Elongation Factor 1-alpha (EF1-alpha) protein family; EF1 is responsible for the GTP-dependent binding of aminoacyl-tRNAs to the ribosomes. EF1 is composed of four subunits: the alpha chain which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This subfamily is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha interacts with the actin of the eukaryotic cytoskeleton and may thereby play a role in cellular transformation and apoptosis. EF-Tu can have no such role in bacteria. In humans, the isoform eEF1A2 is overexpressed in 2/3 of breast cancers and has been identified as a putative oncogene. This subfamily also includes Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation in yeast, and to associate with Dom34. It has been speculated that yeast Hbs1 and Dom34 proteins may function as part of a complex with a role in gene expression.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2057581928   1 FEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFIKNMITG 64
Cdd:cd01883    34 YEKEAKEMGKESFKYAWVLDKLKEERERGVTIDVGLAKFETEKYRFTIIDAPGHRDFVKNMITG 97

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2057581928   1 FEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFIKNMITG 64
Cdd:TIGR00483  42 FEKEAQEKGKASFEFAWVMDRLKEERERGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITG 105

Elongation Factor 1-alpha (EF1-alpha) protein family; EF1 is responsible for the GTP-dependent binding of aminoacyl-tRNAs to the ribosomes. EF1 is composed of four subunits: the alpha chain which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This subfamily is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha interacts with the actin of the eukaryotic cytoskeleton and may thereby play a role in cellular transformation and apoptosis. EF-Tu can have no such role in bacteria. In humans, the isoform eEF1A2 is overexpressed in 2/3 of breast cancers and has been identified as a putative oncogene. This subfamily also includes Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation in yeast, and to associate with Dom34. It has been speculated that yeast Hbs1 and Dom34 proteins may function as part of a complex with a role in gene expression.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2057581928   1 FEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFIKNMITG 64
Cdd:cd01883    34 YEKEAKEMGKESFKYAWVLDKLKEERERGVTIDVGLAKFETEKYRFTIIDAPGHRDFVKNMITG 97

elongation factor 1-alpha; Reviewed

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2057581928   1 FEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFIKNMITG 64
Cdd:PRK12317   41 LREEAKEKGKESFKFAWVMDRLKEERERGVTIDLAHKKFETDKYYFTIVDCPGHRDFVKNMITG 104

elongation factor 1-alpha; Provisional

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2057581928   1 FEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFIKNMITG 64
Cdd:PLN00043   42 FEKEAAEMNKRSFKYAWVLDKLKAERERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITG 105

GTP translation factor family primarily contains translation initiation, elongation and release factors; The GTP translation factor 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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2057581928  17 WVLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFIKNMITG 64
Cdd:cd00881    35 TFLDTLKEERERGITIKTGVVEFEWPKRRINFIDTPGHEDFSKETVRG 82

Sulfate adenylyltransferase subunit 1, EFTu-like GTPase family [Inorganic ion transport and metabolism]; Sulfate adenylyltransferase subunit 1, EFTu-like GTPase family is part of the Pathway/BioSystem: Cysteine biosynthesis

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2057581928   2 EKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFIKNMITG 64
Cdd:COG2895    53 ERDSKKRGTQEIDLALLTDGLQAEREQGITIDVAYRYFSTPKRKFIIADTPGHEQYTRNMVTG 115

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        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2057581928  11 GSFKYAWVLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFIKNMITG 64
Cdd:TIGR02034  47 GEIDLALLVDGLQAEREQGITIDVAYRYFSTDKRKFIVADTPGHEQYTRNMATG 100

sulfate adenylyltransferase subunit 1; Provisional

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2057581928  15 YAWVLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFIKNMITG 64
Cdd:PRK05124   78 LALLVDGLQAEREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATG 127

elongation factor Tu; Reviewed

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2057581928   3 KEAAELGKGSFK-YAWVlDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFIKNMITG 64
Cdd:PRK12736   34 KVLAERGLNQAKdYDSI-DAAPEEKERGITINTAHVEYETEKRHYAHVDCPGHADYVKNMITG 95

elongation factor Tu; Reviewed

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2057581928   3 KEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFIKNMITG 64
Cdd:PRK12735   34 KVLAKKGGGEAKAYDQIDNAPEEKARGITINTSHVEYETANRHYAHVDCPGHADYVKNMITG 95

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 2057581928   6 AELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFIKNMITG 64
Cdd:TIGR00485  37 AKEGGAAARAYDQIDNAPEEKARGITINTAHVEYETETRHYAHVDCPGHADYVKNMITG 95

Elongation factor Tu; Provisional

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2057581928  19 LDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFIKNMITG 64
Cdd:PLN03127   99 IDKAPEEKARGITIATAHVEYETAKRHYAHVDCPGHADYVKNMITG 144

Elongation factor Tu; Provisional

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2057581928   6 AELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFIKNMITG 64
Cdd:PLN03126  106 ASMGGSAPKKYDEIDAAPEERARGITINTATVEYETENRHYAHVDCPGHADYVKNMITG 164

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2057581928  19 LDKLKAERERGITIDIALWKFETPK--------------YSITVIDAPGHRDFIKNMITG 64
Cdd:cd01889    29 FDKNPQSQERGITLDLGFSSFEVDKpkhlednenpqienYQITLVDCPGHASLIRTIIGG 88

Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group contains both eukaryotic and bacterial members.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2057581928  18 VLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDF 57
Cdd:cd01886    38 TMDWMEQERERGITIQSAATTCFWKDHRINIIDTPGHVDF 77

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 2057581928  19 LDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFIKNM 61
Cdd:cd04168    39 TDSMELERQRGITIFSAVASFQWEDTKVNIIDTPGHMDFIAEV 81

elongation factor EF-2; Reviewed

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2057581928  18 VLDKLKAERERGITIDIA----LWKFETPKYSITVIDAPGHRDF 57
Cdd:PRK07560   57 ALDFDEEEQARGITIKAAnvsmVHEYEGKEYLINLIDTPGHVDF 100

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        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2057581928  18 VLDKLKAERERGITIdiaLWK---FETPKYSITVIDAPGHRDF------IKNMITG 64
Cdd:cd01891    39 VMDSNDLERERGITI---LAKntaITYKDTKINIIDTPGHADFggeverVLSMVDG 91

Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and activate the release of the nascent polypeptide. The class II release factor RF3 then initiates the release of the class I RF from the ribosome. RF3 binds to the RF/ribosome complex in the inactive (GDP-bound) state. GDP/GTP exchange occurs, followed by the release of the class I RF. Subsequent hydrolysis of GTP to GDP triggers the release of RF3 from the ribosome. RF3 also enhances the efficiency of class I RFs at less preferred stop codons and at stop codons in weak contexts.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2057581928   9 GKGSFKYAwVLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDF 57
Cdd:cd04169    37 ARKSRKHA-TSDWMEIEKQRGISVTSSVMQFEYKGCVINLLDTPGHEDF 84

Predicted membrane GTPase TypA/BipA involved in stress response [Signal transduction mechanisms];

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2057581928  25 ERERGITI---DIAL-WKfetpKYSITVIDAPGHRDF 57
Cdd:COG1217    50 ERERGITIlakNTAVrYK----GVKINIVDTPGHADF 82

translational GTPase TypA;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2057581928  18 VLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDF 57
Cdd:PRK10218   42 VMDSNDLEKERGITILAKNTAIKWNDYRINIVDTPGHADF 81

translation elongation factor EF-2 subunit; Provisional

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2057581928  20 DKLKAERERGITID---IALWkFETP--------------KYSITVIDAPGHRDF 57
Cdd:PLN00116   58 DTRADEAERGITIKstgISLY-YEMTdeslkdfkgerdgnEYLINLIDSPGHVDF 111

Elongation factor G (EF-G) family; Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group contains only bacterial members.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2057581928  18 VLDKLKAERERGITIDIALWKFETPKYSITVIDAPGHRDFI 58
Cdd:cd04170    38 VSDYDPEEKKRKMSIETSVAPLEWNGHKINLIDTPGYADFV 78