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Conserved domains on  [gi|451702721|gb|EMD57123|]
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ribosome maturation factor rimP [Treponema denticola US-Trep]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK14637 PRK14637
ribosome maturation factor RimP;
2-148 4.08e-90

ribosome maturation factor RimP;


:

Pssm-ID: 237774 [Multi-domain]  Cd Length: 151  Bit Score: 258.64  E-value: 4.08e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721   2 EFIQKKDIPYFSECEPLVEGLGFKLVDLNVLHKKDVWQVKAVIKSEKGVGIKDCTSVHRTLQPRIEALIGSQDVTMEVSS 81
Cdd:PRK14637   1 MNFSKKDLGYFSECEPVVEGLGCKLVDLSRRVQQAQGRVRAVIYSAGGVGLDDCARVHRILVPRLEALGGVRDVFLEVSS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 451702721  82 PGINRLVKRAVEFYAFVGEEAQIWDNSITDWRHGIIKEVNSEGLVLNSDNQDIQIPYQDIKKARCNL 148
Cdd:PRK14637  81 PGIERVIKNAAEFSIFVGETVKVWFECTGQWQVGTIAEADETCLVLTSDGVPVTIPYVQITKAQLHP 147
 
Name Accession Description Interval E-value
PRK14637 PRK14637
ribosome maturation factor RimP;
2-148 4.08e-90

ribosome maturation factor RimP;


Pssm-ID: 237774 [Multi-domain]  Cd Length: 151  Bit Score: 258.64  E-value: 4.08e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721   2 EFIQKKDIPYFSECEPLVEGLGFKLVDLNVLHKKDVWQVKAVIKSEKGVGIKDCTSVHRTLQPRIEALIGSQDVTMEVSS 81
Cdd:PRK14637   1 MNFSKKDLGYFSECEPVVEGLGCKLVDLSRRVQQAQGRVRAVIYSAGGVGLDDCARVHRILVPRLEALGGVRDVFLEVSS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 451702721  82 PGINRLVKRAVEFYAFVGEEAQIWDNSITDWRHGIIKEVNSEGLVLNSDNQDIQIPYQDIKKARCNL 148
Cdd:PRK14637  81 PGIERVIKNAAEFSIFVGETVKVWFECTGQWQVGTIAEADETCLVLTSDGVPVTIPYVQITKAQLHP 147
RimP COG0779
Ribosome maturation factor RimP [Translation, ribosomal structure and biogenesis];
16-145 2.69e-27

Ribosome maturation factor RimP [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440542 [Multi-domain]  Cd Length: 151  Bit Score: 99.04  E-value: 2.69e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721  16 EPLVEGLGFKLVDLNVLHKKDVWQVKAVIKSEKGVGIKDCTSVHRTLQPRIEAL-IGSQDVTMEVSSPGINRLVKRAVEF 94
Cdd:COG0779   13 EPVLEELGLELVDVEVVKEGKRWVLRVYIDKDGGVTLDDCAAVSRALSAVLDVEdPIPGAYTLEVSSPGLDRPLKKPRDF 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 451702721  95 YAFVGEEAQIWDNSITDWRH---GIIKEVNSEGLVLNSDNQDIQIPYQDIKKAR 145
Cdd:COG0779   93 ERFIGRLVKVKLREPIDGRKkftGRLLGVDDDGVTLEVDGKEVEIPLDDIAKAR 146
RimP_N pfam02576
RimP N-terminal domain; This entry represents the N-terminal domain of the ribosome maturation ...
 15-84 9.02e-12

RimP N-terminal domain; This entry represents the N-terminal domain of the ribosome maturation factor RimP (also known as yhbC). RimP facilitates the maturation of the 30S ribosomal subunit. The N-terminal domain contains two alpha-helices and a three-stranded beta-sheet. It is suggested that the N-terminal domain of SP14.3 (RimP orthologue) could function as a protein module that binds to other proteins, especially those that contain highly positively charged surfaces..


Pssm-ID: 460600  Cd Length: 73  Bit Score: 56.84  E-value: 9.02e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 451702721   15 CEPLVEGLGFKLVDLNVLHKKDVWQVKAVIKSEKGVGIKDCTSVHRTLQPRIEA--LIgSQDVTMEVSSPGI 84
Cdd:pfam02576   2 IEPVVESLGFELVDVEFVKEGGGWTLRIYIDKDGGVTIDDCAKVSRAISAVLDVedPI-SGEYTLEVSSPGL 72
YlxS_C cd01734
Bacillus subtilis YxlS-like, C-terminal domain; YxlS is a Bacillus subtilis gene of unknown ...
 83-145 9.59e-07

Bacillus subtilis YxlS-like, C-terminal domain; YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.


Pssm-ID: 212481  Cd Length: 72  Bit Score: 43.97  E-value: 9.59e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 451702721  83 GINRLVKRAVEFYAFVGEEAQIWDNSITDWR---HGIIKEVNSEGLVLN-SDNQDIQIPYQDIKKAR 145
Cdd:cd01734    1 GLDRPLKKPEDFERFIGKEVKVKLKEPIDGRkkfTGELLGVDDDTVTLEvDDGKEVEIPFDNIAKAR 67
 
Name Accession Description Interval E-value
PRK14637 PRK14637
ribosome maturation factor RimP;
2-148 4.08e-90

ribosome maturation factor RimP;


Pssm-ID: 237774 [Multi-domain]  Cd Length: 151  Bit Score: 258.64  E-value: 4.08e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721   2 EFIQKKDIPYFSECEPLVEGLGFKLVDLNVLHKKDVWQVKAVIKSEKGVGIKDCTSVHRTLQPRIEALIGSQDVTMEVSS 81
Cdd:PRK14637   1 MNFSKKDLGYFSECEPVVEGLGCKLVDLSRRVQQAQGRVRAVIYSAGGVGLDDCARVHRILVPRLEALGGVRDVFLEVSS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 451702721  82 PGINRLVKRAVEFYAFVGEEAQIWDNSITDWRHGIIKEVNSEGLVLNSDNQDIQIPYQDIKKARCNL 148
Cdd:PRK14637  81 PGIERVIKNAAEFSIFVGETVKVWFECTGQWQVGTIAEADETCLVLTSDGVPVTIPYVQITKAQLHP 147
RimP COG0779
Ribosome maturation factor RimP [Translation, ribosomal structure and biogenesis];
16-145 2.69e-27

Ribosome maturation factor RimP [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440542 [Multi-domain]  Cd Length: 151  Bit Score: 99.04  E-value: 2.69e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721  16 EPLVEGLGFKLVDLNVLHKKDVWQVKAVIKSEKGVGIKDCTSVHRTLQPRIEAL-IGSQDVTMEVSSPGINRLVKRAVEF 94
Cdd:COG0779   13 EPVLEELGLELVDVEVVKEGKRWVLRVYIDKDGGVTLDDCAAVSRALSAVLDVEdPIPGAYTLEVSSPGLDRPLKKPRDF 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 451702721  95 YAFVGEEAQIWDNSITDWRH---GIIKEVNSEGLVLNSDNQDIQIPYQDIKKAR 145
Cdd:COG0779   93 ERFIGRLVKVKLREPIDGRKkftGRLLGVDDDGVTLEVDGKEVEIPLDDIAKAR 146
PRK00092 PRK00092
ribosome maturation protein RimP; Reviewed
 16-145 7.40e-21

ribosome maturation protein RimP; Reviewed


Pssm-ID: 234627 [Multi-domain]  Cd Length: 154  Bit Score: 82.54  E-value: 7.40e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721  16 EPLVEGLGFKLVDLNVLHKKDVWQVKAVIKSEKGVGIKDCTSVHRTLQPR--IEALIgSQDVTMEVSSPGINRLVKRAVE 93
Cdd:PRK00092  14 EPVVEALGYELVDVEYVKEGRDSTLRIYIDKEGGIDLDDCEEVSRQISAVldVEDPI-PGAYTLEVSSPGLDRPLKKARD 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 451702721  94 FYAFVGEEAQI-----WDNSiTDWRhGIIKEVNSEGLVLNSDNQD--IQIPYQDIKKAR 145
Cdd:PRK00092  93 FRRFIGREVKVklyepIDGR-KKFQ-GILLAVDGETVTLEVEGKEkeVEIPLDNIAKAR 149
PRK14630 PRK14630
ribosome maturation factor RimP;
18-145 2.62e-14

ribosome maturation factor RimP;


Pssm-ID: 173093 [Multi-domain]  Cd Length: 143  Bit Score: 65.59  E-value: 2.62e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721  18 LVEGLGFKLVDLNVLHKKDVWQVKAVIKSEKGVGIKDCTSVHRTLQPRIEALIgSQDVTMEVSSPGINRLVKRAVEFYAF 97
Cdd:PRK14630  17 VTDRLGIEIIEINTFRNRNEGKIQIVLYKKDSFGVDTLCDLHKMILLILEAVL-KYNFSLEISTPGINRKIKSDREFKIF 95

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 451702721  98 VGEEAQIWDNSitDWRHGIIKEVNSEGLVLNSDNQDIQIPYQDIKKAR 145
Cdd:PRK14630  96 EGKKIKLMLDN--DFEEGFILEAKADSFIFKTDSKEVNVLYSDVKKAK 141
RimP_N pfam02576
RimP N-terminal domain; This entry represents the N-terminal domain of the ribosome maturation ...
 15-84 9.02e-12

RimP N-terminal domain; This entry represents the N-terminal domain of the ribosome maturation factor RimP (also known as yhbC). RimP facilitates the maturation of the 30S ribosomal subunit. The N-terminal domain contains two alpha-helices and a three-stranded beta-sheet. It is suggested that the N-terminal domain of SP14.3 (RimP orthologue) could function as a protein module that binds to other proteins, especially those that contain highly positively charged surfaces..


Pssm-ID: 460600  Cd Length: 73  Bit Score: 56.84  E-value: 9.02e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 451702721   15 CEPLVEGLGFKLVDLNVLHKKDVWQVKAVIKSEKGVGIKDCTSVHRTLQPRIEA--LIgSQDVTMEVSSPGI 84
Cdd:pfam02576   2 IEPVVESLGFELVDVEFVKEGGGWTLRIYIDKDGGVTIDDCAKVSRAISAVLDVedPI-SGEYTLEVSSPGL 72
PRK14636 PRK14636
ribosome maturation protein RimP;
8-145 3.37e-11

ribosome maturation protein RimP;


Pssm-ID: 237773 [Multi-domain]  Cd Length: 176  Bit Score: 57.87  E-value: 3.37e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721   8 DIPYFSE-CEPLVEGLGFKLVDLNVLHKKD--VWQVKAVIKSEKGVGIKDCTSVHRTLQPRIEALIGSQDV-TMEVSSPG 83
Cdd:PRK14636   3 DIAALTAlIEPEAKALGLDLVRVAMFGGKSdpTLQIMAERPDTRQLVIEDCAALSRRLSDVFDELDPIEDAyRLEVSSPG 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 451702721  84 INRLVKRAVEFYAFVGEEAQIWDNSITDWR---HGIIKEVNSEGLVLnSDNQ--DIQIPYQDIKKAR 145
Cdd:PRK14636  83 IDRPLTRPKDFADWAGHEARIALSEPLDGRkqfRGELKGIDGDTVTI-ADNKagEVILPFAAIESAK 148
PRK14640 PRK14640
hypothetical protein; Provisional
 17-144 7.39e-11

hypothetical protein; Provisional


Pssm-ID: 173103 [Multi-domain]  Cd Length: 152  Bit Score: 56.56  E-value: 7.39e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721  17 PLVeGLGFKLVDLNVLHKKDVWQVKAVIKSEKGVGIKDCTSVHRtlqpRIEALIGSQD-VT----MEVSSPGINRLVKRA 91
Cdd:PRK14640  15 PVV-ALGFELWGIEFIRAGKHSTLRVYIDGENGVSVENCAEVSH----QVGAIMDVEDpITeeyyLEVSSPGLDRPLFKV 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 451702721  92 VEFYAFVGEEAQIWDNSITDWRH---GIIKEVNSEGLVLNSDNQDIQIPYQDIKKA 144
Cdd:PRK14640  90 AQFEKYVGQEAAVTLRMATNNRRkfkGVIKAVQGDMITLTVDGKDEVLAFTNIQKA 145
PRK14639 PRK14639
ribosome maturation factor RimP;
16-145 5.81e-09

ribosome maturation factor RimP;


Pssm-ID: 173102 [Multi-domain]  Cd Length: 140  Bit Score: 51.36  E-value: 5.81e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721  16 EPLVEGLGFKLVDLNVLHKKDVWQVKAVIKSEKGVGIKDCTSVHRTLQP--RIEALIgSQDVTMEVSSPGINRLVKRAVE 93
Cdd:PRK14639   4 EALCKECGVSFYDDELVSENGRKIYRVYITKEGGVNLDDCERLSELLSPifDVEPPV-SGEYFLEVSSPGLERKLSKIEH 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 451702721  94 FYAFVGEEAQIWDNSITDWRHGIIKeVNSEGLVLNS--DNQDIQIPYQDIKKAR 145
Cdd:PRK14639  83 FAKSIGELVKITTNEKEKFEGKIVS-VDDENITLENleNKEKTTINFNDIKKAK 135
PRK14647 PRK14647
ribosome maturation factor RimP;
16-104 6.05e-09

ribosome maturation factor RimP;


Pssm-ID: 173110 [Multi-domain]  Cd Length: 159  Bit Score: 51.67  E-value: 6.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721  16 EPLVEGLGFKLVDLNVLHKKDVWQVKAVIKSEKGVGIKDCTSVHRTL--QPRIEALIgSQDVTMEVSSPGINRLVKRAVE 93
Cdd:PRK14647  15 EQVLSSLGLELVELEYKREGREMVLRLFIDKEGGVNLDDCAEVSRELseILDVEDFI-PERYTLEVSSPGLDRPLKKEAD 93

                         90
                 ....*....|.
gi 451702721  94 FYAFVGEEAQI 104
Cdd:PRK14647  94 YERYAGRLVKV 104
PRK14642 PRK14642
ribosome maturation factor RimP;
16-104 1.03e-08

ribosome maturation factor RimP;


Pssm-ID: 237775 [Multi-domain]  Cd Length: 197  Bit Score: 51.79  E-value: 1.03e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721  16 EPLVEGLGFKLVDLNV----LHKKDV---WQV---KAVIKSEKGVGIKDCTSVHRTLQPRIEaLIGSQDVTMEVSSPGIN 85
Cdd:PRK14642   8 EQTVTGLGYDLVEIERsaggLLRVTIdlpWVPpteGAPVGPEQFVTVEDCEKVTRQLQFALE-VDGVDYKRLEVSSPGID 86

                         90
                 ....*....|....*....
gi 451702721  86 RLVKRAVEFYAFVGEEAQI 104
Cdd:PRK14642  87 RPLRHEQDFERFAGEVIDI 105
PRK14638 PRK14638
ribosome maturation factor RimP;
14-145 4.62e-08

ribosome maturation factor RimP;


Pssm-ID: 184777 [Multi-domain]  Cd Length: 150  Bit Score: 49.09  E-value: 4.62e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721  14 ECEPLVEGLGFKLVDLNVLHKKDVWQVKAVIKSEKG-VGIKDCTSVHRTLQPRI--EALIGSQdVTMEVSSPGINRLVKR 90
Cdd:PRK14638  13 EAERIAEEQGLEIFDVQYRRESRGWVLRIIIDNPVGyVSVRDCELFSREIERFLdrEDLIEHS-YTLEVSSPGLDRPLRG 91

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 451702721  91 AVEFYAFVGEEAQIWdnsITDWRH--GIIKEVnSEGLVLNSDNQD-IQIPYQDIKKAR 145
Cdd:PRK14638  92 PKDYVRFTGKLAKIV---TKDGKTfiGRIESF-VDGTITISDEKEkYEINIDDVKRAN 145
YlxS_C cd01734
Bacillus subtilis YxlS-like, C-terminal domain; YxlS is a Bacillus subtilis gene of unknown ...
 83-145 9.59e-07

Bacillus subtilis YxlS-like, C-terminal domain; YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.


Pssm-ID: 212481  Cd Length: 72  Bit Score: 43.97  E-value: 9.59e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 451702721  83 GINRLVKRAVEFYAFVGEEAQIWDNSITDWR---HGIIKEVNSEGLVLN-SDNQDIQIPYQDIKKAR 145
Cdd:cd01734    1 GLDRPLKKPEDFERFIGKEVKVKLKEPIDGRkkfTGELLGVDDDTVTLEvDDGKEVEIPFDNIAKAR 67
PRK14633 PRK14633
ribosome maturation factor RimP;
16-145 8.93e-05

ribosome maturation factor RimP;


Pssm-ID: 173096 [Multi-domain]  Cd Length: 150  Bit Score: 40.34  E-value: 8.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721  16 EPLVEGLGFKLVDLNVLHKKDVwQVKAVIKSEKGVGIKDCTSVHRtlqpRIEALIGSQD-----VTMEVSSPGINRLVKR 90
Cdd:PRK14633  11 EPITADLGYILWGIEVVGSGKL-TIRIFIDHENGVSVDDCQIVSK----EISAVFDVEDpvsgkYILEVSSPGMNRQIFN 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721  91 AVEFYAFVGEEAQIWD----NSITDWRhGIIKEVNSEGLVLN-SDNQDIQIPYQDIKKAR 145
Cdd:PRK14633  86 IIQAQALVGFNVKAVTlapvGSQTKFK-GVLERVEGNNVILNlEDGKEISFDFDELKKLR 144
DUF150_C pfam17384
RimP C-terminal SH3 domain; This family represents the C-terminal domain from RimP.
 89-145 2.16e-04

RimP C-terminal SH3 domain; This family represents the C-terminal domain from RimP.


Pssm-ID: 465408  Cd Length: 67  Bit Score: 37.60  E-value: 2.16e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 451702721   89 KRAVEFYAFVGEEAQIWDNSITDWRH---GIIKEVNSEGLVLNSDNQ-DIQIPYQDIKKAR 145
Cdd:pfam17384   2 FTAEHFARFIGELVKVKLKLPIDGRKkfqGKIVAVDGETITLEVDGKtEVTIPFDDIDKAR 62
PRK14634 PRK14634
ribosome maturation factor RimP;
10-136 1.61e-03

ribosome maturation factor RimP;


Pssm-ID: 173097 [Multi-domain]  Cd Length: 155  Bit Score: 36.70  E-value: 1.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 451702721  10 PYFSECEPLVE----GLGFKLVDLNVLHKKDVWQVKAVIKSEKG--VGIKDCTSVHRTLQpriEALIGSQDVT----MEV 79
Cdd:PRK14634   4 PLLPDLETLASataaDKGFELCGIQVLTHLQPMTLQVQIRRSSGsdVSLDDCAGFSGPMG---EALEASQLLTeayvLEI 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 451702721  80 SSPGINRLVKRAVEFYAFVGEEAQIW--DNSITDWRHgiikevnsEGLVLNSDNQDIQI 136
Cdd:PRK14634  81 SSPGIGDQLSSDRDFQTFRGFPVEVShrDDDGSEQRL--------EGLLLERNEDHLQI 131
 
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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