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Conserved domains on  [gi|498910755|ref|WP_010845980|]
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23S rRNA pseudouridine(2605) synthase RluB [Xenorhabdus nematophila]

Protein Classification

23S rRNA pseudouridine(2605) synthase RluB( domain architecture ID 11484875)

23S rRNA pseudouridine(2605) synthase RluB catalyzes 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
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
4-291 0e+00

23S rRNA pseudouridine(2605) synthase RluB;


:

Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 562.85  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755   4 KTEKLQKILARSGHGSRREIEGYIQQGRISIDGKTATLGDRIEVKPSIKIRLDGRILNIKEPQKTVCRVLAYYKPEGELC 83
Cdd:PRK10700   1 MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELC 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  84 TRHDPEGRPTVFDRLPRMQGARWIAVGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFGEVDTAKLRQLTQGV 163
Cdd:PRK10700  81 TRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755 164 QLEDGPASFKTITFKGGEGINQWYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINLPKGLPRGGWTELGLEQTNYL 243
Cdd:PRK10700 161 QLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYL 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 498910755 244 RQLVGLGDEMVTKVAVERDQRRIKANQIRRAVKRHAKVASRP-AGKRPA 291
Cdd:PRK10700 241 RELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRrSGGRNN 289
 
Name Accession Description Interval E-value
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
4-291 0e+00

23S rRNA pseudouridine(2605) synthase RluB;


Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 562.85  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755   4 KTEKLQKILARSGHGSRREIEGYIQQGRISIDGKTATLGDRIEVKPSIKIRLDGRILNIKEPQKTVCRVLAYYKPEGELC 83
Cdd:PRK10700   1 MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELC 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  84 TRHDPEGRPTVFDRLPRMQGARWIAVGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFGEVDTAKLRQLTQGV 163
Cdd:PRK10700  81 TRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755 164 QLEDGPASFKTITFKGGEGINQWYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINLPKGLPRGGWTELGLEQTNYL 243
Cdd:PRK10700 161 QLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYL 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 498910755 244 RQLVGLGDEMVTKVAVERDQRRIKANQIRRAVKRHAKVASRP-AGKRPA 291
Cdd:PRK10700 241 RELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRrSGGRNN 289
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 4-235 4.43e-106

Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ribosomal structure and biogenesis]; Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440800 [Multi-domain]  Cd Length: 226  Bit Score: 308.12  E-value: 4.43e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755   4 KTEKLQKILARSGHGSRREIEGYIQQGRISIDGKTAT-LGDRieVKPSIKIRLDGRILNIKEPqktvCRVLAYYKPEGEL 82
Cdd:COG1187    1 EGMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTeLGTK--VDPGDEVTVDGKPLKLPEE----PVYLLLNKPAGVV 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  83 CTRHDPEGRPTVFDRLPRMQGARWIAVGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFGEVDTAKLRQLTQG 162
Cdd:COG1187   75 STTKDPEGRPTVFDLLPEARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREG 154

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 498910755 163 VQLEDGPASFKTITFKGGEGiNQWYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINLpKGLPRGGWTEL 235
Cdd:COG1187  155 VELEDGPTKPAKVEILSGEA-NTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTL-GDLPPGEWREL 225
PseudoU_synth_RluB cd02556
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ...
 71-236 2.86e-98

Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.


Pssm-ID: 211330 [Multi-domain]  Cd Length: 167  Bit Score: 286.13  E-value: 2.86e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  71 RVLAYYKPEGELCTRHDPEGRPTVFDRLPRMQGARWIAVGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFGE 150
Cdd:cd02556    1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755 151 VDTAKLRQLTQGVQLEDGPASFKTITFKGGEGINQWYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINLPKGLPRG 230
Cdd:cd02556   81 VTDEQLKSLKKGVELEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRG 160


                 ....*.
gi 498910755 231 GWTELG 236
Cdd:cd02556  161 QWEELP 166
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 109-235 4.38e-60

pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 272902  Cd Length: 128  Bit Score: 187.92  E-value: 4.38e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  109 VGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFGEVDTAKLRQLTQGVQLEDGPASFKTITFKGGEGINQWYN 188
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFPTWLR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 498910755  189 VTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINLpKGLPRGGWTEL 235
Cdd:TIGR00093  81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSL-NGLPPGEWRPL 126
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 72-201 6.76e-17

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: 76.29  E-value: 6.76e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755   72 VLAYYKPEGELCTRHDPEGRPTVFDRLPRMQGA---RWIAVGRLDINTCGLLLFTTDGELANRLMH--PSQEVEREYAVR 146
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLSLLALLLRRELgvkRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 498910755  147 VFGEVDTAKLRQL----------TQGVQLEDGPAS---FKTITFKGGEGINqWYNVTLTEGRNREVRR 201
Cdd:pfam00849  81 VDKPEEEEGTIKSpikkeknkspFRKEEELGGKKAvthLKVLKSGSKGDYS-LLELELVTGRKHQIRA 147
S4 smart00363
S4 RNA-binding domain;
8-65 2.86e-04

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 38.34  E-value: 2.86e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 498910755     8 LQKILARSG-HGSRREIEGYIQQGRISIDGKTATLGDRIeVKPSIKIRLDGRILNIKEP 65
Cdd:smart00363   3 LDKFLARLGlAPSRSQARRLIEQGRVKVNGKKVTKPSYI-VKPGDVISVRGKELKRLKK 60
 
Name Accession Description Interval E-value
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
4-291 0e+00

23S rRNA pseudouridine(2605) synthase RluB;


Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 562.85  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755   4 KTEKLQKILARSGHGSRREIEGYIQQGRISIDGKTATLGDRIEVKPSIKIRLDGRILNIKEPQKTVCRVLAYYKPEGELC 83
Cdd:PRK10700   1 MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELC 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  84 TRHDPEGRPTVFDRLPRMQGARWIAVGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFGEVDTAKLRQLTQGV 163
Cdd:PRK10700  81 TRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755 164 QLEDGPASFKTITFKGGEGINQWYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINLPKGLPRGGWTELGLEQTNYL 243
Cdd:PRK10700 161 QLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYL 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 498910755 244 RQLVGLGDEMVTKVAVERDQRRIKANQIRRAVKRHAKVASRP-AGKRPA 291
Cdd:PRK10700 241 RELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRrSGGRNN 289
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 4-235 4.43e-106

Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ribosomal structure and biogenesis]; Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440800 [Multi-domain]  Cd Length: 226  Bit Score: 308.12  E-value: 4.43e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755   4 KTEKLQKILARSGHGSRREIEGYIQQGRISIDGKTAT-LGDRieVKPSIKIRLDGRILNIKEPqktvCRVLAYYKPEGEL 82
Cdd:COG1187    1 EGMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTeLGTK--VDPGDEVTVDGKPLKLPEE----PVYLLLNKPAGVV 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  83 CTRHDPEGRPTVFDRLPRMQGARWIAVGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFGEVDTAKLRQLTQG 162
Cdd:COG1187   75 STTKDPEGRPTVFDLLPEARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREG 154

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 498910755 163 VQLEDGPASFKTITFKGGEGiNQWYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINLpKGLPRGGWTEL 235
Cdd:COG1187  155 VELEDGPTKPAKVEILSGEA-NTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTL-GDLPPGEWREL 225
PseudoU_synth_RluB cd02556
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ...
 71-236 2.86e-98

Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.


Pssm-ID: 211330 [Multi-domain]  Cd Length: 167  Bit Score: 286.13  E-value: 2.86e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  71 RVLAYYKPEGELCTRHDPEGRPTVFDRLPRMQGARWIAVGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFGE 150
Cdd:cd02556    1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755 151 VDTAKLRQLTQGVQLEDGPASFKTITFKGGEGINQWYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINLPKGLPRG 230
Cdd:cd02556   81 VTDEQLKSLKKGVELEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRG 160


                 ....*.
gi 498910755 231 GWTELG 236
Cdd:cd02556  161 QWEELP 166
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 109-235 4.38e-60

pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 272902  Cd Length: 128  Bit Score: 187.92  E-value: 4.38e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  109 VGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFGEVDTAKLRQLTQGVQLEDGPASFKTITFKGGEGINQWYN 188
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFPTWLR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 498910755  189 VTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINLpKGLPRGGWTEL 235
Cdd:TIGR00093  81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSL-NGLPPGEWRPL 126
PseudoU_synth_RsuA_like cd02870
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ...
 72-218 3.11e-59

Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.


Pssm-ID: 211347 [Multi-domain]  Cd Length: 146  Bit Score: 186.16  E-value: 3.11e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  72 VLAYYKPEGELCTRHDPEGRPTVFDRLPRmQGARWIAVGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFGEV 151
Cdd:cd02870    1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKD-VGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVP 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498910755 152 DTAKLRQLTQGVQLEDGPASFKTITFKGGEGINQWYNVTLTEGRNREVRRLWESVGVQVSRLIRVRY 218
Cdd:cd02870   80 SEEELRRLRAGVELDDGKTAPAKVKVLSRDPKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146
PseudoU_synth_Rsu_Rlu_like cd02550
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ...
 72-218 7.27e-51

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: 165.24  E-value: 7.27e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  72 VLAYYKPEGELCTRHDPEGRPTVFDRLPRMQGARWIAVGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFGEV 151
Cdd:cd02550    1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 498910755 152 DTAKLRQL-------TQGVQLEDGPASFKTITFKGGEGINQWYNVTLTEGRNREVRRLWESVGVQVSRLIRVRY 218
Cdd:cd02550   81 DEEGIEDLatvrrgrLSGLVDEGVPLAVTKVRVIGEHGGTGRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI 154
PseudoU_synth_RsuA cd02553
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ...
 74-239 3.74e-37

Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.


Pssm-ID: 211327 [Multi-domain]  Cd Length: 167  Bit Score: 130.33  E-value: 3.74e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  74 AYY---KPEGELCTRHDPEGrPTVFDRLPRMQGARWI-AVGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFG 149
Cdd:cd02553    1 VYLmlnKPAGVVCATKDPHH-PTVIDLLPEPDRRRDLfPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755 150 EVDTAKLRQLTQGVQLEDG----PASFKTITfkggegiNQWYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINLPK 225
Cdd:cd02553   80 PLTEDDIEAFAEGVLLHDGyptkPAKLEILS-------PTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDD 152

                        170
                 ....*....|....
gi 498910755 226 GLPRGGWTELGLEQ 239
Cdd:cd02553  153 DLAPGEWRPLTEEE 166
PRK10475 PRK10475
23S rRNA pseudouridine(2604) synthase RluF;
1-300 1.11e-30

23S rRNA pseudouridine(2604) synthase RluF;


Pssm-ID: 236698 [Multi-domain]  Cd Length: 290  Bit Score: 116.75  E-value: 1.11e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755   1 MSDKTEKLQKILARSGHGSRREIEGYIQQGRISIDGKTATLGDRieVKPSIKIRLDGRILNIKEPQKTVcrVLAYYKPEG 80
Cdd:PRK10475   2 LTDSSTRLNKYISESGICSRREADRYIEQGNVFINGKRATIGDQ--VKAGDVVKVNGQLIEPREAEDLV--LIALNKPVG 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  81 ELCTRHDPEgRPTVFDRLPrmQGARWIAVGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFGEVDTAKLRQLT 160
Cdd:PRK10475  78 IVSTTEDGE-RDNIVDFVN--HSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMG 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755 161 QGVQLedgpasFKTITFK---GGEGINQwYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINLpKGLPRGGWTELGL 237
Cdd:PRK10475 155 AGVPI------LGTVTKKckvKKEAPFV-FRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSL-SGIPLGEWRDLTD 226

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 498910755 238 EQTNYLRQLVglgdEMVTKVAVERDQRRIKANQIRRAVKRHAKVASR-----PAGKRPASSSRQNAGR 300
Cdd:PRK10475 227 DELIDLFKLI----ENSSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKggrpaSNGKRFTSPGRKKKGR 290
PseudoU_synth_RluE cd02566
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ...
 72-223 7.26e-27

Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved.


Pssm-ID: 211334 [Multi-domain]  Cd Length: 168  Bit Score: 103.23  E-value: 7.26e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  72 VLAYYKPEGELCT-RHDPEGRPTVFDRLPrMQGARwiAVGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFGE 150
Cdd:cd02566    1 LILFNKPYGVLSQfTDESEKHKTLKDYID-DPGVY--AAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755 151 VDTAKLRQLTQGVQLEDGPASFKTItFKGGEGI----------------NQWYNVTLTEGRNREVRRLWESVGVQVSRLI 214
Cdd:cd02566   78 PTEDALEQLRNGVELGDGLTLPAKV-EKVDEPPwlwereppirfrknipTSWIEITICEGKNRQVRRMTAAVGFPTLRLI 156


                 ....*....
gi 498910755 215 RVRYGDINL 223
Cdd:cd02566  157 RVSIGDIGL 165
PseudoU_synth_RluF cd02554
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ...
 73-235 4.79e-23

Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.


Pssm-ID: 211328 [Multi-domain]  Cd Length: 164  Bit Score: 93.14  E-value: 4.79e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  73 LAYYKPEGELCTRHDPEgRPTVFDRLPrmQGARWIAVGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFGEVD 152
Cdd:cd02554    3 IAYNKPVGIDCTLERAD-EDNIIDFVN--PPPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPIT 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755 153 TAKLRQLTQGVQLEDG---PASFKTITFKGgeginqwYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINLpKGLPR 229
Cdd:cd02554   80 DEFIEGMSNGVVILGTvtkPCKVERLAKDK-------FRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIEL-GDLAP 151


                 ....*.
gi 498910755 230 GGWTEL 235
Cdd:cd02554  152 GEWRPL 157
PRK10839 PRK10839
16S rRNA pseudouridine(516) synthase RsuA;
7-241 8.48e-22

16S rRNA pseudouridine(516) synthase RsuA;


Pssm-ID: 236774 [Multi-domain]  Cd Length: 232  Bit Score: 91.71  E-value: 8.48e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755   7 KLQKILARSGHGSRREIEGYIQQGRISIDGKTATLGdRIEVKPSIKIRLDGRILNikepQKTVCRVLAYYKPEGELCTRH 86
Cdd:PRK10839   2 RLDKFISQQLGVSRAIAGRELRANRVTVDGEIVKNG-AFKLLPEHDVAYDGNPLA----QQHGPRYFMLNKPQGYVCSTD 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  87 DPEgRPTVFDRLPRMQGARWIAVGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVFGEV--DTAKlrQLTQGVQ 164
Cdd:PRK10839  77 DPD-HPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVadDTAE--QFAKGVQ 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755 165 LED-----GPASFKTITfkggegiNQWYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINLPKGLPRGGWTELGLEQ 239
Cdd:PRK10839 154 LHNekdltKPAVLEVIT-------PTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDADLAPGEYRPLTEEE 226


                 ..
gi 498910755 240 TN 241
Cdd:PRK10839 227 IA 228
PRK11394 PRK11394
23S rRNA pseudouridine(2457) synthase RluE;
63-234 1.71e-18

23S rRNA pseudouridine(2457) synthase RluE;


Pssm-ID: 183115  Cd Length: 217  Bit Score: 82.10  E-value: 1.71e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  63 KEPQKTVCRVLAYYKPEGELCTRHDPEGRPTVFDRLPrMQGArwIAVGRLDINTCGLLLFTTDGELANRLMHPSQEVERE 142
Cdd:PRK11394  32 RKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP-VQGV--YAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKI 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755 143 YAVRVFGEVDTAKLRQLTQGVQLEDGPasfktiTFKGGEGI---------------------NQWYNVTLTEGRNREVRR 201
Cdd:PRK11394 109 YYVQVEGIPTQDALEALRNGVTLNDGP------TLPAGAELvdepawlwprnppirerksipTSWLKITLYEGRNRQVRR 182

                        170       180       190
                 ....*....|....*....|....*....|...
gi 498910755 202 LWESVGVQVSRLIRVRYGDINLpKGLPRGGWTE 234
Cdd:PRK11394 183 MTAHVGFPTLRLIRYAMGDYSL-DNLANGEWRE 214
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 72-201 6.76e-17

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: 76.29  E-value: 6.76e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755   72 VLAYYKPEGELCTRHDPEGRPTVFDRLPRMQGA---RWIAVGRLDINTCGLLLFTTDGELANRLMH--PSQEVEREYAVR 146
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLSLLALLLRRELgvkRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 498910755  147 VFGEVDTAKLRQL----------TQGVQLEDGPAS---FKTITFKGGEGINqWYNVTLTEGRNREVRR 201
Cdd:pfam00849  81 VDKPEEEEGTIKSpikkeknkspFRKEEELGGKKAvthLKVLKSGSKGDYS-LLELELVTGRKHQIRA 147
PSSA_1 cd02555
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ...
 76-236 1.04e-14

Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial proteins assigned to the RsuA 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 TruA family is comprised of proteins related to Escherichia coli RsuA.


Pssm-ID: 211329 [Multi-domain]  Cd Length: 177  Bit Score: 70.90  E-value: 1.04e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755  76 YKPEGELCTRHDP---EGRPTVFDRLPRM----QGARWIAVGRLDINTCGLLLFTTDGELANRLMHPSQEVEREYAVRVF 148
Cdd:cd02555   10 HKPAGMVSEQALAllgPGQRSAADRSGRRplkgHFARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQEYLVEVR 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498910755 149 GEVDTAKLRQLTQGVQLEDGPASFKTITfkggeginqWYNVT-----LTEGRNREVRRLWESVGVQVSRLIRVRYGDINL 223
Cdd:cd02555   90 GELTAGGLERLNHGLTYDGRELPPAKVS---------WQNEQrlrfaLKEPQPGQIRRMCESVGLEVVALRRIRIGRVSL 160

                        170
                 ....*....|...
gi 498910755 224 PKgLPRGGWTELG 236
Cdd:cd02555  161 GK-LPLGQWRYLT 172
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 8-72 2.11e-05

S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.


Pssm-ID: 238095 [Multi-domain]  Cd Length: 70  Bit Score: 41.85  E-value: 2.11e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498910755   8 LQKILARSG-HGSRREIEGYIQQGRISIDGKTAT-LGDRIEVKPSIKIRLDGRILNIKEPQKTVCRV 72
Cdd:cd00165    3 LDKILARLGlAPSRSEARQLIKHGHVLVNGKVVTkPSYKVKPGDVIEVDGKSIEEDIVYEDKKLLVV 69
S4 smart00363
S4 RNA-binding domain;
8-65 2.86e-04

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 38.34  E-value: 2.86e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 498910755     8 LQKILARSG-HGSRREIEGYIQQGRISIDGKTATLGDRIeVKPSIKIRLDGRILNIKEP 65
Cdd:smart00363   3 LDKFLARLGlAPSRSQARRLIEQGRVKVNGKKVTKPSYI-VKPGDVISVRGKELKRLKK 60
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 6-40 1.75e-03

S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA.


Pssm-ID: 396182 [Multi-domain]  Cd Length: 48  Bit Score: 35.55  E-value: 1.75e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 498910755    6 EKLQKILARSGHG-SRREIEGYIQQGRISIDGKTAT 40
Cdd:pfam01479   1 RRLDKVLARLGLAsSRSQARQLIEHGRVLVNGKVVK 36
PseudoU_synth_ScRIB2 cd02557
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, ...
 111-150 5.56e-03

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: 37.22  E-value: 5.56e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 498910755 111 RLDINTCGLLLFTTDGELANRL--MHPSQEVEREYAVRVFGE 150
Cdd:cd02557   65 RLDRLTSGLLLFAKTSQTASRLqqQIRSREVKKEYLARVKGE 106
 
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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