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Conserved domains on  [gi|1476710189|gb|RIE71255|]
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ribosome maturation factor RimP [Shigella flexneri]

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 9.27e-85

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: 244.92  E-value: 9.27e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189   1 MSTLEQKLTEMITAPVEALGFELVGIEFIR-GHTSTLRIYIDSEDGINVDDCADVSHQVSAVLDVEDPITVAYNLEVSSP 79
Cdd:PRK14640    1 MATLEQRLTDLLEAPVVALGFELWGIEFIRaGKHSTLRVYIDGENGVSVENCAEVSHQVGAIMDVEDPITEEYYLEVSSP 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1476710189  80 GLDRPLFTAEHYARFVGEEVTLVLRMAVQNRRKWQGVIKAVDGEMITVTVEGKDEVFALSNIQKANLVPHF 150
Cdd:PRK14640   81 GLDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVDGKDEVLAFTNIQKANIVPNF 151
 
Name Accession Description Interval E-value
PRK14640 PRK14640
hypothetical protein; Provisional
 1-150 9.27e-85

hypothetical protein; Provisional


Pssm-ID: 173103 [Multi-domain]  Cd Length: 152  Bit Score: 244.92  E-value: 9.27e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189   1 MSTLEQKLTEMITAPVEALGFELVGIEFIR-GHTSTLRIYIDSEDGINVDDCADVSHQVSAVLDVEDPITVAYNLEVSSP 79
Cdd:PRK14640    1 MATLEQRLTDLLEAPVVALGFELWGIEFIRaGKHSTLRVYIDGENGVSVENCAEVSHQVGAIMDVEDPITEEYYLEVSSP 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1476710189  80 GLDRPLFTAEHYARFVGEEVTLVLRMAVQNRRKWQGVIKAVDGEMITVTVEGKDEVFALSNIQKANLVPHF 150
Cdd:PRK14640   81 GLDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVDGKDEVLAFTNIQKANIVPNF 151
RimP COG0779
Ribosome maturation factor RimP [Translation, ribosomal structure and biogenesis];
1-150 2.16e-74

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


Pssm-ID: 440542 [Multi-domain]  Cd Length: 151  Bit Score: 218.84  E-value: 2.16e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189   1 MSTLEQKLTEMITAPVEALGFELVGIEFIR-GHTSTLRIYIDSEDGINVDDCADVSHQVSAVLDVEDPITVAYNLEVSSP 79
Cdd:COG0779     1 MSGLEERLEELLEPVLEELGLELVDVEVVKeGKRWVLRVYIDKDGGVTLDDCAAVSRALSAVLDVEDPIPGAYTLEVSSP 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1476710189  80 GLDRPLFTAEHYARFVGEEVTLVLRMAVQNRRKWQGVIKAVDGEMITVTVEGKDEVFALSNIQKANLVPHF 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 2.63e-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: 111.92  E-value: 2.63e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1476710189  11 MITAPVEALGFELVGIEFIR-GHTSTLRIYIDSEDGINVDDCADVSHQVSAVLDVEDPITVAYNLEVSSPGLD 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 9.43e-28

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: 97.90  E-value: 9.43e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1476710189  80 GLDRPLFTAEHYARFVGEEVTLVLRMAVQNRRKWQGVIKAVDGEMITVTVEGKDEV-FALSNIQKANLVPHF 150
Cdd:cd01734     1 GLDRPLKKPEDFERFIGKEVKVKLKEPIDGRKKFTGELLGVDDDTVTLEVDDGKEVeIPFDNIAKARLVPEF 72
 
Name Accession Description Interval E-value
PRK14640 PRK14640
hypothetical protein; Provisional
 1-150 9.27e-85

hypothetical protein; Provisional


Pssm-ID: 173103 [Multi-domain]  Cd Length: 152  Bit Score: 244.92  E-value: 9.27e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189   1 MSTLEQKLTEMITAPVEALGFELVGIEFIR-GHTSTLRIYIDSEDGINVDDCADVSHQVSAVLDVEDPITVAYNLEVSSP 79
Cdd:PRK14640    1 MATLEQRLTDLLEAPVVALGFELWGIEFIRaGKHSTLRVYIDGENGVSVENCAEVSHQVGAIMDVEDPITEEYYLEVSSP 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1476710189  80 GLDRPLFTAEHYARFVGEEVTLVLRMAVQNRRKWQGVIKAVDGEMITVTVEGKDEVFALSNIQKANLVPHF 150
Cdd:PRK14640   81 GLDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVDGKDEVLAFTNIQKANIVPNF 151
PRK00092 PRK00092
ribosome maturation protein RimP; Reviewed
 1-150 5.75e-80

ribosome maturation protein RimP; Reviewed


Pssm-ID: 234627 [Multi-domain]  Cd Length: 154  Bit Score: 232.77  E-value: 5.75e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189   1 MSTLEQKLTEMITAPVEALGFELVGIEFIR-GHTSTLRIYIDSEDGINVDDCADVSHQVSAVLDVEDPITVAYNLEVSSP 79
Cdd:PRK00092    2 MSPLEEQLTELIEPVVEALGYELVDVEYVKeGRDSTLRIYIDKEGGIDLDDCEEVSRQISAVLDVEDPIPGAYTLEVSSP 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1476710189  80 GLDRPLFTAEHYARFVGEEVTLVLRMAVQNRRKWQGVIKAVDGEMITVTVEGKDEV--FALSNIQKANLVPHF 150
Cdd:PRK00092   82 GLDRPLKKARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGETVTLEVEGKEKEveIPLDNIAKARLVVEF 154
RimP COG0779
Ribosome maturation factor RimP [Translation, ribosomal structure and biogenesis];
1-150 2.16e-74

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


Pssm-ID: 440542 [Multi-domain]  Cd Length: 151  Bit Score: 218.84  E-value: 2.16e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189   1 MSTLEQKLTEMITAPVEALGFELVGIEFIR-GHTSTLRIYIDSEDGINVDDCADVSHQVSAVLDVEDPITVAYNLEVSSP 79
Cdd:COG0779     1 MSGLEERLEELLEPVLEELGLELVDVEVVKeGKRWVLRVYIDKDGGVTLDDCAAVSRALSAVLDVEDPIPGAYTLEVSSP 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1476710189  80 GLDRPLFTAEHYARFVGEEVTLVLRMAVQNRRKWQGVIKAVDGEMITVTVEGKDEVFALSNIQKANLVPHF 150
Cdd:COG0779    81 GLDRPLKKPRDFERFIGRLVKVKLREPIDGRKKFTGRLLGVDDDGVTLEVDGKEVEIPLDDIAKARLVIEF 151
PRK14631 PRK14631
ribosome maturation factor RimP;
1-147 3.36e-45

ribosome maturation factor RimP;


Pssm-ID: 237772 [Multi-domain]  Cd Length: 174  Bit Score: 145.80  E-value: 3.36e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189   1 MSTLEQKLTEMITAPVEALGFELVGIEFI-RGHTSTLRIYIDS-----------EDG-------INVDDCADVSHQVSAV 61
Cdd:PRK14631    3 LSNKSQALTDIIAPAVAACGVDLWGIEFLpQGKRSLLRIYIDRlveenaepvinEDGeveqgrgIGVEDCVRVTQQVGAM 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189  62 LDVEDPITVAYNLEVSSPGLDRPLFTAEHYARFVGEEVTLVLRMAVQNRRKWQGVIKAVD--GEMITVTVEGKDEV-FAL 138
Cdd:PRK14631   83 LDVHDPISGEYALEVSSPGWDRPFFQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDleNEEIQVEVEGKHVLdIDS 162


                  ....*....
gi 1476710189 139 SNIQKANLV 147
Cdd:PRK14631  163 NNIDKANLI 171
RimP_N pfam02576
RimP N-terminal domain; This entry represents the N-terminal domain of the ribosome maturation ...
 11-82 2.63e-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: 111.92  E-value: 2.63e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1476710189  11 MITAPVEALGFELVGIEFIR-GHTSTLRIYIDSEDGINVDDCADVSHQVSAVLDVEDPITVAYNLEVSSPGLD 82
Cdd:pfam02576   1 LIEPVVESLGFELVDVEFVKeGGGWTLRIYIDKDGGVTIDDCAKVSRAISAVLDVEDPISGEYTLEVSSPGLD 73
PRK14647 PRK14647
ribosome maturation factor RimP;
6-146 5.81e-33

ribosome maturation factor RimP;


Pssm-ID: 173110 [Multi-domain]  Cd Length: 159  Bit Score: 114.07  E-value: 5.81e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189   6 QKLTEMITAPVEALGFELVGIEFIR-GHTSTLRIYIDSEDGINVDDCADVSHQVSAVLDVEDPITVAYNLEVSSPGLDRP 84
Cdd:PRK14647    8 DRVTELAEQVLSSLGLELVELEYKReGREMVLRLFIDKEGGVNLDDCAEVSRELSEILDVEDFIPERYTLEVSSPGLDRP 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1476710189  85 LFTAEHYARFVGEEVTL----VLRMAVQNRRK-WQGVIKAVDGEMITVTV-EGKDEVFALSNIQKANL 146
Cdd:PRK14647   88 LKKEADYERYAGRLVKVrtfeLLADEAGNKRKtFLGELEGLADGVVTIALkEGQQARIPLDKIAKANL 155
PRK14636 PRK14636
ribosome maturation protein RimP;
7-147 3.35e-30

ribosome maturation protein RimP;


Pssm-ID: 237773 [Multi-domain]  Cd Length: 176  Bit Score: 107.56  E-value: 3.35e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189   7 KLTEMITAPVEALGFELVGIEFIRGHTS-TLRIYIDSEDG--INVDDCADVSHQVSAVLDVEDPITVAYNLEVSSPGLDR 83
Cdd:PRK14636    6 ALTALIEPEAKALGLDLVRVAMFGGKSDpTLQIMAERPDTrqLVIEDCAALSRRLSDVFDELDPIEDAYRLEVSSPGIDR 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1476710189  84 PLFTAEHYARFVGEEVTLVLRMAVQNRRKWQGVIKAVDGEMITVTVEGKDEV-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 9.43e-28

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: 97.90  E-value: 9.43e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1476710189  80 GLDRPLFTAEHYARFVGEEVTLVLRMAVQNRRKWQGVIKAVDGEMITVTVEGKDEV-FALSNIQKANLVPHF 150
Cdd:cd01734     1 GLDRPLKKPEDFERFIGKEVKVKLKEPIDGRKKFTGELLGVDDDTVTLEVDDGKEVeIPFDNIAKARLVPEF 72
PRK14633 PRK14633
ribosome maturation factor RimP;
12-150 2.98e-26

ribosome maturation factor RimP;


Pssm-ID: 173096 [Multi-domain]  Cd Length: 150  Bit Score: 96.57  E-value: 2.98e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189  12 ITAPVEA-LGFELVGIEFIRGHTSTLRIYIDSEDGINVDDCADVSHQVSAVLDVEDPITVAYNLEVSSPGLDRPLFTAEH 90
Cdd:PRK14633    9 IVEPITAdLGYILWGIEVVGSGKLTIRIFIDHENGVSVDDCQIVSKEISAVFDVEDPVSGKYILEVSSPGMNRQIFNIIQ 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1476710189  91 YARFVGEEVTLVLRMAVQNRRKWQGVIKAVDGEMITVTVE-GKDEVFALSNIQKANLVPHF 150
Cdd:PRK14633   89 AQALVGFNVKAVTLAPVGSQTKFKGVLERVEGNNVILNLEdGKEISFDFDELKKLRVSPDF 149
PRK14632 PRK14632
ribosome maturation factor RimP;
1-150 3.35e-25

ribosome maturation factor RimP;


Pssm-ID: 173095 [Multi-domain]  Cd Length: 172  Bit Score: 94.36  E-value: 3.35e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189   1 MST--LEQKLTEMITAPVEALGFELVGIEFIRGHTSTLRIYIDSEDGINVDDCADVSHQVSAVLDVEDPITVAYNLEVSS 78
Cdd:PRK14632    1 MTKqaLDATIADMAGPFLASLGLELWGIELSYGGRTVVRLFVDGPEGVTIDQCAEVSRHVGLALEVEDVISSAYVLEVSS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189  79 PGLDRPLFTAEHYARFVGEEVTLVLRMA---VQNRRKWQGVIKAVDGEMITV---TVEGKDE-----VFALSNIQKANLV 147
Cdd:PRK14632   81 PGLERPFFRAEQMSPYVGRQIELTLIDPtpeWPGRRKFRGELLAVEGDTVVLrpeGAPAPEAeeavlRTSWQGVRKANLI 160


                  ...
gi 1476710189 148 PHF 150
Cdd:PRK14632  161 HVF 163
PRK14639 PRK14639
ribosome maturation factor RimP;
37-144 8.97e-25

ribosome maturation factor RimP;


Pssm-ID: 173102 [Multi-domain]  Cd Length: 140  Bit Score: 92.58  E-value: 8.97e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189  37 RIYIDSEDGINVDDCADVSHQVSAVLDVEDPITVAYNLEVSSPGLDRPLFTAEHYARFVGEEVTLVLrmavQNRRKWQGV 116
Cdd:PRK14639   29 RVYITKEGGVNLDDCERLSELLSPIFDVEPPVSGEYFLEVSSPGLERKLSKIEHFAKSIGELVKITT----NEKEKFEGK 104

                          90       100       110
                  ....*....|....*....|....*....|
gi 1476710189 117 IKAVDGEMITVTVEGKDEVFAL--SNIQKA 144
Cdd:PRK14639  105 IVSVDDENITLENLENKEKTTInfNDIKKA 134
DUF150_C pfam17384
RimP C-terminal SH3 domain; This family represents the C-terminal domain from RimP.
 85-150 2.99e-24

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


Pssm-ID: 465408  Cd Length: 67  Bit Score: 88.84  E-value: 2.99e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1476710189  85 LFTAEHYARFVGEEVTLVLRMAVQNRRKWQGVIKAVDGEMITVTVEGKDEV-FALSNIQKANLVPHF 150
Cdd:pfam17384   1 LFTAEHFARFIGELVKVKLKLPIDGRKKFQGKIVAVDGETITLEVDGKTEVtIPFDDIDKARLVPEF 67
PRK14645 PRK14645
ribosome maturation factor RimP;
8-146 8.18e-23

ribosome maturation factor RimP;


Pssm-ID: 184780 [Multi-domain]  Cd Length: 154  Bit Score: 87.90  E-value: 8.18e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189   8 LTEMITAPVEALGFELVGIEFIRGHTS---TLRIYIDSEDGINVDDCADVSHQVSAVLDVEDPITVAYNLEVSSPGLDRP 84
Cdd:PRK14645   11 LQQLAEGALEPLGYEVLEVQVQRSGGKrivLVRIDRKDEQPVTVEDLERASRALEAELDRLDPIEGEYRLEVESPGPKRP 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1476710189  85 LFTAEHYARFVGeevtlvLRMAVQNR-RKWQGVIKAVDGEMITVTVEGKDEVFALSNIQkANL 146
Cdd:PRK14645   91 LFTARHFERFAG------LKAKVRGPgENFTGRIKAVSGDQVTFDVGGEDRTLRIGTFQ-ANL 146
PRK14642 PRK14642
ribosome maturation factor RimP;
8-122 2.76e-18

ribosome maturation factor RimP;


Pssm-ID: 237775 [Multi-domain]  Cd Length: 197  Bit Score: 77.21  E-value: 2.76e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189   8 LTEMITAPVEALGFELVGIEfiRGHTSTLRIYID-------------SEDGINVDDCADVSHQVSAVLDVEDpitVAYN- 73
Cdd:PRK14642    3 LQQIVEQTVTGLGYDLVEIE--RSAGGLLRVTIDlpwvpptegapvgPEQFVTVEDCEKVTRQLQFALEVDG---VDYKr 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1476710189  74 LEVSSPGLDRPLFTAEHYARFVGEEVTLVLRMAV---------QNRRKWQGVIKAVDG 122
Cdd:PRK14642   78 LEVSSPGIDRPLRHEQDFERFAGEVIDITLKAPIgaaaggqvsANRKKFRGTLERAES 135
PRK14638 PRK14638
ribosome maturation factor RimP;
6-150 7.40e-18

ribosome maturation factor RimP;


Pssm-ID: 184777 [Multi-domain]  Cd Length: 150  Bit Score: 74.90  E-value: 7.40e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189   6 QKLTEMITAPVEALGFELVGIEFIRGHTS-TLRIYIDSEDG-INVDDCADVSHQVSAVLDVEDPITVAYNLEVSSPGLDR 83
Cdd:PRK14638    8 EKVRKEAERIAEEQGLEIFDVQYRRESRGwVLRIIIDNPVGyVSVRDCELFSREIERFLDREDLIEHSYTLEVSSPGLDR 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1476710189  84 PLFTAEHYARFVGEEVTLVLRmavqNRRKWQGVIKAVDGEMITVTVEGKDEVFALSNIQKANLVPHF 150
Cdd:PRK14638   88 PLRGPKDYVRFTGKLAKIVTK----DGKTFIGRIESFVDGTITISDEKEKYEINIDDVKRANLEVEF 150
PRK14637 PRK14637
ribosome maturation factor RimP;
16-148 5.25e-15

ribosome maturation factor RimP;


Pssm-ID: 237774 [Multi-domain]  Cd Length: 151  Bit Score: 67.58  E-value: 5.25e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189  16 VEALGFELVgiEFIRGHTST---LRIYIDSEDGINVDDCADVSH----QVSAVLDVEDpitvaYNLEVSSPGLDRPLFTA 88
Cdd:PRK14637   18 VEGLGCKLV--DLSRRVQQAqgrVRAVIYSAGGVGLDDCARVHRilvpRLEALGGVRD-----VFLEVSSPGIERVIKNA 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1476710189  89 EHYARFVGEEVTLVLRMAVQnrrkWQ-GVIKAVDGEMITVTVEGKDEVFALSNIQKANLVP 148
Cdd:PRK14637   91 AEFSIFVGETVKVWFECTGQ----WQvGTIAEADETCLVLTSDGVPVTIPYVQITKAQLHP 147
PRK02001 PRK02001
ribosome assembly cofactor RimP;
35-144 4.34e-13

ribosome assembly cofactor RimP;


Pssm-ID: 179358 [Multi-domain]  Cd Length: 152  Bit Score: 62.69  E-value: 4.34e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189  35 TLRIYIDSEDGINVDDCADVSHQVSAVLDVEDpitVAYNLEVSSPGLDRPLFTAEHYARFVGEEVTLVLRmavqNRRKWQ 114
Cdd:PRK02001   32 KIVVEIDGDEGVWIEDCVELSRAIEHNLDREE---EDFELEVGSAGLTSPLKVPRQYKKNIGRELEVLTK----NGKKIE 104

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1476710189 115 GVIKAVDGEMITVTVEG--------------KDEVFALSNIQKA 144
Cdd:PRK02001  105 GELKSADENDITLEVKArepkeggkgkvtveKEETITYDDIKEA 148
PRK14634 PRK14634
ribosome maturation factor RimP;
8-132 4.27e-09

ribosome maturation factor RimP;


Pssm-ID: 173097 [Multi-domain]  Cd Length: 155  Bit Score: 52.10  E-value: 4.27e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189   8 LTEMITAPVEALGFELVGIEFIRgHTS--TLRIYIDSEDG--INVDDCADVSHQVSAVLDVEDPITVAYNLEVSSPGLDR 83
Cdd:PRK14634    9 LETLASATAADKGFELCGIQVLT-HLQpmTLQVQIRRSSGsdVSLDDCAGFSGPMGEALEASQLLTEAYVLEISSPGIGD 87

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1476710189  84 PLFTAEHYARFVGEEVTLVLRMAVQNRRKWQGVIKAVDGEMITVTVEGK 132
Cdd:PRK14634   88 QLSSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNEDHLQINIRGR 136
PRK14641 PRK14641
ribosome maturation factor RimP;
13-96 1.89e-07

ribosome maturation factor RimP;


Pssm-ID: 173104 [Multi-domain]  Cd Length: 173  Bit Score: 47.85  E-value: 1.89e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189  13 TAPVEALGFELVGIEfIRG---HTStLRIYIDSEDGINVDDCADVSHQVSAVLDVEDPITVA----YNLEVSSPGLDRPL 85
Cdd:PRK14641   16 SAGTKGEGVYLVSMT-VKGsgkGRK-IEVLLDADTGIRIDQCAFFSRRIRERLEEDEELLGLvgedFDLMVSSPGLGEPI 93

                          90
                  ....*....|.
gi 1476710189  86 FTAEHYARFVG 96
Cdd:PRK14641   94 ILPRQYGRHVG 104
PRK14644 PRK14644
hypothetical protein; Provisional
 34-146 7.81e-05

hypothetical protein; Provisional


Pssm-ID: 184779 [Multi-domain]  Cd Length: 136  Bit Score: 40.21  E-value: 7.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189  34 STLRIYIDSEDginVDDCADVSHQVSAVLDVEDPITVAYNLEVSSPGLDRPLFTAEhYARFVGEEVTLVLRMAVQNRRKW 113
Cdd:PRK14644   27 LFLEVILNSRD---LKDIEELTKEISDFIDNLSVEFDFDSLDISSPGFDMDYETDE-LENHIGEIIDVSLNKEVNKTDFI 102

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1476710189 114 QGVIKAVDGEMITVTVEGKDEvFALSNIQKANL 146
Cdd:PRK14644  103 TGELLENNPETITLKWNCKGQ-FRKVEINKENI 134
PRK14646 PRK14646
ribosome maturation factor RimP;
42-139 6.17e-04

ribosome maturation factor RimP;


Pssm-ID: 173109 [Multi-domain]  Cd Length: 155  Bit Score: 38.00  E-value: 6.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189  42 SEDGINVDDCADVSHQVSAVLDVEDPITVAYNLEVSSPGLDRPLFTAEHYARFVGEEVTLVLRMAVQNRRKWQGVIKAVD 121
Cdd:PRK14646   46 NGDDISLDDCALFNTPASEEIENSNLLNCSYVLEISSQGVSDELTSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKS 125

                          90       100
                  ....*....|....*....|....
gi 1476710189 122 GEMITVTVEGK------DEVFALS 139
Cdd:PRK14646  126 KDYLAINIKGKikkipfNEVLKIS 149
PRK14635 PRK14635
ribosome maturation factor RimP;
46-146 2.20e-03

ribosome maturation factor RimP;


Pssm-ID: 184774 [Multi-domain]  Cd Length: 162  Bit Score: 36.43  E-value: 2.20e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189  46 INVDDCADVSHQVSAVLDVEDPiTVAYNLEVSSPGLDRPLFTAEHYARFVGEEVTLVLRMavQNRRKWQ-GVIKAV--DG 122
Cdd:PRK14635   50 VSLLECEQVSRKLKEELERISP-DLDFTLKVSSAGAERKLRLPEDLDRFRGIPVRLVFRS--EESEKWQeGIFRLVnrDG 126

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1476710189 123 EMITVT--------VEGKDEVFALSNIQKANL 146
Cdd:PRK14635  127 DQVELEkfqkgkksKVKKQTTLNLKDILKGNL 158
PRK14630 PRK14630
ribosome maturation factor RimP;
11-147 9.03e-03

ribosome maturation factor RimP;


Pssm-ID: 173093 [Multi-domain]  Cd Length: 143  Bit Score: 34.39  E-value: 9.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1476710189  11 MITAPVEALGFELVGIE-FIRGHTSTLRIYIDSEDGINVDDCADVSHQVsaVLDVEDPITVAYNLEVSSPGLDRPLFTAE 89
Cdd:PRK14630   13 LIKNVTDRLGIEIIEINtFRNRNEGKIQIVLYKKDSFGVDTLCDLHKMI--LLILEAVLKYNFSLEISTPGINRKIKSDR 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1476710189  90 HYARFVGEEVTLVLrmavqNRRKWQGVIKAVDGEMITVTVEGKDEVFALSNIQKANLV 147
Cdd:PRK14630   91 EFKIFEGKKIKLML-----DNDFEEGFILEAKADSFIFKTDSKEVNVLYSDVKKAKLS 143
 
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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