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Conserved domains on  [gi|746124497|ref|WP_039190021|]
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MULTISPECIES: tRNA lysidine(34) synthetase TilS [Hafnia]

Protein Classification

adenine nucleotide alpha hydrolase family protein( domain architecture ID 188)

AANH (adenine nucleotide alpha hydrolase) family protein

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 ...
 3-439 0e+00

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 PRK10660:

Pssm-ID: 469708 [Multi-domain]  Cd Length: 436  Bit Score: 689.44  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497   3 SSEIQMRIASKLQGRSQLMVAFSGGLDSTVLLHALAQLRMQNfPHLQLRAVHVHHGLSRYADLWVDHCESVCRQWQVPLK 82
Cdd:PRK10660   1 DNMLTLTLNRQLLTSRQILVAFSGGLDSTVLLHLLVQWRTEN-PGVTLRAIHVHHGLSPNADSWVKHCEQVCQQWQVPLV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497  83 VLRVKVDSQRSGVEAAARDARYHAIADEISHHETLLTAQHLDDQCETFLLALKRGSGPTGLSAMASHMPFFSTEQLRPLL 162
Cdd:PRK10660  80 VERVQLDQRGLGIEAAARQARYQAFARTLLPGEVLVTAQHLDDQCETFLLALKRGSGPAGLSAMAEVSPFAGTRLIRPLL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497 163 DISRAQLEEYAANYDLKWVEDDSNQDDRFDRNFLRLRVIPNLRDRWPHFPEAVARSASLCAEQEQLLDELLLESLQSLMS 242
Cdd:PRK10660 160 ARSREELEQYAQAHGLRWIEDDSNQDDRYDRNFLRLRVLPLLQQRWPHFAEATARSAALCAEQEQLLDELLAEDLAHLQT 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497 243 EDDSLNIDGLLPMSEAKRYALLRRWIACFGVMMPTREQLQLLWSEVAMAREDAEPQLQLGKSQIRRYRQHLYLLPPLRSL 322
Cdd:PRK10660 240 PDGTLSIDPLLAMSDARRAAILRRWLAGQGAPMPSRDQLQRIWQEVALAREDAEPCLRLGAFEIRRYQSQLWLIKSVAGQ 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497 323 KEQVIAWDP-RESLSLPDGLGELQLGSrGICVRAPKFDEAVSIRFAAHGTLRIVGRRHSRPIKKIWQEHNIPPWERERTP 401
Cdd:PRK10660 320 SETILPWQTwLQPLELPAGLGSLQLVA-GGDVRPPRADEAVSVRFKAQGLLHIVGRNHGRKLKKIWQELGVPPWLRDRTP 398

                        410       420       430
                 ....*....|....*....|....*....|....*...
gi 746124497 402 MLYYGETLIAALGVFITQNGQAVANEPVWNIHWTKDWM 439
Cdd:PRK10660 399 LLFYGETLIAAAGVFVTQEGQAEEGENGVSLVWQKTLS 436
 
Name Accession Description Interval E-value
tilS PRK10660
tRNA(Ile)-lysidine synthetase; Provisional
 3-439 0e+00

tRNA(Ile)-lysidine synthetase; Provisional


Pssm-ID: 182626 [Multi-domain]  Cd Length: 436  Bit Score: 689.44  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497   3 SSEIQMRIASKLQGRSQLMVAFSGGLDSTVLLHALAQLRMQNfPHLQLRAVHVHHGLSRYADLWVDHCESVCRQWQVPLK 82
Cdd:PRK10660   1 DNMLTLTLNRQLLTSRQILVAFSGGLDSTVLLHLLVQWRTEN-PGVTLRAIHVHHGLSPNADSWVKHCEQVCQQWQVPLV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497  83 VLRVKVDSQRSGVEAAARDARYHAIADEISHHETLLTAQHLDDQCETFLLALKRGSGPTGLSAMASHMPFFSTEQLRPLL 162
Cdd:PRK10660  80 VERVQLDQRGLGIEAAARQARYQAFARTLLPGEVLVTAQHLDDQCETFLLALKRGSGPAGLSAMAEVSPFAGTRLIRPLL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497 163 DISRAQLEEYAANYDLKWVEDDSNQDDRFDRNFLRLRVIPNLRDRWPHFPEAVARSASLCAEQEQLLDELLLESLQSLMS 242
Cdd:PRK10660 160 ARSREELEQYAQAHGLRWIEDDSNQDDRYDRNFLRLRVLPLLQQRWPHFAEATARSAALCAEQEQLLDELLAEDLAHLQT 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497 243 EDDSLNIDGLLPMSEAKRYALLRRWIACFGVMMPTREQLQLLWSEVAMAREDAEPQLQLGKSQIRRYRQHLYLLPPLRSL 322
Cdd:PRK10660 240 PDGTLSIDPLLAMSDARRAAILRRWLAGQGAPMPSRDQLQRIWQEVALAREDAEPCLRLGAFEIRRYQSQLWLIKSVAGQ 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497 323 KEQVIAWDP-RESLSLPDGLGELQLGSrGICVRAPKFDEAVSIRFAAHGTLRIVGRRHSRPIKKIWQEHNIPPWERERTP 401
Cdd:PRK10660 320 SETILPWQTwLQPLELPAGLGSLQLVA-GGDVRPPRADEAVSVRFKAQGLLHIVGRNHGRKLKKIWQELGVPPWLRDRTP 398

                        410       420       430
                 ....*....|....*....|....*....|....*...
gi 746124497 402 MLYYGETLIAALGVFITQNGQAVANEPVWNIHWTKDWM 439
Cdd:PRK10660 399 LLFYGETLIAAAGVFVTQEGQAEEGENGVSLVWQKTLS 436
TilS COG0037
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 14-223 7.70e-79

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: 243.97  E-value: 7.70e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497  14 LQGRSQLMVAFSGGLDSTVLLHALAQLRMQnfPHLQLRAVHVHHGLSRYADLWVDHCESVCRQWQVPLKVLRVKVDS--- 90
Cdd:COG0037   12 LEPGDRILVAVSGGKDSLALLHLLAKLRRR--LGFELVAVHVDHGLREESDEDAEFVAELCEELGIPLHVVRVDVPAiak 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497  91 -QRSGVEAAARDARYHAIADEISHH--ETLLTAQHLDDQCETFLLALKRGSGPTGLSAMASHMPFFsTEQLRPLLDISRA 167
Cdd:COG0037   90 kEGKSPEAAARRARYGALYELARELgaDKIATGHHLDDQAETFLLNLLRGSGLAGLAGMPPSRGGG-VRLIRPLLYVSRK 168

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 746124497 168 QLEEYAANYDLKWVEDDSNQDDRFDRNFLRLRVIPNLRDRWPHFPEAVARSASLCA 223
Cdd:COG0037  169 EIEAYAKENGLPWIEDPCNYDPRYTRNRIRHLVLPELEERNPGFKENLARSAENLA 224
ATP_bind_3 pfam01171
PP-loop family; This family of proteins belongs to the PP-loop superfamily.
 22-197 1.38e-70

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


Pssm-ID: 426097 [Multi-domain]  Cd Length: 178  Bit Score: 220.96  E-value: 1.38e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497   22 VAFSGGLDSTVLLHALAQLRMQNFphLQLRAVHVHHGLSRYADLWVDHCESVCRQWQVPLKVLRVKVDSQR-SGVEAAAR 100
Cdd:pfam01171   1 VAVSGGPDSMALLYLLAKLKIKLG--IELTAAHVNHGLREESDREAEHVQALCRQLGIPLEILRVDVAKKSgENLEAAAR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497  101 DARYHAIADEISHH--ETLLTAQHLDDQCETFLLALKRGSGPTGLSAMASHMPFFSTEQLRPLLDISRAQLEEYAANYDL 178
Cdd:pfam01171  79 EARYDFFEEALKKHgaDVLLTAHHLDDQLETFLMRLKRGSGLAGLAGIPPVREFAGGRIIRPLLKVSKAEIEAYAKEHKI 158

                         170
                  ....*....|....*....
gi 746124497  179 KWVEDDSNQDDRFDRNFLR 197
Cdd:pfam01171 159 PWFEDESNADDKYTRNRIR 177
TilS_N cd01992
N-terminal domain of tRNA(Ile)-lysidine synthase and similar proteins; tRNA(Ile)-lysidine ...
 22-202 1.47e-64

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: 205.52  E-value: 1.47e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497  22 VAFSGGLDSTVLLHALAQLRMQNFphLQLRAVHVHHGLSRYADLWVDHCESVCRQWQVPLKVLRVKVDS-QRSGVEAAAR 100
Cdd:cd01992    4 VAVSGGPDSMALLHLLKELRPKLG--LKLVAVHVDHGLREESAEEAQFVAKLCKKLGIPLHILTVTEAPkSGGNLEAAAR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497 101 DARYHAIADEISHH--ETLLTAQHLDDQCETFLLALKRGSGPTGLSAMASHMPFFSTEQLRPLLDISRAQLEEYAANYDL 178
Cdd:cd01992   82 EARYAFLERAAKEHgiDVLLTAHHLDDQAETVLMRLLRGSGLSGLAGMAARSKAGGIRLIRPLLGISKAELLAYCRENGL 161

                        170       180
                 ....*....|....*....|....
gi 746124497 179 KWVEDDSNQDDRFDRNFLRLRVIP 202
Cdd:cd01992  162 PWVEDPSNADLKYTRNRIRHELLP 185
lysidine_TilS_N TIGR02432
tRNA(Ile)-lysidine synthetase, N-terminal domain; The only examples in which the wobble ...
 19-202 4.36e-62

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: 199.40  E-value: 4.36e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497   19 QLMVAFSGGLDSTVLLHALAQLrmQNFPHLQLRAVHVHHGLSRYADLWVDHCESVCRQWQVPLKVLRVKVDSQ----RSG 94
Cdd:TIGR02432   1 RILVAVSGGVDSMALLHLLLKL--QPKIKIKLIAAHVDHGLRPESDEEAEFVQQFCRKLNIPLEIKKVDVKALakgkKKN 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497   95 VEAAARDARYHAIAD--EISHHETLLTAQHLDDQCETFLLALKRGSGPTGLSAMASHMPFFSTEQL-RPLLDISRAQLEE 171
Cdd:TIGR02432  79 LEEAAREARYDFFEEiaKKHGADYILTAHHADDQAETILMRLLRGSGLRGLSGMKPIRILGSGIQIiRPLLGISKSEIEE 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 746124497  172 YAANYDLKWVEDDSNQDDRFDRNFLRLRVIP 202
Cdd:TIGR02432 159 YLKENGLPWFEDETNQDDKYLRNRIRHELLP 189
TilS_C smart00977
TilS substrate C-terminal domain; This domain is found in the tRNA(Ile) lysidine synthetase ...
 362-429 2.95e-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: 81.46  E-value: 2.95e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 746124497   362 VSIRF-AAHGTLRIVGRRHSRPIKKIWQEHNIPPWERERTPMLYYGETLIAALGVFITQNGQAVANEPV 429
Cdd:smart00977   1 LTVRFrQPGDRLRPLGRGGSKKLKKLFQDAKVPPWERDRIPLLFYGDEIVWVVGLRVDARFKAKETTKR 69
 
Name Accession Description Interval E-value
tilS PRK10660
tRNA(Ile)-lysidine synthetase; Provisional
 3-439 0e+00

tRNA(Ile)-lysidine synthetase; Provisional


Pssm-ID: 182626 [Multi-domain]  Cd Length: 436  Bit Score: 689.44  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497   3 SSEIQMRIASKLQGRSQLMVAFSGGLDSTVLLHALAQLRMQNfPHLQLRAVHVHHGLSRYADLWVDHCESVCRQWQVPLK 82
Cdd:PRK10660   1 DNMLTLTLNRQLLTSRQILVAFSGGLDSTVLLHLLVQWRTEN-PGVTLRAIHVHHGLSPNADSWVKHCEQVCQQWQVPLV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497  83 VLRVKVDSQRSGVEAAARDARYHAIADEISHHETLLTAQHLDDQCETFLLALKRGSGPTGLSAMASHMPFFSTEQLRPLL 162
Cdd:PRK10660  80 VERVQLDQRGLGIEAAARQARYQAFARTLLPGEVLVTAQHLDDQCETFLLALKRGSGPAGLSAMAEVSPFAGTRLIRPLL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497 163 DISRAQLEEYAANYDLKWVEDDSNQDDRFDRNFLRLRVIPNLRDRWPHFPEAVARSASLCAEQEQLLDELLLESLQSLMS 242
Cdd:PRK10660 160 ARSREELEQYAQAHGLRWIEDDSNQDDRYDRNFLRLRVLPLLQQRWPHFAEATARSAALCAEQEQLLDELLAEDLAHLQT 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497 243 EDDSLNIDGLLPMSEAKRYALLRRWIACFGVMMPTREQLQLLWSEVAMAREDAEPQLQLGKSQIRRYRQHLYLLPPLRSL 322
Cdd:PRK10660 240 PDGTLSIDPLLAMSDARRAAILRRWLAGQGAPMPSRDQLQRIWQEVALAREDAEPCLRLGAFEIRRYQSQLWLIKSVAGQ 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497 323 KEQVIAWDP-RESLSLPDGLGELQLGSrGICVRAPKFDEAVSIRFAAHGTLRIVGRRHSRPIKKIWQEHNIPPWERERTP 401
Cdd:PRK10660 320 SETILPWQTwLQPLELPAGLGSLQLVA-GGDVRPPRADEAVSVRFKAQGLLHIVGRNHGRKLKKIWQELGVPPWLRDRTP 398

                        410       420       430
                 ....*....|....*....|....*....|....*...
gi 746124497 402 MLYYGETLIAALGVFITQNGQAVANEPVWNIHWTKDWM 439
Cdd:PRK10660 399 LLFYGETLIAAAGVFVTQEGQAEEGENGVSLVWQKTLS 436
TilS COG0037
tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]; tRNA ...
 14-223 7.70e-79

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: 243.97  E-value: 7.70e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497  14 LQGRSQLMVAFSGGLDSTVLLHALAQLRMQnfPHLQLRAVHVHHGLSRYADLWVDHCESVCRQWQVPLKVLRVKVDS--- 90
Cdd:COG0037   12 LEPGDRILVAVSGGKDSLALLHLLAKLRRR--LGFELVAVHVDHGLREESDEDAEFVAELCEELGIPLHVVRVDVPAiak 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497  91 -QRSGVEAAARDARYHAIADEISHH--ETLLTAQHLDDQCETFLLALKRGSGPTGLSAMASHMPFFsTEQLRPLLDISRA 167
Cdd:COG0037   90 kEGKSPEAAARRARYGALYELARELgaDKIATGHHLDDQAETFLLNLLRGSGLAGLAGMPPSRGGG-VRLIRPLLYVSRK 168

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 746124497 168 QLEEYAANYDLKWVEDDSNQDDRFDRNFLRLRVIPNLRDRWPHFPEAVARSASLCA 223
Cdd:COG0037  169 EIEAYAKENGLPWIEDPCNYDPRYTRNRIRHLVLPELEERNPGFKENLARSAENLA 224
ATP_bind_3 pfam01171
PP-loop family; This family of proteins belongs to the PP-loop superfamily.
 22-197 1.38e-70

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


Pssm-ID: 426097 [Multi-domain]  Cd Length: 178  Bit Score: 220.96  E-value: 1.38e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497   22 VAFSGGLDSTVLLHALAQLRMQNFphLQLRAVHVHHGLSRYADLWVDHCESVCRQWQVPLKVLRVKVDSQR-SGVEAAAR 100
Cdd:pfam01171   1 VAVSGGPDSMALLYLLAKLKIKLG--IELTAAHVNHGLREESDREAEHVQALCRQLGIPLEILRVDVAKKSgENLEAAAR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497  101 DARYHAIADEISHH--ETLLTAQHLDDQCETFLLALKRGSGPTGLSAMASHMPFFSTEQLRPLLDISRAQLEEYAANYDL 178
Cdd:pfam01171  79 EARYDFFEEALKKHgaDVLLTAHHLDDQLETFLMRLKRGSGLAGLAGIPPVREFAGGRIIRPLLKVSKAEIEAYAKEHKI 158

                         170
                  ....*....|....*....
gi 746124497  179 KWVEDDSNQDDRFDRNFLR 197
Cdd:pfam01171 159 PWFEDESNADDKYTRNRIR 177
TilS_N cd01992
N-terminal domain of tRNA(Ile)-lysidine synthase and similar proteins; tRNA(Ile)-lysidine ...
 22-202 1.47e-64

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: 205.52  E-value: 1.47e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497  22 VAFSGGLDSTVLLHALAQLRMQNFphLQLRAVHVHHGLSRYADLWVDHCESVCRQWQVPLKVLRVKVDS-QRSGVEAAAR 100
Cdd:cd01992    4 VAVSGGPDSMALLHLLKELRPKLG--LKLVAVHVDHGLREESAEEAQFVAKLCKKLGIPLHILTVTEAPkSGGNLEAAAR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497 101 DARYHAIADEISHH--ETLLTAQHLDDQCETFLLALKRGSGPTGLSAMASHMPFFSTEQLRPLLDISRAQLEEYAANYDL 178
Cdd:cd01992   82 EARYAFLERAAKEHgiDVLLTAHHLDDQAETVLMRLLRGSGLSGLAGMAARSKAGGIRLIRPLLGISKAELLAYCRENGL 161

                        170       180
                 ....*....|....*....|....
gi 746124497 179 KWVEDDSNQDDRFDRNFLRLRVIP 202
Cdd:cd01992  162 PWVEDPSNADLKYTRNRIRHELLP 185
lysidine_TilS_N TIGR02432
tRNA(Ile)-lysidine synthetase, N-terminal domain; The only examples in which the wobble ...
 19-202 4.36e-62

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: 199.40  E-value: 4.36e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497   19 QLMVAFSGGLDSTVLLHALAQLrmQNFPHLQLRAVHVHHGLSRYADLWVDHCESVCRQWQVPLKVLRVKVDSQ----RSG 94
Cdd:TIGR02432   1 RILVAVSGGVDSMALLHLLLKL--QPKIKIKLIAAHVDHGLRPESDEEAEFVQQFCRKLNIPLEIKKVDVKALakgkKKN 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497   95 VEAAARDARYHAIAD--EISHHETLLTAQHLDDQCETFLLALKRGSGPTGLSAMASHMPFFSTEQL-RPLLDISRAQLEE 171
Cdd:TIGR02432  79 LEEAAREARYDFFEEiaKKHGADYILTAHHADDQAETILMRLLRGSGLRGLSGMKPIRILGSGIQIiRPLLGISKSEIEE 158

                         170       180       190
                  ....*....|....*....|....*....|.
gi 746124497  172 YAANYDLKWVEDDSNQDDRFDRNFLRLRVIP 202
Cdd:TIGR02432 159 YLKENGLPWFEDETNQDDKYLRNRIRHELLP 189
TilS_C pfam11734
TilS substrate C-terminal domain; This domain is found in the tRNA(Ile) lysidine synthetase ...
 362-434 1.02e-22

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


Pssm-ID: 463335 [Multi-domain]  Cd Length: 73  Bit Score: 91.11  E-value: 1.02e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 746124497  362 VSIRF-AAHGTLRIVGRRHSRPIKKIWQEHNIPPWERERTPMLYYGETLIAALGVFITQNGQAVANEPVwNIHW 434
Cdd:pfam11734   1 LSVRFrRGGERLRPAGRGGSRKLKKLFQEAGVPPWLRDRLPLLFYGDQLVAVAGLGVAAGFEAQPGEAG-RLEW 73
TilS_C smart00977
TilS substrate C-terminal domain; This domain is found in the tRNA(Ile) lysidine synthetase ...
 362-429 2.95e-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: 81.46  E-value: 2.95e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 746124497   362 VSIRF-AAHGTLRIVGRRHSRPIKKIWQEHNIPPWERERTPMLYYGETLIAALGVFITQNGQAVANEPV 429
Cdd:smart00977   1 LTVRFrQPGDRLRPLGRGGSKKLKKLFQDAKVPPWERDRIPLLFYGDEIVWVVGLRVDARFKAKETTKR 69
TilS pfam09179
TilS substrate binding domain; This domain is found in the tRNA(Ile) lysidine synthetase (TilS) ...
 249-314 7.02e-17

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


Pssm-ID: 462708  Cd Length: 66  Bit Score: 74.59  E-value: 7.02e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 746124497  249 IDGLLPMSEAKRYALLRRWIACFGVMMPTREQLQLLWSEVAMAREDAEPQLQLGKSQIRRYRQHLY 314
Cdd:pfam09179   1 IAALAALSPARRRRLLRRWLAQLGLPMPSAAHLEEILRQLLLARPDAQPRLQLPDGGVRRYRGRLY 66
TtcA-like cd24138
tRNA-cytidine(32) 2-sulfurtransferase and similar proteins; tRNA-cytidine(32) ...
 17-183 1.90e-14

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: 71.54  E-value: 1.90e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497  17 RSQLMVAFSGGLDSTVLLHALAQLRMQNFPHLQLRAVHVHHGLSRYADLWvDHCESVCrqwqVPLKVLRVKVDSQRSGVE 96
Cdd:cd24138    8 GDRILVGLSGGKDSLTLLHLLEELKRRAPIKFELVAVTVDPGYPGYRPPR-EELAEIL----EELGEILEDEESEIIIIE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497  97 ---------------------AAARDARYHAIAdeishhetllTAQHLDDQCETFLLALKRGSgptGLSAM--ASHMPFF 153
Cdd:cd24138   83 kereekspcslcsrlrrgilySLAKELGCNKLA----------LGHHLDDAVETLLMNLLYGG---RLKTMppKVTMDRG 149

                        170       180       190
                 ....*....|....*....|....*....|
gi 746124497 154 STEQLRPLLDISRAQLEEYAANYDLKWVED 183
Cdd:cd24138  150 GLTVIRPLIYVREKDIRAFAEENGLPKIEC 179
CTU1-like cd01713
cytoplasmic tRNA 2-thiolation protein 1 and similar proteins; This subfamily includes human ...
 21-137 1.29e-11

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: 63.76  E-value: 1.29e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497  21 MVAFSGGLDSTVLLHALAQLRMQNFPHLQLRAVHVHHGLSRYADLWVDHCESVCRQWQVPLKVLR-------------VK 87
Cdd:cd01713   22 AVGLSGGKDSTVLLYVLKELNKRHDYGVELIAVTIDEGIKGYRDDSLEAARKLAEEYGIPLEIVSfedefgftldeliVG 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 746124497  88 VDSQRS-----GV------EAAARdaRYHAiadeishhETLLTAQHLDDQCETFLLALKRG 137
Cdd:cd01713  102 KGGKKNactycGVfrrralNRGAR--ELGA--------DKLATGHNLDDEAETILMNLLRG 152
lysidine_TilS_C TIGR02433
tRNA(Ile)-lysidine synthetase, C-terminal domain; TIGRFAMs model TIGR02432 describes the ...
 362-407 3.21e-11

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: 57.94  E-value: 3.21e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 746124497  362 VSIRFAAHG-TLRIVGRRHSRPIKKIWQEHNIPPWERERTPMLYYGE 407
Cdd:TIGR02433   1 LTVRFRQGGdRIKLLGRKGSKKLKKLFIDAKVPPWLRDRIPLLFYGD 47
AANH-like cd01986
adenine nucleotide alpha hydrolase (AANH)-like proteins; This group of adenine nucleotide ...
 21-77 3.44e-06

adenine nucleotide alpha hydrolase (AANH)-like proteins; This group of adenine nucleotide alpha hydrolase (AANH)-like proteins includes N-type ATP PPases and ATP sulfurylases. The domain forms an alpha/beta/alpha fold which binds to adenosine nucleotide.


Pssm-ID: 467490 [Multi-domain]  Cd Length: 74  Bit Score: 44.75  E-value: 3.44e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 746124497  21 MVAFSGGLDSTVLLHALAQLrmqnFPHLQLRAVHVHHGLSRyadlwVDHCESVCRQW 77
Cdd:cd01986    2 VVGYSGGKDSSVALHLASRL----GRKAEVAVVHIDHGIGF-----KEEAESVASIA 49
TtuA-like cd01993
tRNA-5-methyluridine(54) 2-sulfurtransferase and similar proteins; tRNA-5-methyluridine(54) ...
 21-173 1.58e-04

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: 42.31  E-value: 1.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497  21 MVAFSGGLDSTVLLHALAQLrmqnfpHLQLRAVHVHHGLSRYADLWVDHCESVCRQWQVPLKVLRVKvDSQRSGVEAAAR 100
Cdd:cd01993   12 LVAVSGGKDSLALLAVLKKL------GYNVEALYINLGIGEYSEKSEEVVKKLAEKLNLPLHVVDLK-EEYGLGIPELAK 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497 101 DA------------RY--HAIADEIShHETLLTAQHLDDQCeTFLLA--LKRgsgptGLSAMASHMPFFSTEQ------L 158
Cdd:cd01993   85 KSrrppcsvcglvkRYimNKFAVENG-FDVVATGHNLDDEA-AFLLGniLNW-----NEEYLAKQGPFLLPEHgglvtrV 157

                        170
                 ....*....|....*
gi 746124497 159 RPLLDISRAQLEEYA 173
Cdd:cd01993  158 KPLYEITEEEIALYA 172
CysD COG0175
3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase or ...
 9-103 2.86e-03

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


Pssm-ID: 439945 [Multi-domain]  Cd Length: 232  Bit Score: 39.06  E-value: 2.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 746124497   9 RIASKLQGRsqLMVAFSGGLDSTVLLHALAQLRmqnfphLQLRAVHVHHGL-----SRYADlwvdhceSVCRQWQVPLKV 83
Cdd:COG0175   27 EAAAEFGGR--VVVSSSGGKDSTVLLHLAAKFK------PPIPVLFLDTGYefpetYEFRD-------RLAERLGLDLIV 91

                         90       100
                 ....*....|....*....|....
gi 746124497  84 LRVKVDSQRS----GVEAAARDAR 103
Cdd:COG0175   92 VRPEDAFAEQlaefGPPLFYRDPR 115
COG1606 COG1606
ATP-utilizing enzyme, PP-loop superfamily [General function prediction only];
14-36 8.24e-03

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


Pssm-ID: 441214 [Multi-domain]  Cd Length: 265  Bit Score: 37.78  E-value: 8.24e-03
                         10        20
                 ....*....|....*....|...
gi 746124497  14 LQGRSQLMVAFSGGLDSTVLLHA 36
Cdd:COG1606   12 LKELGSVLVAFSGGVDSTLLAKV 34
 
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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