RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780648|ref|YP_003065061.1| GTPase ObgE [Candidatus Liberibacter asiaticus str. psy62] (335 letters) >gnl|CDD|30882 COG0536, Obg, Predicted GTPase [General function prediction only]. Length = 369 Score = 436 bits (1124), Expect = e-123 Identities = 179/340 (52%), Positives = 243/340 (71%), Gaps = 6/340 (1%) Query: 1 MKFLDEAKVYIRSGDGGAGGISFRREKFIEFGGPDGGSGGRGGDVWIQATSNLNTLIDFR 60 MKF+DE K+ +++GDGG G +SFRREKF+ GGPDGG GGRGG V +A NLNTLIDFR Sbjct: 1 MKFVDEVKIEVKAGDGGNGCVSFRREKFVPKGGPDGGDGGRGGSVIFEADENLNTLIDFR 60 Query: 61 YQQHFKAQHGEKGMKRNRSGAKGEDVVLTVPVGTQVFEEDGISLICDLDQEGQRIILAPG 120 Y++HFKA++GE GM RNR+GAKG+D+V+ VPVGT V +ED L+ DL + GQR ++A G Sbjct: 61 YKKHFKAENGENGMGRNRTGAKGKDLVIKVPVGTVVRDEDTGELLADLTEHGQRFLVAKG 120 Query: 121 GNGGFGNAHFKSSTNQAPYYANPGILGQEKIIWLKLKLIADIGIIGLPNAGKSTFLASVT 180 G GG GNAHFKSS N+AP +A PG G+E+ + L+LKL+AD+G++GLPNAGKST L++V+ Sbjct: 121 GRGGLGNAHFKSSVNRAPRFATPGEPGEERDLRLELKLLADVGLVGLPNAGKSTLLSAVS 180 Query: 181 RAKPKIADYPFTTLYPNLGIVK-EGYKEFILADIPGIIKNAHQGAGIGDRFLKHTERTHV 239 AKPKIADYPFTTL PNLG+V+ +G + F++ADIPG+I+ A +G G+G RFL+H ERT V Sbjct: 181 AAKPKIADYPFTTLVPNLGVVRVDGGESFVVADIPGLIEGASEGVGLGLRFLRHIERTRV 240 Query: 240 LLHIVSALEENVQ---AAYQCILDELSAYNSELRKKIEIVGLSQIDTV-DSDTLARKKNE 295 LLH++ + + YQ I +EL Y+ +L +K IV L++ID D + L K Sbjct: 241 LLHVIDLSPIDGRDPIEDYQTIRNELEKYSPKLAEKPRIVVLNKIDLPLDEEELEELKKA 300 Query: 296 LATQCGQVPFEF-SSITGHGIPQILECLHDKIFSIRGENE 334 LA G F S++T G+ ++L L + + + E E Sbjct: 301 LAEALGWEVFYLISALTREGLDELLRALAELLEETKAEAE 340 >gnl|CDD|36702 KOG1489, KOG1489, KOG1489, Predicted GTP-binding protein (ODN superfamily) [General function prediction only]. Length = 366 Score = 274 bits (702), Expect = 3e-74 Identities = 120/326 (36%), Positives = 185/326 (56%), Gaps = 8/326 (2%) Query: 2 KFLDEAKVYIRSGDGGAGGISFRREKFIEFGGPDGGSGGRGGDVWIQATSNLNTLIDFRY 61 F+D+ +V I+ G GG+G SF R GGPDGG GG GG V+ A + Sbjct: 40 NFIDKRRVRIKGGSGGSGASSFFRGYRRPRGGPDGGDGGNGGHVYFVAKPGAFKQLSHVG 99 Query: 62 QQHFKAQHGEKGMKRNRSGAKGEDVVLTVPVGTQVFEEDGISLICDLDQEGQRIILAPGG 121 +A +GE G + G+ + + VPVGT V + + L+ +L +EG R+I A GG Sbjct: 100 SLI-QAPNGENGKSKMCHGSNAKHSEIRVPVGTVVKDIEQGKLVAELTKEGDRVIAARGG 158 Query: 122 NGGFGNAHFKSSTNQAPYYANPGILGQEKIIWLKLKLIADIGIIGLPNAGKSTFLASVTR 181 GG GN F S+ N++P ++ PG+ G+E++I L+LK IAD+G++G PNAGKST L +++R Sbjct: 159 EGGKGNKFFLSNENRSPKFSKPGLNGEERVIELELKSIADVGLVGFPNAGKSTLLNALSR 218 Query: 182 AKPKIADYPFTTLYPNLGIV-KEGYKEFILADIPGIIKNAHQGAGIGDRFLKHTERTHVL 240 AKPK+A Y FTTL P++G V + + + +ADIPGII+ AH G+G +FL+H ER L Sbjct: 219 AKPKVAHYAFTTLRPHIGTVNYDDFSQITVADIPGIIEGAHMNKGLGYKFLRHIERCKGL 278 Query: 241 LHIV---SALEENVQAAYQCILDELSAYNSELRKKIEIVGLSQIDTVDSDTLARKKNELA 297 L +V N Q +++EL Y L + ++ ++ID +++ + LA Sbjct: 279 LFVVDLSGKQLRNPWQQLQLLIEELELYEKGLADRPALIVANKIDLPEAE--KNLLSSLA 336 Query: 298 TQCGQVP-FEFSSITGHGIPQILECL 322 + S+ +G G+ ++L L Sbjct: 337 KRLQNPHVVPVSAKSGEGLEELLNGL 362 >gnl|CDD|110047 pfam01018, GTP1_OBG, GTP1/OBG. The N-terminal domain of the Spo0B-associated GTP-binding protein has the OBG fold, which is formed by three glycine-rich regions inserted into a small 8-stranded beta-sandwich these regions form six left-handed collagen-like helices packed and H-bonded together. Length = 156 Score = 223 bits (571), Expect = 4e-59 Identities = 84/156 (53%), Positives = 112/156 (71%) Query: 3 FLDEAKVYIRSGDGGAGGISFRREKFIEFGGPDGGSGGRGGDVWIQATSNLNTLIDFRYQ 62 F+D+ ++Y+ +G+GG G +SFRREK++ GGPDGG+GGRGGDV +A NL+TL+DFRY+ Sbjct: 1 FVDQVEIYVAAGNGGNGCVSFRREKYVPKGGPDGGNGGRGGDVIFEADENLDTLLDFRYK 60 Query: 63 QHFKAQHGEKGMKRNRSGAKGEDVVLTVPVGTQVFEEDGISLICDLDQEGQRIILAPGGN 122 +HFKA+ G+ G RN G GED+V+ VP GT V + D L+ DL GQR++ A GG Sbjct: 61 KHFKAEDGKHGGSRNCHGKNGEDLVIKVPPGTVVLDLDNGELLADLVHHGQRLLAAKGGK 120 Query: 123 GGFGNAHFKSSTNQAPYYANPGILGQEKIIWLKLKL 158 GG GNA FKS N+AP YA G G+E+ I L+LKL Sbjct: 121 GGLGNAAFKSPVNRAPGYALNGEPGEERDIRLELKL 156 >gnl|CDD|133298 cd01898, Obg, Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans. The E. coli homolog, ObgE is believed to function in ribosomal biogenesis. Members of the subfamily contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain. Length = 170 Score = 220 bits (563), Expect = 5e-58 Identities = 78/170 (45%), Positives = 118/170 (69%), Gaps = 3/170 (1%) Query: 160 ADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVK-EGYKEFILADIPGIIK 218 AD+G++GLPNAGKST L++++ AKPKIADYPFTTL PNLG+V+ + + F++ADIPG+I+ Sbjct: 1 ADVGLVGLPNAGKSTLLSAISNAKPKIADYPFTTLVPNLGVVRVDDGRSFVVADIPGLIE 60 Query: 219 NAHQGAGIGDRFLKHTERTHVLLHIVS-ALEENVQAAYQCILDELSAYNSELRKKIEIVG 277 A +G G+G RFL+H ERT +LLH++ + +++ Y+ I +EL YN EL +K IV Sbjct: 61 GASEGKGLGHRFLRHIERTRLLLHVIDLSGDDDPVEDYKTIRNELELYNPELLEKPRIVV 120 Query: 278 LSQIDTVDSDTLARKKNELATQCGQVP-FEFSSITGHGIPQILECLHDKI 326 L++ID +D + L EL + P F S++TG G+ ++L L + + Sbjct: 121 LNKIDLLDEEELFELLKELLKELWGKPVFPISALTGEGLDELLRKLAELL 170 >gnl|CDD|133281 cd01881, Obg_like, The Obg-like subfamily consists of five well-delimited, ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210, and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and Ygr210) are characterized by a distinct glycine-rich motif immediately following the Walker B motif (G3 box). Obg/CgtA is an essential gene that is involved in the initiation of sporulation and DNA replication in the bacteria Caulobacter and Bacillus, but its exact molecular role is unknown. Furthermore, several OBG family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. Nog1 is a nucleolar protein that might function in ribosome assembly. The DRG and Nog1 subfamilies are ubiquitous in archaea and eukaryotes, the Ygr210 subfamily is present in archaea and fungi, and the Obg and YyaF/YchF subfamilies are ubiquitous in bacteria and eukaryotes. The Obg/Nog1 and DRG subfamilies appear to form one major branch of the Obg family and the Ygr210 and YchF subfamilies form another branch. No GEFs, GAPs, or GDIs for Obg have been identified. Length = 176 Score = 166 bits (422), Expect = 1e-41 Identities = 65/176 (36%), Positives = 102/176 (57%), Gaps = 13/176 (7%) Query: 164 IIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVK-EGYKEFILADIPGIIKNAHQ 222 ++GLPN GKST L ++T AKPK+A+YPFTTL PNLG+V+ +ADIPG+I+ A + Sbjct: 1 LVGLPNVGKSTLLNALTNAKPKVANYPFTTLEPNLGVVEVPDGARIQVADIPGLIEGASE 60 Query: 223 GAGIGDRFLKHTERTHVLLHIVSALEE------NVQAAYQCILDELSAYNSE-----LRK 271 G G+G++FL H R +LH+V A E+ + Y+ + EL Y+ E L Sbjct: 61 GRGLGNQFLAHIRRADAILHVVDASEDDDIGGVDPLEDYEILNAELKLYDLETILGLLTA 120 Query: 272 KIEIVGLSQIDTVDSDTLARKK-NELATQCGQVPFEFSSITGHGIPQILECLHDKI 326 K I L++ID D++ L + ELA + G S+ T G+ +++ +++ + Sbjct: 121 KPVIYVLNKIDLDDAEELEEELVRELALEEGAEVVPISAKTEEGLDELIRAIYELL 176 >gnl|CDD|30362 COG0012, COG0012, Predicted GTPase, probable translation factor [Translation, ribosomal structure and biogenesis]. Length = 372 Score = 95.6 bits (238), Expect = 2e-20 Identities = 39/108 (36%), Positives = 60/108 (55%), Gaps = 22/108 (20%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVK----------EGYK----- 206 IGI+GLPN GKST ++T+A +IA+YPF T+ PN+G+V E K Sbjct: 5 IGIVGLPNVGKSTLFNALTKAGAEIANYPFCTIEPNVGVVYVPDCRLDELAEIVKCPPKI 64 Query: 207 -----EFILADIPGIIKNAHQGAGIGDRFLKHTERTHVLLHIVSALEE 249 EF+ DI G++K A +G G+G++FL + ++H+V + Sbjct: 65 RPAPVEFV--DIAGLVKGASKGEGLGNKFLDNIREVDAIIHVVRCFGD 110 >gnl|CDD|133299 cd01899, Ygr210, Ygr210 subfamily. Ygr210 is a member of Obg-like family and present in archaea and fungi. They are characterized by a distinct glycine-rich motif immediately following the Walker B motif. The Ygr210 and YyaF/YchF subfamilies appear to form one major branch of the Obg-like family. Among eukaryotes, the Ygr210 subfamily is represented only in fungi. These fungal proteins form a tight cluster with their archaeal orthologs, which suggests the possibility of horizontal transfer from archaea to fungi. Length = 318 Score = 91.9 bits (229), Expect = 2e-19 Identities = 39/109 (35%), Positives = 59/109 (54%), Gaps = 24/109 (22%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGI-----------------VKEG 204 IG++G PNAGKSTF + T A +IA+YPFTT+ PN+G+ + G Sbjct: 1 IGLVGKPNAGKSTFFNAATLADVEIANYPFTTIDPNVGVGYVRVECPCKELGVSCNPRYG 60 Query: 205 Y----KEFI---LADIPGIIKNAHQGAGIGDRFLKHTERTHVLLHIVSA 246 K ++ L D+ G++ AH+G G+G++FL L+H+V A Sbjct: 61 KCIDGKRYVPVELIDVAGLVPGAHEGKGLGNKFLDDLRDADALIHVVDA 109 >gnl|CDD|36704 KOG1491, KOG1491, KOG1491, Predicted GTP-binding protein (ODN superfamily) [General function prediction only]. Length = 391 Score = 87.3 bits (216), Expect = 5e-18 Identities = 50/180 (27%), Positives = 82/180 (45%), Gaps = 28/180 (15%) Query: 147 GQEKIIWLKLKLIADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIV----- 201 ++K++ + IGI+GLPN GKSTF ++T++K A++PF T+ PN V Sbjct: 8 EEKKVLLGRDGNNLKIGIVGLPNVGKSTFFNALTKSKAGAANFPFCTIDPNEARVEVPDS 67 Query: 202 -----KEGYKE------FI-LADIPGIIKNAHQGAGIGDRFLKHTERTHVLLHIVSALEE 249 Y F+ + DI G++K A G G+G++FL H + H+V A E+ Sbjct: 68 RFDLLCPIYGPKSKVPAFLTVYDIAGLVKGASAGEGLGNKFLSHIRHVDAIFHVVRAFED 127 Query: 250 N----VQAAY------QCILDELSAYNSE-LRKKIEIVGLSQIDTVDSDTLARKKNELAT 298 V+ + I +EL + E L K++E + T + + K E Sbjct: 128 TDIIHVEGGVDPVRDIEIIQEELRLKDLEFLEKRLEKLEKKHKRTKSNLETKQLKFEYGL 187 >gnl|CDD|145217 pfam01926, MMR_HSR1, GTPase of unknown function. Length = 106 Score = 83.5 bits (207), Expect = 8e-17 Identities = 38/98 (38%), Positives = 56/98 (57%), Gaps = 3/98 (3%) Query: 171 GKSTFLASVT-RAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAHQGAG-IGD 228 GKST + ++T + + ++DYP TT PN G V+ K+ IL D PGII+ A +G G +G+ Sbjct: 1 GKSTLINALTGKKRAIVSDYPGTTRDPNEGRVELDGKQIILVDTPGIIEGASKGEGELGN 60 Query: 229 RFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYN 266 R L+ E ++LH+V A E + ILD L Sbjct: 61 RTLEAIEEADLILHVVDASEG-LTEEDLEILDLLLELG 97 >gnl|CDD|133300 cd01900, YchF, YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated with the ribosome. Several members of the family, including YchF, possess the TGS domain related to the RNA-binding proteins. Experimental data and genomic analysis suggest that YchF may be part of a nucleoprotein complex and may function as a GTP-dependent translational factor. Length = 274 Score = 82.1 bits (204), Expect = 2e-16 Identities = 46/138 (33%), Positives = 72/138 (52%), Gaps = 25/138 (18%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVK----------EGYK----- 206 IGI+GLPN GKST ++T+A + A+YPF T+ PN+GIV E K Sbjct: 1 IGIVGLPNVGKSTLFNALTKAGAEAANYPFCTIEPNVGIVPVPDERLDKLAEIVKPKKIV 60 Query: 207 ----EFILADIPGIIKNAHQGAGIGDRFLKHTERTHVLLHIVSALE-ENVQAAYQCI--L 259 EF+ DI G++K A +G G+G++FL H + H+V E +++ + + Sbjct: 61 PATIEFV--DIAGLVKGASKGEGLGNKFLSHIREVDAIAHVVRCFEDDDITHVEGSVDPV 118 Query: 260 DELSAYNSELRKK-IEIV 276 ++ N+EL +E V Sbjct: 119 RDIEIINTELILADLETV 136 >gnl|CDD|31357 COG1163, DRG, Predicted GTPase [General function prediction only]. Length = 365 Score = 81.4 bits (201), Expect = 3e-16 Identities = 48/150 (32%), Positives = 69/150 (46%), Gaps = 15/150 (10%) Query: 159 IADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIK 218 A + ++G P+ GKST L +T K ++ADYPFTTL P G+++ + L D+PGII+ Sbjct: 63 DATVALVGFPSVGKSTLLNKLTNTKSEVADYPFTTLEPVPGMLEYKGAQIQLLDLPGIIE 122 Query: 219 NAHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKK------ 272 A G G G + L R L+ IV + E+ I EL L K+ Sbjct: 123 GASSGRGRGRQVLS-VARNADLIIIVLDVFEDPH-HRDIIERELEDVGIRLNKRPPDVTI 180 Query: 273 -------IEIVGLSQIDTVDSDTLARKKNE 295 I I G + +D DT+ E Sbjct: 181 KKKESGGIRINGTGPLTHLDEDTVRAILRE 210 >gnl|CDD|133296 cd01896, DRG, The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding. Length = 233 Score = 76.0 bits (188), Expect = 1e-14 Identities = 34/104 (32%), Positives = 55/104 (52%), Gaps = 4/104 (3%) Query: 160 ADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKN 219 A + ++G P+ GKST L+ +T K ++A Y FTTL G+++ + L D+PGII+ Sbjct: 1 ARVALVGFPSVGKSTLLSKLTNTKSEVAAYEFTTLTCVPGVLEYKGAKIQLLDLPGIIEG 60 Query: 220 AHQGAGIGDRFLKHTERTHVLLHIV-SALEENVQAAYQCILDEL 262 A G G G + + RT L+ +V A + + + EL Sbjct: 61 AADGKGRGRQVIA-VARTADLILMVLDATKPEGH--REILEREL 101 >gnl|CDD|133297 cd01897, NOG, NOG1 is a nucleolar GTP-binding protein present in eukaryotes ranging from trypanosomes to humans. NOG1 is functionally linked to ribosome biogenesis and found in association with the nuclear pore complexes and identified in many preribosomal complexes. Thus, defects in NOG1 can lead to defects in 60S biogenesis. The S. cerevisiae NOG1 gene is essential for cell viability, and mutations in the predicted G motifs abrogate function. It is a member of the ODN family of GTP-binding proteins that also includes the bacterial Obg and DRG proteins. Length = 168 Score = 74.1 bits (183), Expect = 6e-14 Identities = 47/176 (26%), Positives = 81/176 (46%), Gaps = 28/176 (15%) Query: 164 IIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAHQG 223 I G PN GKS+ + +TRAKP++A YPFTT +G Y + + D PG++ Sbjct: 5 IAGYPNVGKSSLVNKLTRAKPEVAPYPFTTKSLFVGHFDYKYLRWQVIDTPGLL------ 58 Query: 224 AGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILD--ELSAY------------NSEL 269 DR L+ ER + + ++AL +++AA + D E Y Sbjct: 59 ----DRPLE--ERNTIEMQAITAL-AHLRAAVLFLFDPSETCGYSLEEQLSLFEEIKPLF 111 Query: 270 RKKIEIVGLSQIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILECLHDK 325 + K IV L++ID + + L+ + E G+ + S++T G+ ++ + Sbjct: 112 KNKPVIVVLNKIDLLTFEDLSEIEEEEE-LEGEEVLKISTLTEEGVDEVKNKACEL 166 >gnl|CDD|31281 COG1084, COG1084, Predicted GTPase [General function prediction only]. Length = 346 Score = 70.7 bits (173), Expect = 5e-13 Identities = 46/170 (27%), Positives = 79/170 (46%), Gaps = 26/170 (15%) Query: 164 IIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAHQG 223 + G PN GKS+ + +T AKP++A YPFTT ++G + GY + D PG++ Sbjct: 173 VAGYPNVGKSSLVRKLTTAKPEVAPYPFTTKGIHVGHFERGYLRIQVIDTPGLL------ 226 Query: 224 AGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILD--ELSAYNSE-----------LR 270 DR L+ ER + + AL ++ + D E Y+ E L Sbjct: 227 ----DRPLE--ERNEIERQAILAL-RHLAGVILFLFDPSETCGYSLEEQISLLEEIKELF 279 Query: 271 KKIEIVGLSQIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILE 320 K +V +++ID D + L + + + G+ P + S+ G G+ ++ E Sbjct: 280 KAPIVVVINKIDIADEEKLEEIEASVLEEGGEEPLKISATKGCGLDKLRE 329 >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 = 68.9 bits (169), Expect = 2e-12 Identities = 39/165 (23%), Positives = 70/165 (42%), Gaps = 12/165 (7%) Query: 164 IIGLPNAGKSTFLASVTRAKP-KIADYPFTTLYPNLGIVKEGYK-EFILADIPGIIKNAH 221 + G NAGKS+ L ++ + ++ P TT P + + G +L D PGI + Sbjct: 1 LFGRTNAGKSSLLNALLGQEVAIVSPVPGTTTDPVEYVWELGPLGPVVLIDTPGIDEAGG 60 Query: 222 QGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIVGLSQI 281 G + + ER ++L +V A + +L+ L K + ++ L++I Sbjct: 61 LGREREELARRVLERADLILFVVDADLRAD-EEEEKLLELLRERG----KPV-LLVLNKI 114 Query: 282 DTVDSD----TLARKKNELATQCGQVPFEFSSITGHGIPQILECL 322 D + + L + L G S++TG GI ++ E L Sbjct: 115 DLLPEEEEEELLELRLLILLLLLGLPVIAVSALTGEGIDELREAL 159 >gnl|CDD|36699 KOG1486, KOG1486, KOG1486, GTP-binding protein DRG2 (ODN superfamily) [Signal transduction mechanisms]. Length = 364 Score = 65.3 bits (159), Expect = 2e-11 Identities = 36/113 (31%), Positives = 56/113 (49%), Gaps = 2/113 (1%) Query: 160 ADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKN 219 A + +IG P+ GKST L+ +T + A Y FTTL G++ L D+PGII+ Sbjct: 63 ARVALIGFPSVGKSTLLSKITSTHSEAASYEFTTLTCIPGVIHYNGANIQLLDLPGIIEG 122 Query: 220 AHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKK 272 A QG G G + + ++L ++ A + Q + + EL A L K+ Sbjct: 123 ASQGKGRGRQVIAVARTADLILMVLDATKSEDQR--EILEKELEAVGIRLNKR 173 >gnl|CDD|31353 COG1159, Era, GTPase [General function prediction only]. Length = 298 Score = 57.5 bits (139), Expect = 5e-09 Identities = 47/173 (27%), Positives = 74/173 (42%), Gaps = 20/173 (11%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPKI-ADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNA 220 + IIG PN GKST L ++ K I + P TT GIV + I D PGI K Sbjct: 9 VAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNAQIIFVDTPGIHKPK 68 Query: 221 HQGAGIGDRFLKHTERT----HVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIV 276 H +G+ K ++L +V A +E + IL++L K I+ Sbjct: 69 HA---LGELMNKAARSALKDVDLILFVVDA-DEGWGPGDEFILEQLKK-----TKTPVIL 119 Query: 277 GLSQIDTVDSDTLARKKNELATQCGQVPF----EFSSITGHGIPQILECLHDK 325 +++ID V T+ K + +PF S++ G + +LE + + Sbjct: 120 VVNKIDKVKPKTVLLKLIAFLKK--LLPFKEIVPISALKGDNVDTLLEIIKEY 170 >gnl|CDD|32443 COG2262, HflX, GTPases [General function prediction only]. Length = 411 Score = 56.8 bits (137), Expect = 8e-09 Identities = 40/176 (22%), Positives = 81/176 (46%), Gaps = 8/176 (4%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVK-EGYKEFILADIPGIIKN- 219 + ++G NAGKST ++T A +AD F TL P ++ ++ +L D G I++ Sbjct: 195 VALVGYTNAGKSTLFNALTGADVYVADQLFATLDPTTRRIELGDGRKVLLTDTVGFIRDL 254 Query: 220 AHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIVGLS 279 H L+ + +LLH+V A + + + + D L+ ++ + I+ L+ Sbjct: 255 PHPLVEAFKSTLEEVKEADLLLHVVDASDPEILEKLEAVEDVLAEIGAD--EIPIILVLN 312 Query: 280 QIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILECLHDKIFSIRGENEF 335 +ID ++ + + + + P S+ TG G+ + E + + + +R E Sbjct: 313 KIDLLEDEEILAELERGSPN----PVFISAKTGEGLDLLRERIIELLSGLRTEVTL 364 >gnl|CDD|36637 KOG1423, KOG1423, KOG1423, Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. Length = 379 Score = 54.3 bits (130), Expect = 4e-08 Identities = 56/282 (19%), Positives = 93/282 (32%), Gaps = 70/282 (24%) Query: 95 QVFEEDGISLICDLDQEGQRIILAPGGNGG-------FGNAHFKSSTNQAPYYANPGILG 147 EE G + L A FG + +++S P Y Sbjct: 7 YEMEELGHMINTHLASSLFVFSSASTSTYRERVEKLFFGYSDWETSV--GPLYPAALESR 64 Query: 148 QEKIIWLKLKLIADIGIIGLPNAGKSTFLASVTRAKPKIA-DYPFTTLYPNLGIVKEGYK 206 E+ + + + +IG PN GKST + K TT + LGI+ G Sbjct: 65 DEE----EAQKSLYVAVIGAPNVGKSTLTNQMIGQKVSAVSRKVHTTRHRILGIITSGET 120 Query: 207 EFILADIPGIIKNAHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCI-------- 258 + + D PG++ K R H+++ ++ + Q A C+ Sbjct: 121 QLVFYDTPGLVSK------------KMHRRHHLMMSVLQNPRDAAQNA-DCVVVVVDASA 167 Query: 259 ---------LDELSAY---------NSELRKKIEIVGLSQIDTVDSDTLARKKNELA--- 297 L L Y N + K + + L+ D + + LA+ K E+ Sbjct: 168 TRTPLHPRVLHMLEEYSKIPSILVMNKIDKLKQKRLLLNLKDLLTNGELAKLKLEVQEKF 227 Query: 298 ----------TQCGQVPFE----FSSITGHGIPQILECLHDK 325 T CG FE S++ G GI + + L + Sbjct: 228 TDVPSDEKWRTICGWSHFERVFMVSALYGEGIKDLKQYLMSQ 269 >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 = 52.8 bits (128), Expect = 1e-07 Identities = 46/175 (26%), Positives = 73/175 (41%), Gaps = 24/175 (13%) Query: 162 IGIIGLPNAGKSTFLASVTRAK-----PKIADYPFTTLYPNLGIVKEGYKEFILADIPGI 216 + I+G PN GKST L ++ K PK P TT GI + + I D PGI Sbjct: 6 VAIVGRPNVGKSTLLNALVGQKISIVSPK----PQTTRNRIRGIYTDDDAQIIFVDTPGI 61 Query: 217 IKNAHQGAGIGDRFLKHTERT----HVLLHIVSALEENVQAAYQCILDELSAYNSELRKK 272 K + +G+R +K ++L +V A E + IL+ L Sbjct: 62 HKPKKK---LGERMVKAAWSALKDVDLVLFVVDASEPIGEGDEF-ILELLKKSK----TP 113 Query: 273 IEIVGLSQIDTV-DSDTLARKKNEL-ATQCGQVPFEFSSITGHGIPQILECLHDK 325 + I+ L++ID V D + L +L F S++ G + ++LE + Sbjct: 114 V-ILVLNKIDLVKDKEDLLPLLEKLKELGPFAEIFPISALKGENVDELLEEIVKY 167 >gnl|CDD|36703 KOG1490, KOG1490, KOG1490, GTP-binding protein CRFG/NOG1 (ODN superfamily) [General function prediction only]. Length = 620 Score = 52.7 bits (126), Expect = 1e-07 Identities = 39/142 (27%), Positives = 65/142 (45%), Gaps = 11/142 (7%) Query: 164 IIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAHQG 223 + G PN GKS+F VTRA ++ Y FTT +G + Y + + D PGI+ Sbjct: 173 VCGYPNVGKSSFNNKVTRADDEVQPYAFTTKLLLVGHLDYKYLRWQVIDTPGILDRP--- 229 Query: 224 AGIGDRFLKHTERTHVLLHIVSALEENVQAAYQC---ILDELSAYNS---ELRKKIEIVG 277 DR + + L H+ SA+ + + C + ++ Y+S K+ I+ Sbjct: 230 --EEDRNIIEMQIITALAHLRSAVLYFMDLSEMCGYSVAAQVKLYHSIKPLFANKVTILV 287 Query: 278 LSQIDTVDSDTLARKKNELATQ 299 L++ID + + L +K EL Sbjct: 288 LNKIDAMRPEDLDQKNQELLQT 309 >gnl|CDD|30719 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion transport and metabolism]. Length = 653 Score = 52.2 bits (125), Expect = 2e-07 Identities = 38/175 (21%), Positives = 74/175 (42%), Gaps = 27/175 (15%) Query: 161 DIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIK-N 219 + ++G PN GK+T ++T A K+ ++P T+ G +K E + D+PG Sbjct: 5 TVALVGNPNVGKTTLFNALTGANQKVGNWPGVTVEKKEGKLKYKGHEIEIVDLPGTYSLT 64 Query: 220 AHQG-AGIGDRFLKHTERTHVLLHIVSA--LEENVQAAYQCILDELSAYNSELRKKIEIV 276 A+ + FL + +++++V A LE N+ Q + EL + I+ Sbjct: 65 AYSEDEKVARDFLL-EGKPDLIVNVVDATNLERNLYLTLQLL---------ELGIPM-IL 113 Query: 277 GLSQIDTVDSDTLARKKN------ELATQCGQVPFEFSSITGHGIPQILECLHDK 325 L+ ID A+K+ +L+ G + G G+ ++ + + Sbjct: 114 ALNMID------EAKKRGIRIDIEKLSKLLGVPVVPTVAKRGEGLEELKRAIIEL 162 >gnl|CDD|36700 KOG1487, KOG1487, KOG1487, GTP-binding protein DRG1 (ODN superfamily) [Signal transduction mechanisms]. Length = 358 Score = 49.2 bits (117), Expect = 1e-06 Identities = 32/86 (37%), Positives = 48/86 (55%), Gaps = 1/86 (1%) Query: 159 IADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIK 218 A +G +G P+ GKST L+ +T ++A Y FTTL G+++ + L D+PGII+ Sbjct: 59 DARVGFVGFPSVGKSTLLSKLTGTFSEVAAYEFTTLTTVPGVIRYKGAKIQLLDLPGIIE 118 Query: 219 NAHQGAGIGDRFLKHTERTHVLLHIV 244 A G G G + + RT L+ IV Sbjct: 119 GAKDGKGRGKQVIA-VARTCNLIFIV 143 >gnl|CDD|31354 COG1160, COG1160, Predicted GTPases [General function prediction only]. Length = 444 Score = 44.8 bits (106), Expect = 4e-05 Identities = 40/162 (24%), Positives = 65/162 (40%), Gaps = 12/162 (7%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPKI-ADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNA 220 + I+G PN GKST +T + I +D P T G + +EFIL D G+ Sbjct: 6 VAIVGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDAEWLGREFILIDTGGLDDGD 65 Query: 221 HQGAG--IGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIVGL 278 I ++ L E V+L +V E + A + I L R K ++ + Sbjct: 66 EDELQELIREQALIAIEEADVILFVVDG-REGITPADEEIAKIL------RRSKKPVILV 118 Query: 279 SQIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILE 320 ++ +D+ E + P S+ G GI +L+ Sbjct: 119 --VNKIDNLKAEELAYEFYSLGFGEPVPISAEHGRGIGDLLD 158 Score = 41.7 bits (98), Expect = 3e-04 Identities = 43/190 (22%), Positives = 79/190 (41%), Gaps = 19/190 (10%) Query: 147 GQEKIIWLKLKLIADIGIIGLPNAGKSTFLASVTRAKPKIA-DYPFTTLYPNLGIVKEGY 205 E+ + I IIG PN GKS+ + ++ + I D TT + Sbjct: 166 PDEEEEEEEETDPIKIAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDSIDIEFERDG 225 Query: 206 KEFILADIPGI-----IKNAHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILD 260 ++++L D GI I + + + R LK ER V+L ++ A E D Sbjct: 226 RKYVLIDTAGIRRKGKITESVEKYSVA-RTLKAIERADVVLLVIDATEGI------SEQD 278 Query: 261 ELSAYNSELRKKIEIVGLSQIDTVDSD--TLARKKNELATQCGQVPFE----FSSITGHG 314 A E + ++ +++ D V+ D T+ K +L + + F S++TG G Sbjct: 279 LRIAGLIEEAGRGIVIVVNKWDLVEEDEATMEEFKKKLRRKLPFLDFAPIVFISALTGQG 338 Query: 315 IPQILECLHD 324 + ++ E + + Sbjct: 339 LDKLFEAIKE 348 >gnl|CDD|133280 cd01879, FeoB, Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent. Length = 158 Score = 44.3 bits (106), Expect = 4e-05 Identities = 43/172 (25%), Positives = 80/172 (46%), Gaps = 29/172 (16%) Query: 164 IIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGI--IKNAH 221 ++G PN GK+T ++T A+ K+ ++P T+ G K G KE + D+PG + Sbjct: 1 LVGNPNVGKTTLFNALTGARQKVGNWPGVTVEKKEGRFKLGGKEIEIVDLPGTYSLSPYS 60 Query: 222 QGAGIGDRFLKHTERTHVLLHIV--SALEENVQAAYQCILDELSAYNSELRKKIEIVGLS 279 + + FL E+ +++++V + LE N+ Q + EL + +V L+ Sbjct: 61 EDEKVARDFL-LGEKPDLIVNVVDATNLERNLYLTLQLL---------ELGLPV-VVALN 109 Query: 280 QIDTVDSDTLARKK------NELATQCGQVP-FEFSSITGHGIPQILECLHD 324 ID A K+ ++L+ G VP S+ G GI ++ + + + Sbjct: 110 MID------EAEKRGIKIDLDKLSELLG-VPVVPTSARKGEGIDELKDAIAE 154 >gnl|CDD|35631 KOG0410, KOG0410, KOG0410, Predicted GTP binding protein [General function prediction only]. Length = 410 Score = 41.2 bits (96), Expect = 4e-04 Identities = 44/184 (23%), Positives = 75/184 (40%), Gaps = 27/184 (14%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVK-EGYKEFILADIPGIIKN- 219 I ++G NAGKST + ++T+A D F TL P L +L D G I + Sbjct: 181 IAVVGYTNAGKSTLIKALTKAALYPNDRLFATLDPTLHSAHLPSGNFVLLTDTVGFISDL 240 Query: 220 AHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIVGLS 279 Q L+ +LLH+V ++S N+E +++ + L+ Sbjct: 241 PIQLVAAFQATLEEVAEADLLLHVV----------------DISHPNAEEQRETVLHVLN 284 Query: 280 QIDTVDSDTLARK---KNELATQCGQVPFE------FSSITGHGIPQILECLHDKIFSIR 330 QI L N++ + +V E S++TG G+ ++L+ K+ S Sbjct: 285 QIGVPSEPKLQNMIEVDNKIDYEEDEVEEEKNLDVGISALTGDGLEELLKAEETKVASET 344 Query: 331 GENE 334 +E Sbjct: 345 TVDE 348 >gnl|CDD|145523 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent. Length = 188 Score = 40.5 bits (96), Expect = 7e-04 Identities = 42/170 (24%), Positives = 75/170 (44%), Gaps = 29/170 (17%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGI--IKN 219 I ++G PN GK+T ++T A+ + ++P T+ G K E + D+PG + Sbjct: 2 IALVGNPNVGKTTLFNALTGARQHVGNWPGVTVEKKEGTFKYKGYEIEIVDLPGTYSLSP 61 Query: 220 AHQGAGIGDRFLKHTERTHVLLHIVSA--LEENVQAAYQCILDELSAYNSELRKKIEIVG 277 + + +L E+ V++++V A LE N+ Q + EL + +V Sbjct: 62 YSEEEKVARDYL-LEEKPDVIINVVDATNLERNLYLTLQLL---------ELGIPV-VVA 110 Query: 278 LSQIDTVDSDTLARKK------NELATQCGQVP-FEFSSITGHGIPQILE 320 L+ +D A KK +L+ G VP S+ G GI ++ + Sbjct: 111 LNMMD------EAEKKGIKIDIKKLSELLG-VPVVPTSARKGEGIDELKD 153 >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 = 38.6 bits (91), Expect = 0.002 Identities = 45/182 (24%), Positives = 76/182 (41%), Gaps = 38/182 (20%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNL-GIVKEGYKEFILADIPGIIKNA 220 + ++G NAGKST ++T A D F TL P + +E +L D G I++ Sbjct: 44 VALVGYTNAGKSTLFNALTGADVYAEDQLFATLDPTTRRLRLPDGREVLLTDTVGFIRD- 102 Query: 221 HQGAGIGDRFLKHT----------ERTH--VLLHIVSA----LEENVQAAYQCILDELSA 264 L H E +LLH+V A EE ++ + +L EL A Sbjct: 103 ----------LPHQLVEAFRSTLEEVAEADLLLHVVDASDPDYEEQIETVEK-VLKELGA 151 Query: 265 YNSELRKKIEIVGLSQIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILECLHD 324 + I+ L++ID +D + L + + S+ TG G+ ++LE + + Sbjct: 152 ED-----IPMILVLNKIDLLDDEELEERLEAGRPDAVFI----SAKTGEGLDELLEAIEE 202 Query: 325 KI 326 + Sbjct: 203 LL 204 >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 = 0.002 Identities = 29/166 (17%), Positives = 54/166 (32%), Gaps = 18/166 (10%) Query: 164 IIGLPNAGKSTFLASVTRAKPKIADYPFT--TLYPNLGIVKEGYKEFILADIPGIIKNAH 221 ++G GK++ L + + +Y T Y V + + D G Sbjct: 1 VVGDSGVGKTSLLNRLLGGEFVPEEYETTIIDFYSKTIEVDGKKVKLQIWDTAGQE---- 56 Query: 222 QGAGIGDRFLKHTER-THVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIVG--- 277 + R ++ + + + L + I +VG Sbjct: 57 ----RFRSLRRLYYRGADGIILVYDVTDRESFENVKEWLLLILINKEGENIPIILVGNKI 112 Query: 278 -LSQIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILECL 322 L + V + LA + LA + G FE S+ TG + ++ E L Sbjct: 113 DLPEERVVSEEELAEQ---LAKELGVPYFETSAKTGENVEELFEEL 155 >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 = 38.2 bits (90), Expect = 0.003 Identities = 28/93 (30%), Positives = 43/93 (46%), Gaps = 7/93 (7%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIA-DYPFTTLYPNLGIVKEGYKEFILADIPGIIKNA 220 I IIG PN GKS+ + ++ + I D TT + K++ L D GI + Sbjct: 5 IAIIGRPNVGKSSLVNALLGEERVIVSDIAGTTRDSIDVPFEYDGKKYTLIDTAGIRRKG 64 Query: 221 HQGAGIGDRF-----LKHTERTHVLLHIVSALE 248 GI +++ LK ER V+L ++ A E Sbjct: 65 KVEEGI-EKYSVLRTLKAIERADVVLLVIDATE 96 >gnl|CDD|31355 COG1161, COG1161, Predicted GTPases [General function prediction only]. Length = 322 Score = 37.7 bits (87), Expect = 0.005 Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 8/77 (10%) Query: 146 LGQEKIIWLK----LKLIADIGIIGLPNAGKSTFL-ASVTRAKPKIADYPFTTLYPNLGI 200 L +EKI LK LK +G++G PN GKST + + + K ++ P TT Sbjct: 115 LSEEKIKRLKKKGLLKRKIRVGVVGYPNVGKSTLINRLLGKKVAKTSNRPGTTKGIQWIK 174 Query: 201 VKEGYKEFILADIPGII 217 + +G L D PGII Sbjct: 175 LDDG---IYLLDTPGII 188 >gnl|CDD|36405 KOG1191, KOG1191, KOG1191, Mitochondrial GTPase [Translation, ribosomal structure and biogenesis]. Length = 531 Score = 37.7 bits (87), Expect = 0.005 Identities = 45/184 (24%), Positives = 76/184 (41%), Gaps = 20/184 (10%) Query: 156 LKLIADIGIIGLPNAGKSTFLASVTRAKPKI-ADYPFTT---LYPNLGIVKEGYKEFILA 211 L+ I I+G PN GKS+ L +++R I + P TT + + + G L+ Sbjct: 265 LQSGLQIAIVGRPNVGKSSLLNALSREDRSIVSPVPGTTRDAIEAQVTV--NGVP-VRLS 321 Query: 212 DIPGIIKNAHQG-AGIG-DRFLKHTERTHVLLHIVSA----LEENVQAA--YQCILDELS 263 D GI + ++ G +G +R K ER V+L +V A E +++ A + L Sbjct: 322 DTAGIREESNDGIEALGIERARKRIERADVILLVVDAEESDTESDLKIARILETEGVGLV 381 Query: 264 AYNSELRKKIEIVGLSQIDTV---DSDTLARKKNELATQCGQVPF--EFSSITGHGIPQI 318 +++ K+ I+ ++ D V T A P E S T G ++ Sbjct: 382 VIVNKMEKQRIILVANKSDLVSKIPEMTKIPVVYPSAEGRSVFPIVVEVSCTTKEGCERL 441 Query: 319 LECL 322 L Sbjct: 442 STAL 445 >gnl|CDD|30833 COG0486, ThdF, Predicted GTPase [General function prediction only]. Length = 454 Score = 36.7 bits (85), Expect = 0.010 Identities = 42/179 (23%), Positives = 69/179 (38%), Gaps = 19/179 (10%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPKI-ADYPFTT---LYPNLGIVKEGYKEFILADIPGII 217 + IIG PN GKS+ L ++ I D TT + ++ + G L D GI Sbjct: 220 VVIIGRPNVGKSSLLNALLGRDRAIVTDIAGTTRDVIEEDINL--NGIP-VRLVDTAGIR 276 Query: 218 KNAHQGAGIG-DRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIV 276 + IG +R K E ++L ++ A + + ++L+ +KK IV Sbjct: 277 ETDDVVERIGIERAKKAIEEADLVLFVLDASQPLDK-------EDLALIELLPKKKPIIV 329 Query: 277 GLSQIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILECLHDKIFSIRGENEF 335 L++ D V L +K S+ TG G+ + E + G E Sbjct: 330 VLNKADLVSKIELESEKLANGDAI----ISISAKTGEGLDALREAIKQLFGKGLGNQEG 384 >gnl|CDD|30567 COG0218, COG0218, Predicted GTPase [General function prediction only]. Length = 200 Score = 36.4 bits (84), Expect = 0.013 Identities = 38/190 (20%), Positives = 68/190 (35%), Gaps = 33/190 (17%) Query: 162 IGIIGLPNAGKSTFLASVTRAKP--KIADYPFTTLYPNLGIVKEGYKEFILADIPG---- 215 I G N GKS+ + ++T K + + P T N V + E L D+PG Sbjct: 27 IAFAGRSNVGKSSLINALTNQKNLARTSKTPGRTQLINFFEVDD---ELRLVDLPGYGYA 83 Query: 216 ---IIKNAHQGAGIGDRFLKHTE--RTHVLLHIVSALEENVQAAYQCILDELSAYNSELR 270 I + K +L+ ++ + + +L EL Sbjct: 84 KVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPPKDLDREMIEFLL--------ELG 135 Query: 271 KKIEIVGLSQIDTVDSDTLARKKNELATQCGQVP------FEFSSITGHGIPQILECLHD 324 + +V L++ D + ++ N++A + + P FSS+ GI + L Sbjct: 136 IPVIVV-LTKADKLKKSERNKQLNKVAEELKKPPPDDQWVVLFSSLKKKGIDE----LKA 190 Query: 325 KIFSIRGENE 334 KI E + Sbjct: 191 KILEWLKEAK 200 >gnl|CDD|57927 cd01856, YlqF, YlqF. Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. The YlqF subfamily is represented in a phylogenetically diverse array of bacteria (including gram-positive bacteria, proteobacteria, Synechocystis, Borrelia, and Thermotoga) and in all eukaryotes.. Length = 171 Score = 35.6 bits (82), Expect = 0.021 Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 4/54 (7%) Query: 164 IIGLPNAGKSTFLASVTRAK-PKIADYPFTTLYPNLGIVKEGYKEFILADIPGI 216 ++G+PN GKST + + K K+ + P T + +K ++L D PGI Sbjct: 120 VVGIPNVGKSTLINRLRGKKVAKVGNKPGVT--KGIQWIKISPGIYLL-DTPGI 170 >gnl|CDD|57924 cd01849, YlqF_related_GTPase, YlqF-related GTPases. These proteins are found in bacteria, eukaryotes, and archaea. They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases.. Length = 155 Score = 33.8 bits (77), Expect = 0.075 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 6/58 (10%) Query: 161 DIGIIGLPNAGKSTFLASVTRA-KPKIADYP-FTTLYPNLGIVKEGYKEFILADIPGI 216 +G+IG PN GKS+ + ++ K K+ + P TT + + + L D PGI Sbjct: 102 TVGVIGYPNVGKSSVINALLNKLKLKVGNVPGTTTSQQEVKLDNKIK----LLDTPGI 155 >gnl|CDD|31297 COG1100, COG1100, GTPase SAR1 and related small G proteins [General function prediction only]. Length = 219 Score = 33.4 bits (75), Expect = 0.079 Identities = 13/59 (22%), Positives = 20/59 (33%), Gaps = 2/59 (3%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYP-FTTLYPNLGIVKEGYK-EFILADIPGIIK 218 I ++G GK+T L + + P L P I + L D G + Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEE 66 >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 = 33.3 bits (77), Expect = 0.089 Identities = 38/126 (30%), Positives = 52/126 (41%), Gaps = 30/126 (23%) Query: 208 FILADIPG---IIKNAHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCI--LDEL 262 FI D+PG IKN GAG D VLL V A +E + Q L+ L Sbjct: 55 FI--DVPGHEKFIKNMLAGAGGID---------LVLL--VVAADEGIMP--QTREHLEIL 99 Query: 263 SAYNSELRKKIEIVGLSQIDTVDSDTLARKKNELATQCGQVP------FEFSSITGHGIP 316 K+ +V L++ D VD D L + E+ F S++TG GI Sbjct: 100 ELLGI---KRG-LVVLTKADLVDEDWLELVEEEIRELLAGTFLADAPIFPVSAVTGEGIE 155 Query: 317 QILECL 322 ++ E L Sbjct: 156 ELKEYL 161 >gnl|CDD|57928 cd01857, HSR1_MMR1, HSR1/MMR1. Human HSR1, is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with sequence NKXD) are relocated to the N terminus.. Length = 141 Score = 32.4 bits (74), Expect = 0.18 Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 14/77 (18%) Query: 147 GQEKIIWLKLKLIADIGIIGLPNAGKSTFL-ASVTRAKPKIADYP-----FTTLYPNLGI 200 G + + LK A IG++G PN GKS+ + A V + K ++ P F T++ Sbjct: 71 GIVVVFFSALKENATIGLVGYPNVGKSSLINALVGKKKVSVSATPGKTKHFQTIFLT--- 127 Query: 201 VKEGYKEFILADIPGII 217 L D PG++ Sbjct: 128 -----PTITLCDCPGLV 139 >gnl|CDD|57931 cd04178, Nucleostemin_like, Nucleostemin-like. Nucleostemin (NS) is a nucleolar protein that functions as a regulator of cell growth and proliferation in stem cells and in several types of cancer cells, but is not expressed in the differentiated cells of most mammalian adult tissues. NS shuttles between the nucleolus and nucleoplasm bidirectionally at a rate that is fast and independent of cell type. Lowering GTP levels decreases the nucleolar retention of NS, and expression of NS is abruptly down-regulated during differentiation prior to terminal cell division. Found only in eukaryotes, NS consists of an N-terminal basic domain, a coiled-coil domain, a GTP-binding domain, an intermediate domain, and a C-terminal acidic domain. Experimental evidence indicates that NS uses its GTP-binding property as a molecular switch to control the transition between the nucleolus and nucleoplasm, and this process involves interaction between the basic, GTP-binding, and intermediate domains of the protein.. Length = 172 Score = 32.1 bits (73), Expect = 0.22 Identities = 9/22 (40%), Positives = 17/22 (77%) Query: 162 IGIIGLPNAGKSTFLASVTRAK 183 +G++G PN GKS+ + S+ R++ Sbjct: 120 VGVVGFPNVGKSSLINSLKRSR 141 >gnl|CDD|133294 cd01894, EngA1, EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability. Length = 157 Score = 32.0 bits (74), Expect = 0.23 Identities = 23/61 (37%), Positives = 30/61 (49%), Gaps = 7/61 (11%) Query: 164 IIGLPNAGKSTFLASVTRAKPKI-ADYPFTT---LYPNLGIVKEGYKEFILADIPGIIKN 219 I+G PN GKST +T + I D P T +Y G + G +EFIL D GI + Sbjct: 2 IVGRPNVGKSTLFNRLTGRRDAIVEDTPGVTRDRIY---GEAEWGGREFILIDTGGIEPD 58 Query: 220 A 220 Sbjct: 59 D 59 >gnl|CDD|57926 cd01855, YqeH, YqeH. YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts. Proteins of the YqeH family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases.. Length = 190 Score = 31.8 bits (72), Expect = 0.26 Identities = 22/71 (30%), Positives = 29/71 (40%), Gaps = 6/71 (8%) Query: 152 IWLKLKLIADIGIIGLPNAGKSTF---LASVTRAKPKIADYPFTTLYPN--LGIVK-EGY 205 I K D+ ++G N GKST L K K+ D T+ P L ++K Sbjct: 120 IKKLAKKGGDVYVVGATNVGKSTLINALLKKDNGKKKLKDLLTTSPIPGTTLDLIKIPLG 179 Query: 206 KEFILADIPGI 216 L D PGI Sbjct: 180 NGKKLYDTPGI 190 >gnl|CDD|37695 KOG2484, KOG2484, KOG2484, GTPase [General function prediction only]. Length = 435 Score = 31.1 bits (70), Expect = 0.46 Identities = 26/105 (24%), Positives = 39/105 (37%), Gaps = 16/105 (15%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAH 221 +GIIG PN GKS+ + S+ R K + ++ VK K+ L D PGI+ Sbjct: 255 VGIIGYPNVGKSSVINSLKRRKACNVG-NVPGVTRSMQEVK-LDKKIRLLDSPGIV---- 308 Query: 222 QGAGIGDRFLKHTERTHVLLHIVSALEENVQ--AAYQCILDELSA 264 E+ + L + + CIL S Sbjct: 309 --------PPSIDEKDALALRNCIPIGKVADPVTPVSCILKRCSK 345 >gnl|CDD|30834 COG0488, Uup, ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]. Length = 530 Score = 31.0 bits (70), Expect = 0.53 Identities = 28/119 (23%), Positives = 46/119 (38%), Gaps = 10/119 (8%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGY--KEFILADIPGIIKN 219 IG++G AGKST L + P + ++ GY +E L ++ Sbjct: 32 IGLVGRNGAGKSTLLKILAG-----ELEPDSGEVTRPKGLRVGYLSQEPPLDPEKTVLDY 86 Query: 220 AHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEIVGL 278 +G G L E + LL A + +L+EL + E R + ++GL Sbjct: 87 VIEGFGELRELLAELEEAYALLADPDDEL---LAELEALLEELDGWTLEARAEEALLGL 142 >gnl|CDD|39822 KOG4622, KOG4622, KOG4622, Predicted nucleotide kinase [General function prediction only]. Length = 291 Score = 30.9 bits (69), Expect = 0.55 Identities = 28/117 (23%), Positives = 45/117 (38%), Gaps = 18/117 (15%) Query: 159 IADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIK 218 IA + +IG+P AGKS+F + A + I + +F++ P K Sbjct: 1 IALLALIGIPAAGKSSFCRKILGAHAALRVRH---------IEHLCFDDFLMDATPSADK 51 Query: 219 NAHQGAGIGDRFLKHTERTHVLLHIVSALEENVQAAYQCILDELSAYNSELRKKIEI 275 A + G RF H E+ +SA++E+ Q S + R I Sbjct: 52 AAKEQRG---RFECHIEK------CISAIQEDTDWPPQVRRISSSGDYNSGRHIILC 99 >gnl|CDD|133364 cd04164, trmE, TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance. Length = 157 Score = 30.5 bits (70), Expect = 0.59 Identities = 8/13 (61%), Positives = 10/13 (76%) Query: 164 IIGLPNAGKSTFL 176 I+G PN GKS+ L Sbjct: 6 IVGKPNVGKSSLL 18 >gnl|CDD|36638 KOG1424, KOG1424, KOG1424, Predicted GTP-binding protein MMR1 [General function prediction only]. Length = 562 Score = 29.2 bits (65), Expect = 1.8 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 4/57 (7%) Query: 162 IGIIGLPNAGKSTFLAS-VTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGII 217 +G +G PN GKS+ + + V R K ++ P T + + L D PG++ Sbjct: 317 VGFVGYPNVGKSSTINALVGRKKVSVSSTPGKTKHFQTIFLSPSVC---LCDCPGLV 370 >gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems. Length = 267 Score = 28.9 bits (65), Expect = 1.9 Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 19/68 (27%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAH 221 +GI G+P AGKST + ++ + + + G++ +LA P Sbjct: 32 VGITGVPGAGKSTLIEALG-----------------MELRRRGHRVAVLAVDPS--SPFT 72 Query: 222 QGAGIGDR 229 G+ +GDR Sbjct: 73 GGSILGDR 80 >gnl|CDD|133278 cd01876, YihA_EngB, The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be involved in organellar targeting). Homologs of yihA are found in most Gram-positive and Gram-negative pathogenic bacteria, with the exception of Mycobacterium tuberculosis. The broad-spectrum nature of YihA and its essentiality for cell viability in bacteria make it an attractive antibacterial target. Length = 170 Score = 29.0 bits (66), Expect = 2.1 Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 5/56 (8%) Query: 162 IGIIGLPNAGKSTFLASVTRAK--PKIADYPFTTLYPNLGIVKEGYKEFILADIPG 215 I G N GKS+ + ++T K + + P T N V + +F L D+PG Sbjct: 2 IAFAGRSNVGKSSLINALTNRKKLARTSKTPGKTQLINFFNVND---KFRLVDLPG 54 >gnl|CDD|133360 cd04160, Arfrp1, Arfrp1 subfamily. Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development. Length = 167 Score = 28.8 bits (65), Expect = 2.1 Identities = 10/13 (76%), Positives = 12/13 (92%) Query: 164 IIGLPNAGKSTFL 176 I+GL NAGK+TFL Sbjct: 4 ILGLDNAGKTTFL 16 >gnl|CDD|133359 cd04159, Arl10_like, Arl10-like subfamily. Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved. Length = 159 Score = 28.8 bits (65), Expect = 2.3 Identities = 7/20 (35%), Positives = 14/20 (70%) Query: 161 DIGIIGLPNAGKSTFLASVT 180 +I ++GL N+GK+T + + Sbjct: 1 EITLVGLQNSGKTTLVNVIA 20 >gnl|CDD|133254 cd00878, Arf_Arl, Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions. Length = 158 Score = 28.7 bits (65), Expect = 2.3 Identities = 13/39 (33%), Positives = 17/39 (43%), Gaps = 7/39 (17%) Query: 161 DIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLG 199 I I+GL AGK+T L K+ T P +G Sbjct: 1 RILILGLDGAGKTTILY-------KLKLGEVVTTIPTIG 32 >gnl|CDD|35298 KOG0075, KOG0075, KOG0075, GTP-binding ADP-ribosylation factor-like protein [General function prediction only]. Length = 186 Score = 28.4 bits (63), Expect = 2.7 Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 5/71 (7%) Query: 148 QEKIIWLK---LKLIADIGIIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEG 204 ++K++W+ K ++ ++GL N+GK+T + + A+ + + T+ N+ V +G Sbjct: 6 RKKLVWICNSFWKEEMELSLVGLQNSGKTTLVNVI--ARGQYLEDMIPTVGFNMRKVTKG 63 Query: 205 YKEFILADIPG 215 L D+ G Sbjct: 64 NVTIKLWDLGG 74 >gnl|CDD|133305 cd04105, SR_beta, Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are synthesized with an N-terminal hydrophobic signal sequence that binds SRP54, a component of the SRP. SRP directs targeting of the ribosome-nascent chain complex (RNC) to the ER membrane via interaction with the SR, which is localized to the ER membrane. The RNC is then transferred to the protein-conducting channel, or translocon, which facilitates polypeptide translation across the ER membrane or integration into the ER membrane. SR-beta is found only in eukaryotes; it is believed to control the release of the signal sequence from SRP54 upon binding of the ribosome to the translocon. High expression of SR-beta has been observed in human colon cancer, suggesting it may play a role in the development of this type of cancer. Length = 203 Score = 28.4 bits (64), Expect = 3.0 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 17/61 (27%) Query: 164 IIGLPNAGKSTFL---------ASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIP 214 ++G ++GK+ ++VT +P +A + L +G K+F L D+P Sbjct: 5 LLGPSDSGKTALFTKLTTGKYRSTVTSIEPNVATF-------ILNSEGKG-KKFRLVDVP 56 Query: 215 G 215 G Sbjct: 57 G 57 >gnl|CDD|72978 cd03219, ABC_Mj1267_LivG_branched, The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E. coli branched-chain amino acid transporter. MJ1267 contains an insertion from residues 114 to 123 characteristic of LivG (Leucine-Isoleucine-Valine) homologs. The branched-chain amino acid transporter from E. coli comprises a heterodimer of ABCs (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ).. Length = 236 Score = 28.1 bits (63), Expect = 3.9 Identities = 38/151 (25%), Positives = 58/151 (38%), Gaps = 41/151 (27%) Query: 163 GIIGLPN-AGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFILADIPGIIKNAH 221 G+IG PN AGK+T ++ L P G V F DI G+ + Sbjct: 30 GLIG-PNGAGKTTLFNLISGF-----------LRPTSGSVL-----FDGEDITGLPPHEI 72 Query: 222 QGAGIGDRFLKHTERTHVLLHIVSAL--EENVQAAYQC------ILDELSAYNSELRKK- 272 GIG RT + + L ENV A Q +L E R++ Sbjct: 73 ARLGIG--------RTFQIPRLFPELTVLENVMVAAQARTGSGLLLARARREEREARERA 124 Query: 273 ---IEIVGLSQIDTVDSDTLA---RKKNELA 297 +E VGL+ + + L+ +++ E+A Sbjct: 125 EELLERVGLADLADRPAGELSYGQQRRLEIA 155 >gnl|CDD|146182 pfam03408, Foamy_virus_ENV, Foamy virus envelope protein. Expression of the envelope (Env) glycoprotein is essential for viral particle egress. This feature is unique to the Spumavirinae, a subclass of the Retroviridae. Length = 985 Score = 27.8 bits (62), Expect = 3.9 Identities = 9/23 (39%), Positives = 16/23 (69%) Query: 272 KIEIVGLSQIDTVDSDTLARKKN 294 K ++GLSQ+ ++S+T+A N Sbjct: 157 KERVLGLSQVVMINSETIANSAN 179 >gnl|CDD|33380 COG3580, COG3580, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 351 Score = 27.9 bits (62), Expect = 4.0 Identities = 26/128 (20%), Positives = 40/128 (31%), Gaps = 12/128 (9%) Query: 204 GYKEFILADIPGIIKNAHQGAGIGDRFLKHTERTHVLLHI--VSALEENVQAAYQCILDE 261 Y E I +IP + D K + + +E + A Q E Sbjct: 119 SYPEVIKNNIPDLRDGVMYLYPFLDLENKELLKEQFYKVFKEIGLSKEENEEAVQKAWKE 178 Query: 262 LSAYNSELRKKIEIVGLSQIDTVDSDTLARKKNELATQCGQVPFEFSSITGHGIPQILEC 321 Y ++RKK E V L + + E P+ F HGIP+ + Sbjct: 179 GEEYREDIRKKGEEV-LKYLK---------ENGEKGVVLAGRPYHFDPEINHGIPEKINS 228 Query: 322 LHDKIFSI 329 I + Sbjct: 229 RGIPILTE 236 >gnl|CDD|48378 cd03114, ArgK-like, The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.. Length = 148 Score = 27.9 bits (62), Expect = 4.6 Identities = 11/21 (52%), Positives = 15/21 (71%) Query: 162 IGIIGLPNAGKSTFLASVTRA 182 IGI G+P AGKST + ++ A Sbjct: 2 IGITGVPGAGKSTLIDALITA 22 >gnl|CDD|31414 COG1221, PspF, Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]. Length = 403 Score = 27.7 bits (61), Expect = 4.6 Identities = 20/74 (27%), Positives = 27/74 (36%), Gaps = 9/74 (12%) Query: 155 KLKLIADIG----IIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGIVKEGYKEFIL 210 ++K A G IIG GK F + + A+ PF N E Sbjct: 93 QIKAYAPSGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAF--NCAAYSE---NLQE 147 Query: 211 ADIPGIIKNAHQGA 224 A++ G K A GA Sbjct: 148 AELFGHEKGAFTGA 161 >gnl|CDD|35280 KOG0057, KOG0057, KOG0057, Mitochondrial Fe/S cluster exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 591 Score = 27.5 bits (61), Expect = 5.4 Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 10/72 (13%) Query: 110 QEGQRIILAPGGNGGFGNAHFKSSTNQAPYYANPGILGQEKIIWLKLKLIADIGIIGLPN 169 QE I GG+ F + HF Y +L K + + + I+G Sbjct: 339 QEAALPIELFGGSIEFDDVHFS-------YGPKRKVL---KGVSFTIPKGEKVAIVGSNG 388 Query: 170 AGKSTFLASVTR 181 +GKST L + R Sbjct: 389 SGKSTILRLLLR 400 >gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]. Length = 323 Score = 27.6 bits (61), Expect = 5.7 Identities = 11/20 (55%), Positives = 15/20 (75%) Query: 162 IGIIGLPNAGKSTFLASVTR 181 IGI G+P AGKST + ++ R Sbjct: 54 IGITGVPGAGKSTLIEALGR 73 >gnl|CDD|37696 KOG2485, KOG2485, KOG2485, Conserved ATP/GTP binding protein [General function prediction only]. Length = 335 Score = 27.6 bits (61), Expect = 5.7 Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 6/66 (9%) Query: 164 IIGLPNAGKSTFLASVTRAKPKIADYPFTTLYPNLGI-VKEGYKEF-----ILADIPGII 217 ++G+PN GKS+ + ++ + P + V E + L D PGI+ Sbjct: 148 VVGVPNVGKSSLINALRNVHLRKKKAARVGAEPGVTRRVSERIRISHRPPVYLIDTPGIL 207 Query: 218 KNAHQG 223 + Sbjct: 208 VPSIVD 213 >gnl|CDD|73015 cd03256, ABC_PhnC_transporter, ABC-type phosphate/phosphonate transport system. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only procaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.. Length = 241 Score = 27.1 bits (60), Expect = 6.8 Identities = 8/20 (40%), Positives = 11/20 (55%) Query: 162 IGIIGLPNAGKSTFLASVTR 181 + +IG AGKST L + Sbjct: 30 VALIGPSGAGKSTLLRCLNG 49 >gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2l1/Arl13 subfamily. Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene. Length = 167 Score = 27.0 bits (60), Expect = 7.6 Identities = 9/24 (37%), Positives = 16/24 (66%) Query: 162 IGIIGLPNAGKSTFLASVTRAKPK 185 + +GL NAGK+T ++++ PK Sbjct: 2 LLTVGLDNAGKTTLVSALQGEIPK 25 >gnl|CDD|36145 KOG0927, KOG0927, KOG0927, Predicted transporter (ABC superfamily) [General function prediction only]. Length = 614 Score = 26.8 bits (59), Expect = 7.7 Identities = 11/38 (28%), Positives = 16/38 (42%), Gaps = 4/38 (10%) Query: 163 GIIGLPNAGKSTFLASVTR----AKPKIADYPFTTLYP 196 G+IG +GKSTFL ++ I Y + Sbjct: 105 GLIGPNGSGKSTFLRAIAGREVPIPEHIDFYLLSREIE 142 >gnl|CDD|57930 cd01859, MJ1464, MJ1464. This family represents archaeal GTPase typified by the protein MJ1464 from Methanococcus jannaschii. The members of this family show a circular permutation of the GTPase signature motifs so that C-terminal strands 5, 6, and 7 (strands 6 contain the NKxD motif) are relocated to the N terminus.. Length = 156 Score = 26.8 bits (59), Expect = 8.5 Identities = 7/20 (35%), Positives = 14/20 (70%) Query: 162 IGIIGLPNAGKSTFLASVTR 181 +G++G PN GKS+ + ++ Sbjct: 104 VGVVGYPNVGKSSIINALKG 123 >gnl|CDD|72979 cd03220, ABC_KpsT_Wzt, ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ABC. In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenzae) and a cytoplasmic membrane protein MPA2.. Length = 224 Score = 26.7 bits (59), Expect = 9.0 Identities = 10/15 (66%), Positives = 11/15 (73%) Query: 162 IGIIGLPNAGKSTFL 176 IG+IG AGKST L Sbjct: 51 IGLIGRNGAGKSTLL 65 >gnl|CDD|31329 COG1134, TagH, ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]. Length = 249 Score = 26.7 bits (59), Expect = 9.1 Identities = 10/15 (66%), Positives = 11/15 (73%) Query: 162 IGIIGLPNAGKSTFL 176 +GIIG AGKST L Sbjct: 56 VGIIGHNGAGKSTLL 70 >gnl|CDD|57929 cd01858, NGP_1, NGP-1. Autoantigen NGP-1 (Nucleolar G-protein gene 1) has been shown to localize in the nucleolus and nucleolar organizers in all cell types analyzed, which is indicative of a function in ribosomal assembly. NGP-1 and its homologs show a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with NKXD motif) are relocated to the N terminus.. Length = 157 Score = 26.7 bits (59), Expect = 9.2 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 6/57 (10%) Query: 162 IGIIGLPNAGKSTFLASVTRAKP-KIADYPF-TTLYPNLGIVKEGYKEFILADIPGI 216 +G IG PN GKS+ + ++ K K+A P T ++ + ++K Y L D PG+ Sbjct: 105 VGFIGYPNVGKSSIINTLRSKKVCKVAPIPGETKVWQYITLMKRIY----LIDCPGV 157 >gnl|CDD|133353 cd04153, Arl5_Arl8, Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library. It is found in brain, heart, lung, cartilage, and kidney. No function has been assigned for Arl8 to date. Length = 174 Score = 26.5 bits (59), Expect = 9.8 Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 4/22 (18%) Query: 155 KLKLIADIGIIGLPNAGKSTFL 176 + K+I I+GL NAGK+T L Sbjct: 15 EYKVI----IVGLDNAGKTTIL 32 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 0.140 0.412 Gapped Lambda K H 0.267 0.0656 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,096,663 Number of extensions: 218810 Number of successful extensions: 791 Number of sequences better than 10.0: 1 Number of HSP's gapped: 771 Number of HSP's successfully gapped: 80 Length of query: 335 Length of database: 6,263,737 Length adjustment: 94 Effective length of query: 241 Effective length of database: 4,232,491 Effective search space: 1020030331 Effective search space used: 1020030331 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 58 (26.3 bits)