|
Name |
Accession |
Description |
Interval |
E-value |
| rimM |
PRK00122 |
16S rRNA-processing protein RimM; Provisional |
1-172 |
1.18e-66 |
|
16S rRNA-processing protein RimM; Provisional
Pssm-ID: 234650 [Multi-domain] Cd Length: 172 Bit Score: 201.52 E-value: 1.18e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 1 MTKLENPVLMATIGGAQGLRGEVRAKAYTADPGALGDYGHLHSMDG---RSFEVLEIREMKNVVVVRFRGVNDRNAAEAL 77
Cdd:PRK00122 1 MSKPEDLLVVGKIVSAHGIKGEVKVKSFTDFPERIFDYGPWLLGKGgewQEVEIESGRFHKGFLIVKFEGVDDRNAAEAL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 78 NGLELYIERDNLPdeELEDDEFYYADLEGLEARDDKGVSYGTVTGVFDFGAGDLLELKGPGKRPVLIPFSEASVLEIDLE 157
Cdd:PRK00122 81 KGCELFVPRSQLP--ELEEDEYYWHDLIGLEVVDEDGEELGKVTDILETGANDVLVVLKDKKEERLIPFVEEVVKEVDLE 158
|
170
....*....|....*
gi 502309687 158 AGTLLIDPLaAGLVE 172
Cdd:PRK00122 159 AKRITVDWP-EGLLD 172
|
|
| RimM |
COG0806 |
Ribosomal 30S subunit maturation factor RimM, required for 16S rRNA processing [Translation, ... |
3-173 |
5.77e-62 |
|
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: 189.55 E-value: 5.77e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 3 KLENPVLMATIGGAQGLRGEVRAKAYTADPGALGDYGHLHSMDG----RSFEVLEIREMKNVVVVRFRGVNDRNAAEALN 78
Cdd:COG0806 2 KMEDLVVVGRIVKAHGVKGEVKVKSFTDDPERFFDYGPVFLEDPdgelRPLTVESVRPHKGGLLVKFEGVDDREAAEALR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 79 GLELYIERDNLPdeELEDDEFYYADLEGLEARDDKGVSYGTVTGVFDFGAGDLLELKGPGKRPVLIPFSEASVLEIDLEA 158
Cdd:COG0806 82 GAELYVPRDDLP--ELEEDEFYWHDLIGLEVVDEDGEELGKVTDVLETGANDVLVVKGPGGKEVLIPFVDEFVPEVDLEA 159
|
170
....*....|....*
gi 502309687 159 GTLLIDPLaAGLVED 173
Cdd:COG0806 160 GRIVVDPP-EGLLDL 173
|
|
| 16S_RimM |
TIGR02273 |
16S rRNA processing protein RimM; This family consists of the bacterial protein RimM (YfjA, ... |
7-167 |
2.25e-51 |
|
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: 162.38 E-value: 2.25e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 7 PVLMATIGGAQGLRGEVRAKAYTADPGALGDYGHLHSMDG----RSFEVLEIREMKNVVVVRFRGVNDRNAAEALNGLEL 82
Cdd:TIGR02273 1 LLVVGKIGGPHGIKGEVKVKSFTDFPESLFDYGPWLILKGskqwQTVKVARVRKQNNKLIVKFEGIDDREAAEALKGLEL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 83 YIERDNLPdeELEDDEFYYADLEGLEARDDKGVSYGTVTGVFDFGAGDLLELKGP-GKRPVLIPFSEASVLEIDLEAGTL 161
Cdd:TIGR02273 81 FVPREALP--ELEEDEYYWTDLIGLEVVTEEGEELGKVVEILETGANDVLVVRSKkGKKEVLIPFVEEIVKEIDLEKKII 158
|
....*.
gi 502309687 162 LIDPLA 167
Cdd:TIGR02273 159 TVDWPE 164
|
|
| RimM |
pfam01782 |
RimM N-terminal domain; The RimM protein is essential for efficient processing of 16S rRNA. ... |
9-87 |
1.03e-21 |
|
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: 84.15 E-value: 1.03e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 9 LMATIGGAQGLRGEVRAKAYTADPGALGDYGHL----HSMDGRSFEVLEIREMKNVVVVRFRGVNDRNAAEALNGLELYI 84
Cdd:pfam01782 1 VVGKIVGTHGLKGEVKVKSFTDFPEDRFDYGPVfllkKKGKWQTLTVESVRVHKKGLILKFEGIDDRDAAEALKGAELYV 80
|
...
gi 502309687 85 ERD 87
Cdd:pfam01782 81 PRS 83
|
|
|
|
Name |
Accession |
Description |
Interval |
E-value |
| rimM |
PRK00122 |
16S rRNA-processing protein RimM; Provisional |
1-172 |
1.18e-66 |
|
16S rRNA-processing protein RimM; Provisional
Pssm-ID: 234650 [Multi-domain] Cd Length: 172 Bit Score: 201.52 E-value: 1.18e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 1 MTKLENPVLMATIGGAQGLRGEVRAKAYTADPGALGDYGHLHSMDG---RSFEVLEIREMKNVVVVRFRGVNDRNAAEAL 77
Cdd:PRK00122 1 MSKPEDLLVVGKIVSAHGIKGEVKVKSFTDFPERIFDYGPWLLGKGgewQEVEIESGRFHKGFLIVKFEGVDDRNAAEAL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 78 NGLELYIERDNLPdeELEDDEFYYADLEGLEARDDKGVSYGTVTGVFDFGAGDLLELKGPGKRPVLIPFSEASVLEIDLE 157
Cdd:PRK00122 81 KGCELFVPRSQLP--ELEEDEYYWHDLIGLEVVDEDGEELGKVTDILETGANDVLVVLKDKKEERLIPFVEEVVKEVDLE 158
|
170
....*....|....*
gi 502309687 158 AGTLLIDPLaAGLVE 172
Cdd:PRK00122 159 AKRITVDWP-EGLLD 172
|
|
| RimM |
COG0806 |
Ribosomal 30S subunit maturation factor RimM, required for 16S rRNA processing [Translation, ... |
3-173 |
5.77e-62 |
|
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: 189.55 E-value: 5.77e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 3 KLENPVLMATIGGAQGLRGEVRAKAYTADPGALGDYGHLHSMDG----RSFEVLEIREMKNVVVVRFRGVNDRNAAEALN 78
Cdd:COG0806 2 KMEDLVVVGRIVKAHGVKGEVKVKSFTDDPERFFDYGPVFLEDPdgelRPLTVESVRPHKGGLLVKFEGVDDREAAEALR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 79 GLELYIERDNLPdeELEDDEFYYADLEGLEARDDKGVSYGTVTGVFDFGAGDLLELKGPGKRPVLIPFSEASVLEIDLEA 158
Cdd:COG0806 82 GAELYVPRDDLP--ELEEDEFYWHDLIGLEVVDEDGEELGKVTDVLETGANDVLVVKGPGGKEVLIPFVDEFVPEVDLEA 159
|
170
....*....|....*
gi 502309687 159 GTLLIDPLaAGLVED 173
Cdd:COG0806 160 GRIVVDPP-EGLLDL 173
|
|
| rimM |
PRK13828 |
16S rRNA-processing protein RimM; Provisional |
19-186 |
2.01e-57 |
|
16S rRNA-processing protein RimM; Provisional
Pssm-ID: 184351 [Multi-domain] Cd Length: 161 Bit Score: 177.83 E-value: 2.01e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 19 LRGEVRAKAYTADPGALGDYGHLHSMDG-RSFEVLEIREMKNVVVVRFRGVNDRNAAEALNGLELYIERDNLPdeELEDD 97
Cdd:PRK13828 1 VRGEVRLKSFTEDPLAIADYGPLTTEDGaRSFTVALARPAKDGLVARLKGVATREAAEALRGLELYVPRDRLP--ELDDD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 98 EFYYADLEGLEARDDKGVSYGTVTGVFDFGAGDLLELKGPGKRP-VLIPFSEASVLEIDLEAGTLLIDPlaaglvedPEE 176
Cdd:PRK13828 79 EFYHADLIGLAAVDTGGALLGRVKAVHNFGAGDILEIAPPGGGPtLLLPFTRAVVPTVDLAAGRVVADP--------PAE 150
|
170
....*....|
gi 502309687 177 LSKFTPDKPK 186
Cdd:PRK13828 151 IEGDEPPEPD 160
|
|
| 16S_RimM |
TIGR02273 |
16S rRNA processing protein RimM; This family consists of the bacterial protein RimM (YfjA, ... |
7-167 |
2.25e-51 |
|
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: 162.38 E-value: 2.25e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 7 PVLMATIGGAQGLRGEVRAKAYTADPGALGDYGHLHSMDG----RSFEVLEIREMKNVVVVRFRGVNDRNAAEALNGLEL 82
Cdd:TIGR02273 1 LLVVGKIGGPHGIKGEVKVKSFTDFPESLFDYGPWLILKGskqwQTVKVARVRKQNNKLIVKFEGIDDREAAEALKGLEL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 83 YIERDNLPdeELEDDEFYYADLEGLEARDDKGVSYGTVTGVFDFGAGDLLELKGP-GKRPVLIPFSEASVLEIDLEAGTL 161
Cdd:TIGR02273 81 FVPREALP--ELEEDEYYWTDLIGLEVVTEEGEELGKVVEILETGANDVLVVRSKkGKKEVLIPFVEEIVKEIDLEKKII 158
|
....*.
gi 502309687 162 LIDPLA 167
Cdd:TIGR02273 159 TVDWPE 164
|
|
| rimM |
PRK14592 |
16S rRNA-processing protein RimM; Provisional |
8-165 |
3.20e-30 |
|
16S rRNA-processing protein RimM; Provisional
Pssm-ID: 173056 [Multi-domain] Cd Length: 165 Bit Score: 108.66 E-value: 3.20e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 8 VLMATIGGAQGLRGEVRAKAYTADPGALGDYGHLhsMDG-RSFEVLEIREMK-NVVVVRFRGVNDRNAAEALNGLELYIE 85
Cdd:PRK14592 3 ICLGVITSPHGIKGHVKIKTFTEDPENISAYGKL--TDGsNTYKISVVSVIGaNLVIAKISGINSRTEAELLRNKKLYVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 86 RDNLPdeELEDDEFYYADLEGLEARDDKGVSYGTVTGVFDFGAGDLLELKG-PGKRPVLIPFSEASVLEIDLEAGTLLID 164
Cdd:PRK14592 81 RSKLP--NLNEDEFYQSDLIGMEVKLEDNTIYGYIKKIYNFGSCDIIEISLtSTKKSTMLPFTKEIFPHINVKERYIILV 158
|
.
gi 502309687 165 P 165
Cdd:PRK14592 159 P 159
|
|
| RimM |
pfam01782 |
RimM N-terminal domain; The RimM protein is essential for efficient processing of 16S rRNA. ... |
9-87 |
1.03e-21 |
|
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: 84.15 E-value: 1.03e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 9 LMATIGGAQGLRGEVRAKAYTADPGALGDYGHL----HSMDGRSFEVLEIREMKNVVVVRFRGVNDRNAAEALNGLELYI 84
Cdd:pfam01782 1 VVGKIVGTHGLKGEVKVKSFTDFPEDRFDYGPVfllkKKGKWQTLTVESVRVHKKGLILKFEGIDDRDAAEALKGAELYV 80
|
...
gi 502309687 85 ERD 87
Cdd:pfam01782 81 PRS 83
|
|
| rimM |
PRK13829 |
16S rRNA-processing protein RimM; Provisional |
51-167 |
8.41e-13 |
|
16S rRNA-processing protein RimM; Provisional
Pssm-ID: 184352 [Multi-domain] Cd Length: 162 Bit Score: 63.23 E-value: 8.41e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 51 VLEIREMKNVVVVRFRGVNDRNAAEALNGLELYIERDNLPDeeLEDDEFYYADLEGLEARDDkGVSYGTVTGVFDFGAGD 130
Cdd:PRK13829 43 IERAERVGPELVLHLAGVTSREGAEALVGLRVYADDADLPP--LEEGSYYYHELRGLPVYVD-GEPLGEVVDVEDAGAQD 119
|
90 100 110 120
....*....|....*....|....*....|....*....|..
gi 502309687 131 LLELKGPG-----KRPVLIPFSEASVLeidLEAGTLLIDPLA 167
Cdd:PRK13829 120 LLVIRHVGgslraRATYFVPLQAPYVR---VELDGITADAIP 158
|
|
| PRC |
pfam05239 |
PRC-barrel domain; The PRC-barrel is an all beta barrel domain found in photosystem reaction ... |
96-170 |
4.12e-10 |
|
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: 53.83 E-value: 4.12e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 96 DDEFYYADLEGLEARDDKGVSYGTVTGV-FDFGAGDLLEL-----KGPGKRPVLIPFSEasvLEIDLEAGTLLIDPLAAG 169
Cdd:pfam05239 1 EDEFYASDLIGLEVYTEDGEKLGKVKDVvIDEGEGRVRYLvvsvgGFLGGKEVLIPFDK---LNVKLGKDRIIVDPPKEL 77
|
.
gi 502309687 170 L 170
Cdd:pfam05239 78 L 78
|
|
| rimM |
PRK14590 |
16S rRNA-processing protein RimM; Provisional |
51-165 |
4.84e-10 |
|
16S rRNA-processing protein RimM; Provisional
Pssm-ID: 173054 [Multi-domain] Cd Length: 171 Bit Score: 56.02 E-value: 4.84e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 51 VLEIREMKNVVVVRFRGVNDRNAAEALNGLELYIERDNLPDEELEdDEFYYADLEGLEARDDKGVSYG-TVTGVFDFGAG 129
Cdd:PRK14590 50 LLEIRPHGGKFLVRFEGYDTPEEAVKWRGGSLFLPQELLPKIETK-GEFYSEDLIGLQAIDETGKPLNwKLTDVQDNPAH 128
|
90 100 110
....*....|....*....|....*....|....*..
gi 502309687 130 DLLELKGPGKRPVLIPFSEASVLEIDLEAGTL-LIDP 165
Cdd:PRK14590 129 PILVFIKGEGEEILIPFLNVFVGDLDLEKQTIvLIQP 165
|
|
| rimM |
PRK14591 |
16S rRNA-processing protein RimM; Provisional |
61-164 |
1.28e-05 |
|
16S rRNA-processing protein RimM; Provisional
Pssm-ID: 173055 [Multi-domain] Cd Length: 169 Bit Score: 43.49 E-value: 1.28e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 61 VVVRFRGVNDRNAAEALNGLELYIERDNLPdeELEDDEFYYADLEGLEARDDKGVSYGTVTGVFDFGAGDLLELKGPGKR 140
Cdd:PRK14591 64 VYIKLANINNADTAKKYVNALIGVPKRALP--QLAEDEVYFKDLIGCSVKNINNDSFGVVVDIIETGANEVLVCKEDNSE 141
|
90 100
....*....|....*....|....
gi 502309687 141 pVLIPFSEASVLEIDLEAGTLLID 164
Cdd:PRK14591 142 -YLIPYVKQYIVSEDLNSKKIVVD 164
|
|
| rimM |
PRK14594 |
16S rRNA-processing protein RimM; Provisional |
50-161 |
2.54e-04 |
|
16S rRNA-processing protein RimM; Provisional
Pssm-ID: 173058 [Multi-domain] Cd Length: 166 Bit Score: 39.77 E-value: 2.54e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502309687 50 EVLEIREMKNVVVVRFRGVNDRNAAEALNGLELYIErDNLPdEELEDDEFYYADLEGLEARDDkGVSYGTVTGVFDFGAG 129
Cdd:PRK14594 50 KVEDVSLKNNSLLLKFEEFNAPEPIKPLIGFELWVD-DELA-SKLEEGEYYFGKLIGYAIVND-GKELGEVVSFFECLNS 126
|
90 100 110
....*....|....*....|....*....|..
gi 502309687 130 DLLELKgPGKRPVLIPFSEASVLEIDLEAGTL 161
Cdd:PRK14594 127 VLLEVK-VGIKLFFVPFLSIYLGDINRELKTI 157
|
|
|