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Conserved domains on  [gi|16130652|ref|NP_417225|]
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tRNA pseudouridine(13) synthase [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

tRNA pseudouridine(13) synthase TruD( domain architecture ID 10011603)

tRNA pseudouridine(13) synthase TruD catalyzes the isomerization of uridines at positions 13 in tRNA to pseudouridines

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
truD PRK00984
tRNA pseudouridine synthase D; Reviewed
1-341 0e+00

tRNA pseudouridine synthase D; Reviewed


:

Pssm-ID: 234884 [Multi-domain]  Cd Length: 341  Bit Score: 517.46  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652    1 MIEFDNLTYLHGKPQGTGLLKANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKD 80
Cdd:PRK00984   1 MMEFGNLLYLHGKPGITGRLKANPEDFVVREILGFEPSGEGEHLLVRIRKRGWNTLFVARALAKFLGISLRDVGYAGLKD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652   81 KHAVTEQWLCARVPGKEMPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVS-NRDDVEQRLIDICVKGVPNY 159
Cdd:PRK00984  81 RHAVTTQWFSIHLPGKEEPDLSAFQLEGLEILELGRHNRKLRLGDLKGNRFTIRLREVSkDRDKVEQRLEEIAAGGVPNY 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  160 FGAQRFGIGGSNLQGAQRWAQTNTPVRDRNKRSFWLSAARSALFNQIVAERLKKAD-VNQVVDGDALQLAGRGSWFVATT 238
Cdd:PRK00984 161 FGEQRFGSGGKNLQEALRWANGEKKVLDRNLRSFFLSAAQSYLFNRILSERLEKGLpLNQVLEGDALQLAGRGSWFVAEE 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  239 EElAELQRRVNDKELMITAALPGSGEWGTQREALAFEQAAVAAETELQALLVREKVEAARRAMLLYPQQLSwnWWDDVTV 318
Cdd:PRK00984 241 LE-EELQRRLKRGDLHITAPLPGSGELGTQGEALAIEQEILAEETALFALLGREKVEGARRAILLYPQNLS--WNDDETL 317
                        330       340
                 ....*....|....*....|...
gi 16130652  319 EIRFWLPAGSFATSVVRELINTT 341
Cdd:PRK00984 318 ELEFWLPKGSYATSVLRELLKTD 340
 
Name Accession Description Interval E-value
truD PRK00984
tRNA pseudouridine synthase D; Reviewed
1-341 0e+00

tRNA pseudouridine synthase D; Reviewed


Pssm-ID: 234884 [Multi-domain]  Cd Length: 341  Bit Score: 517.46  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652    1 MIEFDNLTYLHGKPQGTGLLKANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKD 80
Cdd:PRK00984   1 MMEFGNLLYLHGKPGITGRLKANPEDFVVREILGFEPSGEGEHLLVRIRKRGWNTLFVARALAKFLGISLRDVGYAGLKD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652   81 KHAVTEQWLCARVPGKEMPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVS-NRDDVEQRLIDICVKGVPNY 159
Cdd:PRK00984  81 RHAVTTQWFSIHLPGKEEPDLSAFQLEGLEILELGRHNRKLRLGDLKGNRFTIRLREVSkDRDKVEQRLEEIAAGGVPNY 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  160 FGAQRFGIGGSNLQGAQRWAQTNTPVRDRNKRSFWLSAARSALFNQIVAERLKKAD-VNQVVDGDALQLAGRGSWFVATT 238
Cdd:PRK00984 161 FGEQRFGSGGKNLQEALRWANGEKKVLDRNLRSFFLSAAQSYLFNRILSERLEKGLpLNQVLEGDALQLAGRGSWFVAEE 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  239 EElAELQRRVNDKELMITAALPGSGEWGTQREALAFEQAAVAAETELQALLVREKVEAARRAMLLYPQQLSwnWWDDVTV 318
Cdd:PRK00984 241 LE-EELQRRLKRGDLHITAPLPGSGELGTQGEALAIEQEILAEETALFALLGREKVEGARRAILLYPQNLS--WNDDETL 317
                        330       340
                 ....*....|....*....|...
gi 16130652  319 EIRFWLPAGSFATSVVRELINTT 341
Cdd:PRK00984 318 ELEFWLPKGSYATSVLRELLKTD 340
TruD COG0585
tRNA(Glu) U13 pseudouridine synthase TruD [Translation, ribosomal structure and biogenesis]; ...
1-341 2.40e-160

tRNA(Glu) U13 pseudouridine synthase TruD [Translation, ribosomal structure and biogenesis]; tRNA(Glu) U13 pseudouridine synthase TruD is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440350 [Multi-domain]  Cd Length: 349  Bit Score: 452.34  E-value: 2.40e-160
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652   1 MIEFDNLTYLHGKPQGTGLLKANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKD 80
Cdd:COG0585   1 MERDLGLPYATGTPGIGGRLKASPEDFIVEEILGFEPSGEGEHLLLRIEKRGWNTLDVARRLARALGISRRRVGYAGLKD 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  81 KHAVTEQWLCARVpGKEMPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREV-SNRDDVEQRLIDICVKGVPNY 159
Cdd:COG0585  81 RHAVTTQWFSVHL-GKDEPDLSALELEGVEVLEVGRHRRKLRRGDLKGNRFTIVLRDVdGDRERLEARLEEIAAQGVPNY 159
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652 160 FGAQRFGIGGSNLQGAQRWAQTNT------PVRDRNKRSFWLSAARSALFNQIVAERLKKADVNQVVDGDALQLAGRGSW 233
Cdd:COG0585 160 FGEQRFGSDGPNLFVAKALLRGDYegagalRRLPRNLRSLFLSAAQSYLFNRVLSERLERGLWNRPLAGDVLQLAGSGSW 239
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652 234 FVATTEELAELQRRVNDKELMITAALPGSGEWGTQREALAFEQAAVAAETELQALLV---REKVEAARRAMLLYPQQLSW 310
Cdd:COG0585 240 FVVEELDLETLQRRLARGDIHPTGPLPGRGTLLADGEAGEIEREVLAEEGLLLEDLRlpeRLGLKGERRALRLRPQDLSW 319
                       330       340       350
                ....*....|....*....|....*....|.
gi 16130652 311 NwWDDVTVEIRFWLPAGSFATSVVRELINTT 341
Cdd:COG0585 320 E-WDDDTLTLSFSLPKGSYATSVLRELMKVD 349
tRNA_TruD_broad TIGR00094
tRNA pseudouridine synthase, TruD family; an EGAD loading error caused one member to be called ...
1-343 1.71e-156

tRNA pseudouridine synthase, TruD family; an EGAD loading error caused one member to be called surE, but that's an adjacent gene. MJ11364 is a strong partial match from 50 to 230 aa. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 272903 [Multi-domain]  Cd Length: 387  Bit Score: 444.22  E-value: 1.71e-156
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652     1 MIEFDNLTYLHGKPQGTGLLKANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKD 80
Cdd:TIGR00094   2 MLNEMPLNTLTNHPGTTGLIKASPRDFIVEEIPGYEFSGEGEFIHITVEKENWDTLEVLRVIAKFLGVSRREIGFAGTKD 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652    81 KHAVTEQWLCARVPGKEMPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVS-NRDDVEQRLIDICVKGVPNY 159
Cdd:TIGR00094  82 KRAVTTQWVCLPVKLEEEPDASNFQLKGVKILSYNYHNRKIRLGDLKGNRFRIRIRDVElNSDELEETLNELCKKGFPNY 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652   160 FGAQRFG-----------------IGGSNLQGAQRWAQTNTPVRDRNKRSFWLSAARSALFNQIVAERLKKADVNQVVDG 222
Cdd:TIGR00094 162 FGSQRFGtfriithtvgrelllsnWKGANHQYALKPLQGETKKSKEARRIFWESDAKSALFNMPKAKRYERALLNSLLEG 241
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652   223 DALQLAGRGSWFVAT-TEELAELQRRV-----NDKELMITAALPGSGE-WGTQREALAFEQAAVAAETELQ-----ALLV 290
Cdd:TIGR00094 242 DNSYLAAIMSLPKNLrTMFVHAYQSYLfniksERIELMGTAPLPGDGLiDELEREALRFEKKEVAPEGALDvkykkALYA 321
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16130652   291 R----EKVEAARRAMLLY------PQQLSWNWWDDVT---VEIRFWLPAGSFATSVVRELINTTGD 343
Cdd:TIGR00094 322 RilsvEDFKALRVPKLKShaktlgSRRFSWDFWEHVTsqkVVLKFYLPKGSYATSVLRELMKTKGS 387
PseudoU_synth_EcTruD cd02575
Pseudouridine synthase, similar to Escherichia coli TruD; This group consists of bacterial ...
18-338 1.78e-126

Pseudouridine synthase, similar to Escherichia coli TruD; This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD makes the highly phylogenetically conserved psi13 in tRNAs.


Pssm-ID: 211340 [Multi-domain]  Cd Length: 253  Bit Score: 362.68  E-value: 1.78e-126
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  18 GLLKANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCARVPGKE 97
Cdd:cd02575   1 GHLKATPEDFQVEEVLGYEPSGEGEHLLLHIRKTGLNTREVAKELAKALGVKERDVGYAGLKDRHAVTTQWFSVHLPGKE 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  98 MPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVS-NRDDVEQRLIDICVKGVPNYFGAQRFGIGGSNLQGAQ 176
Cdd:cd02575  81 APDLSALQLEGVKILEVTRHNRKLRRGHLKGNRFVIRLRGVSgNADKLEQRLETIAQKGVPNYFGPQRFGRDGGNLLQGL 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652 177 RWAQTNTPVRDRNKRSFWLSAARSALFNQIVAERLKKADVNQVVDGDALQLAGRGSWFVatteelaelqrrvndkelmit 256
Cdd:cd02575 161 RLLAGERKVRDRNKRSFLLSAARSYLFNRVLSERLEQGSWNRVLDGDVLQLAGSGSWFV--------------------- 219
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652 257 aalpgsgewgtqrealafeqaavaaetelqallvrekveaarramllyPQQLSWNWWDDVTVEIRFWLPAGSFATSVVRE 336
Cdd:cd02575 220 ------------------------------------------------PQRLAWQWPEDAGLELSFYLPAGSYATSVLRE 251

                ..
gi 16130652 337 LI 338
Cdd:cd02575 252 LL 253
TruD pfam01142
tRNA pseudouridine synthase D (TruD); TruD is responsible for synthesis of pseudouridine from ...
18-337 1.29e-57

tRNA pseudouridine synthase D (TruD); TruD is responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs. The structure of TruD reveals an overall V-shaped molecule which contains an RNA-binding cleft.


Pssm-ID: 426077 [Multi-domain]  Cd Length: 414  Bit Score: 192.02  E-value: 1.29e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652    18 GLLKANPEDFVVVE---DLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCarVP 94
Cdd:pfam01142  16 GRLRERPEDFIVEEiplFSGEEDGDEGPYLILRLEKRNWDTNDAVRELARALGISRKRIGFAGTKDKRAVTTQYIS--IY 93
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652    95 GKEMPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVSNRDD---VEQRLIDICVKGVPNYFGAQRFG----- 166
Cdd:pfam01142  94 GVDPEELEALNLKDIEIEVVGRANRKLRLGDLAGNRFRIRVRDADEDEAasrAEAILEELKEFGVPNYFGYQRFGsirpv 173
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652   167 ---IGGSNLQG----------------------AQRWAQTNT----------PVR------------------------- 186
Cdd:pfam01142 174 thlVGKAILRGdyeeavdtyvgkpfpgepedtrEAREAYAETgdweealelfPKSlryeramlhrlaenpgdyegalral 253
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652   187 DRNKRSFWLSAARSALFNQIVAERLKK-ADVNQVVDGDALQLAGRGSW-----FVATTEELAELQRRVNDKELMITAALP 260
Cdd:pfam01142 254 PPNLLRMFVHAYQSYLFNRVLSERLERgLPLNEPVEGDIVCFADERLPdtdrtQRVTEKNIEAVRRLIKRGRAFPTGPLP 333
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652   261 GSGEWGTQREALAFEQAAVAAE-TELQALLVREKVEAA----RRAMLLYPQQLSWNWWDDvTVEIRFWLPAGSFATSVVR 335
Cdd:pfam01142 334 GYDTELAEGEPGEIEREVLEEEgLTLEDFKLPGIPELSskgtRRPILLPIDDFSYSALGD-GLTLSFSLPKGSYATTVLR 412

                  ..
gi 16130652   336 EL 337
Cdd:pfam01142 413 EY 414
 
Name Accession Description Interval E-value
truD PRK00984
tRNA pseudouridine synthase D; Reviewed
1-341 0e+00

tRNA pseudouridine synthase D; Reviewed


Pssm-ID: 234884 [Multi-domain]  Cd Length: 341  Bit Score: 517.46  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652    1 MIEFDNLTYLHGKPQGTGLLKANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKD 80
Cdd:PRK00984   1 MMEFGNLLYLHGKPGITGRLKANPEDFVVREILGFEPSGEGEHLLVRIRKRGWNTLFVARALAKFLGISLRDVGYAGLKD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652   81 KHAVTEQWLCARVPGKEMPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVS-NRDDVEQRLIDICVKGVPNY 159
Cdd:PRK00984  81 RHAVTTQWFSIHLPGKEEPDLSAFQLEGLEILELGRHNRKLRLGDLKGNRFTIRLREVSkDRDKVEQRLEEIAAGGVPNY 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  160 FGAQRFGIGGSNLQGAQRWAQTNTPVRDRNKRSFWLSAARSALFNQIVAERLKKAD-VNQVVDGDALQLAGRGSWFVATT 238
Cdd:PRK00984 161 FGEQRFGSGGKNLQEALRWANGEKKVLDRNLRSFFLSAAQSYLFNRILSERLEKGLpLNQVLEGDALQLAGRGSWFVAEE 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  239 EElAELQRRVNDKELMITAALPGSGEWGTQREALAFEQAAVAAETELQALLVREKVEAARRAMLLYPQQLSwnWWDDVTV 318
Cdd:PRK00984 241 LE-EELQRRLKRGDLHITAPLPGSGELGTQGEALAIEQEILAEETALFALLGREKVEGARRAILLYPQNLS--WNDDETL 317
                        330       340
                 ....*....|....*....|...
gi 16130652  319 EIRFWLPAGSFATSVVRELINTT 341
Cdd:PRK00984 318 ELEFWLPKGSYATSVLRELLKTD 340
TruD COG0585
tRNA(Glu) U13 pseudouridine synthase TruD [Translation, ribosomal structure and biogenesis]; ...
1-341 2.40e-160

tRNA(Glu) U13 pseudouridine synthase TruD [Translation, ribosomal structure and biogenesis]; tRNA(Glu) U13 pseudouridine synthase TruD is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440350 [Multi-domain]  Cd Length: 349  Bit Score: 452.34  E-value: 2.40e-160
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652   1 MIEFDNLTYLHGKPQGTGLLKANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKD 80
Cdd:COG0585   1 MERDLGLPYATGTPGIGGRLKASPEDFIVEEILGFEPSGEGEHLLLRIEKRGWNTLDVARRLARALGISRRRVGYAGLKD 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  81 KHAVTEQWLCARVpGKEMPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREV-SNRDDVEQRLIDICVKGVPNY 159
Cdd:COG0585  81 RHAVTTQWFSVHL-GKDEPDLSALELEGVEVLEVGRHRRKLRRGDLKGNRFTIVLRDVdGDRERLEARLEEIAAQGVPNY 159
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652 160 FGAQRFGIGGSNLQGAQRWAQTNT------PVRDRNKRSFWLSAARSALFNQIVAERLKKADVNQVVDGDALQLAGRGSW 233
Cdd:COG0585 160 FGEQRFGSDGPNLFVAKALLRGDYegagalRRLPRNLRSLFLSAAQSYLFNRVLSERLERGLWNRPLAGDVLQLAGSGSW 239
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652 234 FVATTEELAELQRRVNDKELMITAALPGSGEWGTQREALAFEQAAVAAETELQALLV---REKVEAARRAMLLYPQQLSW 310
Cdd:COG0585 240 FVVEELDLETLQRRLARGDIHPTGPLPGRGTLLADGEAGEIEREVLAEEGLLLEDLRlpeRLGLKGERRALRLRPQDLSW 319
                       330       340       350
                ....*....|....*....|....*....|.
gi 16130652 311 NwWDDVTVEIRFWLPAGSFATSVVRELINTT 341
Cdd:COG0585 320 E-WDDDTLTLSFSLPKGSYATSVLRELMKVD 349
tRNA_TruD_broad TIGR00094
tRNA pseudouridine synthase, TruD family; an EGAD loading error caused one member to be called ...
1-343 1.71e-156

tRNA pseudouridine synthase, TruD family; an EGAD loading error caused one member to be called surE, but that's an adjacent gene. MJ11364 is a strong partial match from 50 to 230 aa. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 272903 [Multi-domain]  Cd Length: 387  Bit Score: 444.22  E-value: 1.71e-156
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652     1 MIEFDNLTYLHGKPQGTGLLKANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKD 80
Cdd:TIGR00094   2 MLNEMPLNTLTNHPGTTGLIKASPRDFIVEEIPGYEFSGEGEFIHITVEKENWDTLEVLRVIAKFLGVSRREIGFAGTKD 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652    81 KHAVTEQWLCARVPGKEMPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVS-NRDDVEQRLIDICVKGVPNY 159
Cdd:TIGR00094  82 KRAVTTQWVCLPVKLEEEPDASNFQLKGVKILSYNYHNRKIRLGDLKGNRFRIRIRDVElNSDELEETLNELCKKGFPNY 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652   160 FGAQRFG-----------------IGGSNLQGAQRWAQTNTPVRDRNKRSFWLSAARSALFNQIVAERLKKADVNQVVDG 222
Cdd:TIGR00094 162 FGSQRFGtfriithtvgrelllsnWKGANHQYALKPLQGETKKSKEARRIFWESDAKSALFNMPKAKRYERALLNSLLEG 241
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652   223 DALQLAGRGSWFVAT-TEELAELQRRV-----NDKELMITAALPGSGE-WGTQREALAFEQAAVAAETELQ-----ALLV 290
Cdd:TIGR00094 242 DNSYLAAIMSLPKNLrTMFVHAYQSYLfniksERIELMGTAPLPGDGLiDELEREALRFEKKEVAPEGALDvkykkALYA 321
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16130652   291 R----EKVEAARRAMLLY------PQQLSWNWWDDVT---VEIRFWLPAGSFATSVVRELINTTGD 343
Cdd:TIGR00094 322 RilsvEDFKALRVPKLKShaktlgSRRFSWDFWEHVTsqkVVLKFYLPKGSYATSVLRELMKTKGS 387
PseudoU_synth_EcTruD cd02575
Pseudouridine synthase, similar to Escherichia coli TruD; This group consists of bacterial ...
18-338 1.78e-126

Pseudouridine synthase, similar to Escherichia coli TruD; This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD makes the highly phylogenetically conserved psi13 in tRNAs.


Pssm-ID: 211340 [Multi-domain]  Cd Length: 253  Bit Score: 362.68  E-value: 1.78e-126
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  18 GLLKANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCARVPGKE 97
Cdd:cd02575   1 GHLKATPEDFQVEEVLGYEPSGEGEHLLLHIRKTGLNTREVAKELAKALGVKERDVGYAGLKDRHAVTTQWFSVHLPGKE 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  98 MPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVS-NRDDVEQRLIDICVKGVPNYFGAQRFGIGGSNLQGAQ 176
Cdd:cd02575  81 APDLSALQLEGVKILEVTRHNRKLRRGHLKGNRFVIRLRGVSgNADKLEQRLETIAQKGVPNYFGPQRFGRDGGNLLQGL 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652 177 RWAQTNTPVRDRNKRSFWLSAARSALFNQIVAERLKKADVNQVVDGDALQLAGRGSWFVatteelaelqrrvndkelmit 256
Cdd:cd02575 161 RLLAGERKVRDRNKRSFLLSAARSYLFNRVLSERLEQGSWNRVLDGDVLQLAGSGSWFV--------------------- 219
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652 257 aalpgsgewgtqrealafeqaavaaetelqallvrekveaarramllyPQQLSWNWWDDVTVEIRFWLPAGSFATSVVRE 336
Cdd:cd02575 220 ------------------------------------------------PQRLAWQWPEDAGLELSFYLPAGSYATSVLRE 251

                ..
gi 16130652 337 LI 338
Cdd:cd02575 252 LL 253
PseudoU_synth_TruD_like cd02552
Pseudouridine synthase, TruD family; This group consists of eukaryotic, bacterial and archeal ...
18-338 1.95e-73

Pseudouridine synthase, TruD family; This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruD and Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD and S. cerevisiae Pus7 make psi13 in cytoplasmic tRNAs. In addition S. cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA) and psi35 in pre-tRNATyr. Psi35 in U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35.


Pssm-ID: 211326 [Multi-domain]  Cd Length: 232  Bit Score: 227.09  E-value: 1.95e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  18 GLLKANPEDFVVVEDLGFEP------DGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCA 91
Cdd:cd02552   1 GRLKQRPEDFVVNEILLDGPvvhlwpKGEGEYLHFTLYKENKDTMEALREIAKALGVPPRDIGYAGTKDKRAVTTQRVSV 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  92 RVPGKEMPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVSNRDD--VEQRLIDICVKGVPNYFGAQRFGigg 169
Cdd:cd02552  81 HKPGKERLALLNLELKGIRILEFGRHDKKLRLGDLKGNRFTITLRGVSPEEDelIERRLESLKEKGFPNYFGLQRFG--- 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652 170 snlqgaqrwaqtntpvrdrnkrSFWLSAARSALFNQIVAERLKKADVNQVVDGDalqlagrgswfvatteelaelqrrvn 249
Cdd:cd02552 158 ----------------------SMYLHAYQSYLFNEVLSERIELYGFNRVVEGD-------------------------- 189
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652 250 dkelmitaALPGSGEWGTQREALafeqaavaaetelqallvrekveaarramllypqqlswNWWDDVTVEIRFWLPAGSF 329
Cdd:cd02552 190 --------VKPKNLKWSEERYDD--------------------------------------LEGEKLALKLSFSLPRGSY 223

                ....*....
gi 16130652 330 ATSVVRELI 338
Cdd:cd02552 224 ATMVLRELL 232
TruD pfam01142
tRNA pseudouridine synthase D (TruD); TruD is responsible for synthesis of pseudouridine from ...
18-337 1.29e-57

tRNA pseudouridine synthase D (TruD); TruD is responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs. The structure of TruD reveals an overall V-shaped molecule which contains an RNA-binding cleft.


Pssm-ID: 426077 [Multi-domain]  Cd Length: 414  Bit Score: 192.02  E-value: 1.29e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652    18 GLLKANPEDFVVVE---DLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCarVP 94
Cdd:pfam01142  16 GRLRERPEDFIVEEiplFSGEEDGDEGPYLILRLEKRNWDTNDAVRELARALGISRKRIGFAGTKDKRAVTTQYIS--IY 93
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652    95 GKEMPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVSNRDD---VEQRLIDICVKGVPNYFGAQRFG----- 166
Cdd:pfam01142  94 GVDPEELEALNLKDIEIEVVGRANRKLRLGDLAGNRFRIRVRDADEDEAasrAEAILEELKEFGVPNYFGYQRFGsirpv 173
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652   167 ---IGGSNLQG----------------------AQRWAQTNT----------PVR------------------------- 186
Cdd:pfam01142 174 thlVGKAILRGdyeeavdtyvgkpfpgepedtrEAREAYAETgdweealelfPKSlryeramlhrlaenpgdyegalral 253
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652   187 DRNKRSFWLSAARSALFNQIVAERLKK-ADVNQVVDGDALQLAGRGSW-----FVATTEELAELQRRVNDKELMITAALP 260
Cdd:pfam01142 254 PPNLLRMFVHAYQSYLFNRVLSERLERgLPLNEPVEGDIVCFADERLPdtdrtQRVTEKNIEAVRRLIKRGRAFPTGPLP 333
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652   261 GSGEWGTQREALAFEQAAVAAE-TELQALLVREKVEAA----RRAMLLYPQQLSWNWWDDvTVEIRFWLPAGSFATSVVR 335
Cdd:pfam01142 334 GYDTELAEGEPGEIEREVLEEEgLTLEDFKLPGIPELSskgtRRPILLPIDDFSYSALGD-GLTLSFSLPKGSYATTVLR 412

                  ..
gi 16130652   336 EL 337
Cdd:pfam01142 413 EY 414
PSTD1 cd02577
Pseudouridine synthase, a subgroup of the TruD family; This group consists of several ...
18-338 2.23e-33

Pseudouridine synthase, a subgroup of the TruD family; This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). The TruD family is comprised of proteins related to Escherichia coli TruD.


Pssm-ID: 211342 [Multi-domain]  Cd Length: 319  Bit Score: 125.90  E-value: 2.23e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  18 GLLKANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCARVPgke 97
Cdd:cd02577   1 GRLKQYPEDFIVEEITPFDIGKKGKYLIYLLEKKNWDTLDAVRRIAKALGISRKRIGYAGTKDKHAVTTQYISIFDP--- 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  98 mPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVSNRD-DVEQRLIDICVK-GVPNYFGAQRFGiggsnlqga 175
Cdd:cd02577  78 -KDEEKLSIKDIELKVLGRSRKPLRLGDLWGNRFEITVRDLGDEEiERIETLVEEVEKgGFPNYFGSQRFG--------- 147
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652 176 qrwaqtntPVRDRNKrsfwlsaarsalfnqIVAERLKKADVNqvvdgDALQLAGRGSWFVATTEElAELQRRVNDKELMI 255
Cdd:cd02577 148 --------SVRPVTH---------------FVGKLILEGDYE-----EAAKTYLTARYPLEETGD-KKRALRLFPKWGDW 198
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652 256 TAALPGSGEWGTQREALA-------FEQAAVAAETELQALLV------------REKVEA------------ARRAMLLY 304
Cdd:cd02577 199 ERCLKEYPTNLEERRVKHllaepkdYKGAFLALPKNLRRMFVhayqsylfneilSERIEEggplneavegdiLERKASVK 278
                       330       340       350       360
                ....*....|....*....|....*....|....*....|.
gi 16130652 305 PQ-------QLSWNWWDDVTVEIRFWLPAGSFATSVVRELI 338
Cdd:cd02577 279 PGdfkigeeRPDELNPGKDKVVLSFTLPRGSYATSVLRELI 319
PseudoU_synth_ScPUS7 cd02576
Pseudouridine synthase, TruD family; This group consists of eukaryotic pseudouridine synthases ...
17-338 4.14e-22

Pseudouridine synthase, TruD family; This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Saccharomyces cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA), psi13 in cytoplasmic tRNAs and psi35 in pre-tRNATyr. Psi35 in yeast U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35.


Pssm-ID: 211341 [Multi-domain]  Cd Length: 371  Bit Score: 95.76  E-value: 4.14e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  17 TGLLKANPEDFVVVEdlgFEPDGEgehiLVRiLKNGCntRFV--------ADAL---AKFLKIHAREVSFAGQKDKHAVT 85
Cdd:cd02576   3 RGIIKQRYSDFVVNE---IDLDGS----VVH-LTDYL--HFTlykenkdtMEAInkiAKLLRVKPSDFSYAGTKDKRAVT 72
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652  86 EQWLCARvpgKEMPD-LSA--FQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREV--SNRDDVEQRLIDICVKGVPNYF 160
Cdd:cd02576  73 VQRVSVK---KVTASrLKAlnSKLRGIRVGNFEYKDEPLKLGDLKGNEFTIVIRNVkaDSEELIKQALESLKEKGFINYY 149
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652 161 GAQRFG--------IGGSNLQG------------------------AQRWAQT--------NTPVRD------------- 187
Cdd:cd02576 150 GLQRFGtfsiptheIGIAILKEnwkeavdlilkprseleegdlveaREIWKETgdakaalkKLPRKKvaekallrglsky 229
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652 188 ---------------RNKRSFWLSAARSALFNQIVAERLKKADvNQVVDGDalqlagrgswfvatteelaeLQRRVNDke 252
Cdd:cd02576 230 gngpndylgaigsipRNLRSMYVHAYQSYVWNLAVSKRIKLYG-LKVVEGD--------------------LVIVIYD-- 286
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130652 253 lmITAALPGS---------GEWgtqrealaFEQAAVAAETELQALLVREK----VEAARRaMLLYPQQLSWNWwddVTVE 319
Cdd:cd02576 287 --VVLPLPGHdviypsneiGEW--------YKEVLSKDGLDPDNMRRKERefslSGGYRK-ILVKPKNLEYSF---LALK 352
                       410
                ....*....|....*....
gi 16130652 320 IRFWLPAGSFATSVVRELI 338
Cdd:cd02576 353 LKFSLPSSSYATMALRELM 371
PseudoU_synth cd01291
Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to ...
50-92 8.45e-12

Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).


Pssm-ID: 211324 [Multi-domain]  Cd Length: 87  Bit Score: 60.66  E-value: 8.45e-12
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 16130652  50 KNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCAR 92
Cdd:cd01291   3 KPGGDTMEAARQLAKLLGIPPKRVGYAGRKDKRAVTTQLVSNR 45
PseudoU_synth cd01291
Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to ...
303-338 4.94e-04

Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).


Pssm-ID: 211324 [Multi-domain]  Cd Length: 87  Bit Score: 38.70  E-value: 4.94e-04
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 16130652 303 LYPQQLSWNWWDD--VTVEIRFWLPAGSFATSVVRELI 338
Cdd:cd01291  50 LRVKPLNLKWPEErkRALVLEFTLPRGSYATMLLRELG 87
 
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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