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Conserved domains on  [gi|145337616|ref|NP_177744|]
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2-thiocytidine tRNA biosynthesis protein, TtcA [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

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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 ...
 20-225 1.83e-119

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: 342.65  E-value: 1.83e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  20 FEEEIHQVIVGNRLFKFGERVAIGASGGKDSSVLAYVLSELNRRHSYGLDLFLLSIDEGITGYRDDSLETVKRNEVQYGL 99
Cdd:cd01713    1 IERRVHRTIRKYRLIKPGDRVAVGLSGGKDSTVLLYVLKELNKRHDYGVELIAVTIDEGIKGYRDDSLEAARKLAEEYGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616 100 PLQIVSYKDLYGWTMDE-IVKMIGLKNNCTFCGVFRRQALDRGAALLKVDKLVTGHNADDIAETVVLNILRGDIARLSR- 177
Cdd:cd01713   81 PLEIVSFEDEFGFTLDElIVGKGGKKNACTYCGVFRRRALNRGARELGADKLATGHNLDDEAETILMNLLRGDVARLLRt 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 145337616 178 CTSITTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNA 225
Cdd:cd01713  161 GPEPRSEGEGLVPRIKPLRYIPEKEIVLYAHLNGLPYFSTECPYAPEA 208
TIGR00269 super family cl42867
TIGR00269 family protein; [Hypothetical proteins, Conserved]
 189-290 2.06e-17

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: 76.39  E-value: 2.06e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  189 IPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNAYRGFACEFINDLERLRPRAILDIIKSGEdfRIATTTK----MP 264
Cdd:TIGR00269   1 VPRIKPLRYIPEKEVVLYAFLNELKVHLDECPYSSLSVRARIRDFLYDLENKKPGVKFSVLRGFE--KLIPLLKelseQE 78

                          90       100
                  ....*....|....*....|....*.
gi 145337616  265 EQGTCERCGYISSQKWCKACVLLEGL 290
Cdd:TIGR00269  79 DLRRCERCGEPTSGRICKACKFLEEL 104
 
Name Accession Description Interval E-value
CTU1-like cd01713
cytoplasmic tRNA 2-thiolation protein 1 and similar proteins; This subfamily includes human ...
 20-225 1.83e-119

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: 342.65  E-value: 1.83e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  20 FEEEIHQVIVGNRLFKFGERVAIGASGGKDSSVLAYVLSELNRRHSYGLDLFLLSIDEGITGYRDDSLETVKRNEVQYGL 99
Cdd:cd01713    1 IERRVHRTIRKYRLIKPGDRVAVGLSGGKDSTVLLYVLKELNKRHDYGVELIAVTIDEGIKGYRDDSLEAARKLAEEYGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616 100 PLQIVSYKDLYGWTMDE-IVKMIGLKNNCTFCGVFRRQALDRGAALLKVDKLVTGHNADDIAETVVLNILRGDIARLSR- 177
Cdd:cd01713   81 PLEIVSFEDEFGFTLDElIVGKGGKKNACTYCGVFRRRALNRGARELGADKLATGHNLDDEAETILMNLLRGDVARLLRt 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 145337616 178 CTSITTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNA 225
Cdd:cd01713  161 GPEPRSEGEGLVPRIKPLRYIPEKEIVLYAHLNGLPYFSTECPYAPEA 208
TilS COG0037
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 23-256 1.25e-47

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: 160.38  E-value: 1.25e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  23 EIHQVIVGNRLFKFGERVAIGASGGKDSSVLAYVLSELNRRhsYGLDLFLLSIDEGITGYRDDSLETVKRNEVQYGLPLQ 102
Cdd:COG0037    1 KVRKAIRDYRLLEPGDRILVAVSGGKDSLALLHLLAKLRRR--LGFELVAVHVDHGLREESDEDAEFVAELCEELGIPLH 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616 103 IVSYKDLYgwtmdeIVKMIGlKNNCTFCGVFRRQALDRGAALLKVDKLVTGHNADDIAETVVLNILRGD-IARLSrctSI 181
Cdd:COG0037   79 VVRVDVPA------IAKKEG-KSPEAAARRARYGALYELARELGADKIATGHHLDDQAETFLLNLLRGSgLAGLA---GM 148

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 145337616 182 TTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNAYRGFA-CEFINDLERLRPRAILDIIKSGEDFR 256
Cdd:COG0037  149 PPSRGGGVRLIRPLLYVSRKEIEAYAKENGLPWIEDPCNYDPRYTRNRIrHLVLPELEERNPGFKENLARSAENLA 224
TIGR00269 TIGR00269
TIGR00269 family protein; [Hypothetical proteins, Conserved]
 189-290 2.06e-17

TIGR00269 family protein; [Hypothetical proteins, Conserved]


Pssm-ID: 129370 [Multi-domain]  Cd Length: 104  Bit Score: 76.39  E-value: 2.06e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  189 IPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNAYRGFACEFINDLERLRPRAILDIIKSGEdfRIATTTK----MP 264
Cdd:TIGR00269   1 VPRIKPLRYIPEKEVVLYAFLNELKVHLDECPYSSLSVRARIRDFLYDLENKKPGVKFSVLRGFE--KLIPLLKelseQE 78

                          90       100
                  ....*....|....*....|....*.
gi 145337616  265 EQGTCERCGYISSQKWCKACVLLEGL 290
Cdd:TIGR00269  79 DLRRCERCGEPTSGRICKACKFLEEL 104
PRK10696 PRK10696
tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional
 37-207 2.73e-16

tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional


Pssm-ID: 236737 [Multi-domain]  Cd Length: 258  Bit Score: 77.20  E-value: 2.73e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  37 GERVAIGASGGKDSSVLAYVLSELNRRHSYGLDLFLLSIDEGITGYRDDSLETVKRnevQYGLPLQIVsYKDLYGwtmde 116
Cdd:PRK10696  29 GDRVMVCLSGGKDSYTLLDILLNLQKRAPINFELVAVNLDQKQPGFPEHVLPEYLE---SLGVPYHIE-EQDTYS----- 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616 117 IVKMI---GlKNNCTFCGVFRRQALDRGAALLKVDKLVTGHNADDIAETVVLNILRGdiARLSRCTSITTGEDGPIPRCK 193
Cdd:PRK10696 100 IVKEKipeG-KTTCSLCSRLRRGILYRTARELGATKIALGHHRDDILETLFLNMFYG--GKLKAMPPKLLSDDGKHIVIR 176

                        170
                 ....*....|....
gi 145337616 194 PFKYTYEKEIVMYA 207
Cdd:PRK10696 177 PLAYVAEKDIIKFA 190
lysidine_TilS_N TIGR02432
tRNA(Ile)-lysidine synthetase, N-terminal domain; The only examples in which the wobble ...
 39-215 2.76e-16

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: 75.75  E-value: 2.76e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616   39 RVAIGASGGKDSSVLAYVLSELNRRhsYGLDLFLLSIDEGItgyRDDSLET---VKRNEVQYGLPLQIVSYKdlygWTMD 115
Cdd:TIGR02432   1 RILVAVSGGVDSMALLHLLLKLQPK--IKIKLIAAHVDHGL---RPESDEEaefVQQFCRKLNIPLEIKKVD----VKAL 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  116 EIVKMIGLKNNCTFcgvFRRQALDRGAALLKVDKLVTGHNADDIAETVVLNILRG-DIARLSRCTSITT-GEDGPIPRck 193
Cdd:TIGR02432  72 AKGKKKNLEEAARE---ARYDFFEEIAKKHGADYILTAHHADDQAETILMRLLRGsGLRGLSGMKPIRIlGSGIQIIR-- 146

                         170       180
                  ....*....|....*....|..
gi 145337616  194 PFKYTYEKEIVMYAYFKKLDYF 215
Cdd:TIGR02432 147 PLLGISKSEIEEYLKENGLPWF 168
zn-ribbon_14 pfam16503
Zinc-ribbon; This is a family of zinc-ribbons largely from eukaryotes that lie at the ...
 267-298 5.02e-15

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: 67.96  E-value: 5.02e-15
                          10        20        30
                  ....*....|....*....|....*....|..
gi 145337616  267 GTCERCGYISSQKWCKACVLLEGLNRGLPKMG 298
Cdd:pfam16503   1 GRCERCGYISSQKICKACVLLEGLNKGRPKIA 32
ATP_bind_3 pfam01171
PP-loop family; This family of proteins belongs to the PP-loop superfamily.
 42-215 5.15e-14

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


Pssm-ID: 426097 [Multi-domain]  Cd Length: 178  Bit Score: 69.19  E-value: 5.15e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616   42 IGASGGKDSSVLAYVLSELNRrhSYGLDLFLLSIDEGITGYRDDSLETVKRNEVQYGLPLQI--VSYKDLYGWTMDEIVK 119
Cdd:pfam01171   1 VAVSGGPDSMALLYLLAKLKI--KLGIELTAAHVNHGLREESDREAEHVQALCRQLGIPLEIlrVDVAKKSGENLEAAAR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  120 MiglknnctfcgvFRRQALDRGAALLKVDKLVTGHNADDIAETVVLNILRGD-IARLSRCTSITTGEDGPIPRckPFKYT 198
Cdd:pfam01171  79 E------------ARYDFFEEALKKHGADVLLTAHHLDDQLETFLMRLKRGSgLAGLAGIPPVREFAGGRIIR--PLLKV 144

                         170
                  ....*....|....*..
gi 145337616  199 YEKEIVMYAYFKKLDYF 215
Cdd:pfam01171 145 SKAEIEAYAKEHKIPWF 161
 
Name Accession Description Interval E-value
CTU1-like cd01713
cytoplasmic tRNA 2-thiolation protein 1 and similar proteins; This subfamily includes human ...
 20-225 1.83e-119

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: 342.65  E-value: 1.83e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  20 FEEEIHQVIVGNRLFKFGERVAIGASGGKDSSVLAYVLSELNRRHSYGLDLFLLSIDEGITGYRDDSLETVKRNEVQYGL 99
Cdd:cd01713    1 IERRVHRTIRKYRLIKPGDRVAVGLSGGKDSTVLLYVLKELNKRHDYGVELIAVTIDEGIKGYRDDSLEAARKLAEEYGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616 100 PLQIVSYKDLYGWTMDE-IVKMIGLKNNCTFCGVFRRQALDRGAALLKVDKLVTGHNADDIAETVVLNILRGDIARLSR- 177
Cdd:cd01713   81 PLEIVSFEDEFGFTLDElIVGKGGKKNACTYCGVFRRRALNRGARELGADKLATGHNLDDEAETILMNLLRGDVARLLRt 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 145337616 178 CTSITTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNA 225
Cdd:cd01713  161 GPEPRSEGEGLVPRIKPLRYIPEKEIVLYAHLNGLPYFSTECPYAPEA 208
TilS COG0037
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 23-256 1.25e-47

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: 160.38  E-value: 1.25e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  23 EIHQVIVGNRLFKFGERVAIGASGGKDSSVLAYVLSELNRRhsYGLDLFLLSIDEGITGYRDDSLETVKRNEVQYGLPLQ 102
Cdd:COG0037    1 KVRKAIRDYRLLEPGDRILVAVSGGKDSLALLHLLAKLRRR--LGFELVAVHVDHGLREESDEDAEFVAELCEELGIPLH 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616 103 IVSYKDLYgwtmdeIVKMIGlKNNCTFCGVFRRQALDRGAALLKVDKLVTGHNADDIAETVVLNILRGD-IARLSrctSI 181
Cdd:COG0037   79 VVRVDVPA------IAKKEG-KSPEAAARRARYGALYELARELGADKIATGHHLDDQAETFLLNLLRGSgLAGLA---GM 148

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 145337616 182 TTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNAYRGFA-CEFINDLERLRPRAILDIIKSGEDFR 256
Cdd:COG0037  149 PPSRGGGVRLIRPLLYVSRKEIEAYAKENGLPWIEDPCNYDPRYTRNRIrHLVLPELEERNPGFKENLARSAENLA 224
TtuA-like cd01993
tRNA-5-methyluridine(54) 2-sulfurtransferase and similar proteins; tRNA-5-methyluridine(54) ...
 31-225 5.12e-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: 154.79  E-value: 5.12e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  31 NRLFKFGERVAIGASGGKDSSVLAYVLSELnrrhsyGLDLFLLSIDEGITGYRDDSLETVKRNEVQYGLPLQIVSYKDLY 110
Cdd:cd01993    2 YKMFEKDDKILVAVSGGKDSLALLAVLKKL------GYNVEALYINLGIGEYSEKSEEVVKKLAEKLNLPLHVVDLKEEY 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616 111 GWTMDEIVKMIGlKNNCTFCGVFRRQALDRGAALLKVDKLVTGHNADDIAETVVLNILRGDIARLSRCTSIT-TGEDGPI 189
Cdd:cd01993   76 GLGIPELAKKSR-RPPCSVCGLVKRYIMNKFAVENGFDVVATGHNLDDEAAFLLGNILNWNEEYLAKQGPFLlPEHGGLV 154

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 145337616 190 PRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNA 225
Cdd:cd01993  155 TRVKPLYEITEEEIALYALLNGIPYLEEECPYAEGA 190
TtcA-like cd24138
tRNA-cytidine(32) 2-sulfurtransferase and similar proteins; tRNA-cytidine(32) ...
 32-222 1.86e-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: 108.52  E-value: 1.86e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  32 RLFKFGERVAIGASGGKDSSVLAYVLSELNRRHSYGLDLFLLSIDEGITGYRDDSlETVKRNEVQYGLPLQIVSYKDLyg 111
Cdd:cd24138    3 KMIEPGDRILVGLSGGKDSLTLLHLLEELKRRAPIKFELVAVTVDPGYPGYRPPR-EELAEILEELGEILEDEESEII-- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616 112 wtmdEIVKMIGLKNNCTFCGVFRRQALDRGAALLKVDKLVTGHNADDIAETVVLNILRGdiARLSRCTSITTGEDGPIPR 191
Cdd:cd24138   80 ----IIEKEREEKSPCSLCSRLRRGILYSLAKELGCNKLALGHHLDDAVETLLMNLLYG--GRLKTMPPKVTMDRGGLTV 153

                        170       180       190
                 ....*....|....*....|....*....|.
gi 145337616 192 CKPFKYTYEKEIVMYAYFKKLDYFSTECIYS 222
Cdd:cd24138  154 IRPLIYVREKDIRAFAEENGLPKIECPCPYC 184
TIGR00269 TIGR00269
TIGR00269 family protein; [Hypothetical proteins, Conserved]
 189-290 2.06e-17

TIGR00269 family protein; [Hypothetical proteins, Conserved]


Pssm-ID: 129370 [Multi-domain]  Cd Length: 104  Bit Score: 76.39  E-value: 2.06e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  189 IPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNAYRGFACEFINDLERLRPRAILDIIKSGEdfRIATTTK----MP 264
Cdd:TIGR00269   1 VPRIKPLRYIPEKEVVLYAFLNELKVHLDECPYSSLSVRARIRDFLYDLENKKPGVKFSVLRGFE--KLIPLLKelseQE 78

                          90       100
                  ....*....|....*....|....*.
gi 145337616  265 EQGTCERCGYISSQKWCKACVLLEGL 290
Cdd:TIGR00269  79 DLRRCERCGEPTSGRICKACKFLEEL 104
TilS_N cd01992
N-terminal domain of tRNA(Ile)-lysidine synthase and similar proteins; tRNA(Ile)-lysidine ...
 39-227 5.88e-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: 77.63  E-value: 5.88e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  39 RVAIGASGGKDSSVLAYVLSELNRRhsYGLDLFLLSIDEGItgyRDDSLE---TVKRNEVQYGLPLQIVSYKDLYGWTMD 115
Cdd:cd01992    1 KILVAVSGGPDSMALLHLLKELRPK--LGLKLVAVHVDHGL---REESAEeaqFVAKLCKKLGIPLHILTVTEAPKSGGN 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616 116 ------EIvkmiglknnctfcgvfRRQALDRGAALLKVDKLVTGHNADDIAETVVLNILRG-DIARLSRCTSITTGEDGP 188
Cdd:cd01992   76 leaaarEA----------------RYAFLERAAKEHGIDVLLTAHHLDDQAETVLMRLLRGsGLSGLAGMAARSKAGGIR 139

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 145337616 189 IprCKPFKYTYEKEIVMYAYFKKLDYF----STECIYSPNAYR 227
Cdd:cd01992  140 L--IRPLLGISKAELLAYCRENGLPWVedpsNADLKYTRNRIR 180
PRK10696 PRK10696
tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional
 37-207 2.73e-16

tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional


Pssm-ID: 236737 [Multi-domain]  Cd Length: 258  Bit Score: 77.20  E-value: 2.73e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  37 GERVAIGASGGKDSSVLAYVLSELNRRHSYGLDLFLLSIDEGITGYRDDSLETVKRnevQYGLPLQIVsYKDLYGwtmde 116
Cdd:PRK10696  29 GDRVMVCLSGGKDSYTLLDILLNLQKRAPINFELVAVNLDQKQPGFPEHVLPEYLE---SLGVPYHIE-EQDTYS----- 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616 117 IVKMI---GlKNNCTFCGVFRRQALDRGAALLKVDKLVTGHNADDIAETVVLNILRGdiARLSRCTSITTGEDGPIPRCK 193
Cdd:PRK10696 100 IVKEKipeG-KTTCSLCSRLRRGILYRTARELGATKIALGHHRDDILETLFLNMFYG--GKLKAMPPKLLSDDGKHIVIR 176

                        170
                 ....*....|....
gi 145337616 194 PFKYTYEKEIVMYA 207
Cdd:PRK10696 177 PLAYVAEKDIIKFA 190
lysidine_TilS_N TIGR02432
tRNA(Ile)-lysidine synthetase, N-terminal domain; The only examples in which the wobble ...
 39-215 2.76e-16

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: 75.75  E-value: 2.76e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616   39 RVAIGASGGKDSSVLAYVLSELNRRhsYGLDLFLLSIDEGItgyRDDSLET---VKRNEVQYGLPLQIVSYKdlygWTMD 115
Cdd:TIGR02432   1 RILVAVSGGVDSMALLHLLLKLQPK--IKIKLIAAHVDHGL---RPESDEEaefVQQFCRKLNIPLEIKKVD----VKAL 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  116 EIVKMIGLKNNCTFcgvFRRQALDRGAALLKVDKLVTGHNADDIAETVVLNILRG-DIARLSRCTSITT-GEDGPIPRck 193
Cdd:TIGR02432  72 AKGKKKNLEEAARE---ARYDFFEEIAKKHGADYILTAHHADDQAETILMRLLRGsGLRGLSGMKPIRIlGSGIQIIR-- 146

                         170       180
                  ....*....|....*....|..
gi 145337616  194 PFKYTYEKEIVMYAYFKKLDYF 215
Cdd:TIGR02432 147 PLLGISKSEIEEYLKENGLPWF 168
zn-ribbon_14 pfam16503
Zinc-ribbon; This is a family of zinc-ribbons largely from eukaryotes that lie at the ...
 267-298 5.02e-15

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: 67.96  E-value: 5.02e-15
                          10        20        30
                  ....*....|....*....|....*....|..
gi 145337616  267 GTCERCGYISSQKWCKACVLLEGLNRGLPKMG 298
Cdd:pfam16503   1 GRCERCGYISSQKICKACVLLEGLNKGRPKIA 32
ATP_bind_3 pfam01171
PP-loop family; This family of proteins belongs to the PP-loop superfamily.
 42-215 5.15e-14

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


Pssm-ID: 426097 [Multi-domain]  Cd Length: 178  Bit Score: 69.19  E-value: 5.15e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616   42 IGASGGKDSSVLAYVLSELNRrhSYGLDLFLLSIDEGITGYRDDSLETVKRNEVQYGLPLQI--VSYKDLYGWTMDEIVK 119
Cdd:pfam01171   1 VAVSGGPDSMALLYLLAKLKI--KLGIELTAAHVNHGLREESDREAEHVQALCRQLGIPLEIlrVDVAKKSGENLEAAAR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  120 MiglknnctfcgvFRRQALDRGAALLKVDKLVTGHNADDIAETVVLNILRGD-IARLSRCTSITTGEDGPIPRckPFKYT 198
Cdd:pfam01171  79 E------------ARYDFFEEALKKHGADVLLTAHHLDDQLETFLMRLKRGSgLAGLAGIPPVREFAGGRIIR--PLLKV 144

                         170
                  ....*....|....*..
gi 145337616  199 YEKEIVMYAYFKKLDYF 215
Cdd:pfam01171 145 SKAEIEAYAKEHKIPWF 161
tRNA_Me_trans pfam03054
tRNA methyl transferase HUP domain; This family represents the N-terminal HUP domain in tRNA ...
 38-156 6.32e-05

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: 43.40  E-value: 6.32e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616   38 ERVAIGASGGKDSSVLAYVLselnrrHSYGLD---LFL------LSIDEGITGYRDDSLETVKRNEVQYGLPLQIVSYKD 108
Cdd:pfam03054   1 MKVVVAMSGGVDSSVAAYLL------KEQGHNvigVFMknwdeeQSLDEEGKCCSEEDLADAQRVCEQLGIPLYVVNFEK 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 145337616  109 LYgW------TMDEIVKmiGLK-NNCTFC------GVFRRQALDRgaalLKVDKLVTGHNA 156
Cdd:pfam03054  75 EY-WedvfepFLDEYKN--GRTpNPDVLCnkeikfGALLDYALEN----LGADYVATGHYA 128
CysD COG0175
3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase or ...
 35-105 9.55e-05

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: 42.91  E-value: 9.55e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 145337616  35 KFGERVAIGASGGKDSSVLAYVLSELNrrhsygLDLFLLSIDegiTGYR-DDSLETVKRNEVQYGLPLQIVS 105
Cdd:COG0175   31 EFGGRVVVSSSGGKDSTVLLHLAAKFK------PPIPVLFLD---TGYEfPETYEFRDRLAERLGLDLIVVR 93
MnmA_TRMU-like cd01998
MnmA/TRMU family 2-thiouridylases and similar proteins; This family is composed of bacterial ...
 39-154 6.90e-04

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: 40.95  E-value: 6.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  39 RVAIGASGGKDSSVLAYVLSElnrrhsYGLD---LFLLSIDEGITGYR----DDSLETVKRNEVQYGLPLQIVSYKDLYg 111
Cdd:cd01998    1 KVAVAMSGGVDSSVAAALLKE------QGYDvigVFMKNWDDEDNEKGgccsEEDIEDARRVADQLGIPLYVVDFSEEY- 73

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 145337616 112 WtmDEIVK-MI-----GLKNN-CTFC------GVFRRQALDRGAallkvDKLVTGH 154
Cdd:cd01998   74 W--ERVFDpFLeeykaGRTPNpDVLCnreikfGALLDAAKKLGA-----DYIATGH 122
MnmA COG0482
tRNA U34 2-thiouridine synthase MnmA/TrmU, contains the PP-loop ATPase domain [Translation, ...
 39-154 2.02e-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: 39.65  E-value: 2.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  39 RVAIGASGGKDSSVLAYVLSELnrrhsyGLD---LFL-LSIDEGITGYRD----DSLETVKRNEVQYGLPLQIVSYKDLY 110
Cdd:COG0482    2 RVVVGMSGGVDSSVAAALLKEQ------GYEvigVTMkLWDDDDASGSGGccslEDIEDARRVADKLGIPHYVVDFEEEF 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 145337616 111 GwtmDEIVK-MIG--LK----NNCTFC------GVFRRQALDRGAallkvDKLVTGH 154
Cdd:COG0482   76 K---DRVIDyFLDeyLAgrtpNPCVLCnreikfGALLEKALELGA-----DYIATGH 124
PAPS_reductase-like_YbdN cd23947
uncharacterized phosphoadenosine phosphosulfate reductase-like proteins, similar to ...
 32-119 4.62e-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: 37.75  E-value: 4.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145337616  32 RLFKFGERVAIGASGGKDSSVLAY-VLSELNRRHSyglDLFLLSIDegiTGYR-DDSLETVKRNEVQYGLPLQIVSYKDL 109
Cdd:cd23947    7 KVFEEFDPVIVSFSGGKDSLVLLHlALEALRRLRK---DVYVVFID---TGIEfPETIDFVEKLAETLGLDVEAARPPLF 80

                         90
                 ....*....|
gi 145337616 110 YGWTMDEIVK 119
Cdd:cd23947   81 LEWLTSNFQP 90
 
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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