDTPGQIELFTHWDSLARGVEALEASRLGAVY 126 Query: 108 VVDATQGVEAQT-LANVYQA--IDNNHEI--ITVLNKADLPSA--------DPDRVKKQI 154 +VD + + + + A I + + LNK DL S DPD ++ + Sbjct: 127 LVDTRRLTDPIDFFSGLLYALSIMLRLGLPFVVALNKFDLLSLEFALKWFTDPDDLQLLL 186 Query: 155 E-------ETIGISTEDALLV------SAKTGEGIPLLLERI 183 E E I ++ + LV + +TGE + LL I Sbjct: 187 ELDYRYLNEAIRLALDLFYLVPRFLCDARETGESMEDLLTLI 228 >gnl|CDD|57924 cd01849, YlqF_related_GTPase, YlqF-related GTPases. These proteins are found in bacteria, eukaryotes, and archaea. They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases.. Length = 155 Score = 30.7 bits (69), Expect = 1.2 Identities = 22/98 (22%), Positives = 37/98 (37%), Gaps = 5/98 (5%) Query: 106 LLVVDATQGVEAQTLANVYQAIDNNHE--IITVLNKADLPSADPDRVKKQIEETIGISTE 163 L V+DA + ++ + + +I VLNKADL + ++K + Sbjct: 4 LEVLDA-RDPLGTRSPDIERVLIKEKGKKLILVLNKADL--VPKEVLRKWLAYLRHSYPT 60 Query: 164 DALLVSAKTGEGIPLLLERIVQQLPSPTSPEGANAPLK 201 +SA G+GI +Q S + LK Sbjct: 61 IPFKISATNGQGIEKKESAFTKQTNSNLKSYAKDGKLK 98 >gnl|CDD|143978 pfam00223, PsaA_PsaB, Photosystem I psaA/psaB protein. Length = 682 Score = 30.4 bits (69), Expect = 1.3 Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 6/36 (16%) Query: 383 LYMHDGSMQKLSNPIDMPEVTKIAELREP----WIQ 414 LY+H+ +MQ L P DM +I L EP WIQ Sbjct: 403 LYIHNDTMQALGRPQDMFSDKQI--LLEPVFAQWIQ 436 >gnl|CDD|31357 COG1163, DRG, Predicted GTPase [General function prediction only]. Length = 365 Score = 30.2 bits (68), Expect = 1.5 Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 10/55 (18%) Query: 134 ITVLNKADLPSADP-DRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQL 187 + V+NK DLP + +R+ ++ +++ +SAK G + L ERI L Sbjct: 243 LYVVNKIDLPGLEELERLARKP---------NSVPISAKKGINLDELKERIWDVL 288 >gnl|CDD|36637 KOG1423, KOG1423, KOG1423, Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. Length = 379 Score = 30.0 bits (67), Expect = 1.7 Identities = 44/233 (18%), Positives = 70/233 (30%), Gaps = 68/233 (29%) Query: 1 MQKKPTPLSRIRNFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGIT 60 + + +++ + GKSTL ++ I S V + R R + Sbjct: 62 ESRDEEEAQKSLYVAVIGAPNVGKSTLTNQMIGQ--------KVSAVSRKVHTTRHRILG 113 Query: 61 IKAQTVRLNYTSTDAKDYQLNLIDTPGHV------------DFTYEVSRSLSACEGSLLV 108 I TS + QL DTPG V + + ++V Sbjct: 114 I--------ITS---GETQLVFYDTPGLVSKKMHRRHHLMMSVLQNPRDAAQNADCVVVV 162 Query: 109 VDATQGVEAQTLANVYQAIDNNHEI-----ITVLNKADLP-------------------- 143 VDA+ +T + + + E I V+NK D Sbjct: 163 VDAS---ATRTPLHP-RVLHMLEEYSKIPSILVMNKIDKLKQKRLLLNLKDLLTNGELAK 218 Query: 144 --------SADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQLP 188 D +K E +VSA GEGI L + ++ Q P Sbjct: 219 LKLEVQEKFTDVPSDEKWRTICGWSHFERVFMVSALYGEGIKDLKQYLMSQAP 271 >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 = 29.7 bits (67), Expect = 2.1 Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 9/42 (21%) Query: 217 VLVRIINGQLTKGQSIRLMGTN---------AKYQVERIGIL 249 RI +G + KGQ ++++G N + R+ IL Sbjct: 19 AFGRIYSGTIKKGQKVKVLGENYSLDDEEDMTICTIGRLWIL 60 >gnl|CDD|35317 KOG0094, KOG0094, KOG0094, GTPase Rab6/YPT6/Ryh1, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 221 Score = 29.9 bits (67), Expect = 2.2 Identities = 32/130 (24%), Positives = 46/130 (35%), Gaps = 22/130 (16%) Query: 78 YQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNHE----- 132 +L L DT G F + + +++V D T + + N + I++ Sbjct: 71 VRLQLWDTAGQERFRSLIPSYIRDSSVAVIVYDIT---DRNSFENTSKWIEDVRRERGSD 127 Query: 133 ---IITVLNKADLPSADPDRVKKQIEETIGISTEDAL-----LVSAKTGEGIPLLLERIV 184 I V NK DL K+Q+ G L SAK GE + L RI Sbjct: 128 DVIIFLVGNKTDLSD------KRQVSIEEGERKAKELNAEFIETSAKAGENVKQLFRRIA 181 Query: 185 QQLPSPTSPE 194 LP E Sbjct: 182 AALPGMEVLE 191 >gnl|CDD|133319 cd04119, RJL, RJL (RabJ-Like) subfamily. RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Length = 168 Score = 29.6 bits (67), Expect = 2.5 Identities = 29/119 (24%), Positives = 41/119 (34%), Gaps = 16/119 (13%) Query: 81 NLIDTPGHVDFTYEVSRSL-SACEGSLLVVDATQGVEAQTL------ANVYQAIDNNHEI 133 N D GH EV +G LLV D T + L N E Sbjct: 52 NFFDLSGH-PEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMEN 110 Query: 134 ITVL---NKADLPSADPDRVKKQIEETIGISTEDALL--VSAKTGEGIPLLLERIVQQL 187 I V+ NK DL R + E + ++ SA TGEG+ + + + + Sbjct: 111 IVVVVCANKIDLTKH---RAVSEDEGRLWAESKGFKYFETSACTGEGVNEMFQTLFSSI 166 >gnl|CDD|39948 KOG4751, KOG4751, KOG4751, DNA recombinational repair protein BRCA2 [Replication, recombination and repair]. Length = 756 Score = 29.7 bits (66), Expect = 2.5 Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 2/40 (5%) Query: 204 LIDSWY--NSYLGVMVLVRIINGQLTKGQSIRLMGTNAKY 241 L D WY N+ L V++ ++ G+L GQ +R Y Sbjct: 669 LTDGWYSMNAALDVVLTKQLNAGKLFVGQKLRHAYVLISY 708 >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 = 29.8 bits (67), Expect = 2.6 Identities = 14/68 (20%), Positives = 33/68 (48%), Gaps = 11/68 (16%) Query: 218 LVRIINGQLTKGQSIRLMGTN---------AKYQVERIGIL-TPKMIDIEALYPGEIGVM 267 R+ +G + KGQ +R++G N +K ++R+ ++ ++ + G I V+ Sbjct: 20 FGRVFSGTIRKGQKVRVLGPNYSPEDEEDLSKKTIQRLYLMMGRYREPVDEVPAGNI-VL 78 Query: 268 IASIKEVS 275 I + ++ Sbjct: 79 IVGLDQLK 86 >gnl|CDD|133264 cd01861, Rab6, Rab6 subfamily. Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 161 Score = 29.5 bits (67), Expect = 2.9 Identities = 40/148 (27%), Positives = 59/148 (39%), Gaps = 38/148 (25%) Query: 58 GITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSL--------SACEGSLLVV 109 GI ++T+ L + K +L L DT G F RSL S ++V Sbjct: 34 GIDFLSKTMYL-----EDKTVRLQLWDTAGQERF-----RSLIPSYIRDSSVA---VVVY 80 Query: 110 DATQGVEAQTLANVYQAIDN-----NHEIITVL--NKADLPSADPDRVKKQIEETIGIST 162 D T Q+ N + ID+ +++I VL NK DL D+ + EE + Sbjct: 81 DIT---NRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDLS----DKRQVSTEEGEKKAK 133 Query: 163 EDALL---VSAKTGEGIPLLLERIVQQL 187 E + SAK G + L +I L Sbjct: 134 ELNAMFIETSAKAGHNVKELFRKIASAL 161 >gnl|CDD|30727 COG0378, HypB, Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]. Length = 202 Score = 29.0 bits (65), Expect = 3.4 Identities = 26/117 (22%), Positives = 46/117 (39%), Gaps = 12/117 (10%) Query: 74 DAKDYQLNLIDTPGHV--DFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNH 131 D D L I++ G++ F+ ++ L V+D T+G + I Sbjct: 93 DFPDLDLLFIESVGNLVCPFSPDLGDHLRVV-----VIDVTEGED--IPRKGGPGIFKAD 145 Query: 132 EIITVLNKADLPSADPDRVKKQIEETIGISTE-DALLVSAKTGEGIPLLLERIVQQL 187 + V+NK DL ++ + ++ E + + KTGEG+ L I Q Sbjct: 146 --LLVINKTDLAPYVGADLEVMARDAKEVNPEAPIIFTNLKTGEGLDEWLRFIEPQA 200 >gnl|CDD|35309 KOG0086, KOG0086, KOG0086, GTPase Rab4, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 214 Score = 29.2 bits (65), Expect = 3.8 Identities = 45/171 (26%), Positives = 66/171 (38%), Gaps = 31/171 (18%) Query: 14 FSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTST 73 F ++ GKS L +FI+ ++ D D G+ ++ V + Sbjct: 12 FLVIGSAGTGKSCLLHQFIE-----------NKFKD--DSSHTIGVEFGSRIV-----NV 53 Query: 74 DAKDYQLNLIDTPGHVDFTYEVSRSL-SACEGSLLVVDATQGVEAQTLANVYQAI----D 128 K +L + DT G F V+RS G+LLV D T L N Sbjct: 54 GGKTVKLQIWDTAGQERFR-SVTRSYYRGAAGALLVYDITSRDSFNALTNWLTDARTLAS 112 Query: 129 NNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALL---VSAKTGEGI 176 N +I NK DL DP+R + E + E+ L+ SA TGE + Sbjct: 113 PNIVVILCGNKKDL---DPER-EVTFLEASRFAQENELMFLETSALTGENV 159 >gnl|CDD|110038 pfam01007, IRK, Inward rectifier potassium channel. Length = 336 Score = 28.8 bits (65), Expect = 4.7 Identities = 9/19 (47%), Positives = 14/19 (73%) Query: 331 ASFSFELENSTALGFGFRC 349 ++F F +E T +G+GFRC Sbjct: 86 SAFLFSIETQTTIGYGFRC 104 >gnl|CDD|31355 COG1161, COG1161, Predicted GTPases [General function prediction only]. Length = 322 Score = 28.8 bits (64), Expect = 4.8 Identities = 26/97 (26%), Positives = 40/97 (41%), Gaps = 9/97 (9%) Query: 82 LIDTPGHV-DFTYEVSRSLSACEGSLLVVDA--TQGVEAQTLANVYQAIDNNHEIITVLN 138 + PGH+ ++ L + + + VVDA G T + I + VLN Sbjct: 14 IQWFPGHMKKAKRQLKEVLKSVDVVVEVVDARDPLG----TRNPELERIVKEKPKLLVLN 69 Query: 139 KADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEG 175 KADL A + KK + + VSAK+ +G Sbjct: 70 KADL--APKEVTKKWKKYFKKEEGIKPIFVSAKSRQG 104 >gnl|CDD|39031 KOG3827, KOG3827, KOG3827, Inward rectifier K+ channel [Inorganic ion transport and metabolism]. Length = 400 Score = 28.8 bits (64), Expect = 4.9 Identities = 8/19 (42%), Positives = 13/19 (68%) Query: 331 ASFSFELENSTALGFGFRC 349 ++F F +E T +G+GFR Sbjct: 115 SAFLFSIETQTTIGYGFRY 133 >gnl|CDD|57927 cd01856, YlqF, YlqF. Proteins of the YlqF 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. The YlqF subfamily is represented in a phylogenetically diverse array of bacteria (including gram-positive bacteria, proteobacteria, Synechocystis, Borrelia, and Thermotoga) and in all eukaryotes.. Length = 171 Score = 28.7 bits (64), Expect = 4.9 Identities = 25/85 (29%), Positives = 42/85 (49%), Gaps = 6/85 (7%) Query: 124 YQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERI 183 + I N I VLNKADL ADP + KK ++ + L V+AK+G+G+ LL+ Sbjct: 40 LEKILGNKPRIIVLNKADL--ADPKKTKKWLKYFESKGEK-VLFVNAKSGKGVKKLLKAA 96 Query: 184 VQQLPSP---TSPEGANAPLKALLI 205 + L + ++A+++ Sbjct: 97 KKLLKDIEKLKAKGLLPRGIRAMVV 121 >gnl|CDD|176112 cd08420, PBP2_CysL_like, C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold. CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 201 Score = 28.2 bits (64), Expect = 6.2 Identities = 8/24 (33%), Positives = 13/24 (54%) Query: 12 RNFSIVAHIDHGKSTLADRFIQHC 35 R FS++ H D S A+ F++ Sbjct: 178 RPFSLIYHKDKYLSPAAEAFLEFL 201 >gnl|CDD|143894 pfam00120, Gln-synt_C, Glutamine synthetase, catalytic domain. Length = 257 Score = 28.3 bits (64), Expect = 6.4 Identities = 10/43 (23%), Positives = 17/43 (39%), Gaps = 1/43 (2%) Query: 282 TITDDSSPTTSALPGFKPIQPVVFCGLFPVDAT-QFENLRTAI 323 + DD P G+ + + G FPV + ++R I Sbjct: 31 FLFDDVRPGGGPPGGYPDPRGPYYGGYFPVAPLDEARDIRRDI 73 >gnl|CDD|177045 CHL00122, secA, preprotein translocase subunit SecA; Validated. Length = 870 Score = 28.0 bits (63), Expect = 7.4 Identities = 26/92 (28%), Positives = 40/92 (43%), Gaps = 17/92 (18%) Query: 415 VTIITPNEYL--------GSILKLCQERRG-IQIDMSHLDNR----AMIVYELPLNEVIF 461 V I+T N+YL G I + G IQ MS + + I Y + +E+ F Sbjct: 120 VHIVTVNDYLAKRDQEWMGQIYRFLGLTVGLIQEGMSSEERKKNYLKDITY-VTNSELGF 178 Query: 462 DFYDRLKSVSKG---YASFDYNVIDYRDSDLV 490 D+ ++S F+Y +ID DS L+ Sbjct: 179 DYLRDNMALSLSDVVQRPFNYCIIDEVDSILI 210 >gnl|CDD|133273 cd01870, RhoA_like, RhoA-like subfamily. The RhoA subfamily consists of RhoA, RhoB, and RhoC. RhoA promotes the formation of stress fibers and focal adhesions, regulating cell shape, attachment, and motility. RhoA can bind to multiple effector proteins, thereby triggering different downstream responses. In many cell types, RhoA mediates local assembly of the contractile ring, which is necessary for cytokinesis. RhoA is vital for muscle contraction; in vascular smooth muscle cells, RhoA plays a key role in cell contraction, differentiation, migration, and proliferation. RhoA activities appear to be elaborately regulated in a time- and space-dependent manner to control cytoskeletal changes. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. RhoA and RhoC are observed only in geranylgeranylated forms; however, RhoB can be present in palmitoylated, farnesylated, and geranylgeranylated forms. RhoA and RhoC are highly relevant for tumor progression and invasiveness; however, RhoB has recently been suggested to be a tumor suppressor. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 175 Score = 27.8 bits (62), Expect = 9.1 Identities = 35/143 (24%), Positives = 58/143 (40%), Gaps = 25/143 (17%) Query: 65 TVRLNYTS---TDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVV-------DATQG 114 TV NY + D K +L L DT G D Y+ R LS + ++++ D+ + Sbjct: 33 TVFENYVADIEVDGKQVELALWDTAGQED--YDRLRPLSYPDTDVILMCFSIDSPDSLEN 90 Query: 115 VEAQTLANVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLV------ 168 + + V + N II V NK DL + + R + + + E+ + Sbjct: 91 IPEKWTPEV-KHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANKIGA 149 Query: 169 ------SAKTGEGIPLLLERIVQ 185 SAKT EG+ + E + Sbjct: 150 FGYMECSAKTKEGVREVFEMATR 172 >gnl|CDD|143815 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a number of different Prosite families together. Length = 174 Score = 27.6 bits (62), Expect = 9.4 Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 4/58 (6%) Query: 133 IITVLNKADLPSA-DPDRVKKQIEETIGISTEDALLV--SAKTGEGIPLLLERIVQQL 187 ++ + NK DLP A +++ + + + + SA TGEG+ L+ + + Sbjct: 118 LLILANKQDLPGAMSEAEIRELLGLH-ELKSRPWEIQGCSAVTGEGLDEGLDWLSNYI 174 >gnl|CDD|144151 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins. Length = 196 Score = 27.9 bits (63), Expect = 9.5 Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 8/57 (14%) Query: 75 AKDYQLNLIDTPG--HVDFTY-----EVSRSLSACEGSLLVVDATQGVEAQTLANVY 124 A++Y + L+DT G D ++ R ++ E LLV+DAT G A A + Sbjct: 81 AENYDVVLVDTAGRLQNDKNLMDELKKIKRVIAPDE-VLLVLDATTGQNALNQAKAF 136 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 0.319 0.136 0.384 Gapped Lambda K H 0.267 0.0787 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 7,064,335 Number of extensions: 379845 Number of successful extensions: 1284 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1125 Number of HSP's successfully gapped: 160 Length of query: 606 Length of database: 6,263,737 Length adjustment: 99 Effective length of query: 507 Effective length of database: 4,124,446 Effective search space: 2091094122 Effective search space used: 2091094122 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 60 (26.8 bits)