RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780226|ref|YP_003064639.1| translation-associated GTPase [Candidatus Liberibacter asiaticus str. psy62] (367 letters) >gnl|CDD|30362 COG0012, COG0012, Predicted GTPase, probable translation factor [Translation, ribosomal structure and biogenesis]. Length = 372 Score = 481 bits (1239), Expect = e-136 Identities = 214/373 (57%), Positives = 267/373 (71%), Gaps = 7/373 (1%) Query: 1 MGFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAE 60 M K GI+GLPNVGKSTLFNALT+ A A+ ANYPFCTIEPN G V VPD R+ +LAEI + Sbjct: 1 MSLKIGIVGLPNVGKSTLFNALTK-AGAEIANYPFCTIEPNVGVVYVPDCRLDELAEIVK 59 Query: 61 -SKDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGR 119 + P + FVDIAGLV+GASKGEGLGN+FL +IREVDAIIHV+RCF D +I HVEG+ Sbjct: 60 CPPKIRPAPVEFVDIAGLVKGASKGEGLGNKFLDNIREVDAIIHVVRCFGDTDIEHVEGK 119 Query: 120 IDPINDIETIETELMLSDLERLERLFEK-NKKYRNHKSEEIVLLQ--SIISSSLRLIEEG 176 +DP+ DIE I TEL+L DLE LE+ +E+ K+ + K + L + S++ +EEG Sbjct: 120 VDPVEDIEIINTELILWDLESLEKRWERLEKRAKAGKKLDKELKEELSLLGKLEEHLEEG 179 Query: 177 KPVRSL-LESLDSDAIPIFKSLNLLTAKPILYICNVSEHDCKKGNIYTEAVQRLASQQNA 235 KP R L L + + SLNLLTAKP+LY+ NVSE D N Y + ++ LA+++NA Sbjct: 180 KPARGLDLSKWSEEDLEALASLNLLTAKPMLYVANVSEDDLANLNEYVKRLKELAAKENA 239 Query: 236 EMIIISAAIEAEISQLPE-EERALFMEELDISISGLELLIRSGYRLLDLITYFTVGPKET 294 E++ +SAAIE E+ +L + EE+ F+ EL SGL LIR+GY LL L TYFT G KE Sbjct: 240 EVVPVSAAIELELRELADAEEKGEFLIELGQKESGLNELIRAGYGLLGLQTYFTAGVKEV 299 Query: 295 RAWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGKEYI 354 RAWTI G+ A AAGVIH DFEKGFIRA ISY D + GGE AAKEAGK R EGK+YI Sbjct: 300 RAWTIKDGSKAPDAAGVIHPDFEKGFIRAEVISYADLIHYGGEAAAKEAGKRRLEGKDYI 359 Query: 355 VKDGDILHFRFNV 367 V+DGD++HF+FNV Sbjct: 360 VQDGDVIHFKFNV 372 >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 = 412 bits (1061), Expect = e-115 Identities = 165/281 (58%), Positives = 207/281 (73%), Gaps = 11/281 (3%) Query: 5 CGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDL 64 GI+GLPNVGKSTLFNALT+ A A+AANYPFCTIEPN G V VPD R+ KLAEI + K + Sbjct: 1 IGIVGLPNVGKSTLFNALTK-AGAEAANYPFCTIEPNVGIVPVPDERLDKLAEIVKPKKI 59 Query: 65 VPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPIN 124 VP + FVDIAGLV+GASKGEGLGN+FL+HIREVDAI HV+RCF+D++I HVEG +DP+ Sbjct: 60 VPATIEFVDIAGLVKGASKGEGLGNKFLSHIREVDAIAHVVRCFEDDDITHVEGSVDPVR 119 Query: 125 DIETIETELMLSDLERLERLFEK-NKKYRNHKSE---EIVLLQSIISSSLRLIEEGKPVR 180 DIE I TEL+L+DLE +E+ E+ KK ++ E E+ LL+ I +EEGKP R Sbjct: 120 DIEIINTELILADLETVEKRLERLEKKAKSGDKEAKAELELLEKIKE----HLEEGKPAR 175 Query: 181 SLLESLDSDAIPIFKSLNLLTAKPILYICNVSEHDCKKGNIYTEAVQRLASQQNAEMIII 240 SL L + I I SL LLTAKP+LY+ NVSE D GN V+ +A+++ AE+I I Sbjct: 176 SL--ELTEEEIEILNSLQLLTAKPVLYVANVSEDDLANGNNKVLKVREIAAKEGAEVIPI 233 Query: 241 SAAIEAEISQLPEEERALFMEELDISISGLELLIRSGYRLL 281 SA IEAE+++L EEE A F+EEL + SGL+ LIR+GY LL Sbjct: 234 SAKIEAELAELDEEEAAEFLEELGLEESGLDRLIRAGYELL 274 >gnl|CDD|36704 KOG1491, KOG1491, KOG1491, Predicted GTP-binding protein (ODN superfamily) [General function prediction only]. Length = 391 Score = 378 bits (971), Expect = e-105 Identities = 182/376 (48%), Positives = 238/376 (63%), Gaps = 12/376 (3%) Query: 1 MGFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAE 60 K GI+GLPNVGKST FNALT+ + A AAN+PFCTI+PN V VPD R L I Sbjct: 19 NNLKIGIVGLPNVGKSTFFNALTK-SKAGAANFPFCTIDPNEARVEVPDSRFDLLCPIYG 77 Query: 61 SKDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRI 120 K VP ++ DIAGLV+GAS GEGLGN+FL+HIR VDAI HV+R F+D +IIHVEG + Sbjct: 78 PKSKVPAFLTVYDIAGLVKGASAGEGLGNKFLSHIRHVDAIFHVVRAFEDTDIIHVEGGV 137 Query: 121 DPINDIETIETELMLSDLERLERLFEKNKKYRNHKSEEIVLLQSIISSSL------RLIE 174 DP+ DIE I+ EL L DLE LE+ EK +K + Q L +L++ Sbjct: 138 DPVRDIEIIQEELRLKDLEFLEKRLEKLEKKHKRTKSNLETKQLKFEYGLLEKVKEKLLD 197 Query: 175 EGKPVRSLLESLDSDAIPIFKSLNLLTAKPILYICNVSEHD-CKKGNIYTEAVQRLASQQ 233 KPVR E + + I I L LLTAKP +Y+ N+SEHD +K N ++ + Sbjct: 198 GKKPVRP-KEKWNDEEIEILNKLFLLTAKPTVYLLNLSEHDYARKKNKKLPKIKEWVDEV 256 Query: 234 N--AEMIIISAAIEAEISQLPEEERALFMEELDISISGLELLIRSGYRLLDLITYFTVGP 291 + +I+ SAA E+++ +L EEE +E+L S S L +I++GY L+LI +FT G Sbjct: 257 SPGDVVIVFSAAFESQLFELYEEEAVKELEDLGDS-SALPKIIKTGYSALNLIVFFTCGE 315 Query: 292 KETRAWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGK 351 E RAWTI +GT A +AAGVIH+DFEKGFI A + ++D+ E+A K AGK R GK Sbjct: 316 DEVRAWTIRKGTKAPQAAGVIHSDFEKGFIMAEVMKFEDFKEYKSESACKAAGKYRQVGK 375 Query: 352 EYIVKDGDILHFRFNV 367 EYIV+DGDI+ F+FN Sbjct: 376 EYIVEDGDIIFFKFNP 391 >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 = 180 bits (460), Expect = 5e-46 Identities = 92/275 (33%), Positives = 119/275 (43%), Gaps = 99/275 (36%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66 ++GLPNVGKSTL NALT A + ANYPF T+EPN G V VPD Sbjct: 1 LVGLPNVGKSTLLNALTN-AKPKVANYPFTTLEPNLGVVEVPDG---------------- 43 Query: 67 TRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPINDI 126 R+ DI GL+ GAS+G GLGNQFLAHIR DAI+HV+ +D++I G +DP+ D Sbjct: 44 ARIQVADIPGLIEGASEGRGLGNQFLAHIRRADAILHVVDASEDDDI----GGVDPLEDY 99 Query: 127 ETIETELMLSDLERLERLFEKNKKYRNHKSEEIVLLQSIISSSLRLIEEGKPVRSLLESL 186 E + EL L DLE + L KPV Sbjct: 100 EILNAELKLYDLETILGLLTA-----------------------------KPV------- 123 Query: 187 DSDAIPIFKSLNLLTAKPILYICNVSEHDCKKGNIYTEAVQRLASQQNAEMIIISAAIEA 246 +Y+ N + D + E V+ LA ++ AE++ ISA E Sbjct: 124 -------------------IYVLNKIDLDDAEELEE-ELVRELALEEGAEVVPISAKTEE 163 Query: 247 EISQLPEEERALFMEELDISISGLELLIRSGYRLL 281 GL+ LIR+ Y LL Sbjct: 164 ----------------------GLDELIRAIYELL 176 >gnl|CDD|133440 cd04867, TGS_YchF_C, TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the family contain a C-terminal TGS domain. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role. Length = 83 Score = 160 bits (406), Expect = 8e-40 Identities = 55/83 (66%), Positives = 67/83 (80%) Query: 283 LITYFTVGPKETRAWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKE 342 LI++FT GP E RAWTI +GT A +AAGVIHTDFEKGFIRA + Y+D V +G E AAKE Sbjct: 1 LISFFTAGPDEVRAWTIRKGTKAPQAAGVIHTDFEKGFIRAEVMKYEDLVELGSEAAAKE 60 Query: 343 AGKARDEGKEYIVKDGDILHFRF 365 AGK R EGK+Y+V+DGDI+ F+F Sbjct: 61 AGKYRQEGKDYVVQDGDIIFFKF 83 >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 = 123 bits (312), Expect = 5e-29 Identities = 79/266 (29%), Positives = 122/266 (45%), Gaps = 40/266 (15%) Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGE----VAVPDPRMHKLAEIAES 61 G++G PN GKST FNA T A + ANYPF TI+PN G V P + Sbjct: 2 GLVGKPNAGKSTFFNAATL-ADVEIANYPFTTIDPNVGVGYVRVECPCKELGVSCNPRYG 60 Query: 62 KD-----LVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKD------ 110 K VP + +D+AGLV GA +G+GLGN+FL +R+ DA+IHV+ D Sbjct: 61 KCIDGKRYVPVEL--IDVAGLVPGAHEGKGLGNKFLDDLRDADALIHVV----DASGGTD 114 Query: 111 -ENIIHVEGRIDPINDIETIETELMLSDLERLERLFEKNKKYRNHKSEEIVLLQSIIS-S 168 E G DP+ DIE +E E+ + LE+ +EK R +E+ +++++ Sbjct: 115 AEGNGVETGGHDPLEDIEFLENEIDMWIYGILEKNWEKIV--RKADAEKTDIVEALSEQL 172 Query: 169 SLRLIEEGKPVRSLLESLDSDAIP-------IFKSLNLLT--AKPILYICNVSEHDCKKG 219 S + E V LE L+ + + L +KP++ N ++ + Sbjct: 173 SGFGVNEKD-VIEALEELELPEDLSKWTDEDLLRLARALRKRSKPMVIAANKADIPDAEN 231 Query: 220 NIYTEAVQRLASQQNAEMIIISAAIE 245 NI ++ + ++ SA E Sbjct: 232 NISKLRLKYP----DEIVVPTSAEAE 253 >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 = 95.9 bits (240), Expect = 1e-20 Identities = 53/138 (38%), Positives = 74/138 (53%), Gaps = 26/138 (18%) Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65 G++GLPN GKSTL +A++ A + A+YPF T+ PN G V V D R Sbjct: 4 GLVGLPNAGKSTLLSAISN-AKPKIADYPFTTLVPNLGVVRVDDGR-------------- 48 Query: 66 PTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPIND 125 DI GL+ GAS+G+GLG++FL HI ++HV+ D+ DP+ D Sbjct: 49 --SFVVADIPGLIEGASEGKGLGHRFLRHIERTRLLLHVIDLSGDD---------DPVED 97 Query: 126 IETIETELMLSDLERLER 143 +TI EL L + E LE+ Sbjct: 98 YKTIRNELELYNPELLEK 115 >gnl|CDD|30882 COG0536, Obg, Predicted GTPase [General function prediction only]. Length = 369 Score = 96.0 bits (239), Expect = 2e-20 Identities = 50/130 (38%), Positives = 66/130 (50%), Gaps = 28/130 (21%) Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65 G++GLPN GKSTL +A++ A + A+YPF T+ PN G V V Sbjct: 163 GLVGLPNAGKSTLLSAVSA-AKPKIADYPFTTLVPNLGVVRVDGGE-------------- 207 Query: 66 PTRMSFV--DIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPI 123 SFV DI GL+ GAS+G GLG +FL HI ++HV+ + DPI Sbjct: 208 ----SFVVADIPGLIEGASEGVGLGLRFLRHIERTRVLLHVIDLSPIDG-------RDPI 256 Query: 124 NDIETIETEL 133 D +TI EL Sbjct: 257 EDYQTIRNEL 266 >gnl|CDD|145217 pfam01926, MMR_HSR1, GTPase of unknown function. Length = 106 Score = 86.6 bits (215), Expect = 9e-18 Identities = 38/105 (36%), Positives = 51/105 (48%), Gaps = 18/105 (17%) Query: 14 GKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVPTRMSFVD 73 GKSTL NALT A ++YP T +PN G V + ++ VD Sbjct: 1 GKSTLINALTGKKRAIVSDYPGTTRDPNEGRVELDGKQII-----------------LVD 43 Query: 74 IAGLVRGASKGEG-LGNQFLAHIREVDAIIHVLRCFKDENIIHVE 117 G++ GASKGEG LGN+ L I E D I+HV+ + +E Sbjct: 44 TPGIIEGASKGEGELGNRTLEAIEEADLILHVVDASEGLTEEDLE 88 >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 = 82.6 bits (205), Expect = 2e-16 Identities = 41/129 (31%), Positives = 57/129 (44%), Gaps = 30/129 (23%) Query: 5 CGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDL 64 ++G P+VGKSTL + LT T S A Y F T+ VP +K A+I Sbjct: 3 VALVGFPSVGKSTLLSKLTNTKSE-VAAYEFTTLTC------VPGVLEYKGAKI------ 49 Query: 65 VPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPIN 124 +D+ G++ GA+ G+G G Q +A R D I+ VL K E Sbjct: 50 -----QLLDLPGIIEGAADGKGRGRQVIAVARTADLILMVLDATKPE------------G 92 Query: 125 DIETIETEL 133 E +E EL Sbjct: 93 HREILEREL 101 >gnl|CDD|31357 COG1163, DRG, Predicted GTPase [General function prediction only]. Length = 365 Score = 76.8 bits (189), Expect = 1e-14 Identities = 81/364 (22%), Positives = 139/364 (38%), Gaps = 78/364 (21%) Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65 ++G P+VGKSTL N LT T S + A+YPF T+EP G + +K A+I Sbjct: 67 ALVGFPSVGKSTLLNKLTNTKS-EVADYPFTTLEPVPGMLE------YKGAQI------- 112 Query: 66 PTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPIND 125 +D+ G++ GAS G G G Q L+ R D II VL F+D Sbjct: 113 ----QLLDLPGIIEGASSGRGRGRQVLSVARNADLIIIVLDVFEDP-------------- 154 Query: 126 IETIETELMLSDLERLERLFEKNKKYRNHKSEEIVLLQSIISSSLRLIEEGKPVRSLLES 185 + +ER E N + ++ + + I L Sbjct: 155 ----------HHRDIIERELEDVGIRLNKRPPDVTIKKKESGG----IRINGTGP--LTH 198 Query: 186 LDSDAI-PIFKSLNLLTAKPILYICNVSEHDCKKGNIYTEAVQRLASQQNAEMII--ISA 242 LD D + I + + A +L +V+ D +A++ + A ++ I Sbjct: 199 LDEDTVRAILREYRIHNAD-VLIREDVTLDD------LIDALEGNRVYKPALYVVNKIDL 251 Query: 243 AIEAEISQLPEEERALFME-ELDISISGLELLIRSGYRLLDLITYFT----VGPKETRAW 297 E+ +L + ++ + + I L+ L + +L LI +T P Sbjct: 252 PGLEELERLARKPNSVPISAKKGI---NLDELKERIWDVLGLIRVYTKPPGEEPDFDEPL 308 Query: 298 TIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGKEYIVKD 357 + RG+ IH D + F Y + G++ + G +++++D Sbjct: 309 ILRRGSTVGDVCRKIHRDLVENF---------RYARVWGKSVKHPGQRV---GLDHVLED 356 Query: 358 GDIL 361 DI+ Sbjct: 357 EDIV 360 >gnl|CDD|36702 KOG1489, KOG1489, KOG1489, Predicted GTP-binding protein (ODN superfamily) [General function prediction only]. Length = 366 Score = 73.4 bits (180), Expect = 9e-14 Identities = 36/102 (35%), Positives = 51/102 (50%), Gaps = 17/102 (16%) Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65 G++G PN GKSTL NAL+R A + A+Y F T+ P+ G V D +A Sbjct: 200 GLVGFPNAGKSTLLNALSR-AKPKVAHYAFTTLRPHIGTVNYDD---FSQITVA------ 249 Query: 66 PTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRC 107 DI G++ GA +GLG +FL HI ++ V+ Sbjct: 250 -------DIPGIIEGAHMNKGLGYKFLRHIERCKGLLFVVDL 284 >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 = 69.7 bits (171), Expect = 1e-12 Identities = 19/101 (18%), Positives = 30/101 (29%), Gaps = 16/101 (15%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66 + G N GKS+L NAL A + P T +P + Sbjct: 1 LFGRTNAGKSSLLNALLGQEVAIVSPVPGTTTDPVEYVWELGPLG--------------- 45 Query: 67 TRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRC 107 + +D G+ G + D I+ V+ Sbjct: 46 -PVVLIDTPGIDEAGGLGREREELARRVLERADLILFVVDA 85 >gnl|CDD|133441 cd04938, TGS_Obg-like, TGS_Obg-like: The C-terminal TGS domain of Obg-like GTPases such as those present in DRG (developmentally regulated GTP-binding protein), and GTP-binding proteins Ygr210 and YchF. The TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role. Length = 76 Score = 61.7 bits (150), Expect = 4e-10 Identities = 26/94 (27%), Positives = 34/94 (36%), Gaps = 29/94 (30%) Query: 283 LITYFTV-----------GPKETRAWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDY 331 LI + V G + +GT A IH D EKGFI A+ Sbjct: 1 LIPVYPVKNIHTFTNGSGGNVFRDCVLVKKGTTVGDVARKIHGDLEKGFIEAVG------ 54 Query: 332 VAMGGENAAKEAGKARDEGKEYIVKDGDILHFRF 365 G+ R EGK+ I+ DIL F+ Sbjct: 55 ------------GRRRLEGKDVILGKNDILKFKT 76 >gnl|CDD|36699 KOG1486, KOG1486, KOG1486, GTP-binding protein DRG2 (ODN superfamily) [Signal transduction mechanisms]. Length = 364 Score = 60.3 bits (146), Expect = 8e-10 Identities = 35/105 (33%), Positives = 52/105 (49%), Gaps = 18/105 (17%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66 +IG P+VGKSTL + +T T S +AA+Y F T+ G + Sbjct: 67 LIGFPSVGKSTLLSKITSTHS-EAASYEFTTLTCIPGVIHYNG----------------- 108 Query: 67 TRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDE 111 + +D+ G++ GAS+G+G G Q +A R D I+ VL K E Sbjct: 109 ANIQLLDLPGIIEGASQGKGRGRQVIAVARTADLILMVLDATKSE 153 >gnl|CDD|36700 KOG1487, KOG1487, KOG1487, GTP-binding protein DRG1 (ODN superfamily) [Signal transduction mechanisms]. Length = 358 Score = 51.9 bits (124), Expect = 3e-07 Identities = 41/130 (31%), Positives = 59/130 (45%), Gaps = 30/130 (23%) Query: 4 KCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKD 63 + G +G P+VGKSTL + LT T S + A Y F T+ VP +K A+I Sbjct: 61 RVGFVGFPSVGKSTLLSKLTGTFS-EVAAYEFTTL------TTVPGVIRYKGAKIQ---- 109 Query: 64 LVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPI 123 +D+ G++ GA G+G G Q +A R + I VL K P+ Sbjct: 110 -------LLDLPGIIEGAKDGKGRGKQVIAVARTCNLIFIVLDVLK------------PL 150 Query: 124 NDIETIETEL 133 + + IE EL Sbjct: 151 SHKKIIEKEL 160 >gnl|CDD|133435 cd01616, TGS, The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role. Length = 60 Score = 50.0 bits (120), Expect = 1e-06 Identities = 21/82 (25%), Positives = 28/82 (34%), Gaps = 22/82 (26%) Query: 284 ITYFTVGPKETRAWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEA 343 + FT A +P+G A A IHTD KGFI AL Sbjct: 1 MIIFTPD---GSAVELPKGATAMDFALKIHTDLGKGFIGALVN----------------- 40 Query: 344 GKARDEGKEYIVKDGDILHFRF 365 + Y ++DGD + Sbjct: 41 --GQLVDLSYTLQDGDTVSIVT 60 >gnl|CDD|31354 COG1160, COG1160, Predicted GTPases [General function prediction only]. Length = 444 Score = 49.0 bits (117), Expect = 2e-06 Identities = 30/101 (29%), Positives = 41/101 (40%), Gaps = 19/101 (18%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66 I+G PNVGKSTLFN LT A ++ P T + G+ + + Sbjct: 8 IVGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDA-----------------EWLG 50 Query: 67 TRMSFVDIAGLVRGASK--GEGLGNQFLAHIREVDAIIHVL 105 +D GL G E + Q L I E D I+ V+ Sbjct: 51 REFILIDTGGLDDGDEDELQELIREQALIAIEEADVILFVV 91 Score = 35.5 bits (82), Expect = 0.025 Identities = 22/103 (21%), Positives = 35/103 (33%), Gaps = 19/103 (18%) Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAES 61 K IIG PNVGKS+L NA+ ++ T + + + Sbjct: 178 PIKIAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDS------IDIEFERDGRKY--- 228 Query: 62 KDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHV 104 +D AG+ R E + + + R + AI Sbjct: 229 --------VLIDTAGIRRKGKITESV--EKYSVARTLKAIERA 261 >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 = 47.4 bits (114), Expect = 6e-06 Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 1/43 (2%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPD 49 ++G PNVGK+TLFNALT A + N+P T+E G + Sbjct: 1 LVGNPNVGKTTLFNALTG-ARQKVGNWPGVTVEKKEGRFKLGG 42 >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 = 47.4 bits (114), Expect = 7e-06 Identities = 16/28 (57%), Positives = 18/28 (64%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYP 34 I+G PNVGKSTLFN LT A + P Sbjct: 2 IVGRPNVGKSTLFNRLTGRRDAIVEDTP 29 >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 = 46.0 bits (109), Expect = 2e-05 Identities = 15/33 (45%), Positives = 20/33 (60%) Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYP 34 G + ++G+PNVGKSTL N L A+ N P Sbjct: 115 GIRAMVVGIPNVGKSTLINRLRGKKVAKVGNKP 147 >gnl|CDD|30719 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion transport and metabolism]. Length = 653 Score = 46.0 bits (109), Expect = 2e-05 Identities = 29/102 (28%), Positives = 47/102 (46%), Gaps = 21/102 (20%) Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65 ++G PNVGK+TLFNALT A+ + N+P T+E G++ + Sbjct: 7 ALVGNPNVGKTTLFNALTG-ANQKVGNWPGVTVEKKEGKLKYKGHEIE------------ 53 Query: 66 PTRMSFVDIAGL--VRGASKGEGLGNQFLAHIREVDAIIHVL 105 VD+ G + S+ E + FL + D I++V+ Sbjct: 54 -----IVDLPGTYSLTAYSEDEKVARDFLLE-GKPDLIVNVV 89 >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 = 44.4 bits (106), Expect = 5e-05 Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 1/40 (2%) Query: 4 KCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSG 43 ++G PNVGK+TLFNALT A N+P T+E G Sbjct: 1 TIALVGNPNVGKTTLFNALTG-ARQHVGNWPGVTVEKKEG 39 >gnl|CDD|32443 COG2262, HflX, GTPases [General function prediction only]. Length = 411 Score = 44.1 bits (104), Expect = 6e-05 Identities = 36/136 (26%), Positives = 58/136 (42%), Gaps = 18/136 (13%) Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65 ++G N GKSTLFNALT A A+ F T++P + + + D R L + + Sbjct: 196 ALVGYTNAGKSTLFNALT-GADVYVADQLFATLDPTTRRIELGDGRKVLLTDTVGFIRDL 254 Query: 66 PTRM--SF---------VDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENII 114 P + +F D+ V AS E L + V+ ++ + + II Sbjct: 255 PHPLVEAFKSTLEEVKEADLLLHVVDASDPE-----ILEKLEAVEDVLAEIGA-DEIPII 308 Query: 115 HVEGRIDPINDIETIE 130 V +ID + D E + Sbjct: 309 LVLNKIDLLEDEEILA 324 >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 = 44.1 bits (105), Expect = 6e-05 Identities = 19/31 (61%), Positives = 21/31 (67%), Gaps = 1/31 (3%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCT 37 I G PNVGKS+L N LTR A + A YPF T Sbjct: 5 IAGYPNVGKSSLVNKLTR-AKPEVAPYPFTT 34 >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 = 43.2 bits (103), Expect = 1e-04 Identities = 16/23 (69%), Positives = 17/23 (73%), Gaps = 3/23 (13%) Query: 3 FKCG---IIGLPNVGKSTLFNAL 22 FK G I+G PNVGKSTL NAL Sbjct: 1 FKSGFVAIVGRPNVGKSTLLNAL 23 >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 = 41.3 bits (98), Expect = 4e-04 Identities = 14/23 (60%), Positives = 16/23 (69%) Query: 2 GFKCGIIGLPNVGKSTLFNALTR 24 G K I+G PNVGKS+L NAL Sbjct: 1 GIKVVIVGKPNVGKSSLLNALAG 23 >gnl|CDD|31355 COG1161, COG1161, Predicted GTPases [General function prediction only]. Length = 322 Score = 41.2 bits (96), Expect = 4e-04 Identities = 15/34 (44%), Positives = 20/34 (58%) Query: 1 MGFKCGIIGLPNVGKSTLFNALTRTASAQAANYP 34 + G++G PNVGKSTL N L A+ +N P Sbjct: 131 RKIRVGVVGYPNVGKSTLINRLLGKKVAKTSNRP 164 >gnl|CDD|31353 COG1159, Era, GTPase [General function prediction only]. Length = 298 Score = 40.5 bits (95), Expect = 6e-04 Identities = 31/110 (28%), Positives = 49/110 (44%), Gaps = 21/110 (19%) Query: 1 MGFKCG---IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAE 57 M FK G IIG PNVGKSTL NAL + + P T +++ Sbjct: 2 MKFKSGFVAIIGRPNVGKSTLLNALVGQKISIVSPKPQTT--------------RNRIRG 47 Query: 58 IAESKDLVPTRMSFVDIAGLVRGASK-GEGLGNQFLAHIREVDAIIHVLR 106 I + + ++ FVD G+ + GE + + +++VD I+ V+ Sbjct: 48 IVTTDN---AQIIFVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVD 94 >gnl|CDD|30833 COG0486, ThdF, Predicted GTPase [General function prediction only]. Length = 454 Score = 39.8 bits (93), Expect = 0.001 Identities = 16/33 (48%), Positives = 18/33 (54%) Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYP 34 G K IIG PNVGKS+L NAL A + Sbjct: 217 GLKVVIIGRPNVGKSSLLNALLGRDRAIVTDIA 249 >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 = 39.3 bits (93), Expect = 0.002 Identities = 29/110 (26%), Positives = 41/110 (37%), Gaps = 38/110 (34%) Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65 ++G N GKSTLFNALT A A + F T+ DP +L + Sbjct: 45 ALVGYTNAGKSTLFNALTG-ADVYAEDQLFATL----------DPTTRRL--------RL 85 Query: 66 PTRMSFV--DIAGLVRG------ASKGEGLGNQF---LAHIREVDAIIHV 104 P + D G +R + F L + E D ++HV Sbjct: 86 PDGREVLLTDTVGFIRDLPHQLVEA--------FRSTLEEVAEADLLLHV 127 >gnl|CDD|31281 COG1084, COG1084, Predicted GTPase [General function prediction only]. Length = 346 Score = 39.1 bits (91), Expect = 0.002 Identities = 17/31 (54%), Positives = 20/31 (64%), Gaps = 1/31 (3%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCT 37 + G PNVGKS+L LT TA + A YPF T Sbjct: 173 VAGYPNVGKSSLVRKLT-TAKPEVAPYPFTT 202 >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 = 38.8 bits (90), Expect = 0.002 Identities = 14/29 (48%), Positives = 18/29 (62%) Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYP 34 G+IG PNVGKS++ NAL + N P Sbjct: 104 GVIGYPNVGKSSVINALLNKLKLKVGNVP 132 >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 = 37.9 bits (88), Expect = 0.004 Identities = 13/31 (41%), Positives = 19/31 (61%) Query: 4 KCGIIGLPNVGKSTLFNALTRTASAQAANYP 34 G++G PNVGKS+L N+L R+ + P Sbjct: 119 TVGVVGFPNVGKSSLINSLKRSRACNVGATP 149 >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 = 37.4 bits (88), Expect = 0.007 Identities = 13/22 (59%), Positives = 15/22 (68%) Query: 2 GFKCGIIGLPNVGKSTLFNALT 23 + IIG PNVGKS+L NAL Sbjct: 2 PIRIAIIGRPNVGKSSLVNALL 23 >gnl|CDD|37695 KOG2484, KOG2484, KOG2484, GTPase [General function prediction only]. Length = 435 Score = 36.9 bits (85), Expect = 0.008 Identities = 15/29 (51%), Positives = 19/29 (65%) Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYP 34 GIIG PNVGKS++ N+L R + N P Sbjct: 256 GIIGYPNVGKSSVINSLKRRKACNVGNVP 284 >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 = 36.8 bits (85), Expect = 0.009 Identities = 15/32 (46%), Positives = 20/32 (62%) Query: 3 FKCGIIGLPNVGKSTLFNALTRTASAQAANYP 34 K G++G PNVGKS++ NAL SA + P Sbjct: 102 GKVGVVGYPNVGKSSIINALKGRHSASTSPSP 133 >gnl|CDD|36637 KOG1423, KOG1423, KOG1423, Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. Length = 379 Score = 35.8 bits (82), Expect = 0.022 Identities = 19/73 (26%), Positives = 27/73 (36%), Gaps = 17/73 (23%) Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65 +IG PNVGKSTL N + + + T G + + Sbjct: 76 AVIGAPNVGKSTLTNQMIGQKVSAVSRKVHTTRHRILGIITSGE---------------- 119 Query: 66 PTRMSFVDIAGLV 78 T++ F D GLV Sbjct: 120 -TQLVFYDTPGLV 131 >gnl|CDD|35631 KOG0410, KOG0410, KOG0410, Predicted GTP binding protein [General function prediction only]. Length = 410 Score = 35.4 bits (81), Expect = 0.028 Identities = 29/144 (20%), Positives = 53/144 (36%), Gaps = 23/144 (15%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66 ++G N GKSTL ALT+ A+ + F T++P +P L + +P Sbjct: 183 VVGYTNAGKSTLIKALTK-AALYPNDRLFATLDPTLHSAHLPSGNFVLLTDTVGFISDLP 241 Query: 67 TRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPINDI 126 LV L + E D ++HV+ +I H + Sbjct: 242 I--------QLVAAFQAT-------LEEVAEADLLLHVV------DISHPNAEEQ-RETV 279 Query: 127 ETIETELMLSDLERLERLFEKNKK 150 + ++ + +L+ + E + K Sbjct: 280 LHVLNQIGVPSEPKLQNMIEVDNK 303 >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 = 34.4 bits (80), Expect = 0.050 Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 1/36 (2%) Query: 7 IIGLPNVGKSTLFNALTRTAS-AQAANYPFCTIEPN 41 G NVGKS+L NALT A+ + P T N Sbjct: 4 FAGRSNVGKSSLINALTNRKKLARTSKTPGKTQLIN 39 >gnl|CDD|173737 cd07834, STKc_MAPK, Catalytic domain of the Serine/Threonine Kinase, Mitogen-Activated Protein Kinase. Serine/Threonine Kinases (STKs), Mitogen-Activated Protein Kinase (MAPK) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAPK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MAPKs serve as important mediators of cellular responses to extracellular signals. They control critical cellular functions including differentiation, proliferation, migration, and apoptosis. They are also implicated in the pathogenesis of many diseases including multiple types of cancer, stroke, diabetes, and chronic inflammation. Typical MAPK pathways involve a triple kinase core cascade comprising of the MAPK, which is phosphorylated and activated by a MAPK kinase (MAP2K or MKK), which itself is phosphorylated and activated by a MAPK kinase kinase (MAP3K or MKKK). Each cascade is activated either by a small GTP-binding protein or by an adaptor protein, which transmits the signal either directly to a MAP3K to start the triple kinase core cascade or indirectly through a mediator kinase, a MAP4K. There are three main typical MAPK subfamilies: Extracellular signal-Regulated Kinase (ERK), c-Jun N-terminal Kinase (JNK), and p38. Some MAPKs are atypical in that they are not regulated by MAP2Ks. These include MAPK4, MAPK6, NLK, and ERK7. Length = 330 Score = 34.4 bits (80), Expect = 0.053 Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 10/51 (19%) Query: 96 REVDAIIHVLRCFKDENIIHVEGRIDPINDIET-----IETELMLSDLERL 141 RE I +LR + ENII + I E I TELM +DL ++ Sbjct: 48 RE----IKLLRHLRHENIIGLL-DILRPPSPEDFNDVYIVTELMETDLHKV 93 >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 = 34.1 bits (78), Expect = 0.060 Identities = 11/19 (57%), Positives = 14/19 (73%) Query: 7 IIGLPNVGKSTLFNALTRT 25 ++G NVGKSTL NAL + Sbjct: 132 VVGATNVGKSTLINALLKK 150 >gnl|CDD|31297 COG1100, COG1100, GTPase SAR1 and related small G proteins [General function prediction only]. Length = 219 Score = 34.2 bits (77), Expect = 0.065 Identities = 38/211 (18%), Positives = 63/211 (29%), Gaps = 15/211 (7%) Query: 3 FKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKL-----AE 57 FK ++G VGK+TL N L YP + + P R KL A Sbjct: 6 FKIVVLGDGGVGKTTLLNRLVG--DEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAG 63 Query: 58 IAESKDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVE 117 E + L P + +V ++ E E + L D I+ V Sbjct: 64 QEEYRSLRPEYYRGANGILIVYDSTLRESSDE----LTEEWLEELREL-APDDVPILLVG 118 Query: 118 GRIDPINDIETIETELMLSDLERLERLFEKNKKYRNHKSEEIVLLQSIISSSLRLIEEGK 177 +ID ++ + E + + E + L + SL + Sbjct: 119 NKIDLFDEQSSSE---EILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNE 175 Query: 178 PVRSLLESLDSDAIPIFKSLNLLTAKPILYI 208 + LL L + + L + Sbjct: 176 LFKELLRKLLEEIEKLVLKNELRQLDRLNNP 206 >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 = 33.6 bits (77), Expect = 0.081 Identities = 12/17 (70%), Positives = 15/17 (88%) Query: 6 GIIGLPNVGKSTLFNAL 22 G++G PNVGKS+L NAL Sbjct: 87 GLVGYPNVGKSSLINAL 103 >gnl|CDD|36405 KOG1191, KOG1191, KOG1191, Mitochondrial GTPase [Translation, ribosomal structure and biogenesis]. Length = 531 Score = 33.4 bits (76), Expect = 0.088 Identities = 14/23 (60%), Positives = 18/23 (78%) Query: 2 GFKCGIIGLPNVGKSTLFNALTR 24 G + I+G PNVGKS+L NAL+R Sbjct: 268 GLQIAIVGRPNVGKSSLLNALSR 290 >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 = 33.1 bits (76), Expect = 0.11 Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 16/76 (21%) Query: 5 CGIIGLPN-VGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKL--AEIAES 61 GI+G PN GKSTL L ++P+SGE+ + + L E+A Sbjct: 28 VGILG-PNGAGKSTLLKTLAG------------LLKPSSGEILLDGKDLASLSPKELARK 74 Query: 62 KDLVPTRMSFVDIAGL 77 VP + + +A L Sbjct: 75 IAYVPQALELLGLAHL 90 >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 = 32.9 bits (75), Expect = 0.13 Identities = 13/29 (44%), Positives = 16/29 (55%) Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYP 34 G IG PNVGKS++ N L + A P Sbjct: 106 GFIGYPNVGKSSIINTLRSKKVCKVAPIP 134 >gnl|CDD|133439 cd01669, TGS_Ygr210_C, TGS_Ygr210_C: The C-terminal TGS domain of Ygr210 GTP-binding protein which is a member of Obg-like family of GTPases, and present in archaea. Several Obg-like 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. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role. Length = 76 Score = 32.6 bits (75), Expect = 0.16 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 17/67 (25%) Query: 296 AWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGKEYIV 355 A+ +P+G+ A+ A IHTD GF+ A+ +A R G++Y + Sbjct: 24 AFLLPKGSTARDLAYAIHTDIGDGFLHAI-----------------DARTGRRVGEDYEL 66 Query: 356 KDGDILH 362 K D++ Sbjct: 67 KHRDVIK 73 >gnl|CDD|37696 KOG2485, KOG2485, KOG2485, Conserved ATP/GTP binding protein [General function prediction only]. Length = 335 Score = 32.6 bits (74), Expect = 0.18 Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 5/37 (13%) Query: 7 IIGLPNVGKSTLFNALTR-----TASAQAANYPFCTI 38 ++G+PNVGKS+L NAL +A+ P T Sbjct: 148 VVGVPNVGKSSLINALRNVHLRKKKAARVGAEPGVTR 184 >gnl|CDD|37634 KOG2423, KOG2423, KOG2423, Nucleolar GTPase [General function prediction only]. Length = 572 Score = 31.5 bits (71), Expect = 0.36 Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 8/42 (19%) Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAV 47 G IG PNVGKS++ N L C + P GE V Sbjct: 311 GFIGYPNVGKSSIINTLR--------KKKVCKVAPIPGETKV 344 >gnl|CDD|36638 KOG1424, KOG1424, KOG1424, Predicted GTP-binding protein MMR1 [General function prediction only]. Length = 562 Score = 31.1 bits (70), Expect = 0.43 Identities = 11/17 (64%), Positives = 13/17 (76%) Query: 6 GIIGLPNVGKSTLFNAL 22 G +G PNVGKS+ NAL Sbjct: 318 GFVGYPNVGKSSTINAL 334 >gnl|CDD|30567 COG0218, COG0218, Predicted GTPase [General function prediction only]. Length = 200 Score = 31.0 bits (70), Expect = 0.48 Identities = 17/40 (42%), Positives = 21/40 (52%), Gaps = 1/40 (2%) Query: 8 IGLPNVGKSTLFNALT-RTASAQAANYPFCTIEPNSGEVA 46 G NVGKS+L NALT + A+ + P T N EV Sbjct: 30 AGRSNVGKSSLINALTNQKNLARTSKTPGRTQLINFFEVD 69 >gnl|CDD|48378 cd03114, ArgK-like, The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.. Length = 148 Score = 30.2 bits (68), Expect = 0.84 Identities = 15/37 (40%), Positives = 20/37 (54%) Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNS 42 GI G+P GKSTL +AL A+ I+P+S Sbjct: 3 GITGVPGAGKSTLIDALITALRARGKRVAVLAIDPSS 39 >gnl|CDD|31317 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]. Length = 258 Score = 30.1 bits (68), Expect = 0.86 Identities = 26/111 (23%), Positives = 40/111 (36%), Gaps = 23/111 (20%) Query: 5 CGIIGLPN-VGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKD 63 GI+G PN GKSTL L ++P SGEV + + L+ +K Sbjct: 31 TGILG-PNGSGKSTLLKCLAG------------LLKPKSGEVLLDGKDIASLSPKELAKK 77 Query: 64 L--------VPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLR 106 L P ++ ++ L R G G V+ + +L Sbjct: 78 LAYVPQSPSAPFGLTVYELVLLGRYPHLG-LFGRPSKEDEEIVEEALELLG 127 >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 = 30.1 bits (68), Expect = 0.91 Identities = 16/54 (29%), Positives = 21/54 (38%), Gaps = 12/54 (22%) Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKL 55 G +IG GKSTL L +EP SG V + ++KL Sbjct: 27 GEFVALIGPSGAGKSTLLRCLNG------------LVEPTSGSVLIDGTDINKL 68 >gnl|CDD|36703 KOG1490, KOG1490, KOG1490, GTP-binding protein CRFG/NOG1 (ODN superfamily) [General function prediction only]. Length = 620 Score = 30.0 bits (67), Expect = 0.97 Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 1/31 (3%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCT 37 + G PNVGKS+ N +TR A + Y F T Sbjct: 173 VCGYPNVGKSSFNNKVTR-ADDEVQPYAFTT 202 >gnl|CDD|143354 cd07849, STKc_ERK1_2_like, Catalytic domain of Extracellular signal-Regulated Kinase 1 and 2-like Serine/Threonine Kinases. Serine/Threonine Kinases (STKs), Extracellular signal-regulated kinases 1 and 2 (ERK1/2) and Fus3 subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This ERK1/2-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. This subfamily is composed of the mitogen-activated protein kinases (MAPKs) ERK1, ERK2, baker's yeast Fus3, and similar proteins. MAPK pathways are important mediators of cellular responses to extracellular signals. ERK1/2 activation is preferentially by mitogenic factors, differentiation stimuli, and cytokines, through a kinase cascade involving the MAPK kinases MEK1/2 and a MAPK kinase kinase from the Raf family. ERK1/2 have numerous substrates, many of which are nuclear and participate in transcriptional regulation of many cellular processes. They regulate cell growth, cell proliferation, and cell cycle progression from G1 to S phase. Although the distinct roles of ERK1 and ERK2 have not been fully determined, it is known that ERK2 can maintain most functions in the absence of ERK1, and that the deletion of ERK2 is embryonically lethal. The MAPK, Fus3, regulates yeast mating processes including mating-specific gene expression, G1 arrest, mating projection, and cell fusion. Length = 336 Score = 29.6 bits (67), Expect = 1.5 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 10/54 (18%) Query: 95 IREVDAIIHVLRCFKDENIIHV-----EGRIDPINDIETIETELMLSDLERLER 143 +RE I +LR FK ENII + + ND+ ++ ELM +DL +L + Sbjct: 51 LRE----IKILRRFKHENIIGILDIIRPPSFESFNDVYIVQ-ELMETDLYKLIK 99 >gnl|CDD|39443 KOG4242, KOG4242, KOG4242, Predicted myosin-I-binding protein [Cell motility]. Length = 553 Score = 29.3 bits (65), Expect = 1.7 Identities = 15/71 (21%), Positives = 25/71 (35%) Query: 248 ISQLPEEERALFMEELDISISGLELLIRSGYRLLDLITYFTVGPKETRAWTIPRGTNAQK 307 IS+L + L++ ELD+S +G + I + T + T+ Sbjct: 204 ISKLLIQSGRLWLTELDLSTNGGKDDIPRTLNKKAGTLVLFKLDRSTTGIRLDLLTSPLA 263 Query: 308 AAGVIHTDFEK 318 A F K Sbjct: 264 AGRTTKLTFGK 274 >gnl|CDD|73053 cd03294, ABC_Pro_Gly_Bertaine, This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation. 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 = 269 Score = 29.4 bits (66), Expect = 1.9 Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 13/66 (19%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66 I+GL GKSTL + R IEP SG+V + + ++ E ++L Sbjct: 55 IMGLSGSGKSTLLRCINR------------LIEPTSGKVLIDGQDIAAMSR-KELRELRR 101 Query: 67 TRMSFV 72 ++S V Sbjct: 102 KKISMV 107 >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 = 29.3 bits (66), Expect = 1.9 Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 12/49 (24%) Query: 1 MGFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPD 49 G + G++G GKSTL + +EP+ G V Sbjct: 25 PGDRIGLVGRNGAGKSTLLKLIA------------GELEPDEGIVTWGS 61 >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 = 29.0 bits (65), Expect = 2.0 Identities = 19/98 (19%), Positives = 27/98 (27%), Gaps = 23/98 (23%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66 ++G VGK++L N E E + D Sbjct: 1 VVGDSGVGKTSLLNR-------------LLGGEFVPEEYETTIIDFYS---KTIEVDGKK 44 Query: 67 TRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHV 104 ++ D AG R S + R D II V Sbjct: 45 VKLQIWDTAGQERFRSLRR-------LYYRGADGIILV 75 >gnl|CDD|37772 KOG2561, KOG2561, KOG2561, Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms]. Length = 568 Score = 29.2 bits (65), Expect = 2.0 Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 4/60 (6%) Query: 142 ERLFEKNKKYRNHKSEEIVLLQSIISSSLRLIEEGKPVRSLLESLDSDAIPIFKSLNLLT 201 ER + KKY N ++ V +S+ RL+ G E+L + I K+L+LL Sbjct: 356 EREILERKKYGNTPMKKWVNPRSLE----RLVSMGYERELAAEALRRNENDIQKALDLLQ 411 >gnl|CDD|72978 cd03219, ABC_Mj1267_LivG_branched, The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E. coli branched-chain amino acid transporter. MJ1267 contains an insertion from residues 114 to 123 characteristic of LivG (Leucine-Isoleucine-Valine) homologs. The branched-chain amino acid transporter from E. coli comprises a heterodimer of ABCs (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ).. Length = 236 Score = 28.9 bits (65), Expect = 2.2 Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 14/42 (33%) Query: 5 CGIIGLPN-VGKSTLFNALTRTASAQAANYPFCTIEPNSGEV 45 G+IG PN GK+TLFN ++ + P SG V Sbjct: 29 HGLIG-PNGAGKTTLFNLISG------------FLRPTSGSV 57 >gnl|CDD|36138 KOG0920, KOG0920, KOG0920, ATP-dependent RNA helicase A [RNA processing and modification]. Length = 924 Score = 28.7 bits (64), Expect = 2.5 Identities = 18/91 (19%), Positives = 33/91 (36%), Gaps = 13/91 (14%) Query: 108 FKDENIIHVEGRIDPINDIETIETELMLSD-LERLERLFEKNKKYRNHKSEEIVLLQSII 166 F +I + GR P+ E L D L + + E + + ++ L + + Sbjct: 338 FGGCPVITIPGRTFPV-------KEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKL 390 Query: 167 SSS---LRLIEEGKPVRSLLESLDSDAIPIF 194 LIE+ + + E AI +F Sbjct: 391 WEPEIDYDLIED--LIEYIDEREFEGAILVF 419 >gnl|CDD|33915 COG4175, ProV, ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]. Length = 386 Score = 28.8 bits (64), Expect = 2.8 Identities = 28/94 (29%), Positives = 40/94 (42%), Gaps = 27/94 (28%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEV-------------AVPDPRMH 53 I+GL GKSTL L R IEP GE+ + + R Sbjct: 59 IMGLSGSGKSTLVRLLNR------------LIEPTRGEILVDGKDIAKLSAAELRELRRK 106 Query: 54 KLAEIAESKDLVPTRMSFVDIA-GL-VRGASKGE 85 K++ + +S L+P R ++A GL V+G K E Sbjct: 107 KISMVFQSFALLPHRTVLENVAFGLEVQGVPKAE 140 >gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]. Length = 323 Score = 28.4 bits (63), Expect = 3.1 Identities = 14/37 (37%), Positives = 19/37 (51%) Query: 6 GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNS 42 GI G+P GKSTL AL R + ++P+S Sbjct: 55 GITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSS 91 >gnl|CDD|30909 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide transport and metabolism]. Length = 178 Score = 28.3 bits (63), Expect = 3.3 Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 10/63 (15%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFC---TIEPNSGEVAVPDPRMHKLAEIAESKD 63 I+G P GKSTL A A T + +A ++ + + + Sbjct: 5 ILGPPGAGKSTL-------AKKLAKKLGLPHLDTGDILRAAIAERTELGEEIKKYIDKGE 57 Query: 64 LVP 66 LVP Sbjct: 58 LVP 60 >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 = 3.3 Identities = 8/20 (40%), Positives = 10/20 (50%) Query: 3 FKCGIIGLPNVGKSTLFNAL 22 F C ++G GKS L A Sbjct: 5 FLCFVLGAKGSGKSALLRAF 24 >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 = 28.2 bits (63), Expect = 3.6 Identities = 26/134 (19%), Positives = 54/134 (40%), Gaps = 25/134 (18%) Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAES 61 G K ++G GKSTL LT ++P GE+ + +++ Sbjct: 28 GEKIALLGRSGSGKSTLLQLLTG------------DLKPQQGEITLDG------VPVSDL 69 Query: 62 KDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHV----E 117 + + + +S ++ + + LG +F R+ A+ +L +D I+ + Sbjct: 70 EKALSSLISVLNQRPYLFDTTLRNNLGRRFSGGERQRLALARIL--LQDAPIVLLDEPTV 127 Query: 118 GRIDPINDIETIET 131 G +DPI + + + Sbjct: 128 G-LDPITERQLLSL 140 >gnl|CDD|33698 COG3911, COG3911, Predicted ATPase [General function prediction only]. Length = 183 Score = 28.0 bits (62), Expect = 3.7 Identities = 20/64 (31%), Positives = 25/64 (39%), Gaps = 2/64 (3%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNS--GEVAVPDPRMHKLAEIAESKDL 64 + G P GK+TL AL R A I S G A+P AE+ + L Sbjct: 14 LTGGPGAGKTTLLAALARAGFATVEEAGRDIIALESAQGGTALPWTDPGAFAELVGLQRL 73 Query: 65 VPTR 68 TR Sbjct: 74 RQTR 77 >gnl|CDD|146421 pfam03770, IPK, Inositol polyphosphate kinase. ArgRIII has has been demonstrated to be an inositol polyphosphate kinase. Length = 184 Score = 28.3 bits (64), Expect = 3.8 Identities = 15/81 (18%), Positives = 22/81 (27%), Gaps = 19/81 (23%) Query: 103 HVLRCFKDENIIH-----VEGRIDPINDIETIETELMLSDLERLERLFEKNKKYRNHKSE 157 + R E + + I L L+ L E + YR Sbjct: 73 YYGRSLSAEEVKEALKRFFSNGKSLRRSKKLIPR--FLERLQELRNWLESQESYR----- 125 Query: 158 EIVLLQSIISSSLRLIEEGKP 178 SSSL + +G P Sbjct: 126 -------FYSSSLLFVYDGDP 139 >gnl|CDD|36463 KOG1249, KOG1249, KOG1249, Predicted GTPases [General function prediction only]. Length = 572 Score = 28.0 bits (62), Expect = 4.0 Identities = 28/115 (24%), Positives = 40/115 (34%), Gaps = 17/115 (14%) Query: 8 IGLPNVGKSTLFNALTR-----------TASAQAANYPFCTIEPNSGEVAVPDP-RMHKL 55 +G NVGKSTLFNAL A +++P T+ V VP P R+ Sbjct: 219 VGATNVGKSTLFNALLESDLCSVNAPKLVDRATISDWPGTTLSLLKFPVLVPHPYRLGGR 278 Query: 56 -----AEIAESKDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVL 105 +K + R G A +G F ++A+ L Sbjct: 279 RKRLGVHSVSAKKDMGERDLLALETGDAGKAGPVAAVGRTFAGSEELINAMAKEL 333 >gnl|CDD|132953 cd06622, PKc_MAPKK_PBS2_like, Catalytic domain of fungal PBS2-like dual-specificity MAP kinase kinases. Protein kinases (PKs), MAP kinase kinase (MAPKK) subfamily, fungal PBS2-like proteins, catalytic (c) domain. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. The MAPKK subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. The mitogen-activated protein (MAP) kinase signaling pathways are important mediators of cellular responses to extracellular signals. The pathways involve a triple kinase core cascade comprising of the MAP kinase (MAPK), which is phosphorylated and activated by a MAPK kinase (MAPKK or MKK), which itself is phosphorylated and activated by a MAPK kinase kinase (MAPKKK or MKKK). Members of this group include the MAPKKs Polymyxin B resistance protein 2 (PBS2) from Saccharomyces cerevisiae, Wis1 from Schizosaccharomyces pombe, and related proteins. PBS2 and Wis1 are components of stress-activated MAPK cascades in budding and fission yeast, respectively. PBS2 is the specific activator of the MAPK Hog1, which plays a central role in the response of budding yeast to stress including exposure to arsenite and hyperosmotic environments. Wis1 phosphorylates and activates the MAPK Sty1 (also called Spc1 or Phh1), which stimulates a transcriptional response to a wide range of cellular insults through the bZip transcription factors Atf1, Pcr1, and Pap1. Length = 286 Score = 27.9 bits (62), Expect = 4.2 Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 6/51 (11%) Query: 69 MSFVD---IAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDE-NIIH 115 M ++D + L G EG+ L I A++ L+ K+E NIIH Sbjct: 78 MEYMDAGSLDKLYAGGVATEGIPEDVLRRI--TYAVVKGLKFLKEEHNIIH 126 >gnl|CDD|35277 KOG0054, KOG0054, KOG0054, Multidrug resistance-associated protein/mitoxantrone resistance protein, ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]. Length = 1381 Score = 27.9 bits (62), Expect = 4.3 Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 12/46 (26%) Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAV 47 G K GI+G GKS+L AL R +EP GE+ + Sbjct: 1166 GEKVGIVGRTGAGKSSLILALFR------------LVEPAEGEILI 1199 >gnl|CDD|143363 cd07858, STKc_TEY_MAPK_plant, Catalytic domain of the Serine/Threonine Kinases, TEY Mitogen-Activated Protein Kinases from Plants. Serine/Threonine Kinases (STKs), Plant TEY Mitogen-Activated Protein Kinase (MAPK) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The TEY MAPK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. MAPKs are important mediators of cellular responses to extracellular signals. In plants, MAPKs are associated with physiological, developmental, hormonal, and stress responses. Some plants show numerous gene duplications of MAPKs. Arabidopsis thaliana harbors at least 20 MAPKs, named AtMPK1-20. There are two subtypes of plant MAPKs based on the conserved phosphorylation motif present in the activation loop, TEY and TDY. This subfamily represents the TEY subtype and is further subdivided into three groups (A, B, and C). Group A is represented by AtMPK3, AtMPK6, Nicotiana tabacum BTF4 (NtNTF4), among others. They are mostly involved in environmental and hormonal responses. AtMPK3 and AtMPK6 are also key regulators for stomatal development and patterning. Group B is represented by AtMPK4, AtMPK13, and NtNTF6, among others. They may be involved in both cell division and environmental stress response. AtMPK4 also participates in regulating innate immunity. Group C is represented by AtMPK1, AtMPK2, NtNTF3, Oryza sativa MAPK4 (OsMAPK4), among others. They may also be involved in stress responses. AtMPK1 and AtMPK2 are activated following mechanical injury and in the presence of stress chemicals such as jasmonic acid, hydrogen peroxide and abscisic acid. OsMAPK4 is also called OsMSRMK3 for Multiple Stress-Responsive MAPK3. Length = 337 Score = 28.1 bits (63), Expect = 4.4 Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 6/47 (12%) Query: 102 IHVLRCFKDENIIHVEGRIDPI-----NDIETIETELMLSDLERLER 143 I +LR EN+I ++ + P ND+ I ELM +DL ++ R Sbjct: 55 IKLLRHLDHENVIAIKDIMPPPHREAFNDV-YIVYELMDTDLHQIIR 100 >gnl|CDD|37292 KOG2081, KOG2081, KOG2081, Nuclear transport regulator [Intracellular trafficking, secretion, and vesicular transport]. Length = 559 Score = 28.0 bits (62), Expect = 4.8 Identities = 17/71 (23%), Positives = 26/71 (36%), Gaps = 2/71 (2%) Query: 195 KSLNLLTAKPILYICNVSEHD--CKKGNIYTEAVQRLASQQNAEMIIISAAIEAEISQLP 252 K L A IC+ C ++ ++Q N E + I IS LP Sbjct: 480 KRLASAAALAFHRICSACRVQMTCLIPSLLELIRSLDSTQINEEAACLLQGISLIISNLP 539 Query: 253 EEERALFMEEL 263 + + +EEL Sbjct: 540 AHKAKIALEEL 550 >gnl|CDD|147781 pfam05816, TelA, Toxic anion resistance protein (TelA). This family consists of several prokaryotic TelA like proteins. TelA and KlA are associated with tellurite resistance and plasmid fertility inhibition. Length = 333 Score = 27.9 bits (63), Expect = 5.0 Identities = 14/37 (37%), Positives = 24/37 (64%), Gaps = 2/37 (5%) Query: 116 VEGRIDPI-NDIETIETELMLSDLERLERLFEKNKKY 151 V G+ID I ++E + EL+ D L++L++KN +Y Sbjct: 96 VGGQIDKILVELEKGKDELL-KDNAMLDQLYDKNLEY 131 >gnl|CDD|110135 pfam01112, Asparaginase_2, Asparaginase. Length = 296 Score = 27.8 bits (62), Expect = 5.2 Identities = 9/56 (16%), Positives = 19/56 (33%) Query: 305 AQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGKEYIVKDGDI 360 A+ AA I +G + +++K + A ++G + I Sbjct: 238 AEAAAKRITKALPRGSGGLIALNHKGEIGAPCNTTGMFRATATEDGTTLEYSEIGI 293 >gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems. Length = 267 Score = 27.7 bits (62), Expect = 5.6 Identities = 11/18 (61%), Positives = 12/18 (66%) Query: 6 GIIGLPNVGKSTLFNALT 23 GI G+P GKSTL AL Sbjct: 33 GITGVPGAGKSTLIEALG 50 >gnl|CDD|30834 COG0488, Uup, ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]. Length = 530 Score = 27.5 bits (61), Expect = 5.6 Identities = 27/145 (18%), Positives = 50/145 (34%), Gaps = 30/145 (20%) Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAES 61 G + G++G GKSTL L +EP+SGEV P ++ +++ Sbjct: 29 GERIGLVGRNGAGKSTLLKILAG------------ELEPDSGEVTRPKG--LRVGYLSQE 74 Query: 62 KDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRID 121 L P + + + E++ +L DE + +E ++ Sbjct: 75 PPLDPEKTVLDYVIEGFGELR----------ELLAELEEAYALLADPDDELLAELEALLE 124 Query: 122 PIN------DIETIETELMLSDLER 140 ++ E L D +R Sbjct: 125 ELDGWTLEARAEEALLGLGFPDEDR 149 >gnl|CDD|38920 KOG3716, KOG3716, KOG3716, Carnitine O-acyltransferase CPTI [Lipid transport and metabolism]. Length = 764 Score = 27.6 bits (61), Expect = 5.6 Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 5/41 (12%) Query: 311 VIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGK 351 ++ TDF KGFI+ +S ++ M A + RD+GK Sbjct: 540 LVFTDFGKGFIKKCGVSPDAFIQM-----ALQLAYYRDQGK 575 >gnl|CDD|133359 cd04159, Arl10_like, Arl10-like subfamily. Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved. Length = 159 Score = 27.3 bits (61), Expect = 6.5 Identities = 8/18 (44%), Positives = 12/18 (66%) Query: 6 GIIGLPNVGKSTLFNALT 23 ++GL N GK+TL N + Sbjct: 3 TLVGLQNSGKTTLVNVIA 20 >gnl|CDD|39796 KOG4596, KOG4596, KOG4596, Uncharacterized conserved protein [Function unknown]. Length = 1936 Score = 27.3 bits (60), Expect = 7.1 Identities = 46/222 (20%), Positives = 80/222 (36%), Gaps = 58/222 (26%) Query: 53 HKLAEIAESKDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDA-IIHVLRCFKDE 111 H++ E +D T + F GNQ +AHI EV A II + +K Sbjct: 1072 HEIYNWTELQDTSLTCIEF----------------GNQKIAHINEVHAAIILLTSKYKGI 1115 Query: 112 NIIHVEGRID----------PINDIETIETELMLSDLERLERLFEKNKKYRNHKSEEIVL 161 + EG +D ET E+ +L D +LE + +S Sbjct: 1116 SDPEFEGLLDLWFPPNKPIPNAFLRETGESNQLLPDWLKLEMI----------RSVV--- 1162 Query: 162 LQSIISSSLRLIEE----------GKPVRS---LLESLDSDAIPIFKSL--NLLTAKPIL 206 Q ++ ++L + G PV S LL+ LD+ +P + +L+ + Sbjct: 1163 -QRLVDAALIDLSPHQAQLFVQVFGMPVESMSKLLKMLDNAVMPDLDRIDHQILSKMYLA 1221 Query: 207 YICNVSEHDCKKGNIYTEAVQRLASQQNAEMIIISAAIEAEI 248 ++ + + R+ SQ + + I+ EI Sbjct: 1222 HLIEGQRMRGAQSGETL--INRIHSQMDNLLPFIAKEEPMEI 1261 >gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family, nucleotide-binding domain. This family includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho. Length = 213 Score = 27.0 bits (61), Expect = 7.9 Identities = 10/33 (30%), Positives = 13/33 (39%), Gaps = 3/33 (9%) Query: 2 GFKCGIIGLPNVGKSTLFNALTRTASAQAANYP 34 G + GI G GK+ L L A A+ Sbjct: 15 GQRIGIFGGSGTGKTVL---LGMIARNAKADVV 44 >gnl|CDD|33396 COG3596, COG3596, Predicted GTPase [General function prediction only]. Length = 296 Score = 27.2 bits (60), Expect = 8.1 Identities = 9/35 (25%), Positives = 15/35 (42%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPN 41 ++G GKS+L NAL + + + T Sbjct: 44 LMGATGAGKSSLINALFQGEVKEVSKVGVGTDITT 78 >gnl|CDD|34791 COG5192, BMS1, GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]. Length = 1077 Score = 27.1 bits (59), Expect = 8.3 Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 7/69 (10%) Query: 3 FKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGE------VAVPDPRMHKLA 56 F ++G P GKSTL +L R + Q + I SG+ + P +H++ Sbjct: 70 FIVAVVGPPGTGKSTLIRSLVRRFTKQTIDEIRGPITVVSGKTRRITFLECPSD-LHQMI 128 Query: 57 EIAESKDLV 65 ++A+ DLV Sbjct: 129 DVAKIADLV 137 >gnl|CDD|133282 cd01882, BMS1, Bms1. Bms1 is an essential, evolutionarily conserved, nucleolar protein. Its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits. Bms1, the putative endonuclease Rc11, and the essential U3 small nucleolar RNA form a stable subcomplex that is believed to control an early step in the formation of the 40S subumit. The C-terminal domain of Bms1 contains a GTPase-activating protein (GAP) that functions intramolecularly. It is believed that Rc11 activates Bms1 by acting as a guanine-nucleotide exchange factor (GEF) to promote GDP/GTP exchange, and that activated (GTP-bound) Bms1 delivers Rc11 to the preribosomes. Length = 225 Score = 26.9 bits (60), Expect = 8.3 Identities = 9/23 (39%), Positives = 15/23 (65%) Query: 7 IIGLPNVGKSTLFNALTRTASAQ 29 ++G P VGK+TL +L + + Q Sbjct: 44 VVGPPGVGKTTLIKSLVKNYTKQ 66 >gnl|CDD|88298 cd05027, S-100B, S-100B: S-100B domain found in proteins similar to S100B. S100B is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100B group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100B is most abundant in glial cells of the central nervous system, predominately in astrocytes. S100B is involved in signal transduction via the inhibition of protein phoshorylation, regulation of enzyme activity and by affecting the calcium homeostasis. Upon calcium binding the S100B homodimer changes conformation to expose a hydrophobic cleft, which represents the interaction site of S100B with its more than 20 known target proteins. These target proteins include several cellular architecture proteins such as tubulin and GFAP; S100B can inhibit polymerization of these oligomeric molecules. Furthermore, S100B inhibits the phosphorylation of multiple kinase substrates including the Alzheimer protein tau and neuromodulin (GAP-43) through a calcium-sensitive interaction with the protein substrates.. Length = 88 Score = 26.9 bits (59), Expect = 8.3 Identities = 15/40 (37%), Positives = 25/40 (62%) Query: 150 KYRNHKSEEIVLLQSIISSSLRLIEEGKPVRSLLESLDSD 189 K++ KSE L+ + +S L I+E + V ++E+LDSD Sbjct: 24 KHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSD 63 >gnl|CDD|36919 KOG1707, KOG1707, KOG1707, Predicted Ras related/Rac-GTP binding protein [Defense mechanisms]. Length = 625 Score = 26.9 bits (59), Expect = 9.0 Identities = 8/20 (40%), Positives = 12/20 (60%) Query: 3 FKCGIIGLPNVGKSTLFNAL 22 F+C ++G N GKS L + Sbjct: 426 FQCFVVGPKNCGKSALLQSF 445 >gnl|CDD|99995 cd04299, GT1_Glycogen_Phosphorylase_like, This family is most closely related to the oligosaccharide phosphorylase domain family and other unidentified sequences. Oligosaccharide phosphorylase catalyzes the breakdown of oligosaccharides into glucose-1-phosphate units. They are important allosteric enzymes in carbohydrate metabolism. The members of this family are found in bacteria and Archaea.. Length = 778 Score = 26.7 bits (60), Expect = 9.1 Identities = 8/12 (66%), Positives = 10/12 (83%) Query: 133 LMLSDLERLERL 144 L+L D ERL+RL Sbjct: 495 LLLRDPERLKRL 506 >gnl|CDD|146089 pfam03280, Lipase_chap, Proteobacterial lipase chaperone protein. Length = 195 Score = 26.8 bits (60), Expect = 9.1 Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 2/35 (5%) Query: 225 AVQRLASQQNAEMIIIS--AAIEAEISQLPEEERA 257 A++RL +Q+ + + A I+QLPE+ R Sbjct: 65 ALERLRIKQDPSLSDEQKARRLAALIAQLPEDLRE 99 >gnl|CDD|33644 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria [Function unknown]. Length = 308 Score = 26.9 bits (59), Expect = 9.6 Identities = 11/28 (39%), Positives = 14/28 (50%) Query: 7 IIGLPNVGKSTLFNALTRTASAQAANYP 34 IIG P VGK+TL + R S + Sbjct: 142 IIGPPQVGKTTLLRDIARLLSDGINQFL 169 >gnl|CDD|30807 COG0459, GroL, Chaperonin GroEL (HSP60 family) [Posttranslational modification, protein turnover, chaperones]. Length = 524 Score = 26.7 bits (59), Expect = 9.6 Identities = 21/94 (22%), Positives = 37/94 (39%), Gaps = 12/94 (12%) Query: 159 IVLLQSIISSSLRLIEEG-----------KPVRSLLESLDSDAIPIFKSLNLLTAKPILY 207 +VL +++ + +LI G V +E L A P+ S L Sbjct: 89 VVLAGALLKEAEKLIAAGIHPTVIKRGYRLAVEKAVEELKEIAKPVSDSEEELKIAITSV 148 Query: 208 ICNVSEHDCKKGNIYTEAVQRLA-SQQNAEMIII 240 + D + G + EAV+++ Q + + III Sbjct: 149 ASKSANSDEEIGELVVEAVEKVGKEQSDLDGIII 182 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 0.136 0.383 Gapped Lambda K H 0.267 0.0790 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,297,598 Number of extensions: 229035 Number of successful extensions: 1029 Number of sequences better than 10.0: 1 Number of HSP's gapped: 989 Number of HSP's successfully gapped: 139 Length of query: 367 Length of database: 6,263,737 Length adjustment: 95 Effective length of query: 272 Effective length of database: 4,210,882 Effective search space: 1145359904 Effective search space used: 1145359904 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 58 (26.0 bits)