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Conserved domains on  [gi|938482088|gb|ALJ46319|]
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tRNA(Ile)-lysidine synthase [Bacteroides ovatus]

Protein Classification

tRNA lysidine(34) synthetase( domain architecture ID 10113386)

tRNA lysidine(34) synthetase TilS ligates 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

CATH:  3.40.50.620
EC:  6.3.4.19
Gene Ontology:  GO:0005524|GO:0016879|GO:0006400
PubMed:  18073113|12012333|15894617
SCOP:  3001593|4002775

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TilS COG0037
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 5-233 5.12e-89

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: 269.78  E-value: 5.12e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088   5 RVTKYIEKEHLFSPDDKILVALSGGADSVALLYILH----TAGYHCEAAHCNFHLRGkESDRDELFVRQLCERMEIHLHT 80
Cdd:COG0037    1 KVRKAIRDYRLLEPGDRILVAVSGGKDSLALLHLLAklrrRLGFELVAVHVDHGLRE-ESDEDAEFVAELCEELGIPLHV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  81 IDFNTTQYATEKHISIEMAARELRYQWFEKIRKECQADVVAVAHHQDDSIETILLNLIRGTGITGLLGIRPRNG---TIV 157
Cdd:COG0037   80 VRVDVPAIAKKEGKSPEAAARRARYGALYELARELGADKIATGHHLDDQAETFLLNLLRGSGLAGLAGMPPSRGggvRLI 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 938482088 158 RPLLCINREEIIRYLQNIGQDYVTDSTNLEDEYTRNKIRLNLLPLMQEINPSVKNTLIDTSNYLNDVATIYNKCIE 233
Cdd:COG0037  160 RPLLYVSRKEIEAYAKENGLPWIEDPCNYDPRYTRNRIRHLVLPELEERNPGFKENLARSAENLAEEEDLLDELAE 235
TilS_C smart00977
TilS substrate C-terminal domain; This domain is found in the tRNA(Ile) lysidine synthetase ...
 354-419 3.61e-19

TilS substrate C-terminal domain; This domain is found in the tRNA(Ile) lysidine synthetase (TilS) protein.


:

Pssm-ID: 198045 [Multi-domain]  Cd Length: 69  Bit Score: 81.08  E-value: 3.61e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 938482088   354 RKWQPGDTFIPFGMKGKKKISDYLTDRKFSISQKERQWVLCCGEHIAWLIGERTDNRFRIDETTKR 419
Cdd:smart00977   4 RFRQPGDRLRPLGRGGSKKLKKLFQDAKVPPWERDRIPLLFYGDEIVWVVGLRVDARFKAKETTKR 69
 
Name Accession Description Interval E-value
TilS COG0037
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 5-233 5.12e-89

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: 269.78  E-value: 5.12e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088   5 RVTKYIEKEHLFSPDDKILVALSGGADSVALLYILH----TAGYHCEAAHCNFHLRGkESDRDELFVRQLCERMEIHLHT 80
Cdd:COG0037    1 KVRKAIRDYRLLEPGDRILVAVSGGKDSLALLHLLAklrrRLGFELVAVHVDHGLRE-ESDEDAEFVAELCEELGIPLHV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  81 IDFNTTQYATEKHISIEMAARELRYQWFEKIRKECQADVVAVAHHQDDSIETILLNLIRGTGITGLLGIRPRNG---TIV 157
Cdd:COG0037   80 VRVDVPAIAKKEGKSPEAAARRARYGALYELARELGADKIATGHHLDDQAETFLLNLLRGSGLAGLAGMPPSRGggvRLI 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 938482088 158 RPLLCINREEIIRYLQNIGQDYVTDSTNLEDEYTRNKIRLNLLPLMQEINPSVKNTLIDTSNYLNDVATIYNKCIE 233
Cdd:COG0037  160 RPLLYVSRKEIEAYAKENGLPWIEDPCNYDPRYTRNRIRHLVLPELEERNPGFKENLARSAENLAEEEDLLDELAE 235
lysidine_TilS_N TIGR02432
tRNA(Ile)-lysidine synthetase, N-terminal domain; The only examples in which the wobble ...
 21-201 2.58e-75

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: 232.91  E-value: 2.58e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088   21 KILVALSGGADSVALLYILHTA----GYHCEAAHCNFHLRGkESDRDELFVRQLCERMEIHLHTIDFNTTQYATEKHISI 96
Cdd:TIGR02432   1 RILVAVSGGVDSMALLHLLLKLqpkiKIKLIAAHVDHGLRP-ESDEEAEFVQQFCRKLNIPLEIKKVDVKALAKGKKKNL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088   97 EMAARELRYQWFEKIRKECQADVVAVAHHQDDSIETILLNLIRGTGITGLLGIRPR-----NGTIVRPLLCINREEIIRY 171
Cdd:TIGR02432  80 EEAAREARYDFFEEIAKKHGADYILTAHHADDQAETILMRLLRGSGLRGLSGMKPIrilgsGIQIIRPLLGISKSEIEEY 159

                         170       180       190
                  ....*....|....*....|....*....|
gi 938482088  172 LQNIGQDYVTDSTNLEDEYTRNKIRLNLLP 201
Cdd:TIGR02432 160 LKENGLPWFEDETNQDDKYLRNRIRHELLP 189
TilS_N cd01992
N-terminal domain of tRNA(Ile)-lysidine synthase and similar proteins; tRNA(Ile)-lysidine ...
 21-201 7.20e-74

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: 229.02  E-value: 7.20e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  21 KILVALSGGADSVALLYILHTAGYHCE----AAHCNFHLRgKESDRDELFVRQLCERMEIHLHTIdfnTTQYATEKHISI 96
Cdd:cd01992    1 KILVAVSGGPDSMALLHLLKELRPKLGlklvAVHVDHGLR-EESAEEAQFVAKLCKKLGIPLHIL---TVTEAPKSGGNL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  97 EMAARELRYQWFEKIRKECQADVVAVAHHQDDSIETILLNLIRGTGITGLLGIRPR----NGTIVRPLLCINREEIIRYL 172
Cdd:cd01992   77 EAAAREARYAFLERAAKEHGIDVLLTAHHLDDQAETVLMRLLRGSGLSGLAGMAARskagGIRLIRPLLGISKAELLAYC 156

                        170       180
                 ....*....|....*....|....*....
gi 938482088 173 QNIGQDYVTDSTNLEDEYTRNKIRLNLLP 201
Cdd:cd01992  157 RENGLPWVEDPSNADLKYTRNRIRHELLP 185
ATP_bind_3 pfam01171
PP-loop family; This family of proteins belongs to the PP-loop superfamily.
 24-196 1.05e-56

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


Pssm-ID: 426097 [Multi-domain]  Cd Length: 178  Bit Score: 184.75  E-value: 1.05e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088   24 VALSGGADSVALLYILH---TAGYHC-EAAHCNFHLRgKESDRDELFVRQLCERMEIHLHTIDFNttqYATEKHISIEMA 99
Cdd:pfam01171   1 VAVSGGPDSMALLYLLAklkIKLGIElTAAHVNHGLR-EESDREAEHVQALCRQLGIPLEILRVD---VAKKSGENLEAA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  100 ARELRYQWFEKIRKECQADVVAVAHHQDDSIETILLNLIRGTGITGLLGIRPRN----GTIVRPLLCINREEIIRYLQNI 175
Cdd:pfam01171  77 AREARYDFFEEALKKHGADVLLTAHHLDDQLETFLMRLKRGSGLAGLAGIPPVRefagGRIIRPLLKVSKAEIEAYAKEH 156

                         170       180
                  ....*....|....*....|.
gi 938482088  176 GQDYVTDSTNLEDEYTRNKIR 196
Cdd:pfam01171 157 KIPWFEDESNADDKYTRNRIR 177
tilS PRK10660
tRNA(Ile)-lysidine synthetase; Provisional
 18-205 2.00e-24

tRNA(Ile)-lysidine synthetase; Provisional


Pssm-ID: 182626 [Multi-domain]  Cd Length: 436  Bit Score: 104.70  E-value: 2.00e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  18 PDDKILVALSGGADSVALLYIL-----HTAGYHCEAAHCNFHLrgkeSDRDELFV---RQLCERMEIHLH----TIDfnt 85
Cdd:PRK10660  14 TSRQILVAFSGGLDSTVLLHLLvqwrtENPGVTLRAIHVHHGL----SPNADSWVkhcEQVCQQWQVPLVvervQLD--- 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  86 tqyatEKHISIEMAARELRYQWFEkiRKECQADVVAVAHHQDDSIETILLNLIRGTGITGLLGIRPR---NGT-IVRPLL 161
Cdd:PRK10660  87 -----QRGLGIEAAARQARYQAFA--RTLLPGEVLVTAQHLDDQCETFLLALKRGSGPAGLSAMAEVspfAGTrLIRPLL 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 938482088 162 CINREEIIRYLQNIGQDYVTDSTNLEDEYTRNKIRLNLLPLMQE 205
Cdd:PRK10660 160 ARSREELEQYAQAHGLRWIEDDSNQDDRYDRNFLRLRVLPLLQQ 203
TilS_C smart00977
TilS substrate C-terminal domain; This domain is found in the tRNA(Ile) lysidine synthetase ...
 354-419 3.61e-19

TilS substrate C-terminal domain; This domain is found in the tRNA(Ile) lysidine synthetase (TilS) protein.


Pssm-ID: 198045 [Multi-domain]  Cd Length: 69  Bit Score: 81.08  E-value: 3.61e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 938482088   354 RKWQPGDTFIPFGMKGKKKISDYLTDRKFSISQKERQWVLCCGEHIAWLIGERTDNRFRIDETTKR 419
Cdd:smart00977   4 RFRQPGDRLRPLGRGGSKKLKKLFQDAKVPPWERDRIPLLFYGDEIVWVVGLRVDARFKAKETTKR 69
B3_4 pfam03483
B3/4 domain; This domain is found in tRNA synthetase beta subunits as well as in some non tRNA ...
 339-422 3.13e-05

B3/4 domain; This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins.


Pssm-ID: 427327 [Multi-domain]  Cd Length: 174  Bit Score: 44.08  E-value: 3.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  339 IACFDADKLNGEIHYRKWQPGDTFIPFGMKGKKKISDYLtdrkfsisqkerqwVLCCGE---HIA-WLIGERTdnrfRID 414
Cdd:pfam03483  53 LHAFDLDKIAGDIVVRLAKGGEKFTTLDGKERELDPGDL--------------VIADDDgpvALAgIMGGEES----EVT 114


                  ....*...
gi 938482088  415 ETTKRVVI 422
Cdd:pfam03483 115 EDTTNIFL 122
lysidine_TilS_C TIGR02433
tRNA(Ile)-lysidine synthetase, C-terminal domain; TIGRFAMs model TIGR02432 describes the ...
 351-390 7.85e-04

tRNA(Ile)-lysidine synthetase, C-terminal domain; TIGRFAMs model TIGR02432 describes the family of the N-terminal domain of tRNA(Ile)-lysidine synthetase. This family (TIGR02433) describes a small C-terminal domain of about 50 residues present in about half the members of family TIGR02432,and in no other protein. Characterized examples of tRNA(Ile)-lysidine synthetase from E. coli and Bacillus subtilis both contain this domain. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 274130 [Multi-domain]  Cd Length: 47  Bit Score: 37.14  E-value: 7.85e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 938482088  351 IHYRKWQPGDTFIPFGMKGKKKISDYLTDRKfsISQKERQ 390
Cdd:TIGR02433   1 LTVRFRQGGDRIKLLGRKGSKKLKKLFIDAK--VPPWLRD 38
 
Name Accession Description Interval E-value
TilS COG0037
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 5-233 5.12e-89

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: 269.78  E-value: 5.12e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088   5 RVTKYIEKEHLFSPDDKILVALSGGADSVALLYILH----TAGYHCEAAHCNFHLRGkESDRDELFVRQLCERMEIHLHT 80
Cdd:COG0037    1 KVRKAIRDYRLLEPGDRILVAVSGGKDSLALLHLLAklrrRLGFELVAVHVDHGLRE-ESDEDAEFVAELCEELGIPLHV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  81 IDFNTTQYATEKHISIEMAARELRYQWFEKIRKECQADVVAVAHHQDDSIETILLNLIRGTGITGLLGIRPRNG---TIV 157
Cdd:COG0037   80 VRVDVPAIAKKEGKSPEAAARRARYGALYELARELGADKIATGHHLDDQAETFLLNLLRGSGLAGLAGMPPSRGggvRLI 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 938482088 158 RPLLCINREEIIRYLQNIGQDYVTDSTNLEDEYTRNKIRLNLLPLMQEINPSVKNTLIDTSNYLNDVATIYNKCIE 233
Cdd:COG0037  160 RPLLYVSRKEIEAYAKENGLPWIEDPCNYDPRYTRNRIRHLVLPELEERNPGFKENLARSAENLAEEEDLLDELAE 235
lysidine_TilS_N TIGR02432
tRNA(Ile)-lysidine synthetase, N-terminal domain; The only examples in which the wobble ...
 21-201 2.58e-75

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: 232.91  E-value: 2.58e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088   21 KILVALSGGADSVALLYILHTA----GYHCEAAHCNFHLRGkESDRDELFVRQLCERMEIHLHTIDFNTTQYATEKHISI 96
Cdd:TIGR02432   1 RILVAVSGGVDSMALLHLLLKLqpkiKIKLIAAHVDHGLRP-ESDEEAEFVQQFCRKLNIPLEIKKVDVKALAKGKKKNL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088   97 EMAARELRYQWFEKIRKECQADVVAVAHHQDDSIETILLNLIRGTGITGLLGIRPR-----NGTIVRPLLCINREEIIRY 171
Cdd:TIGR02432  80 EEAAREARYDFFEEIAKKHGADYILTAHHADDQAETILMRLLRGSGLRGLSGMKPIrilgsGIQIIRPLLGISKSEIEEY 159

                         170       180       190
                  ....*....|....*....|....*....|
gi 938482088  172 LQNIGQDYVTDSTNLEDEYTRNKIRLNLLP 201
Cdd:TIGR02432 160 LKENGLPWFEDETNQDDKYLRNRIRHELLP 189
TilS_N cd01992
N-terminal domain of tRNA(Ile)-lysidine synthase and similar proteins; tRNA(Ile)-lysidine ...
 21-201 7.20e-74

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: 229.02  E-value: 7.20e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  21 KILVALSGGADSVALLYILHTAGYHCE----AAHCNFHLRgKESDRDELFVRQLCERMEIHLHTIdfnTTQYATEKHISI 96
Cdd:cd01992    1 KILVAVSGGPDSMALLHLLKELRPKLGlklvAVHVDHGLR-EESAEEAQFVAKLCKKLGIPLHIL---TVTEAPKSGGNL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  97 EMAARELRYQWFEKIRKECQADVVAVAHHQDDSIETILLNLIRGTGITGLLGIRPR----NGTIVRPLLCINREEIIRYL 172
Cdd:cd01992   77 EAAAREARYAFLERAAKEHGIDVLLTAHHLDDQAETVLMRLLRGSGLSGLAGMAARskagGIRLIRPLLGISKAELLAYC 156

                        170       180
                 ....*....|....*....|....*....
gi 938482088 173 QNIGQDYVTDSTNLEDEYTRNKIRLNLLP 201
Cdd:cd01992  157 RENGLPWVEDPSNADLKYTRNRIRHELLP 185
ATP_bind_3 pfam01171
PP-loop family; This family of proteins belongs to the PP-loop superfamily.
 24-196 1.05e-56

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


Pssm-ID: 426097 [Multi-domain]  Cd Length: 178  Bit Score: 184.75  E-value: 1.05e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088   24 VALSGGADSVALLYILH---TAGYHC-EAAHCNFHLRgKESDRDELFVRQLCERMEIHLHTIDFNttqYATEKHISIEMA 99
Cdd:pfam01171   1 VAVSGGPDSMALLYLLAklkIKLGIElTAAHVNHGLR-EESDREAEHVQALCRQLGIPLEILRVD---VAKKSGENLEAA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  100 ARELRYQWFEKIRKECQADVVAVAHHQDDSIETILLNLIRGTGITGLLGIRPRN----GTIVRPLLCINREEIIRYLQNI 175
Cdd:pfam01171  77 AREARYDFFEEALKKHGADVLLTAHHLDDQLETFLMRLKRGSGLAGLAGIPPVRefagGRIIRPLLKVSKAEIEAYAKEH 156

                         170       180
                  ....*....|....*....|.
gi 938482088  176 GQDYVTDSTNLEDEYTRNKIR 196
Cdd:pfam01171 157 KIPWFEDESNADDKYTRNRIR 177
tilS PRK10660
tRNA(Ile)-lysidine synthetase; Provisional
 18-205 2.00e-24

tRNA(Ile)-lysidine synthetase; Provisional


Pssm-ID: 182626 [Multi-domain]  Cd Length: 436  Bit Score: 104.70  E-value: 2.00e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  18 PDDKILVALSGGADSVALLYIL-----HTAGYHCEAAHCNFHLrgkeSDRDELFV---RQLCERMEIHLH----TIDfnt 85
Cdd:PRK10660  14 TSRQILVAFSGGLDSTVLLHLLvqwrtENPGVTLRAIHVHHGL----SPNADSWVkhcEQVCQQWQVPLVvervQLD--- 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  86 tqyatEKHISIEMAARELRYQWFEkiRKECQADVVAVAHHQDDSIETILLNLIRGTGITGLLGIRPR---NGT-IVRPLL 161
Cdd:PRK10660  87 -----QRGLGIEAAARQARYQAFA--RTLLPGEVLVTAQHLDDQCETFLLALKRGSGPAGLSAMAEVspfAGTrLIRPLL 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 938482088 162 CINREEIIRYLQNIGQDYVTDSTNLEDEYTRNKIRLNLLPLMQE 205
Cdd:PRK10660 160 ARSREELEQYAQAHGLRWIEDDSNQDDRYDRNFLRLRVLPLLQQ 203
TtuA-like cd01993
tRNA-5-methyluridine(54) 2-sulfurtransferase and similar proteins; tRNA-5-methyluridine(54) ...
 15-171 1.02e-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: 92.00  E-value: 1.02e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  15 LFSPDDKILVALSGGADSVALLYILHTAGYHCEAAHCNFHLrGKESDRDELFVRQLCERMEIHLHTIDFNTTQYATEKHI 94
Cdd:cd01993    4 MFEKDDKILVAVSGGKDSLALLAVLKKLGYNVEALYINLGI-GEYSEKSEEVVKKLAEKLNLPLHVVDLKEEYGLGIPEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  95 SIEMAAREL-------RYqWFEKIRKECQADVVAVAHHQDDsIETILLNLIRGTGITGLLGIRPRNGTI-------VRPL 160
Cdd:cd01993   83 AKKSRRPPCsvcglvkRY-IMNKFAVENGFDVVATGHNLDD-EAAFLLGNILNWNEEYLAKQGPFLLPEhgglvtrVKPL 160

                        170
                 ....*....|.
gi 938482088 161 LCINREEIIRY 171
Cdd:cd01993  161 YEITEEEIALY 171
TilS_C smart00977
TilS substrate C-terminal domain; This domain is found in the tRNA(Ile) lysidine synthetase ...
 354-419 3.61e-19

TilS substrate C-terminal domain; This domain is found in the tRNA(Ile) lysidine synthetase (TilS) protein.


Pssm-ID: 198045 [Multi-domain]  Cd Length: 69  Bit Score: 81.08  E-value: 3.61e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 938482088   354 RKWQPGDTFIPFGMKGKKKISDYLTDRKFSISQKERQWVLCCGEHIAWLIGERTDNRFRIDETTKR 419
Cdd:smart00977   4 RFRQPGDRLRPLGRGGSKKLKKLFQDAKVPPWERDRIPLLFYGDEIVWVVGLRVDARFKAKETTKR 69
TtcA-like cd24138
tRNA-cytidine(32) 2-sulfurtransferase and similar proteins; tRNA-cytidine(32) ...
 15-176 1.03e-17

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: 80.78  E-value: 1.03e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  15 LFSPDDKILVALSGGADSVALLYILHT----AGYHCE--AAHCNFHLRGKESDRDELfvRQLCERMEIHLHTIDFN-TTQ 87
Cdd:cd24138    4 MIEPGDRILVGLSGGKDSLTLLHLLEElkrrAPIKFElvAVTVDPGYPGYRPPREEL--AEILEELGEILEDEESEiIII 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  88 YATEKHISI-EMAARELRYQWFEKIRKEcQADVVAVAHHQDDSIETILLNLIRGtgiTGLLGIRPR------NGTIVRPL 160
Cdd:cd24138   82 EKEREEKSPcSLCSRLRRGILYSLAKEL-GCNKLALGHHLDDAVETLLMNLLYG---GRLKTMPPKvtmdrgGLTVIRPL 157

                        170
                 ....*....|....*.
gi 938482088 161 LCINREEIIRYLQNIG 176
Cdd:cd24138  158 IYVREKDIRAFAEENG 173
CTU1-like cd01713
cytoplasmic tRNA 2-thiolation protein 1 and similar proteins; This subfamily includes human ...
 2-171 1.79e-16

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: 77.63  E-value: 1.79e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088   2 IQQRVTKYIEKEHLFSPDDKILVALSGGADSVALLYILHTagyhceaahcnfhLRGKESDRDELF--------------- 66
Cdd:cd01713    1 IERRVHRTIRKYRLIKPGDRVAVGLSGGKDSTVLLYVLKE-------------LNKRHDYGVELIavtidegikgyrdds 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  67 ---VRQLCERMEIHLHTIDFNTTQYATEKHISIEMAARE--------LRYQWFEKIRKECQADVVAVAHHQDDSIETILL 135
Cdd:cd01713   68 leaARKLAEEYGIPLEIVSFEDEFGFTLDELIVGKGGKKnactycgvFRRRALNRGARELGADKLATGHNLDDEAETILM 147

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 938482088 136 NLIRG-------TGI---TGLLGIRPRngtiVRPLLCINREEIIRY 171
Cdd:cd01713  148 NLLRGdvarllrTGPeprSEGEGLVPR----IKPLRYIPEKEIVLY 189
MnmA_TRMU-like cd01998
MnmA/TRMU family 2-thiouridylases and similar proteins; This family is composed of bacterial ...
 21-83 2.53e-08

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: 55.20  E-value: 2.53e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  21 KILVALSGGADS-VAlLYILHTAGYHCEAAHCNFHL------RGKESDRDELFVRQLCERMEIHLHTIDF 83
Cdd:cd01998    1 KVAVAMSGGVDSsVA-AALLKEQGYDVIGVFMKNWDdednekGGCCSEEDIEDARRVADQLGIPLYVVDF 69
PRK10696 PRK10696
tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional
 2-174 1.22e-07

tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional


Pssm-ID: 236737 [Multi-domain]  Cd Length: 258  Bit Score: 52.55  E-value: 1.22e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088   2 IQQRVTKYIEKEHLFSPDDKILVALSGGADSVALLYILHT----AGYHCEAAHCNfhLRGKESDRDELFVRQLCERMEIH 77
Cdd:PRK10696  12 LRRQVGQAIADFNMIEEGDRVMVCLSGGKDSYTLLDILLNlqkrAPINFELVAVN--LDQKQPGFPEHVLPEYLESLGVP 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  78 LHTIDFNTTQYATEK------HISIemAAReLRYQWFEKIRKECQADVVAVAHHQDDSIETILLNLIRGTGITG----LL 147
Cdd:PRK10696  90 YHIEEQDTYSIVKEKipegktTCSL--CSR-LRRGILYRTARELGATKIALGHHRDDILETLFLNMFYGGKLKAmppkLL 166

                        170       180
                 ....*....|....*....|....*..
gi 938482088 148 GIRPRNgTIVRPLLCINREEIIRYLQN 174
Cdd:PRK10696 167 SDDGKH-IVIRPLAYVAEKDIIKFAEA 192
tRNA_Me_trans pfam03054
tRNA methyl transferase HUP domain; This family represents the N-terminal HUP domain in tRNA ...
 20-83 2.43e-06

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: 48.02  E-value: 2.43e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 938482088   20 DKILVALSGGADSVALLYILHTAGYHCEAAHCNFHLRGKESD--------RDELFVRQLCERMEIHLHTIDF 83
Cdd:pfam03054   1 MKVVVAMSGGVDSSVAAYLLKEQGHNVIGVFMKNWDEEQSLDeegkccseEDLADAQRVCEQLGIPLYVVNF 72
B3_4 pfam03483
B3/4 domain; This domain is found in tRNA synthetase beta subunits as well as in some non tRNA ...
 339-422 3.13e-05

B3/4 domain; This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins.


Pssm-ID: 427327 [Multi-domain]  Cd Length: 174  Bit Score: 44.08  E-value: 3.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  339 IACFDADKLNGEIHYRKWQPGDTFIPFGMKGKKKISDYLtdrkfsisqkerqwVLCCGE---HIA-WLIGERTdnrfRID 414
Cdd:pfam03483  53 LHAFDLDKIAGDIVVRLAKGGEKFTTLDGKERELDPGDL--------------VIADDDgpvALAgIMGGEES----EVT 114


                  ....*...
gi 938482088  415 ETTKRVVI 422
Cdd:pfam03483 115 EDTTNIFL 122
QueC COG0603
7-cyano-7-deazaguanine synthase (queuosine biosynthesis) [Translation, ribosomal structure and ...
 21-179 4.43e-05

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


Pssm-ID: 440368 [Multi-domain]  Cd Length: 223  Bit Score: 44.38  E-value: 4.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  21 KILVALSGGADSVALLYILHTAGYHCEAAHCNFHLRGKEsdrdELFV-RQLCERMEI-HLHTIDFNT-TQYA----TEKH 93
Cdd:COG0603    4 KAVVLLSGGLDSTTCLAWALARGYEVYALSFDYGQRHRK----ELEAaRRIAKALGVgEHKVIDLDFlGEIGgsalTDDS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088  94 ISIEMAARELRYQ------------------WFEKIrkecQADVVAVAHHQDDSI-------ETI-----LLNLIRGTGI 143
Cdd:COG0603   80 IEVPEGHYAEEGIpstyvpgrnliflsiaaaYAEAL----GAEDIFIGVNATDYSgypdcrpEFIeafnaALNLGTKRPV 155

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 938482088 144 tgllgirprngTIVRPLLCINREEIIRYLQNIGQDY 179
Cdd:COG0603  156 -----------RIHTPLMHLSKAEIVKLGLELGVPY 180
lysidine_TilS_C TIGR02433
tRNA(Ile)-lysidine synthetase, C-terminal domain; TIGRFAMs model TIGR02432 describes the ...
 351-390 7.85e-04

tRNA(Ile)-lysidine synthetase, C-terminal domain; TIGRFAMs model TIGR02432 describes the family of the N-terminal domain of tRNA(Ile)-lysidine synthetase. This family (TIGR02433) describes a small C-terminal domain of about 50 residues present in about half the members of family TIGR02432,and in no other protein. Characterized examples of tRNA(Ile)-lysidine synthetase from E. coli and Bacillus subtilis both contain this domain. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 274130 [Multi-domain]  Cd Length: 47  Bit Score: 37.14  E-value: 7.85e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 938482088  351 IHYRKWQPGDTFIPFGMKGKKKISDYLTDRKfsISQKERQ 390
Cdd:TIGR02433   1 LTVRFRQGGDRIKLLGRKGSKKLKKLFIDAK--VPPWLRD 38
QueC-like cd01995
7-cyano-7-deazaguanine synthase QueC and similar proteins; 7-cyano-7-deazaguanine synthase (EC ...
 21-84 9.12e-04

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


Pssm-ID: 467499 [Multi-domain]  Cd Length: 208  Bit Score: 40.29  E-value: 9.12e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 938482088  21 KILVALSGGADSVALLYILHTAGYHCEAAHcnFHLRGKESDRDELFVRQLCERMEIHLHTIDFN 84
Cdd:cd01995    2 KAVVLLSGGLDSTTLLYWALKEGYEVHALT--FDYGQRHAKEELEAAKLIAKLLGIEHKVIDLS 63
COG1606 COG1606
ATP-utilizing enzyme, PP-loop superfamily [General function prediction only];
7-84 4.62e-03

ATP-utilizing enzyme, PP-loop superfamily [General function prediction only];


Pssm-ID: 441214 [Multi-domain]  Cd Length: 265  Bit Score: 38.55  E-value: 4.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 938482088   7 TKYIEKEHLFSPDDKILVALSGGADSVALLYILH-TAGYHCEAAHCN--FHLRgkeSDRDElfVRQLCERMEIHLHTIDF 83
Cdd:COG1606    3 EKLERLKAILKELGSVLVAFSGGVDSTLLAKVAHdVLGDRVLAVTADspSLPE---RELEE--AKELAKEIGIRHEVIET 77


                 .
gi 938482088  84 N 84
Cdd:COG1606   78 D 78
 
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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