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Conserved domains on  [gi|497579894|ref|WP_009894078|]
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ATP-binding protein [Clostridioides difficile]

Protein Classification

tRNA 2-thiocytidine biosynthesis TtcA family protein( domain architecture ID 19235256)

tRNA 2-thiocytidine biosynthesis TtcA family protein belonging to the adenine nucleotide alpha hydrolase superfamily may have sulfurtransferase activity

CATH:  3.40.50.620
Gene Ontology:  GO:0005524|GO:0016740|GO:0000049
PubMed:  12012333
SCOP:  3001593

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TtcA-like cd24138
tRNA-cytidine(32) 2-sulfurtransferase and similar proteins; tRNA-cytidine(32) ...
 16-195 7.48e-86

tRNA-cytidine(32) 2-sulfurtransferase and similar proteins; tRNA-cytidine(32) 2-sulfurtransferase, also called two-thiocytidine biosynthesis protein A or tRNA 2-thiocytidine biosynthesis protein TtcA, catalyzes the ATP-dependent 2-thiolation of cytidine in position 32 of tRNA, to form 2-thiocytidine (s(2)C32). TtcA belongs to the adenine nucleotide alpha hydrolase superfamily (AANH) that includes N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to the adenosine group. This domain has a strongly conserved motif SGGKD at the N-terminus.


:

Pssm-ID: 467514 [Multi-domain]  Cd Length: 187  Bit Score: 252.97  E-value: 7.48e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  16 DFDMIQENDKIAVGLSGGKDSLTLLHILKSYQRFSPQNFELIAITLNTGGVDNSPLDKLCKEINVPFYEFQTDIKE---I 92
Cdd:cd24138    1 DFKMIEPGDRILVGLSGGKDSLTLLHLLEELKRRAPIKFELVAVTVDPGYPGYRPPREELAEILEELGEILEDEESeiiI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  93 VFDIRQEKNPCALCANLRRGALNDNAKKLGCNKVALGHHKDDAIETFLMSMFYEGRVNCFSPKTYLDRQDLTVIRPMIYI 172
Cdd:cd24138   81 IEKEREEKSPCSLCSRLRRGILYSLAKELGCNKLALGHHLDDAVETLLMNLLYGGRLKTMPPKVTMDRGGLTVIRPLIYV 160

                        170       180
                 ....*....|....*....|...
gi 497579894 173 EEYMTKKISKDSNYPIITNPCPA 195
Cdd:cd24138  161 REKDIRAFAEENGLPKIECPCPY 183
 
Name Accession Description Interval E-value
TtcA-like cd24138
tRNA-cytidine(32) 2-sulfurtransferase and similar proteins; tRNA-cytidine(32) ...
 16-195 7.48e-86

tRNA-cytidine(32) 2-sulfurtransferase and similar proteins; tRNA-cytidine(32) 2-sulfurtransferase, also called two-thiocytidine biosynthesis protein A or tRNA 2-thiocytidine biosynthesis protein TtcA, catalyzes the ATP-dependent 2-thiolation of cytidine in position 32 of tRNA, to form 2-thiocytidine (s(2)C32). TtcA belongs to the adenine nucleotide alpha hydrolase superfamily (AANH) that includes N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to the adenosine group. This domain has a strongly conserved motif SGGKD at the N-terminus.


Pssm-ID: 467514 [Multi-domain]  Cd Length: 187  Bit Score: 252.97  E-value: 7.48e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  16 DFDMIQENDKIAVGLSGGKDSLTLLHILKSYQRFSPQNFELIAITLNTGGVDNSPLDKLCKEINVPFYEFQTDIKE---I 92
Cdd:cd24138    1 DFKMIEPGDRILVGLSGGKDSLTLLHLLEELKRRAPIKFELVAVTVDPGYPGYRPPREELAEILEELGEILEDEESeiiI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  93 VFDIRQEKNPCALCANLRRGALNDNAKKLGCNKVALGHHKDDAIETFLMSMFYEGRVNCFSPKTYLDRQDLTVIRPMIYI 172
Cdd:cd24138   81 IEKEREEKSPCSLCSRLRRGILYSLAKELGCNKLALGHHLDDAVETLLMNLLYGGRLKTMPPKVTMDRGGLTVIRPLIYV 160

                        170       180
                 ....*....|....*....|...
gi 497579894 173 EEYMTKKISKDSNYPIITNPCPA 195
Cdd:cd24138  161 REKDIRAFAEENGLPKIECPCPY 183
TilS COG0037
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 9-228 7.33e-77

tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA(Ile)-lysidine synthase TilS/MesJ is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439807 [Multi-domain]  Cd Length: 235  Bit Score: 232.03  E-value: 7.33e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894   9 KARKAIQDFDMIQENDKIAVGLSGGKDSLTLLHILKSYQRFSpqNFELIAITLNTGGVDNSPLD-----KLCKEINVPFY 83
Cdd:COG0037    1 KVRKAIRDYRLLEPGDRILVAVSGGKDSLALLHLLAKLRRRL--GFELVAVHVDHGLREESDEDaefvaELCEELGIPLH 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  84 EFQTDIKEIVfdIRQEKNPCALCANLRRGALNDNAKKLGCNKVALGHHKDDAIETFLMSMFYEGRVNCFSPKTYLDRQDL 163
Cdd:COG0037   79 VVRVDVPAIA--KKEGKSPEAAARRARYGALYELARELGADKIATGHHLDDQAETFLLNLLRGSGLAGLAGMPPSRGGGV 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 497579894 164 TVIRPMIYIEEYMTKKISKDSNYPIITNPCPANGHTRREYIKN-LIANLNKEMPDFKRNVFGALNN 228
Cdd:COG0037  157 RLIRPLLYVSRKEIEAYAKENGLPWIEDPCNYDPRYTRNRIRHlVLPELEERNPGFKENLARSAEN 222
PRK10696 PRK10696
tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional
 5-228 2.74e-70

tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional


Pssm-ID: 236737 [Multi-domain]  Cd Length: 258  Bit Score: 215.88  E-value: 2.74e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894   5 KLLSKARKAIQDFDMIQENDKIAVGLSGGKDSLTLLHILKSYQRFSPQNFELIAITLNTG--GVDNSPLDKLCKEINVPF 82
Cdd:PRK10696  11 RLRRQVGQAIADFNMIEEGDRVMVCLSGGKDSYTLLDILLNLQKRAPINFELVAVNLDQKqpGFPEHVLPEYLESLGVPY 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  83 YEFQTDIKEIVFD-IRQEKNPCALCANLRRGALNDNAKKLGCNKVALGHHKDDAIETFLMSMFYEGRVNCFSPKTYLDRQ 161
Cdd:PRK10696  91 HIEEQDTYSIVKEkIPEGKTTCSLCSRLRRGILYRTARELGATKIALGHHRDDILETLFLNMFYGGKLKAMPPKLLSDDG 170

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894 162 DLTVIRPMIYIEEYMTKKISKDSNYPIItnPCPANGHT---RREYIKNLIANLNKEMPDFKRNVFGALNN 228
Cdd:PRK10696 171 KHIVIRPLAYVAEKDIIKFAEAKEFPII--PCNLCGSQenlQRQVVKEMLRDWEKEYPGRIETMFRALQN 238
lysidine_TilS_N TIGR02432
tRNA(Ile)-lysidine synthetase, N-terminal domain; The only examples in which the wobble ...
 25-172 3.74e-21

tRNA(Ile)-lysidine synthetase, N-terminal domain; The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This family describes a protein domain found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain archictecture of this protein family is variable; some, including characterized proteins of E. coli and B. subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family ( pfam01171). It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer). [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 274129 [Multi-domain]  Cd Length: 189  Bit Score: 87.30  E-value: 3.74e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894   25 KIAVGLSGGKDSLTLLHILKSYQRFSpqNFELIAITLNTGGVDNSPLD-----KLCKEINVPFYEFQTDIKEivFDIRQE 99
Cdd:TIGR02432   1 RILVAVSGGVDSMALLHLLLKLQPKI--KIKLIAAHVDHGLRPESDEEaefvqQFCRKLNIPLEIKKVDVKA--LAKGKK 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 497579894  100 KNPCALCANLRRGALNDNAKKLGCNKVALGHHKDDAIETFLMSMF----YEGrVNCFSPKTYLDRQdLTVIRPMIYI 172
Cdd:TIGR02432  77 KNLEEAAREARYDFFEEIAKKHGADYILTAHHADDQAETILMRLLrgsgLRG-LSGMKPIRILGSG-IQIIRPLLGI 151
ATP_bind_3 pfam01171
PP-loop family; This family of proteins belongs to the PP-loop superfamily.
 28-175 6.75e-15

PP-loop family; This family of proteins belongs to the PP-loop superfamily.


Pssm-ID: 426097 [Multi-domain]  Cd Length: 178  Bit Score: 70.35  E-value: 6.75e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894   28 VGLSGGKDSLTLLHILKSYQRFSPqnFELIAITLNTGGVDNSPLD-----KLCKEINVPFYEFQTDIKEIVFDIRQEKnp 102
Cdd:pfam01171   1 VAVSGGPDSMALLYLLAKLKIKLG--IELTAAHVNHGLREESDREaehvqALCRQLGIPLEILRVDVAKKSGENLEAA-- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  103 calcA-NLRRGALNDNAKKLGCNKVALGHHKDDAIETFLMSMF-YEGRVNCFSPKTYLDRQDLTVIRPMIY-----IEEY 175
Cdd:pfam01171  77 ----ArEARYDFFEEALKKHGADVLLTAHHLDDQLETFLMRLKrGSGLAGLAGIPPVREFAGGRIIRPLLKvskaeIEAY 152
 
Name Accession Description Interval E-value
TtcA-like cd24138
tRNA-cytidine(32) 2-sulfurtransferase and similar proteins; tRNA-cytidine(32) ...
 16-195 7.48e-86

tRNA-cytidine(32) 2-sulfurtransferase and similar proteins; tRNA-cytidine(32) 2-sulfurtransferase, also called two-thiocytidine biosynthesis protein A or tRNA 2-thiocytidine biosynthesis protein TtcA, catalyzes the ATP-dependent 2-thiolation of cytidine in position 32 of tRNA, to form 2-thiocytidine (s(2)C32). TtcA belongs to the adenine nucleotide alpha hydrolase superfamily (AANH) that includes N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to the adenosine group. This domain has a strongly conserved motif SGGKD at the N-terminus.


Pssm-ID: 467514 [Multi-domain]  Cd Length: 187  Bit Score: 252.97  E-value: 7.48e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  16 DFDMIQENDKIAVGLSGGKDSLTLLHILKSYQRFSPQNFELIAITLNTGGVDNSPLDKLCKEINVPFYEFQTDIKE---I 92
Cdd:cd24138    1 DFKMIEPGDRILVGLSGGKDSLTLLHLLEELKRRAPIKFELVAVTVDPGYPGYRPPREELAEILEELGEILEDEESeiiI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  93 VFDIRQEKNPCALCANLRRGALNDNAKKLGCNKVALGHHKDDAIETFLMSMFYEGRVNCFSPKTYLDRQDLTVIRPMIYI 172
Cdd:cd24138   81 IEKEREEKSPCSLCSRLRRGILYSLAKELGCNKLALGHHLDDAVETLLMNLLYGGRLKTMPPKVTMDRGGLTVIRPLIYV 160

                        170       180
                 ....*....|....*....|...
gi 497579894 173 EEYMTKKISKDSNYPIITNPCPA 195
Cdd:cd24138  161 REKDIRAFAEENGLPKIECPCPY 183
TilS COG0037
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 9-228 7.33e-77

tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA(Ile)-lysidine synthase TilS/MesJ is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439807 [Multi-domain]  Cd Length: 235  Bit Score: 232.03  E-value: 7.33e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894   9 KARKAIQDFDMIQENDKIAVGLSGGKDSLTLLHILKSYQRFSpqNFELIAITLNTGGVDNSPLD-----KLCKEINVPFY 83
Cdd:COG0037    1 KVRKAIRDYRLLEPGDRILVAVSGGKDSLALLHLLAKLRRRL--GFELVAVHVDHGLREESDEDaefvaELCEELGIPLH 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  84 EFQTDIKEIVfdIRQEKNPCALCANLRRGALNDNAKKLGCNKVALGHHKDDAIETFLMSMFYEGRVNCFSPKTYLDRQDL 163
Cdd:COG0037   79 VVRVDVPAIA--KKEGKSPEAAARRARYGALYELARELGADKIATGHHLDDQAETFLLNLLRGSGLAGLAGMPPSRGGGV 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 497579894 164 TVIRPMIYIEEYMTKKISKDSNYPIITNPCPANGHTRREYIKN-LIANLNKEMPDFKRNVFGALNN 228
Cdd:COG0037  157 RLIRPLLYVSRKEIEAYAKENGLPWIEDPCNYDPRYTRNRIRHlVLPELEERNPGFKENLARSAEN 222
PRK10696 PRK10696
tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional
 5-228 2.74e-70

tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional


Pssm-ID: 236737 [Multi-domain]  Cd Length: 258  Bit Score: 215.88  E-value: 2.74e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894   5 KLLSKARKAIQDFDMIQENDKIAVGLSGGKDSLTLLHILKSYQRFSPQNFELIAITLNTG--GVDNSPLDKLCKEINVPF 82
Cdd:PRK10696  11 RLRRQVGQAIADFNMIEEGDRVMVCLSGGKDSYTLLDILLNLQKRAPINFELVAVNLDQKqpGFPEHVLPEYLESLGVPY 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  83 YEFQTDIKEIVFD-IRQEKNPCALCANLRRGALNDNAKKLGCNKVALGHHKDDAIETFLMSMFYEGRVNCFSPKTYLDRQ 161
Cdd:PRK10696  91 HIEEQDTYSIVKEkIPEGKTTCSLCSRLRRGILYRTARELGATKIALGHHRDDILETLFLNMFYGGKLKAMPPKLLSDDG 170

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894 162 DLTVIRPMIYIEEYMTKKISKDSNYPIItnPCPANGHT---RREYIKNLIANLNKEMPDFKRNVFGALNN 228
Cdd:PRK10696 171 KHIVIRPLAYVAEKDIIKFAEAKEFPII--PCNLCGSQenlQRQVVKEMLRDWEKEYPGRIETMFRALQN 238
CTU1-like cd01713
cytoplasmic tRNA 2-thiolation protein 1 and similar proteins; This subfamily includes human ...
 9-174 1.05e-35

cytoplasmic tRNA 2-thiolation protein 1 and similar proteins; This subfamily includes human cytoplasmic tRNA 2-thiolation protein 1, also called cytosolic thiouridylase subunit 1 (CTU1), ATP-binding domain-containing protein 3 (ATPBD3), cancer-associated gene protein, or cytoplasmic tRNA adenylyltransferase 1. CTU1 plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln). It directly binds tRNAs and probably acts by catalyzing adenylation of tRNAs, an intermediate required for 2-thiolation. The CTU1-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.


Pssm-ID: 467486  Cd Length: 208  Bit Score: 125.78  E-value: 1.05e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894   9 KARKAIQDFDMIQENDKIAVGLSGGKDSLTLLHILKSYQRFSPQNFELIAITLNTG--GVDNSPLD---KLCKEINVPFY 83
Cdd:cd01713    4 RVHRTIRKYRLIKPGDRVAVGLSGGKDSTVLLYVLKELNKRHDYGVELIAVTIDEGikGYRDDSLEaarKLAEEYGIPLE 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  84 ------EFQTDIKEIVFDIRQEKNPCALCANLRRGALNDNAKKLGCNKVALGHHKDDAIETFLMSMFyEGRVN---CFSP 154
Cdd:cd01713   84 ivsfedEFGFTLDELIVGKGGKKNACTYCGVFRRRALNRGARELGADKLATGHNLDDEAETILMNLL-RGDVArllRTGP 162

                        170       180
                 ....*....|....*....|.
gi 497579894 155 KTYLDRQDLTV-IRPMIYIEE 174
Cdd:cd01713  163 EPRSEGEGLVPrIKPLRYIPE 183
TilS_N cd01992
N-terminal domain of tRNA(Ile)-lysidine synthase and similar proteins; tRNA(Ile)-lysidine ...
 25-179 3.24e-22

N-terminal domain of tRNA(Ile)-lysidine synthase and similar proteins; tRNA(Ile)-lysidine synthase (EC 6.3.4.19), also called tRNA(Ile)-2-lysyl-cytidine synthase or tRNA(Ile)-lysidine synthetase, catalyzes the ligation of lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine. This subfamily belongs to the adenine nucleotide alpha hydrolase superfamily that also includes N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to adenosine group. This domain has a strongly conserved motif SGGXD at the N-terminus.


Pssm-ID: 467496 [Multi-domain]  Cd Length: 185  Bit Score: 89.96  E-value: 3.24e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  25 KIAVGLSGGKDSLTLLHILKSYQRfsPQNFELIAITLNTGGVDNSPLD-----KLCKEINVPFYefqtdIKEIVFDIRQE 99
Cdd:cd01992    1 KILVAVSGGPDSMALLHLLKELRP--KLGLKLVAVHVDHGLREESAEEaqfvaKLCKKLGIPLH-----ILTVTEAPKSG 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894 100 KNPCALCANLRRGALNDNAKKLGCNKVALGHHKDDAIETFLMSMFY-EGRVNCFSPKTYLDRQDLTVIRPMIY-----IE 173
Cdd:cd01992   74 GNLEAAAREARYAFLERAAKEHGIDVLLTAHHLDDQAETVLMRLLRgSGLSGLAGMAARSKAGGIRLIRPLLGiskaeLL 153


                 ....*.
gi 497579894 174 EYMTKK 179
Cdd:cd01992  154 AYCREN 159
lysidine_TilS_N TIGR02432
tRNA(Ile)-lysidine synthetase, N-terminal domain; The only examples in which the wobble ...
 25-172 3.74e-21

tRNA(Ile)-lysidine synthetase, N-terminal domain; The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This family describes a protein domain found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain archictecture of this protein family is variable; some, including characterized proteins of E. coli and B. subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family ( pfam01171). It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer). [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 274129 [Multi-domain]  Cd Length: 189  Bit Score: 87.30  E-value: 3.74e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894   25 KIAVGLSGGKDSLTLLHILKSYQRFSpqNFELIAITLNTGGVDNSPLD-----KLCKEINVPFYEFQTDIKEivFDIRQE 99
Cdd:TIGR02432   1 RILVAVSGGVDSMALLHLLLKLQPKI--KIKLIAAHVDHGLRPESDEEaefvqQFCRKLNIPLEIKKVDVKA--LAKGKK 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 497579894  100 KNPCALCANLRRGALNDNAKKLGCNKVALGHHKDDAIETFLMSMF----YEGrVNCFSPKTYLDRQdLTVIRPMIYI 172
Cdd:TIGR02432  77 KNLEEAAREARYDFFEEIAKKHGADYILTAHHADDQAETILMRLLrgsgLRG-LSGMKPIRILGSG-IQIIRPLLGI 151
TtuA-like cd01993
tRNA-5-methyluridine(54) 2-sulfurtransferase and similar proteins; tRNA-5-methyluridine(54) ...
 17-194 8.20e-21

tRNA-5-methyluridine(54) 2-sulfurtransferase and similar proteins; tRNA-5-methyluridine(54) 2-sulfurtransferase, also called tRNA thiouridine synthetase TtuA, catalyzes the ATP-dependent 2-thiolation of 5-methyluridine residue at position 54 in the T loop of tRNAs, leading to 5-methyl-2-thiouridine (m(5)s(2)U or s(2)T). TtuA belongs to the adenine nucleotide alpha hydrolase superfamily (AANH) that includes N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to the adenosine group. This domain has a strongly conserved motif SGGKD at the N-terminus.


Pssm-ID: 467497 [Multi-domain]  Cd Length: 190  Bit Score: 86.22  E-value: 8.20e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  17 FDMIQENDKIAVGLSGGKDSLTLLHILKSYQrfspQNFELIAITLNTGGVDNSPLD---KLCKEINVPFY------EFQT 87
Cdd:cd01993    2 YKMFEKDDKILVAVSGGKDSLALLAVLKKLG----YNVEALYINLGIGEYSEKSEEvvkKLAEKLNLPLHvvdlkeEYGL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  88 DIKEIVFDIRQEknPCALCANLRRGALNDNAKKLGCNKVALGHHKDDAIETFLMSMFYEGRVncfspktYLDRQD----- 162
Cdd:cd01993   78 GIPELAKKSRRP--PCSVCGLVKRYIMNKFAVENGFDVVATGHNLDDEAAFLLGNILNWNEE-------YLAKQGpfllp 148

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 497579894 163 -----LTVIRPMIYIEEYMTKKISKDSNYPIITNPCP 194
Cdd:cd01993  149 ehgglVTRVKPLYEITEEEIALYALLNGIPYLEEECP 185
ATP_bind_3 pfam01171
PP-loop family; This family of proteins belongs to the PP-loop superfamily.
 28-175 6.75e-15

PP-loop family; This family of proteins belongs to the PP-loop superfamily.


Pssm-ID: 426097 [Multi-domain]  Cd Length: 178  Bit Score: 70.35  E-value: 6.75e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894   28 VGLSGGKDSLTLLHILKSYQRFSPqnFELIAITLNTGGVDNSPLD-----KLCKEINVPFYEFQTDIKEIVFDIRQEKnp 102
Cdd:pfam01171   1 VAVSGGPDSMALLYLLAKLKIKLG--IELTAAHVNHGLREESDREaehvqALCRQLGIPLEILRVDVAKKSGENLEAA-- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  103 calcA-NLRRGALNDNAKKLGCNKVALGHHKDDAIETFLMSMF-YEGRVNCFSPKTYLDRQDLTVIRPMIY-----IEEY 175
Cdd:pfam01171  77 ----ArEARYDFFEEALKKHGADVLLTAHHLDDQLETFLMRLKrGSGLAGLAGIPPVREFAGGRIIRPLLKvskaeIEAY 152
MnmA_TRMU-like cd01998
MnmA/TRMU family 2-thiouridylases and similar proteins; This family is composed of bacterial ...
 25-130 5.67e-12

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: 64.45  E-value: 5.67e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  25 KIAVGLSGGKDSLTLLHILKSyqrfspQNFELIAITL-------NTGGVDNSPLD-----KLCKEINVPFYE--FQTDIK 90
Cdd:cd01998    1 KVAVAMSGGVDSSVAAALLKE------QGYDVIGVFMknwddedNEKGGCCSEEDiedarRVADQLGIPLYVvdFSEEYW 74

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 497579894  91 EIVFD--IRQEK-----NPCALCaNlRR---GALNDNAKKLGCNKVALGH 130
Cdd:cd01998   75 ERVFDpfLEEYKagrtpNPDVLC-N-REikfGALLDAAKKLGADYIATGH 122
tRNA_Me_trans pfam03054
tRNA methyl transferase HUP domain; This family represents the N-terminal HUP domain in tRNA ...
 24-130 3.55e-11

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: 60.73  E-value: 3.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894   24 DKIAVGLSGGKDSLTLLHILKSyqrfspQNFELIAITL----NTGGVDN-----SPLD-----KLCKEINVPFY--EFQT 87
Cdd:pfam03054   1 MKVVVAMSGGVDSSVAAYLLKE------QGHNVIGVFMknwdEEQSLDEegkccSEEDladaqRVCEQLGIPLYvvNFEK 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 497579894   88 DIKEIVFD--IRQEK-----NPCALCaN--LRRGALNDNAK-KLGCNKVALGH 130
Cdd:pfam03054  75 EYWEDVFEpfLDEYKngrtpNPDVLC-NkeIKFGALLDYALeNLGADYVATGH 126
mnmA PRK00143
tRNA-specific 2-thiouridylase MnmA; Reviewed
 25-131 2.40e-08

tRNA-specific 2-thiouridylase MnmA; Reviewed


Pssm-ID: 234664 [Multi-domain]  Cd Length: 346  Bit Score: 53.54  E-value: 2.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  25 KIAVGLSGGKDSLTLLHILKSyqrfspQNFELIAITL--------NTGGVDNSPLD-----KLCKEINVPFY--EFQTDI 89
Cdd:PRK00143   2 RVVVGMSGGVDSSVAAALLKE------QGYEVIGVFMklwddddeTGKGGCCAEEDiadarRVADKLGIPHYvvDFEKEF 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 497579894  90 KEIVFD--IRQEK-----NPCALCaNlRR---GALNDNAKKLGCNKVALGHH 131
Cdd:PRK00143  76 WDRVIDyfLDEYKagrtpNPCVLC-N-KEikfKAFLEYARELGADYIATGHY 125
MnmA COG0482
tRNA U34 2-thiouridine synthase MnmA/TrmU, contains the PP-loop ATPase domain [Translation, ...
 25-130 2.71e-07

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: 50.44  E-value: 2.71e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  25 KIAVGLSGGKDSLTLLHILKSyqrfspQNFELIAITL--------NTGGVDNSPLD-----KLCKEINVPFY--EFQTDI 89
Cdd:COG0482    2 RVVVGMSGGVDSSVAAALLKE------QGYEVIGVTMklwddddaSGSGGCCSLEDiedarRVADKLGIPHYvvDFEEEF 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 497579894  90 KEIVFD--IRQEK-----NPCALCaNlRR---GALNDNAKKLGCNKVALGH 130
Cdd:COG0482   76 KDRVIDyfLDEYLagrtpNPCVLC-N-REikfGALLEKALELGADYIATGH 124
LarE-like cd01990
Lactate racemization operon protein LarE and similar proteins; This subfamily includes ...
 25-134 1.02e-06

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: 48.02  E-value: 1.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  25 KIAVGLSGGKDSLTLLHILKsyqRFSPQNfeLIAITLNTGGVDNSPLDK---LCKEINVPFYEFQTDIKEIVFDIRQEKN 101
Cdd:cd01990    1 KVVVAFSGGVDSSLLAKLAK---EVLGDN--VVAVTADSPLVPREELEEakrIAEEIGIRHEIIKTDELDDEEYVANDPD 75

                         90       100       110
                 ....*....|....*....|....*....|...
gi 497579894 102 PCALCANLRRGALNDNAKKLGCNKVALGHHKDD 134
Cdd:cd01990   76 RCYHCKKALYSTLKEIAKERGYDVVLDGTNADD 108
COG1365 COG1365
Predicted ATPase, PP-loop superfamily [General function prediction only];
3-129 1.81e-06

Predicted ATPase, PP-loop superfamily [General function prediction only];


Pssm-ID: 440976  Cd Length: 256  Bit Score: 47.74  E-value: 1.81e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894   3 IQKLLSKARKAIQDFDMIQ--ENDKIAVGLSGGKDSLTLLHILKSYqrfspqNFELIAITLN-----TGGVDNSpLDKLC 75
Cdd:COG1365   38 LRELLEKRLNGPKEFLKRSkeKNPKVVVAFSGGVDSSASLIIAKWI------GFDVEAVTVKstiilPQMFKKN-IKELC 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 497579894  76 KEINVPFYEFQTDIKEIVFDIRQEK-NPCALCANLRRGALNDNAKKLGCNKVALG 129
Cdd:COG1365  111 KKLNVKHEFIEIDLGEIIEDALKGKfHPCGRCHSLIEEAVEDYAKKNGIKIVIFG 165
PRK14664 PRK14664
tRNA-specific 2-thiouridylase MnmA; Provisional
 19-131 3.29e-06

tRNA-specific 2-thiouridylase MnmA; Provisional


Pssm-ID: 173127 [Multi-domain]  Cd Length: 362  Bit Score: 47.26  E-value: 3.29e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894  19 MIQENDKIAVGLSGGKDSLTLLHILKSyqrfspQNFELIAITLNTGGVDNSPLDKLCKEINVPFY------EF-QTDIKE 91
Cdd:PRK14664   1 MKESKKRVLVGMSGGIDSTATCLMLQE------QGYEIVGVTMRVWGDEPQDARELAARMGIEHYvadervPFkDTIVKN 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 497579894  92 IVFDIRQEK--NPCALCANL-RRGALNDNAKKLGCNKVALGHH 131
Cdd:PRK14664  75 FIDEYRQGRtpNPCVMCNPLfKFRMLIEWADKLGCAWIATGHY 117
QueC COG0603
7-cyano-7-deazaguanine synthase (queuosine biosynthesis) [Translation, ribosomal structure and ...
 22-64 7.47e-04

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: 39.76  E-value: 7.47e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 497579894  22 ENDKIAVGLSGGKDSLTLLHILKSyqrfspQNFELIAITLNTG 64
Cdd:COG0603    1 MMKKAVVLLSGGLDSTTCLAWALA------RGYEVYALSFDYG 37
CysD COG0175
3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase or ...
 11-64 1.60e-03

3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase or related enzyme [Amino acid transport and metabolism, Coenzyme transport and metabolism]; 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase or related enzyme is part of the Pathway/BioSystem: Cysteine biosynthesis


Pssm-ID: 439945 [Multi-domain]  Cd Length: 232  Bit Score: 38.67  E-value: 1.60e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 497579894  11 RKAIQDFdmiqeNDKIAVGLSGGKDSLTLLHILKsyqRFSPqNFELiaITLNTG 64
Cdd:COG0175   26 REAAAEF-----GGRVVVSSSGGKDSTVLLHLAA---KFKP-PIPV--LFLDTG 68
PAPS_reductase-like_YbdN cd23947
uncharacterized phosphoadenosine phosphosulfate reductase-like proteins, similar to ...
 10-42 1.72e-03

uncharacterized phosphoadenosine phosphosulfate reductase-like proteins, similar to Escherichia coli YbdN; This subgroup contains Escherichia coli YbdN and other phosphoadenosine phosphosulfate (PAPS) reductase (or PAPS sulfotransferase EC 1.8.4.8)-like proteins. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N-type ATP PPases and ATP sulfurylases. A highly modified version of the P loop, the fingerprint peptide of mononucleotide-binding proteins, is present in the active site of the protein, which appears to be a positively charged cleft containing a number of conserved arginine and lysine residues. Although PAPS reductase has no ATPase activity, it shows a striking similarity to the structure of the ATP pyrophosphatase (ATP PPase) domain of GMP synthetase, indicating that both enzyme families have evolved from a common ancestral nucleotide-binding fold. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP).


Pssm-ID: 467512 [Multi-domain]  Cd Length: 206  Bit Score: 38.53  E-value: 1.72e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 497579894  10 ARKAIQDFdmIQENDKIAVGLSGGKDSLTLLHI 42
Cdd:cd23947    1 ALERIRKV--FEEFDPVIVSFSGGKDSLVLLHL 31
PRK13795 PRK13795
hypothetical protein; Provisional
 3-82 7.35e-03

hypothetical protein; Provisional


Pssm-ID: 237510 [Multi-domain]  Cd Length: 636  Bit Score: 37.28  E-value: 7.35e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497579894   3 IQKLLSKARKAIQDFDMiQENDKIAVGLSGGKDSLTLLHI-LKSYQRFSpqnfeliAITLNTG-----GVDNspLDKLCK 76
Cdd:PRK13795 224 LEEKEKEAVNFIRGVAE-KYNLPVSVSFSGGKDSLVVLDLaREALKDFK-------AFFNNTGlefpeTVEN--VKEVAE 293


                 ....*.
gi 497579894  77 EINVPF 82
Cdd:PRK13795 294 EYGIEL 299
AANH-like cd01986
adenine nucleotide alpha hydrolase (AANH)-like proteins; This group of adenine nucleotide ...
 26-44 7.82e-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: 34.35  E-value: 7.82e-03
                         10
                 ....*....|....*....
gi 497579894  26 IAVGLSGGKDSLTLLHILK 44
Cdd:cd01986    1 VVVGYSGGKDSSVALHLAS 19
QueC pfam06508
Queuosine biosynthesis protein QueC; This family of proteins participate in the biosynthesis ...
 25-92 7.94e-03

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: 36.44  E-value: 7.94e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 497579894   25 KIAVGLSGGKDSLTLLHILKSyqrfspQNFELIAITLNTGGVDNSPLD---KLCKEINVPFYEFQTD-IKEI 92
Cdd:pfam06508   1 KAVVLLSGGLDSTTCLAWAKK------EGYEVYALSFDYGQRHRKELEcakKIAKALGVEHKILDLDfLKQI 66
 
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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