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Conserved domains on  [gi|2130561025|ref|WP_228315223|]
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MULTISPECIES: pseudouridine synthase [unclassified Xanthomonas]

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

 Zoom to residue level

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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, ...
 27-255 5.70e-85

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: 262.66  E-value: 5.70e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  27 EERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVasaLTEPSRVLIYNKPEGEVTTRE 105
Cdd:COG1187     2 GMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTElGTKVDPGDEVTVDGKPLK---LPEEPVYLLLNKPAGVVSTTK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 106 DPEGRPTVFESLPALKGSRWIAIGRLDINttgllllttDGELANAMMHPSYEVEREYVVRVRAPegeetVSDAIIERLSR 185
Cdd:COG1187    79 DPEGRPTVFDLLPEARKERLFPVGRLDKDteglllltnDGELAHRLTHPKYGVEKEYLVRVDGP-----VTEEDLERLRE 153

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 186 GVLLEDGGAKFDEIERIGGTDSHdWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPrELLRGQ 255
Cdd:COG1187   154 GVELEDGPTKPAKVEILSGEANT-WLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLG-DLPPGE 221
 
Name Accession Description Interval E-value
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 27-255 5.70e-85

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: 262.66  E-value: 5.70e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  27 EERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVasaLTEPSRVLIYNKPEGEVTTRE 105
Cdd:COG1187     2 GMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTElGTKVDPGDEVTVDGKPLK---LPEEPVYLLLNKPAGVVSTTK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 106 DPEGRPTVFESLPALKGSRWIAIGRLDINttgllllttDGELANAMMHPSYEVEREYVVRVRAPegeetVSDAIIERLSR 185
Cdd:COG1187    79 DPEGRPTVFDLLPEARKERLFPVGRLDKDteglllltnDGELAHRLTHPKYGVEKEYLVRVDGP-----VTEEDLERLRE 153

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 186 GVLLEDGGAKFDEIERIGGTDSHdWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPrELLRGQ 255
Cdd:COG1187   154 GVELEDGPTKPAKVEILSGEANT-WLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLG-DLPPGE 221
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
28-296 2.46e-78

23S rRNA pseudouridine(2605) synthase RluB;


Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 248.14  E-value: 2.46e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  28 ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQTG--MSVRSGDKIELDGRSF-VASALTEPSRVLIYNKPEGEVTTR 104
Cdd:PRK10700    3 EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGdrVEVTPGLKIRIDGHLIsVKESAEQICRVLAYYKPEGELCTR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 105 EDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRapeGEetVSDAIIERLS 184
Cdd:PRK10700   83 NDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVF---GQ--VDDAKLRQLS 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 185 RGVLLEDGGAKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSVEVAQEKV 264
Cdd:PRK10700  158 RGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQT 237

                         250       260       270
                  ....*....|....*....|....*....|..
gi 2130561025 265 ESLRaelKLEEGAPSALTLQPVIGQRRAAKST 296
Cdd:PRK10700  238 NYLR---ELVELPPETSSKVAVEKDRRRMKAN 266
PseudoU_synth_RluB cd02556
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ...
 90-259 1.46e-68

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: 218.33  E-value: 1.46e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  90 RVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAp 169
Cdd:cd02556     1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFG- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 170 egeeTVSDAIIERLSRGVLLEDGGAKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPR 249
Cdd:cd02556    80 ----QVTDEQLKSLKKGVELEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPG 155

                         170
                  ....*....|
gi 2130561025 250 ELLRGQSVEV 259
Cdd:cd02556   156 NLKRGQWEEL 165
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 128-247 4.71e-33

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: 122.44  E-value: 4.71e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 128 IGRLDINTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPegeetVSDAIIERLSRGVLLEDGGAKFDEIERIGGTDS 207
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGP-----VTDEDLEALRKGVQLEDGKTKPAKLKVITEPGF 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2130561025 208 HDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISL 247
Cdd:TIGR00093  76 PTWLRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSL 115
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 91-225 4.50e-11

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: 61.27  E-value: 4.50e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  91 VLIYNKPEGEVTTREDPEG---RPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGELANAMMH--PSYEVEREYVVR 165
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTkllSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2130561025 166 VRAPEGEET-----VSDAIIERLSRGVLLEDGGAKFDEIERI--GGTDSHDWFRVVVKEGRNREVRR 225
Cdd:pfam00849  81 VDKPEEEEGtikspIKKEKNKSPFRKEEELGGKKAVTHLKVLksGSKGDYSLLELELVTGRKHQIRA 147
S4 smart00363
S4 RNA-binding domain;
29-79 4.98e-06

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 44.12  E-value: 4.98e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2130561025   29 RLHKVLAQAGLG-SRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRS 79
Cdd:smart00363   2 RLDKFLARLGLApSRSQARRLIEQGRVKVNGKKVTKpSYIVKPGDVISVRGKE 54
 
Name Accession Description Interval E-value
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 27-255 5.70e-85

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: 262.66  E-value: 5.70e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  27 EERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVasaLTEPSRVLIYNKPEGEVTTRE 105
Cdd:COG1187     2 GMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTElGTKVDPGDEVTVDGKPLK---LPEEPVYLLLNKPAGVVSTTK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 106 DPEGRPTVFESLPALKGSRWIAIGRLDINttgllllttDGELANAMMHPSYEVEREYVVRVRAPegeetVSDAIIERLSR 185
Cdd:COG1187    79 DPEGRPTVFDLLPEARKERLFPVGRLDKDteglllltnDGELAHRLTHPKYGVEKEYLVRVDGP-----VTEEDLERLRE 153

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 186 GVLLEDGGAKFDEIERIGGTDSHdWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPrELLRGQ 255
Cdd:COG1187   154 GVELEDGPTKPAKVEILSGEANT-WLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLG-DLPPGE 221
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
28-296 2.46e-78

23S rRNA pseudouridine(2605) synthase RluB;


Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 248.14  E-value: 2.46e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  28 ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQTG--MSVRSGDKIELDGRSF-VASALTEPSRVLIYNKPEGEVTTR 104
Cdd:PRK10700    3 EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGdrVEVTPGLKIRIDGHLIsVKESAEQICRVLAYYKPEGELCTR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 105 EDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRapeGEetVSDAIIERLS 184
Cdd:PRK10700   83 NDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVF---GQ--VDDAKLRQLS 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 185 RGVLLEDGGAKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSVEVAQEKV 264
Cdd:PRK10700  158 RGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQT 237

                         250       260       270
                  ....*....|....*....|....*....|..
gi 2130561025 265 ESLRaelKLEEGAPSALTLQPVIGQRRAAKST 296
Cdd:PRK10700  238 NYLR---ELVELPPETSSKVAVEKDRRRMKAN 266
PseudoU_synth_RluB cd02556
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ...
 90-259 1.46e-68

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: 218.33  E-value: 1.46e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  90 RVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAp 169
Cdd:cd02556     1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFG- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 170 egeeTVSDAIIERLSRGVLLEDGGAKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPR 249
Cdd:cd02556    80 ----QVTDEQLKSLKKGVELEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPG 155

                         170
                  ....*....|
gi 2130561025 250 ELLRGQSVEV 259
Cdd:cd02556   156 NLKRGQWEEL 165
PseudoU_synth_RsuA_like cd02870
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ...
 91-242 1.29e-44

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: 154.57  E-value: 1.29e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  91 VLIYNKPEGEVTTREDPEGRPTVFESLPAlKGSRWIAIGRLDINTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPe 170
Cdd:cd02870     1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKD-VGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGV- 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2130561025 171 geetVSDAIIERLSRGVLLEDGGAKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRY 242
Cdd:cd02870    79 ----PSEEELRRLRAGVELDDGKTAPAKVKVLSRDPKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 128-247 4.71e-33

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: 122.44  E-value: 4.71e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 128 IGRLDINTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPegeetVSDAIIERLSRGVLLEDGGAKFDEIERIGGTDS 207
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGP-----VTDEDLEALRKGVQLEDGKTKPAKLKVITEPGF 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2130561025 208 HDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISL 247
Cdd:TIGR00093  76 PTWLRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSL 115
PseudoU_synth_Rsu_Rlu_like cd02550
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ...
 91-242 1.19e-31

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: 119.40  E-value: 1.19e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  91 VLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPE 170
Cdd:cd02550     1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2130561025 171 GEETVSDAIIERLSR--GVLLEDGGAKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRY 242
Cdd:cd02550    81 DEEGIEDLATVRRGRlsGLVDEGVPLAVTKVRVIGEHGGTGRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI 154
PseudoU_synth_RsuA cd02553
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ...
 90-255 2.13e-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: 102.60  E-value: 2.13e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  90 RVLIYNKPEGEVTTREDPEGrPTVFESLPALKGSRWIAI-GRLDINTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRA 168
Cdd:cd02553     1 VYLMLNKPAGVVCATKDPHH-PTVIDLLPEPDRRRDLFPvGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 169 PegeetVSDAIIERLSRGVLLEDGG-AKFDEIERIGGTdshdWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISL 247
Cdd:cd02553    80 P-----LTEDDIEAFAEGVLLHDGYpTKPAKLEILSPT----TVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLEL 150


                  ....*...
gi 2130561025 248 PRELLRGQ 255
Cdd:cd02553   151 DDDLAPGE 158
PseudoU_synth_RluF cd02554
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ...
 92-247 2.51e-21

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: 90.83  E-value: 2.51e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  92 LIYNKPEGEVTTREDPEgRPTVFESLPalKGSRWIAIGRLDINTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPeg 171
Cdd:cd02554     3 IAYNKPVGIDCTLERAD-EDNIIDFVN--PPPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKP-- 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2130561025 172 eetVSDAIIERLSRGVLLEDGGAKFDEIERIggtdSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISL 247
Cdd:cd02554    78 ---ITDEFIEGMSNGVVILGTVTKPCKVERL----AKDKFRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIEL 146
PRK10475 PRK10475
23S rRNA pseudouridine(2604) synthase RluF;
29-307 9.33e-20

23S rRNA pseudouridine(2604) synthase RluF;


Pssm-ID: 236698 [Multi-domain]  Cd Length: 290  Bit Score: 89.79  E-value: 9.33e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  29 RLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQTGMSVRSGDKIELDGRsfvasaLTEP----SRVLI-YNKPEGEVTT 103
Cdd:PRK10475    8 RLNKYISESGICSRREADRYIEQGNVFINGKRATIGDQVKAGDVVKVNGQ------LIEPreaeDLVLIaLNKPVGIVST 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 104 REDPEGRPTV-FESlpalKGSRWIAIGRLDINTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPegeetVSDAIIER 182
Cdd:PRK10475   82 TEDGERDNIVdFVN----HSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKP-----ITDEFIRG 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 183 LSRGVLLEDGGAKFDEIERiggtDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLP-------RELlrgq 255
Cdd:PRK10475  153 MGAGVPILGTVTKKCKVKK----EAPFVFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSgiplgewRDL---- 224

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2130561025 256 sveVAQEKVESLRA-ELKLEEGAPSALTLQPVIGQRRAAKSTVHVSRDGRSNA 307
Cdd:PRK10475  225 ---TDDELIDLFKLiENSSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPA 274
PRK10839 PRK10839
16S rRNA pseudouridine(516) synthase RsuA;
29-267 1.07e-14

16S rRNA pseudouridine(516) synthase RsuA;


Pssm-ID: 236774 [Multi-domain]  Cd Length: 232  Bit Score: 73.60  E-value: 1.07e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  29 RLHKVLAQAgLGSRRALEQR-IADGLIKVNGAVAQTG-MSVRSGDKIELDGRSFvasALTEPSRVLIYNKPEGEVTTRED 106
Cdd:PRK10839    2 RLDKFISQQ-LGVSRAIAGReLRANRVTVDGEIVKNGaFKLLPEHDVAYDGNPL---AQQHGPRYFMLNKPQGYVCSTDD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 107 PEgRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPEGEETVsdaiiERLSRG 186
Cdd:PRK10839   78 PD-HPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTA-----EQFAKG 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 187 VLL--EDGGAKFDEIERIGGTDshdwFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSVEVAQEKV 264
Cdd:PRK10839  152 VQLhnEKDLTKPAVLEVITPTQ----VRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDADLAPGEYRPLTEEEI 227


                  ...
gi 2130561025 265 ESL 267
Cdd:PRK10839  228 ASV 230
PseudoU_synth_RluE cd02566
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ...
 91-247 4.12e-13

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: 67.41  E-value: 4.12e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  91 VLIYNKPEGEVTT-REDPEGRPTVFESLPaLKGSRwiAIGRLDINTTGLLLLTTDGELANAMMHPSYEVEREYVVRVrap 169
Cdd:cd02566     1 LILFNKPYGVLSQfTDESEKHKTLKDYID-DPGVY--AAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQV--- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 170 EGEETvSDAiIERLSRGVLLEDGGAKFDEIERIGGTDS---------------HDWFRVVVKEGRNREVRRLWESQGCQV 234
Cdd:cd02566    75 EGVPT-EDA-LEQLRNGVELGDGLTLPAKVEKVDEPPWlwereppirfrknipTSWIEITICEGKNRQVRRMTAAVGFPT 152

                         170
                  ....*....|...
gi 2130561025 235 SRLKRSRYGKISL 247
Cdd:cd02566   153 LRLIRVSIGDIGL 165
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 91-225 4.50e-11

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: 61.27  E-value: 4.50e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  91 VLIYNKPEGEVTTREDPEG---RPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGELANAMMH--PSYEVEREYVVR 165
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTkllSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2130561025 166 VRAPEGEET-----VSDAIIERLSRGVLLEDGGAKFDEIERI--GGTDSHDWFRVVVKEGRNREVRR 225
Cdd:pfam00849  81 VDKPEEEEGtikspIKKEKNKSPFRKEEELGGKKAVTHLKVLksGSKGDYSLLELELVTGRKHQIRA 147
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 28-95 2.78e-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: 56.49  E-value: 2.78e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  28 ERLHKVLAQAGL-GSRRALEQRIADGLIKVNGAVA-QTGMSVRSGDKIELDGRSFVASALTEPSRVLIYN 95
Cdd:cd00165     1 MRLDKILARLGLaPSRSEARQLIKHGHVLVNGKVVtKPSYKVKPGDVIEVDGKSIEEDIVYEDKKLLVVN 70
PSSA_1 cd02555
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ...
 92-247 7.36e-09

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: 55.49  E-value: 7.36e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  92 LIYNKPEGEVTTREDPEGRPTVF-----ESLPALKG--SRWIAIGRLDINTTGLLLLTTDGELANAMMHPSYEVEREYVV 164
Cdd:cd02555     7 LLLHKPAGMVSEQALALLGPGQRsaadrSGRRPLKGhfARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQEYLV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 165 RVRApegeETVSDAiIERLSRGVLLEDGGAKFDEIERIggtdSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGK 244
Cdd:cd02555    87 EVRG----ELTAGG-LERLNHGLTYDGRELPPAKVSWQ----NEQRLRFALKEPQPGQIRRMCESVGLEVVALRRIRIGR 157


                  ...
gi 2130561025 245 ISL 247
Cdd:cd02555   158 VSL 160
PRK11394 PRK11394
23S rRNA pseudouridine(2457) synthase RluE;
87-247 1.50e-08

23S rRNA pseudouridine(2457) synthase RluE;


Pssm-ID: 183115  Cd Length: 217  Bit Score: 55.13  E-value: 1.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025  87 EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPaLKGSrwIAIGRLDINTTGLLLLTTDGELANAMMHPSYEVEREYVVRV 166
Cdd:PRK11394   37 QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP-VQGV--YAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQV 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2130561025 167 rapEGEETvSDAIiERLSRGVLLEDGG---AKFDEIE------------RIGGTDSHDWFRVVVKEGRNREVRRLWESQG 231
Cdd:PRK11394  114 ---EGIPT-QDAL-EALRNGVTLNDGPtlpAGAELVDepawlwprnppiRERKSIPTSWLKITLYEGRNRQVRRMTAHVG 188

                         170
                  ....*....|....*.
gi 2130561025 232 CQVSRLKRSRYGKISL 247
Cdd:PRK11394  189 FPTLRLIRYAMGDYSL 204
S4 smart00363
S4 RNA-binding domain;
29-79 4.98e-06

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 44.12  E-value: 4.98e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2130561025   29 RLHKVLAQAGLG-SRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRS 79
Cdd:smart00363   2 RLDKFLARLGLApSRSQARRLIEQGRVKVNGKKVTKpSYIVKPGDVISVRGKE 54
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 28-73 1.56e-05

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: 42.09  E-value: 1.56e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2130561025  28 ERLHKVLAQAGLG-SRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKI 73
Cdd:pfam01479   1 RRLDKVLARLGLAsSRSQARQLIEHGRVLVNGKVVKDpSYRVKPGDEI 48
 
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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