NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1002247740|ref|XP_015628038|]
View 

uncharacterized protein [Oryza sativa Japonica Group]

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
PRK05618 super family cl35350
50S ribosomal protein L25/general stress protein Ctc; Reviewed
 36-236 3.49e-32

50S ribosomal protein L25/general stress protein Ctc; Reviewed


The actual alignment was detected with superfamily member PRK05618:

Pssm-ID: 235534 [Multi-domain]  Cd Length: 197  Bit Score: 116.07  E-value: 3.49e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740  36 HTIQALPRETAGPRAAARERRSGRVPAVLLalagaGPGEGVAHrklLTADRKQLGEILKqSPYFLSTPVRLQVRAGERst 115
Cdd:PRK05618    4 ITLEAEVREEFGKGAARRLRRAGKVPAVIY-----GKGKEPVS---ISVDEKELIKALK-KGAFLSTLLDLEVGGKKQ-- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740 116 avvhsgTVLPIKVHRDETTGNILNLVLVEADEGTMLKVNLPVEFKGEDVCPGLKKGGFLQKIRTSLVYLCPAEHIPPKIE 195
Cdd:PRK05618   73 ------KVLVKDVQRHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGVKLGGVLNQVLHELEVECLPEDIPEFIE 146

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1002247740 196 VDLANLDIGDRVSMNDIPVHPSLRLLSkNETMPVCKILASK 236
Cdd:PRK05618  147 VDVSGLEIGDSIHVSDLKLPEGVKLLD-DPDEVVATVVAPR 186
 
Name Accession Description Interval E-value
PRK05618 PRK05618
50S ribosomal protein L25/general stress protein Ctc; Reviewed
 36-236 3.49e-32

50S ribosomal protein L25/general stress protein Ctc; Reviewed


Pssm-ID: 235534 [Multi-domain]  Cd Length: 197  Bit Score: 116.07  E-value: 3.49e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740  36 HTIQALPRETAGPRAAARERRSGRVPAVLLalagaGPGEGVAHrklLTADRKQLGEILKqSPYFLSTPVRLQVRAGERst 115
Cdd:PRK05618    4 ITLEAEVREEFGKGAARRLRRAGKVPAVIY-----GKGKEPVS---ISVDEKELIKALK-KGAFLSTLLDLEVGGKKQ-- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740 116 avvhsgTVLPIKVHRDETTGNILNLVLVEADEGTMLKVNLPVEFKGEDVCPGLKKGGFLQKIRTSLVYLCPAEHIPPKIE 195
Cdd:PRK05618   73 ------KVLVKDVQRHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGVKLGGVLNQVLHELEVECLPEDIPEFIE 146

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1002247740 196 VDLANLDIGDRVSMNDIPVHPSLRLLSkNETMPVCKILASK 236
Cdd:PRK05618  147 VDVSGLEIGDSIHVSDLKLPEGVKLLD-DPDEVVATVVAPR 186
Ribosomal_TL5_C pfam14693
Ribosomal protein TL5, C-terminal domain; This family contains the C-terminal domain of ...
 151-236 8.57e-23

Ribosomal protein TL5, C-terminal domain; This family contains the C-terminal domain of ribosomal protein TL5. The N-terminal domain, which binds to 5S rRNA, is contained in family Ribosomal_L25p, pfam01386. Full length (N- and C-terminal domain) homologs of TL5 are also known as CTC proteins. TL5 or CTC are not found in Eukarya or Archaea. In some Bacteria, including E. coli, this ribosomal subunit occurs as a single domain protein (named Ribosomal subunit L25), where the only domain is homologous to TL5 N-terminal domain (hence included in family pfam01386). The function of the C-terminal domain of TLC is at present unknown.


Pssm-ID: 464265  Cd Length: 84  Bit Score: 88.23  E-value: 8.57e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740 151 LKVNLPVEFKGEdvCPGLKKGGFLQKIRTSLVYLCPAEHIPPKIEVDLANLDIGDRVSMNDIPVHPSLRLLSKNETmPVC 230
Cdd:pfam14693   2 VTVEVPVHFVGE--APGVKKGGVLNQVLRELEVECLPKDIPEFIEVDVSGLEIGDSIHVSDLKLPEGVELLTDPDT-VVV 78


                  ....*.
gi 1002247740 231 KILASK 236
Cdd:pfam14693  79 SVVAPR 84
RplY COG1825
Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and ...
 37-214 4.80e-21

Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis]; Ribosomal protein L25 (general stress protein Ctc) is part of the Pathway/BioSystem: Ribosome 50S subunit


Pssm-ID: 441430 [Multi-domain]  Cd Length: 182  Bit Score: 86.49  E-value: 4.80e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740  37 TIQALPRETAGPRAAARERRSGRVPAVLlalagAGPGEGVAHrklLTADRKQLGEILKQspYFLSTPVRLQVrAGERSTA 116
Cdd:COG1825     5 TLKAEKREETGKGAARRLRREGKVPAVI-----YGGGKEPVS---ISVDAKELRKLLRK--EGENTLITLDI-DGKKEKV 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740 117 VVHSgtvlpikVHRDETTGNILNLVLVEADEGTMLKVNLPVEFKGEDVCPGLKKGGFLQKIRTSLVYLCPAehIPPKIEV 196
Cdd:COG1825    74 LIKD-------VQRHPVKDEILHVDFLRVSAGEKVTVEVPVHFVGEAAGVKVGGGLVLTLHELEVEALPPD--IPEPIEV 144

                         170
                  ....*....|....*...
gi 1002247740 197 DLANLDIGDRVSMNDIPV 214
Cdd:COG1825   145 DVSDLGLGDSISVHDLDL 162
bL25_bact_ctc TIGR00731
ribosomal protein bL25, Ctc-form; This model models a family of proteins with full-length ...
 43-225 4.84e-17

ribosomal protein bL25, Ctc-form; This model models a family of proteins with full-length homology to the general stress protein Ctc of Bacillus subtilis, a mesophile, and ribosomal protein TL5 of Thermus thermophilus, a thermophile. Ribosomal protein L25 of Escherichia coli and H. influenzae appear to be orthologous but consist only of the N-terminal half of Ctc and TL5. Both short (L25-like) and full-length (CTC-like) members of this family bind the E-loop of bacterial 5S rRNA. This protein appears to be restricted to bacteria and organelles, and consists of at most one copy per prokaryotic genome.Ctc of Bacillus subtilis has now been localized to ribosomes and can be viewed as the long form, or Ctc form, of L25. The C-terminal domain of sll1824, an apparent L25 of Synechocystis PCC6803, matches the N-terminal domain of this family. Examples of L25 and Ctc are not separated by a UPGMA tree built on the region of shared homology. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273237 [Multi-domain]  Cd Length: 176  Bit Score: 75.86  E-value: 4.84e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740  43 RETAGPRAAARERRSGRVPAVLLalagaGPGEGVAHrklLTADRKQLGEILKQSPyfLSTPVRLQVRAGERStavvhsgt 122
Cdd:TIGR00731   6 RTSFGKSAARRIRKEGRIPAVVY-----GKGKENVN---LELKSKEFIKYLRKGA--TSTVLTLEIGGKEFK-------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740 123 VLPIKVHRDETTGNILNLVLVEADEGTMLKVNLPVEFKGEDVCpgLKKGGFLQKIRTSLVYLCPAEHIPPKIEVDLANLD 202
Cdd:TIGR00731  68 VLVKDYQYNPVTNEVIHVDFLEVVEGVKLKVEVPIKLIGTPIG--VKNGGILTQVKRRIEVECKPKDIPDFLELDVSSLG 145

                         170       180
                  ....*....|....*....|...
gi 1002247740 203 IGDRVSMNDIPVHPSLRLLSKNE 225
Cdd:TIGR00731 146 VGESLKLSDLELPAGVSFITDDD 168
Ribosomal_L25_TL5_CTC cd00495
Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; L25 is a single-domain protein, ...
 37-140 1.29e-08

Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC. CTC is a known stress protein, and proteins of this family are believed to have two functions, acting as both ribosomal and stress proteins. In Escherichia coli, cells deleted for L25 were found to be viable; however, these cells grew slowly and had impaired protein synthesis capability. In Bacillus subtilis, CTC is induced under stress conditions and located in the ribosome; it has been proposed that CTC may be necessary for accurate translation under stress conditions. Ribosomal_L25_TL5_CTC is mostly found in bacteria, with a few exceptions such as plants or stramenopiles. Due to its limited taxonomic diversity and the viability of cells deleted for L25, this protein is not believed to be necessary for ribosomal assembly. Eukaryotes contain a protein called L25, which is not homologous to bacterial L25, but rather to bacterial L23.


Pssm-ID: 198379  Cd Length: 90  Bit Score: 50.93  E-value: 1.29e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740  37 TIQALPRETAGPRAAARERRSGRVPAVLLalagaGPGEgvaHRKLLTADRKQLGEILKQSPYflSTPVRLQVrAGERSTA 116
Cdd:cd00495     1 TLKAEKREETGKGAARRLRREGKVPAVIY-----GKGE---EPIPISVDAKELEKLLRKEGE--NTVIELEI-DGKKENV 69

                          90       100
                  ....*....|....*....|....
gi 1002247740 117 VVHSgtvlpikVHRDETTGNILNL 140
Cdd:cd00495    70 LIKD-------VQRHPVKDEILHV 86
 
Name Accession Description Interval E-value
PRK05618 PRK05618
50S ribosomal protein L25/general stress protein Ctc; Reviewed
 36-236 3.49e-32

50S ribosomal protein L25/general stress protein Ctc; Reviewed


Pssm-ID: 235534 [Multi-domain]  Cd Length: 197  Bit Score: 116.07  E-value: 3.49e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740  36 HTIQALPRETAGPRAAARERRSGRVPAVLLalagaGPGEGVAHrklLTADRKQLGEILKqSPYFLSTPVRLQVRAGERst 115
Cdd:PRK05618    4 ITLEAEVREEFGKGAARRLRRAGKVPAVIY-----GKGKEPVS---ISVDEKELIKALK-KGAFLSTLLDLEVGGKKQ-- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740 116 avvhsgTVLPIKVHRDETTGNILNLVLVEADEGTMLKVNLPVEFKGEDVCPGLKKGGFLQKIRTSLVYLCPAEHIPPKIE 195
Cdd:PRK05618   73 ------KVLVKDVQRHPVKDFILHVDFLRVDAGEKVKVEVPVHFVGEAKGVGVKLGGVLNQVLHELEVECLPEDIPEFIE 146

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1002247740 196 VDLANLDIGDRVSMNDIPVHPSLRLLSkNETMPVCKILASK 236
Cdd:PRK05618  147 VDVSGLEIGDSIHVSDLKLPEGVKLLD-DPDEVVATVVAPR 186
Ribosomal_TL5_C pfam14693
Ribosomal protein TL5, C-terminal domain; This family contains the C-terminal domain of ...
 151-236 8.57e-23

Ribosomal protein TL5, C-terminal domain; This family contains the C-terminal domain of ribosomal protein TL5. The N-terminal domain, which binds to 5S rRNA, is contained in family Ribosomal_L25p, pfam01386. Full length (N- and C-terminal domain) homologs of TL5 are also known as CTC proteins. TL5 or CTC are not found in Eukarya or Archaea. In some Bacteria, including E. coli, this ribosomal subunit occurs as a single domain protein (named Ribosomal subunit L25), where the only domain is homologous to TL5 N-terminal domain (hence included in family pfam01386). The function of the C-terminal domain of TLC is at present unknown.


Pssm-ID: 464265  Cd Length: 84  Bit Score: 88.23  E-value: 8.57e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740 151 LKVNLPVEFKGEdvCPGLKKGGFLQKIRTSLVYLCPAEHIPPKIEVDLANLDIGDRVSMNDIPVHPSLRLLSKNETmPVC 230
Cdd:pfam14693   2 VTVEVPVHFVGE--APGVKKGGVLNQVLRELEVECLPKDIPEFIEVDVSGLEIGDSIHVSDLKLPEGVELLTDPDT-VVV 78


                  ....*.
gi 1002247740 231 KILASK 236
Cdd:pfam14693  79 SVVAPR 84
RplY COG1825
Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and ...
 37-214 4.80e-21

Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis]; Ribosomal protein L25 (general stress protein Ctc) is part of the Pathway/BioSystem: Ribosome 50S subunit


Pssm-ID: 441430 [Multi-domain]  Cd Length: 182  Bit Score: 86.49  E-value: 4.80e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740  37 TIQALPRETAGPRAAARERRSGRVPAVLlalagAGPGEGVAHrklLTADRKQLGEILKQspYFLSTPVRLQVrAGERSTA 116
Cdd:COG1825     5 TLKAEKREETGKGAARRLRREGKVPAVI-----YGGGKEPVS---ISVDAKELRKLLRK--EGENTLITLDI-DGKKEKV 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740 117 VVHSgtvlpikVHRDETTGNILNLVLVEADEGTMLKVNLPVEFKGEDVCPGLKKGGFLQKIRTSLVYLCPAehIPPKIEV 196
Cdd:COG1825    74 LIKD-------VQRHPVKDEILHVDFLRVSAGEKVTVEVPVHFVGEAAGVKVGGGLVLTLHELEVEALPPD--IPEPIEV 144

                         170
                  ....*....|....*...
gi 1002247740 197 DLANLDIGDRVSMNDIPV 214
Cdd:COG1825   145 DVSDLGLGDSISVHDLDL 162
bL25_bact_ctc TIGR00731
ribosomal protein bL25, Ctc-form; This model models a family of proteins with full-length ...
 43-225 4.84e-17

ribosomal protein bL25, Ctc-form; This model models a family of proteins with full-length homology to the general stress protein Ctc of Bacillus subtilis, a mesophile, and ribosomal protein TL5 of Thermus thermophilus, a thermophile. Ribosomal protein L25 of Escherichia coli and H. influenzae appear to be orthologous but consist only of the N-terminal half of Ctc and TL5. Both short (L25-like) and full-length (CTC-like) members of this family bind the E-loop of bacterial 5S rRNA. This protein appears to be restricted to bacteria and organelles, and consists of at most one copy per prokaryotic genome.Ctc of Bacillus subtilis has now been localized to ribosomes and can be viewed as the long form, or Ctc form, of L25. The C-terminal domain of sll1824, an apparent L25 of Synechocystis PCC6803, matches the N-terminal domain of this family. Examples of L25 and Ctc are not separated by a UPGMA tree built on the region of shared homology. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273237 [Multi-domain]  Cd Length: 176  Bit Score: 75.86  E-value: 4.84e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740  43 RETAGPRAAARERRSGRVPAVLLalagaGPGEGVAHrklLTADRKQLGEILKQSPyfLSTPVRLQVRAGERStavvhsgt 122
Cdd:TIGR00731   6 RTSFGKSAARRIRKEGRIPAVVY-----GKGKENVN---LELKSKEFIKYLRKGA--TSTVLTLEIGGKEFK-------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740 123 VLPIKVHRDETTGNILNLVLVEADEGTMLKVNLPVEFKGEDVCpgLKKGGFLQKIRTSLVYLCPAEHIPPKIEVDLANLD 202
Cdd:TIGR00731  68 VLVKDYQYNPVTNEVIHVDFLEVVEGVKLKVEVPIKLIGTPIG--VKNGGILTQVKRRIEVECKPKDIPDFLELDVSSLG 145

                         170       180
                  ....*....|....*....|...
gi 1002247740 203 IGDRVSMNDIPVHPSLRLLSKNE 225
Cdd:TIGR00731 146 VGESLKLSDLELPAGVSFITDDD 168
Ribosomal_L25_TL5_CTC cd00495
Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; L25 is a single-domain protein, ...
 37-140 1.29e-08

Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC. CTC is a known stress protein, and proteins of this family are believed to have two functions, acting as both ribosomal and stress proteins. In Escherichia coli, cells deleted for L25 were found to be viable; however, these cells grew slowly and had impaired protein synthesis capability. In Bacillus subtilis, CTC is induced under stress conditions and located in the ribosome; it has been proposed that CTC may be necessary for accurate translation under stress conditions. Ribosomal_L25_TL5_CTC is mostly found in bacteria, with a few exceptions such as plants or stramenopiles. Due to its limited taxonomic diversity and the viability of cells deleted for L25, this protein is not believed to be necessary for ribosomal assembly. Eukaryotes contain a protein called L25, which is not homologous to bacterial L25, but rather to bacterial L23.


Pssm-ID: 198379  Cd Length: 90  Bit Score: 50.93  E-value: 1.29e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740  37 TIQALPRETAGPRAAARERRSGRVPAVLLalagaGPGEgvaHRKLLTADRKQLGEILKQSPYflSTPVRLQVrAGERSTA 116
Cdd:cd00495     1 TLKAEKREETGKGAARRLRREGKVPAVIY-----GKGE---EPIPISVDAKELEKLLRKEGE--NTVIELEI-DGKKENV 69

                          90       100
                  ....*....|....*....|....
gi 1002247740 117 VVHSgtvlpikVHRDETTGNILNL 140
Cdd:cd00495    70 LIKD-------VQRHPVKDEILHV 86
Ribosomal_L25p pfam01386
Ribosomal L25p family; Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. ...
 38-140 1.10e-04

Ribosomal L25p family; Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis, which is induced by stress.


Pssm-ID: 460185  Cd Length: 87  Bit Score: 39.73  E-value: 1.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247740  38 IQALPRETAGPRAAARERRSGRVPAVLlalagAGPGEGVAHrklLTADRKQLGEILKQspYFLSTPVRLQVrAGERSTAV 117
Cdd:pfam01386   1 LKAEKRTEFGKGAARRLRREGKVPAVL-----YGGGKEPIS---ISVDAKELRKLLRT--EGENTVIELDI-DGKKYKVL 69

                          90       100
                  ....*....|....*....|...
gi 1002247740 118 VHSgtvlpikVHRDETTGNILNL 140
Cdd:pfam01386  70 IKD-------VQRHPVKDEILHV 85
 
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