GTPase CgtA; Reviewed

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907141399 117 VADIPGIIRGAHQNKGLGLSFLRHIERCRFFLFVVDLTLPE---PWTQVDDLKYELEKFEEGLSERSHVIIANKIDLPQA 193
Cdd:PRK12297  210 MADIPGLIEGASEGVGLGHQFLRHIERTRVIVHVIDMSGSEgrdPIEDYEKINKELKLYNPRLLERPQIVVANKMDLPEA 289

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1907141399 194 RARLPQLQARLGQEAIGLSALTGENLEQLLLHLKELHDAHIEAELEQ 240
Cdd:PRK12297  290 EENLEEFKEKLGPKVFPISALTGQGLDELLYAVAELLEETPEFPLEE 336

Obg family GTPase CgtA; This model describes a univeral, mostly one-gene-per-genome GTP-binding protein that associates with ribosomal subunits and appears to play a role in ribosomal RNA maturation. This GTPase, related to the nucleolar protein Obg, is designated CgtA in bacteria. Mutations in this gene are pleiotropic, but it appears that effects on cellular functions such as chromosome partition may be secondary to the effect on ribosome structure. Recent work done in Vibrio cholerae shows an essential role in the stringent response, in which RelA-dependent ability to synthesize the alarmone ppGpp is required for deletion of this GTPase to be lethal. [Protein synthesis, Other]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907141399 117 VADIPGIIRGAHQNKGLGLSFLRHIERCRFFLFVVDLTLPEPWTQVDDLKY---ELEKFEEGLSERSHVIIANKIDLP-- 191
Cdd:TIGR02729 209 IADIPGLIEGASEGAGLGHRFLKHIERTRVLLHLIDISPEDGSDPVEDYEIirnELKKYSPELAEKPRIVVLNKIDLLde 288

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1907141399 192 -QARARLPQLQARLGQEAIGLSALTGENLEQLLLHLKEL 229
Cdd:TIGR02729 289 eELEELLKELKKELGKPVFPISALTGEGLDELLDALAEL 327

GTPase CgtA; Reviewed

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907141399 117 VADIPGIIRGAHQNKGLGLSFLRHIERCRFFLFVVDLTLPE---PWTQVDDLKYELEKFEEGLSERSHVIIANKIDLPQA 193
Cdd:PRK12297  210 MADIPGLIEGASEGVGLGHQFLRHIERTRVIVHVIDMSGSEgrdPIEDYEKINKELKLYNPRLLERPQIVVANKMDLPEA 289

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1907141399 194 RARLPQLQARLGQEAIGLSALTGENLEQLLLHLKELHDAHIEAELEQ 240
Cdd:PRK12297  290 EENLEEFKEKLGPKVFPISALTGQGLDELLYAVAELLEETPEFPLEE 336

Obg family GTPase CgtA; This model describes a univeral, mostly one-gene-per-genome GTP-binding protein that associates with ribosomal subunits and appears to play a role in ribosomal RNA maturation. This GTPase, related to the nucleolar protein Obg, is designated CgtA in bacteria. Mutations in this gene are pleiotropic, but it appears that effects on cellular functions such as chromosome partition may be secondary to the effect on ribosome structure. Recent work done in Vibrio cholerae shows an essential role in the stringent response, in which RelA-dependent ability to synthesize the alarmone ppGpp is required for deletion of this GTPase to be lethal. [Protein synthesis, Other]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907141399 117 VADIPGIIRGAHQNKGLGLSFLRHIERCRFFLFVVDLTLPEPWTQVDDLKY---ELEKFEEGLSERSHVIIANKIDLP-- 191
Cdd:TIGR02729 209 IADIPGLIEGASEGAGLGHRFLKHIERTRVLLHLIDISPEDGSDPVEDYEIirnELKKYSPELAEKPRIVVLNKIDLLde 288

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1907141399 192 -QARARLPQLQARLGQEAIGLSALTGENLEQLLLHLKEL 229
Cdd:TIGR02729 289 eELEELLKELKKELGKPVFPISALTGEGLDELLDALAEL 327

GTPase CgtA; Reviewed

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907141399 117 VADIPGIIRGAHQNKGLGLSFLRHIERCRFFLFVVDLTlpePWTQVDDLK------YELEKFEEGLSERSHVIIANKIDL 190
Cdd:PRK12298  211 VADIPGLIEGASEGAGLGIRFLKHLERCRVLLHLIDIA---PIDGSDPVEnariiiNELEKYSPKLAEKPRWLVFNKIDL 287

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907141399 191 ---PQARARLPQLQARLGQEA--IGLSALTGENLEQLLLHLKELHDAHIEAELEQGRQP 244
Cdd:PRK12298  288 ldeEEAEERAKAIVEALGWEGpvYLISAASGLGVKELCWDLMTFIEENPREEAEEAEAP 346

Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1; 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907141399 116 RVADIPGIIRGAHQNKGLGLSFLRHIERCRFFLFVVDLTLPEPWTQVDDLK---YELEKFEEGLSERSHVIIANKIDLPQ 192
Cdd:cd01881    48 QIIDLPGLLDGASEGRGLGEQILAHLYRSDLILHVIDASEDCVGDPLEDQKtlnEEVSGSFLFLKNKPEMIVANKIDMAS 127

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1907141399 193 AR--ARLPQLQARLGQEAIGLSALTGENLEQLL 223
Cdd:cd01881   128 ENnlKRLKLDKLKRGIPVVPTSALTRLGLDRVI 160

E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngB), 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907141399 119 DIPGIIRGAHQNKGLGLSFLRHIERCRFFLFVVDLTLPEpwtqvDDLKYELEKFEEglSERSHVIIANKIDLPQARARL- 197
Cdd:cd00880    52 DTPGLDEEGGLGRERVEEARQVADRADLVLLVVDSDLTP-----VEEEAKLGLLRE--RGKPVLLVLNKIDLVPESEEEe 124

                          90       100       110
                  ....*....|....*....|....*....|
gi 1907141399 198 ----PQLQARLGQEAIGLSALTGENLEQLL 223
Cdd:cd00880   125 llreRKLELLPDLPVIAVSALPGEGIDELR 154

tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal structure and biogenesis]; tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE is part of the Pathway/BioSystem: tRNA modification

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907141399 138 LRHIERCRFFLFVVDLTlpEPWTQVDdlkyelEKFEEGLSERSHVIIANKIDLPQARARlpQLQARLGQEAIGLSALTGE 217
Cdd:COG0486   287 REAIEEADLVLLLLDAS--EPLTEED------EEILEKLKDKPVIVVLNKIDLPSEADG--ELKSLPGEPVIAISAKTGE 356

                          90
                  ....*....|..
gi 1907141399 218 NLEQLLLHLKEL 229
Cdd:COG0486   357 GIDELKEAILEL 368

trmE is a tRNA modification GTPase; 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907141399 148 LFVVDLTlpEPWTQVDDLKYELekfeegLSERSHVIIANKIDLPQARARLPQLqarLGQEAIGLSALTGENLEQLLLHLK 227
Cdd:cd04164    87 LLVVDAS--EGLDEEDLEILEL------PAKKPVIVVLNKSDLLSDAEGISEL---NGKPIIAISAKTGEGIDELKEALL 155

                  ..
gi 1907141399 228 EL 229
Cdd:cd04164   156 EL 157

MnmE helical domain; The tRNA modification GTPase MnmE consists of three domains. An N-terminal domain, a helical domain and a GTPase domain which is nested within the helical domain. This family represents the helical domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907141399 138 LRHIERCRFFLFVVDLTlpEPWTQVDdlkyelEKFEEGLSERSHVI-IANKIDLPQArarLPQLQARLGQEAIGLSALTG 216
Cdd:pfam12631 168 REAIEEADLVLLVLDAS--RPLDEED------LEILELLKDKKPIIvVLNKSDLLGE---IDELEELKGKPVLAISAKTG 236

                          90
                  ....*....|...
gi 1907141399 217 ENLEQLLLHLKEL 229
Cdd:pfam12631 237 EGLDELEEAIKEL 249

ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907141399 148 LFVVDLTLPEpwtQVDDLKYELEKF--EEGLSERSHVIIANKIDLPQARaRLPQLQARLGQEAI--------GLSALTGE 217
Cdd:cd00878    71 IFVVDSSDRE---RIEEAKNELHKLlnEEELKGAPLLILANKQDLPGAL-TESELIELLGLESIkgrrwhiqPCSAVTGD 146

                  ....*.
gi 1907141399 218 NLEQLL 223
Cdd:cd00878   147 GLDEGL 152

GTPase Era; Reviewed

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907141399 148 LFVVDLTlpEPWTQVDdlKYELEKFEEglSERSHVIIANKIDLPQARARLPQLQARLGQ-----EAIGLSALTGENLEQL 222
Cdd:PRK00089   89 LFVVDAD--EKIGPGD--EFILEKLKK--VKTPVILVLNKIDLVKDKEELLPLLEELSElmdfaEIVPISALKGDNVDEL 162

                  ....*..
gi 1907141399 223 LLHLKEL 229
Cdd:PRK00089  163 LDVIAKY 169

E. coli Ras-like protein (Era) is a multifunctional GTPase; 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907141399 119 DIPGIIrgaHQNKGLGLSFLRH----IERCRFFLFVVDLTlpEPWTqvDDLKYELEKFEEglSERSHVIIANKIDLPQAR 194
Cdd:cd04163    57 DTPGIH---KPKKKLGERMVKAawsaLKDVDLVLFVVDAS--EWIG--EGDEFILELLKK--SKTPVILVLNKIDLVKDK 127

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1907141399 195 ARLPQLQARL-----GQEAIGLSALTGENLEQLLLHLKEL 229
Cdd:cd04163   128 EDLLPLLEKLkelhpFAEIFPISALKGENVDELLEYIVEY 167

HflX GTPase family; 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907141399 148 LFVVDLTLPEPWTQVDDLKYELEkfEEGLSERSHVIIANKIDLPQARARLPQLQARLGqEAIGLSALTGENLEQLLLHLK 227
Cdd:cd01878   125 LHVVDASDPDREEQIETVEEVLK--ELGADDIPIILVLNKIDLLDDEELEERLRAGRP-DAVFISAKTGEGLDLLKEAIE 201

                  ..
gi 1907141399 228 EL 229
Cdd:cd01878   202 EL 203

GTPase RsgA; Reviewed

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907141399 182 VIIANKIDL----PQARARLpQLQARLGQEAIGLSALTGENLEQLLLHLKE 228
Cdd:PRK00098  115 IIVLNKIDLlddlEEARELL-ALYRAIGYDVLELSAKEGEGLDELKPLLAG 164

Rab GTPase family 28 (Rab28); Rab28 subfamily. First identified in maize, Rab28 has been shown to be a late embryogenesis-abundant (Lea) protein that is regulated by the plant hormone abcisic acid (ABA). In Arabidopsis, Rab28 is expressed during embryo development and is generally restricted to provascular tissues in mature embryos. Unlike maize Rab28, it is not ABA-inducible. Characterization of the human Rab28 homolog revealed two isoforms, which differ by a 95-base pair insertion, producing an alternative sequence for the 30 amino acids at the C-terminus. The two human isoforms are presumably the result of alternative splicing. Since they differ at the C-terminus but not in the GTP-binding region, they are predicted to be targeted to different cellular locations. 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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907141399 148 LFVVDLTLPEPWTQVDDLKYELEK-FEEGLSERSHVIIANKIDLPQARARLPQLQARLGQE----AIGLSALTGE 217
Cdd:cd04109    78 CLVYDITNSQSFENLEDWLSVVKKvNEESETKPKMVLVGNKTDLEHNRQVTAEKHARFAQEndmeSIFVSAKTGD 152

LepA also known as Elongation Factor 4 (EF4); LepA (also known as elongation factor 4, EF4) belongs to the GTPase family and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and eukaryota (e.g. yeast GUF1p), but is missing from archaea. This pattern of phyletic distribution suggests that LepA evolved through a duplication of the EF-G gene in bacteria, followed by early transfer into the eukaryotic lineage, most likely from the promitochondrial endosymbiont. Yeast GUF1p is not essential and mutant cells did not reveal any marked phenotype.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907141399 178 ERSHVIIA--NKIDLPQA---RARLpQLQARLG---QEAIGLSALTGENLEQLL 223
Cdd:cd01890   117 ENNLEIIPviNKIDLPAAdpdRVKQ-EIEDVLGldaSEAILVSAKTGLGVEDLL 169