RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780809|ref|YP_003065222.1| tRNA modification GTPase TrmE [Candidatus Liberibacter asiaticus str. psy62] (440 letters) >gnl|CDD|30833 COG0486, ThdF, Predicted GTPase [General function prediction only]. Length = 454 Score = 441 bits (1135), Expect = e-124 Identities = 186/454 (40%), Positives = 261/454 (57%), Gaps = 19/454 (4%) Query: 4 EKETIFAVSTGALPSAISIIRLSGPSCFQVCEFICKKKK-PFPRKASLRYFFGLDGRILD 62 +TI A++T AI I+R+SGP ++ + + K P PR A + +G I+D Sbjct: 3 MFDTIAAIATAPGEGAIGIVRISGPDALEIAQKLFGGLKLPKPRTAHYGHIKDENGEIID 62 Query: 63 KGLLIVFPSPESFTGEDSAEFHVHGGIAVVNGILEELAKMPNLRLANPGEFSRRAFENGK 122 + L++ F +P SFTGED E HGG VVN ILE L K+ RLA PGEFS+RAF NGK Sbjct: 63 EVLVLYFKAPNSFTGEDVVEIQCHGGPVVVNLILELLLKLG-ARLAEPGEFSKRAFLNGK 121 Query: 123 IDLLEAESLADLISSETEMQRRLSMEGMSGELSSLYGQWIDKLTHIRSFIEADLDFSEEE 182 +DL +AE++ADLI ++TE R+++ + G LS L + + L + + +EA++DF EE+ Sbjct: 122 LDLTQAEAIADLIDAKTEQAARIALRQLQGALSQLINELREALLELLAQVEANIDFPEED 181 Query: 183 DVQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKK 242 + K + + L ++ ++ K G+I+R G K+VI+G N GKSSL NAL + Sbjct: 182 IEELVLEK-IREKLEELIAELDELLATAKQGKILREGLKVVIIGRPNVGKSSLLNALLGR 240 Query: 243 DVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLEVENADLI 302 D AIVTDI GTTRDV+ D++L G V++ DTAGIRETDD+VE+ GI+R +E ADL+ Sbjct: 241 DRAIVTDIAGTTRDVIEEDINLNGIPVRLVDTAGIRETDDVVERIGIERAKKAIEEADLV 300 Query: 303 LLL-------KEINSKKEISFPKNIDFIFIGTKSDLYSTYTEEYDHL--------ISSFT 347 L + + + PK I + K+DL S E + L IS+ T Sbjct: 301 LFVLDASQPLDKEDLALIELLPKKKPIIVVLNKADLVSKIELESEKLANGDAIISISAKT 360 Query: 348 GEGLEELINKIKSILSNKFKKLPFSIPSHKRHLYHLSQTVRYLEMA-SLNEKDCGLDIIA 406 GEGL+ L IK + S+ RH+ L Q +LE A E LD++A Sbjct: 361 GEGLDALREAIKQLFGKGLGNQEGLFLSNLRHIQLLEQAAEHLEDALQQLELGQPLDLLA 420 Query: 407 ENLRLASVSLGKITGCVDVEQLLDIIFSKFCIGK 440 E+LRLA +LG+ITG E LLD IFS FCIGK Sbjct: 421 EDLRLAQEALGEITGEFVSEDLLDEIFSNFCIGK 454 >gnl|CDD|36405 KOG1191, KOG1191, KOG1191, Mitochondrial GTPase [Translation, ribosomal structure and biogenesis]. Length = 531 Score = 296 bits (758), Expect = 1e-80 Identities = 175/490 (35%), Positives = 249/490 (50%), Gaps = 57/490 (11%) Query: 7 TIFAVSTGA-LPSAISIIRLSGP-SCFQVCEFICKKKKPFPRKASLR---------YFFG 55 TIFA+STG L SAI+I R+SGP + + P R A LR Y Sbjct: 43 TIFALSTGIGLTSAIAIFRISGPDATKVARRLLRSVMVPKRRNAGLRALYNPEVRVYVVD 102 Query: 56 LDGRILDKGLLIVFPSPESFTGEDSAEFHVHGGIAVVNGILEELAK--MPNLRLANPGEF 113 DG D+ L + F P+SFTGED E HG AVV G+L L +P +RLA PGEF Sbjct: 103 EDGVTRDRALGLYFLGPQSFTGEDVVELQTHGSSAVVVGVLTALGASGIPGIRLAEPGEF 162 Query: 114 SRRAFENGKIDLLEAESLADLISSETEMQRRLSMEGMSGELSSLYGQWIDKLTHIRSFIE 173 +RRAF NGK+DL +AE + DLI +ETE QRR +++ ++GE +L W L + +E Sbjct: 163 TRRAFLNGKLDLTQAEGIIDLIVAETESQRRAALDEVAGEALALCFGWRKILIEALAGLE 222 Query: 174 ADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKS 233 A +DF EE ++ + E+ + L L +D+ SH+++ E +++G +I I+G N GKS Sbjct: 223 ARIDFEEERPLEEIETVEIFIESLSLLDDVLSHLNKADEIERLQSGLQIAIVGRPNVGKS 282 Query: 234 SLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRE-TDDIVEKEGIKRT 292 SL NAL+++D +IV+ +PGTTRD + + + G V++SDTAGIRE ++D +E GI+R Sbjct: 283 SLLNALSREDRSIVSPVPGTTRDAIEAQVTVNGVPVRLSDTAGIREESNDGIEALGIERA 342 Query: 293 FLEVENADLILLLKEINS----------------KKEISFPKNIDF----IFIGTKSDLY 332 +E AD+ILL+ + + N I + KSDL Sbjct: 343 RKRIERADVILLVVDAEESDTESDLKIARILETEGVGLVVIVNKMEKQRIILVANKSDLV 402 Query: 333 STYTE-----------------EYDHLISSFTGEGLEELINKIKSIL---SNKFKKLPFS 372 S E +S T EG E L + +I+ P + Sbjct: 403 SKIPEMTKIPVVYPSAEGRSVFPIVVEVSCTTKEGCERLSTALLNIVERLVVSPHSAPPT 462 Query: 373 IPSHKRHLYHLSQTVRY-LEMASL-NEKDCGLDIIAENLRLASVSLGKITGCVDVEQLLD 430 + S KR L LE L + +D+ E LRLA S+ +ITG E++L Sbjct: 463 L-SQKRIKELLRTCAAPELERRFLAKQLKEDIDLAGEPLRLAQRSIARITGGGGTEEVLS 521 Query: 431 IIFSKFCIGK 440 IF KFCIGK Sbjct: 522 SIFQKFCIGK 531 >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 = 181 bits (463), Expect = 2e-46 Identities = 64/156 (41%), Positives = 90/156 (57%), Gaps = 12/156 (7%) Query: 219 GYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR 278 G K+VI+G N GKSSL NALA +D AIV+DI GTTRDV+ +D+ G V++ DTAGIR Sbjct: 1 GIKVVIVGKPNVGKSSLLNALAGRDRAIVSDIAGTTRDVIEESIDIGGIPVRLIDTAGIR 60 Query: 279 ETDDIVEKEGIKRTFLEVENADLILLL----KEINS--KKEISFPKNIDFIFIGTKSDLY 332 ET+D +EK GI+R +E ADL+L + + ++ + + P + I + KSDL Sbjct: 61 ETEDEIEKIGIERAREAIEEADLVLFVIDASRGLDEEDLEILELPADKPIIVVLNKSDLL 120 Query: 333 STYTEEYD------HLISSFTGEGLEELINKIKSIL 362 IS+ TGEGL+EL + + Sbjct: 121 PDSELLSLLAGKPIIAISAKTGEGLDELKEALLELA 156 >gnl|CDD|145217 pfam01926, MMR_HSR1, GTPase of unknown function. Length = 106 Score = 93.9 bits (234), Expect = 8e-20 Identities = 35/75 (46%), Positives = 44/75 (58%) Query: 231 GKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIK 290 GKS+L NAL K AIV+D PGTTRD ++L+G + + DT GI E E E Sbjct: 1 GKSTLINALTGKKRAIVSDYPGTTRDPNEGRVELDGKQIILVDTPGIIEGASKGEGELGN 60 Query: 291 RTFLEVENADLILLL 305 RT +E ADLIL + Sbjct: 61 RTLEAIEEADLILHV 75 >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 = 89.8 bits (224), Expect = 1e-18 Identities = 37/88 (42%), Positives = 55/88 (62%), Gaps = 3/88 (3%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRE- 279 +I I+G N GKSSL NAL ++ IV+DI GTTRD + + + +G + DTAGIR Sbjct: 4 RIAIIGRPNVGKSSLVNALLGEERVIVSDIAGTTRDSIDVPFEYDGKKYTLIDTAGIRRK 63 Query: 280 --TDDIVEKEGIKRTFLEVENADLILLL 305 ++ +EK + RT +E AD++LL+ Sbjct: 64 GKVEEGIEKYSVLRTLKAIERADVVLLV 91 >gnl|CDD|31354 COG1160, COG1160, Predicted GTPases [General function prediction only]. Length = 444 Score = 85.2 bits (211), Expect = 3e-17 Identities = 57/183 (31%), Positives = 87/183 (47%), Gaps = 33/183 (18%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR-- 278 KI I+G N GKSSL NA+ ++ IV+DI GTTRD + I+ + +G + DTAGIR Sbjct: 180 KIAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDSIDIEFERDGRKYVLIDTAGIRRK 239 Query: 279 -ETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEIS--FPKNIDFI--------FIGT 327 + + VEK + RT +E AD++LL+ I++ + IS + I + Sbjct: 240 GKITESVEKYSVARTLKAIERADVVLLV--IDATEGISEQDLRIAGLIEEAGRGIVIVVN 297 Query: 328 KSDLYSTYTEEYDHL------------------ISSFTGEGLEELINKIKSILSNKFKKL 369 K DL + IS+ TG+GL++L IK I +++ Sbjct: 298 KWDLVEEDEATMEEFKKKLRRKLPFLDFAPIVFISALTGQGLDKLFEAIKEIYECATRRI 357 Query: 370 PFS 372 S Sbjct: 358 STS 360 Score = 81.4 bits (201), Expect = 5e-16 Identities = 43/166 (25%), Positives = 77/166 (46%), Gaps = 24/166 (14%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRE- 279 + I+G N GKS+LFN L + +AIV+D PG TRD + D + G + DT G+ + Sbjct: 5 VVAIVGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDAEWLGREFILIDTGGLDDG 64 Query: 280 TDDIVEKEGIKRTFLEVENADLILLLKEINSKKEIS----------FPKNIDFIFIGTKS 329 +D +++ ++ + +E AD+IL + ++ ++ I+ I + K Sbjct: 65 DEDELQELIREQALIAIEEADVILFV--VDGREGITPADEEIAKILRRSKKPVILVVNKI 122 Query: 330 D----------LYSTYTEEYDHLISSFTGEGLEELINKIKSILSNK 365 D YS E IS+ G G+ +L++ + +L Sbjct: 123 DNLKAEELAYEFYSLGFGEP-VPISAEHGRGIGDLLDAVLELLPPD 167 >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 = 83.1 bits (206), Expect = 1e-16 Identities = 48/164 (29%), Positives = 73/164 (44%), Gaps = 26/164 (15%) Query: 224 ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGY-LVKISDTAGIRETDD 282 + G +NAGKSSL NAL ++VAIV+ +PGTT D + +L V + DT GI E Sbjct: 1 LFGRTNAGKSSLLNALLGQEVAIVSPVPGTTTDPVEYVWELGPLGPVVLIDTPGIDEAGG 60 Query: 283 IVEKEGIKRTFLEVENADLILLLKEINSKKEISFPK--------NIDFIFIGTKSDLYST 334 + +E + +E ADLIL + + + + + K + + K DL Sbjct: 61 L-GREREELARRVLERADLILFVVDADLRADEEEEKLLELLRERGKPVLLVLNKIDLLPE 119 Query: 335 YTEEYD----------------HLISSFTGEGLEELINKIKSIL 362 EE +S+ TGEG++EL + L Sbjct: 120 EEEEELLELRLLILLLLLGLPVIAVSALTGEGIDELREALIEAL 163 >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 = 82.5 bits (205), Expect = 2e-16 Identities = 45/157 (28%), Positives = 70/157 (44%), Gaps = 17/157 (10%) Query: 223 VILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDD 282 I+G N GKS+LFN L + AIV D PG TRD + + + G + DT GI D+ Sbjct: 1 AIVGRPNVGKSTLFNRLTGRRDAIVEDTPGVTRDRIYGEAEWGGREFILIDTGGIEPDDE 60 Query: 283 IVEKEGIKRTFLEVENADLILLL---KEINSKKEISF-----PKNIDFIFIGTKSDLYST 334 + KE ++ L +E AD+IL + +E + + I + K D Sbjct: 61 GISKEIREQAELAIEEADVILFVVDGREGLTPADEEIAKYLRKSKKPVILVVNKVDNIKE 120 Query: 335 YTEEYD---------HLISSFTGEGLEELINKIKSIL 362 E + IS+ G G+ +L++ I +L Sbjct: 121 EDEAAEFYSLGFGEPIPISAEHGRGIGDLLDAILELL 157 >gnl|CDD|30719 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion transport and metabolism]. Length = 653 Score = 56.8 bits (137), Expect = 1e-08 Identities = 49/238 (20%), Positives = 88/238 (36%), Gaps = 27/238 (11%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRE 279 + ++G+ N GK++LFNAL + V + PG T + L +G+ ++I D G Sbjct: 4 LTVALVGNPNVGKTTLFNALTGANQK-VGNWPGVTVEKKEGKLKYKGHEIEIVDLPGTYS 62 Query: 280 TDDIVEKEGIKRTFLEVENADLIL-LLKEINSKKEISFPK-----NIDFIFIGTKSDLYS 333 E E + R FL DLI+ ++ N ++ + I I D Sbjct: 63 LTAYSEDEKVARDFLLEGKPDLIVNVVDATNLERNLYLTLQLLELGIPMILALNMIDEAK 122 Query: 334 TYTEEYDH------------LISSFTGEGLEELINKIKSILSNKFKKL----PFSIPSHK 377 D + GEGLEEL I + +K I Sbjct: 123 KRGIRIDIEKLSKLLGVPVVPTVAKRGEGLEELKRAIIELAESKTTPREVDYGEEIEEEI 182 Query: 378 RHLYHLSQTVRYLEMASLNEKDCGLDIIAENLRLASVSLGKITGCVDVEQLLDIIFSK 435 + L LS+ R+L + L +++ L+ + ++ + E+ ++ + Sbjct: 183 KELEALSEDPRWLAIKLLE----DDELVEAVLKEPEKRVEELLEELSEEEGHLLLIAD 236 >gnl|CDD|57925 cd01854, YjeQ_engC, YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.. Length = 287 Score = 56.3 bits (136), Expect = 1e-08 Identities = 35/136 (25%), Positives = 56/136 (41%), Gaps = 18/136 (13%) Query: 174 ADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQG--KLGEIIRNGYKIVILGHSNAG 231 ADL EEE+++ + + +L +S+ +G +L E ++ V++G S G Sbjct: 119 ADLLDDEEEELELVEALALGYPVLA----VSAKTGEGLDELREYLKGK-TSVLVGQSGVG 173 Query: 232 KSSLFNALAKKDVAIVTDIPG-------TTRDVLTIDLDLEGYLVKISDTAGIRETDDI- 283 KS+L NAL +I TT L G L+ DT G RE + Sbjct: 174 KSTLINALLPDLDLATGEISEKLGRGRHTTTHRELFPLPGGGLLI---DTPGFREFGLLH 230 Query: 284 VEKEGIKRTFLEVENA 299 ++ E + F E Sbjct: 231 IDPEELAHYFPEFREL 246 >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 = 55.9 bits (136), Expect = 2e-08 Identities = 40/170 (23%), Positives = 69/170 (40%), Gaps = 34/170 (20%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTR-DVLTIDLDLEGYLVKISDTAGIRE 279 + I+G N GKS+L NAL + ++IV+ P TTR + I D + ++ + DT GI Sbjct: 5 FVAIVGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIYTDDDAQIIFV-DTPGI-- 61 Query: 280 TDDIVEKEGIKRTFLEV-----ENADLILLLKEINSKK--------EISFPKNIDFIFIG 326 K+ + ++ ++ DL+L + + + E+ I + Sbjct: 62 ---HKPKKKLGERMVKAAWSALKDVDLVLFVVDASEPIGEGDEFILELLKKSKTPVILVL 118 Query: 327 TKSDL----------YSTYTEEYD----HLISSFTGEGLEELINKIKSIL 362 K DL E IS+ GE ++EL+ +I L Sbjct: 119 NKIDLVKDKEDLLPLLEKLKELGPFAEIFPISALKGENVDELLEEIVKYL 168 >gnl|CDD|31353 COG1159, Era, GTPase [General function prediction only]. Length = 298 Score = 55.2 bits (133), Expect = 3e-08 Identities = 38/165 (23%), Positives = 66/165 (40%), Gaps = 24/165 (14%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRD-VLTIDLDLEGYLVKISDTAGIRET 280 + I+G N GKS+L NAL + ++IV+ P TTR+ + I ++ + DT GI + Sbjct: 9 VAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNAQIIFV-DTPGIHKP 67 Query: 281 DDIVEKEGIKRTFLEVENADLILLLKEINSKK--------EISFPKNIDFIFIGTKSDLY 332 + + K +++ DLIL + + + E I + K D Sbjct: 68 KHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLKKTKTPVILVVNKIDKV 127 Query: 333 STYTEEYDHL--------------ISSFTGEGLEELINKIKSILS 363 T + IS+ G+ ++ L+ IK L Sbjct: 128 KPKTVLLKLIAFLKKLLPFKEIVPISALKGDNVDTLLEIIKEYLP 172 >gnl|CDD|32443 COG2262, HflX, GTPases [General function prediction only]. Length = 411 Score = 55.3 bits (133), Expect = 3e-08 Identities = 57/184 (30%), Positives = 81/184 (44%), Gaps = 29/184 (15%) Query: 217 RNGYKIV-ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLE-GYLVKISDT 274 R+G +V ++G++NAGKS+LFNAL DV V D T D T ++L G V ++DT Sbjct: 189 RSGIPLVALVGYTNAGKSTLFNALTGADVY-VADQLFATLDPTTRRIELGDGRKVLLTDT 247 Query: 275 AG-IRETD-DIVEKEGIKRTFLEVENADLILL-------------------LKEIN--SK 311 G IR+ +VE K T EV+ ADL+L L EI Sbjct: 248 VGFIRDLPHPLVE--AFKSTLEEVKEADLLLHVVDASDPEILEKLEAVEDVLAEIGADEI 305 Query: 312 KEISFPKNIDFIFIGTKSDLYSTYTEEYDHLISSFTGEGLEELINKIKSILSNKFKKLPF 371 I ID + + IS+ TGEGL+ L +I +LS ++ Sbjct: 306 PIILVLNKIDLLEDEEILAELERGSPNP-VFISAKTGEGLDLLRERIIELLSGLRTEVTL 364 Query: 372 SIPS 375 +P Sbjct: 365 ELPY 368 >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 = 54.0 bits (130), Expect = 8e-08 Identities = 33/156 (21%), Positives = 57/156 (36%), Gaps = 22/156 (14%) Query: 224 ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKIS--DTAGIRETD 281 ++G S GK+SL N L + T D + ++++G VK+ DTAG Sbjct: 1 VVGDSGVGKTSLLNRLLGGEFVPEEYET-TIIDFYSKTIEVDGKKVKLQIWDTAGQERFR 59 Query: 282 DIVEK-----EGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFIFIGTKSDLYSTYT 336 + +GI + + + + + +NI I +G K DL Sbjct: 60 SLRRLYYRGADGIILVYDVTDRESFENVKEWLLLILINKEGENIPIILVGNKIDLPEERV 119 Query: 337 EEYD--------------HLISSFTGEGLEELINKI 358 + S+ TGE +EEL ++ Sbjct: 120 VSEEELAEQLAKELGVPYFETSAKTGENVEELFEEL 155 >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 = 53.7 bits (129), Expect = 9e-08 Identities = 26/69 (37%), Positives = 36/69 (52%), Gaps = 11/69 (15%) Query: 217 RNGYKIVILGHSNAGKSSLFNALAKKD--------VAIVTDIPGTTRDVLTIDLDLEGYL 268 + G + ++G +N GKS+L NAL KKD + + IPGTT D++ I L L Sbjct: 125 KKGGDVYVVGATNVGKSTLINALLKKDNGKKKLKDLLTTSPIPGTTLDLIKIPLGNGKKL 184 Query: 269 VKISDTAGI 277 DT GI Sbjct: 185 Y---DTPGI 190 Score = 32.9 bits (75), Expect = 0.19 Identities = 18/62 (29%), Positives = 21/62 (33%), Gaps = 20/62 (32%) Query: 318 KNIDFIFIGTKSDLYSTYTEEYD--------------------HLISSFTGEGLEELINK 357 N I +G K DL LIS+ G G+EELIN Sbjct: 60 GNNPVILVGNKIDLLPKDKNLVRIKNWLRAKAAAGLGLKPKDVILISAKKGWGVEELINA 119 Query: 358 IK 359 IK Sbjct: 120 IK 121 >gnl|CDD|146027 pfam03193, DUF258, Protein of unknown function, DUF258. Length = 161 Score = 53.7 bits (130), Expect = 1e-07 Identities = 25/86 (29%), Positives = 33/86 (38%), Gaps = 11/86 (12%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPG-------TTRDVLTIDLDLEGYLVKISDT 274 V+ G S GKS+L NAL + +I TT V L G L+ DT Sbjct: 38 SVLAGQSGVGKSTLLNALLPELDLRTGEISEKLGRGRHTTTHVELFPLPGGGLLI---DT 94 Query: 275 AGIRETD-DIVEKEGIKRTFLEVENA 299 G RE ++ E + F E Sbjct: 95 PGFRELGLWHLDPEELAEYFPEFREL 120 >gnl|CDD|31356 COG1162, COG1162, Predicted GTPases [General function prediction only]. Length = 301 Score = 53.4 bits (128), Expect = 1e-07 Identities = 32/133 (24%), Positives = 49/133 (36%), Gaps = 14/133 (10%) Query: 177 DFSEEEDVQNFSSKEVLNDIL--FLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSS 234 D ++E+ DI L + +L E++ V+LG S GKS+ Sbjct: 121 DLLDDEEAAVKELLREYEDIGYPVLFVSAKNGDGLEELAELLAGKI-TVLLGQSGVGKST 179 Query: 235 LFNALAKKDVAIVTDIPG-------TTRDVLTIDLDLEGYLVKISDTAGIRETD-DIVEK 286 L NAL + +I TT V L G+++ DT G R +E Sbjct: 180 LINALLPELNQKTGEISEKLGRGRHTTTHVELFPLPGGGWII---DTPGFRSLGLAHLEP 236 Query: 287 EGIKRTFLEVENA 299 E + + F E Sbjct: 237 EDLVQAFPEFAEL 249 >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 = 52.1 bits (125), Expect = 3e-07 Identities = 29/88 (32%), Positives = 43/88 (48%), Gaps = 7/88 (7%) Query: 190 KEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTD 249 K++L L DI ++G L IR +++G N GKS+L N L K VA V + Sbjct: 90 KKLLKAAKKLLKDIEKLKAKGLLPRGIR----AMVVGIPNVGKSTLINRLRGKKVAKVGN 145 Query: 250 IPGTTRDVLTIDLDLEGYLVKISDTAGI 277 PG T+ + I + + + DT GI Sbjct: 146 KPGVTKGIQWIKI---SPGIYLLDTPGI 170 >gnl|CDD|31355 COG1161, COG1161, Predicted GTPases [General function prediction only]. Length = 322 Score = 51.2 bits (122), Expect = 5e-07 Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 3/85 (3%) Query: 207 ISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEG 266 I + K +++ ++ ++G+ N GKS+L N L K VA ++ PGTT+ + I LD Sbjct: 120 IKRLKKKGLLKRKIRVGVVGYPNVGKSTLINRLLGKKVAKTSNRPGTTKGIQWIKLDDGI 179 Query: 267 YLVKISDTAGIRETDDIVEKEGIKR 291 YL+ DT GI ++ + + Sbjct: 180 YLL---DTPGIIPPKFDDDELVLLK 201 >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 = 50.5 bits (122), Expect = 8e-07 Identities = 58/180 (32%), Positives = 81/180 (45%), Gaps = 47/180 (26%) Query: 217 RNGYKIV-ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLT--IDLDLEGYLVKISD 273 R+G V ++G++NAGKS+LFNAL DV D T D T + L +G V ++D Sbjct: 38 RSGIPTVALVGYTNAGKSTLFNALTGADVY-AEDQLFATLDPTTRRLRLP-DGREVLLTD 95 Query: 274 TAG-IRETD---DIVEKEGIKRTFLEVENADLILL-------------------LKEINS 310 T G IR D +V E + T EV ADL+L LKE+ + Sbjct: 96 TVGFIR--DLPHQLV--EAFRSTLEEVAEADLLLHVVDASDPDYEEQIETVEKVLKELGA 151 Query: 311 KKEISFPKNIDFIFIGTKSDLYSTYTEEYD--------HLISSFTGEGLEELINKIKSIL 362 ++I I + K DL E IS+ TGEGL+EL+ I+ +L Sbjct: 152 -------EDIPMILVLNKIDLLDDEELEERLEAGRPDAVFISAKTGEGLDELLEAIEELL 204 >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 = 50.2 bits (121), Expect = 1e-06 Identities = 46/181 (25%), Positives = 70/181 (38%), Gaps = 52/181 (28%) Query: 222 IVILGHSNAGKSSLFNALA-KKDVAIVTDIPGTTRDVLTI---DLDLEGYLV-------- 269 I G SN GKSSL NAL +K +A + PG T+ I +++ + LV Sbjct: 2 IAFAGRSNVGKSSLINALTNRKKLARTSKTPGKTQ---LINFFNVNDKFRLVDLPGYGYA 58 Query: 270 KISDTAGIRETDDIVEKEGIKRTFLEV-ENADLILLLKEINSKKEIS----------FPK 318 K+S + I E +LE EN ++LL I+S+ + Sbjct: 59 KVSKEVKEKWGKLIEE-------YLENRENLKGVVLL--IDSRHGPTEIDLEMLDWLEEL 109 Query: 319 NIDFIFIGTKSD-------------LYSTYTEEYDH----LISSFTGEGLEELINKIKSI 361 I F+ + TK+D + L SS G+G++EL I+ Sbjct: 110 GIPFLVVLTKADKLKKSELAKALKEIKKELKLFEIDPPIILFSSLKGQGIDELRALIEKW 169 Query: 362 L 362 L Sbjct: 170 L 170 >gnl|CDD|33396 COG3596, COG3596, Predicted GTPase [General function prediction only]. Length = 296 Score = 48.8 bits (116), Expect = 3e-06 Identities = 30/123 (24%), Positives = 60/123 (48%), Gaps = 5/123 (4%) Query: 192 VLNDILFLKNDISSHIS-QGKLGEIIRNGY-KIVILGHSNAGKSSLFNALAKKDVAIVTD 249 VL +L L + +S I Q ++ ++ ++++G + AGKSSL NAL + +V V+ Sbjct: 10 VLKGLLGLPSLLSERILEQLRMLQLTEKEPVNVLLMGATGAGKSSLINALFQGEVKEVSK 69 Query: 250 IPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLEVEN-ADLILLLKEI 308 + T + L +G + + DT G+ D + ++ + + DL+L L + Sbjct: 70 VGVGTDITTRLRLSYDGENLVLWDTPGLG--DGKDKDAEHRQLYRDYLPKLDLVLWLIKA 127 Query: 309 NSK 311 + + Sbjct: 128 DDR 130 >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 = 47.9 bits (115), Expect = 6e-06 Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 1/83 (1%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRET 280 I ++G+ N GK++LFNAL V + PG T + +GY ++I D G Sbjct: 1 TIALVGNPNVGKTTLFNALTGARQ-HVGNWPGVTVEKKEGTFKYKGYEIEIVDLPGTYSL 59 Query: 281 DDIVEKEGIKRTFLEVENADLIL 303 E+E + R +L E D+I+ Sbjct: 60 SPYSEEEKVARDYLLEEKPDVII 82 >gnl|CDD|35631 KOG0410, KOG0410, KOG0410, Predicted GTP binding protein [General function prediction only]. Length = 410 Score = 47.3 bits (112), Expect = 9e-06 Identities = 48/181 (26%), Positives = 73/181 (40%), Gaps = 35/181 (19%) Query: 209 QGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYL 268 Q ++G + I ++G++NAGKS+L AL K + D L LD + Sbjct: 168 QRRVGREGESSPVIAVVGYTNAGKSTLIKALTKAAL--------YPNDRLFATLDPTLHS 219 Query: 269 VKI--------SDTAGIRETDDIVEKEGIKRTFLEVENADLIL----------------L 304 + +DT G I + T EV ADL+L + Sbjct: 220 AHLPSGNFVLLTDTVGFISDLPIQLVAAFQATLEEVAEADLLLHVVDISHPNAEEQRETV 279 Query: 305 LKEINSKKEISFPKNIDFIFIGTKSDLYSTYTEEYDHL---ISSFTGEGLEELINKIKSI 361 L +N S PK + I + K D EE +L IS+ TG+GLEEL+ ++ Sbjct: 280 LHVLNQIGVPSEPKLQNMIEVDNKIDYEEDEVEEEKNLDVGISALTGDGLEELLKAEETK 339 Query: 362 L 362 + Sbjct: 340 V 340 >gnl|CDD|133250 cd00154, Rab, Rab family. Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members, several have been found to possess 60 or more Rabs; for many of these Rab isoforms, homologous proteins are not found in other organisms. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Since crystal structures often lack C-terminal residues, the lipid modification site is not available for annotation in many of the CDs in the hierarchy, but is included where possible. Length = 159 Score = 46.7 bits (112), Expect = 1e-05 Identities = 42/173 (24%), Positives = 66/173 (38%), Gaps = 50/173 (28%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTT--RDVLTIDLDLEGYLVKIS--DTA 275 +KIV++G S GK+SL + +T D + ++++G VK+ DTA Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDG---KFDENYKSTIGVDFKSKTIEIDGKTVKLQIWDTA 57 Query: 276 G-----------IRETD------DIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPK 318 G R DI +E +F ++ LKE+ P+ Sbjct: 58 GQERFRSITPSYYRGAHGAILVYDITNRE----SFENLDK-----WLKELKEY----APE 104 Query: 319 NIDFIFIGTKSDLYST----------YTEEYD---HLISSFTGEGLEELINKI 358 NI I +G K DL + +E S+ TGE +EEL + Sbjct: 105 NIPIILVGNKIDLEDQRQVSTEEAQQFAKENGLLFFETSAKTGENVEELFQSL 157 >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 = 46.3 bits (111), Expect = 2e-05 Identities = 41/182 (22%), Positives = 72/182 (39%), Gaps = 49/182 (26%) Query: 224 ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRD----VLTIDLDLEGYLVKISDTAGIRE 279 ++G N GKS+L NAL + + P TT + V+ + ++++D G+ Sbjct: 1 LVGLPNVGKSTLLNALTNAKPKV-ANYPFTTLEPNLGVVEVPDGAR---IQVADIPGL-- 54 Query: 280 TDDIVEKEGIKRTFL-EVENADLILLL------------------KEINSKKEISFPKNI 320 + E G+ FL + AD IL + + +N++ ++ + I Sbjct: 55 IEGASEGRGLGNQFLAHIRRADAILHVVDASEDDDIGGVDPLEDYEILNAELKLYDLETI 114 Query: 321 DF-------IFIGTKSDLYSTYTEEYDHL-------------ISSFTGEGLEELINKIKS 360 I++ K DL E + + IS+ T EGL+ELI I Sbjct: 115 LGLLTAKPVIYVLNKIDLDDAEELEEELVRELALEEGAEVVPISAKTEEGLDELIRAIYE 174 Query: 361 IL 362 +L Sbjct: 175 LL 176 >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 = 46.3 bits (111), Expect = 2e-05 Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 1/80 (1%) Query: 224 ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDI 283 ++G+ N GK++LFNAL V + PG T + L G ++I D G Sbjct: 1 LVGNPNVGKTTLFNALTGAR-QKVGNWPGVTVEKKEGRFKLGGKEIEIVDLPGTYSLSPY 59 Query: 284 VEKEGIKRTFLEVENADLIL 303 E E + R FL E DLI+ Sbjct: 60 SEDEKVARDFLLGEKPDLIV 79 >gnl|CDD|31297 COG1100, COG1100, GTPase SAR1 and related small G proteins [General function prediction only]. Length = 219 Score = 45.0 bits (105), Expect = 4e-05 Identities = 32/154 (20%), Positives = 53/154 (34%), Gaps = 16/154 (10%) Query: 218 NGYKIVILGHSNAGKSSLFNALAK------KDVAIVTDIPGTTRDVLTIDLDLEGYLVKI 271 +KIV+LG GK++L N L I P T + ++ L+ + Sbjct: 4 KEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQ-----L 58 Query: 272 SDTAGIRETDDIVEK-----EGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFIFIG 326 DTAG E + + GI + L +E + P ++ + +G Sbjct: 59 WDTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVG 118 Query: 327 TKSDLYSTYTEEYDHLISSFTGEGLEELINKIKS 360 K DL+ + + L L L K Sbjct: 119 NKIDLFDEQSSSEEILNQLNREVVLLVLAPKAVL 152 >gnl|CDD|31281 COG1084, COG1084, Predicted GTPase [General function prediction only]. Length = 346 Score = 44.9 bits (106), Expect = 4e-05 Identities = 43/184 (23%), Positives = 78/184 (42%), Gaps = 23/184 (12%) Query: 190 KEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTD 249 K++ +D+ FL H+ KL I + IV+ G+ N GKSSL L + Sbjct: 142 KKIDDDLEFL-RKARDHLK--KLPAIDPDLPTIVVAGYPNVGKSSLVRKLTTAKPEV-AP 197 Query: 250 IPGTTRDVLTIDLDLEGYLVKISDTAGI--RETDDIVEKEGIKRTFLEVEN-ADLILLL- 305 P TT+ + + +++ DT G+ R ++ E E ++ L + + A +IL L Sbjct: 198 YPFTTKGIHVGHFERGYLRIQVIDTPGLLDRPLEERNEIE--RQAILALRHLAGVILFLF 255 Query: 306 -----------KEINSKKEISFPKNIDFIFIGTKSDLYSTYTEEYDHLISSFTGEGLEEL 354 ++I+ +EI + + K D+ E+ + + +S EG EE Sbjct: 256 DPSETCGYSLEEQISLLEEIKELFKAPIVVVINKIDI--ADEEKLEEIEASVLEEGGEEP 313 Query: 355 INKI 358 + Sbjct: 314 LKIS 317 >gnl|CDD|30567 COG0218, COG0218, Predicted GTPase [General function prediction only]. Length = 200 Score = 44.9 bits (106), Expect = 4e-05 Identities = 42/179 (23%), Positives = 68/179 (37%), Gaps = 37/179 (20%) Query: 221 KIVILGHSNAGKSSLFNALA-KKDVAIVTDIPGTTRDVLTIDLDLEGYLV--------KI 271 +I G SN GKSSL NAL +K++A + PG T+ + ++D E LV K+ Sbjct: 26 EIAFAGRSNVGKSSLINALTNQKNLARTSKTPGRTQLINFFEVDDELRLVDLPGYGYAKV 85 Query: 272 SDTAGIRETDDIVE----KEGIKRTFLEVENADLILLLKEINSKKEISFPK--NIDFIFI 325 + I E + +K L ++ + ++ I F I I + Sbjct: 86 PKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPP----KDLDREMIEFLLELGIPVIVV 141 Query: 326 GTKSD------------------LYSTYTEEYDHLISSFTGEGLEELINKIKSILSNKF 366 TK+D +++ L SS +G++EL KI L Sbjct: 142 LTKADKLKKSERNKQLNKVAEELKKPPPDDQWVVLFSSLKKKGIDELKAKILEWLKEAK 200 >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 = 44.2 bits (104), Expect = 7e-05 Identities = 28/118 (23%), Positives = 44/118 (37%), Gaps = 11/118 (9%) Query: 160 QWIDKLTHIRSFIEADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNG 219 +W+ L H S+ S + + + K Sbjct: 49 KWLAYLRH--SYPTIPFKISATNGQGIEKKESAFTKQTNSNLKSYAKDGKLK------KS 100 Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGI 277 + ++G+ N GKSS+ NAL K V ++PGTT + LD + L+ DT GI Sbjct: 101 ITVGVIGYPNVGKSSVINALLNKLKLKVGNVPGTTTSQQEVKLDNKIKLL---DTPGI 155 >gnl|CDD|36637 KOG1423, KOG1423, KOG1423, Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. Length = 379 Score = 42.3 bits (99), Expect = 3e-04 Identities = 22/105 (20%), Positives = 45/105 (42%), Gaps = 17/105 (16%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETD 281 + ++G N GKS+L N + + V+ V+ TTR + + + DT G Sbjct: 75 VAVIGAPNVGKSTLTNQMIGQKVSAVSRKVHTTRHRILGIITSGETQLVFYDTPG----- 129 Query: 282 DIVEKEGIKRTFLE----------VENADLILLLKEI-NSKKEIS 315 +V K+ +R L +NAD ++++ + ++ + Sbjct: 130 -LVSKKMHRRHHLMMSVLQNPRDAAQNADCVVVVVDASATRTPLH 173 >gnl|CDD|37696 KOG2485, KOG2485, KOG2485, Conserved ATP/GTP binding protein [General function prediction only]. Length = 335 Score = 42.2 bits (99), Expect = 3e-04 Identities = 29/81 (35%), Positives = 36/81 (44%), Gaps = 6/81 (7%) Query: 219 GYKIVILGHSNAGKSSLFNA-----LAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISD 273 Y ++++G N GKSSL NA L KK A V PG TR V V + D Sbjct: 143 EYNVMVVGVPNVGKSSLINALRNVHLRKKKAARVGAEPGVTRRVSERIRISHRPPVYLID 202 Query: 274 TAGIRETDDIVEKEGIKRTFL 294 T GI IV+ E + L Sbjct: 203 TPGIL-VPSIVDVEDGLKLAL 222 >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 = 39.9 bits (94), Expect = 0.002 Identities = 50/175 (28%), Positives = 75/175 (42%), Gaps = 44/175 (25%) Query: 222 IVILGHSNAGKSSLFNAL--AKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGI-- 277 +VI G+ N GKSSL N L AK +VA P TT+ + D + ++ DT G+ Sbjct: 3 LVIAGYPNVGKSSLVNKLTRAKPEVA---PYPFTTKSLFVGHFDYKYLRWQVIDTPGLLD 59 Query: 278 RETDD--IVEKEGIKRTFLE-VENADL----------------ILLLKEINSKKEISFPK 318 R ++ +E + I T L + A L + L +EI K + K Sbjct: 60 RPLEERNTIEMQAI--TALAHLRAAVLFLFDPSETCGYSLEEQLSLFEEI---KPLFKNK 114 Query: 319 NIDFIFIGTKSDL-----YSTYTEEYD------HLISSFTGEGLEELINKIKSIL 362 + I + K DL S EE + IS+ T EG++E+ NK +L Sbjct: 115 PV--IVVLNKIDLLTFEDLSEIEEEEELEGEEVLKISTLTEEGVDEVKNKACELL 167 >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 = 39.5 bits (92), Expect = 0.002 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 3/62 (4%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTA 275 I+ + ++G N GKSSL N+L + V PG T+ + + LD + VK+ D+ Sbjct: 114 IKTSITVGVVGFPNVGKSSLINSLKRSRACNVGATPGVTKSMQEVHLDKK---VKLLDSP 170 Query: 276 GI 277 GI Sbjct: 171 GI 172 >gnl|CDD|37634 KOG2423, KOG2423, KOG2423, Nucleolar GTPase [General function prediction only]. Length = 572 Score = 38.5 bits (89), Expect = 0.003 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 3/74 (4%) Query: 225 LGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIV 284 +G+ N GKSS+ N L KK V V IPG T+ I L +L+ D G+ Sbjct: 313 IGYPNVGKSSIINTLRKKKVCKVAPIPGETKVWQYITLMKRIFLI---DCPGVVYPSSDS 369 Query: 285 EKEGIKRTFLEVEN 298 E + + + + VEN Sbjct: 370 ETDIVLKGVVRVEN 383 >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 = 38.2 bits (89), Expect = 0.004 Identities = 20/52 (38%), Positives = 26/52 (50%), Gaps = 3/52 (5%) Query: 226 GHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGI 277 G+ N GKSSL NAL K V+ PG T+ TI L + + D G+ Sbjct: 90 GYPNVGKSSLINALVGKKKVSVSATPGKTKHFQTIFLTPT---ITLCDCPGL 138 >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 = 37.9 bits (88), Expect = 0.005 Identities = 15/32 (46%), Positives = 19/32 (59%) Query: 224 ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTR 255 +G+ N GKSS+ N L K V V IPG T+ Sbjct: 107 FIGYPNVGKSSIINTLRSKKVCKVAPIPGETK 138 >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 = 37.6 bits (87), Expect = 0.006 Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 3/67 (4%) Query: 211 KLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVK 270 +L +I K+ ++G+ N GKSS+ NAL + A + PG T+ + + + YL+ Sbjct: 93 ELAKIDGKEGKVGVVGYPNVGKSSIINALKGRHSASTSPSPGYTKGEQLVKITSKIYLL- 151 Query: 271 ISDTAGI 277 DT G+ Sbjct: 152 --DTPGV 156 >gnl|CDD|133251 cd00157, Rho, Rho (Ras homology) family. Members of the Rho family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Since crystal structures often lack C-terminal residues, this feature is not available for annotation in many of the CDs in the hierarchy. Length = 171 Score = 37.5 bits (88), Expect = 0.008 Identities = 32/130 (24%), Positives = 48/130 (36%), Gaps = 34/130 (26%) Query: 221 KIVILGHSNAGKSSLFNALAK-----KDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTA 275 KIV++G GK+ L + + V V D T+ +D + + + DTA Sbjct: 2 KIVVVGDGAVGKTCLLISYTTGKFPTEYVPTVFDN-----YSATVTVDGKQVNLGLWDTA 56 Query: 276 GIRETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNID-------------- 321 G E D + R L N D+ L+ ++S SF Sbjct: 57 GQEEYDRL-------RP-LSYPNTDVFLICFSVDSPS--SFENVKTKWIPEIRHYCPNVP 106 Query: 322 FIFIGTKSDL 331 I +GTK DL Sbjct: 107 IILVGTKIDL 116 >gnl|CDD|144080 pfam00350, Dynamin_N, Dynamin family. Length = 168 Score = 37.2 bits (87), Expect = 0.008 Identities = 26/102 (25%), Positives = 38/102 (37%), Gaps = 15/102 (14%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETD 281 I ++G +AGKSS+ NAL +D+ P TTR L + L G A E Sbjct: 1 IAVVGDQSAGKSSVLNALLGRDILPRGPGP-TTRRPLVLRL---GEEPGAIPGAVKVEYK 56 Query: 282 DIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFI 323 D ++K D L +EI + + Sbjct: 57 DGLKKF-----------EDFSELREEIEDETDKISGTGKGIS 87 >gnl|CDD|35317 KOG0094, KOG0094, KOG0094, GTPase Rab6/YPT6/Ryh1, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 221 Score = 36.8 bits (85), Expect = 0.012 Identities = 39/188 (20%), Positives = 63/188 (33%), Gaps = 37/188 (19%) Query: 203 ISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDL 262 + YK+V LG + GK+SL D T D L+ + Sbjct: 6 VCLACQTMATFGAPLKKYKLVFLGDQSVGKTSLITRF-MYDKFDNTYQATIGIDFLSKTM 64 Query: 263 DLEGYLVKIS--DTAG-----------IRETDDIVEKEGI--KRTFLEVENADLILLLKE 307 LE V++ DTAG IR++ V I + +F K Sbjct: 65 YLEDRTVRLQLWDTAGQERFRSLIPSYIRDSSVAVIVYDITDRNSFENTS--------KW 116 Query: 308 INSKKEISFPKNIDFIFIGTKSDLYS---TYTEEYDHL----------ISSFTGEGLEEL 354 I + ++ +G K+DL EE + S+ GE +++L Sbjct: 117 IEDVRRERGSDDVIIFLVGNKTDLSDKRQVSIEEGERKAKELNAEFIETSAKAGENVKQL 176 Query: 355 INKIKSIL 362 +I + L Sbjct: 177 FRRIAAAL 184 >gnl|CDD|30362 COG0012, COG0012, Predicted GTPase, probable translation factor [Translation, ribosomal structure and biogenesis]. Length = 372 Score = 36.3 bits (84), Expect = 0.016 Identities = 15/29 (51%), Positives = 17/29 (58%) Query: 218 NGYKIVILGHSNAGKSSLFNALAKKDVAI 246 KI I+G N GKS+LFNAL K I Sbjct: 1 MSLKIGIVGLPNVGKSTLFNALTKAGAEI 29 >gnl|CDD|36638 KOG1424, KOG1424, KOG1424, Predicted GTP-binding protein MMR1 [General function prediction only]. Length = 562 Score = 35.8 bits (82), Expect = 0.023 Identities = 16/39 (41%), Positives = 21/39 (53%) Query: 225 LGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLD 263 +G+ N GKSS NAL + V+ PG T+ TI L Sbjct: 320 VGYPNVGKSSTINALVGRKKVSVSSTPGKTKHFQTIFLS 358 >gnl|CDD|143853 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices. Length = 162 Score = 35.9 bits (84), Expect = 0.023 Identities = 33/131 (25%), Positives = 50/131 (38%), Gaps = 35/131 (26%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTD-IPGTTRDVLTIDLDLEGYLVK--ISDTAG- 276 K+V++G GKSSL + + IP D T ++++G VK I DTAG Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNK--FPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQ 58 Query: 277 ----------IRETD------DIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNI 320 R DI ++ +F V+ L+EI N+ Sbjct: 59 ERFRALRPLYYRGAQGFLLVYDITSRD----SFENVKK-----WLEEILRHA----DDNV 105 Query: 321 DFIFIGTKSDL 331 + +G K DL Sbjct: 106 PIVLVGNKCDL 116 >gnl|CDD|133293 cd01893, Miro1, Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature. Length = 166 Score = 35.4 bits (82), Expect = 0.028 Identities = 26/130 (20%), Positives = 53/130 (40%), Gaps = 23/130 (17%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDV-LTIDLDLEGYLVKISDTAGIRE 279 +IV++G GKSSL +L ++ ++P ++ + D+ E I DT+ + Sbjct: 2 RIVLIGDEGVGKSSLIMSLVSEE--FPENVPRVLPEITIPADVTPERVPTTIVDTSSRPQ 59 Query: 280 TDDIVEKEGIKRTFLEVENADLILLLKEINSKKEI------------SFPKNIDFIFIGT 327 + E I++ A++I L+ ++ + + I +G Sbjct: 60 DRANLAAE-IRK-------ANVICLVYSVDRPSTLERIRTKWLPLIRRLGVKVPIILVGN 111 Query: 328 KSDLYSTYTE 337 KSDL ++ Sbjct: 112 KSDLRDGSSQ 121 >gnl|CDD|35314 KOG0091, KOG0091, KOG0091, GTPase Rab39, small G protein superfamily [General function prediction only]. Length = 213 Score = 35.3 bits (81), Expect = 0.032 Identities = 35/131 (26%), Positives = 57/131 (43%), Gaps = 24/131 (18%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLE-GYLVKIS--DTAG 276 ++++++G S GKSSL + A ++D P D ++L GY +K+ DTAG Sbjct: 9 FRLIVIGDSTVGKSSLLRYFTEGKFAELSD-PTVGVDFFARLIELRPGYRIKLQLWDTAG 67 Query: 277 IRETDDIVEKE-----GI--------KRTFLEVENADLILLLKEINSKKEISFPKNIDFI 323 I + G+ + +F VEN +KE + P + F+ Sbjct: 68 QERFRSITKSYYRNSVGVLLVYDITNRESFEHVEN-----WVKE--AAMATQGPDKVVFL 120 Query: 324 FIGTKSDLYST 334 +G KSDL S Sbjct: 121 LVGHKSDLQSQ 131 >gnl|CDD|37695 KOG2484, KOG2484, KOG2484, GTPase [General function prediction only]. Length = 435 Score = 34.6 bits (79), Expect = 0.060 Identities = 19/62 (30%), Positives = 38/62 (61%), Gaps = 3/62 (4%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTA 275 ++ ++ I+G+ N GKSS+ N+L ++ V ++PG TR + + LD + +++ D+ Sbjct: 249 LKTSIRVGIIGYPNVGKSSVINSLKRRKACNVGNVPGVTRSMQEVKLDKK---IRLLDSP 305 Query: 276 GI 277 GI Sbjct: 306 GI 307 >gnl|CDD|30882 COG0536, Obg, Predicted GTPase [General function prediction only]. Length = 369 Score = 34.0 bits (78), Expect = 0.073 Identities = 41/177 (23%), Positives = 71/177 (40%), Gaps = 42/177 (23%) Query: 224 ILGHSNAGKSSLFNAL--AKKDVAIVTDIPGTTR--DVLTIDLDLEGYLVKISDTAGIRE 279 ++G NAGKS+L +A+ AK +A D P TT ++ + +D V ++D G+ E Sbjct: 164 LVGLPNAGKSTLLSAVSAAKPKIA---DYPFTTLVPNLGVVRVDGGESFV-VADIPGLIE 219 Query: 280 TDDIVEKEGIKRTFLE-VENADLILLLKEINSKKEISFPKNI-----------------D 321 E G+ FL +E ++L + +++ ++ Sbjct: 220 --GASEGVGLGLRFLRHIERTRVLLHVIDLSPIDGRDPIEDYQTIRNELEKYSPKLAEKP 277 Query: 322 FIFIGTKSD--------------LYSTYTEEYDHLISSFTGEGLEELINKIKSILSN 364 I + K D L E +LIS+ T EGL+EL+ + +L Sbjct: 278 RIVVLNKIDLPLDEEELEELKKALAEALGWEVFYLISALTREGLDELLRALAELLEE 334 >gnl|CDD|31357 COG1163, DRG, Predicted GTPase [General function prediction only]. Length = 365 Score = 34.0 bits (78), Expect = 0.074 Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 2/84 (2%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETD 281 + ++G + GKS+L N L V D P TT + + L+ +G +++ D GI E Sbjct: 66 VALVGFPSVGKSTLLNKLTNTKSE-VADYPFTTLEPVPGMLEYKGAQIQLLDLPGIIE-G 123 Query: 282 DIVEKEGIKRTFLEVENADLILLL 305 + ++ NADLI+++ Sbjct: 124 ASSGRGRGRQVLSVARNADLIIIV 147 >gnl|CDD|35315 KOG0092, KOG0092, KOG0092, GTPase Rab5/YPT51 and related small G protein superfamily GTPases [Intracellular trafficking, secretion, and vesicular transport]. Length = 200 Score = 34.1 bits (78), Expect = 0.076 Identities = 47/196 (23%), Positives = 75/196 (38%), Gaps = 47/196 (23%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVK--ISDTAGIR 278 K+V+LG S GKSSL K P LT + ++ +K I DTAG + Sbjct: 7 KVVLLGDSGVGKSSLVLRFVKDQFH-ENIEPTIGAAFLTKTVTVDDNTIKFEIWDTAG-Q 64 Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISF--------------PKNIDFIF 324 E + + A+ +++ +I ++ SF NI Sbjct: 65 ERYHSLAP-------MYYRGANAAIVVYDITDEE--SFEKAKNWVKELQRQASPNIVIAL 115 Query: 325 IGTKSDLYSTYTEEYD---------HLI----SSFTGEGLEELINKIKSILSNKFKKLPF 371 +G K+DL E++ L+ S+ TGE + E+ I +KLP Sbjct: 116 VGNKADLLERREVEFEEAQAYAESQGLLFFETSAKTGENVNEIFQAI-------AEKLPC 168 Query: 372 SIPSHKRHLYHLSQTV 387 S P ++ L + Q V Sbjct: 169 SDPQERQGLPNRRQGV 184 >gnl|CDD|133265 cd01862, Rab7, Rab7 subfamily. Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 172 Score = 34.2 bits (79), Expect = 0.085 Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 5/60 (8%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTT-RDVLTIDLDLEGYLV--KISDTAG 276 K++ILG S GK+SL N K + T D LT ++ ++ LV +I DTAG Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFS--NQYKATIGADFLTKEVTVDDKLVTLQIWDTAG 58 >gnl|CDD|133335 cd04135, Tc10, TC10 subfamily. TC10 is a Rho family protein that has been shown to induce microspike formation and neurite outgrowth in vitro. Its expression changes dramatically after peripheral nerve injury, suggesting an important role in promoting axonal outgrowth and regeneration. TC10 regulates translocation of insulin-stimulated GLUT4 in adipocytes and has also been shown to bind directly to Golgi COPI coat proteins. GTP-bound TC10 in vitro can bind numerous potential effectors. Depending on its subcellular localization and distinct functional domains, TC10 can differentially regulate two types of filamentous actin in adipocytes. TC10 mRNAs are highly expressed in three types of mouse muscle tissues: leg skeletal muscle, cardiac muscle, and uterus; they were also present in brain, with higher levels in adults than in newborns. TC10 has also been shown to play a role in regulating the expression of cystic fibrosis transmembrane conductance regulator (CFTR) through interactions with CFTR-associated ligand (CAL). The GTP-bound form of TC10 directs the trafficking of CFTR from the juxtanuclear region to the secretory pathway toward the plasma membrane, away from CAL-mediated DFTR degradation in the lysosome. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 174 Score = 33.7 bits (77), Expect = 0.098 Identities = 28/125 (22%), Positives = 51/125 (40%), Gaps = 24/125 (19%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRD--VLTIDLDLEGYLVKISDTAGIR 278 K V++G GK+ L + A A + T D +++ + + YL+ + DTAG Sbjct: 2 KCVVVGDGAVGKTCLLMSYAND--AFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQE 59 Query: 279 ETDDIVEKEGIKRTFLEVENADLILLL------KEINSKKEISFPK------NIDFIFIG 326 + D + L D+ L+ + KE P+ N+ ++ +G Sbjct: 60 DYDRLRP--------LSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPYLLVG 111 Query: 327 TKSDL 331 T+ DL Sbjct: 112 TQIDL 116 >gnl|CDD|36919 KOG1707, KOG1707, KOG1707, Predicted Ras related/Rac-GTP binding protein [Defense mechanisms]. Length = 625 Score = 33.4 bits (76), Expect = 0.11 Identities = 27/140 (19%), Positives = 52/140 (37%), Gaps = 26/140 (18%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDV-LTIDLDLEGYLVKISDTAGIRE 279 +IV++G GK+SL +L +++ V +P + + D+ E I DT+ + Sbjct: 11 RIVLIGDEGVGKTSLIMSLLEEE--FVDAVPRRLPRILIPADVTPENVPTSIVDTSSDSD 68 Query: 280 TDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISF---------------PKNIDFIF 324 + KE I++ AD+I L+ ++ + + I Sbjct: 69 DRLCLRKE-IRK-------ADVICLVYAVDDESTVDRISTKWLPLIRQLFGDYHETPVIL 120 Query: 325 IGTKSDLYSTYTEEYDHLIS 344 +G KSD + Sbjct: 121 VGNKSDNGDNENNSDEVNTL 140 >gnl|CDD|133252 cd00876, Ras, Ras family. The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 160 Score = 33.7 bits (78), Expect = 0.12 Identities = 34/130 (26%), Positives = 54/130 (41%), Gaps = 33/130 (25%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRD--VLTIDLDLEGYLVKISDTAG-- 276 K+V+LG GKS++ K V + T D TI +D E Y + I DTAG Sbjct: 1 KVVVLGAGGVGKSAITIQFVKGT--FVEEYDPTIEDSYRKTIVVDGETYTLDILDTAGQE 58 Query: 277 ---------IRETD------DIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNID 321 IR+ D I ++E +F E++ ++I + ++I Sbjct: 59 EFSAMRDLYIRQGDGFILVYSITDRE----SFEEIKG-----YREQI---LRVKDDEDIP 106 Query: 322 FIFIGTKSDL 331 + +G K DL Sbjct: 107 IVLVGNKCDL 116 >gnl|CDD|34593 COG4988, CydD, ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]. Length = 559 Score = 33.3 bits (76), Expect = 0.13 Identities = 11/26 (42%), Positives = 15/26 (57%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALAK 241 I+ G ++G S AGKS+L N L Sbjct: 344 IKAGQLTALVGASGAGKSTLLNLLLG 369 >gnl|CDD|35616 KOG0395, KOG0395, KOG0395, Ras-related GTPase [General function prediction only]. Length = 196 Score = 33.0 bits (75), Expect = 0.17 Identities = 34/134 (25%), Positives = 50/134 (37%), Gaps = 29/134 (21%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLT--IDLDLEGYLVKISDTAGI 277 YK+V+LG GKS+L V D T D + +D E +++I DTAG Sbjct: 4 YKVVVLGAGGVGKSALTIQFLTGRF--VEDYDPTIEDSYRKELTVDGEVCMLEILDTAGQ 61 Query: 278 RETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISF---------------PKNIDF 322 E + + L + N D LL+ I + SF ++ Sbjct: 62 EEFSAMRD--------LYIRNGDGFLLVYSITDRS--SFEEAKQLREQILRVKGRDDVPI 111 Query: 323 IFIGTKSDLYSTYT 336 I +G K DL Sbjct: 112 ILVGNKCDLERERQ 125 >gnl|CDD|36703 KOG1490, KOG1490, KOG1490, GTP-binding protein CRFG/NOG1 (ODN superfamily) [General function prediction only]. Length = 620 Score = 32.7 bits (74), Expect = 0.23 Identities = 28/91 (30%), Positives = 45/91 (49%), Gaps = 7/91 (7%) Query: 203 ISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDL 262 + H+S +L I N +++ G+ N GKSS N + + D V TT+ +L L Sbjct: 154 VRQHLS--RLPAIDPNTRTLLVCGYPNVGKSSFNNKVTRADDE-VQPYAFTTKLLLVGHL 210 Query: 263 DLEGYLVKISDTAGI--RETDD--IVEKEGI 289 D + ++ DT GI R +D I+E + I Sbjct: 211 DYKYLRWQVIDTPGILDRPEEDRNIIEMQII 241 >gnl|CDD|133355 cd04155, Arl3, Arl3 subfamily. Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation. Length = 173 Score = 32.7 bits (75), Expect = 0.23 Identities = 12/28 (42%), Positives = 21/28 (75%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVT 248 +I+ILG NAGK+++ LA +D++ +T Sbjct: 16 RILILGLDNAGKTTILKQLASEDISHIT 43 >gnl|CDD|35669 KOG0448, KOG0448, KOG0448, Mitofusin 1 GTPase, involved in mitochondrila biogenesis [Posttranslational modification, protein turnover, chaperones]. Length = 749 Score = 32.3 bits (73), Expect = 0.28 Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 6/80 (7%) Query: 166 THIRSFIEADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQGKLGEII-RNGYKIVI 224 + R+F+E E D F+ +E L + + + + E++ R K+ I Sbjct: 60 SEPRTFLEGTYKNPELND---FALEERLLEDEVMSGGYEDKLDA--IDEVLARRHMKVAI 114 Query: 225 LGHSNAGKSSLFNALAKKDV 244 G ++AGKS++ NA+ K + Sbjct: 115 FGRTSAGKSTVINAMLHKKL 134 >gnl|CDD|33918 COG4178, COG4178, ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]. Length = 604 Score = 32.2 bits (73), Expect = 0.31 Identities = 13/25 (52%), Positives = 18/25 (72%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240 +R G +++I G S AGK+SL ALA Sbjct: 416 VRPGERLLITGESGAGKTSLLRALA 440 >gnl|CDD|133377 cd04177, RSR1, RSR1 subgroup. RSR1/Bud1p is a member of the Rap subfamily of the Ras family that is found in fungi. In budding yeasts, RSR1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization. The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site. It is believed that cdc42 interacts directly with RSR1 in vivo. In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha. In Ashbya gossypii, RSR1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Length = 168 Score = 32.1 bits (73), Expect = 0.31 Identities = 35/121 (28%), Positives = 56/121 (46%), Gaps = 13/121 (10%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVL--TIDLDLEGYLVKISDTAGI 277 YKIV+LG GKS+L ++V I + P T D +++D ++I DTAG Sbjct: 2 YKIVVLGAGGVGKSAL-TVQFVQNVFIESYDP-TIEDSYRKQVEIDGRQCDLEILDTAGT 59 Query: 278 RE---TDDIVEKEGIKRTFLEVENADLILLLKEINSKKE----ISFPKNIDFIFIGTKSD 330 + ++ K G + FL V + L E+ +E I N+ + +G K+D Sbjct: 60 EQFTAMRELYIKSG--QGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKAD 117 Query: 331 L 331 L Sbjct: 118 L 118 >gnl|CDD|133262 cd01853, Toc34_like, Toc34-like (Translocon at the Outer-envelope membrane of Chloroplasts). This family contains several Toc proteins, including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125, and Toc90. The Toc complex at the outer envelope membrane of chloroplasts is a molecular machine of ~500 kDa that contains a single Toc159 protein, four Toc75 molecules, and four or five copies of Toc34. Toc64 and Toc12 are associated with the translocon, but do not appear to be part of the core complex. The Toc translocon initiates the import of nuclear-encoded preproteins from the cytosol into the organelle. Toc34 and Toc159 are both GTPases, while Toc75 is a beta-barrel integral membrane protein. Toc159 is equally distributed between a soluble cytoplasmic form and a membrane-inserted form, suggesting that assembly of the Toc complex is dynamic. Toc34 and Toc75 act sequentially to mediate docking and insertion of Toc159 resulting in assembly of the functional translocon. Length = 249 Score = 31.9 bits (73), Expect = 0.38 Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 7/79 (8%) Query: 209 QGKLGEIIRNGYK-------IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTID 261 Q K E+ G + I++LG + GKSS N++ + A + T V + Sbjct: 14 QTKALELEAKGKEELDFSLTILVLGKTGVGKSSTINSIFGERKAATSAFQSETLRVREVS 73 Query: 262 LDLEGYLVKISDTAGIRET 280 ++G+ + I DT G+ E+ Sbjct: 74 GTVDGFKLNIIDTPGLLES 92 >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 = 31.8 bits (73), Expect = 0.43 Identities = 16/33 (48%), Positives = 20/33 (60%), Gaps = 1/33 (3%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTT 254 I ++G NAGKS+ FNA DV I + P TT Sbjct: 1 IGLVGKPNAGKSTFFNAATLADVEI-ANYPFTT 32 >gnl|CDD|72984 cd03225, ABC_cobalt_CbiO_domain1, Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.. Length = 211 Score = 31.6 bits (72), Expect = 0.46 Identities = 9/25 (36%), Positives = 16/25 (64%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240 I+ G ++I+G + +GKS+L L Sbjct: 24 IKKGEFVLIVGPNGSGKSTLLRLLN 48 >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 = 31.4 bits (72), Expect = 0.46 Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 7/38 (18%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAI-----VTDIPGTT 254 I ++GHS +GK++L AL AI V D GTT Sbjct: 2 IALVGHSGSGKTTLAEALLYATGAIDRLGSVED--GTT 37 >gnl|CDD|37697 KOG2486, KOG2486, KOG2486, Predicted GTPase [General function prediction only]. Length = 320 Score = 31.2 bits (70), Expect = 0.59 Identities = 35/168 (20%), Positives = 56/168 (33%), Gaps = 23/168 (13%) Query: 169 RSFIEADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHS 228 +S+ + L S DV F +++ + + D S + + G S Sbjct: 91 KSYRKRVLSGSNI-DVSPFLARKQVKSEKRVHGDGSVTAEDCPKDKRPE----LAFYGRS 145 Query: 229 NAGKSSLFNALAKKDVAIVTDIPGTTRDVLTID----------LDLEGYLVKISDTAGIR 278 N GKSSL N L + T I+ +DL GY Sbjct: 146 NVGKSSLLNDLVRVKNIADTSKS-KNGKTQAINHFHVGKSWYEVDLPGYGRAGYGFELPA 204 Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFIFIG 326 + D K LE EN + LL +++ I N + ++G Sbjct: 205 DWDKFT-----KSYLLERENLVRVFLL--VDASVPIQPTDNPEIAWLG 245 >gnl|CDD|30753 COG0404, GcvT, Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]. Length = 379 Score = 31.0 bits (70), Expect = 0.60 Identities = 20/102 (19%), Positives = 39/102 (38%), Gaps = 8/102 (7%) Query: 3 HEKETIFAVSTGALPSAISIIRLSGPSCFQVCEFICKKKKPFPRKASLRYFFGLDGRILD 62 H+ V+ ++ ++++ L GP +V K +L +F + I Sbjct: 131 HQAGPDLDVTLTSVTEDLAVLALQGPKAREVLA----KLVDGDLVEALPFFAFKEVTIGG 186 Query: 63 KGLLIVFPSPESFTGEDSAEFHVHG--GIAVVNGILEELAKM 102 + + + +TGE E +V AV + +LE K Sbjct: 187 GVPVRISRT--GYTGELGFEIYVPAEDAAAVWDALLEAGEKF 226 >gnl|CDD|72972 cd03213, ABCG_EPDR, ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR). DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.. Length = 194 Score = 31.3 bits (71), Expect = 0.63 Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 9/61 (14%) Query: 182 EDVQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAK 241 ++ L ++S G+L I+G S AGKS+L NALA Sbjct: 7 RNLTVTVKSSPSKSGKQLLKNVSGKAKPGEL---------TAIMGPSGAGKSTLLNALAG 57 Query: 242 K 242 + Sbjct: 58 R 58 >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 = 30.9 bits (71), Expect = 0.73 Identities = 12/22 (54%), Positives = 14/22 (63%) Query: 224 ILGHSNAGKSSLFNALAKKDVA 245 I+G N GKS+LFNAL K Sbjct: 3 IVGLPNVGKSTLFNALTKAGAE 24 >gnl|CDD|133263 cd01860, Rab5_related, Rab5-related subfamily. This subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 163 Score = 30.9 bits (71), Expect = 0.74 Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 7/61 (11%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTT--RDVLTIDLDLEGYLVK--ISDTA 275 +K+V+LG S+ GKSSL K + ++ +T LT ++L+ VK I DTA Sbjct: 2 FKLVLLGDSSVGKSSLVLRFVKNE---FSENQESTIGAAFLTQTVNLDDTTVKFEIWDTA 58 Query: 276 G 276 G Sbjct: 59 G 59 >gnl|CDD|133334 cd04134, Rho3, Rho3 subfamily. Rho3 is a member of the Rho family found only in fungi. Rho3 is believed to regulate cell polarity by interacting with the diaphanous/formin family protein For3 to control both the actin cytoskeleton and microtubules. Rho3 is also believed to have a direct role in exocytosis that is independent of its role in regulating actin polarity. The function in exocytosis may be two-pronged: first, in the transport of post-Golgi vesicles from the mother cell to the bud, mediated by myosin (Myo2); second, in the docking and fusion of vesicles to the plasma membrane, mediated by an exocyst (Exo70) protein. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Length = 189 Score = 31.0 bits (70), Expect = 0.75 Identities = 27/93 (29%), Positives = 46/93 (49%), Gaps = 12/93 (12%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKIS--DTAGIR 278 K+V+LG GK+SL N + V + P T + D+ ++G +++S DTAG Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYE-P-TVFENYVHDIFVDGLHIELSLWDTAGQE 59 Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINSK 311 E D + R+ L + D+I+L ++S Sbjct: 60 EFDRL-------RS-LSYADTDVIMLCFSVDSP 84 >gnl|CDD|72971 cd00267, ABC_ATPase, ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. 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 = 157 Score = 30.7 bits (69), Expect = 0.80 Identities = 8/25 (32%), Positives = 17/25 (68%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240 ++ G + ++G + +GKS+L A+A Sbjct: 22 LKAGEIVALVGPNGSGKSTLLRAIA 46 >gnl|CDD|35280 KOG0057, KOG0057, KOG0057, Mitochondrial Fe/S cluster exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 591 Score = 30.6 bits (69), Expect = 0.83 Identities = 23/91 (25%), Positives = 37/91 (40%), Gaps = 6/91 (6%) Query: 153 ELSSLYGQWIDKLTHIR-SFIEADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQGK 211 L S+Y + LT +R FI ++D +E I F S + Sbjct: 310 FLGSVYRELRQALTDMRTLFILLEVDEDIQEAALPIELFG--GSIEFDDVHFSYGPKRKV 367 Query: 212 LGEI---IRNGYKIVILGHSNAGKSSLFNAL 239 L + I G K+ I+G + +GKS++ L Sbjct: 368 LKGVSFTIPKGEKVAIVGSNGSGKSTILRLL 398 >gnl|CDD|35615 KOG0394, KOG0394, KOG0394, Ras-related GTPase [General function prediction only]. Length = 210 Score = 30.7 bits (69), Expect = 0.86 Identities = 34/131 (25%), Positives = 51/131 (38%), Gaps = 31/131 (23%) Query: 221 KIVILGHSNAGKSSLFNALAKKDV-----AIVTDIPGTTRDVLTIDLDLEGYLV--KISD 273 K++ILG S GK+SL N K A + D LT ++ ++ V +I D Sbjct: 11 KVIILGDSGVGKTSLMNQYVNKKFSQQYKATI------GADFLTKEVQVDDRSVTLQIWD 64 Query: 274 TAG-----------IRETDDIVEKE--GIKRTFLEVENADLILLLKEINSKKEISFPKNI 320 TAG R D V ++F +EN KE + P+ Sbjct: 65 TAGQERFQSLGVAFYRGADCCVLVYDVNNPKSFENLENWR-----KEFLIQASPQDPETF 119 Query: 321 DFIFIGTKSDL 331 F+ +G K D+ Sbjct: 120 PFVILGNKIDV 130 >gnl|CDD|133332 cd04132, Rho4_like, Rho4-like subfamily. Rho4 is a GTPase that controls septum degradation by regulating secretion of Eng1 or Agn1 during cytokinesis. Rho4 also plays a role in cell morphogenesis. Rho4 regulates septation and cell morphology by controlling the actin cytoskeleton and cytoplasmic microtubules. The localization of Rho4 is modulated by Rdi1, which may function as a GDI, and by Rga9, which is believed to function as a GAP. In S. pombe, both Rho4 deletion and Rho4 overexpression result in a defective cell wall, suggesting a role for Rho4 in maintaining cell wall integrity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Length = 187 Score = 30.7 bits (70), Expect = 0.87 Identities = 30/136 (22%), Positives = 50/136 (36%), Gaps = 39/136 (28%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVA----------IVTDIPGTTRDVLTIDLDLEGYLVK 270 KIV++G GK+ L ++ VT+I G I+L L Sbjct: 2 KIVVVGDGGCGKTCLLIVYSQGKFPEEYVPTVFENYVTNIQGPNGK--IIELAL------ 53 Query: 271 ISDTAGIRETDDIVEKEGIKRTFLEVENADLILLLKEINSK------KEISFP------K 318 DTAG E D + R L + D++L+ +++ ++ FP Sbjct: 54 -WDTAGQEEYDRL-------RP-LSYPDVDVLLICYAVDNPTSLDNVEDKWFPEVNHFCP 104 Query: 319 NIDFIFIGTKSDLYST 334 + +G K+DL Sbjct: 105 GTPIMLVGLKTDLRKD 120 >gnl|CDD|72982 cd03223, ABCD_peroxisomal_ALDP, Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asymptomatic).. Length = 166 Score = 30.5 bits (69), Expect = 0.99 Identities = 14/25 (56%), Positives = 18/25 (72%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240 I+ G +++I G S GKSSLF ALA Sbjct: 24 IKPGDRLLITGPSGTGKSSLFRALA 48 >gnl|CDD|133311 cd04111, Rab39, Rab39 subfamily. Found in eukaryotes, Rab39 is mainly found in epithelial cell lines, but is distributed widely in various human tissues and cell lines. It is believed to be a novel Rab protein involved in regulating Golgi-associated vesicular transport during cellular endocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Length = 211 Score = 30.5 bits (69), Expect = 1.0 Identities = 35/131 (26%), Positives = 60/131 (45%), Gaps = 31/131 (23%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLE-GYLVKIS--DTAG 276 ++++++G S GKSSL + A V+D P D + +++E G +K+ DTAG Sbjct: 3 FRLIVIGDSTVGKSSLLKRFTEGRFAEVSD-PTVGVDFFSRLIEIEPGVRIKLQLWDTAG 61 Query: 277 IRETDDIVEK-EGIKRTFLEVENADLILLLKEINSKKEISF---------------PKNI 320 E+ I R++ N+ +LL+ +I +++ SF P Sbjct: 62 -------QERFRSITRSYY--RNSVGVLLVFDITNRE--SFEHVHDWLEEARSHIQPHRP 110 Query: 321 DFIFIGTKSDL 331 FI +G K DL Sbjct: 111 VFILVGHKCDL 121 >gnl|CDD|33698 COG3911, COG3911, Predicted ATPase [General function prediction only]. Length = 183 Score = 30.4 bits (68), Expect = 1.1 Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 1/36 (2%) Query: 217 RNGYKIVIL-GHSNAGKSSLFNALAKKDVAIVTDIP 251 N +K IL G AGK++L ALA+ A V + Sbjct: 6 FNRHKRFILTGGPGAGKTTLLAALARAGFATVEEAG 41 >gnl|CDD|35307 KOG0084, KOG0084, KOG0084, GTPase Rab1/YPT1, small G protein superfamily, and related GTP-binding proteins [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport]. Length = 205 Score = 30.2 bits (68), Expect = 1.1 Identities = 30/128 (23%), Positives = 53/128 (41%), Gaps = 27/128 (21%) Query: 220 YKIVILGHSNAGKSSL---FNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAG 276 +KI+++G S GK+ L F + I T G + T++LD + ++I DTAG Sbjct: 10 FKIILIGDSGVGKTCLLLRFKDDTFTESYISTI--GVDFKIRTVELDGKTIKLQIWDTAG 67 Query: 277 IRETDDIVEKEGIKRTFLEV-ENADLILLLKEINSK----------KEISF--PKNIDFI 323 +E + A I+ + +I + +EI +N+ + Sbjct: 68 ---------QERFRTITSSYYRGAHGIIFVYDITKQESFNNVKRWIQEIDRYASENVPKL 118 Query: 324 FIGTKSDL 331 +G K DL Sbjct: 119 LVGNKCDL 126 >gnl|CDD|133271 cd01868, Rab11_like, Rab11-like. Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 165 Score = 30.2 bits (69), Expect = 1.1 Identities = 38/134 (28%), Positives = 61/134 (45%), Gaps = 39/134 (29%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDV--LTIDLDLEGYLVK--ISDTA 275 +KIV++G S GKS+L + + + + + +T V T + ++G +K I DTA Sbjct: 4 FKIVLIGDSGVGKSNLLSRFTRNEFNLDSK---STIGVEFATRSIQIDGKTIKAQIWDTA 60 Query: 276 GIRE-----TD-------------DIVEKEGIKRTFLEVENADLILLLKEINSKKEISFP 317 G +E T DI + K+TF VE LKE+ ++ + Sbjct: 61 G-QERYRAITSAYYRGAVGALLVYDITK----KQTFENVE-----RWLKEL---RDHA-D 106 Query: 318 KNIDFIFIGTKSDL 331 NI + +G KSDL Sbjct: 107 SNIVIMLVGNKSDL 120 >gnl|CDD|72987 cd03228, ABCC_MRP_Like, The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). 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 = 171 Score = 30.4 bits (69), Expect = 1.1 Identities = 11/26 (42%), Positives = 17/26 (65%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALAK 241 I+ G K+ I+G S +GKS+L L + Sbjct: 25 IKPGEKVAIVGPSGSGKSTLLKLLLR 50 >gnl|CDD|73003 cd03244, ABCC_MRP_domain2, Domain 2 of the ABC subfamily C. This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.. Length = 221 Score = 30.1 bits (68), Expect = 1.1 Identities = 12/24 (50%), Positives = 17/24 (70%) Query: 216 IRNGYKIVILGHSNAGKSSLFNAL 239 I+ G K+ I+G + +GKSSL AL Sbjct: 27 IKPGEKVGIVGRTGSGKSSLLLAL 50 >gnl|CDD|35310 KOG0087, KOG0087, KOG0087, GTPase Rab11/YPT3, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 222 Score = 30.3 bits (68), Expect = 1.2 Identities = 35/137 (25%), Positives = 57/137 (41%), Gaps = 26/137 (18%) Query: 219 GYKIVILGHSNAGKSSLFNALAKKDVAIVTDIP-GTTRDVLTIDLDLEGYLVKISDTAGI 277 +KIV++G S GKS+L + + + ++ + G T+++D + +I DTAG Sbjct: 14 LFKIVLIGDSAVGKSNLLSRFTRNEFSLESKSTIGVEFATRTVNVDGKTVKAQIWDTAGQ 73 Query: 278 RETDDI-------------VEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFIF 324 I V ++TF VE LKE+ NI + Sbjct: 74 ERYRAITSAYYRGAVGALLVYDITRRQTFENVE-----RWLKELRD----HADSNIVIML 124 Query: 325 IGTKSDLY---STYTEE 338 +G KSDL + TE+ Sbjct: 125 VGNKSDLNHLRAVPTED 141 >gnl|CDD|31298 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase component [General function prediction only]. Length = 263 Score = 30.2 bits (68), Expect = 1.2 Identities = 9/19 (47%), Positives = 15/19 (78%) Query: 222 IVILGHSNAGKSSLFNALA 240 + ++G + AGKS+L NA+A Sbjct: 35 VTVIGSNGAGKSTLLNAIA 53 >gnl|CDD|35277 KOG0054, KOG0054, KOG0054, Multidrug resistance-associated protein/mitoxantrone resistance protein, ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]. Length = 1381 Score = 30.2 bits (68), Expect = 1.2 Identities = 13/24 (54%), Positives = 17/24 (70%) Query: 216 IRNGYKIVILGHSNAGKSSLFNAL 239 I+ G K+ I+G + AGKSSL AL Sbjct: 1163 IKPGEKVGIVGRTGAGKSSLILAL 1186 >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 = 30.0 bits (68), Expect = 1.3 Identities = 32/130 (24%), Positives = 54/130 (41%), Gaps = 17/130 (13%) Query: 222 IVILGHSNAGKSSLFNAL-AKKDVAIVTDIPGTTRDVLTIDLDLE--GYLVKISDTAG-- 276 +++LG S++GK++LF L K + VT I +V T L+ E G ++ D G Sbjct: 3 VLLLGPSDSGKTALFTKLTTGKYRSTVTSI---EPNVATFILNSEGKGKKFRLVDVPGHP 59 Query: 277 -IRETDDIVEKEGIKRTFLEVENADLI-------LLLKEINSKKEISFPKNIDFIFIGTK 328 +R+ K K V++A L +I + E K I + K Sbjct: 60 KLRDKLLETLKNSAKGIVFVVDSATFQKNLKDVAEFLYDILTDLEKVKNK-IPVLIACNK 118 Query: 329 SDLYSTYTEE 338 DL++ + Sbjct: 119 QDLFTAKPAK 128 >gnl|CDD|34590 COG4985, COG4985, ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]. Length = 289 Score = 30.0 bits (67), Expect = 1.4 Identities = 22/121 (18%), Positives = 47/121 (38%), Gaps = 20/121 (16%) Query: 53 FFGLDGRILDKGLLIVFPSPESFTGEDSAEFHVHGGIAVVNGILEELAKMP--NLRLANP 110 +G R G + D E + + V + +++ KM +R+ N Sbjct: 143 LYGKLLRFDSNGQELD---------GDPLERELQKRLLEVETLRDQVDKMVEQQVRVINS 193 Query: 111 GEFSRRAFENGKIDL---LEAESLADLISSETEMQRRLS-----MEGMSGELSSLYGQWI 162 R E ++ L L+ E ++ ++E+Q+RL+ ++ + EL + + Sbjct: 194 Q-LERLRLEKRRLQLNGQLDDEFQQHYVAEKSELQKRLAQLQTELDALRAELERQFLYLV 252 Query: 163 D 163 D Sbjct: 253 D 253 >gnl|CDD|143815 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a number of different Prosite families together. Length = 174 Score = 29.9 bits (68), Expect = 1.4 Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 2/32 (6%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIP 251 +I+ILG NAGK+++ L + IVT IP Sbjct: 15 MRILILGLDNAGKTTILYKLKLGE--IVTTIP 44 >gnl|CDD|72980 cd03221, ABCF_EF-3, ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.. Length = 144 Score = 30.0 bits (68), Expect = 1.4 Identities = 10/36 (27%), Positives = 18/36 (50%) Query: 215 IIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDI 250 I G +I ++G + AGKS+L +A + + Sbjct: 22 TINPGDRIGLVGRNGAGKSTLLKLIAGELEPDEGIV 57 >gnl|CDD|31313 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 248 Score = 29.8 bits (67), Expect = 1.4 Identities = 10/25 (40%), Positives = 14/25 (56%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240 + G + ILG S GKS+L +A Sbjct: 26 VEKGEFVAILGPSGCGKSTLLRLIA 50 >gnl|CDD|34592 COG4987, CydC, ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]. Length = 573 Score = 29.8 bits (67), Expect = 1.4 Identities = 12/26 (46%), Positives = 16/26 (61%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALAK 241 + G K+ ILG S +GKS+L LA Sbjct: 361 LAQGEKVAILGRSGSGKSTLLQLLAG 386 >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 = 29.7 bits (68), Expect = 1.6 Identities = 47/180 (26%), Positives = 68/180 (37%), Gaps = 55/180 (30%) Query: 224 ILGHSNAGKSSLFNAL--AKKDVAIVTDIPGTTRDVLTIDLDLEGYL--VKISDTAGIRE 279 ++G NAGKS+L +A+ AK +A D P TT L L V++ D Sbjct: 5 LVGLPNAGKSTLLSAISNAKPKIA---DYPFTT---------LVPNLGVVRVDDGRSFVV 52 Query: 280 TD--DIVE--KEG----------IKRTFL--------EVEN--ADLILLLKEINSKKEIS 315 D ++E EG I+RT L ++ D + E+ Sbjct: 53 ADIPGLIEGASEGKGLGHRFLRHIERTRLLLHVIDLSGDDDPVEDYKTIRNELELYNPEL 112 Query: 316 FPKNIDFIFIGTKSDLYSTYT------EEYDHL-------ISSFTGEGLEELINKIKSIL 362 K I + K DL E L IS+ TGEGL+EL+ K+ +L Sbjct: 113 LEKPR--IVVLNKIDLLDEEELFELLKELLKELWGKPVFPISALTGEGLDELLRKLAELL 170 >gnl|CDD|30834 COG0488, Uup, ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]. Length = 530 Score = 29.8 bits (67), Expect = 1.6 Identities = 12/29 (41%), Positives = 17/29 (58%) Query: 215 IIRNGYKIVILGHSNAGKSSLFNALAKKD 243 I G +I I+G + AGKS+L LA + Sbjct: 344 RIDRGDRIAIVGPNGAGKSTLLKLLAGEL 372 Score = 27.1 bits (60), Expect = 9.5 Identities = 10/31 (32%), Positives = 17/31 (54%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALAKKDVAI 246 + G +I ++G + AGKS+L LA + Sbjct: 26 LNPGERIGLVGRNGAGKSTLLKILAGELEPD 56 >gnl|CDD|73051 cd03292, ABC_FtsE_transporter, FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane. The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.. Length = 214 Score = 29.5 bits (66), Expect = 1.8 Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 10/55 (18%) Query: 189 SKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKD 243 +K N L + I+ IS G+ + ++G S AGKS+L + K++ Sbjct: 7 TKTYPNGTAAL-DGINISISAGEF---------VFLVGPSGAGKSTLLKLIYKEE 51 >gnl|CDD|31317 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]. Length = 258 Score = 29.8 bits (67), Expect = 1.8 Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 9/40 (22%) Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALA 240 +D+S I +G++ ILG + +GKS+L LA Sbjct: 19 DDLSFSIPKGEI---------TGILGPNGSGKSTLLKCLA 49 >gnl|CDD|36704 KOG1491, KOG1491, KOG1491, Predicted GTP-binding protein (ODN superfamily) [General function prediction only]. Length = 391 Score = 29.5 bits (66), Expect = 1.9 Identities = 14/24 (58%), Positives = 16/24 (66%) Query: 218 NGYKIVILGHSNAGKSSLFNALAK 241 N KI I+G N GKS+ FNAL K Sbjct: 19 NNLKIGIVGLPNVGKSTFFNALTK 42 >gnl|CDD|36463 KOG1249, KOG1249, KOG1249, Predicted GTPases [General function prediction only]. Length = 572 Score = 29.6 bits (66), Expect = 1.9 Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 11/40 (27%) Query: 226 GHSNAGKSSLFNALAKKD-----------VAIVTDIPGTT 254 G +N GKS+LFNAL + D A ++D PGTT Sbjct: 220 GATNVGKSTLFNALLESDLCSVNAPKLVDRATISDWPGTT 259 >gnl|CDD|133316 cd04116, Rab9, Rab9 subfamily. Rab9 is found in late endosomes, together with mannose 6-phosphate receptors (MPRs) and the tail-interacting protein of 47 kD (TIP47). Rab9 is a key mediator of vesicular transport from late endosomes to the trans-Golgi network (TGN) by redirecting the MPRs. Rab9 has been identified as a key component for the replication of several viruses, including HIV1, Ebola, Marburg, and measles, making it a potential target for inhibiting a variety of viruses. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 170 Score = 29.4 bits (66), Expect = 2.0 Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 15/64 (23%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTR------DVLTIDLDLEGYLV--KIS 272 K+++LG GKSSL N VT+ T + L DL+++G+ V +I Sbjct: 7 KVILLGDGGVGKSSLMNRY-------VTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIW 59 Query: 273 DTAG 276 DTAG Sbjct: 60 DTAG 63 >gnl|CDD|36702 KOG1489, KOG1489, KOG1489, Predicted GTP-binding protein (ODN superfamily) [General function prediction only]. Length = 366 Score = 29.5 bits (66), Expect = 2.0 Identities = 44/176 (25%), Positives = 75/176 (42%), Gaps = 47/176 (26%) Query: 224 ILGHSNAGKSSLFNAL--AKKDVAIVTDIPGTT--RDVLTIDLDLEGYLVKISDTAGIRE 279 ++G NAGKS+L NAL AK VA TT + T++ D + + ++D GI E Sbjct: 201 LVGFPNAGKSTLLNALSRAKPKVA---HYAFTTLRPHIGTVNYD-DFSQITVADIPGIIE 256 Query: 280 TDDIVEKEGIKRTFLE-VENADLILLLKEINSKKEISFPKNIDF---------------- 322 +G+ FL +E +L + +++ K+ + + + Sbjct: 257 --GAHMNKGLGYKFLRHIERCKGLLFVVDLSGKQLRNPWQQLQLLIEELELYEKGLADRP 314 Query: 323 -IFIGTKSDLYSTYTEEYDHLISSF---------------TGEGLEELINKIKSIL 362 + + K DL E +L+SS +GEGLEEL+N ++ +L Sbjct: 315 ALIVANKIDL----PEAEKNLLSSLAKRLQNPHVVPVSAKSGEGLEELLNGLRELL 366 >gnl|CDD|133372 cd04172, Rnd3_RhoE_Rho8, Rnd3/RhoE/Rho8 subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7. Rnd3/RhoE is known to bind the serine-threonine kinase ROCK I. Unphosphorylated Rnd3/RhoE associates primarily with membranes, but ROCK I-phosphorylated Rnd3/RhoE localizes in the cytosol. Phosphorylation of Rnd3/RhoE correlates with its activity in disrupting RhoA-induced stress fibers and inhibiting Ras-induced fibroblast transformation. In cells that lack stress fibers, such as macrophages and monocytes, Rnd3/RhoE induces a redistribution of actin, causing morphological changes in the cell. In addition, Rnd3/RhoE has been shown to inhibit cell cycle progression in G1 phase at a point upstream of the pRb family pocket protein checkpoint. Rnd3/RhoE has also been shown to inhibit Ras- and Raf-induced fibroblast transformation. In mammary epithelial tumor cells, Rnd3/RhoE regulates the assembly of the apical junction complex and tight junction formation. Rnd3/RhoE is underexpressed in prostate cancer cells both in vitro and in vivo; re-expression of Rnd3/RhoE suppresses cell cycle progression and increases apoptosis, suggesting it may play a role in tumor suppression. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 182 Score = 29.3 bits (65), Expect = 2.1 Identities = 36/138 (26%), Positives = 62/138 (44%), Gaps = 27/138 (19%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKIS--DTAGIR 278 KIV++G S GK++L + A KD +P T + T +++ +++S DT+G Sbjct: 7 KIVVVGDSQCGKTALLHVFA-KDCFPENYVP-TVFENYTASFEIDTQRIELSLWDTSGSP 64 Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINS-----------KKEIS-FPKNIDFIFIG 326 D++ L ++D +L+ +I+ K EI F N + +G Sbjct: 65 YYDNVRP--------LSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVG 116 Query: 327 TKSDL---YSTYTEEYDH 341 KSDL +T E +H Sbjct: 117 CKSDLRTDLTTLVELSNH 134 >gnl|CDD|143431 cd07113, ALDH_PADH_NahF, Escherichia coli NAD+-dependent phenylacetaldehyde dehydrogenase PadA-like. NAD+-dependent, homodimeric, phenylacetaldehyde dehydrogenase (PADH, EC=1.2.1.39) PadA of Escherichia coli involved in the catabolism of 2-phenylethylamine, and other related sequences, are present in this CD. Also included is the Pseudomonas fluorescens ST StyD PADH involved in styrene catabolism, the Sphingomonas sp. LB126 FldD protein involved in fluorene degradation, and the Novosphingobium aromaticivorans NahF salicylaldehyde dehydrogenase involved in the NAD+-dependent conversion of salicylaldehyde to salicylate. Length = 477 Score = 29.3 bits (66), Expect = 2.2 Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 3/47 (6%) Query: 50 LRYFFGLDGRILDKGLLIVFPSPESFTGEDSAEFHVHGGIAVVNGIL 96 LRYF G +I + L PS + GE F + VV GI+ Sbjct: 107 LRYFAGWATKINGETLAPSIPSMQ---GERYTAFTRREPVGVVAGIV 150 >gnl|CDD|35309 KOG0086, KOG0086, KOG0086, GTPase Rab4, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 214 Score = 29.2 bits (65), Expect = 2.2 Identities = 35/167 (20%), Positives = 62/167 (37%), Gaps = 24/167 (14%) Query: 220 YKIVILGHSNAGKSSLFNALAKK----DVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTA 275 +K +++G + GKS L + + D + + +R +++ + ++I DTA Sbjct: 10 FKFLVIGSAGTGKSCLLHQFIENKFKDDSSHTIGVEFGSR---IVNVGGKTVKLQIWDTA 66 Query: 276 GIRETDDIVEK--EGIKRTFL--EVENADLILLLKEINSKKEISFPKNIDFIFIGTKSDL 331 G + G L ++ + D L + NI I G K DL Sbjct: 67 GQERFRSVTRSYYRGAAGALLVYDITSRDSFNALTNWLTDARTLASPNIVVILCGNKKDL 126 Query: 332 ----------YSTYTEEYD---HLISSFTGEGLEELINKIKSILSNK 365 S + +E + S+ TGE +EE K + NK Sbjct: 127 DPEREVTFLEASRFAQENELMFLETSALTGENVEEAFLKCARTILNK 173 >gnl|CDD|31319 COG1122, CbiO, ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 235 Score = 29.1 bits (65), Expect = 2.2 Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 14/77 (18%) Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTI 260 D+S I +G+ ++++G + +GKS+L L ++ G V + Sbjct: 21 KDVSLEIEKGER---------VLLIGPNGSGKSTLLKLLN----GLLKPTSGEVL-VDGL 66 Query: 261 DLDLEGYLVKISDTAGI 277 D E L+++ G+ Sbjct: 67 DTSSEKSLLELRQKVGL 83 >gnl|CDD|113806 pfam05049, IIGP, Interferon-inducible GTPase (IIGP). Interferon-inducible GTPase (IIGP) is thought to play a role in in intracellular defence. IIGP is predominantly associated with the Golgi apparatus and also localizes to the endoplasmic reticulum and exerts a distinct role in IFN-induced intracellular membrane trafficking or processing. Length = 375 Score = 29.4 bits (66), Expect = 2.3 Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 4/55 (7%) Query: 189 SKEVLNDIL--FLKNDISSHISQGK--LGEIIRNGYKIVILGHSNAGKSSLFNAL 239 S EV+ I + ++ +S K + EI KI + G S GKSS NAL Sbjct: 1 SPEVITLIETALREGNLQKVVSIIKKAIQEISSAPLKIAVTGDSGNGKSSFINAL 55 >gnl|CDD|133374 cd04174, Rnd1_Rho6, Rnd1/Rho6 subfamily. Rnd1/Rho6 is a member of the novel Rho subfamily Rnd, together with Rnd2/Rho7 and Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not hydrolyze it to GDP, indicating that it is constitutively active. In rat, Rnd1/Rho6 is highly expressed in the cerebral cortex and hippocampus during synapse formation, and plays a role in spine formation. Rnd1/Rho6 is also expressed in the liver and in endothelial cells, and is upregulated in uterine myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8, Rnd1/Rho6 is believed to function as an antagonist to RhoA. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 232 Score = 29.3 bits (65), Expect = 2.3 Identities = 34/125 (27%), Positives = 57/125 (45%), Gaps = 24/125 (19%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKIS--DTAGIR 278 K+V++G GK+++ LA KD T +P T + T L+ E V++S DT+G Sbjct: 15 KLVLVGDVQCGKTAMLQVLA-KDCYPETYVP-TVFENYTAGLETEEQRVELSLWDTSGSP 72 Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINS-----------KKEI-SFPKNIDFIFIG 326 D++ L ++D +LL +I+ K EI + + + IG Sbjct: 73 YYDNVRP--------LCYSDSDAVLLCFDISRPETVDSALKKWKAEIMDYCPSTRILLIG 124 Query: 327 TKSDL 331 K+DL Sbjct: 125 CKTDL 129 >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 = 29.1 bits (66), Expect = 2.4 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 2/31 (6%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIP 251 +I+ILG AGK+++ L +V VT IP Sbjct: 1 RILILGLDGAGKTTILYKLKLGEV--VTTIP 29 >gnl|CDD|30909 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide transport and metabolism]. Length = 178 Score = 29.1 bits (65), Expect = 2.7 Identities = 13/22 (59%), Positives = 16/22 (72%) Query: 221 KIVILGHSNAGKSSLFNALAKK 242 +I+ILG AGKS+L LAKK Sbjct: 2 RILILGPPGAGKSTLAKKLAKK 23 >gnl|CDD|73006 cd03247, ABCC_cytochrome_bd, The CYD subfamily implicated in cytochrome bd biogenesis. The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.. Length = 178 Score = 29.0 bits (65), Expect = 2.7 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%) Query: 192 VLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALA 240 +N++ F + + + L ++ G KI +LG S +GKS+L L Sbjct: 2 SINNVSFSYPEQEQQVLKN-LSLELKQGEKIALLGRSGSGKSTLLQLLT 49 >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 = 28.9 bits (65), Expect = 2.7 Identities = 9/25 (36%), Positives = 16/25 (64%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDV 244 YK++I+G NAGK+++ +V Sbjct: 16 YKVIIVGLDNAGKTTILYQFLLGEV 40 >gnl|CDD|73009 cd03250, ABCC_MRP_domain1, Domain 1 of the ABC subfamily C. This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.. Length = 204 Score = 28.9 bits (65), Expect = 2.9 Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 9/54 (16%) Query: 186 NFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNAL 239 +F+ + F DI+ + +G+L + I+G +GKSSL +AL Sbjct: 7 SFTWDSGEQETSFTLKDINLEVPKGEL---------VAIVGPVGSGKSSLLSAL 51 >gnl|CDD|35300 KOG0077, KOG0077, KOG0077, Vesicle coat complex COPII, GTPase subunit SAR1 [Intracellular trafficking, secretion, and vesicular transport]. Length = 193 Score = 28.8 bits (64), Expect = 2.9 Identities = 31/133 (23%), Positives = 53/133 (39%), Gaps = 29/133 (21%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPG--TTRDVLTID------LDLEGYLVK-- 270 K++ LG NAGK++L + L KD + +P T + L+I DL G+L Sbjct: 22 KLLFLGLDNAGKTTLLHML--KDDRLGQHVPTLHPTSEELSIGGMTFTTFDLGGHLQARR 79 Query: 271 -----ISDTAGIRETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFIFI 325 I D ++E F E + KE+++ + F+ + Sbjct: 80 VWKDYFPQVDAIVYLVDAYDQE----RFAESK--------KELDALLSDESLATVPFLIL 127 Query: 326 GTKSDLYSTYTEE 338 G K D+ +E+ Sbjct: 128 GNKIDIPYAASED 140 >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 = 28.6 bits (65), Expect = 3.0 Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 4/85 (4%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETD 281 + ++G + GKS+L + L V TT + L+ +G +++ D GI E Sbjct: 3 VALVGFPSVGKSTLLSKLTNTKSE-VAAYEFTTLTCVPGVLEYKGAKIQLLDLPGIIE-- 59 Query: 282 DIVEKEGIKRTFLEV-ENADLILLL 305 + +G R + V ADLIL++ Sbjct: 60 GAADGKGRGRQVIAVARTADLILMV 84 >gnl|CDD|73022 cd03263, ABC_subfamily_A, The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.. Length = 220 Score = 28.6 bits (64), Expect = 3.3 Identities = 8/25 (32%), Positives = 13/25 (52%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240 + G +LGH+ AGK++ L Sbjct: 25 VYKGEIFGLLGHNGAGKTTTLKMLT 49 >gnl|CDD|32455 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]. Length = 709 Score = 28.6 bits (64), Expect = 3.4 Identities = 11/25 (44%), Positives = 15/25 (60%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240 I G K+ I+G S +GKS+L L Sbjct: 496 IPPGEKVAIVGRSGSGKSTLLKLLL 520 >gnl|CDD|133336 cd04136, Rap_like, Rap-like subfamily. The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres. Rap2 is involved in multiple functions, including activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton and activation of the Wnt/beta-catenin signaling pathway in embryonic Xenopus. A number of effector proteins for Rap2 have been identified, including isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK), and the RalGEFs RalGDS, RGL, and Rlf, which also interact with Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and Rap2. In budding yeasts, it is involved in selecting a site for bud growth, which directs the establishment of cell polarization. The Rho family GTPase Cdc42 and its GEF, Cdc24, then establish an axis of polarized growth. It is believed that Cdc42 interacts directly with RSR1 in vivo. In filamentous fungi such as Ashbya gossypii, RSR1 is a key regulator of polar growth in the hypha. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 163 Score = 28.4 bits (64), Expect = 3.5 Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 16/66 (24%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDI------PGTTRDVL--TIDLDLEGYLVKI 271 YK+V+LG GKS+L V V I P T D I++D + +++I Sbjct: 2 YKVVVLGSGGVGKSAL-------TVQFVQGIFVEKYDP-TIEDSYRKQIEVDGQQCMLEI 53 Query: 272 SDTAGI 277 DTAG Sbjct: 54 LDTAGT 59 >gnl|CDD|73018 cd03259, ABC_Carb_Solutes_like, ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. 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 = 213 Score = 28.6 bits (64), Expect = 3.6 Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 19/67 (28%) Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALA------KKDVAI----VTDI 250 +D+S + G+ + +LG S GK++L +A ++ I VT + Sbjct: 17 DDLSLTVEPGEF---------LALLGPSGCGKTTLLRLIAGLERPDSGEILIDGRDVTGV 67 Query: 251 PGTTRDV 257 P R++ Sbjct: 68 PPERRNI 74 >gnl|CDD|133310 cd04110, Rab35, Rab35 subfamily. Rab35 is one of several Rab proteins to be found to participate in the regulation of osteoclast cells in rats. In addition, Rab35 has been identified as a protein that interacts with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) in human cells. Overexpression of NPM-ALK is a key oncogenic event in some anaplastic large-cell lymphomas; since Rab35 interacts with N|PM-ALK, it may provide a target for cancer treatments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Length = 199 Score = 28.7 bits (64), Expect = 3.8 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 3/59 (5%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVA--IVTDIPGTTRDVLTIDLDLEGYLVKISDTAG 276 +K++I+G S GKSSL A + +T I G + T++++ E ++I DTAG Sbjct: 7 FKLLIIGDSGVGKSSLLLRFADNTFSGSYITTI-GVDFKIRTVEINGERVKLQIWDTAG 64 >gnl|CDD|72973 cd03214, ABC_Iron-Siderophores_B12_Hemin, ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.. Length = 180 Score = 28.5 bits (64), Expect = 4.0 Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 9/41 (21%) Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAK 241 +D+S I G++ + ILG + AGKS+L LA Sbjct: 16 DDLSLSIEAGEI---------VGILGPNGAGKSTLLKTLAG 47 >gnl|CDD|133292 cd01892, Miro2, Miro2 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature. Length = 169 Score = 28.3 bits (64), Expect = 4.0 Identities = 27/131 (20%), Positives = 51/131 (38%), Gaps = 28/131 (21%) Query: 217 RNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTID-LDLEG---YLVKIS 272 RN + +LG +GKS+L A + + + T + ++ +++ G YL+ Sbjct: 2 RNVFLCFVLGAKGSGKSALLRAFLGRSFS-LNAYSPTIKPRYAVNTVEVYGQEKYLI--- 57 Query: 273 DTAGIRETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISFP------------KNI 320 +RE ++ I E+ D+ L+ +S SF I Sbjct: 58 ----LREVG--EDEVAILLNDAELAACDVACLV--YDSSDPKSFSYCAEVYKKYFMLGEI 109 Query: 321 DFIFIGTKSDL 331 +F+ K+DL Sbjct: 110 PCLFVAAKADL 120 >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 = 28.2 bits (63), Expect = 4.5 Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 9/39 (23%) Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNAL 239 D+S I+ G+ + ++G S AGKS+L L Sbjct: 18 KDVSLSINPGEF---------VALIGPSGAGKSTLLRCL 47 >gnl|CDD|176731 cd08316, Death_FAS_TNFRSF6, Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. Length = 97 Score = 28.1 bits (63), Expect = 4.7 Identities = 8/36 (22%), Positives = 18/36 (50%) Query: 260 IDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLE 295 D+DL ++ I+D +++ V K G+ ++ Sbjct: 3 SDVDLSKHIPDIADVMTLKDVKKFVRKSGLSEPKID 38 >gnl|CDD|73052 cd03293, ABC_NrtD_SsuB_transporters, NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. 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 = 220 Score = 28.1 bits (63), Expect = 4.7 Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 9/40 (22%) Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALA 240 DIS + +G+ + ++G S GKS+L +A Sbjct: 21 EDISLSVEEGEF---------VALVGPSGCGKSTLLRIIA 51 >gnl|CDD|133304 cd04104, p47_IIGP_like, p47 (47-kDa) family. The p47 GTPase family consists of several highly homologous proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. They are found in higher eukaryotes where they play a role in immune resistance against intracellular pathogens. p47 proteins exist at low resting levels in mouse cells, but are strongly induced by Type II interferon (IFN-gamma). ITGP is critical for resistance to Toxoplasma gondii infection and in involved in inhibition of Coxsackievirus-B3-induced apoptosis. TGTP was shown to limit vesicular stomatitis virus (VSV) infection of fibroblasts in vitro. IRG-47 is involved in resistance to T. gondii infection. LRG-47 has been implicated in resistance to T. gondii, Listeria monocytogenes, Leishmania, and mycobacterial infections. IIGP1 has been shown to localize to the ER and to the Golgi membranes in IFN-induced cells and inflamed tissues. In macrophages, IIGP1 interacts with hook3, a microtubule binding protein that participates in the organization of the cis-Golgi compartment. Length = 197 Score = 28.1 bits (63), Expect = 4.7 Identities = 11/19 (57%), Positives = 12/19 (63%) Query: 221 KIVILGHSNAGKSSLFNAL 239 I + G S AGKSS NAL Sbjct: 3 NIAVTGESGAGKSSFINAL 21 >gnl|CDD|110369 pfam01364, Peptidase_C25, Peptidase family C25. Length = 349 Score = 28.1 bits (62), Expect = 5.1 Identities = 21/98 (21%), Positives = 38/98 (38%), Gaps = 12/98 (12%) Query: 269 VKISDTAGIRETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFIFIGTK 328 VK+++ T + + ++ +K+ + + N +LL + K+I G K Sbjct: 40 VKVAEDIASPVTANAI-QQFVKQEYEKEGNDLTYVLL--VGDHKDIPAKITP-----GIK 91 Query: 329 SDLYSTYTEEYDHLISSFTG----EGLEELINKIKSIL 362 SD DH F G E E+L +I + Sbjct: 92 SDQVYGQIVGNDHYNEVFIGRFSCESKEDLKTQIDRTI 129 >gnl|CDD|33631 COG3839, MalK, ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]. Length = 338 Score = 27.9 bits (62), Expect = 5.1 Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 10/52 (19%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA------KKDVAI----VTDIPGTTRDV 257 I +G +V+LG S GKS+L +A ++ I VTD+P R + Sbjct: 26 IEDGEFVVLLGPSGCGKSTLLRMIAGLEEPTSGEILIDGRDVTDLPPEKRGI 77 >gnl|CDD|133255 cd00879, Sar1, Sar1 subfamily. Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation. Length = 190 Score = 28.0 bits (63), Expect = 5.1 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 2/31 (6%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIP 251 KI+ LG NAGK++L + L KD + +P Sbjct: 21 KILFLGLDNAGKTTLLHML--KDDRLAQHVP 49 >gnl|CDD|33632 COG3840, ThiQ, ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]. Length = 231 Score = 28.0 bits (62), Expect = 5.2 Identities = 12/25 (48%), Positives = 16/25 (64%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240 + G + ILG S AGKS+L N +A Sbjct: 22 VPAGEIVAILGPSGAGKSTLLNLIA 46 >gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab33B/Rab33A subfamily. Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II. Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells. In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 170 Score = 28.2 bits (63), Expect = 5.3 Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 15/65 (23%) Query: 220 YKIVILGHSNAGKSSL-FNALAKKDVAIVTDIPGTTRDVLTID-----LDLEGYLVKIS- 272 +KI+++G SN GK+ L + A + P T + +D ++++G +K+ Sbjct: 3 FKIIVIGDSNVGKTCLTYRFCAGR-------FPERTEATIGVDFRERTVEIDGERIKVQL 55 Query: 273 -DTAG 276 DTAG Sbjct: 56 WDTAG 60 >gnl|CDD|72993 cd03234, ABCG_White, The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors. The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan. The pigment precursors are encoded by the white, brown, and scarlet genes, respectively. Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan. However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes. Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in macrophages, hepatocytes, and intestinal mucosa cells. ABCG1 (ABC8), the human homolog of the Drosophila white gene is induced in monocyte-derived macrophages during cholesterol influx mediated by acetylated low-density lipoprotein. It is possible that human ABCG1 forms heterodimers with several heterologous partners.. Length = 226 Score = 27.9 bits (62), Expect = 5.4 Identities = 13/43 (30%), Positives = 25/43 (58%), Gaps = 9/43 (20%) Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKD 243 ND+S H+ G++ + ILG S +GK++L +A++ + Sbjct: 24 NDVSLHVESGQV---------MAILGSSGSGKTTLLDAISGRV 57 >gnl|CDD|31445 COG1253, TlyC, Hemolysins and related proteins containing CBS domains [General function prediction only]. Length = 429 Score = 28.0 bits (62), Expect = 5.6 Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 6/87 (6%) Query: 240 AKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLEVENA 299 + +AIV D G ++T++ +E + +I D E +DI++++ +L Sbjct: 300 ERTHMAIVVDEYGGVEGLVTLEDIIEEIVGEIPDEHDEDEEEDIIQRDD--DGWL----V 353 Query: 300 DLILLLKEINSKKEISFPKNIDFIFIG 326 D + L+E+ I + D+ I Sbjct: 354 DGRVPLEELEELLGIDLDEEEDYDTIA 380 >gnl|CDD|30002 cd01136, ATPase_flagellum-secretory_path_III, Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.. Length = 326 Score = 27.9 bits (62), Expect = 5.8 Identities = 28/92 (30%), Positives = 41/92 (44%), Gaps = 24/92 (26%) Query: 219 GYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR 278 G ++ I S GKS+L +A+ GTT DV I L I + R Sbjct: 69 GQRLGIFAGSGVGKSTLLGMIAR----------GTTADVNVIAL--------IGERG--R 108 Query: 279 ETDDIVEK----EGIKRTFLEVENADLILLLK 306 E + +EK EG+KR+ + V +D LL+ Sbjct: 109 EVREFIEKDLGEEGLKRSVVVVATSDESPLLR 140 >gnl|CDD|33436 COG3638, COG3638, ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 258 Score = 27.9 bits (62), Expect = 6.2 Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 9/40 (22%) Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALA 240 D++ I+QG++ + I+G S AGKS+L +L Sbjct: 21 KDVNLEINQGEM---------VAIIGPSGAGKSTLLRSLN 51 >gnl|CDD|72991 cd03232, ABC_PDR_domain2, The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters. PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. 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 = 192 Score = 27.8 bits (62), Expect = 6.3 Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 10/51 (19%) Query: 199 LKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAK-KDVAIVT 248 L N+IS ++ G L ++G S AGK++L + LA K ++T Sbjct: 22 LLNNISGYVKPGTL---------TALMGESGAGKTTLLDVLAGRKTAGVIT 63 >gnl|CDD|35296 KOG0073, KOG0073, KOG0073, GTP-binding ADP-ribosylation factor-like protein ARL2 [Intracellular trafficking, secretion, and vesicular transport, Cytoskeleton]. Length = 185 Score = 27.9 bits (62), Expect = 6.4 Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 4/59 (6%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRE 279 +I+ILG N+GK+++ L +D TD T L+ +GY + I D G + Sbjct: 18 RILILGLDNSGKTTIVKKLLGED----TDTISPTLGFQIKTLEYKGYTLNIWDVGGQKT 72 >gnl|CDD|30543 COG0194, Gmk, Guanylate kinase [Nucleotide transport and metabolism]. Length = 191 Score = 27.8 bits (62), Expect = 6.6 Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTR 255 IV+ G S GKS+L AL + D + + TTR Sbjct: 7 IVLSGPSGVGKSTLVKALLEDD-KLRFSVSATTR 39 >gnl|CDD|147764 pfam05789, Baculo_VP1054, Baculovirus VP1054 protein. This family consists of several VP1054 proteins from the Baculoviruses. VP1054 is a virus structural protein required for nucleocapsid assembly. Length = 314 Score = 27.6 bits (62), Expect = 6.6 Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 5/43 (11%) Query: 277 IRETDDIVEKEGIKRTFLEVENADLILLLKEIN----SKKEIS 315 + E D+ V + I +TFL V N L ++LK+ N + K IS Sbjct: 178 VPEYDEAVASQDIYKTFL-VYNTVLTMMLKQKNPFNDANKSIS 219 >gnl|CDD|39086 KOG3883, KOG3883, KOG3883, Ras family small GTPase [Signal transduction mechanisms]. Length = 198 Score = 27.7 bits (61), Expect = 6.6 Identities = 24/128 (18%), Positives = 55/128 (42%), Gaps = 25/128 (19%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEG---YLVKISDTAGI 277 K+V+ G + GK+++ L + T++ T D+ ++ + +++ DTAG+ Sbjct: 11 KVVVCGMKSVGKTAILEQLLYGNHVPGTELHPTIEDIYVASVETDRGAREQLRLYDTAGL 70 Query: 278 RETDDIVEKEGIKRTFLEVENADLI--------------LLLKEINSKKEISFPKNIDFI 323 + ++ + R + + +A ++ LL KEI+ K+ K + + Sbjct: 71 QG-----GQQELPRHYFQFADAFVLVYSPMDPESFQRVELLKKEIDKHKD---KKEVPIV 122 Query: 324 FIGTKSDL 331 + K D Sbjct: 123 VLANKRDR 130 >gnl|CDD|35301 KOG0078, KOG0078, KOG0078, GTP-binding protein SEC4, small G protein superfamily, and related Ras family GTP-binding proteins [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport]. Length = 207 Score = 27.5 bits (61), Expect = 6.7 Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 3/59 (5%) Query: 220 YKIVILGHSNAGKSSLFNALAKK--DVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAG 276 +K++++G S GK+ L + + + ++ I G + TI+LD + ++I DTAG Sbjct: 13 FKLLLIGDSGVGKTCLLLRFSDDSFNTSFISTI-GIDFKIKTIELDGKKIKLQIWDTAG 70 >gnl|CDD|73021 cd03262, ABC_HisP_GlnQ_permeases, HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP has properties intermediate between those of integral and peripheral membrane proteins and is accessible from both sides of the membrane, presumably by its interaction with HisQ and HisM. The two HisP subunits form a homodimer within the complex. The domain structure of the amino acid uptake systems is typical for prokaryote extracellular solute binding protein-dependent uptake systems. All of the amino acid uptake systems also have at least one, and in a few cases, two extracellular solute binding proteins located in the periplasm of Gram-negative bacteria, or attached to the cell membrane of Gram-positive bacteria. The best-studied member of the PAAT (polar amino acid transport) family is the HisJQMP system of S. typhimurium, where HisJ is the extracellular solute binding proteins and HisP is the ABC protein.. Length = 213 Score = 27.4 bits (61), Expect = 7.1 Identities = 16/81 (19%), Positives = 29/81 (35%), Gaps = 23/81 (28%) Query: 187 FSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSL---FNALAKKD 243 F VL I ++ G +VI+G S +GKS+L N L + D Sbjct: 10 FGDFHVLKGIDL----------------TVKKGEVVVIIGPSGSGKSTLLRCINLLEEPD 53 Query: 244 VAIVT----DIPGTTRDVLTI 260 + + +++ + Sbjct: 54 SGTIIIDGLKLTDDKKNINEL 74 >gnl|CDD|133331 cd04131, Rnd, Rnd subfamily. The Rnd subfamily contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These novel Rho family proteins have substantial structural differences compared to other Rho members, including N- and C-terminal extensions relative to other Rhos. Rnd3/RhoE is farnesylated at the C-terminal prenylation site, unlike most other Rho proteins that are geranylgeranylated. In addition, Rnd members are unable to hydrolyze GTP and are resistant to GAP activity. They are believed to exist only in the GTP-bound conformation, and are antagonists of RhoA activity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 178 Score = 27.6 bits (61), Expect = 7.3 Identities = 31/125 (24%), Positives = 56/125 (44%), Gaps = 24/125 (19%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKIS--DTAGIR 278 KIV++G GK++L A KD T +P T + T +++ +++S DT+G Sbjct: 3 KIVVVGDVQCGKTALLQVFA-KDCYPETYVP-TVFENYTASFEIDEQRIELSLWDTSGSP 60 Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINS-----------KKEI-SFPKNIDFIFIG 326 D++ L ++D +L+ +I+ + EI F N + +G Sbjct: 61 YYDNVRP--------LCYPDSDAVLICFDISRPETLDSVLKKWRGEIQEFCPNTKVLLVG 112 Query: 327 TKSDL 331 K+DL Sbjct: 113 CKTDL 117 >gnl|CDD|73004 cd03245, ABCC_bacteriocin_exporters, ABC-type bacteriocin exporters. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2. A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.. Length = 220 Score = 27.4 bits (61), Expect = 7.5 Identities = 12/25 (48%), Positives = 16/25 (64%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240 IR G K+ I+G +GKS+L LA Sbjct: 27 IRAGEKVAIIGRVGSGKSTLLKLLA 51 >gnl|CDD|133356 cd04156, ARLTS1, ARLTS1 subfamily. ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling. ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers. ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL). ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter. In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity. In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation. The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in high-risk familial breast cancer. Length = 160 Score = 27.4 bits (61), Expect = 8.2 Identities = 44/176 (25%), Positives = 71/176 (40%), Gaps = 51/176 (28%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLD----------------- 263 ++++LG +AGKS+L L K +VT IP +V + L+ Sbjct: 1 QVLLLGLDSAGKSTLLYKL--KHAELVTTIPTVGFNVEMLQLEKHLSLTVWDVGGQEKMR 58 Query: 264 ------LEG-----YLVKISDTAGI----RETDDIVEKEGIKRTFLEVENADLILLLKEI 308 LE Y+V SD A + +E I++ E IK ++LL Sbjct: 59 TVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIK-------GVPVVLLA--- 108 Query: 309 NSKKEISFPKNIDFIFIGTKSDLYSTYTEEYDHLI---SSFTGEGLEELINKIKSI 361 +K+++ P + I + L Y + D + S+ TGEGL E K+ S Sbjct: 109 -NKQDL--PGALTAEEITRRFKL-KKYCSDRDWYVQPCSAVTGEGLAEAFRKLASF 160 >gnl|CDD|36358 KOG1143, KOG1143, KOG1143, Predicted translation elongation factor [Translation, ribosomal structure and biogenesis]. Length = 591 Score = 27.3 bits (60), Expect = 8.4 Identities = 40/199 (20%), Positives = 77/199 (38%), Gaps = 28/199 (14%) Query: 178 FSEEEDVQNFSSKEVLNDILFLKN--DISSHISQGKLGEIIRNGYKIVIL----GHSNAG 231 F ++Q+ + + N++L N + ++ EI+ K+V GH+ Sbjct: 204 FRHPHEIQSGRTSSISNEVLGFDNRGKVVNYAQNMTAEEIVEKSSKLVTFIDLAGHAKYQ 263 Query: 232 KSSLFNA------LAKKDVAIVTDIPGTTRDVLTIDLDLE-GYLVKISDTAGIRETDDIV 284 K+++ A V+ I TTR+ L + L + V ++ D+V Sbjct: 264 KTTIHGLTGYTPHFACLVVSADRGITWTTREHLGLIAALNIPFFVLVTKM-------DLV 316 Query: 285 EKEGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFIFIGTKSDLYSTYTEEYDHLIS 344 +++G+K+T ++ N LL + K D + + +S Sbjct: 317 DRQGLKKTVKDLSN-----LLAKAGCTKVPKRVTTKDDAVKAAQELCSGNIVPIF--AVS 369 Query: 345 SFTGEGLEELINKIKSILS 363 S +GEGL L+ + LS Sbjct: 370 SVSGEGL-RLLRTFLNCLS 387 >gnl|CDD|39877 KOG4679, KOG4679, KOG4679, Uncharacterized protein PSP1 (suppressor of DNA polymerase alpha mutations in yeast) [General function prediction only]. Length = 572 Score = 27.4 bits (60), Expect = 8.5 Identities = 22/63 (34%), Positives = 29/63 (46%), Gaps = 12/63 (19%) Query: 105 LRLANPGEFSRRAFENGKIDLLEAESLADLISSETEMQRRLSMEGMSGELSSLYGQW-ID 163 LR A P E + D LEA +LA E + R+L+ME ++ E QW Sbjct: 470 LRKATPWELDTLKQK----DELEALALA--QCRERVLNRKLNMEILNCEY-----QWDRK 518 Query: 164 KLT 166 KLT Sbjct: 519 KLT 521 >gnl|CDD|39539 KOG4338, KOG4338, KOG4338, Predicted lipoprotein [Lipid transport and metabolism]. Length = 1680 Score = 27.3 bits (60), Expect = 8.7 Identities = 25/124 (20%), Positives = 45/124 (36%), Gaps = 11/124 (8%) Query: 284 VEKEGIKRTFLEVENADLIL----LLKEINSKKEISFPKNIDFIFIG-----TKSDLYST 334 E E + +N L E NS++ + + N+ + +DL Sbjct: 1528 EECEKELERESKEKNYRDKSDRLEELSEYNSEQTMDYEGNLMEKYPERTIHFGFNDLTGK 1587 Query: 335 YTE-EYDHLISSFTGEGLEELINKIKSILSNKFKKLPFSIPSHKRHLYHLSQTVRYLEMA 393 E+ H I F+ E + E ++S S+ +KK +P H L + +R + Sbjct: 1588 TAIKEFSHRIC-FSIEPVSECRRGLESEESHNWKKRFTCLPRHSSRARRLLKEIRSQKNL 1646 Query: 394 SLNE 397 L Sbjct: 1647 DLVN 1650 >gnl|CDD|35284 KOG0061, KOG0061, KOG0061, Transporter, ABC superfamily (Breast cancer resistance protein) [Secondary metabolites biosynthesis, transport and catabolism]. Length = 613 Score = 27.3 bits (60), Expect = 9.2 Identities = 11/26 (42%), Positives = 17/26 (65%) Query: 215 IIRNGYKIVILGHSNAGKSSLFNALA 240 + G + I+G S +GK++L NALA Sbjct: 52 TAKPGELLAIMGPSGSGKTTLLNALA 77 >gnl|CDD|133346 cd04146, RERG_RasL11_like, RERG/RasL11-like subfamily. RERG (Ras-related and Estrogen- Regulated Growth inhibitor) and Ras-like 11 are members of a novel subfamily of Ras that were identified based on their behavior in breast and prostate tumors, respectively. RERG expression was decreased or lost in a significant fraction of primary human breast tumors that lack estrogen receptor and are correlated with poor clinical prognosis. Elevated RERG expression correlated with favorable patient outcome in a breast tumor subtype that is positive for estrogen receptor expression. In contrast to most Ras proteins, RERG overexpression inhibited the growth of breast tumor cells in vitro and in vivo. RasL11 was found to be ubiquitously expressed in human tissue, but down-regulated in prostate tumors. Both RERG and RasL11 lack the C-terminal CaaX prenylation motif, where a = an aliphatic amino acid and X = any amino acid, and are localized primarily in the cytoplasm. Both are believed to have tumor suppressor activity. Length = 165 Score = 27.2 bits (61), Expect = 9.2 Identities = 9/15 (60%), Positives = 11/15 (73%) Query: 221 KIVILGHSNAGKSSL 235 KI +LG S GKS+L Sbjct: 1 KIAVLGASGVGKSAL 15 >gnl|CDD|29996 cd01130, VirB11-like_ATPase, Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.. Length = 186 Score = 27.1 bits (60), Expect = 9.8 Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 3/40 (7%) Query: 212 LGEIIRNGYKIVILGHSNAGKSSLFNALAK---KDVAIVT 248 L + I+I G + +GK++L NAL D I+T Sbjct: 18 LWLAVEARKNILISGGTGSGKTTLLNALLAFIPPDERIIT 57 >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 = 27.0 bits (60), Expect = 9.9 Identities = 10/25 (40%), Positives = 16/25 (64%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240 + G +I ++G + AGKS+L LA Sbjct: 45 VPRGERIGLIGRNGAGKSTLLRLLA 69 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 0.138 0.385 Gapped Lambda K H 0.267 0.0762 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,222,913 Number of extensions: 285839 Number of successful extensions: 1254 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1211 Number of HSP's successfully gapped: 217 Length of query: 440 Length of database: 6,263,737 Length adjustment: 97 Effective length of query: 343 Effective length of database: 4,167,664 Effective search space: 1429508752 Effective search space used: 1429508752 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: 59 (26.4 bits)