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Conserved domains on  [gi|504092043|ref|WP_014326037|]
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23S rRNA pseudouridine(2605) synthase RluB [Pasteurella multocida]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10700 super family cl32559
23S rRNA pseudouridine(2605) synthase RluB;
62-342 4.76e-174

23S rRNA pseudouridine(2605) synthase RluB;


The actual alignment was detected with superfamily member PRK10700:

Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 484.65  E-value: 4.76e-174
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043  62 EGEKLQKVLARAGQGSRREIEAMIAENRVSVDGKIATLGDRIDVHAGVKIRIDGHLINLLHAQKEVCRVLMYYKPEGELC 141
Cdd:PRK10700   1 MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELC 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 142 TRHDPEGRPTVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDEAMLHRLKKGV 221
Cdd:PRK10700  81 TRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 222 QLEDGPANFKEIKFAGGVGMNQWFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLMKSLPRGGWEEMDLTNVNYL 301
Cdd:PRK10700 161 QLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYL 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 504092043 302 RELVGLPAEVETKLDVTKPRRRAKTGQIRKAVKRYAELNKR 342
Cdd:PRK10700 241 RELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGG 281
 
Name Accession Description Interval E-value
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
62-342 4.76e-174

23S rRNA pseudouridine(2605) synthase RluB;


Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 484.65  E-value: 4.76e-174
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043  62 EGEKLQKVLARAGQGSRREIEAMIAENRVSVDGKIATLGDRIDVHAGVKIRIDGHLINLLHAQKEVCRVLMYYKPEGELC 141
Cdd:PRK10700   1 MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELC 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 142 TRHDPEGRPTVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDEAMLHRLKKGV 221
Cdd:PRK10700  81 TRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 222 QLEDGPANFKEIKFAGGVGMNQWFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLMKSLPRGGWEEMDLTNVNYL 301
Cdd:PRK10700 161 QLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYL 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 504092043 302 RELVGLPAEVETKLDVTKPRRRAKTGQIRKAVKRYAELNKR 342
Cdd:PRK10700 241 RELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGG 281
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 62-294 7.31e-110

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: 319.29  E-value: 7.31e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043  62 EGEKLQKVLARAGQGSRREIEAMIAENRVSVDGKIAT-LGDRIDVHAgvKIRIDGHLINLlhaqKEVCRVLMYYKPEGEL 140
Cdd:COG1187    1 EGMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTeLGTKVDPGD--EVTVDGKPLKL----PEEPVYLLLNKPAGVV 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 141 CTRHDPEGRPTVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDEAMLHRLKKG 220
Cdd:COG1187   75 STTKDPEGRPTVFDLLPEARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREG 154

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504092043 221 VQLEDGPANFKEIKFAGGvGMNQWFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLmKSLPRGGWEEMD 294
Cdd:COG1187  155 VELEDGPTKPAKVEILSG-EANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTL-GDLPPGEWRELT 226
PseudoU_synth_RluB cd02556
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ...
 129-294 1.88e-97

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: 285.74  E-value: 1.88e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 129 RVLMYYKPEGELCTRHDPEGRPTVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQ 208
Cdd:cd02556    1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 209 VDEAMLHRLKKGVQLEDGPANFKEIKFAGGVGMNQWFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLMKSLPRG 288
Cdd:cd02556   81 VTDEQLKSLKKGVELEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRG 160


                 ....*.
gi 504092043 289 GWEEMD 294
Cdd:cd02556  161 QWEELP 166
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 167-295 6.02e-62

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: 193.70  E-value: 6.02e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043  167 VGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDEAMLHRLKKGVQLEDGPANFKEIKFAGGVGMNQWFD 246
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFPTWLR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 504092043  247 VTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLmKSLPRGGWEEMDL 295
Cdd:TIGR00093  81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSL-NGLPPGEWRPLTL 128
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 130-259 3.85e-16

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: 74.36  E-value: 3.85e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043  130 VLMYYKPEGELCTRHDPEG---RPTVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMH--PSREVEREYSVR 204
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTkllSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504092043  205 VFG----------QVDEAMLHRLKKGVQLEDG---PANFKEIKFAGGVGmNQWFDVTLMEGRNREVRR 259
Cdd:pfam00849  81 VDKpeeeegtiksPIKKEKNKSPFRKEEELGGkkaVTHLKVLKSGSKGD-YSLLELELVTGRKHQIRA 147
S4 smart00363
S4 RNA-binding domain;
66-113 5.34e-04

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 37.57  E-value: 5.34e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 504092043    66 LQKVLARAG-QGSRREIEAMIAENRVSVDGKIAT-------LGDRIDVHAGVKIRI 113
Cdd:smart00363   3 LDKFLARLGlAPSRSQARRLIEQGRVKVNGKKVTkpsyivkPGDVISVRGKELKRL 58
 
Name Accession Description Interval E-value
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
62-342 4.76e-174

23S rRNA pseudouridine(2605) synthase RluB;


Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 484.65  E-value: 4.76e-174
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043  62 EGEKLQKVLARAGQGSRREIEAMIAENRVSVDGKIATLGDRIDVHAGVKIRIDGHLINLLHAQKEVCRVLMYYKPEGELC 141
Cdd:PRK10700   1 MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELC 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 142 TRHDPEGRPTVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDEAMLHRLKKGV 221
Cdd:PRK10700  81 TRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 222 QLEDGPANFKEIKFAGGVGMNQWFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLMKSLPRGGWEEMDLTNVNYL 301
Cdd:PRK10700 161 QLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYL 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 504092043 302 RELVGLPAEVETKLDVTKPRRRAKTGQIRKAVKRYAELNKR 342
Cdd:PRK10700 241 RELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGG 281
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 62-294 7.31e-110

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: 319.29  E-value: 7.31e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043  62 EGEKLQKVLARAGQGSRREIEAMIAENRVSVDGKIAT-LGDRIDVHAgvKIRIDGHLINLlhaqKEVCRVLMYYKPEGEL 140
Cdd:COG1187    1 EGMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTeLGTKVDPGD--EVTVDGKPLKL----PEEPVYLLLNKPAGVV 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 141 CTRHDPEGRPTVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDEAMLHRLKKG 220
Cdd:COG1187   75 STTKDPEGRPTVFDLLPEARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREG 154

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504092043 221 VQLEDGPANFKEIKFAGGvGMNQWFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLmKSLPRGGWEEMD 294
Cdd:COG1187  155 VELEDGPTKPAKVEILSG-EANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTL-GDLPPGEWRELT 226
PseudoU_synth_RluB cd02556
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ...
 129-294 1.88e-97

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: 285.74  E-value: 1.88e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 129 RVLMYYKPEGELCTRHDPEGRPTVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQ 208
Cdd:cd02556    1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 209 VDEAMLHRLKKGVQLEDGPANFKEIKFAGGVGMNQWFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLMKSLPRG 288
Cdd:cd02556   81 VTDEQLKSLKKGVELEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRG 160


                 ....*.
gi 504092043 289 GWEEMD 294
Cdd:cd02556  161 QWEELP 166
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 167-295 6.02e-62

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: 193.70  E-value: 6.02e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043  167 VGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDEAMLHRLKKGVQLEDGPANFKEIKFAGGVGMNQWFD 246
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFPTWLR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 504092043  247 VTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLmKSLPRGGWEEMDL 295
Cdd:TIGR00093  81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSL-NGLPPGEWRPLTL 128
PseudoU_synth_RsuA_like cd02870
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ...
 130-276 2.34e-57

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: 182.69  E-value: 2.34e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 130 VLMYYKPEGELCTRHDPEGRPTVFDRLPRlTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQV 209
Cdd:cd02870    1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKD-VGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVP 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504092043 210 DEAMLHRLKKGVQLEDGPANFKEIKFAGGVGMNQWFDVTLMEGRNREVRRLWESQGVQVSRLIRTRY 276
Cdd:cd02870   80 SEEELRRLRAGVELDDGKTAPAKVKVLSRDPKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146
PseudoU_synth_Rsu_Rlu_like cd02550
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ...
 130-276 1.00e-47

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: 158.30  E-value: 1.00e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 130 VLMYYKPEGELCTRHDPEGRPTVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQV 209
Cdd:cd02550    1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504092043 210 DEAMLHRLKK-------GVQLEDGPANFKEIKFAGGVGMNQWFDVTLMEGRNREVRRLWESQGVQVSRLIRTRY 276
Cdd:cd02550   81 DEEGIEDLATvrrgrlsGLVDEGVPLAVTKVRVIGEHGGTGRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI 154
PseudoU_synth_RsuA cd02553
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ...
 129-293 9.76e-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: 129.95  E-value: 9.76e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 129 RVLMYYKPEGELCTRHDPEGrPTVFDRLPRLTGSRWI-AVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFG 207
Cdd:cd02553    1 VYLMLNKPAGVVCATKDPHH-PTVIDLLPEPDRRRDLfPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 208 QVDEAMLHRLKKGVQLEDG----PANFKEIKfaggvgmNQWFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLMK 283
Cdd:cd02553   80 PLTEDDIEAFAEGVLLHDGyptkPAKLEILS-------PTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDD 152

                        170
                 ....*....|
gi 504092043 284 SLPRGGWEEM 293
Cdd:cd02553  153 DLAPGEWRPL 162
PRK10475 PRK10475
23S rRNA pseudouridine(2604) synthase RluF;
65-334 2.72e-26

23S rRNA pseudouridine(2604) synthase RluF;


Pssm-ID: 236698 [Multi-domain]  Cd Length: 290  Bit Score: 105.97  E-value: 2.72e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043  65 KLQKVLARAGQGSRREIEAMIAENRVSVDGKIATLGDRidVHAGVKIRIDGHLINLLHAQKEVCRVLmyYKPEGELCTRH 144
Cdd:PRK10475   8 RLNKYISESGICSRREADRYIEQGNVFINGKRATIGDQ--VKAGDVVKVNGQLIEPREAEDLVLIAL--NKPVGIVSTTE 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 145 DPEgRPTVFDRLPRltGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDEAMLHRLKKGVQL- 223
Cdd:PRK10475  84 DGE-RDNIVDFVNH--SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPIl 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 224 ----EDGPANfKEIKFAggvgmnqwFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLmKSLPRGGWEemDLTNvn 299
Cdd:PRK10475 161 gtvtKKCKVK-KEAPFV--------FRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSL-SGIPLGEWR--DLTD-- 226

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 504092043 300 ylRELVGLPAEVETKLDVTKPRRRA--KTGQIRKAVK 334
Cdd:PRK10475 227 --DELIDLFKLIENSSSEAKPKAKAkpKTAGIKRPVV 261
PseudoU_synth_RluE cd02566
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ...
 130-281 3.05e-26

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: 102.46  E-value: 3.05e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 130 VLMYYKPEGELCT-RHDPEGRPTVFDRLPrLTGSRwiAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQ 208
Cdd:cd02566    1 LILFNKPYGVLSQfTDESEKHKTLKDYID-DPGVY--AAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 209 VDEAMLHRLKKGVQLEDG---PANFKEIKFAGGVGMNQ------------WFDVTLMEGRNREVRRLWESQGVQVSRLIR 273
Cdd:cd02566   78 PTEDALEQLRNGVELGDGltlPAKVEKVDEPPWLWEREppirfrkniptsWIEITICEGKNRQVRRMTAAVGFPTLRLIR 157


                 ....*...
gi 504092043 274 TRYGNISL 281
Cdd:cd02566  158 VSIGDIGL 165
PseudoU_synth_RluF cd02554
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ...
 131-296 8.15e-22

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: 90.45  E-value: 8.15e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 131 LMYYKPEGELCTRHDPEgRPTVFDRLPRltGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVD 210
Cdd:cd02554    3 IAYNKPVGIDCTLERAD-EDNIIDFVNP--PPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPIT 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 211 EAMLHRLKKGVQLEDGPANFKEIKFAGGVGmnqwFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLmKSLPRGGW 290
Cdd:cd02554   80 DEFIEGMSNGVVILGTVTKPCKVERLAKDK----FRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIEL-GDLAPGEW 154


                 ....*.
gi 504092043 291 EemDLT 296
Cdd:cd02554  155 R--PLT 158
PRK10839 PRK10839
16S rRNA pseudouridine(516) synthase RsuA;
65-288 3.99e-19

16S rRNA pseudouridine(516) synthase RsuA;


Pssm-ID: 236774 [Multi-domain]  Cd Length: 232  Bit Score: 84.77  E-value: 3.99e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043  65 KLQKVLARAGQGSR----REIEAmiaeNRVSVDGKIATLGdRIDVHAGVKIRIDGhliNLLHaQKEVCRVLMYYKPEGEL 140
Cdd:PRK10839   2 RLDKFISQQLGVSRaiagRELRA----NRVTVDGEIVKNG-AFKLLPEHDVAYDG---NPLA-QQHGPRYFMLNKPQGYV 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 141 CTRHDPEgRPTVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDEAMLHRLKKG 220
Cdd:PRK10839  73 CSTDDPD-HPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKG 151

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 504092043 221 VQLED-----GPANFKEIKfaggvgmNQWFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLMKSLPRG 288
Cdd:PRK10839 152 VQLHNekdltKPAVLEVIT-------PTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDADLAPG 217
PRK11394 PRK11394
23S rRNA pseudouridine(2457) synthase RluE;
124-292 3.81e-18

23S rRNA pseudouridine(2457) synthase RluE;


Pssm-ID: 183115  Cd Length: 217  Bit Score: 81.71  E-value: 3.81e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 124 QKEVCRVLMYYKPEGELCTRHDPEGRPTVFDRLPrLTGSrwIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSV 203
Cdd:PRK11394  35 ENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP-VQGV--YAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYV 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 204 RVFGQVDEAMLHRLKKGVQLEDGPAnfkeikFAGGVGM---------------------NQWFDVTLMEGRNREVRRLWE 262
Cdd:PRK11394 112 QVEGIPTQDALEALRNGVTLNDGPT------LPAGAELvdepawlwprnppirerksipTSWLKITLYEGRNRQVRRMTA 185

                        170       180       190
                 ....*....|....*....|....*....|
gi 504092043 263 SQGVQVSRLIRTRYGNISLmKSLPRGGWEE 292
Cdd:PRK11394 186 HVGFPTLRLIRYAMGDYSL-DNLANGEWRE 214
PSSA_1 cd02555
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ...
 131-290 1.87e-16

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: 76.29  E-value: 1.87e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 131 LMYYKPEGELCTRHDP---EGRPTVFDRLPR--LTG--SRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSV 203
Cdd:cd02555    7 LLLHKPAGMVSEQALAllgPGQRSAADRSGRrpLKGhfARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQEYLV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043 204 RVFGQVDEAMLHRLKKGVQLED---GPA-----NFKEIKFAggvgmnqwfdvtLMEGRNREVRRLWESQGVQVSRLIRTR 275
Cdd:cd02555   87 EVRGELTAGGLERLNHGLTYDGrelPPAkvswqNEQRLRFA------------LKEPQPGQIRRMCESVGLEVVALRRIR 154

                        170
                 ....*....|....*
gi 504092043 276 YGNISLMKsLPRGGW 290
Cdd:cd02555  155 IGRVSLGK-LPLGQW 168
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 130-259 3.85e-16

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: 74.36  E-value: 3.85e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504092043  130 VLMYYKPEGELCTRHDPEG---RPTVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMH--PSREVEREYSVR 204
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTkllSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504092043  205 VFG----------QVDEAMLHRLKKGVQLEDG---PANFKEIKFAGGVGmNQWFDVTLMEGRNREVRR 259
Cdd:pfam00849  81 VDKpeeeegtiksPIKKEKNKSPFRKEEELGGkkaVTHLKVLKSGSKGD-YSLLELELVTGRKHQIRA 147
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 66-130 4.73e-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: 41.08  E-value: 4.73e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504092043  66 LQKVLARAG-QGSRREIEAMIAENRVSVDGKIAT-LGDRIDVHAGVKIRIDGHLINLLHAQKEVCRV 130
Cdd:cd00165    3 LDKILARLGlAPSRSEARQLIKHGHVLVNGKVVTkPSYKVKPGDVIEVDGKSIEEDIVYEDKKLLVV 69
PseudoU_synth_ScRIB2 cd02557
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, ...
 169-207 3.76e-04

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: 41.08  E-value: 3.76e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 504092043 169 RLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFG 207
Cdd:cd02557   65 RLDRLTSGLLLFAKTSQTASRLqqQIRSREVKKEYLARVKG 105
S4 smart00363
S4 RNA-binding domain;
66-113 5.34e-04

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 37.57  E-value: 5.34e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 504092043    66 LQKVLARAG-QGSRREIEAMIAENRVSVDGKIAT-------LGDRIDVHAGVKIRI 113
Cdd:smart00363   3 LDKFLARLGlAPSRSQARRLIEQGRVKVNGKKVTkpsyivkPGDVISVRGKELKRL 58
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 64-98 1.51e-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: 35.93  E-value: 1.51e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 504092043   64 EKLQKVLARAGQG-SRREIEAMIAENRVSVDGKIAT 98
Cdd:pfam01479   1 RRLDKVLARLGLAsSRSQARQLIEHGRVLVNGKVVK 36
 
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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