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Conserved domains on  [gi|1631450803|gb|TJX41458|]
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TRAM domain-containing protein, partial [Soehngenia saccharolytica]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MiaB super family cl33981
tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-137 9.67e-60

tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA A37 methylthiotransferase MiaB is part of the Pathway/BioSystem: tRNA modification


The actual alignment was detected with superfamily member COG0621:

Pssm-ID: 440386 [Multi-domain]  Cd Length: 435  Bit Score: 189.91  E-value: 9.67e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1631450803   1 TDIIVGFPGETEEDFEETMDVVRRVRYDSAFTFIYSKRTGTPAATMDDQIPEEVIKERFDRLLHEVQTISAEKAGKLTGQ 80
Cdd:COG0621   298 TDIIVGFPGETEEDFEETLDFVEEVRFDRLHVFPYSPRPGTPAAKMPDQVPEEVKKERLARLMELQEEISAERNQRLVGK 377

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1631450803  81 TLPVLVEEVNGQDASLVTGKLTNNSTVHFPGTADMIGTIQNVVLEECKGFYYIGRLA 137
Cdd:COG0621   378 TVEVLVEGPSKKDDGQLIGRTENYALVVFPGDELLPGDFVDVKITEADEYDLIGELV 434
 
Name Accession Description Interval E-value
MiaB COG0621
tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-137 9.67e-60

tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA A37 methylthiotransferase MiaB is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440386 [Multi-domain]  Cd Length: 435  Bit Score: 189.91  E-value: 9.67e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1631450803   1 TDIIVGFPGETEEDFEETMDVVRRVRYDSAFTFIYSKRTGTPAATMDDQIPEEVIKERFDRLLHEVQTISAEKAGKLTGQ 80
Cdd:COG0621   298 TDIIVGFPGETEEDFEETLDFVEEVRFDRLHVFPYSPRPGTPAAKMPDQVPEEVKKERLARLMELQEEISAERNQRLVGK 377

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1631450803  81 TLPVLVEEVNGQDASLVTGKLTNNSTVHFPGTADMIGTIQNVVLEECKGFYYIGRLA 137
Cdd:COG0621   378 TVEVLVEGPSKKDDGQLIGRTENYALVVFPGDELLPGDFVDVKITEADEYDLIGELV 434
PRK14328 PRK14328
(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
 1-136 5.53e-57

(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional


Pssm-ID: 237675 [Multi-domain]  Cd Length: 439  Bit Score: 182.88  E-value: 5.53e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1631450803   1 TDIIVGFPGETEEDFEETMDVVRRVRYDSAFTFIYSKRTGTPAATMDDQIPEEVIKERFDRLLHEVQTISAEKAGKLTGQ 80
Cdd:PRK14328  302 TDIIVGFPGETEEDFEETLDLVKEVRYDSAFTFIYSKRKGTPAAKMEDQVPEDVKHERFNRLVELQNKISLEKNKEYEGK 381

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1631450803  81 TLPVLVEEVNGQDASLVTGKLTNNSTVHFPGTADMIGTIQNVVLEECKGFYYIGRL 136
Cdd:PRK14328  382 IVEVLVEGPSKNDENKLTGRTRTNKLVNFIGDKELIGKLVNVKITKANSFSLTGEV 437
TIGR00089 TIGR00089
radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 ...
 1-134 2.27e-51

radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 modification enzyme, MiaB (TIGR01574). The phylogenetic tree indicates 4 distinct clades, one of which corresponds to MiaB. The other three clades are modelled by hypothetical equivalogs (TIGR01125, TIGR01579 and TIGR01578). Together, the four models hit every sequence hit by the subfamily model without any overlap between them. This subfamily is aparrently a part of a larger superfamily of enzymes utilizing both a 4Fe4S cluster and S-adenosyl methionine (SAM) to initiate radical reactions. MiaB acts on a particular isoprenylated Adenine base of certain tRNAs causing thiolation at an aromatic carbon, and probably also transferring a methyl grouyp from SAM to the thiol. The particular substrate of the three other clades is unknown but may be very closely related.


Pssm-ID: 272900 [Multi-domain]  Cd Length: 429  Bit Score: 168.19  E-value: 2.27e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1631450803   1 TDIIVGFPGETEEDFEETMDVVRRVRYDSAFTFIYSKRTGTPAATMDDQIPEEVIKERFDRLLHEVQTISAEKAGKLTGQ 80
Cdd:TIGR00089 294 TDIIVGFPGETEEDFEETLDLVEEVKFDKLHSFIYSPRPGTPAADMKDQVPEEVKKERLERLIALQKEISLEKNKKYVGK 373

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1631450803  81 TLPVLVEEVNGQDASLVTGKLTNNSTVHFPG--TADMIGTIQNVVLEECKGFYYIG 134
Cdd:TIGR00089 374 TLEVLVEGKEGKKEGELTGRTENYKPVVFEGgvGKSLIGKFVKVKITEAAEYDLIG 429
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 1-62 3.56e-16

Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.


Pssm-ID: 214792 [Multi-domain]  Cd Length: 216  Bit Score: 71.66  E-value: 3.56e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1631450803    1 TDIIVGFPGETEEDFEETMDVVRRVRYDSAFTFIYSKRTGTPAATMDDQIPEEVIKERFDRL 62
Cdd:smart00729 155 TDLIVGLPGETEEDFEETLKLLKELGPDRVSIFPLSPRPGTPLAKMYKRLKPPTKEERAELL 216
 
Name Accession Description Interval E-value
MiaB COG0621
tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-137 9.67e-60

tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA A37 methylthiotransferase MiaB is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440386 [Multi-domain]  Cd Length: 435  Bit Score: 189.91  E-value: 9.67e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1631450803   1 TDIIVGFPGETEEDFEETMDVVRRVRYDSAFTFIYSKRTGTPAATMDDQIPEEVIKERFDRLLHEVQTISAEKAGKLTGQ 80
Cdd:COG0621   298 TDIIVGFPGETEEDFEETLDFVEEVRFDRLHVFPYSPRPGTPAAKMPDQVPEEVKKERLARLMELQEEISAERNQRLVGK 377

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1631450803  81 TLPVLVEEVNGQDASLVTGKLTNNSTVHFPGTADMIGTIQNVVLEECKGFYYIGRLA 137
Cdd:COG0621   378 TVEVLVEGPSKKDDGQLIGRTENYALVVFPGDELLPGDFVDVKITEADEYDLIGELV 434
PRK14328 PRK14328
(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
 1-136 5.53e-57

(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional


Pssm-ID: 237675 [Multi-domain]  Cd Length: 439  Bit Score: 182.88  E-value: 5.53e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1631450803   1 TDIIVGFPGETEEDFEETMDVVRRVRYDSAFTFIYSKRTGTPAATMDDQIPEEVIKERFDRLLHEVQTISAEKAGKLTGQ 80
Cdd:PRK14328  302 TDIIVGFPGETEEDFEETLDLVKEVRYDSAFTFIYSKRKGTPAAKMEDQVPEDVKHERFNRLVELQNKISLEKNKEYEGK 381

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1631450803  81 TLPVLVEEVNGQDASLVTGKLTNNSTVHFPGTADMIGTIQNVVLEECKGFYYIGRL 136
Cdd:PRK14328  382 IVEVLVEGPSKNDENKLTGRTRTNKLVNFIGDKELIGKLVNVKITKANSFSLTGEV 437
TIGR00089 TIGR00089
radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 ...
 1-134 2.27e-51

radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 modification enzyme, MiaB (TIGR01574). The phylogenetic tree indicates 4 distinct clades, one of which corresponds to MiaB. The other three clades are modelled by hypothetical equivalogs (TIGR01125, TIGR01579 and TIGR01578). Together, the four models hit every sequence hit by the subfamily model without any overlap between them. This subfamily is aparrently a part of a larger superfamily of enzymes utilizing both a 4Fe4S cluster and S-adenosyl methionine (SAM) to initiate radical reactions. MiaB acts on a particular isoprenylated Adenine base of certain tRNAs causing thiolation at an aromatic carbon, and probably also transferring a methyl grouyp from SAM to the thiol. The particular substrate of the three other clades is unknown but may be very closely related.


Pssm-ID: 272900 [Multi-domain]  Cd Length: 429  Bit Score: 168.19  E-value: 2.27e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1631450803   1 TDIIVGFPGETEEDFEETMDVVRRVRYDSAFTFIYSKRTGTPAATMDDQIPEEVIKERFDRLLHEVQTISAEKAGKLTGQ 80
Cdd:TIGR00089 294 TDIIVGFPGETEEDFEETLDLVEEVKFDKLHSFIYSPRPGTPAADMKDQVPEEVKKERLERLIALQKEISLEKNKKYVGK 373

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1631450803  81 TLPVLVEEVNGQDASLVTGKLTNNSTVHFPG--TADMIGTIQNVVLEECKGFYYIG 134
Cdd:TIGR00089 374 TLEVLVEGKEGKKEGELTGRTENYKPVVFEGgvGKSLIGKFVKVKITEAAEYDLIG 429
miaB-methiolase TIGR01574
tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB; This model represents ...
 1-129 5.29e-44

tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB; This model represents homologs of the MiaB enzyme responsible for the modification of the isopentenylated adenine-37 base of most bacterial and eukaryotic tRNAs that read codons beginning with uracil (all except tRNA(I,V) Ser). Adenine-37 is next to the anticodon on the 3' side in these tRNA's, and lack of modification at this site leads to an increased spontaneous mutation frequency. Isopentenylated A-37 is modified by methylthiolation at position 2, either by MiaB alone or in concert with a separate methylase yet to be discovered (MiaC?). MiaB contains a 4Fe-4S cluster which is labile under oxidizing conditions. Additionally, the sequence is homologous (via PSI-BLAST searches) to the biotin synthetase, BioB, which utilizes both an iron-sulfur cluster and S-adenosym methionine (SAM) to generate a radical which is responsible for initiating the insertion of sulfur into the substrate. It is reasonable to surmise that the methyl group of SAM becomes the methyl group of the product, but this has not been shown, and the possibility of a separate methylase exists. This equivalog is a member of a subfamily (TIGR00089) which contains several other hypothetical equivalogs which are all probably enzymes with similar function acting on different substrates. These enzymes contain a TRAM domain (pfam01938) which is believed to be responsible for binding to tRNAs. Hits to this model span all major groups of bacteria and eukaryotes, but not archaea, which are known to lack this particular tRNA modification. The enzyme from Thermotoga maritima has been cloned, expressed, spectroscopically characterized and shown to complement the E. coli MiaB enzyme. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 273700 [Multi-domain]  Cd Length: 438  Bit Score: 149.19  E-value: 5.29e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1631450803   1 TDIIVGFPGETEEDFEETMDVVRRVRYDSAFTFIYSKRTGTPAATMDDQIPEEVIKERFDRLLHEVQTISAEKAGKLTGQ 80
Cdd:TIGR01574 302 TDIIVGFPGETEEDFEETLDLLREVEFDSAFSFIYSPRPGTPAADMPDQIPEEIKKRRLQRLQARHNEILDKKMRKQEGK 381

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1631450803  81 TLPVLVEEVNGQDASLVTGKLTNNSTVHFPGTADMIGTIQNVVLEECKG 129
Cdd:TIGR01574 382 TFKVLVEGLSRNNPEELAGRTENNFLVNFEGSEDLIGKFVDVKITNVKR 430
TIGR01125 TIGR01125
ribosomal protein S12 methylthiotransferase RimO; Members of this protein are the ...
 1-130 1.27e-26

ribosomal protein S12 methylthiotransferase RimO; Members of this protein are the methylthiotransferase RimO, which modifies a conserved Asp residue in ribosomal protein S12. This clade of radical SAM family proteins is closely related to the tRNA modification bifunctional enzyme MiaB (see TIGR01574), and it catalyzes the same two types of reactions: a radical-mechanism sulfur insertion, and a methylation of the inserted sulfur. This clade spans alpha and gamma proteobacteria, cyano bacteria, Deinococcus, Porphyromonas, Aquifex, Helicobacter, Campylobacter, Thermotoga, Chlamydia, Streptococcus coelicolor and Clostridium, but does not include most other gram positive bacteria, archaea or eukaryotes. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273453 [Multi-domain]  Cd Length: 426  Bit Score: 102.52  E-value: 1.27e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1631450803   1 TDIIVGFPGETEEDFEETMDVVRRVRYDSAFTFIYSKRTGTPAATMDDQIPEEVIKERFDRLLHEVQTISAEKAGKLTGQ 80
Cdd:TIGR01125 290 TTFIVGFPGETEEDFQELLDFVEEGQFDRLGAFTYSPEEGTDAFALPDQVPEEVKEERLERLMQLQQRISAKKLQEFVGK 369

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1631450803  81 TLPVLVEEVNGQdaslvTGKLTNNSTVHFPGT--------ADMIGTIQNVVLEECKGF 130
Cdd:TIGR01125 370 KIEVLIDGYEPE-----FNLLIGRTYGQAPEVdgvvyvngKGKIGDILRVVITETDEY 422
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 1-62 3.56e-16

Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.


Pssm-ID: 214792 [Multi-domain]  Cd Length: 216  Bit Score: 71.66  E-value: 3.56e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1631450803    1 TDIIVGFPGETEEDFEETMDVVRRVRYDSAFTFIYSKRTGTPAATMDDQIPEEVIKERFDRL 62
Cdd:smart00729 155 TDLIVGLPGETEEDFEETLKLLKELGPDRVSIFPLSPRPGTPLAKMYKRLKPPTKEERAELL 216
PRK14336 PRK14336
(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
 1-122 6.95e-15

(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional


Pssm-ID: 184632 [Multi-domain]  Cd Length: 418  Bit Score: 69.94  E-value: 6.95e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1631450803   1 TDIIVGFPGETEEDFEETMDVVRRVRYDSAFTFIYSKRTGTPAA-TMDDQIPEEVIKERfdrlLHEVQTISAEKAGK--- 76
Cdd:PRK14336  279 TDLIVGFPSETEEQFNQSYKLMADIGYDAIHVAAYSPRPQTVAArDMADDVPVIEKKRR----LKLIEDLQKETVGKana 354

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1631450803  77 -LTGQTLPVLVEevnGQDASLVTGKLTNNSTVHFPGTADMIGTIQNV 122
Cdd:PRK14336  355 aLMDTFAEVLVE---GLQKNKWQGRTLGGKLVFLESDLPLEGCLVNV 398
YgiQ COG1032
Radical SAM superfamily enzyme YgiQ, UPF0313 family [General function prediction only];
2-42 4.04e-07

Radical SAM superfamily enzyme YgiQ, UPF0313 family [General function prediction only];


Pssm-ID: 440655 [Multi-domain]  Cd Length: 394  Bit Score: 47.63  E-value: 4.04e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1631450803   2 DIIVGFPGETEEDFEETMDVVRRVRYDSAFTFIYSKRTGTP 42
Cdd:COG1032   321 YFIIGLPGETEEDIEETIEFIKELGPDQAQVSIFTPLPGTP 361
PRK08207 PRK08207
coproporphyrinogen III oxidase; Provisional
 2-29 1.75e-04

coproporphyrinogen III oxidase; Provisional


Pssm-ID: 236187 [Multi-domain]  Cd Length: 488  Bit Score: 39.86  E-value: 1.75e-04
                          10        20
                  ....*....|....*....|....*...
gi 1631450803   2 DIIVGFPGETEEDFEETMDVVRRVRYDS 29
Cdd:PRK08207  325 DLIIGLPGEGLEEVKHTLEEIEKLNPES 352
 
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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