NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1907118126|ref|XP_036015865|]
View 

large ribosomal subunit protein mL39 isoform X3 [Mus musculus]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PLN02908 super family cl31949
threonyl-tRNA synthetase
 144-316 1.20e-22

threonyl-tRNA synthetase


The actual alignment was detected with superfamily member PLN02908:

Pssm-ID: 178496 [Multi-domain]  Cd Length: 686  Bit Score: 99.85  E-value: 1.20e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907118126 144 SKSILALVDGQPWDMYKPLTKSCEIKFLTFKDPDPKEVnkaYWRSCAMMLGCVIERAfkddYVVSLVRAPEVPVIAGaFC 223
Cdd:PLN02908   84 NSALIAQVDGVLWDMTRPLEGDCKLKLFKFDDDEGRDT---FWHSSAHILGEALELE----YGCKLCIGPCTTRGEG-FY 155

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907118126 224 YDVTLDKR-LDEwmptkENLRSFTKDAHALIYRDLPFETLDVDARVALEIFQHNKYKVDFIEEKasqnPE-RIVKLHRIG 301
Cdd:PLN02908  156 YDAFYGDRtLNE-----EDFKPIEARAEKAVKEKQPFERIEVTREEALEMFSENKFKVEIINDL----PEdATITVYRCG 226

                         170
                  ....*....|....*
gi 1907118126 302 DFIDVSEGPLIPRTS 316
Cdd:PLN02908  227 PLVDLCRGPHIPNTS 241
Ubl1_cv_Nsp3_N-like super family cl28922
first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV ...
 63-171 7.29e-15

first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV non-structural protein 3 (Nsp3) and related proteins; This ubiquitin-like (Ubl) domain (Ubl1) is found at the N-terminus of coronavirus Nsp3, a large multi-functional multi-domain protein which is an essential component of the replication/transcription complex (RTC). The functions of Ubl1 in CoVs are related to single-stranded RNA (ssRNA) binding and to interacting with the nucleocapsid (N) protein. SARS-CoV Ubl1 has been shown to bind ssRNA having AUA patterns, and since the 5'-UTR of the SARS-CoV genome has a number of AUA repeats, it may bind there. In mouse hepatitis virus (MHV), this Ubl1 domain binds the cognate N protein. Adjacent to Ubl1 is a Glu-rich acidic region (also referred to as hypervariable region, HVR); Ubl1 together with HVR has been called Nsp3a. Currently, the function of HVR in CoVs is unknown. This model corresponds to one of two Ubl domains in Nsp3; the other is located N-terminal to the papain-like protease (PLpro) and is not represented by this model.


The actual alignment was detected with superfamily member cd01616:

Pssm-ID: 475130 [Multi-domain]  Cd Length: 61  Bit Score: 68.40  E-value: 7.29e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907118126  63 EVKHVGKTdPGTVFVMNKnISTPYSCAMRkqqnnvdhftravqstaegnmlsllgeaveficshfathcplcfvdLSEWY 142
Cdd:cd01616     1 EVFTVGKT-PGTVFVMNK-GATAYSCAMH----------------------------------------------LHEDY 32

                          90       100
                  ....*....|....*....|....*....
gi 1907118126 143 CSKSILALVDGQPWDMYKPLTKSCEIKFL 171
Cdd:cd01616    33 CRKSILALVDGQLWDMYYPLTKGDEIKFL 61
 
Name Accession Description Interval E-value
PLN02908 PLN02908
threonyl-tRNA synthetase
 144-316 1.20e-22

threonyl-tRNA synthetase


Pssm-ID: 178496 [Multi-domain]  Cd Length: 686  Bit Score: 99.85  E-value: 1.20e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907118126 144 SKSILALVDGQPWDMYKPLTKSCEIKFLTFKDPDPKEVnkaYWRSCAMMLGCVIERAfkddYVVSLVRAPEVPVIAGaFC 223
Cdd:PLN02908   84 NSALIAQVDGVLWDMTRPLEGDCKLKLFKFDDDEGRDT---FWHSSAHILGEALELE----YGCKLCIGPCTTRGEG-FY 155

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907118126 224 YDVTLDKR-LDEwmptkENLRSFTKDAHALIYRDLPFETLDVDARVALEIFQHNKYKVDFIEEKasqnPE-RIVKLHRIG 301
Cdd:PLN02908  156 YDAFYGDRtLNE-----EDFKPIEARAEKAVKEKQPFERIEVTREEALEMFSENKFKVEIINDL----PEdATITVYRCG 226

                         170
                  ....*....|....*
gi 1907118126 302 DFIDVSEGPLIPRTS 316
Cdd:PLN02908  227 PLVDLCRGPHIPNTS 241
ThrS COG0441
Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Threonyl-tRNA ...
 145-318 4.16e-20

Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Threonyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases


Pssm-ID: 440210 [Multi-domain]  Cd Length: 639  Bit Score: 92.02  E-value: 4.16e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907118126 145 KSILALVDGQPWDMYKPLTKSCEIKFLTFKDPDPKEVnkaYWRSCAMMLGCVIERAFkddyvvslvraPEV-----PVIA 219
Cdd:COG0441    34 AAVAAKVNGELVDLSTPIEEDAELEIVTFDDEEGLEI---LRHSAAHLLAQAVKRLY-----------PDAkltigPVIE 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907118126 220 GAFCYDVTLDKRLdewmpTKENLRSFTKDAHALIYRDLPFETLDVDARVALEIFQ--HNKYKVDFIEEKASqnpERIVKL 297
Cdd:COG0441   100 NGFYYDFDLERPF-----TPEDLEKIEKEMKEIIKEDLPIEREEVSREEAIELFKekGEPYKVELIEDIPE---DEEISL 171

                         170       180
                  ....*....|....*....|.
gi 1907118126 298 HRIGDFIDVSEGPLIPRTSVC 318
Cdd:COG0441   172 YRQGEFVDLCRGPHVPSTGKI 192
TGS cd01616
TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold; ...
 63-171 7.29e-15

TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold; This family includes eukaryotic and some bacterial threonyl-tRNA synthetases (ThrRSs), a distinct Obg family GTPases, and guanosine polyphosphate hydrolase (SpoT) and synthetase (RelA), which are involved in stringent response in bacteria, as well as uridine kinase (UDK) from Thermotogales. All family members contain a TGS domain named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs. It is a small domain with a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions. The functions of the TGS domain remains unclear, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, with a regulatory role.


Pssm-ID: 340455 [Multi-domain]  Cd Length: 61  Bit Score: 68.40  E-value: 7.29e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907118126  63 EVKHVGKTdPGTVFVMNKnISTPYSCAMRkqqnnvdhftravqstaegnmlsllgeaveficshfathcplcfvdLSEWY 142
Cdd:cd01616     1 EVFTVGKT-PGTVFVMNK-GATAYSCAMH----------------------------------------------LHEDY 32

                          90       100
                  ....*....|....*....|....*....
gi 1907118126 143 CSKSILALVDGQPWDMYKPLTKSCEIKFL 171
Cdd:cd01616    33 CRKSILALVDGQLWDMYYPLTKGDEIKFL 61
TGS_ThrRS cd01667
TGS (ThrRS, GTPase and SpoT) domain found in threonyl-tRNA synthetase (ThrRS) and similar ...
 134-177 7.51e-13

TGS (ThrRS, GTPase and SpoT) domain found in threonyl-tRNA synthetase (ThrRS) and similar proteins; ThrRS, also termed cytoplasmic threonine--tRNA ligase, is a class II aminoacyl-tRNA synthetase (aaRS) that plays an essential role in protein synthesis by catalyzing the aminoacylation of tRNA(Thr), generating aminoacyl-tRNA, and editing misacylation. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs. TGS is a small domain with a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions.


Pssm-ID: 340458 [Multi-domain]  Cd Length: 65  Bit Score: 62.89  E-value: 7.51e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1907118126 134 CFVDLSEWYCSKSILALVDGQPWDMYKPLTKSCEIKFLTFKDPD 177
Cdd:cd01667    22 IAKSISPGLAKKAVAAKVNGELVDLSRPLEEDAELEILTFDDPE 65
 
Name Accession Description Interval E-value
PLN02908 PLN02908
threonyl-tRNA synthetase
 144-316 1.20e-22

threonyl-tRNA synthetase


Pssm-ID: 178496 [Multi-domain]  Cd Length: 686  Bit Score: 99.85  E-value: 1.20e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907118126 144 SKSILALVDGQPWDMYKPLTKSCEIKFLTFKDPDPKEVnkaYWRSCAMMLGCVIERAfkddYVVSLVRAPEVPVIAGaFC 223
Cdd:PLN02908   84 NSALIAQVDGVLWDMTRPLEGDCKLKLFKFDDDEGRDT---FWHSSAHILGEALELE----YGCKLCIGPCTTRGEG-FY 155

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907118126 224 YDVTLDKR-LDEwmptkENLRSFTKDAHALIYRDLPFETLDVDARVALEIFQHNKYKVDFIEEKasqnPE-RIVKLHRIG 301
Cdd:PLN02908  156 YDAFYGDRtLNE-----EDFKPIEARAEKAVKEKQPFERIEVTREEALEMFSENKFKVEIINDL----PEdATITVYRCG 226

                         170
                  ....*....|....*
gi 1907118126 302 DFIDVSEGPLIPRTS 316
Cdd:PLN02908  227 PLVDLCRGPHIPNTS 241
ThrS COG0441
Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Threonyl-tRNA ...
 145-318 4.16e-20

Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Threonyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases


Pssm-ID: 440210 [Multi-domain]  Cd Length: 639  Bit Score: 92.02  E-value: 4.16e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907118126 145 KSILALVDGQPWDMYKPLTKSCEIKFLTFKDPDPKEVnkaYWRSCAMMLGCVIERAFkddyvvslvraPEV-----PVIA 219
Cdd:COG0441    34 AAVAAKVNGELVDLSTPIEEDAELEIVTFDDEEGLEI---LRHSAAHLLAQAVKRLY-----------PDAkltigPVIE 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907118126 220 GAFCYDVTLDKRLdewmpTKENLRSFTKDAHALIYRDLPFETLDVDARVALEIFQ--HNKYKVDFIEEKASqnpERIVKL 297
Cdd:COG0441   100 NGFYYDFDLERPF-----TPEDLEKIEKEMKEIIKEDLPIEREEVSREEAIELFKekGEPYKVELIEDIPE---DEEISL 171

                         170       180
                  ....*....|....*....|.
gi 1907118126 298 HRIGDFIDVSEGPLIPRTSVC 318
Cdd:COG0441   172 YRQGEFVDLCRGPHVPSTGKI 192
TGS cd01616
TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold; ...
 63-171 7.29e-15

TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold; This family includes eukaryotic and some bacterial threonyl-tRNA synthetases (ThrRSs), a distinct Obg family GTPases, and guanosine polyphosphate hydrolase (SpoT) and synthetase (RelA), which are involved in stringent response in bacteria, as well as uridine kinase (UDK) from Thermotogales. All family members contain a TGS domain named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs. It is a small domain with a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions. The functions of the TGS domain remains unclear, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, with a regulatory role.


Pssm-ID: 340455 [Multi-domain]  Cd Length: 61  Bit Score: 68.40  E-value: 7.29e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907118126  63 EVKHVGKTdPGTVFVMNKnISTPYSCAMRkqqnnvdhftravqstaegnmlsllgeaveficshfathcplcfvdLSEWY 142
Cdd:cd01616     1 EVFTVGKT-PGTVFVMNK-GATAYSCAMH----------------------------------------------LHEDY 32

                          90       100
                  ....*....|....*....|....*....
gi 1907118126 143 CSKSILALVDGQPWDMYKPLTKSCEIKFL 171
Cdd:cd01616    33 CRKSILALVDGQLWDMYYPLTKGDEIKFL 61
TGS_ThrRS cd01667
TGS (ThrRS, GTPase and SpoT) domain found in threonyl-tRNA synthetase (ThrRS) and similar ...
 134-177 7.51e-13

TGS (ThrRS, GTPase and SpoT) domain found in threonyl-tRNA synthetase (ThrRS) and similar proteins; ThrRS, also termed cytoplasmic threonine--tRNA ligase, is a class II aminoacyl-tRNA synthetase (aaRS) that plays an essential role in protein synthesis by catalyzing the aminoacylation of tRNA(Thr), generating aminoacyl-tRNA, and editing misacylation. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs. TGS is a small domain with a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions.


Pssm-ID: 340458 [Multi-domain]  Cd Length: 65  Bit Score: 62.89  E-value: 7.51e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1907118126 134 CFVDLSEWYCSKSILALVDGQPWDMYKPLTKSCEIKFLTFKDPD 177
Cdd:cd01667    22 IAKSISPGLAKKAVAAKVNGELVDLSRPLEEDAELEILTFDDPE 65
PRK12444 PRK12444
threonyl-tRNA synthetase; Reviewed
 145-315 5.90e-10

threonyl-tRNA synthetase; Reviewed


Pssm-ID: 183530 [Multi-domain]  Cd Length: 639  Bit Score: 60.92  E-value: 5.90e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907118126 145 KSILALVDGQPWDMYKPLTKSCEIKFLTFkdpDPKEVNKAYWRSCAMMLGCVIERAFKDdyvVSLVRAPevpVIAGAFCY 224
Cdd:PRK12444   38 KAVAGKVNDKLYDLRRNLEEDAEVEIITI---DSNEGVEIARHSAAHILAQAVKRLYGD---VNLGVGP---VIENGFYY 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907118126 225 DVTLDKRLdewmpTKENLRSFTKDAHALIYRDLPFETLDVDARVALEIFQ--HNKYKVDFIEEKASqnpERIVKLHRIGD 302
Cdd:PRK12444  109 DMDLPSSV-----NVEDLRKIEKEMKKIINENIKIERVEVSREEAAKLFQemNDRLKLELLEAIPS---GESITLYKQGE 180

                         170
                  ....*....|...
gi 1907118126 303 FIDVSEGPLIPRT 315
Cdd:PRK12444  181 FVDLCRGPHLPST 193
 
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