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Conserved domains on  [gi|490433988|gb|AGL12643|]
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initiation translation factor 2, partial [Klebsiella oxytoca]

Protein Classification

translation initiation factor IF-2( domain architecture ID 11425233)

translation initiation factor IF-2 protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits; also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex

CATH:  3.40.50.300
Gene Ontology:  GO:0006413|GO:0003743|GO:0005525|GO:0003924
PubMed:  11738593|11916378|22308033

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
InfB COG0532
Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; ...
 1-205 1.26e-134

Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; Translation initiation factor IF-2, a GTPase is part of the Pathway/BioSystem: Translation factors


:

Pssm-ID: 440298 [Multi-domain]  Cd Length: 502  Bit Score: 386.29  E-value: 1.26e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   1 SMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKPEADPDRVKNELSQYGILPEEWGGESQFVH 80
Cdd:COG0532   66 AMRARGAQVTDIVILVVAADDGVMPQTIEAINHAKAAGVPIIVAINKIDKPGANPDRVKQELAEHGLVPEEWGGDTIFVP 145

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  81 VSAKAGTGIDELLDAILLQAEVLELKAVRKGMASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGFEYGRVRAMRNE 160
Cdd:COG0532  146 VSAKTGEGIDELLEMILLQAEVLELKANPDRPARGTVIEAKLDKGRGPVATVLVQNGTLKVGDIVVAGTAYGRVRAMFDD 225

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 490433988 161 LGQEVLEAGPSIPVEILGLSGVPAAGDEVTVVRDEKKAREVALYR 205
Cdd:COG0532  226 RGKRVKEAGPSTPVEILGLSGVPQAGDEFVVVEDEKKAREIAEKR 270
 
Name Accession Description Interval E-value
InfB COG0532
Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; ...
 1-205 1.26e-134

Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; Translation initiation factor IF-2, a GTPase is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440298 [Multi-domain]  Cd Length: 502  Bit Score: 386.29  E-value: 1.26e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   1 SMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKPEADPDRVKNELSQYGILPEEWGGESQFVH 80
Cdd:COG0532   66 AMRARGAQVTDIVILVVAADDGVMPQTIEAINHAKAAGVPIIVAINKIDKPGANPDRVKQELAEHGLVPEEWGGDTIFVP 145

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  81 VSAKAGTGIDELLDAILLQAEVLELKAVRKGMASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGFEYGRVRAMRNE 160
Cdd:COG0532  146 VSAKTGEGIDELLEMILLQAEVLELKANPDRPARGTVIEAKLDKGRGPVATVLVQNGTLKVGDIVVAGTAYGRVRAMFDD 225

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 490433988 161 LGQEVLEAGPSIPVEILGLSGVPAAGDEVTVVRDEKKAREVALYR 205
Cdd:COG0532  226 RGKRVKEAGPSTPVEILGLSGVPQAGDEFVVVEDEKKAREIAEKR 270
IF-2 TIGR00487
translation initiation factor IF-2; This model discriminates eubacterial (and mitochondrial) ...
 1-205 3.01e-120

translation initiation factor IF-2; This model discriminates eubacterial (and mitochondrial) translation initiation factor 2 (IF-2), encoded by the infB gene in bacteria, from similar proteins in the Archaea and Eukaryotes. In the bacteria and in organelles, the initiator tRNA is charged with N-formyl-Met instead of Met. This translation factor acts in delivering the initator tRNA to the ribosome. It is one of a number of GTP-binding translation factors recognized by the pfam model GTP_EFTU. [Protein synthesis, Translation factors]


Pssm-ID: 273102 [Multi-domain]  Cd Length: 587  Bit Score: 352.92  E-value: 3.01e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988    1 SMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKPEADPDRVKNELSQYGILPEEWGGESQFVH 80
Cdd:TIGR00487 150 SMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVPIIVAINKIDKPEANPDRVKQELSEYGLVPEDWGGDTIFVP 229

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   81 VSAKAGTGIDELLDAILLQAEVLELKAVRKGMASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGFEYGRVRAMRNE 160
Cdd:TIGR00487 230 VSALTGDGIDELLDMILLQSEVEELKANPNGQASGVVIEAQLDKGRGPVATVLVQSGTLRVGDIVVVGAAYGRVRAMIDE 309

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 490433988  161 LGQEVLEAGPSIPVEILGLSGVPAAGDEVTVVRDEKKAREVALYR 205
Cdd:TIGR00487 310 NGKSVKEAGPSKPVEILGLSDVPAAGDEFIVFKDEKDARLVAEKR 354
infB CHL00189
translation initiation factor 2; Provisional
 1-202 1.24e-80

translation initiation factor 2; Provisional


Pssm-ID: 177089 [Multi-domain]  Cd Length: 742  Bit Score: 254.37  E-value: 1.24e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   1 SMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKPEADPDRVKNELSQYGILPEEWGGESQFVH 80
Cdd:CHL00189 310 SMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANVPIIVAINKIDKANANTERIKQQLAKYNLIPEKWGGDTPMIP 389

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  81 VSAKAGTGIDELLDAILLQAEVLELKAVRKGMASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGFEYGRVRAMRNE 160
Cdd:CHL00189 390 ISASQGTNIDKLLETILLLAEIEDLKADPTQLAQGIILEAHLDKTKGPVATILVQNGTLHIGDIIVIGTSYAKIRGMINS 469

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 490433988 161 LGQEVLEAGPSIPVEILGLSGVPAAGDEVTVVRDEKKAREVA 202
Cdd:CHL00189 470 LGNKINLATPSSVVEIWGLSSVPATGEHFQVFNSEKEAKLKI 511
IF2_eIF5B cd01887
Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; IF2/eIF5B ...
 1-103 9.37e-49

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: 156.48  E-value: 9.37e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   1 SMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKP---EADPDRVKNELSQYGILPEEWGGESQ 77
Cdd:cd01887   64 NMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAANVPIIVAINKIDKPygtEADPERVKNELSELGLVGEEWGGDVS 143

                         90       100
                 ....*....|....*....|....*.
gi 490433988  78 FVHVSAKAGTGIDELLDAILLQAEVL 103
Cdd:cd01887  144 IVPISAKTGEGIDDLLEAILLLAEVL 169
GTP_EFTU pfam00009
Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ...
 3-96 1.08e-16

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: 74.48  E-value: 1.08e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988    3 RARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKP-EADPDRVKNELSQ-YGILPEEWGGESQFVH 80
Cdd:pfam00009  86 VIRGLAQADGAILVVDAVEGVMPQTREHLRLARQLGVPIIVFINKMDRVdGAELEEVVEEVSReLLEKYGEDGEFVPVVP 165

                          90
                  ....*....|....*.
gi 490433988   81 VSAKAGTGIDELLDAI 96
Cdd:pfam00009 166 GSALKGEGVQTLLDAL 181
 
Name Accession Description Interval E-value
InfB COG0532
Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; ...
 1-205 1.26e-134

Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; Translation initiation factor IF-2, a GTPase is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440298 [Multi-domain]  Cd Length: 502  Bit Score: 386.29  E-value: 1.26e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   1 SMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKPEADPDRVKNELSQYGILPEEWGGESQFVH 80
Cdd:COG0532   66 AMRARGAQVTDIVILVVAADDGVMPQTIEAINHAKAAGVPIIVAINKIDKPGANPDRVKQELAEHGLVPEEWGGDTIFVP 145

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  81 VSAKAGTGIDELLDAILLQAEVLELKAVRKGMASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGFEYGRVRAMRNE 160
Cdd:COG0532  146 VSAKTGEGIDELLEMILLQAEVLELKANPDRPARGTVIEAKLDKGRGPVATVLVQNGTLKVGDIVVAGTAYGRVRAMFDD 225

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 490433988 161 LGQEVLEAGPSIPVEILGLSGVPAAGDEVTVVRDEKKAREVALYR 205
Cdd:COG0532  226 RGKRVKEAGPSTPVEILGLSGVPQAGDEFVVVEDEKKAREIAEKR 270
IF-2 TIGR00487
translation initiation factor IF-2; This model discriminates eubacterial (and mitochondrial) ...
 1-205 3.01e-120

translation initiation factor IF-2; This model discriminates eubacterial (and mitochondrial) translation initiation factor 2 (IF-2), encoded by the infB gene in bacteria, from similar proteins in the Archaea and Eukaryotes. In the bacteria and in organelles, the initiator tRNA is charged with N-formyl-Met instead of Met. This translation factor acts in delivering the initator tRNA to the ribosome. It is one of a number of GTP-binding translation factors recognized by the pfam model GTP_EFTU. [Protein synthesis, Translation factors]


Pssm-ID: 273102 [Multi-domain]  Cd Length: 587  Bit Score: 352.92  E-value: 3.01e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988    1 SMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKPEADPDRVKNELSQYGILPEEWGGESQFVH 80
Cdd:TIGR00487 150 SMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVPIIVAINKIDKPEANPDRVKQELSEYGLVPEDWGGDTIFVP 229

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   81 VSAKAGTGIDELLDAILLQAEVLELKAVRKGMASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGFEYGRVRAMRNE 160
Cdd:TIGR00487 230 VSALTGDGIDELLDMILLQSEVEELKANPNGQASGVVIEAQLDKGRGPVATVLVQSGTLRVGDIVVVGAAYGRVRAMIDE 309

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 490433988  161 LGQEVLEAGPSIPVEILGLSGVPAAGDEVTVVRDEKKAREVALYR 205
Cdd:TIGR00487 310 NGKSVKEAGPSKPVEILGLSDVPAAGDEFIVFKDEKDARLVAEKR 354
infB CHL00189
translation initiation factor 2; Provisional
 1-202 1.24e-80

translation initiation factor 2; Provisional


Pssm-ID: 177089 [Multi-domain]  Cd Length: 742  Bit Score: 254.37  E-value: 1.24e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   1 SMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKPEADPDRVKNELSQYGILPEEWGGESQFVH 80
Cdd:CHL00189 310 SMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANVPIIVAINKIDKANANTERIKQQLAKYNLIPEKWGGDTPMIP 389

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  81 VSAKAGTGIDELLDAILLQAEVLELKAVRKGMASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGFEYGRVRAMRNE 160
Cdd:CHL00189 390 ISASQGTNIDKLLETILLLAEIEDLKADPTQLAQGIILEAHLDKTKGPVATILVQNGTLHIGDIIVIGTSYAKIRGMINS 469

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 490433988 161 LGQEVLEAGPSIPVEILGLSGVPAAGDEVTVVRDEKKAREVA 202
Cdd:CHL00189 470 LGNKINLATPSSVVEIWGLSSVPATGEHFQVFNSEKEAKLKI 511
IF2_eIF5B cd01887
Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; IF2/eIF5B ...
 1-103 9.37e-49

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: 156.48  E-value: 9.37e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   1 SMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKP---EADPDRVKNELSQYGILPEEWGGESQ 77
Cdd:cd01887   64 NMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAANVPIIVAINKIDKPygtEADPERVKNELSELGLVGEEWGGDVS 143

                         90       100
                 ....*....|....*....|....*.
gi 490433988  78 FVHVSAKAGTGIDELLDAILLQAEVL 103
Cdd:cd01887  144 IVPISAKTGEGIDDLLEAILLLAEVL 169
IF2_mtIF2_II cd03702
Domain II of bacterial and mitochondrial Initiation Factor 2; This family represents domain II ...
 113-205 1.13e-48

Domain II of bacterial and mitochondrial Initiation Factor 2; This family represents domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homolog mtIF2. IF2, the largest initiation factor, is an essential GTP binding protein. In E. coli, three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2.


Pssm-ID: 293903 [Multi-domain]  Cd Length: 96  Bit Score: 153.73  E-value: 1.13e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988 113 ASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGFEYGRVRAMRNELGQEVLEAGPSIPVEILGLSGVPAAGDEVTVV 192
Cdd:cd03702    2 ARGVVIESKLDKGRGPVATVLVQNGTLKVGDILVAGTTYGKVRAMIDDNGKRIKEAGPSTPVEILGLNGVPQAGDKFIVV 81

                         90
                 ....*....|...
gi 490433988 193 RDEKKAREVALYR 205
Cdd:cd03702   82 DSEKEAREIAEKR 94
GTP_EFTU pfam00009
Elongation factor Tu GTP binding domain; This domain contains a P-loop motif, also found in ...
 3-96 1.08e-16

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: 74.48  E-value: 1.08e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988    3 RARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKP-EADPDRVKNELSQ-YGILPEEWGGESQFVH 80
Cdd:pfam00009  86 VIRGLAQADGAILVVDAVEGVMPQTREHLRLARQLGVPIIVFINKMDRVdGAELEEVVEEVSReLLEKYGEDGEFVPVVP 165

                          90
                  ....*....|....*.
gi 490433988   81 VSAKAGTGIDELLDAI 96
Cdd:pfam00009 166 GSALKGEGVQTLLDAL 181
PRK04004 PRK04004
translation initiation factor IF-2; Validated
 1-157 3.76e-12

translation initiation factor IF-2; Validated


Pssm-ID: 235195 [Multi-domain]  Cd Length: 586  Bit Score: 64.43  E-value: 3.76e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   1 SMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDK----------P-----EADPDRVKNELSQ- 64
Cdd:PRK04004  86 NLRKRGGALADIAILVVDINEGFQPQTIEAINILKRRKTPFVVAANKIDRipgwkstedaPflesiEKQSQRVQQELEEk 165

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  65 -YGILPE--EWGGESQF-------------VHVSAKAGTGIDELLdAIL--LQAEVLE--LKAVRKGMASGAVIESFLDK 124
Cdd:PRK04004 166 lYELIGQlsELGFSADRfdrvkdftktvaiVPVSAKTGEGIPDLL-MVLagLAQRYLEerLKIDVEGPGKGTVLEVKEER 244

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 490433988 125 GRGPVATVLVREGTLHKGDIVLCGFEYG----RVRAM 157
Cdd:PRK04004 245 GLGTTIDVILYDGTLRKGDTIVVGGKDGpivtKVRAL 281
GTP_translation_factor cd00881
GTP translation factor family primarily contains translation initiation, elongation and ...
 5-101 7.69e-12

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: 61.16  E-value: 7.69e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   5 RGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDK-PEADPDRV----KNELSQYGILPEEWGGESqFV 79
Cdd:cd00881   81 RGLAQADGALLVVDANEGVEPQTREHLNIALAGGLPIIVAVNKIDRvGEEDFDEVlreiKELLKLIGFTFLKGKDVP-II 159

                         90       100
                 ....*....|....*....|..
gi 490433988  80 HVSAKAGTGIDELLDAILLQAE 101
Cdd:cd00881  160 PISALTGEGIEELLDAIVEHLP 181
LepA cd01890
LepA also known as Elongation Factor 4 (EF4); LepA (also known as elongation factor 4, EF4) ...
 9-96 4.32e-11

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: 59.08  E-value: 4.32e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   9 ATDIVVLVVAADDGVMPQTIE----AIQHAKAAGVPVvvavNKIDKPEADPDRVKNELSQY-GILPEEwggesqFVHVSA 83
Cdd:cd01890   90 ACEGALLVVDATQGVEAQTLAnfylALENNLEIIPVI----NKIDLPAADPDRVKQEIEDVlGLDASE------AILVSA 159

                         90
                 ....*....|...
gi 490433988  84 KAGTGIDELLDAI 96
Cdd:cd01890  160 KTGLGVEDLLEAI 172
SelB COG3276
Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure ...
 11-170 5.05e-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: 5.05e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  11 DIVVLVVAADDGVMPQTIE---------------AIqhakaagvpvvvavNKIDKpeADPDR-------VKNELSQYGIl 68
Cdd:COG3276   76 DLVLLVVAADEGVMPQTREhlaildllgikrgivVL--------------TKADL--VDEEWlelveeeIRELLAGTFL- 138

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  69 peewgGESQFVHVSAKAGTGIDELLDAILLQAEVLELKAvrkgmASG----AVIESFLDKGRGPVATVLVREGTLHKGD- 143
Cdd:COG3276  139 -----EDAPIVPVSAVTGEGIDELRAALDALAAAVPARD-----ADGpfrlPIDRVFSIKGFGTVVTGTLLSGTVRVGDe 208

                        170       180
                 ....*....|....*....|....*...
gi 490433988 144 IVLCGFEY-GRVRAMRNElGQEVLEAGP 170
Cdd:COG3276  209 LELLPSGKpVRVRGIQVH-GQPVEEAYA 235
PRK14845 PRK14845
translation initiation factor IF-2; Provisional
 1-148 1.01e-10

translation initiation factor IF-2; Provisional


Pssm-ID: 237833 [Multi-domain]  Cd Length: 1049  Bit Score: 60.28  E-value: 1.01e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988    1 SMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDK-----PEADPDRVKN--ELSQYGI------ 67
Cdd:PRK14845  541 SLRKRGGSLADLAVLVVDINEGFKPQTIEAINILRQYKTPFVVAANKIDLipgwnISEDEPFLLNfnEQDQHALteleik 620

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   68 LPE------EWGGESQ-------------FVHVSAKAGTGIDELLDAIL-LQAEVLE--LKAVRKGMASGAVIESFLDKG 125
Cdd:PRK14845  621 LYEligklyELGFDADrfdrvqdftrtvaIVPVSAKTGEGIPELLMMVAgLAQKYLEerLKLNVEGYAKGTILEVKEEKG 700

                         170       180
                  ....*....|....*....|...
gi 490433988  126 RGPVATVLVREGTLHKGDIVLCG 148
Cdd:PRK14845  701 LGTTIDAIIYDGTLRRGDTIVVG 723
SelB cd04171
SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ...
 6-97 6.15e-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: 55.69  E-value: 6.15e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   6 GAQATDIVVLVVAADDGVMPQTIE--AIQHaKAAGVPVVVAVNKIDKPEAD-PDRVKNELSQYgiLPEEWGGESQFVHVS 82
Cdd:cd04171   70 GAGGIDAVLLVVAADEGIMPQTREhlEILE-LLGIKKGLVVLTKADLVDEDrLELVEEEILEL--LAGTFLADAPIFPVS 146

                         90
                 ....*....|....*
gi 490433988  83 AKAGTGIDELLDAIL 97
Cdd:cd04171  147 SVTGEGIEELKNYLD 161
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 2-97 1.06e-05

small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General]


Pssm-ID: 272973 [Multi-domain]  Cd Length: 162  Bit Score: 43.90  E-value: 1.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988    2 MRARGAQATDIVVLVVAADDGVMPQTIEaIQHAKAAGVPVVVAVNKIDKPEADpdrvknELSQYGILPEEWGGESqFVHV 81
Cdd:TIGR00231  74 QVERSLRVFDIVILVLDVEEILEKQTKE-IIHHADSGVPIILVGNKIDLKDAD------LKTHVASEFAKLNGEP-IIPL 145

                          90
                  ....*....|....*.
gi 490433988   82 SAKAGTGIDELLDAIL 97
Cdd:TIGR00231 146 SAETGKNIDSAFKIVE 161
IF2_IF5B_II cd03701
Domain II of prokaryotic Initiation Factor 2 and archaeal and eukaryotic Initiation Factor 5; ...
 113-192 1.53e-05

Domain II of prokaryotic Initiation Factor 2 and archaeal and eukaryotic Initiation Factor 5; This family represents domain II of prokaryotic Initiation Factor 2 (IF2) and its archaeal and eukaryotic homologue aeIF5B. IF2, the largest initiation factor, is an essential GTP binding protein. In E. coli, three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma.


Pssm-ID: 293902 [Multi-domain]  Cd Length: 96  Bit Score: 42.27  E-value: 1.53e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988 113 ASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCG----FEYGRVRAM----------RNELGQEVLEAGPSIPVEILG 178
Cdd:cd03701    2 PRGVILEVKLDKGAGITIDMLVQEGTLRVGDTIVAGeskdVIYTRIRALldpdpleemeSRKKGNKRKEVGAASGVKILG 81

                         90
                 ....*....|....*
gi 490433988 179 LS-GVPAAGDEVTVV 192
Cdd:cd03701   82 FGqELPHAGDPLEVV 96
TypA_BipA cd01891
Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; BipA ...
 5-97 2.06e-05

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: 43.35  E-value: 2.06e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   5 RGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKPEADPDRVKNELsqYGILPEEWGGESQ----FVH 80
Cdd:cd01891   84 RVLSMVDGVLLLVDASEGPMPQTRFVLKKALEAGLKPIVVINKIDRPDARPEEVVDEV--FDLFLELNATDEQldfpIVY 161

                         90       100
                 ....*....|....*....|....*..
gi 490433988  81 VSAKAG----------TGIDELLDAIL 97
Cdd:cd01891  162 ASAKNGwaslnlddpsEDLDPLFETII 188
Arf_Arl cd00878
ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ...
 46-94 7.61e-05

ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions.


Pssm-ID: 206644 [Multi-domain]  Cd Length: 158  Bit Score: 41.41  E-value: 7.61e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 490433988  46 NKIDKPEA-DPDRVKNELSQYGILPEEWggesQFVHVSAKAGTGIDELLD 94
Cdd:cd00878  108 NKQDLPGAlTESELIELLGLESIKGRRW----HIQPCSAVTGDGLDEGLD 153
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 10-97 7.88e-05

Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions.


Pssm-ID: 206648 [Multi-domain]  Cd Length: 161  Bit Score: 41.29  E-value: 7.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  10 TDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVA--VNKIDKPEADPDRVKNELSQYGILPEEwggesQFVHVSAKAGT 87
Cdd:cd00882   76 ADLILLVVDSTDRESEEDAKLLILRRLRKEGIPIIlvGNKIDLLEEREVEELLRLEELAKILGV-----PVFEVSAKTGE 150

                         90
                 ....*....|
gi 490433988  88 GIDELLDAIL 97
Cdd:cd00882  151 GVDELFEKLI 160
PRK10512 PRK10512
selenocysteinyl-tRNA-specific translation factor; Provisional
 11-158 1.31e-04

selenocysteinyl-tRNA-specific translation factor; Provisional


Pssm-ID: 182508 [Multi-domain]  Cd Length: 614  Bit Score: 41.96  E-value: 1.31e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  11 DIVVLVVAADDGVMPQTIE--AIQHAKAAGVPVVV--AVNKIDKPEADPDR--VKNELSQYGilpeeWGGESQFVhVSAK 84
Cdd:PRK10512  76 DHALLVVACDDGVMAQTREhlAILQLTGNPMLTVAltKADRVDEARIAEVRrqVKAVLREYG-----FAEAKLFV-TAAT 149

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490433988  85 AGTGIDELLDAILLQAEVLELKAVRKGMasgAVIESFLDKGRGPVATVLVREGTLHKGDIV-LCGFEYG-RVRAMR 158
Cdd:PRK10512 150 EGRGIDALREHLLQLPEREHAAQHRFRL---AIDRAFTVKGAGLVVTGTALSGEVKVGDTLwLTGVNKPmRVRGLH 222
Era_like cd00880
E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ...
 7-100 2.54e-04

E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngB), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family.


Pssm-ID: 206646 [Multi-domain]  Cd Length: 161  Bit Score: 39.92  E-value: 2.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   7 AQATDIVVLVVAADdgvMPQTIEAIQHAKAAGVPVVV--AVNKIDKPEADPDRVKNELSQYGILPEEwggesQFVHVSAK 84
Cdd:cd00880   74 ADRADLVLLVVDSD---LTPVEEEAKLGLLRERGKPVllVLNKIDLVPESEEEELLRERKLELLPDL-----PVIAVSAL 145

                         90
                 ....*....|....*.
gi 490433988  85 AGTGIDELLDAILLQA 100
Cdd:cd00880  146 PGEGIDELRKKIAELL 161
SelB_euk cd01889
SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ...
 6-92 6.69e-04

SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryotes, they do share a common feature. Unlike in E. coli, these SECIS elements are located in the 3' UTRs. This group contains eukaryotic SelBs and some from archaea.


Pssm-ID: 206676 [Multi-domain]  Cd Length: 192  Bit Score: 38.89  E-value: 6.69e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   6 GAQATDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDK-PEADPDRVKNELSQ--YGILPEEWGGESQFVHVS 82
Cdd:cd01889   88 GAQIIDLMLLVVDAKKGIQTQTAECLVIGELLCKPLIVVLNKIDLiPEEERKRKIEKMKKrlQKTLEKTRLKDSPIIPVS 167

                         90
                 ....*....|
gi 490433988  83 AKAGTGIDEL 92
Cdd:cd01889  168 AKPGEGEAEL 177
TypA COG1217
Predicted membrane GTPase TypA/BipA involved in stress response [Signal transduction ...
 11-61 6.84e-04

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


Pssm-ID: 440830 [Multi-domain]  Cd Length: 606  Bit Score: 40.00  E-value: 6.84e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490433988  11 DIVVLVVAADDGVMPQT-------IEA----IqhakaagvpvvVAVNKIDKPEADPDRVKNE 61
Cdd:COG1217   94 DGVLLLVDAFEGPMPQTrfvlkkaLELglkpI-----------VVINKIDRPDARPDEVVDE 144
EF_Tu cd01884
Elongation Factor Tu (EF-Tu) GTP-binding proteins; EF-Tu subfamily. This subfamily includes ...
 6-31 7.59e-04

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: 39.10  E-value: 7.59e-04
                         10        20
                 ....*....|....*....|....*.
gi 490433988   6 GAQATDIVVLVVAADDGVMPQTIEAI 31
Cdd:cd01884   85 GAAQMDGAILVVSATDGPMPQTREHL 110
Era COG1159
GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis];
11-97 9.59e-04

GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440773 [Multi-domain]  Cd Length: 290  Bit Score: 39.20  E-value: 9.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  11 DIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKpeADPDRVKNELSQYgilpEEWGGESQFVHVSAKAGTGID 90
Cdd:COG1159   84 DVILFVVDATEKIGEGDEFILELLKKLKTPVILVINKIDL--VKKEELLPLLAEY----SELLDFAEIVPISALKGDNVD 157


                 ....*..
gi 490433988  91 ELLDAIL 97
Cdd:COG1159  158 ELLDEIA 164
MnmE COG0486
tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal ...
 3-97 1.20e-03

tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal structure and biogenesis]; tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440253 [Multi-domain]  Cd Length: 448  Bit Score: 38.89  E-value: 1.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   3 RARGAQAtDIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVavNKIDKPEADPDRVKNElsqygilpeewgGESQFVHVS 82
Cdd:COG0486  287 REAIEEA-DLVLLLLDASEPLTEEDEEILEKLKDKPVIVVL--NKIDLPSEADGELKSL------------PGEPVIAIS 351

                         90
                 ....*....|....*
gi 490433988  83 AKAGTGIDELLDAIL 97
Cdd:COG0486  352 AKTGEGIDELKEAIL 366
EngA1 cd01894
EngA1 GTPase contains the first domain of EngA; This EngA1 subfamily CD represents the first ...
 11-97 1.42e-03

EngA1 GTPase contains the first domain of EngA; This EngA1 subfamily CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.


Pssm-ID: 206681 [Multi-domain]  Cd Length: 157  Bit Score: 37.80  E-value: 1.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  11 DIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKPEADPDrvKNELSQYGIlpeewggeSQFVHVSAKAGTGID 90
Cdd:cd01894   78 DVILFVVDGREGLTPADEEIAKYLRKSKKPVILVVNKIDNIKEEEE--AAEFYSLGF--------GEPIPISAEHGRGIG 147


                 ....*..
gi 490433988  91 ELLDAIL 97
Cdd:cd01894  148 DLLDAIL 154
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
11-97 1.53e-03

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 38.04  E-value: 1.53e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  11 DIVVLVVaadDGVMPQTIEAIQHAKAAGVPVVVAV------NKIDkpEADPDRVKNELSQYGILPEEWGGEsqFVHVSAK 84
Cdd:COG1100   81 SLYLFVV---DGTREETLQSLYELLESLRRLGKKSpiilvlNKID--LYDEEEIEDEERLKEALSEDNIVE--VVATSAK 153

                         90
                 ....*....|...
gi 490433988  85 AGTGIDELLDAIL 97
Cdd:COG1100  154 TGEGVEELFAALA 166
TufA COG0050
Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis] ...
 6-145 2.01e-03

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


Pssm-ID: 439820 [Multi-domain]  Cd Length: 396  Bit Score: 38.21  E-value: 2.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   6 GAQATDIVVLVVAADDGVMPQTIEAI----QhakAAGVPVVVAVNKIDKPEaDPD-------RVKNELSQYGiLPeewGG 74
Cdd:COG0050   95 GAAQMDGAILVVSATDGPMPQTREHIllarQ---VGVPYIVVFLNKCDMVD-DEEllelvemEVRELLSKYG-FP---GD 166

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  75 ESQFVHVSA-KAGTG---------IDELLDAILLQAEVLElKAVRKG--MAsgavIES-FLDKGRGPVATVLVREGTLHK 141
Cdd:COG0050  167 DTPIIRGSAlKALEGdpdpewekkILELMDAVDSYIPEPE-RDTDKPflMP----VEDvFSITGRGTVVTGRVERGIIKV 241


                 ....
gi 490433988 142 GDIV 145
Cdd:COG0050  242 GDEV 245
trmE cd04164
trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in ...
 3-97 2.60e-03

trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance.


Pssm-ID: 206727 [Multi-domain]  Cd Length: 159  Bit Score: 37.09  E-value: 2.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   3 RARGAQAtDIVVLVVaadDGVMPQTIE-AIQHAKAAGVPVVVAVNKIDKPEADPDRVKNElsqygilpeewggESQFVHV 81
Cdd:cd04164   77 REAIEEA-DLVLLVV---DASEGLDEEdLEILELPAKKPVIVVLNKSDLLSDAEGISELN-------------GKPIIAI 139

                         90
                 ....*....|....*.
gi 490433988  82 SAKAGTGIDELLDAIL 97
Cdd:cd04164  140 SAKTGEGIDELKEALL 155
PRK12317 PRK12317
elongation factor 1-alpha; Reviewed
 6-91 2.73e-03

elongation factor 1-alpha; Reviewed


Pssm-ID: 237055 [Multi-domain]  Cd Length: 425  Bit Score: 37.98  E-value: 2.73e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   6 GAQATDIVVLVVAADD--GVMPQTIE-AIQHAKAAGVPVVVAVNKIDKPEADPDR---VKNELSQ----YGILPEewggE 75
Cdd:PRK12317 104 GASQADAAVLVVAADDagGVMPQTREhVFLARTLGINQLIVAINKMDAVNYDEKRyeeVKEEVSKllkmVGYKPD----D 179

                         90
                 ....*....|....*.
gi 490433988  76 SQFVHVSAKAGTGIDE 91
Cdd:PRK12317 180 IPFIPVSAFEGDNVVK 195
era PRK00089
GTPase Era; Reviewed
 11-97 5.80e-03

GTPase Era; Reviewed


Pssm-ID: 234624 [Multi-domain]  Cd Length: 292  Bit Score: 36.56  E-value: 5.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  11 DIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKpEADPDRVKNELSQYgilpEEWGGESQFVHVSAKAGTGID 90
Cdd:PRK00089  86 DLVLFVVDADEKIGPGDEFILEKLKKVKTPVILVLNKIDL-VKDKEELLPLLEEL----SELMDFAEIVPISALKGDNVD 160


                 ....*..
gi 490433988  91 ELLDAIL 97
Cdd:PRK00089 161 ELLDVIA 167
Era cd04163
E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ...
 11-97 7.05e-03

E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.


Pssm-ID: 206726 [Multi-domain]  Cd Length: 168  Bit Score: 35.90  E-value: 7.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988  11 DIVVLVVAADDGVMPQTIEAIQHAKAAGVPVVVAVNKIDKpEADPDRVKNELSQYGILPEEWggesQFVHVSAKAGTGID 90
Cdd:cd04163   84 DLVLFVVDASEWIGEGDEFILELLKKSKTPVILVLNKIDL-VKDKEDLLPLLEKLKELHPFA----EIFPISALKGENVD 158


                 ....*..
gi 490433988  91 ELLDAIL 97
Cdd:cd04163  159 ELLEYIV 165
HflX cd01878
HflX GTPase family; HflX subfamily. A distinct conserved domain with a glycine-rich segment ...
 46-96 8.55e-03

HflX GTPase family; HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.


Pssm-ID: 206666 [Multi-domain]  Cd Length: 204  Bit Score: 35.90  E-value: 8.55e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 490433988  46 NKIDKpeADPDRVKNELSQygilpeewgGESQFVHVSAKAGTGIDELLDAI 96
Cdd:cd01878  161 NKIDL--LDDEELEERLRA---------GRPDAVFISAKTGEGLDLLKEAI 200
TEF1 COG5256
Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ...
 6-89 9.17e-03

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: 36.45  E-value: 9.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490433988   6 GAQATDIVVLVVAADDGVMPQTIE-AIQHAKAAGVPVVVAVNKIDKPEADPDR---VKNELSQY----GILPEewggESQ 77
Cdd:COG5256  105 GASQADAAILVVSAKDGVMGQTREhAFLARTLGINQLIVAVNKMDAVNYSEKRyeeVKEEVSKLlkmvGYKVD----KIP 180

                         90
                 ....*....|..
gi 490433988  78 FVHVSAKAGTGI 89
Cdd:COG5256  181 FIPVSAWKGDNV 192
 
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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