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Conserved domains on  [gi|1609542363|gb|QBY35202|]
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elongation factor 1-alpha, partial [Trachymyrmex nogalensis]

Protein Classification

P-loop NTPase family protein( domain architecture ID 1562424)

P-loop NTPase (nucleoside triphosphate hydrolase) family protein contains two conserved sequence signatures, the Walker A motif (the P-loop proper) and Walker B motif which bind, respectively, the beta and gamma phosphate moieties of the bound nucleotide (typically ATP or GTP), and a Mg(2+) cation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 1-125 2.49e-85

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.


The actual alignment was detected with superfamily member PTZ00141:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 446  Bit Score: 255.44  E-value: 2.49e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609542363   1 ALTTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNQPPRGAADFTAQVIVLNHPGQISNGYTPVLDC 80
Cdd:PTZ00141  272 GVTTEVKSVEMHHEQLAEAVPGDNVGFNVKNVSVKDIKRGYVASDSKNDPAKECADFTAQVIVLNHPGQIKNGYTPVLDC 351

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1609542363  81 HTAHIACKFAEIKEKCDRRTGKTTEENPKGIKSGDAAIVMLQPTK 125
Cdd:PTZ00141  352 HTAHIACKFAEIESKIDRRSGKVLEENPKAIKSGDAAIVKMVPTK 396
 
Name Accession Description Interval E-value
PTZ00141 PTZ00141
elongation factor 1- alpha; Provisional
 1-125 2.49e-85

elongation factor 1- alpha; Provisional


Pssm-ID: 185474 [Multi-domain]  Cd Length: 446  Bit Score: 255.44  E-value: 2.49e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609542363   1 ALTTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNQPPRGAADFTAQVIVLNHPGQISNGYTPVLDC 80
Cdd:PTZ00141  272 GVTTEVKSVEMHHEQLAEAVPGDNVGFNVKNVSVKDIKRGYVASDSKNDPAKECADFTAQVIVLNHPGQIKNGYTPVLDC 351

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1609542363  81 HTAHIACKFAEIKEKCDRRTGKTTEENPKGIKSGDAAIVMLQPTK 125
Cdd:PTZ00141  352 HTAHIACKFAEIESKIDRRSGKVLEENPKAIKSGDAAIVKMVPTK 396
EF-1_alpha TIGR00483
translation elongation factor EF-1 alpha; This model represents the counterpart of bacterial ...
 2-125 8.68e-61

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]


Pssm-ID: 129574 [Multi-domain]  Cd Length: 426  Bit Score: 192.00  E-value: 8.68e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609542363   2 LTTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNqPPRGAADFTAQVIVLNHPGQISNGYTPVLDCH 81
Cdd:TIGR00483 267 VSGEVKSIEMHHEQIEQAEPGDNIGFNVRGVSKKDIRRGDVCGHPDN-PPKVAKEFTAQIVVLQHPGAITVGYTPVFHCH 345

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1609542363  82 TAHIACKFAEIKEKCDRRTGKTTEENPKGIKSGDAAIVMLQPTK 125
Cdd:TIGR00483 346 TAQIACRFDELLKKNDPRTGQVLEENPQFLKTGDAAIVKFKPTK 389
TEF1 COG5256
Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ...
 3-125 3.37e-59

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


Pssm-ID: 444074 [Multi-domain]  Cd Length: 423  Bit Score: 187.83  E-value: 3.37e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609542363   3 TTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNqPPRGAADFTAQVIVLNHPGQISNGYTPVLDCHT 82
Cdd:COG5256   265 VGEVKSIEMHHEELEQAEPGDNIGFNVRGVEKNDIKRGDVAGHPDN-PPTVAEEFTAQIVVLQHPSAITVGYTPVFHVHT 343

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1609542363  83 AHIACKFAEIKEKCDRRTGKTTEENPKGIKSGDAAIVMLQPTK 125
Cdd:COG5256   344 AQVACTFVELVSKLDPRTGQVKEENPQFLKTGDAAIVKIKPTK 386
EF1_alpha_III cd03705
Domain III of Elongation Factor 1; Eukaryotic elongation factor 1 (EF-1) is responsible for ...
 52-125 4.96e-49

Domain III of Elongation Factor 1; Eukaryotic elongation factor 1 (EF-1) is responsible for the GTP-dependent binding of aminoacyl-tRNAs to ribosomes. EF-1 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 model represents the alpha subunit, which is the counterpart of bacterial EF-Tu for archaea (aEF-1 alpha) and eukaryotes (eEF-1 alpha).


Pssm-ID: 294004 [Multi-domain]  Cd Length: 104  Bit Score: 151.96  E-value: 4.96e-49
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1609542363  52 RGAADFTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPKGIKSGDAAIVMLQPTK 125
Cdd:cd03705     1 KEAKSFTAQVIILNHPGQIKAGYTPVLDCHTAHVACKFAELKEKIDRRTGKKLEENPKFLKSGDAAIVKMVPTK 74
GTP_EFTU_D3 pfam03143
Elongation factor Tu C-terminal domain; Elongation factor Tu consists of three structural ...
 50-125 5.00e-23

Elongation factor Tu C-terminal domain; Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA and binding to EF-Ts pfam00889.


Pssm-ID: 397314 [Multi-domain]  Cd Length: 105  Bit Score: 85.78  E-value: 5.00e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609542363  50 PPRGAADFTAQVIVLNH-----PGQISNGYTPVLDCHTAHIACKFAEIKEKCDrrTGKTTeENPKGIKSGDAAIVMLQPT 124
Cdd:pfam03143   1 PIKPHTKFEAQVYILNKeeggrHTPFFNGYRPQFYFRTADVTGKFVELLHKLD--PGGVS-ENPEFVMPGDNVIVTVELI 77


                  .
gi 1609542363 125 K 125
Cdd:pfam03143  78 K 78
 
Name Accession Description Interval E-value
PTZ00141 PTZ00141
elongation factor 1- alpha; Provisional
 1-125 2.49e-85

elongation factor 1- alpha; Provisional


Pssm-ID: 185474 [Multi-domain]  Cd Length: 446  Bit Score: 255.44  E-value: 2.49e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609542363   1 ALTTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNQPPRGAADFTAQVIVLNHPGQISNGYTPVLDC 80
Cdd:PTZ00141  272 GVTTEVKSVEMHHEQLAEAVPGDNVGFNVKNVSVKDIKRGYVASDSKNDPAKECADFTAQVIVLNHPGQIKNGYTPVLDC 351

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1609542363  81 HTAHIACKFAEIKEKCDRRTGKTTEENPKGIKSGDAAIVMLQPTK 125
Cdd:PTZ00141  352 HTAHIACKFAEIESKIDRRSGKVLEENPKAIKSGDAAIVKMVPTK 396
PLN00043 PLN00043
elongation factor 1-alpha; Provisional
 1-125 6.31e-61

elongation factor 1-alpha; Provisional


Pssm-ID: 165621 [Multi-domain]  Cd Length: 447  Bit Score: 193.00  E-value: 6.31e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609542363   1 ALTTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNQPPRGAADFTAQVIVLNHPGQISNGYTPVLDC 80
Cdd:PLN00043  272 GLTTEVKSVEMHHESLQEALPGDNVGFNVKNVAVKDLKRGYVASNSKDDPAKEAANFTSQVIIMNHPGQIGNGYAPVLDC 351

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1609542363  81 HTAHIACKFAEIKEKCDRRTGKTTEENPKGIKSGDAAIVMLQPTK 125
Cdd:PLN00043  352 HTSHIAVKFAEILTKIDRRSGKELEKEPKFLKNGDAGFVKMIPTK 396
EF-1_alpha TIGR00483
translation elongation factor EF-1 alpha; This model represents the counterpart of bacterial ...
 2-125 8.68e-61

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]


Pssm-ID: 129574 [Multi-domain]  Cd Length: 426  Bit Score: 192.00  E-value: 8.68e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609542363   2 LTTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNqPPRGAADFTAQVIVLNHPGQISNGYTPVLDCH 81
Cdd:TIGR00483 267 VSGEVKSIEMHHEQIEQAEPGDNIGFNVRGVSKKDIRRGDVCGHPDN-PPKVAKEFTAQIVVLQHPGAITVGYTPVFHCH 345

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1609542363  82 TAHIACKFAEIKEKCDRRTGKTTEENPKGIKSGDAAIVMLQPTK 125
Cdd:TIGR00483 346 TAQIACRFDELLKKNDPRTGQVLEENPQFLKTGDAAIVKFKPTK 389
TEF1 COG5256
Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ...
 3-125 3.37e-59

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


Pssm-ID: 444074 [Multi-domain]  Cd Length: 423  Bit Score: 187.83  E-value: 3.37e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609542363   3 TTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNqPPRGAADFTAQVIVLNHPGQISNGYTPVLDCHT 82
Cdd:COG5256   265 VGEVKSIEMHHEELEQAEPGDNIGFNVRGVEKNDIKRGDVAGHPDN-PPTVAEEFTAQIVVLQHPSAITVGYTPVFHVHT 343

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1609542363  83 AHIACKFAEIKEKCDRRTGKTTEENPKGIKSGDAAIVMLQPTK 125
Cdd:COG5256   344 AQVACTFVELVSKLDPRTGQVKEENPQFLKTGDAAIVKIKPTK 386
PRK12317 PRK12317
elongation factor 1-alpha; Reviewed
 5-125 4.17e-59

elongation factor 1-alpha; Reviewed


Pssm-ID: 237055 [Multi-domain]  Cd Length: 425  Bit Score: 187.44  E-value: 4.17e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609542363   5 EVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNqPPRGAADFTAQVIVLNHPGQISNGYTPVLDCHTAH 84
Cdd:PRK12317  268 EVKSIEMHHEELPQAEPGDNIGFNVRGVGKKDIKRGDVCGHPDN-PPTVAEEFTAQIVVLQHPSAITVGYTPVFHAHTAQ 346

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1609542363  85 IACKFAEIKEKCDRRTGKTTEENPKGIKSGDAAIVMLQPTK 125
Cdd:PRK12317  347 VACTFEELVKKLDPRTGQVAEENPQFIKTGDAAIVKIKPTK 387
EF1_alpha_III cd03705
Domain III of Elongation Factor 1; Eukaryotic elongation factor 1 (EF-1) is responsible for ...
 52-125 4.96e-49

Domain III of Elongation Factor 1; Eukaryotic elongation factor 1 (EF-1) is responsible for the GTP-dependent binding of aminoacyl-tRNAs to ribosomes. EF-1 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 model represents the alpha subunit, which is the counterpart of bacterial EF-Tu for archaea (aEF-1 alpha) and eukaryotes (eEF-1 alpha).


Pssm-ID: 294004 [Multi-domain]  Cd Length: 104  Bit Score: 151.96  E-value: 4.96e-49
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1609542363  52 RGAADFTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPKGIKSGDAAIVMLQPTK 125
Cdd:cd03705     1 KEAKSFTAQVIILNHPGQIKAGYTPVLDCHTAHVACKFAELKEKIDRRTGKKLEENPKFLKSGDAAIVKMVPTK 74
EF1_alpha_II cd03693
Domain II of elongation factor 1-alpha; This family represents domain II of elongation factor ...
 2-49 1.25e-26

Domain II of elongation factor 1-alpha; This family represents domain II of elongation factor 1-alpha (EF-1A) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF-1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF-1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.


Pssm-ID: 293894 [Multi-domain]  Cd Length: 91  Bit Score: 94.56  E-value: 1.25e-26
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1609542363   2 LTTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNQ 49
Cdd:cd03693    44 VTGEVKSVEMHHEPLEEAIPGDNVGFNVKGVSVKDIKRGDVAGDSKND 91
GTP_EFTU_D3 pfam03143
Elongation factor Tu C-terminal domain; Elongation factor Tu consists of three structural ...
 50-125 5.00e-23

Elongation factor Tu C-terminal domain; Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA and binding to EF-Ts pfam00889.


Pssm-ID: 397314 [Multi-domain]  Cd Length: 105  Bit Score: 85.78  E-value: 5.00e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609542363  50 PPRGAADFTAQVIVLNH-----PGQISNGYTPVLDCHTAHIACKFAEIKEKCDrrTGKTTeENPKGIKSGDAAIVMLQPT 124
Cdd:pfam03143   1 PIKPHTKFEAQVYILNKeeggrHTPFFNGYRPQFYFRTADVTGKFVELLHKLD--PGGVS-ENPEFVMPGDNVIVTVELI 77


                  .
gi 1609542363 125 K 125
Cdd:pfam03143  78 K 78
Translation_factor_III cd01513
Domain III of Elongation factor (EF) Tu (EF-TU) and related proteins; Elongation factor (EF) ...
 57-125 7.58e-16

Domain III of Elongation factor (EF) Tu (EF-TU) and related proteins; Elongation factor (EF) EF-Tu participates in the elongation phase during protein biosynthesis on the ribosome. Its functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Experimental findings indicate an essential contribution of domain III to activation of GTP hydrolysis. This domain III, which is distinct from the domain III in EFG and related elongation factors, is found in several eukaryotic translation factors, like peptide chain release factors RF3, elongation factor 1, selenocysteine (Sec)-specific elongation factor, and in GT-1 family of GTPase (GTPBP1).


Pssm-ID: 275447 [Multi-domain]  Cd Length: 102  Bit Score: 67.42  E-value: 7.58e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1609542363  57 FTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKttEENPKGIKSGDAAIVMLQPTK 125
Cdd:cd01513     6 FDAKVIVLEHPKPIRPGYKPVMDVGTAHVPGRIAKLLSKEDGKTKE--KKPPDSLQPGENGTVEVELQK 72
eRF3_C_III cd03704
C-terminal domain of eRF3; This model represents the eEF1alpha-like C-terminal region of eRF3, ...
 57-122 3.67e-10

C-terminal domain of eRF3; This model represents the eEF1alpha-like C-terminal region of eRF3, which is homologous to the domain III of EF-Tu. eRF3 is a GTPase which enhances termination efficiency by stimulating eRF1 activity in a GTP-dependent manner. The C-terminal region is responsible for translation termination activity and is essential for viability. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions: N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils.


Pssm-ID: 294003 [Multi-domain]  Cd Length: 108  Bit Score: 52.94  E-value: 3.67e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1609542363  57 FTAQVIVLNHPGQI-SNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPKGIKSGDAAIVMLQ 122
Cdd:cd03704     6 FEAQIVILDLLKSIiTAGYSAVLHIHTAVEEVTITKLLATIDKKTGKKKKKKPKFVKSGQVVIARLE 72
SelB_II cd03696
Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor ...
 3-42 2.88e-09

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.


Pssm-ID: 293897 [Multi-domain]  Cd Length: 83  Bit Score: 50.22  E-value: 2.88e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1609542363   3 TTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYV 42
Cdd:cd03696    41 EVRVRSIQVHDKPVEEAKAGDRVALNLTGVDAKELERGFV 80
GTP_EFTU_D2 pfam03144
Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this ...
 2-42 7.57e-08

Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to pfam03143, and in fact has weak sequence matches to this domain.


Pssm-ID: 427163 [Multi-domain]  Cd Length: 73  Bit Score: 46.10  E-value: 7.57e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1609542363   2 LTTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYV 42
Cdd:pfam03144  31 IVTRVTSLLMFHAPLREAVAGDNAGLILAGVGLEDIRVGDT 71
HBS1_C_III cd04093
C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1); This model represents the ...
 57-122 1.03e-07

C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1); This model represents the C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1), which is homologous to the domain III of EF-1alpha. This group contains proteins similar to yeast Hbs1, which together with Dom34, promotes the No-go decay (NGD) of mRNA. The NGD targets mRNAs whose elongation stalled for degradation initiated by endonucleolytic cleavage in the vicinity of the stalled ribosome.


Pssm-ID: 294008 [Multi-domain]  Cd Length: 109  Bit Score: 46.77  E-value: 1.03e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1609542363  57 FTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPKGIKSGDAAIVMLQ 122
Cdd:cd04093     8 FEARIVTFDLQVPILKGTPVVLHRHSLSEPATISKLVSTLDKSTGEVIKKKPRCLGKNQSAVVEIE 73
EFTU_II cd03697
Domain II of elongation factor Tu; Elongation factors Tu (EF-Tu) are three-domain GTPases with ...
 2-42 7.05e-07

Domain II of elongation factor Tu; Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven alpha helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Both non-catalytic domains are composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA; and an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher affinity for GDP than for GTP.


Pssm-ID: 293898 [Multi-domain]  Cd Length: 87  Bit Score: 44.05  E-value: 7.05e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1609542363   2 LTTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYV 42
Cdd:cd03697    42 LKTTVTGIEMFRKTLDEAEAGDNVGVLLRGVKKEDVERGMV 82
Translation_Factor_II_like cd01342
Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of ...
 3-42 1.80e-06

Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of three structural domains. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought to be involved in binding of E. coli IF-2 to 30S subunits.


Pssm-ID: 293888 [Multi-domain]  Cd Length: 80  Bit Score: 42.64  E-value: 1.80e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1609542363   3 TTEVKSVEMHHEALTEALPGDNVGFNVKNisVKELRRGYV 42
Cdd:cd01342    41 TGRVTSIERFHEEVDEAKAGDIVGIGILG--VKDILTGDT 78
GTPBP_III cd03708
Domain III of the GP-1 family of GTPases; This family includes proteins similar to GTPBP1 and ...
 57-122 8.04e-06

Domain III of the GP-1 family of GTPases; This family includes proteins similar to GTPBP1 and GTPBP2. GTPBP1 is structurally related to elongation factor 1 alpha, a key component of the protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in the cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.


Pssm-ID: 294007 [Multi-domain]  Cd Length: 87  Bit Score: 41.35  E-value: 8.04e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1609542363  57 FTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRrtgktteenpkgikSGDAAIVMLQ 122
Cdd:cd03708     6 FEAEVLVLHHPTTISPGYQPVVHCGTIRQTARIISIDKEVLR--------------TGDRALVRFR 57
GTPBP_II cd03694
Domain II of the GTPBP family of GTP binding proteins; This group includes proteins similar to ...
 2-42 2.15e-05

Domain II of the GTPBP family of GTP binding proteins; This group includes proteins similar to GTPBP1 and GTPBP2. GTPBP1 is structurally related to elongation factor 1 alpha, a key component of the protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.


Pssm-ID: 293895 [Multi-domain]  Cd Length: 87  Bit Score: 39.90  E-value: 2.15e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1609542363   2 LTTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYV 42
Cdd:cd03694    44 RPVTVKSIHRNRQPVDRARAGQSASFALKKIKRESLRKGMV 84
tufA CHL00071
elongation factor Tu
 3-65 3.36e-05

elongation factor Tu


Pssm-ID: 177010 [Multi-domain]  Cd Length: 409  Bit Score: 41.48  E-value: 3.36e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1609542363   3 TTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNQPPRgaADFTAQVIVLN 65
Cdd:CHL00071  263 TTTVTGLEMFQKTLDEGLAGDNVGILLRGIQKEDIERGMVLAKPGTITPH--TKFEAQVYILT 323
PLN03126 PLN03126
Elongation factor Tu; Provisional
 3-92 6.86e-05

Elongation factor Tu; Provisional


Pssm-ID: 215592 [Multi-domain]  Cd Length: 478  Bit Score: 40.75  E-value: 6.86e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609542363   3 TTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNQPPRgaADFTAQVIVLNHP--GQIS---NGYTPV 77
Cdd:PLN03126  332 STTVTGVEMFQKILDEALAGDNVGLLLRGIQKADIQRGMVLAKPGSITPH--TKFEAIVYVLKKEegGRHSpffAGYRPQ 409

                          90
                  ....*....|....*
gi 1609542363  78 LDCHTAHIACKFAEI 92
Cdd:PLN03126  410 FYMRTTDVTGKVTSI 424
EF-Tu TIGR00485
translation elongation factor TU; This model models orthologs of translation elongation factor ...
 4-64 2.38e-03

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]


Pssm-ID: 129576 [Multi-domain]  Cd Length: 394  Bit Score: 36.29  E-value: 2.38e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1609542363   4 TEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNQPPRgaADFTAQVIVL 64
Cdd:TIGR00485 254 TTVTGVEMFRKELDEGRAGDNVGLLLRGIKREEIERGMVLAKPGSIKPH--TKFEAEVYVL 312
PRK12735 PRK12735
elongation factor Tu; Reviewed
 2-64 2.69e-03

elongation factor Tu; Reviewed


Pssm-ID: 183708 [Multi-domain]  Cd Length: 396  Bit Score: 35.97  E-value: 2.69e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1609542363   2 LTTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNQPPRgaADFTAQVIVL 64
Cdd:PRK12735  254 QKTTVTGVEMFRKLLDEGQAGDNVGVLLRGTKREDVERGQVLAKPGSIKPH--TKFEAEVYVL 314
TufA COG0050
Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis] ...
 3-64 4.48e-03

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


Pssm-ID: 439820 [Multi-domain]  Cd Length: 396  Bit Score: 35.51  E-value: 4.48e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1609542363   3 TTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNQPPRgaADFTAQVIVL 64
Cdd:COG0050   255 KTVVTGVEMFRKLLDEGEAGDNVGLLLRGIKREDVERGQVLAKPGSITPH--TKFEAEVYVL 314
PRK00049 PRK00049
elongation factor Tu; Reviewed
 3-64 4.85e-03

elongation factor Tu; Reviewed


Pssm-ID: 234596 [Multi-domain]  Cd Length: 396  Bit Score: 35.55  E-value: 4.85e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1609542363   3 TTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNQPPRgaADFTAQVIVL 64
Cdd:PRK00049  255 KTTVTGVEMFRKLLDEGQAGDNVGALLRGIKREDVERGQVLAKPGSITPH--TKFEAEVYVL 314
PRK12736 PRK12736
elongation factor Tu; Reviewed
 3-64 5.07e-03

elongation factor Tu; Reviewed


Pssm-ID: 237184 [Multi-domain]  Cd Length: 394  Bit Score: 35.31  E-value: 5.07e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1609542363   3 TTEVKSVEMHHEALTEALPGDNVGFNVKNISVKELRRGYVAGDSKNQPPRgaADFTAQVIVL 64
Cdd:PRK12736  253 KTVVTGVEMFRKLLDEGQAGDNVGVLLRGVDRDEVERGQVLAKPGSIKPH--TKFKAEVYIL 312
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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