NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2312126190|ref|WP_262316221|]
View 

ribosome maturation factor RimM [Lacticaseibacillus parakribbianus]

Protein Classification

ribosome maturation factor RimM( domain architecture ID 11478117)

ribosome maturation factor RimM is an accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region

Gene Ontology:  GO:0043022|GO:0042274
PubMed:  23293003

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
rimM PRK00122
16S rRNA-processing protein RimM; Provisional
 1-169 4.02e-68

16S rRNA-processing protein RimM; Provisional


:

Pssm-ID: 234650 [Multi-domain]  Cd Length: 172  Bit Score: 204.61  E-value: 4.02e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190   1 MANLYHVGKIVNTHGIRGELKVVPITDFPETRFAKGSKLVIEATPNVEVEVAQSRQQKGMYLLTLKGYTDINAVLPFKGQ 80
Cdd:PRK00122    4 PEDLLVVGKIVSAHGIKGEVKVKSFTDFPERIFDYGPWLLGKGGEWQEVEIESGRFHKGFLIVKFEGVDDRNAAEALKGC 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190  81 VLSVAESEMQDLADGEYYYHDIIGLTVIDQNDQVLGQVSEILSPGPNDVWVIPRPGKTDVLLPFLNSVVSRIDLAAHTAW 160
Cdd:PRK00122   84 ELFVPRSQLPELEEDEYYWHDLIGLEVVDEDGEELGKVTDILETGANDVLVVLKDKKEERLIPFVEEVVKEVDLEAKRIT 163


                  ....*....
gi 2312126190 161 VTVPEGLID 169
Cdd:PRK00122  164 VDWPEGLLD 172
 
Name Accession Description Interval E-value
rimM PRK00122
16S rRNA-processing protein RimM; Provisional
 1-169 4.02e-68

16S rRNA-processing protein RimM; Provisional


Pssm-ID: 234650 [Multi-domain]  Cd Length: 172  Bit Score: 204.61  E-value: 4.02e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190   1 MANLYHVGKIVNTHGIRGELKVVPITDFPETRFAKGSKLVIEATPNVEVEVAQSRQQKGMYLLTLKGYTDINAVLPFKGQ 80
Cdd:PRK00122    4 PEDLLVVGKIVSAHGIKGEVKVKSFTDFPERIFDYGPWLLGKGGEWQEVEIESGRFHKGFLIVKFEGVDDRNAAEALKGC 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190  81 VLSVAESEMQDLADGEYYYHDIIGLTVIDQNDQVLGQVSEILSPGPNDVWVIPRPGKTDVLLPFLNSVVSRIDLAAHTAW 160
Cdd:PRK00122   84 ELFVPRSQLPELEEDEYYWHDLIGLEVVDEDGEELGKVTDILETGANDVLVVLKDKKEERLIPFVEEVVKEVDLEAKRIT 163


                  ....*....
gi 2312126190 161 VTVPEGLID 169
Cdd:PRK00122  164 VDWPEGLLD 172
RimM COG0806
Ribosomal 30S subunit maturation factor RimM, required for 16S rRNA processing [Translation, ...
 1-170 1.23e-60

Ribosomal 30S subunit maturation factor RimM, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]; Ribosomal 30S subunit maturation factor RimM, required for 16S rRNA processing is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440569 [Multi-domain]  Cd Length: 173  Bit Score: 185.70  E-value: 1.23e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190   1 MANLYHVGKIVNTHGIRGELKVVPITDFPEtRFAKGSKLVIEATPN--VEVEVAQSRQQKGMYLLTLKGYTDINAVLPFK 78
Cdd:COG0806     3 MEDLVVVGRIVKAHGVKGEVKVKSFTDDPE-RFFDYGPVFLEDPDGelRPLTVESVRPHKGGLLVKFEGVDDREAAEALR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190  79 GQVLSVAESEMQDLADGEYYYHDIIGLTVIDQNDQVLGQVSEILSPGPNDVWVIPRPGKTDVLLPFLNSVVSRIDLAAHT 158
Cdd:COG0806    82 GAELYVPRDDLPELEEDEFYWHDLIGLEVVDEDGEELGKVTDVLETGANDVLVVKGPGGKEVLIPFVDEFVPEVDLEAGR 161

                         170
                  ....*....|..
gi 2312126190 159 AWVTVPEGLIDD 170
Cdd:COG0806   162 IVVDPPEGLLDL 173
16S_RimM TIGR02273
16S rRNA processing protein RimM; This family consists of the bacterial protein RimM (YfjA, ...
 7-166 5.18e-48

16S rRNA processing protein RimM; This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a PRC-barrel domain that it shares with other protein families (pfam05239) and a unique domain (pfam01782). This model describes the full-length protein. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide. [Transcription, RNA processing]


Pssm-ID: 274061 [Multi-domain]  Cd Length: 165  Bit Score: 153.13  E-value: 5.18e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190   7 VGKIVNTHGIRGELKVVPITDFPETRFAKGSKLVIEATPNV-EVEVAQSRQQKGMYLLTLKGYTDINAVLPFKGQVLSVA 85
Cdd:TIGR02273   4 VGKIGGPHGIKGEVKVKSFTDFPESLFDYGPWLILKGSKQWqTVKVARVRKQNNKLIVKFEGIDDREAAEALKGLELFVP 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190  86 ESEMQDLADGEYYYHDIIGLTVIDQNDQVLGQVSEILSPGPNDVWVI-PRPGKTDVLLPFLNSVVSRIDLAAHTAWVTVP 164
Cdd:TIGR02273  84 REALPELEEDEYYWTDLIGLEVVTEEGEELGKVVEILETGANDVLVVrSKKGKKEVLIPFVEEIVKEIDLEKKIITVDWP 163


                  ..
gi 2312126190 165 EG 166
Cdd:TIGR02273 164 EG 165
RimM pfam01782
RimM N-terminal domain; The RimM protein is essential for efficient processing of 16S rRNA. ...
 7-88 3.48e-25

RimM N-terminal domain; The RimM protein is essential for efficient processing of 16S rRNA. The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes. This N-terminal domain is found associated with a PRC-barrel domain.


Pssm-ID: 460327  Cd Length: 84  Bit Score: 92.62  E-value: 3.48e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190   7 VGKIVNTHGIRGELKVVPITDFPETRFAKGSKLVIEATPNV-EVEVAQSRQQKGMYLLTLKGYTDINAVLPFKGQVLSVA 85
Cdd:pfam01782   2 VGKIVGTHGLKGEVKVKSFTDFPEDRFDYGPVFLLKKKGKWqTLTVESVRVHKKGLILKFEGIDDRDAAEALKGAELYVP 81


                  ...
gi 2312126190  86 ESE 88
Cdd:pfam01782  82 RSD 84
 
Name Accession Description Interval E-value
rimM PRK00122
16S rRNA-processing protein RimM; Provisional
 1-169 4.02e-68

16S rRNA-processing protein RimM; Provisional


Pssm-ID: 234650 [Multi-domain]  Cd Length: 172  Bit Score: 204.61  E-value: 4.02e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190   1 MANLYHVGKIVNTHGIRGELKVVPITDFPETRFAKGSKLVIEATPNVEVEVAQSRQQKGMYLLTLKGYTDINAVLPFKGQ 80
Cdd:PRK00122    4 PEDLLVVGKIVSAHGIKGEVKVKSFTDFPERIFDYGPWLLGKGGEWQEVEIESGRFHKGFLIVKFEGVDDRNAAEALKGC 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190  81 VLSVAESEMQDLADGEYYYHDIIGLTVIDQNDQVLGQVSEILSPGPNDVWVIPRPGKTDVLLPFLNSVVSRIDLAAHTAW 160
Cdd:PRK00122   84 ELFVPRSQLPELEEDEYYWHDLIGLEVVDEDGEELGKVTDILETGANDVLVVLKDKKEERLIPFVEEVVKEVDLEAKRIT 163


                  ....*....
gi 2312126190 161 VTVPEGLID 169
Cdd:PRK00122  164 VDWPEGLLD 172
RimM COG0806
Ribosomal 30S subunit maturation factor RimM, required for 16S rRNA processing [Translation, ...
 1-170 1.23e-60

Ribosomal 30S subunit maturation factor RimM, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]; Ribosomal 30S subunit maturation factor RimM, required for 16S rRNA processing is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440569 [Multi-domain]  Cd Length: 173  Bit Score: 185.70  E-value: 1.23e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190   1 MANLYHVGKIVNTHGIRGELKVVPITDFPEtRFAKGSKLVIEATPN--VEVEVAQSRQQKGMYLLTLKGYTDINAVLPFK 78
Cdd:COG0806     3 MEDLVVVGRIVKAHGVKGEVKVKSFTDDPE-RFFDYGPVFLEDPDGelRPLTVESVRPHKGGLLVKFEGVDDREAAEALR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190  79 GQVLSVAESEMQDLADGEYYYHDIIGLTVIDQNDQVLGQVSEILSPGPNDVWVIPRPGKTDVLLPFLNSVVSRIDLAAHT 158
Cdd:COG0806    82 GAELYVPRDDLPELEEDEFYWHDLIGLEVVDEDGEELGKVTDVLETGANDVLVVKGPGGKEVLIPFVDEFVPEVDLEAGR 161

                         170
                  ....*....|..
gi 2312126190 159 AWVTVPEGLIDD 170
Cdd:COG0806   162 IVVDPPEGLLDL 173
16S_RimM TIGR02273
16S rRNA processing protein RimM; This family consists of the bacterial protein RimM (YfjA, ...
 7-166 5.18e-48

16S rRNA processing protein RimM; This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a PRC-barrel domain that it shares with other protein families (pfam05239) and a unique domain (pfam01782). This model describes the full-length protein. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide. [Transcription, RNA processing]


Pssm-ID: 274061 [Multi-domain]  Cd Length: 165  Bit Score: 153.13  E-value: 5.18e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190   7 VGKIVNTHGIRGELKVVPITDFPETRFAKGSKLVIEATPNV-EVEVAQSRQQKGMYLLTLKGYTDINAVLPFKGQVLSVA 85
Cdd:TIGR02273   4 VGKIGGPHGIKGEVKVKSFTDFPESLFDYGPWLILKGSKQWqTVKVARVRKQNNKLIVKFEGIDDREAAEALKGLELFVP 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190  86 ESEMQDLADGEYYYHDIIGLTVIDQNDQVLGQVSEILSPGPNDVWVI-PRPGKTDVLLPFLNSVVSRIDLAAHTAWVTVP 164
Cdd:TIGR02273  84 REALPELEEDEYYWTDLIGLEVVTEEGEELGKVVEILETGANDVLVVrSKKGKKEVLIPFVEEIVKEIDLEKKIITVDWP 163


                  ..
gi 2312126190 165 EG 166
Cdd:TIGR02273 164 EG 165
RimM pfam01782
RimM N-terminal domain; The RimM protein is essential for efficient processing of 16S rRNA. ...
 7-88 3.48e-25

RimM N-terminal domain; The RimM protein is essential for efficient processing of 16S rRNA. The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes. This N-terminal domain is found associated with a PRC-barrel domain.


Pssm-ID: 460327  Cd Length: 84  Bit Score: 92.62  E-value: 3.48e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190   7 VGKIVNTHGIRGELKVVPITDFPETRFAKGSKLVIEATPNV-EVEVAQSRQQKGMYLLTLKGYTDINAVLPFKGQVLSVA 85
Cdd:pfam01782   2 VGKIVGTHGLKGEVKVKSFTDFPEDRFDYGPVFLLKKKGKWqTLTVESVRVHKKGLILKFEGIDDRDAAEALKGAELYVP 81


                  ...
gi 2312126190  86 ESE 88
Cdd:pfam01782  82 RSD 84
rimM PRK13828
16S rRNA-processing protein RimM; Provisional
 16-170 3.00e-20

16S rRNA-processing protein RimM; Provisional


Pssm-ID: 184351 [Multi-domain]  Cd Length: 161  Bit Score: 81.92  E-value: 3.00e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190  16 IRGELKVVPITDFPE--TRF-----AKGSKlvieatpnvEVEVAQSRQQKGMYLLTLKGYTDINAVLPFKGQVLSVAESE 88
Cdd:PRK13828    1 VRGEVRLKSFTEDPLaiADYgplttEDGAR---------SFTVALARPAKDGLVARLKGVATREAAEALRGLELYVPRDR 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190  89 MQDLADGEYYYHDIIGLTVIDQNDQVLGQVSEILSPGPNDVWVI-PRPGKTDVLLPFLNSVVSRIDLAAHTAWVTVPEGL 167
Cdd:PRK13828   72 LPELDDDEFYHADLIGLAAVDTGGALLGRVKAVHNFGAGDILEIaPPGGGPTLLLPFTRAVVPTVDLAAGRVVADPPAEI 151


                  ...
gi 2312126190 168 IDD 170
Cdd:PRK13828  152 EGD 154
rimM PRK14592
16S rRNA-processing protein RimM; Provisional
 3-165 1.91e-13

16S rRNA-processing protein RimM; Provisional


Pssm-ID: 173056 [Multi-domain]  Cd Length: 165  Bit Score: 64.36  E-value: 1.91e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190   3 NLYHVGKIVNTHGIRGELKVVPITDFPETRFAKGSklVIEATPNVEVEVAqSRQQKGMYLLTLKGYTDINAVLPFKGQVL 82
Cdd:PRK14592    1 DLICLGVITSPHGIKGHVKIKTFTEDPENISAYGK--LTDGSNTYKISVV-SVIGANLVIAKISGINSRTEAELLRNKKL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190  83 SVAESEMQDLADGEYYYHDIIGLTVIDQNDQVLGQVSEILSPGPNDVWVI-PRPGKTDVLLPFLNSVVSRIDLAAHTAWV 161
Cdd:PRK14592   78 YVERSKLPNLNEDEFYQSDLIGMEVKLEDNTIYGYIKKIYNFGSCDIIEIsLTSTKKSTMLPFTKEIFPHINVKERYIIL 157


                  ....
gi 2312126190 162 TVPE 165
Cdd:PRK14592  158 VPPE 161
rimM PRK13829
16S rRNA-processing protein RimM; Provisional
 7-169 9.68e-09

16S rRNA-processing protein RimM; Provisional


Pssm-ID: 184352 [Multi-domain]  Cd Length: 162  Bit Score: 51.67  E-value: 9.68e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190   7 VGKIVNTHGIRGELKVvpitdfpetrfaKGSKlVIEATPNVEVE------VAQSRQQKGMYLLTLKGYTDINAVLPFKGQ 80
Cdd:PRK13829    6 IGRFGGPYGVQGGLKF------------RGEP-VVLDLPRVYVEglgwraIERAERVGPELVLHLAGVTSREGAEALVGL 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190  81 VLSVAESEMQDLADGEYYYHDIIGLTVIdQNDQVLGQVSEILSPGPNDVWVIPRPGKT-----DVLLPFLNSVVSRIDLA 155
Cdd:PRK13829   73 RVYADDADLPPLEEGSYYYHELRGLPVY-VDGEPLGEVVDVEDAGAQDLLVIRHVGGSlraraTYFVPLQAPYVRVELDG 151

                         170
                  ....*....|....
gi 2312126190 156 AHtawVTVPEGLID 169
Cdd:PRK13829  152 IT---ADAIPGLLD 162
rimM PRK14591
16S rRNA-processing protein RimM; Provisional
 7-154 1.87e-08

16S rRNA-processing protein RimM; Provisional


Pssm-ID: 173055 [Multi-domain]  Cd Length: 169  Bit Score: 51.19  E-value: 1.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190   7 VGKIVNTHGIRGELKVVPITDFPETRFAKGSKLVIEATPNVEVEVAQS---RQQKGMYLlTLKGYTDINAVLPFKGQVLS 83
Cdd:PRK14591    8 IAKIGATYKLNGELNLYPLANSIETLLSYGDWYIQLPATNVWQQLKGEsvlKRADKVYI-KLANINNADTAKKYVNALIG 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2312126190  84 VAESEMQDLADGEYYYHDIIGLTVIDQNDQVLGQVSEILSPGPNDVWVIpRPGKTDVLLPFLNSVVSRIDL 154
Cdd:PRK14591   87 VPKRALPQLAEDEVYFKDLIGCSVKNINNDSFGVVVDIIETGANEVLVC-KEDNSEYLIPYVKQYIVSEDL 156
rimM PRK14590
16S rRNA-processing protein RimM; Provisional
 7-165 9.47e-08

16S rRNA-processing protein RimM; Provisional


Pssm-ID: 173054 [Multi-domain]  Cd Length: 171  Bit Score: 49.08  E-value: 9.47e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190   7 VGKIVNTHGIRGELKV-VPITDFPETRFAKGSKLVIEAT--PNVEVEVAQSRQQKGMYLLTLKGYTDINAVLPFKGQVLS 83
Cdd:PRK14590    3 LGQLGKPFGIKGWLRVnVRGETLHTLKAPATLKLGKEDPqfPESEIALLEIRPHGGKFLVRFEGYDTPEEAVKWRGGSLF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190  84 VAESEMQDL-ADGEYYYHDIIGLTVIDQNDQVLG-QVSEILSPGPNDVWVIPRPGKTDVLLPFLNSVVSRIDLAAHTAWV 161
Cdd:PRK14590   83 LPQELLPKIeTKGEFYSEDLIGLQAIDETGKPLNwKLTDVQDNPAHPILVFIKGEGEEILIPFLNVFVGDLDLEKQTIVL 162


                  ....
gi 2312126190 162 TVPE 165
Cdd:PRK14590  163 IQPE 166
rimM PRK14593
ribosome maturation factor RimM;
1-121 3.37e-07

ribosome maturation factor RimM;


Pssm-ID: 237760 [Multi-domain]  Cd Length: 184  Bit Score: 47.71  E-value: 3.37e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190   1 MANLYHVGKIVNTHGIRGELKVVPITDFPETrFAKGSKLVIE-------ATPNVEVEVAQSRQQKGMYLLTLKGYTDINA 73
Cdd:PRK14593    1 MVSMLLVGRIGKSVGLNGGLKLHLESDFPEC-LKKGVKVSVAplnafscASSFKDYVIHSYEHAKNLLFLETIHTPEKAK 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2312126190  74 VLPFKGQVLSVAESE-MQDLADGEYYYHDIIGLTVIDQNdQVLGQVSEI 121
Cdd:PRK14593   80 ELTNLGLFMSEAESKkLCVLKEGEFFYCDLVGLSVVEEN-EILGKVIEI 127
PRC pfam05239
PRC-barrel domain; The PRC-barrel is an all beta barrel domain found in photosystem reaction ...
 94-153 5.95e-07

PRC-barrel domain; The PRC-barrel is an all beta barrel domain found in photosystem reaction centre subunit H of the purple bacteria and RNA metabolism proteins of the RimM group. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the carboxyl terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain.


Pssm-ID: 398765  Cd Length: 78  Bit Score: 44.97  E-value: 5.95e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2312126190  94 DGEYYYHDIIGLTVIDQNDQVLGQVSEI-LSPGPNDVWVI-----PRPGKTDVLLPFLNSVVSRID 153
Cdd:pfam05239   1 EDEFYASDLIGLEVYTEDGEKLGKVKDVvIDEGEGRVRYLvvsvgGFLGGKEVLIPFDKLNVKLGK 66
rimM PRK14594
16S rRNA-processing protein RimM; Provisional
 8-153 1.41e-05

16S rRNA-processing protein RimM; Provisional


Pssm-ID: 173058 [Multi-domain]  Cd Length: 166  Bit Score: 43.23  E-value: 1.41e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2312126190   8 GKIVNTHGIRGELKVVPITD-FPETRFAKGSKLVI--EATPNVEVEVAQSRQQKGMYLLTLKGYTDINAVLPFKGQVLSV 84
Cdd:PRK14594    5 GIILSSYGINGYAKVKSISNnFCDFINLKNNKLVLkkSNCSSIEVKVEDVSLKNNSLLLKFEEFNAPEPIKPLIGFELWV 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2312126190  85 AESEMQDLADGEYYYHDIIGLTVIDqNDQVLGQVSEILSpGPNDVWVIPRPGKTDVLLPFLNSVVSRID 153
Cdd:PRK14594   85 DDELASKLEEGEYYFGKLIGYAIVN-DGKELGEVVSFFE-CLNSVLLEVKVGIKLFFVPFLSIYLGDIN 151
 
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