NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|489959858|ref|WP_003863165|]
View 

MULTISPECIES: 23S rRNA pseudouridine(1911/1915/1917) synthase RluD [Enterobacter]

Protein Classification

23S rRNA pseudouridine(1911/1915/1917) synthase RluD( domain architecture ID 11485254)

23S rRNA pseudouridine(1911/1915/1917) synthase RluD is responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
rluD PRK11180
23S rRNA pseudouridine(1911/1915/1917) synthase RluD;
1-325 0e+00

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


:

Pssm-ID: 183020 [Multi-domain]  Cd Length: 325  Bit Score: 722.23  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858   1 MAQRVELTATVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKIWDKPKEKVFGGEAVAINAEIEEEIRFEPQ 80
Cdd:PRK11180   1 MAQQVQLTATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEPQ 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  81 DIPLDIVYEDDDILVINKPRDFVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE 160
Cdd:PRK11180  81 DIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 161 SLQLREITREYEAVAIGHMTSGGTVEEPISRHPTKRTHMSVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHM 240
Cdd:PRK11180 161 ALQKREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHM 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 241 AHITHPLVGDPVYGGRPRPPKGASDEFISVLRKFDRQALHATMLRLYHPITGIQMEWHAPIPQDMVELIDAMRADFEEHK 320
Cdd:PRK11180 241 AHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPITGIEMEWHAPLPQDMVELIEALRADFEEHK 320

                 ....*
gi 489959858 321 DHVDW 325
Cdd:PRK11180 321 DEVDW 325
 
Name Accession Description Interval E-value
rluD PRK11180
23S rRNA pseudouridine(1911/1915/1917) synthase RluD;
1-325 0e+00

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


Pssm-ID: 183020 [Multi-domain]  Cd Length: 325  Bit Score: 722.23  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858   1 MAQRVELTATVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKIWDKPKEKVFGGEAVAINAEIEEEIRFEPQ 80
Cdd:PRK11180   1 MAQQVQLTATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEPQ 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  81 DIPLDIVYEDDDILVINKPRDFVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE 160
Cdd:PRK11180  81 DIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 161 SLQLREITREYEAVAIGHMTSGGTVEEPISRHPTKRTHMSVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHM 240
Cdd:PRK11180 161 ALQKREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHM 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 241 AHITHPLVGDPVYGGRPRPPKGASDEFISVLRKFDRQALHATMLRLYHPITGIQMEWHAPIPQDMVELIDAMRADFEEHK 320
Cdd:PRK11180 241 AHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPITGIEMEWHAPLPQDMVELIEALRADFEEHK 320

                 ....*
gi 489959858 321 DHVDW 325
Cdd:PRK11180 321 DEVDW 325
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
13-313 2.01e-150

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: 424.43  E-value: 2.01e-150
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858   13 ENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKIWDKPKEKVFGGEAVAINAEIEEEIRFEPQDIPLDIVYEDDD 92
Cdd:TIGR00005   1 EEQAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDED 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858   93 ILVINKPRDFVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172
Cdd:TIGR00005  81 IIVINKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYV 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  173 AVAIGH-MTSGGTVEEPISRHPTKRTHMSVHPM--GKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMAHITHPLVG 249
Cdd:TIGR00005 161 ALVHGQfDSGGGTVDAPLGRVPNNRGLMAVHPSseGKPAVTHFRVLERFGNASLVECELETGRTHQIRVHLQYLGHPLAG 240
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489959858  250 DPVYGGRPRPPKGAsdefiSVLRKFDRQALHATMLRLYHPITGIQMEWHAPIPQDMVELIDAMR 313
Cdd:TIGR00005 241 DPLYGNKPVPGNNL-----NGLLNFDRQALHAYELGFIHPATGEILEFEAPLPADLVLLLEALR 299
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
86-311 7.34e-106

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: 308.22  E-value: 7.34e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  86 IVYEDDDILVINKPRDFVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLR 165
Cdd:COG0564    1 ILYEDEDLLVVNKPAGLVVHPGSGGDDGTLVNALRAHLGELSGVPRPGLVHRLDRDTSGLLLVAKTRKAARRLSEQFRER 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 166 EITREYEAVAIGHMT-SGGTVEEPISRHPTKRTHMSV-HPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMAHI 243
Cdd:COG0564   81 EVEKRYLALVEGKPKeDEGTIDAPLGRDPKDRKKMAVvDEDGKPAVTHYRVLERFGGYSLVEVRLETGRTHQIRVHLAHI 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489959858 244 THPLVGDPVYGGRPRPPkgasdefisvLRKFDRQALHATMLRLYHPITGIQMEWHAPIPQDMVELIDA 311
Cdd:COG0564  161 GHPIVGDPLYGGDRSNR----------LLGLDRQALHAYRLGFPHPVTGEPLEFEAPLPEDFQALLEK 218
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
93-286 1.88e-73

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: 224.52  E-value: 1.88e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  93 ILVINKPRDFVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172
Cdd:cd02869    1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 173 AVAIGHMT-SGGTVEEPISRH-PTKRTHMSVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMAHITHPLVGD 250
Cdd:cd02869   81 ALVDGKPPeDEGTIDAPLGRKkRKKRARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLASIGHPIVGD 160
                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 489959858 251 PVYGGRPRPPKGasdefisvlrkFDRQALHATMLRL 286
Cdd:cd02869  161 PKYGGKASDSPG-----------LKRLALHAYRLSF 185
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
93-242 2.68e-34

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: 122.90  E-value: 2.68e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858   93 ILVINKPRDFVVHPGAGNPDGTVLNALlhYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLSLLAL--LLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLFPERKIEKEYL 78
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489959858  173 AVAIGHMTSGGTVEEPISRHPTKR-THMSVHPMGKPAVTHYRIMEHFRI--HTRLRLRLETGRTHQIRVHMAH 242
Cdd:pfam00849  79 ALVDKPEEEEGTIKSPIKKEKNKSpFRKEEELGGKKAVTHLKVLKSGSKgdYSLLELELVTGRKHQIRAHLAA 151
S4 smart00363
S4 RNA-binding domain;
18-76 9.74e-09

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 51.05  E-value: 9.74e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 489959858    18 QRLDQALAELFPDYSRSRIKEWILDQRVLVNGKIWDKPKEKVFGGEAVAINAEIEEEIR 76
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELKRLK 59
 
Name Accession Description Interval E-value
rluD PRK11180
23S rRNA pseudouridine(1911/1915/1917) synthase RluD;
1-325 0e+00

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


Pssm-ID: 183020 [Multi-domain]  Cd Length: 325  Bit Score: 722.23  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858   1 MAQRVELTATVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKIWDKPKEKVFGGEAVAINAEIEEEIRFEPQ 80
Cdd:PRK11180   1 MAQQVQLTATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEPQ 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  81 DIPLDIVYEDDDILVINKPRDFVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE 160
Cdd:PRK11180  81 DIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 161 SLQLREITREYEAVAIGHMTSGGTVEEPISRHPTKRTHMSVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHM 240
Cdd:PRK11180 161 ALQKREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHM 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 241 AHITHPLVGDPVYGGRPRPPKGASDEFISVLRKFDRQALHATMLRLYHPITGIQMEWHAPIPQDMVELIDAMRADFEEHK 320
Cdd:PRK11180 241 AHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPITGIEMEWHAPLPQDMVELIEALRADFEEHK 320

                 ....*
gi 489959858 321 DHVDW 325
Cdd:PRK11180 321 DEVDW 325
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
13-313 2.01e-150

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: 424.43  E-value: 2.01e-150
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858   13 ENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKIWDKPKEKVFGGEAVAINAEIEEEIRFEPQDIPLDIVYEDDD 92
Cdd:TIGR00005   1 EEQAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDED 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858   93 ILVINKPRDFVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172
Cdd:TIGR00005  81 IIVINKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYV 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  173 AVAIGH-MTSGGTVEEPISRHPTKRTHMSVHPM--GKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMAHITHPLVG 249
Cdd:TIGR00005 161 ALVHGQfDSGGGTVDAPLGRVPNNRGLMAVHPSseGKPAVTHFRVLERFGNASLVECELETGRTHQIRVHLQYLGHPLAG 240
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489959858  250 DPVYGGRPRPPKGAsdefiSVLRKFDRQALHATMLRLYHPITGIQMEWHAPIPQDMVELIDAMR 313
Cdd:TIGR00005 241 DPLYGNKPVPGNNL-----NGLLNFDRQALHAYELGFIHPATGEILEFEAPLPADLVLLLEALR 299
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
86-311 7.34e-106

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: 308.22  E-value: 7.34e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  86 IVYEDDDILVINKPRDFVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLR 165
Cdd:COG0564    1 ILYEDEDLLVVNKPAGLVVHPGSGGDDGTLVNALRAHLGELSGVPRPGLVHRLDRDTSGLLLVAKTRKAARRLSEQFRER 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 166 EITREYEAVAIGHMT-SGGTVEEPISRHPTKRTHMSV-HPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMAHI 243
Cdd:COG0564   81 EVEKRYLALVEGKPKeDEGTIDAPLGRDPKDRKKMAVvDEDGKPAVTHYRVLERFGGYSLVEVRLETGRTHQIRVHLAHI 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489959858 244 THPLVGDPVYGGRPRPPkgasdefisvLRKFDRQALHATMLRLYHPITGIQMEWHAPIPQDMVELIDA 311
Cdd:COG0564  161 GHPIVGDPLYGGDRSNR----------LLGLDRQALHAYRLGFPHPVTGEPLEFEAPLPEDFQALLEK 218
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
93-286 1.88e-73

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: 224.52  E-value: 1.88e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  93 ILVINKPRDFVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172
Cdd:cd02869    1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 173 AVAIGHMT-SGGTVEEPISRH-PTKRTHMSVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMAHITHPLVGD 250
Cdd:cd02869   81 ALVDGKPPeDEGTIDAPLGRKkRKKRARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLASIGHPIVGD 160
                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 489959858 251 PVYGGRPRPPKGasdefisvlrkFDRQALHATMLRL 286
Cdd:cd02869  161 PKYGGKASDSPG-----------LKRLALHAYRLSF 185
PseudoU_synth_Rsu_Rlu_like cd02550
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ...
93-248 5.89e-47

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: 155.61  E-value: 5.89e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  93 ILVINKPRDFVVHPGAGNPDGTVLNallhyYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEslQLREITREYE 172
Cdd:cd02550    1 ILVLNKPSGLVCHPTDRDRDPTVVV-----RLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTE--PRREIEKEYL 73
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489959858 173 AVAIGHMTSGGTVEEPISRhpTKRTHMSVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMAHITHPLV 248
Cdd:cd02550   74 VTVRGELDEEGIEDLATVR--RGRLSGLVDEGVPLAVTKVRVIGEHGGTGRLRLTLKTGRTHQIRRHCAAVGFPVL 147
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
93-242 2.68e-34

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: 122.90  E-value: 2.68e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858   93 ILVINKPRDFVVHPGAGNPDGTVLNALlhYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYE 172
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLSLLAL--LLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLFPERKIEKEYL 78
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489959858  173 AVAIGHMTSGGTVEEPISRHPTKR-THMSVHPMGKPAVTHYRIMEHFRI--HTRLRLRLETGRTHQIRVHMAH 242
Cdd:pfam00849  79 ALVDKPEEEEGTIKSPIKKEKNKSpFRKEEELGGKKAVTHLKVLKSGSKgdYSLLELELVTGRKHQIRAHLAA 151
PRK11025 PRK11025
23S rRNA pseudouridine(955/2504/2580) synthase RluC;
10-314 3.52e-33

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


Pssm-ID: 182909 [Multi-domain]  Cd Length: 317  Bit Score: 124.46  E-value: 3.52e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  10 TVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVN-GKIwdKPKEKVFGGEAVAIN----AEIEEEirfePQDIPL 84
Cdd:PRK11025  12 TISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNkKRI--KPEYKLEAGDEVRIPpvrvAEREEE----AVSPKL 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  85 D--------IVYEDDDILVINKPRDFVVHPGAGNPDGtVLNALLHYYPpiaDVPRAGIVHRLDKDTTGLMVVAKTVPAQT 156
Cdd:PRK11025  86 QkvaaladvILYEDDHILVLNKPSGTAVHGGSGLSFG-VIEGLRALRP---EARFLELVHRLDRDTSGVLLVAKKRSALR 161
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 157 RLVESLQLREITREYEAVAIGHMTSG-GTVEEPISRHPTKRTH--MSVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRT 233
Cdd:PRK11025 162 SLHEQLREKGMQKDYLALVRGQWQSHvKVVQAPLLKNILQSGEriVRVSQEGKPSETRFKVEERYAFATLVRASPVTGRT 241
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 234 HQIRVHMAHITHPLVGDPVYGGRprppkgasdEFISVLRK--FDRQALHATMLRLYHPITGIQMEWHAPIPQDMVELIDA 311
Cdd:PRK11025 242 HQIRVHTQYAGHPIAFDDRYGDR---------EFDQQLTGtgLNRLFLHAAALKFTHPGTGEVMRIEAPLDEQLKRCLQK 312

                 ...
gi 489959858 312 MRA 314
Cdd:PRK11025 313 LRN 315
PseudoU_synth_TruC cd02563
tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific ...
84-302 3.61e-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: 119.36  E-value: 3.61e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  84 LDIVYEDDDILVINKPRDFVVHPGAGNPDGTV-----LNALL--HYYPpiadvpragiVHRLDKDTTGLMVVAKTVPAQT 156
Cdd:cd02563    1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRfalqtLRDQLgqHVYP----------VHRLDRPTSGVLLFALSSEVAR 70
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 157 RLVESLQLREITREYEAVAIGHMTSGGTVEEPISRHPTKR--THMSVHPMGKPAVTHYRIMEHFRIHTR----------- 223
Cdd:cd02563   71 KLGEQFTEHRVHKTYLAVVRGYVPESGTIDYPLSEELDKLadKFASDDKAPQAATTHYRLLAVEELPVVvgkyptsrysl 150
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489959858 224 LRLRLETGRTHQIRVHMAHITHPLVGDPVYGgrprppKGASDEFISVLRKFDRQALHATMLRLYHPITGIQMEWHAPIP 302
Cdd:cd02563  151 VELTPHTGRKHQLRRHLAHIRHPIIGDTTHG------DGRHNRFFREHFGCHRLLLAATRLEFTHPVTGERLLIEAPLD 223
PseudoU_synth_ScRIB2 cd02557
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, ...
79-254 2.95e-30

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: 113.88  E-value: 2.95e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  79 PQDI-PLDIVYEDDDILVINKPRDFVVHPgAGNPDG-TVLNALLHYYPPIADVPragiVHRLDKDTTGLMVVAKTVPAQT 156
Cdd:cd02557   10 PVTNdPIKIVHEDDDLLVVDKPSGIPVHP-TGRYRYnTVTEILKSEYGLTELRP----CHRLDRLTSGLLLFAKTSQTAS 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 157 RLVESLQLREITREYEAVAIGHMTSGG-TVEEPI-SRHPTKRTHMSVHPMGKPAVTH-YRIMEHFRIHTRL-RLRLETGR 232
Cdd:cd02557   85 RLQQQIRSREVKKEYLARVKGEFPDGEvVVDQPIgLVSPKGGLRNDVDEKGKDARTIfKRLSYNGDLNTSVvLCKPITGR 164
                        170       180
                 ....*....|....*....|..
gi 489959858 233 THQIRVHMAHITHPLVGDPVYG 254
Cdd:cd02557  165 THQIRVHLQYLGHPIVNDPIYN 186
PRK10158 PRK10158
bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;
79-301 3.47e-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: 3.47e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  79 PQDIPLDIVYEDDDILVINKPRDFVVHPG--AGNPDgTVLNALLHyyppiaDVPRAGIVHRLDKDTTGLMVVAKTVPAQT 156
Cdd:PRK10158   9 PQEPWLVILYQDEHIMVVNKPSGLLSVPGrlEEHKD-SVMTRIQR------DYPQAESVHRLDMATSGVIVVALTKAAER 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 157 RLVESLQLREITREYEAVAIGH-MTSGGTVEEP-ISRHPTKRTHMSVHPMGKPAVTHYRIMEHFRIHT-RLRLRLETGRT 233
Cdd:PRK10158  82 ELKRQFREREPKKQYVARVWGHpSPAEGLVDLPlICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTaRVVLKPITGRS 161
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489959858 234 HQIRVHMAHITHPLVGDPVYggrprppkgASDEfisVLRKFDRQALHATMLRLYHPITGIQMEWHAPI 301
Cdd:PRK10158 162 HQLRVHMLALGHPILGDRFY---------ASPE---ARAMAPRLLLHAEMLTITHPAYGNSMTFKAPA 217
PRK11112 PRK11112
tRNA pseudouridine synthase C; Provisional
84-316 3.75e-24

tRNA pseudouridine synthase C; Provisional


Pssm-ID: 182971 [Multi-domain]  Cd Length: 257  Bit Score: 98.97  E-value: 3.75e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  84 LDIVYEDDDILVINKPRDFVVHPGAGNPDGT--VLNAL-----LHYYPpiadvpragiVHRLDKDTTGLMVVAKTVPAQT 156
Cdd:PRK11112   2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETvfVMQTVrdqigQHVFT----------AHRLDRPTSGVLLMALSSEVAR 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 157 RLVESLQLREITREYEAVAIGHMTSGGTVEEPIS----RHPTKRTHMSVHPmgKPAVTHYRIMEHFRI--------HTR- 223
Cdd:PRK11112  72 LLAQQFEQHQIQKTYHAIVRGWLMEEAVLDYPLKeeldKIADKFAREDKAP--QPAVTHYRGLATVEMpvatgrypTTRy 149
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 224 --LRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRpRPPKGASDEFISvlrkfDRQALHATMLRLYHPITG----IQMEW 297
Cdd:PRK11112 150 slVELEPKTGRKHQLRRHMAHLRHPIIGDTKHGDL-RQNRSLAEHFGC-----SRLMLHASELSLTHPFTGepltITAGL 223
                        250       260
                 ....*....|....*....|....*
gi 489959858 298 HAPIPQDM------VELIDAMRADF 316
Cdd:PRK11112 224 DETWQQLLsqfgwrGLLPENERVEF 248
RluA-like TIGR01621
pseudouridine synthase Rlu family protein, TIGR01621; This model represents a clade of ...
84-303 2.20e-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: 87.65  E-value: 2.20e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858   84 LDIVYEDDDILVINKPRDFVVHPGAGNpdgtvlNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQ 163
Cdd:TIGR01621   2 FEILFTHPDFLLINKHPGISVHKDDGE------TGLLQEVATQLGVGQVWLVHRLDKMTSGILLLALNAESASELSQGFA 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  164 LREITREYEAVAighmtsggtveepiSRHPTKRTHMSVHPMGK--------------PAVTHYrimEHFRIHTRLRLRL- 228
Cdd:TIGR01621  76 KRKIEKTYLALS--------------SKKPKKKQGLICGDMEKsrrgswklvnsqenPAITRF---FSASAATGLRLFIl 138
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489959858  229 --ETGRTHQIRVHMAHITHPLVGDPVYGGRprppkgasdefisvlRKFDRQALHATMLRLYHpiTGIQMEWHAPIPQ 303
Cdd:TIGR01621 139 kpHTGKTHQLRVAMKSLGSPILGDPLYGTT---------------DESDRGYLHAFALRFDY--QNEVIQWLCDPRQ 198
PSRA_1 cd02558
Pseudouridine synthase, a subgroup of the RluA family; This group is comprised of bacterial ...
70-293 1.71e-19

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: 85.79  E-value: 1.71e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  70 EIEEEIRfepqdIPLD--IVYEDDDILVINKPRDFVVHPGAGNpdgtVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMV 147
Cdd:cd02558   28 ELPDEPP-----IPFEetILHQDEHLLVADKPHFLPVTPRGRY----VTETLLVRLRRQTGNPDLTPAHRLDRLTAGLVL 98
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858 148 VAKTvPAQTRLVESL-QLREITREYEAVAighmtsggTVEEPISRHPTKRTHM--------SVHPMGKP-AVTHYRIMEH 217
Cdd:cd02558   99 FSKR-PETRGAYQTLfARREVSKTYEAVA--------PYVPALTFPLTVRSRIvkgrgffqAREVEGEPnAETRIELLAR 169
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489959858 218 FRIHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYggrPRPPKGASDEFISVLRkfdrqaLHATMLRLYHPITGI 293
Cdd:cd02558  170 RGGWGLYRLSPHTGKTHQLRVHMAALGVPILNDPFY---PVLLDKDPDDFSRPLQ------LLAKELEFTDPLTGR 236
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
18-97 1.24e-13

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: 64.96  E-value: 1.24e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  18 QRLDQALAELFPDYSRSRIKEWILDQRVLVNGKIWDKPKEKVfggeavainaEIEEEIRFEPQDIPLDIVYEDDDILVIN 97
Cdd:cd00165    1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKV----------KPGDVIEVDGKSIEEDIVYEDKKLLVVN 70
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
17-147 2.42e-09

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: 56.58  E-value: 2.42e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489959858  17 GQRLDQALAELfPDYSRSRIKEWILDQRVLVNGKIWDKPKEKVFGGEAVAINaeiEEEIRFEPQDipldiVYedddiLVI 96
Cdd:COG1187    2 GMRLQKFLANA-GVGSRREAEELIEAGRVTVNGKVVTELGTKVDPGDEVTVD---GKPLKLPEEP-----VY-----LLL 67
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 489959858  97 NKPRDFVV--HPGAGNPdgTVLNALlhyypPIADVPRAGIVHRLDKDTTGLMV 147
Cdd:COG1187   68 NKPAGVVSttKDPEGRP--TVFDLL-----PEARKERLFPVGRLDKDTEGLLL 113
S4 smart00363
S4 RNA-binding domain;
18-76 9.74e-09

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 51.05  E-value: 9.74e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 489959858    18 QRLDQALAELFPDYSRSRIKEWILDQRVLVNGKIWDKPKEKVFGGEAVAINAEIEEEIR 76
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELKRLK 59
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
18-65 1.86e-08

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: 49.80  E-value: 1.86e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 489959858   18 QRLDQALAELFPDYSRSRIKEWILDQRVLVNGKIWDKPKEKVFGGEAV 65
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
YqxC COG1189
Predicted rRNA methylase YqxC, contains S4 and FtsJ domains [Translation, ribosomal structure ...
18-77 3.50e-07

Predicted rRNA methylase YqxC, contains S4 and FtsJ domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440802 [Multi-domain]  Cd Length: 248  Bit Score: 50.44  E-value: 3.50e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489959858  18 QRLDQALAELFPDYSRSRIKEWILDQRVLVNGKIWDKPkekvfgGEAVAINAEIE---EEIRF 77
Cdd:COG1189    1 ERLDVLLVERGLAESREKAQRLIMAGRVLVNGQVVDKP------GTKVPEDAEIEvkgEELPY 57
tly TIGR00478
TlyA family rRNA methyltransferase/putative hemolysin; Members of this family include TlyA ...
19-59 7.58e-04

TlyA family rRNA methyltransferase/putative hemolysin; Members of this family include TlyA from Mycobacterium tuberculosis, an rRNA methylase whose modifications are necessary to confer sensitivity to ribosome-targeting antibiotics capreomycin and viomycin. Homology supports identification as a methyltransferase. However, a parallel literature persists in calling some members hemolysins. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. A recent study (2013) on SCO1782 from Streptomyces coelicolor shows hemolysin activity as earlier described for a homolog from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. [Unknown function, General]


Pssm-ID: 129570 [Multi-domain]  Cd Length: 228  Bit Score: 40.17  E-value: 7.58e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 489959858   19 RLDQALAELFPDYSRSRIKEWILDQRVLVNGKIWDKPKEKV 59
Cdd:TIGR00478   1 RLDILLVRRGLFESREKAKRLILKGFVLVNGKKVDKPSALV 41
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH