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Conserved domains on  [gi|2315541556|dbj|GIV44776|]
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MAG: hypothetical protein KatS3mg035_1899 [Bacteroidia bacterium]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RsgA super family cl34152
Ribosome biogenesis GTPase RsgA [Translation, ribosomal structure and biogenesis];
1-42 1.44e-10

Ribosome biogenesis GTPase RsgA [Translation, ribosomal structure and biogenesis];


The actual alignment was detected with superfamily member COG1162:

Pssm-ID: 440776 [Multi-domain]  Cd Length: 300  Bit Score: 53.58  E-value: 1.44e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2315541556   1 MHQNEPGCAVRNAVHENLFDEERYINYLNILnsEELKKKPLR 42
Cdd:COG1162   261 THLHEPGCAVKAAVEAGEISPERYESYLKLL--EELEERKRR 300
 
Name Accession Description Interval E-value
RsgA COG1162
Ribosome biogenesis GTPase RsgA [Translation, ribosomal structure and biogenesis];
1-42 1.44e-10

Ribosome biogenesis GTPase RsgA [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440776 [Multi-domain]  Cd Length: 300  Bit Score: 53.58  E-value: 1.44e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2315541556   1 MHQNEPGCAVRNAVHENLFDEERYINYLNILnsEELKKKPLR 42
Cdd:COG1162   261 THLHEPGCAVKAAVEAGEISPERYESYLKLL--EELEERKRR 300
YjeQ_EngC cd01854
Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; ...
 2-32 1.57e-10

Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; YjeQ (YloQ in Bacillus subtilis) is a ribosomal small subunit-dependent GTPase; hence also known as RsgA. YjeQ is a late-stage ribosomal biogenesis factor involved in the 30S subunit maturation, and it represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain.


Pssm-ID: 206747 [Multi-domain]  Cd Length: 211  Bit Score: 52.79  E-value: 1.57e-10
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2315541556   2 HQNEPGCAVRNAVHENLFDEERYINYLNILN 32
Cdd:cd01854   181 HINEPGCAVKAAVEAGEISEERYESYLKLLE 211
PRK00098 PRK00098
GTPase RsgA; Reviewed
 1-40 5.79e-10

GTPase RsgA; Reviewed


Pssm-ID: 234631 [Multi-domain]  Cd Length: 298  Bit Score: 51.74  E-value: 5.79e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2315541556   1 MHQNEPGCAVRNAVHENLFDEERYINYLNILNSEELKKKP 40
Cdd:PRK00098  259 THLHEPGCAVKAAVEEGEIAPSRYESYLQILEEIENRRER 298
TIGR00157 TIGR00157
ribosome small subunit-dependent GTPase A; Members of this protein were designated YjeQ and ...
 2-32 9.60e-06

ribosome small subunit-dependent GTPase A; Members of this protein were designated YjeQ and are now designated RsgA (ribosome small subunit-dependent GTPase A). The strongest motif in the alignment of these proteins is GXSGVGKS[ST], a classic P-loop for nucleotide binding. This protein has been shown to cleave GTP and remain bound to GDP. A role as a regulator of translation has been suggested. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option). [Protein synthesis, Translation factors]


Pssm-ID: 272934 [Multi-domain]  Cd Length: 245  Bit Score: 39.71  E-value: 9.60e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2315541556   2 HQNEPGCAVRNAVHENLFDEERYINYLNILN 32
Cdd:TIGR00157 215 HQSEPGCAVRQAVEQGEISEWRYENYLKLIE 245
 
Name Accession Description Interval E-value
RsgA COG1162
Ribosome biogenesis GTPase RsgA [Translation, ribosomal structure and biogenesis];
1-42 1.44e-10

Ribosome biogenesis GTPase RsgA [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440776 [Multi-domain]  Cd Length: 300  Bit Score: 53.58  E-value: 1.44e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2315541556   1 MHQNEPGCAVRNAVHENLFDEERYINYLNILnsEELKKKPLR 42
Cdd:COG1162   261 THLHEPGCAVKAAVEAGEISPERYESYLKLL--EELEERKRR 300
YjeQ_EngC cd01854
Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; ...
 2-32 1.57e-10

Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; YjeQ (YloQ in Bacillus subtilis) is a ribosomal small subunit-dependent GTPase; hence also known as RsgA. YjeQ is a late-stage ribosomal biogenesis factor involved in the 30S subunit maturation, and it represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain.


Pssm-ID: 206747 [Multi-domain]  Cd Length: 211  Bit Score: 52.79  E-value: 1.57e-10
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2315541556   2 HQNEPGCAVRNAVHENLFDEERYINYLNILN 32
Cdd:cd01854   181 HINEPGCAVKAAVEAGEISEERYESYLKLLE 211
PRK00098 PRK00098
GTPase RsgA; Reviewed
 1-40 5.79e-10

GTPase RsgA; Reviewed


Pssm-ID: 234631 [Multi-domain]  Cd Length: 298  Bit Score: 51.74  E-value: 5.79e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2315541556   1 MHQNEPGCAVRNAVHENLFDEERYINYLNILNSEELKKKP 40
Cdd:PRK00098  259 THLHEPGCAVKAAVEEGEIAPSRYESYLQILEEIENRRER 298
PRK12288 PRK12288
small ribosomal subunit biogenesis GTPase RsgA;
2-33 2.32e-07

small ribosomal subunit biogenesis GTPase RsgA;


Pssm-ID: 237039 [Multi-domain]  Cd Length: 347  Bit Score: 44.46  E-value: 2.32e-07
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2315541556   2 HQNEPGCAVRNAVHENLFDEERYINYLNILNS 33
Cdd:PRK12288  301 HDDDPGCALREAVEEGKIAETRFENYHRILES 332
PRK01889 PRK01889
GTPase RsgA; Reviewed
 2-27 7.71e-07

GTPase RsgA; Reviewed


Pssm-ID: 234988 [Multi-domain]  Cd Length: 356  Bit Score: 43.00  E-value: 7.71e-07
                          10        20
                  ....*....|....*....|....*.
gi 2315541556   2 HQNEPGCAVRNAVHENLFDEERYINY 27
Cdd:PRK01889  290 HEAEPGCAVQAAIENGELDERRLQSY 315
TIGR00157 TIGR00157
ribosome small subunit-dependent GTPase A; Members of this protein were designated YjeQ and ...
 2-32 9.60e-06

ribosome small subunit-dependent GTPase A; Members of this protein were designated YjeQ and are now designated RsgA (ribosome small subunit-dependent GTPase A). The strongest motif in the alignment of these proteins is GXSGVGKS[ST], a classic P-loop for nucleotide binding. This protein has been shown to cleave GTP and remain bound to GDP. A role as a regulator of translation has been suggested. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option). [Protein synthesis, Translation factors]


Pssm-ID: 272934 [Multi-domain]  Cd Length: 245  Bit Score: 39.71  E-value: 9.60e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2315541556   2 HQNEPGCAVRNAVHENLFDEERYINYLNILN 32
Cdd:TIGR00157 215 HQSEPGCAVRQAVEQGEISEWRYENYLKLIE 245
PRK12289 PRK12289
small ribosomal subunit biogenesis GTPase RsgA;
2-31 1.29e-03

small ribosomal subunit biogenesis GTPase RsgA;


Pssm-ID: 237040 [Multi-domain]  Cd Length: 352  Bit Score: 33.84  E-value: 1.29e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 2315541556   2 HQNEPGCAVRNavhenlfDEERYINYLNIL 31
Cdd:PRK12289  269 HRDEPNCAVRG-------DWERYEHYLEFL 291
 
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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