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Conserved domains on  [gi|332170279|gb|AEE19534|]
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protein of unknown function DUF150 [Dokdonia sp. 4H-3-7-5]

Protein Classification

ribosome assembly cofactor RimP( domain architecture ID 10011741)

ribosome assembly cofactor RimP is important for the maturation of 30S ribosome subunits

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK02001 PRK02001
ribosome assembly cofactor RimP;
1-152 1.09e-74

ribosome assembly cofactor RimP;


:

Pssm-ID: 179358 [Multi-domain]  Cd Length: 152  Bit Score: 219.85  E-value: 1.09e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279   1 MLKEKVTNLLQEALDENPSLFLISLDIQGNNEVKIIIDGDSGVTVEDCMAVSRKVEHNLDREEEDFSLEVMSAGATSPLE 80
Cdd:PRK02001   1 MIKKKVVELLVEELLEGPELFLVDLTISPDNKIVVEIDGDEGVWIEDCVELSRAIEHNLDREEEDFELEVGSAGLTSPLK 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 332170279  81 IPRQYKKNIGRHLEVKTQDGEKIEGLMTEATDAEITLTWKTREPKPVGKGKVTVEKIETFPYNEIVQAKVMI 152
Cdd:PRK02001  81 VPRQYKKNIGRELEVLTKNGKKIEGELKSADENDITLEVKAREPKEGGKGKVTVEKEETITYDDIKEAKVII 152
 
Name Accession Description Interval E-value
PRK02001 PRK02001
ribosome assembly cofactor RimP;
1-152 1.09e-74

ribosome assembly cofactor RimP;


Pssm-ID: 179358 [Multi-domain]  Cd Length: 152  Bit Score: 219.85  E-value: 1.09e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279   1 MLKEKVTNLLQEALDENPSLFLISLDIQGNNEVKIIIDGDSGVTVEDCMAVSRKVEHNLDREEEDFSLEVMSAGATSPLE 80
Cdd:PRK02001   1 MIKKKVVELLVEELLEGPELFLVDLTISPDNKIVVEIDGDEGVWIEDCVELSRAIEHNLDREEEDFELEVGSAGLTSPLK 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 332170279  81 IPRQYKKNIGRHLEVKTQDGEKIEGLMTEATDAEITLTWKTREPKPVGKGKVTVEKIETFPYNEIVQAKVMI 152
Cdd:PRK02001  81 VPRQYKKNIGRELEVLTKNGKKIEGELKSADENDITLEVKAREPKEGGKGKVTVEKEETITYDDIKEAKVII 152
RimP COG0779
Ribosome maturation factor RimP [Translation, ribosomal structure and biogenesis];
2-154 9.62e-37

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


Pssm-ID: 440542 [Multi-domain]  Cd Length: 151  Bit Score: 123.31  E-value: 9.62e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279   2 LKEKVTNLLQEALdENPSLFLISLDIQG---NNEVKIIIDGDSGVTVEDCMAVSRKVEHNLDREE---EDFSLEVMSAGA 75
Cdd:COG0779    4 LEERLEELLEPVL-EELGLELVDVEVVKegkRWVLRVYIDKDGGVTLDDCAAVSRALSAVLDVEDpipGAYTLEVSSPGL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279  76 TSPLEIPRQYKKNIGRHLEVKT---QDGEK-IEGLMTEATDAEITLTWKtrepkpvgkgkvtvEKIETFPYNEIVQAKVM 151
Cdd:COG0779   83 DRPLKKPRDFERFIGRLVKVKLrepIDGRKkFTGRLLGVDDDGVTLEVD--------------GKEVEIPLDDIAKARLV 148


                 ...
gi 332170279 152 IKF 154
Cdd:COG0779  149 IEF 151
RimP_N pfam02576
RimP N-terminal domain; This entry represents the N-terminal domain of the ribosome maturation ...
 19-75 2.09e-07

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: 45.67  E-value: 2.09e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 332170279   19 SLFLISLDIQGNNE-VKIIIDGDSGVTVEDCMAVSRKVEHNLDRE---EEDFSLEVMSAGA 75
Cdd:pfam02576  12 ELVDVEFVKEGGGWtLRIYIDKDGGVTIDDCAKVSRAISAVLDVEdpiSGEYTLEVSSPGL 72
YlxS_C cd01734
Bacillus subtilis YxlS-like, C-terminal domain; YxlS is a Bacillus subtilis gene of unknown ...
 74-154 7.57e-06

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: 41.66  E-value: 7.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279  74 GATSPLEIPRQYKKNIGRHLEVKT----QDGEKIEGLMTEATDAEITLtwktrepkpvgkgKVTVEKIETFPYNEIVQAK 149
Cdd:cd01734    1 GLDRPLKKPEDFERFIGKEVKVKLkepiDGRKKFTGELLGVDDDTVTL-------------EVDDGKEVEIPFDNIAKAR 67


                 ....*
gi 332170279 150 VMIKF 154
Cdd:cd01734   68 LVPEF 72
 
Name Accession Description Interval E-value
PRK02001 PRK02001
ribosome assembly cofactor RimP;
1-152 1.09e-74

ribosome assembly cofactor RimP;


Pssm-ID: 179358 [Multi-domain]  Cd Length: 152  Bit Score: 219.85  E-value: 1.09e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279   1 MLKEKVTNLLQEALDENPSLFLISLDIQGNNEVKIIIDGDSGVTVEDCMAVSRKVEHNLDREEEDFSLEVMSAGATSPLE 80
Cdd:PRK02001   1 MIKKKVVELLVEELLEGPELFLVDLTISPDNKIVVEIDGDEGVWIEDCVELSRAIEHNLDREEEDFELEVGSAGLTSPLK 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 332170279  81 IPRQYKKNIGRHLEVKTQDGEKIEGLMTEATDAEITLTWKTREPKPVGKGKVTVEKIETFPYNEIVQAKVMI 152
Cdd:PRK02001  81 VPRQYKKNIGRELEVLTKNGKKIEGELKSADENDITLEVKAREPKEGGKGKVTVEKEETITYDDIKEAKVII 152
RimP COG0779
Ribosome maturation factor RimP [Translation, ribosomal structure and biogenesis];
2-154 9.62e-37

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


Pssm-ID: 440542 [Multi-domain]  Cd Length: 151  Bit Score: 123.31  E-value: 9.62e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279   2 LKEKVTNLLQEALdENPSLFLISLDIQG---NNEVKIIIDGDSGVTVEDCMAVSRKVEHNLDREE---EDFSLEVMSAGA 75
Cdd:COG0779    4 LEERLEELLEPVL-EELGLELVDVEVVKegkRWVLRVYIDKDGGVTLDDCAAVSRALSAVLDVEDpipGAYTLEVSSPGL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279  76 TSPLEIPRQYKKNIGRHLEVKT---QDGEK-IEGLMTEATDAEITLTWKtrepkpvgkgkvtvEKIETFPYNEIVQAKVM 151
Cdd:COG0779   83 DRPLKKPRDFERFIGRLVKVKLrepIDGRKkFTGRLLGVDDDGVTLEVD--------------GKEVEIPLDDIAKARLV 148


                 ...
gi 332170279 152 IKF 154
Cdd:COG0779  149 IEF 151
PRK00092 PRK00092
ribosome maturation protein RimP; Reviewed
 1-154 7.20e-21

ribosome maturation protein RimP; Reviewed


Pssm-ID: 234627 [Multi-domain]  Cd Length: 154  Bit Score: 82.93  E-value: 7.20e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279   1 MLKEKVTNLLQEALDENP-SLFLISLDIQGNNE-VKIIIDGDSGVTVEDCMAVSRKVEHNLDREE---EDFSLEVMSAGA 75
Cdd:PRK00092   4 PLEEQLTELIEPVVEALGyELVDVEYVKEGRDStLRIYIDKEGGIDLDDCEEVSRQISAVLDVEDpipGAYTLEVSSPGL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279  76 TSPLEIPRQYKKNIGRHLEVKT----QDGEKIEGLMTEATDAEITLTwktrepkpVGKGKVTVEkietFPYNEIVQAKVM 151
Cdd:PRK00092  84 DRPLKKARDFRRFIGREVKVKLyepiDGRKKFQGILLAVDGETVTLE--------VEGKEKEVE----IPLDNIAKARLV 151


                 ...
gi 332170279 152 IKF 154
Cdd:PRK00092 152 VEF 154
PRK14641 PRK14641
ribosome maturation factor RimP;
2-131 2.38e-13

ribosome maturation factor RimP;


Pssm-ID: 173104 [Multi-domain]  Cd Length: 173  Bit Score: 63.64  E-value: 2.38e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279   2 LKEKVTNLLQEALDENPS-----LFLISLDIQGN---NEVKIIIDGDSGVTVEDCMAVSRKVEHNLDREE-------EDF 66
Cdd:PRK14641   1 MEEKINNCVLQVLEASAGtkgegVYLVSMTVKGSgkgRKIEVLLDADTGIRIDQCAFFSRRIRERLEEDEellglvgEDF 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 332170279  67 SLEVMSAGATSPLEIPRQYKKNIGRHLEVKTQDGEKIEG---------LMTEATDAEITLtwktrepKPVGKGK 131
Cdd:PRK14641  81 DLMVSSPGLGEPIILPRQYGRHVGRLLRVTYRDEEGSEHevtghlqevSLTEGEGASIVL-------KPEQKKK 147
PRK14640 PRK14640
hypothetical protein; Provisional
 2-123 4.30e-11

hypothetical protein; Provisional


Pssm-ID: 173103 [Multi-domain]  Cd Length: 152  Bit Score: 57.33  E-value: 4.30e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279   2 LKEKVTNLLQEALDE-NPSLFLISLDIQGNNE-VKIIIDGDSGVTVEDCMAVSRKVEHNLDREE---EDFSLEVMSAGAT 76
Cdd:PRK14640   4 LEQRLTDLLEAPVVAlGFELWGIEFIRAGKHStLRVYIDGENGVSVENCAEVSHQVGAIMDVEDpitEEYYLEVSSPGLD 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 332170279  77 SPLEIPRQYKKNIGR----HLEVKTQDGEKIEGLMTEATDAEITLTWKTRE 123
Cdd:PRK14640  84 RPLFKVAQFEKYVGQeaavTLRMATNNRRKFKGVIKAVQGDMITLTVDGKD 134
PRK14638 PRK14638
ribosome maturation factor RimP;
1-154 1.77e-10

ribosome maturation factor RimP;


Pssm-ID: 184777 [Multi-domain]  Cd Length: 150  Bit Score: 55.64  E-value: 1.77e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279   1 MLKEKVTNLLQ-EALDENPSLFLISLDIQGNNE-----VKIIIDGDSG-VTVEDCMAVSRKVEHNLDRE---EEDFSLEV 70
Cdd:PRK14638   1 MFEEMILEKVRkEAERIAEEQGLEIFDVQYRREsrgwvLRIIIDNPVGyVSVRDCELFSREIERFLDREdliEHSYTLEV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279  71 MSAGATSPLEIPRQYKKNIGRHLEVKTQDGEKIEGLMTEATDAEITLTwktrepkpvgKGKvtveKIETFPYNEIVQAKV 150
Cdd:PRK14638  81 SSPGLDRPLRGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDGTITIS----------DEK----EKYEINIDDVKRANL 146


                 ....
gi 332170279 151 MIKF 154
Cdd:PRK14638 147 EVEF 150
PRK14639 PRK14639
ribosome maturation factor RimP;
34-117 1.69e-08

ribosome maturation factor RimP;


Pssm-ID: 173102 [Multi-domain]  Cd Length: 140  Bit Score: 50.21  E-value: 1.69e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279  34 KIIIDGDSGVTVEDCMAVSRKVEHNLDREEE---DFSLEVMSAGATSPLEIPRQYKKNIGRHLEVKTQDGEKIEGLMTEA 110
Cdd:PRK14639  29 RVYITKEGGVNLDDCERLSELLSPIFDVEPPvsgEYFLEVSSPGLERKLSKIEHFAKSIGELVKITTNEKEKFEGKIVSV 108


                 ....*..
gi 332170279 111 TDAEITL 117
Cdd:PRK14639 109 DDENITL 115
PRK14647 PRK14647
ribosome maturation factor RimP;
4-97 5.58e-08

ribosome maturation factor RimP;


Pssm-ID: 173110 [Multi-domain]  Cd Length: 159  Bit Score: 49.36  E-value: 5.58e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279   4 EKVTNLLQEALDenpSLFLISLDIQGNNE-----VKIIIDGDSGVTVEDCMAVSRKVEHNLDREE---EDFSLEVMSAGA 75
Cdd:PRK14647   8 DRVTELAEQVLS---SLGLELVELEYKREgremvLRLFIDKEGGVNLDDCAEVSRELSEILDVEDfipERYTLEVSSPGL 84

                         90       100
                 ....*....|....*....|..
gi 332170279  76 TSPLEIPRQYKKNIGRHLEVKT 97
Cdd:PRK14647  85 DRPLKKEADYERYAGRLVKVRT 106
RimP_N pfam02576
RimP N-terminal domain; This entry represents the N-terminal domain of the ribosome maturation ...
 19-75 2.09e-07

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: 45.67  E-value: 2.09e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 332170279   19 SLFLISLDIQGNNE-VKIIIDGDSGVTVEDCMAVSRKVEHNLDRE---EEDFSLEVMSAGA 75
Cdd:pfam02576  12 ELVDVEFVKEGGGWtLRIYIDKDGGVTIDDCAKVSRAISAVLDVEdpiSGEYTLEVSSPGL 72
YlxS_C cd01734
Bacillus subtilis YxlS-like, C-terminal domain; YxlS is a Bacillus subtilis gene of unknown ...
 74-154 7.57e-06

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: 41.66  E-value: 7.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279  74 GATSPLEIPRQYKKNIGRHLEVKT----QDGEKIEGLMTEATDAEITLtwktrepkpvgkgKVTVEKIETFPYNEIVQAK 149
Cdd:cd01734    1 GLDRPLKKPEDFERFIGKEVKVKLkepiDGRKKFTGELLGVDDDTVTL-------------EVDDGKEVEIPFDNIAKAR 67


                 ....*
gi 332170279 150 VMIKF 154
Cdd:cd01734   68 LVPEF 72
PRK14645 PRK14645
ribosome maturation factor RimP;
43-143 1.26e-05

ribosome maturation factor RimP;


Pssm-ID: 184780 [Multi-domain]  Cd Length: 154  Bit Score: 42.83  E-value: 1.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279  43 VTVEDCMAVSRKVEHNLDRE---EEDFSLEVMSAGATSPLEIPRQYKKNIGRHLEVKTqDGEKIEGLMTEATDAEITLTw 119
Cdd:PRK14645  52 VTVEDLERASRALEAELDRLdpiEGEYRLEVESPGPKRPLFTARHFERFAGLKAKVRG-PGENFTGRIKAVSGDQVTFD- 129

                         90       100
                 ....*....|....*....|....
gi 332170279 120 ktrepkpVGKGKVTVeKIETFPYN 143
Cdd:PRK14645 130 -------VGGEDRTL-RIGTFQAN 145
PRK14635 PRK14635
ribosome maturation factor RimP;
3-102 7.92e-05

ribosome maturation factor RimP;


Pssm-ID: 184774 [Multi-domain]  Cd Length: 162  Bit Score: 40.67  E-value: 7.92e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332170279   3 KEKVTNLLQEALdeNPSLFLISLDIQGN-NEVKIIIDGDS------GVTVEDCMAVSRKVEHNLDR--EEEDFSLEVMSA 73
Cdd:PRK14635   5 EEEISEILDRVL--ALPVKLYSLKVNQRpNHSLIEVVLDNlehpygSVSLLECEQVSRKLKEELERisPDLDFTLKVSSA 82

                         90       100       110
                 ....*....|....*....|....*....|.
gi 332170279  74 GATSPLEIPRQYKK--NIGRHLEVKTQDGEK 102
Cdd:PRK14635  83 GAERKLRLPEDLDRfrGIPVRLVFRSEESEK 113
SM-ATX pfam14438
Ataxin 2 SM domain; This SM domain is found in Ataxin-2.
 89-147 3.50e-04

Ataxin 2 SM domain; This SM domain is found in Ataxin-2.


Pssm-ID: 464173  Cd Length: 78  Bit Score: 37.15  E-value: 3.50e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 332170279   89 IGRHLEVKTQDGEKIEGLMTEAT---DAEITL--TWKTREPKPVGKGKVTVEKIET--FPYNEIVQ 147
Cdd:pfam14438   9 VGLVVEVTTKNGEVYEGIFSTASlekDFGVVLkmARRIKKSNGSGLNPVRGEIVDTmiFPAKDIVD 74
PRK14642 PRK14642
ribosome maturation factor RimP;
43-95 4.38e-03

ribosome maturation factor RimP;


Pssm-ID: 237775 [Multi-domain]  Cd Length: 197  Bit Score: 35.99  E-value: 4.38e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 332170279  43 VTVEDCMAVSRKVEHNLDREEEDFS-LEVMSAGATSPLEIPRQYKKNIGRHLEV 95
Cdd:PRK14642  52 VTVEDCEKVTRQLQFALEVDGVDYKrLEVSSPGIDRPLRHEQDFERFAGEVIDI 105
PRK14636 PRK14636
ribosome maturation protein RimP;
43-105 7.64e-03

ribosome maturation protein RimP;


Pssm-ID: 237773 [Multi-domain]  Cd Length: 176  Bit Score: 35.14  E-value: 7.64e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 332170279  43 VTVEDCMAVSRKVEHNLDREEE---DFSLEVMSAGATSPLEIPRQYKKNIGRhlEVKTQDGEKIEG 105
Cdd:PRK14636  48 LVIEDCAALSRRLSDVFDELDPiedAYRLEVSSPGIDRPLTRPKDFADWAGH--EARIALSEPLDG 111
 
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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