NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|488296114|ref|WP_002367322|]
View 

MULTISPECIES: tRNA uracil 4-sulfurtransferase ThiI [Enterococcus]

Protein Classification

tRNA sulfurtransferase( domain architecture ID 11416748)

tRNA sulfurtransferase catalyzes the ATP-dependent transfer of sulfur to tRNA to produce 4-thiouridine, which is important for tRNA stability, as well as to sulfur carrier protein ThiS, forming ThiS-thiocarboxylate, as part of thiamine biosynthesis

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
ThiI COG0301
Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) [Coenzyme ...
 3-384 0e+00

Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) [Coenzyme transport and metabolism, Translation, ribosomal structure and biogenesis]; Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) is part of the Pathway/BioSystem: Thiamine biosynthesis


:

Pssm-ID: 440070 [Multi-domain]  Cd Length: 382  Bit Score: 582.05  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114   3 YTEIMVRYGELSTKGKNRKTFIMQLAQNVKRALADFPALKIHADRDRMHILLNGEDSEEVIPKLSKVFGIQNFSPSIRIE 82
Cdd:COG0301    1 YKVILVRYGEIALKGKNRKRFEKRLVKNIRAALKDLGEVKVKREWGRIYVETDGEDAEEAIERLKKVFGIVSFSPAVEVE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114  83 KEMPAIRAMVQEVVREVYtPGKTFKITAKRSDHSFELDSNGLNQELGGAVIEAIPEIQVQMKKPDINLRIEIRKDAAYLS 162
Cdd:COG0301   81 KDLEDIKEAALELAKEEL-KGKTFKVRAKRAGKHFPFTSPELEREVGGALLENTPGLKVDLKNPDVTIRVEVRDDKAYVY 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 163 YETIRGAGGLPVGTSGRGMLMLSGGIDSPVAGYLAMKRGVEVEAVHFASPPYTSEQALQKAKDLAEKLVPYVGT-IQFIE 241
Cdd:COG0301  160 TERIPGPGGLPVGTQGKVLLLLSGGIDSPVAAYLMMKRGVEVEAVHFHSGPYTSERAEEKVKDLARKLSRYGGHrVKLYV 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 242 VPFTEIQEEIKRVVPQGYLMTITRRLMLRLTDAIREMRKGLVIINGESLGQVASQTLQSMVAINEVTSTPIIRPVVSMDK 321
Cdd:COG0301  240 VPFTEVQEEILEKVPERYRTVLLRRMMMRIAERIAEKEGALALVTGESLGQVASQTLENLAVIDAVTDLPVLRPLIGMDK 319

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488296114 322 TEIIEIAEKIDTFELAIQPFEDCCTIFAPPQPKTRPRLDKAQEYEARLDLEGLMARALEGLKI 384
Cdd:COG0301  320 EEIIEIARKIGTYEISILPYEDCCTVFVPKHPETKPKLEKVEKEEEKLDLEELLEEAVENAEV 382
 
Name Accession Description Interval E-value
ThiI COG0301
Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) [Coenzyme ...
 3-384 0e+00

Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) [Coenzyme transport and metabolism, Translation, ribosomal structure and biogenesis]; Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) is part of the Pathway/BioSystem: Thiamine biosynthesis


Pssm-ID: 440070 [Multi-domain]  Cd Length: 382  Bit Score: 582.05  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114   3 YTEIMVRYGELSTKGKNRKTFIMQLAQNVKRALADFPALKIHADRDRMHILLNGEDSEEVIPKLSKVFGIQNFSPSIRIE 82
Cdd:COG0301    1 YKVILVRYGEIALKGKNRKRFEKRLVKNIRAALKDLGEVKVKREWGRIYVETDGEDAEEAIERLKKVFGIVSFSPAVEVE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114  83 KEMPAIRAMVQEVVREVYtPGKTFKITAKRSDHSFELDSNGLNQELGGAVIEAIPEIQVQMKKPDINLRIEIRKDAAYLS 162
Cdd:COG0301   81 KDLEDIKEAALELAKEEL-KGKTFKVRAKRAGKHFPFTSPELEREVGGALLENTPGLKVDLKNPDVTIRVEVRDDKAYVY 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 163 YETIRGAGGLPVGTSGRGMLMLSGGIDSPVAGYLAMKRGVEVEAVHFASPPYTSEQALQKAKDLAEKLVPYVGT-IQFIE 241
Cdd:COG0301  160 TERIPGPGGLPVGTQGKVLLLLSGGIDSPVAAYLMMKRGVEVEAVHFHSGPYTSERAEEKVKDLARKLSRYGGHrVKLYV 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 242 VPFTEIQEEIKRVVPQGYLMTITRRLMLRLTDAIREMRKGLVIINGESLGQVASQTLQSMVAINEVTSTPIIRPVVSMDK 321
Cdd:COG0301  240 VPFTEVQEEILEKVPERYRTVLLRRMMMRIAERIAEKEGALALVTGESLGQVASQTLENLAVIDAVTDLPVLRPLIGMDK 319

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488296114 322 TEIIEIAEKIDTFELAIQPFEDCCTIFAPPQPKTRPRLDKAQEYEARLDLEGLMARALEGLKI 384
Cdd:COG0301  320 EEIIEIARKIGTYEISILPYEDCCTVFVPKHPETKPKLEKVEKEEEKLDLEELLEEAVENAEV 382
TIGR00342 TIGR00342
tRNA sulfurtransferase ThiI; Members of this protein family are "ThiI", a sulfurtransferase ...
 6-372 3.89e-129

tRNA sulfurtransferase ThiI; Members of this protein family are "ThiI", a sulfurtransferase involved in 4-thiouridine modification of tRNA. This protein often is bifunctional, with genetically separable activities, where the C-terminal rhodanese-like domain (residues 385 to 482 in E. coli ThiI), a domain not included in this model, is sufficient to synthesize the thiazole moiety of thiamine (see TIGR04271). Note that ThiI, because of its role in tRNA modification, may occur in species (such as Mycoplasma genitalium) that lack de novo thiamine biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine, Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 273025 [Multi-domain]  Cd Length: 371  Bit Score: 376.36  E-value: 3.89e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114    6 IMVRYGELSTKGKNRKTFIMQLAQNVKRALADFP---ALKIHADRdRMHILLNGEDSEEVIPKLSKVFGIQNFSPSIRIE 82
Cdd:TIGR00342   1 ILARYGEIGIKGKNRLRFEKILKKNIKKALKKYEilrAVVYHFDR-IVVIAIDKEQRDALLDLLTKIPGIVSFSPAFKCD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114   83 KEMPAIRAMvQEVVREVYTPGKTFKITAKRSDHSFELDSNGLNQELGGAVIEAIpEIQVQMKKPDINLRIEIRKDAAYLS 162
Cdd:TIGR00342  80 LPFDEIHIL-LKALKQLRKEGKTFKVRTKRRGKDFPLNSVEVNKYVGGGIVEKI-GLKVDLTNPDITVHIEIREDEFLII 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114  163 YETIRGAGGLPVGTSGRGMLMLSGGIDSPVAGYLAMKRGVEVEAVHFASPPYTSEQALQKAKDLAEKLVPYVGTIQFIEV 242
Cdd:TIGR00342 158 TERYEGIGGLPVGTQGKVLALLSGGIDSPVAAFMMMKRGCRVVAVHFFNEPAASEKAREKVERLANSLNETGGSVKLYVF 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114  243 PFTEIQEEIKRVVPQGYLMTITRRLMLRLTDAIREMRKGLVIINGESLGQVASQTLQSMVAINEVTSTPIIRPVVSMDKT 322
Cdd:TIGR00342 238 DFTDVQEEIIHIIPEGYTCVLCRRMMYKAASKVAEKEGCLAIVTGESLGQVASQTLENLRVIQAVSNTPILRPLIGMDKE 317

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 488296114  323 EIIEIAEKIDTFELAIQPFEDCCTIFAPPQPKTRPRLDKAQEYEARLDLE 372
Cdd:TIGR00342 318 EIIELAKEIGTYEISIEPHEDCCTIFKPKHPTTKAKPEKVEKLEEKLDFS 367
PPase_ThiI cd01712
pyrophosphatase domain of thiamine biosynthesis protein ThiI; ThiI is required for thiazole ...
 174-357 3.63e-90

pyrophosphatase domain of thiamine biosynthesis protein ThiI; ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. ThiI is also responsible for the 4-thiouridine (S4U) modification at position 8 in some prokaryotic tRNAs. ThiI contains a PP-loop pyrophosphatase domain which binds ATP and activates tRNA by adenylation. The PP-loop pyrophosphatase catalytic domain of ThiI proteins is always accompanied by a THUMP domain towards the N terminus. THUMP domains are predicted to bind RNA and are widespread in bacteria, archaea, and eukaryotes. The acronym was derived from the names of RNA-modifying enzymes in which this domain is found, namely, thiouridine synthases (ThiI), methylases, and archaeal pseudouridine synthases. ThiI proteins from gamma-proteobacteria and from archaea of the genus Thermoplasma also contain a C-terminal extension of approximately 100 amino acid residues which accepts sulfur in the form of a persulfide on a cysteine residue. This persulfide is responsible for a nucleophilic attack of the adenylated tRNA substrate, completing the sulfur insertion forming a disulfide-bridge between the rhodanese-like domain and a second cysteine residue located in the PP-loop domain. The reaction releases AMP and modified tRNA, and leaves the enzyme in an oxidized state. The disulfide is then reductively cleaved to complete the enzymatic cycle. The pyrophosphatase domain of ThiI belongs to the adenine nucleotide hydrolase (AANH) superfamily and it binds to adenosine nucleotide.


Pssm-ID: 467485 [Multi-domain]  Cd Length: 185  Bit Score: 269.81  E-value: 3.63e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 174 VGTSGRGMLMLSGGIDSPVAGYLAMKRGVEVEAVHFASPPYTSEQALQKAKDLAEKLVPYVGTIQFIEVPFTE-IQEEIK 252
Cdd:cd01712    1 VGTSGKVLVLLSGGIDSPVAAWMMMKRGVEVDFLHFHSGPYTSEKAVEKVKDLARVLSEYQGGVKLYLVPFTDkIQKEIL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 253 RVVPQGYLMTITRRLMLRLTDAIREMRKGLVIINGESLGQVASQTLQSMVAINEVTSTPIIRPVVSMDKTEIIEIAEKID 332
Cdd:cd01712   81 EKVPESYRIVLMRRMMYRIAEKIAERLGADALVTGESLGQVASQTLENLKVIDSVTDLPVLRPLIGMDKEEIIDIARRIG 160

                        170       180
                 ....*....|....*....|....*
gi 488296114 333 TFELAIQPFEDCCTIFAPPQPKTRP 357
Cdd:cd01712  161 TYEISILPYEDCCCLFAPKNPVTKP 185
ThiI pfam02568
Thiamine biosynthesis protein (ThiI); ThiI is required for thiazole synthesis, required for ...
 175-371 3.68e-64

Thiamine biosynthesis protein (ThiI); ThiI is required for thiazole synthesis, required for thiamine biosynthesis.


Pssm-ID: 280691 [Multi-domain]  Cd Length: 197  Bit Score: 203.81  E-value: 3.68e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114  175 GTSGRGMLMLSGGIDSPVAGYLAMKRGVEVEAVHFASPPYTSEQALQKAKDLAEKLVPYVG--TIQFIEVPFTEIQEEIK 252
Cdd:pfam02568   1 GTQGKVLALISGGIDSPVAAYMMMRRGCRVVALHFINNPGTSAEAIGKVQKLAELLARYGTshEVRLVVFDFTDVQKEIL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114  253 RVVPQGYLMTITRRLMLRLTDAIREMRKGLVIINGESLGQVASQTLQSMVAINEVTSTPIIRPVVSMDKTEIIEIAEKID 332
Cdd:pfam02568  81 EKAPEGYRCVLLKRCMYRIAEKVAEEEGADALVTGESLGQVASQTLDNLRVISAVSNTPILRPLIGLDKEDIINLAKEIG 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 488296114  333 TFELAIQPfEDCCTIFaPPQPKTRPRLDKAQEYEARLDL 371
Cdd:pfam02568 161 TYEISIEP-YDCCTVF-AKHPTTKAKPEEVEKEEEKLDL 197
PRK08349 PRK08349
hypothetical protein; Validated
 183-359 6.91e-39

hypothetical protein; Validated


Pssm-ID: 169396  Cd Length: 198  Bit Score: 138.33  E-value: 6.91e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 183 MLSGGIDSPVAGYLAMKRGVEVEAVHFASppytSEQALQKAKDLAEKLVPYVGTI--QFIEVPFTEIQ----EEIKRVVP 256
Cdd:PRK08349   6 LLSSGIDSPVAIYLMLRRGVEVYPVHFRQ----DEKKEEKVRELVERLQELHGGKlkDPVVVDAFEEQgpvfEKLRELKK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 257 QGYLMTITRRLMLRLTDAIREMRKGLVIINGESLGQVASQTLQSMVAINEVTSTPIIRPVVSMDKTEIIEIAEKIDTFEL 336
Cdd:PRK08349  82 EKWTCIFCKYTMYRKAERIAHEIGASAIITGDSLGQVASQTLDNLMVISTATDLPVLRPLIGLDKEEIVKIAKEIGTFEI 161

                        170       180
                 ....*....|....*....|...
gi 488296114 337 AIQPfEDCCTiFAPPQPKTRPRL 359
Cdd:PRK08349 162 SIEP-EPPCP-FVPKYPVVRASL 182
THUMP smart00981
The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP ...
 92-164 1.39e-17

The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 214952 [Multi-domain]  Cd Length: 83  Bit Score: 76.93  E-value: 1.39e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488296114    92 VQEVVREVY--TPGKTFKITAKRSDHSFELDSNGLNQELGGAVIEAIPEIQVQMKKPDINLRIEIRKDAAYLSYE 164
Cdd:smart00981   9 ALELIRWEKifKEGKTFAVRAKRRGKNHEFTSLEVKRAIGDKLLEKTGGRKVDLKNPDVVIRVELRKDKAYLSID 83
 
Name Accession Description Interval E-value
ThiI COG0301
Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) [Coenzyme ...
 3-384 0e+00

Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) [Coenzyme transport and metabolism, Translation, ribosomal structure and biogenesis]; Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) is part of the Pathway/BioSystem: Thiamine biosynthesis


Pssm-ID: 440070 [Multi-domain]  Cd Length: 382  Bit Score: 582.05  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114   3 YTEIMVRYGELSTKGKNRKTFIMQLAQNVKRALADFPALKIHADRDRMHILLNGEDSEEVIPKLSKVFGIQNFSPSIRIE 82
Cdd:COG0301    1 YKVILVRYGEIALKGKNRKRFEKRLVKNIRAALKDLGEVKVKREWGRIYVETDGEDAEEAIERLKKVFGIVSFSPAVEVE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114  83 KEMPAIRAMVQEVVREVYtPGKTFKITAKRSDHSFELDSNGLNQELGGAVIEAIPEIQVQMKKPDINLRIEIRKDAAYLS 162
Cdd:COG0301   81 KDLEDIKEAALELAKEEL-KGKTFKVRAKRAGKHFPFTSPELEREVGGALLENTPGLKVDLKNPDVTIRVEVRDDKAYVY 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 163 YETIRGAGGLPVGTSGRGMLMLSGGIDSPVAGYLAMKRGVEVEAVHFASPPYTSEQALQKAKDLAEKLVPYVGT-IQFIE 241
Cdd:COG0301  160 TERIPGPGGLPVGTQGKVLLLLSGGIDSPVAAYLMMKRGVEVEAVHFHSGPYTSERAEEKVKDLARKLSRYGGHrVKLYV 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 242 VPFTEIQEEIKRVVPQGYLMTITRRLMLRLTDAIREMRKGLVIINGESLGQVASQTLQSMVAINEVTSTPIIRPVVSMDK 321
Cdd:COG0301  240 VPFTEVQEEILEKVPERYRTVLLRRMMMRIAERIAEKEGALALVTGESLGQVASQTLENLAVIDAVTDLPVLRPLIGMDK 319

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488296114 322 TEIIEIAEKIDTFELAIQPFEDCCTIFAPPQPKTRPRLDKAQEYEARLDLEGLMARALEGLKI 384
Cdd:COG0301  320 EEIIEIARKIGTYEISILPYEDCCTVFVPKHPETKPKLEKVEKEEEKLDLEELLEEAVENAEV 382
TIGR00342 TIGR00342
tRNA sulfurtransferase ThiI; Members of this protein family are "ThiI", a sulfurtransferase ...
 6-372 3.89e-129

tRNA sulfurtransferase ThiI; Members of this protein family are "ThiI", a sulfurtransferase involved in 4-thiouridine modification of tRNA. This protein often is bifunctional, with genetically separable activities, where the C-terminal rhodanese-like domain (residues 385 to 482 in E. coli ThiI), a domain not included in this model, is sufficient to synthesize the thiazole moiety of thiamine (see TIGR04271). Note that ThiI, because of its role in tRNA modification, may occur in species (such as Mycoplasma genitalium) that lack de novo thiamine biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine, Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 273025 [Multi-domain]  Cd Length: 371  Bit Score: 376.36  E-value: 3.89e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114    6 IMVRYGELSTKGKNRKTFIMQLAQNVKRALADFP---ALKIHADRdRMHILLNGEDSEEVIPKLSKVFGIQNFSPSIRIE 82
Cdd:TIGR00342   1 ILARYGEIGIKGKNRLRFEKILKKNIKKALKKYEilrAVVYHFDR-IVVIAIDKEQRDALLDLLTKIPGIVSFSPAFKCD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114   83 KEMPAIRAMvQEVVREVYTPGKTFKITAKRSDHSFELDSNGLNQELGGAVIEAIpEIQVQMKKPDINLRIEIRKDAAYLS 162
Cdd:TIGR00342  80 LPFDEIHIL-LKALKQLRKEGKTFKVRTKRRGKDFPLNSVEVNKYVGGGIVEKI-GLKVDLTNPDITVHIEIREDEFLII 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114  163 YETIRGAGGLPVGTSGRGMLMLSGGIDSPVAGYLAMKRGVEVEAVHFASPPYTSEQALQKAKDLAEKLVPYVGTIQFIEV 242
Cdd:TIGR00342 158 TERYEGIGGLPVGTQGKVLALLSGGIDSPVAAFMMMKRGCRVVAVHFFNEPAASEKAREKVERLANSLNETGGSVKLYVF 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114  243 PFTEIQEEIKRVVPQGYLMTITRRLMLRLTDAIREMRKGLVIINGESLGQVASQTLQSMVAINEVTSTPIIRPVVSMDKT 322
Cdd:TIGR00342 238 DFTDVQEEIIHIIPEGYTCVLCRRMMYKAASKVAEKEGCLAIVTGESLGQVASQTLENLRVIQAVSNTPILRPLIGMDKE 317

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 488296114  323 EIIEIAEKIDTFELAIQPFEDCCTIFAPPQPKTRPRLDKAQEYEARLDLE 372
Cdd:TIGR00342 318 EIIELAKEIGTYEISIEPHEDCCTIFKPKHPTTKAKPEKVEKLEEKLDFS 367
PPase_ThiI cd01712
pyrophosphatase domain of thiamine biosynthesis protein ThiI; ThiI is required for thiazole ...
 174-357 3.63e-90

pyrophosphatase domain of thiamine biosynthesis protein ThiI; ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. ThiI is also responsible for the 4-thiouridine (S4U) modification at position 8 in some prokaryotic tRNAs. ThiI contains a PP-loop pyrophosphatase domain which binds ATP and activates tRNA by adenylation. The PP-loop pyrophosphatase catalytic domain of ThiI proteins is always accompanied by a THUMP domain towards the N terminus. THUMP domains are predicted to bind RNA and are widespread in bacteria, archaea, and eukaryotes. The acronym was derived from the names of RNA-modifying enzymes in which this domain is found, namely, thiouridine synthases (ThiI), methylases, and archaeal pseudouridine synthases. ThiI proteins from gamma-proteobacteria and from archaea of the genus Thermoplasma also contain a C-terminal extension of approximately 100 amino acid residues which accepts sulfur in the form of a persulfide on a cysteine residue. This persulfide is responsible for a nucleophilic attack of the adenylated tRNA substrate, completing the sulfur insertion forming a disulfide-bridge between the rhodanese-like domain and a second cysteine residue located in the PP-loop domain. The reaction releases AMP and modified tRNA, and leaves the enzyme in an oxidized state. The disulfide is then reductively cleaved to complete the enzymatic cycle. The pyrophosphatase domain of ThiI belongs to the adenine nucleotide hydrolase (AANH) superfamily and it binds to adenosine nucleotide.


Pssm-ID: 467485 [Multi-domain]  Cd Length: 185  Bit Score: 269.81  E-value: 3.63e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 174 VGTSGRGMLMLSGGIDSPVAGYLAMKRGVEVEAVHFASPPYTSEQALQKAKDLAEKLVPYVGTIQFIEVPFTE-IQEEIK 252
Cdd:cd01712    1 VGTSGKVLVLLSGGIDSPVAAWMMMKRGVEVDFLHFHSGPYTSEKAVEKVKDLARVLSEYQGGVKLYLVPFTDkIQKEIL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 253 RVVPQGYLMTITRRLMLRLTDAIREMRKGLVIINGESLGQVASQTLQSMVAINEVTSTPIIRPVVSMDKTEIIEIAEKID 332
Cdd:cd01712   81 EKVPESYRIVLMRRMMYRIAEKIAERLGADALVTGESLGQVASQTLENLKVIDSVTDLPVLRPLIGMDKEEIIDIARRIG 160

                        170       180
                 ....*....|....*....|....*
gi 488296114 333 TFELAIQPFEDCCTIFAPPQPKTRP 357
Cdd:cd01712  161 TYEISILPYEDCCCLFAPKNPVTKP 185
THUMP_ThiI cd11716
THUMP domain of thiamine biosynthesis protein ThiI; ThiI is an enzyme responsible for the ...
 6-170 4.05e-73

THUMP domain of thiamine biosynthesis protein ThiI; ThiI is an enzyme responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNAs. This modification acts as a signal for UV exposure, triggering a response that provides protection against its damaging effects. ThiI consists of an N-terminal THUMP domain, followed by an NFLD domain, and a C-terminal PP-loop pyrophosphatase domain. The N-terminal THUMP domain has been implicated in the recognition of the acceptor-stem region. The THUMP domain is named after thiouridine synthases, methylases and PSUSs. The domain consists of about 110 amino acid residues. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 212585  Cd Length: 166  Bit Score: 225.79  E-value: 4.05e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114   6 IMVRYGELSTKGKNRKTFIMQLAQNVKRALADFPALKIHADRDRMHILLNGEDSEEVIPKLSKVFGIQNFSPSIRIEKEM 85
Cdd:cd11716    2 ILVRYGEIALKGKNRKRFEKRLVKNIRRALKDLPDVKVEREWGRIYVELNGEDLEEVIERLKKVFGIVSFSPAVEVEKDL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114  86 PAIRAMVQEVVREVYTPGKTFKITAKRSDHSFELDSNGLNQELGGAVIEAIPEIQVQMKKPDINLRIEIRKDAAYLSYET 165
Cdd:cd11716   82 EDIKEAALELLKEELKKGKTFKVRAKRADKSFPFTSMEINREVGAALLENTPDLKVDLKNPDVTIRVEIREDGAYVYTER 161


                 ....*
gi 488296114 166 IRGAG 170
Cdd:cd11716  162 IPGPG 166
ThiI pfam02568
Thiamine biosynthesis protein (ThiI); ThiI is required for thiazole synthesis, required for ...
 175-371 3.68e-64

Thiamine biosynthesis protein (ThiI); ThiI is required for thiazole synthesis, required for thiamine biosynthesis.


Pssm-ID: 280691 [Multi-domain]  Cd Length: 197  Bit Score: 203.81  E-value: 3.68e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114  175 GTSGRGMLMLSGGIDSPVAGYLAMKRGVEVEAVHFASPPYTSEQALQKAKDLAEKLVPYVG--TIQFIEVPFTEIQEEIK 252
Cdd:pfam02568   1 GTQGKVLALISGGIDSPVAAYMMMRRGCRVVALHFINNPGTSAEAIGKVQKLAELLARYGTshEVRLVVFDFTDVQKEIL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114  253 RVVPQGYLMTITRRLMLRLTDAIREMRKGLVIINGESLGQVASQTLQSMVAINEVTSTPIIRPVVSMDKTEIIEIAEKID 332
Cdd:pfam02568  81 EKAPEGYRCVLLKRCMYRIAEKVAEEEGADALVTGESLGQVASQTLDNLRVISAVSNTPILRPLIGLDKEDIINLAKEIG 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 488296114  333 TFELAIQPfEDCCTIFaPPQPKTRPRLDKAQEYEARLDL 371
Cdd:pfam02568 161 TYEISIEP-YDCCTVF-AKHPTTKAKPEEVEKEEEKLDL 197
PRK08349 PRK08349
hypothetical protein; Validated
 183-359 6.91e-39

hypothetical protein; Validated


Pssm-ID: 169396  Cd Length: 198  Bit Score: 138.33  E-value: 6.91e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 183 MLSGGIDSPVAGYLAMKRGVEVEAVHFASppytSEQALQKAKDLAEKLVPYVGTI--QFIEVPFTEIQ----EEIKRVVP 256
Cdd:PRK08349   6 LLSSGIDSPVAIYLMLRRGVEVYPVHFRQ----DEKKEEKVRELVERLQELHGGKlkDPVVVDAFEEQgpvfEKLRELKK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 257 QGYLMTITRRLMLRLTDAIREMRKGLVIINGESLGQVASQTLQSMVAINEVTSTPIIRPVVSMDKTEIIEIAEKIDTFEL 336
Cdd:PRK08349  82 EKWTCIFCKYTMYRKAERIAHEIGASAIITGDSLGQVASQTLDNLMVISTATDLPVLRPLIGLDKEEIVKIAKEIGTFEI 161

                        170       180
                 ....*....|....*....|...
gi 488296114 337 AIQPfEDCCTiFAPPQPKTRPRL 359
Cdd:PRK08349 162 SIEP-EPPCP-FVPKYPVVRASL 182
THUMP smart00981
The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP ...
 92-164 1.39e-17

The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 214952 [Multi-domain]  Cd Length: 83  Bit Score: 76.93  E-value: 1.39e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488296114    92 VQEVVREVY--TPGKTFKITAKRSDHSFELDSNGLNQELGGAVIEAIPEIQVQMKKPDINLRIEIRKDAAYLSYE 164
Cdd:smart00981   9 ALELIRWEKifKEGKTFAVRAKRRGKNHEFTSLEVKRAIGDKLLEKTGGRKVDLKNPDVVIRVELRKDKAYLSID 83
THUMP pfam02926
THUMP domain; The THUMP domain is named after after thiouridine synthases, methylases and ...
 57-162 4.48e-13

THUMP domain; The THUMP domain is named after after thiouridine synthases, methylases and PSUSs. The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterized RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 460749  Cd Length: 143  Bit Score: 66.31  E-value: 4.48e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114   57 EDSEEVIPKLSKVFGIQNFSPSIRIEKEMPAIRAMVQEVVRE-VYTPGKTFKITAKRSDHSFELDSNGLNQELGGAVIEA 135
Cdd:pfam02926  35 EDRELLKEALEKAPGIERFPVAETCEADLEDILELAKEIIKDkFKKEGETFAVRVKRRGKNHEFTSLEINREVGKAIVEK 114

                          90       100
                  ....*....|....*....|....*..
gi 488296114  136 IPEIqVQMKKPDINLRIEIRKDAAYLS 162
Cdd:pfam02926 115 TGLK-VDLENPDIVVHVEIIKDKAYIS 140
QueC pfam06508
Queuosine biosynthesis protein QueC; This family of proteins participate in the biosynthesis ...
 184-230 2.75e-05

Queuosine biosynthesis protein QueC; This family of proteins participate in the biosynthesis of 7-carboxy-7-deazaguanine. They catalyze the conversion of 7-deaza-7-carboxyguanine to preQ0.


Pssm-ID: 428982 [Multi-domain]  Cd Length: 210  Bit Score: 44.92  E-value: 2.75e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 488296114  184 LSGGIDSPVAGYLAMKRGVEVEAVHFAsppYTSEQA--LQKAKDLAEKL 230
Cdd:pfam06508   6 LSGGLDSTTCLAWAKKEGYEVYALSFD---YGQRHRkeLECAKKIAKAL 51
MnmA_TRMU-like cd01998
MnmA/TRMU family 2-thiouridylases and similar proteins; This family is composed of bacterial ...
 183-246 2.80e-05

MnmA/TRMU family 2-thiouridylases and similar proteins; This family is composed of bacterial tRNA-specific 2-thiouridylase MnmA (EC 2.8.1.13) and mitochondrial tRNA-specific 2-thiouridylase 1 (TRMU or MTU1, EC 2.8.1.14). MnmA catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. TRMU/MTU1 catalyzes the 2-thiolation of uridine at the wobble position (U34) of mitochondrial tRNA(Lys), tRNA(Glu) and tRNA(Gln); this is required for the formation of 5-taurinomethyl-2-thiouridine (tm5s2U) of mitochondrial tRNA(Lys), tRNA(Glu), and tRNA(Gln) at the wobble position. This family belongs to the adenine nucleotide alpha hydrolase (AANH) superfamily that also includes other N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to the adenosine group.


Pssm-ID: 467502 [Multi-domain]  Cd Length: 349  Bit Score: 45.57  E-value: 2.80e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488296114 183 MLSGGIDSPVAGYLAMKRGVEVEAVHF--------ASPPYTSEQALQKAKDLAEKLvpyvgTIQFIEVPFTE 246
Cdd:cd01998    5 AMSGGVDSSVAAALLKEQGYDVIGVFMknwddednEKGGCCSEEDIEDARRVADQL-----GIPLYVVDFSE 71
QueC COG0603
7-cyano-7-deazaguanine synthase (queuosine biosynthesis) [Translation, ribosomal structure and ...
 183-331 4.51e-05

7-cyano-7-deazaguanine synthase (queuosine biosynthesis) [Translation, ribosomal structure and biogenesis]; 7-cyano-7-deazaguanine synthase (queuosine biosynthesis) is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440368 [Multi-domain]  Cd Length: 223  Bit Score: 44.38  E-value: 4.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 183 MLSGGIDSPVAGYLAMKRGVEVEAVHFAsppY----TSEqaLQKAKDLAEKL---------VPYVGTI-------QFIEV 242
Cdd:COG0603    8 LLSGGLDSTTCLAWALARGYEVYALSFD---YgqrhRKE--LEAARRIAKALgvgehkvidLDFLGEIggsaltdDSIEV 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 243 PFTEIQEEIKR--VVPQgylmtitrR--LMLRLTDAIREMRKGLVIINGESLGQVASQ------TLQSM-VAINEVTSTP 311
Cdd:COG0603   83 PEGHYAEEGIPstYVPG--------RnlIFLSIAAAYAEALGAEDIFIGVNATDYSGYpdcrpeFIEAFnAALNLGTKRP 154

                        170       180
                 ....*....|....*....|..
gi 488296114 312 --IIRPVVSMDKTEIIEIAEKI 331
Cdd:COG0603  155 vrIHTPLMHLSKAEIVKLGLEL 176
PRK13980 PRK13980
NAD synthetase; Provisional
 164-256 2.93e-04

NAD synthetase; Provisional


Pssm-ID: 184435 [Multi-domain]  Cd Length: 265  Bit Score: 42.12  E-value: 2.93e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 164 ETIRGAGglpvgtSGRGMLMLSGGIDSPVAGYLAmKRGVEVEAVHFASPPY--TSEQALQKAKDLAEKLvpyvgTIQFIE 241
Cdd:PRK13980  23 EEVEKAG------AKGVVLGLSGGIDSAVVAYLA-VKALGKENVLALLMPSsvSPPEDLEDAELVAEDL-----GIEYKV 90

                         90
                 ....*....|....*
gi 488296114 242 VPFTEIQEEIKRVVP 256
Cdd:PRK13980  91 IEITPIVDAFFSAIP 105
THUMP cd11688
THUMP domain, predicted to bind RNA; The THUMP domain is named after THioUridine synthases, ...
 27-162 5.67e-04

THUMP domain, predicted to bind RNA; The THUMP domain is named after THioUridine synthases, RNA Methyltransferases and Pseudo-uridine synthases. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 212583  Cd Length: 148  Bit Score: 40.16  E-value: 5.67e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114  27 LAQNVKRALADF-PALKIHADRD-RMHILLNGEDSEEVIpkLSKVFGIQNFSPsirIEKEMPA----IRAMVQEVVR-EV 99
Cdd:cd11688   13 LAAELYELLEVRgFDAEIQVVPHgRVHFKTDTDEAVYQL--VMWSRLISRIMP---PLGECKAdledLYETALEINEpEM 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488296114 100 YTPGKTFKITAKRSDHSFeLDSNGLNQELGgAVIEAIPEIQVQMKKPDINLRIEIRKDAAYLS 162
Cdd:cd11688   88 GNEGAKFAVRARRRNKTI-LNSQEIAMKVG-DAIVDAFNPEVDLDNPDIVVNVEVHKEIASIA 148
NAD_synthase pfam02540
NAD synthase; NAD synthase (EC:6.3.5.1) is involved in the de novo synthesis of NAD and is ...
 167-247 6.80e-04

NAD synthase; NAD synthase (EC:6.3.5.1) is involved in the de novo synthesis of NAD and is induced by stress factors such as heat shock and glucose limitation.


Pssm-ID: 396888 [Multi-domain]  Cd Length: 241  Bit Score: 40.83  E-value: 6.80e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114  167 RGAGGLPVGtsgrgmlmLSGGIDSPVAGYLAmKRGVEVEAVHFASPP--YTSEQALQKAKDLAEKLvpyvgTIQFIEVPF 244
Cdd:pfam02540  16 AGFKGVVLG--------LSGGIDSSLVAYLA-VKALGKENVLALIMPssQSSEEDVQDALALAENL-----GIEYKTIDI 81


                  ...
gi 488296114  245 TEI 247
Cdd:pfam02540  82 KPI 84
nadE TIGR00552
NAD+ synthetase; NAD+ synthetase is a nearly ubiquitous enzyme for the final step in the ...
 167-230 7.29e-04

NAD+ synthetase; NAD+ synthetase is a nearly ubiquitous enzyme for the final step in the biosynthesis of the essensial cofactor NAD. The member of this family from Bacillus subtilis is a strictly NH(3)-dependent NAD(+) synthetase of 272 amino acids. Proteins consisting only of the domain modeled here may be named as NH3-dependent NAD+ synthetase. Amidotransferase activity may reside in a separate protein, or not be present. Some other members of the family, such as from Mycobacterium tuberculosis, are considerably longer, contain an apparent amidotransferase domain, and show glutamine-dependent as well as NH(3)-dependent activity. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridine nucleotides]


Pssm-ID: 273132 [Multi-domain]  Cd Length: 250  Bit Score: 40.83  E-value: 7.29e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488296114  167 RGAGGLPVGtsgrgmlmLSGGIDSPVAGYLAMKR-GVEVEAVHFASPPYTSEQALQKAKDLAEKL 230
Cdd:TIGR00552  20 SGAKGVVLG--------LSGGIDSAVVAALCVEAlGEQNHALLLPHSVQTPEQDVQDALALAEPL 76
mnmA PRK00143
tRNA-specific 2-thiouridylase MnmA; Reviewed
 184-233 8.05e-04

tRNA-specific 2-thiouridylase MnmA; Reviewed


Pssm-ID: 234664 [Multi-domain]  Cd Length: 346  Bit Score: 41.21  E-value: 8.05e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 184 LSGGIDSPVAGYLAMKRGVEVEAVH---------FASPPYTSEQALQKAKDLAEKL-VPY 233
Cdd:PRK00143   7 MSGGVDSSVAAALLKEQGYEVIGVFmklwddddeTGKGGCCAEEDIADARRVADKLgIPH 66
QueC-like cd01995
7-cyano-7-deazaguanine synthase QueC and similar proteins; 7-cyano-7-deazaguanine synthase (EC ...
 184-209 1.66e-03

7-cyano-7-deazaguanine synthase QueC and similar proteins; 7-cyano-7-deazaguanine synthase (EC 6.3.4.20) is also called 7-cyano-7-carbaguanine synthase, preQ(0) synthase, or queuosine biosynthesis protein QueC. It catalyzes the ATP-dependent conversion of 7-carboxy-7-deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)), as part of the biosynthesis pathway of queuosine (Q). Q is one of the most complex modifications occurring at the wobble position of tRNAs with GUN anticodons, and is implicated in a number of biological activities, including accuracy of decoding, virulence, and cellular differentiation. This subfamily belongs to the adenine nucleotide alpha hydrolase (AANH) superfamily that also includes other N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to the adenosine group.


Pssm-ID: 467499 [Multi-domain]  Cd Length: 208  Bit Score: 39.52  E-value: 1.66e-03
                         10        20
                 ....*....|....*....|....*.
gi 488296114 184 LSGGIDSPVAGYLAMKRGVEVEAVHF 209
Cdd:cd01995    7 LSGGLDSTTLLYWALKEGYEVHALTF 32
Tan1 COG1818
tRNA(Ser,Leu) C12 N-acetylase TAN1, contains THUMP domain [Translation, ribosomal structure ...
 88-162 3.27e-03

tRNA(Ser,Leu) C12 N-acetylase TAN1, contains THUMP domain [Translation, ribosomal structure and biogenesis]; tRNA(Ser,Leu) C12 N-acetylase TAN1, contains THUMP domain is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441423  Cd Length: 162  Bit Score: 37.95  E-value: 3.27e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488296114  88 IRAMVQEVVREVYTPGKTFKITAKRSDHSfELDSNGLNQELGGAVIEAIPeiqVQMKKPDINLRIEIRKDAAYLS 162
Cdd:COG1818   83 IVEAAKELAKKKIPEGETFAVRCEKRGKS-KLSSREVIRAIGEAIKRGAK---VDLENPDWVVLVEILGDKAGIS 153
NAD_synthase cd00553
NAD(+) synthase; NAD(+) synthase (EC 6.3.5.1), a homodimer, catalyzes the final step in the de ...
 184-247 3.66e-03

NAD(+) synthase; NAD(+) synthase (EC 6.3.5.1), a homodimer, catalyzes the final step in the de novo nicotinamide adenine dinucleotide (NAD(+)) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD(+) occurs via a NAD-adenylate intermediate and requires ATP and Mg(2+). The intermediate is subsequently cleaved into NAD(+) and AMP. In many prokaryotes, such as Escherichia coli, NAD synthase consists of a single domain and is strictly ammonia dependent. In contrast, eukaryotes and other prokaryotes have an additional N-terminal amidohydrolase domain that prefer glutamine. Interestingly, NAD(+) synthases in these prokaryotes, can also utilize ammonia as an amide source.


Pssm-ID: 467484 [Multi-domain]  Cd Length: 248  Bit Score: 38.69  E-value: 3.66e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488296114 184 LSGGIDSPVAGYLAmKRGVEVEAVHFASPP--YTSEQALQKAKDLAEKLvpyvGtIQFIEVPFTEI 247
Cdd:cd00553   30 LSGGIDSAVVAALA-VRALGAENVLALIMPsrYSSKETRDDAKALAENL----G-IEYRTIDIDPI 89
NadE COG0171
NH3-dependent NAD+ synthetase [Coenzyme transport and metabolism]; NH3-dependent NAD+ ...
 184-256 4.11e-03

NH3-dependent NAD+ synthetase [Coenzyme transport and metabolism]; NH3-dependent NAD+ synthetase is part of the Pathway/BioSystem: NAD biosynthesis


Pssm-ID: 439941 [Multi-domain]  Cd Length: 542  Bit Score: 39.44  E-value: 4.11e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488296114 184 LSGGIDSPVAGYLAmKRGVEVEAVHFASPP--YTSEQALQKAKDLAEKLvpyvGtIQFIEVPFTEIQEEIKRVVP 256
Cdd:COG0171  293 LSGGIDSALVAALA-VDALGPENVLGVTMPsrYTSDESLEDAEELAENL----G-IEYEEIDITPAVEAFLEALP 361
LarE-like cd01990
Lactate racemization operon protein LarE and similar proteins; This subfamily includes ...
 181-253 4.27e-03

Lactate racemization operon protein LarE and similar proteins; This subfamily includes Lactiplantibacillus plantarum LarE, a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family. LarE is part of the lar operon, encoding five Lar proteins (LarA-E) that collaboratively synthesize and incorporate a niacin-derived Ni-containing cofactor into LarA, an Ni-dependent lactate racemase. It catalyzes successive thiolation reactions by donating the sulfur atom of their exclusive cysteine residues to the substrate. The LarE-like subfamily belongs to the nucleotide alpha hydrolase (AANH) superfamily that includes N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to the adenosine group. Proteins from this subfamily probably binds ATP. This domain is about 200 amino acids long with a strongly conserved motif SGGxDS at the N-terminus.


Pssm-ID: 467494 [Multi-domain]  Cd Length: 222  Bit Score: 38.39  E-value: 4.27e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488296114 181 MLMLSGGIDSPVAGYLAMKR-GVEVEAVhFASPPYTSEQALQKAKDLAEKLvpyvgTIQFIEVPFTEIQ-EEIKR 253
Cdd:cd01990    3 VVAFSGGVDSSLLAKLAKEVlGDNVVAV-TADSPLVPREELEEAKRIAEEI-----GIRHEIIKTDELDdEEYVA 71
tRNA_Me_trans pfam03054
tRNA methyl transferase HUP domain; This family represents the N-terminal HUP domain in tRNA ...
 184-233 4.37e-03

tRNA methyl transferase HUP domain; This family represents the N-terminal HUP domain in tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs.


Pssm-ID: 460787 [Multi-domain]  Cd Length: 202  Bit Score: 38.00  E-value: 4.37e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488296114  184 LSGGIDSPVAGYLAMKRGVEVEAVHFASPPY----------TSEQALQKAKDLAEKL-VPY 233
Cdd:pfam03054   7 MSGGVDSSVAAYLLKEQGHNVIGVFMKNWDEeqsldeegkcCSEEDLADAQRVCEQLgIPL 67
MnmA COG0482
tRNA U34 2-thiouridine synthase MnmA/TrmU, contains the PP-loop ATPase domain [Translation, ...
 184-233 4.61e-03

tRNA U34 2-thiouridine synthase MnmA/TrmU, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; tRNA U34 2-thiouridine synthase MnmA/TrmU, contains the PP-loop ATPase domain is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440250 [Multi-domain]  Cd Length: 353  Bit Score: 38.88  E-value: 4.61e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114 184 LSGGIDSPVAGYLAMKRGVEVEAVHFA---------SPPYTSEQALQKAKDLAEKL-VPY 233
Cdd:COG0482    7 MSGGVDSSVAAALLKEQGYEVIGVTMKlwddddasgSGGCCSLEDIEDARRVADKLgIPH 66
THUMP_SPOUT cd11718
THUMP domain associated with SPOUT RNA Methylases; Members of this archaeal protein family are ...
 52-162 6.76e-03

THUMP domain associated with SPOUT RNA Methylases; Members of this archaeal protein family are characterized by containing an N-terminal THUMP domain and a C-terminal SPOUT RNA methyltransferase domain. No functional information is available The THUMP domain is named after thiouridine synthases, methylases and PSUSs. The domain consists of about 110 amino acid residues. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 212587  Cd Length: 145  Bit Score: 36.88  E-value: 6.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488296114  52 ILLNGEDSEEV----IPKLSKVfgiqnfspsIRIEKEMPA----IRAMVQEVVREvYTPGKTFKI-TAKRSDHSFEldSN 122
Cdd:cd11718   38 LVESDEDKKDElalrVPEVERV---------IPVDAEVKAdldeIVRVAEEIAKH-ISEGETFAVrTTRRGKHDFT--SI 105

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 488296114 123 GLNQELGGAVIEAIpEIQVQMKKPDINLRIEIRKDAAYLS 162
Cdd:cd11718  106 DVNVVLGAAVKELT-GAEVDLNNPDKVVYVEIIGDRAYIS 144
AANH-like cd01986
adenine nucleotide alpha hydrolase (AANH)-like proteins; This group of adenine nucleotide ...
 181-229 8.09e-03

adenine nucleotide alpha hydrolase (AANH)-like proteins; This group of adenine nucleotide alpha hydrolase (AANH)-like proteins includes N-type ATP PPases and ATP sulfurylases. The domain forms an alpha/beta/alpha fold which binds to adenosine nucleotide.


Pssm-ID: 467490 [Multi-domain]  Cd Length: 74  Bit Score: 35.12  E-value: 8.09e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 488296114 181 MLMLSGGIDSPVAGYLAMK--RGVEVEAVHFASpPYTSEQALQKAKDLAEK 229
Cdd:cd01986    2 VVGYSGGKDSSVALHLASRlgRKAEVAVVHIDH-GIGFKEEAESVASIARR 51
 
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