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Conserved domains on  [gi|339903526|gb|AEK18968|]
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deoxyribonuclease [Methanococcus maripaludis X1]

Protein Classification

TRAM domain-containing protein( domain architecture ID 10007143)

TRAM domain-containing protein similar to Methanocaldococcus jannaschii protein MJ0660

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG3269 COG3269
Predicted RNA-binding protein, contains TRAM domain [General function prediction only];
8-69 1.22e-24

Predicted RNA-binding protein, contains TRAM domain [General function prediction only];


:

Pssm-ID: 442500 [Multi-domain]  Cd Length: 129  Bit Score: 88.57  E-value: 1.22e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 339903526   8 MKNVPVEAGKEYEVTIEDMGKGGDGIARIDGFVVFVPNAEKGSVINVKVTAVKEKFAFAERV 69
Cdd:COG3269   65 ELTPPVEEGEEYEVEIEDIGKKGDGIARVEGFVIFVPGAEVGDRVKVKITKVKRNFAFAEVV 126
 
Name Accession Description Interval E-value
COG3269 COG3269
Predicted RNA-binding protein, contains TRAM domain [General function prediction only];
8-69 1.22e-24

Predicted RNA-binding protein, contains TRAM domain [General function prediction only];


Pssm-ID: 442500 [Multi-domain]  Cd Length: 129  Bit Score: 88.57  E-value: 1.22e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 339903526   8 MKNVPVEAGKEYEVTIEDMGKGGDGIARIDGFVVFVPNAEKGSVINVKVTAVKEKFAFAERV 69
Cdd:COG3269   65 ELTPPVEEGEEYEVEIEDIGKKGDGIARVEGFVIFVPGAEVGDRVKVKITKVKRNFAFAEVV 126
PRK12336 PRK12336
translation initiation factor IF-2 subunit beta; Provisional
 13-69 1.98e-18

translation initiation factor IF-2 subunit beta; Provisional


Pssm-ID: 183451 [Multi-domain]  Cd Length: 201  Bit Score: 74.21  E-value: 1.98e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 339903526  13 VEAGKEYEVTIEDMGKGGDGIARIDGFVVFVPNAEKGSVINVKVTAVKEKFAFAERV 69
Cdd:PRK12336 145 IEEGKTYEVEITGTGRKGDGVAKKGKYTIFVPGAKKGEVVKVKIKKISGNLAFAERA 201
TRAM pfam01938
TRAM domain; This small domain has no known function. However it may perform a nucleic acid ...
 12-67 8.17e-12

TRAM domain; This small domain has no known function. However it may perform a nucleic acid binding role (Bateman A. unpublished observation).


Pssm-ID: 396497 [Multi-domain]  Cd Length: 59  Bit Score: 53.76  E-value: 8.17e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 339903526  12 PVEAGKEYEVTIEDMGKGGDGIARID-GFVVFVPNAEKGSVINVKVTAVKEKFAFAE 67
Cdd:pfam01938  1 RRYVGQTQEVLVEGLSSNGEGIGRTDnGKVVFVPGALPGEFVEVKITKVKRNYLRGE 57
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 30-66 1.93e-07

23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129571 [Multi-domain]  Cd Length: 431  Bit Score: 45.58  E-value: 1.93e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 339903526   30 GDGIARIDGFVVFVPNAEKGSVINVKVTAVKEKFAFA 66
Cdd:TIGR00479   5 GEGVARFNGKTVFVPGALPGEKAEVRVTEVKKQYARA 41
 
Name Accession Description Interval E-value
COG3269 COG3269
Predicted RNA-binding protein, contains TRAM domain [General function prediction only];
8-69 1.22e-24

Predicted RNA-binding protein, contains TRAM domain [General function prediction only];


Pssm-ID: 442500 [Multi-domain]  Cd Length: 129  Bit Score: 88.57  E-value: 1.22e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 339903526   8 MKNVPVEAGKEYEVTIEDMGKGGDGIARIDGFVVFVPNAEKGSVINVKVTAVKEKFAFAERV 69
Cdd:COG3269   65 ELTPPVEEGEEYEVEIEDIGKKGDGIARVEGFVIFVPGAEVGDRVKVKITKVKRNFAFAEVV 126
PRK12336 PRK12336
translation initiation factor IF-2 subunit beta; Provisional
 13-69 1.98e-18

translation initiation factor IF-2 subunit beta; Provisional


Pssm-ID: 183451 [Multi-domain]  Cd Length: 201  Bit Score: 74.21  E-value: 1.98e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 339903526  13 VEAGKEYEVTIEDMGKGGDGIARIDGFVVFVPNAEKGSVINVKVTAVKEKFAFAERV 69
Cdd:PRK12336 145 IEEGKTYEVEITGTGRKGDGVAKKGKYTIFVPGAKKGEVVKVKIKKISGNLAFAERA 201
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 17-67 4.36e-15

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 67.12  E-value: 4.36e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 339903526  17 KEYEVTIEDMGKGGDGIARIDGFVVFVPNAEKGSVINVKVTAVKEKFAFAE 67
Cdd:COG2265    1 EILELTIEDLAHGGDGVARHDGKVVFVPGALPGERVRVRVTKVKKSFARAK 51
TRAM pfam01938
TRAM domain; This small domain has no known function. However it may perform a nucleic acid ...
 12-67 8.17e-12

TRAM domain; This small domain has no known function. However it may perform a nucleic acid binding role (Bateman A. unpublished observation).


Pssm-ID: 396497 [Multi-domain]  Cd Length: 59  Bit Score: 53.76  E-value: 8.17e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 339903526  12 PVEAGKEYEVTIEDMGKGGDGIARID-GFVVFVPNAEKGSVINVKVTAVKEKFAFAE 67
Cdd:pfam01938  1 RRYVGQTQEVLVEGLSSNGEGIGRTDnGKVVFVPGALPGEFVEVKITKVKRNYLRGE 57
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 30-66 1.93e-07

23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129571 [Multi-domain]  Cd Length: 431  Bit Score: 45.58  E-value: 1.93e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 339903526   30 GDGIARIDGFVVFVPNAEKGSVINVKVTAVKEKFAFA 66
Cdd:TIGR00479   5 GEGVARFNGKTVFVPGALPGEKAEVRVTEVKKQYARA 41
rumA PRK13168
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;
17-67 9.35e-07

23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;


Pssm-ID: 237291 [Multi-domain]  Cd Length: 443  Bit Score: 43.61  E-value: 9.35e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 339903526  17 KEYEVTIEDMGKGGDGIARIDGFVVFVPNAEKGSVINVKVTAVKEKFAFAE 67
Cdd:PRK13168  14 QIITVTIESLDHDGRGVARHNGKTVFIEGALPGERVEVQVTEDKKQYARAK 64
 
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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