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Conserved domains on  [gi|6322695|ref|NP_012768|]
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Signal recognition particle receptor subunit beta [Saccharomyces cerevisiae S288C]

Protein Classification

SR_beta domain-containing protein( domain architecture ID 12100135)

SR_beta domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SRPRB pfam09439
Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition ...
 36-221 1.45e-74

Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane.


:

Pssm-ID: 462797 [Multi-domain]  Cd Length: 181  Bit Score: 224.24  E-value: 1.45e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695     36 SYQPSIIIAGPQNSGKTSLLTLLTTDSVRPTVVSQEPLSAADY---DGSGVTLVDFPGHVKLRYKLSDYLKTRAKfVKGL 112
Cdd:pfam09439   1 SSQPAVIIAGLCDSGKTSLFTLLTTDSVRPTVTSQEPSAAYRYmlnKGNSFTLIDFPGHVKLRYKLLETLKDSSS-LKGI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695    113 IFMVDSTVDPKKLTTTAEFLVDILSITESScENGIDILIACNKSELFTARPPSKIKDALESEIQKVIERRKKSLNEVErk 192
Cdd:pfam09439  80 VFVVDSTIFPKEVTDTAEFLYDILSITELL-KNGIDILIACNKQESFTARPPKKIKQALEKEINTIRERRSKALSGLD-- 156

                         170       180
                  ....*....|....*....|....*....
gi 6322695    193 iNEEDyaeNTLDVLQSTDGFKFANLEASV 221
Cdd:pfam09439 157 -GSED---LSAVLGKKGKGFKFDQLEANV 181
 
Name Accession Description Interval E-value
SRPRB pfam09439
Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition ...
 36-221 1.45e-74

Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane.


Pssm-ID: 462797 [Multi-domain]  Cd Length: 181  Bit Score: 224.24  E-value: 1.45e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695     36 SYQPSIIIAGPQNSGKTSLLTLLTTDSVRPTVVSQEPLSAADY---DGSGVTLVDFPGHVKLRYKLSDYLKTRAKfVKGL 112
Cdd:pfam09439   1 SSQPAVIIAGLCDSGKTSLFTLLTTDSVRPTVTSQEPSAAYRYmlnKGNSFTLIDFPGHVKLRYKLLETLKDSSS-LKGI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695    113 IFMVDSTVDPKKLTTTAEFLVDILSITESScENGIDILIACNKSELFTARPPSKIKDALESEIQKVIERRKKSLNEVErk 192
Cdd:pfam09439  80 VFVVDSTIFPKEVTDTAEFLYDILSITELL-KNGIDILIACNKQESFTARPPKKIKQALEKEINTIRERRSKALSGLD-- 156

                         170       180
                  ....*....|....*....|....*....
gi 6322695    193 iNEEDyaeNTLDVLQSTDGFKFANLEASV 221
Cdd:pfam09439 157 -GSED---LSAVLGKKGKGFKFDQLEANV 181
SR_beta cd04105
Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ...
 39-243 7.24e-66

Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms the heterodimeric signal recognition particle (SRP); Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are synthesized with an N-terminal hydrophobic signal sequence that binds SRP54, a component of the SRP. SRP directs targeting of the ribosome-nascent chain complex (RNC) to the ER membrane via interaction with the SR, which is localized to the ER membrane. The RNC is then transferred to the protein-conducting channel, or translocon, which facilitates polypeptide translation across the ER membrane or integration into the ER membrane. SR-beta is found only in eukaryotes; it is believed to control the release of the signal sequence from SRP54 upon binding of the ribosome to the translocon. High expression of SR-beta has been observed in human colon cancer, suggesting it may play a role in the development of this type of cancer.


Pssm-ID: 206691 [Multi-domain]  Cd Length: 202  Bit Score: 202.94  E-value: 7.24e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695   39 PSIIIAGPQNSGKTSLLTLLTTDSVRPTVVSQEPLSAADYDGSG----VTLVDFPGHVKLRYKLSDYLKTRAKfvkGLIF 114
Cdd:cd04105   1 PTVLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSkgkkLTLVDVPGHEKLRDKLLEYLKASLK---AIVF 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695  115 MVDSTVDPKKLTTTAEFLVDILSITESSCeNGIDILIACNKSELFTARPPSKIKDALESEIQKVIERRKKSLNEVERKIN 194
Cdd:cd04105  78 VVDSATFQKNIRDVAEFLYDILTDLEKIK-NKIPILIACNKQDLFTAKPAKKIKELLEKEINTLRESRSKSLESLDGDDG 156

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
gi 6322695  195 EEDYAEntldvLQSTDGFKFANLEASVVAFEGSINKRK--ISQWREWIDEK 243
Cdd:cd04105 157 SKDTLG-----DKGGKDFEFDQLEGEVDFVEGSVKKSKggIDDIEEWIDEL 202
 
Name Accession Description Interval E-value
SRPRB pfam09439
Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition ...
 36-221 1.45e-74

Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane.


Pssm-ID: 462797 [Multi-domain]  Cd Length: 181  Bit Score: 224.24  E-value: 1.45e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695     36 SYQPSIIIAGPQNSGKTSLLTLLTTDSVRPTVVSQEPLSAADY---DGSGVTLVDFPGHVKLRYKLSDYLKTRAKfVKGL 112
Cdd:pfam09439   1 SSQPAVIIAGLCDSGKTSLFTLLTTDSVRPTVTSQEPSAAYRYmlnKGNSFTLIDFPGHVKLRYKLLETLKDSSS-LKGI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695    113 IFMVDSTVDPKKLTTTAEFLVDILSITESScENGIDILIACNKSELFTARPPSKIKDALESEIQKVIERRKKSLNEVErk 192
Cdd:pfam09439  80 VFVVDSTIFPKEVTDTAEFLYDILSITELL-KNGIDILIACNKQESFTARPPKKIKQALEKEINTIRERRSKALSGLD-- 156

                         170       180
                  ....*....|....*....|....*....
gi 6322695    193 iNEEDyaeNTLDVLQSTDGFKFANLEASV 221
Cdd:pfam09439 157 -GSED---LSAVLGKKGKGFKFDQLEANV 181
SR_beta cd04105
Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ...
 39-243 7.24e-66

Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms the heterodimeric signal recognition particle (SRP); Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are synthesized with an N-terminal hydrophobic signal sequence that binds SRP54, a component of the SRP. SRP directs targeting of the ribosome-nascent chain complex (RNC) to the ER membrane via interaction with the SR, which is localized to the ER membrane. The RNC is then transferred to the protein-conducting channel, or translocon, which facilitates polypeptide translation across the ER membrane or integration into the ER membrane. SR-beta is found only in eukaryotes; it is believed to control the release of the signal sequence from SRP54 upon binding of the ribosome to the translocon. High expression of SR-beta has been observed in human colon cancer, suggesting it may play a role in the development of this type of cancer.


Pssm-ID: 206691 [Multi-domain]  Cd Length: 202  Bit Score: 202.94  E-value: 7.24e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695   39 PSIIIAGPQNSGKTSLLTLLTTDSVRPTVVSQEPLSAADYDGSG----VTLVDFPGHVKLRYKLSDYLKTRAKfvkGLIF 114
Cdd:cd04105   1 PTVLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSkgkkLTLVDVPGHEKLRDKLLEYLKASLK---AIVF 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695  115 MVDSTVDPKKLTTTAEFLVDILSITESSCeNGIDILIACNKSELFTARPPSKIKDALESEIQKVIERRKKSLNEVERKIN 194
Cdd:cd04105  78 VVDSATFQKNIRDVAEFLYDILTDLEKIK-NKIPILIACNKQDLFTAKPAKKIKELLEKEINTLRESRSKSLESLDGDDG 156

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
gi 6322695  195 EEDYAEntldvLQSTDGFKFANLEASVVAFEGSINKRK--ISQWREWIDEK 243
Cdd:cd04105 157 SKDTLG-----DKGGKDFEFDQLEGEVDFVEGSVKKSKggIDDIEEWIDEL 202
Arf_Arl cd00878
ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ...
 41-172 8.46e-08

ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions.


Pssm-ID: 206644 [Multi-domain]  Cd Length: 158  Bit Score: 50.27  E-value: 8.46e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695   41 IIIAGPQNSGK---TSLLTLLTTDSVRPTVVSQepLSAADYDGSGVTLVDFPGHVKLRYKLSDYLKTrakfVKGLIFMVD 117
Cdd:cd00878   2 ILMLGLDGAGKttiLYKLKLGEVVTTIPTIGFN--VETVEYKNVKFTVWDVGGQDKIRPLWKHYYEN----TDGLIFVVD 75

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 6322695  118 STvDPKKLTTTAEFLVDILSITESScenGIDILIACNKSELFTARPPSKIKDALE 172
Cdd:cd00878  76 SS-DRERIEEAKNELHKLLNEEELK---GAPLLILANKQDLPGALTESELIELLG 126
Arl3 cd04155
Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most ...
 32-172 1.55e-05

Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.


Pssm-ID: 206721 [Multi-domain]  Cd Length: 174  Bit Score: 43.92  E-value: 1.55e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695   32 IKQKSYQ-PSIIIAGPQNSGKTSLLTLLTTDSVRPTVVSQE-PLSAADYDGSGVTLVDFPGHVKLRYKLSDYLKTrakfV 109
Cdd:cd04155   8 LKPSSRQeVRILLLGLDNAGKTTILKQLASEDISHITPTQGfNIKNVQADGFKLNVWDIGGQRKIRPYWRNYFEN----T 83

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6322695  110 KGLIFMVDSTvDPKKLTTTAEFLVDILsitESSCENGIDILIACNKSELFTARPPSKIKDALE 172
Cdd:cd04155  84 DVLIYVIDSA-DRKRFEEAGQELVELL---EEEKLAGVPVLVFANKQDLLTAAPAEEVAEALN 142
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 43-180 5.08e-05

Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions.


Pssm-ID: 206648 [Multi-domain]  Cd Length: 161  Bit Score: 42.44  E-value: 5.08e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695   43 IAGPQNSGK-----------TSLLTLLTTDSVRPTVVSQEplsaADYDGSGVTLVDFPGHVKLRYKLSDYLKTR-AKFVK 110
Cdd:cd00882   2 VVGRGGVGKssllnallggeVGEVSDVPGTTRDPDVYVKE----LDKGKVKLVLVDTPGLDEFGGLGREELARLlLRGAD 77

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695  111 GLIFMVDSTVDPkkltttaEFLVDILSITESSCENGIDILIACNKSELFTARPPSKIKDALESEIQKVIE 180
Cdd:cd00882  78 LILLVVDSTDRE-------SEEDAKLLILRRLRKEGIPIILVGNKIDLLEEREVEELLRLEELAKILGVP 140
SelB_euk cd01889
SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ...
 69-184 5.04e-04

SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryotes, they do share a common feature. Unlike in E. coli, these SECIS elements are located in the 3' UTRs. This group contains eukaryotic SelBs and some from archaea.


Pssm-ID: 206676 [Multi-domain]  Cd Length: 192  Bit Score: 40.04  E-value: 5.04e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695   69 SQEPLSAADYDGSGVTLVDFPGHVKLryklsdyLKT---RAKFVKGLIFMVDSTVDPKklTTTAEFLVdILSITesscen 145
Cdd:cd01889  56 HLEDNENPQIENYQITLVDCPGHASL-------IRTiigGAQIIDLMLLVVDAKKGIQ--TQTAECLV-IGELL------ 119

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 6322695  146 GIDILIACNKSELFtarPPSKIKDALE---SEIQKVIERRKK 184
Cdd:cd01889 120 CKPLIVVLNKIDLI---PEEERKRKIEkmkKRLQKTLEKTRL 158
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
 84-172 3.14e-03

ADP-ribosylation factor family; Pfam combines a number of different Prosite families together


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 37.20  E-value: 3.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322695     84 TLVDFPGHVKLRYKLSDYLKTrakfVKGLIFMVDSTvDPKKLTTTAEFLVDILSITESScenGIDILIACNKSELFTARP 163
Cdd:pfam00025  47 TVWDVGGQESLRPLWRNYFPN----TDAVIFVVDSA-DRDRIEEAKEELHALLNEEELA---DAPLLILANKQDLPGAMS 118


                  ....*....
gi 6322695    164 PSKIKDALE 172
Cdd:pfam00025 119 EAEIRELLG 127
 
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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