NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|145360979|ref|NP_181956|]
View 

repressor of lrx1 [Arabidopsis thaliana]

Protein Classification

tRNA 2-thiolation protein( domain architecture ID 18932641)

tRNA 2-thiolation protein is a nucleotide alpha hydrolase (AANH) superfamily protein that directly binds tRNAs and probably acts by catalyzing adenylation of tRNAs, an intermediate required for 2-thiolation; such as cytoplasmic tRNA 2-thiolation protein 1

CATH:  3.40.50.620
EC:  2.7.7.-
Gene Ontology:  GO:0000049|GO:0034227|GO:0016779
PubMed:  12012333|18391219
SCOP:  3001593

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CTU1-like cd01713
cytoplasmic tRNA 2-thiolation protein 1 and similar proteins; This subfamily includes human ...
 42-247 1.95e-120

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: 346.11  E-value: 1.95e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  42 FEEEIHQVIVQNRLFKSGERVAIGASGGKDSTVLAYVLSELNRRHNYGLDLFLLSIDEGITGYRDDSLETVKRNEVQYGL 121
Cdd:cd01713    1 IERRVHRTIRKYRLIKPGDRVAVGLSGGKDSTVLLYVLKELNKRHDYGVELIAVTIDEGIKGYRDDSLEAARKLAEEYGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979 122 PLKIVSYKDLYGWTMDE-IVKMIGLKNNCTFCGVFRRQALDRGAALLKVEKLVTGHNADDIAETVLLNILRGDIARLSR- 199
Cdd:cd01713   81 PLEIVSFEDEFGFTLDElIVGKGGKKNACTYCGVFRRRALNRGARELGADKLATGHNLDDEAETILMNLLRGDVARLLRt 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 145360979 200 CTSITTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNA 247
Cdd:cd01713  161 GPEPRSEGEGLVPRIKPLRYIPEKEIVLYAHLNGLPYFSTECPYAPEA 208
TIGR00269 super family cl42867
TIGR00269 family protein; [Hypothetical proteins, Conserved]
 211-312 9.16e-18

TIGR00269 family protein; [Hypothetical proteins, Conserved]


The actual alignment was detected with superfamily member TIGR00269:

Pssm-ID: 129370 [Multi-domain]  Cd Length: 104  Bit Score: 77.54  E-value: 9.16e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  211 IPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNAYRGFAREFIKDLERIRPRAILDIIKSGEDFRIATTTKMP--EQ 288
Cdd:TIGR00269   1 VPRIKPLRYIPEKEVVLYAFLNELKVHLDECPYSSLSVRARIRDFLYDLENKKPGVKFSVLRGFEKLIPLLKELSEqeDL 80

                          90       100
                  ....*....|....*....|....
gi 145360979  289 GTCERCGYISSQKWCKACVLLEGL 312
Cdd:TIGR00269  81 RRCERCGEPTSGRICKACKFLEEL 104
 
Name Accession Description Interval E-value
CTU1-like cd01713
cytoplasmic tRNA 2-thiolation protein 1 and similar proteins; This subfamily includes human ...
 42-247 1.95e-120

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: 346.11  E-value: 1.95e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  42 FEEEIHQVIVQNRLFKSGERVAIGASGGKDSTVLAYVLSELNRRHNYGLDLFLLSIDEGITGYRDDSLETVKRNEVQYGL 121
Cdd:cd01713    1 IERRVHRTIRKYRLIKPGDRVAVGLSGGKDSTVLLYVLKELNKRHDYGVELIAVTIDEGIKGYRDDSLEAARKLAEEYGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979 122 PLKIVSYKDLYGWTMDE-IVKMIGLKNNCTFCGVFRRQALDRGAALLKVEKLVTGHNADDIAETVLLNILRGDIARLSR- 199
Cdd:cd01713   81 PLEIVSFEDEFGFTLDElIVGKGGKKNACTYCGVFRRRALNRGARELGADKLATGHNLDDEAETILMNLLRGDVARLLRt 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 145360979 200 CTSITTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNA 247
Cdd:cd01713  161 GPEPRSEGEGLVPRIKPLRYIPEKEIVLYAHLNGLPYFSTECPYAPEA 208
TilS COG0037
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 45-278 4.05e-51

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: 170.01  E-value: 4.05e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  45 EIHQVIVQNRLFKSGERVAIGASGGKDSTVLAYVLSELNRRHNYglDLFLLSIDEGITGYRDDSLETVKRNEVQYGLPLK 124
Cdd:COG0037    1 KVRKAIRDYRLLEPGDRILVAVSGGKDSLALLHLLAKLRRRLGF--ELVAVHVDHGLREESDEDAEFVAELCEELGIPLH 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979 125 IVSYKDLYgwtmdeiVKMIGLKNNCTFCGVFRRQALDRGAALLKVEKLVTGHNADDIAETVLLNILRGD-IARLSrctSI 203
Cdd:COG0037   79 VVRVDVPA-------IAKKEGKSPEAAARRARYGALYELARELGADKIATGHHLDDQAETFLLNLLRGSgLAGLA---GM 148

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 145360979 204 TTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNAYRGFAR-EFIKDLERIRPRAILDIIKSGEDFR 278
Cdd:COG0037  149 PPSRGGGVRLIRPLLYVSRKEIEAYAKENGLPWIEDPCNYDPRYTRNRIRhLVLPELEERNPGFKENLARSAENLA 224
TIGR00269 TIGR00269
TIGR00269 family protein; [Hypothetical proteins, Conserved]
 211-312 9.16e-18

TIGR00269 family protein; [Hypothetical proteins, Conserved]


Pssm-ID: 129370 [Multi-domain]  Cd Length: 104  Bit Score: 77.54  E-value: 9.16e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  211 IPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNAYRGFAREFIKDLERIRPRAILDIIKSGEDFRIATTTKMP--EQ 288
Cdd:TIGR00269   1 VPRIKPLRYIPEKEVVLYAFLNELKVHLDECPYSSLSVRARIRDFLYDLENKKPGVKFSVLRGFEKLIPLLKELSEqeDL 80

                          90       100
                  ....*....|....*....|....
gi 145360979  289 GTCERCGYISSQKWCKACVLLEGL 312
Cdd:TIGR00269  81 RRCERCGEPTSGRICKACKFLEEL 104
PRK10696 PRK10696
tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional
 48-264 1.46e-17

tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional


Pssm-ID: 236737 [Multi-domain]  Cd Length: 258  Bit Score: 81.06  E-value: 1.46e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  48 QVIVQNRLFKSGERVAIGASGGKDSTVLAYVLSELNRRHNYGLDLFLLSIDEGITGYRDDSLETVKRnevQYGLPLKIVs 127
Cdd:PRK10696  18 QAIADFNMIEEGDRVMVCLSGGKDSYTLLDILLNLQKRAPINFELVAVNLDQKQPGFPEHVLPEYLE---SLGVPYHIE- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979 128 YKDLYGwtmdeIVKMI---GlKNNCTFCGVFRRQALDRGAALLKVEKLVTGHNADDIAETVLLNILRGdiARLSRCTSIT 204
Cdd:PRK10696  94 EQDTYS-----IVKEKipeG-KTTCSLCSRLRRGILYRTARELGATKIALGHHRDDILETLFLNMFYG--GKLKAMPPKL 165

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 145360979 205 TGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYS-PNAYRGFAREFIKDLERIRP 264
Cdd:PRK10696 166 LSDDGKHIVIRPLAYVAEKDIIKFAEAKEFPIIPCNLCGSqENLQRQVVKEMLRDWEKEYP 226
lysidine_TilS_N TIGR02432
tRNA(Ile)-lysidine synthetase, N-terminal domain; The only examples in which the wobble ...
 61-237 7.35e-17

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: 77.67  E-value: 7.35e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979   61 RVAIGASGGKDSTVLAYVLSELNRrhNYGLDLFLLSIDEGItgyRDDSLET---VKRNEVQYGLPLKIVSYKdlygWTMD 137
Cdd:TIGR02432   1 RILVAVSGGVDSMALLHLLLKLQP--KIKIKLIAAHVDHGL---RPESDEEaefVQQFCRKLNIPLEIKKVD----VKAL 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  138 EIVKMIGLKNNCTFcgvFRRQALDRGAALLKVEKLVTGHNADDIAETVLLNILRG-DIARLSRCTSITT-GEDGPIPRck 215
Cdd:TIGR02432  72 AKGKKKNLEEAARE---ARYDFFEEIAKKHGADYILTAHHADDQAETILMRLLRGsGLRGLSGMKPIRIlGSGIQIIR-- 146

                         170       180
                  ....*....|....*....|..
gi 145360979  216 PFKYTYEKEIVMYAYFKKLDYF 237
Cdd:TIGR02432 147 PLLGISKSEIEEYLKENGLPWF 168
ATP_bind_3 pfam01171
PP-loop family; This family of proteins belongs to the PP-loop superfamily.
 64-253 2.13e-14

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: 2.13e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979   64 IGASGGKDSTVLAYVLSELNRrhNYGLDLFLLSIDEGITGYRDDSLETVKRNEVQYGLPLKI--VSYKDLYGWTMDEIVK 141
Cdd:pfam01171   1 VAVSGGPDSMALLYLLAKLKI--KLGIELTAAHVNHGLREESDREAEHVQALCRQLGIPLEIlrVDVAKKSGENLEAAAR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  142 MiglknnctfcgvFRRQALDRGAALLKVEKLVTGHNADDIAETVLLNILRGD-IARLSRCTSITTGEDGPIPRckPFKYT 220
Cdd:pfam01171  79 E------------ARYDFFEEALKKHGADVLLTAHHLDDQLETFLMRLKRGSgLAGLAGIPPVREFAGGRIIR--PLLKV 144

                         170       180       190
                  ....*....|....*....|....*....|...
gi 145360979  221 YEKEIVMYAYFKKLDYFSTECIYSPNAYRGFAR 253
Cdd:pfam01171 145 SKAEIEAYAKEHKIPWFEDESNADDKYTRNRIR 177
zn-ribbon_14 pfam16503
Zinc-ribbon; This is a family of zinc-ribbons largely from eukaryotes that lie at the ...
 289-320 2.86e-14

Zinc-ribbon; This is a family of zinc-ribbons largely from eukaryotes that lie at the C-terminus of cytoplasmic tRNA adenylyltransferase 1 proteins. Most of these proteins carry an ATP-binding domain towards the N-terminus.


Pssm-ID: 465147  Cd Length: 32  Bit Score: 66.03  E-value: 2.86e-14
                          10        20        30
                  ....*....|....*....|....*....|..
gi 145360979  289 GTCERCGYISSQKWCKACVLLEGLNRGLPKMG 320
Cdd:pfam16503   1 GRCERCGYISSQKICKACVLLEGLNKGRPKIA 32
 
Name Accession Description Interval E-value
CTU1-like cd01713
cytoplasmic tRNA 2-thiolation protein 1 and similar proteins; This subfamily includes human ...
 42-247 1.95e-120

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: 346.11  E-value: 1.95e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  42 FEEEIHQVIVQNRLFKSGERVAIGASGGKDSTVLAYVLSELNRRHNYGLDLFLLSIDEGITGYRDDSLETVKRNEVQYGL 121
Cdd:cd01713    1 IERRVHRTIRKYRLIKPGDRVAVGLSGGKDSTVLLYVLKELNKRHDYGVELIAVTIDEGIKGYRDDSLEAARKLAEEYGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979 122 PLKIVSYKDLYGWTMDE-IVKMIGLKNNCTFCGVFRRQALDRGAALLKVEKLVTGHNADDIAETVLLNILRGDIARLSR- 199
Cdd:cd01713   81 PLEIVSFEDEFGFTLDElIVGKGGKKNACTYCGVFRRRALNRGARELGADKLATGHNLDDEAETILMNLLRGDVARLLRt 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 145360979 200 CTSITTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNA 247
Cdd:cd01713  161 GPEPRSEGEGLVPRIKPLRYIPEKEIVLYAHLNGLPYFSTECPYAPEA 208
TilS COG0037
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 45-278 4.05e-51

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: 170.01  E-value: 4.05e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  45 EIHQVIVQNRLFKSGERVAIGASGGKDSTVLAYVLSELNRRHNYglDLFLLSIDEGITGYRDDSLETVKRNEVQYGLPLK 124
Cdd:COG0037    1 KVRKAIRDYRLLEPGDRILVAVSGGKDSLALLHLLAKLRRRLGF--ELVAVHVDHGLREESDEDAEFVAELCEELGIPLH 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979 125 IVSYKDLYgwtmdeiVKMIGLKNNCTFCGVFRRQALDRGAALLKVEKLVTGHNADDIAETVLLNILRGD-IARLSrctSI 203
Cdd:COG0037   79 VVRVDVPA-------IAKKEGKSPEAAARRARYGALYELARELGADKIATGHHLDDQAETFLLNLLRGSgLAGLA---GM 148

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 145360979 204 TTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNAYRGFAR-EFIKDLERIRPRAILDIIKSGEDFR 278
Cdd:COG0037  149 PPSRGGGVRLIRPLLYVSRKEIEAYAKENGLPWIEDPCNYDPRYTRNRIRhLVLPELEERNPGFKENLARSAENLA 224
TtuA-like cd01993
tRNA-5-methyluridine(54) 2-sulfurtransferase and similar proteins; tRNA-5-methyluridine(54) ...
 52-247 4.19e-46

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: 155.56  E-value: 4.19e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  52 QNRLFKSGERVAIGASGGKDSTVLAYVLSELnrrhnyGLDLFLLSIDEGITGYRDDSLETVKRNEVQYGLPLKIVSYKDL 131
Cdd:cd01993    1 RYKMFEKDDKILVAVSGGKDSLALLAVLKKL------GYNVEALYINLGIGEYSEKSEEVVKKLAEKLNLPLHVVDLKEE 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979 132 YGWTMDEIVKMIGlKNNCTFCGVFRRQALDRGAALLKVEKLVTGHNADDIAETVLLNILRGDIARLSRCTSIT-TGEDGP 210
Cdd:cd01993   75 YGLGIPELAKKSR-RPPCSVCGLVKRYIMNKFAVENGFDVVATGHNLDDEAAFLLGNILNWNEEYLAKQGPFLlPEHGGL 153

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 145360979 211 IPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNA 247
Cdd:cd01993  154 VTRVKPLYEITEEEIALYALLNGIPYLEEECPYAEGA 190
TtcA-like cd24138
tRNA-cytidine(32) 2-sulfurtransferase and similar proteins; tRNA-cytidine(32) ...
 54-244 1.67e-28

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: 109.29  E-value: 1.67e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  54 RLFKSGERVAIGASGGKDSTVLAYVLSELNRRHNYGLDLFLLSIDEGITGYRDDSlETVKRNEVQYGLPLKIVSYKDLyg 133
Cdd:cd24138    3 KMIEPGDRILVGLSGGKDSLTLLHLLEELKRRAPIKFELVAVTVDPGYPGYRPPR-EELAEILEELGEILEDEESEII-- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979 134 wtmdEIVKMIGLKNNCTFCGVFRRQALDRGAALLKVEKLVTGHNADDIAETVLLNILRGdiARLSRCTSITTGEDGPIPR 213
Cdd:cd24138   80 ----IIEKEREEKSPCSLCSRLRRGILYSLAKELGCNKLALGHHLDDAVETLLMNLLYG--GRLKTMPPKVTMDRGGLTV 153

                        170       180       190
                 ....*....|....*....|....*....|.
gi 145360979 214 CKPFKYTYEKEIVMYAYFKKLDYFSTECIYS 244
Cdd:cd24138  154 IRPLIYVREKDIRAFAEENGLPKIECPCPYC 184
TIGR00269 TIGR00269
TIGR00269 family protein; [Hypothetical proteins, Conserved]
 211-312 9.16e-18

TIGR00269 family protein; [Hypothetical proteins, Conserved]


Pssm-ID: 129370 [Multi-domain]  Cd Length: 104  Bit Score: 77.54  E-value: 9.16e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  211 IPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNAYRGFAREFIKDLERIRPRAILDIIKSGEDFRIATTTKMP--EQ 288
Cdd:TIGR00269   1 VPRIKPLRYIPEKEVVLYAFLNELKVHLDECPYSSLSVRARIRDFLYDLENKKPGVKFSVLRGFEKLIPLLKELSEqeDL 80

                          90       100
                  ....*....|....*....|....
gi 145360979  289 GTCERCGYISSQKWCKACVLLEGL 312
Cdd:TIGR00269  81 RRCERCGEPTSGRICKACKFLEEL 104
PRK10696 PRK10696
tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional
 48-264 1.46e-17

tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional


Pssm-ID: 236737 [Multi-domain]  Cd Length: 258  Bit Score: 81.06  E-value: 1.46e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  48 QVIVQNRLFKSGERVAIGASGGKDSTVLAYVLSELNRRHNYGLDLFLLSIDEGITGYRDDSLETVKRnevQYGLPLKIVs 127
Cdd:PRK10696  18 QAIADFNMIEEGDRVMVCLSGGKDSYTLLDILLNLQKRAPINFELVAVNLDQKQPGFPEHVLPEYLE---SLGVPYHIE- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979 128 YKDLYGwtmdeIVKMI---GlKNNCTFCGVFRRQALDRGAALLKVEKLVTGHNADDIAETVLLNILRGdiARLSRCTSIT 204
Cdd:PRK10696  94 EQDTYS-----IVKEKipeG-KTTCSLCSRLRRGILYRTARELGATKIALGHHRDDILETLFLNMFYG--GKLKAMPPKL 165

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 145360979 205 TGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYS-PNAYRGFAREFIKDLERIRP 264
Cdd:PRK10696 166 LSDDGKHIVIRPLAYVAEKDIIKFAEAKEFPIIPCNLCGSqENLQRQVVKEMLRDWEKEYP 226
TilS_N cd01992
N-terminal domain of tRNA(Ile)-lysidine synthase and similar proteins; tRNA(Ile)-lysidine ...
 61-249 1.81e-17

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: 79.18  E-value: 1.81e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  61 RVAIGASGGKDSTVLAYVLSELNRRhnYGLDLFLLSIDEGItgyRDDSLE---TVKRNEVQYGLPLKIVSYKDLYGWTMD 137
Cdd:cd01992    1 KILVAVSGGPDSMALLHLLKELRPK--LGLKLVAVHVDHGL---REESAEeaqFVAKLCKKLGIPLHILTVTEAPKSGGN 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979 138 ------EIvkmiglknnctfcgvfRRQALDRGAALLKVEKLVTGHNADDIAETVLLNILRG-DIARLSRCTSITTGEDGP 210
Cdd:cd01992   76 leaaarEA----------------RYAFLERAAKEHGIDVLLTAHHLDDQAETVLMRLLRGsGLSGLAGMAARSKAGGIR 139

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 145360979 211 IprCKPFKYTYEKEIVMYAYFKKLDYF----STECIYSPNAYR 249
Cdd:cd01992  140 L--IRPLLGISKAELLAYCRENGLPWVedpsNADLKYTRNRIR 180
lysidine_TilS_N TIGR02432
tRNA(Ile)-lysidine synthetase, N-terminal domain; The only examples in which the wobble ...
 61-237 7.35e-17

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: 77.67  E-value: 7.35e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979   61 RVAIGASGGKDSTVLAYVLSELNRrhNYGLDLFLLSIDEGItgyRDDSLET---VKRNEVQYGLPLKIVSYKdlygWTMD 137
Cdd:TIGR02432   1 RILVAVSGGVDSMALLHLLLKLQP--KIKIKLIAAHVDHGL---RPESDEEaefVQQFCRKLNIPLEIKKVD----VKAL 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  138 EIVKMIGLKNNCTFcgvFRRQALDRGAALLKVEKLVTGHNADDIAETVLLNILRG-DIARLSRCTSITT-GEDGPIPRck 215
Cdd:TIGR02432  72 AKGKKKNLEEAARE---ARYDFFEEIAKKHGADYILTAHHADDQAETILMRLLRGsGLRGLSGMKPIRIlGSGIQIIR-- 146

                         170       180
                  ....*....|....*....|..
gi 145360979  216 PFKYTYEKEIVMYAYFKKLDYF 237
Cdd:TIGR02432 147 PLLGISKSEIEEYLKENGLPWF 168
ATP_bind_3 pfam01171
PP-loop family; This family of proteins belongs to the PP-loop superfamily.
 64-253 2.13e-14

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: 2.13e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979   64 IGASGGKDSTVLAYVLSELNRrhNYGLDLFLLSIDEGITGYRDDSLETVKRNEVQYGLPLKI--VSYKDLYGWTMDEIVK 141
Cdd:pfam01171   1 VAVSGGPDSMALLYLLAKLKI--KLGIELTAAHVNHGLREESDREAEHVQALCRQLGIPLEIlrVDVAKKSGENLEAAAR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  142 MiglknnctfcgvFRRQALDRGAALLKVEKLVTGHNADDIAETVLLNILRGD-IARLSRCTSITTGEDGPIPRckPFKYT 220
Cdd:pfam01171  79 E------------ARYDFFEEALKKHGADVLLTAHHLDDQLETFLMRLKRGSgLAGLAGIPPVREFAGGRIIR--PLLKV 144

                         170       180       190
                  ....*....|....*....|....*....|...
gi 145360979  221 YEKEIVMYAYFKKLDYFSTECIYSPNAYRGFAR 253
Cdd:pfam01171 145 SKAEIEAYAKEHKIPWFEDESNADDKYTRNRIR 177
zn-ribbon_14 pfam16503
Zinc-ribbon; This is a family of zinc-ribbons largely from eukaryotes that lie at the ...
 289-320 2.86e-14

Zinc-ribbon; This is a family of zinc-ribbons largely from eukaryotes that lie at the C-terminus of cytoplasmic tRNA adenylyltransferase 1 proteins. Most of these proteins carry an ATP-binding domain towards the N-terminus.


Pssm-ID: 465147  Cd Length: 32  Bit Score: 66.03  E-value: 2.86e-14
                          10        20        30
                  ....*....|....*....|....*....|..
gi 145360979  289 GTCERCGYISSQKWCKACVLLEGLNRGLPKMG 320
Cdd:pfam16503   1 GRCERCGYISSQKICKACVLLEGLNKGRPKIA 32
CysD COG0175
3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase or ...
 59-127 3.36e-04

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: 41.37  E-value: 3.36e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  59 GERVAIGASGGKDSTVLAYVLSELNrrhnygLDLFLLSIDegiTGYR-DDSLETVKRNEVQYGLPLKIVS 127
Cdd:COG0175   33 GGRVVVSSSGGKDSTVLLHLAAKFK------PPIPVLFLD---TGYEfPETYEFRDRLAERLGLDLIVVR 93
PAPS_reductase-like_YbdN cd23947
uncharacterized phosphoadenosine phosphosulfate reductase-like proteins, similar to ...
 54-141 6.35e-04

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: 40.45  E-value: 6.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  54 RLFKSGERVAIGASGGKDSTVLAY-VLSELNRRHnygLDLFLLSIDegiTGYR-DDSLETVKRNEVQYGLPLKIVSYKDL 131
Cdd:cd23947    7 KVFEEFDPVIVSFSGGKDSLVLLHlALEALRRLR---KDVYVVFID---TGIEfPETIDFVEKLAETLGLDVEAARPPLF 80

                         90
                 ....*....|
gi 145360979 132 YGWTMDEIVK 141
Cdd:cd23947   81 LEWLTSNFQP 90
MnmA_TRMU-like cd01998
MnmA/TRMU family 2-thiouridylases and similar proteins; This family is composed of bacterial ...
 61-176 9.99e-03

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: 37.49  E-value: 9.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145360979  61 RVAIGASGGKDSTVLAYVLSElnRRHNY-GldLFLLSIDEGITGYR----DDSLETVKRNEVQYGLPLKIVSYKDLYgWt 135
Cdd:cd01998    1 KVAVAMSGGVDSSVAAALLKE--QGYDViG--VFMKNWDDEDNEKGgccsEEDIEDARRVADQLGIPLYVVDFSEEY-W- 74

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 145360979 136 mDEIVK-MI-----GLKNN-CTFC------GVFRRQALDRGAallkvEKLVTGH 176
Cdd:cd01998   75 -ERVFDpFLeeykaGRTPNpDVLCnreikfGALLDAAKKLGA-----DYIATGH 122
 
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