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Conserved domains on  [gi|495265659|ref|WP_007990414|]
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MULTISPECIES: 23S rRNA pseudouridine(1911/1915/1917) synthase RluD [Pseudomonas]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
rluD super family cl32656
23S rRNA pseudouridine(1911/1915/1917) synthase RluD;
1-318 7.37e-175

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


The actual alignment was detected with superfamily member PRK11180:

Pssm-ID: 183020 [Multi-domain]  Cd Length: 325  Bit Score: 486.88  E-value: 7.37e-175
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659   1 MSDKIELRAEVPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVI-RPRDIVHGGAILELTAEQEAQGEWVAQ 79
Cdd:PRK11180   1 MAQQVQLTATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVInKPKEKVLGGEQVAIDAEIEEEARFEPQ 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  80 DIALDIVYEDDDILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVT 159
Cdd:PRK11180  81 DIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 160 QLQSRSVSRIYECIVIGVVTAGGKINAPIGRHGQQRQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHM 239
Cdd:PRK11180 161 ALQKREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHM 240
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 495265659 240 AHINYPLVGDPAYGGRFRIPPAANPTMVESLKNFPRQALHARFLELDHPTTGKRMSWESPLPEDFVWLLTLLKQDREAF 318
Cdd:PRK11180 241 AHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPITGIEMEWHAPLPQDMVELIEALRADFEEH 319
 
Name Accession Description Interval E-value
rluD PRK11180
23S rRNA pseudouridine(1911/1915/1917) synthase RluD;
1-318 7.37e-175

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


Pssm-ID: 183020 [Multi-domain]  Cd Length: 325  Bit Score: 486.88  E-value: 7.37e-175
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659   1 MSDKIELRAEVPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVI-RPRDIVHGGAILELTAEQEAQGEWVAQ 79
Cdd:PRK11180   1 MAQQVQLTATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVInKPKEKVLGGEQVAIDAEIEEEARFEPQ 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  80 DIALDIVYEDDDILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVT 159
Cdd:PRK11180  81 DIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 160 QLQSRSVSRIYECIVIGVVTAGGKINAPIGRHGQQRQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHM 239
Cdd:PRK11180 161 ALQKREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHM 240
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 495265659 240 AHINYPLVGDPAYGGRFRIPPAANPTMVESLKNFPRQALHARFLELDHPTTGKRMSWESPLPEDFVWLLTLLKQDREAF 318
Cdd:PRK11180 241 AHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPITGIEMEWHAPLPQDMVELIEALRADFEEH 319
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
17-312 1.43e-120

pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 161659 [Multi-domain]  Cd Length: 299  Bit Score: 348.54  E-value: 1.43e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659   17 GQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVIR-PRDIVHGGAILELTAEQEAQGEWVAQDIALDIVYEDDDILVI 95
Cdd:TIGR00005   5 GQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTAnPKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDEDIIVI 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659   96 NKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVI 175
Cdd:TIGR00005  85 NKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYVALVH 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  176 GVV-TAGGKINAPIGRHGQQRQRMAV--MEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYPLVGDPAY 252
Cdd:TIGR00005 165 GQFdSGGGTVDAPLGRVPNNRGLMAVhpSSEGKPAVTHFRVLERFGNASLVECELETGRTHQIRVHLQYLGHPLAGDPLY 244
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  253 GGRFRIPPAANptmveSLKNFPRQALHARFLELDHPTTGKRMSWESPLPEDFVWLLTLLK 312
Cdd:TIGR00005 245 GNKPVPGNNLN-----GLLNFDRQALHAYELGFIHPATGEILEFEAPLPADLVLLLEALR 299
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
85-309 4.60e-113

Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]; Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440330 [Multi-domain]  Cd Length: 218  Bit Score: 326.32  E-value: 4.60e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  85 IVYEDDDILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSR 164
Cdd:COG0564    1 ILYEDEDLLVVNKPAGLVVHPGSGGDDGTLVNALRAHLGELSGVPRPGLVHRLDRDTSGLLLVAKTRKAARRLSEQFRER 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 165 SVSRIYECIVIGVVT-AGGKINAPIGRHGQQRQRMAVME-GGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHI 242
Cdd:COG0564   81 EVEKRYLALVEGKPKeDEGTIDAPLGRDPKDRKKMAVVDeDGKPAVTHYRVLERFGGYSLVEVRLETGRTHQIRVHLAHI 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 495265659 243 NYPLVGDPAYGGRFRIPpaanptmvesLKNFPRQALHARFLELDHPTTGKRMSWESPLPEDFVWLLT 309
Cdd:COG0564  161 GHPIVGDPLYGGDRSNR----------LLGLDRQALHAYRLGFPHPVTGEPLEFEAPLPEDFQALLE 217
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
92-285 1.85e-77

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: 234.54  E-value: 1.85e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  92 ILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYE 171
Cdd:cd02869    1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 172 CIVIGVVT-AGGKINAPIGRHGQQ-RQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYPLVGD 249
Cdd:cd02869   81 ALVDGKPPeDEGTIDAPLGRKKRKkRARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLASIGHPIVGD 160
                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 495265659 250 PAYGGRFRIPPaanptmveslkNFPRQALHARFLEL 285
Cdd:cd02869  161 PKYGGKASDSP-----------GLKRLALHAYRLSF 185
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
92-241 2.23e-37

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: 130.60  E-value: 2.23e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659   92 ILVINKPAGLVVHPAAGHADGTLLNALLhhVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYE 171
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLSLLALL--LRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLFPERKIEKEYL 78
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495265659  172 CIVIGVVTAGGKINAPIGRHGQQRQRMAV-MEGGKQAVSHYRVLERFRS--HTHVRVKLETGRTHQIRVHMAH 241
Cdd:pfam00849  79 ALVDKPEEEEGTIKSPIKKEKNKSPFRKEeELGGKKAVTHLKVLKSGSKgdYSLLELELVTGRKHQIRAHLAA 151
 
Name Accession Description Interval E-value
rluD PRK11180
23S rRNA pseudouridine(1911/1915/1917) synthase RluD;
1-318 7.37e-175

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


Pssm-ID: 183020 [Multi-domain]  Cd Length: 325  Bit Score: 486.88  E-value: 7.37e-175
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659   1 MSDKIELRAEVPSELGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVI-RPRDIVHGGAILELTAEQEAQGEWVAQ 79
Cdd:PRK11180   1 MAQQVQLTATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVInKPKEKVLGGEQVAIDAEIEEEARFEPQ 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  80 DIALDIVYEDDDILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVT 159
Cdd:PRK11180  81 DIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 160 QLQSRSVSRIYECIVIGVVTAGGKINAPIGRHGQQRQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHM 239
Cdd:PRK11180 161 ALQKREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHM 240
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 495265659 240 AHINYPLVGDPAYGGRFRIPPAANPTMVESLKNFPRQALHARFLELDHPTTGKRMSWESPLPEDFVWLLTLLKQDREAF 318
Cdd:PRK11180 241 AHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPITGIEMEWHAPLPQDMVELIEALRADFEEH 319
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
17-312 1.43e-120

pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 161659 [Multi-domain]  Cd Length: 299  Bit Score: 348.54  E-value: 1.43e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659   17 GQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVIR-PRDIVHGGAILELTAEQEAQGEWVAQDIALDIVYEDDDILVI 95
Cdd:TIGR00005   5 GQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTAnPKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDEDIIVI 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659   96 NKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVI 175
Cdd:TIGR00005  85 NKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYVALVH 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  176 GVV-TAGGKINAPIGRHGQQRQRMAV--MEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYPLVGDPAY 252
Cdd:TIGR00005 165 GQFdSGGGTVDAPLGRVPNNRGLMAVhpSSEGKPAVTHFRVLERFGNASLVECELETGRTHQIRVHLQYLGHPLAGDPLY 244
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  253 GGRFRIPPAANptmveSLKNFPRQALHARFLELDHPTTGKRMSWESPLPEDFVWLLTLLK 312
Cdd:TIGR00005 245 GNKPVPGNNLN-----GLLNFDRQALHAYELGFIHPATGEILEFEAPLPADLVLLLEALR 299
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
85-309 4.60e-113

Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]; Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440330 [Multi-domain]  Cd Length: 218  Bit Score: 326.32  E-value: 4.60e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  85 IVYEDDDILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSR 164
Cdd:COG0564    1 ILYEDEDLLVVNKPAGLVVHPGSGGDDGTLVNALRAHLGELSGVPRPGLVHRLDRDTSGLLLVAKTRKAARRLSEQFRER 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 165 SVSRIYECIVIGVVT-AGGKINAPIGRHGQQRQRMAVME-GGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHI 242
Cdd:COG0564   81 EVEKRYLALVEGKPKeDEGTIDAPLGRDPKDRKKMAVVDeDGKPAVTHYRVLERFGGYSLVEVRLETGRTHQIRVHLAHI 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 495265659 243 NYPLVGDPAYGGRFRIPpaanptmvesLKNFPRQALHARFLELDHPTTGKRMSWESPLPEDFVWLLT 309
Cdd:COG0564  161 GHPIVGDPLYGGDRSNR----------LLGLDRQALHAYRLGFPHPVTGEPLEFEAPLPEDFQALLE 217
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
92-285 1.85e-77

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: 234.54  E-value: 1.85e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  92 ILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYE 171
Cdd:cd02869    1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 172 CIVIGVVT-AGGKINAPIGRHGQQ-RQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYPLVGD 249
Cdd:cd02869   81 ALVDGKPPeDEGTIDAPLGRKKRKkRARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLASIGHPIVGD 160
                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 495265659 250 PAYGGRFRIPPaanptmveslkNFPRQALHARFLEL 285
Cdd:cd02869  161 PKYGGKASDSP-----------GLKRLALHAYRLSF 185
PseudoU_synth_ScRIB2 cd02557
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, ...
83-253 2.50e-39

Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.


Pssm-ID: 211331 [Multi-domain]  Cd Length: 213  Bit Score: 137.76  E-value: 2.50e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  83 LDIVYEDDDILVINKPAGLVVHPAAGHADGTLLNALLHHvpdiINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQ 162
Cdd:cd02557   16 IKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSE----YGLTELRPCHRLDRLTSGLLLFAKTSQTASRLQQQIR 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 163 SRSVSRIYECIVIGVVTAGGKI-NAPIGRHG-QQRQRMAVMEGGKQAVSHYRVLeRFRSHTH---VRVKLETGRTHQIRV 237
Cdd:cd02557   92 SREVKKEYLARVKGEFPDGEVVvDQPIGLVSpKGGLRNDVDEKGKDARTIFKRL-SYNGDLNtsvVLCKPITGRTHQIRV 170
                        170
                 ....*....|....*.
gi 495265659 238 HMAHINYPLVGDPAYG 253
Cdd:cd02557  171 HLQYLGHPIVNDPIYN 186
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
92-241 2.23e-37

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: 130.60  E-value: 2.23e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659   92 ILVINKPAGLVVHPAAGHADGTLLNALLhhVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYE 171
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLSLLALL--LRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLFPERKIEKEYL 78
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495265659  172 CIVIGVVTAGGKINAPIGRHGQQRQRMAV-MEGGKQAVSHYRVLERFRS--HTHVRVKLETGRTHQIRVHMAH 241
Cdd:pfam00849  79 ALVDKPEEEEGTIKSPIKKEKNKSPFRKEeELGGKKAVTHLKVLKSGSKgdYSLLELELVTGRKHQIRAHLAA 151
PseudoU_synth_Rsu_Rlu_like cd02550
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ...
92-247 6.44e-37

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: 129.41  E-value: 6.44e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  92 ILVINKPAGLVVHPAAGHADGTLLNALlhhvpDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQlqSRSVSRIYE 171
Cdd:cd02550    1 ILVLNKPSGLVCHPTDRDRDPTVVVRL-----DKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEP--RREIEKEYL 73
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495265659 172 CIVIGVVTAGGKINAPIGRHGQQRQRmaVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYPLV 247
Cdd:cd02550   74 VTVRGELDEEGIEDLATVRRGRLSGL--VDEGVPLAVTKVRVIGEHGGTGRLRLTLKTGRTHQIRRHCAAVGFPVL 147
PseudoU_synth_TruC cd02563
tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific ...
83-301 8.84e-32

tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.


Pssm-ID: 211333 [Multi-domain]  Cd Length: 223  Bit Score: 118.21  E-value: 8.84e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  83 LDIVYEDDDILVINKPAGLVVHPA--AGHAD----GTLLNALLHHV-PdiinvpragiVHRLDKDTTGLMVVAKTIQAQT 155
Cdd:cd02563    1 LEILYQDEHLVAINKPSGLLVHRSelDRHETrfalQTLRDQLGQHVyP----------VHRLDRPTSGVLLFALSSEVAR 70
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 156 QLVTQLQSRSVSRIYECIVIGVVTAGGKINAPIGRHGQQRQRMAVMEGGKQ--AVSHYRVL---------ERFRSHTHVR 224
Cdd:cd02563   71 KLGEQFTEHRVHKTYLAVVRGYVPESGTIDYPLSEELDKLADKFASDDKAPqaATTHYRLLaveelpvvvGKYPTSRYSL 150
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 225 VKLE--TGRTHQIRVHMAHINYPLVGDPAYG-GRfrippaANPTMVESLkNFPRQALHARFLELDHPTTGKRMSWESPLP 301
Cdd:cd02563  151 VELTphTGRKHQLRRHLAHIRHPIIGDTTHGdGR------HNRFFREHF-GCHRLLLAATRLEFTHPVTGERLLIEAPLD 223
PRK10158 PRK10158
bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;
79-299 3.05e-30

bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;


Pssm-ID: 236659 [Multi-domain]  Cd Length: 219  Bit Score: 114.32  E-value: 3.05e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  79 QDIALDIVYEDDDILVINKPAGLVVHPA--AGHADGTLLNALLhhvpdiiNVPRAGIVHRLDKDTTGLMVVAKTIQAQTQ 156
Cdd:PRK10158  10 QEPWLVILYQDEHIMVVNKPSGLLSVPGrlEEHKDSVMTRIQR-------DYPQAESVHRLDMATSGVIVVALTKAAERE 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 157 LVTQLQSRSVSRIYECIVIG-VVTAGGKINAPIGRHGQQRQRMAV-MEGGKQAVSHYRVLERFRSHT-HVRVKLETGRTH 233
Cdd:PRK10158  83 LKRQFREREPKKQYVARVWGhPSPAEGLVDLPLICDWPNRPKQKVcYETGKPAQTEYEVVEYAADNTaRVVLKPITGRSH 162
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495265659 234 QIRVHMAHINYPLVGDPAYggrfrippaANPtmvESLKNFPRQALHARFLELDHPTTGKRMSWESP 299
Cdd:PRK10158 163 QLRVHMLALGHPILGDRFY---------ASP---EARAMAPRLLLHAEMLTITHPAYGNSMTFKAP 216
PRK11025 PRK11025
23S rRNA pseudouridine(955/2504/2580) synthase RluC;
85-315 3.62e-30

23S rRNA pseudouridine(955/2504/2580) synthase RluC;


Pssm-ID: 182909 [Multi-domain]  Cd Length: 317  Bit Score: 116.37  E-value: 3.62e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  85 IVYEDDDILVINKPAGLVVHPAAGHADGTL--LNALLhhvpdiinvPRA---GIVHRLDKDTTGLMVVAKTIQAQTQLVT 159
Cdd:PRK11025  95 ILYEDDHILVLNKPSGTAVHGGSGLSFGVIegLRALR---------PEArflELVHRLDRDTSGVLLVAKKRSALRSLHE 165
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 160 QLQSRSVSRIYECIVIGVVTAGGK-INAPIGRHG-QQRQRMA-VMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIR 236
Cdd:PRK11025 166 QLREKGMQKDYLALVRGQWQSHVKvVQAPLLKNIlQSGERIVrVSQEGKPSETRFKVEERYAFATLVRASPVTGRTHQIR 245
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 495265659 237 VHMAHINYPLVGDPAYGGRfrippAANPTMVESLKNfpRQALHARFLELDHPTTGKRMSWESPLPEDFVWLLTLLKQDR 315
Cdd:PRK11025 246 VHTQYAGHPIAFDDRYGDR-----EFDQQLTGTGLN--RLFLHAAALKFTHPGTGEVMRIEAPLDEQLKRCLQKLRNAK 317
PRK11112 PRK11112
tRNA pseudouridine synthase C; Provisional
83-318 4.45e-28

tRNA pseudouridine synthase C; Provisional


Pssm-ID: 182971 [Multi-domain]  Cd Length: 257  Bit Score: 109.37  E-value: 4.45e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  83 LDIVYEDDDILVINKPAGLVVHPA--AGH----ADGTLLNALLHHV-PdiinvpragiVHRLDKDTTGLMVVAKTIQAQT 155
Cdd:PRK11112   2 LEILYQDEWLVAVNKPAGWLVHRSwlDRHetvfVMQTVRDQIGQHVfT----------AHRLDRPTSGVLLMALSSEVAR 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 156 QLVTQLQSRSVSRIYECIVIGVVTAGGKINAPIGrhgQQRQRMA-----VMEGGKQAVSHYRVLE---------RFRS-- 219
Cdd:PRK11112  72 LLAQQFEQHQIQKTYHAIVRGWLMEEAVLDYPLK---EELDKIAdkfarEDKAPQPAVTHYRGLAtvempvatgRYPTtr 148
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 220 HTHVRVKLETGRTHQIRVHMAHINYPLVGDPAYG-GRfrippaANPTMVESLkNFPRQALHARFLELDHPTTGKRMSWES 298
Cdd:PRK11112 149 YSLVELEPKTGRKHQLRRHMAHLRHPIIGDTKHGdLR------QNRSLAEHF-GCSRLMLHASELSLTHPFTGEPLTITA 221
                        250       260
                 ....*....|....*....|....*..
gi 495265659 299 PLPE-------DFVWLLTLLKQDREAF 318
Cdd:PRK11112 222 GLDEtwqqllsQFGWRGLLPENERVEF 248
PSRA_1 cd02558
Pseudouridine synthase, a subgroup of the RluA family; This group is comprised of bacterial ...
85-301 2.74e-23

Pseudouridine synthase, a subgroup of the RluA family; This group is comprised of bacterial proteins assigned to the RluA 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 RluA family is comprised of proteins related to Escherichia coli RluA.


Pssm-ID: 211332 [Multi-domain]  Cd Length: 246  Bit Score: 96.19  E-value: 2.74e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  85 IVYEDDDILVINKPAGLVVHPAAGHADGTLLNAL--LHHVPDIinVPragiVHRLDKDTTGLMVVAKTIQAQTQLVTQLQ 162
Cdd:cd02558   41 ILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLrrQTGNPDL--TP----AHRLDRLTAGLVLFSKRPETRGAYQTLFA 114
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 163 SRSVSRIYECIvigvvtagGKINAPIGRHGQQRQR---------MAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTH 233
Cdd:cd02558  115 RREVSKTYEAV--------APYVPALTFPLTVRSRivkgrgffqAREVEGEPNAETRIELLARRGGWGLYRLSPHTGKTH 186
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 234 QIRVHMAHINYPLVGDPAYggrfripPAANPTMVEslkNF--PRQaLHARFLELDHPTTGKRMSWESPLP 301
Cdd:cd02558  187 QLRVHMAALGVPILNDPFY-------PVLLDKDPD---DFsrPLQ-LLAKELEFTDPLTGRPRRFESGRS 245
RluA-like TIGR01621
pseudouridine synthase Rlu family protein, TIGR01621; This model represents a clade of ...
83-306 4.27e-20

pseudouridine synthase Rlu family protein, TIGR01621; This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 130682 [Multi-domain]  Cd Length: 217  Bit Score: 86.88  E-value: 4.27e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659   83 LDIVYEDDDILVINKPAGLVVHPAAGHadgtllNALLHHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQ 162
Cdd:TIGR01621   2 FEILFTHPDFLLINKHPGISVHKDDGE------TGLLQEVATQLGVGQVWLVHRLDKMTSGILLLALNAESASELSQGFA 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  163 SRSVSRIYecIVIGVVTAGGKINAPIGRHGQQRQRMAVMEGGKQAVShyrvLERFRS---HTHVRV---KLETGRTHQIR 236
Cdd:TIGR01621  76 KRKIEKTY--LALSSKKPKKKQGLICGDMEKSRRGSWKLVNSQENPA----ITRFFSasaATGLRLfilKPHTGKTHQLR 149
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  237 VHMAHINYPLVGDPAYGGRFRIppaanptmveslknfPRQALHARFLELDHptTGKRMSWESPLPEDFVW 306
Cdd:TIGR01621 150 VAMKSLGSPILGDPLYGTTDES---------------DRGYLHAFALRFDY--QNEVIQWLCDPRQFQKW 202
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
16-245 7.80e-11

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: 60.82  E-value: 7.80e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  16 GGQRLDQV-AAQLFAehSRSRLSAWIKDGRLTVDGAVIR-------PRDIVH-GGAILELTAEQeaqgewvaqdialdiV 86
Cdd:COG1187    1 EGMRLQKFlANAGVG--SRREAEELIEAGRVTVNGKVVTelgtkvdPGDEVTvDGKPLKLPEEP---------------V 63
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  87 YedddiLVINKPAGLVVHPAAGHADGTLLnallhhvpDIINVPRAGIVH---RLDKDTTGLMVVaktiqaqT---QLVTQ 160
Cdd:COG1187   64 Y-----LLLNKPAGVVSTTKDPEGRPTVF--------DLLPEARKERLFpvgRLDKDTEGLLLL-------TndgELAHR 123
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 161 LQ--SRSVSRIYECIVIGVVTAGgkinapigrhgqQRQRMA---VMEGGKQAVSHYRVLERfRSHTHVRVKLETGRTHQI 235
Cdd:COG1187  124 LThpKYGVEKEYLVRVDGPVTEE------------DLERLRegvELEDGPTKPAKVEILSG-EANTWLRITLTEGRNRQV 190
                        250
                 ....*....|
gi 495265659 236 RVHMAHINYP 245
Cdd:COG1187  191 RRMFEAVGLP 200
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
18-96 4.33e-08

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: 49.56  E-value: 4.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  18 QRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVIR-PRDIVHGGAILELTAEQeaqgewvaqdIALDIVYEDDDILVIN 96
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTkPSYKVKPGDVIEVDGKS----------IEEDIVYEDKKLLVVN 70
PseudoU_synth_RsuA_like cd02870
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ...
93-247 2.07e-07

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: 49.41  E-value: 2.07e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  93 LVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVpraGivhRLDKDTTGLMvvaktiqaqtqLVT---QLQSR----- 164
Cdd:cd02870    2 LLLNKPRGVVSTVRDPEGRPTVLDLLKDVGERLFPV---G---RLDYDTEGLL-----------LLTndgELANRlthpr 64
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 165 -SVSRIYECIVIGVVTAggkinapigRHGQQRQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHIN 243
Cdd:cd02870   65 yGVEKTYLVKVRGVPSE---------EELRRLRAGVELDDGKTAPAKVKVLSRDPKNTLLEVTLHEGRNRQVRRMFEAVG 135

                 ....
gi 495265659 244 YPLV 247
Cdd:cd02870  136 HPVL 139
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
18-64 2.54e-04

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: 38.24  E-value: 2.54e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 495265659   18 QRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVIR-PRDIVHGGAIL 64
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKdPSYRVKPGDEI 48
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
134-248 2.57e-04

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: 40.39  E-value: 2.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659  134 VHRLDKDTTGLMvvaktiqaqtqLVT---QLQSRSVSRIYECIVIGVVTAGGkinaPIGRHGQQRQRMAVM-EGGKQAVS 209
Cdd:TIGR00093   1 VGRLDRDSEGLL-----------LLTndgELVHRLTHPGHHHEKEYLVTVEG----PVTDEDLEALRKGVQlEDGKTKPA 65
                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 495265659  210 HYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYPLVG 248
Cdd:TIGR00093  66 KLKVITEPGFPTWLRVTLSEGRNRQVRRMFAAVGFPVLR 104
M20_Acy1_YkuR-like cd05670
M20 Peptidase aminoacyclase-1 YkuR-like proteins, including YkuR and Ama/HipO/HyuC proteins; ...
150-308 3.98e-03

M20 Peptidase aminoacyclase-1 YkuR-like proteins, including YkuR and Ama/HipO/HyuC proteins; Peptidase M20 family, aminoacyclase-1 YkuR-like subfamily including YkuR and Ama/HipO/HyuC proteins, most of which have not been well characterized to date. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in the protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity; substrates include indoleacetic acid (IAA) N-conjugates of amino acids, N-acetyl-L-amino acids and aminobenzoylglutamate. ACY1 breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as in the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). ACY1 appears to physically interact with Sphingosine kinase type 1 (SphK1) and may influence its physiological functions; SphK1 and its product sphingosine-1-phosphate have been shown to promote cell growth and inhibit apoptosis of tumor cells. Strong expression of the human gene and its mouse ortholog Acy1 in brain, liver, and kidney suggest a role of the enzyme in amino acid metabolism of these organs.


Pssm-ID: 349920 [Multi-domain]  Cd Length: 367  Bit Score: 38.40  E-value: 3.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 150 TIQAQTQLVTQLQ---SRSVSRIYECIV-IGVVTAGGKINAPIGRhgqqrqrmAVMEGGKQAVSHyRVLERFRShthvRV 225
Cdd:cd05670  195 MVVAAANFVTQLQtivSRNVDPIDGAVVtIGKIHAGTARNVIAGT--------AHLEGTIRTLTQ-EMMELVKQ----RV 261
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495265659 226 K-----LETGRTHQIRVHMAHINYPLVGDPAYggrfrippaanptmVESLKNFPRQALHARFLELDHPTTGkrmswespl 300
Cdd:cd05670  262 RdiaegIELAFDCEVKVDLGQGYYPVENDPDL--------------TTEFIDFMKKADGVNFVEAEPAMTG--------- 318

                 ....*...
gi 495265659 301 pEDFVWLL 308
Cdd:cd05670  319 -EDFGYLL 325
 
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.
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