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Conserved domains on  [gi|16130515|ref|NP_417085|]
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23S rRNA pseudouridine(1911/1915/1917) synthase [Escherichia coli str. K-12 substr. MG1655]

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

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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: 720.69  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515    1 MAQRVQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQ 80
Cdd:PRK11180   1 MAQQVQLTATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEPQ 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515   81 DIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE 160
Cdd:PRK11180  81 DIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  161 SLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHM 240
Cdd:PRK11180 161 ALQKREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHM 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  241 AHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEHK 320
Cdd:PRK11180 241 AHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPITGIEMEWHAPLPQDMVELIEALRADFEEHK 320

                 ....*
gi 16130515  321 DEVDW 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: 720.69  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515    1 MAQRVQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQ 80
Cdd:PRK11180   1 MAQQVQLTATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEPQ 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515   81 DIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE 160
Cdd:PRK11180  81 DIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  161 SLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHM 240
Cdd:PRK11180 161 ALQKREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHM 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  241 AHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEHK 320
Cdd:PRK11180 241 AHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPITGIEMEWHAPLPQDMVELIEALRADFEEHK 320

                 ....*
gi 16130515  321 DEVDW 325
Cdd:PRK11180 321 DEVDW 325
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
13-313 2.15e-156

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: 439.45  E-value: 2.15e-156
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515    13 ENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDED 92
Cdd:TIGR00005   1 EEQAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDED 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515    93 IIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172
Cdd:TIGR00005  81 IIVINKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYV 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515   173 AVAIGH-MTAGGTVDEPISRHPTKRTHMAVHPM--GKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVG 249
Cdd:TIGR00005 161 ALVHGQfDSGGGTVDAPLGRVPNNRGLMAVHPSseGKPAVTHFRVLERFGNASLVECELETGRTHQIRVHLQYLGHPLAG 240
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16130515   250 DPVYGGRPRPPKGAseafiSTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMR 313
Cdd:TIGR00005 241 DPLYGNKPVPGNNL-----NGLLNFDRQALHAYELGFIHPATGEILEFEAPLPADLVLLLEALR 299
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
86-310 4.05e-108

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: 314.00  E-value: 4.05e-108
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  86 IVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRR 165
Cdd:COG0564   1 ILYEDEDLLVVNKPAGLVVHPGSGGDDGTLVNALRAHLGELSGVPRPGLVHRLDRDTSGLLLVAKTRKAARRLSEQFRER 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515 166 EITREYEAVAIGHMT-AGGTVDEPISRHPTKRTHMAV-HPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHI 243
Cdd:COG0564  81 EVEKRYLALVEGKPKeDEGTIDAPLGRDPKDRKKMAVvDEDGKPAVTHYRVLERFGGYSLVEVRLETGRTHQIRVHLAHI 160
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16130515 244 THPLVGDPVYGGRPRPPkgaseafistLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIE 310
Cdd:COG0564 161 GHPIVGDPLYGGDRSNR----------LLGLDRQALHAYRLGFPHPVTGEPLEFEAPLPEDFQALLE 217
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
93-286 4.31e-75

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: 228.76  E-value: 4.31e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  93 IIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172
Cdd:cd02869   1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYL 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515 173 AVAIGHMT-AGGTVDEPISRH-PTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGD 250
Cdd:cd02869  81 ALVDGKPPeDEGTIDAPLGRKkRKKRARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLASIGHPIVGD 160
                       170       180       190
                ....*....|....*....|....*....|....*.
gi 16130515 251 PVYGGRPRPPKGaseafistlrkFDRQALHATMLRL 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 3.95e-35

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: 124.83  E-value: 3.95e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515    93 IIIINKPRDLVVHPGAGNPDGTVLNALlhYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLSLLAL--LLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLFPERKIEKEYL 78
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16130515   173 AVAIGHMTAGGTVDEPISRHPTKR-THMAVHPMGKPAVTHYRIMEHFRV--HTRLRLRLETGRTHQIRVHMAH 242
Cdd:pfam00849  79 ALVDKPEEEEGTIKSPIKKEKNKSpFRKEEELGGKKAVTHLKVLKSGSKgdYSLLELELVTGRKHQIRAHLAA 151
S4 smart00363
S4 RNA-binding domain;
18-76 2.71e-10

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 55.29  E-value: 2.71e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 16130515     18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEAR 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: 720.69  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515    1 MAQRVQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQ 80
Cdd:PRK11180   1 MAQQVQLTATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEPQ 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515   81 DIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE 160
Cdd:PRK11180  81 DIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  161 SLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHM 240
Cdd:PRK11180 161 ALQKREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHM 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  241 AHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEHK 320
Cdd:PRK11180 241 AHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPITGIEMEWHAPLPQDMVELIEALRADFEEHK 320

                 ....*
gi 16130515  321 DEVDW 325
Cdd:PRK11180 321 DEVDW 325
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
13-313 2.15e-156

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: 439.45  E-value: 2.15e-156
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515    13 ENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDED 92
Cdd:TIGR00005   1 EEQAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDED 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515    93 IIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172
Cdd:TIGR00005  81 IIVINKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYV 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515   173 AVAIGH-MTAGGTVDEPISRHPTKRTHMAVHPM--GKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVG 249
Cdd:TIGR00005 161 ALVHGQfDSGGGTVDAPLGRVPNNRGLMAVHPSseGKPAVTHFRVLERFGNASLVECELETGRTHQIRVHLQYLGHPLAG 240
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16130515   250 DPVYGGRPRPPKGAseafiSTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMR 313
Cdd:TIGR00005 241 DPLYGNKPVPGNNL-----NGLLNFDRQALHAYELGFIHPATGEILEFEAPLPADLVLLLEALR 299
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
86-310 4.05e-108

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: 314.00  E-value: 4.05e-108
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  86 IVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRR 165
Cdd:COG0564   1 ILYEDEDLLVVNKPAGLVVHPGSGGDDGTLVNALRAHLGELSGVPRPGLVHRLDRDTSGLLLVAKTRKAARRLSEQFRER 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515 166 EITREYEAVAIGHMT-AGGTVDEPISRHPTKRTHMAV-HPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHI 243
Cdd:COG0564  81 EVEKRYLALVEGKPKeDEGTIDAPLGRDPKDRKKMAVvDEDGKPAVTHYRVLERFGGYSLVEVRLETGRTHQIRVHLAHI 160
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16130515 244 THPLVGDPVYGGRPRPPkgaseafistLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIE 310
Cdd:COG0564 161 GHPIVGDPLYGGDRSNR----------LLGLDRQALHAYRLGFPHPVTGEPLEFEAPLPEDFQALLE 217
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
93-286 4.31e-75

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: 228.76  E-value: 4.31e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  93 IIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172
Cdd:cd02869   1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYL 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515 173 AVAIGHMT-AGGTVDEPISRH-PTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGD 250
Cdd:cd02869  81 ALVDGKPPeDEGTIDAPLGRKkRKKRARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLASIGHPIVGD 160
                       170       180       190
                ....*....|....*....|....*....|....*.
gi 16130515 251 PVYGGRPRPPKGaseafistlrkFDRQALHATMLRL 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 1.12e-49

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: 162.54  E-value: 1.12e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  93 IIIINKPRDLVVHPGAGNPDGTVLNallhyYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEslQRREITREYE 172
Cdd:cd02550   1 ILVLNKPSGLVCHPTDRDRDPTVVV-----RLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTE--PRREIEKEYL 73
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16130515 173 AVAIGHMTAGGTVDEPISRhpTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLV 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 3.95e-35

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: 124.83  E-value: 3.95e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515    93 IIIINKPRDLVVHPGAGNPDGTVLNALlhYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYE 172
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLSLLAL--LLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLFPERKIEKEYL 78
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16130515   173 AVAIGHMTAGGTVDEPISRHPTKR-THMAVHPMGKPAVTHYRIMEHFRV--HTRLRLRLETGRTHQIRVHMAH 242
Cdd:pfam00849  79 ALVDKPEEEEGTIKSPIKKEKNKSpFRKEEELGGKKAVTHLKVLKSGSKgdYSLLELELVTGRKHQIRAHLAA 151
PseudoU_synth_TruC cd02563
tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific ...
84-302 1.68e-34

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: 125.53  E-value: 1.68e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  84 LDIVYEDEDIIIINKPRDLVVHPGAGNPDGTV-----LNALL--HYYPpiadvpragiVHRLDKDTTGLMVVAKTVPAQT 156
Cdd:cd02563   1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRfalqtLRDQLgqHVYP----------VHRLDRPTSGVLLFALSSEVAR 70
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515 157 RLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKR--THMAVHPMGKPAVTHYR---IMEHFRVHTR-------- 223
Cdd:cd02563  71 KLGEQFTEHRVHKTYLAVVRGYVPESGTIDYPLSEELDKLadKFASDDKAPQAATTHYRllaVEELPVVVGKyptsrysl 150
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16130515 224 LRLRLETGRTHQIRVHMAHITHPLVGDPVYGgrprppKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIP 302
Cdd:cd02563 151 VELTPHTGRKHQLRRHLAHIRHPIIGDTTHG------DGRHNRFFREHFGCHRLLLAATRLEFTHPVTGERLLIEAPLD 223
PRK10158 PRK10158
bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;
79-301 8.21e-32

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


Pssm-ID: 236659 [Multi-domain]  Cd Length: 219  Bit Score: 118.56  E-value: 8.21e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515   79 PQDIPLDIVYEDEDIIIINKPRDLVVHPG--AGNPDgTVLNALLHyyppiaDVPRAGIVHRLDKDTTGLMVVAKTVPAQT 156
Cdd:PRK10158   9 PQEPWLVILYQDEHIMVVNKPSGLLSVPGrlEEHKD-SVMTRIQR------DYPQAESVHRLDMATSGVIVVALTKAAER 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  157 RLVESLQRREITREYEAVAIGH-MTAGGTVDEP-ISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHT-RLRLRLETGRT 233
Cdd:PRK10158  82 ELKRQFREREPKKQYVARVWGHpSPAEGLVDLPlICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTaRVVLKPITGRS 161
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16130515  234 HQIRVHMAHITHPLVGDPVYggrprppkgaseAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPI 301
Cdd:PRK10158 162 HQLRVHMLALGHPILGDRFY------------ASPEARAMAPRLLLHAEMLTITHPAYGNSMTFKAPA 217
PRK11025 PRK11025
23S rRNA pseudouridine(955/2504/2580) synthase RluC;
10-314 1.44e-30

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


Pssm-ID: 182909 [Multi-domain]  Cd Length: 317  Bit Score: 117.52  E-value: 1.44e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515   10 TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVN-GKVcdKPKEKVLGGEQVAIN----AEIEEE---------A 75
Cdd:PRK11025  12 TISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNkKRI--KPEYKLEAGDEVRIPpvrvAEREEEavspklqkvA 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515   76 RFEPQdipldIVYEDEDIIIINKPRDLVVHPGAGNPDGtVLNALLHYYPpiaDVPRAGIVHRLDKDTTGLMVVAKTVPAQ 155
Cdd:PRK11025  90 ALADV-----ILYEDDHILVLNKPSGTAVHGGSGLSFG-VIEGLRALRP---EARFLELVHRLDRDTSGVLLVAKKRSAL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  156 TRLVESLQRREITREYEAVAIGHMTAG-GTVDEPISRHPTKRTH--MAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGR 232
Cdd:PRK11025 161 RSLHEQLREKGMQKDYLALVRGQWQSHvKVVQAPLLKNILQSGEriVRVSQEGKPSETRFKVEERYAFATLVRASPVTGR 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  233 THQIRVHMAHITHPLVGDPVYGGRprppkgaseAFISTLRK--FDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIE 310
Cdd:PRK11025 241 THQIRVHTQYAGHPIAFDDRYGDR---------EFDQQLTGtgLNRLFLHAAALKFTHPGTGEVMRIEAPLDEQLKRCLQ 311

                 ....
gi 16130515  311 VMRA 314
Cdd:PRK11025 312 KLRN 315
PseudoU_synth_ScRIB2 cd02557
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, ...
79-254 7.82e-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: 113.11  E-value: 7.82e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  79 PQDI-PLDIVYEDEDIIIINKPRDLVVHPgAGNPDG-TVLNALLHYYPPIADVPragiVHRLDKDTTGLMVVAKTVPAQT 156
Cdd:cd02557  10 PVTNdPIKIVHEDDDLLVVDKPSGIPVHP-TGRYRYnTVTEILKSEYGLTELRP----CHRLDRLTSGLLLFAKTSQTAS 84
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515 157 RLVESLQRREITREYEAVAIGHMTAGG-TVDEPI-SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV--HTRLRLRLETGR 232
Cdd:cd02557  85 RLQQQIRSREVKKEYLARVKGEFPDGEvVVDQPIgLVSPKGGLRNDVDEKGKDARTIFKRLSYNGDlnTSVVLCKPITGR 164
                       170       180
                ....*....|....*....|..
gi 16130515 233 THQIRVHMAHITHPLVGDPVYG 254
Cdd:cd02557 165 THQIRVHLQYLGHPIVNDPIYN 186
PRK11112 PRK11112
tRNA pseudouridine synthase C; Provisional
84-301 4.55e-25

tRNA pseudouridine synthase C; Provisional


Pssm-ID: 182971 [Multi-domain]  Cd Length: 257  Bit Score: 101.28  E-value: 4.55e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515   84 LDIVYEDEDIIIINKPRDLVVHPGAGNPDGT--VLNAL-----LHYYPpiadvpragiVHRLDKDTTGLMVVAKTVPAQT 156
Cdd:PRK11112   2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETvfVMQTVrdqigQHVFT----------AHRLDRPTSGVLLMALSSEVAR 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  157 RLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHP--MGKPAVTHYRIMEHFRV--------HTR--- 223
Cdd:PRK11112  72 LLAQQFEQHQIQKTYHAIVRGWLMEEAVLDYPLKEELDKIADKFAREdkAPQPAVTHYRGLATVEMpvatgrypTTRysl 151
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16130515  224 LRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRpRPPKGASEAFIStlrkfDRQALHATMLRLYHPISGIEMEWHAPI 301
Cdd:PRK11112 152 VELEPKTGRKHQLRRHMAHLRHPIIGDTKHGDL-RQNRSLAEHFGC-----SRLMLHASELSLTHPFTGEPLTITAGL 223
RluA-like TIGR01621
pseudouridine synthase Rlu family protein, TIGR01621; This model represents a clade of ...
84-303 4.25e-21

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: 89.57  E-value: 4.25e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515    84 LDIVYEDEDIIIINKPRDLVVHPGAGNpdgtvlNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQ 163
Cdd:TIGR01621   2 FEILFTHPDFLLINKHPGISVHKDDGE------TGLLQEVATQLGVGQVWLVHRLDKMTSGILLLALNAESASELSQGFA 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515   164 RREITREYEAVAighmtaggtvdepiSRHPTKRTHMAVHPMGK--------------PAVTHYrimEHFRVHTRLRLRL- 228
Cdd:TIGR01621  76 KRKIEKTYLALS--------------SKKPKKKQGLICGDMEKsrrgswklvnsqenPAITRF---FSASAATGLRLFIl 138
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16130515   229 --ETGRTHQIRVHMAHITHPLVGDPVYGGRprppkgaseafistlRKFDRQALHATMLRLYHpiSGIEMEWHAPIPQ 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 ...
82-294 1.05e-20

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: 89.25  E-value: 1.05e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  82 IPLD--IVYEDEDIIIINKPRDLVVHPGAGNpdgtVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTvPAQTRLV 159
Cdd:cd02558  35 IPFEetILHQDEHLLVADKPHFLPVTPRGRY----VTETLLVRLRRQTGNPDLTPAHRLDRLTAGLVLFSKR-PETRGAY 109
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515 160 ESL-QRREITREYEAVAighmtaggTVDEPISRHPTKRTHM--------AVHPMGKP-AVTHYRIMEHFRVHTRLRLRLE 229
Cdd:cd02558 110 QTLfARREVSKTYEAVA--------PYVPALTFPLTVRSRIvkgrgffqAREVEGEPnAETRIELLARRGGWGLYRLSPH 181
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16130515 230 TGRTHQIRVHMAHITHPLVGDPVYggrPRPPKGASEAFISTLRkfdrqaLHATMLRLYHPISGIE 294
Cdd:cd02558 182 TGKTHQLRVHMAALGVPILNDPFY---PVLLDKDPDDFSRPLQ------LLAKELEFTDPLTGRP 237
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
18-97 7.68e-15

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: 68.43  E-value: 7.68e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINaeieeearfePQDIPLDIVYEDEDIIIIN 97
Cdd:cd00165   1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVD----------GKSIEEDIVYEDKKLLVVN 70
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
17-237 1.78e-12

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: 65.83  E-value: 1.78e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  17 GQRLDQALAEMfPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAE-IEEEARFepqdipldiVYedediII 95
Cdd:COG1187   2 GMRLQKFLANA-GVGSRREAEELIEAGRVTVNGKVVTELGTKVDPGDEVTVDGKpLKLPEEP---------VY-----LL 66
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130515  96 INKPRDLVV--HPGAGNPdgTVLNALlhyypPIADVPRAGIVHRLDKDTTGLMVVaktvpaqT---RLVESLQ--RREIT 168
Cdd:COG1187  67 LNKPAGVVSttKDPEGRP--TVFDLL-----PEARKERLFPVGRLDKDTEGLLLL-------TndgELAHRLThpKYGVE 132
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 16130515 169 REYEAvaighmtaggTVDEPISrhPTKRTHMA--VHPMGKPA-VTHYRIMEHFRvHTRLRLRLETGRTHQIR 237
Cdd:COG1187 133 KEYLV----------RVDGPVT--EEDLERLRegVELEDGPTkPAKVEILSGEA-NTWLRITLTEGRNRQVR 191
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
18-65 5.02e-11

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: 57.12  E-value: 5.02e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 16130515    18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQV 65
Cdd:pfam01479   1 RRLDKVLARLGLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
S4 smart00363
S4 RNA-binding domain;
18-76 2.71e-10

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 55.29  E-value: 2.71e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 16130515     18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEAR 76
Cdd:smart00363   1 RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELKRLK 59
YqxC COG1189
Predicted rRNA methylase YqxC, contains S4 and FtsJ domains [Translation, ribosomal structure ...
18-72 3.00e-08

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


Pssm-ID: 440802 [Multi-domain]  Cd Length: 248  Bit Score: 53.52  E-value: 3.00e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 16130515  18 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPkekvlgGEQVAINAEIE 72
Cdd:COG1189   1 ERLDVLLVERGLAESREKAQRLIMAGRVLVNGQVVDKP------GTKVPEDAEIE 49
tly TIGR00478
TlyA family rRNA methyltransferase/putative hemolysin; Members of this family include TlyA ...
19-59 1.66e-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: 42.10  E-value: 1.66e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 16130515    19 RLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKV 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.
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