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Conserved domains on  [gi|1196647648|ref|WP_086233589|]
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MULTISPECIES: pseudouridine synthase [Campylobacter]

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, ...
 1-236 9.23e-78

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: 234.16  E-value: 9.23e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648   1 MRINKFISHNTNYSRREADELIKAGKVSINGRIISDLSTDIKDGDKVRIGSRLVKLKKEFSVIVYNKPKGELVTKRDDRG 80
Cdd:COG1187     3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTELGTKVDPGDEVTVDGKPLKLPEEPVYLLLNKPAGVVSTTKDPEG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  81 RRTIYDSLPR-GFSKFISIGRLDFASEGLLLLTDAPAIAQALM--DSDIEREYYLKIKGNITEQVINAMREGFFAKDatk 157
Cdd:COG1187    83 RPTVFDLLPEaRKERLFPVGRLDKDTEGLLLLTNDGELAHRLThpKYGVEKEYLVRVDGPVTEEDLERLREGVELED--- 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1196647648 158 gahAKTKqismefkpFLAYRIISQsGGYTRLKVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLDQLGEGKWRYFT 236
Cdd:COG1187   160 ---GPTK--------PAKVEILSG-EANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLGDLPPGEWRELT 226
 
Name Accession Description Interval E-value
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 1-236 9.23e-78

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: 234.16  E-value: 9.23e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648   1 MRINKFISHNTNYSRREADELIKAGKVSINGRIISDLSTDIKDGDKVRIGSRLVKLKKEFSVIVYNKPKGELVTKRDDRG 80
Cdd:COG1187     3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTELGTKVDPGDEVTVDGKPLKLPEEPVYLLLNKPAGVVSTTKDPEG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  81 RRTIYDSLPR-GFSKFISIGRLDFASEGLLLLTDAPAIAQALM--DSDIEREYYLKIKGNITEQVINAMREGFFAKDatk 157
Cdd:COG1187    83 RPTVFDLLPEaRKERLFPVGRLDKDTEGLLLLTNDGELAHRLThpKYGVEKEYLVRVDGPVTEEDLERLREGVELED--- 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1196647648 158 gahAKTKqismefkpFLAYRIISQsGGYTRLKVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLDQLGEGKWRYFT 236
Cdd:COG1187   160 ---GPTK--------PAKVEILSG-EANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLGDLPPGEWRELT 226
PseudoU_synth_RluB cd02556
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ...
 62-237 6.86e-35

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: 122.80  E-value: 6.86e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  62 VIVYNKPKGELVTKRDDRGRRTIYDSLPR-GFSKFISIGRLDFASEGLLLLTDAPAIAQALM--DSDIEREYYLKIKGNI 138
Cdd:cd02556     2 VLIYHKPEGLICTRKDPKGRPTVFDLLPKlGIPRWISVGRLDLNTEGLLLFTNDGELANRLMhpSNEIEREYAVRVFGQV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648 139 TEQVINAMREGFFAKDATkgahAKTKQISMEfkpflayriiSQSGGYTRLKVIINEGQNRELRRFFGYFDLEVMDLKRVS 218
Cdd:cd02556    82 TDEQLKSLKKGVELEDGF----AGFKSIQLE----------GGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIR 147

                         170       180
                  ....*....|....*....|
gi 1196647648 219 FGR-VSLDQLGEGKWRYFTN 237
Cdd:cd02556   148 YGPiFLPGNLKRGQWEELPP 167
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 98-236 5.85e-34

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: 118.97  E-value: 5.85e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  98 IGRLDFASEGLLLLTDAPAIAQALM--DSDIEREYYLKIKGNITEQVINAMREGFFAKDATKGAHAKTKQISMEFKpfla 175
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLThpGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFP---- 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1196647648 176 yriisqsggyTRLKVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLDQLGEGKWRYFT 236
Cdd:TIGR00093  77 ----------TWLRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPLT 127
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
14-232 1.18e-29

23S rRNA pseudouridine(2605) synthase RluB;


Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 112.55  E-value: 1.18e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  14 SRREADELIKAGKVSINGRI--ISDlSTDIKDGDKVRIGSRLVKLKKEFS----VIVYNKPKGELVTKRDDRGRRTIYDS 87
Cdd:PRK10700   16 SRREIESIIEAGRVSVDGKIatLGD-RVEVTPGLKIRIDGHLISVKESAEqicrVLAYYKPEGELCTRNDPEGRPTVFDR 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  88 LPR-GFSKFISIGRLDFASEGLLLLTDAPAIAQALM--DSDIEREYYLKIKGNITEQVINAMREGffakdatkgahaktk 164
Cdd:PRK10700   95 LPKlRGARWIAVGRLDVNTCGLLLFTTDGELANRLMhpSREVEREYAVRVFGQVDDAKLRQLSRG--------------- 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1196647648 165 qISMEFKPfLAYRIISQSGG------YTrlkVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLDQ-LGEGKW 232
Cdd:PRK10700  160 -VQLEDGP-AAFKTIKFSGGeginqwYN---VTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKgLPRGGW 229
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 62-204 3.21e-12

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: 62.42  E-value: 3.21e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  62 VIVYNKPKGELVTKRDDRGRRTIYDSLPRGFS----KFISIGRLDFASEGLLLLTDAPAIAQALMDS----DIEREYYLK 133
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLSLLALLLRRElgvkRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLfperKIEKEYLAL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1196647648 134 IKGNITEQVI--NAMREGFFAKDATKGAHAKTKQISMEFKPfLAYRIIsqsGGYTRLKVIINEGQNRELRRFF 204
Cdd:pfam00849  81 VDKPEEEEGTikSPIKKEKNKSPFRKEEELGGKKAVTHLKV-LKSGSK---GDYSLLELELVTGRKHQIRAHL 149
S4 smart00363
S4 RNA-binding domain;
1-59 2.02e-08

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 49.51  E-value: 2.02e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648    1 MRINKFI-SHNTNYSRREADELIKAGKVSINGRIISDLSTDIKDGDKVRIGSRLVKLKKE 59
Cdd:smart00363   1 RRLDKFLaRLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELKRLKK 60
 
Name Accession Description Interval E-value
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 1-236 9.23e-78

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: 234.16  E-value: 9.23e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648   1 MRINKFISHNTNYSRREADELIKAGKVSINGRIISDLSTDIKDGDKVRIGSRLVKLKKEFSVIVYNKPKGELVTKRDDRG 80
Cdd:COG1187     3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTELGTKVDPGDEVTVDGKPLKLPEEPVYLLLNKPAGVVSTTKDPEG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  81 RRTIYDSLPR-GFSKFISIGRLDFASEGLLLLTDAPAIAQALM--DSDIEREYYLKIKGNITEQVINAMREGFFAKDatk 157
Cdd:COG1187    83 RPTVFDLLPEaRKERLFPVGRLDKDTEGLLLLTNDGELAHRLThpKYGVEKEYLVRVDGPVTEEDLERLREGVELED--- 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1196647648 158 gahAKTKqismefkpFLAYRIISQsGGYTRLKVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLDQLGEGKWRYFT 236
Cdd:COG1187   160 ---GPTK--------PAKVEILSG-EANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLGDLPPGEWRELT 226
PseudoU_synth_RluB cd02556
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ...
 62-237 6.86e-35

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: 122.80  E-value: 6.86e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  62 VIVYNKPKGELVTKRDDRGRRTIYDSLPR-GFSKFISIGRLDFASEGLLLLTDAPAIAQALM--DSDIEREYYLKIKGNI 138
Cdd:cd02556     2 VLIYHKPEGLICTRKDPKGRPTVFDLLPKlGIPRWISVGRLDLNTEGLLLFTNDGELANRLMhpSNEIEREYAVRVFGQV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648 139 TEQVINAMREGFFAKDATkgahAKTKQISMEfkpflayriiSQSGGYTRLKVIINEGQNRELRRFFGYFDLEVMDLKRVS 218
Cdd:cd02556    82 TDEQLKSLKKGVELEDGF----AGFKSIQLE----------GGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIR 147

                         170       180
                  ....*....|....*....|
gi 1196647648 219 FGR-VSLDQLGEGKWRYFTN 237
Cdd:cd02556   148 YGPiFLPGNLKRGQWEELPP 167
PseudoU_synth_RsuA_like cd02870
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ...
 62-219 1.42e-34

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: 121.06  E-value: 1.42e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  62 VIVYNKPKGELVTKRDDRGRRTIYDSLPRGFSKFISIGRLDFASEGLLLLTDAPAIAQALMD--SDIEREYYLKIKGNIT 139
Cdd:cd02870     1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKDVGERLFPVGRLDYDTEGLLLLTNDGELANRLTHprYGVEKTYLVKVRGVPS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648 140 EQVINAMREGF-FAKDATKGAHAKtkqismefkpflayrIISQSGGYTRLKVIINEGQNRELRRFFGYFDLEVMDLKRVS 218
Cdd:cd02870    81 EEELRRLRAGVeLDDGKTAPAKVK---------------VLSRDPKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVR 145


                  .
gi 1196647648 219 F 219
Cdd:cd02870   146 I 146
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 98-236 5.85e-34

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: 118.97  E-value: 5.85e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  98 IGRLDFASEGLLLLTDAPAIAQALM--DSDIEREYYLKIKGNITEQVINAMREGFFAKDATKGAHAKTKQISMEFKpfla 175
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLThpGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFP---- 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1196647648 176 yriisqsggyTRLKVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLDQLGEGKWRYFT 236
Cdd:TIGR00093  77 ----------TWLRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPLT 127
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
14-232 1.18e-29

23S rRNA pseudouridine(2605) synthase RluB;


Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 112.55  E-value: 1.18e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  14 SRREADELIKAGKVSINGRI--ISDlSTDIKDGDKVRIGSRLVKLKKEFS----VIVYNKPKGELVTKRDDRGRRTIYDS 87
Cdd:PRK10700   16 SRREIESIIEAGRVSVDGKIatLGD-RVEVTPGLKIRIDGHLISVKESAEqicrVLAYYKPEGELCTRNDPEGRPTVFDR 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  88 LPR-GFSKFISIGRLDFASEGLLLLTDAPAIAQALM--DSDIEREYYLKIKGNITEQVINAMREGffakdatkgahaktk 164
Cdd:PRK10700   95 LPKlRGARWIAVGRLDVNTCGLLLFTTDGELANRLMhpSREVEREYAVRVFGQVDDAKLRQLSRG--------------- 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1196647648 165 qISMEFKPfLAYRIISQSGG------YTrlkVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLDQ-LGEGKW 232
Cdd:PRK10700  160 -VQLEDGP-AAFKTIKFSGGeginqwYN---VTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKgLPRGGW 229
PRK10475 PRK10475
23S rRNA pseudouridine(2604) synthase RluF;
1-243 7.65e-27

23S rRNA pseudouridine(2604) synthase RluF;


Pssm-ID: 236698 [Multi-domain]  Cd Length: 290  Bit Score: 105.20  E-value: 7.65e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648   1 MRINKFISHNTNYSRREADELIKAGKVSINGRIISdLSTDIKDGDKVRIGSRLVKLKKE--FSVIVYNKPKGeLVTKRDD 78
Cdd:PRK10475    7 TRLNKYISESGICSRREADRYIEQGNVFINGKRAT-IGDQVKAGDVVKVNGQLIEPREAedLVLIALNKPVG-IVSTTED 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  79 RGRRTIYDSLprGFSKFI-SIGRLDFASEGLLLLTDAPAIAQALMDS--DIEREYYLKIKGNITEQVINAMREGF-FAKD 154
Cdd:PRK10475   85 GERDNIVDFV--NHSKRVfPIGRLDKDSQGLIFLTNHGDLVNKILRAgnDHEKEYLVTVDKPITDEFIRGMGAGVpILGT 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648 155 ATKgaHAKTKQISmefkPFlAYRIIsqsggytrlkviINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLDQLGEGKWRY 234
Cdd:PRK10475  163 VTK--KCKVKKEA----PF-VFRIT------------LVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGIPLGEWRD 223


                  ....*....
gi 1196647648 235 FTNSEYDDL 243
Cdd:PRK10475  224 LTDDELIDL 232
PseudoU_synth_RsuA cd02553
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ...
 63-239 3.40e-25

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: 97.59  E-value: 3.40e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  63 IVYNKPKGeLVTKRDDRGRRTIYDSLPRGFSKFI--SIGRLDFASEGLLLLTDAPAIAQALMD--SDIEREYYLKIKGNI 138
Cdd:cd02553     3 LMLNKPAG-VVCATKDPHHPTVIDLLPEPDRRRDlfPVGRLDKDTTGLLLLTNDGQLAHRLTSpkKHVPKTYEVTLAGPL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648 139 TEQVINAMREGFFAKDATKGAHAKTKQISmefkpflayriisqsggYTRLKVIINEGQNRELRRFFGYFDLEVMDLKRVS 218
Cdd:cd02553    82 TEDDIEAFAEGVLLHDGYPTKPAKLEILS-----------------PTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIR 144

                         170       180
                  ....*....|....*....|..
gi 1196647648 219 FGRVSLD-QLGEGKWRYFTNSE 239
Cdd:cd02553   145 IGGLELDdDLAPGEWRPLTEEE 166
PseudoU_synth_Rsu_Rlu_like cd02550
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ...
 62-218 3.35e-22

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: 89.35  E-value: 3.35e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  62 VIVYNKPKGELVTKRDDRGRRTIYDSLP-RGFSKFISIGRLDFASEGLLLLTDAPAIAQALMDS--DIEREYYLKIKGNI 138
Cdd:cd02550     1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDkLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPrrEIEKEYLVTVRGEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648 139 TEQVINAMREGFFAKDA----TKGAHAKTKqismefkpflaYRIISQSGGYTRLKVIINEGQNRELRRFFGYFDLEVMDL 214
Cdd:cd02550    81 DEEGIEDLATVRRGRLSglvdEGVPLAVTK-----------VRVIGEHGGTGRLRLTLKTGRTHQIRRHCAAVGFPVLRL 149


                  ....
gi 1196647648 215 KRVS 218
Cdd:cd02550   150 HRVR 153
PSSA_1 cd02555
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ...
 77-239 1.06e-19

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: 83.22  E-value: 1.06e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  77 DDR-GRRtiydSLPRGFSKFISIGRLDFASEGLLLLTDAPAIAQALMD--SDIEREYYLKIKGNITEQVINAMREGFFAK 153
Cdd:cd02555    32 ADRsGRR----PLKGHFARLAPIGPLDKDASGLLVFSQDGRVLRKLIGdaSRLEQEYLVEVRGELTAGGLERLNHGLTYD 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648 154 DatkgahaktkqismefKPFLAYRIISQSGgyTRLKVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLDQLGEGKWR 233
Cdd:cd02555   108 G----------------RELPPAKVSWQNE--QRLRFALKEPQPGQIRRMCESVGLEVVALRRIRIGRVSLGKLPLGQWR 169


                  ....*.
gi 1196647648 234 YFTNSE 239
Cdd:cd02555   170 YLTTGE 175
PseudoU_synth_RluE cd02566
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ...
 62-227 1.13e-17

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: 77.81  E-value: 1.13e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  62 VIVYNKPKGELVTKRDD-RGRRTIYDSLPrgFSKFISIGRLDFASEGLLLLTDAPAIAQALMD--SDIEREYYLKIKGNI 138
Cdd:cd02566     1 LILFNKPYGVLSQFTDEsEKHKTLKDYID--DPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDpsFKHPKTYYVQVEGVP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648 139 TEQVINAMREGFFAKD-ATKGAHAKtkqiSMEFKPFLAYRI----ISQSGGYTRLKVIINEGQNRELRRFFGYFDLEVMD 213
Cdd:cd02566    79 TEDALEQLRNGVELGDgLTLPAKVE----KVDEPPWLWEREppirFRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLR 154

                         170
                  ....*....|....
gi 1196647648 214 LKRVSFGRVSLDQL 227
Cdd:cd02566   155 LIRVSIGDIGLDNL 168
PRK11394 PRK11394
23S rRNA pseudouridine(2457) synthase RluE;
62-237 3.90e-16

23S rRNA pseudouridine(2457) synthase RluE;


Pssm-ID: 183115  Cd Length: 217  Bit Score: 74.78  E-value: 3.90e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  62 VIVYNKPKGELVTKRDDRGRRTIYDSLPrgFSKFISIGRLDFASEGLLLLTDAPAIaQALMDSDIERE---YYLKIKGNI 138
Cdd:PRK11394   41 VILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL-QARLTQPGKRTgkiYYVQVEGIP 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648 139 TEQVINAMREGFFAKDA-TKGAHAKTKQISMEFKPFLAYRIISQSGGYTRLKVIINEGQNRELRRFFGYFDLEVMDLKRV 217
Cdd:PRK11394  118 TQDALEALRNGVTLNDGpTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRY 197

                         170       180
                  ....*....|....*....|
gi 1196647648 218 SFGRVSLDQLGEGKWRYFTN 237
Cdd:PRK11394  198 AMGDYSLDNLANGEWREATD 217
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 62-204 3.21e-12

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: 62.42  E-value: 3.21e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  62 VIVYNKPKGELVTKRDDRGRRTIYDSLPRGFS----KFISIGRLDFASEGLLLLTDAPAIAQALMDS----DIEREYYLK 133
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLSLLALLLRRElgvkRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLfperKIEKEYLAL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1196647648 134 IKGNITEQVI--NAMREGFFAKDATKGAHAKTKQISMEFKPfLAYRIIsqsGGYTRLKVIINEGQNRELRRFF 204
Cdd:pfam00849  81 VDKPEEEEGTikSPIKKEKNKSPFRKEEELGGKKAVTHLKV-LKSGSK---GDYSLLELELVTGRKHQIRAHL 149
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 1-66 9.34e-10

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: 53.41  E-value: 9.34e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648   1 MRINKFISH-NTNYSRREADELIKAGKVSINGRIISDLSTDIKDGDKVRIGSRLVKLKKEFS---VIVYN 66
Cdd:cd00165     1 MRLDKILARlGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYEdkkLLVVN 70
PRK10839 PRK10839
16S rRNA pseudouridine(516) synthase RsuA;
1-239 3.27e-09

16S rRNA pseudouridine(516) synthase RsuA;


Pssm-ID: 236774 [Multi-domain]  Cd Length: 232  Bit Score: 55.50  E-value: 3.27e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648   1 MRINKFISHNTNYSRREADELIKAGKVSINGRIISDLSTDIKDGDKVRIGSRLVKLKKEFSVIVYNKPKGeLVTKRDDRG 80
Cdd:PRK10839    1 MRLDKFISQQLGVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQG-YVCSTDDPD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  81 RRTIYDSL--PRGFsKFISIGRLDFASEGLLLLTDAPAIAQALMDS--DIEREYYLKIKGNITEQVInamrEGFFAKDAT 156
Cdd:PRK10839   80 HPTVLYFLdePVAY-KLHAAGRLDIDTTGLVLMTDDGQWSHRITSPrhHCEKTYLVTLESPVADDTA----EQFAKGVQL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648 157 KGAHAKTKQISMEfkpflayrIISQsggyTRLKVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLD-QLGEGKWRYF 235
Cdd:PRK10839  155 HNEKDLTKPAVLE--------VITP----TQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDaDLAPGEYRPL 222


                  ....
gi 1196647648 236 TNSE 239
Cdd:PRK10839  223 TEEE 226
S4 smart00363
S4 RNA-binding domain;
1-59 2.02e-08

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 49.51  E-value: 2.02e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648    1 MRINKFI-SHNTNYSRREADELIKAGKVSINGRIISDLSTDIKDGDKVRIGSRLVKLKKE 59
Cdd:smart00363   1 RRLDKFLaRLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELKRLKK 60
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 1-47 1.57e-06

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: 44.02  E-value: 1.57e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1196647648   1 MRINKFISH-NTNYSRREADELIKAGKVSINGRIISDLSTDIKDGDKV 47
Cdd:pfam01479   1 RRLDKVLARlGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
rluD PRK11180
23S rRNA pseudouridine(1911/1915/1917) synthase RluD;
11-201 6.65e-04

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


Pssm-ID: 183020 [Multi-domain]  Cd Length: 325  Bit Score: 40.43  E-value: 6.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  11 TNYSRREADELIKAGKVSINGRIISDLSTDIKDGDKVRIGSRL----------VKLK---KEFSVIVYNKPKGELVTKRD 77
Cdd:PRK11180   29 PDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIeeearfepqdIPLDivyEDDDILVINKPRDLVVHPGA 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648  78 DRGRRTIYDSL----------PR-GFskfisIGRLDFASEGLLLLTDA-PA---IAQALMDSDIEREYYLKIKGNITEqv 142
Cdd:PRK11180  109 GNPDGTVLNALlhyyppiadvPRaGI-----VHRLDKDTTGLMVVAKTvPAqtrLVEALQKREITREYEAVAIGHMTA-- 181

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1196647648 143 iNAMREGFFAKDATKGAHAKTKQISmefKPFLA-YRIISQSGGYTRLKVIINEGQNRELR 201
Cdd:PRK11180  182 -GGTVDEPISRHPTKRTHMAVHPMG---KPAVThYRIMEHFRVHTRLRLRLETGRTHQIR 237
TyrS COG0162
Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Tyrosyl-tRNA ...
 14-57 8.62e-03

Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Tyrosyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases


Pssm-ID: 439932 [Multi-domain]  Cd Length: 409  Bit Score: 36.94  E-value: 8.62e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1196647648  14 SRREADELIKAGKVSINGRIISDLSTDIKDGD-------KVRIGSR---LVKLK 57
Cdd:COG0162   356 SKSEARRLIKQGGVSVNGEKVTDPDAVLTAGDllhggylVLRVGKKkfaLVKLK 409
 
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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