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Conserved domains on  [gi|488214761|ref|WP_002285969|]
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MULTISPECIES: pseudouridine synthase [Enterococcus]

Protein Classification

pseudouridine synthase( domain architecture ID 11439600)

pseudouridine synthase may catalyze the formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit, or at position 2605 in 23S rRNA

CATH:  3.30.2350.10
EC:  5.4.99.-
Gene Ontology:  GO:0140098|GO:0001522|GO:0009451|GO:0003723|GO:0009982

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 1-229 3.00e-98

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: 285.77  E-value: 3.00e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761   1 MRLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEfEDAVTYLGEIIT-YQKDFYYILHKPAGVISATQDNH 79
Cdd:COG1187    3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTELGTKVDP-GDEVTVDGKPLKlPEEPVYLLLNKPAGVVSTTKDPE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  80 D-QTVIDLLEDqDYREDLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDgD 158
Cdd:COG1187   82 GrPTVFDLLPE-ARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELE-D 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488214761 159 EQTLPAKLQIDQVDQETEtsiIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLpKDLNKGQYRPMT 229
Cdd:COG1187  160 GPTKPAKVEILSGEANTW---LRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTL-GDLPPGEWRELT 226
 
Name Accession Description Interval E-value
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 1-229 3.00e-98

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: 285.77  E-value: 3.00e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761   1 MRLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEfEDAVTYLGEIIT-YQKDFYYILHKPAGVISATQDNH 79
Cdd:COG1187    3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTELGTKVDP-GDEVTVDGKPLKlPEEPVYLLLNKPAGVVSTTKDPE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  80 D-QTVIDLLEDqDYREDLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDgD 158
Cdd:COG1187   82 GrPTVFDLLPE-ARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELE-D 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488214761 159 EQTLPAKLQIDQVDQETEtsiIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLpKDLNKGQYRPMT 229
Cdd:COG1187  160 GPTKPAKVEILSGEANTW---LRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTL-GDLPPGEWRELT 226
PseudoU_synth_RsuA cd02553
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ...
 61-233 9.62e-90

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: 262.07  E-value: 9.62e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  61 FYYILHKPAGVISATQDNHDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGI 140
Cdd:cd02553    1 VYLMLNKPAGVVCATKDPHHPTVIDLLPEPDRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAGP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761 141 MTEEDIRLFAEGLIIDGDEQTLPAKLQIdqvdqeTETSIIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLPKDL 220
Cdd:cd02553   81 LTEDDIEAFAEGVLLHDGYPTKPAKLEI------LSPTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDDDL 154

                        170
                 ....*....|...
gi 488214761 221 NKGQYRPMTKEEL 233
Cdd:cd02553  155 APGEWRPLTEEEL 167
PRK10839 PRK10839
16S rRNA pseudouridine(516) synthase RsuA;
1-236 5.16e-46

16S rRNA pseudouridine(516) synthase RsuA;


Pssm-ID: 236774 [Multi-domain]  Cd Length: 232  Bit Score: 152.95  E-value: 5.16e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761   1 MRLDKFLADMgLG-SRKEVKGLIKKGTIEVNGQVVKSDKAQVNEfEDAVTYLGEIITYQKD-FYYILHKPAGVISATQDN 78
Cdd:PRK10839   1 MRLDKFISQQ-LGvSRAIAGRELRANRVTVDGEIVKNGAFKLLP-EHDVAYDGNPLAQQHGpRYFMLNKPQGYVCSTDDP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  79 HDQTVIDLLeDQDYREDLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGD 158
Cdd:PRK10839  79 DHPTVLYFL-DEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNE 157

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488214761 159 EQ-TLPAKLQIdqvdqeTETSIIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLPKDLNKGQYRPMTKEELEQV 236
Cdd:PRK10839 158 KDlTKPAVLEV------ITPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDADLAPGEYRPLTEEEIASV 230
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 99-229 1.18e-38

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: 130.53  E-value: 1.18e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761   99 VGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDgDEQTLPAKLQIdqVDQETETS 178
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLE-DGKTKPAKLKV--ITEPGFPT 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 488214761  179 IIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLpKDLNKGQYRPMT 229
Cdd:TIGR00093  78 WLRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSL-NGLPPGEWRPLT 127
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 62-195 1.42e-20

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: 84.76  E-value: 1.42e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761   62 YYILHKPAGVISATQDN---HDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVFAHQL--LSPKKHVEKEYLAE 136
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSltkLLSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLnkLFPERKIEKEYLAL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488214761  137 VSGIMTEEDIR----LFAEGLIIDGDEQTLPAKLQIDQVDQ-----ETETSIIRLILHEGKFHQVKRM 195
Cdd:pfam00849  81 VDKPEEEEGTIkspiKKEKNKSPFRKEEELGGKKAVTHLKVlksgsKGDYSLLELELVTGRKHQIRAH 148
S4 smart00363
S4 RNA-binding domain;
1-54 2.76e-05

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 40.65  E-value: 2.76e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 488214761     1 MRLDKFLADMGLG-SRKEVKGLIKKGTIEVNGQVVKSDKAQVNEfEDAVTYLGEI 54
Cdd:smart00363   1 RRLDKFLARLGLApSRSQARRLIEQGRVKVNGKKVTKPSYIVKP-GDVISVRGKE 54
 
Name Accession Description Interval E-value
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 1-229 3.00e-98

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: 285.77  E-value: 3.00e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761   1 MRLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEfEDAVTYLGEIIT-YQKDFYYILHKPAGVISATQDNH 79
Cdd:COG1187    3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTELGTKVDP-GDEVTVDGKPLKlPEEPVYLLLNKPAGVVSTTKDPE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  80 D-QTVIDLLEDqDYREDLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDgD 158
Cdd:COG1187   82 GrPTVFDLLPE-ARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELE-D 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488214761 159 EQTLPAKLQIDQVDQETEtsiIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLpKDLNKGQYRPMT 229
Cdd:COG1187  160 GPTKPAKVEILSGEANTW---LRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTL-GDLPPGEWRELT 226
PseudoU_synth_RsuA cd02553
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ...
 61-233 9.62e-90

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: 262.07  E-value: 9.62e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  61 FYYILHKPAGVISATQDNHDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGI 140
Cdd:cd02553    1 VYLMLNKPAGVVCATKDPHHPTVIDLLPEPDRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAGP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761 141 MTEEDIRLFAEGLIIDGDEQTLPAKLQIdqvdqeTETSIIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLPKDL 220
Cdd:cd02553   81 LTEDDIEAFAEGVLLHDGYPTKPAKLEI------LSPTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDDDL 154

                        170
                 ....*....|...
gi 488214761 221 NKGQYRPMTKEEL 233
Cdd:cd02553  155 APGEWRPLTEEEL 167
PseudoU_synth_RsuA_like cd02870
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ...
 62-210 9.99e-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: 177.30  E-value: 9.99e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  62 YYILHKPAGVISATQDNHD-QTVIDLLEDQDYRedLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGI 140
Cdd:cd02870    1 YLLLNKPRGVVSTVRDPEGrPTVLDLLKDVGER--LFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGV 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761 141 MTEEDIRLFAEGLIIDgDEQTLPAKlqIDQVDQETETSIIRLILHEGKFHQVKRMVKAVGKEVLYLKRIR 210
Cdd:cd02870   79 PSEEELRRLRAGVELD-DGKTAPAK--VKVLSRDPKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVR 145
PRK10839 PRK10839
16S rRNA pseudouridine(516) synthase RsuA;
1-236 5.16e-46

16S rRNA pseudouridine(516) synthase RsuA;


Pssm-ID: 236774 [Multi-domain]  Cd Length: 232  Bit Score: 152.95  E-value: 5.16e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761   1 MRLDKFLADMgLG-SRKEVKGLIKKGTIEVNGQVVKSDKAQVNEfEDAVTYLGEIITYQKD-FYYILHKPAGVISATQDN 78
Cdd:PRK10839   1 MRLDKFISQQ-LGvSRAIAGRELRANRVTVDGEIVKNGAFKLLP-EHDVAYDGNPLAQQHGpRYFMLNKPQGYVCSTDDP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  79 HDQTVIDLLeDQDYREDLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGD 158
Cdd:PRK10839  79 DHPTVLYFL-DEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNE 157

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488214761 159 EQ-TLPAKLQIdqvdqeTETSIIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLPKDLNKGQYRPMTKEELEQV 236
Cdd:PRK10839 158 KDlTKPAVLEV------ITPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDADLAPGEYRPLTEEEIASV 230
PseudoU_synth_RluF cd02554
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ...
 62-235 6.77e-39

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: 132.43  E-value: 6.77e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  62 YYILHKPAGVISATQDNHDQTVIDLLedqDYREDLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGIM 141
Cdd:cd02554    2 YIAYNKPVGIDCTLERADEDNIIDFV---NPPPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761 142 TEEDIRLFAEGLIIdGDEQTLPAKlqidqVDQETETSiIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLpKDLN 221
Cdd:cd02554   79 TDEFIEGMSNGVVI-LGTVTKPCK-----VERLAKDK-FRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIEL-GDLA 150

                        170
                 ....*....|....
gi 488214761 222 KGQYRPMTKEELEQ 235
Cdd:cd02554  151 PGEWRPLTDAELFE 164
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 99-229 1.18e-38

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: 130.53  E-value: 1.18e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761   99 VGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDgDEQTLPAKLQIdqVDQETETS 178
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLE-DGKTKPAKLKV--ITEPGFPT 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 488214761  179 IIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLpKDLNKGQYRPMT 229
Cdd:TIGR00093  78 WLRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSL-NGLPPGEWRPLT 127
PseudoU_synth_Rsu_Rlu_like cd02550
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ...
 62-211 3.10e-36

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: 125.18  E-value: 3.10e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  62 YYILHKPAGVISATQD-NHDQTVIDLLEDQDYrEDLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGI 140
Cdd:cd02550    1 ILVLNKPSGLVCHPTDrDRDPTVVVRLDKLHG-PRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGE 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488214761 141 MTEEDIRLFAEGLIIDG----DEQTLPAKLQIDQVDQETETSIIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRM 211
Cdd:cd02550   80 LDEEGIEDLATVRRGRLsglvDEGVPLAVTKVRVIGEHGGTGRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI 154
PRK10475 PRK10475
23S rRNA pseudouridine(2604) synthase RluF;
1-233 2.54e-32

23S rRNA pseudouridine(2604) synthase RluF;


Pssm-ID: 236698 [Multi-domain]  Cd Length: 290  Bit Score: 119.07  E-value: 2.54e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761   1 MRLDKFLADMGLGSRKEVKGLIKKGTIEVNG-------QVVKSDKAQVNefedavtylGEIIT--YQKDFYYI-LHKPAG 70
Cdd:PRK10475   7 TRLNKYISESGICSRREADRYIEQGNVFINGkratigdQVKAGDVVKVN---------GQLIEprEAEDLVLIaLNKPVG 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  71 VISATQDNHDQTVIDLLedqDYREDLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFA 150
Cdd:PRK10475  78 IVSTTEDGERDNIVDFV---NHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMG 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761 151 EGLIIDGdeqTLPAKLQIDQVdqetETSIIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLpKDLNKGQYRPMTK 230
Cdd:PRK10475 155 AGVPILG---TVTKKCKVKKE----APFVFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSL-SGIPLGEWRDLTD 226


                 ...
gi 488214761 231 EEL 233
Cdd:PRK10475 227 DEL 229
PseudoU_synth_RluB cd02556
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ...
 64-230 1.23e-30

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: 111.25  E-value: 1.23e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  64 ILHKPAGVISATQDNHDQ-TVIDLLEdQDYREDLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGIMT 142
Cdd:cd02556    4 IYHKPEGLICTRKDPKGRpTVFDLLP-KLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQVT 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761 143 EEDIRLFAEGLIIDGdeqTLPAKLQIDQVDQETETSIIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLPKDLNK 222
Cdd:cd02556   83 DEQLKSLKKGVELED---GFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKR 159


                 ....*...
gi 488214761 223 GQYRPMTK 230
Cdd:cd02556  160 GQWEELPP 167
PseudoU_synth_RluE cd02566
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ...
 62-216 1.16e-28

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: 106.31  E-value: 1.16e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  62 YYILHKPAGVISA-TQDNHDQ-TVIDLLEDQDyredLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSG 139
Cdd:cd02566    1 LILFNKPYGVLSQfTDESEKHkTLKDYIDDPG----VYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEG 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761 140 IMTEEDIRLFAEGLIIdGDEQTLPAK-LQIDQVDQETE------------TSIIRLILHEGKFHQVKRMVKAVGKEVLYL 206
Cdd:cd02566   77 VPTEDALEQLRNGVEL-GDGLTLPAKvEKVDEPPWLWEreppirfrknipTSWIEITICEGKNRQVRRMTAAVGFPTLRL 155

                        170
                 ....*....|
gi 488214761 207 KRIRMGKFWL 216
Cdd:cd02566  156 IRVSIGDIGL 165
PSSA_1 cd02555
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ...
 63-232 2.34e-24

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: 95.17  E-value: 2.34e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  63 YILHKPAGVIS---------ATQDNHDQTVIDLLEDQDYRedLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEY 133
Cdd:cd02555    7 LLLHKPAGMVSeqalallgpGQRSAADRSGRRPLKGHFAR--LAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQEY 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761 134 LAEVSGIMTEEDIRLFAEGLIIDGDEQTlPAKlqidqVDQETETSiIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGK 213
Cdd:cd02555   85 LVEVRGELTAGGLERLNHGLTYDGRELP-PAK-----VSWQNEQR-LRFALKEPQPGQIRRMCESVGLEVVALRRIRIGR 157

                        170
                 ....*....|....*....
gi 488214761 214 FWLpKDLNKGQYRPMTKEE 232
Cdd:cd02555  158 VSL-GKLPLGQWRYLTTGE 175
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
2-238 3.47e-24

23S rRNA pseudouridine(2605) synthase RluB;


Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 97.53  E-value: 3.47e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761   2 RLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVK-SDKAQVNEfEDAVTYLGEIITY---QKDFYYIL--HKPAGVISAT 75
Cdd:PRK10700   4 KLQKVLARAGHGSRREIESIIEAGRVSVDGKIATlGDRVEVTP-GLKIRIDGHLISVkesAEQICRVLayYKPEGELCTR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  76 QDNHDQ-TVIDLLED-QDYRedLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGL 153
Cdd:PRK10700  83 NDPEGRpTVFDRLPKlRGAR--WIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761 154 II-DGdeqtlPAKLQ-IDQVDQETETSIIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLPKDLNKGQYRPMTKE 231
Cdd:PRK10700 161 QLeDG-----PAAFKtIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLA 235


                 ....*..
gi 488214761 232 ELEQVRE 238
Cdd:PRK10700 236 QTNYLRE 242
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 62-195 1.42e-20

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: 84.76  E-value: 1.42e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761   62 YYILHKPAGVISATQDN---HDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVFAHQL--LSPKKHVEKEYLAE 136
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSltkLLSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLnkLFPERKIEKEYLAL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488214761  137 VSGIMTEEDIR----LFAEGLIIDGDEQTLPAKLQIDQVDQ-----ETETSIIRLILHEGKFHQVKRM 195
Cdd:pfam00849  81 VDKPEEEEGTIkspiKKEKNKSPFRKEEELGGKKAVTHLKVlksgsKGDYSLLELELVTGRKHQIRAH 148
PRK11394 PRK11394
23S rRNA pseudouridine(2457) synthase RluE;
94-229 7.12e-19

23S rRNA pseudouridine(2457) synthase RluE;


Pssm-ID: 183115  Cd Length: 217  Bit Score: 81.71  E-value: 7.12e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  94 EDLFPVGRLDKDTEGLLILTNDGVFAHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDgDEQTLPAKlqIDQVDQ 173
Cdd:PRK11394  70 QGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLN-DGPTLPAG--AELVDE 146

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488214761 174 ---------------ETETSIIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLpKDLNKGQYRPMT 229
Cdd:PRK11394 147 pawlwprnppirerkSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSL-DNLANGEWREAT 216
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 62-191 3.45e-13

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: 65.82  E-value: 3.45e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  62 YYILHKPAGVIS-ATQDNHDQTVIDLLEDQDYRED----LFPVGRLDKDTEGLLILTNDGvFAHQLLS---PKKHVEKEY 133
Cdd:cd02869    1 LLVVNKPAGLPVhPGPGHLTGTLVNALLKLLLLLGeefrPGLVHRLDKDTSGLLLVAKNK-KAAAKLSkqfKERKVKKTY 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488214761 134 LAEVSGIMTEEDIRLFAE--------GLIIDGDEQTLPAKLQIDQVDQETETSIIRLILHEGKFHQ 191
Cdd:cd02869   80 LALVDGKPPEDEGTIDAPlgrkkrkkRARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQ 145
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
 57-191 1.65e-12

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: 64.39  E-value: 1.65e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  57 YQKDFYYILHKPAGVIS-ATQDNHDQTVIDLLEDQDYR----EDLFPVGRLDKDTEGLLILT-NDgvFAHQLLSP---KK 127
Cdd:COG0564    3 YEDEDLLVVNKPAGLVVhPGSGGDDGTLVNALRAHLGElsgvPRPGLVHRLDRDTSGLLLVAkTR--KAARRLSEqfrER 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488214761 128 HVEKEYLAEVSGIMTEEDIRLFA----------EGLIIDGDEQtlPAKLQIDQVDQETETSIIRLILHEGKFHQ 191
Cdd:COG0564   81 EVEKRYLALVEGKPKEDEGTIDAplgrdpkdrkKMAVVDEDGK--PAVTHYRVLERFGGYSLVEVRLETGRTHQ 152
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
 1-193 2.67e-12

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: 65.04  E-value: 2.67e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761    1 MRLDKFLADM-GLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEfEDAVTYLGEI--------------ITYQKDFYYIL 65
Cdd:TIGR00005   6 QRLDDFLASLlPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKD-GDRITVRVPEeeehevppqdipldILFEDEDIIVI 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761   66 HKPAGVIS-ATQDNHDQTVIDLLEDQDYR----EDLFPVGRLDKDTEGLLIL--TNDG--VFAHQLlsPKKHVEKEYLAE 136
Cdd:TIGR00005  85 NKPSGLVVhPGGGNPFGTVLNALLAHCPPiagvERVGIVHRLDRDTSGLMVVakTPLAlrELQRQL--KNRTVTKEYVAL 162

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488214761  137 VSGIMTEED---------IRLFAEGLIIDGDEQTLPAKLQIDQVDQETETSIIRLILHEGKFHQVK 193
Cdd:TIGR00005 163 VHGQFDSGGgtvdaplgrVPNNRGLMAVHPSSEGKPAVTHFRVLERFGNASLVECELETGRTHQIR 228
PseudoU_synth_ScRIB2 cd02557
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, ...
 55-192 1.34e-11

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: 61.88  E-value: 1.34e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  55 ITYQKDFYYILHKPAGV-ISATQDNHDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVFAHQLLSP--KKHVEK 131
Cdd:cd02557   18 IVHEDDDLLVVDKPSGIpVHPTGRYRYNTVTEILKSEYGLTELRPCHRLDRLTSGLLLFAKTSQTASRLQQQirSREVKK 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488214761 132 EYLAEVSGIMTEEDIRLFAE--------GLIIDGDEQTLPAKLQIDQV--DQETETSIIRLILHEGKFHQV 192
Cdd:cd02557   98 EYLARVKGEFPDGEVVVDQPiglvspkgGLRNDVDEKGKDARTIFKRLsyNGDLNTSVVLCKPITGRTHQI 168
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 1-66 2.32e-09

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: 52.25  E-value: 2.32e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488214761   1 MRLDKFLADMGL-GSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEfEDAVTYLGEI----ITYQKDFYYILH 66
Cdd:cd00165    1 MRLDKILARLGLaPSRSEARQLIKHGHVLVNGKVVTKPSYKVKP-GDVIEVDGKSieedIVYEDKKLLVVN 70
rluD PRK11180
23S rRNA pseudouridine(1911/1915/1917) synthase RluD;
1-142 2.02e-07

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


Pssm-ID: 183020 [Multi-domain]  Cd Length: 325  Bit Score: 50.83  E-value: 2.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761   1 MRLDKFLADMGLG-SRKEVKGLIKKGTIEVNGQVVKSDKAQV---------NEFEDAVTYLGEI----ITYQKDFYYILH 66
Cdd:PRK11180  18 QRLDQALAELFPDySRSRIKEWILDQRVLVNGKVINKPKEKVlggeqvaidAEIEEEARFEPQDipldIVYEDDDILVIN 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  67 KPAG-VISATQDNHDQTVIDLLEDQDYREDLFP----VGRLDKDTEGLLILTNDGVFAHQLLSP--KKHVEKEYLAEVSG 139
Cdd:PRK11180  98 KPRDlVVHPGAGNPDGTVLNALLHYYPPIADVPragiVHRLDKDTTGLMVVAKTVPAQTRLVEAlqKREITREYEAVAIG 177


                 ...
gi 488214761 140 IMT 142
Cdd:PRK11180 178 HMT 180
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 1-36 6.46e-07

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: 44.79  E-value: 6.46e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 488214761    1 MRLDKFLADMGLG-SRKEVKGLIKKGTIEVNGQVVKS 36
Cdd:pfam01479   1 RRLDKVLARLGLAsSRSQARQLIEHGRVLVNGKVVKD 37
PseudoU_synth_TruC cd02563
tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific ...
 55-146 1.59e-06

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: 47.33  E-value: 1.59e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  55 ITYQKDFYYILHKPAG--VISATQDNH-DQTVIDLLEDQdYREDLFPVGRLDKDTEGLLILTNDGVFAHQL--LSPKKHV 129
Cdd:cd02563    3 ILYQDEHLVAINKPSGllVHRSELDRHeTRFALQTLRDQ-LGQHVYPVHRLDRPTSGVLLFALSSEVARKLgeQFTEHRV 81

                         90
                 ....*....|....*..
gi 488214761 130 EKEYLAEVSGIMTEEDI 146
Cdd:cd02563   82 HKTYLAVVRGYVPESGT 98
PRK11112 PRK11112
tRNA pseudouridine synthase C; Provisional
 53-146 5.70e-06

tRNA pseudouridine synthase C; Provisional


Pssm-ID: 182971 [Multi-domain]  Cd Length: 257  Bit Score: 46.19  E-value: 5.70e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488214761  53 EIItYQKDFYYILHKPAG--VISATQDNHD-QTVIDLLEDQdYREDLFPVGRLDKDTEGLLILTNDGVFAHqLLSPK--- 126
Cdd:PRK11112   3 EIL-YQDEWLVAVNKPAGwlVHRSWLDRHEtVFVMQTVRDQ-IGQHVFTAHRLDRPTSGVLLMALSSEVAR-LLAQQfeq 79

                         90       100
                 ....*....|....*....|
gi 488214761 127 KHVEKEYLAEVSGIMTEEDI 146
Cdd:PRK11112  80 HQIQKTYHAIVRGWLMEEAV 99
S4 smart00363
S4 RNA-binding domain;
1-54 2.76e-05

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 40.65  E-value: 2.76e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 488214761     1 MRLDKFLADMGLG-SRKEVKGLIKKGTIEVNGQVVKSDKAQVNEfEDAVTYLGEI 54
Cdd:smart00363   1 RRLDKFLARLGLApSRSQARRLIEQGRVKVNGKKVTKPSYIVKP-GDVISVRGKE 54
 
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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