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Conserved domains on  [gi|756787017|gb|AJM90031|]
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translation elongation factor 1-alpha, partial [Stephanospora novae-caledoniae]

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 ...
 1-161 3.87e-98

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: 289.73  E-value: 3.87e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   1 RDFIKNMITGTSQADCAILIIAGGTGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMD--TTKWSEDRFNEIIKETS 78
Cdd:PTZ00141  96 RDFIKNMITGTSQADVAILVVASTAGEFEAGISKDGQTREHALLAFTLGVKQMIVCINKMDdkTVNYSQERYDEIKKEVS 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  79 TFIKKVGYNPKAVAFVPISGWHGDNMLEESPNMPWYkgwtkenkggavKGKTLLDAIDAIEPPVRPSDKPLRLPLQDVYK 158
Cdd:PTZ00141 176 AYLKKVGYNPEKVPFIPISGWQGDNMIEKSDNMPWY------------KGPTLLEALDTLEPPKRPVDKPLRLPLQDVYK 243


                 ...
gi 756787017 159 IGG 161
Cdd:PTZ00141 244 IGG 246
 
Name Accession Description Interval E-value
PTZ00141 PTZ00141
elongation factor 1- alpha; Provisional
 1-161 3.87e-98

elongation factor 1- alpha; Provisional


Pssm-ID: 185474 [Multi-domain]  Cd Length: 446  Bit Score: 289.73  E-value: 3.87e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   1 RDFIKNMITGTSQADCAILIIAGGTGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMD--TTKWSEDRFNEIIKETS 78
Cdd:PTZ00141  96 RDFIKNMITGTSQADVAILVVASTAGEFEAGISKDGQTREHALLAFTLGVKQMIVCINKMDdkTVNYSQERYDEIKKEVS 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  79 TFIKKVGYNPKAVAFVPISGWHGDNMLEESPNMPWYkgwtkenkggavKGKTLLDAIDAIEPPVRPSDKPLRLPLQDVYK 158
Cdd:PTZ00141 176 AYLKKVGYNPEKVPFIPISGWQGDNMIEKSDNMPWY------------KGPTLLEALDTLEPPKRPVDKPLRLPLQDVYK 243


                 ...
gi 756787017 159 IGG 161
Cdd:PTZ00141 244 IGG 246
EF1_alpha cd01883
Elongation Factor 1-alpha (EF1-alpha) protein family; EF1 is responsible for the GTP-dependent ...
 1-142 1.01e-83

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: 245.09  E-value: 1.01e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   1 RDFIKNMITGTSQADCAILIIAGGTGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDTT--KWSEDRFNEIIKETS 78
Cdd:cd01883   88 RDFVKNMITGASQADVAVLVVSARKGEFEAGFEKGGQTREHALLARTLGVKQLIVAVNKMDDVtvNWSQERYDEIKKKVS 167

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 756787017  79 TFIKKVGYNPKAVAFVPISGWHGDNMLEESPNMPWYKGWtkenkggavkgkTLLDAIDAIEPPV 142
Cdd:cd01883  168 PFLKKVGYNPKDVPFIPISGFTGDNLIEKSENMPWYKGP------------TLLEALDSLEPPE 219
TEF1 COG5256
Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ...
 1-161 1.69e-74

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: 228.66  E-value: 1.69e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   1 RDFIKNMITGTSQADCAILIIAGGTGEfeagiskDGQTREHALLAFTLGVRQLIVAVNKMDTTKWSEDRFNEIIKETSTF 80
Cdd:COG5256   96 RDFVKNMITGASQADAAILVVSAKDGV-------MGQTREHAFLARTLGINQLIVAVNKMDAVNYSEKRYEEVKEEVSKL 168

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  81 IKKVGYNPKAVAFVPISGWHGDNMLEESPNMPWYkgwtkenkggavKGKTLLDAIDAIEPPVRPSDKPLRLPLQDVYKIG 160
Cdd:COG5256  169 LKMVGYKVDKIPFIPVSAWKGDNVVKKSDNMPWY------------NGPTLLEALDNLKEPEKPVDKPLRIPIQDVYSIS 236


                 .
gi 756787017 161 G 161
Cdd:COG5256  237 G 237
GTP_EFTU pfam00009
Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ...
 1-141 6.77e-32

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: 112.62  E-value: 6.77e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017    1 RDFIKNMITGTSQADCAILIIAGGTGefeagisKDGQTREHALLAFTLGVRqLIVAVNKMDTTkwSEDRFNEIIKETS-T 79
Cdd:pfam00009  80 VDFVKEVIRGLAQADGAILVVDAVEG-------VMPQTREHLRLARQLGVP-IIVFINKMDRV--DGAELEEVVEEVSrE 149

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 756787017   80 FIKKVGYNPKAVAFVPISGWHGDNMleespnmpwykgwtkenkggavkgKTLLDAIDAIEPP 141
Cdd:pfam00009 150 LLEKYGEDGEFVPVVPGSALKGEGV------------------------QTLLDALDEYLPS 187
CysN TIGR02034
sulfate adenylyltransferase, large subunit; Metabolic assimilation of sulfur from inorganic ...
 3-156 7.26e-32

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: 117.47  E-value: 7.26e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017    3 FIKNMITGTSQADCAILIIAGGTGEFEagiskdgQTREHALLAFTLGVRQLIVAVNKMDTTKWSEDRFNEIIKETSTFIK 82
Cdd:TIGR02034  93 YTRNMATGASTADLAVLLVDARKGVLE-------QTRRHSYIASLLGIRHVVLAVNKMDLVDYDEEVFENIKKDYLAFAE 165

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 756787017   83 KVGynPKAVAFVPISGWHGDNMLEESPNMPWYkgwtkenkggavKGKTLLDAIDAIEPPVRPSDKPLRLPLQDV 156
Cdd:TIGR02034 166 QLG--FRDVTFIPLSALKGDNVVSRSESMPWY------------SGPTLLEILETVEVERDAQDLPLRFPVQYV 225
 
Name Accession Description Interval E-value
PTZ00141 PTZ00141
elongation factor 1- alpha; Provisional
 1-161 3.87e-98

elongation factor 1- alpha; Provisional


Pssm-ID: 185474 [Multi-domain]  Cd Length: 446  Bit Score: 289.73  E-value: 3.87e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   1 RDFIKNMITGTSQADCAILIIAGGTGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMD--TTKWSEDRFNEIIKETS 78
Cdd:PTZ00141  96 RDFIKNMITGTSQADVAILVVASTAGEFEAGISKDGQTREHALLAFTLGVKQMIVCINKMDdkTVNYSQERYDEIKKEVS 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  79 TFIKKVGYNPKAVAFVPISGWHGDNMLEESPNMPWYkgwtkenkggavKGKTLLDAIDAIEPPVRPSDKPLRLPLQDVYK 158
Cdd:PTZ00141 176 AYLKKVGYNPEKVPFIPISGWQGDNMIEKSDNMPWY------------KGPTLLEALDTLEPPKRPVDKPLRLPLQDVYK 243


                 ...
gi 756787017 159 IGG 161
Cdd:PTZ00141 244 IGG 246
EF1_alpha cd01883
Elongation Factor 1-alpha (EF1-alpha) protein family; EF1 is responsible for the GTP-dependent ...
 1-142 1.01e-83

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: 245.09  E-value: 1.01e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   1 RDFIKNMITGTSQADCAILIIAGGTGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDTT--KWSEDRFNEIIKETS 78
Cdd:cd01883   88 RDFVKNMITGASQADVAVLVVSARKGEFEAGFEKGGQTREHALLARTLGVKQLIVAVNKMDDVtvNWSQERYDEIKKKVS 167

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 756787017  79 TFIKKVGYNPKAVAFVPISGWHGDNMLEESPNMPWYKGWtkenkggavkgkTLLDAIDAIEPPV 142
Cdd:cd01883  168 PFLKKVGYNPKDVPFIPISGFTGDNLIEKSENMPWYKGP------------TLLEALDSLEPPE 219
TEF1 COG5256
Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ...
 1-161 1.69e-74

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: 228.66  E-value: 1.69e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   1 RDFIKNMITGTSQADCAILIIAGGTGEfeagiskDGQTREHALLAFTLGVRQLIVAVNKMDTTKWSEDRFNEIIKETSTF 80
Cdd:COG5256   96 RDFVKNMITGASQADAAILVVSAKDGV-------MGQTREHAFLARTLGINQLIVAVNKMDAVNYSEKRYEEVKEEVSKL 168

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  81 IKKVGYNPKAVAFVPISGWHGDNMLEESPNMPWYkgwtkenkggavKGKTLLDAIDAIEPPVRPSDKPLRLPLQDVYKIG 160
Cdd:COG5256  169 LKMVGYKVDKIPFIPVSAWKGDNVVKKSDNMPWY------------NGPTLLEALDNLKEPEKPVDKPLRIPIQDVYSIS 236


                 .
gi 756787017 161 G 161
Cdd:COG5256  237 G 237
PRK12317 PRK12317
elongation factor 1-alpha; Reviewed
 1-161 1.01e-72

elongation factor 1-alpha; Reviewed


Pssm-ID: 237055 [Multi-domain]  Cd Length: 425  Bit Score: 224.03  E-value: 1.01e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   1 RDFIKNMITGTSQADCAILIIAGgtgefEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDTTKWSEDRFNEIIKETSTF 80
Cdd:PRK12317  95 RDFVKNMITGASQADAAVLVVAA-----DDAGGVMPQTREHVFLARTLGINQLIVAINKMDAVNYDEKRYEEVKEEVSKL 169

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  81 IKKVGYNPKAVAFVPISGWHGDNMLEESPNMPWYkgwtkenkggavKGKTLLDAIDAIEPPVRPSDKPLRLPLQDVYKIG 160
Cdd:PRK12317 170 LKMVGYKPDDIPFIPVSAFEGDNVVKKSENMPWY------------NGPTLLEALDNLKPPEKPTDKPLRIPIQDVYSIS 237


                 .
gi 756787017 161 G 161
Cdd:PRK12317 238 G 238
PLN00043 PLN00043
elongation factor 1-alpha; Provisional
 1-161 2.08e-72

elongation factor 1-alpha; Provisional


Pssm-ID: 165621 [Multi-domain]  Cd Length: 447  Bit Score: 224.20  E-value: 2.08e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   1 RDFIKNMITGTSQADCAILIIAGGTGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDTT--KWSEDRFNEIIKETS 78
Cdd:PLN00043  96 RDFIKNMITGTSQADCAVLIIDSTTGGFEAGISKDGQTREHALLAFTLGVKQMICCCNKMDATtpKYSKARYDEIVKEVS 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  79 TFIKKVGYNPKAVAFVPISGWHGDNMLEESPNMPWYkgwtkenkggavKGKTLLDAIDAIEPPVRPSDKPLRLPLQDVYK 158
Cdd:PLN00043 176 SYLKKVGYNPDKIPFVPISGFEGDNMIERSTNLDWY------------KGPTLLEALDQINEPKRPSDKPLRLPLQDVYK 243


                 ...
gi 756787017 159 IGG 161
Cdd:PLN00043 244 IGG 246
CysN COG2895
Sulfate adenylyltransferase subunit 1, EFTu-like GTPase family [Inorganic ion transport and ...
 1-158 1.14e-48

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: 162.18  E-value: 1.14e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   1 RDFI-----------KNMITGTSQADCAILIIaggtgefEA--GISKdgQTREHALLAFTLGVRQLIVAVNKMDTTKWSE 67
Cdd:COG2895   95 RKFIiadtpgheqytRNMVTGASTADLAILLI-------DArkGVLE--QTRRHSYIASLLGIRHVVVAVNKMDLVDYSE 165

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  68 DRFNEIIKETSTFIKKVGYNPkaVAFVPISGWHGDNMLEESPNMPWYkgwtkenkggavKGKTLLDAIDAIEPPVRPSDK 147
Cdd:COG2895  166 EVFEEIVADYRAFAAKLGLED--ITFIPISALKGDNVVERSENMPWY------------DGPTLLEHLETVEVAEDRNDA 231

                        170
                 ....*....|.
gi 756787017 148 PLRLPLQDVYK 158
Cdd:COG2895  232 PFRFPVQYVNR 242
CysN_ATPS cd04166
CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; CysN_ATPS ...
 3-141 1.81e-39

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: 132.31  E-value: 1.81e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   3 FIKNMITGTSQADCAILIIAGGTGEFEagiskdgQTREHALLAFTLGVRQLIVAVNKMDTTKWSEDRFNEIIKETSTFIK 82
Cdd:cd04166   91 YTRNMVTGASTADLAILLVDARKGVLE-------QTRRHSYIASLLGIRHVVVAVNKMDLVDYDEEVFEEIKADYLAFAA 163

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 756787017  83 KVGYNPkaVAFVPISGWHGDNMLEESPNMPWYkgwtkenkggavKGKTLLDAIDAIEPP 141
Cdd:cd04166  164 SLGIED--ITFIPISALEGDNVVSRSENMPWY------------KGPTLLEHLETVEIA 208
cysN PRK05124
sulfate adenylyltransferase subunit 1; Provisional
 5-156 4.72e-35

sulfate adenylyltransferase subunit 1; Provisional


Pssm-ID: 235349 [Multi-domain]  Cd Length: 474  Bit Score: 126.95  E-value: 4.72e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   5 KNMITGTSQADCAILIIAGGTGEFEagiskdgQTREHALLAFTLGVRQLIVAVNKMDTTKWSEDRFNEIIKETSTFIKKV 84
Cdd:PRK05124 122 RNMATGASTCDLAILLIDARKGVLD-------QTRRHSFIATLLGIKHLVVAVNKMDLVDYSEEVFERIREDYLTFAEQL 194

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 756787017  85 GYNPKaVAFVPISGWHGDNMLEESPNMPWYkgwtkenkggavKGKTLLDAIDAIEPPVRPSDKPLRLPLQDV 156
Cdd:PRK05124 195 PGNLD-IRFVPLSALEGDNVVSQSESMPWY------------SGPTLLEVLETVDIQRVVDAQPFRFPVQYV 253
PRK05506 PRK05506
bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional
 5-156 8.53e-34

bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional


Pssm-ID: 180120 [Multi-domain]  Cd Length: 632  Bit Score: 124.66  E-value: 8.53e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   5 KNMITGTSQADCAILIIAGGTGEFEagiskdgQTREHALLAFTLGVRQLIVAVNKMDTTKWSEDRFNEIIKETSTFIKKV 84
Cdd:PRK05506 119 RNMVTGASTADLAIILVDARKGVLT-------QTRRHSFIASLLGIRHVVLAVNKMDLVDYDQEVFDEIVADYRAFAAKL 191

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 756787017  85 GYNpkAVAFVPISGWHGDNMLEESPNMPWYkgwtkenkggavKGKTLLDAIDAIEPPVRPSDKPLRLPLQDV 156
Cdd:PRK05506 192 GLH--DVTFIPISALKGDNVVTRSARMPWY------------EGPSLLEHLETVEIASDRNLKDFRFPVQYV 249
GTP_EFTU pfam00009
Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ...
 1-141 6.77e-32

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: 112.62  E-value: 6.77e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017    1 RDFIKNMITGTSQADCAILIIAGGTGefeagisKDGQTREHALLAFTLGVRqLIVAVNKMDTTkwSEDRFNEIIKETS-T 79
Cdd:pfam00009  80 VDFVKEVIRGLAQADGAILVVDAVEG-------VMPQTREHLRLARQLGVP-IIVFINKMDRV--DGAELEEVVEEVSrE 149

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 756787017   80 FIKKVGYNPKAVAFVPISGWHGDNMleespnmpwykgwtkenkggavkgKTLLDAIDAIEPP 141
Cdd:pfam00009 150 LLEKYGEDGEFVPVVPGSALKGEGV------------------------QTLLDALDEYLPS 187
CysN TIGR02034
sulfate adenylyltransferase, large subunit; Metabolic assimilation of sulfur from inorganic ...
 3-156 7.26e-32

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: 117.47  E-value: 7.26e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017    3 FIKNMITGTSQADCAILIIAGGTGEFEagiskdgQTREHALLAFTLGVRQLIVAVNKMDTTKWSEDRFNEIIKETSTFIK 82
Cdd:TIGR02034  93 YTRNMATGASTADLAVLLVDARKGVLE-------QTRRHSYIASLLGIRHVVLAVNKMDLVDYDEEVFENIKKDYLAFAE 165

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 756787017   83 KVGynPKAVAFVPISGWHGDNMLEESPNMPWYkgwtkenkggavKGKTLLDAIDAIEPPVRPSDKPLRLPLQDV 156
Cdd:TIGR02034 166 QLG--FRDVTFIPLSALKGDNVVSRSESMPWY------------SGPTLLEILETVEVERDAQDLPLRFPVQYV 225
GTP_translation_factor cd00881
GTP translation factor family primarily contains translation initiation, elongation and ...
 1-141 7.27e-22

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: 86.58  E-value: 7.27e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   1 RDFIKNMITGTSQADCAILIIAGGTGEfeagiskDGQTREHALLAFtLGVRQLIVAVNKMDTTKwsEDRFNEIIKETSTF 80
Cdd:cd00881   73 EDFSKETVRGLAQADGALLVVDANEGV-------EPQTREHLNIAL-AGGLPIIVAVNKIDRVG--EEDFDEVLREIKEL 142

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 756787017  81 IKKVGY---NPKAVAFVPISGWHGDNMLEespnmpwykgwtkenkggavkgktLLDAIDAIEPP 141
Cdd:cd00881  143 LKLIGFtflKGKDVPIIPISALTGEGIEE------------------------LLDAIVEHLPP 182
TufA COG0050
Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis] ...
 2-161 5.12e-21

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: 87.90  E-value: 5.12e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   2 DFIKNMITGTSQADCAILIIAGgtgefeagisKDG---QTREHALLAFTLGVRQLIVAVNKMDTTkwsEDrfNEIIK--- 75
Cdd:COG0050   87 DYVKNMITGAAQMDGAILVVSA----------TDGpmpQTREHILLARQVGVPYIVVFLNKCDMV---DD--EELLElve 151

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  76 -ETSTFIKKVGYNPKAVAFVPISGWhgdNMLEESPNMPWYKgwtkenkggavKGKTLLDAIDA-IEPPVRPSDKPLRLPL 153
Cdd:COG0050  152 mEVRELLSKYGFPGDDTPIIRGSAL---KALEGDPDPEWEK-----------KILELMDAVDSyIPEPERDTDKPFLMPV 217


                 ....*...
gi 756787017 154 QDVYKIGG 161
Cdd:COG0050  218 EDVFSITG 225
tufA CHL00071
elongation factor Tu
 2-161 1.38e-19

elongation factor Tu


Pssm-ID: 177010 [Multi-domain]  Cd Length: 409  Bit Score: 83.85  E-value: 1.38e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   2 DFIKNMITGTSQADCAILIIAGGTGEFEagiskdgQTREHALLAFTLGVRQLIVAVNKMDttKWSEDRFNEIIK-ETSTF 80
Cdd:CHL00071  87 DYVKNMITGAAQMDGAILVVSAADGPMP-------QTKEHILLAKQVGVPNIVVFLNKED--QVDDEELLELVElEVREL 157

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  81 IKKVGYNPKAVAFVPISGWHGDNMLEESPNM-PWYKGWTKenkggavKGKTLLDAIDA-IEPPVRPSDKPLRLPLQDVYK 158
Cdd:CHL00071 158 LSKYDFPGDDIPIVSGSALLALEALTENPKIkRGENKWVD-------KIYNLMDAVDSyIPTPERDTDKPFLMAIEDVFS 230


                 ...
gi 756787017 159 IGG 161
Cdd:CHL00071 231 ITG 233
PRK12736 PRK12736
elongation factor Tu; Reviewed
 2-161 1.73e-19

elongation factor Tu; Reviewed


Pssm-ID: 237184 [Multi-domain]  Cd Length: 394  Bit Score: 83.46  E-value: 1.73e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   2 DFIKNMITGTSQADCAILIIAggtgefeagiSKDG---QTREHALLAFTLGVRQLIVAVNKMDTTkwSEDRFNEIIK-ET 77
Cdd:PRK12736  87 DYVKNMITGAAQMDGAILVVA----------ATDGpmpQTREHILLARQVGVPYLVVFLNKVDLV--DDEELLELVEmEV 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  78 STFIKKVGYNPKAVAFVPISGWHGdnmLEESPnmPWYKgwtkenkggavKGKTLLDAIDA-IEPPVRPSDKPLRLPLQDV 156
Cdd:PRK12736 155 RELLSEYDFPGDDIPVIRGSALKA---LEGDP--KWED-----------AIMELMDAVDEyIPTPERDTDKPFLMPVEDV 218


                 ....*
gi 756787017 157 YKIGG 161
Cdd:PRK12736 219 FTITG 223
PRK00049 PRK00049
elongation factor Tu; Reviewed
 2-161 7.02e-18

elongation factor Tu; Reviewed


Pssm-ID: 234596 [Multi-domain]  Cd Length: 396  Bit Score: 79.08  E-value: 7.02e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   2 DFIKNMITGTSQADCAILIIAGGtgefeagiskDG---QTREHALLAFTLGVRQLIVAVNKMDTtkwSEDRfnEIIK--- 75
Cdd:PRK00049  87 DYVKNMITGAAQMDGAILVVSAA----------DGpmpQTREHILLARQVGVPYIVVFLNKCDM---VDDE--ELLElve 151

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  76 -ETSTFIKKVGYNPKAVAFVPISGWHGdnmLEESPNMPWYKgwtkenkggavKGKTLLDAIDA-IEPPVRPSDKPLRLPL 153
Cdd:PRK00049 152 mEVRELLSKYDFPGDDTPIIRGSALKA---LEGDDDEEWEK-----------KILELMDAVDSyIPTPERAIDKPFLMPI 217


                 ....*...
gi 756787017 154 QDVYKIGG 161
Cdd:PRK00049 218 EDVFSISG 225
PLN03127 PLN03127
Elongation factor Tu; Provisional
 2-161 4.74e-16

Elongation factor Tu; Provisional


Pssm-ID: 178673 [Multi-domain]  Cd Length: 447  Bit Score: 74.09  E-value: 4.74e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   2 DFIKNMITGTSQADCAILIIAGGTGEFEagiskdgQTREHALLAFTLGVRQLIVAVNKMDTTKWSE--DRFNEIIKETST 79
Cdd:PLN03127 136 DYVKNMITGAAQMDGGILVVSAPDGPMP-------QTKEHILLARQVGVPSLVVFLNKVDVVDDEEllELVEMELRELLS 208

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  80 FIKKVGYNPKAVAFVPISGWHGDNmleespnmpwykgwtkeNKGGAVKGKTLLDAIDAIEP-PVRPSDKPLRLPLQDVYK 158
Cdd:PLN03127 209 FYKFPGDEIPIIRGSALSALQGTN-----------------DEIGKNAILKLMDAVDEYIPePVRVLDKPFLMPIEDVFS 271


                 ...
gi 756787017 159 IGG 161
Cdd:PLN03127 272 IQG 274
EF_Tu cd01884
Elongation Factor Tu (EF-Tu) GTP-binding proteins; EF-Tu subfamily. This subfamily includes ...
 2-61 6.62e-16

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: 71.08  E-value: 6.62e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   2 DFIKNMITGTSQADCAILIIAGGTGEFEagiskdgQTREHALLAFTLGVRQLIVAVNKMD 61
Cdd:cd01884   77 DYIKNMITGAAQMDGAILVVSATDGPMP-------QTREHLLLARQVGVPYIVVFLNKAD 129
PRK12735 PRK12735
elongation factor Tu; Reviewed
 2-161 1.18e-15

elongation factor Tu; Reviewed


Pssm-ID: 183708 [Multi-domain]  Cd Length: 396  Bit Score: 72.95  E-value: 1.18e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   2 DFIKNMITGTSQADCAILIIAggtgefeagiSKDG---QTREHALLAFTLGVRQLIVAVNKMDTTKWSEdrFNEIIK-ET 77
Cdd:PRK12735  87 DYVKNMITGAAQMDGAILVVS----------AADGpmpQTREHILLARQVGVPYIVVFLNKCDMVDDEE--LLELVEmEV 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  78 STFIKKVGYNpkavafvpisgwhGDNM----------LEESPNMPWYKgwtkenkggavKGKTLLDAIDA-IEPPVRPSD 146
Cdd:PRK12735 155 RELLSKYDFP-------------GDDTpiirgsalkaLEGDDDEEWEA-----------KILELMDAVDSyIPEPERAID 210

                        170
                 ....*....|....*
gi 756787017 147 KPLRLPLQDVYKIGG 161
Cdd:PRK12735 211 KPFLMPIEDVFSISG 225
PLN03126 PLN03126
Elongation factor Tu; Provisional
 2-161 1.72e-15

Elongation factor Tu; Provisional


Pssm-ID: 215592 [Multi-domain]  Cd Length: 478  Bit Score: 72.73  E-value: 1.72e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   2 DFIKNMITGTSQADCAILIIAGGTGEFEagiskdgQTREHALLAFTLGVRQLIVAVNKMDTTKwSEDRFNEIIKETSTFI 81
Cdd:PLN03126 156 DYVKNMITGAAQMDGAILVVSGADGPMP-------QTKEHILLAKQVGVPNMVVFLNKQDQVD-DEELLELVELEVRELL 227

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  82 KKVGYNPKAVAFVPISGWHGDNMLEESPNMPwyKGwtkENKgGAVKGKTLLDAIDAIEP-PVRPSDKPLRLPLQDVYKIG 160
Cdd:PLN03126 228 SSYEFPGDDIPIISGSALLALEALMENPNIK--RG---DNK-WVDKIYELMDAVDSYIPiPQRQTDLPFLLAVEDVFSIT 301


                 .
gi 756787017 161 G 161
Cdd:PLN03126 302 G 302
EF-Tu TIGR00485
translation elongation factor TU; This model models orthologs of translation elongation factor ...
 2-161 2.00e-15

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: 72.12  E-value: 2.00e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017    2 DFIKNMITGTSQADCAILIIAGGTGEFEagiskdgQTREHALLAFTLGVRQLIVAVNKMDTTKWSE--DRFNEIIKETST 79
Cdd:TIGR00485  87 DYVKNMITGAAQMDGAILVVSATDGPMP-------QTREHILLARQVGVPYIVVFLNKCDMVDDEEllELVEMEVRELLS 159

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   80 FIKKVGYNPKAVAFVPISGWHGDNMLEEspnmpwykgwtkenkggavKGKTLLDAIDA-IEPPVRPSDKPLRLPLQDVYK 158
Cdd:TIGR00485 160 QYDFPGDDTPIIRGSALKALEGDAEWEA-------------------KILELMDAVDEyIPTPEREIDKPFLLPIEDVFS 220


                  ...
gi 756787017  159 IGG 161
Cdd:TIGR00485 221 ITG 223
SelB COG3276
Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure ...
 2-152 1.57e-11

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: 61.08  E-value: 1.57e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   2 DFIKNMITGTSQADCAILIIAggtgefeagiSKDG---QTREH-ALLAFtLGVRQLIVAVNKMDTTkwSEDRFNEIIKET 77
Cdd:COG3276   63 KFIKNMLAGAGGIDLVLLVVA----------ADEGvmpQTREHlAILDL-LGIKRGIVVLTKADLV--DEEWLELVEEEI 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  78 STFIKkvGYNPKAVAFVPISgwhgdnmleespnmpwykgwtkenkggAVKGK---TLLDAIDAI--EPPVRPSDKPLRLP 152
Cdd:COG3276  130 RELLA--GTFLEDAPIVPVS---------------------------AVTGEgidELRAALDALaaAVPARDADGPFRLP 180
SelB cd04171
SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ...
 2-86 3.52e-10

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: 55.30  E-value: 3.52e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   2 DFIKNMITGTSQADCAILIIAGgtgefEAGISKdgQTREHALLAFTLGVRQLIVAVNKMDTTkwSEDRFNEIIKETSTFI 81
Cdd:cd04171   62 KFVKNMLAGAGGIDAVLLVVAA-----DEGIMP--QTREHLEILELLGIKKGLVVLTKADLV--DEDRLELVEEEILELL 132


                 ....*
gi 756787017  82 KKVGY 86
Cdd:cd04171  133 AGTFL 137
selB TIGR00475
selenocysteine-specific elongation factor SelB; In prokaryotes, the incorporation of ...
 3-161 6.33e-10

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: 56.42  E-value: 6.33e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017    3 FIKNMITGTSQADCAILIIAggtgefeagiSKDG---QTREHALLAFTLGVRQLIVAVNKMDTTkwSEDRFNEIIKETST 79
Cdd:TIGR00475  63 FISNAIAGGGGIDAALLVVD----------ADEGvmtQTGEHLAVLDLLGIPHTIVVITKADRV--NEEEIKRTEMFMKQ 130

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   80 FIKKVGYNPKAVAFVpISGWHGDNMLEESPNMpwykgwtkenkggavkgKTLLDAIDAieppvRPSDKPLRLPLQDVYKI 159
Cdd:TIGR00475 131 ILNSYIFLKNAKIFK-TSAKTGQGIGELKKEL-----------------KNLLESLDI-----KRIQKPLRMAIDRAFKV 187


                  ..
gi 756787017  160 GG 161
Cdd:TIGR00475 188 KG 189
EF1_alpha_II cd03693
Domain II of elongation factor 1-alpha; This family represents domain II of elongation factor ...
 145-161 6.03e-06

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: 42.56  E-value: 6.03e-06
                         10
                 ....*....|....*..
gi 756787017 145 SDKPLRLPLQDVYKIGG 161
Cdd:cd03693    1 TDKPLRLPIQDVYKIGG 17
PRK04000 PRK04000
translation initiation factor IF-2 subunit gamma; Validated
 7-151 6.52e-05

translation initiation factor IF-2 subunit gamma; Validated


Pssm-ID: 235194 [Multi-domain]  Cd Length: 411  Bit Score: 41.76  E-value: 6.52e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   7 MITGTSQADCAILIIAGGTGEFEAgiskdgQTREHaLLAFT-LGVRQLIVAVNKMDTTkwSEDR----FNEiIKEtstFI 81
Cdd:PRK04000 102 MLSGAALMDGAILVIAANEPCPQP------QTKEH-LMALDiIGIKNIVIVQNKIDLV--SKERalenYEQ-IKE---FV 168

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 756787017  82 KkvGYNPKAVAFVPISGWHGDNMleespnmpwykgwtkenkggavkgKTLLDAIDA-IEPPVRPSDKPLRL 151
Cdd:PRK04000 169 K--GTVAENAPIIPVSALHKVNI------------------------DALIEAIEEeIPTPERDLDKPPRM 213
IF2_eIF5B cd01887
Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; IF2/eIF5B ...
 10-104 1.56e-03

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: 37.07  E-value: 1.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017  10 GTSQADCAILIIAGGTGeFEAgiskdgQTRE---HALLAFTlgvrQLIVAVNKMDTTKWSE---DRFNEIIKETSTFIKK 83
Cdd:cd01887   69 GASVTDIAILVVAADDG-VMP------QTIEainHAKAANV----PIIVAINKIDKPYGTEadpERVKNELSELGLVGEE 137

                         90       100
                 ....*....|....*....|.
gi 756787017  84 VGynpKAVAFVPISGWHGDNM 104
Cdd:cd01887  138 WG---GDVSIVPISAKTGEGI 155
PTZ00327 PTZ00327
eukaryotic translation initiation factor 2 gamma subunit; Provisional
 7-97 2.53e-03

eukaryotic translation initiation factor 2 gamma subunit; Provisional


Pssm-ID: 240362 [Multi-domain]  Cd Length: 460  Bit Score: 37.29  E-value: 2.53e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 756787017   7 MITGTSQADCAILIIAGGTGefeagiSKDGQTREHALLAFTLGVRQLIVAVNKMDTTKWSE--DRFNEIIKetstFIKkv 84
Cdd:PTZ00327 134 MLNGAAVMDAALLLIAANES------CPQPQTSEHLAAVEIMKLKHIIILQNKIDLVKEAQaqDQYEEIRN----FVK-- 201

                         90
                 ....*....|...
gi 756787017  85 GYNPKAVAFVPIS 97
Cdd:PTZ00327 202 GTIADNAPIIPIS 214
 
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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