|
Name |
Accession |
Description |
Interval |
E-value |
| RsuA |
COG1187 |
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ... |
46-326 |
3.81e-69 |
|
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: 215.28 E-value: 3.81e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 46 IRLNKLISMKRNISRRKSDEFIKDGKVKINNKIITNPGTHVHIGkDSLRIYDKKIKLtniinmikqneNKLHKWIVLHKP 125
Cdd:COG1187 3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTELGTKVDPG-DEVTVDGKPLKL-----------PEEPVYLLLNKP 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 126 KGLLCTSNDEKNRKSIYTLFPEEmlQKYRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEGPVKMNAL 205
Cdd:COG1187 71 AGVVSTTKDPEGRPTVFDLLPEA--RKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDL 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 206 KELARGIYLeEDEKTQPKKiynykesreksniddkkkkkmskmkkktnpafIEILREEkikikedtkKITVLNISIKEGR 285
Cdd:COG1187 149 ERLREGVEL-EDGPTKPAK--------------------------------VEILSGE---------ANTWLRITLTEGR 186
|
250 260 270 280
....*....|....*....|....*....|....*....|.
gi 124801447 286 NRQIRKMFQQINQPVIKIKRTSFENITLKNIyFPKQYRELN 326
Cdd:COG1187 187 NRQVRRMFEAVGLPVVRLKRVRIGPLTLGDL-PPGEWRELT 226
|
|
| PseudoU_synth_RsuA_like |
cd02870 |
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ... |
119-308 |
1.60e-43 |
|
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: 146.87 E-value: 1.60e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 119 WIVLHKPKGLLCTSNDEKNRKsiyTLFPEEMLQKYRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEG 198
Cdd:cd02870 1 YLLLNKPRGVVSTVRDPEGRP---TVLDLLKDVGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 199 PVKMNALKELARGIYLeEDEKTQPkkiynykesreksniddkkkkkmskmkkktnpafieilreEKIKIKEDTKKITVLN 278
Cdd:cd02870 78 VPSEEELRRLRAGVEL-DDGKTAP----------------------------------------AKVKVLSRDPKNTLLE 116
|
170 180 190
....*....|....*....|....*....|
gi 124801447 279 ISIKEGRNRQIRKMFQQINQPVIKIKRTSF 308
Cdd:cd02870 117 VTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146
|
|
| TIGR00093 |
TIGR00093 |
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ... |
158-327 |
4.89e-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: 118.97 E-value: 4.89e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 158 VGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEGPVKMNALKELARGIYLeEDEKTQPKKiynykesreksni 237
Cdd:TIGR00093 1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQL-EDGKTKPAK------------- 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 238 ddkkkkkmskmkkktnpafIEILREEKIKIKedtkkitvLNISIKEGRNRQIRKMFQQINQPVIKIKRTSFENITLKNIY 317
Cdd:TIGR00093 67 -------------------LKVITEPGFPTW--------LRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLP 119
|
170
....*....|
gi 124801447 318 fPKQYRELNQ 327
Cdd:TIGR00093 120 -PGEWRPLTL 128
|
|
| PRK10700 |
PRK10700 |
23S rRNA pseudouridine(2605) synthase RluB; |
47-334 |
6.53e-25 |
|
23S rRNA pseudouridine(2605) synthase RluB;
Pssm-ID: 182659 [Multi-domain] Cd Length: 289 Bit Score: 101.77 E-value: 6.53e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 47 RLNKLISMKRNISRRKSDEFIKDGKVKINNKIITnPGTHVHIGKDSlriydkKIKLTNIINMIKQNENKLHKWIVLHKPK 126
Cdd:PRK10700 4 KLQKVLARAGHGSRREIESIIEAGRVSVDGKIAT-LGDRVEVTPGL------KIRIDGHLISVKESAEQICRVLAYYKPE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 127 GLLCTSNDEKNRKSIYTLFPEemLQKYRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEGPVKMNALK 206
Cdd:PRK10700 77 GELCTRNDPEGRPTVFDRLPK--LRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLR 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 207 ELARGIYLEEdektqpkkiynykesreksniddkkkkkmskmkkktNPAFIEILR---EEKIKikedtkkiTVLNISIKE 283
Cdd:PRK10700 155 QLSRGVQLED------------------------------------GPAAFKTIKfsgGEGIN--------QWYNVTLTE 190
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*.
gi 124801447 284 GRNRQIRKMFQQINQPVIKIKRTSFENITLkniyfPK-----QYRELNQKEVNDLK 334
Cdd:PRK10700 191 GRNREVRRLWEAVGVQVSRLIRVRYGDIPL-----PKglprgGWTELDLAQTNYLR 241
|
|
| PseudoU_synth_2 |
pfam00849 |
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ... |
119-295 |
1.22e-18 |
|
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: 81.30 E-value: 1.22e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 119 WIVLHKPKGLLCTSNDEKN-RKSIYTLFPEEMLQKYRLVTVGRLDRNTSGVLLLTNDYAWVNKLTH--PKYQRIRTYRVH 195
Cdd:pfam00849 1 YIVVNKPAGVPVHPTDSLTkLLSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 196 IEGPvkmnalkELARGIYLEEDEKTQPKKIYNYKESREKSNIddkkkkkmskmkkktnPAFIEILREEKIkikedtKKIT 275
Cdd:pfam00849 81 VDKP-------EEEEGTIKSPIKKEKNKSPFRKEEELGGKKA----------------VTHLKVLKSGSK------GDYS 131
|
170 180
....*....|....*....|
gi 124801447 276 VLNISIKEGRNRQIRKMFQQ 295
Cdd:pfam00849 132 LLELELVTGRKHQIRAHLAA 151
|
|
| S4 |
smart00363 |
S4 RNA-binding domain; |
47-101 |
1.61e-05 |
|
S4 RNA-binding domain;
Pssm-ID: 214638 [Multi-domain] Cd Length: 60 Bit Score: 41.81 E-value: 1.61e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 124801447 47 RLNKLI-SMKRNISRRKSDEFIKDGKVKINNKIITNPGTHVHIGkDSLRIYDKKIK 101
Cdd:smart00363 2 RLDKFLaRLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPG-DVISVRGKELK 56
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RsuA |
COG1187 |
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ... |
46-326 |
3.81e-69 |
|
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: 215.28 E-value: 3.81e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 46 IRLNKLISMKRNISRRKSDEFIKDGKVKINNKIITNPGTHVHIGkDSLRIYDKKIKLtniinmikqneNKLHKWIVLHKP 125
Cdd:COG1187 3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTELGTKVDPG-DEVTVDGKPLKL-----------PEEPVYLLLNKP 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 126 KGLLCTSNDEKNRKSIYTLFPEEmlQKYRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEGPVKMNAL 205
Cdd:COG1187 71 AGVVSTTKDPEGRPTVFDLLPEA--RKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDL 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 206 KELARGIYLeEDEKTQPKKiynykesreksniddkkkkkmskmkkktnpafIEILREEkikikedtkKITVLNISIKEGR 285
Cdd:COG1187 149 ERLREGVEL-EDGPTKPAK--------------------------------VEILSGE---------ANTWLRITLTEGR 186
|
250 260 270 280
....*....|....*....|....*....|....*....|.
gi 124801447 286 NRQIRKMFQQINQPVIKIKRTSFENITLKNIyFPKQYRELN 326
Cdd:COG1187 187 NRQVRRMFEAVGLPVVRLKRVRIGPLTLGDL-PPGEWRELT 226
|
|
| PseudoU_synth_RsuA_like |
cd02870 |
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ... |
119-308 |
1.60e-43 |
|
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: 146.87 E-value: 1.60e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 119 WIVLHKPKGLLCTSNDEKNRKsiyTLFPEEMLQKYRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEG 198
Cdd:cd02870 1 YLLLNKPRGVVSTVRDPEGRP---TVLDLLKDVGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 199 PVKMNALKELARGIYLeEDEKTQPkkiynykesreksniddkkkkkmskmkkktnpafieilreEKIKIKEDTKKITVLN 278
Cdd:cd02870 78 VPSEEELRRLRAGVEL-DDGKTAP----------------------------------------AKVKVLSRDPKNTLLE 116
|
170 180 190
....*....|....*....|....*....|
gi 124801447 279 ISIKEGRNRQIRKMFQQINQPVIKIKRTSF 308
Cdd:cd02870 117 VTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146
|
|
| PseudoU_synth_RsuA |
cd02553 |
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ... |
120-330 |
7.65e-36 |
|
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: 127.64 E-value: 7.65e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 120 IVLHKPKGLLCTSNDEKNrKSIYTLFPEEMLQKyRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEGP 199
Cdd:cd02553 3 LMLNKPAGVVCATKDPHH-PTVIDLLPEPDRRR-DLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAGP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 200 VKMNALKELARGIYLEEDEKTQPKKiynykesreksniddkkkkkmskmkkktnpafIEILREEKIKikedtkkitvlnI 279
Cdd:cd02553 81 LTEDDIEAFAEGVLLHDGYPTKPAK--------------------------------LEILSPTTVR------------L 116
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 124801447 280 SIKEGRNRQIRKMFQQINQPVIKIKRTSFENITLKNIYFPKQYRELNQKEV 330
Cdd:cd02553 117 TITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDDDLAPGEWRPLTEEEL 167
|
|
| PseudoU_synth_RluB |
cd02556 |
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ... |
118-327 |
9.93e-34 |
|
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: 122.03 E-value: 9.93e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 118 KWIVLHKPKGLLCTSNDEKNRKSIYTLFPEemLQKYRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIE 197
Cdd:cd02556 1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPK--LGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVF 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 198 GPVKMNALKELARGIYLeEDEKTQPKKIYNykESREKSNiddkkkkkmskmkkktnpafieilreekikikedtkkiTVL 277
Cdd:cd02556 79 GQVTDEQLKSLKKGVEL-EDGFAGFKSIQL--EGGEGKN--------------------------------------SWY 117
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 124801447 278 NISIKEGRNRQIRKMFQQINQPVIKIKRTSFENITLKNIYFPKQYRELNQ 327
Cdd:cd02556 118 RVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRGQWEELPP 167
|
|
| TIGR00093 |
TIGR00093 |
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ... |
158-327 |
4.89e-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: 118.97 E-value: 4.89e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 158 VGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEGPVKMNALKELARGIYLeEDEKTQPKKiynykesreksni 237
Cdd:TIGR00093 1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQL-EDGKTKPAK------------- 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 238 ddkkkkkmskmkkktnpafIEILREEKIKIKedtkkitvLNISIKEGRNRQIRKMFQQINQPVIKIKRTSFENITLKNIY 317
Cdd:TIGR00093 67 -------------------LKVITEPGFPTW--------LRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLP 119
|
170
....*....|
gi 124801447 318 fPKQYRELNQ 327
Cdd:TIGR00093 120 -PGEWRPLTL 128
|
|
| PseudoU_synth_Rsu_Rlu_like |
cd02550 |
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ... |
120-307 |
6.12e-26 |
|
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: 101.30 E-value: 6.12e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 120 IVLHKPKGLLCTSNDEKNRKSIYTLFPEEMLqkYRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEGP 199
Cdd:cd02550 2 LVLNKPSGLVCHPTDRDRDPTVVVRLDKLHG--PRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 200 VKMNALKELARGIYLE----EDEKTQPKKiynykesreksniddkkkkkmskmkkktnpafieilreEKIKIKEDTKKIT 275
Cdd:cd02550 80 LDEEGIEDLATVRRGRlsglVDEGVPLAV--------------------------------------TKVRVIGEHGGTG 121
|
170 180 190
....*....|....*....|....*....|..
gi 124801447 276 VLNISIKEGRNRQIRKMFQQINQPVIKIKRTS 307
Cdd:cd02550 122 RLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVR 153
|
|
| PRK10700 |
PRK10700 |
23S rRNA pseudouridine(2605) synthase RluB; |
47-334 |
6.53e-25 |
|
23S rRNA pseudouridine(2605) synthase RluB;
Pssm-ID: 182659 [Multi-domain] Cd Length: 289 Bit Score: 101.77 E-value: 6.53e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 47 RLNKLISMKRNISRRKSDEFIKDGKVKINNKIITnPGTHVHIGKDSlriydkKIKLTNIINMIKQNENKLHKWIVLHKPK 126
Cdd:PRK10700 4 KLQKVLARAGHGSRREIESIIEAGRVSVDGKIAT-LGDRVEVTPGL------KIRIDGHLISVKESAEQICRVLAYYKPE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 127 GLLCTSNDEKNRKSIYTLFPEemLQKYRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEGPVKMNALK 206
Cdd:PRK10700 77 GELCTRNDPEGRPTVFDRLPK--LRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLR 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 207 ELARGIYLEEdektqpkkiynykesreksniddkkkkkmskmkkktNPAFIEILR---EEKIKikedtkkiTVLNISIKE 283
Cdd:PRK10700 155 QLSRGVQLED------------------------------------GPAAFKTIKfsgGEGIN--------QWYNVTLTE 190
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*.
gi 124801447 284 GRNRQIRKMFQQINQPVIKIKRTSFENITLkniyfPK-----QYRELNQKEVNDLK 334
Cdd:PRK10700 191 GRNREVRRLWEAVGVQVSRLIRVRYGDIPL-----PKglprgGWTELDLAQTNYLR 241
|
|
| PRK10839 |
PRK10839 |
16S rRNA pseudouridine(516) synthase RsuA; |
46-335 |
1.11e-23 |
|
16S rRNA pseudouridine(516) synthase RsuA;
Pssm-ID: 236774 [Multi-domain] Cd Length: 232 Bit Score: 97.10 E-value: 1.11e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 46 IRLNKLISMKRNISRRKSDEFIKDGKVKINNKIITNpgTHVHIGKDSLRIYDKkikltniiNMIKQNENKlhKWIVLHKP 125
Cdd:PRK10839 1 MRLDKFISQQLGVSRAIAGRELRANRVTVDGEIVKN--GAFKLLPEHDVAYDG--------NPLAQQHGP--RYFMLNKP 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 126 KGLLCTSNDEKNRKSIYtlFPEEMLqKYRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEGPVKMNAL 205
Cdd:PRK10839 69 QGYVCSTDDPDHPTVLY--FLDEPV-AYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTA 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 206 KELARGIYLeEDEKTqpkkiynykesreksniddkkkkkmskmkkKTNPAFIEILREEKIKikedtkkitvlnISIKEGR 285
Cdd:PRK10839 146 EQFAKGVQL-HNEKD------------------------------LTKPAVLEVITPTQVR------------LTISEGR 182
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|
gi 124801447 286 NRQIRKMFQQINQPVIKIKRTSFENITLKNIYFPKQYRELNQKEVNDLKL 335
Cdd:PRK10839 183 YHQVKRMFAAVGNHVVELHRERIGAITLDADLAPGEYRPLTEEEIASVGA 232
|
|
| PseudoU_synth_RluE |
cd02566 |
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ... |
120-316 |
6.59e-21 |
|
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: 87.82 E-value: 6.59e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 120 IVLHKPKGLLCTSNDEKN-RKSIYTLFPEEmlqkyRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEG 198
Cdd:cd02566 2 ILFNKPYGVLSQFTDESEkHKTLKDYIDDP-----GVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEG 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 199 PVKMNALKELARGIYLeEDEKTQPKKIYNYKESreksniddkkkkkmskmkkktnPAFIEilREEKIKIKedtKKITV-- 276
Cdd:cd02566 77 VPTEDALEQLRNGVEL-GDGLTLPAKVEKVDEP----------------------PWLWE--REPPIRFR---KNIPTsw 128
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 124801447 277 LNISIKEGRNRQIRKMFQQINQPVIKIKRTSFENITLKNI 316
Cdd:cd02566 129 IEITICEGKNRQVRRMTAAVGFPTLRLIRVSIGDIGLDNL 168
|
|
| PseudoU_synth_RluF |
cd02554 |
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ... |
119-330 |
8.05e-19 |
|
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: 82.36 E-value: 8.05e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 119 WIVLHKPKGLLCTSNDEKNRKSIYTLFPEEmlqkyRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEG 198
Cdd:cd02554 2 YIAYNKPVGIDCTLERADEDNIIDFVNPPP-----RIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNK 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 199 PVKMNALKELARGI-YLEEdektqpkkiynykesreksniddkkkkkmskmkkKTNPAFIEILREEKIKIkedtkkitVL 277
Cdd:cd02554 77 PITDEFIEGMSNGVvILGT----------------------------------VTKPCKVERLAKDKFRI--------VL 114
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 124801447 278 NisikEGRNRQIRKMFQQINQPVIKIKRTSFENITLKNIYfPKQYRELNQKEV 330
Cdd:cd02554 115 T----QGLNRQIRRMCEALGYRVTDLKRVRIMNIELGDLA-PGEWRPLTDAEL 162
|
|
| PseudoU_synth_2 |
pfam00849 |
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ... |
119-295 |
1.22e-18 |
|
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: 81.30 E-value: 1.22e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 119 WIVLHKPKGLLCTSNDEKN-RKSIYTLFPEEMLQKYRLVTVGRLDRNTSGVLLLTNDYAWVNKLTH--PKYQRIRTYRVH 195
Cdd:pfam00849 1 YIVVNKPAGVPVHPTDSLTkLLSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 196 IEGPvkmnalkELARGIYLEEDEKTQPKKIYNYKESREKSNIddkkkkkmskmkkktnPAFIEILREEKIkikedtKKIT 275
Cdd:pfam00849 81 VDKP-------EEEEGTIKSPIKKEKNKSPFRKEEELGGKKA----------------VTHLKVLKSGSK------GDYS 131
|
170 180
....*....|....*....|
gi 124801447 276 VLNISIKEGRNRQIRKMFQQ 295
Cdd:pfam00849 132 LLELELVTGRKHQIRAHLAA 151
|
|
| PRK10475 |
PRK10475 |
23S rRNA pseudouridine(2604) synthase RluF; |
46-333 |
1.88e-16 |
|
23S rRNA pseudouridine(2604) synthase RluF;
Pssm-ID: 236698 [Multi-domain] Cd Length: 290 Bit Score: 78.23 E-value: 1.88e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 46 IRLNKLISMKRNISRRKSDEFIKDGKVKINNKIITnPGTHVHIGkDSLRIYDKKIKltniinmiKQNENKLhKWIVLHKP 125
Cdd:PRK10475 7 TRLNKYISESGICSRREADRYIEQGNVFINGKRAT-IGDQVKAG-DVVKVNGQLIE--------PREAEDL-VLIALNKP 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 126 KGLLCTSND-EKNRKSIYTLFPEemlqkyRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEGPVKMNA 204
Cdd:PRK10475 76 VGIVSTTEDgERDNIVDFVNHSK------RVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEF 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 205 LKELARGIyleedektqpkkiynykesreksniddkkkkkmskmkkktnPAFIEILREEKIKiKEDTkkiTVLNISIKEG 284
Cdd:PRK10475 150 IRGMGAGV-----------------------------------------PILGTVTKKCKVK-KEAP---FVFRITLVQG 184
|
250 260 270 280
....*....|....*....|....*....|....*....|....*....
gi 124801447 285 RNRQIRKMFQQINQPVIKIKRTSFENITLKNIYfPKQYRELNQKEVNDL 333
Cdd:PRK10475 185 LNRQIRRMCEHFGYEVTKLERTRIMNVSLSGIP-LGEWRDLTDDELIDL 232
|
|
| PRK11394 |
PRK11394 |
23S rRNA pseudouridine(2457) synthase RluE; |
110-316 |
3.28e-15 |
|
23S rRNA pseudouridine(2457) synthase RluE;
Pssm-ID: 183115 Cd Length: 217 Bit Score: 73.62 E-value: 3.28e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 110 KQNENKLHKWIVLHKPKGLLCTSNDEKNRKSIYTLFPEEmlqkyRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRI 189
Cdd:PRK11394 32 RKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQ-----GVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTG 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 190 RTYRVHIEGPVKMNALKELARGIYLeEDEKTQPKKIYNYKESReksniddkkkkkmskMKKKTNPAfieiLREEKikike 269
Cdd:PRK11394 107 KIYYVQVEGIPTQDALEALRNGVTL-NDGPTLPAGAELVDEPA---------------WLWPRNPP----IRERK----- 161
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 124801447 270 dTKKITVLNISIKEGRNRQIRKMFQQINQPVIKIKRTSFENITLKNI 316
Cdd:PRK11394 162 -SIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNL 207
|
|
| PseudoU_synth_RluA_like |
cd02869 |
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ... |
119-301 |
8.18e-08 |
|
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: 51.57 E-value: 8.18e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 119 WIVLHKPKGLLCTSNDEKNRKSIYTLFPEEMLQK---YRLVTVGRLDRNTSGVLLLTNDYAWVNKLTHP-KYQRI-RTYR 193
Cdd:cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLgeeFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQfKERKVkKTYL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 194 VhiegpvkmnalkeLARGIyLEEDEKTQPKKIYNYKESREKSNIDDkkkkkmskmkKKTNPAfieILReekIKIKEDTKK 273
Cdd:cd02869 81 A-------------LVDGK-PPEDEGTIDAPLGRKKRKKRARVVVS----------EDGKPA---ITH---YKVLERFGN 130
|
170 180
....*....|....*....|....*...
gi 124801447 274 ITVLNISIKEGRNRQIRKMFQQINQPVI 301
Cdd:cd02869 131 VTLVELQLETGRTHQIRVHLASIGHPIV 158
|
|
| PSSA_1 |
cd02555 |
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ... |
120-305 |
3.38e-06 |
|
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: 46.63 E-value: 3.38e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 120 IVLHKPKGLLCTSNDEK---NRKSIYTLFPEEMLQKY--RLVTVGRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRV 194
Cdd:cd02555 7 LLLHKPAGMVSEQALALlgpGQRSAADRSGRRPLKGHfaRLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQEYLV 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124801447 195 HIEGPVKMNALKELARGiyLEEDEKTQPkkiynykesreksniddkkkkkmskmkkktnPAFIEILREEKikikedtkki 274
Cdd:cd02555 87 EVRGELTAGGLERLNHG--LTYDGRELP-------------------------------PAKVSWQNEQR---------- 123
|
170 180 190
....*....|....*....|....*....|.
gi 124801447 275 tvLNISIKEGRNRQIRKMFQQINQPVIKIKR 305
Cdd:cd02555 124 --LRFALKEPQPGQIRRMCESVGLEVVALRR 152
|
|
| S4 |
pfam01479 |
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ... |
47-89 |
1.14e-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: 1.14e-05
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 124801447 47 RLNKLIS-MKRNISRRKSDEFIKDGKVKINNKIITNPGTHVHIG 89
Cdd:pfam01479 2 RLDKVLArLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPG 45
|
|
| S4 |
smart00363 |
S4 RNA-binding domain; |
47-101 |
1.61e-05 |
|
S4 RNA-binding domain;
Pssm-ID: 214638 [Multi-domain] Cd Length: 60 Bit Score: 41.81 E-value: 1.61e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 124801447 47 RLNKLI-SMKRNISRRKSDEFIKDGKVKINNKIITNPGTHVHIGkDSLRIYDKKIK 101
Cdd:smart00363 2 RLDKFLaRLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPG-DVISVRGKELK 56
|
|
| S4 |
cd00165 |
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ... |
46-101 |
2.19e-05 |
|
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Pssm-ID: 238095 [Multi-domain] Cd Length: 70 Bit Score: 41.85 E-value: 2.19e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 124801447 46 IRLNKLIS-MKRNISRRKSDEFIKDGKVKINNKIITNPGTHVHIGkDSLRIYDKKIK 101
Cdd:cd00165 1 MRLDKILArLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPG-DVIEVDGKSIE 56
|
|
| YlmH |
COG2302 |
RNA-binding protein YlmH, contains S4-like domain [General function prediction only]; |
47-110 |
3.71e-03 |
|
RNA-binding protein YlmH, contains S4-like domain [General function prediction only];
Pssm-ID: 441877 Cd Length: 260 Bit Score: 38.60 E-value: 3.71e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 124801447 47 RLNKLISMKRNISRRKSDEFIKDGKVKINNKIITNPGTHVHIGkD--SLRIYDkKIKLTNIINMIK 110
Cdd:COG2302 185 RLDAVASAGFGLSRSKAAELIESGKVKVNWKVVDKPSFEVKEG-DliSVRGFG-RLKVLEIGGKTK 248
|
|
| |
