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Conserved domains on  [gi|17563220|ref|NP_506245|]
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Signal recognition particle receptor subunit beta [Caenorhabditis elegans]

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 ...
 36-215 6.57e-77

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: 230.02  E-value: 6.57e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220    36 SNKNRVLFVGLMDCGKTTIFTQLSQKeaeypTTTKTYTSMvENKITLRI---KDKEKEIIDYPGNDRLRQKLIENHLHSR 112
Cdd:pfam09439   1 SSQPAVIIAGLCDSGKTSLFTLLTTD-----SVRPTVTSQ-EPSAAYRYmlnKGNSFTLIDFPGHVKLRYKLLETLKDSS 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220   113 SLLRIVFVVDSAAFSKNARDVAELFYTVALENV---DKVPILIACHKQDLSLAKTEKVIRNSLEKEIGLINKSRAAALIG 189
Cdd:pfam09439  75 SLKGIVFVVDSTIFPKEVTDTAEFLYDILSITEllkNGIDILIACNKQESFTARPPKKIKQALEKEINTIRERRSKALSG 154

                         170       180
                  ....*....|....*....|....*.
gi 17563220   190 TDGSEEKRSTLTDTGIDFKWEDLKKQ 215
Cdd:pfam09439 155 LDGSEDLSAVLGKKGKGFKFDQLEAN 180
 
Name Accession Description Interval E-value
SRPRB pfam09439
Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition ...
 36-215 6.57e-77

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: 230.02  E-value: 6.57e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220    36 SNKNRVLFVGLMDCGKTTIFTQLSQKeaeypTTTKTYTSMvENKITLRI---KDKEKEIIDYPGNDRLRQKLIENHLHSR 112
Cdd:pfam09439   1 SSQPAVIIAGLCDSGKTSLFTLLTTD-----SVRPTVTSQ-EPSAAYRYmlnKGNSFTLIDFPGHVKLRYKLLETLKDSS 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220   113 SLLRIVFVVDSAAFSKNARDVAELFYTVALENV---DKVPILIACHKQDLSLAKTEKVIRNSLEKEIGLINKSRAAALIG 189
Cdd:pfam09439  75 SLKGIVFVVDSTIFPKEVTDTAEFLYDILSITEllkNGIDILIACNKQESFTARPPKKIKQALEKEINTIRERRSKALSG 154

                         170       180
                  ....*....|....*....|....*.
gi 17563220   190 TDGSEEKRSTLTDTGIDFKWEDLKKQ 215
Cdd:pfam09439 155 LDGSEDLSAVLGKKGKGFKFDQLEAN 180
SR_beta cd04105
Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ...
 39-234 3.93e-63

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: 195.62  E-value: 3.93e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220  39 NRVLFVGLMDCGKTTIFTQLSQKeaeypTTTKTYTSMVEN---KITLRIKDKEKEIIDYPGNDRLRQKLIENHLHSrsLL 115
Cdd:cd04105   1 PTVLLLGPSDSGKTALFTKLTTG-----KVRSTVTSIEPNvasFYSNSSKGKKLTLVDVPGHEKLRDKLLEYLKAS--LK 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220 116 RIVFVVDSAAFSKNARDVAELFYTVALENV---DKVPILIACHKQDLSLAKTEKVIRNSLEKEIGLINKSRAAALIGTDG 192
Cdd:cd04105  74 AIVFVVDSATFQKNIRDVAEFLYDILTDLEkikNKIPILIACNKQDLFTAKPAKKIKELLEKEINTLRESRSKSLESLDG 153

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 17563220 193 SEEKRSTLTDTGIDFKWEDLKKQEVSFVSTSSNSEDFGVHEI 234
Cdd:cd04105 154 DDGSKDTLGDKGGKDFEFDQLEGEVDFVEGSVKKSKGGIDDI 195
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 40-188 1.64e-09

small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General]


Pssm-ID: 272973 [Multi-domain]  Cd Length: 162  Bit Score: 55.07  E-value: 1.64e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220    40 RVLFVGLMDCGKTTIFTQLSQKE----AEYPTTTKTYtsmVENKITLRIKDKEKEIIDYPGNDRLRQkliENHLHSRSLL 115
Cdd:TIGR00231   3 KIVIVGHPNVGKSTLLNSLLGNKgsitEYYPGTTRNY---VTTVIEEDGKTYKFNLLDTAGQEDYDA---IRRLYYPQVE 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17563220   116 RIVFVVDSAAFSKNARDVAELfYTVALENV--DKVPILIACHKQDLslaktekVIRNSLEKEIGLINKSRAAALI 188
Cdd:TIGR00231  77 RSLRVFDIVILVLDVEEILEK-QTKEIIHHadSGVPIILVGNKIDL-------KDADLKTHVASEFAKLNGEPII 143
SAR smart00178
Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene ...
 40-194 2.32e-06

Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene required for transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 197556 [Multi-domain]  Cd Length: 184  Bit Score: 46.47  E-value: 2.32e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220     40 RVLFVGLMDCGKTTIFTQLSQKEaeyptttktytsMVENKITLRIKDKEKEIidypGNDRLRQKLIENHLHSRSLLR--- 116
Cdd:smart00178  19 KILFLGLDNAGKTTLLHMLKNDR------------LAQHQPTQHPTSEELAI----GNIKFTTFDLGGHQQARRLWKdyf 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220    117 -----IVFVVDSAAFSKNARDVAELFYTVALENVDKVPILIACHKQDLSLAKTEKVIRNSLekeiGLINKSRAAALIGTD 191
Cdd:smart00178  83 pevngIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAASEDELRYAL----GLTNTTTGKGKVGVR 158


                   ...
gi 17563220    192 GSE 194
Cdd:smart00178 159 PVE 161
PTZ00133 PTZ00133
ADP-ribosylation factor; Provisional
 40-172 3.01e-05

ADP-ribosylation factor; Provisional


Pssm-ID: 173423  Cd Length: 182  Bit Score: 43.30  E-value: 3.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220   40 RVLFVGLMDCGKTTIFTQLsqKEAEYPTTTKTYTSMVEnkiTLRIKDKEKEIIDYPGNDRLRQklIENHLHSRSlLRIVF 119
Cdd:PTZ00133  19 RILMVGLDAAGKTTILYKL--KLGEVVTTIPTIGFNVE---TVEYKNLKFTMWDVGGQDKLRP--LWRHYYQNT-NGLIF 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 17563220  120 VVDSAAFSKNARDVAELFYTVALENVDKVPILIACHKQDLSLAK-----TEKVIRNSL 172
Cdd:PTZ00133  91 VVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMsttevTEKLGLHSV 148
FeoB COG0370
Fe2+ transporter FeoB [Inorganic ion transport and metabolism];
40-96 2.46e-04

Fe2+ transporter FeoB [Inorganic ion transport and metabolism];


Pssm-ID: 440139 [Multi-domain]  Cd Length: 662  Bit Score: 41.64  E-value: 2.46e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17563220  40 RVLFVGLMDCGKTTIF---TQLSQKEAEYPTTTktytsmVENKI-TLRIKDKEKEIIDYPG 96
Cdd:COG0370   5 TIALVGNPNVGKTTLFnalTGSRQKVGNWPGVT------VEKKEgKFKLKGKEIELVDLPG 59
 
Name Accession Description Interval E-value
SRPRB pfam09439
Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition ...
 36-215 6.57e-77

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: 230.02  E-value: 6.57e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220    36 SNKNRVLFVGLMDCGKTTIFTQLSQKeaeypTTTKTYTSMvENKITLRI---KDKEKEIIDYPGNDRLRQKLIENHLHSR 112
Cdd:pfam09439   1 SSQPAVIIAGLCDSGKTSLFTLLTTD-----SVRPTVTSQ-EPSAAYRYmlnKGNSFTLIDFPGHVKLRYKLLETLKDSS 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220   113 SLLRIVFVVDSAAFSKNARDVAELFYTVALENV---DKVPILIACHKQDLSLAKTEKVIRNSLEKEIGLINKSRAAALIG 189
Cdd:pfam09439  75 SLKGIVFVVDSTIFPKEVTDTAEFLYDILSITEllkNGIDILIACNKQESFTARPPKKIKQALEKEINTIRERRSKALSG 154

                         170       180
                  ....*....|....*....|....*.
gi 17563220   190 TDGSEEKRSTLTDTGIDFKWEDLKKQ 215
Cdd:pfam09439 155 LDGSEDLSAVLGKKGKGFKFDQLEAN 180
SR_beta cd04105
Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ...
 39-234 3.93e-63

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: 195.62  E-value: 3.93e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220  39 NRVLFVGLMDCGKTTIFTQLSQKeaeypTTTKTYTSMVEN---KITLRIKDKEKEIIDYPGNDRLRQKLIENHLHSrsLL 115
Cdd:cd04105   1 PTVLLLGPSDSGKTALFTKLTTG-----KVRSTVTSIEPNvasFYSNSSKGKKLTLVDVPGHEKLRDKLLEYLKAS--LK 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220 116 RIVFVVDSAAFSKNARDVAELFYTVALENV---DKVPILIACHKQDLSLAKTEKVIRNSLEKEIGLINKSRAAALIGTDG 192
Cdd:cd04105  74 AIVFVVDSATFQKNIRDVAEFLYDILTDLEkikNKIPILIACNKQDLFTAKPAKKIKELLEKEINTLRESRSKSLESLDG 153

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 17563220 193 SEEKRSTLTDTGIDFKWEDLKKQEVSFVSTSSNSEDFGVHEI 234
Cdd:cd04105 154 DDGSKDTLGDKGGKDFEFDQLEGEVDFVEGSVKKSKGGIDDI 195
Arf_Arl cd00878
ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ...
 40-173 4.66e-11

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: 59.13  E-value: 4.66e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220  40 RVLFVGLMDCGKTTIFTQLSQKEAEYPTTTKTYtsmveNKITLRIKDKEKEIIDYPGNDRLRQklIENHLHSRSLLrIVF 119
Cdd:cd00878   1 RILMLGLDGAGKTTILYKLKLGEVVTTIPTIGF-----NVETVEYKNVKFTVWDVGGQDKIRP--LWKHYYENTDG-LIF 72

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 17563220 120 VVDSA-----AFSKNardvaELFYTVALENVDKVPILIACHKQDLSLAKTEKVIRNSLE 173
Cdd:cd00878  73 VVDSSdreriEEAKN-----ELHKLLNEEELKGAPLLILANKQDLPGALTESELIELLG 126
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
 40-173 1.46e-09

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


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 55.31  E-value: 1.46e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220    40 RVLFVGLMDCGKTTIFTQLSQKEAEypTTTKTYTSMVEnkiTLRIKDKEKEIIDYPGNDRLRqKLIENHLhsRSLLRIVF 119
Cdd:pfam00025   2 RILILGLDNAGKTTILYKLKLGEIV--TTIPTIGFNVE---TVTYKNVKFTVWDVGGQESLR-PLWRNYF--PNTDAVIF 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 17563220   120 VVDSAAFSKNARDVAELFYTVALENVDKVPILIACHKQDLSLAKTEKVIRNSLE 173
Cdd:pfam00025  74 VVDSADRDRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLG 127
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 40-188 1.64e-09

small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General]


Pssm-ID: 272973 [Multi-domain]  Cd Length: 162  Bit Score: 55.07  E-value: 1.64e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220    40 RVLFVGLMDCGKTTIFTQLSQKE----AEYPTTTKTYtsmVENKITLRIKDKEKEIIDYPGNDRLRQkliENHLHSRSLL 115
Cdd:TIGR00231   3 KIVIVGHPNVGKSTLLNSLLGNKgsitEYYPGTTRNY---VTTVIEEDGKTYKFNLLDTAGQEDYDA---IRRLYYPQVE 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17563220   116 RIVFVVDSAAFSKNARDVAELfYTVALENV--DKVPILIACHKQDLslaktekVIRNSLEKEIGLINKSRAAALI 188
Cdd:TIGR00231  77 RSLRVFDIVILVLDVEEILEK-QTKEIIHHadSGVPIILVGNKIDL-------KDADLKTHVASEFAKLNGEPII 143
Arl5_Arl8 cd04153
Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like ...
 32-172 2.05e-09

Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library. It is found in brain, heart, lung, cartilage, and kidney. No function has been assigned for Arl8 to date.


Pssm-ID: 133353 [Multi-domain]  Cd Length: 174  Bit Score: 55.05  E-value: 2.05e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220  32 SFASSNKNRVLFVGLMDCGKTTIFTQLSQKEAeyPTTTKTYTSMVENkitLRIKDKEKEIIDYPGNDRLR----QKLIEN 107
Cdd:cd04153   9 LFFPRKEYKVIIVGLDNAGKTTILYQFLLGEV--VHTSPTIGSNVEE---IVYKNIRFLMWDIGGQESLRsswnTYYTNT 83

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17563220 108 HLhsrsllrIVFVVDSAAFSKNARDVAELFYTVALENVDKVPILIACHKQDLSLAKTEKVIRNSL 172
Cdd:cd04153  84 DA-------VILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGAMTPAEISESL 141
Arl3 cd04155
Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most ...
 40-173 4.81e-07

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: 48.55  E-value: 4.81e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220  40 RVLFVGLMDCGKTTIFTQLSQKEAEYPTTTKTYTSMVENKITLRIKdkekeIIDYPGNDRLRQkLIENHLHSRSLLriVF 119
Cdd:cd04155  17 RILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGFKLN-----VWDIGGQRKIRP-YWRNYFENTDVL--IY 88

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 17563220 120 VVDSAAFSKNARDVAELFYTVALENVDKVPILIACHKQDLSLAKTEKVIRNSLE 173
Cdd:cd04155  89 VIDSADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLTAAPAEEVAEALN 142
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 42-181 7.87e-07

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: 47.45  E-value: 7.87e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220  42 LFVGLMDCGKTTIFTQLSQKE-----AEYPTTTKtytsmvENKITLRIKDKEK--EIIDYPGNDRLRQKLIENhlHSRSL 114
Cdd:cd00882   1 VVVGRGGVGKSSLLNALLGGEvgevsDVPGTTRD------PDVYVKELDKGKVklVLVDTPGLDEFGGLGREE--LARLL 72

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17563220 115 LR----IVFVVDSaafSKNARDVAELFYTVALENVDKVPILIACHKQDLSLAKTEKVIRNSLEKEIGLINK 181
Cdd:cd00882  73 LRgadlILLVVDS---TDRESEEDAKLLILRRLRKEGIPIILVGNKIDLLEEREVEELLRLEELAKILGVP 140
SAR smart00178
Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene ...
 40-194 2.32e-06

Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene required for transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 197556 [Multi-domain]  Cd Length: 184  Bit Score: 46.47  E-value: 2.32e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220     40 RVLFVGLMDCGKTTIFTQLSQKEaeyptttktytsMVENKITLRIKDKEKEIidypGNDRLRQKLIENHLHSRSLLR--- 116
Cdd:smart00178  19 KILFLGLDNAGKTTLLHMLKNDR------------LAQHQPTQHPTSEELAI----GNIKFTTFDLGGHQQARRLWKdyf 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220    117 -----IVFVVDSAAFSKNARDVAELFYTVALENVDKVPILIACHKQDLSLAKTEKVIRNSLekeiGLINKSRAAALIGTD 191
Cdd:smart00178  83 pevngIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAASEDELRYAL----GLTNTTTGKGKVGVR 158


                   ...
gi 17563220    192 GSE 194
Cdd:smart00178 159 PVE 161
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
 40-172 6.76e-06

ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular transport. Activator 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. Contains ATP/GTP-binding motif (P-loop).


Pssm-ID: 128474 [Multi-domain]  Cd Length: 175  Bit Score: 45.30  E-value: 6.76e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220     40 RVLFVGLMDCGKTTIFTQLsqKEAEYPTTTKTYTSMVEnkiTLRIKDKEKEIIDYPGNDRLRQklIENHLHsRSLLRIVF 119
Cdd:smart00177  15 RILMVGLDAAGKTTILYKL--KLGESVTTIPTIGFNVE---TVTYKNISFTVWDVGGQDKIRP--LWRHYY-TNTQGLIF 86

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 17563220    120 VVDSAAFSKNARDVAELFYTVALENVDKVPILIACHKQDLSLAKTEKVIRNSL 172
Cdd:smart00177  87 VVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKL 139
Arl1 cd04151
ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi ...
 40-206 8.83e-06

ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi complex, where it is believed to recruit effector proteins to the trans-Golgi network. Like most members of the Arf family, Arl1 is myristoylated at its N-terminal helix and mutation of the myristoylation site disrupts Golgi targeting. In humans, the Golgi-localized proteins golgin-97 and golgin-245 have been identified as Arl1 effectors. Golgins are large coiled-coil proteins found in the Golgi, and these golgins contain a C-terminal GRIP domain, which is the site of Arl1 binding. Additional Arl1 effectors include the GARP (Golgi-associated retrograde protein)/VFT (Vps53) vesicle-tethering complex and Arfaptin 2. Arl1 is not required for exocytosis, but appears necessary for trafficking from the endosomes to the Golgi. In Drosophila zygotes, mutation of Arl1 is lethal, and in the host-bloodstream form of Trypanosoma brucei, Arl1 is essential for viability.


Pssm-ID: 206718 [Multi-domain]  Cd Length: 158  Bit Score: 44.32  E-value: 8.83e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220  40 RVLFVGLMDCGKTTIFTQLsqKEAEYPTTTKTYTSMVEnkiTLRIKDKEKEIIDYPGNDRLRqklienhLHSRSLLR--- 116
Cdd:cd04151   1 RILILGLDGAGKTTILYRL--QVGEVVTTIPTIGFNVE---TVTYKNLKFQVWDLGGQTSIR-------PYWRCYYSntd 68

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220 117 -IVFVVDSAAFSKNARDVAELFYTVALENVDKVPILIACHKQDLSLAKTEKVIRNSLekeiGLIN-KSRAAALIGTdgse 194
Cdd:cd04151  69 aIIYVVDSTDRDRLGISKSELHAMLEEEELKDAVLLVFANKQDMPGALSEAEVAEKL----GLSElKDRTWQIFKT---- 140

                       170
                ....*....|..
gi 17563220 195 ekrSTLTDTGID 206
Cdd:cd04151 141 ---SATKGEGLD 149
PTZ00133 PTZ00133
ADP-ribosylation factor; Provisional
 40-172 3.01e-05

ADP-ribosylation factor; Provisional


Pssm-ID: 173423  Cd Length: 182  Bit Score: 43.30  E-value: 3.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220   40 RVLFVGLMDCGKTTIFTQLsqKEAEYPTTTKTYTSMVEnkiTLRIKDKEKEIIDYPGNDRLRQklIENHLHSRSlLRIVF 119
Cdd:PTZ00133  19 RILMVGLDAAGKTTILYKL--KLGEVVTTIPTIGFNVE---TVEYKNLKFTMWDVGGQDKLRP--LWRHYYQNT-NGLIF 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 17563220  120 VVDSAAFSKNARDVAELFYTVALENVDKVPILIACHKQDLSLAK-----TEKVIRNSL 172
Cdd:PTZ00133  91 VVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMsttevTEKLGLHSV 148
Arl2l1_Arl13_like cd04161
Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ...
 41-184 4.31e-05

Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene.


Pssm-ID: 133361 [Multi-domain]  Cd Length: 167  Bit Score: 42.77  E-value: 4.31e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220  41 VLFVGLMDCGKTTIFTQLsQKEAEypttTKTYTSMVENKITLRIKDKEKEIIDYPGNDRLRQKLIeNHLHSRSllRIVFV 120
Cdd:cd04161   2 LLTVGLDNAGKTTLVSAL-QGEIP----KKVAPTVGFTPTKLRLDKYEVCIFDLGGGANFRGIWV-NYYAEAH--GLVFV 73

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17563220 121 VDSAAfSKNARDVAELFYTVALE-NVDKVPILIACHKQDLSLAKTE-KVIRN-SLEKeigLINKSRA 184
Cdd:cd04161  74 VDSSD-DDRVQEVKEILRELLQHpRVSGKPILVLANKQDKKNALLGaDVIEYlSLEK---LVNENKS 136
Arf6 cd04149
ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins ...
 40-173 6.20e-05

ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins localize to the plasma membrane, where they perform a wide variety of functions. In its active, GTP-bound form, Arf6 is involved in cell spreading, Rac-induced formation of plasma membrane ruffles, cell migration, wound healing, and Fc-mediated phagocytosis. Arf6 appears to change the actin structure at the plasma membrane by activating Rac, a Rho family protein involved in membrane ruffling. Arf6 is required for and enhances Rac formation of ruffles. Arf6 can regulate dendritic branching in hippocampal neurons, and in yeast it localizes to the growing bud, where it plays a role in polarized growth and bud site selection. In leukocytes, Arf6 is required for chemokine-stimulated migration across endothelial cells. Arf6 also plays a role in down-regulation of beta2-adrenergic receptors and luteinizing hormone receptors by facilitating the release of sequestered arrestin to allow endocytosis. Arf6 is believed to function at multiple sites on the plasma membrane through interaction with a specific set of GEFs, GAPs, and effectors. Arf6 has been implicated in breast cancer and melanoma cell invasion, and in actin remodelling at the invasion site of Chlamydia infection.


Pssm-ID: 206716  Cd Length: 168  Bit Score: 42.07  E-value: 6.20e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220  40 RVLFVGLMDCGKTTIFTQLsqKEAEYPTTTKTYTSMVEnkiTLRIKDKEKEIIDYPGNDRLRQklIENHLHSRSLlRIVF 119
Cdd:cd04149  11 RILMLGLDAAGKTTILYKL--KLGQSVTTIPTVGFNVE---TVTYKNVKFNVWDVGGQDKIRP--LWRHYYTGTQ-GLIF 82

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 17563220 120 VVDSAAFSKNARDVAELFYTVALENVDKVPILIACHKQDLSLAKTEKVIRNSLE 173
Cdd:cd04149  83 VVDSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPDAMKPHEIQEKLG 136
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
 40-172 9.34e-05

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 41.88  E-value: 9.34e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220   40 RVLFVGLMDCGKTTIFTQLsqKEAEYPTTTKTYTSMVEnkiTLRIKDKEKEIIDYPGNDRLRqKLIENHLHSRSLLriVF 119
Cdd:PLN00223  19 RILMVGLDAAGKTTILYKL--KLGEIVTTIPTIGFNVE---TVEYKNISFTVWDVGGQDKIR-PLWRHYFQNTQGL--IF 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 17563220  120 VVDSAAFSK--NARDvaELFYTVALENVDKVPILIACHKQDLSLAKTEKVIRNSL 172
Cdd:PLN00223  91 VVDSNDRDRvvEARD--ELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKL 143
FeoB COG0370
Fe2+ transporter FeoB [Inorganic ion transport and metabolism];
40-96 2.46e-04

Fe2+ transporter FeoB [Inorganic ion transport and metabolism];


Pssm-ID: 440139 [Multi-domain]  Cd Length: 662  Bit Score: 41.64  E-value: 2.46e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17563220  40 RVLFVGLMDCGKTTIF---TQLSQKEAEYPTTTktytsmVENKI-TLRIKDKEKEIIDYPG 96
Cdd:COG0370   5 TIALVGNPNVGKTTLFnalTGSRQKVGNWPGVT------VEKKEgKFKLKGKEIELVDLPG 59
FeoB_N pfam02421
Ferrous iron transport protein B; Escherichia coli has an iron(II) transport system (feo) ...
 40-96 3.29e-04

Ferrous iron transport protein B; Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.


Pssm-ID: 460552 [Multi-domain]  Cd Length: 156  Bit Score: 39.74  E-value: 3.29e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17563220    40 RVLFVGLMDCGKTTIFTQLS---QKEAEYPTTTktytsmVENKI-TLRIKDKEKEIIDYPG 96
Cdd:pfam02421   2 TIALVGNPNVGKTTLFNALTganQHVGNWPGVT------VEKKEgKFKYKGYEIEIVDLPG 56
ARD1 cd04158
(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein ...
 40-162 3.92e-04

(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein 1) is an unusual member of the Arf family. In addition to the C-terminal Arf domain, ARD1 has an additional 46-kDa N-terminal domain that contains a RING finger domain, two predicted B-Boxes, and a coiled-coil protein interaction motif. This domain belongs to the TRIM (tripartite motif) or RBCC (RING, B-Box, coiled-coil) family. Like most Arfs, the ARD1 Arf domain lacks detectable GTPase activity. However, unlike most Arfs, the full-length ARD1 protein has significant GTPase activity due to the GAP (GTPase-activating protein) activity exhibited by the 46-kDa N-terminal domain. The GAP domain of ARD1 is specific for its own Arf domain and does not bind other Arfs. The rate of GDP dissociation from the ARD1 Arf domain is slowed by the adjacent 15 amino acids, which act as a GDI (GDP-dissociation inhibitor) domain. ARD1 is ubiquitously expressed in cells and localizes to the Golgi and to the lysosomal membrane. Two Tyr-based motifs in the Arf domain are responsible for Golgi localization, while the GAP domain controls lysosomal localization.


Pssm-ID: 206723 [Multi-domain]  Cd Length: 169  Bit Score: 40.01  E-value: 3.92e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220  40 RVLFVGLMDCGKTTIFTQLSQKEAEYPTTTKTYtsmveNKITLRIKDKEKEIIDYPGNDRLRQKLIENHLHSRSllrIVF 119
Cdd:cd04158   1 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGF-----NVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQA---VVF 72

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 17563220 120 VVDSAAFSKNARDVAELFYTVALENVDKVPILIACHKQDLSLA 162
Cdd:cd04158  73 VIDSSHRDRVSEAHSELAKLLTEKELRDALLLIFANKQDVAGA 115
Arl6 cd04157
Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small ...
 41-175 4.41e-04

Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases. Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development. Arl6 is also believed to have a role in cilia or flagella function. Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p. Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.


Pssm-ID: 206722 [Multi-domain]  Cd Length: 162  Bit Score: 39.72  E-value: 4.41e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220  41 VLFVGLMDCGKTTIFTQLSQKEAEYPTTTKTYTSMVEN--KITLRIKdkekeIIDYPGNDRLRQkLIENHLHSRSllRIV 118
Cdd:cd04157   2 ILVLGLDNSGKTTIINQLKPSNAQSQNIVPTVGFNVESfkKGNLSFT-----AFDMSGQGKYRG-LWEHYYKNIQ--GII 73

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17563220 119 FVVDSAafsknardvAELFYTVALENVD-----------KVPILIACHKQDLSLAKTEKVIRNSLEKE 175
Cdd:cd04157  74 FVIDSS---------DRLRMVVAKDELElllnhpdikhrRIPILFYANKMDLPDALTAVKITQLLCLE 132
FeoB cd01879
Ferrous iron transport protein B (FeoB) family; Ferrous iron transport protein B (FeoB) ...
 43-96 4.79e-04

Ferrous iron transport protein B (FeoB) family; Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.


Pssm-ID: 206667 [Multi-domain]  Cd Length: 159  Bit Score: 39.36  E-value: 4.79e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 17563220  43 FVGLMDCGKTTIFTQLS---QKEAEYPTTTktytsmVENKI-TLRIKDKEKEIIDYPG 96
Cdd:cd01879   2 LVGNPNVGKTTLFNALTgarQKVGNWPGVT------VEKKEgEFKLGGKEIEIVDLPG 53
Obg_like cd01881
Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1; ...
 43-206 5.00e-04

Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1; The Obg-like subfamily consists of five well-delimited, ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210, and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and Ygr210) are characterized by a distinct glycine-rich motif immediately following the Walker B motif (G3 box). Obg/CgtA is an essential gene that is involved in the initiation of sporulation and DNA replication in the bacteria Caulobacter and Bacillus, but its exact molecular role is unknown. Furthermore, several OBG family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. Nog1 is a nucleolar protein that might function in ribosome assembly. The DRG and Nog1 subfamilies are ubiquitous in archaea and eukaryotes, the Ygr210 subfamily is present in archaea and fungi, and the Obg and YyaF/YchF subfamilies are ubiquitous in bacteria and eukaryotes. The Obg/Nog1 and DRG subfamilies appear to form one major branch of the Obg family and the Ygr210 and YchF subfamilies form another branch. No GEFs, GAPs, or GDIs for Obg have been identified.


Pssm-ID: 206668 [Multi-domain]  Cd Length: 167  Bit Score: 39.68  E-value: 5.00e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220  43 FVGLMDCGKTTIFTQLSQ---KEAEYPTTTKT-YTSMVENKITLRIkdkekEIIDYPG------NDRLRQKLIENHLHSR 112
Cdd:cd01881   2 LVGLPNVGKSTLLSALTSakvEIASYPFTTLEpNVGVFEFGDGVDI-----QIIDLPGlldgasEGRGLGEQILAHLYRS 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220 113 SLlrIVFVVDsaAFSKNARDVAE----LFYTVAL--ENVDKVPILIACHKQDlslakteKVIRNSLeKEIGLINKSRAAA 186
Cdd:cd01881  77 DL--ILHVID--ASEDCVGDPLEdqktLNEEVSGsfLFLKNKPEMIVANKID-------MASENNL-KRLKLDKLKRGIP 144

                       170       180
                ....*....|....*....|
gi 17563220 187 LIGTdgseekrSTLTDTGID 206
Cdd:cd01881 145 VVPT-------SALTRLGLD 157
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 40-156 5.70e-04

50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotide.


Pssm-ID: 460387 [Multi-domain]  Cd Length: 113  Bit Score: 38.37  E-value: 5.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220    40 RVLFVGLMDCGKTTIFTQLSQKEAE---YPTTTKTytsmvENKITLRIKDKEKEIIDYPG---NDRLRQKLIENHLHSRS 113
Cdd:pfam01926   1 RVALVGRPNVGKSTLINALTGAKAIvsdYPGTTRD-----PNEGRLELKGKQIILVDTPGlieGASEGEGLGRAFLAIIE 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 17563220   114 LLRIVFVVDSAA-FSKNARDVAELfytvaLENVDKvPILIACHK 156
Cdd:pfam01926  76 ADLILFVVDSEEgITPLDEELLEL-----LRENKK-PIILVLNK 113
ARLTS1 cd04156
Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), ...
 40-172 1.02e-03

Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling. ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers. ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL). ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter. In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity. In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation. The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in high-risk familial breast cancer.


Pssm-ID: 133356 [Multi-domain]  Cd Length: 160  Bit Score: 38.55  E-value: 1.02e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220  40 RVLFVGLMDCGKTTIFTQLsqKEAEYPTTTKTYTSMVEnkiTLRIKDK-EKEIIDYPGNDRLRQKLIENHLHSRSLlriV 118
Cdd:cd04156   1 QVLLLGLDSAGKSTLLYKL--KHAELVTTIPTVGFNVE---MLQLEKHlSLTVWDVGGQEKMRTVWKCYLENTDGL---V 72

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 17563220 119 FVVDSAAFSKNARDVAELFYTVALENVDKVPILIACHKQDLSLAKTEKVIRNSL 172
Cdd:cd04156  73 YVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDLPGALTAEEITRRF 126
Arf1_5_like cd04150
ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like ...
 40-162 1.52e-03

ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and related proteins. Arfs1-5 are soluble proteins that are crucial for assembling coat proteins during vesicle formation. Each contains an N-terminal myristoylated amphipathic helix that is folded into the protein in the GDP-bound state. GDP/GTP exchange exposes the helix, which anchors to the membrane. Following GTP hydrolysis, the helix dissociates from the membrane and folds back into the protein. A general feature of Arf1-5 signaling may be the cooperation of two Arfs at the same site. Arfs1-5 are generally considered to be interchangeable in function and location, but some specific functions have been assigned. Arf1 localizes to the early/cis-Golgi, where it is activated by GBF1 and recruits the coat protein COPI. It also localizes to the trans-Golgi network (TGN), where it is activated by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA proteins. Humans, but not rodents and other lower eukaryotes, lack Arf2. Human Arf3 shares 96% sequence identity with Arf1 and is believed to generally function interchangeably with Arf1. Human Arf4 in the activated (GTP-bound) state has been shown to interact with the cytoplasmic domain of epidermal growth factor receptor (EGFR) and mediate the EGF-dependent activation of phospholipase D2 (PLD2), leading to activation of the activator protein 1 (AP-1) transcription factor. Arf4 has also been shown to recognize the C-terminal sorting signal of rhodopsin and regulate its incorporation into specialized post-Golgi rhodopsin transport carriers (RTCs). There is some evidence that Arf5 functions at the early-Golgi and the trans-Golgi to affect Golgi-associated alpha-adaptin homology Arf-binding proteins (GGAs).


Pssm-ID: 206717 [Multi-domain]  Cd Length: 159  Bit Score: 38.16  E-value: 1.52e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220  40 RVLFVGLMDCGKTTIFTQLsqKEAEYPTTTKTYTSMVEnkiTLRIKDKEKEIIDYPGNDRLRqkLIENHLHSRSlLRIVF 119
Cdd:cd04150   2 RILMVGLDAAGKTTILYKL--KLGEIVTTIPTIGFNVE---TVEYKNISFTVWDVGGQDKIR--PLWRHYFQNT-QGLIF 73

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 17563220 120 VVDSAAFSKNARDVAELFYTVALENVDKVPILIACHKQDLSLA 162
Cdd:cd04150  74 VVDSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNA 116
Arl2 cd04154
Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind ...
 40-173 8.33e-03

Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis.


Pssm-ID: 206720 [Multi-domain]  Cd Length: 173  Bit Score: 36.15  E-value: 8.33e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563220  40 RVLFVGLMDCGKTTIFTQLSQKEAE--YPTTTKTYTSMVENKITLrikdkekEIIDYPGNDRLRQkLIENHLHSRSLLri 117
Cdd:cd04154  16 RILMLGLDNAGKTTILKKFNGEDIStiSPTLGFNIKTLEYNGYKL-------NIWDVGGQKSLRS-YWRNYFESTDAL-- 85

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 17563220 118 VFVVDSAAFSKNARDVAELFYTVALENVDKVPILIACHKQDLSLAKTEKVIRNSLE 173
Cdd:cd04154  86 IWVVDSSDRARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALSPEEIREVLE 141
 
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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