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Conserved domains on  [gi|491006355|ref|WP_004868075|]
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MULTISPECIES: ribosome maturation factor RimP [Klebsiella/Raoultella group]

Protein Classification

LSm family protein( domain architecture ID 249)

LSm family protein such as eukaryotic LSm (Sm-like proteins) and bacterial LSm-related Hfq proteins, that have an Sm fold consisting of a five-stranded beta-sheet and an alpha-helix at the N-terminus, and are involved in processes associated with RNA processing and gene expression regulation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sm_like super family cl00259
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 1-150 1.39e-83

Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.


The actual alignment was detected with superfamily member PRK14640:

Pssm-ID: 469694 [Multi-domain]  Cd Length: 152  Bit Score: 242.22  E-value: 1.39e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355   1 MSTLEQKLTEMLTAPVEALGFELVGIEFIR-GRTSTLRIYIDSDDGINVDDCADVSHQVSAVMDVEDPITVAYNLEVSSP 79
Cdd:PRK14640   1 MATLEQRLTDLLEAPVVALGFELWGIEFIRaGKHSTLRVYIDGENGVSVENCAEVSHQVGAIMDVEDPITEEYYLEVSSP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 491006355  80 GLDRPMFTAEHYERFSGEEVALVLRMAVQNRRKWQGIIKAVDGEMITVTVEGKDEVFALSNIQKANLVPHF 150
Cdd:PRK14640  81 GLDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVDGKDEVLAFTNIQKANIVPNF 151
 
Name Accession Description Interval E-value
PRK14640 PRK14640
hypothetical protein; Provisional
 1-150 1.39e-83

hypothetical protein; Provisional


Pssm-ID: 173103 [Multi-domain]  Cd Length: 152  Bit Score: 242.22  E-value: 1.39e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355   1 MSTLEQKLTEMLTAPVEALGFELVGIEFIR-GRTSTLRIYIDSDDGINVDDCADVSHQVSAVMDVEDPITVAYNLEVSSP 79
Cdd:PRK14640   1 MATLEQRLTDLLEAPVVALGFELWGIEFIRaGKHSTLRVYIDGENGVSVENCAEVSHQVGAIMDVEDPITEEYYLEVSSP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 491006355  80 GLDRPMFTAEHYERFSGEEVALVLRMAVQNRRKWQGIIKAVDGEMITVTVEGKDEVFALSNIQKANLVPHF 150
Cdd:PRK14640  81 GLDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVDGKDEVLAFTNIQKANIVPNF 151
RimP COG0779
Ribosome maturation factor RimP [Translation, ribosomal structure and biogenesis];
1-150 2.39e-73

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


Pssm-ID: 440542 [Multi-domain]  Cd Length: 151  Bit Score: 216.14  E-value: 2.39e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355   1 MSTLEQKLTEMLTAPVEALGFELVGIEFIR-GRTSTLRIYIDSDDGINVDDCADVSHQVSAVMDVEDPITVAYNLEVSSP 79
Cdd:COG0779    1 MSGLEERLEELLEPVLEELGLELVDVEVVKeGKRWVLRVYIDKDGGVTLDDCAAVSRALSAVLDVEDPIPGAYTLEVSSP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 491006355  80 GLDRPMFTAEHYERFSGEEVALVLRMAVQNRRKWQGIIKAVDGEMITVTVEGKDEVFALSNIQKANLVPHF 150
Cdd:COG0779   81 GLDRPLKKPRDFERFIGRLVKVKLREPIDGRKKFTGRLLGVDDDGVTLEVDGKEVEIPLDDIAKARLVIEF 151
RimP_N pfam02576
RimP N-terminal domain; This entry represents the N-terminal domain of the ribosome maturation ...
 11-82 2.31e-33

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: 112.31  E-value: 2.31e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491006355   11 MLTAPVEALGFELVGIEFIR-GRTSTLRIYIDSDDGINVDDCADVSHQVSAVMDVEDPITVAYNLEVSSPGLD 82
Cdd:pfam02576   1 LIEPVVESLGFELVDVEFVKeGGGWTLRIYIDKDGGVTIDDCAKVSRAISAVLDVEDPISGEYTLEVSSPGLD 73
YlxS_C cd01734
Bacillus subtilis YxlS-like, C-terminal domain; YxlS is a Bacillus subtilis gene of unknown ...
 80-150 2.48e-26

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: 94.44  E-value: 2.48e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 491006355  80 GLDRPMFTAEHYERFSGEEVALVLRMAVQNRRKWQGIIKAVDGEMITVTVEGKDEV-FALSNIQKANLVPHF 150
Cdd:cd01734    1 GLDRPLKKPEDFERFIGKEVKVKLKEPIDGRKKFTGELLGVDDDTVTLEVDDGKEVeIPFDNIAKARLVPEF 72
 
Name Accession Description Interval E-value
PRK14640 PRK14640
hypothetical protein; Provisional
 1-150 1.39e-83

hypothetical protein; Provisional


Pssm-ID: 173103 [Multi-domain]  Cd Length: 152  Bit Score: 242.22  E-value: 1.39e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355   1 MSTLEQKLTEMLTAPVEALGFELVGIEFIR-GRTSTLRIYIDSDDGINVDDCADVSHQVSAVMDVEDPITVAYNLEVSSP 79
Cdd:PRK14640   1 MATLEQRLTDLLEAPVVALGFELWGIEFIRaGKHSTLRVYIDGENGVSVENCAEVSHQVGAIMDVEDPITEEYYLEVSSP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 491006355  80 GLDRPMFTAEHYERFSGEEVALVLRMAVQNRRKWQGIIKAVDGEMITVTVEGKDEVFALSNIQKANLVPHF 150
Cdd:PRK14640  81 GLDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVDGKDEVLAFTNIQKANIVPNF 151
PRK00092 PRK00092
ribosome maturation protein RimP; Reviewed
 1-150 8.54e-80

ribosome maturation protein RimP; Reviewed


Pssm-ID: 234627 [Multi-domain]  Cd Length: 154  Bit Score: 232.39  E-value: 8.54e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355   1 MSTLEQKLTEMLTAPVEALGFELVGIEFIR-GRTSTLRIYIDSDDGINVDDCADVSHQVSAVMDVEDPITVAYNLEVSSP 79
Cdd:PRK00092   2 MSPLEEQLTELIEPVVEALGYELVDVEYVKeGRDSTLRIYIDKEGGIDLDDCEEVSRQISAVLDVEDPIPGAYTLEVSSP 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491006355  80 GLDRPMFTAEHYERFSGEEVALVLRMAVQNRRKWQGIIKAVDGEMITVTVEGKDEV--FALSNIQKANLVPHF 150
Cdd:PRK00092  82 GLDRPLKKARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGETVTLEVEGKEKEveIPLDNIAKARLVVEF 154
RimP COG0779
Ribosome maturation factor RimP [Translation, ribosomal structure and biogenesis];
1-150 2.39e-73

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


Pssm-ID: 440542 [Multi-domain]  Cd Length: 151  Bit Score: 216.14  E-value: 2.39e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355   1 MSTLEQKLTEMLTAPVEALGFELVGIEFIR-GRTSTLRIYIDSDDGINVDDCADVSHQVSAVMDVEDPITVAYNLEVSSP 79
Cdd:COG0779    1 MSGLEERLEELLEPVLEELGLELVDVEVVKeGKRWVLRVYIDKDGGVTLDDCAAVSRALSAVLDVEDPIPGAYTLEVSSP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 491006355  80 GLDRPMFTAEHYERFSGEEVALVLRMAVQNRRKWQGIIKAVDGEMITVTVEGKDEVFALSNIQKANLVPHF 150
Cdd:COG0779   81 GLDRPLKKPRDFERFIGRLVKVKLREPIDGRKKFTGRLLGVDDDGVTLEVDGKEVEIPLDDIAKARLVIEF 151
PRK14631 PRK14631
ribosome maturation factor RimP;
1-147 3.99e-44

ribosome maturation factor RimP;


Pssm-ID: 237772 [Multi-domain]  Cd Length: 174  Bit Score: 142.72  E-value: 3.99e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355   1 MSTLEQKLTEMLTAPVEALGFELVGIEFI-RGRTSTLRIYIDS------------------DDGINVDDCADVSHQVSAV 61
Cdd:PRK14631   3 LSNKSQALTDIIAPAVAACGVDLWGIEFLpQGKRSLLRIYIDRlveenaepvinedgeveqGRGIGVEDCVRVTQQVGAM 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355  62 MDVEDPITVAYNLEVSSPGLDRPMFTAEHYERFSGEEVALVLRMAVQNRRKWQGIIKAVD--GEMITVTVEGKDEV-FAL 138
Cdd:PRK14631  83 LDVHDPISGEYALEVSSPGWDRPFFQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDleNEEIQVEVEGKHVLdIDS 162


                 ....*....
gi 491006355 139 SNIQKANLV 147
Cdd:PRK14631 163 NNIDKANLI 171
PRK14647 PRK14647
ribosome maturation factor RimP;
6-146 1.86e-33

ribosome maturation factor RimP;


Pssm-ID: 173110 [Multi-domain]  Cd Length: 159  Bit Score: 115.23  E-value: 1.86e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355   6 QKLTEMLTAPVEALGFELVGIEFIR-GRTSTLRIYIDSDDGINVDDCADVSHQVSAVMDVEDPITVAYNLEVSSPGLDRP 84
Cdd:PRK14647   8 DRVTELAEQVLSSLGLELVELEYKReGREMVLRLFIDKEGGVNLDDCAEVSRELSEILDVEDFIPERYTLEVSSPGLDRP 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491006355  85 MFTAEHYERFSGEEVAL----VLRMAVQNRRK-WQGIIKAVDGEMITVTV-EGKDEVFALSNIQKANL 146
Cdd:PRK14647  88 LKKEADYERYAGRLVKVrtfeLLADEAGNKRKtFLGELEGLADGVVTIALkEGQQARIPLDKIAKANL 155
RimP_N pfam02576
RimP N-terminal domain; This entry represents the N-terminal domain of the ribosome maturation ...
 11-82 2.31e-33

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: 112.31  E-value: 2.31e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491006355   11 MLTAPVEALGFELVGIEFIR-GRTSTLRIYIDSDDGINVDDCADVSHQVSAVMDVEDPITVAYNLEVSSPGLD 82
Cdd:pfam02576   1 LIEPVVESLGFELVDVEFVKeGGGWTLRIYIDKDGGVTIDDCAKVSRAISAVLDVEDPISGEYTLEVSSPGLD 73
PRK14636 PRK14636
ribosome maturation protein RimP;
7-147 5.62e-28

ribosome maturation protein RimP;


Pssm-ID: 237773 [Multi-domain]  Cd Length: 176  Bit Score: 101.78  E-value: 5.62e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355   7 KLTEMLTAPVEALGFELVGIEFIRGRTS-TLRIYIDSDDG--INVDDCADVSHQVSAVMDVEDPITVAYNLEVSSPGLDR 83
Cdd:PRK14636   6 ALTALIEPEAKALGLDLVRVAMFGGKSDpTLQIMAERPDTrqLVIEDCAALSRRLSDVFDELDPIEDAYRLEVSSPGIDR 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 491006355  84 PMFTAEHYERFSGEEVALVLRMAVQNRRKWQGIIKAVDGEMITVTVEGKDEV-FALSNIQKANLV 147
Cdd:PRK14636  86 PLTRPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGDTVTIADNKAGEViLPFAAIESAKLI 150
YlxS_C cd01734
Bacillus subtilis YxlS-like, C-terminal domain; YxlS is a Bacillus subtilis gene of unknown ...
 80-150 2.48e-26

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: 94.44  E-value: 2.48e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 491006355  80 GLDRPMFTAEHYERFSGEEVALVLRMAVQNRRKWQGIIKAVDGEMITVTVEGKDEV-FALSNIQKANLVPHF 150
Cdd:cd01734    1 GLDRPLKKPEDFERFIGKEVKVKLKEPIDGRKKFTGELLGVDDDTVTLEVDDGKEVeIPFDNIAKARLVPEF 72
PRK14633 PRK14633
ribosome maturation factor RimP;
8-150 1.61e-24

ribosome maturation factor RimP;


Pssm-ID: 173096 [Multi-domain]  Cd Length: 150  Bit Score: 91.95  E-value: 1.61e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355   8 LTEMLTAPVEALGFELVGIEFIRGRTSTLRIYIDSDDGINVDDCADVSHQVSAVMDVEDPITVAYNLEVSSPGLDRPMFT 87
Cdd:PRK14633   6 LYEIVEPITADLGYILWGIEVVGSGKLTIRIFIDHENGVSVDDCQIVSKEISAVFDVEDPVSGKYILEVSSPGMNRQIFN 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 491006355  88 AEHYERFSGEEVALVLRMAVQNRRKWQGIIKAVDGEMITVTVE-GKDEVFALSNIQKANLVPHF 150
Cdd:PRK14633  86 IIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGNNVILNLEdGKEISFDFDELKKLRVSPDF 149
DUF150_C pfam17384
RimP C-terminal SH3 domain; This family represents the C-terminal domain from RimP.
 85-150 4.99e-24

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


Pssm-ID: 465408  Cd Length: 67  Bit Score: 88.45  E-value: 4.99e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491006355   85 MFTAEHYERFSGEEVALVLRMAVQNRRKWQGIIKAVDGEMITVTVEGKDEV-FALSNIQKANLVPHF 150
Cdd:pfam17384   1 LFTAEHFARFIGELVKVKLKLPIDGRKKFQGKIVAVDGETITLEVDGKTEVtIPFDDIDKARLVPEF 67
PRK14645 PRK14645
ribosome maturation factor RimP;
8-146 1.77e-23

ribosome maturation factor RimP;


Pssm-ID: 184780 [Multi-domain]  Cd Length: 154  Bit Score: 89.44  E-value: 1.77e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355   8 LTEMLTAPVEALGFELVGIEFIR-GRTSTLRIYIDSDDG--INVDDCADVSHQVSAVMDVEDPITVAYNLEVSSPGLDRP 84
Cdd:PRK14645  11 LQQLAEGALEPLGYEVLEVQVQRsGGKRIVLVRIDRKDEqpVTVEDLERASRALEAELDRLDPIEGEYRLEVESPGPKRP 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491006355  85 MFTAEHYERFSGeevalvLRMAVQNR-RKWQGIIKAVDGEMITVTVEGKDEVFALSNIQkANL 146
Cdd:PRK14645  91 LFTARHFERFAG------LKAKVRGPgENFTGRIKAVSGDQVTFDVGGEDRTLRIGTFQ-ANL 146
PRK14632 PRK14632
ribosome maturation factor RimP;
1-150 1.93e-23

ribosome maturation factor RimP;


Pssm-ID: 173095 [Multi-domain]  Cd Length: 172  Bit Score: 90.13  E-value: 1.93e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355   1 MST--LEQKLTEMLTAPVEALGFELVGIEFIRGRTSTLRIYIDSDDGINVDDCADVSHQVSAVMDVEDPITVAYNLEVSS 78
Cdd:PRK14632   1 MTKqaLDATIADMAGPFLASLGLELWGIELSYGGRTVVRLFVDGPEGVTIDQCAEVSRHVGLALEVEDVISSAYVLEVSS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355  79 PGLDRPMFTAEHYERFSGEEVALVLRMA---VQNRRKWQGIIKAVDGEMITV---TVEGKDE-----VFALSNIQKANLV 147
Cdd:PRK14632  81 PGLERPFFRAEQMSPYVGRQIELTLIDPtpeWPGRRKFRGELLAVEGDTVVLrpeGAPAPEAeeavlRTSWQGVRKANLI 160


                 ...
gi 491006355 148 PHF 150
Cdd:PRK14632 161 HVF 163
PRK14639 PRK14639
ribosome maturation factor RimP;
12-144 5.17e-23

ribosome maturation factor RimP;


Pssm-ID: 173102 [Multi-domain]  Cd Length: 140  Bit Score: 87.95  E-value: 5.17e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355  12 LTAPVEALGFELVGIEFI--RGRtSTLRIYIDSDDGINVDDCADVSHQVSAVMDVEDPITVAYNLEVSSPGLDRPMFTAE 89
Cdd:PRK14639   3 LEALCKECGVSFYDDELVseNGR-KIYRVYITKEGGVNLDDCERLSELLSPIFDVEPPVSGEYFLEVSSPGLERKLSKIE 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 491006355  90 HYERFSGEEVALVLrmavQNRRKWQGIIKAVDGEMITVTVEGKDEVFAL--SNIQKA 144
Cdd:PRK14639  82 HFAKSIGELVKITT----NEKEKFEGKIVSVDDENITLENLENKEKTTInfNDIKKA 134
PRK14638 PRK14638
ribosome maturation factor RimP;
4-150 3.20e-17

ribosome maturation factor RimP;


Pssm-ID: 184777 [Multi-domain]  Cd Length: 150  Bit Score: 73.36  E-value: 3.20e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355   4 LEQKLTEMLTAPV----EALGFELVGIEFIR-GRTSTLRIYIDSDDG-INVDDCADVSHQVSAVMDVEDPITVAYNLEVS 77
Cdd:PRK14638   2 FEEMILEKVRKEAeriaEEQGLEIFDVQYRReSRGWVLRIIIDNPVGyVSVRDCELFSREIERFLDREDLIEHSYTLEVS 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491006355  78 SPGLDRPMFTAEHYERFSGEEVALVLRmavqNRRKWQGIIKAVDGEMITVTVEGKDEVFALSNIQKANLVPHF 150
Cdd:PRK14638  82 SPGLDRPLRGPKDYVRFTGKLAKIVTK----DGKTFIGRIESFVDGTITISDEKEKYEINIDDVKRANLEVEF 150
PRK14642 PRK14642
ribosome maturation factor RimP;
8-122 3.69e-16

ribosome maturation factor RimP;


Pssm-ID: 237775 [Multi-domain]  Cd Length: 197  Bit Score: 71.43  E-value: 3.69e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355   8 LTEMLTAPVEALGFELVGIEfiRGRTSTLRIYID-------------SDDGINVDDCADVSHQVSAVMDVEDpitVAYN- 73
Cdd:PRK14642   3 LQQIVEQTVTGLGYDLVEIE--RSAGGLLRVTIDlpwvpptegapvgPEQFVTVEDCEKVTRQLQFALEVDG---VDYKr 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 491006355  74 LEVSSPGLDRPMFTAEHYERFSGEEVALVLRMAV---------QNRRKWQGIIKAVDG 122
Cdd:PRK14642  78 LEVSSPGIDRPLRHEQDFERFAGEVIDITLKAPIgaaaggqvsANRKKFRGTLERAES 135
PRK14637 PRK14637
ribosome maturation factor RimP;
16-148 9.39e-14

ribosome maturation factor RimP;


Pssm-ID: 237774 [Multi-domain]  Cd Length: 151  Bit Score: 64.12  E-value: 9.39e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355  16 VEALGFELVGIE-FIRGRTSTLRIYIDSDDGINVDDCADVSH----QVSAVMDVEDpitvaYNLEVSSPGLDRPMFTAEH 90
Cdd:PRK14637  18 VEGLGCKLVDLSrRVQQAQGRVRAVIYSAGGVGLDDCARVHRilvpRLEALGGVRD-----VFLEVSSPGIERVIKNAAE 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 491006355  91 YERFSGEEVALVLRMAVQnrrkWQ-GIIKAVDGEMITVTVEGKDEVFALSNIQKANLVP 148
Cdd:PRK14637  93 FSIFVGETVKVWFECTGQ----WQvGTIAEADETCLVLTSDGVPVTIPYVQITKAQLHP 147
PRK02001 PRK02001
ribosome assembly cofactor RimP;
35-144 5.36e-13

ribosome assembly cofactor RimP;


Pssm-ID: 179358 [Multi-domain]  Cd Length: 152  Bit Score: 62.30  E-value: 5.36e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355  35 TLRIYIDSDDGINVDDCADVSHQVSAVMDVEDpitVAYNLEVSSPGLDRPMFTAEHYERFSGEEVALVLRmavqNRRKWQ 114
Cdd:PRK02001  32 KIVVEIDGDEGVWIEDCVELSRAIEHNLDREE---EDFELEVGSAGLTSPLKVPRQYKKNIGRELEVLTK----NGKKIE 104

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 491006355 115 GIIKAVDGEMITVTVEG--------------KDEVFALSNIQKA 144
Cdd:PRK02001 105 GELKSADENDITLEVKArepkeggkgkvtveKEETITYDDIKEA 148
PRK14634 PRK14634
ribosome maturation factor RimP;
8-132 1.32e-08

ribosome maturation factor RimP;


Pssm-ID: 173097 [Multi-domain]  Cd Length: 155  Bit Score: 50.56  E-value: 1.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355   8 LTEMLTAPVEALGFELVGIE-FIRGRTSTLRIYIDSDDG--INVDDCADVSHQVSAVMDVEDPITVAYNLEVSSPGLDRP 84
Cdd:PRK14634   9 LETLASATAADKGFELCGIQvLTHLQPMTLQVQIRRSSGsdVSLDDCAGFSGPMGEALEASQLLTEAYVLEISSPGIGDQ 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 491006355  85 MFTAEHYERFSGEEVALVLRMAVQNRRKWQGIIKAVDGEMITVTVEGK 132
Cdd:PRK14634  89 LSSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNEDHLQINIRGR 136
PRK14641 PRK14641
ribosome maturation factor RimP;
13-96 4.43e-06

ribosome maturation factor RimP;


Pssm-ID: 173104 [Multi-domain]  Cd Length: 173  Bit Score: 44.00  E-value: 4.43e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355  13 TAPVEALGFELVGIEfIRGRTSTLRIYI--DSDDGINVDDCADVSHQVSAVMDVEDPITVA----YNLEVSSPGLDRPMF 86
Cdd:PRK14641  16 SAGTKGEGVYLVSMT-VKGSGKGRKIEVllDADTGIRIDQCAFFSRRIRERLEEDEELLGLvgedFDLMVSSPGLGEPII 94

                         90
                 ....*....|
gi 491006355  87 TAEHYERFSG 96
Cdd:PRK14641  95 LPRQYGRHVG 104
PRK14644 PRK14644
hypothetical protein; Provisional
 34-146 1.17e-04

hypothetical protein; Provisional


Pssm-ID: 184779 [Multi-domain]  Cd Length: 136  Bit Score: 39.82  E-value: 1.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355  34 STLRIYIDSDDginVDDCADVSHQVSAVMDVEDPITVAYNLEVSSPGLDRPMFTAEhYERFSGEEVALVLRMAVQNRRKW 113
Cdd:PRK14644  27 LFLEVILNSRD---LKDIEELTKEISDFIDNLSVEFDFDSLDISSPGFDMDYETDE-LENHIGEIIDVSLNKEVNKTDFI 102

                         90       100       110
                 ....*....|....*....|....*....|...
gi 491006355 114 QGIIKAVDGEMITVTVEGKDEvFALSNIQKANL 146
Cdd:PRK14644 103 TGELLENNPETITLKWNCKGQ-FRKVEINKENI 134
PRK14646 PRK14646
ribosome maturation factor RimP;
44-139 1.23e-03

ribosome maturation factor RimP;


Pssm-ID: 173109 [Multi-domain]  Cd Length: 155  Bit Score: 37.23  E-value: 1.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355  44 DGINVDDCADVSHQVSAVMDVEDPITVAYNLEVSSPGLDRPMFTAEHYERFSGEEVALVLRMAVQNRRKWQGIIKAVDGE 123
Cdd:PRK14646  48 DDISLDDCALFNTPASEEIENSNLLNCSYVLEISSQGVSDELTSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD 127

                         90       100
                 ....*....|....*....|..
gi 491006355 124 MITVTVEGK------DEVFALS 139
Cdd:PRK14646 128 YLAINIKGKikkipfNEVLKIS 149
PRK14630 PRK14630
ribosome maturation factor RimP;
17-147 2.04e-03

ribosome maturation factor RimP;


Pssm-ID: 173093 [Multi-domain]  Cd Length: 143  Bit Score: 36.31  E-value: 2.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355  17 EALGFELVGIEFIRGRTS-TLRIYIDSDDGINVDDCADVSHQVsaVMDVEDPITVAYNLEVSSPGLDRPMFTAEHYERFS 95
Cdd:PRK14630  19 DRLGIEIIEINTFRNRNEgKIQIVLYKKDSFGVDTLCDLHKMI--LLILEAVLKYNFSLEISTPGINRKIKSDREFKIFE 96

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 491006355  96 GEEVALVLRMAVQnrrkwQGIIKAVDGEMITVTVEGKDEVFALSNIQKANLV 147
Cdd:PRK14630  97 GKKIKLMLDNDFE-----EGFILEAKADSFIFKTDSKEVNVLYSDVKKAKLS 143
PRK14635 PRK14635
ribosome maturation factor RimP;
46-146 2.05e-03

ribosome maturation factor RimP;


Pssm-ID: 184774 [Multi-domain]  Cd Length: 162  Bit Score: 36.43  E-value: 2.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491006355  46 INVDDCADVSHQVSAVMDVEDPiTVAYNLEVSSPGLDRPMFTAEHYERFSGEEVALVLRMavQNRRKWQ-GIIKAV--DG 122
Cdd:PRK14635  50 VSLLECEQVSRKLKEELERISP-DLDFTLKVSSAGAERKLRLPEDLDRFRGIPVRLVFRS--EESEKWQeGIFRLVnrDG 126

                         90       100       110
                 ....*....|....*....|....*....|..
gi 491006355 123 EMITVT--------VEGKDEVFALSNIQKANL 146
Cdd:PRK14635 127 DQVELEkfqkgkksKVKKQTTLNLKDILKGNL 158
 
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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