NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|544684181|ref|WP_021116070|]
View 

tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB [Glaesserella parasuis]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
miaB-methiolase super family cl36932
tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB; This model represents ...
3-439 0e+00

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]


The actual alignment was detected with superfamily member TIGR01574:

Pssm-ID: 273700 [Multi-domain]  Cd Length: 438  Bit Score: 703.50  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181    3 KLHITTWGCQMNEYDSSKMADLLNSTHGLELTENPEEADILLLNTCSIREKAQEKVFSQLGRWKNWKKDKPDLIIGVGGC 82
Cdd:TIGR01574   1 KLFIQTYGCQMNVRDSEHMAALLTAKEGYALTEDAKEADVLLINTCSVREKAEHKVFGELGGFKKLKKKNPDLIIGVCGC 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   83 VASQEGEHIRERAPFVDIVFGPQTLHRLPEMINQIRGGKSSVVDISFPEIEKFDRLPEPRAEG-PTAFVSIMEGCNKYCS 161
Cdd:TIGR01574  81 MASHLGNEIFQRAPYVDFVFGTRNIHRLPQAIKTPLTQKFMVVDIDSDESEVAGYFADFRNEGiYKSFINIMIGCNKFCT 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  162 FCVVPYTRGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQNVNAYRGETFDGGICSFAELLRLVASIDGIDRVRYTTSHPI 241
Cdd:TIGR01574 161 YCIVPYTRGDEISRPFDDILQEVQKLAEKGVREITLLGQNVNAYRGKDFEGKTMDFSDLLRELSTIDGIERIRFTSSHPL 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  242 EFTDDIIEVYKDTPELVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREARPDIQISSDFIVGFPGETAQDFEQTM 321
Cdd:TIGR01574 241 DFDDDLIEVFANNPKLCKSMHLPVQSGSSEILKLMKRGYTREWYLNLVRKLRAACPNVSISTDIIVGFPGETEEDFEETL 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  322 KIIEQVNFDMSFSFIYSARPGTPAADLPDDVTEDEKKERLYRLQQRINNQAMQFSRAMLGTEQRILVEGPSKKDIMELTG 401
Cdd:TIGR01574 321 DLLREVEFDSAFSFIYSPRPGTPAADMPDQIPEEIKKRRLQRLQARHNEILDKKMRKQEGKTFKVLVEGLSRNNPEELAG 400
                         410       420       430
                  ....*....|....*....|....*....|....*...
gi 544684181  402 RTESNRIVNFQGTPNMIGKFVDVKITDVYTNSLRGEVV 439
Cdd:TIGR01574 401 RTENNFLVNFEGSEDLIGKFVDVKITNVKRMSLRGEIV 438
 
Name Accession Description Interval E-value
miaB-methiolase TIGR01574
tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB; This model represents ...
3-439 0e+00

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: 703.50  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181    3 KLHITTWGCQMNEYDSSKMADLLNSTHGLELTENPEEADILLLNTCSIREKAQEKVFSQLGRWKNWKKDKPDLIIGVGGC 82
Cdd:TIGR01574   1 KLFIQTYGCQMNVRDSEHMAALLTAKEGYALTEDAKEADVLLINTCSVREKAEHKVFGELGGFKKLKKKNPDLIIGVCGC 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   83 VASQEGEHIRERAPFVDIVFGPQTLHRLPEMINQIRGGKSSVVDISFPEIEKFDRLPEPRAEG-PTAFVSIMEGCNKYCS 161
Cdd:TIGR01574  81 MASHLGNEIFQRAPYVDFVFGTRNIHRLPQAIKTPLTQKFMVVDIDSDESEVAGYFADFRNEGiYKSFINIMIGCNKFCT 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  162 FCVVPYTRGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQNVNAYRGETFDGGICSFAELLRLVASIDGIDRVRYTTSHPI 241
Cdd:TIGR01574 161 YCIVPYTRGDEISRPFDDILQEVQKLAEKGVREITLLGQNVNAYRGKDFEGKTMDFSDLLRELSTIDGIERIRFTSSHPL 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  242 EFTDDIIEVYKDTPELVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREARPDIQISSDFIVGFPGETAQDFEQTM 321
Cdd:TIGR01574 241 DFDDDLIEVFANNPKLCKSMHLPVQSGSSEILKLMKRGYTREWYLNLVRKLRAACPNVSISTDIIVGFPGETEEDFEETL 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  322 KIIEQVNFDMSFSFIYSARPGTPAADLPDDVTEDEKKERLYRLQQRINNQAMQFSRAMLGTEQRILVEGPSKKDIMELTG 401
Cdd:TIGR01574 321 DLLREVEFDSAFSFIYSPRPGTPAADMPDQIPEEIKKRRLQRLQARHNEILDKKMRKQEGKTFKVLVEGLSRNNPEELAG 400
                         410       420       430
                  ....*....|....*....|....*....|....*...
gi 544684181  402 RTESNRIVNFQGTPNMIGKFVDVKITDVYTNSLRGEVV 439
Cdd:TIGR01574 401 RTENNFLVNFEGSEDLIGKFVDVKITNVKRMSLRGEIV 438
MiaB COG0621
tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA ...
1-439 0e+00

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: 662.16  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   1 MAKLHITTWGCQMNEYDSSKMADLLNStHGLELTENPEEADILLLNTCSIREKAQEKVFSQLGRWKNWKKDKPDLIIGVG 80
Cdd:COG0621    1 MKKVYIVTLGCQMNQVDSERMAGLLEA-AGYELVDDPEEADVVVVNTCSVREKAEEKSRQTIGRLAELKRKNPDAKIVVT 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  81 GCVASQEGEHIRERAPFVDIVFGPQTLHRLPEMINQIRGGKSsVVDISfpEIEKFDRLPEP-RAEGPTAFVSIMEGCNKY 159
Cdd:COG0621   80 GCLAQREGEELLEEIPEVDLVVGPQDKHRLPELLEEALAGEK-VVDIS--SEETFDDLPVPrRTGRTRAFVKIQEGCNNF 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 160 CSFCVVPYTRGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQNVNAYRGETfdGGICSFAELLRLVASIDGIDRVRYTTSH 239
Cdd:COG0621  157 CTFCIIPYTRGRERSRPPEDILAEARRLAAQGVKEIVLTGQNVNSYGKDL--YGKTDLADLLRALAEIEGIERIRLSSSH 234
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 240 PIEFTDDIIEVYKDTPELVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREARPDIQISSDFIVGFPGETAQDFEQ 319
Cdd:COG0621  235 PKDFTDELIEAMAESPKVCPHLHLPLQSGSDRVLKRMNRRYTREEYLELVEKIREAIPDIAIRTDIIVGFPGETEEDFEE 314
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 320 TMKIIEQVNFDMSFSFIYSARPGTPAADLPDDVTEDEKKERLYRLQQRINNQAMQFSRAMLGTEQRILVEGPSKKDIMEL 399
Cdd:COG0621  315 TLDFVEEVRFDRLHVFPYSPRPGTPAAKMPDQVPEEVKKERLARLMELQEEISAERNQRLVGKTVEVLVEGPSKKDDGQL 394
                        410       420       430       440
                 ....*....|....*....|....*....|....*....|
gi 544684181 400 TGRTESNRIVNFQGTPNMIGKFVDVKITDVYTNSLRGEVV 439
Cdd:COG0621  395 IGRTENYALVVFPGDELLPGDFVDVKITEADEYDLIGELV 434
PRK14328 PRK14328
(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
1-440 0e+00

(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional


Pssm-ID: 237675 [Multi-domain]  Cd Length: 439  Bit Score: 543.81  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   1 MAKLHITTWGCQMNEYDSSKMADLLNSThGLELTENPEEADILLLNTCSIREKAQEKVFSQLGRWKNWKKDKPDLIIGVG 80
Cdd:PRK14328   1 NKKYFIETYGCQMNEEDSEKLAGMLKSM-GYERTENREEADIIIFNTCCVRENAENKVFGNLGELKKLKEKNPNLIIGVC 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  81 GCVASQEG--EHIRERAPFVDIVFGPQTLHRLPEMINQIRGGKSSVVDISFPEIEKFDRLPEPRAEGPTAFVSIMEGCNK 158
Cdd:PRK14328  80 GCMMQQKGmaEKIKKKFPFVDIIFGTHNIHKFPEYLNRVKEEGKSVIEIWEKEDGIVEGLPIDRKSKVKAFVTIMYGCNN 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 159 YCSFCVVPYTRGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQNVNAYrGETFDGGIcSFAELLRLVASIDGIDRVRYTTS 238
Cdd:PRK14328 160 FCTYCIVPYVRGRERSRKPEDIIAEIKELVSEGYKEVTLLGQNVNSY-GKDLEEKI-DFADLLRRVNEIDGLERIRFMTS 237
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 239 HPIEFTDDIIEVYKDTPELVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREARPDIQISSDFIVGFPGETAQDFE 318
Cdd:PRK14328 238 HPKDLSDDLIEAIADCDKVCEHIHLPVQSGSNRILKKMNRHYTREYYLELVEKIKSNIPDVAITTDIIVGFPGETEEDFE 317
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 319 QTMKIIEQVNFDMSFSFIYSARPGTPAADLPDDVTEDEKKERLYRLQQRINNQAMQFSRAMLGTEQRILVEGPSKKDIME 398
Cdd:PRK14328 318 ETLDLVKEVRYDSAFTFIYSKRKGTPAAKMEDQVPEDVKHERFNRLVELQNKISLEKNKEYEGKIVEVLVEGPSKNDENK 397
                        410       420       430       440
                 ....*....|....*....|....*....|....*....|..
gi 544684181 399 LTGRTESNRIVNFQGTPNMIGKFVDVKITDVYTNSLRGEVVR 440
Cdd:PRK14328 398 LTGRTRTNKLVNFIGDKELIGKLVNVKITKANSFSLTGEVIE 439
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
146-364 8.27e-58

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: 190.31  E-value: 8.27e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   146 PTAFVSIMEGCNKYCSFCVVPYTRGEEVSRPVDDVLFEIAQLAEQGVREVnLLGQNVNAYRGETFDGGIcSFAELLRLVA 225
Cdd:smart00729   1 PLALYIITRGCPRRCTFCSFPSLRGKLRSRYLEALVREIELLAEKGEKEG-LVGTVFIGGGTPTLLSPE-QLEELLEAIR 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   226 SIDGIDRV--RYTTSHPIEFTDDIIEVYKDTPelVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREARPdIQISS 303
Cdd:smart00729  79 EILGLAKDveITIETRPDTLTEELLEALKEAG--VNRVSLGVQSGDDEVLKAINRGHTVEDVLEAVELLREAGP-IKVST 155
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 544684181   304 DFIVGFPGETAQDFEQTMKIIEQVNFDMSFSFIYSARPGTPAADLPDDVTEDEKKERLYRL 364
Cdd:smart00729 156 DLIVGLPGETEEDFEETLKLLKELGPDRVSIFPLSPRPGTPLAKMYKRLKPPTKEERAELL 216
UPF0004 pfam00919
Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite ...
3-103 3.77e-41

Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins. This domain is a nearly always found in conjunction with pfam04055 and pfam01938 although its function is uncertain.


Pssm-ID: 459997 [Multi-domain]  Cd Length: 98  Bit Score: 142.27  E-value: 3.77e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181    3 KLHITTWGCQMNEYDSSKMADLLNStHGLELTENPEEADILLLNTCSIREKAQEKVFSQLGRWKnwKKDKPDLIIGVGGC 82
Cdd:pfam00919   1 KVYIETLGCQMNQADSEIMAGLLEK-AGYEVVEDEEEADVVVINTCTVRENAEQKSRQTIGRLK--RLKKPDAKIVVTGC 77
                          90       100
                  ....*....|....*....|.
gi 544684181   83 VASQEGEHIRERAPFVDIVFG 103
Cdd:pfam00919  78 MAQRYGEELLKLPPEVDLVLG 98
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
155-356 1.22e-09

Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.


Pssm-ID: 100105 [Multi-domain]  Cd Length: 204  Bit Score: 58.11  E-value: 1.22e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 155 GCNKYCSFCVVP--YTRGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQNVNAYRGetfdggicsFAELLRLVASIDGIDR 232
Cdd:cd01335    6 GCNLNCGFCSNPasKGRGPESPPEIEEILDIVLEAKERGVEVVILTGGEPLLYPE---------LAELLRRLKKELPGFE 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 233 VRYTTSHPIEFTDDIIEVYKDTPELVSFlhlPIQSGSDRVL-TMMKRNHTALEYKAIIRKLREArpDIQISSDFIVGFPG 311
Cdd:cd01335   77 ISIETNGTLLTEELLKELKELGLDGVGV---SLDSGDEEVAdKIRGSGESFKERLEALKELREA--GLGLSTTLLVGLGD 151
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 544684181 312 ETAQDFEQTMKIIEQVNFDMSFSFI-YSARPGTPAADLPDDVTEDE 356
Cdd:cd01335  152 EDEEDDLEELELLAEFRSPDRVSLFrLLPEEGTPLELAAPVVPAEK 197
 
Name Accession Description Interval E-value
miaB-methiolase TIGR01574
tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB; This model represents ...
3-439 0e+00

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: 703.50  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181    3 KLHITTWGCQMNEYDSSKMADLLNSTHGLELTENPEEADILLLNTCSIREKAQEKVFSQLGRWKNWKKDKPDLIIGVGGC 82
Cdd:TIGR01574   1 KLFIQTYGCQMNVRDSEHMAALLTAKEGYALTEDAKEADVLLINTCSVREKAEHKVFGELGGFKKLKKKNPDLIIGVCGC 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   83 VASQEGEHIRERAPFVDIVFGPQTLHRLPEMINQIRGGKSSVVDISFPEIEKFDRLPEPRAEG-PTAFVSIMEGCNKYCS 161
Cdd:TIGR01574  81 MASHLGNEIFQRAPYVDFVFGTRNIHRLPQAIKTPLTQKFMVVDIDSDESEVAGYFADFRNEGiYKSFINIMIGCNKFCT 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  162 FCVVPYTRGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQNVNAYRGETFDGGICSFAELLRLVASIDGIDRVRYTTSHPI 241
Cdd:TIGR01574 161 YCIVPYTRGDEISRPFDDILQEVQKLAEKGVREITLLGQNVNAYRGKDFEGKTMDFSDLLRELSTIDGIERIRFTSSHPL 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  242 EFTDDIIEVYKDTPELVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREARPDIQISSDFIVGFPGETAQDFEQTM 321
Cdd:TIGR01574 241 DFDDDLIEVFANNPKLCKSMHLPVQSGSSEILKLMKRGYTREWYLNLVRKLRAACPNVSISTDIIVGFPGETEEDFEETL 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  322 KIIEQVNFDMSFSFIYSARPGTPAADLPDDVTEDEKKERLYRLQQRINNQAMQFSRAMLGTEQRILVEGPSKKDIMELTG 401
Cdd:TIGR01574 321 DLLREVEFDSAFSFIYSPRPGTPAADMPDQIPEEIKKRRLQRLQARHNEILDKKMRKQEGKTFKVLVEGLSRNNPEELAG 400
                         410       420       430
                  ....*....|....*....|....*....|....*...
gi 544684181  402 RTESNRIVNFQGTPNMIGKFVDVKITDVYTNSLRGEVV 439
Cdd:TIGR01574 401 RTENNFLVNFEGSEDLIGKFVDVKITNVKRMSLRGEIV 438
MiaB COG0621
tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA ...
1-439 0e+00

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: 662.16  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   1 MAKLHITTWGCQMNEYDSSKMADLLNStHGLELTENPEEADILLLNTCSIREKAQEKVFSQLGRWKNWKKDKPDLIIGVG 80
Cdd:COG0621    1 MKKVYIVTLGCQMNQVDSERMAGLLEA-AGYELVDDPEEADVVVVNTCSVREKAEEKSRQTIGRLAELKRKNPDAKIVVT 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  81 GCVASQEGEHIRERAPFVDIVFGPQTLHRLPEMINQIRGGKSsVVDISfpEIEKFDRLPEP-RAEGPTAFVSIMEGCNKY 159
Cdd:COG0621   80 GCLAQREGEELLEEIPEVDLVVGPQDKHRLPELLEEALAGEK-VVDIS--SEETFDDLPVPrRTGRTRAFVKIQEGCNNF 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 160 CSFCVVPYTRGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQNVNAYRGETfdGGICSFAELLRLVASIDGIDRVRYTTSH 239
Cdd:COG0621  157 CTFCIIPYTRGRERSRPPEDILAEARRLAAQGVKEIVLTGQNVNSYGKDL--YGKTDLADLLRALAEIEGIERIRLSSSH 234
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 240 PIEFTDDIIEVYKDTPELVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREARPDIQISSDFIVGFPGETAQDFEQ 319
Cdd:COG0621  235 PKDFTDELIEAMAESPKVCPHLHLPLQSGSDRVLKRMNRRYTREEYLELVEKIREAIPDIAIRTDIIVGFPGETEEDFEE 314
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 320 TMKIIEQVNFDMSFSFIYSARPGTPAADLPDDVTEDEKKERLYRLQQRINNQAMQFSRAMLGTEQRILVEGPSKKDIMEL 399
Cdd:COG0621  315 TLDFVEEVRFDRLHVFPYSPRPGTPAAKMPDQVPEEVKKERLARLMELQEEISAERNQRLVGKTVEVLVEGPSKKDDGQL 394
                        410       420       430       440
                 ....*....|....*....|....*....|....*....|
gi 544684181 400 TGRTESNRIVNFQGTPNMIGKFVDVKITDVYTNSLRGEVV 439
Cdd:COG0621  395 IGRTENYALVVFPGDELLPGDFVDVKITEADEYDLIGELV 434
TIGR00089 TIGR00089
radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 ...
3-436 0e+00

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: 574.96  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181    3 KLHITTWGCQMNEYDSSKMADLLnSTHGLELTENPEEADILLLNTCSIREKAQEKVFSQLGRWKNWKKDKPdlIIGVGGC 82
Cdd:TIGR00089   1 KVYIETYGCQMNEADSEIMAGLL-KEGGYEVTDDPEEADVIIINTCAVREKAEQKVRSRLGELAKLKKKNA--KIVVAGC 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   83 VASQEGEHIRERAPFVDIVFGPQTLHRLPEMINQIRGGKSSVVDISFpeiEKFDRLPEPRAEG-PTAFVSIMEGCNKYCS 161
Cdd:TIGR00089  78 LAQREGEELLKEIPEVDIVLGPQDKERIPEAIESAEEGKQVVFDISK---EVYEELPRPRSFGkTRAFLKIQEGCDKFCT 154
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  162 FCVVPYTRGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQNVNAYrGETFDGGIcSFAELLRLVASIDGIDRVRYTTSHPI 241
Cdd:TIGR00089 155 YCIIPYARGRERSRPPEDILEEVKELVSKGVKEIVLLGQNVGAY-GKDLEGKT-NLADLLRELSKIDGIFRIRFGSSHPD 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  242 EFTDDIIEVYKDTPELVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREARPDIQISSDFIVGFPGETAQDFEQTM 321
Cdd:TIGR00089 233 DVTDDLIELIAENPKVCKHLHLPVQSGSDRILKRMNRKYTREEYLDIVEKIRAKIPDAAITTDIIVGFPGETEEDFEETL 312
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  322 KIIEQVNFDMSFSFIYSARPGTPAADLPDDVTEDEKKERLYRLQQRINNQAMQFSRAMLGTEQRILVEGPSKKDIMELTG 401
Cdd:TIGR00089 313 DLVEEVKFDKLHSFIYSPRPGTPAADMKDQVPEEVKKERLERLIALQKEISLEKNKKYVGKTLEVLVEGKEGKKEGELTG 392
                         410       420       430
                  ....*....|....*....|....*....|....*..
gi 544684181  402 RTESNRIVNFQG--TPNMIGKFVDVKITDVYTNSLRG 436
Cdd:TIGR00089 393 RTENYKPVVFEGgvGKSLIGKFVKVKITEAAEYDLIG 429
PRK14328 PRK14328
(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
1-440 0e+00

(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional


Pssm-ID: 237675 [Multi-domain]  Cd Length: 439  Bit Score: 543.81  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   1 MAKLHITTWGCQMNEYDSSKMADLLNSThGLELTENPEEADILLLNTCSIREKAQEKVFSQLGRWKNWKKDKPDLIIGVG 80
Cdd:PRK14328   1 NKKYFIETYGCQMNEEDSEKLAGMLKSM-GYERTENREEADIIIFNTCCVRENAENKVFGNLGELKKLKEKNPNLIIGVC 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  81 GCVASQEG--EHIRERAPFVDIVFGPQTLHRLPEMINQIRGGKSSVVDISFPEIEKFDRLPEPRAEGPTAFVSIMEGCNK 158
Cdd:PRK14328  80 GCMMQQKGmaEKIKKKFPFVDIIFGTHNIHKFPEYLNRVKEEGKSVIEIWEKEDGIVEGLPIDRKSKVKAFVTIMYGCNN 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 159 YCSFCVVPYTRGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQNVNAYrGETFDGGIcSFAELLRLVASIDGIDRVRYTTS 238
Cdd:PRK14328 160 FCTYCIVPYVRGRERSRKPEDIIAEIKELVSEGYKEVTLLGQNVNSY-GKDLEEKI-DFADLLRRVNEIDGLERIRFMTS 237
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 239 HPIEFTDDIIEVYKDTPELVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREARPDIQISSDFIVGFPGETAQDFE 318
Cdd:PRK14328 238 HPKDLSDDLIEAIADCDKVCEHIHLPVQSGSNRILKKMNRHYTREYYLELVEKIKSNIPDVAITTDIIVGFPGETEEDFE 317
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 319 QTMKIIEQVNFDMSFSFIYSARPGTPAADLPDDVTEDEKKERLYRLQQRINNQAMQFSRAMLGTEQRILVEGPSKKDIME 398
Cdd:PRK14328 318 ETLDLVKEVRYDSAFTFIYSKRKGTPAAKMEDQVPEDVKHERFNRLVELQNKISLEKNKEYEGKIVEVLVEGPSKNDENK 397
                        410       420       430       440
                 ....*....|....*....|....*....|....*....|..
gi 544684181 399 LTGRTESNRIVNFQGTPNMIGKFVDVKITDVYTNSLRGEVVR 440
Cdd:PRK14328 398 LTGRTRTNKLVNFIGDKELIGKLVNVKITKANSFSLTGEVIE 439
PRK14336 PRK14336
(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
1-440 1.21e-107

(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional


Pssm-ID: 184632 [Multi-domain]  Cd Length: 418  Bit Score: 325.71  E-value: 1.21e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   1 MAKLHITTWGCQMNEYDSSKMADLLnSTHGLELTENPEEADILLLNTCSIREKAQEKVFSQLGRWKNWKKDKPDLIIGVG 80
Cdd:PRK14336   1 MPGYYLWTIGCQMNQAESERLGRLF-ELWGYSLADKAEDAELVLVNSCVVREHAENKVINRLHLLRKLKNKNPKLKIALT 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  81 GCVASQEGEHIRERAPFVDIVFGPQTLhrlPEMINQIRGgkssvvdisfpeiekfdrLPEPRAEGPTAFVSIMEGCNKYC 160
Cdd:PRK14336  80 GCLVGQDISLIRKKFPFVDYIFGPGSM---PDWREIPEG------------------FILPLKPPVSANVTIMQGCDNFC 138
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 161 SFCVVPYTRGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQNVNAYrGETFDGGICsFAELLRLVASIDGIDRVRYTTSHP 240
Cdd:PRK14336 139 TYCVVPYRRGREKSRSIAEIGCEVAELVRRGSREVVLLGQNVDSY-GHDLPEKPC-LADLLSALHDIPGLLRIRFLTSHP 216
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 241 IEFTDDIIEVYKDTPELVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREARPDIQISSDFIVGFPGETAQDFEQT 320
Cdd:PRK14336 217 KDISQKLIDAMAHLPKVCRSLSLPVQAGDDTILAAMRRGYTNQQYRELVERLKTAMPDISLQTDLIVGFPSETEEQFNQS 296
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 321 MKIIEQVNFDMSFSFIYSARPGTPAA-DLPDDVTEDEKKERLY---RLQQRINNQAmqfSRAMLGTEQRILVEGPSKKdi 396
Cdd:PRK14336 297 YKLMADIGYDAIHVAAYSPRPQTVAArDMADDVPVIEKKRRLKlieDLQKETVGKA---NAALMDTFAEVLVEGLQKN-- 371
                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....
gi 544684181 397 mELTGRTESNRIVNFQGTPNMIGKFVDVKITDVYTNSLRGEVVR 440
Cdd:PRK14336 372 -KWQGRTLGGKLVFLESDLPLEGCLVNVKIFKTSPWSLQAKLVN 414
MiaB-like-C TIGR01579
MiaB-like tRNA modifying enzyme; This clade of sequences is closely related to MiaB, a ...
6-426 2.14e-90

MiaB-like tRNA modifying enzyme; This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see TIGR01574). Sequence alignments suggest that this equivalog performs the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade is a member of a subfamily (TIGR00089) and spans low GC Gram positive bacteria, alpha and epsilon proteobacteria, Campylobacter, Porphyromonas, Aquifex, Thermotoga, Chlamydia, Treponema and Fusobacterium. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 273704 [Multi-domain]  Cd Length: 414  Bit Score: 281.19  E-value: 2.14e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181    6 ITTWGCQMNEYDSSKMADLLnSTHGLELTENPEEADILLLNTCSIREKAQEKVFSQLgrwKNWKKDKPDLIIGVGGCVAS 85
Cdd:TIGR01579   1 IETLGCRVNQYESESLKNQL-IQKGYEVVPDEDKADVYIINTCTVTAKADSKARRAI---RRARRQNPTAKIIVTGCYAQ 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   86 QEGEHIRERaPFVDIVFGPQTLHRLPEM------INQIRGGKSSVVDIS-FPEIEKFDRLPEPRAegptaFVSIMEGCNK 158
Cdd:TIGR01579  77 SNPKELADL-KDVDLVLGNKEKDKINKLlslglkTSFYRVKNKNFSREKgVPEYEEVAFEGHTRA-----FIKVQDGCNF 150
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  159 YCSFCVVPYTRGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQNVNAYrGETFDGGIcSFAELLRLVASIDGIDRVRYTTS 238
Cdd:TIGR01579 151 FCSYCIIPFARGRSRSVPMEAILKQVKILVAKGYKEIVLTGVNLGSY-GDDLKNGT-SLAKLLEQILQIPGIKRIRLSSI 228
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  239 HPIEFTDDIIEVYKDTPELVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREARPDIQISSDFIVGFPGETAQDFE 318
Cdd:TIGR01579 229 DPEDIDEELLEAIASEKRLCPHLHLSLQSGSDRVLKRMRRKYTRDDFLKLVNKLRSVRPDYAFGTDIIVGFPGESEEDFQ 308
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  319 QTMKIIEQVNFDMSFSFIYSARPGTPAADLPDDVTEDEKKERLYRLQQRINNQAMQFSRAMLGTEQRILVEgpsKKDIME 398
Cdd:TIGR01579 309 ETLRMVKEIEFSHLHIFPYSARPGTPASTMKDKVPETIKKERVKRLKELAEKNYQEFLKKNIGKELEVLVE---KEKAGV 385
                         410       420
                  ....*....|....*....|....*....
gi 544684181  399 LTGRTES-NRIVNFQGTPNMIGKFVDVKI 426
Cdd:TIGR01579 386 LTGYSEYyLKVKVESDKGVAAGELISVRI 414
TIGR01125 TIGR01125
ribosomal protein S12 methylthiotransferase RimO; Members of this protein are the ...
3-429 2.13e-84

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: 266.23  E-value: 2.13e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181    3 KLHITTWGCQMNEYDSSKMADLLnSTHGLELTENPEEADILLLNTCSIREKAQEKVFSQLGRWKNWKKDkpdliIGVGGC 82
Cdd:TIGR01125   1 KIGFISLGCPKNLVDSEVLLGVL-REAGYEVVPNYEDADVVIVNTCGFIEDAKQESIDTIGEFADAGKK-----VIVTGC 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   83 VASQEGEHIRERAPFVDIVFGPqtlHRLPEMINQIRGGKSS--VVDISFPEIEKFDR-LPEPRaegPTAFVSIMEGCNKY 159
Cdd:TIGR01125  75 LVQRYKEELKEEIPEVDAITGS---GDVEEILNAIENGEPGdlVPFKSEIEMGEVPRiLLTPR---HYAYLKIAEGCNRR 148
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  160 CSFCVVPYTRGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQNVNAY----RGETfdggicSFAELLRLVASIDGIDRVRY 235
Cdd:TIGR01125 149 CAFCIIPSIRGKLRSRPIEEILREAERLVDQGVKEIILIAQDTTAYgkdlYRES------KLVDLLERLGKLGGIFWIRM 222
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  236 TTSHPIEFTDDIIEVYKDTPELVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREARPDIQISSDFIVGFPGETAQ 315
Cdd:TIGR01125 223 HYLYPDELTDDVIDLMAEGPKVLPYLDIPLQHASDRILKLMRRPGSGEEQLDMIERIREKCPDAVLRTTFIVGFPGETEE 302
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  316 DFEQTMKIIEQVNFDMSFSFIYSARPGTPAADLPDDVTEDEKKERLYRL---QQRINNQAMQfsrAMLGTEQRILVEGpS 392
Cdd:TIGR01125 303 DFQELLDFVEEGQFDRLGAFTYSPEEGTDAFALPDQVPEEVKEERLERLmqlQQRISAKKLQ---EFVGKKIEVLIDG-Y 378
                         410       420       430       440
                  ....*....|....*....|....*....|....*....|..
gi 544684181  393 KKDIMELTGRT-----ESNRIVNFQGTPNmIGKFVDVKITDV 429
Cdd:TIGR01125 379 EPEFNLLIGRTygqapEVDGVVYVNGKGK-IGDILRVVITET 419
MiaB-like-B TIGR01578
MiaB-like tRNA modifying enzyme, archaeal-type; This clade of sequences is closely related to ...
3-439 5.49e-75

MiaB-like tRNA modifying enzyme, archaeal-type; This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see TIGR01574). Sequence alignments suggest that this equivalog performs the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade is a member of a subfamily (TIGR00089) and spans the archaea and eukaryotes. The only archaeal miaB-like genes are in this clade, while eukaryotes have sequences described by this model as well as ones falling within the scope of the MiaB equivalog model. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 273703 [Multi-domain]  Cd Length: 420  Bit Score: 241.61  E-value: 5.49e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181    3 KLHITTWGCQMNEYDSSKMADLLNStHGLELTENPEEADILLLNTCSIREKAQEKVfsqLGRWKNWKKDKPDLIigVGGC 82
Cdd:TIGR01578   1 KVYVETYGCTLNNGDSEIMKNSLAA-YGHELVNNAEEADLAILNTCTVKNKTEDTM---LYRIESLMRNGKHVV--VAGC 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   83 VASQEGEHIRERAPFVDIVfGPQTLHRLPEMINQIRGGKSSVVDIsFPEIEKfdrLPEPRAEGPTAFVSIMEGCNKYCSF 162
Cdd:TIGR01578  75 MPQAQKESVYDNGSVASVL-GVQAIDRLVEVVEETLKKKVHGRRE-AGTPLS---LPKPRKNPLIEIIPINQGCLGNCSY 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  163 CVVPYTRGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQNVNAYrgeTFDGGIcSFAELLRLVASIDGIDRVRYTTSHP-- 240
Cdd:TIGR01578 150 CITKHARGKLASYPPEKIVEKARQLVAEGCKEIWITSQDTGAY---GRDIGS-RLPELLRLITEIPGEFRLRVGMMNPkn 225
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  241 -IEFTDDIIEVYkDTPELVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREARPDIQISSDFIVGFPGETAQDFEQ 319
Cdd:TIGR01578 226 vLEILDELANVY-QHEKVYKFLHLPVQSGSDSVLKEMKREYTVSDFEDIVDKFRERFPDLTLSTDIIVGFPTETDDDFEE 304
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  320 TMKIIEQVNFDMSFSFIYSARPGTPAADLP--DDVTEDEKKERLYRLQQRINNQAMQfsrAMLGTEQRILVEGPSKKDIM 397
Cdd:TIGR01578 305 TMELLRKYRPEKINITKFSPRPGTPAAKMKriPTNIVKKRSKRLTKLYEQVLLEMRD---NLIGTRVHVLVTKEGKGDSL 381
                         410       420       430       440
                  ....*....|....*....|....*....|....*....|..
gi 544684181  398 EltgRTESNRIVNFQGTPNMIGKFVDVKITDVYTNSLRGEVV 439
Cdd:TIGR01578 382 D---DEDAYRQVVIRSRTREPGEFAGVEITGAKTAYLIGEII 420
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
146-364 8.27e-58

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: 190.31  E-value: 8.27e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   146 PTAFVSIMEGCNKYCSFCVVPYTRGEEVSRPVDDVLFEIAQLAEQGVREVnLLGQNVNAYRGETFDGGIcSFAELLRLVA 225
Cdd:smart00729   1 PLALYIITRGCPRRCTFCSFPSLRGKLRSRYLEALVREIELLAEKGEKEG-LVGTVFIGGGTPTLLSPE-QLEELLEAIR 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181   226 SIDGIDRV--RYTTSHPIEFTDDIIEVYKDTPelVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREARPdIQISS 303
Cdd:smart00729  79 EILGLAKDveITIETRPDTLTEELLEALKEAG--VNRVSLGVQSGDDEVLKAINRGHTVEDVLEAVELLREAGP-IKVST 155
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 544684181   304 DFIVGFPGETAQDFEQTMKIIEQVNFDMSFSFIYSARPGTPAADLPDDVTEDEKKERLYRL 364
Cdd:smart00729 156 DLIVGLPGETEEDFEETLKLLKELGPDRVSIFPLSPRPGTPLAKMYKRLKPPTKEERAELL 216
UPF0004 pfam00919
Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite ...
3-103 3.77e-41

Uncharacterized protein family UPF0004; This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins. This domain is a nearly always found in conjunction with pfam04055 and pfam01938 although its function is uncertain.


Pssm-ID: 459997 [Multi-domain]  Cd Length: 98  Bit Score: 142.27  E-value: 3.77e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181    3 KLHITTWGCQMNEYDSSKMADLLNStHGLELTENPEEADILLLNTCSIREKAQEKVFSQLGRWKnwKKDKPDLIIGVGGC 82
Cdd:pfam00919   1 KVYIETLGCQMNQADSEIMAGLLEK-AGYEVVEDEEEADVVVINTCTVRENAEQKSRQTIGRLK--RLKKPDAKIVVTGC 77
                          90       100
                  ....*....|....*....|.
gi 544684181   83 VASQEGEHIRERAPFVDIVFG 103
Cdd:pfam00919  78 MAQRYGEELLKLPPEVDLVLG 98
YgiQ COG1032
Radical SAM superfamily enzyme YgiQ, UPF0313 family [General function prediction only];
69-381 3.87e-35

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


Pssm-ID: 440655 [Multi-domain]  Cd Length: 394  Bit Score: 135.07  E-value: 3.87e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  69 KKDKPDLIIGVGGCVASQEGEHIREraPFVDIVF---GPQTLhrlPEMINQIRGGKS--------------SVVDISFPE 131
Cdd:COG1032   78 KERNPGVPIVLGGPHASLNPEELLE--PFADFVVigeGEETL---PELLEALEEGRDladipglayrddgrIVQNPPRPL 152
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 132 IEKFDRLPEPRAE-------GPTAFVSIMEGCNKYCSFCVVPYTRGEEV-SRPVDDVLFEIAQLAEQ-GVREVNLLGQNV 202
Cdd:COG1032  153 IEDLDELPFPAYDlldleayHRRASIETSRGCPFGCSFCSISALYGRKVrYRSPESVVEEIEELVKRyGIREIFFVDDNF 232
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 203 NAYRGEtfdggicsFAELLRLVasidgIDRvRYTTSHPIE-----FTDDIIEVYKDTPelVSFLHLPIQSGSDRVLTMMK 277
Cdd:COG1032  233 NVDKKR--------LKELLEEL-----IER-GLNVSFPSEvrvdlLDEELLELLKKAG--CRGLFIGIESGSQRVLKAMN 296
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 278 RNHTALEYKAIIRKLREArpDIQISSDFIVGFPGETAQDFEQTMKIIEQVNFDMSFSFIYSARPGTPAADLPddvtedEK 357
Cdd:COG1032  297 KGITVEDILEAVRLLKKA--GIRVKLYFIIGLPGETEEDIEETIEFIKELGPDQAQVSIFTPLPGTPLYEEL------EK 368
                        330       340
                 ....*....|....*....|....
gi 544684181 358 KERLYRLQQRINNQAMQFSRAMLG 381
Cdd:COG1032  369 EGRLYDWEKYEDLLEAVLAPRLSG 392
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
152-320 3.19e-24

Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.


Pssm-ID: 427681 [Multi-domain]  Cd Length: 159  Bit Score: 98.37  E-value: 3.19e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  152 IMEGCNKYCSFCVVPYT--RGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQNVNAYRGetfdggicsFAELLRLVASID- 228
Cdd:pfam04055   1 ITRGCNLRCTYCAFPSIraRGKGRELSPEEILEEAKELKRLGVEVVILGGGEPLLLPD---------LVELLERLLKLEl 71
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181  229 -GIDRVRYTTShPIEFTDDIIEVYKDTPelVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREArpDIQISSDFIV 307
Cdd:pfam04055  72 aEGIRITLETN-GTLLDEELLELLKEAG--LDRVSIGLESGDDEVLKLINRGHTFEEVLEALELLREA--GIPVVTDNIV 146
                         170
                  ....*....|...
gi 544684181  308 GFPGETAQDFEQT 320
Cdd:pfam04055 147 GLPGETDEDLEET 159
TRAM pfam01938
TRAM domain; This small domain has no known function. However it may perform a nucleic acid ...
377-439 1.72e-13

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: 64.93  E-value: 1.72e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544684181  377 RAMLGTEQRILVEGPSkkDIMELTGRTESNRIVNFQGTPNmiGKFVDVKITDVYTNSLRGEVV 439
Cdd:pfam01938   1 RRYVGQTQEVLVEGLS--SNGEGIGRTDNGKVVFVPGALP--GEFVEVKITKVKRNYLRGELL 59
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
155-356 1.22e-09

Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.


Pssm-ID: 100105 [Multi-domain]  Cd Length: 204  Bit Score: 58.11  E-value: 1.22e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 155 GCNKYCSFCVVP--YTRGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQNVNAYRGetfdggicsFAELLRLVASIDGIDR 232
Cdd:cd01335    6 GCNLNCGFCSNPasKGRGPESPPEIEEILDIVLEAKERGVEVVILTGGEPLLYPE---------LAELLRRLKKELPGFE 76
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 233 VRYTTSHPIEFTDDIIEVYKDTPELVSFlhlPIQSGSDRVL-TMMKRNHTALEYKAIIRKLREArpDIQISSDFIVGFPG 311
Cdd:cd01335   77 ISIETNGTLLTEELLKELKELGLDGVGV---SLDSGDEEVAdKIRGSGESFKERLEALKELREA--GLGLSTTLLVGLGD 151
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 544684181 312 ETAQDFEQTMKIIEQVNFDMSFSFI-YSARPGTPAADLPDDVTEDE 356
Cdd:cd01335  152 EDEEDDLEELELLAEFRSPDRVSLFrLLPEEGTPLELAAPVVPAEK 197
HemN COG0635
Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase ...
156-364 2.38e-07

Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase [Coenzyme transport and metabolism]; Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase is part of the Pathway/BioSystem: Heme biosynthesis


Pssm-ID: 440400 [Multi-domain]  Cd Length: 400  Bit Score: 52.88  E-value: 2.38e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 156 CNKYCSFC----VVpyTRGEEVSRPVDDVLFEIAQLAEQ-GVREVnllgqnvnayrgET--FDGG---ICSFAELLRLva 225
Cdd:COG0635   32 CRSKCPYCdfnsHT--TREEPVDRYLDALLKEIELYAALlGGRPV------------STifFGGGtpsLLSPEQLERL-- 95
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 226 sIDGIDRvRYTTSHPIEFT---------DDIIEVYKDTPelVSFLHLPIQSGSDRVLTMMKRNHTALEYKAIIRKLREAR 296
Cdd:COG0635   96 -LDALRE-HFPLAPDAEITleanpgtvtAEKLAALREAG--VNRLSLGVQSFDDEVLKALGRIHTAEEALAAVELAREAG 171
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 297 PDiQISSDFIVGFPGETAQDFEQTmkiIEQVnFDMS------FSFIYsaRPGTPAA--------DLPDdvteDEKKERLY 362
Cdd:COG0635  172 FD-NINLDLIYGLPGQTLESWEET---LEKA-LALGpdhislYSLTH--EPGTPFAqrvrrgklALPD----DDEKADMY 240

                 ..
gi 544684181 363 RL 364
Cdd:COG0635  241 EL 242
PRK08207 PRK08207
coproporphyrinogen III oxidase; Provisional
266-328 7.38e-06

coproporphyrinogen III oxidase; Provisional


Pssm-ID: 236187 [Multi-domain]  Cd Length: 488  Bit Score: 48.34  E-value: 7.38e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 544684181 266 QSGSDRVLTMMKRNHTALEykaIIRKLREARpDI---QISSDFIVGFPGETAQDFEQTMKIIEQVN 328
Cdd:PRK08207 288 QTMNDETLKAIGRHHTVED---IIEKFHLAR-EMgfdNINMDLIIGLPGEGLEEVKHTLEEIEKLN 349
TM1601 COG1031
Radical SAM superfamily enzyme with C-terminal helix-hairpin-helix motif [General function ...
155-390 1.96e-05

Radical SAM superfamily enzyme with C-terminal helix-hairpin-helix motif [General function prediction only];


Pssm-ID: 440654 [Multi-domain]  Cd Length: 555  Bit Score: 47.16  E-value: 1.96e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 155 GCNKY---CSFCVVP-YtrGEEVSRPVDDVLFEIAQLAEQGVREVNLLGQ-NVNAYRGETF-DGGICSFAELLRLVASID 228
Cdd:COG1031  189 GCPRRvggCSFCTEPlY--GRPEFRPPEGVVEEVEALYDAGVRHFRLGRQaDILAYGGKGGgDGPKPNPEALEELYSGIR 266
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 229 G---------IDRV--RYTTSHP---IEFTDDIIEvYkDTP-ELVSFlhlPIQSGSDRVLtmmKRNH---TALE-YKAI- 288
Cdd:COG1031  267 EvapdlktlhIDNVnpGTIARYPeesREALKTIVK-Y-HTPgDVAAF---GLESADPVVI---KANNlkvTPEEvLEAIr 338
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544684181 289 ----IRKLREAR------PDIqissDFIVGFPGETAQDFEQTMKIIEQVnFD-------------MSFsfiysarPGTPA 345
Cdd:COG1031  339 ivneVGGWRGYNglpkllPGI----NFVHGLPGETKETFELNYEFLKRV-LDegllvrrinirqvMAF-------PGTPM 406
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 544684181 346 ADLPDDVTEDEKKERLyRLQQRINNqamQFSRAMLgteQRILVEG 390
Cdd:COG1031  407 WETGADIARKHKKLFK-KYKEWVRE---EIDLPML---RRVVPPG 444
TRAM_2 pfam18693
TRAM domain; This is a C-terminal TRAM (after TRM2, a family of uridine methylases, and MiaB) ...
381-439 2.79e-03

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: 36.29  E-value: 2.79e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 544684181  381 GTEQRILVEGPSKkdiMELTGRT-----ESNRIVNFQGTPNM-IGKFVDVKITDVYTNSLRGEVV 439
Cdd:pfam18693   2 GKTLDVLIDGEEE---GLYVGRSyadapEIDGEVYVTGAEDLkVGDFVNVRITDADEYDLIGEVV 63
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH