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Conserved domains on  [gi|1039744114|ref|XP_017171079|]
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threonylcarbamoyladenosine tRNA methylthiotransferase isoform X4 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MiaB-like-B super family cl36934
MiaB-like tRNA modifying enzyme, archaeal-type; This clade of sequences is closely related to ...
 1-206 4.01e-70

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]


The actual alignment was detected with superfamily member TIGR01578:

Pssm-ID: 273703 [Multi-domain]  Cd Length: 420  Bit Score: 222.73  E-value: 4.01e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114   1 MLRLGMTNPPYILEHLEEMAKILNHPRVYAFLHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKVPGITIATDIICGF 80
Cdd:TIGR01578 215 RLRVGMMNPKNVLEILDELANVYQHEKVYKFLHLPVQSGSDSVLKEMKREYTVSDFEDIVDKFRERFPDLTLSTDIIVGF 294

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114  81 PGETDQDFQETVKLVEEYKFPSLFINQFYPRPGTPAAKAEQVPAHVKKQRTKDLSRVFH--SYNPYDHKIGERQQVLVTE 158
Cdd:TIGR01578 295 PTETDDDFEETMELLRKYRPEKINITKFSPRPGTPAAKMKRIPTNIVKKRSKRLTKLYEqvLLEMRDNLIGTRVHVLVTK 374

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1039744114 159 ESF-DS-KFYVAhnrfYEQVLVPKNPAFMGKMVEVDIYESGKHFLKGQPV 206
Cdd:TIGR01578 375 EGKgDSlDDEDA----YRQVVIRSRTREPGEFAGVEITGAKTAYLIGEII 420
 
Name Accession Description Interval E-value
MiaB-like-B TIGR01578
MiaB-like tRNA modifying enzyme, archaeal-type; This clade of sequences is closely related to ...
 1-206 4.01e-70

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: 222.73  E-value: 4.01e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114   1 MLRLGMTNPPYILEHLEEMAKILNHPRVYAFLHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKVPGITIATDIICGF 80
Cdd:TIGR01578 215 RLRVGMMNPKNVLEILDELANVYQHEKVYKFLHLPVQSGSDSVLKEMKREYTVSDFEDIVDKFRERFPDLTLSTDIIVGF 294

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114  81 PGETDQDFQETVKLVEEYKFPSLFINQFYPRPGTPAAKAEQVPAHVKKQRTKDLSRVFH--SYNPYDHKIGERQQVLVTE 158
Cdd:TIGR01578 295 PTETDDDFEETMELLRKYRPEKINITKFSPRPGTPAAKMKRIPTNIVKKRSKRLTKLYEqvLLEMRDNLIGTRVHVLVTK 374

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1039744114 159 ESF-DS-KFYVAhnrfYEQVLVPKNPAFMGKMVEVDIYESGKHFLKGQPV 206
Cdd:TIGR01578 375 EGKgDSlDDEDA----YRQVVIRSRTREPGEFAGVEITGAKTAYLIGEII 420
MiaB COG0621
tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-207 1.40e-63

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: 206.09  E-value: 1.40e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114   1 MLRLGMTNPPYILEHL-EEMAkilNHPRVYAFLHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKVPGITIATDIICG 79
Cdd:COG0621   227 RIRLSSSHPKDFTDELiEAMA---ESPKVCPHLHLPLQSGSDRVLKRMNRRYTREEYLELVEKIREAIPDIAIRTDIIVG 303

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114  80 FPGETDQDFQETVKLVEEYKFPSLFINQFYPRPGTPAAK-AEQVPAHVKKQRTKDLSRVF--HSYNPYDHKIGERQQVLV 156
Cdd:COG0621   304 FPGETEEDFEETLDFVEEVRFDRLHVFPYSPRPGTPAAKmPDQVPEEVKKERLARLMELQeeISAERNQRLVGKTVEVLV 383

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1039744114 157 TEES-FDSKFYVAHNRFYEQVLVPKNPAFMGKMVEVDIYESGKHFLKGQPVS 207
Cdd:COG0621   384 EGPSkKDDGQLIGRTENYALVVFPGDELLPGDFVDVKITEADEYDLIGELVE 435
PRK14328 PRK14328
(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
 22-207 1.24e-40

(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional


Pssm-ID: 237675 [Multi-domain]  Cd Length: 439  Bit Score: 146.28  E-value: 1.24e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114  22 ILNHPRVYAFLHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKVPGITIATDIICGFPGETDQDFQETVKLVEEYKFP 101
Cdd:PRK14328  250 IADCDKVCEHIHLPVQSGSNRILKKMNRHYTREYYLELVEKIKSNIPDVAITTDIIVGFPGETEEDFEETLDLVKEVRYD 329

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114 102 SLFINQFYPRPGTPAAK-AEQVPAHVKKQRTKDLSRVFH--SYNPYDHKIGERQQVLVTEES-FDSKFYVAHNRFYEQVL 177
Cdd:PRK14328  330 SAFTFIYSKRKGTPAAKmEDQVPEDVKHERFNRLVELQNkiSLEKNKEYEGKIVEVLVEGPSkNDENKLTGRTRTNKLVN 409

                         170       180       190
                  ....*....|....*....|....*....|
gi 1039744114 178 VPKNPAFMGKMVEVDIYESGKHFLKGQPVS 207
Cdd:PRK14328  410 FIGDKELIGKLVNVKITKANSFSLTGEVIE 439
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 7-123 4.90e-30

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: 112.88  E-value: 4.90e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114    7 TNPPYIL-EHLEEMAKILNHprvyaFLHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKVPgITIATDIICGFPGETD 85
Cdd:smart00729  93 TRPDTLTeELLEALKEAGVN-----RVSLGVQSGDDEVLKAINRGHTVEDVLEAVELLREAGP-IKVSTDLIVGLPGETE 166

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1039744114   86 QDFQETVKLVEEYKFPSLFINQFYPRPGTPAAKAEQVP 123
Cdd:smart00729 167 EDFEETLKLLKELGPDRVSIFPLSPRPGTPLAKMYKRL 204
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 7-91 9.26e-11

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: 59.08  E-value: 9.26e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114   7 TNPPYI-LEHLEEMAKiLNHPRVyaflHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKvpGITIATDIICGFPGETD 85
Cdd:pfam04055  81 TNGTLLdEELLELLKE-AGLDRV----SIGLESGDDEVLKLINRGHTFEEVLEALELLREA--GIPVVTDNIVGLPGETD 153


                  ....*.
gi 1039744114  86 QDFQET 91
Cdd:pfam04055 154 EDLEET 159
 
Name Accession Description Interval E-value
MiaB-like-B TIGR01578
MiaB-like tRNA modifying enzyme, archaeal-type; This clade of sequences is closely related to ...
 1-206 4.01e-70

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: 222.73  E-value: 4.01e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114   1 MLRLGMTNPPYILEHLEEMAKILNHPRVYAFLHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKVPGITIATDIICGF 80
Cdd:TIGR01578 215 RLRVGMMNPKNVLEILDELANVYQHEKVYKFLHLPVQSGSDSVLKEMKREYTVSDFEDIVDKFRERFPDLTLSTDIIVGF 294

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114  81 PGETDQDFQETVKLVEEYKFPSLFINQFYPRPGTPAAKAEQVPAHVKKQRTKDLSRVFH--SYNPYDHKIGERQQVLVTE 158
Cdd:TIGR01578 295 PTETDDDFEETMELLRKYRPEKINITKFSPRPGTPAAKMKRIPTNIVKKRSKRLTKLYEqvLLEMRDNLIGTRVHVLVTK 374

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1039744114 159 ESF-DS-KFYVAhnrfYEQVLVPKNPAFMGKMVEVDIYESGKHFLKGQPV 206
Cdd:TIGR01578 375 EGKgDSlDDEDA----YRQVVIRSRTREPGEFAGVEITGAKTAYLIGEII 420
MiaB COG0621
tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-207 1.40e-63

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: 206.09  E-value: 1.40e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114   1 MLRLGMTNPPYILEHL-EEMAkilNHPRVYAFLHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKVPGITIATDIICG 79
Cdd:COG0621   227 RIRLSSSHPKDFTDELiEAMA---ESPKVCPHLHLPLQSGSDRVLKRMNRRYTREEYLELVEKIREAIPDIAIRTDIIVG 303

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114  80 FPGETDQDFQETVKLVEEYKFPSLFINQFYPRPGTPAAK-AEQVPAHVKKQRTKDLSRVF--HSYNPYDHKIGERQQVLV 156
Cdd:COG0621   304 FPGETEEDFEETLDFVEEVRFDRLHVFPYSPRPGTPAAKmPDQVPEEVKKERLARLMELQeeISAERNQRLVGKTVEVLV 383

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1039744114 157 TEES-FDSKFYVAHNRFYEQVLVPKNPAFMGKMVEVDIYESGKHFLKGQPVS 207
Cdd:COG0621   384 EGPSkKDDGQLIGRTENYALVVFPGDELLPGDFVDVKITEADEYDLIGELVE 435
TIGR00089 TIGR00089
radical SAM methylthiotransferase, MiaB/RimO family; This subfamily contains the tRNA-i(6)A37 ...
 2-203 2.35e-52

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: 176.66  E-value: 2.35e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114   2 LRLGMTNPPYILEHLEEMakILNHPRVYAFLHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKVPGITIATDIICGFP 81
Cdd:TIGR00089 224 IRFGSSHPDDVTDDLIEL--IAENPKVCKHLHLPVQSGSDRILKRMNRKYTREEYLDIVEKIRAKIPDAAITTDIIVGFP 301

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114  82 GETDQDFQETVKLVEEYKFPSLFINQFYPRPGTPAAK-AEQVPAHVKKQRTKDLS-RVFH-SYNPYDHKIGERQQVLVTE 158
Cdd:TIGR00089 302 GETEEDFEETLDLVEEVKFDKLHSFIYSPRPGTPAADmKDQVPEEVKKERLERLIaLQKEiSLEKNKKYVGKTLEVLVEG 381

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1039744114 159 ES-FDSKFYVAHNRFYEQVLVP--KNPAFMGKMVEVDIYESGKHFLKG 203
Cdd:TIGR00089 382 KEgKKEGELTGRTENYKPVVFEggVGKSLIGKFVKVKITEAAEYDLIG 429
PRK14328 PRK14328
(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
 22-207 1.24e-40

(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional


Pssm-ID: 237675 [Multi-domain]  Cd Length: 439  Bit Score: 146.28  E-value: 1.24e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114  22 ILNHPRVYAFLHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKVPGITIATDIICGFPGETDQDFQETVKLVEEYKFP 101
Cdd:PRK14328  250 IADCDKVCEHIHLPVQSGSNRILKKMNRHYTREYYLELVEKIKSNIPDVAITTDIIVGFPGETEEDFEETLDLVKEVRYD 329

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114 102 SLFINQFYPRPGTPAAK-AEQVPAHVKKQRTKDLSRVFH--SYNPYDHKIGERQQVLVTEES-FDSKFYVAHNRFYEQVL 177
Cdd:PRK14328  330 SAFTFIYSKRKGTPAAKmEDQVPEDVKHERFNRLVELQNkiSLEKNKEYEGKIVEVLVEGPSkNDENKLTGRTRTNKLVN 409

                         170       180       190
                  ....*....|....*....|....*....|
gi 1039744114 178 VPKNPAFMGKMVEVDIYESGKHFLKGQPVS 207
Cdd:PRK14328  410 FIGDKELIGKLVNVKITKANSFSLTGEVIE 439
miaB-methiolase TIGR01574
tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB; This model represents ...
 19-206 2.63e-36

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: 134.56  E-value: 2.63e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114  19 MAKILNHPRVYAFLHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKVPGITIATDIICGFPGETDQDFQETVKLVEEY 98
Cdd:TIGR01574 247 IEVFANNPKLCKSMHLPVQSGSSEILKLMKRGYTREWYLNLVRKLRAACPNVSISTDIIVGFPGETEEDFEETLDLLREV 326

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114  99 KFPSLFINQFYPRPGTPAAK-AEQVPAHVKKQRtkdLSRVFHSYNPYDHKI-----GERQQVLVTEESFDSKFYVA-HNR 171
Cdd:TIGR01574 327 EFDSAFSFIYSPRPGTPAADmPDQIPEEIKKRR---LQRLQARHNEILDKKmrkqeGKTFKVLVEGLSRNNPEELAgRTE 403

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1039744114 172 FYEQVLVPKNPAFMGKMVEVDIYESGKHFLKGQPV 206
Cdd:TIGR01574 404 NNFLVNFEGSEDLIGKFVDVKITNVKRMSLRGEIV 438
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 7-123 4.90e-30

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: 112.88  E-value: 4.90e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114    7 TNPPYIL-EHLEEMAKILNHprvyaFLHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKVPgITIATDIICGFPGETD 85
Cdd:smart00729  93 TRPDTLTeELLEALKEAGVN-----RVSLGVQSGDDEVLKAINRGHTVEDVLEAVELLREAGP-IKVSTDLIVGLPGETE 166

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1039744114   86 QDFQETVKLVEEYKFPSLFINQFYPRPGTPAAKAEQVP 123
Cdd:smart00729 167 EDFEETLKLLKELGPDRVSIFPLSPRPGTPLAKMYKRL 204
TIGR01125 TIGR01125
ribosomal protein S12 methylthiotransferase RimO; Members of this protein are the ...
 11-175 2.38e-24

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: 101.36  E-value: 2.38e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114  11 YILEHLEEMAK-ILNHPRVYAFLHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKVPGITIATDIICGFPGETDQDFQ 89
Cdd:TIGR01125 226 YPDELTDDVIDlMAEGPKVLPYLDIPLQHASDRILKLMRRPGSGEEQLDMIERIREKCPDAVLRTTFIVGFPGETEEDFQ 305

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114  90 ETVKLVEEYKFPSLFINQFYPRPGTPAAK-AEQVPAHVKKQRTKDLS----RVFHSYNpyDHKIGERQQVLVteESFDSK 164
Cdd:TIGR01125 306 ELLDFVEEGQFDRLGAFTYSPEEGTDAFAlPDQVPEEVKEERLERLMqlqqRISAKKL--QEFVGKKIEVLI--DGYEPE 381

                         170
                  ....*....|.
gi 1039744114 165 FYVAHNRFYEQ 175
Cdd:TIGR01125 382 FNLLIGRTYGQ 392
PRK14336 PRK14336
(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
 2-137 3.38e-24

(dimethylallyl)adenosine tRNA methylthiotransferase; Provisional


Pssm-ID: 184632 [Multi-domain]  Cd Length: 418  Bit Score: 101.14  E-value: 3.38e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114   2 LRLGMTNPPYILEHL-EEMAKIlnhPRVYAFLHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKVPGITIATDIICGF 80
Cdd:PRK14336  209 IRFLTSHPKDISQKLiDAMAHL---PKVCRSLSLPVQAGDDTILAAMRRGYTNQQYRELVERLKTAMPDISLQTDLIVGF 285

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1039744114  81 PGETDQDFQETVKLVEEYKFPSLFINQFYPRPGTPAAK--AEQVPAHVKKQRTKDLSRV 137
Cdd:PRK14336  286 PSETEEQFNQSYKLMADIGYDAIHVAAYSPRPQTVAARdmADDVPVIEKKRRLKLIEDL 344
YgiQ COG1032
Radical SAM superfamily enzyme YgiQ, UPF0313 family [General function prediction only];
17-141 9.59e-18

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


Pssm-ID: 440655 [Multi-domain]  Cd Length: 394  Bit Score: 82.30  E-value: 9.59e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114  17 EEMAKILNHPRVYAfLHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKvpGITIATDIICGFPGETDQDFQETVKLVE 96
Cdd:COG1032   266 EELLELLKKAGCRG-LFIGIESGSQRVLKAMNKGITVEDILEAVRLLKKA--GIRVKLYFIIGLPGETEEDIEETIEFIK 342

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1039744114  97 EYKFPSLFINQFYPRPGTPAAKaeqvpaHVKKQRTKDLSRVFHSY 141
Cdd:COG1032   343 ELGPDQAQVSIFTPLPGTPLYE------ELEKEGRLYDWEKYEDL 381
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 7-91 9.26e-11

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: 59.08  E-value: 9.26e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114   7 TNPPYI-LEHLEEMAKiLNHPRVyaflHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKvpGITIATDIICGFPGETD 85
Cdd:pfam04055  81 TNGTLLdEELLELLKE-AGLDRV----SIGLESGDDEVLKLINRGHTFEEVLEALELLREA--GIPVVTDNIVGLPGETD 153


                  ....*.
gi 1039744114  86 QDFQET 91
Cdd:pfam04055 154 EDLEET 159
HemN COG0635
Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase ...
 36-119 5.23e-06

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: 47.48  E-value: 5.23e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039744114  36 VQSASDSVLMDMKREYCVADFKRVVDFLKE-KVPGITIatDIICGFPGETDQDFQETVKLVEEYKFP--SLFinQFYPRP 112
Cdd:COG0635   140 VQSFDDEVLKALGRIHTAEEALAAVELAREaGFDNINL--DLIYGLPGQTLESWEETLEKALALGPDhiSLY--SLTHEP 215


                  ....*..
gi 1039744114 113 GTPAAKA 119
Cdd:COG0635   216 GTPFAQR 222
PRK08207 PRK08207
coproporphyrinogen III oxidase; Provisional
 37-99 3.31e-03

coproporphyrinogen III oxidase; Provisional


Pssm-ID: 236187 [Multi-domain]  Cd Length: 488  Bit Score: 38.71  E-value: 3.31e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039744114  37 QSASDSVLMDMKREYCVADFKRVVDFLKEkVPGITIATDIICGFPGETDQDFQETVKLVEEYK 99
Cdd:PRK08207  288 QTMNDETLKAIGRHHTVEDIIEKFHLARE-MGFDNINMDLIIGLPGEGLEEVKHTLEEIEKLN 349
 
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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