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Conserved domains on  [gi|1039009589|gb|ANM59617|]
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2-thiocytidine tRNA biosynthesis protein, TtcA [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AANH_superfamily super family cl00292
Adenine nucleotide alpha hydrolase (AANH) superfamily; The adenine nucleotide alpha hydrolase ...
 10-99 1.42e-45

Adenine nucleotide alpha hydrolase (AANH) superfamily; The adenine nucleotide alpha hydrolase (AANH) superfamily includes N-type ATP PPases, ATP sulfurylases, universal stress response proteins (USPs), and electron transfer flavoproteins (ETFs). The domain forms an alpha/beta/alpha fold which binds to adenosine nucleotide.


The actual alignment was detected with superfamily member cd01713:

Pssm-ID: 469708  Cd Length: 208  Bit Score: 149.66  E-value: 1.42e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039009589  10 KALDRGAALLKVDKLVTGHNADDIAETVVLNILRGDIARLSR-CTSITTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDY 88
Cdd:cd01713   118 RALNRGARELGADKLATGHNLDDEAETILMNLLRGDVARLLRtGPEPRSEGEGLVPRIKPLRYIPEKEIVLYAHLNGLPY 197

                          90
                  ....*....|.
gi 1039009589  89 FSTECIYSPNA 99
Cdd:cd01713   198 FSTECPYAPEA 208
TIGR00269 super family cl42867
TIGR00269 family protein; [Hypothetical proteins, Conserved]
 63-164 9.61e-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: 74.85  E-value: 9.61e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039009589  63 IPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNAYRGFACEFINDLERLRPRAILDIIKSGEDFRIATTTKMP--EQ 140
Cdd:TIGR00269   1 VPRIKPLRYIPEKEVVLYAFLNELKVHLDECPYSSLSVRARIRDFLYDLENKKPGVKFSVLRGFEKLIPLLKELSEqeDL 80

                          90       100
                  ....*....|....*....|....
gi 1039009589 141 GTCERCGYISSQKWCKACVLLEGL 164
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 ...
 10-99 1.42e-45

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: 149.66  E-value: 1.42e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039009589  10 KALDRGAALLKVDKLVTGHNADDIAETVVLNILRGDIARLSR-CTSITTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDY 88
Cdd:cd01713   118 RALNRGARELGADKLATGHNLDDEAETILMNLLRGDVARLLRtGPEPRSEGEGLVPRIKPLRYIPEKEIVLYAHLNGLPY 197

                          90
                  ....*....|.
gi 1039009589  89 FSTECIYSPNA 99
Cdd:cd01713   198 FSTECPYAPEA 208
TilS COG0037
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 10-130 2.54e-19

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: 82.57  E-value: 2.54e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039009589  10 KALDRGAALLKVDKLVTGHNADDIAETVVLNILRGD-IARLSrctSITTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDY 88
Cdd:COG0037   105 GALYELARELGADKIATGHHLDDQAETFLLNLLRGSgLAGLA---GMPPSRGGGVRLIRPLLYVSRKEIEAYAKENGLPW 181

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1039009589  89 FSTECIYSPNAYRGFA-CEFINDLERLRPRAILDIIKSGEDFR 130
Cdd:COG0037   182 IEDPCNYDPRYTRNRIrHLVLPELEERNPGFKENLARSAENLA 224
TIGR00269 TIGR00269
TIGR00269 family protein; [Hypothetical proteins, Conserved]
 63-164 9.61e-18

TIGR00269 family protein; [Hypothetical proteins, Conserved]


Pssm-ID: 129370 [Multi-domain]  Cd Length: 104  Bit Score: 74.85  E-value: 9.61e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039009589  63 IPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNAYRGFACEFINDLERLRPRAILDIIKSGEDFRIATTTKMP--EQ 140
Cdd:TIGR00269   1 VPRIKPLRYIPEKEVVLYAFLNELKVHLDECPYSSLSVRARIRDFLYDLENKKPGVKFSVLRGFEKLIPLLKELSEqeDL 80

                          90       100
                  ....*....|....*....|....
gi 1039009589 141 GTCERCGYISSQKWCKACVLLEGL 164
Cdd:TIGR00269  81 RRCERCGEPTSGRICKACKFLEEL 104
zn-ribbon_14 pfam16503
Zinc-ribbon; This is a family of zinc-ribbons largely from eukaryotes that lie at the ...
 141-172 9.39e-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: 65.26  E-value: 9.39e-15
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1039009589 141 GTCERCGYISSQKWCKACVLLEGLNRGLPKMG 172
Cdd:pfam16503   1 GRCERCGYISSQKICKACVLLEGLNKGRPKIA 32
lysidine_TilS_N TIGR02432
tRNA(Ile)-lysidine synthetase, N-terminal domain; The only examples in which the wobble ...
 10-89 8.47e-08

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: 50.32  E-value: 8.47e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039009589  10 KALDRGAALLKVDKLVTGHNADDIAETVVLNILRG-DIARLSRCTSITT-GEDGPIPRckPFKYTYEKEIVMYAYFKKLD 87
Cdd:TIGR02432  89 DFFEEIAKKHGADYILTAHHADDQAETILMRLLRGsGLRGLSGMKPIRIlGSGIQIIR--PLLGISKSEIEEYLKENGLP 166


                  ..
gi 1039009589  88 YF 89
Cdd:TIGR02432 167 WF 168
ATP_bind_3 pfam01171
PP-loop family; This family of proteins belongs to the PP-loop superfamily.
 10-89 6.41e-06

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


Pssm-ID: 426097 [Multi-domain]  Cd Length: 178  Bit Score: 44.93  E-value: 6.41e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039009589  10 KALDRGAALLKVDKLVTGHNADDIAETVVLNILRGD-IARLSRCTSITTGEDGPIPRckPFKYTYEKEIVMYAYFKKLDY 88
Cdd:pfam01171  83 DFFEEALKKHGADVLLTAHHLDDQLETFLMRLKRGSgLAGLAGIPPVREFAGGRIIR--PLLKVSKAEIEAYAKEHKIPW 160


                  .
gi 1039009589  89 F 89
Cdd:pfam01171 161 F 161
 
Name Accession Description Interval E-value
CTU1-like cd01713
cytoplasmic tRNA 2-thiolation protein 1 and similar proteins; This subfamily includes human ...
 10-99 1.42e-45

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: 149.66  E-value: 1.42e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039009589  10 KALDRGAALLKVDKLVTGHNADDIAETVVLNILRGDIARLSR-CTSITTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDY 88
Cdd:cd01713   118 RALNRGARELGADKLATGHNLDDEAETILMNLLRGDVARLLRtGPEPRSEGEGLVPRIKPLRYIPEKEIVLYAHLNGLPY 197

                          90
                  ....*....|.
gi 1039009589  89 FSTECIYSPNA 99
Cdd:cd01713   198 FSTECPYAPEA 208
TilS COG0037
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 10-130 2.54e-19

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: 82.57  E-value: 2.54e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039009589  10 KALDRGAALLKVDKLVTGHNADDIAETVVLNILRGD-IARLSrctSITTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDY 88
Cdd:COG0037   105 GALYELARELGADKIATGHHLDDQAETFLLNLLRGSgLAGLA---GMPPSRGGGVRLIRPLLYVSRKEIEAYAKENGLPW 181

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1039009589  89 FSTECIYSPNAYRGFA-CEFINDLERLRPRAILDIIKSGEDFR 130
Cdd:COG0037   182 IEDPCNYDPRYTRNRIrHLVLPELEERNPGFKENLARSAENLA 224
TtuA-like cd01993
tRNA-5-methyluridine(54) 2-sulfurtransferase and similar proteins; tRNA-5-methyluridine(54) ...
 12-99 5.54e-18

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: 77.75  E-value: 5.54e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039009589  12 LDRGAALLKVDKLVTGHNADDIAETVVLNILRGDIARLSRCTSIT-TGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDYFS 90
Cdd:cd01993   102 MNKFAVENGFDVVATGHNLDDEAAFLLGNILNWNEEYLAKQGPFLlPEHGGLVTRVKPLYEITEEEIALYALLNGIPYLE 181


                  ....*....
gi 1039009589  91 TECIYSPNA 99
Cdd:cd01993   182 EECPYAEGA 190
TIGR00269 TIGR00269
TIGR00269 family protein; [Hypothetical proteins, Conserved]
 63-164 9.61e-18

TIGR00269 family protein; [Hypothetical proteins, Conserved]


Pssm-ID: 129370 [Multi-domain]  Cd Length: 104  Bit Score: 74.85  E-value: 9.61e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039009589  63 IPRCKPFKYTYEKEIVMYAYFKKLDYFSTECIYSPNAYRGFACEFINDLERLRPRAILDIIKSGEDFRIATTTKMP--EQ 140
Cdd:TIGR00269   1 VPRIKPLRYIPEKEVVLYAFLNELKVHLDECPYSSLSVRARIRDFLYDLENKKPGVKFSVLRGFEKLIPLLKELSEqeDL 80

                          90       100
                  ....*....|....*....|....
gi 1039009589 141 GTCERCGYISSQKWCKACVLLEGL 164
Cdd:TIGR00269  81 RRCERCGEPTSGRICKACKFLEEL 104
zn-ribbon_14 pfam16503
Zinc-ribbon; This is a family of zinc-ribbons largely from eukaryotes that lie at the ...
 141-172 9.39e-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: 65.26  E-value: 9.39e-15
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1039009589 141 GTCERCGYISSQKWCKACVLLEGLNRGLPKMG 172
Cdd:pfam16503   1 GRCERCGYISSQKICKACVLLEGLNKGRPKIA 32
TilS_N cd01992
N-terminal domain of tRNA(Ile)-lysidine synthase and similar proteins; tRNA(Ile)-lysidine ...
 10-101 6.87e-08

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: 50.29  E-value: 6.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039009589  10 KALDRGAALLKVDKLVTGHNADDIAETVVLNILRG-DIARLSRCTSITTGEDGPIprCKPFKYTYEKEIVMYAYFKKLDY 88
Cdd:cd01992    86 AFLERAAKEHGIDVLLTAHHLDDQAETVLMRLLRGsGLSGLAGMAARSKAGGIRL--IRPLLGISKAELLAYCRENGLPW 163

                          90
                  ....*....|....*..
gi 1039009589  89 F----STECIYSPNAYR 101
Cdd:cd01992   164 VedpsNADLKYTRNRIR 180
lysidine_TilS_N TIGR02432
tRNA(Ile)-lysidine synthetase, N-terminal domain; The only examples in which the wobble ...
 10-89 8.47e-08

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: 50.32  E-value: 8.47e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039009589  10 KALDRGAALLKVDKLVTGHNADDIAETVVLNILRG-DIARLSRCTSITT-GEDGPIPRckPFKYTYEKEIVMYAYFKKLD 87
Cdd:TIGR02432  89 DFFEEIAKKHGADYILTAHHADDQAETILMRLLRGsGLRGLSGMKPIRIlGSGIQIIR--PLLGISKSEIEEYLKENGLP 166


                  ..
gi 1039009589  88 YF 89
Cdd:TIGR02432 167 WF 168
ATP_bind_3 pfam01171
PP-loop family; This family of proteins belongs to the PP-loop superfamily.
 10-89 6.41e-06

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


Pssm-ID: 426097 [Multi-domain]  Cd Length: 178  Bit Score: 44.93  E-value: 6.41e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039009589  10 KALDRGAALLKVDKLVTGHNADDIAETVVLNILRGD-IARLSRCTSITTGEDGPIPRckPFKYTYEKEIVMYAYFKKLDY 88
Cdd:pfam01171  83 DFFEEALKKHGADVLLTAHHLDDQLETFLMRLKRGSgLAGLAGIPPVREFAGGRIIR--PLLKVSKAEIEAYAKEHKIPW 160


                  .
gi 1039009589  89 F 89
Cdd:pfam01171 161 F 161
TtcA-like cd24138
tRNA-cytidine(32) 2-sulfurtransferase and similar proteins; tRNA-cytidine(32) ...
 11-96 1.51e-05

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: 43.80  E-value: 1.51e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039009589  11 ALDRGAALLKVDKLVTGHNADDIAETVVLNILRGdiARLSRCTSITTGEDGPIPRCKPFKYTYEKEIVMYAYFKKLDYFS 90
Cdd:cd24138   101 ILYSLAKELGCNKLALGHHLDDAVETLLMNLLYG--GRLKTMPPKVTMDRGGLTVIRPLIYVREKDIRAFAEENGLPKIE 178


                  ....*.
gi 1039009589  91 TECIYS 96
Cdd:cd24138   179 CPCPYC 184
 
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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