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)