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)