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Conserved domains on  [gi|564397942|ref|XP_006256512|]
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GTP-binding protein SAR1a isoform X1 [Rattus norvegicus]

Protein Classification

GTP-binding protein Sar1( domain architecture ID 10096332)

GTP-binding protein Sar1 is a small GTPase component of COPII vesicle coats involved in export of cargo from the endoplasmic reticulum (ER), and functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER

CATH:  3.40.50.300
Gene Ontology:  GO:0003924|GO:0005525
PubMed:  1898771|12429613|11995995|2122258
SCOP:  4004043

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
Sar1 cd00879
Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII ...
 3-197 1.14e-131

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: 366.99  E-value: 1.14e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942   3 FIFEWIYNgfssVLQFLGLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQA 82
Cdd:cd00879    1 FIFDWFYN----VLSSLGLYKKEAKIVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTIGNVKFTTFDLGGHEQA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  83 RRVWKNYLPAINGIVFLVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYGQTTGKGN 162
Cdd:cd00879   77 RRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANVPILILGNKIDKPGAVSEEELREALGLYGTTTGKGG 156

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 564397942 163 VTLKELNARPMEVFMCSVLKRQGYGEGFRWLSQYI 197
Cdd:cd00879  157 VSLKVSNIRPVEVFMCSVVKRQGYGEGFRWLSQYL 191
 
Name Accession Description Interval E-value
Sar1 cd00879
Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII ...
 3-197 1.14e-131

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: 366.99  E-value: 1.14e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942   3 FIFEWIYNgfssVLQFLGLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQA 82
Cdd:cd00879    1 FIFDWFYN----VLSSLGLYKKEAKIVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTIGNVKFTTFDLGGHEQA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  83 RRVWKNYLPAINGIVFLVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYGQTTGKGN 162
Cdd:cd00879   77 RRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANVPILILGNKIDKPGAVSEEELREALGLYGTTTGKGG 156

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 564397942 163 VTLKELNARPMEVFMCSVLKRQGYGEGFRWLSQYI 197
Cdd:cd00879  157 VSLKVSNIRPVEVFMCSVVKRQGYGEGFRWLSQYL 191
SAR smart00178
Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene ...
 5-197 4.53e-98

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: 282.21  E-value: 4.53e-98
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942     5 FEWIYNgfssVLQFLGLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARR 84
Cdd:smart00178   1 FDWFYD----ILASLGLWNKHAKILFLGLDNAGKTTLLHMLKNDRLAQHQPTQHPTSEELAIGNIKFTTFDLGGHQQARR 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942    85 VWKNYLPAINGIVFLVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYGQTTGKGNVt 164
Cdd:smart00178  77 LWKDYFPEVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAASEDELRYALGLTNTTTGKGKV- 155

                          170       180       190
                   ....*....|....*....|....*....|...
gi 564397942   165 lkelNARPMEVFMCSVLKRQGYGEGFRWLSQYI 197
Cdd:smart00178 156 ----GVRPVEVFMCSVVRRMGYGEGFKWLSQYI 184
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
 26-197 1.66e-84

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


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 246.75  E-value: 1.66e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942   26 GKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADH 105
Cdd:pfam00025   1 MRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  106 SRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYgqttgkgnvtlkELNARPMEVFMCSVLKRQG 185
Cdd:pfam00025  81 DRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLH------------ELKDRPWEIQGCSAVTGEG 148

                         170
                  ....*....|..
gi 564397942  186 YGEGFRWLSQYI 197
Cdd:pfam00025 149 LDEGLDWLSNYI 160
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
 12-197 1.62e-27

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 102.35  E-value: 1.62e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  12 FSSVLQFLgLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLP 91
Cdd:PLN00223   5 FTKLFSRL-FAKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQ 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  92 AINGIVFLVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYGqttgkgnvtlkeLNAR 171
Cdd:PLN00223  84 NTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHS------------LRQR 151

                        170       180
                 ....*....|....*....|....*.
gi 564397942 172 PMEVFMCSVLKRQGYGEGFRWLSQYI 197
Cdd:PLN00223 152 HWYIQSTCATSGEGLYEGLDWLSNNI 177
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 26-151 2.88e-13

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: 64.70  E-value: 2.88e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942   26 GKLVFLGLDNAGKTTLLHMLKDD--RLGQHVP--TLHPTSEELTIAGMT--FTTFDLGGHEQARRVWKNYLPAINGIVFL 99
Cdd:TIGR00231   2 IKIVIVGHPNVGKSTLLNSLLGNkgSITEYYPgtTRNYVTTVIEEDGKTykFNLLDTAGQEDYDAIRRLYYPQVERSLRV 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 564397942  100 VDCADHSRLMESKVELNA-LMTDETISNVPILILGNKIDRTDAISEEKLREIF 151
Cdd:TIGR00231  82 FDIVILVLDVEEILEKQTkEIIHHADSGVPIILVGNKIDLKDADLKTHVASEF 134
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
27-155 8.53e-07

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 47.28  E-value: 8.53e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  27 KLVFLGLDNAGKTTLLHMLKDDR--LGQHVPTLHPTSE--ELTIAGMTFTT--FDLGGH---EQARRVWKNYLPAINGIV 97
Cdd:COG1100    5 KIVVVGTGGVGKTSLVNRLVGDIfsLEKYLSTNGVTIDkkELKLDGLDVDLviWDTPGQdefRETRQFYARQLTGASLYL 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564397942  98 FLVDCaDHSRLMESKVELNALMTdETISNVPILILGNKIDRTDA---ISEEKLREIFGLYG 155
Cdd:COG1100   85 FVVDG-TREETLQSLYELLESLR-RLGKKSPIILVLNKIDLYDEeeiEDEERLKEALSEDN 143
 
Name Accession Description Interval E-value
Sar1 cd00879
Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII ...
 3-197 1.14e-131

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: 366.99  E-value: 1.14e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942   3 FIFEWIYNgfssVLQFLGLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQA 82
Cdd:cd00879    1 FIFDWFYN----VLSSLGLYKKEAKIVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTIGNVKFTTFDLGGHEQA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  83 RRVWKNYLPAINGIVFLVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYGQTTGKGN 162
Cdd:cd00879   77 RRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANVPILILGNKIDKPGAVSEEELREALGLYGTTTGKGG 156

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 564397942 163 VTLKELNARPMEVFMCSVLKRQGYGEGFRWLSQYI 197
Cdd:cd00879  157 VSLKVSNIRPVEVFMCSVVKRQGYGEGFRWLSQYL 191
SAR smart00178
Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene ...
 5-197 4.53e-98

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: 282.21  E-value: 4.53e-98
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942     5 FEWIYNgfssVLQFLGLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARR 84
Cdd:smart00178   1 FDWFYD----ILASLGLWNKHAKILFLGLDNAGKTTLLHMLKNDRLAQHQPTQHPTSEELAIGNIKFTTFDLGGHQQARR 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942    85 VWKNYLPAINGIVFLVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYGQTTGKGNVt 164
Cdd:smart00178  77 LWKDYFPEVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAASEDELRYALGLTNTTTGKGKV- 155

                          170       180       190
                   ....*....|....*....|....*....|...
gi 564397942   165 lkelNARPMEVFMCSVLKRQGYGEGFRWLSQYI 197
Cdd:smart00178 156 ----GVRPVEVFMCSVVRRMGYGEGFKWLSQYI 184
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
 26-197 1.66e-84

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


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 246.75  E-value: 1.66e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942   26 GKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADH 105
Cdd:pfam00025   1 MRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  106 SRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYgqttgkgnvtlkELNARPMEVFMCSVLKRQG 185
Cdd:pfam00025  81 DRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLH------------ELKDRPWEIQGCSAVTGEG 148

                         170
                  ....*....|..
gi 564397942  186 YGEGFRWLSQYI 197
Cdd:pfam00025 149 LDEGLDWLSNYI 160
Arf_Arl cd00878
ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ...
 27-195 1.22e-47

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: 153.12  E-value: 1.22e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  27 KLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADHS 106
Cdd:cd00878    1 RILMLGLDGAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSDRE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942 107 RLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYgqttgkgnvtlkELNARPMEVFMCSVLKRQGY 186
Cdd:cd00878   81 RIEEAKNELHKLLNEEELKGAPLLILANKQDLPGALTESELIELLGLE------------SIKGRRWHIQPCSAVTGDGL 148


                 ....*....
gi 564397942 187 GEGFRWLSQ 195
Cdd:cd00878  149 DEGLDWLIE 157
Arf6 cd04149
ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins ...
 23-195 1.24e-32

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: 115.26  E-value: 1.24e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  23 KKSGKLVFLGLDNAGKTTLLHMLKddrLGQHV---PTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLPAINGIVFL 99
Cdd:cd04149    7 NKEMRILMLGLDAAGKTTILYKLK---LGQSVttiPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFV 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942 100 VDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGlygqttgkgnvtLKELNARPMEVFMCS 179
Cdd:cd04149   84 VDSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPDAMKPHEIQEKLG------------LTRIRDRNWYVQPSC 151

                        170
                 ....*....|....*.
gi 564397942 180 VLKRQGYGEGFRWLSQ 195
Cdd:cd04149  152 ATSGDGLYEGLTWLSS 167
ARLTS1 cd04156
Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), ...
 27-196 1.05e-31

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: 112.51  E-value: 1.05e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  27 KLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAG-MTFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADH 105
Cdd:cd04156    1 QVLLLGLDSAGKSTLLYKLKHAELVTTIPTVGFNVEMLQLEKhLSLTVWDVGGQEKMRTVWKCYLENTDGLVYVVDSSDE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942 106 SRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYgqttgkgnvtlKELNARPMEVFMCSVLKRQG 185
Cdd:cd04156   81 ARLDESQKELKHILKNEHIKGVPVVLLANKQDLPGALTAEEITRRFKLK-----------KYCSDRDWYVQPCSAVTGEG 149

                        170
                 ....*....|.
gi 564397942 186 YGEGFRWLSQY 196
Cdd:cd04156  150 LAEAFRKLASF 160
Arl5_Arl8 cd04153
Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like ...
 12-195 1.04e-30

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: 110.52  E-value: 1.04e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  12 FSSVLQFLGLYKKSgKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLP 91
Cdd:cd04153    3 FSSLWSLFFPRKEY-KVIIVGLDNAGKTTILYQFLLGEVVHTSPTIGSNVEEIVYKNIRFLMWDIGGQESLRSSWNTYYT 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  92 AINGIVFLVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREifglygqttgkgNVTLKELNAR 171
Cdd:cd04153   82 NTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGAMTPAEISE------------SLGLTSIRDH 149

                        170       180
                 ....*....|....*....|....
gi 564397942 172 PMEVFMCSVLKRQGYGEGFRWLSQ 195
Cdd:cd04153  150 TWHIQGCCALTGEGLPEGLDWIAS 173
Arl1 cd04151
ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi ...
 27-194 7.54e-30

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: 107.88  E-value: 7.54e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  27 KLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADHS 106
Cdd:cd04151    1 RILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTDRD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942 107 RLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGlygqttgkgnvtLKELNARPMEVFMCSVLKRQGY 186
Cdd:cd04151   81 RLGISKSELHAMLEEEELKDAVLLVFANKQDMPGALSEAEVAEKLG------------LSELKDRTWQIFKTSATKGEGL 148


                 ....*...
gi 564397942 187 GEGFRWLS 194
Cdd:cd04151  149 DEGMDWLV 156
Arl6 cd04157
Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small ...
 28-195 1.63e-29

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: 107.13  E-value: 1.63e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  28 LVFLGLDNAGKTTLLHMLKDDRLGQH--VPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADH 105
Cdd:cd04157    2 ILVLGLDNSGKTTIINQLKPSNAQSQniVPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942 106 SRLMESKVELNALMTDETISN--VPILILGNKIDRTDAISEEKLREIFGlygqttgkgnvtLKELNARPMEVFMCSVLKR 183
Cdd:cd04157   82 LRMVVAKDELELLLNHPDIKHrrIPILFYANKMDLPDALTAVKITQLLC------------LENIKDKPWHIFASSALTG 149

                        170
                 ....*....|..
gi 564397942 184 QGYGEGFRWLSQ 195
Cdd:cd04157  150 EGLDEGVDWLQA 161
Arl3 cd04155
Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most ...
 23-193 5.11e-29

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: 105.94  E-value: 5.11e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  23 KKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLPAINGIVFLVDC 102
Cdd:cd04155   13 RQEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGFKLNVWDIGGQRKIRPYWRNYFENTDVLIYVIDS 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942 103 ADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREifglygqttgkgNVTLKELNARPMEVFMCSVLK 182
Cdd:cd04155   93 ADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLTAAPAEEVAE------------ALNLHDIRDRSWHIQACSAKT 160

                        170
                 ....*....|.
gi 564397942 183 RQGYGEGFRWL 193
Cdd:cd04155  161 GEGLQEGMNWV 171
Arfrp1 cd04160
Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a ...
 29-194 8.71e-29

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: 105.12  E-value: 8.71e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  29 VFLGLDNAGKTTLLHMLKDdRLGQHVPTLHP----TSEELTIA-----GMTFTTFDLGGHEQARRVWKNYLPAINGIVFL 99
Cdd:cd04160    3 LILGLDNAGKTTFLEQTKT-KFSKNYKGLNPskitPTVGLNIGtievgKARLMFWDLGGQEELRSLWDKYYAESHGVIYV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942 100 VDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYGQTTGKGNVTlkelnarpmeVFMCS 179
Cdd:cd04160   82 IDSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDLPDALSVAEIKEVFDDCIALIGRRDCL----------VQPVS 151

                        170
                 ....*....|....*
gi 564397942 180 VLKRQGYGEGFRWLS 194
Cdd:cd04160  152 ALEGEGVEEGIEWLV 166
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
 18-194 1.33e-28

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: 105.00  E-value: 1.33e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942    18 FLGLY-KKSGKLVFLGLDNAGKTTLLHMLKddrLGQHV---PTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLPAI 93
Cdd:smart00177   5 FSKLFgNKEMRILMVGLDAAGKTTILYKLK---LGESVttiPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTNT 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942    94 NGIVFLVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYgqttgkgnvtlkELNARPM 173
Cdd:smart00177  82 QGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLH------------SIRDRNW 149

                          170       180
                   ....*....|....*....|.
gi 564397942   174 EVFMCSVLKRQGYGEGFRWLS 194
Cdd:smart00177 150 YIQPTCATSGDGLYEGLTWLS 170
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
 12-197 1.62e-27

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 102.35  E-value: 1.62e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  12 FSSVLQFLgLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLP 91
Cdd:PLN00223   5 FTKLFSRL-FAKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQ 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  92 AINGIVFLVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYGqttgkgnvtlkeLNAR 171
Cdd:PLN00223  84 NTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHS------------LRQR 151

                        170       180
                 ....*....|....*....|....*.
gi 564397942 172 PMEVFMCSVLKRQGYGEGFRWLSQYI 197
Cdd:PLN00223 152 HWYIQSTCATSGEGLYEGLDWLSNNI 177
Arl10_like cd04159
Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from ...
 31-195 1.86e-26

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: 98.93  E-value: 1.86e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  31 LGLDNAGKTTLLHMLKDdrlGQHVPTLHPT----SEELTIAGMTFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADHS 106
Cdd:cd04159    5 VGLQNSGKTTLVNVIAS---GQFSEDTIPTvgfnMRKVTKGNVTIKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADRE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942 107 RLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREifglygqttgkgNVTLKELNARPMEVFMCSVLKRQGY 186
Cdd:cd04159   82 KLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELIE------------QMNLKSITDREVSCYSISAKEKTNI 149


                 ....*....
gi 564397942 187 GEGFRWLSQ 195
Cdd:cd04159  150 DIVLDWLIK 158
Arl2 cd04154
Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind ...
 14-195 9.95e-26

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: 97.40  E-value: 9.95e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  14 SVLQFLGLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLPAI 93
Cdd:cd04154    3 TILRKTKQKEREMRILMLGLDNAGKTTILKKFNGEDISTISPTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYFEST 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  94 NGIVFLVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGlygqttgkgnvtLKELNARPM 173
Cdd:cd04154   83 DALIWVVDSSDRARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALSPEEIREVLE------------LDSIKSHHW 150

                        170       180
                 ....*....|....*....|..
gi 564397942 174 EVFMCSVLKRQGYGEGFRWLSQ 195
Cdd:cd04154  151 RIFGCSAVTGENLLDGIDWLVD 172
PTZ00133 PTZ00133
ADP-ribosylation factor; Provisional
 7-197 4.89e-25

ADP-ribosylation factor; Provisional


Pssm-ID: 173423  Cd Length: 182  Bit Score: 96.07  E-value: 4.89e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942   7 WIYNGFSSVLQflglyKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARRVW 86
Cdd:PTZ00133   4 WLSSAFKSLFG-----KKEVRILMVGLDAAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNLKFTMWDVGGQDKLRPLW 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  87 KNYLPAINGIVFLVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYGqttgkgnvtlk 166
Cdd:PTZ00133  79 RHYYQNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMSTTEVTEKLGLHS----------- 147

                        170       180       190
                 ....*....|....*....|....*....|.
gi 564397942 167 eLNARPMEVFMCSVLKRQGYGEGFRWLSQYI 197
Cdd:PTZ00133 148 -VRQRNWYIQGCCATTAQGLYEGLDWLSANI 177
ARD1 cd04158
(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein ...
 27-195 1.28e-24

(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: 94.71  E-value: 1.28e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  27 KLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADHS 106
Cdd:cd04158    1 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942 107 RLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYGQTTGkgnvtlkelnaRPMEVFMCSVLKRQGY 186
Cdd:cd04158   81 RVSEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEMTELLSLHKLCCG-----------RSWYIQGCDARSGMGL 149


                 ....*....
gi 564397942 187 GEGFRWLSQ 195
Cdd:cd04158  150 YEGLDWLSR 158
Arl4_Arl7 cd04152
Arf-like 4 (Arl4) and 7 (Arl7) GTPases; Arl4 (Arf-like 4) is highly expressed in testicular ...
 28-197 1.40e-24

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: 94.87  E-value: 1.40e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  28 LVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIA-----GMTFTTFDLGGHEQARRVWKNYLPAINGIVFLVDC 102
Cdd:cd04152    6 IVMLGLDSAGKTTVLYRLKFNEFVNTVPTKGFNTEKIKVSlgnakGVTFHFWDVGGQEKLRPLWKSYTRCTDGIVFVVDS 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942 103 ADHSRLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYgqttgkgnvtlkEL-NARPMEVFMCSVL 181
Cdd:cd04152   86 VDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLPNALPVSEVEKLLALH------------ELsSSTPWHVQPACAI 153

                        170
                 ....*....|....*.
gi 564397942 182 KRQGYGEGFRWLSQYI 197
Cdd:cd04152  154 IGEGLQEGLEKLYEMI 169
Arl2l1_Arl13_like cd04161
Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ...
 28-153 1.02e-23

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: 92.07  E-value: 1.02e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  28 LVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADHSR 107
Cdd:cd04161    2 LLTVGLDNAGKTTLVSALQGEIPKKVAPTVGFTPTKLRLDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSDDDR 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 564397942 108 LMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGL 153
Cdd:cd04161   82 VQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLGADVIEYLSL 127
Arl9_Arfrp2_like cd04162
Arf-like 9 (Arl9)/Arfrp2-like GTPase; Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first ...
 28-161 1.31e-23

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: 91.74  E-value: 1.31e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  28 LVFLGLDNAGKTTLLHMLKDDR-LGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADHS 106
Cdd:cd04162    2 ILVLGLDGAGKTSLLHSLSSERsLESVVPTTGFNSVAIPTQDAIMELLEIGGSQNLRKYWKRYLSGSQGLIFVVDSADSE 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 564397942 107 RLMESKVELNALMTDEtiSNVPILILGNKIDRTDAISEEKLREIFGLYGQTTGKG 161
Cdd:cd04162   82 RLPLARQELHQLLQHP--PDLPLVVLANKQDLPAARSVQEIHKELELEPIARGRR 134
Arf1_5_like cd04150
ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like ...
 27-196 6.45e-23

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: 89.77  E-value: 6.45e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  27 KLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADHS 106
Cdd:cd04150    2 RILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942 107 RLMESKVELNALMTDETISNVPILILGNKIDRTDAISEEKLREIFGLYgqttgkgnvtlkELNARPMEVFMCSVLKRQGY 186
Cdd:cd04150   82 RIGEAREELQRMLNEDELRDAVLLVFANKQDLPNAMSAAEVTDKLGLH------------SLRNRNWYIQATCATSGDGL 149

                        170
                 ....*....|
gi 564397942 187 GEGFRWLSQY 196
Cdd:cd04150  150 YEGLDWLSNN 159
SR_beta cd04105
Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ...
 29-149 2.77e-15

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: 70.81  E-value: 2.77e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  29 VFLGLDNAGKTTLLHMLKDDRLGQHVPTLHP---TSEELTIAGMTFTTFDLGGHEQAR-RVWKNYLPAINGIVFLVDCAD 104
Cdd:cd04105    4 LLLGPSDSGKTALFTKLTTGKVRSTVTSIEPnvaSFYSNSSKGKKLTLVDVPGHEKLRdKLLEYLKASLKAIVFVVDSAT 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 564397942 105 HSRLMESKVEL--NALMTDETISN-VPILILGNKIDRTDAISEEKLRE 149
Cdd:cd04105   84 FQKNIRDVAEFlyDILTDLEKIKNkIPILIACNKQDLFTAKPAKKIKE 131
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 26-151 2.88e-13

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: 64.70  E-value: 2.88e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942   26 GKLVFLGLDNAGKTTLLHMLKDD--RLGQHVP--TLHPTSEELTIAGMT--FTTFDLGGHEQARRVWKNYLPAINGIVFL 99
Cdd:TIGR00231   2 IKIVIVGHPNVGKSTLLNSLLGNkgSITEYYPgtTRNYVTTVIEEDGKTykFNLLDTAGQEDYDAIRRLYYPQVERSLRV 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 564397942  100 VDCADHSRLMESKVELNA-LMTDETISNVPILILGNKIDRTDAISEEKLREIF 151
Cdd:TIGR00231  82 FDIVILVLDVEEILEKQTkEIIHHADSGVPIILVGNKIDLKDADLKTHVASEF 134
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 29-195 2.74e-11

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: 59.39  E-value: 2.74e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  29 VFLGLDNAGKTTLLHMLKDDRLGQ----HVPTLHPTSEELTIAGM--TFTTFDLGGHEQARRVW-----KNYLPAINGIV 97
Cdd:cd00882    1 VVVGRGGVGKSSLLNALLGGEVGEvsdvPGTTRDPDVYVKELDKGkvKLVLVDTPGLDEFGGLGreelaRLLLRGADLIL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  98 FLVDCADHSRLMESKVELNALMTDEtisNVPILILGNKIDRTDAISEEKLREIFglygqttgkgnvtlKELNARPMEVFM 177
Cdd:cd00882   81 LVVDSTDRESEEDAKLLILRRLRKE---GIPIILVGNKIDLLEEREVEELLRLE--------------ELAKILGVPVFE 143

                        170
                 ....*....|....*...
gi 564397942 178 CSVLKRQGYGEGFRWLSQ 195
Cdd:cd00882  144 VSAKTGEGVDELFEKLIE 161
SRPRB pfam09439
Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition ...
 23-149 2.88e-08

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: 51.29  E-value: 2.88e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942   23 KKSGKLVFLGLDNAGKTTLLHMLKddrLGQHVPTLhpTSEELTIA-------GMTFTTFDLGGHEQARRVWKNYLPA--- 92
Cdd:pfam09439   1 SSQPAVIIAGLCDSGKTSLFTLLT---TDSVRPTV--TSQEPSAAyrymlnkGNSFTLIDFPGHVKLRYKLLETLKDsss 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942   93 INGIVFLVDCADHSRLMESKVEL--NALMTDETISN-VPILILGNKIDRTDAISEEKLRE 149
Cdd:pfam09439  76 LKGIVFVVDSTIFPKEVTDTAEFlyDILSITELLKNgIDILIACNKQESFTARPPKKIKQ 135
G-alpha pfam00503
G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular ...
 54-148 4.72e-07

G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular signaling pathways. The G protein alpha subunit binds guanyl nucleotide and is a weak GTPase. A set of residues that are unique to G-alpha as compared to its ancestor the Arf-like family form a ring of residues centered on the nucleotide binding site. A Ggamma is found fused to an inactive Galpha in the Dictyostelium protein gbqA.


Pssm-ID: 459835 [Multi-domain]  Cd Length: 316  Bit Score: 48.74  E-value: 4.72e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942   54 VPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCAD----------HSRLMESKVELNALMTDET 123
Cdd:pfam00503 152 VKTTGIIETKFEFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVSLSEydqvlyeddsTNRMEESLKLFEEICNSPW 231

                          90       100
                  ....*....|....*....|....*
gi 564397942  124 ISNVPILILGNKIDrtdaISEEKLR 148
Cdd:pfam00503 232 FKNTPIILFLNKKD----LFEEKLK 252
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
27-155 8.53e-07

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 47.28  E-value: 8.53e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  27 KLVFLGLDNAGKTTLLHMLKDDR--LGQHVPTLHPTSE--ELTIAGMTFTT--FDLGGH---EQARRVWKNYLPAINGIV 97
Cdd:COG1100    5 KIVVVGTGGVGKTSLVNRLVGDIfsLEKYLSTNGVTIDkkELKLDGLDVDLviWDTPGQdefRETRQFYARQLTGASLYL 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564397942  98 FLVDCaDHSRLMESKVELNALMTdETISNVPILILGNKIDRTDA---ISEEKLREIFGLYG 155
Cdd:COG1100   85 FVVDG-TREETLQSLYELLESLR-RLGKKSPIILVLNKIDLYDEeeiEDEERLKEALSEDN 143
DLP_2 cd09912
Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The ...
 27-150 5.19e-05

Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; The dynamin family of large mechanochemical GTPases includes the classical dynamins and dynamin-like proteins (DLPs) that are found throughout the Eukarya. This family also includes bacterial DLPs. These proteins catalyze membrane fission during clathrin-mediated endocytosis. Dynamin consists of five domains; an N-terminal G domain that binds and hydrolyzes GTP, a middle domain (MD) involved in self-assembly and oligomerization, a pleckstrin homology (PH) domain responsible for interactions with the plasma membrane, GED, which is also involved in self-assembly, and a proline arginine rich domain (PRD) that interacts with SH3 domains on accessory proteins. To date, three vertebrate dynamin genes have been identified; dynamin 1, which is brain specific, mediates uptake of synaptic vesicles in presynaptic terminals; dynamin-2 is expressed ubiquitously and similarly participates in membrane fission; mutations in the MD, PH and GED domains of dynamin 2 have been linked to human diseases such as Charcot-Marie-Tooth peripheral neuropathy and rare forms of centronuclear myopathy. Dynamin 3 participates in megakaryocyte progenitor amplification, and is also involved in cytoplasmic enlargement and the formation of the demarcation membrane system. This family also includes mitofusins (MFN1 and MFN2 in mammals) that are involved in mitochondrial fusion. Dynamin oligomerizes into helical structures around the neck of budding vesicles in a GTP hydrolysis-dependent manner.


Pssm-ID: 206739 [Multi-domain]  Cd Length: 180  Bit Score: 42.15  E-value: 5.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  27 KLVFLGLDNAGKTTLL-HMLKDDRLgqhvPT-LHPTSEELTI------AGMTFttFD---LGGHEQARRVW-KNYLPAIN 94
Cdd:cd09912    2 LLAVVGEFSAGKSTLLnALLGEEVL----PTgVTPTTAVITVlrygllKGVVL--VDtpgLNSTIEHHTEItESFLPRAD 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 564397942  95 GIVFLVDcADHSrLMESkvELNALMTDETISNVPILILGNKIdrtDAISEEKLREI 150
Cdd:cd09912   76 AVIFVLS-ADQP-LTES--EREFLKEILKWSGKKIFFVLNKI---DLLSEEELEEV 124
Rab cd00154
Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ...
 27-149 6.90e-05

Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members, several have been found to possess 60 or more Rabs; for many of these Rab isoforms, homologous proteins are not found in other organisms. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Since crystal structures often lack C-terminal residues, the lipid modification site is not available for annotation in many of the CDs in the hierarchy, but is included where possible.


Pssm-ID: 206640 [Multi-domain]  Cd Length: 159  Bit Score: 41.29  E-value: 6.90e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  27 KLVFLGLDNAGKTTLLHMLKDDRL-GQHVPTLHP--TSEELTIAGMTFTT--FDLGGHEQARRVWKNYLPAINGIVFLVD 101
Cdd:cd00154    2 KIVLIGDSGVGKTSLLLRFVDNKFsENYKSTIGVdfKSKTIEVDGKKVKLqiWDTAGQERFRSITSSYYRGAHGAILVYD 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 564397942 102 CADHsrlmESKVELNALMTD---ETISNVPILILGNKIDRTD--AISEEKLRE 149
Cdd:cd00154   82 VTNR----ESFENLDKWLNElkeYAPPNIPIILVGNKSDLEDerQVSTEEAQQ 130
Era_like cd00880
E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ...
 29-167 4.88e-04

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: 39.15  E-value: 4.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  29 VFLGLDNAGKTTLLHMLkddrLGQHV--------PTLHPTSEELTIAGmtFTTFDL--------GGHEQARRVwKNYLPA 92
Cdd:cd00880    1 AIFGRPNVGKSSLLNAL----LGQNVgivspipgTTRDPVRKEWELLP--LGPVVLidtpgldeEGGLGRERV-EEARQV 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  93 IN---GIVFLVDcADH--SRLMESKVELNAlmtdetiSNVPILILGNKIDRTDAISEEKL--REIFGLYGQ--------T 157
Cdd:cd00880   74 ADradLVLLVVD-SDLtpVEEEAKLGLLRE-------RGKPVLLVLNKIDLVPESEEEELlrERKLELLPDlpviavsaL 145

                        170
                 ....*....|
gi 564397942 158 TGKGNVTLKE 167
Cdd:cd00880  146 PGEGIDELRK 155
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 27-135 9.54e-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: 37.60  E-value: 9.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942   27 KLVFLGLDNAGKTTLLHMLkddrLGQHVP-------TLHPTSEELTIAGMTFTTFDLGG-------HEQARRVWKNYLPA 92
Cdd:pfam01926   1 RVALVGRPNVGKSTLINAL----TGAKAIvsdypgtTRDPNEGRLELKGKQIILVDTPGliegaseGEGLGRAFLAIIEA 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 564397942   93 iNGIVFLVDcaDHSRLMESKVELNALMTDetiSNVPILILGNK 135
Cdd:pfam01926  77 -DLILFVVD--SEEGITPLDEELLELLRE---NKKPIILVLNK 113
Rho cd00157
Ras homology family (Rho) of small guanosine triphosphatases (GTPases); Members of the Rho ...
 27-185 2.14e-03

Ras homology family (Rho) of small guanosine triphosphatases (GTPases); Members of the Rho (Ras homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Since crystal structures often lack C-terminal residues, this feature is not available for annotation in many of the CDs in the hierarchy.


Pssm-ID: 206641 [Multi-domain]  Cd Length: 171  Bit Score: 37.14  E-value: 2.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  27 KLVFLGLDNAGKTTLLHMLKDDR-LGQHVPTL---HPTSeeLTIAGMTFTT--FDLGGHEQARRvWKNYL-PAINgiVFL 99
Cdd:cd00157    2 KIVVVGDGAVGKTCLLISYTTNKfPTEYVPTVfdnYSAN--VTVDGKQVNLglWDTAGQEEYDR-LRPLSyPQTD--VFL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942 100 ----VDCADHSRLMESK--VELNalmtdETISNVPILILGNKID-RTDAISEEKLREIFGLYgqTTGKGNVTLKELNARP 172
Cdd:cd00157   77 lcfsVDSPSSFENVKTKwyPEIK-----HYCPNVPIILVGTKIDlRDDGNTLKKLEKKQKPI--TPEEGEKLAKEIGAVK 149

                        170
                 ....*....|....
gi 564397942 173 -MEvfmCSVLKRQG 185
Cdd:cd00157  150 yME---CSALTQEG 160
Rab18 cd01863
Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic ...
 27-138 2.61e-03

Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206656 [Multi-domain]  Cd Length: 161  Bit Score: 36.91  E-value: 2.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  27 KLVFLGLDNAGKTTLLHMLKDDrlgQHVPTLHPT------SEELTIAGMTF--TTFDLGGHEQARRVWKNYLPAINGIVF 98
Cdd:cd01863    2 KILLIGDSGVGKSSLLLRFTDD---TFDEDLSSTigvdfkVKTVTVDGKKVklAIWDTAGQERFRTLTSSYYRGAQGVIL 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 564397942  99 LVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDR 138
Cdd:cd01863   79 VYDVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGNKIDK 118
Rab27A cd04127
Rab GTPase family 27a (Rab27a); The Rab27a subfamily consists of Rab27a and its highly ...
 27-155 2.85e-03

Rab GTPase family 27a (Rab27a); The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated insulin secretion, making it a potential target for diabetes therapy. When bound to JFC1 in prostate cells, Rab27a is believed to regulate the exocytosis of prostate- specific markers. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206700 [Multi-domain]  Cd Length: 180  Bit Score: 37.09  E-value: 2.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  27 KLVFLGLDNAGKTTLLHMLKDDRL-GQHVPT----------LHPTSEELTIAGMTFTT----FDLGGHEQARRVWKNYLP 91
Cdd:cd04127    6 KLLALGDSGVGKTTFLYRYTDNKFnPKFITTvgidfrekrvVYNSQGPDGTSGKAFRVhlqlWDTAGQERFRSLTTAFFR 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564397942  92 AINGIVFLVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRTD--AISEEKLREIFGLYG 155
Cdd:cd04127   86 DAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPDIVLIGNKADLPDqrEVSERQARELADKYG 151
G_alpha smart00275
G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding ...
 54-148 3.54e-03

G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding site


Pssm-ID: 214595 [Multi-domain]  Cd Length: 342  Bit Score: 37.17  E-value: 3.54e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942    54 VPTLHPTSEELTIAGMTFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADH----------SRLMESKVELNALMTDET 123
Cdd:smart00275 169 VPTTGIQETAFIVKKLFFRMFDVGGQRSERKKWIHCFDNVTAIIFCVALSEYdqvleedestNRMQESLNLFESICNSRW 248

                           90       100
                   ....*....|....*....|....*
gi 564397942   124 ISNVPILILGNKIDrtdaISEEKLR 148
Cdd:smart00275 249 FANTSIILFLNKID----LFEEKIK 269
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
 27-193 7.92e-03

Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.


Pssm-ID: 425451 [Multi-domain]  Cd Length: 162  Bit Score: 35.57  E-value: 7.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942   27 KLVFLGLDNAGKTTLLHMLKDDR-LGQHVPTLHPTSEELTIAG----MTFTTFDLGGHEQARRVWKNYLPAINGIVFLVD 101
Cdd:pfam00071   1 KLVLVGDGGVGKSSLLIRFTQNKfPEEYIPTIGVDFYTKTIEVdgktVKLQIWDTAGQERFRALRPLYYRGADGFLLVYD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397942  102 CADHSRLMESKVELNALMtDETISNVPILILGNKIDrtdaisEEKLREIfglygqTTGKGNVTLKELNARPMEvfmCSVL 181
Cdd:pfam00071  81 ITSRDSFENVKKWVEEIL-RHADENVPIVLVGNKCD------LEDQRVV------STEEGEALAKELGLPFME---TSAK 144

                         170
                  ....*....|..
gi 564397942  182 KRQGYGEGFRWL 193
Cdd:pfam00071 145 TNENVEEAFEEL 156
COG4586 COG4586
ABC-type uncharacterized transport system, ATPase component [General function prediction only]; ...
 30-70 8.90e-03

ABC-type uncharacterized transport system, ATPase component [General function prediction only];


Pssm-ID: 443643 [Multi-domain]  Cd Length: 323  Bit Score: 36.22  E-value: 8.90e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 564397942  30 FLGLDNAGKTTLLHMLkddrlgqhvpT--LHPTSEELTIAGMT 70
Cdd:COG4586   53 FIGPNGAGKSTTIKML----------TgiLVPTSGEVRVLGYV 85
 
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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