RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780484|ref|YP_003064897.1| GTPase EngB [Candidatus Liberibacter asiaticus str. psy62] (212 letters) >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 = 220 bits (563), Expect = 2e-58 Identities = 81/180 (45%), Positives = 113/180 (62%), Gaps = 10/180 (5%) Query: 31 EIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVD 90 EIAF+GRSNVGKSSLIN L NRK LARTS PG+TQ +NFF N+ + LVD Sbjct: 1 EIAFAGRSNVGKSSLINALTNRKKLARTSKTPGKTQLINFF------NVNDKF---RLVD 51 Query: 91 MPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKAV 150 +PGYGYA+ K+ + WG LI YL R L+ V LLID RHG +ID ++ +L++ + Sbjct: 52 LPGYGYAKVSKEVKEKWGKLIEEYLENRENLKGVVLLIDSRHGPTEIDLEMLDWLEELGI 111 Query: 151 SYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILETI 210 + +VLTK DKL + + L++ K ++ + P +I SS+K +GI+ LR I + + Sbjct: 112 PFLVVLTKADKLKKSELAKALKEIKKELKLFE-IDPPIILFSSLKGQGIDELRALIEKWL 170 >gnl|CDD|30567 COG0218, COG0218, Predicted GTPase [General function prediction only]. Length = 200 Score = 217 bits (553), Expect = 3e-57 Identities = 89/206 (43%), Positives = 120/206 (58%), Gaps = 9/206 (4%) Query: 6 IFTKSAWIFLRGVPEIGLLPKAGPPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRT 65 F+ P+I P+ PEIAF+GRSNVGKSSLIN L N+KNLARTS PGRT Sbjct: 1 KLNYHKAKFITSAPDIKQYPEDDLPEIAFAGRSNVGKSSLINALTNQKNLARTSKTPGRT 60 Query: 66 QHLNFFVPKDFSNLKNNLPAMALVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVY 125 Q +NFF D + LVD+PGYGYA+ PK+ + W LI YL +R+ L+ V Sbjct: 61 QLINFFEVDD---------ELRLVDLPGYGYAKVPKEVKEKWKKLIEEYLEKRANLKGVV 111 Query: 126 LLIDCRHGVKQIDQDVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAH 185 LLID RH K +D+++ FL + + +VLTK DKL + + L K ++ P Sbjct: 112 LLIDARHPPKDLDREMIEFLLELGIPVIVVLTKADKLKKSERNKQLNKVAEELKKPPPDD 171 Query: 186 PEVIPTSSVKRKGIEVLRKAILETIN 211 V+ SS+K+KGI+ L+ ILE + Sbjct: 172 QWVVLFSSLKKKGIDELKAKILEWLK 197 >gnl|CDD|37697 KOG2486, KOG2486, KOG2486, Predicted GTPase [General function prediction only]. Length = 320 Score = 111 bits (278), Expect = 2e-25 Identities = 67/196 (34%), Positives = 88/196 (44%), Gaps = 16/196 (8%) Query: 24 LPKAGPPEIAFSGRSNVGKSSLINILVNRKNLARTSNA-PGRTQHLNFFVPKDFSNLKNN 82 PK PE+AF GRSNVGKSSL+N LV KN+A TS + G+TQ +N F + Sbjct: 131 CPKDKRPELAFYGRSNVGKSSLLNDLVRVKNIADTSKSKNGKTQAINHF---------HV 181 Query: 83 LPAMALVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVF 142 + VD+PGYG A + W YL ER L V+LL+D ++ D Sbjct: 182 GKSWYEVDLPGYGRAGYGFELPADWDKFTKSYLLERENLVRVFLLVDASVPIQPTDNPEI 241 Query: 143 SFLDKKAVSYQIVLTKIDKLS---PTTAQETLEKTKY---LIRNYPTAHPEVIPTSSVKR 196 ++L + V V TK DK T + L LIR I SSV Sbjct: 242 AWLGENNVPMTSVFTKCDKQKKVKRTGKKPGLNIKINFQGLIRGVFLVDLPWIYVSSVTS 301 Query: 197 KGIEVLRKAILETINY 212 G ++L I + Y Sbjct: 302 LGRDLLLLHIAQLRGY 317 >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 = 76.2 bits (188), Expect = 6e-15 Identities = 41/173 (23%), Positives = 70/173 (40%), Gaps = 14/173 (8%) Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDMPGYG 95 GR+N GKSSL+N L+ + +A S PG T +V + + L+D PG Sbjct: 3 GRTNAGKSSLLNALLG-QEVAIVSPVPGTTTDPVEYVWELGPLGP-----VVLIDTPGID 56 Query: 96 YARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKAVSYQIV 155 A + ++D + ++ + L ++ +V Sbjct: 57 EAG------GLGREREELARRVLERADLILFVVDADLRADEEEEKLLELLRERGKPVLLV 110 Query: 156 LTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILE 208 L KID L +E LE ++ VI S++ +GI+ LR+A++E Sbjct: 111 LNKIDLLPEEEEEELLELRLLILLLLLGLP--VIAVSALTGEGIDELREALIE 161 >gnl|CDD|145217 pfam01926, MMR_HSR1, GTPase of unknown function. Length = 106 Score = 72.7 bits (179), Expect = 6e-14 Identities = 30/118 (25%), Positives = 49/118 (41%), Gaps = 12/118 (10%) Query: 41 GKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDMPGYGYARAP 100 GKS+LIN L +K A S+ PG T+ N ++ + + LVD PG + Sbjct: 1 GKSTLINALTGKKR-AIVSDYPGTTRDPNEGR------VELDGKQIILVDTPGIIEGASK 53 Query: 101 KKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKAVSYQIVLTK 158 + G L R L + ++D G+ + D ++ L + +VL K Sbjct: 54 GE-----GELGNRTLEAIEEADLILHVVDASEGLTEEDLEILDLLLELGKPVILVLNK 106 >gnl|CDD|31353 COG1159, Era, GTPase [General function prediction only]. Length = 298 Score = 56.0 bits (135), Expect = 7e-09 Identities = 48/183 (26%), Positives = 82/183 (44%), Gaps = 28/183 (15%) Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQH-LNFFVPKDFSNLKNNLPAMALVD 90 +A GR NVGKS+L+N LV +K ++ S P T++ + V D + + VD Sbjct: 9 VAIIGRPNVGKSTLLNALVGQK-ISIVSPKPQTTRNRIRGIVTTDNAQI-------IFVD 60 Query: 91 MPGYGYARAPKKNVDSWGGLIVRYLSE--RSTLR---CVYLLIDCRHGVKQIDQDVFSFL 145 PG PK + +++ RS L+ + ++D G D+ + L Sbjct: 61 TPGI---HKPKHALG-------ELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQL 110 Query: 146 DKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKA 205 K +V+ KIDK+ P L+ +L + P E++P S++K ++ L + Sbjct: 111 KKTKTPVILVVNKIDKVKP--KTVLLKLIAFLKKLLP--FKEIVPISALKGDNVDTLLEI 166 Query: 206 ILE 208 I E Sbjct: 167 IKE 169 >gnl|CDD|30833 COG0486, ThdF, Predicted GTPase [General function prediction only]. Length = 454 Score = 55.2 bits (133), Expect = 1e-08 Identities = 46/186 (24%), Positives = 71/186 (38%), Gaps = 33/186 (17%) Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRT-----QHLNFFVPKDFSNLKNNLPAM 86 + GR NVGKSSL+N L+ R + A ++ G T + +N N +P + Sbjct: 220 VVIIGRPNVGKSSLLNALLGR-DRAIVTDIAGTTRDVIEEDINL----------NGIP-V 267 Query: 87 ALVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLD 146 LVD G R V+ G I R V ++D + + D + L Sbjct: 268 RLVDTAGI---RETDDVVERIG--IERAKKAIEEADLVLFVLDASQPLDKEDLALIELLP 322 Query: 147 KKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAI 206 KK +VL K D +S + I I S+ +G++ LR+AI Sbjct: 323 KK-KPIIVVLNKADLVSKIELESEKLANGDAI----------ISISAKTGEGLDALREAI 371 Query: 207 LETINY 212 + Sbjct: 372 KQLFGK 377 >gnl|CDD|31354 COG1160, COG1160, Predicted GTPases [General function prediction only]. Length = 444 Score = 54.0 bits (130), Expect = 3e-08 Identities = 47/185 (25%), Positives = 75/185 (40%), Gaps = 30/185 (16%) Query: 29 PPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNF----FVPKDFSNLKNNLP 84 P +A GR NVGKS+L N L + +A S+ PG T+ + ++ ++F Sbjct: 3 TPVVAIVGRPNVGKSTLFNRLT-GRRIAIVSDTPGVTRDRIYGDAEWLGREF-------- 53 Query: 85 AMALVDMPGYGYARAPKKNVDSWGGLIVRY-LSERSTLRCVYLLIDCRHGVKQIDQDVFS 143 L+D G + D LI L + ++D R G+ D+++ Sbjct: 54 --ILIDTGGL-----DDGDEDELQELIREQALIAIEEADVILFVVDGREGITPADEEIAK 106 Query: 144 FLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLR 203 L + +V+ KID L E+ Y Y E +P S+ +GI L Sbjct: 107 ILRRSKKPVILVVNKIDNLKA-------EELAYEF--YSLGFGEPVPISAEHGRGIGDLL 157 Query: 204 KAILE 208 A+LE Sbjct: 158 DAVLE 162 Score = 52.5 bits (126), Expect = 7e-08 Identities = 51/206 (24%), Positives = 85/206 (41%), Gaps = 25/206 (12%) Query: 14 FLRGVPEIGLLPKAGPPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVP 73 L E + P +IA GR NVGKSSLIN ++ + S+ G T+ + Sbjct: 163 LLPPDEEEEEEEETDPIKIAIIGRPNVGKSSLINAILG-EERVIVSDIAGTTRDS---ID 218 Query: 74 KDFSNLKNNLPAMALVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRC------VYLL 127 +F + + L+D G R K +S V S TL+ V L+ Sbjct: 219 IEF---ERDGRKYVLIDTAG---IRRKGKITES-----VEKYSVARTLKAIERADVVLLV 267 Query: 128 IDCRHGVKQIDQDVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRN--YPTAH 185 ID G+ + D + +++ IV+ K D + A T+E+ K +R Sbjct: 268 IDATEGISEQDLRIAGLIEEAGRGIVIVVNKWDLVEEDEA--TMEEFKKKLRRKLPFLDF 325 Query: 186 PEVIPTSSVKRKGIEVLRKAILETIN 211 ++ S++ +G++ L +AI E Sbjct: 326 APIVFISALTGQGLDKLFEAIKEIYE 351 >gnl|CDD|133363 cd04163, Era, Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA. Length = 168 Score = 52.4 bits (127), Expect = 8e-08 Identities = 46/183 (25%), Positives = 81/183 (44%), Gaps = 28/183 (15%) Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQH-LNFFVPKDFSNLKNNLPAMALVD 90 +A GR NVGKS+L+N LV +K ++ S P T++ + D + + VD Sbjct: 6 VAIVGRPNVGKSTLLNALVGQK-ISIVSPKPQTTRNRIRGIYTDDDAQI-------IFVD 57 Query: 91 MPGYGYARAPKKNVDSWGGLIVRYLSE--RSTLR---CVYLLIDCRHGVKQIDQDVFSFL 145 PG PKK + + + S L+ V ++D + + D+ + L Sbjct: 58 TPGI---HKPKKKLG-------ERMVKAAWSALKDVDLVLFVVDASEPIGEGDEFILELL 107 Query: 146 DKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKA 205 K +VL KID + ++ L + L P A E+ P S++K + ++ L + Sbjct: 108 KKSKTPVILVLNKIDLVKD--KEDLLPLLEKLKELGPFA--EIFPISALKGENVDELLEE 163 Query: 206 ILE 208 I++ Sbjct: 164 IVK 166 >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 = 46.7 bits (112), Expect = 4e-06 Identities = 44/197 (22%), Positives = 70/197 (35%), Gaps = 51/197 (25%) Query: 39 NVGKSSLINILVNRKNLARTSNAPGRTQHLN---FFVPKDFSNLKNNLPAMALVDMPG-- 93 NVGKS+L+N L N K + +N P T N VP + + D+PG Sbjct: 6 NVGKSTLLNALTNAK--PKVANYPFTTLEPNLGVVEVPDGAR--------IQVADIPGLI 55 Query: 94 YGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDC----RHGVKQI------------ 137 G + GL ++L+ + ++D G Sbjct: 56 EG----ASEGR----GLGNQFLAHIRRADAILHVVDASEDDDIGGVDPLEDYEILNAELK 107 Query: 138 ---DQDVFSFL-DKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSS 193 + + L K + VL KID +E L + L EV+P S+ Sbjct: 108 LYDLETILGLLTAKPVI---YVLNKIDLDDAEELEEELVRELALEEG-----AEVVPISA 159 Query: 194 VKRKGIEVLRKAILETI 210 +G++ L +AI E + Sbjct: 160 KTEEGLDELIRAIYELL 176 >gnl|CDD|31355 COG1161, COG1161, Predicted GTPases [General function prediction only]. Length = 322 Score = 46.2 bits (109), Expect = 7e-06 Identities = 23/59 (38%), Positives = 31/59 (52%), Gaps = 10/59 (16%) Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDMPGY 94 G NVGKS+LIN L+ +K A+TSN PG T+ + + D L+D PG Sbjct: 139 GYPNVGKSTLINRLLGKKV-AKTSNRPGTTKGIQWIKLDDGIY---------LLDTPGI 187 >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 = 44.8 bits (107), Expect = 2e-05 Identities = 43/191 (22%), Positives = 69/191 (36%), Gaps = 56/191 (29%) Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRT-----QHLNFFVPKDFSNLKNNLPAMALVD 90 G+ NVGKSSL+N L R + A S+ G T + ++ +P + L+D Sbjct: 8 GKPNVGKSSLLNALAGR-DRAIVSDIAGTTRDVIEESIDI----------GGIP-VRLID 55 Query: 91 MPGY----------GYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQD 140 G G RA R E + L +ID G+ + D + Sbjct: 56 TAGIRETEDEIEKIGIERA-------------REAIEEADLVL--FVIDASRGLDEEDLE 100 Query: 141 VFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIE 200 + K +VL K D L + L +I S+ +G++ Sbjct: 101 ILELPADK--PIIVVLNKSDLLPDSELLSLLAG------------KPIIAISAKTGEGLD 146 Query: 201 VLRKAILETIN 211 L++A+LE Sbjct: 147 ELKEALLELAG 157 >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 = 44.4 bits (105), Expect = 2e-05 Identities = 24/63 (38%), Positives = 29/63 (46%), Gaps = 12/63 (19%) Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLN-FFVPKDFSNLKNNLPAMALVD 90 I G NVGKSSLIN LV +K S PG+T+H F+ + L D Sbjct: 86 IGLVGYPNVGKSSLINALVGKK-KVSVSATPGKTKHFQTIFLTPTIT----------LCD 134 Query: 91 MPG 93 PG Sbjct: 135 CPG 137 >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 = 43.2 bits (103), Expect = 5e-05 Identities = 46/192 (23%), Positives = 79/192 (41%), Gaps = 29/192 (15%) Query: 28 GPPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKD--FSNLKNNLPA 85 P IA GR NVGKSSL+N L+ + S+ G T+ D + + Sbjct: 1 DPIRIAIIGRPNVGKSSLVNALLG-EERVIVSDIAGTTR--------DSIDVPFEYDGKK 51 Query: 86 MALVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLR------CVYLLIDCRHGVKQIDQ 139 L+D G R K + + S TL+ V L+ID G+ + D Sbjct: 52 YTLIDTAG---IRRKGKVEEG-----IEKYSVLRTLKAIERADVVLLVIDATEGITEQDL 103 Query: 140 DVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRN--YPTAHPEVIPTSSVKRK 197 + + ++ + IV+ K D + +T+++ K IR + ++ S++ + Sbjct: 104 RIAGLILEEGKALVIVVNKWDLVEKD--SKTMKEFKKEIRRKLPFLDYAPIVFISALTGQ 161 Query: 198 GIEVLRKAILET 209 G++ L AI E Sbjct: 162 GVDKLFDAIDEV 173 >gnl|CDD|36638 KOG1424, KOG1424, KOG1424, Predicted GTP-binding protein MMR1 [General function prediction only]. Length = 562 Score = 41.9 bits (98), Expect = 1e-04 Identities = 19/36 (52%), Positives = 25/36 (69%), Gaps = 1/36 (2%) Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQH 67 + F G NVGKSS IN LV RK ++ S+ PG+T+H Sbjct: 317 VGFVGYPNVGKSSTINALVGRKKVS-VSSTPGKTKH 351 >gnl|CDD|133371 cd04171, SelB, SelB subfamily. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryotes, they do share a common feature. Unlike in E. coli, these SECIS elements are located in the 3' UTRs. This group contains bacterial SelBs, as well as, one from archaea. Length = 164 Score = 41.4 bits (98), Expect = 2e-04 Identities = 21/91 (23%), Positives = 40/91 (43%), Gaps = 5/91 (5%) Query: 121 LRCVYLLIDCRHGVKQ--IDQ-DVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYL 177 + V L++ G+ + ++ L K +VLTK D + + E+ + L Sbjct: 75 IDLVLLVVAADEGIMPQTREHLEILELLGIKRGL--VVLTKADLVDEDWLELVEEEIREL 132 Query: 178 IRNYPTAHPEVIPTSSVKRKGIEVLRKAILE 208 + A + P S+V +GIE L++ + E Sbjct: 133 LAGTFLADAPIFPVSAVTGEGIEELKEYLDE 163 >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 = 41.0 bits (96), Expect = 3e-04 Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 10/55 (18%) Query: 39 NVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDMPG 93 NVGKS+LIN L K +A+ N PG T+ + + P + L+D PG Sbjct: 125 NVGKSTLINRLRG-KKVAKVGNKPGVTKGIQWIK---------ISPGIYLLDTPG 169 >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 = 40.5 bits (96), Expect = 3e-04 Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 8/67 (11%) Query: 144 FLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLR 203 L+K + +VL KID L E L++ + P V P S++ +G++ L Sbjct: 112 LLEKPRI---VVLNKIDLLDEEELFELLKELLKELWGKP-----VFPISALTGEGLDELL 163 Query: 204 KAILETI 210 + + E + Sbjct: 164 RKLAELL 170 >gnl|CDD|33087 COG3276, SelB, Selenocysteine-specific translation elongation factor [Translation, ribosomal structure and biogenesis]. Length = 447 Score = 39.9 bits (93), Expect = 5e-04 Identities = 37/179 (20%), Positives = 68/179 (37%), Gaps = 24/179 (13%) Query: 32 IAFSGRSNVGKSSLINILVN-RKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVD 90 I +G + GK++L+ L + G T L F K M +D Sbjct: 3 IGTAGHIDHGKTTLLKALTGGVTDRLPEEKKRGITIDLGF------YYRKLEDGVMGFID 56 Query: 91 MPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKAV 150 +PG+ P I L+ + L++ G+ + LD + Sbjct: 57 VPGH-----PDF--------ISNLLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGI 103 Query: 151 SYQI-VLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILE 208 I VLTK D++ +K K ++ + A+ ++ TS+ +GIE L+ +++ Sbjct: 104 KNGIIVLTKADRVDE---ARIEQKIKQILADLSLANAKIFKTSAKTGRGIEELKNELID 159 >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 = 39.3 bits (93), Expect = 9e-04 Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 1/30 (3%) Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRT 65 GR NVGKS+L N L + A + PG T Sbjct: 4 GRPNVGKSTLFNRLT-GRRDAIVEDTPGVT 32 >gnl|CDD|36702 KOG1489, KOG1489, KOG1489, Predicted GTP-binding protein (ODN superfamily) [General function prediction only]. Length = 366 Score = 39.2 bits (91), Expect = 9e-04 Identities = 46/207 (22%), Positives = 76/207 (36%), Gaps = 52/207 (25%) Query: 15 LRGVPEIGLLPKAGPPEIAFSGRSNVGKSSLINILVNRK----NLARTSNAPGRTQHLNF 70 L+ + ++GL+ G N GKS+L+N L K + A T+ P H+ Sbjct: 193 LKSIADVGLV-----------GFPNAGKSTLLNALSRAKPKVAHYAFTTLRP----HIGT 237 Query: 71 FVPKDFSNLKNNLPAMALVDMPGYGYARAPKKNVDSWGGLIVRYLS--ERSTLRCVYLLI 128 DFS + + D+PG K GL ++L ER ++ Sbjct: 238 VNYDDFSQ-------ITVADIPGIIEGAHMNK------GLGYKFLRHIERCKGLL--FVV 282 Query: 129 DCRHGVKQIDQDVFSFLDKKAVSYQ---------IVLTKIDKLSPTTAQETLEKTKYLIR 179 D + L ++ Y+ IV KID A++ L + L + Sbjct: 283 DLSGKQLRNPWQQLQLLIEELELYEKGLADRPALIVANKIDLPE---AEKNLLSS--LAK 337 Query: 180 NYPTAHPEVIPTSSVKRKGIEVLRKAI 206 H V+P S+ +G+E L + Sbjct: 338 RLQNPH--VVPVSAKSGEGLEELLNGL 362 >gnl|CDD|30882 COG0536, Obg, Predicted GTPase [General function prediction only]. Length = 369 Score = 38.3 bits (89), Expect = 0.001 Identities = 40/195 (20%), Positives = 72/195 (36%), Gaps = 36/195 (18%) Query: 31 EIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVD 90 ++ G N GKS+L++ + K + ++ P T N V + + + D Sbjct: 161 DVGLVGLPNAGKSTLLSAVSAAK--PKIADYPFTTLVPNLGVVRVDGG-----ESFVVAD 213 Query: 91 MPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLL----------IDCRHGVKQIDQD 140 +PG + GL +R+L R R LL D + I + Sbjct: 214 IPGL------IEGASEGVGLGLRFL--RHIERTRVLLHVIDLSPIDGRDPIEDYQTIRNE 265 Query: 141 VFSF----LDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKR 196 + + +K + +VL KID +E E K L S++ R Sbjct: 266 LEKYSPKLAEKPRI---VVLNKIDLPLD--EEELEELKKALAEALGW--EVFYLISALTR 318 Query: 197 KGIEVLRKAILETIN 211 +G++ L +A+ E + Sbjct: 319 EGLDELLRALAELLE 333 >gnl|CDD|36405 KOG1191, KOG1191, KOG1191, Mitochondrial GTPase [Translation, ribosomal structure and biogenesis]. Length = 531 Score = 38.0 bits (88), Expect = 0.002 Identities = 42/194 (21%), Positives = 70/194 (36%), Gaps = 24/194 (12%) Query: 29 PPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMAL 88 +IA GR NVGKSSL+N L + + S PG T+ + + + L Sbjct: 268 GLQIAIVGRPNVGKSSLLNALSRE-DRSIVSPVPGTTRDA-IEAQVTVNGVP-----VRL 320 Query: 89 VDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFL--D 146 D G +++ G R ER+ + L++D + D + L + Sbjct: 321 SDTAGIREESN--DGIEALGIERARKRIERADVIL--LVVDAEESDTESDLKIARILETE 376 Query: 147 KKAVSYQ----------IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKR 196 + +V K D +S + T Y + P V+ S + Sbjct: 377 GVGLVVIVNKMEKQRIILVANKSDLVSKIP-EMTKIPVVYPSAEGRSVFPIVVEVSCTTK 435 Query: 197 KGIEVLRKAILETI 210 +G E L A+L + Sbjct: 436 EGCERLSTALLNIV 449 >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 = 37.4 bits (88), Expect = 0.003 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 10/57 (17%) Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILETI 210 +VL KID L +E LE P+ + S+ +G++ L +AI E + Sbjct: 158 LVLNKIDLLDDEELEERLEAG----------RPDAVFISAKTGEGLDELLEAIEELL 204 Score = 29.3 bits (67), Expect = 0.89 Identities = 11/26 (42%), Positives = 16/26 (61%) Query: 26 KAGPPEIAFSGRSNVGKSSLINILVN 51 ++G P +A G +N GKS+L N L Sbjct: 38 RSGIPTVALVGYTNAGKSTLFNALTG 63 >gnl|CDD|133257 cd00881, GTP_translation_factor, GTP translation factor family. This family consists primarily of translation initiation, elongation, and release factors, which play specific roles in protein translation. In addition, the family includes Snu114p, a component of the U5 small nuclear riboprotein particle which is a component of the spliceosome and is involved in excision of introns, TetM, a tetracycline resistance gene that protects the ribosome from tetracycline binding, and the unusual subfamily CysN/ATPS, which has an unrelated function (ATP sulfurylase) acquired through lateral transfer of the EF1-alpha gene and development of a new function. Length = 189 Score = 37.3 bits (87), Expect = 0.003 Identities = 26/134 (19%), Positives = 54/134 (40%), Gaps = 24/134 (17%) Query: 88 LVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDK 147 +D PG+ D + ++R LS L++D GV+ ++ + Sbjct: 66 FIDTPGH---------ED-FSSEVIRGLS---VSDGAILVVDANEGVQPQTREHLRIARE 112 Query: 148 KAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPE-----------VIPTSSVKR 196 + + + KID++ +E L + K L+ + ++P S++ Sbjct: 113 GGLPIIVAINKIDRVGEEDLEEVLREIKELLGLIGFISTKEEGTRNGLLVPIVPGSALTG 172 Query: 197 KGIEVLRKAILETI 210 G+E L +AI+E + Sbjct: 173 IGVEELLEAIVEHL 186 >gnl|CDD|32443 COG2262, HflX, GTPases [General function prediction only]. Length = 411 Score = 37.2 bits (86), Expect = 0.003 Identities = 39/195 (20%), Positives = 74/195 (37%), Gaps = 36/195 (18%) Query: 26 KAGPPEIAFSGRSNVGKSSLINILVNRKNLAR-----TSNAPGRTQHLNFFVPKDFSNLK 80 ++G P +A G +N GKS+L N L T + R L Sbjct: 189 RSGIPLVALVGYTNAGKSTLFNALTGADVYVADQLFATLDPTTRRIELG----------- 237 Query: 81 NNLPAMALVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHG--VKQID 138 + + L D G+ P V+++ L E + ++D +++++ Sbjct: 238 DGRKVL-LTDTVGF-IRDLPHPLVEAFK----STLEEVKEADLLLHVVDASDPEILEKLE 291 Query: 139 Q--DVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKR 196 DV + + + +VL KID L LE+ P + S+ Sbjct: 292 AVEDVLAEIGADEIPIILVLNKIDLLEDEEILAELER----------GSPNPVFISAKTG 341 Query: 197 KGIEVLRKAILETIN 211 +G+++LR+ I+E ++ Sbjct: 342 EGLDLLRERIIELLS 356 >gnl|CDD|30878 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]. Length = 509 Score = 37.1 bits (86), Expect = 0.004 Identities = 41/187 (21%), Positives = 70/187 (37%), Gaps = 33/187 (17%) Query: 29 PPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLN-FFVPKDFSNLKNNLPAMA 87 PP + G + GK++L++ + RK A G TQH+ + VP D +P + Sbjct: 5 PPVVTIMGHVDHGKTTLLDKI--RKTNVAAGEAGGITQHIGAYQVPLD----VIKIPGIT 58 Query: 88 LVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDK 147 +D PG+ + + G S L++ GV + + Sbjct: 59 FIDTPGH----EAFTAMRARGA---------SVTDIAILVVAADDGVMPQTIEAINHAKA 105 Query: 148 KAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPE-------VIPTSSVKRKGIE 200 V + + KIDK + E +Y + PE +P S+ +GI+ Sbjct: 106 AGVPIVVAINKIDKPEANPDKVKQELQEYGLV------PEEWGGDVIFVPVSAKTGEGID 159 Query: 201 VLRKAIL 207 L + IL Sbjct: 160 ELLELIL 166 >gnl|CDD|143801 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This domain contains a P-loop motif, also found in several other families such as pfam00071, pfam00025 and pfam00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains. Length = 185 Score = 36.7 bits (86), Expect = 0.005 Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 3/88 (3%) Query: 126 LLIDCRHGVKQIDQDVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLI---RNYP 182 L++D GV ++ + V + + K+D++ E +E+ + + Sbjct: 96 LVVDAVEGVMPQTREHLLLAKQLGVPIIVFINKMDRVDDAELDEVVEEISRELLEKYGFG 155 Query: 183 TAHPEVIPTSSVKRKGIEVLRKAILETI 210 VIP S++ +GI+ L +A+ + Sbjct: 156 GETIPVIPGSALTGEGIDTLLEALDLYL 183 >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 = 35.5 bits (82), Expect = 0.010 Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 2/37 (5%) Query: 33 AFSGRSNVGKSSLINILVNRKNLA--RTSNAPGRTQH 67 G+S VGKS+LIN L+ +LA S GR +H Sbjct: 165 VLVGQSGVGKSTLINALLPDLDLATGEISEKLGRGRH 201 Score = 33.6 bits (77), Expect = 0.046 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 7/53 (13%) Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAI 206 IVLTK D L +E LE + L YP V+ S+ +G++ LR+ + Sbjct: 114 IVLTKADLLDD--EEEELELVEALALGYP-----VLAVSAKTGEGLDELREYL 159 >gnl|CDD|146027 pfam03193, DUF258, Protein of unknown function, DUF258. Length = 161 Score = 35.2 bits (82), Expect = 0.011 Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 4/39 (10%) Query: 32 IAFSGRSNVGKSSLINILVNRKNLART---SNAPGRTQH 67 +G+S VGKS+L+N L+ +L RT S GR +H Sbjct: 38 SVLAGQSGVGKSTLLNALLPELDL-RTGEISEKLGRGRH 75 >gnl|CDD|33396 COG3596, COG3596, Predicted GTPase [General function prediction only]. Length = 296 Score = 35.3 bits (81), Expect = 0.013 Identities = 43/197 (21%), Positives = 67/197 (34%), Gaps = 29/197 (14%) Query: 29 PPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMAL 88 P + G + GKSSLIN L + S T L + + L Sbjct: 39 PVNVLLMGATGAGKSSLINALFQG-EVKEVSKVGVGTDITTRLR------LSYDGENLVL 91 Query: 89 VDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKK 148 D PG G + L YL + L V LI D+D + Sbjct: 92 WDTPGLGDGKDKDAEHRQ---LYRDYLPK---LDLVLWLIKADDRALGTDEDFLRDVIIL 145 Query: 149 AVSYQI--VLTKIDKL-------------SPTTAQETLEKTKYLIRNYPTAHPEVIPTSS 193 + ++ V+T+ D+ SP Q EK + L R + P V+ S Sbjct: 146 GLDKRVLFVVTQADRAEPGREWDSAGHQPSPAIKQFIEEKAEALGRLFQEVKP-VVAVSG 204 Query: 194 VKRKGIEVLRKAILETI 210 G++ L +A++ + Sbjct: 205 RLPWGLKELVRALITAL 221 >gnl|CDD|36637 KOG1423, KOG1423, KOG1423, Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. Length = 379 Score = 34.6 bits (79), Expect = 0.022 Identities = 37/208 (17%), Positives = 70/208 (33%), Gaps = 47/208 (22%) Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDM 91 +A G NVGKS+L N ++ +K ++ S T+H + + + + D Sbjct: 75 VAVIGAPNVGKSTLTNQMIGQK-VSAVSRKVHTTRHRILGI------ITSGETQLVFYDT 127 Query: 92 PG-------YGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSF 144 PG + + CV +++D + V Sbjct: 128 PGLVSKKMHRRHHLMMSVLQNPRDAAQ--------NADCVVVVVDASATRTPLHPRVLHM 179 Query: 145 LDK-KAVSYQIVLTKIDKLSP---------TTAQETLEKTKYLIRNYPTAHP-------- 186 L++ + +V+ KIDKL L K K ++ T P Sbjct: 180 LEEYSKIPSILVMNKIDKLKQKRLLLNLKDLLTNGELAKLKLEVQEKFTDVPSDEKWRTI 239 Query: 187 -------EVIPTSSVKRKGIEVLRKAIL 207 V S++ +GI+ L++ ++ Sbjct: 240 CGWSHFERVFMVSALYGEGIKDLKQYLM 267 >gnl|CDD|144365 pfam00735, Septin, Septin. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerize to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis. Length = 280 Score = 34.6 bits (80), Expect = 0.022 Identities = 46/171 (26%), Positives = 69/171 (40%), Gaps = 39/171 (22%) Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFS-------NLKNNLPAMAL 88 G S +GK++LIN L +L PG ++ + V + +K NL + Sbjct: 11 GESGLGKTTLINTLFLT-DLYPERGIPGPSEKIKKTVEIKATTVEIEEDGVKLNL---TV 66 Query: 89 VDMPGYGYARAPKKNVDSWGGLIVRYLSER--STLR-----------------CVYLLID 129 +D PG+G A N + W IV Y+ E+ LR C+Y + Sbjct: 67 IDTPGFGDA---IDNSNCW-KPIVEYIDEQFEQYLRDESRLNRTSIVDNRVHCCLYFISP 122 Query: 130 CRHGVKQIDQDVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRN 180 HG+K +D + L +K V+ V+ K D L T E K IR Sbjct: 123 TGHGLKPLDVEFMKKLHEK-VNIIPVIAKADTL---TPDELQR-FKKRIRA 168 >gnl|CDD|30719 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion transport and metabolism]. Length = 653 Score = 34.4 bits (79), Expect = 0.023 Identities = 41/181 (22%), Positives = 74/181 (40%), Gaps = 25/181 (13%) Query: 30 PEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALV 89 +A G NVGK++L N L + N PG T V K LK + +V Sbjct: 4 LTVALVGNPNVGKTTLFNALTGAN--QKVGNWPGVT------VEKKEGKLKYKGHEIEIV 55 Query: 90 DMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKA 149 D+PG Y+ S + R + ++D ++++++ L Sbjct: 56 DLPGT-YSLTAY----SEDEKVARDFLLEGKPDLIVNVVD----ATNLERNLYLTLQLLE 106 Query: 150 VSYQIV--LTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAIL 207 + ++ L ID+ + +EK L+ V+PT + + +G+E L++AI+ Sbjct: 107 LGIPMILALNMIDEAKKRGIRIDIEKLSKLLG------VPVVPTVAKRGEGLEELKRAII 160 Query: 208 E 208 E Sbjct: 161 E 161 >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 = 33.7 bits (77), Expect = 0.039 Identities = 24/68 (35%), Positives = 28/68 (41%), Gaps = 16/68 (23%) Query: 34 FSGRSNVGKSSLINILVNRKN-------LARTSNAPGRTQHLNFFVPKDFSNLKNNLPAM 86 G +NVGKS+LIN L+ + N L TS PG T L L N Sbjct: 132 VVGATNVGKSTLINALLKKDNGKKKLKDLLTTSPIPGTTLDLIKI------PLGNGK--- 182 Query: 87 ALVDMPGY 94 L D PG Sbjct: 183 KLYDTPGI 190 >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 = 33.7 bits (77), Expect = 0.041 Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 1/46 (2%) Query: 26 KAGPPEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFF 71 ++ G NVGKSS+IN L R + A TS +PG T+ Sbjct: 98 DGKEGKVGVVGYPNVGKSSIINALKGRHS-ASTSPSPGYTKGEQLV 142 >gnl|CDD|133288 cd01888, eIF2_gamma, eIF2-gamma (gamma subunit of initiation factor 2). eIF2 is a heterotrimeric translation initiation factor that consists of alpha, beta, and gamma subunits. The GTP-bound gamma subunit also binds initiator methionyl-tRNA and delivers it to the 40S ribosomal subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is released from the ribosome. The gamma subunit has no intrinsic GTPase activity, but is stimulated by the GTPase activating protein (GAP) eIF5, and GDP/GTP exchange is stimulated by the guanine nucleotide exchange factor (GEF) eIF2B. eIF2B is a heteropentamer, and the epsilon chain binds eIF2. Both eIF5 and eIF2B-epsilon are known to bind strongly to eIF2-beta, but have also been shown to bind directly to eIF2-gamma. It is possible that eIF2-beta serves simply as a high-affinity docking site for eIF5 and eIF2B-epsilon, or that eIF2-beta serves a regulatory role. eIF2-gamma is found only in eukaryotes and archaea. It is closely related to SelB, the selenocysteine-specific elongation factor from eubacteria. The translational factor components of the ternary complex, IF2 in eubacteria and eIF2 in eukaryotes are not the same protein (despite their unfortunately similar names). Both factors are GTPases; however, eubacterial IF-2 is a single polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is a member of the same family as eubacterial IF2, but the two proteins are only distantly related. This family includes translation initiation, elongation, and release factors. Length = 203 Score = 32.6 bits (75), Expect = 0.078 Identities = 17/57 (29%), Positives = 29/57 (50%) Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILETI 210 IV KID + A E E+ K ++ + +IP S+ + I+VL + I++ I Sbjct: 142 IVQNKIDLVKEEQALENYEQIKKFVKGTIAENAPIIPISAQLKYNIDVLLEYIVKKI 198 >gnl|CDD|30869 COG0523, COG0523, Putative GTPases (G3E family) [General function prediction only]. Length = 323 Score = 32.6 bits (74), Expect = 0.079 Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 4/65 (6%) Query: 115 LSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKT 174 L++ L V ++D H ++ +D D+ A + IVL K D + E LE Sbjct: 111 LADGVRLDGVVTVVDAAHFLEGLDAIAELAEDQLAFADVIVLNKTDLVDA----EELEAL 166 Query: 175 KYLIR 179 + +R Sbjct: 167 EARLR 171 >gnl|CDD|34854 COG5257, GCD11, Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]. Length = 415 Score = 32.5 bits (74), Expect = 0.084 Identities = 18/57 (31%), Positives = 29/57 (50%) Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILETI 210 IV KID +S A E E+ K ++ + +IP S+ + I+ L +AI + I Sbjct: 145 IVQNKIDLVSRERALENYEQIKEFVKGTVAENAPIIPISAQHKANIDALIEAIEKYI 201 >gnl|CDD|31356 COG1162, COG1162, Predicted GTPases [General function prediction only]. Length = 301 Score = 32.6 bits (74), Expect = 0.084 Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 2/37 (5%) Query: 33 AFSGRSNVGKSSLINILVNRKNLA--RTSNAPGRTQH 67 G+S VGKS+LIN L+ N S GR +H Sbjct: 168 VLLGQSGVGKSTLINALLPELNQKTGEISEKLGRGRH 204 >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 = 32.3 bits (73), Expect = 0.094 Identities = 16/34 (47%), Positives = 21/34 (61%), Gaps = 1/34 (2%) Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRT 65 + G NVGKSS+IN L+N+ L + N PG T Sbjct: 103 VGVIGYPNVGKSSVINALLNKLKL-KVGNVPGTT 135 >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 = 32.1 bits (74), Expect = 0.12 Identities = 11/24 (45%), Positives = 17/24 (70%) Query: 188 VIPTSSVKRKGIEVLRKAILETIN 211 V+PTS+ K +GI+ L+ AI+E Sbjct: 137 VVPTSARKGEGIDELKDAIIEVAE 160 Score = 32.1 bits (74), Expect = 0.13 Identities = 21/62 (33%), Positives = 27/62 (43%), Gaps = 8/62 (12%) Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDM 91 IA G NVGK++L N L + N PG T V K K + +VD+ Sbjct: 2 IALVGNPNVGKTTLFNALTGAR--QHVGNWPGVT------VEKKEGTFKYKGYEIEIVDL 53 Query: 92 PG 93 PG Sbjct: 54 PG 55 >gnl|CDD|37634 KOG2423, KOG2423, KOG2423, Nucleolar GTPase [General function prediction only]. Length = 572 Score = 31.9 bits (72), Expect = 0.14 Identities = 15/35 (42%), Positives = 22/35 (62%), Gaps = 1/35 (2%) Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQ 66 + F G NVGKSS+IN L +K + + + PG T+ Sbjct: 310 VGFIGYPNVGKSSIINTL-RKKKVCKVAPIPGETK 343 >gnl|CDD|30543 COG0194, Gmk, Guanylate kinase [Nucleotide transport and metabolism]. Length = 191 Score = 31.6 bits (72), Expect = 0.17 Identities = 22/91 (24%), Positives = 36/91 (39%), Gaps = 10/91 (10%) Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRT--------QHLNFFVPKDFSNL--KN 81 I SG S VGKS+L+ L+ L + +A R F ++F L ++ Sbjct: 7 IVLSGPSGVGKSTLVKALLEDDKLRFSVSATTRKPRPGEVDGVDYFFVTEEEFEELIERD 66 Query: 82 NLPAMALVDMPGYGYARAPKKNVDSWGGLIV 112 A YG +R P + + G ++ Sbjct: 67 EFLEWAEYHGNYYGTSREPVEQALAEGKDVI 97 >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 = 31.4 bits (71), Expect = 0.20 Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 1/35 (2%) Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQ 66 + F G NVGKSS+IN L K + + + PG T+ Sbjct: 105 VGFIGYPNVGKSSIINTL-RSKKVCKVAPIPGETK 138 >gnl|CDD|39846 KOG4647, KOG4647, KOG4647, Uncharacterized membrane protein [Function unknown]. Length = 263 Score = 30.8 bits (69), Expect = 0.31 Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 2/36 (5%) Query: 165 TTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIE 200 Q + EK + N AH E + V+R+ E Sbjct: 10 VYGQRSEEKDYGSMENLANAHREYL--KVVRRQNRE 43 >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 = 30.7 bits (70), Expect = 0.32 Identities = 11/18 (61%), Positives = 14/18 (77%) Query: 36 GRSNVGKSSLINILVNRK 53 G S VGK+SL+N VN+K Sbjct: 7 GDSGVGKTSLMNQYVNKK 24 >gnl|CDD|37696 KOG2485, KOG2485, KOG2485, Conserved ATP/GTP binding protein [General function prediction only]. Length = 335 Score = 30.7 bits (69), Expect = 0.33 Identities = 21/65 (32%), Positives = 26/65 (40%), Gaps = 6/65 (9%) Query: 6 IFTKSAWIFLRGVPEIGLLPKAGPPEIAFSGRSNVGKSSLINILVN----RKNLARTSNA 61 + + V I L + G NVGKSSLIN L N +K AR Sbjct: 122 LLKILTILSEELVRFIRTLN--SEYNVMVVGVPNVGKSSLINALRNVHLRKKKAARVGAE 179 Query: 62 PGRTQ 66 PG T+ Sbjct: 180 PGVTR 184 >gnl|CDD|35669 KOG0448, KOG0448, KOG0448, Mitofusin 1 GTPase, involved in mitochondrila biogenesis [Posttranslational modification, protein turnover, chaperones]. Length = 749 Score = 30.4 bits (68), Expect = 0.36 Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 6/37 (16%) Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHL 68 +A GR++ GKS++IN ++++K L P H Sbjct: 112 VAIFGRTSAGKSTVINAMLHKKLL------PSGIGHT 142 >gnl|CDD|36359 KOG1144, KOG1144, KOG1144, Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]. Length = 1064 Score = 30.4 bits (68), Expect = 0.36 Identities = 30/145 (20%), Positives = 57/145 (39%), Gaps = 27/145 (18%) Query: 30 PEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHL--NFF----------VPKDFS 77 P G + GK+ L++ + R + A G TQ + +F K + Sbjct: 476 PICCILGHVDTGKTKLLDKI--RGTNVQEGEAGGITQQIGATYFPAENIREKTKELKKDA 533 Query: 78 NLKNNLPAMALVDMPGYGYARAPKKNVDSWGGLIVRYLSERSTLRCVYLLIDCRHGVKQI 137 + +P + ++D PG+ +S+ L R S L++D HG++ Sbjct: 534 KKRLKVPGLLVIDTPGH----------ESFTNLRSRGSS---LCDLAILVVDIMHGLEPQ 580 Query: 138 DQDVFSFLDKKAVSYQIVLTKIDKL 162 + + L + + + L KID+L Sbjct: 581 TIESINLLRMRKTPFIVALNKIDRL 605 >gnl|CDD|29456 cd02760, MopB_Phenylacetyl-CoA-OR, The MopB_Phenylacetyl-CoA-OR CD contains the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), and other related proteins. The phenylacetyl-CoA:acceptor oxidoreductase has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins.. Length = 760 Score = 30.4 bits (68), Expect = 0.38 Identities = 13/36 (36%), Positives = 19/36 (52%) Query: 8 TKSAWIFLRGVPEIGLLPKAGPPEIAFSGRSNVGKS 43 T+ AW+FLR VP P++ F+ R+N S Sbjct: 492 TQLAWMFLREVPLDWKFELPTLPDVWFNYRTNPAIS 527 >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 = 29.8 bits (67), Expect = 0.58 Identities = 15/33 (45%), Positives = 17/33 (51%), Gaps = 1/33 (3%) Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQHL 68 G NVGKSSLIN L R PG T+ + Sbjct: 124 GFPNVGKSSLINSL-KRSRACNVGATPGVTKSM 155 >gnl|CDD|31357 COG1163, DRG, Predicted GTPase [General function prediction only]. Length = 365 Score = 29.4 bits (66), Expect = 0.79 Identities = 13/30 (43%), Positives = 19/30 (63%) Query: 24 LPKAGPPEIAFSGRSNVGKSSLINILVNRK 53 + K+G +A G +VGKS+L+N L N K Sbjct: 58 VKKSGDATVALVGFPSVGKSTLLNKLTNTK 87 >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 = 29.1 bits (66), Expect = 0.83 Identities = 13/27 (48%), Positives = 14/27 (51%), Gaps = 8/27 (29%) Query: 27 AGPPEIAFSGRSNVGKSSLINILVNRK 53 AG P NVGKSSL+N L K Sbjct: 6 AGYP--------NVGKSSLVNKLTRAK 24 >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 = 29.3 bits (67), Expect = 0.88 Identities = 11/22 (50%), Positives = 16/22 (72%) Query: 188 VIPTSSVKRKGIEVLRKAILET 209 V+PTS+ K +GI+ L+ AI E Sbjct: 134 VVPTSARKGEGIDELKDAIAEL 155 Score = 28.9 bits (66), Expect = 1.0 Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 8/58 (13%) Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDMPG 93 G NVGK++L N L + + N PG T V K K + +VD+PG Sbjct: 3 GNPNVGKTTLFNALTGAR--QKVGNWPGVT------VEKKEGRFKLGGKEIEIVDLPG 52 >gnl|CDD|37695 KOG2484, KOG2484, KOG2484, GTPase [General function prediction only]. Length = 435 Score = 29.2 bits (65), Expect = 0.93 Identities = 16/34 (47%), Positives = 19/34 (55%), Gaps = 1/34 (2%) Query: 35 SGRSNVGKSSLINILVNRKNLARTSNAPGRTQHL 68 G NVGKSS+IN L RK N PG T+ + Sbjct: 258 IGYPNVGKSSVINSLKRRKACN-VGNVPGVTRSM 290 >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 = 28.6 bits (64), Expect = 1.3 Identities = 11/28 (39%), Positives = 14/28 (50%) Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTS 59 A G S GKS+L+N L R+ S Sbjct: 38 TAIMGPSGAGKSTLLNALAGRRTGLGVS 65 >gnl|CDD|146036 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop. Length = 122 Score = 28.5 bits (64), Expect = 1.3 Identities = 8/22 (36%), Positives = 13/22 (59%) Query: 30 PEIAFSGRSNVGKSSLINILVN 51 P + G + GK++LI L+N Sbjct: 1 PIVLVVGPKDSGKTTLIRKLLN 22 >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 = 1.5 Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 3/62 (4%) Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRN---YPTAHPEVIPTSSVKRKGIEVLRKAILETI 210 IV+ K D+ A L L+R P V+ TS+++ +GI+ L AI + Sbjct: 194 IVINKADRKGAEKAARELRSALDLLREVWRENGWRPPVVTTSALEGEGIDELWDAIEDHR 253 Query: 211 NY 212 + Sbjct: 254 KF 255 >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 = 1.7 Identities = 12/21 (57%), Positives = 13/21 (61%) Query: 29 PPEIAFSGRSNVGKSSLINIL 49 P IA +G S GKSS IN L Sbjct: 1 PLNIAVTGESGAGKSSFINAL 21 >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 = 28.2 bits (63), Expect = 1.8 Identities = 32/175 (18%), Positives = 62/175 (35%), Gaps = 22/175 (12%) Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVDMPGYG 95 G S VGK+SL+N L+ + + F K + + + D G Sbjct: 3 GDSGVGKTSLLNRLLGGEFVPEEYETTIID-----FYSKTIEVDGKKVK-LQIWDTAGQE 56 Query: 96 YARAPKKNVDSWG-GLIVRY-LSERSTLRCVYLLIDCRHGVKQIDQDVFSFLDKKAVSYQ 153 R+ ++ G+I+ Y +++R + VK+ + + + + Sbjct: 57 RFRSLRRLYYRGADGIILVYDVTDRESFEN----------VKEWLLLILINKEGENIPII 106 Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILE 208 +V KID L E + L + TS+ + +E L + + E Sbjct: 107 LVGNKID-LPEERVVSEEELAEQLAKEL---GVPYFETSAKTGENVEELFEELAE 157 >gnl|CDD|99853 cd06099, CS_ACL-C_CCL, Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) from citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. Some CS proteins function as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. CCL cleaves citryl-CoA (CiCoA) to AcCoA and OAA. ACLs catalyze an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA; they do this in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate CiCoA, and c) the hydrolysis of CiCoA to produce citrate and CoA. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). Some type II CSs are strongly and specifically inhibited by NADH through an allosteric mechanism. In fungi, yeast, plants, and animals ACL is cytosolic and generates AcCoA for lipogenesis. In several groups of autotrophic prokaryotes and archaea, ACL carries out the citrate-cleavage reaction of the reductive tricarboxylic acid (rTCA) cycle. In the family Aquificaceae this latter reaction in the rTCA cycle is carried out via a two enzyme system the second enzyme of which is CCL.. Length = 213 Score = 28.1 bits (63), Expect = 1.9 Identities = 10/57 (17%), Positives = 18/57 (31%), Gaps = 6/57 (10%) Query: 64 RTQHLNFFVPKDFSNLKNNLPAMALVD-----MPGYGYARAPKKNVDSWGGLIVRYL 115 R L F + + P L Y + NVD + G++ + + Sbjct: 118 RATVLKKFAEELLKE-DGDDPMFELAAELEKIAEEVLYEKKLYPNVDFYSGVLYKAM 173 >gnl|CDD|34624 COG5019, CDC3, Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]. Length = 373 Score = 27.9 bits (62), Expect = 1.9 Identities = 37/174 (21%), Positives = 65/174 (37%), Gaps = 43/174 (24%) Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNL-------KNNLPAMAL 88 G S +GK++ IN L + T R + + + + NL + Sbjct: 30 GESGLGKTTFINTLFGTSLVDETEIDDIRAEGTSPTLEIKITKAELEEDGFHLNL---TV 86 Query: 89 VDMPGYGYARAPKKNVD---SWGGLIV-------RYLSERSTLR------------CVYL 126 +D PG+G +D W ++ +YL E ++ C+Y Sbjct: 87 IDTPGFG------DFIDNSKCWEPIVDYIDDQFDQYLDEEQKIKRNPKFKDTRVHACLYF 140 Query: 127 LIDCRHGVKQIDQDVFSFLDKKAVSYQIVLTKIDKLSPTTAQETLEKTKYLIRN 180 + HG+K +D + L K+ V+ V+ K D L+ + L + K IR Sbjct: 141 IRPTGHGLKPLDIEAMKRLSKR-VNLIPVIAKADTLTD----DELAEFKERIRE 189 >gnl|CDD|35615 KOG0394, KOG0394, KOG0394, Ras-related GTPase [General function prediction only]. Length = 210 Score = 27.6 bits (61), Expect = 2.4 Identities = 12/28 (42%), Positives = 17/28 (60%) Query: 26 KAGPPEIAFSGRSNVGKSSLINILVNRK 53 K ++ G S VGK+SL+N VN+K Sbjct: 6 KRTLLKVIILGDSGVGKTSLMNQYVNKK 33 >gnl|CDD|48380 cd03116, MobB, Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.. Length = 159 Score = 27.5 bits (61), Expect = 2.4 Identities = 8/22 (36%), Positives = 12/22 (54%) Query: 29 PPEIAFSGRSNVGKSSLINILV 50 I F G S GK++L+ L+ Sbjct: 1 MKVIGFVGYSGSGKTTLLEKLI 22 >gnl|CDD|133287 cd01887, IF2_eIF5B, IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases, IF2/IF5B undergoes conformational changes between its GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess three characteristic segments, including a divergent N-terminal region followed by conserved central and C-terminal segments. This core region is conserved among all known eukaryotic and archaeal IF2/eIF5Bs and eubacterial IF2s. Length = 168 Score = 27.5 bits (62), Expect = 2.9 Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 14/63 (22%) Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPE--------VIPTSSVKRKGIEVLRKA 205 + L KIDK E+ K + E ++PTS+ +GI+ L +A Sbjct: 107 VALNKIDKP-----NANPERVKNELSEL-GLQGEDEWGGDVQIVPTSAKTGEGIDDLLEA 160 Query: 206 ILE 208 IL Sbjct: 161 ILL 163 >gnl|CDD|145920 pfam03029, ATP_bind_1, Conserved hypothetical ATP binding protein. Members of this family are found in a range of archaea and eukaryotes and have hypothesized ATP binding activity. Length = 234 Score = 27.3 bits (61), Expect = 2.9 Identities = 15/76 (19%), Positives = 22/76 (28%), Gaps = 17/76 (22%) Query: 154 IVLTKIDKLSPTTAQETLEKTKYL--------------IRNY---PTAHPEVIPTSSVKR 196 + L K D LS A + L IR P + + Sbjct: 159 VALNKFDLLSLEFALKWFTDPDDLQLLLELDYRYLNEAIRLALDLFYLVPRFLCDARETG 218 Query: 197 KGIEVLRKAILETINY 212 + +E L I E + Y Sbjct: 219 ESMEDLLTLIDEALQY 234 >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 = 27.5 bits (61), Expect = 3.0 Identities = 9/19 (47%), Positives = 13/19 (68%) Query: 32 IAFSGRSNVGKSSLINILV 50 +A GRS GKS+L+ +L Sbjct: 367 VAILGRSGSGKSTLLQLLA 385 >gnl|CDD|31281 COG1084, COG1084, Predicted GTPase [General function prediction only]. Length = 346 Score = 27.5 bits (61), Expect = 3.1 Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 4/47 (8%) Query: 7 FTKSAWIFLRGVPEIGLLPKAGPPEIAFSGRSNVGKSSLINILVNRK 53 F + A L+ +P I P I +G NVGKSSL+ L K Sbjct: 150 FLRKARDHLKKLPAI----DPDLPTIVVAGYPNVGKSSLVRKLTTAK 192 >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 = 27.1 bits (61), Expect = 3.4 Identities = 6/20 (30%), Positives = 9/20 (45%) Query: 32 IAFSGRSNVGKSSLINILVN 51 + G VGKS++ V Sbjct: 2 VVVLGAGGVGKSAITIQFVK 21 >gnl|CDD|35687 KOG0466, KOG0466, KOG0466, Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]. Length = 466 Score = 27.2 bits (60), Expect = 3.6 Identities = 15/57 (26%), Positives = 29/57 (50%) Query: 154 IVLTKIDKLSPTTAQETLEKTKYLIRNYPTAHPEVIPTSSVKRKGIEVLRKAILETI 210 I+ KID + + A E E+ + I+ +IP S+ + I+V+ + I++ I Sbjct: 184 ILQNKIDLIKESQALEQHEQIQKFIQGTVAEGAPIIPISAQLKYNIDVVCEYIVKKI 240 >gnl|CDD|37302 KOG2091, KOG2091, KOG2091, Predicted member of glycosyl hydrolase family 18 [Carbohydrate transport and metabolism]. Length = 392 Score = 26.9 bits (59), Expect = 4.0 Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 2/64 (3%) Query: 65 TQHLNFFVPKDFSNLKNNLPAMALVDMPGYGYARAPKKNV-DSWGGLIVRYLSERSTLRC 123 L FF P++FS L +L+ Y + P N W + +L S R Sbjct: 235 NGQLKFFTPEEFSKLVAVYDGFSLMTY-DYSLVQGPGPNAPLEWIRHCLHHLGGSSAKRP 293 Query: 124 VYLL 127 LL Sbjct: 294 KILL 297 >gnl|CDD|31532 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General function prediction only]. Length = 398 Score = 26.8 bits (59), Expect = 4.4 Identities = 8/38 (21%), Positives = 13/38 (34%) Query: 15 LRGVPEIGLLPKAGPPEIAFSGRSNVGKSSLINILVNR 52 + E + G + GKS+L L N+ Sbjct: 59 IADTWESKSESAGKVGVVMVVGPVDSGKSTLTTYLANK 96 >gnl|CDD|35284 KOG0061, KOG0061, KOG0061, Transporter, ABC superfamily (Breast cancer resistance protein) [Secondary metabolites biosynthesis, transport and catabolism]. Length = 613 Score = 26.9 bits (59), Expect = 4.5 Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 1/30 (3%) Query: 26 KAGPPEI-AFSGRSNVGKSSLINILVNRKN 54 A P E+ A G S GK++L+N L R N Sbjct: 52 TAKPGELLAIMGPSGSGKTTLLNALAGRLN 81 >gnl|CDD|35667 KOG0446, KOG0446, KOG0446, Vacuolar sorting protein VPS1, dynamin, and related proteins [Intracellular trafficking, secretion, and vesicular transport, General function prediction only]. Length = 657 Score = 26.9 bits (59), Expect = 4.7 Identities = 12/36 (33%), Positives = 16/36 (44%) Query: 30 PEIAFSGRSNVGKSSLINILVNRKNLARTSNAPGRT 65 P+I G + GKSS++ LV L R R Sbjct: 30 PQIVVVGGQSSGKSSVLESLVGFVFLPRGVGIVTRR 65 >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 = 26.3 bits (58), Expect = 5.6 Identities = 9/22 (40%), Positives = 14/22 (63%) Query: 33 AFSGRSNVGKSSLINILVNRKN 54 A G S GK++L+++L RK Sbjct: 37 ALMGESGAGKTTLLDVLAGRKT 58 >gnl|CDD|36704 KOG1491, KOG1491, KOG1491, Predicted GTP-binding protein (ODN superfamily) [General function prediction only]. Length = 391 Score = 26.4 bits (58), Expect = 5.8 Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 2/33 (6%) Query: 30 PEIAFSGRSNVGKSSLINILVNRKNLARTSNAP 62 +I G NVGKS+ N L K A +N P Sbjct: 21 LKIGIVGLPNVGKSTFFNALTKSK--AGAANFP 51 >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 = 26.3 bits (58), Expect = 5.9 Identities = 9/18 (50%), Positives = 12/18 (66%) Query: 32 IAFSGRSNVGKSSLINIL 49 A G S GKS+L+N+L Sbjct: 350 TALVGASGAGKSTLLNLL 367 >gnl|CDD|30834 COG0488, Uup, ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]. Length = 530 Score = 26.0 bits (57), Expect = 7.4 Identities = 8/20 (40%), Positives = 12/20 (60%) Query: 32 IAFSGRSNVGKSSLINILVN 51 IA G + GKS+L+ +L Sbjct: 351 IAIVGPNGAGKSTLLKLLAG 370 >gnl|CDD|133259 cd01850, CDC_Septin, CDC/Septin. Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis. In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments. Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities. Length = 276 Score = 26.0 bits (58), Expect = 7.7 Identities = 30/135 (22%), Positives = 44/135 (32%), Gaps = 44/135 (32%) Query: 36 GRSNVGKSSLINILVNRKNLARTSNAPGRTQ-----------HLNFFVPKDFS-NLKNNL 83 G S +GKS+ IN L N L + P + L Sbjct: 11 GESGLGKSTFINTLFN-TKLIPSDYPPDPAEEHIDKTVEIKSSKAEIEENGVKLKLT--- 66 Query: 84 PAMALVDMPGYGYARAPKKNVDSWGGLIVRYLSER--STLR------------------C 123 ++D PG+G N D W IV Y+ ++ LR C Sbjct: 67 ----VIDTPGFGDN---INNSDCWK-PIVDYIDDQFDQYLREESRIKRNPRIPDTRVHAC 118 Query: 124 VYLLIDCRHGVKQID 138 +Y + HG+K +D Sbjct: 119 LYFIEPTGHGLKPLD 133 >gnl|CDD|30190 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).. Length = 200 Score = 26.0 bits (57), Expect = 7.9 Identities = 9/21 (42%), Positives = 12/21 (57%) Query: 32 IAFSGRSNVGKSSLINILVNR 52 I F G GK++LI +L R Sbjct: 3 IVFEGIDGAGKTTLIELLAER 23 >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 = 25.9 bits (57), Expect = 7.9 Identities = 12/21 (57%), Positives = 14/21 (66%) Query: 29 PPEIAFSGRSNVGKSSLINIL 49 P +IA +G S GKSS IN L Sbjct: 35 PLKIAVTGDSGNGKSSFINAL 55 >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 = 26.1 bits (58), Expect = 8.4 Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 1/36 (2%) Query: 18 VPEIGLLPKAGPPEI-AFSGRSNVGKSSLINILVNR 52 VP + P+ PP + A G VGK++LI LV Sbjct: 27 VPVVDRTPEEPPPLVVAVVGPPGVGKTTLIKSLVKN 62 >gnl|CDD|111954 pfam03115, Astro_capsid, Astrovirus capsid protein precursor. This product is encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The 87kD precursor protein undergoes an intracellular cleavage to form a 79kD protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion. Length = 787 Score = 25.9 bits (57), Expect = 8.4 Identities = 10/38 (26%), Positives = 17/38 (44%) Query: 64 RTQHLNFFVPKDFSNLKNNLPAMALVDMPGYGYARAPK 101 RT +F+V + + +N PA+ +P R P Sbjct: 361 RTGARSFYVYASYQDALSNKPALCTGGVPAGARVREPV 398 >gnl|CDD|37866 KOG2655, KOG2655, KOG2655, Septin family protein (P-loop GTPase) [Cell cycle control, cell division, chromosome partitioning, Nuclear structure, Intracellular trafficking, secretion, and vesicular transport]. Length = 366 Score = 26.1 bits (57), Expect = 8.4 Identities = 39/174 (22%), Positives = 59/174 (33%), Gaps = 45/174 (25%) Query: 36 GRSNVGKSSLIN-----ILVNRKNLARTSNAPGRT----QHLNFFVPKDFSNLKNNLPAM 86 G S +GKS+ IN L + + S T Sbjct: 28 GESGLGKSTFINSLFLTDLSGNREVPGASERIKETVEIESTKVEIEENGVKLNLT----- 82 Query: 87 ALVDMPGYGYA-------RAPKKNVDSWGGLIVRYLSERSTLR-----------CVYLLI 128 ++D PG+G A R +DS +YL E S L C+Y + Sbjct: 83 -VIDTPGFGDAVDNSNCWRPIVNYIDS---QFDQYLDEESRLNRSKIKDNRVHCCLYFIS 138 Query: 129 DCRHGVKQIDQDVFSFLDKKAVSYQI--VLTKIDKLSPTTAQETLEKTKYLIRN 180 HG+K +D F+ K + + V+ K D L+ + L + K IR Sbjct: 139 PTGHGLKPLD---IEFMKKLSKKVNLIPVIAKADTLTK----DELNQFKKRIRQ 185 >gnl|CDD|31858 COG1672, COG1672, Predicted ATPase (AAA+ superfamily) [General function prediction only]. Length = 359 Score = 25.9 bits (56), Expect = 8.8 Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 1/39 (2%) Query: 18 VPEIGLLPKAGPPEIAF-SGRSNVGKSSLINILVNRKNL 55 + E+ + ++ PP I F GR VGK+SL+ + K Sbjct: 11 LEELLKIIESEPPSIVFIYGRRRVGKTSLLKEFIKEKLG 49 >gnl|CDD|30362 COG0012, COG0012, Predicted GTPase, probable translation factor [Translation, ribosomal structure and biogenesis]. Length = 372 Score = 25.9 bits (57), Expect = 9.1 Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 2/33 (6%) Query: 30 PEIAFSGRSNVGKSSLINILVNRKNLARTSNAP 62 +I G NVGKS+L N L K A +N P Sbjct: 3 LKIGIVGLPNVGKSTLFNALT--KAGAEIANYP 33 >gnl|CDD|33687 COG3899, COG3899, Predicted ATPase [General function prediction only]. Length = 849 Score = 25.7 bits (56), Expect = 9.2 Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 11/59 (18%) Query: 32 IAFSGRSNVGKSSLINILVNRKNLARTSNAPGRTQHLNFFVPKDFSNLKNNLPAMALVD 90 + +G S +GKS+L+N + R + F + N+P LV Sbjct: 27 VLVAGESGIGKSALVNEVHKP-------ITQQRGYFIKGK----FDQFERNIPLSPLVQ 74 >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 = 25.8 bits (57), Expect = 9.2 Identities = 7/21 (33%), Positives = 12/21 (57%) Query: 32 IAFSGRSNVGKSSLINILVNR 52 I GR+ GKS+L+ ++ Sbjct: 29 IGLVGRNGAGKSTLLKLIAGE 49 >gnl|CDD|133302 cd04102, RabL3, RabL3 (Rab-like3) subfamily. RabL3s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL3 lacks a prenylation site at the C-terminus. The specific function of RabL3 remains unknown. Length = 202 Score = 25.5 bits (56), Expect = 9.9 Identities = 11/24 (45%), Positives = 16/24 (66%) Query: 36 GRSNVGKSSLINILVNRKNLARTS 59 G S VGKSSL++++ + L R S Sbjct: 7 GDSGVGKSSLVHLICKNQVLGRPS 30 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 0.320 0.136 0.399 Gapped Lambda K H 0.267 0.0648 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,532,246 Number of extensions: 127256 Number of successful extensions: 562 Number of sequences better than 10.0: 1 Number of HSP's gapped: 535 Number of HSP's successfully gapped: 128 Length of query: 212 Length of database: 6,263,737 Length adjustment: 90 Effective length of query: 122 Effective length of database: 4,318,927 Effective search space: 526909094 Effective search space used: 526909094 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 (21.8 bits) S2: 55 (25.1 bits)