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Conserved domains on  [gi|926677750|gb|ALD53755|]
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elongation factor 1-alpha, partial [Agenioideus biedermani]

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 ...
 1-206 2.02e-133

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: 381.79  E-value: 2.02e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   1 KYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYS 80
Cdd:PTZ00141  84 KYYFTIIDAPGHRDFIKNMITGTSQADVAILVVASTAGEFEAGISKDGQTREHALLAFTLGVKQMIVCINKMDDKTVNYS 163

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  81 ETRFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEVSSKMPWFKgwmverkegkaeGKCLIEALDAILPPTRPTD 160
Cdd:PTZ00141 164 QERYDEIKKEVSAYLKKVGYNPEKVPFIPISGWQGDNMIEKSDNMPWYK------------GPTLLEALDTLEPPKRPVD 231

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 926677750 161 KALRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:PTZ00141 232 KPLRLPLQDVYKIGGIGTVPVGRVETGILKPGMVVTFAPSGVTTEV 277
 
Name Accession Description Interval E-value
PTZ00141 PTZ00141
elongation factor 1- alpha; Provisional
 1-206 2.02e-133

elongation factor 1- alpha; Provisional


Pssm-ID: 185474 [Multi-domain]  Cd Length: 446  Bit Score: 381.79  E-value: 2.02e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   1 KYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYS 80
Cdd:PTZ00141  84 KYYFTIIDAPGHRDFIKNMITGTSQADVAILVVASTAGEFEAGISKDGQTREHALLAFTLGVKQMIVCINKMDDKTVNYS 163

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  81 ETRFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEVSSKMPWFKgwmverkegkaeGKCLIEALDAILPPTRPTD 160
Cdd:PTZ00141 164 QERYDEIKKEVSAYLKKVGYNPEKVPFIPISGWQGDNMIEKSDNMPWYK------------GPTLLEALDTLEPPKRPVD 231

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 926677750 161 KALRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:PTZ00141 232 KPLRLPLQDVYKIGGIGTVPVGRVETGILKPGMVVTFAPSGVTTEV 277
TEF1 COG5256
Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ...
 1-206 1.53e-102

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: 302.24  E-value: 1.53e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   1 KYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEfeagiskNGQTREHALLAFTLGVKQLIVGVNKMDSTEppYS 80
Cdd:COG5256   84 KYYFTIIDAPGHRDFVKNMITGASQADAAILVVSAKDGV-------MGQTREHAFLARTLGINQLIVAVNKMDAVN--YS 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  81 ETRFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEVSSKMPWFKGwmverkegkaegKCLIEALDAILPPTRPTD 160
Cdd:COG5256  155 EKRYEEVKEEVSKLLKMVGYKVDKIPFIPVSAWKGDNVVKKSDNMPWYNG------------PTLLEALDNLKEPEKPVD 222

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 926677750 161 KALRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:COG5256  223 KPLRIPIQDVYSISGIGTVPVGRVETGVLKVGDKVVFMPAGVVGEV 268
EF-1_alpha TIGR00483
translation elongation factor EF-1 alpha; This model represents the counterpart of bacterial ...
 1-206 1.46e-98

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: 292.15  E-value: 1.46e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750    1 KYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagisKNGQTREHALLAFTLGVKQLIVGVNKMDSTEppYS 80
Cdd:TIGR00483  84 KYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGDGEFE----VQPQTREHAFLARTLGINQLIVAINKMDSVN--YD 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   81 ETRFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEVSSKMPWFKgwmverkegkaeGKCLIEALDAILPPTRPTD 160
Cdd:TIGR00483 158 EEEFEAIKKEVSNLIKKVGYNPDTVPFIPISAWNGDNVIKKSENTPWYK------------GKTLLEALDALEPPEKPTD 225

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 926677750  161 KALRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:TIGR00483 226 KPLRIPIQDVYSITGVGTVPVGRVETGVLKPGDKVVFEPAGVSGEV 271
EF1_alpha cd01883
Elongation Factor 1-alpha (EF1-alpha) protein family; EF1 is responsible for the GTP-dependent ...
 1-155 1.28e-96

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.


Pssm-ID: 206670 [Multi-domain]  Cd Length: 219  Bit Score: 279.76  E-value: 1.28e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   1 KYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYS 80
Cdd:cd01883   76 KYRFTIIDAPGHRDFVKNMITGASQADVAVLVVSARKGEFEAGFEKGGQTREHALLARTLGVKQLIVAVNKMDDVTVNWS 155

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 926677750  81 ETRFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEVSSKMPWFKGWmverkegkaegkCLIEALDAILPP 155
Cdd:cd01883  156 QERYDEIKKKVSPFLKKVGYNPKDVPFIPISGFTGDNLIEKSENMPWYKGP------------TLLEALDSLEPP 218
GTP_EFTU pfam00009
Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ...
 1-121 3.27e-40

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.


Pssm-ID: 425418 [Multi-domain]  Cd Length: 187  Bit Score: 135.35  E-value: 3.27e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750    1 KYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGefeagisKNGQTREHALLAFTLGVKqLIVGVNKMDSTeppyS 80
Cdd:pfam00009  68 DYLINLIDTPGHVDFVKEVIRGLAQADGAILVVDAVEG-------VMPQTREHLRLARQLGVP-IIVFINKMDRV----D 135

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 926677750   81 ETRFEEIKKEVSS-YIKKIGYNPAAVAFVPISGWHGDNMLEV 121
Cdd:pfam00009 136 GAELEEVVEEVSReLLEKYGEDGEFVPVVPGSALKGEGVQTL 177
 
Name Accession Description Interval E-value
PTZ00141 PTZ00141
elongation factor 1- alpha; Provisional
 1-206 2.02e-133

elongation factor 1- alpha; Provisional


Pssm-ID: 185474 [Multi-domain]  Cd Length: 446  Bit Score: 381.79  E-value: 2.02e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   1 KYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYS 80
Cdd:PTZ00141  84 KYYFTIIDAPGHRDFIKNMITGTSQADVAILVVASTAGEFEAGISKDGQTREHALLAFTLGVKQMIVCINKMDDKTVNYS 163

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  81 ETRFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEVSSKMPWFKgwmverkegkaeGKCLIEALDAILPPTRPTD 160
Cdd:PTZ00141 164 QERYDEIKKEVSAYLKKVGYNPEKVPFIPISGWQGDNMIEKSDNMPWYK------------GPTLLEALDTLEPPKRPVD 231

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 926677750 161 KALRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:PTZ00141 232 KPLRLPLQDVYKIGGIGTVPVGRVETGILKPGMVVTFAPSGVTTEV 277
TEF1 COG5256
Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ...
 1-206 1.53e-102

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: 302.24  E-value: 1.53e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   1 KYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEfeagiskNGQTREHALLAFTLGVKQLIVGVNKMDSTEppYS 80
Cdd:COG5256   84 KYYFTIIDAPGHRDFVKNMITGASQADAAILVVSAKDGV-------MGQTREHAFLARTLGINQLIVAVNKMDAVN--YS 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  81 ETRFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEVSSKMPWFKGwmverkegkaegKCLIEALDAILPPTRPTD 160
Cdd:COG5256  155 EKRYEEVKEEVSKLLKMVGYKVDKIPFIPVSAWKGDNVVKKSDNMPWYNG------------PTLLEALDNLKEPEKPVD 222

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 926677750 161 KALRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:COG5256  223 KPLRIPIQDVYSISGIGTVPVGRVETGVLKVGDKVVFMPAGVVGEV 268
PLN00043 PLN00043
elongation factor 1-alpha; Provisional
 1-206 4.50e-102

elongation factor 1-alpha; Provisional


Pssm-ID: 165621 [Multi-domain]  Cd Length: 447  Bit Score: 302.01  E-value: 4.50e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   1 KYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYS 80
Cdd:PLN00043  84 KYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGGFEAGISKDGQTREHALLAFTLGVKQMICCCNKMDATTPKYS 163

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  81 ETRFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEVSSKMPWFKgwmverkegkaeGKCLIEALDAILPPTRPTD 160
Cdd:PLN00043 164 KARYDEIVKEVSSYLKKVGYNPDKIPFVPISGFEGDNMIERSTNLDWYK------------GPTLLEALDQINEPKRPSD 231

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 926677750 161 KALRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:PLN00043 232 KPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFGPTGLTTEV 277
PRK12317 PRK12317
elongation factor 1-alpha; Reviewed
 1-206 5.81e-101

elongation factor 1-alpha; Reviewed


Pssm-ID: 237055 [Multi-domain]  Cd Length: 425  Bit Score: 298.38  E-value: 5.81e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   1 KYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAgtgefEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEppYS 80
Cdd:PRK12317  83 KYYFTIVDCPGHRDFVKNMITGASQADAAVLVVAA-----DDAGGVMPQTREHVFLARTLGINQLIVAINKMDAVN--YD 155

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  81 ETRFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEVSSKMPWFKGwmverkegkaegKCLIEALDAILPPTRPTD 160
Cdd:PRK12317 156 EKRYEEVKEEVSKLLKMVGYKPDDIPFIPVSAFEGDNVVKKSENMPWYNG------------PTLLEALDNLKPPEKPTD 223

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 926677750 161 KALRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:PRK12317 224 KPLRIPIQDVYSISGVGTVPVGRVETGVLKVGDKVVFMPAGVVGEV 269
EF-1_alpha TIGR00483
translation elongation factor EF-1 alpha; This model represents the counterpart of bacterial ...
 1-206 1.46e-98

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: 292.15  E-value: 1.46e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750    1 KYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagisKNGQTREHALLAFTLGVKQLIVGVNKMDSTEppYS 80
Cdd:TIGR00483  84 KYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGDGEFE----VQPQTREHAFLARTLGINQLIVAINKMDSVN--YD 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   81 ETRFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEVSSKMPWFKgwmverkegkaeGKCLIEALDAILPPTRPTD 160
Cdd:TIGR00483 158 EEEFEAIKKEVSNLIKKVGYNPDTVPFIPISAWNGDNVIKKSENTPWYK------------GKTLLEALDALEPPEKPTD 225

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 926677750  161 KALRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:TIGR00483 226 KPLRIPIQDVYSITGVGTVPVGRVETGVLKPGDKVVFEPAGVSGEV 271
EF1_alpha cd01883
Elongation Factor 1-alpha (EF1-alpha) protein family; EF1 is responsible for the GTP-dependent ...
 1-155 1.28e-96

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.


Pssm-ID: 206670 [Multi-domain]  Cd Length: 219  Bit Score: 279.76  E-value: 1.28e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   1 KYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYS 80
Cdd:cd01883   76 KYRFTIIDAPGHRDFVKNMITGASQADVAVLVVSARKGEFEAGFEKGGQTREHALLARTLGVKQLIVAVNKMDDVTVNWS 155

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 926677750  81 ETRFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEVSSKMPWFKGWmverkegkaegkCLIEALDAILPP 155
Cdd:cd01883  156 QERYDEIKKKVSPFLKKVGYNPKDVPFIPISGFTGDNLIEKSENMPWYKGP------------TLLEALDSLEPP 218
CysN COG2895
Sulfate adenylyltransferase subunit 1, EFTu-like GTPase family [Inorganic ion transport and ...
 6-206 9.19e-56

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


Pssm-ID: 442140 [Multi-domain]  Cd Length: 430  Bit Score: 182.21  E-value: 9.19e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   6 IIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVGVNKMDSTEppYSETRFE 85
Cdd:COG2895   99 IADTPGHEQYTRNMVTGASTADLAILLIDARKGVLE-------QTRRHSYIASLLGIRHVVVAVNKMDLVD--YSEEVFE 169

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  86 EIKKEVSSYIKKIGYNPaaVAFVPISGWHGDNMLEVSSKMPWFKgwmverkegkaeGKCLIEALDAILPPTRPTDKALRL 165
Cdd:COG2895  170 EIVADYRAFAAKLGLED--ITFIPISALKGDNVVERSENMPWYD------------GPTLLEHLETVEVAEDRNDAPFRF 235

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 926677750 166 PLQDVYKiggigtvP-------VGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:COG2895  236 PVQYVNR-------PnldfrgyAGTIASGTVRVGDEVVVLPSGKTSTV 276
CysN_ATPS cd04166
CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; CysN_ATPS ...
 6-152 2.95e-42

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.


Pssm-ID: 206729 [Multi-domain]  Cd Length: 209  Bit Score: 141.17  E-value: 2.95e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   6 IIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVGVNKMDSTEppYSETRFE 85
Cdd:cd04166   82 IADTPGHEQYTRNMVTGASTADLAILLVDARKGVLE-------QTRRHSYIASLLGIRHVVVAVNKMDLVD--YDEEVFE 152

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 926677750  86 EIKKEVSSYIKKIGYNPaaVAFVPISGWHGDNMLEVSSKMPWFKgwmverkegkaeGKCLIEALDAI 152
Cdd:cd04166  153 EIKADYLAFAASLGIED--ITFIPISALEGDNVVSRSENMPWYK------------GPTLLEHLETV 205
GTP_EFTU pfam00009
Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ...
 1-121 3.27e-40

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.


Pssm-ID: 425418 [Multi-domain]  Cd Length: 187  Bit Score: 135.35  E-value: 3.27e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750    1 KYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGefeagisKNGQTREHALLAFTLGVKqLIVGVNKMDSTeppyS 80
Cdd:pfam00009  68 DYLINLIDTPGHVDFVKEVIRGLAQADGAILVVDAVEG-------VMPQTREHLRLARQLGVP-IIVFINKMDRV----D 135

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 926677750   81 ETRFEEIKKEVSS-YIKKIGYNPAAVAFVPISGWHGDNMLEV 121
Cdd:pfam00009 136 GAELEEVVEEVSReLLEKYGEDGEFVPVVPGSALKGEGVQTL 177
CysN TIGR02034
sulfate adenylyltransferase, large subunit; Metabolic assimilation of sulfur from inorganic ...
 6-206 1.02e-36

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]


Pssm-ID: 213679 [Multi-domain]  Cd Length: 406  Bit Score: 132.11  E-value: 1.02e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750    6 IIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVGVNKMDSTEppYSETRFE 85
Cdd:TIGR02034  84 VADTPGHEQYTRNMATGASTADLAVLLVDARKGVLE-------QTRRHSYIASLLGIRHVVLAVNKMDLVD--YDEEVFE 154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   86 EIKKEVSSYIKKIGynPAAVAFVPISGWHGDNMLEVSSKMPWFkgwmverkegkaEGKCLIEALDAILPPTRPTDKALRL 165
Cdd:TIGR02034 155 NIKKDYLAFAEQLG--FRDVTFIPLSALKGDNVVSRSESMPWY------------SGPTLLEILETVEVERDAQDLPLRF 220

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 926677750  166 PLQDVYKI-----GGIGTVPVGRVetgvlKPGMVVTFAPAGLTTEV 206
Cdd:TIGR02034 221 PVQYVNRPnldfrGYAGTIASGSV-----HVGDEVVVLPSGRSSRV 261
cysN PRK05124
sulfate adenylyltransferase subunit 1; Provisional
 6-206 7.06e-36

sulfate adenylyltransferase subunit 1; Provisional


Pssm-ID: 235349 [Multi-domain]  Cd Length: 474  Bit Score: 130.80  E-value: 7.06e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   6 IIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVGVNKMDSTEppYSETRFE 85
Cdd:PRK05124 111 IADTPGHEQYTRNMATGASTCDLAILLIDARKGVLD-------QTRRHSFIATLLGIKHLVVAVNKMDLVD--YSEEVFE 181

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  86 EIKKEVSSYIKKIGYNPaAVAFVPISGWHGDNMLEVSSKMPWFkgwmverkegkaEGKCLIEALDAILPPTRPTDKALRL 165
Cdd:PRK05124 182 RIREDYLTFAEQLPGNL-DIRFVPLSALEGDNVVSQSESMPWY------------SGPTLLEVLETVDIQRVVDAQPFRF 248

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 926677750 166 PLQDVYKI-----GGIGTvpvgrVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:PRK05124 249 PVQYVNRPnldfrGYAGT-----LASGVVKVGDRVKVLPSGKESNV 289
PRK05506 PRK05506
bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional
 6-206 5.57e-35

bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional


Pssm-ID: 180120 [Multi-domain]  Cd Length: 632  Bit Score: 130.05  E-value: 5.57e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   6 IIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVGVNKMDSTEppYSETRFE 85
Cdd:PRK05506 108 VADTPGHEQYTRNMVTGASTADLAIILVDARKGVLT-------QTRRHSFIASLLGIRHVVLAVNKMDLVD--YDQEVFD 178

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  86 EIKKEVSSYIKKIGYnpAAVAFVPISGWHGDNMLEVSSKMPWFkgwmverkegkaEGKCLIEALDAILPPTRPTDKALRL 165
Cdd:PRK05506 179 EIVADYRAFAAKLGL--HDVTFIPISALKGDNVVTRSARMPWY------------EGPSLLEHLETVEIASDRNLKDFRF 244

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 926677750 166 PLQDVYKI-----GGIGTvpvgrVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:PRK05506 245 PVQYVNRPnldfrGFAGT-----VASGVVRPGDEVVVLPSGKTSRV 285
TufA COG0050
Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis] ...
 7-192 2.66e-30

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: 114.86  E-value: 2.66e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   7 IDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVGVNKMDSTEPPY-SETRFE 85
Cdd:COG0050   80 VDCPGHADYVKNMITGAAQMDGAILVVSATDGPMP-------QTREHILLARQVGVPYIVVFLNKCDMVDDEElLELVEM 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  86 EIKKEVSSYikkiGYNPAAVAFVPISGWhgdNMLEVSSKMPWFKGwMVErkegkaegkcLIEALDAILP-PTRPTDKALR 164
Cdd:COG0050  153 EVRELLSKY----GFPGDDTPIIRGSAL---KALEGDPDPEWEKK-ILE----------LMDAVDSYIPePERDTDKPFL 214

                        170       180
                 ....*....|....*....|....*...
gi 926677750 165 LPLQDVYKIGGIGTVPVGRVETGVLKPG 192
Cdd:COG0050  215 MPVEDVFSITGRGTVVTGRVERGIIKVG 242
EF1_alpha_II cd03693
Domain II of elongation factor 1-alpha; This family represents domain II of elongation factor ...
 159-206 1.31e-29

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: 105.35  E-value: 1.31e-29
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 926677750 159 TDKALRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:cd03693    1 TDKPLRLPIQDVYKIGGIGTVPVGRVETGILKPGMVVTFAPAGVTGEV 48
tufA CHL00071
elongation factor Tu
 7-195 2.87e-29

elongation factor Tu


Pssm-ID: 177010 [Multi-domain]  Cd Length: 409  Bit Score: 111.97  E-value: 2.87e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   7 IDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVGVNKMDSTEppySETRFEE 86
Cdd:CHL00071  80 VDCPGHADYVKNMITGAAQMDGAILVVSAADGPMP-------QTKEHILLAKQVGVPNIVVFLNKEDQVD---DEELLEL 149

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  87 IKKEVSSYIKKIGYNPAAVAFVPISGWHGdnmLEVSSKMPwfkgwMVERKEGKAEGKC--LIEALDAILP-PTRPTDKAL 163
Cdd:CHL00071 150 VELEVRELLSKYDFPGDDIPIVSGSALLA---LEALTENP-----KIKRGENKWVDKIynLMDAVDSYIPtPERDTDKPF 221

                        170       180       190
                 ....*....|....*....|....*....|..
gi 926677750 164 RLPLQDVYKIGGIGTVPVGRVETGVLKPGMVV 195
Cdd:CHL00071 222 LMAIEDVFSITGRGTVATGRIERGTVKVGDTV 253
PRK00049 PRK00049
elongation factor Tu; Reviewed
 7-192 9.60e-29

elongation factor Tu; Reviewed


Pssm-ID: 234596 [Multi-domain]  Cd Length: 396  Bit Score: 110.66  E-value: 9.60e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   7 IDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVGVNKMDSTE-PPYSETRFE 85
Cdd:PRK00049  80 VDCPGHADYVKNMITGAAQMDGAILVVSAADGPMP-------QTREHILLARQVGVPYIVVFLNKCDMVDdEELLELVEM 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  86 EIKKEVSSYikkigynpaavafvpisGWHGDNmlevsskMPWFKGWMVERKEGKAEGKC------LIEALDAILP-PTRP 158
Cdd:PRK00049 153 EVRELLSKY-----------------DFPGDD-------TPIIRGSALKALEGDDDEEWekkileLMDAVDSYIPtPERA 208

                        170       180       190
                 ....*....|....*....|....*....|....
gi 926677750 159 TDKALRLPLQDVYKIGGIGTVPVGRVETGVLKPG 192
Cdd:PRK00049 209 IDKPFLMPIEDVFSISGRGTVVTGRVERGIIKVG 242
PRK12736 PRK12736
elongation factor Tu; Reviewed
 7-192 3.03e-28

elongation factor Tu; Reviewed


Pssm-ID: 237184 [Multi-domain]  Cd Length: 394  Bit Score: 109.26  E-value: 3.03e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   7 IDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVGVNKMDSTEppySETRFEE 86
Cdd:PRK12736  80 VDCPGHADYVKNMITGAAQMDGAILVVAATDGPMP-------QTREHILLARQVGVPYLVVFLNKVDLVD---DEELLEL 149

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  87 IKKEVSSYIKKIGYNPAAVAFVPISGWH---GDnmlevsskmpwfkgwmvERKEGKAEGkcLIEALDAILP-PTRPTDKA 162
Cdd:PRK12736 150 VEMEVRELLSEYDFPGDDIPVIRGSALKaleGD-----------------PKWEDAIME--LMDAVDEYIPtPERDTDKP 210

                        170       180       190
                 ....*....|....*....|....*....|
gi 926677750 163 LRLPLQDVYKIGGIGTVPVGRVETGVLKPG 192
Cdd:PRK12736 211 FLMPVEDVFTITGRGTVVTGRVERGTVKVG 240
GTP_translation_factor cd00881
GTP translation factor family primarily contains translation initiation, elongation and ...
 1-120 5.67e-28

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.


Pssm-ID: 206647 [Multi-domain]  Cd Length: 183  Bit Score: 103.91  E-value: 5.67e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   1 KYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEfeagiskNGQTREHALLAFtLGVKQLIVGVNKMDSTeppyS 80
Cdd:cd00881   61 KRRINFIDTPGHEDFSKETVRGLAQADGALLVVDANEGV-------EPQTREHLNIAL-AGGLPIIVAVNKIDRV----G 128

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 926677750  81 ETRFEEIKKEVSSYIKKIGY---NPAAVAFVPISGWHGDNMLE 120
Cdd:cd00881  129 EEDFDEVLREIKELLKLIGFtflKGKDVPIIPISALTGEGIEE 171
PRK12735 PRK12735
elongation factor Tu; Reviewed
 7-192 6.71e-28

elongation factor Tu; Reviewed


Pssm-ID: 183708 [Multi-domain]  Cd Length: 396  Bit Score: 108.39  E-value: 6.71e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   7 IDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVGVNKMDSTEPPyseTRFEE 86
Cdd:PRK12735  80 VDCPGHADYVKNMITGAAQMDGAILVVSAADGPMP-------QTREHILLARQVGVPYIVVFLNKCDMVDDE---ELLEL 149

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  87 IKKEVSSYIKKIGYNpaavafvpisgwhGDNmlevsskMPWFKGWMVERKEGKAEGKC------LIEALDAILP-PTRPT 159
Cdd:PRK12735 150 VEMEVRELLSKYDFP-------------GDD-------TPIIRGSALKALEGDDDEEWeakileLMDAVDSYIPePERAI 209

                        170       180       190
                 ....*....|....*....|....*....|...
gi 926677750 160 DKALRLPLQDVYKIGGIGTVPVGRVETGVLKPG 192
Cdd:PRK12735 210 DKPFLMPIEDVFSISGRGTVVTGRVERGIVKVG 242
PLN03127 PLN03127
Elongation factor Tu; Provisional
 7-192 1.68e-27

Elongation factor Tu; Provisional


Pssm-ID: 178673 [Multi-domain]  Cd Length: 447  Bit Score: 107.99  E-value: 1.68e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   7 IDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSETRFEE 86
Cdd:PLN03127 129 VDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMP-------QTKEHILLARQVGVPSLVVFLNKVDVVDDEELLELVEM 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  87 IKKEVSSYIKkigynpaavafvpisgWHGDNmlevsskMPWFKGWMVERKEGKAE--GKC----LIEALDAILP-PTRPT 159
Cdd:PLN03127 202 ELRELLSFYK----------------FPGDE-------IPIIRGSALSALQGTNDeiGKNailkLMDAVDEYIPePVRVL 258

                        170       180       190
                 ....*....|....*....|....*....|...
gi 926677750 160 DKALRLPLQDVYKIGGIGTVPVGRVETGVLKPG 192
Cdd:PLN03127 259 DKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVG 291
EF-Tu TIGR00485
translation elongation factor TU; This model models orthologs of translation elongation factor ...
 7-192 3.48e-27

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: 106.40  E-value: 3.48e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750    7 IDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVGVNKMD-STEPPYSETRFE 85
Cdd:TIGR00485  80 VDCPGHADYVKNMITGAAQMDGAILVVSATDGPMP-------QTREHILLARQVGVPYIVVFLNKCDmVDDEELLELVEM 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   86 EIKKEVSSYikkigynpaavafvpisGWHGDNmlevsskMPWFKGWMVERKEGKAEGKC----LIEALDAILP-PTRPTD 160
Cdd:TIGR00485 153 EVRELLSQY-----------------DFPGDD-------TPIIRGSALKALEGDAEWEAkileLMDAVDEYIPtPEREID 208

                         170       180       190
                  ....*....|....*....|....*....|..
gi 926677750  161 KALRLPLQDVYKIGGIGTVPVGRVETGVLKPG 192
Cdd:TIGR00485 209 KPFLLPIEDVFSITGRGTVVTGRVERGIIKVG 240
SelB COG3276
Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure ...
 4-206 5.46e-25

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


Pssm-ID: 442507 [Multi-domain]  Cd Length: 630  Bit Score: 101.53  E-value: 5.46e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   4 VTIIDAPGHRDFIKNMITGTSQADCAVLIVAAgtgefEAGISKngQTREH-ALLAFtLGVKQLIVGVNKMDSTEPpyseT 82
Cdd:COG3276   53 LGFVDVPGHEKFIKNMLAGAGGIDLVLLVVAA-----DEGVMP--QTREHlAILDL-LGIKRGIVVLTKADLVDE----E 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  83 RFEEIKKEVSSYIKKigynpaavafvpiSGWHGDNMLEVSSKmpwfkgwmveRKEGKAEgkcLIEALDAIL--PPTRPTD 160
Cdd:COG3276  121 WLELVEEEIRELLAG-------------TFLEDAPIVPVSAV----------TGEGIDE---LRAALDALAaaVPARDAD 174

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 926677750 161 KALRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:COG3276  175 GPFRLPIDRVFSIKGFGTVVTGTLLSGTVRVGDELELLPSGKPVRV 220
PLN03126 PLN03126
Elongation factor Tu; Provisional
 7-195 2.60e-24

Elongation factor Tu; Provisional


Pssm-ID: 215592 [Multi-domain]  Cd Length: 478  Bit Score: 99.30  E-value: 2.60e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   7 IDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVGVNKMDSTEppySETRFEE 86
Cdd:PLN03126 149 VDCPGHADYVKNMITGAAQMDGAILVVSGADGPMP-------QTKEHILLAKQVGVPNMVVFLNKQDQVD---DEELLEL 218

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  87 IKKEVSSYIKKIGYNPAAvafVPISGWHGDNMLEVSSKMPwfkgwMVERKEGKAEGKC--LIEALDAILP-PTRPTDKAL 163
Cdd:PLN03126 219 VELEVRELLSSYEFPGDD---IPIISGSALLALEALMENP-----NIKRGDNKWVDKIyeLMDAVDSYIPiPQRQTDLPF 290

                        170       180       190
                 ....*....|....*....|....*....|..
gi 926677750 164 RLPLQDVYKIGGIGTVPVGRVETGVLKPGMVV 195
Cdd:PLN03126 291 LLAVEDVFSITGRGTVATGRVERGTVKVGETV 322
EF_Tu cd01884
Elongation Factor Tu (EF-Tu) GTP-binding proteins; EF-Tu subfamily. This subfamily includes ...
 7-155 1.64e-21

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.


Pssm-ID: 206671 [Multi-domain]  Cd Length: 195  Bit Score: 87.25  E-value: 1.64e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   7 IDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVGVNKMDSTEppySETRFEE 86
Cdd:cd01884   70 VDCPGHADYIKNMITGAAQMDGAILVVSATDGPMP-------QTREHLLLARQVGVPYIVVFLNKADMVD---DEELLEL 139

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 926677750  87 IKKEVSSYIKKIGYNPAAVAFVPISGWhgdNMLEvsskmpwfkgwmvERKEGKAEGKC--LIEALDAILPP 155
Cdd:cd01884  140 VEMEVRELLSKYGFDGDDTPIVRGSAL---KALE-------------GDDPNKWVDKIleLLDALDSYIPT 194
selB TIGR00475
selenocysteine-specific elongation factor SelB; In prokaryotes, the incorporation of ...
 2-206 2.26e-19

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]


Pssm-ID: 129567 [Multi-domain]  Cd Length: 581  Bit Score: 85.31  E-value: 2.26e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750    2 YYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVGVNKMDSTEppysE 81
Cdd:TIGR00475  50 YRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVMT-------QTGEHLAVLDLLGIPHTIVVITKADRVN----E 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   82 TRFEEIKKEVSSYIKKIGYNPAAVAFVpISGWHGDNMLEVsskmpwfkgwmverkegKAEGKCLIEALDailppTRPTDK 161
Cdd:TIGR00475 119 EEIKRTEMFMKQILNSYIFLKNAKIFK-TSAKTGQGIGEL-----------------KKELKNLLESLD-----IKRIQK 175

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 926677750  162 ALRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:TIGR00475 176 PLRMAIDRAFKVKGAGTVVTGTAFSGEVKVGDNLRLLPINHEVRV 220
SelB cd04171
SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ...
 6-108 1.94e-17

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.


Pssm-ID: 206734 [Multi-domain]  Cd Length: 170  Bit Score: 76.10  E-value: 1.94e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   6 IIDAPGHRDFIKNMITGTSQADCAVLIVAAgtgefEAGISKngQTREHALLAFTLGVKQLIVGVNKMDSTEPPysetRFE 85
Cdd:cd04171   54 FIDVPGHEKFVKNMLAGAGGIDAVLLVVAA-----DEGIMP--QTREHLEILELLGIKKGLVVLTKADLVDED----RLE 122

                         90       100
                 ....*....|....*....|...
gi 926677750  86 EIKKEVSSYIKKIGYNPAAVAFV 108
Cdd:cd04171  123 LVEEEILELLAGTFLADAPIFPV 145
PRK10512 PRK10512
selenocysteinyl-tRNA-specific translation factor; Provisional
 7-108 1.24e-09

selenocysteinyl-tRNA-specific translation factor; Provisional


Pssm-ID: 182508 [Multi-domain]  Cd Length: 614  Bit Score: 56.98  E-value: 1.24e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   7 IDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFeagisknGQTREH-ALLAFTlGVKQLIVGVNKMDSTEPPysetRFE 85
Cdd:PRK10512  56 IDVPGHEKFLSNMLAGVGGIDHALLVVACDDGVM-------AQTREHlAILQLT-GNPMLTVALTKADRVDEA----RIA 123

                         90       100
                 ....*....|....*....|...
gi 926677750  86 EIKKEVSSYIKKIGYnPAAVAFV 108
Cdd:PRK10512 124 EVRRQVKAVLREYGF-AEAKLFV 145
PRK04000 PRK04000
translation initiation factor IF-2 subunit gamma; Validated
 4-118 5.49e-09

translation initiation factor IF-2 subunit gamma; Validated


Pssm-ID: 235194 [Multi-domain]  Cd Length: 411  Bit Score: 54.86  E-value: 5.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   4 VTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAgiskngQTREHaLLAFT-LGVKQLIVGVNKMDSTEPPYSET 82
Cdd:PRK04000  87 VSFVDAPGHETLMATMLSGAALMDGAILVIAANEPCPQP------QTKEH-LMALDiIGIKNIVIVQNKIDLVSKERALE 159

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 926677750  83 RFEEIKKEVSSYIkkigynpAAVA-FVPISGWHGDNM 118
Cdd:PRK04000 160 NYEQIKEFVKGTV-------AENApIIPVSALHKVNI 189
eIF2_gamma cd01888
Gamma subunit of initiation factor 2 (eIF2 gamma); eIF2 is a heterotrimeric translation ...
 4-118 8.47e-09

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.


Pssm-ID: 206675 [Multi-domain]  Cd Length: 197  Bit Score: 53.04  E-value: 8.47e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   4 VTIIDAPGHRDFIKNMITGTSQADCAVLIVAAgtgefeagiskN-----GQTREHaLLAF-TLGVKQLIVGVNKMDSTEP 77
Cdd:cd01888   79 VSFVDCPGHEILMATMLSGAAVMDGALLLIAA-----------NepcpqPQTSEH-LAALeIMGLKHIIILQNKIDLVKE 146

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 926677750  78 PYSETRFEEIKKevssYIKKIGYNPAAVafVPISGWHGDNM 118
Cdd:cd01888  147 EQALENYEQIKE----FVKGTIAENAPI--IPISAQLKYNI 181
IF2_eIF5B cd01887
Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; IF2/eIF5B ...
 4-118 4.19e-08

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.


Pssm-ID: 206674 [Multi-domain]  Cd Length: 169  Bit Score: 50.55  E-value: 4.19e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   4 VTIIDAPGHRDFiKNMIT-GTSQADCAVLIVAAGTGeFEAgiskngQTRE---HALLAFTlgvkQLIVGVNKMDstEPPY 79
Cdd:cd01887   51 ITFIDTPGHEAF-TNMRArGASVTDIAILVVAADDG-VMP------QTIEainHAKAANV----PIIVAINKID--KPYG 116

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 926677750  80 SETRFEEIKKEVSSY---IKKIGYNpaaVAFVPISGWHGDNM 118
Cdd:cd01887  117 TEADPERVKNELSELglvGEEWGGD---VSIVPISAKTGEGI 155
Translation_Factor_II_like cd01342
Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of ...
 163-206 2.68e-07

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: 46.49  E-value: 2.68e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 926677750 163 LRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:cd01342    1 LVMQVFKVFYIPGRGRVAGGRVESGTLKVGDEIRILPKGITGRV 44
GTPBP1_like cd04165
GTP binding protein 1 (GTPBP1)-like family includes GTPBP2; Mammalian GTP binding protein 1 ...
 4-99 5.89e-07

GTP binding protein 1 (GTPBP1)-like family includes GTPBP2; Mammalian GTP binding protein 1 (GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1 are GTPases whose specific functions remain unknown. In mouse, GTPBP1 is expressed in macrophages, in smooth muscle cells of various tissues and in some neurons of the cerebral cortex; GTPBP2 tissue distribution appears to overlap that of GTPBP1. In human leukemia and macrophage cell lines, expression of both GTPBP1 and GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The chromosomal location of both genes has been identified in humans, with GTPBP1 located in chromosome 22q12-13.1 and GTPBP2 located in chromosome 6p21-12. Human glioblastoma multiforme (GBM), a highly-malignant astrocytic glioma and the most common cancer in the central nervous system, has been linked to chromosomal deletions and a translocation on chromosome 6. The GBM translocation results in a fusion of GTPBP2 and PTPRZ1, a protein involved in oligodendrocyte differentiation, recovery, and survival. This fusion product may contribute to the onset of GBM.


Pssm-ID: 206728 [Multi-domain]  Cd Length: 224  Bit Score: 48.06  E-value: 5.89e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   4 VTIIDAPGHRDFIKNMITGTS--QADCAVLIVAAGTGEfeagiskNGQTREHALLAFTLGVKQLIVgVNKMDSTeppySE 81
Cdd:cd04165   86 VTFIDLAGHERYLKTTVFGMTgyAPDYAMLVVGANAGI-------IGMTKEHLGLALALKVPVFVV-VTKIDMT----PA 153

                         90
                 ....*....|....*...
gi 926677750  82 TRFEEIKKEVSSYIKKIG 99
Cdd:cd04165  154 NVLQETLKDLKRLLKSPG 171
PTZ00327 PTZ00327
eukaryotic translation initiation factor 2 gamma subunit; Provisional
 1-111 7.52e-06

eukaryotic translation initiation factor 2 gamma subunit; Provisional


Pssm-ID: 240362 [Multi-domain]  Cd Length: 460  Bit Score: 45.77  E-value: 7.52e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   1 KYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAgtgefeagiskN-----GQTREHALLAFTLGVKQLIVGVNKMDST 75
Cdd:PTZ00327 116 KRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAA-----------NescpqPQTSEHLAAVEIMKLKHIIILQNKIDLV 184

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 926677750  76 EPPYSETRFEEIKKEVSSYIKKigynpaAVAFVPIS 111
Cdd:PTZ00327 185 KEAQAQDQYEEIRNFVKGTIAD------NAPIIPIS 214
Snu114p cd04167
Snu114p, a spliceosome protein, is a GTPase; Snu114p subfamily. Snu114p is one of several ...
 2-128 2.94e-05

Snu114p, a spliceosome protein, is a GTPase; Snu114p subfamily. Snu114p is one of several proteins that make up the U5 small nuclear ribonucleoprotein (snRNP) particle. U5 is a component of the spliceosome, which catalyzes the splicing of pre-mRNA to remove introns. Snu114p is homologous to EF-2, but typically contains an additional N-terminal domain not found in Ef-2. This protein is part of the GTP translation factor family and the Ras superfamily, characterized by five G-box motifs.


Pssm-ID: 206730 [Multi-domain]  Cd Length: 213  Bit Score: 43.03  E-value: 2.94e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   2 YYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTgefeaGISKNGQT--REhallAFTLGVKQLIVgVNKMDS--TE- 76
Cdd:cd04167   71 YLINIIDTPGHVNFMDEVAAALRLCDGVVLVVDVVE-----GLTSVTERliRH----AIQEGLPMVLV-INKIDRliLEl 140

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 926677750  77 --PP---YSETRfeEIKKEVSSYIKKIGyNPAAVAFVPISGwhgdNMLEVSSKMPWF 128
Cdd:cd04167  141 klPPtdaYYKLR--HTIDEINNYIASFS-TTEGFLVSPELG----NVLFASSKFGFC 190
HBS1-like_II cd16267
Domain II of Hbs1-like proteins; S. cerevisiae Hbs1 is closely related to the eukaryotic class ...
 163-206 8.39e-05

Domain II of Hbs1-like proteins; S. cerevisiae Hbs1 is closely related to the eukaryotic class II release factor (eRF3). Hbs1, together with Dom34 (pelota), plays an important role in termination and recycling, but in contrast to eRF3/eRF1, Hbs1, together with Dom34 (pelota), functions on mRNA-bound ribosomes in a codon-independent manner and promotes subunit splitting on completely empty ribosomes.


Pssm-ID: 293912 [Multi-domain]  Cd Length: 84  Bit Score: 39.80  E-value: 8.39e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 926677750 163 LRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:cd16267    2 FRLSVSDVFKGQGSGFTVSGRIEAGSVQVGDKVLVMPSNETATV 45
TetM_like cd04168
Tet(M)-like family includes Tet(M), Tet(O), Tet(W), and OtrA, containing tetracycline ...
 4-95 1.04e-04

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.


Pssm-ID: 206731 [Multi-domain]  Cd Length: 237  Bit Score: 41.84  E-value: 1.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   4 VTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGefeagisKNGQTRehaLLAFTLgvKQL----IVGVNKMDsTEPPY 79
Cdd:cd04168   66 VNIIDTPGHMDFIAEVERSLSVLDGAILVISAVEG-------VQAQTR---ILFRLL--RKLniptIIFVNKID-RAGAD 132

                         90
                 ....*....|....*.
gi 926677750  80 SETRFEEIKKEVSSYI 95
Cdd:cd04168  133 LEKVYQEIKEKLSPDI 148
EFTU_II cd03697
Domain II of elongation factor Tu; Elongation factors Tu (EF-Tu) are three-domain GTPases with ...
 165-197 2.10e-04

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: 38.65  E-value: 2.10e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 926677750 165 LPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTF 197
Cdd:cd03697    3 MPIEDVFSIPGRGTVVTGRIERGVIKVGDEVEI 35
PRK10218 PRK10218
translational GTPase TypA;
2-196 5.14e-04

translational GTPase TypA;


Pssm-ID: 104396 [Multi-domain]  Cd Length: 607  Bit Score: 40.46  E-value: 5.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   2 YYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEagiskngQTREHALLAFTLGVKQLIVgVNKMD--STEPPY 79
Cdd:PRK10218  68 YRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMP-------QTRFVTKKAFAYGLKPIVV-INKVDrpGARPDW 139

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750  80 SETRFEEIKKEVSSYIKKIGYnPA--AVAFVPISGWHGDNMLEvsSKMPWFKGwmverkegkaegkclieALDAILPPTR 157
Cdd:PRK10218 140 VVDQVFDLFVNLDATDEQLDF-PIvyASALNGIAGLDHEDMAE--DMTPLYQA-----------------IVDHVPAPDV 199

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 926677750 158 PTDKALRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVT 196
Cdd:PRK10218 200 DLDGPFQMQISQLDYNSYVGVIGIGRIKRGKVKPNQQVT 238
CysN_NodQ_II cd03695
Domain II of the large subunit of ATP sulfurylase; This subfamily represents domain II of the ...
 163-206 1.11e-03

Domain II of the large subunit of ATP sulfurylase; This subfamily represents domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction, APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sulfation of a nodulation factor. In Rhizobium meliloti, the heterodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, archaea, and eukaryotes use a different ATP sulfurylase, which shows no amino acid sequence similarity to CysN or NodQ. CysN and the N-terminal portion of NodQ show similarity to GTPases involved in translation, in particular, EF-Tu and EF-1alpha.


Pssm-ID: 293896 [Multi-domain]  Cd Length: 81  Bit Score: 36.77  E-value: 1.11e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 926677750 163 LRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:cd03695    1 FRFPVQYVNRPNLDFRGYAGTIASGSIRVGDEVTVLPSGKTSRV 44
TypA_BipA cd01891
Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; BipA ...
 2-91 1.57e-03

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.


Pssm-ID: 206678 [Multi-domain]  Cd Length: 194  Bit Score: 37.96  E-value: 1.57e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   2 YYVTIIDAPGHRDF------IKNMitgtsqADCAVLIVAAGTGEFEagiskngQTR---EHALLAftlGVKqLIVGVNKM 72
Cdd:cd01891   65 TKINIIDTPGHADFggeverVLSM------VDGVLLLVDASEGPMP-------QTRfvlKKALEA---GLK-PIVVINKI 127

                         90
                 ....*....|....*....
gi 926677750  73 DSteppySETRFEEIKKEV 91
Cdd:cd01891  128 DR-----PDARPEEVVDEV 141
eRF3_II cd04089
Domain II of the eukaryotic class II release factor; In eukaryotes, translation termination is ...
 163-206 7.08e-03

Domain II of the eukaryotic class II release factor; In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribosome. eRF3 is a GTPase, which enhances termination efficiency by stimulating eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF-1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. 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: 293906 [Multi-domain]  Cd Length: 82  Bit Score: 34.38  E-value: 7.08e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 926677750 163 LRLPLQDVYKigGIGTVPVGRVETGVLKPGMVVTFAPAGLTTEV 206
Cdd:cd04089    2 LRMPILDKYK--DMGTVVMGKVESGTIRKGQKLVLMPNKTKVEV 43
TypA COG1217
Predicted membrane GTPase TypA/BipA involved in stress response [Signal transduction ...
 6-73 7.29e-03

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


Pssm-ID: 440830 [Multi-domain]  Cd Length: 606  Bit Score: 36.92  E-value: 7.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   6 IIDAPGHRDF------IKNMitgtsqADCAVLIVAAgtgeFEagisknG---QTR---EHALlafTLGVKqLIVGVNKMD 73
Cdd:COG1217   73 IVDTPGHADFggeverVLSM------VDGVLLLVDA----FE------GpmpQTRfvlKKAL---ELGLK-PIVVINKID 132
LepA cd01890
LepA also known as Elongation Factor 4 (EF4); LepA (also known as elongation factor 4, EF4) ...
 2-95 8.16e-03

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.


Pssm-ID: 206677 [Multi-domain]  Cd Length: 179  Bit Score: 35.59  E-value: 8.16e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 926677750   2 YYVTIIDAPGHRDFikNMITGTSQADC--AVLIVAAGTGeFEAgiskngQTREHALLAFTLGVKQLIVgVNKMD--STEP 77
Cdd:cd01890   67 YLLNLIDTPGHVDF--SYEVSRSLAACegALLVVDATQG-VEA------QTLANFYLALENNLEIIPV-INKIDlpAADP 136

                         90
                 ....*....|....*...
gi 926677750  78 pysetrfEEIKKEVSSYI 95
Cdd:cd01890  137 -------DRVKQEIEDVL 147
 
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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