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
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2513084814   1 KEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFIK 57
Cdd:PTZ00141   44 KEAAEMGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYYFTIIDAPGHRDFIK 100

elongation factor 1- alpha; Provisional

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2513084814   1 KEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFIK 57
Cdd:PTZ00141   44 KEAAEMGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYYFTIIDAPGHRDFIK 100

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
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2513084814   1 KEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFIK 57
Cdd:COG5256    44 EEAEKKGKESFKFAWVMDRLKEERERGVTIDLAHKKFETDKYYFTIIDAPGHRDFVK 100

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
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2513084814   5 ELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFIK 57
Cdd:pfam00009  32 KRGEVKGEGEAGLDNLPEERERGITIKSAAVSFETKDYLINLIDTPGHVDFVK 84

elongation factor 1- alpha; Provisional

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2513084814   1 KEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFIK 57
Cdd:PTZ00141   44 KEAAEMGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYYFTIIDAPGHRDFIK 100

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
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2513084814   1 KEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFIK 57
Cdd:COG5256    44 EEAEKKGKESFKFAWVMDRLKEERERGVTIDLAHKKFETDKYYFTIIDAPGHRDFVK 100

translation elongation factor EF-1 alpha; This model represents the counterpart of bacterial EF-Tu for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1 alpha). The trusted cutoff is set fairly high so that incomplete sequences will score between suggested and trusted cutoff levels. [Protein synthesis, Translation factors]

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2513084814   1 KEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFIK 57
Cdd:TIGR00483  44 KEAQEKGKASFEFAWVMDRLKEERERGVTIDVAHWKFETDKYEVTIVDCPGHRDFIK 100

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
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2513084814   5 ELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFIK 57
Cdd:pfam00009  32 KRGEVKGEGEAGLDNLPEERERGITIKSAAVSFETKDYLINLIDTPGHVDFVK 84

CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; CysN_ATPS subfamily. CysN, together with protein CysD, form the ATP sulfurylase (ATPS) complex in some bacteria and lower eukaryotes. ATPS catalyzes the production of ATP sulfurylase (APS) and pyrophosphate (PPi) from ATP and sulfate. CysD, which catalyzes ATP hydrolysis, is a member of the ATP pyrophosphatase (ATP PPase) family. CysN hydrolysis of GTP is required for CysD hydrolysis of ATP; however, CysN hydrolysis of GTP is not dependent on CysD hydrolysis of ATP. CysN is an example of lateral gene transfer followed by acquisition of new function. In many organisms, an ATPS exists which is not GTP-dependent and shares no sequence or structural similarity to CysN.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2513084814   7 GKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFIK 57
Cdd:cd04166    43 QGEKLDLALLVDGLQAEREQGITIDVAYRYFSTPKRKFIIADTPGHEQYTR 93

sulfate adenylyltransferase, large subunit; Metabolic assimilation of sulfur from inorganic sulfate, requires sulfate activation by coupling to a nucleoside, for the production of high-energy nucleoside phosphosulfates. This pathway appears to be similar in all prokaryotic organisms. Activation is first achieved through sulfation of sulfate with ATP by sulfate adenylyltransferase (ATP sulfurylase) to produce 5'-phosphosulfate (APS), coupled by GTP hydrolysis. Subsequently, APS is phosphorylated by an APS kinase to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In Escherichia coli, ATP sulfurylase is a heterodimer composed of two subunits encoded by cysD and cysN, with APS kinase encoded by cysC. These genes are located in a unidirectionally transcribed gene cluster, and have been shown to be required for the synthesis of sulfur-containing amino acids. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules. With members of the Rhizobiaceae family, nodQ often appears as a fusion of cysN (large subunit of ATP sulfurase) and cysC (APS kinase). [Central intermediary metabolism, Sulfur metabolism]

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2513084814   9 GSFKYAWVLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGH 52
Cdd:TIGR02034  47 GEIDLALLVDGLQAEREQGITIDVAYRYFSTDKRKFIVADTPGH 90

Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis]; Translation elongation factor EF-Tu, a GTPase is part of the Pathway/BioSystem: Translation factors

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2513084814   4 AELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFIK 57
Cdd:COG0050    37 AKKGGAKAKAYDQIDKAPEEKERGITINTSHVEYETEKRHYAHVDCPGHADYVK 90

elongation factor Tu; Reviewed

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2513084814   1 KEAAELGKGSFK-YAWVlDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFIK 57
Cdd:PRK12736   34 KVLAERGLNQAKdYDSI-DAAPEEKERGITINTAHVEYETEKRHYAHVDCPGHADYVK 90

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
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2513084814   4 AELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFIK 57
Cdd:TIGR00485  37 AKEGGAAARAYDQIDNAPEEKARGITINTAHVEYETETRHYAHVDCPGHADYVK 90

Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure and biogenesis]; Selenocysteine-specific translation elongation factor SelB is part of the Pathway/BioSystem: Translation factors

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2513084814  18 DKLKAERERGITIDIALWKFETPKYY-VTVIDAPGHRDFIK 57
Cdd:COG3276    26 DRLKEEKKRGITIDLGFAYLPLPDGRrLGFVDVPGHEKFIK 66

Elongation Factor Tu (EF-Tu) GTP-binding proteins; EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors. The eukaryotic counterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this family. 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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2513084814   4 AELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFIK 57
Cdd:cd01884    27 AKKGGAKAKKYDEIDKAPEEKARGITINTAHVEYETANRHYAHVDCPGHADYIK 80

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
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2513084814  17 LDKLKAERERGITIDIALWKFETPK--------------YYVTVIDAPGHRDFIK 57
Cdd:cd01889    29 FDKNPQSQERGITLDLGFSSFEVDKpkhlednenpqienYQITLVDCPGHASLIR 83

Tet(M)-like family includes Tet(M), Tet(O), Tet(W), and OtrA, containing tetracycline resistant proteins; Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria. Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site. This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are typically found on mobile genetic elements, such as transposons or plasmids, and are often conjugative. Ribosomal protection proteins are homologous to the elongation factors EF-Tu and EF-G. EF-G and Tet(M) compete for binding on the ribosomes. Tet(M) has a higher affinity than EF-G, suggesting these two proteins may have overlapping binding sites and that Tet(M) must be released before EF-G can bind. Tet(M) and Tet(O) have been shown to have ribosome-dependent GTPase activity. These proteins are part of the GTP translation factor family, which includes EF-G, EF-Tu, EF2, LepA, and SelB.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2513084814  17 LDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFI 56
Cdd:cd04168    39 TDSMELERQRGITIFSAVASFQWEDTKVNIIDTPGHMDFI 78

Elongation factor Tu; Provisional

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2513084814  17 LDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFIK 57
Cdd:PLN03127   99 IDKAPEEKARGITIATAHVEYETAKRHYAHVDCPGHADYVK 139

elongation factor EF-2; Reviewed

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2513084814  16 VLDKLKAERERGITIDIA----LWKFETPKYYVTVIDAPGHRDF 55
Cdd:PRK07560   57 ALDFDEEEQARGITIKAAnvsmVHEYEGKEYLINLIDTPGHVDF 100

Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]; Translation elongation factor EF-G, a GTPase is part of the Pathway/BioSystem: Translation factors

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2513084814  16 VLDKLKAERERGITIDIAL----WKfetpKYYVTVIDAPGHRDFI 56
Cdd:COG0480    48 VMDWMPEEQERGITITSAAttceWK----GHKINIIDTPGHVDFT 88

elongation factor G-like protein EF-G2;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2513084814  16 VLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFI 56
Cdd:PRK12740   34 TMDFMPEERERGISITSAATTCEWKGHKINLIDTPGHVDFT 74

Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella typhimurium after exposure to bactericidal/permeability-inducing protein (a cationic antimicrobial protein produced by neutrophils), and has since been identified in E. coli as well. The properties thus far described for BipA are related to its role in the process of pathogenesis by enteropathogenic E. coli. It appears to be involved in the regulation of several processes important for infection, including rearrangements of the cytoskeleton of the host, bacterial resistance to host defense peptides, flagellum-mediated cell motility, and expression of K5 capsular genes. It has been proposed that BipA may utilize a novel mechanism to regulate the expression of target genes. In addition, BipA from enteropathogenic E. coli has been shown to be phosphorylated on a tyrosine residue, while BipA from Salmonella and from E. coli K12 strains is not phosphorylated under the conditions assayed. The phosphorylation apparently modifies the rate of nucleotide hydrolysis, with the phosphorylated form showing greatly increased GTPase activity.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2513084814  16 VLDKLKAERERGITIdiaLWK---FETPKYYVTVIDAPGHRDF 55
Cdd:cd01891    39 VMDSNDLERERGITI---LAKntaITYKDTKINIIDTPGHADF 78

elongation factor G-like protein;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2513084814  16 VLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDF 55
Cdd:PRK13351   47 VTDWMPQEQERGITIESAATSCDWDNHRINLIDTPGHIDF 86

translational GTPase TypA;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2513084814  16 VLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDF 55
Cdd:PRK10218   42 VMDSNDLEKERGITILAKNTAIKWNDYRINIVDTPGHADF 81

translation elongation factor EF-2 subunit; Provisional

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2513084814  18 DKLKAERERGITID---IALWkFETP--------------KYYVTVIDAPGHRDF 55
Cdd:PLN00116   58 DTRADEAERGITIKstgISLY-YEMTdeslkdfkgerdgnEYLINLIDSPGHVDF 111