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Conserved domains on  [gi|341886328|gb|EGT42263|]
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hypothetical protein CAEBREN_04444, partial [Caenorhabditis brenneri]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DUF272 pfam03312
Protein of unknown function (DUF272); This family of proteins is restricted to C.elegans and ...
 208-338 4.84e-44

Protein of unknown function (DUF272); This family of proteins is restricted to C.elegans and has no known function. The protein contains a ubiquitin fold. The GO annotation for the protein indicates that it has a function in nematode larval development.


:

Pssm-ID: 397411  Cd Length: 123  Bit Score: 153.52  E-value: 4.84e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341886328  208 FLWLLDDHVSSVyyFSSREDTISVGHFFEGVFWHTGKG-WECKRYVKSLGKLMDGVVYNDSIELRITVYAYLPASPGRKN 286
Cdd:pfam03312   1 FLWILDKHEEGI--FKSKKHKLELGHFFEGIFEKKPNGkWECKKYVKPIEKLLEGIVVNNKIELTVTIENYQPASGNRKY 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 341886328  287 AETYHNFIGKIvsgIDKHNQLPGDCsSGVKIRIRLYKdrtTDKTNYCWIVAK 338
Cdd:pfam03312  79 PEAYAKYFGKI---LDGKNKLPADC-NGKKINIQRRK---VGEKDYVWVVTE 123
TRAM_2 super family cl40009
TRAM domain; This is a C-terminal TRAM (after TRM2, a family of uridine methylases, and MiaB) ...
 32-60 7.72e-04

TRAM domain; This is a C-terminal TRAM (after TRM2, a family of uridine methylases, and MiaB) domain found in the methylthiotransferases RimO enzymes that catalyze the conversion of aspartate to 2-methylthio-aspartate (msD) in the S12 protein near the decoding center in prokaryotic ribosomes. The TRAM domain in RimO, contains five anti-parallel beta-strands and docks on the surface of the Radical-SAM domain at the distal edge of its open TIM-barrel from its conserved [4Fe-4S] cluster.


The actual alignment was detected with superfamily member pfam18693:

Pssm-ID: 465832 [Multi-domain]  Cd Length: 63  Bit Score: 38.22  E-value: 7.72e-04
                          10        20
                  ....*....|....*....|....*....
gi 341886328   32 PGVDGIVYCSKNRRLKVGDWVEVRFTEAD 60
Cdd:pfam18693  26 PEIDGEVYVTGAEDLKVGDFVNVRITDAD 54
 
Name Accession Description Interval E-value
DUF272 pfam03312
Protein of unknown function (DUF272); This family of proteins is restricted to C.elegans and ...
 208-338 4.84e-44

Protein of unknown function (DUF272); This family of proteins is restricted to C.elegans and has no known function. The protein contains a ubiquitin fold. The GO annotation for the protein indicates that it has a function in nematode larval development.


Pssm-ID: 397411  Cd Length: 123  Bit Score: 153.52  E-value: 4.84e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341886328  208 FLWLLDDHVSSVyyFSSREDTISVGHFFEGVFWHTGKG-WECKRYVKSLGKLMDGVVYNDSIELRITVYAYLPASPGRKN 286
Cdd:pfam03312   1 FLWILDKHEEGI--FKSKKHKLELGHFFEGIFEKKPNGkWECKKYVKPIEKLLEGIVVNNKIELTVTIENYQPASGNRKY 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 341886328  287 AETYHNFIGKIvsgIDKHNQLPGDCsSGVKIRIRLYKdrtTDKTNYCWIVAK 338
Cdd:pfam03312  79 PEAYAKYFGKI---LDGKNKLPADC-NGKKINIQRRK---VGEKDYVWVVTE 123
TRAM_2 pfam18693
TRAM domain; This is a C-terminal TRAM (after TRM2, a family of uridine methylases, and MiaB) ...
 32-60 7.72e-04

TRAM domain; This is a C-terminal TRAM (after TRM2, a family of uridine methylases, and MiaB) domain found in the methylthiotransferases RimO enzymes that catalyze the conversion of aspartate to 2-methylthio-aspartate (msD) in the S12 protein near the decoding center in prokaryotic ribosomes. The TRAM domain in RimO, contains five anti-parallel beta-strands and docks on the surface of the Radical-SAM domain at the distal edge of its open TIM-barrel from its conserved [4Fe-4S] cluster.


Pssm-ID: 465832 [Multi-domain]  Cd Length: 63  Bit Score: 38.22  E-value: 7.72e-04
                          10        20
                  ....*....|....*....|....*....
gi 341886328   32 PGVDGIVYCSKNRRLKVGDWVEVRFTEAD 60
Cdd:pfam18693  26 PEIDGEVYVTGAEDLKVGDFVNVRITDAD 54
 
Name Accession Description Interval E-value
DUF272 pfam03312
Protein of unknown function (DUF272); This family of proteins is restricted to C.elegans and ...
 208-338 4.84e-44

Protein of unknown function (DUF272); This family of proteins is restricted to C.elegans and has no known function. The protein contains a ubiquitin fold. The GO annotation for the protein indicates that it has a function in nematode larval development.


Pssm-ID: 397411  Cd Length: 123  Bit Score: 153.52  E-value: 4.84e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341886328  208 FLWLLDDHVSSVyyFSSREDTISVGHFFEGVFWHTGKG-WECKRYVKSLGKLMDGVVYNDSIELRITVYAYLPASPGRKN 286
Cdd:pfam03312   1 FLWILDKHEEGI--FKSKKHKLELGHFFEGIFEKKPNGkWECKKYVKPIEKLLEGIVVNNKIELTVTIENYQPASGNRKY 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 341886328  287 AETYHNFIGKIvsgIDKHNQLPGDCsSGVKIRIRLYKdrtTDKTNYCWIVAK 338
Cdd:pfam03312  79 PEAYAKYFGKI---LDGKNKLPADC-NGKKINIQRRK---VGEKDYVWVVTE 123
TRAM_2 pfam18693
TRAM domain; This is a C-terminal TRAM (after TRM2, a family of uridine methylases, and MiaB) ...
 32-60 7.72e-04

TRAM domain; This is a C-terminal TRAM (after TRM2, a family of uridine methylases, and MiaB) domain found in the methylthiotransferases RimO enzymes that catalyze the conversion of aspartate to 2-methylthio-aspartate (msD) in the S12 protein near the decoding center in prokaryotic ribosomes. The TRAM domain in RimO, contains five anti-parallel beta-strands and docks on the surface of the Radical-SAM domain at the distal edge of its open TIM-barrel from its conserved [4Fe-4S] cluster.


Pssm-ID: 465832 [Multi-domain]  Cd Length: 63  Bit Score: 38.22  E-value: 7.72e-04
                          10        20
                  ....*....|....*....|....*....
gi 341886328   32 PGVDGIVYCSKNRRLKVGDWVEVRFTEAD 60
Cdd:pfam18693  26 PEIDGEVYVTGAEDLKVGDFVNVRITDAD 54
 
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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