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Conserved domains on  [gi|70608135|ref|NP_001020455|]
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pseudouridylate synthase RPUSD4, mitochondrial [Rattus norvegicus]

Protein Classification

pseudouridine synthase family protein( domain architecture ID 10120734)

pseudouridine synthase family protein may catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
106-329 1.71e-52

Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.


:

Pssm-ID: 211346 [Multi-domain]  Cd Length: 185  Bit Score: 172.52  E-value: 1.71e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135 106 LVVINKPYGLPVHGGPGVQLCiSDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWEKDMAHQVQELFRTRQVEKKY 185
Cdd:cd02869   1 LLVVNKPAGLPVHPGPGHLTG-TLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTY 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135 186 WAITVRVPLPSAGVVDIPImekevagqqqhhkmtlrpsYRMDNGKMVKVRASRDAHVAVTQYQVLSSTPSSALVELQPVT 265
Cdd:cd02869  80 LALVDGKPPEDEGTIDAPL-------------------GRKKRKKRARVVVSEDGKPAITHYKVLERFGNVTLVELQLET 140
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70608135 266 GIKHQLRVHLAFgLDCPILGDHKYSDWNRLAPqklsagtlkklglqqskaRYIPLHLHARQLIL 329
Cdd:cd02869 141 GRTHQIRVHLAS-IGHPIVGDPKYGGKASDSP------------------GLKRLALHAYRLSF 185
 
Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
106-329 1.71e-52

Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.


Pssm-ID: 211346 [Multi-domain]  Cd Length: 185  Bit Score: 172.52  E-value: 1.71e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135 106 LVVINKPYGLPVHGGPGVQLCiSDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWEKDMAHQVQELFRTRQVEKKY 185
Cdd:cd02869   1 LLVVNKPAGLPVHPGPGHLTG-TLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTY 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135 186 WAITVRVPLPSAGVVDIPImekevagqqqhhkmtlrpsYRMDNGKMVKVRASRDAHVAVTQYQVLSSTPSSALVELQPVT 265
Cdd:cd02869  80 LALVDGKPPEDEGTIDAPL-------------------GRKKRKKRARVVVSEDGKPAITHYKVLERFGNVTLVELQLET 140
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70608135 266 GIKHQLRVHLAFgLDCPILGDHKYSDWNRLAPqklsagtlkklglqqskaRYIPLHLHARQLIL 329
Cdd:cd02869 141 GRTHQIRVHLAS-IGHPIVGDPKYGGKASDSP------------------GLKRLALHAYRLSF 185
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
99-355 2.22e-52

Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]; Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440330 [Multi-domain]  Cd Length: 218  Bit Score: 173.40  E-value: 2.22e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135  99 ILHQDKDLVVINKPYGLPVHGGPGVQLciSDVLPILAKMLHGHKAEP-LHLCHRLDKETTGVMVLAWEKDMAHQVQELFR 177
Cdd:COG0564   1 ILYEDEDLLVVNKPAGLVVHPGSGGDD--GTLVNALRAHLGELSGVPrPGLVHRLDRDTSGLLLVAKTRKAARRLSEQFR 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135 178 TRQVEKKYWAITVRVPLPSAGVVDIPIMEKEVagqqqhhkmtlrpsyrmDNGKMVKVRasRDAHVAVTQYQVLSSTPSSA 257
Cdd:COG0564  79 EREVEKRYLALVEGKPKEDEGTIDAPLGRDPK-----------------DRKKMAVVD--EDGKPAVTHYRVLERFGGYS 139
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135 258 LVELQPVTGIKHQLRVHLAFgLDCPILGDHKYSDwnrlapqklsAGTLKKLGLQqskaryiPLHLHARQL--ILPALGsr 335
Cdd:COG0564 140 LVEVRLETGRTHQIRVHLAH-IGHPIVGDPLYGG----------DRSNRLLGLD-------RQALHAYRLgfPHPVTG-- 199
                       250       260
                ....*....|....*....|
gi 70608135 336 tEELLLACKLPHFFARSLRR 355
Cdd:COG0564 200 -EPLEFEAPLPEDFQALLEK 218
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
72-356 5.97e-38

pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 161659 [Multi-domain]  Cd Length: 299  Bit Score: 138.22  E-value: 5.97e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135    72 RVQELVRFTQQLQRVHPN-VLAKELSRRILHQDKDLVVINKPYGLPVHGGPGVQlcISDVLPILAKML-HGHKAEPLHLC 149
Cdd:TIGR00005  46 KVKDGDRITVRVPEEEEHeVPPQDIPLDILFEDEDIIVINKPSGLVVHPGGGNP--FGTVLNALLAHCpPIAGVERVGIV 123
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135   150 HRLDKETTGVMVLAwEKDMAHQV-QELFRTRQVEKKYWAITVRVPLPSAGVVDIPImeKEVAGQQQhhKMTLRPsyrMDN 228
Cdd:TIGR00005 124 HRLDRDTSGLMVVA-KTPLALRElQRQLKNRTVTKEYVALVHGQFDSGGGTVDAPL--GRVPNNRG--LMAVHP---SSE 195
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135   229 GKMvkvrasrdahvAVTQYQVLSSTPSSALVELQPVTGIKHQLRVHLAFgLDCPILGDHKYSDWNRLAPqklSAGTLKKL 308
Cdd:TIGR00005 196 GKP-----------AVTHFRVLERFGNASLVECELETGRTHQIRVHLQY-LGHPLAGDPLYGNKPVPGN---NLNGLLNF 260
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 70608135   309 GLQQskaryipLHLHARQLILPALGsrtEELLLACKLPHFFARSLRRL 356
Cdd:TIGR00005 261 DRQA-------LHAYELGFIHPATG---EILEFEAPLPADLVLLLEAL 298
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
106-276 2.83e-31

RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA.


Pssm-ID: 459961 [Multi-domain]  Cd Length: 151  Bit Score: 115.97  E-value: 2.83e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135   106 LVVINKPYGLPVHGGPGVQLCISDVLPILAKMLHGhkaEPLHLCHRLDKETTGVMVLAWEKDMAHQVQELFRTRQVEKKY 185
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLSLLALLLRRELGV---KRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLFPERKIEKEY 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135   186 WAItVRVPLPSAGVVDIPIMEKEVAGQQQHHKMtlrpsyrmdngkmvkvrasRDAHVAVTQYQVLSSTPSS--ALVELQP 263
Cdd:pfam00849  78 LAL-VDKPEEEEGTIKSPIKKEKNKSPFRKEEE-------------------LGGKKAVTHLKVLKSGSKGdySLLELEL 137
                         170
                  ....*....|...
gi 70608135   264 VTGIKHQLRVHLA 276
Cdd:pfam00849 138 VTGRKHQIRAHLA 150
PRK11112 PRK11112
tRNA pseudouridine synthase C; Provisional
99-325 1.83e-21

tRNA pseudouridine synthase C; Provisional


Pssm-ID: 182971 [Multi-domain]  Cd Length: 257  Bit Score: 92.42  E-value: 1.83e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135   99 ILHQDKDLVVINKPYGLPVHGG-------PGVQLCISD-----VLPIlakmlhghkaeplhlcHRLDKETTGVMVLAWEK 166
Cdd:PRK11112   4 ILYQDEWLVAVNKPAGWLVHRSwldrhetVFVMQTVRDqigqhVFTA----------------HRLDRPTSGVLLMALSS 67
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135  167 DMAHQVQELFRTRQVEKKYWAItVRVPLPSAGVVDIPIMEkevagqqqhhkmtlrpsyRMDNGKMVKVRASRDAHVAVTQ 246
Cdd:PRK11112  68 EVARLLAQQFEQHQIQKTYHAI-VRGWLMEEAVLDYPLKE------------------ELDKIADKFAREDKAPQPAVTH 128
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135  247 YQVLSST---------PSS--ALVELQPVTGIKHQLRVHLAFgLDCPILGDHKYSDW--NRLAPQKLSAGtlkKLGLQQS 313
Cdd:PRK11112 129 YRGLATVempvatgryPTTrySLVELEPKTGRKHQLRRHMAH-LRHPIIGDTKHGDLrqNRSLAEHFGCS---RLMLHAS 204
                        250
                 ....*....|....*...
gi 70608135  314 KARYI------PLHLHAR 325
Cdd:PRK11112 205 ELSLThpftgePLTITAG 222
 
Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
106-329 1.71e-52

Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.


Pssm-ID: 211346 [Multi-domain]  Cd Length: 185  Bit Score: 172.52  E-value: 1.71e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135 106 LVVINKPYGLPVHGGPGVQLCiSDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWEKDMAHQVQELFRTRQVEKKY 185
Cdd:cd02869   1 LLVVNKPAGLPVHPGPGHLTG-TLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTY 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135 186 WAITVRVPLPSAGVVDIPImekevagqqqhhkmtlrpsYRMDNGKMVKVRASRDAHVAVTQYQVLSSTPSSALVELQPVT 265
Cdd:cd02869  80 LALVDGKPPEDEGTIDAPL-------------------GRKKRKKRARVVVSEDGKPAITHYKVLERFGNVTLVELQLET 140
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70608135 266 GIKHQLRVHLAFgLDCPILGDHKYSDWNRLAPqklsagtlkklglqqskaRYIPLHLHARQLIL 329
Cdd:cd02869 141 GRTHQIRVHLAS-IGHPIVGDPKYGGKASDSP------------------GLKRLALHAYRLSF 185
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
99-355 2.22e-52

Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]; Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440330 [Multi-domain]  Cd Length: 218  Bit Score: 173.40  E-value: 2.22e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135  99 ILHQDKDLVVINKPYGLPVHGGPGVQLciSDVLPILAKMLHGHKAEP-LHLCHRLDKETTGVMVLAWEKDMAHQVQELFR 177
Cdd:COG0564   1 ILYEDEDLLVVNKPAGLVVHPGSGGDD--GTLVNALRAHLGELSGVPrPGLVHRLDRDTSGLLLVAKTRKAARRLSEQFR 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135 178 TRQVEKKYWAITVRVPLPSAGVVDIPIMEKEVagqqqhhkmtlrpsyrmDNGKMVKVRasRDAHVAVTQYQVLSSTPSSA 257
Cdd:COG0564  79 EREVEKRYLALVEGKPKEDEGTIDAPLGRDPK-----------------DRKKMAVVD--EDGKPAVTHYRVLERFGGYS 139
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135 258 LVELQPVTGIKHQLRVHLAFgLDCPILGDHKYSDwnrlapqklsAGTLKKLGLQqskaryiPLHLHARQL--ILPALGsr 335
Cdd:COG0564 140 LVEVRLETGRTHQIRVHLAH-IGHPIVGDPLYGG----------DRSNRLLGLD-------RQALHAYRLgfPHPVTG-- 199
                       250       260
                ....*....|....*....|
gi 70608135 336 tEELLLACKLPHFFARSLRR 355
Cdd:COG0564 200 -EPLEFEAPLPEDFQALLEK 218
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
72-356 5.97e-38

pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 161659 [Multi-domain]  Cd Length: 299  Bit Score: 138.22  E-value: 5.97e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135    72 RVQELVRFTQQLQRVHPN-VLAKELSRRILHQDKDLVVINKPYGLPVHGGPGVQlcISDVLPILAKML-HGHKAEPLHLC 149
Cdd:TIGR00005  46 KVKDGDRITVRVPEEEEHeVPPQDIPLDILFEDEDIIVINKPSGLVVHPGGGNP--FGTVLNALLAHCpPIAGVERVGIV 123
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135   150 HRLDKETTGVMVLAwEKDMAHQV-QELFRTRQVEKKYWAITVRVPLPSAGVVDIPImeKEVAGQQQhhKMTLRPsyrMDN 228
Cdd:TIGR00005 124 HRLDRDTSGLMVVA-KTPLALRElQRQLKNRTVTKEYVALVHGQFDSGGGTVDAPL--GRVPNNRG--LMAVHP---SSE 195
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135   229 GKMvkvrasrdahvAVTQYQVLSSTPSSALVELQPVTGIKHQLRVHLAFgLDCPILGDHKYSDWNRLAPqklSAGTLKKL 308
Cdd:TIGR00005 196 GKP-----------AVTHFRVLERFGNASLVECELETGRTHQIRVHLQY-LGHPLAGDPLYGNKPVPGN---NLNGLLNF 260
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 70608135   309 GLQQskaryipLHLHARQLILPALGsrtEELLLACKLPHFFARSLRRL 356
Cdd:TIGR00005 261 DRQA-------LHAYELGFIHPATG---EILEFEAPLPADLVLLLEAL 298
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
106-276 2.83e-31

RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA.


Pssm-ID: 459961 [Multi-domain]  Cd Length: 151  Bit Score: 115.97  E-value: 2.83e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135   106 LVVINKPYGLPVHGGPGVQLCISDVLPILAKMLHGhkaEPLHLCHRLDKETTGVMVLAWEKDMAHQVQELFRTRQVEKKY 185
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLSLLALLLRRELGV---KRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLFPERKIEKEY 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135   186 WAItVRVPLPSAGVVDIPIMEKEVAGQQQHHKMtlrpsyrmdngkmvkvrasRDAHVAVTQYQVLSSTPSS--ALVELQP 263
Cdd:pfam00849  78 LAL-VDKPEEEEGTIKSPIKKEKNKSPFRKEEE-------------------LGGKKAVTHLKVLKSGSKGdySLLELEL 137
                         170
                  ....*....|...
gi 70608135   264 VTGIKHQLRVHLA 276
Cdd:pfam00849 138 VTGRKHQIRAHLA 150
PseudoU_synth_ScRIB2 cd02557
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, ...
83-291 9.65e-27

Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.


Pssm-ID: 211331 [Multi-domain]  Cd Length: 213  Bit Score: 105.79  E-value: 9.65e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135  83 LQRVH---PNVLAKELsrRILHQDKDLVVINKPYGLPVHggPGVQLCISDVLPILAkmlHGHKAEPLHLCHRLDKETTGV 159
Cdd:cd02557   1 SHTVHrhePPVTNDPI--KIVHEDDDLLVVDKPSGIPVH--PTGRYRYNTVTEILK---SEYGLTELRPCHRLDRLTSGL 73
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135 160 MVLAWEKDMAHQVQELFRTRQVEKKYWAitvRV----PlPSAGVVDIPIMEKEVagqqqhhKMTLRPSYRMDngkmvkvr 235
Cdd:cd02557  74 LLFAKTSQTASRLQQQIRSREVKKEYLA---RVkgefP-DGEVVVDQPIGLVSP-------KGGLRNDVDEK-------- 134
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 70608135 236 aSRDAHvavTQYQVLSSTPS--SALVELQPVTGIKHQLRVHLAFgLDCPILGDHKYSD 291
Cdd:cd02557 135 -GKDAR---TIFKRLSYNGDlnTSVVLCKPITGRTHQIRVHLQY-LGHPIVNDPIYNN 187
PseudoU_synth_TruC cd02563
tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific ...
99-291 2.73e-25

tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.


Pssm-ID: 211333 [Multi-domain]  Cd Length: 223  Bit Score: 102.03  E-value: 2.73e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135  99 ILHQDKDLVVINKPYGLPVHGGPGVQLCISDVLPILAKMLHGHkaepLHLCHRLDKETTGVMVLAWEKDMAHQVQELFRT 178
Cdd:cd02563   3 ILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLGQH----VYPVHRLDRPTSGVLLFALSSEVARKLGEQFTE 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135 179 RQVEKKYWAItVRVPLPSAGVVDIPIMEKevagqqqhhkmtlrpsyrMDNGKMVKVRASRDAHVAVTQYQVLSST----- 253
Cdd:cd02563  79 HRVHKTYLAV-VRGYVPESGTIDYPLSEE------------------LDKLADKFASDDKAPQAATTHYRLLAVEelpvv 139
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 70608135 254 ----PSS--ALVELQPVTGIKHQLRVHLAFgLDCPILGDHKYSD 291
Cdd:cd02563 140 vgkyPTSrySLVELTPHTGRKHQLRRHLAH-IRHPIIGDTTHGD 182
PRK11112 PRK11112
tRNA pseudouridine synthase C; Provisional
99-325 1.83e-21

tRNA pseudouridine synthase C; Provisional


Pssm-ID: 182971 [Multi-domain]  Cd Length: 257  Bit Score: 92.42  E-value: 1.83e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135   99 ILHQDKDLVVINKPYGLPVHGG-------PGVQLCISD-----VLPIlakmlhghkaeplhlcHRLDKETTGVMVLAWEK 166
Cdd:PRK11112   4 ILYQDEWLVAVNKPAGWLVHRSwldrhetVFVMQTVRDqigqhVFTA----------------HRLDRPTSGVLLMALSS 67
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135  167 DMAHQVQELFRTRQVEKKYWAItVRVPLPSAGVVDIPIMEkevagqqqhhkmtlrpsyRMDNGKMVKVRASRDAHVAVTQ 246
Cdd:PRK11112  68 EVARLLAQQFEQHQIQKTYHAI-VRGWLMEEAVLDYPLKE------------------ELDKIADKFAREDKAPQPAVTH 128
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135  247 YQVLSST---------PSS--ALVELQPVTGIKHQLRVHLAFgLDCPILGDHKYSDW--NRLAPQKLSAGtlkKLGLQQS 313
Cdd:PRK11112 129 YRGLATVempvatgryPTTrySLVELEPKTGRKHQLRRHMAH-LRHPIIGDTKHGDLrqNRSLAEHFGCS---RLMLHAS 204
                        250
                 ....*....|....*...
gi 70608135  314 KARYI------PLHLHAR 325
Cdd:PRK11112 205 ELSLThpftgePLTITAG 222
PSRA_1 cd02558
Pseudouridine synthase, a subgroup of the RluA family; This group is comprised of bacterial ...
98-289 1.95e-20

Pseudouridine synthase, a subgroup of the RluA family; This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.


Pssm-ID: 211332 [Multi-domain]  Cd Length: 246  Bit Score: 89.25  E-value: 1.95e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135  98 RILHQDKDLVVINKPYGLPVH-GGPGVQLCIsdvlpiLAKMLHGHKAEPLHLCHRLDKETTGVMVLAWEKDMAHQVQELF 176
Cdd:cd02558  40 TILHQDEHLLVADKPHFLPVTpRGRYVTETL------LVRLRRQTGNPDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLF 113
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135 177 RTRQVEKKYWAITVRVPLPSAGVVDIPIMEKEvagqqqhhkmtlRPSYRMDNGkmvkvrasrDAHV-AVTQYQVLSSTPS 255
Cdd:cd02558 114 ARREVSKTYEAVAPYVPALTFPLTVRSRIVKG------------RGFFQAREV---------EGEPnAETRIELLARRGG 172
                       170       180       190
                ....*....|....*....|....*....|....
gi 70608135 256 SALVELQPVTGIKHQLRVHLAfGLDCPILGDHKY 289
Cdd:cd02558 173 WGLYRLSPHTGKTHQLRVHMA-ALGVPILNDPFY 205
PRK11025 PRK11025
23S rRNA pseudouridine(955/2504/2580) synthase RluC;
61-317 3.99e-19

23S rRNA pseudouridine(955/2504/2580) synthase RluC;


Pssm-ID: 182909 [Multi-domain]  Cd Length: 317  Bit Score: 87.09  E-value: 3.99e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135   61 EMRVPtnPVQRRVQELVRFTQQLQRVhpnvlaKELSRRILHQDKDLVVINKPYGLPVHGGPGVQLCISDVLPILAKmlhg 140
Cdd:PRK11025  65 EVRIP--PVRVAEREEEAVSPKLQKV------AALADVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRP---- 132
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135  141 hKAEPLHLCHRLDKETTGVMVLAWEKDMAHQVQELFRTRQVEKKYWAItvrvplpsagvvdipimekeVAGQQQHH-KMT 219
Cdd:PRK11025 133 -EARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL--------------------VRGQWQSHvKVV 191
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135  220 LRPSYR--MDNGKMVkVRASRDAHVAVTQYQVLSSTPSSALVELQPVTGIKHQLRVHLAFGlDCPILGDHKYSDwnRLAP 297
Cdd:PRK11025 192 QAPLLKniLQSGERI-VRVSQEGKPSETRFKVEERYAFATLVRASPVTGRTHQIRVHTQYA-GHPIAFDDRYGD--REFD 267
                        250       260
                 ....*....|....*....|
gi 70608135  298 QKLSAGTLKKLGLQQSKARY 317
Cdd:PRK11025 268 QQLTGTGLNRLFLHAAALKF 287
PseudoU_synth_Rsu_Rlu_like cd02550
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ...
106-276 1.10e-18

Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.


Pssm-ID: 211325 [Multi-domain]  Cd Length: 154  Bit Score: 82.04  E-value: 1.10e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135 106 LVVINKPYGLPVHGGPGvqlcisDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWEKDMAHQVQElfRTRQVEKKY 185
Cdd:cd02550   1 ILVLNKPSGLVCHPTDR------DRDPTVVVRLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTE--PRREIEKEY 72
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135 186 WAiTVRVPLPSAGVVDIPIMEkEVAGQQQHHKmtlrpsyrmdngkmvkvrasrDAHVAVTQYQVLSSTPSSALVELQPVT 265
Cdd:cd02550  73 LV-TVRGELDEEGIEDLATVR-RGRLSGLVDE---------------------GVPLAVTKVRVIGEHGGTGRLRLTLKT 129
                       170
                ....*....|.
gi 70608135 266 GIKHQLRVHLA 276
Cdd:cd02550 130 GRTHQIRRHCA 140
PRK10158 PRK10158
bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;
99-334 8.89e-18

bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;


Pssm-ID: 236659 [Multi-domain]  Cd Length: 219  Bit Score: 81.19  E-value: 8.89e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135   99 ILHQDKDLVVINKPYGLpvHGGPGVQLCISDvlPILAKMLHGH-KAEPLHlchRLDKETTGVMVLAWEKDMAHQVQELFR 177
Cdd:PRK10158  16 ILYQDEHIMVVNKPSGL--LSVPGRLEEHKD--SVMTRIQRDYpQAESVH---RLDMATSGVIVVALTKAAERELKRQFR 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135  178 TRQVEKKYWAITVRVPLPSAGVVDIPIMekevagqqqhHKMTLRPSYRM--DNGKmvkvrasrdahVAVTQYQVLSSTP- 254
Cdd:PRK10158  89 EREPKKQYVARVWGHPSPAEGLVDLPLI----------CDWPNRPKQKVcyETGK-----------PAQTEYEVVEYAAd 147
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135  255 SSALVELQPVTGIKHQLRVHLaFGLDCPILGDHKYSDwnrlapqklsagtlkklglQQSKARYIPLHLHARQLIL--PAL 332
Cdd:PRK10158 148 NTARVVLKPITGRSHQLRVHM-LALGHPILGDRFYAS-------------------PEARAMAPRLLLHAEMLTIthPAY 207

                 ..
gi 70608135  333 GS 334
Cdd:PRK10158 208 GN 209
rluD PRK11180
23S rRNA pseudouridine(1911/1915/1917) synthase RluD;
99-289 1.34e-13

23S rRNA pseudouridine(1911/1915/1917) synthase RluD;


Pssm-ID: 183020 [Multi-domain]  Cd Length: 325  Bit Score: 70.86  E-value: 1.34e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135   99 ILHQDKDLVVINKPYGLPVHGGPGVqlcisdvlP---ILAKMLHGHKAEPL----HLCHRLDKETTGVMVLAweKDMAHQ 171
Cdd:PRK11180  86 IVYEDDDILVINKPRDLVVHPGAGN--------PdgtVLNALLHYYPPIADvpraGIVHRLDKDTTGLMVVA--KTVPAQ 155
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70608135  172 VQ--ELFRTRQVEKKYWAITVRVpLPSAGVVDIPIMEKevAGQQQHhkMTLRPSyrmdnGKmvkvrasrdahVAVTQYQV 249
Cdd:PRK11180 156 TRlvEALQKREITREYEAVAIGH-MTAGGTVDEPISRH--PTKRTH--MAVHPM-----GK-----------PAVTHYRI 214
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 70608135  250 LSSTPSSALVELQPVTGIKHQLRVHLAFgLDCPILGDHKY 289
Cdd:PRK11180 215 MEHFRVHTRLRLRLETGRTHQIRVHMAH-ITHPLVGDQVY 253
 
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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