RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780263|ref|YP_003064676.1| translation elongation factor
Tu [Candidatus Liberibacter asiaticus str. psy62]
         (392 letters)



>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
          Length = 409

 Score =  544 bits (1403), Expect = e-155
 Identities = 226/410 (55%), Positives = 291/410 (70%), Gaps = 19/410 (4%)

Query: 1   MVEKRYVRNKESLGLSTIGHVDHGKTTLTAAIT----KYYSEEKKEYGDIDSAPEEKLRG 56
           M  +++ R K  + + TIGHVDHGKTTLTAAIT         + K+Y +IDSAPEEK RG
Sbjct: 1   MAREKFERKKPHVNIGTIGHVDHGKTTLTAAITMTLAAKGGAKAKKYDEIDSAPEEKARG 60

Query: 57  ITIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHI 116
           ITI TAHV YET+ R Y+H+DCPGHADYVKNMITGA Q DGAILV +A DGP PQT+EHI
Sbjct: 61  ITINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTKEHI 120

Query: 117 LLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKY-SDDTPIIRGSALCAL- 174
           LLA+Q+G+ +IVV++NK D VDD+ELL++ E E+R+LL ++ +  DD PI+ GSAL AL 
Sbjct: 121 LLAKQVGVPNIVVFLNKEDQVDDEELLELVELEVRELLSKYDFPGDDIPIVSGSALLALE 180

Query: 175 ---QGTNKELGE----DSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTG 227
              +    + GE    D I+ LM AVD++IPTP+R  D PFLM IE    I GRGTV TG
Sbjct: 181 ALTENPKIKRGENKWVDKIYNLMDAVDSYIPTPERDTDKPFLMAIEDVFSITGRGTVATG 240

Query: 228 CIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVNRADVPR 287
            I+RG +K G  VEI+G+   K     T +EMF+K LDE +AGDNVG+LLRG+ + D+ R
Sbjct: 241 RIERGTVKVGDTVEIVGLRETKT-TTVTGLEMFQKTLDEGLAGDNVGILLRGIQKEDIER 299

Query: 288 GRVVCAPGSIQEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRI---ILSP 344
           G V+  PG+I  +++F A VYILT  EGGR T F   YRPQF++ T DVTG+I       
Sbjct: 300 GMVLAKPGTITPHTKFEAQVYILTKEEGGRHTPFFPGYRPQFYVRTTDVTGKIESFTADD 359

Query: 345 GSQA--VMPGDRVDLEVELIYPIAMEPNQTFSMREGGKTVGAGLILEIIE 392
           GS+   VMPGDR+ + VELIYPIA+E    F++REGG+TVGAG++ +I++
Sbjct: 360 GSKTEMVMPGDRIKMTVELIYPIAIEKGMRFAIREGGRTVGAGVVSKILK 409


>gnl|CDD|35681 KOG0460, KOG0460, KOG0460, Mitochondrial translation elongation
           factor Tu [Translation, ribosomal structure and
           biogenesis].
          Length = 449

 Score =  523 bits (1348), Expect = e-149
 Identities = 227/395 (57%), Positives = 290/395 (73%), Gaps = 6/395 (1%)

Query: 3   EKRYVRNKESLGLSTIGHVDHGKTTLTAAITKYYSEEK----KEYGDIDSAPEEKLRGIT 58
           +  +VR+K  + + TIGHVDHGKTTLTAAITK  +E+     K+Y +ID APEEK RGIT
Sbjct: 45  KAVFVRDKPHVNVGTIGHVDHGKTTLTAAITKILAEKGGAKFKKYDEIDKAPEEKARGIT 104

Query: 59  IATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILL 118
           I  AHV YET KR Y+H DCPGHADY+KNMITGA Q DGAILV AA DGP PQTREH+LL
Sbjct: 105 INAAHVEYETAKRHYAHTDCPGHADYIKNMITGAAQMDGAILVVAATDGPMPQTREHLLL 164

Query: 119 ARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYS-DDTPIIRGSALCALQGT 177
           ARQ+G+  IVV++NKVD VDD E+L++ E EIR+LL E  +  D+TP+IRGSALCAL+G 
Sbjct: 165 ARQVGVKHIVVFINKVDLVDDPEMLELVEMEIRELLSEFGFDGDNTPVIRGSALCALEGR 224

Query: 178 NKELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAG 237
             E+G ++I  L+ AVD++IPTP+R LD PFL+ IE    I GRGTVVTG ++RG +K G
Sbjct: 225 QPEIGLEAIEKLLDAVDSYIPTPERDLDKPFLLPIEDVFSIPGRGTVVTGRLERGVLKKG 284

Query: 238 SDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVNRADVPRGRVVCAPGSI 297
            +VEI+G   K LK   T +EMFRK LDEA AGDN+G LLRG+ R DV RG V+  PGS+
Sbjct: 285 DEVEIVG-HNKTLKTTVTGIEMFRKSLDEAQAGDNLGALLRGIKREDVKRGMVLAKPGSV 343

Query: 298 QEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRIILSPGSQAVMPGDRVDL 357
           + +++F A +YIL+  EGGR   F+  YRPQ F  T DVTGR+ + P  + VMPG+ V +
Sbjct: 344 KPHNKFEAQLYILSKEEGGRHKPFVSGYRPQMFSRTWDVTGRVDIPPEKEMVMPGENVKV 403

Query: 358 EVELIYPIAMEPNQTFSMREGGKTVGAGLILEIIE 392
           EV LI P+ +E  Q F++REGG+TVG G++ + + 
Sbjct: 404 EVTLIRPMPLEKGQRFTLREGGRTVGTGVVTDTLP 438


>gnl|CDD|30399 COG0050, TufB, GTPases - translation elongation factors
           [Translation, ribosomal structure and biogenesis].
          Length = 394

 Score =  519 bits (1337), Expect = e-148
 Identities = 239/397 (60%), Positives = 292/397 (73%), Gaps = 8/397 (2%)

Query: 1   MVEKRYVRNKESLGLSTIGHVDHGKTTLTAAITKYYSE----EKKEYGDIDSAPEEKLRG 56
           M ++++ R K  + + TIGHVDHGKTTLTAAIT   ++    E K Y  ID+APEEK RG
Sbjct: 1   MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKKGGAEAKAYDQIDNAPEEKARG 60

Query: 57  ITIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHI 116
           ITI TAHV YET  R Y+H+DCPGHADYVKNMITGA Q DGAILV AA DGP PQTREHI
Sbjct: 61  ITINTAHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI 120

Query: 117 LLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYS-DDTPIIRGSALCALQ 175
           LLARQ+G+  IVV++NKVD VDD+ELL++ E E+R+LL E+ +  DDTPIIRGSAL AL+
Sbjct: 121 LLARQVGVPYIVVFLNKVDMVDDEELLELVEMEVRELLSEYGFPGDDTPIIRGSALKALE 180

Query: 176 GTNKELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIK 235
           G  K   E  I  LM AVD++IPTP+R +D PFLM +E    I GRGTVVTG ++RG +K
Sbjct: 181 GDAK--WEAKIEELMDAVDSYIPTPERDIDKPFLMPVEDVFSISGRGTVVTGRVERGILK 238

Query: 236 AGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVNRADVPRGRVVCAPG 295
            G +VEI+G   +  K   T VEMFRK LDE  AGDNVG+LLRGV R DV RG+V+  PG
Sbjct: 239 VGEEVEIVG-IKETQKTTVTGVEMFRKLLDEGQAGDNVGVLLRGVKREDVERGQVLAKPG 297

Query: 296 SIQEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRIILSPGSQAVMPGDRV 355
           SI+ +++F A VY+L+  EGGR T F   YRPQF+  T DVTG I L  G + VMPGD V
Sbjct: 298 SIKPHTKFEAEVYVLSKEEGGRHTPFFHGYRPQFYFRTTDVTGAITLPEGVEMVMPGDNV 357

Query: 356 DLEVELIYPIAMEPNQTFSMREGGKTVGAGLILEIIE 392
            + VELI+PIAME    F++REGG+TVGAG++ +IIE
Sbjct: 358 KMVVELIHPIAMEEGLRFAIREGGRTVGAGVVTKIIE 394


>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 =  339 bits (872), Expect = 7e-94
 Identities = 117/189 (61%), Positives = 147/189 (77%), Gaps = 5/189 (2%)

Query: 17  TIGHVDHGKTTLTAAITKYYSE----EKKEYGDIDSAPEEKLRGITIATAHVSYETDKRF 72
           TIGHVDHGKTTLTAAITK  ++    + K+Y +ID APEEK RGITI TAHV YET  R 
Sbjct: 7   TIGHVDHGKTTLTAAITKVLAKKGGAKFKKYDEIDKAPEEKARGITINTAHVEYETANRH 66

Query: 73  YSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMN 132
           Y+H+DCPGHADY+KNMITGA Q DGAILV +A DGP PQTREH+LLARQ+G+  IVV++N
Sbjct: 67  YAHVDCPGHADYIKNMITGAAQMDGAILVVSATDGPMPQTREHLLLARQVGVPYIVVFLN 126

Query: 133 KVDAVDDDELLDISEYEIRDLLKEHKY-SDDTPIIRGSALCALQGTNKELGEDSIHALMK 191
           K D VDD+ELL++ E E+R+LL ++ +  D+TPI+RGSAL AL+G +       I  L+ 
Sbjct: 127 KADMVDDEELLELVEMEVRELLSKYGFDGDNTPIVRGSALKALEGDDPNKWVKKILELLD 186

Query: 192 AVDTHIPTP 200
           A+D++IPTP
Sbjct: 187 ALDSYIPTP 195


>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 =  221 bits (566), Expect = 2e-58
 Identities = 89/191 (46%), Positives = 122/191 (63%), Gaps = 17/191 (8%)

Query: 15  LSTIGHVDHGKTTLTAAITKY-----YSEEKKEYGDIDSAPEEKLRGITIATAHVSYETD 69
           +  IGHVDHGKTTLT A+           E K+ G++D   EE+ RGITI  A VS+ET 
Sbjct: 6   IGIIGHVDHGKTTLTDALLYVTGAIDKRGEVKQEGELDRLKEERERGITIKIAAVSFETK 65

Query: 70  KRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVV 129
           KR  + ID PGH D+ K MI GA QADGAILV  A +G  PQTREH+LLA+Q+G+  I+V
Sbjct: 66  KRHINIIDTPGHVDFTKEMIRGAAQADGAILVVDAVEGVMPQTREHLLLAKQLGV-PIIV 124

Query: 130 YMNKVDAVDDDELLDISEYEIRDLLKEHKYS-DDTPIIRGSALCALQGTNKELGEDSIHA 188
           ++NK+D VDD EL ++ E   R+LL+++ +  +  P+I GS   AL G         I  
Sbjct: 125 FINKMDRVDDAELDEVVEEISRELLEKYGFGGETIPVIPGS---ALTGEG-------IDT 174

Query: 189 LMKAVDTHIPT 199
           L++A+D ++P+
Sbjct: 175 LLEALDLYLPS 185


>gnl|CDD|34853 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
           [Translation, ribosomal structure and biogenesis].
          Length = 428

 Score =  217 bits (555), Expect = 4e-57
 Identities = 147/435 (33%), Positives = 208/435 (47%), Gaps = 63/435 (14%)

Query: 10  KESLGLSTIGHVDHGKTTLT-----------AAITKYYSEEKKEYGD--------IDSAP 50
           K  L L  IGHVD GK+TL                +   +E KE G         +D   
Sbjct: 5   KPHLNLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVLDKTK 64

Query: 51  EEKLRGITIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDG--- 107
           EE+ RG+TI  AH  +ETDK  ++ ID PGH D+VKNMITGA+QAD A+LV  A DG   
Sbjct: 65  EERERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARDGEFE 124

Query: 108 ----PKPQTREHILLARQIGISSIVVYMNKVDAVD-DDELLDISEYEIRDLLKEHKY-SD 161
                  QTREH  LAR +GI  ++V +NK+D V  D+E  +    E+  LLK   Y   
Sbjct: 125 AGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLLKMVGYNPK 184

Query: 162 DTPIIRGSALCALQGTN-KELGEDS----IHALMKAVDTHIPTPQRSLDAPFLMHIEGSC 216
           D P I  S     +G N  +  E+        L++A+D  +  P+R LD P  + I+   
Sbjct: 185 DVPFIPIS---GFKGDNLTKKSENMPWYKGPTLLEALDQ-LEPPERPLDKPLRLPIQDVY 240

Query: 217 GIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLL 276
            I G GTV  G ++ G IK G  V      G   +VK   +EM  +++ +A  GDNVG  
Sbjct: 241 SISGIGTVPVGRVESGVIKPGQKV-TFMPAGVVGEVK--SIEMHHEEISQAEPGDNVGFN 297

Query: 277 LRGVNRADVPRGRVVCAPGSIQEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADV 336
           +RGV + D+ RG V+    +    S    +  I+    G  T+G    Y P     TA V
Sbjct: 298 VRGVEKNDIRRGDVIGHSDNPPTVSPEFTAQIIVLWHPGIITSG----YTPVLHAHTAQV 353

Query: 337 TGRII-----LSPGS--------QAVMPGDRVDLEVELIYPIAMEPNQ------TFSMRE 377
             RI      L P +        Q +  GD   +++E   P+ +E          F++R+
Sbjct: 354 ACRIAELLSKLDPRTGKKLEENPQFLKRGDAAIVKIEPEKPLCLEKVSEIPQLGRFALRD 413

Query: 378 GGKTVGAGLILEIIE 392
            G+T+ AG +LE+ +
Sbjct: 414 MGQTIAAGKVLEVKK 428


>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 =  162 bits (413), Expect = 1e-40
 Identities = 70/199 (35%), Positives = 104/199 (52%), Gaps = 26/199 (13%)

Query: 16  STIGHVDHGKTTLTAAITKYYSEEKK----EYGDIDSAPEEKLRGITIATAHVSYETDKR 71
              GHVDHGKTTLT  +     + ++    E   +D   EE+ RGITI +   ++E   R
Sbjct: 3   GIAGHVDHGKTTLTERLLYVTGDIERDGTVEETFLDVLKEERERGITIKSGVATFEWPDR 62

Query: 72  FYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYM 131
             + ID PGH D+   +I G + +DGAILV  A +G +PQTREH+ +AR+ G+  I+V +
Sbjct: 63  RVNFIDTPGHEDFSSEVIRGLSVSDGAILVVDANEGVQPQTREHLRIAREGGL-PIIVAI 121

Query: 132 NKVDAVDDDELLDISEYEIRDLLKE----------HKYSDDTPIIRGSALCALQGTNKEL 181
           NK+D V  +E L+    EI++LL             +     PI+ GSAL          
Sbjct: 122 NKIDRV-GEEDLEEVLREIKELLGLIGFISTKEEGTRNGLLVPIVPGSALTG-------- 172

Query: 182 GEDSIHALMKAVDTHIPTP 200
               +  L++A+  H+P P
Sbjct: 173 --IGVEELLEAIVEHLPPP 189


>gnl|CDD|33087 COG3276, SelB, Selenocysteine-specific translation elongation
           factor [Translation, ribosomal structure and
           biogenesis].
          Length = 447

 Score =  155 bits (394), Expect = 2e-38
 Identities = 95/326 (29%), Positives = 157/326 (48%), Gaps = 31/326 (9%)

Query: 17  TIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSHI 76
           T GH+DHGKTTL  A+T          G  D  PEEK RGITI       + +      I
Sbjct: 5   TAGHIDHGKTTLLKALT---------GGVTDRLPEEKKRGITIDLGFYYRKLEDGVMGFI 55

Query: 77  DCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDA 136
           D PGH D++ N++ G    D A+LV AA++G   QT EH+L+   +GI + ++ + K D 
Sbjct: 56  DVPGHPDFISNLLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGIKNGIIVLTKADR 115

Query: 137 VDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALMKAVDTH 196
           VD+  +    E +I+ +L +   + +  I + SA         + G   I  L   +   
Sbjct: 116 VDEARI----EQKIKQILADLSLA-NAKIFKTSA---------KTGRG-IEELKNELIDL 160

Query: 197 IPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTD 256
           +   +R    PF + I+ +  ++G GTVVTG +  G +K G  + +  +  K+++V+   
Sbjct: 161 LEEIERDEQKPFRIAIDRAFTVKGVGTVVTGTVLSGEVKVGDKLYLSPI-NKEVRVR--S 217

Query: 257 VEMFRKKLDEAIAGDNVGLLLRGVNRADVPRGRVVCAPGSIQEYSRFRASVYILTASEGG 316
           ++     ++EA AG  VGL L+GV + ++ RG  +  P  ++  +R    + I    +  
Sbjct: 218 IQAHDVDVEEAKAGQRVGLALKGVEKEEIERGDWLLKPEPLEVTTRLIVELEIDPLFK-- 275

Query: 317 RTTGFMDNYRPQFFMDTADVTGRIIL 342
           +T            +    VTGRI+ 
Sbjct: 276 KTLKQGQPV--HIHVGLRSVTGRIVP 299


>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 =  149 bits (379), Expect = 1e-36
 Identities = 73/194 (37%), Positives = 95/194 (48%), Gaps = 39/194 (20%)

Query: 18  IGHVDHGKTTLTA------------AITKYYSEEKKEYGD--------IDSAPEEKLRGI 57
           IGHVD GK+T T              I KY  +E KE G         +D+  EE+ RG+
Sbjct: 5   IGHVDAGKSTTTGHLLYLLGGVDKRTIEKY-EKEAKEMGKGSFKYAWVLDTLKEERERGV 63

Query: 58  TIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDG-------PKP 110
           TI      +ET+K  ++ +D PGH D+V NMITGA+QAD A+LV  A  G          
Sbjct: 64  TIDVGLAKFETEKYRFTILDAPGHRDFVPNMITGASQADVAVLVVDARKGEFEAGFEKGG 123

Query: 111 QTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEY-EIRD-----LLKEHKYSDDTP 164
           QTREH LLAR +G+  ++V +NK+D V  +       Y EI+      L K      D P
Sbjct: 124 QTREHALLARTLGVKQLIVAVNKMDDVTVN--WSEERYDEIKKELSPFLKKVGYNPKDVP 181

Query: 165 IIRGSALCALQGTN 178
            I  S    L G N
Sbjct: 182 FIPIS---GLTGDN 192


>gnl|CDD|35682 KOG0461, KOG0461, KOG0461, Selenocysteine-specific elongation
           factor [Translation, ribosomal structure and
           biogenesis].
          Length = 522

 Score =  147 bits (373), Expect = 4e-36
 Identities = 86/300 (28%), Positives = 160/300 (53%), Gaps = 30/300 (10%)

Query: 12  SLGLSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITI----------AT 61
           +L L  +GHVD GKTTL  A+++  S         D  P+   RGIT+          + 
Sbjct: 7   NLNLGILGHVDSGKTTLARALSELGSTAA-----FDKHPQSTERGITLDLGFSTMTVLSP 61

Query: 62  AHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQ 121
           A +  + ++  ++ +DCPGHA  ++ +I GA   D  ILV   + G + QT E +++  +
Sbjct: 62  ARLP-QGEQLQFTLVDCPGHASLIRTIIGGAQIIDLMILVIDVQKGKQTQTAECLIIG-E 119

Query: 122 IGISSIVVYMNKVDAVDDDEL---LDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTN 178
           +    +VV +NK+D + +++    ++ S  ++R  L+   +  ++PI+    + A  G  
Sbjct: 120 LLCKKLVVVINKIDVLPENQRASKIEKSAKKVRKTLESTGFDGNSPIV---EVSAADGYF 176

Query: 179 KELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGS 238
           KE     I  L +A+++ I  P+R  + PFLM ++    I+G+GTV+TG + RG ++  +
Sbjct: 177 KEEM---IQELKEALESRIFEPKRDEEGPFLMAVDHCFAIKGQGTVLTGTVLRGVLRLNT 233

Query: 239 DVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVNRADVPRGRVVCAPGSIQ 298
           ++E   +  K+ KVK   ++MF++++  A AGD  G  +   +   + RG +   PG+++
Sbjct: 234 EIEFPALNEKR-KVK--SLQMFKQRVTSAAAGDRAGFCVTQFDEKLLERG-ICGPPGTLK 289


>gnl|CDD|58073 cd03707, EFTU_III, Domain III of elongation factor (EF) Tu. Ef-Tu
           consists of three structural domains, designated I, II
           and III. Domain III adopts a beta barrel structure.
           Domain III is involved in binding to both charged tRNA
           and binding to elongation factor Ts (EF-Ts). EF-Ts is
           the guanine-nucleotide-exchange factor for EF-Tu.  EF-Tu
           and EF-G participate in the elongation phase during
           protein biosynthesis on the ribosome. Their functional
           cycles depend on GTP binding and its hydrolysis. The
           EF-Tu complexed with GTP and aminoacyl-tRNA delivers
           tRNA to the ribosome, whereas EF-G stimulates
           translocation, a process in which tRNA and mRNA
           movements occur in the ribosome. Crystallographic
           studies revealed structural similarities ("molecular
           mimicry") between tertiary structures of EF-G and the
           EF-Tu-aminoacyl-tRNA ternary complex. Domains III, IV,
           and V of EF-G mimic the tRNA structure in the EF-Tu
           ternary complex; domains III, IV and V can be related to
           the acceptor stem, anticodon helix and T stem of tRNA
           respectively..
          Length = 90

 Score =  146 bits (371), Expect = 8e-36
 Identities = 50/90 (55%), Positives = 66/90 (73%)

Query: 298 QEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRIILSPGSQAVMPGDRVDL 357
           + +++F A VY+LT  EGGR T F   YRPQF++ T DVTG I L  G++ VMPGD V +
Sbjct: 1   KPHTKFEAEVYVLTKEEGGRHTPFFSGYRPQFYIRTTDVTGSITLPEGTEMVMPGDNVKM 60

Query: 358 EVELIYPIAMEPNQTFSMREGGKTVGAGLI 387
            VELI+PIA+E    F++REGG+TVGAG+I
Sbjct: 61  TVELIHPIALEKGLRFAIREGGRTVGAGVI 90


>gnl|CDD|35679 KOG0458, KOG0458, KOG0458, Elongation factor 1 alpha [Translation,
           ribosomal structure and biogenesis].
          Length = 603

 Score =  146 bits (370), Expect = 1e-35
 Identities = 110/437 (25%), Positives = 184/437 (42%), Gaps = 62/437 (14%)

Query: 10  KESLGLSTIGHVDHGKTTL------------TAAITKYYSEEKKEYGD--------IDSA 49
           K+ L L  +GHVD GK+TL            + ++ K    E K  G         +D  
Sbjct: 175 KDHLNLVVLGHVDAGKSTLMGHLLYDLGEISSRSMHKL-ERESKNLGKSSFAYAWILDET 233

Query: 50  PEEKLRGITIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDG-- 107
            EE+ RG+T+      +E+  +  + ID PGH D++ NMI+GA+QAD A+LV  A  G  
Sbjct: 234 KEERERGVTMDVKTTWFESKSKIVTLIDAPGHKDFIPNMISGASQADVAVLVVDASTGEF 293

Query: 108 -----PKPQTREHILLARQIGISSIVVYMNKVDAVD-DDELLDISEYEIRDLLKEH-KYS 160
                P  QTREH LL R +GIS ++V +NK+D V    +  +  + ++   LKE   + 
Sbjct: 294 ESGFDPGGQTREHALLLRSLGISQLIVAINKMDLVSWSQDRFEEIKNKLSSFLKESCGFK 353

Query: 161 DD----TPI--IRGSALCALQGTNKELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEG 214
           +      PI  + G  L  ++  N+         L+  +D+    P+R +D P  + I  
Sbjct: 354 ESSVKFIPISGLSGENLIKIEQENELSQWYKGPTLLSQIDS-FKIPERPIDKPLRLTISD 412

Query: 215 SCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVG 274
              +   G  ++G I+ G I+ G  + I      +       +    +    A+AGDNV 
Sbjct: 413 IYPLPSSGVSISGKIESGYIQPGQKLYI---MTSREDATVKGLTSNDEPKTWAVAGDNVS 469

Query: 275 LLLRGVNRADVPRGRVVCA--PGSIQEYSRFRASVYILTAS-----------EGGRTTGF 321
           L L G+    V  G +  +     I + +RF A +     +             G  +  
Sbjct: 470 LKLPGILPNLVQVGDIADSGPQFPISKTTRFVARITTFDINLPITKGSPLILHFGSLSEP 529

Query: 322 MDNYRPQFFMDTADVTGRIILSPGSQAVMPGDRVDLEVELIYPIAMEPNQT------FSM 375
               +      + + +   I+    + +       +E+E   PI +E            +
Sbjct: 530 AVLKK---LTSSINKSTGEIVKKKPRCLTSNQSAIVELETERPICLETFAENRALGRVVL 586

Query: 376 REGGKTVGAGLILEIIE 392
           R+ G T+ AG + EII+
Sbjct: 587 RKSGSTIAAGKVTEIIQ 603


>gnl|CDD|34854 COG5257, GCD11, Translation initiation factor 2, gamma subunit
           (eIF-2gamma; GTPase) [Translation, ribosomal structure
           and biogenesis].
          Length = 415

 Score =  140 bits (355), Expect = 6e-34
 Identities = 114/412 (27%), Positives = 191/412 (46%), Gaps = 82/412 (19%)

Query: 12  SLGLSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITI----ATAHV--- 64
            + +  +GHVDHGKTTLT A++  ++         D   EE  RGITI    A A +   
Sbjct: 10  EVNIGMVGHVDHGKTTLTKALSGVWT---------DRHSEELKRGITIKLGYADAKIYKC 60

Query: 65  -------SYETDK------------RFYSHIDCPGHADYVKNMITGATQADGAILVCAA- 104
                   Y T+             R  S +D PGH   +  M++GA   DGA+LV AA 
Sbjct: 61  PECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGHETLMATMLSGAALMDGALLVIAAN 120

Query: 105 EDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYSDDTP 164
           E  P+PQTREH++    IGI +I++  NK+D V  +  L+ +  +I++ +K    +++ P
Sbjct: 121 EPCPQPQTREHLMALEIIGIKNIIIVQNKIDLVSRERALE-NYEQIKEFVKG-TVAENAP 178

Query: 165 IIRGSALCALQGTNKELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGI------ 218
           II  S   A    N       I AL++A++ +IPTP+R LD P  M++  S  +      
Sbjct: 179 IIPIS---AQHKAN-------IDALIEAIEKYIPTPERDLDKPPRMYVARSFDVNKPGTP 228

Query: 219 --EGRGTVVTGCIKRGRIKAGSDVEI-----IGMGGK----KLKVKCTDVEMFRKKLDEA 267
             E +G V+ G + +G ++ G ++EI     +  GGK     +  +   ++   + ++EA
Sbjct: 229 PEELKGGVIGGSLVQGVLRVGDEIEIRPGIVVEKGGKTVWEPITTEIVSLQAGGEDVEEA 288

Query: 268 IAGDNVGL---LLRGVNRADVPRGRVVCAPGSIQE-YSRFRASVYILTASEGGRTTGFMD 323
             G  VG+   L   + +AD   G+VV  PG++   ++  R   ++L    G +    ++
Sbjct: 289 RPGGLVGVGTKLDPTLTKADALVGQVVGKPGTLPPVWTSIRIEYHLLERVVGTKEELKVE 348

Query: 324 NYRPQ----FFMDTADVTGRIILSPGSQAVMPGDRVDLEVELIYPIAMEPNQ 371
             +        + TA   G +  +   +          EV+L  P+  E  +
Sbjct: 349 PIKTNEVLMLNVGTATTVGVVTSAKKDEI---------EVKLKRPVCAEIGE 391


>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 =  131 bits (331), Expect = 4e-31
 Identities = 67/156 (42%), Positives = 88/156 (56%), Gaps = 14/156 (8%)

Query: 17  TIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITI--ATAHVSYETDKRFYS 74
           T GH+DHGKTTL  A+T           + D  PEEK RGITI    A++   + KR   
Sbjct: 5   TAGHIDHGKTTLIKALTGI---------ETDRLPEEKKRGITIDLGFAYLDLPSGKRL-G 54

Query: 75  HIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKV 134
            ID PGH  ++KNM+ GA   D  +LV AA++G  PQTREH+ +   +GI   +V + K 
Sbjct: 55  FIDVPGHEKFIKNMLAGAGGIDLVLLVVAADEGIMPQTREHLEILELLGIKRGLVVLTKA 114

Query: 135 DAVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSA 170
           D VD+D L  + E EIR+LL     + D PI   SA
Sbjct: 115 DLVDEDWLELVEE-EIRELLAGTFLA-DAPIFPVSA 148


>gnl|CDD|31410 COG1217, TypA, Predicted membrane GTPase involved in stress
           response [Signal transduction mechanisms].
          Length = 603

 Score =  130 bits (329), Expect = 6e-31
 Identities = 91/290 (31%), Positives = 136/290 (46%), Gaps = 22/290 (7%)

Query: 18  IGHVDHGKTTLTAAITK----YYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFY 73
           I HVDHGKTTL  A+ K    +   E+     +DS   EK RGITI   + +   +    
Sbjct: 11  IAHVDHGKTTLVDALLKQSGTFREREEVAERVMDSNDLEKERGITILAKNTAVNYNGTRI 70

Query: 74  SHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNK 133
           + +D PGHAD+   +    +  DG +L+  A +GP PQTR  +  A  +G+  IVV +NK
Sbjct: 71  NIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALALGLKPIVV-INK 129

Query: 134 VD--AVDDDELLDISEYEIRDLLKEHKYSD---DTPIIRGSALCALQGTNKELGEDSIHA 188
           +D      DE++D    E+ DL  E   +D   D PI+  SA       + E   D +  
Sbjct: 130 IDRPDARPDEVVD----EVFDLFVELGATDEQLDFPIVYASARNGTASLDPEDEADDMAP 185

Query: 189 LMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGK 248
           L + +  H+P P+  LD P  M +         G +  G I RG +K    V +I   G 
Sbjct: 186 LFETILDHVPAPKGDLDEPLQMQVTQLDYNSYVGRIGIGRIFRGTVKPNQQVALIKSDGT 245

Query: 249 KLKVKCTDVEMF----RKKLDEAIAGDNVGLLLRGVNRADVPRGRVVCAP 294
               + T +  F    R +++EA AGD V   + G+   ++  G  +C P
Sbjct: 246 TENGRITKLLGFLGLERIEIEEAEAGDIVA--IAGLEDINI--GDTICDP 291


>gnl|CDD|35680 KOG0459, KOG0459, KOG0459, Polypeptide release factor 3
           [Translation, ribosomal structure and biogenesis].
          Length = 501

 Score =  129 bits (326), Expect = 1e-30
 Identities = 108/445 (24%), Positives = 189/445 (42%), Gaps = 63/445 (14%)

Query: 1   MVEKRYVRN-KESLGLSTIGHVDHGKTTLTAAITKY-----------YSEEKKEYGD--- 45
           +V K      KE +    IGHVD GK+T+   I              Y  E KE      
Sbjct: 67  VVVKSCGEYPKEHVNAVFIGHVDAGKSTIGGNILFLTGMVDKRTLEKYEREAKEKNRESW 126

Query: 46  -----IDSAPEEKLRGITIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAIL 100
                +D+  EE+ +G T+      +ET+ + ++ +D PGH  +V NMI GA+QAD A+L
Sbjct: 127 YLSWALDTNGEERDKGKTVEVGRAYFETENKRFTILDAPGHKSFVPNMIGGASQADLAVL 186

Query: 101 VCAAEDGP-------KPQTREHILLARQIGISSIVVYMNKVD---AVDDDELLDISEYEI 150
           V +A  G          QTREH +LA+  G+  ++V +NK+D       +E  +  + ++
Sbjct: 187 VISARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYEECKEKL 246

Query: 151 RDLLKEHKYSDDTPI--IRGSALCAL---QGTNKELGEDSIHALMKAVDTHIPTPQRSLD 205
           +  L++  ++       +  S L        T+           ++ +D  +P  +R L+
Sbjct: 247 QPFLRKLGFNPKPDKHFVPVSGLTGANVKDRTDSVCPWYKGPIFLEYLDE-LPHLERILN 305

Query: 206 APFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLD 265
            P    +      +  GTVV G ++ G IK G  + ++     K  V+   +     + D
Sbjct: 306 GPIRCPVANK--YKDMGTVVGGKVESGSIKKGQQLVVM---PNKTNVEVLGIYSDDVETD 360

Query: 266 EAIAGDNVGLLLRGVNRADVPRGRVVCAPGS-IQEYSRFRASVYILTASEGGR--TTGF- 321
               G+NV L L+G+   D+  G ++C+P +  +    F A + IL   E       G+ 
Sbjct: 361 RVAPGENVKLRLKGIEEEDISPGFILCSPNNPCKSGRTFDAQIVIL---EHKSIICAGYS 417

Query: 322 --------MDNYRPQFFMDTADVTGRIILSPGSQAVMPGDRVDLEVELIYPIAMEPNQT- 372
                   ++    +        TG        + V  G +    +E   PI +E  +  
Sbjct: 418 CVLHIHTAVEEVEIKLIHLIDKKTGEKSKKR-PRFVKQGQKCIARLETEGPICLETFKDY 476

Query: 373 -----FSMREGGKTVGAGLILEIIE 392
                F++R+ GKT+  G +L+++E
Sbjct: 477 PQMGRFTLRDEGKTIAIGKVLKVVE 501


>gnl|CDD|111981 pfam03143, GTP_EFTU_D3, Elongation factor Tu C-terminal domain.
           Elongation factor Tu consists of three structural
           domains, this is the third domain. This domain adopts a
           beta barrel structure. This the third domain is involved
           in binding to both charged tRNA and binding to EF-Ts
           pfam00889.
          Length = 97

 Score =  127 bits (322), Expect = 5e-30
 Identities = 47/97 (48%), Positives = 65/97 (67%), Gaps = 1/97 (1%)

Query: 296 SIQEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRIILSP-GSQAVMPGDR 354
            I+ +++F+A VYIL   EGG  T F D Y PQF+  T DVTG+I +   G + VMPGD 
Sbjct: 1   PIKPHTKFKAQVYILNHPEGGGYTPFFDGYTPQFYCRTTDVTGKIKVLEEGPEFVMPGDN 60

Query: 355 VDLEVELIYPIAMEPNQTFSMREGGKTVGAGLILEII 391
             + VELI PIA+EP   F++REGG+TV  G++ E++
Sbjct: 61  AIVTVELIKPIAVEPGGRFAIREGGRTVAVGVVTEVL 97


>gnl|CDD|34855 COG5258, GTPBP1, GTPase [General function prediction only].
          Length = 527

 Score =  122 bits (307), Expect = 2e-28
 Identities = 115/435 (26%), Positives = 180/435 (41%), Gaps = 75/435 (17%)

Query: 10  KESLGLSTIGHVDHGKTTLTAAITKYYSEEKK--EYGDIDSAPEEKLRGITIATAHVSY- 66
            E + +   GHVDHGK+TL   +     ++        +D    E  RG++   +   Y 
Sbjct: 115 PEHVLVGVAGHVDHGKSTLVGVLVTGRLDDGDGATRSYLDVQKHEVERGLSADISLRVYG 174

Query: 67  ----------------------ETDKRFYSHIDCPGHADYVKNMITG--ATQADGAILVC 102
                                 +   +  S +D  GH  +++  I G    + D  +LV 
Sbjct: 175 FDDGKVVRLKNPLDEAEKAAVVKRADKLVSFVDTVGHEPWLRTTIRGLLGQKVDYGLLVV 234

Query: 103 AAEDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLK------- 155
           AA+DG    T+EH+ +A  + +  IVV + K+D V DD    + E EI  LLK       
Sbjct: 235 AADDGVTKMTKEHLGIALAMELPVIVV-VTKIDMVPDDRFQGVVE-EISALLKRVGRIPL 292

Query: 156 EHKYSDD--------------TPIIRGSALCALQGTNKELGEDSIHALMKAVDTHIPTPQ 201
             K +DD               PI   S++     T + L       L+      +P  +
Sbjct: 293 IVKDTDDVVLAAKAMKAGRGVVPIFYTSSV-----TGEGL------DLLDEFFLLLP-KR 340

Query: 202 RSLDA--PFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIG--MGGKKLKVKCTDV 257
           R  D   PFLM+I+    + G GTVV+G +K G +  G  V ++G    GK  +V    +
Sbjct: 341 RRWDDEGPFLMYIDKIYSVTGVGTVVSGSVKSGILHVGDTV-LLGPFKDGKFREVVVKSI 399

Query: 258 EMFRKKLDEAIAGDNVGLLLRGVNRADVPRGRVVCAPGSIQEYSRFRASVYILTASEGGR 317
           EM   ++D A AG  +G+ L+GV + ++ RG V+ A    +    F A V +L       
Sbjct: 400 EMHHYRVDSAKAGSIIGIALKGVEKEELERGMVLSAGADPKAVREFDAEVLVLR-----H 454

Query: 318 TTGFMDNYRPQFFMDTADVTGRIILSPGSQAVMPGDRVDLEVELIY-PIAMEPNQTFSMR 376
            T     Y P F  +T               +MPGDR  + +   Y P  +E  Q F  R
Sbjct: 455 PTTIRAGYEPVFHYETIREAVYFE-EIDKGFLMPGDRGVVRMRFKYRPHHVEEGQKFVFR 513

Query: 377 EGGKTVGAGLILEII 391
           E G++ G G ++ + 
Sbjct: 514 E-GRSKGVGRVIRVD 527


>gnl|CDD|32720 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
           [Inorganic ion transport and metabolism].
          Length = 431

 Score =  120 bits (303), Expect = 6e-28
 Identities = 93/330 (28%), Positives = 148/330 (44%), Gaps = 42/330 (12%)

Query: 8   RNKESLGLSTIGHVDHGKTTLT---------------AAITKYYSEEKKEYGDIDSA--- 49
           ++K  L   T G VD GK+TL                A++ +    +  +   ID A   
Sbjct: 2   QHKSLLRFITCGSVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLV 61

Query: 50  ---PEEKLRGITIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAED 106
                E+ +GITI  A+  + T+KR +   D PGH  Y +NM TGA+ AD AIL+  A  
Sbjct: 62  DGLEAEREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTADLAILLVDARK 121

Query: 107 GPKPQTREHILLARQIGISSIVVYMNKVDAVD-DDELLDISEYEIRDLLKEHKYSDDTPI 165
           G   QTR H  +A  +GI  +VV +NK+D VD  +E+ +    +      +    D   I
Sbjct: 122 GVLEQTRRHSFIASLLGIRHVVVAVNKMDLVDYSEEVFEAIVADYLAFAAQLGLKDVRFI 181

Query: 166 IRGSALCALQGTNKELGEDSI-----HALMKAVDTHIPTPQRSLDAPFLMHIE--GSCGI 218
                + AL G N     +++       L++ ++T      RS    F   ++      +
Sbjct: 182 ----PISALLGDNVVSKSENMPWYKGPTLLEILETVEIADDRSAK-AFRFPVQYVNRPNL 236

Query: 219 EGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLR 278
           + RG    G I  G +K G +V ++   GK  +VK   +  F  +L +A AG+ V L+L 
Sbjct: 237 DFRG--YAGTIASGSVKVGDEVVVLP-SGKTSRVK--RIVTFDGELAQASAGEAVTLVLA 291

Query: 279 GVNRADVPRGRVVCAPGSIQEYSR-FRASV 307
             +  D+ RG ++ A  +    +  F A V
Sbjct: 292 --DEIDISRGDLIVAADAPPAVADAFDADV 319


>gnl|CDD|58088 cd03697, EFTU_II, EFTU_II: Elongation factor Tu domain II.
           Elongation factors Tu (EF-Tu) are three-domain GTPases
           with an essential function in the elongation phase of
           mRNA translation. The GTPase center of EF-Tu is in the
           N-terminal domain (domain I), also known as the
           catalytic or G-domain. The G-domain is composed of about
           200 amino acid residues, arranged into a predominantly
           parallel six-stranded beta-sheet core surrounded by
           seven a-helices. Non-catalytic domains II and III are
           beta-barrels of seven and six, respectively,
           antiparallel beta-strands that share an extended
           interface. Either non-catalytic domain is composed of
           about 100 amino acid residues.  EF-Tu proteins exist in
           two principal conformations: in a compact one,
           EF-Tu*GTP, with tight interfaces between all three
           domains and a high affinity for aminoacyl-tRNA, and in
           an open one, EF-Tu*GDP, with essentially no
           G-domain-domain II interactions and a low affinity for
           aminoacyl-tRNA. EF-Tu has approximately a 100-fold
           higher affinity for GDP than for GTP..
          Length = 87

 Score =  119 bits (300), Expect = 1e-27
 Identities = 56/88 (63%), Positives = 63/88 (71%), Gaps = 1/88 (1%)

Query: 208 FLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEA 267
           FLM IE    I GRGTVVTG I+RG IK G +VEI+G G + LK   T +EMFRK LDEA
Sbjct: 1   FLMPIEDVFSIPGRGTVVTGRIERGTIKVGDEVEIVGFG-ETLKTTVTGIEMFRKTLDEA 59

Query: 268 IAGDNVGLLLRGVNRADVPRGRVVCAPG 295
            AGDNVG+LLRGV R DV RG V+  PG
Sbjct: 60  EAGDNVGVLLRGVKREDVERGMVLAKPG 87


>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 =  112 bits (282), Expect = 2e-25
 Identities = 60/183 (32%), Positives = 84/183 (45%), Gaps = 26/183 (14%)

Query: 17  TIGHVDHGKTTL-------TAAI-----TKYYSEEKKEYGD-------IDSAPEEKLRGI 57
           T G VD GK+TL       + +I         S+     G+       +D    E+ +GI
Sbjct: 4   TCGSVDDGKSTLIGRLLYDSKSIFEDQLAALESKSCGTGGEPLDLALLVDGLQAEREQGI 63

Query: 58  TIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHIL 117
           TI  A+  + T KR +   D PGH  Y +NM+TGA+ AD AIL+  A  G   QTR H  
Sbjct: 64  TIDVAYRYFSTPKRKFIIADTPGHEQYTRNMVTGASTADLAILLVDARKGVLEQTRRHSY 123

Query: 118 LARQIGISSIVVYMNKVDAVDDDE--LLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQ 175
           +   +GI  +VV +NK+D VD  E    +I   +      +    D T I     + AL 
Sbjct: 124 ILSLLGIRHVVVAVNKMDLVDYSEEVFEEIVA-DYLAFAAKLGIEDITFI----PISALD 178

Query: 176 GTN 178
           G N
Sbjct: 179 GDN 181


>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 =  108 bits (273), Expect = 2e-24
 Identities = 67/222 (30%), Positives = 101/222 (45%), Gaps = 55/222 (24%)

Query: 15  LSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITI----ATAHV------ 64
           + TIGHV HGK+TL  A++  ++   KE         E  R ITI    A A +      
Sbjct: 3   IGTIGHVAHGKSTLVKALSGVWTVRFKE---------ELERNITIKLGYANAKIYKCPNC 53

Query: 65  -------------SYETD----------KRFYSHIDCPGHADYVKNMITGATQADGAILV 101
                        S E +           R  S +DCPGH   +  M++GA   DGA+L+
Sbjct: 54  GCPRPYCYRSKEDSPECECPGCGGETKLVRHVSFVDCPGHEILMATMLSGAAVMDGALLL 113

Query: 102 CAA-EDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYS 160
            AA E  P+PQT EH+     +G+  I++  NK+D V +++ L+  E +I+  +K     
Sbjct: 114 IAANEPCPQPQTSEHLAALEIMGLKHIIIVQNKIDLVKEEQALENYE-QIKKFVKGTIA- 171

Query: 161 DDTPIIRGSALCALQGTNKELGEDSIHALMKAVDTHIPTPQR 202
           ++ PII    + A    N       I  L++ +   IPTP R
Sbjct: 172 ENAPII---PISAQLKYN-------IDVLLEYIVKKIPTPPR 203


>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 = 98.4 bits (246), Expect = 3e-21
 Identities = 65/198 (32%), Positives = 96/198 (48%), Gaps = 26/198 (13%)

Query: 18  IGHVDHGKTTLTAAITKYYSE--EKKEYGD--IDSAPEEKLRGITIATAHVSYETDKRFY 73
           I HVDHGKTTL  A+ K      E +E  +  +DS   E+ RGITI   + +        
Sbjct: 8   IAHVDHGKTTLVDALLKQSGTFRENEEVEERVMDSNDLERERGITILAKNTAVTYKDTKI 67

Query: 74  SHIDCPGHADY------VKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSI 127
           + +D PGHAD+      V +M       DG +L+  A +GP PQTR  +  A ++G+  I
Sbjct: 68  NIVDTPGHADFGGEVERVLSM------VDGVLLLVDASEGPMPQTRFVLKKALELGLKPI 121

Query: 128 VVYMNKVDAVDD--DELLDISEYEIRDL---LKEHKYSDDTPIIRGSALCALQGTNKELG 182
           VV +NK+D  D   +E++D    E+ DL   L   +   D P++  SA       N E  
Sbjct: 122 VV-INKIDRPDARPEEVVD----EVFDLFIELGATEEQLDFPVLYASAKNGWASLNLEDP 176

Query: 183 EDSIHALMKAVDTHIPTP 200
            + +  L   +  H+P P
Sbjct: 177 SEDLEPLFDTIIEHVPAP 194


>gnl|CDD|35683 KOG0462, KOG0462, KOG0462, Elongation factor-type GTP-binding
           protein [Translation, ribosomal structure and
           biogenesis].
          Length = 650

 Score = 97.7 bits (243), Expect = 5e-21
 Identities = 77/264 (29%), Positives = 117/264 (44%), Gaps = 31/264 (11%)

Query: 7   VRNKESLGLSTIGHVDHGKTTLTAAI---TKYYSEEKKEYGDIDSAPEEKLRGITIA--T 61
           +RN      S I HVDHGK+TL   +   T        +   +D    E+ RGITI   T
Sbjct: 60  IRN-----FSIIAHVDHGKSTLADRLLELTGTIDNNIGQEQVLDKLQVERERGITIKAQT 114

Query: 62  AHVSYETDKRFYSH-IDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLAR 120
           A + Y+  + +  + ID PGH D+   +       DGA+LV  A  G + QT  +  LA 
Sbjct: 115 ASIFYKDGQSYLLNLIDTPGHVDFSGEVSRSLAACDGALLVVDASQGVQAQTVANFYLAF 174

Query: 121 QIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKE 180
           + G++ I V +NK+D    D   +  E ++ +L           +I  SA     G N E
Sbjct: 175 EAGLAIIPV-LNKIDLPSAD--PERVENQLFELFDI----PPAEVIYVSAK---TGLNVE 224

Query: 181 LGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDV 240
                   L++A+   +P P+   DAP  M I  S   E RG +    +  G ++ G  V
Sbjct: 225 -------ELLEAIIRRVPPPKGIRDAPLRMLIFDSEYDEYRGVIALVRVVDGVVRKGDKV 277

Query: 241 EIIGMGGKKLKVKCTDVEMFRKKL 264
           +     GK  +VK   V + R ++
Sbjct: 278 QSAA-TGKSYEVK--VVGVMRPEM 298


>gnl|CDD|58072 cd03706, mtEFTU_III, Domain III of mitochondrial EF-TU (mtEF-TU).
           mtEF-TU is highly conserved and is 55-60% identical to
           bacterial EF-TU. The overall structure is similar to
           that observed in the Escherichia coli and Thermus
           aquaticus EF-TU. However, compared with that observed in
           prokaryotic EF-TU the nucleotide-binding domain (domain
           I) of EF-TUmt is in a different orientation relative to
           the rest of the structure. Furthermore, domain III is
           followed by a short 11-amino acid extension that forms
           one helical turn. This extension seems to be specific to
           the mitochondrial factors and has not been observed in
           any of the prokaryotic factors..
          Length = 93

 Score = 94.9 bits (236), Expect = 4e-20
 Identities = 36/89 (40%), Positives = 55/89 (61%)

Query: 302 RFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRIILSPGSQAVMPGDRVDLEVEL 361
           +  A VYIL+ +EGGR   F+ N++PQ F  T D   RI L PG + VMPG+   + + L
Sbjct: 5   KVEAQVYILSKAEGGRHKPFVSNFQPQMFSLTWDCAARIDLPPGKEMVMPGEDTKVTLIL 64

Query: 362 IYPIAMEPNQTFSMREGGKTVGAGLILEI 390
             P+ +E  Q F++R+G +T+G GL+ + 
Sbjct: 65  RRPMVLEKGQRFTLRDGNRTIGTGLVTDT 93


>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 = 88.9 bits (221), Expect = 2e-18
 Identities = 40/137 (29%), Positives = 65/137 (47%), Gaps = 20/137 (14%)

Query: 19  GHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITI--------------ATAHV 64
           GHVD GKT+L  A++     E       D  P+ + RGIT+                  +
Sbjct: 7   GHVDSGKTSLAKALS-----EIASTAAFDKNPQSQERGITLDLGFSSFYVDKPKHLRELI 61

Query: 65  SYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGI 124
           +   +    + +DCPGHA  ++ +I GA   D  +LV  A  G + QT E +++   +  
Sbjct: 62  NPGEENLQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDATKGIQTQTAECLVIGEILCK 121

Query: 125 SSIVVYMNKVDAVDDDE 141
             IVV +NK+D + ++E
Sbjct: 122 KLIVV-LNKIDLIPEEE 137


>gnl|CDD|35275 KOG0052, KOG0052, KOG0052, Translation elongation factor EF-1
           alpha/Tu [Translation, ribosomal structure and
           biogenesis].
          Length = 391

 Score = 86.6 bits (214), Expect = 1e-17
 Identities = 94/326 (28%), Positives = 131/326 (40%), Gaps = 78/326 (23%)

Query: 10  KESLGLSTIGHVDHGKTTLTA----AITKYYSE----EKKEYG--------DIDSAPEEK 53
           K  + +  IGHVD GK+T T      I K   E    E  E G         +D    E+
Sbjct: 5   KIHINIVVIGHVDSGKSTTTGYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAER 64

Query: 54  LRGITIATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDG------ 107
            RGITI  A   +ET K + + ID PGH D++KNMITG +QAD A+L+ AA  G      
Sbjct: 65  ERGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGI 124

Query: 108 -PKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYSDDTPII 166
               QTREH LLA  +G+  ++V +NK+D+                   E  YS+     
Sbjct: 125 SKNGQTREHALLAFTLGVKQLIVGVNKMDST------------------EPPYSEAR--- 163

Query: 167 RGSALCALQGTNKELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVT 226
                       +   E S +  +K +  +        D   +  I    GI   G  VT
Sbjct: 164 ----------YEEIKKEVSSY--IKKIGYNPAAV--LQDVYKIGGIGVETGISEPGMDVT 209

Query: 227 GCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVNRADVP 286
                               G   +VK   V++  +   E + GDNVG  ++ V+  D+ 
Sbjct: 210 ----------------FAPSGVTTEVKS--VKVHHEAGSEDLPGDNVGFNVKNVSVKDID 251

Query: 287 RGRVVCAPGSIQEYSR--FRASVYIL 310
           RG VV    +        F A V IL
Sbjct: 252 RGNVVGDSKNDPPVEAAGFTAQVIIL 277


>gnl|CDD|36360 KOG1145, KOG1145, KOG1145, Mitochondrial translation initiation
           factor 2 (IF-2; GTPase) [Translation, ribosomal
           structure and biogenesis].
          Length = 683

 Score = 86.2 bits (213), Expect = 2e-17
 Identities = 83/261 (31%), Positives = 117/261 (44%), Gaps = 29/261 (11%)

Query: 18  IGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGIT--IATAHVSYETDKRFYSH 75
           +GHVDHGKTTL  A+ K  S    E G           GIT  I    V+  + K   + 
Sbjct: 159 MGHVDHGKTTLLDALRKS-SVAAGEAG-----------GITQHIGAFTVTLPSGKSI-TF 205

Query: 76  IDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVD 135
           +D PGHA +      GA   D  +LV AA+DG  PQT E I  A+   +  IVV +NK+D
Sbjct: 206 LDTPGHAAFSAMRARGANVTDIVVLVVAADDGVMPQTLEAIKHAKSANV-PIVVAINKID 264

Query: 136 AVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALMKAVDT 195
               +      E   + ++ E     D  +I  S   AL G N +L E++I  L + +D 
Sbjct: 265 KPGANPEKVKRELLSQGIVVE-DLGGDVQVIPIS---ALTGENLDLLEEAILLLAEVMDL 320

Query: 196 HIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCT 255
                +     P    +  S   +GRG V T  +KRG +K GS V + G    K++    
Sbjct: 321 -----KADPKGPAEGWVIESSVDKGRGPVATVIVKRGTLKKGS-VLVAGKSWCKVR---A 371

Query: 256 DVEMFRKKLDEAIAGDNVGLL 276
             +   K +DEA     V +L
Sbjct: 372 LFDHNGKPIDEATPSQPVEVL 392


>gnl|CDD|35687 KOG0466, KOG0466, KOG0466, Translation initiation factor 2, gamma
           subunit (eIF-2gamma; GTPase) [Translation, ribosomal
           structure and biogenesis].
          Length = 466

 Score = 84.6 bits (209), Expect = 4e-17
 Identities = 95/374 (25%), Positives = 163/374 (43%), Gaps = 81/374 (21%)

Query: 7   VRNKESLGLSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITI----ATA 62
           +  + ++ + TIGHV HGK+T+  AI+  ++   K          E  R ITI    A A
Sbjct: 33  ISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKN---------ELERNITIKLGYANA 83

Query: 63  HV---------------SYETDK------------------RFYSHIDCPGHADYVKNMI 89
            +               S+ + K                  R  S +DCPGH   +  M+
Sbjct: 84  KIYKCDDPKCPRPGCYRSFGSSKEDRPPCDRPGCEGKMKLVRHVSFVDCPGHDILMATML 143

Query: 90  TGATQADGAILVCAA-EDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEY 148
            GA   D A+L+ A  E  P+PQT EH+     + +  I++  NK+D + + + L+  E 
Sbjct: 144 NGAAVMDAALLLIAGNESCPQPQTSEHLAAVEIMKLKHIIILQNKIDLIKESQALEQHE- 202

Query: 149 EIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALMKAVDTHIPTPQRSLDAP- 207
           +I+  ++    ++  PII  SA         +L  + I  + + +   IP P R   +P 
Sbjct: 203 QIQKFIQ-GTVAEGAPIIPISA---------QLKYN-IDVVCEYIVKKIPVPVRDFTSPP 251

Query: 208 -------FLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEI---IGMGGKKLKVKCTD- 256
                  F ++  GS   + +G V  G I +G +K G ++EI   I    +   +KC   
Sbjct: 252 RLIVIRSFDVNKPGSEVDDLKGGVAGGSILKGVLKVGQEIEIRPGIVTKDENGNIKCRPI 311

Query: 257 ----VEMFRKK--LDEAIAGDNVGL---LLRGVNRADVPRGRVVCAPGSIQE-YSRFRAS 306
               V +F ++  L  A+ G  +G+   +   + RAD   G+V+ A G++ + ++    S
Sbjct: 312 FSRIVSLFAEQNDLQFAVPGGLIGVGTKMDPTLCRADRLVGQVLGAVGTLPDIFTELEIS 371

Query: 307 VYILTASEGGRTTG 320
            ++L    G RT G
Sbjct: 372 YFLLRRLLGVRTKG 385


>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 = 82.2 bits (204), Expect = 2e-16
 Identities = 57/166 (34%), Positives = 75/166 (45%), Gaps = 34/166 (20%)

Query: 18  IGHVDHGKTTLTAAITKYYSEEKKEYGDID--------SAPEEKLRGITIATAHVSYETD 69
           +GHVDHGKTTL   I K  +    E G I          A   K+ GIT           
Sbjct: 6   MGHVDHGKTTLLDKIRKT-NVAAGEAGGITQHIGAFEVPAEVLKIPGITF---------- 54

Query: 70  KRFYSHIDCPGHADYVKNMIT-GATQADGAILVCAAEDGPKPQTREHILLARQIGISSIV 128
                 ID PGH  +  NM   GA+  D AILV AA+DG  PQT E I LA+   +   +
Sbjct: 55  ------IDTPGHEAF-TNMRARGASLTDIAILVVAADDGVMPQTIEAIKLAKAANV-PFI 106

Query: 129 VYMNKVDAVDDDE---LLDISEYEIRDLLKEHKYSDDTPIIRGSAL 171
           V +NK+D  + +      ++SE     L  E ++  D  I+  SA 
Sbjct: 107 VALNKIDKPNANPERVKNELSEL---GLQGEDEWGGDVQIVPTSAK 149


>gnl|CDD|30878 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
           [Translation, ribosomal structure and biogenesis].
          Length = 509

 Score = 81.7 bits (202), Expect = 3e-16
 Identities = 75/243 (30%), Positives = 102/243 (41%), Gaps = 38/243 (15%)

Query: 19  GHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGIT--IATAHVSYETDK-RFYSH 75
           GHVDHGKTTL   I K            + A  E   GIT  I    V  +  K    + 
Sbjct: 12  GHVDHGKTTLLDKIRK-----------TNVAAGEAG-GITQHIGAYQVPLDVIKIPGITF 59

Query: 76  IDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVD 135
           ID PGH  +      GA+  D AILV AA+DG  PQT E I  A+  G+  IVV +NK+D
Sbjct: 60  IDTPGHEAFTAMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAAGV-PIVVAINKID 118

Query: 136 AVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALMKAVDT 195
             + +      E +   L+ E ++  D   +  S   A  G   +   + I  L      
Sbjct: 119 KPEANPDKVKQELQEYGLVPE-EWGGDVIFVPVS---AKTGEGIDELLELILLL------ 168

Query: 196 HIPTPQRSLDAPFLMHIEGSCGIE-----GRGTVVTGCIKRGRIKAGSDVEIIGMGGKKL 250
                   L A       G+  IE     G G V T  ++ G +K G   +II  GG+  
Sbjct: 169 ---AEVLELKANPEGPARGTV-IEVKLDKGLGPVATVIVQDGTLKKG---DIIVAGGEYG 221

Query: 251 KVK 253
           +V+
Sbjct: 222 RVR 224


>gnl|CDD|30828 COG0480, FusA, Translation elongation factors (GTPases)
           [Translation, ribosomal structure and biogenesis].
          Length = 697

 Score = 81.4 bits (201), Expect = 4e-16
 Identities = 39/126 (30%), Positives = 64/126 (50%), Gaps = 10/126 (7%)

Query: 18  IGHVDHGKTTLTAAITKYYSEEKKEYGDI-------DSAPEEKLRGITIATAHVSYET-D 69
           + H+D GKTTLT  I  +Y+    + G++       D   +E+ RGITI +A  +     
Sbjct: 16  VAHIDAGKTTLTERI-LFYTGIISKIGEVHDGAATMDWMEQEQERGITITSAATTLFWKG 74

Query: 70  KRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVV 129
               + ID PGH D+   +       DGA++V  A +G +PQT      A + G+   ++
Sbjct: 75  DYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVEGVEPQTETVWRQADKYGV-PRIL 133

Query: 130 YMNKVD 135
           ++NK+D
Sbjct: 134 FVNKMD 139


>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 = 76.5 bits (189), Expect = 1e-14
 Identities = 53/155 (34%), Positives = 84/155 (54%), Gaps = 22/155 (14%)

Query: 17  TIG---HVDHGKTTLTAAITKYYSEEKKEYGDI-------DSAPEEKLRGITIATAHVSY 66
            IG   HVD GKTTLT ++  Y S   ++ G +       D+   E+ RGITI +A  S+
Sbjct: 1   NIGILAHVDAGKTTLTESLL-YTSGAIRKLGSVDKGTTRTDTMELERQRGITIFSAVASF 59

Query: 67  ETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHIL--LARQIGI 124
           + +    + ID PGH D++  +    +  DGAILV +A +G + QTR  IL  L R++ I
Sbjct: 60  QWEDTKVNLIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTR--ILWRLLRKLNI 117

Query: 125 SSIVVYMNKVDA--VDDDELLDISEYEIRDLLKEH 157
            +I +++NK+D    D +++      EI++ L   
Sbjct: 118 PTI-IFVNKIDRAGADLEKVYQ----EIKEKLSSD 147


>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
          Length = 742

 Score = 76.4 bits (188), Expect = 1e-14
 Identities = 71/238 (29%), Positives = 111/238 (46%), Gaps = 25/238 (10%)

Query: 18  IGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSHID 77
           +GHVDHGKTTL   I K     +KE G I          I        Y+ + +    +D
Sbjct: 250 LGHVDHGKTTLLDKIRKT-QIAQKEAGGITQK-------IGAYEVEFEYKDENQKIVFLD 301

Query: 78  CPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDAV 137
            PGH  +      GA   D AIL+ AA+DG KPQT E I   +   +  I+V +NK+D  
Sbjct: 302 TPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANV-PIIVAINKIDKA 360

Query: 138 DDD-ELL--DISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALMKAVD 194
           + + E +   +++Y    L+ E K+  DTP+I    + A QGTN +   ++I  L +  D
Sbjct: 361 NANTERIKQQLAKYN---LIPE-KWGGDTPMI---PISASQGTNIDKLLETILLLAEIED 413

Query: 195 THIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKV 252
                 Q +       H++ +     +G V T  ++ G +  G D+ +IG    K++ 
Sbjct: 414 LKADPTQLAQGIILEAHLDKT-----KGPVATILVQNGTLHIG-DIIVIGTSYAKIRG 465


>gnl|CDD|30829 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
           outer membrane].
          Length = 603

 Score = 75.2 bits (185), Expect = 3e-14
 Identities = 82/302 (27%), Positives = 134/302 (44%), Gaps = 42/302 (13%)

Query: 1   MVEKRYVRNKESLGLSTIGHVDHGKTTLTAAI---TKYYSEEKKEYGDIDSAPEEKLRGI 57
              ++ +RN      S I H+DHGK+TL   +   T   SE +     +DS   E+ RGI
Sbjct: 3   FTPQKNIRN-----FSIIAHIDHGKSTLADRLLELTGGLSEREMRAQVLDSMDIERERGI 57

Query: 58  TI----ATAHVSYETDKRFYSH-IDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQT 112
           TI       +   +  + +  + ID PGH D+   +       +GA+LV  A  G + QT
Sbjct: 58  TIKAQAVRLNYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQT 117

Query: 113 REHILLARQIGISSIVVYMNKVD--AVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSA 170
             ++ LA +  +  I+  +NK+D  A D + +      EI D++      D +  +  SA
Sbjct: 118 LANVYLALENNL-EIIPVLNKIDLPAADPERVKQ----EIEDIIG----IDASDAVLVSA 168

Query: 171 LCALQGTNKELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIK 230
              +           I  +++A+   IP P+   DAP    I  S      G VV   I 
Sbjct: 169 KTGI----------GIEDVLEAIVEKIPPPKGDPDAPLKALIFDSWYDNYLGVVVLVRIF 218

Query: 231 RGRIKAGSDVEIIGMGGKKLKVKCTDVEMF---RKKLDEAIAGDNVGLLLRGV-NRADVP 286
            G +K G  + ++   GK+ +V   +V +F     K+DE  AG+ VG ++ G+ +  D  
Sbjct: 219 DGTLKKGDKIRMMST-GKEYEV--DEVGIFTPKMVKVDELKAGE-VGYIIAGIKDVRDAR 274

Query: 287 RG 288
            G
Sbjct: 275 VG 276


>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 = 70.7 bits (174), Expect = 7e-13
 Identities = 40/130 (30%), Positives = 61/130 (46%), Gaps = 9/130 (6%)

Query: 18  IGHVDHGKTTLTAAITKYYSEEKKEYGDI-------DSAPEEKLRGITIATAHVSYETDK 70
           +GH   GKTTL  A+  Y +      G +       D  PEE  R ++I+T+    E   
Sbjct: 5   VGHSGSGKTTLAEALL-YATGAIDRLGSVEDGTTVSDYDPEEIKRKMSISTSVAPLEWKG 63

Query: 71  RFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVY 130
              + ID PG+AD+V         AD A++V +A+ G +  T +    A + GI  I+  
Sbjct: 64  HKINLIDTPGYADFVGETRAALRAADAALVVVSAQSGVEVGTEKLWEFADEAGIPRIIF- 122

Query: 131 MNKVDAVDDD 140
           +NK+D    D
Sbjct: 123 INKMDRERAD 132


>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 = 70.3 bits (173), Expect = 8e-13
 Identities = 42/136 (30%), Positives = 66/136 (48%), Gaps = 19/136 (13%)

Query: 16  STIGHVDHGKTTLT-AAITKYYSEEKKEYGDI---DSAPEEKLRGITIATAHVS--YETD 69
             I HVDHGKTTL+ + +       +K  G     DS  +E+ RGIT+ ++ +S  +E +
Sbjct: 4   CIIAHVDHGKTTLSDSLLASAGIISEKLAGKARYMDSREDEQERGITMKSSAISLYFEYE 63

Query: 70  KRFYSH--------IDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQ 121
           +   +         ID PGH D+   +       DGA++V  A +G   QT    +L RQ
Sbjct: 64  EEDKADGNEYLINLIDSPGHVDFSSEVTAALRLCDGALVVVDAVEGVCVQT--ETVL-RQ 120

Query: 122 IGISSI--VVYMNKVD 135
                +  V+ +NK+D
Sbjct: 121 ALKERVKPVLVINKID 136


>gnl|CDD|58087 cd03696, selB_II, selB_II: this subfamily represents the domain of
           elongation factor SelB, homologous to domain II of
           EF-Tu. SelB may function by replacing EF-Tu. In
           prokaryotes, the incorporation of selenocysteine as the
           21st amino acid, encoded by TGA, requires several
           elements: SelC is the tRNA itself, SelD acts as a donor
           of reduced selenium, SelA modifies a serine residue on
           SelC into selenocysteine, and SelB is a
           selenocysteine-specific translation elongation factor.
           3' or 5' non-coding elements of mRNA have been found as
           probable structures for directing selenocysteine
           incorporation..
          Length = 83

 Score = 69.0 bits (169), Expect = 2e-12
 Identities = 32/86 (37%), Positives = 54/86 (62%), Gaps = 3/86 (3%)

Query: 208 FLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEA 267
           F + I+    ++G+GTVVTG +  G +K G  VEI+ +G ++ +V+   +++  K ++EA
Sbjct: 1   FRLPIDRVFTVKGQGTVVTGTVLSGSVKVGDKVEILPLG-EETRVR--SIQVHGKDVEEA 57

Query: 268 IAGDNVGLLLRGVNRADVPRGRVVCA 293
            AGD V L L GV+  D+ RG V+ +
Sbjct: 58  KAGDRVALNLTGVDAKDLERGDVLSS 83


>gnl|CDD|35686 KOG0465, KOG0465, KOG0465, Mitochondrial elongation factor
           [Translation, ribosomal structure and biogenesis].
          Length = 721

 Score = 66.8 bits (163), Expect = 9e-12
 Identities = 41/127 (32%), Positives = 62/127 (48%), Gaps = 13/127 (10%)

Query: 18  IGHVDHGKTTLTAAITKYYSEEKKEYGDI-------DSAPEEKLRGITIATAHVSYETDK 70
             H+D GKTTLT  +  YY+   K  G++       DS   E+ RGITI +A   +    
Sbjct: 45  SAHIDAGKTTLTERML-YYTGRIKHIGEVRGGGATMDSMELERQRGITIQSAATYFTWRD 103

Query: 71  RFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSI--V 128
              + ID PGH D+   +       DGA+LV  A  G + QT     + RQ+   ++  +
Sbjct: 104 YRINIIDTPGHVDFTFEVERALRVLDGAVLVLDAVAGVESQT---ETVWRQMKRYNVPRI 160

Query: 129 VYMNKVD 135
            ++NK+D
Sbjct: 161 CFINKMD 167


>gnl|CDD|33865 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
           ribosomal structure and biogenesis].
          Length = 528

 Score = 66.8 bits (163), Expect = 1e-11
 Identities = 48/170 (28%), Positives = 74/170 (43%), Gaps = 19/170 (11%)

Query: 18  IGHVDHGKTTLTAAITKYYSEEKKEYGDI-----------DSAPEEKLRGITIATAHVSY 66
           I H D GKTTLT  +   +    +E G +           D    EK RGI++ ++ + +
Sbjct: 18  ISHPDAGKTTLTEKLL-LFGGAIQEAGTVKGRKSGKHAKSDWMEIEKQRGISVTSSVMQF 76

Query: 67  ETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISS 126
           +      + +D PGH D+ ++     T  D A++V  A  G +PQT +   + R   I  
Sbjct: 77  DYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIEPQTLKLFEVCRLRDI-P 135

Query: 127 IVVYMNKVDAVDDD--ELLDISEYEIRDLLKEHKYSDDTPIIRGSALCAL 174
           I  ++NK+D    D  ELLD    EI + L         PI  G     +
Sbjct: 136 IFTFINKLDREGRDPLELLD----EIEEELGIQCAPITWPIGMGKDFKGV 181


>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 = 64.6 bits (158), Expect = 4e-11
 Identities = 29/71 (40%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 222 GTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVN 281
           GTV TG ++ G +K G  V I   G  K K + T +EMF   L EA+AG N G++L G+ 
Sbjct: 1   GTVATGRVESGTLKKGDKVVIGPNGTGK-KGRVTSLEMFHGDLREAVAGANAGIILAGIG 59

Query: 282 RADVPRGRVVC 292
             D+ RG  + 
Sbjct: 60  LKDIKRGDTLT 70


>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 = 63.8 bits (156), Expect = 8e-11
 Identities = 36/131 (27%), Positives = 59/131 (45%), Gaps = 15/131 (11%)

Query: 18  IGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPE--------EKLRGITIATAHVSY-ET 68
            GH+ HGKT+L   +    + +    G     P         E+ RGI+I ++ +S    
Sbjct: 6   AGHLHHGKTSLLDMLI-EQTHDLTPSGKDGWKPLRYTDIRKDEQERGISIKSSPISLVLP 64

Query: 69  DKRFYSH----IDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGI 124
           D +  S+    ID PGH +++  +      +DG +LV    +G    T   I  A   G+
Sbjct: 65  DSKGKSYLFNIIDTPGHVNFMDEVAAALRLSDGVVLVVDVVEGVTSNTERLIRHAILEGL 124

Query: 125 SSIVVYMNKVD 135
             IV+ +NK+D
Sbjct: 125 -PIVLVINKID 134


>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 = 63.9 bits (155), Expect = 8e-11
 Identities = 38/137 (27%), Positives = 67/137 (48%), Gaps = 10/137 (7%)

Query: 3   EKRYVRNKESLGLSTIGHVDHGKTTLT----AAITKYYSEEKKEYGDIDSAPEEKLRGIT 58
               +RN     +  + HVDHGKT+L     A+     S    +   +D+  +E+ RGIT
Sbjct: 5   GSEGIRN-----ICLVAHVDHGKTSLADSLVASNGVISSRLAGKIRFLDTREDEQTRGIT 59

Query: 59  IATAHVSYETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILL 118
           + ++ +S        + ID PGH D+   + + +  +DGA+++    +G   QT   +  
Sbjct: 60  MKSSAISLLHKDYLINLIDSPGHVDFSSEVSSASRLSDGALVLVDVVEGVCSQTYAVLRQ 119

Query: 119 ARQIGISSIVVYMNKVD 135
           A   G+  I+V +NK+D
Sbjct: 120 AWIEGLKPILV-INKID 135


>gnl|CDD|58084 cd03693, EF1_alpha_II, EF1_alpha_II: this family represents the
           domain II of elongation factor 1-alpha (EF-1a) that is
           found in archaea and all eukaryotic lineages. EF-1A is
           very abundant in the cytosol, where it is involved in
           the GTP-dependent binding of aminoacyl-tRNAs to the A
           site of the ribosomes in the second step of translation
           from mRNAs to proteins. Both domain II of EF1A and
           domain IV of IF2/eIF5B have been implicated in
           recognition of the 3'-ends of tRNA. More than 61% of
           eukaryotic elongation factor 1A (eEF-1A) in cells is
           estimated to be associated with actin cytoskeleton. The
           binding of eEF1A to actin is a noncanonical function
           that may link two distinct cellular processes,
           cytoskeleton organization and gene expression..
          Length = 91

 Score = 62.8 bits (153), Expect = 2e-10
 Identities = 32/91 (35%), Positives = 46/91 (50%), Gaps = 3/91 (3%)

Query: 205 DAPFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKL 264
           D P  + I+    I G GTV  G ++ G +K G  V      G   +VK   VEM  + L
Sbjct: 2   DKPLRLPIQDVYKIGGIGTVPVGRVETGVLKPGMVV-TFAPAGVTGEVK--SVEMHHEPL 58

Query: 265 DEAIAGDNVGLLLRGVNRADVPRGRVVCAPG 295
           +EA+ GDNVG  ++ V++ D+ RG V     
Sbjct: 59  EEALPGDNVGFNVKNVSKKDIKRGDVAGDSK 89


>gnl|CDD|35690 KOG0469, KOG0469, KOG0469, Elongation factor 2 [Translation,
           ribosomal structure and biogenesis].
          Length = 842

 Score = 61.5 bits (149), Expect = 3e-10
 Identities = 50/157 (31%), Positives = 73/157 (46%), Gaps = 30/157 (19%)

Query: 1   MVEKRYVRNKESLGLSTIGHVDHGKTTLT-AAITKYYSEEKKEYGD---IDSAPEEKLRG 56
           M +K+ +RN     +S I HVDHGK+TLT + + K       + G+    D+  +E+ RG
Sbjct: 13  MDKKKNIRN-----MSVIAHVDHGKSTLTDSLVQKAGIISAAKAGETRFTDTRKDEQERG 67

Query: 57  ITIATAHVSY-----ETDKRFYSH-----------IDCPGHADYVKNMITGATQADGAIL 100
           ITI +  +S      + D +F              ID PGH D+   +       DGA++
Sbjct: 68  ITIKSTAISLFFEMSDDDLKFIKQEGDGNGFLINLIDSPGHVDFSSEVTAALRVTDGALV 127

Query: 101 VCAAEDGPKPQTREHILLARQIGISSI--VVYMNKVD 135
           V     G   QT E +L  RQ     I  V+ MNK+D
Sbjct: 128 VVDCVSGVCVQT-ETVL--RQAIAERIKPVLVMNKMD 161


>gnl|CDD|58069 cd01513, Translation_factor_III, Domain III of Elongation factor
           (EF) Tu (EF-TU) and EF-G.  Elongation factors (EF) EF-Tu
           and EF-G participate in the elongation phase during
           protein biosynthesis on the ribosome. Their functional
           cycles depend on GTP binding and its hydrolysis. The
           EF-Tu complexed with GTP and aminoacyl-tRNA delivers
           tRNA to the ribosome, whereas EF-G stimulates
           translocation, a process in which tRNA and mRNA
           movements occur in the ribosome. Experimental data
           showed that: (1) intrinsic GTPase activity of EF-G is
           influenced by excision of its domain III; (2) that EF-G
           lacking domain III has a 1,000-fold decreased GTPase
           activity on the ribosome and, a slightly decreased
           affinity for GTP; and (3) EF-G lacking domain III does
           not stimulate translocation, despite the physical
           presence of domain IV which is also very important for
           translocation. These findings indicate an essential
           contribution of domain III to activation of GTP
           hydrolysis. Domains III and V of EF-G have the same fold
           (although they are not completely superimposable), the
           double split beta-alpha-beta fold. This fold is observed
           in a large number of ribonucleotide binding proteins and
           is also referred to as the ribonucleoprotein (RNP) or
           RNA recognition (RRM) motif.  This domain III is found
           in several elongation factors, as well as in peptide
           chain release factors and in GT-1 family of GTPase
           (GTPBP1)..
          Length = 102

 Score = 58.8 bits (142), Expect = 2e-09
 Identities = 34/107 (31%), Positives = 49/107 (45%), Gaps = 22/107 (20%)

Query: 298 QEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRIILSP-----------GS 346
           Q   +F A +Y+L   E          Y+P   + TA V GRI                 
Sbjct: 1   QAVDKFVAEIYVLDHPEP-----LSPGYKPVLNVGTAHVPGRIAKLLSKVDGKTEEKKPP 55

Query: 347 QAVMPGDRVDLEVELIYPIAME------PNQTFSMREGGKTVGAGLI 387
           + +  G+R  +EVEL  P+A+E          F++R+GG+TVGAGLI
Sbjct: 56  EFLKSGERGIVEVELQKPVALETFSENQEGGRFALRDGGRTVGAGLI 102


>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 = 57.5 bits (140), Expect = 6e-09
 Identities = 42/135 (31%), Positives = 66/135 (48%), Gaps = 23/135 (17%)

Query: 16  STIGHVDHGKTTL-------TAAITKYYSEEKKEYGDIDSAPEEKLRGITI----ATAHV 64
           S I H+DHGK+TL       T  ++K   E K++   +DS   E+ RGITI       + 
Sbjct: 4   SIIAHIDHGKSTLADRLLELTGTVSK--REMKEQV--LDSMDLERERGITIKAQTVRLNY 59

Query: 65  SYETDKRFYSH-IDCPGHADY---VKNMITGATQADGAILVCAAEDGPKPQTREHILLAR 120
             +  + +  + ID PGH D+   V   +      +GA+L+  A  G + QT  +  LA 
Sbjct: 60  KAKDGQEYLLNLIDTPGHVDFSYEVSRSLAA---CEGALLLVDATQGVEAQTLANFYLAL 116

Query: 121 QIGISSIVVYMNKVD 135
           +  +  I V +NK+D
Sbjct: 117 ENNLEIIPV-INKID 130


>gnl|CDD|35685 KOG0464, KOG0464, KOG0464, Elongation factor G [Translation,
           ribosomal structure and biogenesis].
          Length = 753

 Score = 56.7 bits (136), Expect = 1e-08
 Identities = 41/130 (31%), Positives = 60/130 (46%), Gaps = 13/130 (10%)

Query: 15  LSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSA-------PEEKLRGITIATAHVSYE 67
           +  I H+D GKTT T  I  Y +      GD+D           E+ RGITI +A V+++
Sbjct: 40  IGIIAHIDAGKTTTTERIL-YLAGAIHSAGDVDDGDTVTDFLAIERERGITIQSAAVNFD 98

Query: 68  TDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSI 127
                 + ID PGH D+   +       DGA+ V  A  G + QT   + + RQ     I
Sbjct: 99  WKGHRINLIDTPGHVDFRLEVERCLRVLDGAVAVFDASAGVEAQT---LTVWRQADKFKI 155

Query: 128 --VVYMNKVD 135
               ++NK+D
Sbjct: 156 PAHCFINKMD 165


>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 = 55.3 bits (133), Expect = 2e-08
 Identities = 27/86 (31%), Positives = 45/86 (52%), Gaps = 3/86 (3%)

Query: 208 FLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEA 267
               +      +GRGTV TG ++ G +K G  V +   GG   K K   ++ F+ ++DEA
Sbjct: 1   LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGV-KGKVKSLKRFKGEVDEA 59

Query: 268 IAGDNVGLLLRGVNRADVPRGRVVCA 293
           +AGD VG++L+  +  D+  G  +  
Sbjct: 60  VAGDIVGIVLKDKD--DIKIGDTLTD 83


>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 = 55.6 bits (135), Expect = 2e-08
 Identities = 43/130 (33%), Positives = 63/130 (48%), Gaps = 19/130 (14%)

Query: 18  IGHVDHGKTTLTAAITKYYSEEKKEYGDI-------DSAPEEKLRGITIATAHVSYE-TD 69
           I H+D GKTT T  I  YY+    + G++       D   +E+ RGITI +A  +    D
Sbjct: 5   IAHIDAGKTTTTERIL-YYTGRIHKIGEVHGGGATMDFMEQERERGITIQSAATTCFWKD 63

Query: 70  KRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQT----REHILLARQIGIS 125
            R  + ID PGH D+   +       DGA+ V  A  G +PQT    R+    A +  + 
Sbjct: 64  HRI-NIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVEPQTETVWRQ----ADRYNVP 118

Query: 126 SIVVYMNKVD 135
            I  ++NK+D
Sbjct: 119 RI-AFVNKMD 127


>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 = 53.7 bits (130), Expect = 8e-08
 Identities = 47/151 (31%), Positives = 73/151 (48%), Gaps = 19/151 (12%)

Query: 18  IGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPE-----------EKLRGITIATAHVSY 66
           I H D GKTTLT  +   +    +E G + +              EK RGI++ ++ + +
Sbjct: 8   ISHPDAGKTTLTEKLL-LFGGAIREAGAVKARKSRKHATSDWMEIEKQRGISVTSSVMQF 66

Query: 67  ETDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISS 126
           E      + +D PGH D+ ++     T  D A++V  A  G +PQTR+   + R  GI  
Sbjct: 67  EYRDCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLRGI-P 125

Query: 127 IVVYMNKVD--AVDDDELLDISEYEIRDLLK 155
           I+ ++NK+D    D  ELLD    EI + L 
Sbjct: 126 IITFINKLDREGRDPLELLD----EIEEELG 152


>gnl|CDD|35689 KOG0468, KOG0468, KOG0468, U5 snRNP-specific protein [Translation,
           ribosomal structure and biogenesis].
          Length = 971

 Score = 53.5 bits (128), Expect = 9e-08
 Identities = 30/132 (22%), Positives = 54/132 (40%), Gaps = 15/132 (11%)

Query: 18  IGHVDHGKTTLTAAITKY-----YSEEKKEYGDIDSAPEEKLRGITIATAHVSY-----E 67
           +GH+ HGKT L   + +          + +    D+   E+ RG +I +  V+      +
Sbjct: 134 VGHLHHGKTALMDLLVEQTHPDFSKNTEADLRYTDTLFYEQERGCSIKSTPVTLVLSDSK 193

Query: 68  TDKRFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISS- 126
                 + +D PGH ++          +DG +LV    +G    T     + +    +  
Sbjct: 194 GKSYLMNILDTPGHVNFSDETTASLRLSDGVVLVVDVAEGVMLNTE---RIIKHAIQNRL 250

Query: 127 -IVVYMNKVDAV 137
            IVV +NKVD +
Sbjct: 251 PIVVVINKVDRL 262


>gnl|CDD|35684 KOG0463, KOG0463, KOG0463, GTP-binding protein GP-1 [General
           function prediction only].
          Length = 641

 Score = 47.4 bits (112), Expect = 7e-06
 Identities = 74/343 (21%), Positives = 130/343 (37%), Gaps = 28/343 (8%)

Query: 67  ETDKRFYSHIDCPGHADYVKNMITGAT--QADGAILVCAAEDGPKPQTREHILLARQIGI 124
           E   +  + ID  GH  Y+K  + G T    D  +L+  A  G    T+EH+ LA  + +
Sbjct: 215 EDSAKVITFIDLAGHEKYLKTTVFGMTGHMPDFTMLMIGANAGIIGMTKEHLGLALALHV 274

Query: 125 SSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTN------ 178
              VV + K+D    + +L  +   +  LLK         ++R          N      
Sbjct: 275 PVFVV-VTKIDMCPAN-ILQETMKLLTRLLKSPGCRKLPVLVRSMDDVVHAAVNFPSERV 332

Query: 179 ------KELGEDSIHALMKAVDTHIPTPQRSLDAPFLMHIEGSCGIEGRGTVVTGCIKRG 232
                   +   ++  L   ++      Q + + P    I+    + G GTVV+G +  G
Sbjct: 333 CPIFQVSNVTGTNLPLLKMFLNLLSLRRQLNENDPAEFQIDDIYWVPGVGTVVSGTLLSG 392

Query: 233 RIKAGSDVEIIG--MGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVNRADVPRGRV 290
            I+  +D+ ++G    G  + +    +   R  +     G      L+ + R DV +G V
Sbjct: 393 TIRL-NDILLLGPDSNGDFMPIPIKSIHRKRMPVGIVRCGQTASFALKKIKRKDVRKGMV 451

Query: 291 VCAPG-SIQEYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRIILSPGSQAV 349
           + +P    Q    F A + +L        T     Y+      +   T  I+ S G   +
Sbjct: 452 MVSPKLKPQASWEFEAEILVLH-----HPTTISPRYQAMVHCGSIRQTATIV-SMGKDCL 505

Query: 350 MPGDRVDLEVELI-YPIAMEPNQTFSMREGGKTVGAGLILEII 391
             GD+  ++   I  P  + P Q    RE G+T   G I  ++
Sbjct: 506 RTGDKAKVQFRFIKQPEYIRPGQRLVFRE-GRTKAVGTISSVL 547


>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 = 44.6 bits (106), Expect = 5e-05
 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 8/87 (9%)

Query: 92  ATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIR 151
             +AD  + V  A+     +  + + L R+ G   ++V  NK+D + ++E  ++ E  + 
Sbjct: 73  LERADLILFVVDADLRADEEEEKLLELLRERGKPVLLVL-NKIDLLPEEEEEELLELRLL 131

Query: 152 DLLKEHKYSDDTPIIRGSALCALQGTN 178
            LL         P+I   A+ AL G  
Sbjct: 132 ILLLLLGL----PVI---AVSALTGEG 151


>gnl|CDD|36359 KOG1144, KOG1144, KOG1144, Translation initiation factor 5B
           (eIF-5B) [Translation, ribosomal structure and
           biogenesis].
          Length = 1064

 Score = 42.7 bits (100), Expect = 2e-04
 Identities = 44/148 (29%), Positives = 59/148 (39%), Gaps = 11/148 (7%)

Query: 18  IGHVDHGKTTLTAAITKYYSEEKKEYGDIDSA------PEEKLRGIT-IATAHVSYETDK 70
           +GHVD GKT L   I     +E  E G I         P E +R  T             
Sbjct: 481 LGHVDTGKTKLLDKIRGTNVQEG-EAGGITQQIGATYFPAENIREKTKELKKDAKKRLKV 539

Query: 71  RFYSHIDCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVY 130
                ID PGH  +      G++  D AILV     G +PQT E I L R    +  +V 
Sbjct: 540 PGLLVIDTPGHESFTNLRSRGSSLCDLAILVVDIMHGLEPQTIESINLLRMRK-TPFIVA 598

Query: 131 MNKVDAVDDDELLDISEYEIRDLLKEHK 158
           +NK+D +   +        I + LK+ K
Sbjct: 599 LNKIDRLYGWK--SCPNAPIVEALKKQK 624


>gnl|CDD|31354 COG1160, COG1160, Predicted GTPases [General function prediction
           only].
          Length = 444

 Score = 41.3 bits (97), Expect = 5e-04
 Identities = 51/198 (25%), Positives = 83/198 (41%), Gaps = 30/198 (15%)

Query: 15  LSTIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYS 74
           ++ IG  + GK++L  AI     EE+    DI         G T  +  + +E D R Y 
Sbjct: 181 IAIIGRPNVGKSSLINAILG---EERVIVSDIA--------GTTRDSIDIEFERDGRKYV 229

Query: 75  HIDCPGH------ADYVKNMITGATQ-----ADGAILVCAAEDGPKPQTREHILLARQIG 123
            ID  G        + V+      T      AD  +LV  A +G   Q      L  + G
Sbjct: 230 LIDTAGIRRKGKITESVEKYSVARTLKAIERADVVLLVIDATEGISEQDLRIAGLIEEAG 289

Query: 124 ISSIVVYMNKVDAVDDDEL-LDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELG 182
              ++V +NK D V++DE  ++  + ++R  L    ++   PI+  SAL   QG +K   
Sbjct: 290 RGIVIV-VNKWDLVEEDEATMEEFKKKLRRKLPFLDFA---PIVFISALTG-QGLDKLF- 343

Query: 183 EDSIHALMKAVDTHIPTP 200
            ++I  + +     I T 
Sbjct: 344 -EAIKEIYECATRRISTS 360



 Score = 27.5 bits (61), Expect = 6.8
 Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 3/55 (5%)

Query: 94  QADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEY 148
           +AD  + V    +G  P   E   + R+     I+V +NK+D +  +E     E+
Sbjct: 83  EADVILFVVDGREGITPADEEIAKILRRSKKPVILV-VNKIDNLKAEE--LAYEF 134


>gnl|CDD|58096 cd04089, eRF3_II, eRF3_II: domain II of the eukaryotic class II
           release factor (eRF3). In eukaryotes, translation
           termination is mediated by two interacting release
           factors, eRF1 and eRF3, which act as class I and II
           factors, respectively. eRF1 functions as an omnipotent
           release factor, decoding all three stop codons and
           triggering the release of the nascent peptide catalyzed
           by the ribsome. eRF3 is a GTPase, which enhances the
           termination efficiency by stimulating the eRF1 activity
           in a GTP-dependent manner. Sequence comparison of class
           II release factors with elongation factors shows that
           eRF3 is more similar to eEF1alpha whereas prokaryote RF3
           is more similar to EF-G, implying that their precise
           function may differ. Only eukaryote RF3s are found in
           this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a
           translation termination factor which is divided into
           three regions N, M and a C-terminal eEF1a-like region
           essential for translation termination.  Sup35NM  is a
           non-pathogenic prion-like protein with the property of
           aggregating into polymer-like fibrils..
          Length = 82

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 3/72 (4%)

Query: 221 RGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGV 280
            GTVV G ++ G IK G  + ++     K +V+   +     ++  A  G+NV L L+G+
Sbjct: 13  MGTVVLGKVESGTIKKGDKLLVMP---NKTQVEVLSIYNEDVEVRYARPGENVRLRLKGI 69

Query: 281 NRADVPRGRVVC 292
              D+  G V+C
Sbjct: 70  EEEDISPGFVLC 81


>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 = 38.6 bits (90), Expect = 0.003
 Identities = 32/159 (20%), Positives = 51/159 (32%), Gaps = 20/159 (12%)

Query: 17  TIGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSHI 76
            +G    GKT+L   +           G      E +   I   +  +  +  K      
Sbjct: 1   VVGDSGVGKTSLLNRLL----------GGEFVPEEYETTIIDFYSKTIEVDGKKVKLQIW 50

Query: 77  DCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISS----IVVYMN 132
           D  G   +          ADG ILV    D    +  +  LL   I        I++  N
Sbjct: 51  DTAGQERFRSLRRLYYRGADGIILVYDVTDRESFENVKEWLLLILINKEGENIPIILVGN 110

Query: 133 KVDAVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSAL 171
           K+D  ++     +SE E+ + L +       P    SA 
Sbjct: 111 KIDLPEERV---VSEEELAEQLAKEL---GVPYFETSAK 143


>gnl|CDD|58085 cd03694, GTPBP_II, Domain II of the GP-1 family of GTPase. This
           group includes proteins similar to GTPBP1 and GTPBP2.
           GTPB1 is structurally, related to elongation factor 1
           alpha, a key component of protein biosynthesis
           machinery. Immunohistochemical analyses on mouse tissues
           revealed that GTPBP1 is expressed in some neurons and
           smooth muscle cells of various organs as well as
           macrophages. Immunofluorescence analyses revealed that
           GTPBP1 is localized exclusively in cytoplasm and shows a
           diffuse granular network forming a gradient from the
           nucleus to the periphery of the cells in smooth muscle
           cell lines and macrophages. No significant difference
           was observed in the immune response to protein antigen
           between mutant mice and wild-type mice, suggesting
           normal function of antigen-presenting cells of the
           mutant mice. The absence of an eminent phenotype in
           GTPBP1-deficient mice may be due to functional
           compensation by GTPBP2, which is similar to GTPBP1 in
           structure and tissue distribution..
          Length = 87

 Score = 38.2 bits (89), Expect = 0.004
 Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 208 FLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMG-GKKLKVKCTDVEMFRKKLDE 266
               I+    + G GTVV G + +G I+ G  + +     G    V    +   R  +  
Sbjct: 1   AEFQIDEIYSVPGVGTVVGGTVSKGVIRLGDTLLLGPDQDGSFRPVTVKSIHRNRSPVRV 60

Query: 267 AIAGDNVGLLLRGVNRADVPRGRVV 291
             AG +  L L+ ++R+ + +G V+
Sbjct: 61  VRAGQSASLALKKIDRSLLRKGMVL 85


>gnl|CDD|58089 cd03698, eRF3_II_like, eRF3_II_like: domain similar to domain II of
           the eukaryotic class II release factor (eRF3). In
           eukaryotes, translation termination is mediated by two
           interacting release factors, eRF1 and eRF3, which act as
           class I and II factors, respectively. eRF1 functions as
           an omnipotent release factor, decoding all three stop
           codons and triggering the release of the nascent peptide
           catalyzed by the ribsome. eRF3 is a GTPase, which
           enhances the termination efficiency by stimulating the
           eRF1 activity in a GTP-dependent manner. Sequence
           comparison of class II release factors with elongation
           factors shows that eRF3 is more similar to eEF1alpha
           whereas prokaryote RF3 is more similar to EF-G, implying
           that their precise function may differ. Only eukaryote
           RF3s are found in this group. Saccharomyces cerevisiae
           eRF3 (Sup35p) is a translation termination factor which
           is divided into three regions N, M and a C-terminal
           eEF1a-like region essential for translation termination.
            Sup35NM  is a non-pathogenic prion-like protein with
           the property of aggregating into polymer-like fibrils.
           This group also contains proteins similar to S.
           cerevisiae Hbs1, a G protein known to be important for
           efficient growth and protein synthesis under conditions
           of limiting translation initiation and, to associate
           with Dom34.  It has been speculated that yeast Hbs1 and
           Dom34 proteins may function as part of a complex with a
           role in gene expression..
          Length = 83

 Score = 37.8 bits (88), Expect = 0.005
 Identities = 26/86 (30%), Positives = 50/86 (58%), Gaps = 4/86 (4%)

Query: 207 PFLMHIEGSCGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDE 266
           PF + I      +  GTVV+G ++ G I+ G  + ++    + ++VK   + +  +++D 
Sbjct: 1   PFRLPISDKYK-DQGGTVVSGKVESGSIQKGDTL-LVMPSKESVEVK--SIYVDDEEVDY 56

Query: 267 AIAGDNVGLLLRGVNRADVPRGRVVC 292
           A+AG+NV L L+G++  D+  G V+C
Sbjct: 57  AVAGENVRLKLKGIDEEDISPGDVLC 82


>gnl|CDD|133365 cd04165, GTPBP1_like, GTPBP1-like.  Mammalian GTP binding protein 1
           (GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1
           are GTPases whose specific functions remain unknown.  In
           mouse, GTPBP1 is expressed in macrophages, in smooth
           muscle cells of various tissues and in some neurons of
           the cerebral cortex; GTPBP2 tissue distribution appears
           to overlap that of GTPBP1.  In human leukemia and
           macrophage cell lines, expression of both GTPBP1 and
           GTPBP2 is enhanced by interferon-gamma (IFN-gamma).  The
           chromosomal location of both genes has been identified
           in humans, with GTPBP1 located in chromosome 22q12-13.1
           and GTPBP2 located in chromosome 6p21-12.  Human
           glioblastoma multiforme (GBM), a highly-malignant
           astrocytic glioma and the most common cancer in the
           central nervous system, has been linked to chromosomal
           deletions and a translocation on chromosome 6.  The GBM
           translocation results in a fusion of GTPBP2 and PTPRZ1,
           a protein involved in oligodendrocyte differentiation,
           recovery, and survival.  This fusion product may
           contribute to the onset of GBM.
          Length = 224

 Score = 37.2 bits (87), Expect = 0.008
 Identities = 40/162 (24%), Positives = 65/162 (40%), Gaps = 47/162 (29%)

Query: 18  IGHVDHGKTTLTAAITKYYSEEKKEYGDIDSA-----------PEEKLRGIT--IATAHV 64
           +G+VD GK+TL   +T+         G++D+              E   G T  ++   +
Sbjct: 5   VGNVDAGKSTLLGVLTQ---------GELDNGRGKARLNLFRHKHEVESGRTSSVSNEIL 55

Query: 65  SYETDKRF----YSH------------------IDCPGHADYVKNMITGAT--QADGAIL 100
            +++D        +H                  ID  GH  Y+K  + G T    D A+L
Sbjct: 56  GFDSDGEVVNYPDNHLSESDIEICEKSSKLVTFIDLAGHERYLKTTLFGLTGYAPDYAML 115

Query: 101 VCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDEL 142
           V AA  G    T+EH+ LA  + I  + V + K+D    + L
Sbjct: 116 VVAANAGIIGMTKEHLGLALALNI-PVFVVVTKIDLAPANIL 156


>gnl|CDD|32410 COG2229, COG2229, Predicted GTPase [General function prediction
           only].
          Length = 187

 Score = 37.2 bits (86), Expect = 0.008
 Identities = 42/174 (24%), Positives = 59/174 (33%), Gaps = 16/174 (9%)

Query: 18  IGHVDHGKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSHI- 76
           IG V  GKTT   A++           D  S   +  R  T+A    S E D+    H+ 
Sbjct: 16  IGPVGAGKTTFVRALS--DKPLVITEADASSVSGKGKRPTTVAMDFGSIELDEDTGVHLF 73

Query: 77  DCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDA 136
             PG   +       +  A GAI++  +         E I          +VV +NK D 
Sbjct: 74  GTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPIPVVVAINKQDL 133

Query: 137 VDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALM 190
            D      I E    +LL         P+I   A      T  E   D +  L+
Sbjct: 134 FDALPPEKIREALKLELL-------SVPVIEIDA------TEGEGARDQLDVLL 174


>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 = 36.6 bits (85), Expect = 0.012
 Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 4/58 (6%)

Query: 222 GTVVTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMF----RKKLDEAIAGDNVGL 275
           G +  G I RG +K G  V ++   GK  K K T +  F    R +++EA AGD V +
Sbjct: 15  GRIAIGRIFRGTVKVGQQVAVVKRDGKIEKAKITKLFGFEGLKRVEVEEAEAGDIVAI 72


>gnl|CDD|58075 cd04093, HBS1_C, HBS1_C: this family represents the C-terminal
           domain of Hsp70 subfamily B suppressor 1 (HBS1) which is
           homologous to the domain III of EF-1alpha. This group
           contains proteins similar to yeast Hbs1, a G protein
           known to be important for efficient growth and protein
           synthesis under conditions of limiting translation
           initiation and, to associate with Dom34.  It has been
           speculated that yeast Hbs1 and Dom34 proteins may
           function as part of a complex with a role in gene
           expression..
          Length = 107

 Score = 35.9 bits (83), Expect = 0.018
 Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 13/55 (23%)

Query: 342 LSPGSQAVMPGDRVDLEVELIYPIAMEPNQT------FSMREGGKTVGAGLILEI 390
           L+ G  A++       E+EL  PI +E  +         +R  G+T+ AGL+ EI
Sbjct: 60  LTKGQTAIV-------EIELERPIPLELFKDNKELGRVVLRRDGETIAAGLVTEI 107


>gnl|CDD|58086 cd03695, CysN_NodQ_II, CysN_NodQ_II: This subfamily represents the
           domain II of the large subunit of ATP sulfurylase
           (ATPS): CysN or the N-terminal portion of NodQ, found
           mainly in proteobacteria and homologous to the domain II
           of EF-Tu. Escherichia coli ATPS consists of CysN and a
           smaller subunit CysD and CysN. ATPS produces
           adenosine-5'-phosphosulfate (APS) from ATP and sulfate,
           coupled with GTP hydrolysis. In the subsequent reaction
           APS is phosphorylated by an APS kinase (CysC), to
           produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for
           use in amino acid (aa) biosynthesis. The Rhizobiaceae
           group (alpha-proteobacteria) appears to carry out the
           same chemistry for the sufation of a nodulation factor.
           In Rhizobium meliloti, a the hererodimeric complex
           comprised of NodP and NodQ appears to possess both ATPS
           and APS kinase activities. The N and C termini of NodQ
           correspond to CysN and CysC, respectively.   Other
           eubacteria, Archaea, and eukaryotes use a different ATP
           sulfurylase, which shows no aa sequence similarity to
           CysN or NodQ.   CysN and the N-terminal portion of NodQ
           show similarity to GTPases involved in translation, in
           particular, EF-Tu and EF-1alpha..
          Length = 81

 Score = 34.7 bits (80), Expect = 0.048
 Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 5/69 (7%)

Query: 225 VTGCIKRGRIKAGSDVEIIGMGGKKLKVKCTDVEMFRKKLDEAIAGDNVGLLLRGVNRAD 284
             G I  G I+ G +V ++   GK  +VK   +E F  +LDEA AG++V L L   +  D
Sbjct: 18  YAGTIASGSIRVGDEV-VVLPSGKTSRVK--SIETFDGELDEAGAGESVTLTLE--DEID 72

Query: 285 VPRGRVVCA 293
           V RG V+ A
Sbjct: 73  VSRGDVIVA 81


>gnl|CDD|30567 COG0218, COG0218, Predicted GTPase [General function prediction
           only].
          Length = 200

 Score = 33.3 bits (76), Expect = 0.13
 Identities = 28/124 (22%), Positives = 44/124 (35%), Gaps = 18/124 (14%)

Query: 66  YETDKRFYSHIDCPG---------HADYVKNMI----TGATQADGAILVCAAEDGPKPQT 112
           +E D      +D PG           +  K +I           G +L+  A   PK   
Sbjct: 66  FEVDDELR-LVDLPGYGYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPPKDLD 124

Query: 113 REHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYSDDTPIIRGSALC 172
           RE I    ++GI  IVV + K D +   E       ++ + LK  K   D   +   +  
Sbjct: 125 REMIEFLLELGIPVIVV-LTKADKLKKSERNK-QLNKVAEELK--KPPPDDQWVVLFSSL 180

Query: 173 ALQG 176
             +G
Sbjct: 181 KKKG 184


>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 = 32.4 bits (75), Expect = 0.21
 Identities = 26/101 (25%), Positives = 44/101 (43%), Gaps = 15/101 (14%)

Query: 95  ADGAILVCAAEDGPKPQTREHIL-LARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDL 153
           AD  +LV  A +G   Q    I  L  + G + ++V +NK D V+ D      +   +++
Sbjct: 85  ADVVLLVIDATEGITEQD-LRIAGLILEEGKALVIV-VNKWDLVEKDS--KTMKEFKKEI 140

Query: 154 LKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALMKAVD 194
            ++  + D  PI+  SAL    G         +  L  A+D
Sbjct: 141 RRKLPFLDYAPIVFISALT---GQG-------VDKLFDAID 171


>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 = 31.3 bits (72), Expect = 0.44
 Identities = 24/110 (21%), Positives = 43/110 (39%), Gaps = 18/110 (16%)

Query: 85  VKNMITGATQADGAILVCAAEDGPKPQTREHILLARQI---GISSIVVYMNKVDAVDD-D 140
           VK   +     D  +L     D  +P       +   +       I+V +NK+D V D +
Sbjct: 73  VKAAWSALKDVD-LVLFVV--DASEPIGEGDEFILELLKKSKTPVILV-LNKIDLVKDKE 128

Query: 141 ELLDISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALM 190
           +LL + E     L +   +++  PI       AL+G N +   + I   +
Sbjct: 129 DLLPLLEK----LKELGPFAEIFPI------SALKGENVDELLEEIVKYL 168


>gnl|CDD|73167 cd00655, RNAP_Rpb7_N_like, RNAP_Rpb7_N_like: This conserved domain
           represents the N-terminal ribonucleoprotein (RNP) domain
           of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP)
           II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25
           of eukaryotic RNAP III, and RpoE (subunit E) of archaeal
           RNAP. These proteins have, in addition to their
           N-terminal RNP domain, a C-terminal
           oligonucleotide-binding (OB) domain. Each of these
           subunits heterodimerizes with another RNAP subunit (Rpb7
           to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to
           Rpa14). The heterodimer is thought to tether the RNAP to
           a given promoter via its interactions with a
           promoter-bound transcription factor.The heterodimer is
           also thought to bind and position nascent RNA as it
           exits the polymerase complex..
          Length = 80

 Score = 31.0 bits (70), Expect = 0.58
 Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 3/55 (5%)

Query: 258 EMFRKKLDEAIAGD---NVGLLLRGVNRADVPRGRVVCAPGSIQEYSRFRASVYI 309
            + +  L E   GD    VG++L   +  D+P G +    GS      FRA V+ 
Sbjct: 23  GVKKCLLQEKGEGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVFK 77


>gnl|CDD|58071 cd03705, EF1_alpha_III, Domain III of EF-1. Eukaryotic elongation
           factor 1 (EF-1) is responsible for the GTP-dependent
           binding of aminoacyl-tRNAs to ribosomes. EF-1 is
           composed of four subunits: the alpha chain, which binds
           GTP and aminoacyl-tRNAs, the gamma chain that probably
           plays a role in anchoring the complex to other cellular
           components and the beta and delta (or beta') chains.
           This family is the alpha subunit, and represents the
           counterpart of bacterial EF-Tu for the archaea (aEF-1
           alpha) and eukaryotes (eEF-1 alpha)..
          Length = 104

 Score = 30.5 bits (69), Expect = 0.75
 Identities = 23/108 (21%), Positives = 37/108 (34%), Gaps = 24/108 (22%)

Query: 299 EYSRFRASVYILTASEGGRTTGFMDNYRPQFFMDTADVTGRI-------------ILSPG 345
               F A V +L    G    G    Y P     TA V  R               L   
Sbjct: 2   VAESFTAQVIVL-NHPGQIKPG----YTPVLDCHTAHVACRFAEILSKIDPRTGKKLEEN 56

Query: 346 SQAVMPGDRVDLEVELIYPIAMEPNQT------FSMREGGKTVGAGLI 387
            + +  GD   +++    P+ +E          F++R+ G+TV  G++
Sbjct: 57  PKFLKSGDAAIVKIVPQKPLVVETFSEYPPLGRFAVRDMGQTVAVGIV 104


>gnl|CDD|133282 cd01882, BMS1, Bms1.  Bms1 is an essential, evolutionarily
           conserved, nucleolar protein.  Its depletion interferes
           with processing of the 35S pre-rRNA at sites A0, A1, and
           A2, and the formation of 40S subunits.  Bms1, the
           putative endonuclease Rc11, and the essential U3 small
           nucleolar RNA form a stable subcomplex that is believed
           to control an early step in the formation of the 40S
           subumit.  The C-terminal domain of Bms1 contains a
           GTPase-activating protein (GAP) that functions
           intramolecularly.  It is believed that Rc11 activates
           Bms1 by acting as a guanine-nucleotide exchange factor
           (GEF) to promote GDP/GTP exchange, and that activated
           (GTP-bound) Bms1 delivers Rc11 to the preribosomes.
          Length = 225

 Score = 30.3 bits (69), Expect = 0.89
 Identities = 27/85 (31%), Positives = 39/85 (45%), Gaps = 20/85 (23%)

Query: 24  GKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRG-ITIATAHVSYETDKRFYSHIDCPGHA 82
           GKTTL  ++ K Y+  K+   DI        +G IT+ T        KR  + I+CP   
Sbjct: 51  GKTTLIKSLVKNYT--KQNISDI--------KGPITVVTG------KKRRLTFIECP--- 91

Query: 83  DYVKNMITGATQADGAILVCAAEDG 107
           + +  MI  A  AD  +L+  A  G
Sbjct: 92  NDINAMIDIAKVADLVLLLIDASFG 116


>gnl|CDD|30869 COG0523, COG0523, Putative GTPases (G3E family) [General function
           prediction only].
          Length = 323

 Score = 29.9 bits (67), Expect = 1.4
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 2/58 (3%)

Query: 96  DGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDL 153
           DG + V  A    +       L   Q+  + ++V +NK D VD +E L+  E  +R L
Sbjct: 118 DGVVTVVDAAHFLEGLDAIAELAEDQLAFADVIV-LNKTDLVDAEE-LEALEARLRKL 173


>gnl|CDD|58079 cd03688, eIF2_gamma_II, eIF2_gamma_II: this subfamily represents
           the domain II of the gamma subunit of eukaryotic
           translation initiation factor 2 (eIF2-gamma) found in
           Eukaryota and Archaea. eIF2 is a G protein that delivers
           the methionyl initiator tRNA to the small ribosomal
           subunit and releases it upon GTP hydrolysis after the
           recognition of the initiation codon. eIF2 is composed
           three subunits, alpha, beta and gamma. Subunit gamma
           shows strongest conservation, and it confers both tRNA
           binding and GTP/GDP binding..
          Length = 113

 Score = 29.7 bits (67), Expect = 1.5
 Identities = 30/116 (25%), Positives = 48/116 (41%), Gaps = 26/116 (22%)

Query: 203 SLDAPFLMHIEGSCGI--------EGRGTVVTGCIKRGRIKAGSDVEII-GMGGKKL-KV 252
              +P  M +  S  +        + +G V  G + +G +K G ++EI  G+  K   K+
Sbjct: 1   DFTSPPRMIVIRSFDVNKPGTEVDDLKGGVAGGSLLQGVLKVGDEIEIRPGIVVKDEGKI 60

Query: 253 KC-------TDVEMFRKKLDEAIAGDNVGLLLRGVN------RADVPRGRVVCAPG 295
           KC         ++     L EA+ G   GL+  G        +AD   G+VV  PG
Sbjct: 61  KCRPIFTKIVSLKAENNDLQEAVPG---GLIGVGTKLDPTLTKADRLVGQVVGEPG 113


>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 = 29.7 bits (68), Expect = 1.6
 Identities = 24/114 (21%), Positives = 43/114 (37%), Gaps = 35/114 (30%)

Query: 92  ATQADGAILVCAAEDGPKPQTREHI-----LLARQIGISS---IVVYMNKVDAVDDDELL 143
             +AD  + V    D   P   E I     +L +++G      I+V  NK+D +DD+EL 
Sbjct: 118 VAEADLLLHVV---DASDPDYEEQIETVEKVL-KELGAEDIPMILVL-NKIDLLDDEELE 172

Query: 144 DISEYEIRDLLKEHKYSDDTPIIRGSALCALQGTNKELGEDSIHALMKAVDTHI 197
           +  E    D +                + A  G         +  L++A++  +
Sbjct: 173 ERLEAGRPDAV---------------FISAKTGEG-------LDELLEAIEELL 204


>gnl|CDD|176240 cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase.
           Glutathione-dependent formaldehyde dehydrogenases (FDHs,
           Class III ADH) are members of the zinc-dependent/medium
           chain alcohol dehydrogenase family.  FDH converts
           formaldehyde and NAD(P) to formate and NAD(P)H. The
           initial step in this process the spontaneous formation
           of a S-(hydroxymethyl)glutathione adduct from
           formaldehyde and glutathione, followed by FDH-mediated
           oxidation (and detoxification) of the adduct to
           S-formylglutathione. NAD(P)(H)-dependent oxidoreductases
           are the major enzymes in the interconversion of alcohols
           and aldehydes or ketones.  Alcohol dehydrogenase in the
           liver converts ethanol and NAD+ to acetaldehyde and
           NADH, while in yeast and some other microorganisms ADH
           catalyzes the conversion acetaldehyde to ethanol in
           alcoholic fermentation. Class III ADH are also known as
           glutathione-dependent formaldehyde dehydrogenase (FDH),
           which convert aldehydes to corresponding carboxylic acid
           and alcohol.  ADH is a member of the medium chain
           alcohol dehydrogenase family (MDR), which has a
           NAD(P)(H)-binding domain in a Rossmann fold of an
           beta-alpha form. The NAD(H)-binding region is comprised
           of 2 structurally similar halves, each of which contacts
           a mononucleotide.  A GxGxxG motif after the first
           mononucleotide contact half allows the close contact of
           the coenzyme with the ADH backbone.  The N-terminal
           catalytic domain has a distant homology to GroES.  These
           proteins typically form dimers (typically higher plants,
           mammals) or tetramers (yeast, bacteria), and have 2
           tightly bound zinc atoms per subunit, a catalytic zinc
           at the active site and a structural zinc in a lobe of
           the catalytic domain.  NAD(H) binding occurs in the
           cleft between the catalytic  and coenzyme-binding
           domains at the active site, and coenzyme binding induces
           a conformational closing of this cleft. Coenzyme binding
           typically precedes and contributes to substrate binding.
          Length = 363

 Score = 29.4 bits (67), Expect = 2.0
 Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 9/36 (25%)

Query: 215 SCGIEGRGTVVTGC---IKRGRIKAGSDVEIIGMGG 247
            CG      V TG    +   R++ G  V +IG GG
Sbjct: 164 GCG------VTTGVGAVVNTARVRPGDTVAVIGCGG 193


>gnl|CDD|145217 pfam01926, MMR_HSR1, GTPase of unknown function. 
          Length = 106

 Score = 28.4 bits (64), Expect = 3.7
 Identities = 28/118 (23%), Positives = 42/118 (35%), Gaps = 20/118 (16%)

Query: 24  GKTTLTAAITKYYSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSHIDCPG--- 80
           GK+TL  A+T               A      G T        E D +    +D PG   
Sbjct: 1   GKSTLINALTG-----------KKRAIVSDYPGTTRDPNEGRVELDGKQIILVDTPGIIE 49

Query: 81  HADYVKNMITGAT-----QADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNK 133
            A   +  +   T     +AD  + V  A +G   +  E + L  ++G   I+V  NK
Sbjct: 50  GASKGEGELGNRTLEAIEEADLILHVVDASEGLTEEDLEILDLLLELGKPVILVL-NK 106


>gnl|CDD|29076 cd01445, TST_Repeats, Thiosulfate sulfurtransferases (TST) contain
           2 copies of the Rhodanese Homology Domain. Only the
           second repeat contains the catalytically active Cys
           residue. The role of the 1st repeat is uncertain, but
           believed to be involved in protein interaction. This CD
           aligns the 1st and 2nd repeats..
          Length = 138

 Score = 28.2 bits (62), Expect = 3.7
 Identities = 11/60 (18%), Positives = 23/60 (38%)

Query: 107 GPKPQTREHILLARQIGISSIVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYSDDTPII 166
             +P+     L +  I  +S   +   +D    +E ++ SE E   + +      D  +I
Sbjct: 40  ETQPEPDAVGLDSGHIPGASFFDFEECLDEAGFEESMEPSEAEFAAMFEAKGIDLDKHLI 99


>gnl|CDD|34614 COG5009, MrcA, Membrane carboxypeptidase/penicillin-binding
          protein [Cell envelope biogenesis, outer membrane].
          Length = 797

 Score = 28.3 bits (63), Expect = 3.9
 Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 7/40 (17%)

Query: 36 YSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSH 75
          Y EE++    ID  P+       +  A ++ E DKRFY H
Sbjct: 62 YGEERRIPVPIDDIPDR------LINAFLAAE-DKRFYEH 94


>gnl|CDD|73299 cd02036, MinD, Bacterial cell division requires the formation of a
           septum at mid-cell. The site is determined by the min
           operon products MinC, MinD and MinE. MinC is a
           nonspecific inhibitor of the septum protein FtsZ. MinE
           is the supressor of MinC. MinD plays a pivotal role,
           selecting the mid-cell over other sites through the
           activation and regulation of MinC and MinE. MinD is a
           membrane-associated ATPase, related to nitrogenase iron
           protein. More distantly related proteins include
           flagellar biosynthesis proteins and ParA chromosome
           partitioning proteins. MinD is a monomer..
          Length = 179

 Score = 27.8 bits (62), Expect = 4.8
 Identities = 33/134 (24%), Positives = 50/134 (37%), Gaps = 15/134 (11%)

Query: 24  GKTTLTAAITKYYSEEKKEY----GDIDSAPEEKLRGI---TIATAHVSYETDKRFYSHI 76
           GKTT TA +    ++   +      D+     + + G+    + T H     D   Y  I
Sbjct: 12  GKTTTTANLGTALAQLGYKVVLIDADLGLRNLDLILGLENRVVYTLHDVLAGD---YILI 68

Query: 77  DCPGHADYVKNMITGATQADGAILVCAAEDGPKPQTREHILLARQIGISSIVVYMNKVD- 135
           D P   +  +  IT    AD A+LV   E            L   +GI  + V +N+V  
Sbjct: 69  DSPAGIE--RGFITAIAPADEALLVTTPEISSLRDADRVKGLLEALGIKVVGVIVNRVRP 126

Query: 136 --AVDDDELLDISE 147
                 D + DI E
Sbjct: 127 DMVEGGDMVEDIEE 140


>gnl|CDD|144490 pfam00912, Transgly, Transglycosylase.  The penicillin-binding
          proteins are bifunctional proteins consisting of
          transglycosylase and transpeptidase in the N- and
          C-terminus respectively. The transglycosylase domain
          catalyses the polymerisation of murein glycan chains.
          Length = 174

 Score = 27.6 bits (62), Expect = 6.5
 Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 7/40 (17%)

Query: 36 YSEEKKEYGDIDSAPEEKLRGITIATAHVSYETDKRFYSH 75
          + EE + Y  +D  P        +  A V+ E D+RFYSH
Sbjct: 8  FGEENRVYVPLDEIPP------HLINAVVAIE-DRRFYSH 40


>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 = 27.5 bits (62), Expect = 6.8
 Identities = 10/34 (29%), Positives = 20/34 (58%)

Query: 127 IVVYMNKVDAVDDDELLDISEYEIRDLLKEHKYS 160
           ++V +NK+D +  ++L +I E E  +  +  K S
Sbjct: 116 VIVVLNKIDLLTFEDLSEIEEEEELEGEEVLKIS 149


>gnl|CDD|146149 pfam03361, Herpes_IE2_3, Herpes virus intermediate/early protein
           2/3.  These viral sequences are similar to UL117 protein
           of human and chimpanzee cytomegalovirus, and to
           intermediate/early proteins 2 and 3 of certain herpes
           viruses. UL117 is thought to be a glycoprotein that is
           expressed at early and late times after infection. This
           region is close to the C-terminus of the protein and may
           be a transmembrane region.
          Length = 162

 Score = 27.3 bits (61), Expect = 6.9
 Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 4/39 (10%)

Query: 75  HIDCPGHADYVKNMITGATQAD--GAILVCA--AEDGPK 109
           H  CP  +D    +I  AT  D  GA  +C   A+  PK
Sbjct: 99  HDLCPRSSDVRTMIIQAATPKDFLGAAKLCLPLAQKFPK 137


>gnl|CDD|147030 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region.  GTR1
           was first identified in S. cerevisiae as a suppressor of
           a mutation in RCC1. Biochemical analysis revealed that
           Gtr1 is in fact a G protein of the Ras family. The
           RagA/B proteins are the human homologues of Gtr1.
           Included in this family is the human Rag C, a novel
           protein that has been shown to interact with RagA/B.
          Length = 230

 Score = 27.2 bits (61), Expect = 7.4
 Identities = 28/134 (20%), Positives = 52/134 (38%), Gaps = 29/134 (21%)

Query: 50  PEEKLR-GITIATAHVSYETDKRFYSHI-----DCPGHADYVKNMITGATQAD------G 97
           P + LR G TI           RF  ++     DCPG  D+++N      Q +      G
Sbjct: 25  PRDTLRLGATIDVEQSHV----RFLGNLTLNLWDCPGQDDFMEN--YLTRQKEHIFSNVG 78

Query: 98  AILV---CAAEDGPKPQTR--EHILLARQI--GISSIVVYMNKVDAVDDDELLDISEY-- 148
            ++      + +  +      + I    Q       + V ++K+D + +DE  +I E   
Sbjct: 79  VLIYVFDVESREYEEDLATLVKIIEALYQYSPNA-KVFVLIHKMDLLSEDERKEIFEDRK 137

Query: 149 -EIRDLLKEHKYSD 161
            EI + +++    D
Sbjct: 138 EEIIEEIEDFGIED 151


>gnl|CDD|31527 COG1336, COG1336, Uncharacterized protein predicted to be involved
           in DNA repair (RAMP superfamily) [DNA replication,
           recombination, and repair].
          Length = 298

 Score = 27.2 bits (60), Expect = 8.1
 Identities = 33/178 (18%), Positives = 56/178 (31%), Gaps = 32/178 (17%)

Query: 216 CGIEGRGTVVTGCIK----RGRIKAGSDVEIIGMGGKKLKVKCTDVEM--FRKKLDEAIA 269
             IEG+        K       +    D+ +  + G+  K    D  +     +    I 
Sbjct: 139 NDIEGKALSYPDEGKVYLEEITLNVLEDLTLGDLLGELSKTVFEDDNLPKEFNEQRLVIV 198

Query: 270 GDNVGLLLRGVNRADVPRGRVVCAPGSIQEYSRFRASVYILTASEGGRTTGFMDNYRPQF 329
            DNV   +  ++   V R R+                    T  EGG    + + Y P+ 
Sbjct: 199 SDNVFSDIVNLSTEIVTRIRINRETK---------------TVEEGGL---WYEEYIPE- 239

Query: 330 FMDTADVTGRIILSPGSQAVMPGDRVDLEVELIYPIAMEPNQTFSMREGGKTVGAGLI 387
              T   +   +     + V+  D    EV     +    N  +    G +TVG GL+
Sbjct: 240 --GTLFYSLINVFLIYCEEVLDDDEKVREV-----LKRLSNLRYLQIGGKETVGKGLV 290


>gnl|CDD|146100 pfam03294, Pox_Rap94, RNA polymerase-associated transcription
           specificity factor, Rap94. 
          Length = 796

 Score = 27.0 bits (60), Expect = 8.2
 Identities = 11/33 (33%), Positives = 17/33 (51%)

Query: 128 VVYMNKVDAVDDDELLDISEYEIRDLLKEHKYS 160
             Y N    + ++ LLD  +Y I +L  +H YS
Sbjct: 243 KTYKNNFSEIINNSLLDWGKYIIPNLKNKHLYS 275


>gnl|CDD|73297 cd02034, CooC, The accessory protein CooC, which contains a
          nucleotide-binding domain (P-loop) near the N-terminus,
          participates in the maturation of the nickel center of
          carbon monoxide dehydrogenase (CODH). CODH from
          Rhodospirillum rubrum catalyzes the reversible
          oxidation of CO to CO2. CODH contains a
          nickel-iron-sulfur cluster (C-center) and an
          iron-sulfur cluster (B-center). CO oxidation occurs at
          the C-center. Three accessory proteins encoded by
          cooCTJ genes are involved in nickel incorporation into
          a nickel site. CooC functions as a nickel insertase
          that mobilizes nickel to apoCODH using energy released
          from ATP hydrolysis. CooC is a homodimer and has NTPase
          activities. Mutation at the P-loop abolishs its
          function..
          Length = 116

 Score = 27.1 bits (60), Expect = 9.5
 Identities = 11/29 (37%), Positives = 19/29 (65%)

Query: 24 GKTTLTAAITKYYSEEKKEYGDIDSAPEE 52
          GKTT+ A + +Y +E+ K    ID+ P++
Sbjct: 11 GKTTIAALLARYLAEKGKPVLAIDADPDD 39


>gnl|CDD|30822 COG0474, MgtA, Cation transport ATPase [Inorganic ion transport and
           metabolism].
          Length = 917

 Score = 26.9 bits (59), Expect = 9.8
 Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 19/73 (26%)

Query: 105 EDGPKPQTREHILLARQIGISSIVVYMNKVD-------------------AVDDDELLDI 145
           ED P+   +E I   R+ GI   ++  + V+                    +D  EL  +
Sbjct: 545 EDPPREDVKEAIEELREAGIKVWMITGDHVETAIAIAKECGIEAEAESALVIDGAELDAL 604

Query: 146 SEYEIRDLLKEHK 158
           S+ E+ +L++E  
Sbjct: 605 SDEELAELVEELS 617


>gnl|CDD|176182 cd05279, Zn_ADH1, Liver alcohol dehydrogenase and related
           zinc-dependent alcohol dehydrogenases.
           NAD(P)(H)-dependent oxidoreductases are the major
           enzymes in the interconversion of alcohols and
           aldehydes, or ketones.  Alcohol dehydrogenase in the
           liver converts ethanol and NAD+ to acetaldehyde and
           NADH, while in yeast and some other microorganisms ADH
           catalyzes the conversion acetaldehyde to ethanol in
           alcoholic fermentation.  There are 7 vertebrate ADH 7
           classes, 6 of which have been identified in humans.
           Class III, glutathione-dependent formaldehyde
           dehydrogenase, has been identified as the primordial
           form and exists in diverse species, including plants,
           micro-organisms, vertebrates, and invertebrates. Class
           I, typified by  liver dehydrogenase, is an evolving
           form. Gene duplication and functional specialization of
           ADH into ADH classes and subclasses created numerous
           forms in vertebrates. For example, the A, B and C
           (formerly alpha, beta, gamma) human class I subunits
           have high overall structural similarity, but differ in
           the substrate binding pocket and therefore in substrate
           specificity.  In human ADH catalysis, the zinc ion helps
           coordinate the alcohol, followed by deprotonation of  a
           histidine (His-51), the ribose of NAD, a serine
           (Ser-48), then the alcohol, which allows the transfer of
           a hydride to NAD+, creating NADH and a zinc-bound
           aldehyde or ketone. In yeast and some bacteria, the
           active site zinc binds an aldehyde, polarizing it, and
           leading to the reverse reaction. ADH is a member of the
           medium chain alcohol dehydrogenase family (MDR), which
           has a NAD(P)(H)-binding domain in a Rossmann fold of an
           beta-alpha form.  The NAD(H)-binding region is comprised
           of 2 structurally similar halves, each of which contacts
           a mononucleotide. A GxGxxG motif after the first
           mononucleotide contact half allows the close contact of
           the coenzyme with the ADH backbone.  The N-terminal
           catalytic domain has a distant homology  to GroES.
           These proteins typically form dimers (typically higher
           plants, mammals) or tetramers (yeast, bacteria), and
           have 2 tightly bound zinc atoms per subunit, a catalytic
           zinc at the active site and a structural zinc in a lobe
           of the catalytic domain.  NAD(H) binding occurs in the
           cleft between the catalytic and coenzyme-binding domains
           at the active site, and coenzyme binding induces a
           conformational closing of this cleft. Coenzyme binding
           typically precedes and contributes to substrate binding.
          Length = 365

 Score = 27.0 bits (60), Expect = 10.0
 Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 3/37 (8%)

Query: 216 CGIEGRGTVVTGCIKRGRIKAGSDVEIIGMGGKKLKV 252
           CG     T     +   ++  GS   + G+GG  L V
Sbjct: 166 CGFS---TGYGAAVNTAKVTPGSTCAVFGLGGVGLSV 199


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.318    0.137    0.393 

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: 4,681,549
Number of extensions: 251688
Number of successful extensions: 909
Number of sequences better than 10.0: 1
Number of HSP's gapped: 787
Number of HSP's successfully gapped: 106
Length of query: 392
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 296
Effective length of database: 4,189,273
Effective search space: 1240024808
Effective search space used: 1240024808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.0 bits)