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Conserved domains on  [gi|1148848709|ref|WP_077571105|]
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23S rRNA pseudouridine(2604) synthase RluF [Paenibacillus ihbetae]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10475 super family cl35922
23S rRNA pseudouridine(2604) synthase RluF;
1-229 6.16e-117

23S rRNA pseudouridine(2604) synthase RluF;


The actual alignment was detected with superfamily member PRK10475:

Pssm-ID: 236698 [Multi-domain]  Cd Length: 290  Bit Score: 335.16  E-value: 6.16e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709   1 MRINKFISETGYCSRREADKLVESGKVTINGEIAVLGSQAEEGDDVRINGRPLQEKKQQH-VYIALNKPVGITSTTESHI 79
Cdd:PRK10475    7 TRLNKYISESGICSRREADRYIEQGNVFINGKRATIGDQVKAGDVVKVNGQLIEPREAEDlVLIALNKPVGIVSTTEDGE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  80 KGNIVDFVGHKERIFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPVTPAFLKGMSSGVKILGEMTLP 159
Cdd:PRK10475   87 RDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTKK 166

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709 160 CQVTRISERVFRIILTEGKNRQIRRMCSAFGYEVRRLKRIRIMNILLGDQKVGTWRDLTPAEKQELGKLL 229
Cdd:PRK10475  167 CKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLI 236
 
Name Accession Description Interval E-value
PRK10475 PRK10475
23S rRNA pseudouridine(2604) synthase RluF;
1-229 6.16e-117

23S rRNA pseudouridine(2604) synthase RluF;


Pssm-ID: 236698 [Multi-domain]  Cd Length: 290  Bit Score: 335.16  E-value: 6.16e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709   1 MRINKFISETGYCSRREADKLVESGKVTINGEIAVLGSQAEEGDDVRINGRPLQEKKQQH-VYIALNKPVGITSTTESHI 79
Cdd:PRK10475    7 TRLNKYISESGICSRREADRYIEQGNVFINGKRATIGDQVKAGDVVKVNGQLIEPREAEDlVLIALNKPVGIVSTTEDGE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  80 KGNIVDFVGHKERIFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPVTPAFLKGMSSGVKILGEMTLP 159
Cdd:PRK10475   87 RDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTKK 166

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709 160 CQVTRISERVFRIILTEGKNRQIRRMCSAFGYEVRRLKRIRIMNILLGDQKVGTWRDLTPAEKQELGKLL 229
Cdd:PRK10475  167 CKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLI 236
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 1-218 2.46e-106

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


Pssm-ID: 440800 [Multi-domain]  Cd Length: 226  Bit Score: 305.80  E-value: 2.46e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709   1 MRINKFISETGYCSRREADKLVESGKVTINGEIA-VLGSQAEEGDDVRINGRPLQEKkQQHVYIALNKPVGITSTTESHI 79
Cdd:COG1187     3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVtELGTKVDPGDEVTVDGKPLKLP-EEPVYLLLNKPAGVVSTTKDPE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  80 -KGNIVDFVG--HKERIFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPVTPAFLKGMSSGVKILGEM 156
Cdd:COG1187    82 gRPTVFDLLPeaRKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELEDGP 161

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1148848709 157 TLPCQVTRIS---ERVFRIILTEGKNRQIRRMCSAFGYEVRRLKRIRIMNILLGDQKVGTWRDLT 218
Cdd:COG1187   162 TKPAKVEILSgeaNTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLGDLPPGEWRELT 226
PseudoU_synth_RluF cd02554
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ...
 61-224 3.11e-98

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: 283.05  E-value: 3.11e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  61 VYIALNKPVGITSTTESHIKGNIVDFVGHKERIFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPVTP 140
Cdd:cd02554     1 VYIAYNKPVGIDCTLERADEDNIIDFVNPPPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPITD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709 141 AFLKGMSSGVKILGEMTLPCQVTRISERVFRIILTEGKNRQIRRMCSAFGYEVRRLKRIRIMNILLGDQKVGTWRDLTPA 220
Cdd:cd02554    81 EFIEGMSNGVVILGTVTKPCKVERLAKDKFRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIELGDLAPGEWRPLTDA 160


                  ....
gi 1148848709 221 EKQE 224
Cdd:cd02554   161 ELFE 164
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 96-219 2.33e-49

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: 157.88  E-value: 2.33e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  96 IGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPVTPAFLKGMSSGVKILGEMTLPCQVTRISERVF----R 171
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFptwlR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1148848709 172 IILTEGKNRQIRRMCSAFGYEVRRLKRIRIMNILLGDQKVGTWRDLTP 219
Cdd:TIGR00093  81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPLTL 128
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 62-188 4.86e-22

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: 88.23  E-value: 4.86e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  62 YIALNKPVGITS------TTESHIKGNIVDFVGHKERIFPIGRLDKDSEGLILLTNDGDIVNKI--LRSEGKHEKEYIVT 133
Cdd:pfam00849   1 YIVVNKPAGVPVhptdslTKLLSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLnkLFPERKIEKEYLAL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1148848709 134 VNRPVTPAFL--KGMSSGVKILGEMTLPCQVTRISERVFRII--------------LTEGKNRQIRRMCSA 188
Cdd:pfam00849  81 VDKPEEEEGTikSPIKKEKNKSPFRKEEELGGKKAVTHLKVLksgskgdyslleleLVTGRKHQIRAHLAA 151
S4 smart00363
S4 RNA-binding domain;
1-58 2.70e-06

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 43.74  E-value: 2.70e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709    1 MRINKFISETGY-CSRREADKLVESGKVTINGEIAVLGSQA-EEGDDVRINGRPLQEKKQ 58
Cdd:smart00363   1 RRLDKFLARLGLaPSRSQARRLIEQGRVKVNGKKVTKPSYIvKPGDVISVRGKELKRLKK 60
 
Name Accession Description Interval E-value
PRK10475 PRK10475
23S rRNA pseudouridine(2604) synthase RluF;
1-229 6.16e-117

23S rRNA pseudouridine(2604) synthase RluF;


Pssm-ID: 236698 [Multi-domain]  Cd Length: 290  Bit Score: 335.16  E-value: 6.16e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709   1 MRINKFISETGYCSRREADKLVESGKVTINGEIAVLGSQAEEGDDVRINGRPLQEKKQQH-VYIALNKPVGITSTTESHI 79
Cdd:PRK10475    7 TRLNKYISESGICSRREADRYIEQGNVFINGKRATIGDQVKAGDVVKVNGQLIEPREAEDlVLIALNKPVGIVSTTEDGE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  80 KGNIVDFVGHKERIFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPVTPAFLKGMSSGVKILGEMTLP 159
Cdd:PRK10475   87 RDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTKK 166

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709 160 CQVTRISERVFRIILTEGKNRQIRRMCSAFGYEVRRLKRIRIMNILLGDQKVGTWRDLTPAEKQELGKLL 229
Cdd:PRK10475  167 CKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLI 236
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 1-218 2.46e-106

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


Pssm-ID: 440800 [Multi-domain]  Cd Length: 226  Bit Score: 305.80  E-value: 2.46e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709   1 MRINKFISETGYCSRREADKLVESGKVTINGEIA-VLGSQAEEGDDVRINGRPLQEKkQQHVYIALNKPVGITSTTESHI 79
Cdd:COG1187     3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVtELGTKVDPGDEVTVDGKPLKLP-EEPVYLLLNKPAGVVSTTKDPE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  80 -KGNIVDFVG--HKERIFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPVTPAFLKGMSSGVKILGEM 156
Cdd:COG1187    82 gRPTVFDLLPeaRKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELEDGP 161

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1148848709 157 TLPCQVTRIS---ERVFRIILTEGKNRQIRRMCSAFGYEVRRLKRIRIMNILLGDQKVGTWRDLT 218
Cdd:COG1187   162 TKPAKVEILSgeaNTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLGDLPPGEWRELT 226
PseudoU_synth_RluF cd02554
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ...
 61-224 3.11e-98

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: 283.05  E-value: 3.11e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  61 VYIALNKPVGITSTTESHIKGNIVDFVGHKERIFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPVTP 140
Cdd:cd02554     1 VYIAYNKPVGIDCTLERADEDNIIDFVNPPPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPITD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709 141 AFLKGMSSGVKILGEMTLPCQVTRISERVFRIILTEGKNRQIRRMCSAFGYEVRRLKRIRIMNILLGDQKVGTWRDLTPA 220
Cdd:cd02554    81 EFIEGMSNGVVILGTVTKPCKVERLAKDKFRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIELGDLAPGEWRPLTDA 160


                  ....
gi 1148848709 221 EKQE 224
Cdd:cd02554   161 ELFE 164
PseudoU_synth_RsuA_like cd02870
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ...
 62-201 4.23e-54

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: 170.37  E-value: 4.23e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  62 YIALNKPVGITSTTESHIKGNIV--DFVGHKERIFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPVT 139
Cdd:cd02870     1 YLLLNKPRGVVSTVRDPEGRPTVldLLKDVGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVPS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1148848709 140 PAFLKGMSSGVKILGEMTLPCQVTRISER----VFRIILTEGKNRQIRRMCSAFGYEVRRLKRIRI 201
Cdd:cd02870    81 EEELRRLRAGVELDDGKTAPAKVKVLSRDpkntLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 96-219 2.33e-49

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: 157.88  E-value: 2.33e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  96 IGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPVTPAFLKGMSSGVKILGEMTLPCQVTRISERVF----R 171
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFptwlR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1148848709 172 IILTEGKNRQIRRMCSAFGYEVRRLKRIRIMNILLGDQKVGTWRDLTP 219
Cdd:TIGR00093  81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPLTL 128
PseudoU_synth_RsuA cd02553
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ...
 61-222 1.52e-46

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: 151.90  E-value: 1.52e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  61 VYIALNKPVGITSTTESHIKGNIVDFVGHKER---IFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRP 137
Cdd:cd02553     1 VYLMLNKPAGVVCATKDPHHPTVIDLLPEPDRrrdLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAGP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709 138 VTPAFLKGMSSGVKILGE-MTLPCQVTRISERVFRIILTEGKNRQIRRMCSAFGYEVRRLKRIRIMNILLGDQ-KVGTWR 215
Cdd:cd02553    81 LTEDDIEAFAEGVLLHDGyPTKPAKLEILSPTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDDDlAPGEWR 160


                  ....*..
gi 1148848709 216 DLTPAEK 222
Cdd:cd02553   161 PLTEEEL 167
PseudoU_synth_Rsu_Rlu_like cd02550
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ...
 62-201 4.59e-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: 124.79  E-value: 4.59e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  62 YIALNKPVGITSTTESHIKGNIV---DFVGHKERIFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPV 138
Cdd:cd02550     1 ILVLNKPSGLVCHPTDRDRDPTVvvrLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1148848709 139 TPAFLKGMS-------SGVKILGEMTLPCQVTRISER----VFRIILTEGKNRQIRRMCSAFGYEVRRLKRIRI 201
Cdd:cd02550    81 DEEGIEDLAtvrrgrlSGLVDEGVPLAVTKVRVIGEHggtgRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI 154
PRK10839 PRK10839
16S rRNA pseudouridine(516) synthase RsuA;
1-221 7.09e-33

16S rRNA pseudouridine(516) synthase RsuA;


Pssm-ID: 236774 [Multi-domain]  Cd Length: 232  Bit Score: 119.06  E-value: 7.09e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709   1 MRINKFISETGYCSRREADKLVESGKVTINGEIAVLGS-QAEEGDDVRINGRPLQekkQQH--VYIALNKPVGITSTTES 77
Cdd:PRK10839    1 MRLDKFISQQLGVSRAIAGRELRANRVTVDGEIVKNGAfKLLPEHDVAYDGNPLA---QQHgpRYFMLNKPQGYVCSTDD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  78 HIKGNIVDF----VGHKerIFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPVTPAFLKGMSSGVKIL 153
Cdd:PRK10839   78 PDHPTVLYFldepVAYK--LHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLH 155

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1148848709 154 GEMTL--PCQVTRISERVFRIILTEGKNRQIRRMCSAFGYEVRRLKRIRIMNILLGDQ-KVGTWRDLTPAE 221
Cdd:PRK10839  156 NEKDLtkPAVLEVITPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDADlAPGEYRPLTEEE 226
PSSA_1 cd02555
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ...
 58-222 3.29e-32

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: 115.58  E-value: 3.29e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  58 QQHVYIALNKPVGITST-----------TESHIKGnIVDFVGHKERIFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKH 126
Cdd:cd02555     2 LEPVTLLLHKPAGMVSEqalallgpgqrSAADRSG-RRPLKGHFARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709 127 EKEYIVTVNRPVTPAFLKGMSSGVKILGEMTLPCQVTRISERVFRIILTEGKNRQIRRMCSAFGYEVRRLKRIRIMNILL 206
Cdd:cd02555    81 EQEYLVEVRGELTAGGLERLNHGLTYDGRELPPAKVSWQNEQRLRFALKEPQPGQIRRMCESVGLEVVALRRIRIGRVSL 160

                         170
                  ....*....|....*.
gi 1148848709 207 GDQKVGTWRDLTPAEK 222
Cdd:cd02555   161 GKLPLGQWRYLTTGER 176
PseudoU_synth_RluE cd02566
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ...
 62-208 1.38e-30

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: 110.93  E-value: 1.38e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  62 YIALNKPVGITS--TTESHIKGNIVDFVGHKeRIFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPVT 139
Cdd:cd02566     1 LILFNKPYGVLSqfTDESEKHKTLKDYIDDP-GVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVPT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709 140 PAFLKGMSSGVKILGEMTLPCQVTRISE-----------RV--------FRIILTEGKNRQIRRMCSAFGYEVRRLKRIR 200
Cdd:cd02566    80 EDALEQLRNGVELGDGLTLPAKVEKVDEppwlwereppiRFrkniptswIEITICEGKNRQVRRMTAAVGFPTLRLIRVS 159


                  ....*...
gi 1148848709 201 IMNILLGD 208
Cdd:cd02566   160 IGDIGLDN 167
PseudoU_synth_RluB cd02556
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ...
 63-219 9.86e-26

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: 98.53  E-value: 9.86e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  63 IALNKPVGITSTTESHIKGNIV-DFVGH--KERIFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPVT 139
Cdd:cd02556     3 LIYHKPEGLICTRKDPKGRPTVfDLLPKlgIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQVT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709 140 PAFLKGMSSGVKILGEMTLPCQVTRISERV----FRIILTEGKNRQIRRMCSAFGYEVRRLKRIRIMNI-LLGDQKVGTW 214
Cdd:cd02556    83 DEQLKSLKKGVELEDGFAGFKSIQLEGGEGknswYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIfLPGNLKRGQW 162


                  ....*
gi 1148848709 215 RDLTP 219
Cdd:cd02556   163 EELPP 167
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 62-188 4.86e-22

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: 88.23  E-value: 4.86e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  62 YIALNKPVGITS------TTESHIKGNIVDFVGHKERIFPIGRLDKDSEGLILLTNDGDIVNKI--LRSEGKHEKEYIVT 133
Cdd:pfam00849   1 YIVVNKPAGVPVhptdslTKLLSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLnkLFPERKIEKEYLAL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1148848709 134 VNRPVTPAFL--KGMSSGVKILGEMTLPCQVTRISERVFRII--------------LTEGKNRQIRRMCSA 188
Cdd:pfam00849  81 VDKPEEEEGTikSPIKKEKNKSPFRKEEELGGKKAVTHLKVLksgskgdyslleleLVTGRKHQIRAHLAA 151
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
2-206 3.73e-20

23S rRNA pseudouridine(2605) synthase RluB;


Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 86.36  E-value: 3.73e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709   2 RINKFISETGYCSRREADKLVESGKVTINGEIAVLGSQAE--EGDDVRINGRPLQEKKQQHV---YIALNKPVGiTSTTE 76
Cdd:PRK10700    4 KLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEvtPGLKIRIDGHLISVKESAEQicrVLAYYKPEG-ELCTR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  77 SHIKGNIVDFVG----HKERIFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPVTPAFLKGMSSGVKI 152
Cdd:PRK10700   83 NDPEGRPTVFDRlpklRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGVQL 162

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1148848709 153 ----LGEMTLPCQVTRISERVFRIILTEGKNRQIRRMCSAFGYEVRRLKRIRIMNILL 206
Cdd:PRK10700  163 edgpAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220
PRK11394 PRK11394
23S rRNA pseudouridine(2457) synthase RluE;
63-218 1.10e-14

23S rRNA pseudouridine(2457) synthase RluE;


Pssm-ID: 183115  Cd Length: 217  Bit Score: 70.54  E-value: 1.10e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709  63 IALNKPVGITST-TESHIKGNIVDFVGhKERIFPIGRLDKDSEGLILLTNDGDIVNKILRSEGKHEKEYIVTVNRPVTPA 141
Cdd:PRK11394   42 ILFNKPYDVLPQfTDEAGRKTLKEFIP-VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQD 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709 142 FLKGMSSGVKILGEMTLPCQVTRISERVF-------------------RIILTEGKNRQIRRMCSAFGYEVRRLKRIRIM 202
Cdd:PRK11394  121 ALEALRNGVTLNDGPTLPAGAELVDEPAWlwprnppirerksiptswlKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMG 200

                         170
                  ....*....|....*.
gi 1148848709 203 NILLGDQKVGTWRDLT 218
Cdd:PRK11394  201 DYSLDNLANGEWREAT 216
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 1-66 2.05e-07

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: 46.86  E-value: 2.05e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709   1 MRINKFISETGYC-SRREADKLVESGKVTINGEIAV-LGSQAEEGDDVRINGRPLQEK--KQQHVYIALN 66
Cdd:cd00165     1 MRLDKILARLGLApSRSEARQLIKHGHVLVNGKVVTkPSYKVKPGDVIEVDGKSIEEDivYEDKKLLVVN 70
S4 smart00363
S4 RNA-binding domain;
1-58 2.70e-06

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 43.74  E-value: 2.70e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1148848709    1 MRINKFISETGY-CSRREADKLVESGKVTINGEIAVLGSQA-EEGDDVRINGRPLQEKKQ 58
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 ...
 1-46 4.48e-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: 42.48  E-value: 4.48e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1148848709   1 MRINKFISETGYC-SRREADKLVESGKVTINGEIA-VLGSQAEEGDDV 46
Cdd:pfam01479   1 RRLDKVLARLGLAsSRSQARQLIEHGRVLVNGKVVkDPSYRVKPGDEI 48
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 62-109 3.76e-05

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: 43.09  E-value: 3.76e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1148848709  62 YIALNKPVGITST-TESHIKGNIVDFVGH-------KERIFPIGRLDKDSEGLILL 109
Cdd:cd02869     1 LLVVNKPAGLPVHpGPGHLTGTLVNALLKlllllgeEFRPGLVHRLDKDTSGLLLV 56
 
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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