P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   1 MMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDLLAEGKRQAAIDKMTKKMQKTLENTKFRGAPIIPVAAKPGGPE 80
Cdd:cd01889    95 MLLVVDAKKGIQTQTAECLVIGELLCKPLIVVLNKIDLIPEEERKRKIEKMKKRLQKTLEKTRLKDSPIIPVSAKPGEGE 174

                          90
                  ....*....|....*....
gi 2289442679  81 ApetEAPQGISELIELLKS 99
Cdd:cd01889   175 A---ELGGELKNLIVLPLI 190

SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; 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 eukaryotic SelBs and some from archaea.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   1 MMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDLLAEGKRQAAIDKMTKKMQKTLENTKFRGAPIIPVAAKPGGPE 80
Cdd:cd01889    95 MLLVVDAKKGIQTQTAECLVIGELLCKPLIVVLNKIDLIPEEERKRKIEKMKKRLQKTLEKTRLKDSPIIPVSAKPGEGE 174

                          90
                  ....*....|....*....
gi 2289442679  81 ApetEAPQGISELIELLKS 99
Cdd:cd01889   175 A---ELGGELKNLIVLPLI 190

selenocysteine-specific elongation factor SelB; In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes. [Protein synthesis, Translation factors]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   2 MLVIDVTKGMQTQSAECL-VIGQIACQKLVVVLNKIDLLAEgkrqAAIDKMTKKMQKTLENTKF-RGAPIIPVAAKPGgp 79
Cdd:TIGR00475  78 LLVVDADEGVMTQTGEHLaVLDLLGIPHTIVVITKADRVNE----EEIKRTEMFMKQILNSYIFlKNAKIFKTSAKTG-- 151

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2289442679  80 eapeteapQGISELIELLKSQI-SIPTRDPSGPFLMSVDHCFSIKGQGTVMTGTILSGTISLGDSVEI 146
Cdd:TIGR00475 152 --------QGIGELKKELKNLLeSLDIKRIQKPLRMAIDRAFKVKGAGTVVTGTAFSGEVKVGDNLRL 211

Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor SelB that is homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2289442679 112 FLMSVDHCFSIKGQGTVMTGTILSGTISLGDSVEIPALKVM 152
Cdd:cd03696     1 FRLPIDHVFSIKGAGTVVTGTVLSGKVKVGDELEIPPLGKE 41

SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; 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 eukaryotic SelBs and some from archaea.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   1 MMLVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDLLAEGKRQAAIDKMTKKMQKTLENTKFRGAPIIPVAAKPGGPE 80
Cdd:cd01889    95 MLLVVDAKKGIQTQTAECLVIGELLCKPLIVVLNKIDLIPEEERKRKIEKMKKRLQKTLEKTRLKDSPIIPVSAKPGEGE 174

                          90
                  ....*....|....*....
gi 2289442679  81 ApetEAPQGISELIELLKS 99
Cdd:cd01889   175 A---ELGGELKNLIVLPLI 190

selenocysteine-specific elongation factor SelB; In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes. [Protein synthesis, Translation factors]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   2 MLVIDVTKGMQTQSAECL-VIGQIACQKLVVVLNKIDLLAEgkrqAAIDKMTKKMQKTLENTKF-RGAPIIPVAAKPGgp 79
Cdd:TIGR00475  78 LLVVDADEGVMTQTGEHLaVLDLLGIPHTIVVITKADRVNE----EEIKRTEMFMKQILNSYIFlKNAKIFKTSAKTG-- 151

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2289442679  80 eapeteapQGISELIELLKSQI-SIPTRDPSGPFLMSVDHCFSIKGQGTVMTGTILSGTISLGDSVEI 146
Cdd:TIGR00475 152 --------QGIGELKKELKNLLeSLDIKRIQKPLRMAIDRAFKVKGAGTVVTGTAFSGEVKVGDNLRL 211

translation elongation factor TU; This model models orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts, one of several GTP-binding translation factors found by the more general pfam model GTP_EFTU. The eukaryotic conterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this model. EF-Tu is one of the most abundant proteins in bacteria, as well as one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation. [Protein synthesis, Translation factors]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   2 MLVIDVTKGMQTQSAECLVIG-QIACQKLVVVLNKIDLLAEgkrQAAIDKMTKKMQKTLENTKFRG--APIIPVAAKPGG 78
Cdd:TIGR00485 103 ILVVSATDGPMPQTREHILLArQVGVPYIVVFLNKCDMVDD---EELLELVEMEVRELLSQYDFPGddTPIIRGSALKAL 179

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679  79 PEAPETEAPqgISELIELLKSQISIPTRDPSGPFLMSVDHCFSIKGQGTVMTGTILSGTISLGDSVEIPALKVMDDYSVI 158
Cdd:TIGR00485 180 EGDAEWEAK--ILELMDAVDEYIPTPEREIDKPFLLPIEDVFSITGRGTVVTGRVERGIIKVGEEVEIVGLKDTRKTTVT 257

                  ....*...
gi 2289442679 159 GRSLFKKE 166
Cdd:TIGR00485 258 GVEMFRKE 265

Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor SelB that is homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2289442679 112 FLMSVDHCFSIKGQGTVMTGTILSGTISLGDSVEIPALKVM 152
Cdd:cd03696     1 FRLPIDHVFSIKGAGTVVTGTVLSGKVKVGDELEIPPLGKE 41

elongation factor Tu; Reviewed

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   3 LVIDVTKGMQTQSAE-CLVIGQIACQKLVVVLNKIDLL--AEgkrqaAIDKMTKKMQKTLENTKFRG--APIIPVAAKPG 77
Cdd:PRK12735  104 LVVSAADGPMPQTREhILLARQVGVPYIVVFLNKCDMVddEE-----LLELVEMEVRELLSKYDFPGddTPIIRGSALKA 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679  78 GPEAPETEAPQGISELIELLKSQISIPTRDPSGPFLMSVDHCFSIKGQGTVMTGTILSGTISLGDSVEIPALKVMDDYSV 157
Cdd:PRK12735  179 LEGDDDEEWEAKILELMDAVDSYIPEPERAIDKPFLMPIEDVFSISGRGTVVTGRVERGIVKVGDEVEIVGIKETQKTTV 258

                  ....*....
gi 2289442679 158 IGRSLFKKE 166
Cdd:PRK12735  259 TGVEMFRKL 267

elongation factor Tu; Reviewed

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   3 LVIDVTKGMQTQSAE-CLVIGQIACQKLVVVLNKIDLLAEgkrQAAIDKMTKKMQKTLENTKFRG--APIIPVAAKP--- 76
Cdd:PRK00049  104 LVVSAADGPMPQTREhILLARQVGVPYIVVFLNKCDMVDD---EELLELVEMEVRELLSKYDFPGddTPIIRGSALKale 180

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679  77 GGPEAPETEApqgISELIELLKSQISIPTRDPSGPFLMSVDHCFSIKGQGTVMTGTILSGTISLGDSVEIPALKVMDDYS 156
Cdd:PRK00049  181 GDDDEEWEKK---ILELMDAVDSYIPTPERAIDKPFLMPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIRDTQKTT 257

                  ....*....
gi 2289442679 157 VIGRSLFKK 165
Cdd:PRK00049  258 VTGVEMFRK 266

Elongation factor Tu; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   2 MLVIDVTKGMQTQSAE-CLVIGQIACQKLVVVLNKIDLLAEGKRQAAIDKMTKKMqktLENTKFRG--APIIP------V 72
Cdd:PLN03126  172 ILVVSGADGPMPQTKEhILLAKQVGVPNMVVFLNKQDQVDDEELLELVELEVREL---LSSYEFPGddIPIISgsallaL 248

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679  73 AAKPGGPEAP--ETEAPQGISELIELLKSQISIPTRDPSGPFLMSVDHCFSIKGQGTVMTGTILSGTISLGDSVEIPALK 150
Cdd:PLN03126  249 EALMENPNIKrgDNKWVDKIYELMDAVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVERGTVKVGETVDIVGLR 328

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679 151 VMDDYSVIGRSLFKKETNIQLF---VGL---KVQLSTGEQGIIDSAfgqsgkfkihiPGGLSPESKKILTPTLKKRSRAG 224
Cdd:PLN03126  329 ETRSTTVTGVEMFQKILDEALAgdnVGLllrGIQKADIQRGMVLAK-----------PGSITPHTKFEAIVYVLKKEEGG 397

                  .
gi 2289442679 225 R 225
Cdd:PLN03126  398 R 398

eukaryotic translation initiation factor 2 gamma subunit; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679  12 QTQSAECLVIGQIACQKLVVVL-NKIDLLaegKRQAAIDKMtKKMQKTLENTKFRGAPIIPVAAKPGgpeapeteapQGI 90
Cdd:PTZ00327  156 QPQTSEHLAAVEIMKLKHIIILqNKIDLV---KEAQAQDQY-EEIRNFVKGTIADNAPIIPISAQLK----------YNI 221

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2289442679  91 SELIELLKSQISIPTRDPSGPFLMSVDHCFSIKG--------QGTVMTGTILSGTISLGDSVEI-PALKVMDD 154
Cdd:PTZ00327  222 DVVLEYICTQIPIPKRDLTSPPRMIVIRSFDVNKpgedienlKGGVAGGSILQGVLKVGDEIEIrPGIISKDS 294

SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   1 MMLVIDVTKGMQTQSAECLVIGQI-ACQKLVVVLNKIDLLAEgkrqAAIDKMTKKMQKTLENTKFRGAPIIPVAAKPGgp 79
Cdd:cd04171    77 VLLVVAADEGIMPQTREHLEILELlGIKKGLVVLTKADLVDE----DRLELVEEEILELLAGTFLADAPIFPVSSVTG-- 150

                          90       100
                  ....*....|....*....|
gi 2289442679  80 eapeteapQGISELIELLKS 99
Cdd:cd04171   151 --------EGIEELKNYLDE 162

Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]; Translation elongation factor EF-1alpha (GTPase) is part of the Pathway/BioSystem: Translation factors

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   2 MLVIDVTKGMQTQSAE------CLVIGQIacqklVVVLNKIDLLA-EGKRQAAIDKMTKKMQKTLeNTKFRGAPIIPVAA 74
Cdd:COG5256   113 ILVVSAKDGVMGQTREhaflarTLGINQL-----IVAVNKMDAVNySEKRYEEVKEEVSKLLKMV-GYKVDKIPFIPVSA 186

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2289442679  75 KPG------GPEAPETEAPQgiseLIELLkSQISIPTRDPSGPFLMSVDHCFSIKGQGTVMTGTILSGTISLGDSV 144
Cdd:COG5256   187 WKGdnvvkkSDNMPWYNGPT----LLEAL-DNLKEPEKPVDKPLRIPIQDVYSISGIGTVPVGRVETGVLKVGDKV 257

Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   3 LVIDVTKGMQTQSAECLVIGQIACQKLVVVLNKIDLLaeGKRQAAIDKMTKKMQKTLENTK-FRG-APIIPVAAKPGgpe 80
Cdd:cd01887    78 LVVAADDGVMPQTIEAINHAKAANVPIIVAINKIDKP--YGTEADPERVKNELSELGLVGEeWGGdVSIVPISAKTG--- 152

                          90
                  ....*....|....*..
gi 2289442679  81 apeteapQGISELIELL 97
Cdd:cd01887   153 -------EGIDDLLEAI 162

Gamma subunit of initiation factor 2 (eIF2 gamma); 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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2289442679  12 QTQSAECLV-IGQIACQKLVVVLNKIDLLaegKRQAAIDKMtKKMQKTLENTKFRGAPIIPVAAK 75
Cdd:cd01888   116 QPQTSEHLAaLEIMGLKHIIILQNKIDLV---KEEQALENY-EQIKEFVKGTIAENAPIIPISAQ 176

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   3 LVIDVTKGMQTQSAEclVIGQIACQ--KLVVVLNKIDLLAEGKRQAAIDKMTKK-MQKTLENTKFRgaPIIPVAAKPGgp 79
Cdd:pfam00009  98 LVVDAVEGVMPQTRE--HLRLARQLgvPIIVFINKMDRVDGAELEEVVEEVSRElLEKYGEDGEFV--PVVPGSALKG-- 171

                          90
                  ....*....|....*...
gi 2289442679  80 eapeteapQGISELIELL 97
Cdd:pfam00009 172 --------EGVQTLLDAL 181

Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); 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 regulates 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   1 MMLVIDVTKGMQTQSAECLVIGQIACQK--LVVVLNKIDLLAEGKRQAAIDKMTKKmqktlentKFRGAPIIPVAAKPGg 78
Cdd:cd00882    79 ILLVVDSTDRESEEDAKLLILRRLRKEGipIILVGNKIDLLEEREVEELLRLEELA--------KILGVPVFEVSAKTG- 149

                          90
                  ....*....|....*....
gi 2289442679  79 peapeteapQGISELIELL 97
Cdd:cd00882   150 ---------EGVDELFEKL 159

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 2289442679   3 LVIDVTKGmQTQSAECLVIGQIACQKLVVVLNKIDLLaegkrqaaidkmtkkmQKTLENTKFRGAPIIPVAAKPGgpeap 82
Cdd:pfam12631 179 LVLDASRP-LDEEDLEILELLKDKKPIIVVLNKSDLL----------------GEIDELEELKGKPVLAISAKTG----- 236

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2289442679  83 eteapQGISELIELLKSQISIPTRDPSGPFLMSVDH 118
Cdd:pfam12631 237 -----EGLDELEEAIKELFLAGEIASDGPIITNARH 267

GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   2 MLVIDVTKGMQTQSAEclVIGQIACQK--LVVVLNKIDLLAEGKRQAAIDKMTKKMqktlentKFrgAPIIPVAAKPGgp 79
Cdd:COG1159    87 LFVVDATEKIGEGDEF--ILELLKKLKtpVILVINKIDLVKKEELLPLLAEYSELL-------DF--AEIVPISALKG-- 153

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2289442679  80 eapeteapQGISELIELLKSQIsiptrdPSGPFL 113
Cdd:COG1159   154 --------DNVDELLDEIAKLL------PEGPPY 173

Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; YjeQ (YloQ in Bacillus subtilis) is a ribosomal small subunit-dependent GTPase; hence also known as RsgA. YjeQ is a late-stage ribosomal biogenesis factor involved in the 30S subunit maturation, and it 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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2289442679  30 VVVLNKIDLLAEGKRQAAIDKMTKkmqktlentkfRGAPIIPVAAKpggpeapeteAPQGISELIELLKSQISI 103
Cdd:cd01854    37 VIVLNKADLVDDEELEELLEIYEK-----------LGYPVLAVSAK----------TGEGLDELRELLKGKTSV 89

GTP-binding protein Der; Reviewed

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   3 LVIDVTKGMQTQSAecLVIGQIACQK--LVVVLNKIDLLAEGKRQAAIDKMTKKMQktlentKFRGAPIIPVAAKPGgpe 80
Cdd:PRK00093  261 LVIDATEGITEQDL--RIAGLALEAGraLVIVVNKWDLVDEKTMEEFKKELRRRLP------FLDYAPIVFISALTG--- 329

                          90
                  ....*....|....*.
gi 2289442679  81 apeteapQGISELIEL 96
Cdd:PRK00093  330 -------QGVDKLLEA 338

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2289442679   3 LVIDVTKGMQTQS-AEClvigQIACQ---KLVVVLNKIDLLAegkrqAAIDKMTKKMQKTLentkfrGAP---IIPVAAK 75
Cdd:cd01890    96 LVVDATQGVEAQTlANF----YLALEnnlEIIPVINKIDLPA-----ADPDRVKQEIEDVL------GLDaseAILVSAK 160

                          90       100
                  ....*....|....*....|....*....
gi 2289442679  76 PGgpeapeteapQGISELIELLKSQISIP 104
Cdd:cd01890   161 TG----------LGVEDLLEAIVERIPPP 179

Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The dynamin family of large mechanochemical GTPases includes the classical dynamins and dynamin-like proteins (DLPs) that are found throughout the Eukarya. This family also includes bacterial DLPs. These proteins catalyze membrane fission during clathrin-mediated endocytosis. Dynamin consists of five domains; an N-terminal G domain that binds and hydrolyzes GTP, a middle domain (MD) involved in self-assembly and oligomerization, a pleckstrin homology (PH) domain responsible for interactions with the plasma membrane, GED, which is also involved in self-assembly, and a proline arginine rich domain (PRD) that interacts with SH3 domains on accessory proteins. To date, three vertebrate dynamin genes have been identified; dynamin 1, which is brain specific, mediates uptake of synaptic vesicles in presynaptic terminals; dynamin-2 is expressed ubiquitously and similarly participates in membrane fission; mutations in the MD, PH and GED domains of dynamin 2 have been linked to human diseases such as Charcot-Marie-Tooth peripheral neuropathy and rare forms of centronuclear myopathy. Dynamin 3 participates in megakaryocyte progenitor amplification, and is also involved in cytoplasmic enlargement and the formation of the demarcation membrane system. This family also includes mitofusins (MFN1 and MFN2 in mammals) that are involved in mitochondrial fusion. Dynamin oligomerizes into helical structures around the neck of budding vesicles in a GTP hydrolysis-dependent manner.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2289442679  28 KLVVVLNKIDLLAEGKRQAAIDKMTKKMQKTLENTKFrgAPIIPVAAKPG----GPEAPETEAPQGISELIELLKSQI 101
Cdd:cd09912   105 KIFFVLNKIDLLSEEELEEVLEYSREELGVLELGGGE--PRIFPVSAKEAlearLQGDEELLEQSGFEELEEHLEEFL 180