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Conserved domains on  [gi|334329675|ref|XP_003341253|]
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signal recognition particle receptor subunit beta [Monodelphis domestica]

Protein Classification

signal recognition particle receptor subunit beta( domain architecture ID 10134869)

signal recognition particle (SRP) receptor subunit beta, together with SRP subunit alpha, forms the heterodimeric SRP receptor that binds SRP to regulate protein translocation across the ER membrane

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SR_beta cd04105
Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ...
 62-267 6.84e-93

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: 272.27  E-value: 6.84e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  62 RAVLLVGLCDSGKTLLFVRLLTGLYRNTQTSITDSSAMYRVNNDRGNSLTLIDLPGHESLRLQFLERFKASARAIVFVVD 141
Cdd:cd04105    1 PTVLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKGKKLTLVDVPGHEKLRDKLLEYLKASLKAIVFVVD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675 142 SATFQREVKDVAEFLYQVLIDSMVLKNAPSLLIACNKQDLTMAKSAKLIQQQLEKELNTLRVTRTAAPSTLE-SSGAVIA 220
Cdd:cd04105   81 SATFQKNIRDVAEFLYDILTDLEKIKNKIPILIACNKQDLFTAKPAKKIKELLEKEINTLRESRSKSLESLDgDDGSKDT 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 334329675 221 QLGKKGKEFEFSQLPMKVEFLECSAKGASGddgsaDIQDFEKWLARI 267
Cdd:cd04105  161 LGDKGGKDFEFDQLEGEVDFVEGSVKKSKG-----GIDDIEEWIDEL 202
 
Name Accession Description Interval E-value
SR_beta cd04105
Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ...
 62-267 6.84e-93

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: 272.27  E-value: 6.84e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  62 RAVLLVGLCDSGKTLLFVRLLTGLYRNTQTSITDSSAMYRVNNDRGNSLTLIDLPGHESLRLQFLERFKASARAIVFVVD 141
Cdd:cd04105    1 PTVLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKGKKLTLVDVPGHEKLRDKLLEYLKASLKAIVFVVD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675 142 SATFQREVKDVAEFLYQVLIDSMVLKNAPSLLIACNKQDLTMAKSAKLIQQQLEKELNTLRVTRTAAPSTLE-SSGAVIA 220
Cdd:cd04105   81 SATFQKNIRDVAEFLYDILTDLEKIKNKIPILIACNKQDLFTAKPAKKIKELLEKEINTLRESRSKSLESLDgDDGSKDT 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 334329675 221 QLGKKGKEFEFSQLPMKVEFLECSAKGASGddgsaDIQDFEKWLARI 267
Cdd:cd04105  161 LGDKGGKDFEFDQLEGEVDFVEGSVKKSKG-----GIDDIEEWIDEL 202
SRPRB pfam09439
Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition ...
 59-238 3.77e-85

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: 251.98  E-value: 3.77e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675   59 SSRRAVLLVGLCDSGKTLLFVRLLTGLYRNTQTSItDSSAMYRVNNDRGNSLTLIDLPGHESLRLQFLER--FKASARAI 136
Cdd:pfam09439   1 SSQPAVIIAGLCDSGKTSLFTLLTTDSVRPTVTSQ-EPSAAYRYMLNKGNSFTLIDFPGHVKLRYKLLETlkDSSSLKGI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  137 VFVVDSATFQREVKDVAEFLYQVLIDSMVLKNAPSLLIACNKQDLTMAKSAKLIQQQLEKELNTLRVTRTAAPSTLESSG 216
Cdd:pfam09439  80 VFVVDSTIFPKEVTDTAEFLYDILSITELLKNGIDILIACNKQESFTARPPKKIKQALEKEINTIRERRSKALSGLDGSE 159

                         170       180
                  ....*....|....*....|..
gi 334329675  217 AVIAQLGKKGKEFEFSQLPMKV 238
Cdd:pfam09439 160 DLSAVLGKKGKGFKFDQLEANV 181
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
 51-216 1.37e-07

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 50.35  E-value: 1.37e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  51 WKFIRSRKSSRraVLLVGLCDSGKTLLFVRLLTGLYRNTQTSITDSSAMYRVNNdrgNSLTLIDLPGHESLRLQFLERFK 130
Cdd:PLN00223   9 FSRLFAKKEMR--ILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKN---ISFTVWDVGGQDKIRPLWRHYFQ 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675 131 aSARAIVFVVDSATFQReVKDVAEFLYQVLIDSMvLKNApSLLIACNKQDLTMAKSAKLIQQQLekELNTLRVTRTAAPS 210
Cdd:PLN00223  84 -NTQGLIFVVDSNDRDR-VVEARDELHRMLNEDE-LRDA-VLLVFANKQDLPNAMNAAEITDKL--GLHSLRQRHWYIQS 157


                 ....*.
gi 334329675 211 TLESSG 216
Cdd:PLN00223 158 TCATSG 163
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 61-208 3.99e-06

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: 45.83  E-value: 3.99e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675   61 RRAVLLVGLCDSGKTLLFVRLLTGLYRNTQT--SITDSSAMYRVNND-RGNSLTLIDLPGHESLRLQFLERFKASARAIv 137
Cdd:TIGR00231   1 DIKIVIVGHPNVGKSTLLNSLLGNKGSITEYypGTTRNYVTTVIEEDgKTYKFNLLDTAGQEDYDAIRRLYYPQVERSL- 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334329675  138 FVVDSATFQREVKDVAEFLYQVLIDSmVLKNAPSLLIAcNKQDLTMAKSAKLIQQQLEKeLNTLRVTRTAA 208
Cdd:TIGR00231  80 RVFDIVILVLDVEEILEKQTKEIIHH-ADSGVPIILVG-NKIDLKDADLKTHVASEFAK-LNGEPIIPLSA 147
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
 64-216 4.53e-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: 46.07  E-value: 4.53e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675    64 VLLVGLCDSGKTLLFVRLLTGLYRNTQTSITDSSAMYRVNNdrgNSLTLIDLPGHESLRLQFLERFKASaRAIVFVVDSA 143
Cdd:smart00177  16 ILMVGLDAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKN---ISFTVWDVGGQDKIRPLWRHYYTNT-QGLIFVVDSN 91

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334329675   144 TFQReVKDVAEFLYQVLIDSMvLKNApSLLIACNKQDLTMAKSAKLIQQQLekELNTLRVTRTAAPSTLESSG 216
Cdd:smart00177  92 DRDR-IDEAREELHRMLNEDE-LRDA-VILVFANKQDLPDAMKAAEITEKL--GLHSIRDRNWYIQPTCATSG 159
 
Name Accession Description Interval E-value
SR_beta cd04105
Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ...
 62-267 6.84e-93

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: 272.27  E-value: 6.84e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  62 RAVLLVGLCDSGKTLLFVRLLTGLYRNTQTSITDSSAMYRVNNDRGNSLTLIDLPGHESLRLQFLERFKASARAIVFVVD 141
Cdd:cd04105    1 PTVLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKGKKLTLVDVPGHEKLRDKLLEYLKASLKAIVFVVD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675 142 SATFQREVKDVAEFLYQVLIDSMVLKNAPSLLIACNKQDLTMAKSAKLIQQQLEKELNTLRVTRTAAPSTLE-SSGAVIA 220
Cdd:cd04105   81 SATFQKNIRDVAEFLYDILTDLEKIKNKIPILIACNKQDLFTAKPAKKIKELLEKEINTLRESRSKSLESLDgDDGSKDT 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 334329675 221 QLGKKGKEFEFSQLPMKVEFLECSAKGASGddgsaDIQDFEKWLARI 267
Cdd:cd04105  161 LGDKGGKDFEFDQLEGEVDFVEGSVKKSKG-----GIDDIEEWIDEL 202
SRPRB pfam09439
Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition ...
 59-238 3.77e-85

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: 251.98  E-value: 3.77e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675   59 SSRRAVLLVGLCDSGKTLLFVRLLTGLYRNTQTSItDSSAMYRVNNDRGNSLTLIDLPGHESLRLQFLER--FKASARAI 136
Cdd:pfam09439   1 SSQPAVIIAGLCDSGKTSLFTLLTTDSVRPTVTSQ-EPSAAYRYMLNKGNSFTLIDFPGHVKLRYKLLETlkDSSSLKGI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  137 VFVVDSATFQREVKDVAEFLYQVLIDSMVLKNAPSLLIACNKQDLTMAKSAKLIQQQLEKELNTLRVTRTAAPSTLESSG 216
Cdd:pfam09439  80 VFVVDSTIFPKEVTDTAEFLYDILSITELLKNGIDILIACNKQESFTARPPKKIKQALEKEINTIRERRSKALSGLDGSE 159

                         170       180
                  ....*....|....*....|..
gi 334329675  217 AVIAQLGKKGKEFEFSQLPMKV 238
Cdd:pfam09439 160 DLSAVLGKKGKGFKFDQLEANV 181
Arf_Arl cd00878
ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ...
 64-195 2.95e-13

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: 65.68  E-value: 2.95e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  64 VLLVGLCDSGKTLLFVRLLTGLYRNTQTSITDSSAMYRVNNdrgNSLTLIDLPGHESLRlQFLERFKASARAIVFVVDSA 143
Cdd:cd00878    2 ILMLGLDGAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKN---VKFTVWDVGGQDKIR-PLWKHYYENTDGLIFVVDSS 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 334329675 144 TFQR--EVKdvaEFLYQVLIDSMvLKNAPsLLIACNKQDLTMAKSAKLIQQQLE 195
Cdd:cd00878   78 DRERieEAK---NELHKLLNEEE-LKGAP-LLILANKQDLPGALTESELIELLG 126
Arfrp1 cd04160
Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a ...
 64-216 1.38e-11

Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development.


Pssm-ID: 206725 [Multi-domain]  Cd Length: 168  Bit Score: 61.20  E-value: 1.38e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  64 VLLVGLCDSGKTLLFVRLLTGLYRNT--------QTSITDSSAMYRVNNDRgnsLTLIDLPGHESLRlQFLERFKASARA 135
Cdd:cd04160    2 VLILGLDNAGKTTFLEQTKTKFSKNYkglnpskiTPTVGLNIGTIEVGKAR---LMFWDLGGQEELR-SLWDKYYAESHG 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675 136 IVFVVDSATFQR--EVKDVaeflYQVLIDSMVLKNAPsLLIACNKQDLTMAKSAKLIQQQLE--KELNTLRVTRTAAPST 211
Cdd:cd04160   78 VIYVIDSTDRERfnESKSA----FEKVINNEALEGVP-LLVLANKQDLPDALSVAEIKEVFDdcIALIGRRDCLVQPVSA 152


                 ....*
gi 334329675 212 LESSG 216
Cdd:cd04160  153 LEGEG 157
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
 64-205 2.06e-11

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


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 60.70  E-value: 2.06e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675   64 VLLVGLCDSGKTLLFVRLLTGLYRNTQTSI--TDSSAMYRvnndrGNSLTLIDLPGHESLRlQFLERFKASARAIVFVVD 141
Cdd:pfam00025   3 ILILGLDNAGKTTILYKLKLGEIVTTIPTIgfNVETVTYK-----NVKFTVWDVGGQESLR-PLWRNYFPNTDAVIFVVD 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 334329675  142 SATFQR--EVKDvaEFlyQVLIDSMVLKNAPsLLIACNKQDLTMAKSAKLIQQQLekELNTLRVTR 205
Cdd:pfam00025  77 SADRDRieEAKE--EL--HALLNEEELADAP-LLILANKQDLPGAMSEAEIRELL--GLHELKDRP 135
Arl5_Arl8 cd04153
Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like ...
 64-194 1.86e-10

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: 58.51  E-value: 1.86e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  64 VLLVGLCDSGKTLLFVRLLTGLYRNTQTSITDSSAMYRVNNDRgnsLTLIDLPGHESLRLQFLERFkASARAIVFVVDSA 143
Cdd:cd04153   18 VIIVGLDNAGKTTILYQFLLGEVVHTSPTIGSNVEEIVYKNIR---FLMWDIGGQESLRSSWNTYY-TNTDAVILVIDST 93

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 334329675 144 TFQReVKDVAEFLYQVLIDSMvLKNAPsLLIACNKQDLTMAKSAKLIQQQL 194
Cdd:cd04153   94 DRER-LPLTKEELYKMLAHED-LRKAV-LLVLANKQDLKGAMTPAEISESL 141
Arl3 cd04155
Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most ...
 53-202 1.93e-10

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: 58.18  E-value: 1.93e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  53 FIRSRKSSRRA---VLLVGLCDSGKTLLFVRLltGLYRNTQTSITDSSAMYRVNNDrGNSLTLIDLPGHESLRlQFLERF 129
Cdd:cd04155    4 ILRKLKPSSRQevrILLLGLDNAGKTTILKQL--ASEDISHITPTQGFNIKNVQAD-GFKLNVWDIGGQRKIR-PYWRNY 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334329675 130 KASARAIVFVVDSATfQREVKDVAEFLYQVLIDSMvLKNAPSLLIAcNKQDLTMAKSAKLIQQQLekELNTLR 202
Cdd:cd04155   80 FENTDVLIYVIDSAD-RKRFEEAGQELVELLEEEK-LAGVPVLVFA-NKQDLLTAAPAEEVAEAL--NLHDIR 147
ARLTS1 cd04156
Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), ...
 64-194 1.79e-08

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: 52.42  E-value: 1.79e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  64 VLLVGLCDSGKTLLFVRLLTGLYRNTQTSITDSSAMYRVNndRGNSLTLIDLPGHESLRlQFLERFKASARAIVFVVDSA 143
Cdd:cd04156    2 VLLLGLDSAGKSTLLYKLKHAELVTTIPTVGFNVEMLQLE--KHLSLTVWDVGGQEKMR-TVWKCYLENTDGLVYVVDSS 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 334329675 144 TFQREVKDVAEFlyQVLIDSMVLKNAPSLLIAcNKQDLTMAKSAKLIQQQL 194
Cdd:cd04156   79 DEARLDESQKEL--KHILKNEHIKGVPVVLLA-NKQDLPGALTAEEITRRF 126
Arl2l1_Arl13_like cd04161
Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ...
 64-218 2.70e-08

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: 52.01  E-value: 2.70e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  64 VLLVGLCDSGKTLLfVRLLTGLYrNTQTSITDSSAMYRVNNDRGNsLTLIDLPGHESLRLQFLERFkASARAIVFVVDSA 143
Cdd:cd04161    2 LLTVGLDNAGKTTL-VSALQGEI-PKKVAPTVGFTPTKLRLDKYE-VCIFDLGGGANFRGIWVNYY-AEAHGLVFVVDSS 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 334329675 144 TFQReVKDVAEFLYQVLIDSMVlKNAPSLLIAcNKQDLTMAKS-AKLIQQQLEKELntlrVTRTAAPSTLESSGAV 218
Cdd:cd04161   78 DDDR-VQEVKEILRELLQHPRV-SGKPILVLA-NKQDKKNALLgADVIEYLSLEKL----VNENKSLCHIEPCSAI 146
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
 51-216 1.37e-07

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 50.35  E-value: 1.37e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  51 WKFIRSRKSSRraVLLVGLCDSGKTLLFVRLLTGLYRNTQTSITDSSAMYRVNNdrgNSLTLIDLPGHESLRLQFLERFK 130
Cdd:PLN00223   9 FSRLFAKKEMR--ILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKN---ISFTVWDVGGQDKIRPLWRHYFQ 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675 131 aSARAIVFVVDSATFQReVKDVAEFLYQVLIDSMvLKNApSLLIACNKQDLTMAKSAKLIQQQLekELNTLRVTRTAAPS 210
Cdd:PLN00223  84 -NTQGLIFVVDSNDRDR-VVEARDELHRMLNEDE-LRDA-VLLVFANKQDLPNAMNAAEITDKL--GLHSLRQRHWYIQS 157


                 ....*.
gi 334329675 211 TLESSG 216
Cdd:PLN00223 158 TCATSG 163
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 64-168 2.75e-07

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: 48.00  E-value: 2.75e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675   64 VLLVGLCDSGKTLLFvRLLTGlyRNTQTS----ITDSSAMYRVNNDrGNSLTLIDLPGH---ESLRLQFLERFKASARA- 135
Cdd:pfam01926   2 VALVGRPNVGKSTLI-NALTG--AKAIVSdypgTTRDPNEGRLELK-GKQIILVDTPGLiegASEGEGLGRAFLAIIEAd 77

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 334329675  136 -IVFVVDS-ATFQREVKDVAEFLYQVLIDSMVLKN 168
Cdd:pfam01926  78 lILFVVDSeEGITPLDEELLELLRENKKPIILVLN 112
Arl9_Arfrp2_like cd04162
Arf-like 9 (Arl9)/Arfrp2-like GTPase; Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first ...
 64-222 4.38e-07

Arf-like 9 (Arl9)/Arfrp2-like GTPase; Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first identified as part of the Human Cancer Genome Project. It maps to chromosome 4q12 and is sometimes referred to as Arfrp2 (Arf-related protein 2). This is a novel subfamily identified in human cancers that is uncharacterized to date.


Pssm-ID: 133362 [Multi-domain]  Cd Length: 164  Bit Score: 48.60  E-value: 4.38e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  64 VLLVGLCDSGKTLlFVRLLTGLYRNTQTSITDSSAMYRVNNdRGNSLTLIDLPGHESLRlQFLERFKASARAIVFVVDSA 143
Cdd:cd04162    2 ILVLGLDGAGKTS-LLHSLSSERSLESVVPTTGFNSVAIPT-QDAIMELLEIGGSQNLR-KYWKRYLSGSQGLIFVVDSA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675 144 TFQReVKDVAEFLYQVLIDSMVLknapSLLIACNKQDLTMAKSAKLIQQQLEKE---------LNTLRVTRTAAPSTLES 214
Cdd:cd04162   79 DSER-LPLARQELHQLLQHPPDL----PLVVLANKQDLPAARSVQEIHKELELEpiargrrwiLQGTSLDDDGSPSRMEA 153


                 ....*...
gi 334329675 215 SGAVIAQL 222
Cdd:cd04162  154 VKDLLSQL 161
Sar1 cd00879
Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII ...
 64-199 5.25e-07

Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation.


Pssm-ID: 206645 [Multi-domain]  Cd Length: 191  Bit Score: 48.81  E-value: 5.25e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  64 VLLVGLCDSGKTLLFVRLLTG---LYRNTQTSITDSSAMYRVNndrgnsLTLIDLPGHESLRlQFLERFKASARAIVFVV 140
Cdd:cd00879   22 IVFLGLDNAGKTTLLHMLKDDrlaQHVPTLHPTSEELTIGNVK------FTTFDLGGHEQAR-RVWKDYFPEVDGIVFLV 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334329675 141 DSATFQR--EVKDVAEFLyqvLIDSMvLKNAPsLLIACNKQDLTMAKSakliQQQLEKELN 199
Cdd:cd00879   95 DAADPERfqESKEELDSL---LNDEE-LANVP-ILILGNKIDKPGAVS----EEELREALG 146
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 65-181 7.29e-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: 47.84  E-value: 7.29e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  65 LLVGLCDSGKTLLFVRLLTGLYRNT--QTSITDSSAMYRVNNDRGN-SLTLIDLPGH-ESLRLQFLERFKASAR---AIV 137
Cdd:cd00882    1 VVVGRGGVGKSSLLNALLGGEVGEVsdVPGTTRDPDVYVKELDKGKvKLVLVDTPGLdEFGGLGREELARLLLRgadLIL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 334329675 138 FVVDSAtfQREVKDVAEFLYqvlIDSMVLKNAPSLLIaCNKQDL 181
Cdd:cd00882   81 LVVDST--DRESEEDAKLLI---LRRLRKEGIPIILV-GNKIDL 118
Arl10_like cd04159
Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from ...
 66-194 2.17e-06

Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.


Pssm-ID: 206724 [Multi-domain]  Cd Length: 159  Bit Score: 46.54  E-value: 2.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  66 LVGLCDSGKTLlFVRLLTGLYRNTQTSITDSSAMYRVNndRGN-SLTLIDLPGHESLRLQFlERFKASARAIVFVVDSAT 144
Cdd:cd04159    4 LVGLQNSGKTT-LVNVIASGQFSEDTIPTVGFNMRKVT--KGNvTIKVWDLGGQPRFRSMW-ERYCRGVNAIVYVVDAAD 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 334329675 145 FQRevKDVAEFLYQVLIDSMVLKNAPsLLIACNKQDLTMAKSAKLIQQQL 194
Cdd:cd04159   80 REK--LEVAKNELHDLLEKPSLEGIP-LLVLGNKNDLPGALSVDELIEQM 126
Arl2 cd04154
Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind ...
 52-195 3.68e-06

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: 46.16  E-value: 3.68e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  52 KFIRSRKSSRRA--VLLVGLCDSGKTLLFVRLLtglyrNTQTSITDSSAMYRVNN--DRGNSLTLIDLPGHESLRLQFLE 127
Cdd:cd04154    3 TILRKTKQKEREmrILMLGLDNAGKTTILKKFN-----GEDISTISPTLGFNIKTleYNGYKLNIWDVGGQKSLRSYWRN 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 334329675 128 RFKaSARAIVFVVDSATFQReVKDVAEFLYQVLIDSMVLKnaPSLLIACNKQDLTMAKSAKLIQQQLE 195
Cdd:cd04154   78 YFE-STDALIWVVDSSDRAR-LEDCKRELQKLLVEERLAG--ATLLIFANKQDLPGALSPEEIREVLE 141
Arf1_5_like cd04150
ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like ...
 64-202 3.84e-06

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: 45.86  E-value: 3.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  64 VLLVGLCDSGKTLLFVRLLTGLYRNTQTSITDSSAMYRVNNDrgnSLTLIDLPGHESLRLQFLERFKaSARAIVFVVDSA 143
Cdd:cd04150    3 ILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNI---SFTVWDVGGQDKIRPLWRHYFQ-NTQGLIFVVDSN 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 334329675 144 TFQReVKDVAEFLYQVLIDSMvLKNApSLLIACNKQDLTMAKSAKLIQQQLekELNTLR 202
Cdd:cd04150   79 DRER-IGEAREELQRMLNEDE-LRDA-VLLVFANKQDLPNAMSAAEVTDKL--GLHSLR 132
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 61-208 3.99e-06

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: 45.83  E-value: 3.99e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675   61 RRAVLLVGLCDSGKTLLFVRLLTGLYRNTQT--SITDSSAMYRVNND-RGNSLTLIDLPGHESLRLQFLERFKASARAIv 137
Cdd:TIGR00231   1 DIKIVIVGHPNVGKSTLLNSLLGNKGSITEYypGTTRNYVTTVIEEDgKTYKFNLLDTAGQEDYDAIRRLYYPQVERSL- 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334329675  138 FVVDSATFQREVKDVAEFLYQVLIDSmVLKNAPSLLIAcNKQDLTMAKSAKLIQQQLEKeLNTLRVTRTAA 208
Cdd:TIGR00231  80 RVFDIVILVLDVEEILEKQTKEIIHH-ADSGVPIILVG-NKIDLKDADLKTHVASEFAK-LNGEPIIPLSA 147
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
 64-216 4.53e-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: 46.07  E-value: 4.53e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675    64 VLLVGLCDSGKTLLFVRLLTGLYRNTQTSITDSSAMYRVNNdrgNSLTLIDLPGHESLRLQFLERFKASaRAIVFVVDSA 143
Cdd:smart00177  16 ILMVGLDAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKN---ISFTVWDVGGQDKIRPLWRHYYTNT-QGLIFVVDSN 91

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334329675   144 TFQReVKDVAEFLYQVLIDSMvLKNApSLLIACNKQDLTMAKSAKLIQQQLekELNTLRVTRTAAPSTLESSG 216
Cdd:smart00177  92 DRDR-IDEAREELHRMLNEDE-LRDA-VILVFANKQDLPDAMKAAEITEKL--GLHSIRDRNWYIQPTCATSG 159
Arl6 cd04157
Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small ...
 64-202 7.36e-06

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: 45.11  E-value: 7.36e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  64 VLLVGLCDSGKTLLFVRLLTglyRNTQTSITDSSAMYRVNN-DRGN-SLTLIDLPGHESLRlQFLERFKASARAIVFVVD 141
Cdd:cd04157    2 ILVLGLDNSGKTTIINQLKP---SNAQSQNIVPTVGFNVESfKKGNlSFTAFDMSGQGKYR-GLWEHYYKNIQGIIFVID 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334329675 142 SATFQRE--VKDVAEFLYQVliDSMVLKNAPSLLIAcNKQDLTMAKSAKLIQQQLekELNTLR 202
Cdd:cd04157   78 SSDRLRMvvAKDELELLLNH--PDIKHRRIPILFYA-NKMDLPDALTAVKITQLL--CLENIK 135
PTZ00133 PTZ00133
ADP-ribosylation factor; Provisional
 51-202 8.32e-06

ADP-ribosylation factor; Provisional


Pssm-ID: 173423  Cd Length: 182  Bit Score: 45.22  E-value: 8.32e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  51 WKFIRSRKSSRraVLLVGLCDSGKTLLFVRLLTGLYRNTQTSITDSSAMYRVNNdrgNSLTLIDLPGHESLRlQFLERFK 130
Cdd:PTZ00133   9 FKSLFGKKEVR--ILMVGLDAAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKN---LKFTMWDVGGQDKLR-PLWRHYY 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334329675 131 ASARAIVFVVDSATFQReVKDVAEFLYQVLIDSMvLKNApSLLIACNKQDLTMAKSAKLIQQQLekELNTLR 202
Cdd:PTZ00133  83 QNTNGLIFVVDSNDRER-IGDAREELERMLSEDE-LRDA-VLLVFANKQDLPNAMSTTEVTEKL--GLHSVR 149
Arl1 cd04151
ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi ...
 64-195 9.80e-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: 44.71  E-value: 9.80e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  64 VLLVGLCDSGKTLLFVRLLTGLYRNTQTSITDSSAMYRVNNdrgNSLTLIDLPGHESLRLqFLERFKASARAIVFVVDSA 143
Cdd:cd04151    2 ILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKN---LKFQVWDLGGQTSIRP-YWRCYYSNTDAIIYVVDST 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 334329675 144 TFQREVKDVAEFLYqvLIDSMVLKNAPsLLIACNKQDLTMAKSAKLIQQQLE 195
Cdd:cd04151   78 DRDRLGISKSELHA--MLEEEELKDAV-LLVFANKQDMPGALSEAEVAEKLG 126
Arl4_Arl7 cd04152
Arf-like 4 (Arl4) and 7 (Arl7) GTPases; Arl4 (Arf-like 4) is highly expressed in testicular ...
 64-194 4.55e-05

Arf-like 4 (Arl4) and 7 (Arl7) GTPases; Arl4 (Arf-like 4) is highly expressed in testicular germ cells, and is found in the nucleus and nucleolus. In mice, Arl4 is developmentally expressed during embryogenesis, and a role in somite formation and central nervous system differentiation has been proposed. Arl7 has been identified as the only Arf/Arl protein to be induced by agonists of liver X-receptor and retinoid X-receptor and by cholesterol loading in human macrophages. Arl7 is proposed to play a role in transport between a perinuclear compartment and the plasma membrane, apparently linked to the ABCA1-mediated cholesterol secretion pathway. 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: 206719 [Multi-domain]  Cd Length: 183  Bit Score: 43.25  E-value: 4.55e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  64 VLLVGLCDSGKTLLFVRLLTGLYRNTQTSITDSSAMYRVNNDRGNSLTLI--DLPGHESLRlQFLERFKASARAIVFVVD 141
Cdd:cd04152    6 IVMLGLDSAGKTTVLYRLKFNEFVNTVPTKGFNTEKIKVSLGNAKGVTFHfwDVGGQEKLR-PLWKSYTRCTDGIVFVVD 84

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 334329675 142 SATFQR------EVKDVAEFLYQvlidsmvlKNAPSLLIAcNKQDLTMAKSAKLIQQQL 194
Cdd:cd04152   85 SVDVERmeeaktELHKITKFSEN--------QGVPVLVLA-NKQDLPNALPVSEVEKLL 134
Era_like cd00880
E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ...
 66-208 4.80e-05

E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngB), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family.


Pssm-ID: 206646 [Multi-domain]  Cd Length: 161  Bit Score: 42.62  E-value: 4.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  66 LVGLCDSGKTLLFVRLLtglyrNTQTSITdSSAM--------YRVNNDRGNSLTLIDLPG-HE---SLRLQFLERFKASA 133
Cdd:cd00880    2 IFGRPNVGKSSLLNALL-----GQNVGIV-SPIPgttrdpvrKEWELLPLGPVVLIDTPGlDEeggLGRERVEEARQVAD 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 334329675 134 RA--IVFVVDSatfqrevkDVAEFLYQVLIDSMVLKNAPSLLIAcNKQDL-TMAKSAKLIQQQLEKELNTLRVTRTAA 208
Cdd:cd00880   76 RAdlVLLVVDS--------DLTPVEEEAKLGLLRERGKPVLLVL-NKIDLvPESEEEELLRERKLELLPDLPVIAVSA 144
Arf6 cd04149
ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins ...
 64-198 1.09e-03

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: 38.99  E-value: 1.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  64 VLLVGLCDSGKTLLFVRLLTGlyrntQTSITDSSAMYRVNN--DRGNSLTLIDLPGHESLRLQFLERFKASaRAIVFVVD 141
Cdd:cd04149   12 ILMLGLDAAGKTTILYKLKLG-----QSVTTIPTVGFNVETvtYKNVKFNVWDVGGQDKIRPLWRHYYTGT-QGLIFVVD 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 334329675 142 SATFQReVKDVAEFLYQVLIDSMvLKNApSLLIACNKQDLTMAKSAKLIQQQLEKEL 198
Cdd:cd04149   86 SADRDR-IDEARQELHRIINDRE-MRDA-LLLVFANKQDLPDAMKPHEIQEKLGLTR 139
SAR smart00178
Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene ...
 64-186 1.84e-03

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: 38.38  E-value: 1.84e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675    64 VLLVGLCDSGKTLLFVRLLTGLYRNTQTSITDSSAMYRVNNDRgnsLTLIDLPGHESLRLQFLERFkASARAIVFVVDSA 143
Cdd:smart00178  20 ILFLGLDNAGKTTLLHMLKNDRLAQHQPTQHPTSEELAIGNIK---FTTFDLGGHQQARRLWKDYF-PEVNGIVYLVDAY 95

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 334329675   144 TFQREVKDVAEFlyQVLIDSMVLKNAPsLLIACNKQDLTMAKS 186
Cdd:smart00178  96 DKERFAESKREL--DALLSDEELATVP-FLILGNKIDAPYAAS 135
Roc pfam08477
Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial ...
 64-180 2.57e-03

Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial Rho proteins (Miro-1, and Miro-2) and atypical Rho GTPases. Full-length proteins have a unique domain organization, with tandem GTP-binding domains and two EF hand domains (pfam00036) that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis.


Pssm-ID: 462490 [Multi-domain]  Cd Length: 114  Bit Score: 36.72  E-value: 2.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675   64 VLLVGLCDSGKTLLFVRLLTGLYRNTQTS---ITDSSAMYRVNNDRGNSLTLI--DLPGHeslrlqflERFKA------- 131
Cdd:pfam08477   2 VVLLGDSGVGKTSLLKRFVDDTFDPKYKStigVDFKTKTVLENDDNGKKIKLNiwDTAGQ--------ERFRSlhpfyyr 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 334329675  132 SARAIVFVVDSATFQ------REVKDVAeflyqvlidsmvlKNAPsLLIACNKQD 180
Cdd:pfam08477  74 GAAAALLVYDSRTFSnlkywlRELKKYA-------------GNSP-VILVGNKID 114
FeoB cd01879
Ferrous iron transport protein B (FeoB) family; Ferrous iron transport protein B (FeoB) ...
 66-147 4.90e-03

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: 36.67  E-value: 4.90e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334329675  66 LVGLCDSGKTLLFVRLlTGLYRNTQ----TSITDSSAMYRVNndrGNSLTLIDLPGHESLR---------LQFLErfKAS 132
Cdd:cd01879    2 LVGNPNVGKTTLFNAL-TGARQKVGnwpgVTVEKKEGEFKLG---GKEIEIVDLPGTYSLTpysedekvaRDFLL--GEE 75

                         90
                 ....*....|....*
gi 334329675 133 ARAIVFVVDSATFQR 147
Cdd:cd01879   76 PDLIVNVVDATNLER 90
 
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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