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Conserved domains on  [gi|41152289|ref|NP_957013|]
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ADP ribosylation factor like GTPase 3, like 2 [Danio rerio]

Protein Classification

ADP-ribosylation factor-like protein 3( domain architecture ID 10134973)

ADP-ribosylation factor-like protein 3(Arl3) is a small GTP-binding protein which cycles between an inactive GDP-bound and an active GTP-bound form, and the rate of cycling is regulated by guanine nucleotide exchange factors (GEF) and GTPase-activating proteins (GAP); required for normal cytokinesis and cilia signaling

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Arl3 cd04155
Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most ...
 8-181 8.17e-100

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: 285.44  E-value: 8.17e-100
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289   8 LLSVMQKLKGSSELELRILLLGLDNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYL 87
Cdd:cd04155   1 LLSILRKLKPSSRQEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGFKLNVWDIGGQRKIRPYWRNYF 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  88 ENTDLLVYVIDSADKKRFEETGLELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAIT 167
Cdd:cd04155  81 ENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLTAAPAEEVAEALNLHDIRDRSWHIQACSAKT 160

                       170
                ....*....|....
gi 41152289 168 GEGVQDGMNWICNN 181
Cdd:cd04155 161 GEGLQEGMNWVCKN 174
 
Name Accession Description Interval E-value
Arl3 cd04155
Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most ...
 8-181 8.17e-100

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: 285.44  E-value: 8.17e-100
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289   8 LLSVMQKLKGSSELELRILLLGLDNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYL 87
Cdd:cd04155   1 LLSILRKLKPSSRQEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGFKLNVWDIGGQRKIRPYWRNYF 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  88 ENTDLLVYVIDSADKKRFEETGLELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAIT 167
Cdd:cd04155  81 ENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLTAAPAEEVAEALNLHDIRDRSWHIQACSAKT 160

                       170
                ....*....|....
gi 41152289 168 GEGVQDGMNWICNN 181
Cdd:cd04155 161 GEGLQEGMNWVCKN 174
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
 31-182 1.25e-79

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


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 234.04  E-value: 1.25e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289    31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:pfam00025   9 DNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADRDRIEEAKE 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 41152289   111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAITGEGVQDGMNWICNNL 182
Cdd:pfam00025  89 ELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLHELKDRPWEIQGCSAVTGEGLDEGLDWLSNYI 160
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
 31-185 1.52e-53

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 168.61  E-value: 1.52e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289   31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:PLN00223  26 DAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRDRVVEARD 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41152289  111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAITGEGVQDGMNWICNNLVNR 185
Cdd:PLN00223 106 ELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRQRHWYIQSTCATSGEGLYEGLDWLSNNIANK 180
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
 31-184 1.69e-53

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: 168.18  E-value: 1.69e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289     31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:smart00177  22 DAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDEARE 101

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41152289    111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAITGEGVQDGMNWICNNLVN 184
Cdd:smart00177 102 ELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLHSIRDRNWYIQPTCATSGDGLYEGLTWLSNNLKN 175
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
32-173 1.01e-18

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 78.87  E-value: 1.01e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  32 NAGKTTLLKSLASEDVNT--ITPTQGFNIK----TVASRGMKLNVWDIGGQ---RKIRPFWKKYLENTDLLVYVIDSADK 102
Cdd:COG1100  13 GVGKTSLVNRLVGDIFSLekYLSTNGVTIDkkelKLDGLDVDLVIWDTPGQdefRETRQFYARQLTGASLYLFVVDGTRE 92

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41152289 103 KRFeETGLELSELIDEENLcGVPVLIFANKQDLGTA---APASEIAEGLNlhtyRDRVWQIQACSAITGEGVQD 173
Cdd:COG1100  93 ETL-QSLYELLESLRRLGK-KSPIILVLNKIDLYDEeeiEDEERLKEALS----EDNIVEVVATSAKTGEGVEE 160
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 31-138 3.12e-10

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: 56.23  E-value: 3.12e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289    31 DNAGKTTLLKSLA------SEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSAD-KK 103
Cdd:TIGR00231  10 PNVGKSTLLNSLLgnkgsiTEYYPGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDAIRRLYYPQVERSLRVFDIVIlVL 89

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 41152289   104 RFEETGLELSELIDEENLCGVPVLIFANKQDLGTA 138
Cdd:TIGR00231  90 DVEEILEKQTKEIIHHADSGVPIILVGNKIDLKDA 124
 
Name Accession Description Interval E-value
Arl3 cd04155
Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most ...
 8-181 8.17e-100

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: 285.44  E-value: 8.17e-100
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289   8 LLSVMQKLKGSSELELRILLLGLDNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYL 87
Cdd:cd04155   1 LLSILRKLKPSSRQEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGFKLNVWDIGGQRKIRPYWRNYF 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  88 ENTDLLVYVIDSADKKRFEETGLELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAIT 167
Cdd:cd04155  81 ENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLTAAPAEEVAEALNLHDIRDRSWHIQACSAKT 160

                       170
                ....*....|....
gi 41152289 168 GEGVQDGMNWICNN 181
Cdd:cd04155 161 GEGLQEGMNWVCKN 174
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
 31-182 1.25e-79

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


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 234.04  E-value: 1.25e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289    31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:pfam00025   9 DNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADRDRIEEAKE 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 41152289   111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAITGEGVQDGMNWICNNL 182
Cdd:pfam00025  89 ELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLHELKDRPWEIQGCSAVTGEGLDEGLDWLSNYI 160
Arf_Arl cd00878
ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ...
 31-181 1.71e-74

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: 220.91  E-value: 1.71e-74
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:cd00878   8 DGAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSDRERIEEAKN 87

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41152289 111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAITGEGVQDGMNWICNN 181
Cdd:cd00878  88 ELHKLLNEEELKGAPLLILANKQDLPGALTESELIELLGLESIKGRRWHIQPCSAVTGDGLDEGLDWLIEQ 158
Arl2 cd04154
Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind ...
 8-181 2.30e-70

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: 211.03  E-value: 2.30e-70
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289   8 LLSVMQKLKgSSELELRILLLGLDNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYL 87
Cdd:cd04154   1 LLTILRKTK-QKEREMRILMLGLDNAGKTTILKKFNGEDISTISPTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYF 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  88 ENTDLLVYVIDSADKKRFEETGLELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAIT 167
Cdd:cd04154  80 ESTDALIWVVDSSDRARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALSPEEIREVLELDSIKSHHWRIFGCSAVT 159

                       170
                ....*....|....
gi 41152289 168 GEGVQDGMNWICNN 181
Cdd:cd04154 160 GENLLDGIDWLVDD 173
Arl1 cd04151
ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi ...
 31-180 2.72e-58

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: 179.91  E-value: 2.72e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:cd04151   8 DGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTDRDRLGISKS 87

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289 111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAITGEGVQDGMNWICN 180
Cdd:cd04151  88 ELHAMLEEEELKDAVLLVFANKQDMPGALSEAEVAEKLGLSELKDRTWQIFKTSATKGEGLDEGMDWLVN 157
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
 31-185 1.52e-53

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 168.61  E-value: 1.52e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289   31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:PLN00223  26 DAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRDRVVEARD 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41152289  111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAITGEGVQDGMNWICNNLVNR 185
Cdd:PLN00223 106 ELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRQRHWYIQSTCATSGEGLYEGLDWLSNNIANK 180
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
 31-184 1.69e-53

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: 168.18  E-value: 1.69e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289     31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:smart00177  22 DAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDEARE 101

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41152289    111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAITGEGVQDGMNWICNNLVN 184
Cdd:smart00177 102 ELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLHSIRDRNWYIQPTCATSGDGLYEGLTWLSNNLKN 175
Arl5_Arl8 cd04153
Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like ...
 31-181 2.50e-53

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: 167.91  E-value: 2.50e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:cd04153  24 DNAGKTTILYQFLLGEVVHTSPTIGSNVEEIVYKNIRFLMWDIGGQESLRSSWNTYYTNTDAVILVIDSTDRERLPLTKE 103

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41152289 111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAITGEGVQDGMNWICNN 181
Cdd:cd04153 104 ELYKMLAHEDLRKAVLLVLANKQDLKGAMTPAEISESLGLTSIRDHTWHIQGCCALTGEGLPEGLDWIASR 174
ARLTS1 cd04156
Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), ...
 31-175 1.18e-52

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: 165.67  E-value: 1.18e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  31 DNAGKTTLL-KSLASEDVNTItPTQGFNIKTV-ASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEET 108
Cdd:cd04156   8 DSAGKSTLLyKLKHAELVTTI-PTVGFNVEMLqLEKHLSLTVWDVGGQEKMRTVWKCYLENTDGLVYVVDSSDEARLDES 86

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41152289 109 GLELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRD-RVWQIQACSAITGEGVQDGM 175
Cdd:cd04156  87 QKELKHILKNEHIKGVPVVLLANKQDLPGALTAEEITRRFKLKKYCSdRDWYVQPCSAVTGEGLAEAF 154
Arf6 cd04149
ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins ...
 31-181 1.40e-51

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: 163.02  E-value: 1.40e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:cd04149  18 DAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDSADRDRIDEARQ 97

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41152289 111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAITGEGVQDGMNWICNN 181
Cdd:cd04149  98 ELHRIINDREMRDALLLVFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLSSN 168
Arf1_5_like cd04150
ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like ...
 31-181 1.13e-50

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: 160.65  E-value: 1.13e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:cd04150   9 DAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERIGEARE 88

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41152289 111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAITGEGVQDGMNWICNN 181
Cdd:cd04150  89 ELQRMLNEDELRDAVLLVFANKQDLPNAMSAAEVTDKLGLHSLRNRNWYIQATCATSGDGLYEGLDWLSNN 159
PTZ00133 PTZ00133
ADP-ribosylation factor; Provisional
 31-187 1.68e-50

ADP-ribosylation factor; Provisional


Pssm-ID: 173423  Cd Length: 182  Bit Score: 160.78  E-value: 1.68e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289   31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:PTZ00133  26 DAAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNLKFTMWDVGGQDKLRPLWRHYYQNTNGLIFVVDSNDRERIGDARE 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41152289  111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAITGEGVQDGMNWICNNLVNRKK 187
Cdd:PTZ00133 106 ELERMLSEDELRDAVLLVFANKQDLPNAMSTTEVTEKLGLHSVRQRNWYIQGCCATTAQGLYEGLDWLSANIKKSMQ 182
Arl4_Arl7 cd04152
Arf-like 4 (Arl4) and 7 (Arl7) GTPases; Arl4 (Arf-like 4) is highly expressed in testicular ...
 31-187 3.64e-47

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: 152.26  E-value: 3.64e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  31 DNAGKTTLLKSLA-SEDVNTItPTQGFNIKTV-----ASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKR 104
Cdd:cd04152  12 DSAGKTTVLYRLKfNEFVNTV-PTKGFNTEKIkvslgNAKGVTFHFWDVGGQEKLRPLWKSYTRCTDGIVFVVDSVDVER 90

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289 105 FEETGLELSELID-EENLcGVPVLIFANKQDLGTAAPASEIAEGLNLHT-YRDRVWQIQACSAITGEGVQDGMNWICNNL 182
Cdd:cd04152  91 MEEAKTELHKITKfSENQ-GVPVLVLANKQDLPNALPVSEVEKLLALHElSSSTPWHVQPACAIIGEGLQEGLEKLYEMI 169


                ....*
gi 41152289 183 VNRKK 187
Cdd:cd04152 170 LKRRK 174
Arfrp1 cd04160
Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a ...
 31-178 1.68e-45

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: 147.49  E-value: 1.68e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  31 DNAGKTTLLKSLASEDV--------NTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADK 102
Cdd:cd04160   8 DNAGKTTFLEQTKTKFSknykglnpSKITPTVGLNIGTIEVGKARLMFWDLGGQEELRSLWDKYYAESHGVIYVIDSTDR 87

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41152289 103 KRFEETGLELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLN--LHTYRDRVWQIQACSAITGEGVQDGMNWI 178
Cdd:cd04160  88 ERFNESKSAFEKVINNEALEGVPLLVLANKQDLPDALSVAEIKEVFDdcIALIGRRDCLVQPVSALEGEGVEEGIEWL 165
Arl6 cd04157
Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small ...
 31-178 1.56e-40

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: 134.86  E-value: 1.56e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  31 DNAGKTTLLKSLASEDVNT--ITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEET 108
Cdd:cd04157   8 DNSGKTTIINQLKPSNAQSqnIVPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVA 87

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 41152289 109 GLELSELIDEENLC--GVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAITGEGVQDGMNWI 178
Cdd:cd04157  88 KDELELLLNHPDIKhrRIPILFYANKMDLPDALTAVKITQLLCLENIKDKPWHIFASSALTGEGLDEGVDWL 159
ARD1 cd04158
(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein ...
 31-183 6.56e-40

(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: 133.62  E-value: 6.56e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:cd04158   8 DGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRDRVSEAHS 87

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41152289 111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTY-RDRVWQIQACSAITGEGVQDGMNWICNNLV 183
Cdd:cd04158  88 ELAKLLTEKELRDALLLIFANKQDVAGALSVEEMTELLSLHKLcCGRSWYIQGCDARSGMGLYEGLDWLSRQLV 161
Arl9_Arfrp2_like cd04162
Arf-like 9 (Arl9)/Arfrp2-like GTPase; Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first ...
 31-167 9.45e-38

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: 127.56  E-value: 9.45e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  31 DNAGKTTLLKSLASEDVN-TITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETG 109
Cdd:cd04162   8 DGAGKTSLLHSLSSERSLeSVVPTTGFNSVAIPTQDAIMELLEIGGSQNLRKYWKRYLSGSQGLIFVVDSADSERLPLAR 87

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 41152289 110 LELSELIDEEnlCGVPVLIFANKQDLGTAAPASEIAEGLNLHTY-RDRVWQIQACSAIT 167
Cdd:cd04162  88 QELHQLLQHP--PDLPLVVLANKQDLPAARSVQEIHKELELEPIaRGRRWILQGTSLDD 144
Sar1 cd00879
Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII ...
 31-178 5.69e-37

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: 126.62  E-value: 5.69e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:cd00879  28 DNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTIGNVKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAADPERFQESKE 107

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289 111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLH---TYRDRVWQIQA---------CSAITGEGVQDGMNWI 178
Cdd:cd00879 108 ELDSLLNDEELANVPILILGNKIDKPGAVSEEELREALGLYgttTGKGGVSLKVSnirpvevfmCSVVKRQGYGEGFRWL 187
Arl10_like cd04159
Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from ...
 32-178 7.97e-36

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: 122.81  E-value: 7.97e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  32 NAGKTTLLKSLASED--VNTItPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETG 109
Cdd:cd04159   9 NSGKTTLVNVIASGQfsEDTI-PTVGFNMRKVTKGNVTIKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADREKLEVAK 87

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41152289 110 LELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRVWQIQACSAITGEGVQDGMNWI 178
Cdd:cd04159  88 NELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELIEQMNLKSITDREVSCYSISAKEKTNIDIVLDWL 156
Arl2l1_Arl13_like cd04161
Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ...
 31-181 2.17e-26

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: 98.62  E-value: 2.17e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:cd04161   8 DNAGKTTLVSALQGEIPKKVAPTVGFTPTKLRLDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSDDDRVQEVKE 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289 111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDR---VWQIQACSAITGEG------VQDGMNWICNN 181
Cdd:cd04161  88 ILRELLQHPRVSGKPILVLANKQDKKNALLGADVIEYLSLEKLVNEnksLCHIEPCSAIEGLGkkidpsIVEGLRWLLAA 167
SAR smart00178
Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene ...
 31-178 9.23e-26

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: 97.70  E-value: 9.23e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289     31 DNAGKTTLLKSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGL 110
Cdd:smart00178  26 DNAGKTTLLHMLKNDRLAQHQPTQHPTSEELAIGNIKFTTFDLGGHQQARRLWKDYFPEVNGIVYLVDAYDKERFAESKR 105

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41152289    111 ELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRD-------RVWQIQACSAITGEGVQDGMNWI 178
Cdd:smart00178 106 ELDALLSDEELATVPFLILGNKIDAPYAASEDELRYALGLTNTTTgkgkvgvRPVEVFMCSVVRRMGYGEGFKWL 180
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
32-173 1.01e-18

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 78.87  E-value: 1.01e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  32 NAGKTTLLKSLASEDVNT--ITPTQGFNIK----TVASRGMKLNVWDIGGQ---RKIRPFWKKYLENTDLLVYVIDSADK 102
Cdd:COG1100  13 GVGKTSLVNRLVGDIFSLekYLSTNGVTIDkkelKLDGLDVDLVIWDTPGQdefRETRQFYARQLTGASLYLFVVDGTRE 92

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41152289 103 KRFeETGLELSELIDEENLcGVPVLIFANKQDLGTA---APASEIAEGLNlhtyRDRVWQIQACSAITGEGVQD 173
Cdd:COG1100  93 ETL-QSLYELLESLRRLGK-KSPIILVLNKIDLYDEeeiEDEERLKEALS----EDNIVEVVATSAKTGEGVEE 160
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 32-180 3.42e-18

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: 77.11  E-value: 3.42e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  32 NAGKTTLLKSLASEDV----NTITPTQGFNI--KTVASRGMKLNVWDIGGQRKIRPFW-----KKYLENTDLLVYVIDSA 100
Cdd:cd00882   7 GVGKSSLLNALLGGEVgevsDVPGTTRDPDVyvKELDKGKVKLVLVDTPGLDEFGGLGreelaRLLLRGADLILLVVDST 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289 101 DKKRFEETGLELSELIDEEnlcGVPVLIFANKQDLGTAAPASEIAEGLNLhtYRDRVWQIQACSAITGEGVQDGMNWICN 180
Cdd:cd00882  87 DRESEEDAKLLILRRLRKE---GIPIILVGNKIDLLEEREVEELLRLEEL--AKILGVPVFEVSAKTGEGVDELFEKLIE 161
SR_beta cd04105
Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ...
 32-174 7.36e-14

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: 66.58  E-value: 7.36e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  32 NAGKTTLLKSLAS----EDVNTITPTQGFnIKTVASRGMKLNVWDIGGQRKIRP-FWKKYLENTDLLVYVIDSAD-KKRF 105
Cdd:cd04105  10 DSGKTALFTKLTTgkvrSTVTSIEPNVAS-FYSNSSKGKKLTLVDVPGHEKLRDkLLEYLKASLKAIVFVVDSATfQKNI 88

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41152289 106 EETGLELSE-LIDEENL-CGVPVLIFANKQDLGTAAPASEIAEGL--NLHTYR-DRVWQIQACSAITGEGVQDG 174
Cdd:cd04105  89 RDVAEFLYDiLTDLEKIkNKIPILIACNKQDLFTAKPAKKIKELLekEINTLReSRSKSLESLDGDDGSKDTLG 162
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 31-138 3.12e-10

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: 56.23  E-value: 3.12e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289    31 DNAGKTTLLKSLA------SEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSAD-KK 103
Cdd:TIGR00231  10 PNVGKSTLLNSLLgnkgsiTEYYPGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDAIRRLYYPQVERSLRVFDIVIlVL 89

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 41152289   104 RFEETGLELSELIDEENLCGVPVLIFANKQDLGTA 138
Cdd:TIGR00231  90 DVEEILEKQTKEIIHHADSGVPIILVGNKIDLKDA 124
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
 34-173 5.02e-09

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: 52.90  E-value: 5.02e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289    34 GKTTLLKSLASED-VNTITPTQG--FNIKTVA--SRGMKLNVWDIGGQRKIRPFWKKYLENTD--LLVYVIDSADKkrFE 106
Cdd:pfam00071  11 GKSSLLIRFTQNKfPEEYIPTIGvdFYTKTIEvdGKTVKLQIWDTAGQERFRALRPLYYRGADgfLLVYDITSRDS--FE 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 41152289   107 ETGLELSELIDEENlCGVPVLIFANKQDLG-----TAAPASEIAEGLNLhTYRDrvwqiqaCSAITGEGVQD 173
Cdd:pfam00071  89 NVKKWVEEILRHAD-ENVPIVLVGNKCDLEdqrvvSTEEGEALAKELGL-PFME-------TSAKTNENVEE 151
PLN03118 PLN03118
Rab family protein; Provisional
 34-105 2.11e-08

Rab family protein; Provisional


Pssm-ID: 215587 [Multi-domain]  Cd Length: 211  Bit Score: 51.98  E-value: 2.11e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 41152289   34 GKTTLLKSLASEDVNTITPTQG--FNIK--TVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRF 105
Cdd:PLN03118  26 GKSSLLVSFISSSVEDLAPTIGvdFKIKqlTVGGKRLKLTIWDTAGQERFRTLTSSYYRNAQGIILVYDVTRRETF 101
trmE cd04164
trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in ...
 32-173 6.06e-08

trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance.


Pssm-ID: 206727 [Multi-domain]  Cd Length: 159  Bit Score: 49.80  E-value: 6.06e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  32 NAGKTTLLKSLASEDVNTITPTQG---------FNIKtvasrGMKLNVWDIGGQRK---------IRPFWKKyLENTDLL 93
Cdd:cd04164  13 NVGKSSLLNALAGRDRAIVSDIAGttrdvieeeIDLG-----GIPVRLIDTAGLREtedeiekigIERAREA-IEEADLV 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  94 VYVIDSadkkrfeETGLELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHtyrdrvwqiqACSAITGEGVQD 173
Cdd:cd04164  87 LLVVDA-------SEGLDEEDLEILELPAKKPVIVVLNKSDLLSDAEGISELNGKPII----------AISAKTGEGIDE 149
HflX cd01878
HflX GTPase family; HflX subfamily. A distinct conserved domain with a glycine-rich segment ...
 32-182 1.49e-07

HflX GTPase family; HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.


Pssm-ID: 206666 [Multi-domain]  Cd Length: 204  Bit Score: 49.38  E-value: 1.49e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  32 NAGKTTLLKSLASEDV-------NTITPTqgfniktvaSRGMKLnvwdiGGQRK---------IR--PFW-----KKYLE 88
Cdd:cd01878  51 NAGKSTLFNALTGADVlaedqlfATLDPT---------TRRIKL-----PGGREvlltdtvgfIRdlPHQlveafRSTLE 116

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  89 NT---DLLVYVIDSADKKRFE--ETGLE-LSELideeNLCGVPVLIFANKQDLgtaAPASEIAEGLnLHTYRDRVWqIqa 162
Cdd:cd01878 117 EVaeaDLLLHVVDASDPDREEqiETVEEvLKEL----GADDIPIILVLNKIDL---LDDEELEERL-RAGRPDAVF-I-- 185

                       170       180
                ....*....|....*....|
gi 41152289 163 cSAITGEGVQDGMNWICNNL 182
Cdd:cd01878 186 -SAKTGEGLDLLKEAIEELL 204
Rab cd00154
Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ...
 34-173 2.62e-07

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: 47.84  E-value: 2.62e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  34 GKTTLLKSLASED-VNTITPTQG--FNIKTVASRG--MKLNVWDIGGQ---RKIRPFwkkYLENTD--LLVYviDSADKK 103
Cdd:cd00154  12 GKTSLLLRFVDNKfSENYKSTIGvdFKSKTIEVDGkkVKLQIWDTAGQerfRSITSS---YYRGAHgaILVY--DVTNRE 86

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41152289 104 RFEETgLELSELIDEENLCGVPVLIFANKQDLG-----TAAPASEIAEGLNLHTYrdrvwqiqACSAITGEGVQD 173
Cdd:cd00154  87 SFENL-DKWLNELKEYAPPNIPIILVGNKSDLEderqvSTEEAQQFAKENGLLFF--------ETSAKTGENVDE 152
SRPRB pfam09439
Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition ...
 32-148 2.66e-07

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: 48.21  E-value: 2.66e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289    32 NAGKTTLLKSLASedvNTITPTQ-----GFNIKTVASRGMKLNVWDIGGQRKIRPFWK---KYLENTDLLVYVIDSA-DK 102
Cdd:pfam09439  13 DSGKTSLFTLLTT---DSVRPTVtsqepSAAYRYMLNKGNSFTLIDFPGHVKLRYKLLetlKDSSSLKGIVFVVDSTiFP 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 41152289   103 KRFEETGLELSE--LIDEENLCGVPVLIFANKQDLGTAAPASEIAEGL 148
Cdd:pfam09439  90 KEVTDTAEFLYDilSITELLKNGIDILIACNKQESFTARPPKKIKQAL 137
Roc pfam08477
Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial ...
 32-134 3.88e-07

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: 46.73  E-value: 3.88e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289    32 NAGKTTLLKSLASEDVNTIT-PTQG--FNIKTVASRG-----MKLNVWDIGGQ---RKIRPFwkkYLENTDLLVYVIDSA 100
Cdd:pfam08477   9 GVGKTSLLKRFVDDTFDPKYkSTIGvdFKTKTVLENDdngkkIKLNIWDTAGQerfRSLHPF---YYRGAAAALLVYDSR 85

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 41152289   101 DKKRFEEtglELSELideENLCG-VPVLIFANKQD 134
Cdd:pfam08477  86 TFSNLKY---WLREL---KKYAGnSPVILVGNKID 114
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 32-132 6.83e-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: 46.07  E-value: 6.83e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289    32 NAGKTTLLKSLASEDVNTI-TP--TQGFNIKTVASRGMKLNVWDIGG--------QRKIRPFwkKYLENTDLLVYVIDSA 100
Cdd:pfam01926   9 NVGKSTLINALTGAKAIVSdYPgtTRDPNEGRLELKGKQIILVDTPGliegasegEGLGRAF--LAIIEADLILFVVDSE 86

                          90       100       110
                  ....*....|....*....|....*....|..
gi 41152289   101 DKkrFEETGLELSELIDEENlcgVPVLIFANK 132
Cdd:pfam01926  87 EG--ITPLDEELLELLRENK---KPIILVLNK 113
Era_like cd00880
E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ...
 32-173 8.10e-07

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: 46.86  E-value: 8.10e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  32 NAGKTTLLKSLASEDVNTITPTQGFNiKTVASRGMKLN------------VWDIGGQRKIRP--FWKKyLENTDLLVYVI 97
Cdd:cd00880   7 NVGKSSLLNALLGQNVGIVSPIPGTT-RDPVRKEWELLplgpvvlidtpgLDEEGGLGRERVeeARQV-ADRADLVLLVV 84

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 41152289  98 DSaDKKRFEETglelsELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTYRDRvwQIQACSAITGEGVQD 173
Cdd:cd00880  85 DS-DLTPVEEE-----AKLGLLRERGKPVLLVLNKIDLVPESEEEELLRERKLELLPDL--PVIAVSALPGEGIDE 152
trmE PRK05291
tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE;
32-173 4.29e-06

tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE;


Pssm-ID: 235392 [Multi-domain]  Cd Length: 449  Bit Score: 45.87  E-value: 4.29e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289   32 NAGKTTLLKSLASEDVNTITPTQG---------FNIKtvasrGMKLNVWDIGGQRK---------IRPFWKKyLENTDLL 93
Cdd:PRK05291 225 NVGKSSLLNALLGEERAIVTDIAGttrdvieehINLD-----GIPLRLIDTAGIREtddevekigIERSREA-IEEADLV 298

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289   94 VYVIDSadkkrfeETGLELSELIDEENLCGVPVLIFANKQDLGTAAPASEIAEGLNLHTyrdrvwqiqacSAITGEGVQD 173
Cdd:PRK05291 299 LLVLDA-------SEPLTEEDDEILEELKDKPVIVVLNKADLTGEIDLEEENGKPVIRI-----------SAKTGEGIDE 360
Rab6 cd01861
Rab GTPase family 6 (Rab6); Rab6 is involved in microtubule-dependent transport pathways ...
 34-182 4.64e-06

Rab GTPase family 6 (Rab6); Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. 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: 206654 [Multi-domain]  Cd Length: 161  Bit Score: 44.54  E-value: 4.64e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  34 GKTTLLKSLASEDV-NTITPTQG--FNIKT--VASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEET 108
Cdd:cd01861  12 GKTSIITRFMYDTFdNQYQATIGidFLSKTmyVDDKTVRLQLWDTAGQERFRSLIPSYIRDSSVAVVVYDITNRQSFDNT 91

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41152289 109 GLELSELIDEENlCGVPVLIFANKQDLG-----TAAPASEIAEGLNLHTYRdrvwqiqaCSAITGEGVQDGMNWICNNL 182
Cdd:cd01861  92 DKWIDDVRDERG-NDVIIVLVGNKTDLSdkrqvSTEEGEKKAKENNAMFIE--------TSAKAGHNVKQLFKKIAQAL 161
Obg cd01898
Obg GTPase; The Obg nucleotide binding protein subfamily has been implicated in stress ...
 85-173 5.36e-06

Obg GTPase; The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans. The E. coli homolog, ObgE is believed to function in ribosomal biogenesis. Members of the subfamily contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain.


Pssm-ID: 206685 [Multi-domain]  Cd Length: 170  Bit Score: 44.34  E-value: 5.36e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  85 KYLENTDLLVYVIDSADKKRFEETgleLSELIDE-----ENLCGVPVLIFANKQDLgtaAPASEIAEGLNLHTYRDRVWQ 159
Cdd:cd01898  74 RHIERTRVLLHVIDLSGEDDPVED---YETIRNEleaynPGLAEKPRIVVLNKIDL---LDAEERFEKLKELLKELKGKK 147

                        90
                ....*....|....
gi 41152289 160 IQACSAITGEGVQD 173
Cdd:cd01898 148 VFPISALTGEGLDE 161
RocCOR cd09914
Ras of complex proteins (Roc) C-terminal of Roc (COR) domain family; RocCOR (or Roco) protein ...
 32-180 7.85e-06

Ras of complex proteins (Roc) C-terminal of Roc (COR) domain family; RocCOR (or Roco) protein family is characterized by a superdomain containing a Ras-like GTPase domain, called Roc (Ras of complex proteins), and a characteristic second domain called COR (C-terminal of Roc). A kinase domain and diverse regulatory domains are also often found in Roco proteins. Their functions are diverse; in Dictyostelium discoideum, which encodes 11 Roco proteins, they are involved in cell division, chemotaxis and development, while in human, where 4 Roco proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded, these proteins are involved in epilepsy and cancer. Mutations in LRRK2 (leucine-rich repeat kinase 2) are known to cause familial Parkinson's disease.


Pssm-ID: 206741 [Multi-domain]  Cd Length: 161  Bit Score: 43.86  E-value: 7.85e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  32 NAGKTTLLKSLASEDVNTITPT------QGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKkrF 105
Cdd:cd09914  11 GVGKTSLCKQLIGEKFDGDESSthginvQDWKIPAPERKKIRLNVWDFGGQEIYHATHQFFLTSRSLYLLVFDLRTG--D 88

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41152289 106 EETGLELSELIDEENLCGVPVLIFANKQDlgtAAPASEIAEGLNLHTYRDRVWQIQACSAITGEGVQDGMNWICN 180
Cdd:cd09914  89 EVSRVPYWLRQIKAFGGVSPVILVGTHID---ESCDEDILKKALNKKFPAIINDIHFVSCKNGKGIAELKKAIAK 160
RabL4 cd04101
Rab GTPase-like family 4 (Rab-like4); RabL4 (Rab-like4) subfamily. RabL4s are novel proteins ...
 34-172 2.01e-05

Rab GTPase-like family 4 (Rab-like4); RabL4 (Rab-like4) subfamily. RabL4s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL4 lacks a prenylation site at the C-terminus. The specific function of RabL4 remains unknown.


Pssm-ID: 206688 [Multi-domain]  Cd Length: 167  Bit Score: 42.90  E-value: 2.01e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  34 GKTTLLKSLASEDVN-----TITPTQGFNIKTV----ASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKR 104
Cdd:cd04101  12 GKSALVQMFHSDGATfqknyTMTTGCDLVVKTVpvpdTSDSVELFIFDSAGQELFSDMVENVWEQPAVVCVVYDVTNEVS 91

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41152289 105 FEETGLELSELIDEENLCGVPVLIFANKQDLG-----TAAPASEIAEGLNLHTYRdrvwqiqaCSAITGEGVQ 172
Cdd:cd04101  92 FNNCSRWINRVRTHSHGLHTPGVLVGNKCDLTdrrevDAAQAQALAQANTLKFYE--------TSAKEGVGYE 156
G-alpha pfam00503
G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular ...
 45-135 6.20e-05

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: 42.19  E-value: 6.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289    45 EDV-NTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSA--------DKK--RFEETgLEL- 112
Cdd:pfam00503 145 QDIlRARVKTTGIIETKFEFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVSLSeydqvlyeDDStnRMEES-LKLf 223

                          90       100
                  ....*....|....*....|...
gi 41152289   113 SELIDEENLCGVPVLIFANKQDL 135
Cdd:pfam00503 224 EEICNSPWFKNTPIILFLNKKDL 246
MnmE_helical pfam12631
MnmE helical domain; The tRNA modification GTPase MnmE consists of three domains. An ...
 32-173 6.47e-05

MnmE helical domain; The tRNA modification GTPase MnmE consists of three domains. An N-terminal domain, a helical domain and a GTPase domain which is nested within the helical domain. This family represents the helical domain.


Pssm-ID: 463649 [Multi-domain]  Cd Length: 326  Bit Score: 42.47  E-value: 6.47e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289    32 NAGKTTLLKSLASEDVNTITPTQG---------FNIKtvasrGMKLNVWD-------------IGGQRKirpfwKKYLEN 89
Cdd:pfam12631 104 NVGKSSLLNALLGEERAIVTDIPGttrdvieetINIG-----GIPLRLIDtagiretddevekIGIERA-----REAIEE 173

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289    90 TDLLVYVIDSADKkrFEETGLELSELIDEenlcGVPVLIFANKQDLGTAAPASEIAEGLNlhtyrdrvwqIQACSAITGE 169
Cdd:pfam12631 174 ADLVLLVLDASRP--LDEEDLEILELLKD----KKPIIVVLNKSDLLGEIDELEELKGKP----------VLAISAKTGE 237


                  ....
gi 41152289   170 GVQD 173
Cdd:pfam12631 238 GLDE 241
Rab18 cd01863
Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic ...
 34-173 6.61e-05

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: 41.53  E-value: 6.61e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  34 GKTTLLKSLASEDVN-TITPTQG--FNIKTVASRG--MKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEET 108
Cdd:cd01863  12 GKSSLLLRFTDDTFDeDLSSTIGvdFKVKTVTVDGkkVKLAIWDTAGQERFRTLTSSYYRGAQGVILVYDVTRRDTFDNL 91

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41152289 109 GLELSELideENLCGVPVLIF---ANKQDLGTAAPASEiaEGLNLHtyRDRVWQIQACSAITGEGVQD 173
Cdd:cd01863  92 DTWLNEL---DTYSTNPDAVKmlvGNKIDKENREVTRE--EGQKFA--RKHNMLFIETSAKTRIGVQQ 152
HflX COG2262
50S ribosomal subunit-associated GTPase HflX [Translation, ribosomal structure and biogenesis]; ...
 32-173 6.83e-05

50S ribosomal subunit-associated GTPase HflX [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441863 [Multi-domain]  Cd Length: 419  Bit Score: 42.38  E-value: 6.83e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  32 NAGKTTLLKSLASEDV---N----TITPTqgfniktvaSRGMKLnvwdiGGQRK---------IR--P------FwKKYL 87
Cdd:COG2262 209 NAGKSTLFNRLTGADVlaeDklfaTLDPT---------TRRLEL-----PDGRPvlltdtvgfIRklPhqlveaF-RSTL 273

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  88 ENT---DLLVYVIDSADKKRFE--ETGLE-LSELideeNLCGVPVLIFANKQDLGTAAPASEIAEGlnlhtYRDRVWqIq 161
Cdd:COG2262 274 EEVreaDLLLHVVDASDPDFEEqiETVNEvLEEL----GADDKPIILVFNKIDLLDDEELERLRAG-----YPDAVF-I- 342

                       170
                ....*....|..
gi 41152289 162 acSAITGEGVQD 173
Cdd:COG2262 343 --SAKTGEGIDE 352
Gtr1_RagA pfam04670
Gtr1/RagA G protein conserved region; GTR1 was first identified in S. cerevisiae as a ...
 46-165 1.33e-04

Gtr1/RagA G protein conserved region; GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologs of Gtr1. Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B.


Pssm-ID: 398377 [Multi-domain]  Cd Length: 231  Bit Score: 41.03  E-value: 1.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289    46 DVNTITPTQGFNIKTVASRG-MKLNVWDIGGQRKirpFWKKYL--------ENTDLLVYVIDsADKKRFEETGLELSELI 116
Cdd:pfam04670  27 DTLRLGATIDVEHSHVRFLGnLVLNLWDCGGQDD---FFDNYLtfqkehifSNVGVLIYVFD-VQSREYEEDLARLKETI 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 41152289   117 deENL------CGVPVLIfaNKQDLgtaapaseIAEGLNLHTYRDRVWQIQACSA 165
Cdd:pfam04670 103 --EALyqyspdAKVFVLI--HKMDL--------IQEDHREEIFRDRKQEIREESE 145
MnmE COG0486
tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal ...
 32-173 2.80e-04

tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal structure and biogenesis]; tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440253 [Multi-domain]  Cd Length: 448  Bit Score: 40.43  E-value: 2.80e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  32 NAGKTTLLKSLASEDVNTITPTQG---------FNIktvasRGMKLNVWDIGGQRK---------IRPFWKKyLENTDLL 93
Cdd:COG0486 223 NVGKSSLLNALLGEERAIVTDIAGttrdvieerINI-----GGIPVRLIDTAGLREtedevekigIERAREA-IEEADLV 296

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  94 VYVIDSADkkrfeetGLELSELIDEENLCGVPVLIFANKQDLGTAAPAsEIAEGLNLHTYRdrvwqiqaCSAITGEGVQD 173
Cdd:COG0486 297 LLLLDASE-------PLTEEDEEILEKLKDKPVIVVLNKIDLPSEADG-ELKSLPGEPVIA--------ISAKTGEGIDE 360
Rab12 cd04120
Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was ...
 34-137 3.35e-04

Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was localized to the Golgi complex. The specific function of Rab12 remains unknown, and inconsistent results about its cellular localization have been reported. More recent studies have identified Rab12 associated with post-Golgi vesicles, or with other small vesicle-like structures but not with the Golgi complex. 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. 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.


Pssm-ID: 206699 [Multi-domain]  Cd Length: 202  Bit Score: 40.00  E-value: 3.35e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  34 GKTTLLKSLASEDVNTITPTQ---GFNIKTVASRGMK--LNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEET 108
Cdd:cd04120  12 GKTSLMERFTDDTFCEACKSTvgvDFKIKTVELRGKKirLQIWDTAGQERFNSITSAYYRSAKGIILVYDITKKETFDDL 91

                        90       100
                ....*....|....*....|....*....
gi 41152289 109 GlELSELIDEENLCGVPVLIFANKQDLGT 137
Cdd:cd04120  92 P-KWMKMIDKYASEDAELLLVGNKLDCET 119
Rho cd00157
Ras homology family (Rho) of small guanosine triphosphatases (GTPases); Members of the Rho ...
 34-173 4.19e-04

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: 39.06  E-value: 4.19e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  34 GKTTLLKSLAS-----EDVNTITPTQGFNIkTVASRGMKLNVWDIGGQ---RKIRPFwkKYlENTD--LLVYVIDSAD-- 101
Cdd:cd00157  12 GKTCLLISYTTnkfptEYVPTVFDNYSANV-TVDGKQVNLGLWDTAGQeeyDRLRPL--SY-PQTDvfLLCFSVDSPSsf 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289 102 ---KKRFeetgleLSELIdeENLCGVPVLIFANKQDL-GTAAPASEIAEGLNLHTY---RDRVWQIQA-----CSAITGE 169
Cdd:cd00157  88 envKTKW------YPEIK--HYCPNVPIILVGTKIDLrDDGNTLKKLEKKQKPITPeegEKLAKEIGAvkymeCSALTQE 159


                ....
gi 41152289 170 GVQD 173
Cdd:cd00157 160 GLKE 163
PTZ00099 PTZ00099
rab6; Provisional
 66-136 4.26e-04

rab6; Provisional


Pssm-ID: 185444 [Multi-domain]  Cd Length: 176  Bit Score: 39.34  E-value: 4.26e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41152289   66 MKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEETGLELSELIDEENLcGVPVLIFANKQDLG 136
Cdd:PTZ00099  29 VRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERGK-DVIIALVGNKTDLG 98
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
 34-135 1.16e-03

Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 37.87  E-value: 1.16e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289     34 GKTTLLKSLASEDVNTIT-PTQG--FNIKTVASRGM--KLNVWDIGGQRKIRPFWKKYLENTD--LLVYviDSADKKRFE 106
Cdd:smart00175  12 GKSSLLSRFTDGKFSEQYkSTIGvdFKTKTIEVDGKrvKLQIWDTAGQERFRSITSSYYRGAVgaLLVY--DITNRESFE 89

                           90       100
                   ....*....|....*....|....*....
gi 41152289    107 ETGLELSELIDEENLcGVPVLIFANKQDL 135
Cdd:smart00175  90 NLENWLKELREYASP-NVVIMLVGNKSDL 117
Era cd04163
E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ...
 87-182 1.39e-03

E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.


Pssm-ID: 206726 [Multi-domain]  Cd Length: 168  Bit Score: 37.83  E-value: 1.39e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  87 LENTDLLVYVIDSadkkrFEETGLELSELIDEENLCGVPVLIFANKQDLgtAAPASEIAEGLNLHTYRDRVWQIQACSAI 166
Cdd:cd04163  80 LKDVDLVLFVVDA-----SEWIGEGDEFILELLKKSKTPVILVLNKIDL--VKDKEDLLPLLEKLKELHPFAEIFPISAL 152

                        90
                ....*....|....*.
gi 41152289 167 TGEGVQDGMNWICNNL 182
Cdd:cd04163 153 KGENVDELLEYIVEYL 168
Miro2 cd01892
Mitochondrial Rho family 2 (Miro2), C-terminal; Miro2 subfamily. Miro (mitochondrial Rho) ...
 32-135 1.55e-03

Mitochondrial Rho family 2 (Miro2), C-terminal; Miro2 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.


Pssm-ID: 206679  Cd Length: 180  Bit Score: 37.61  E-value: 1.55e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  32 NAGKTTLLKSLA--SEDVNTITPTQG--FNIKTVASRGMK--LNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRF 105
Cdd:cd01892  14 GSGKSALLQAFLgrSFSQNAYSPTIKprYAVNTVEVPGQEkyLILREVGEDEEAILLNDAELAACDVACLVYDSSDPNSF 93

                        90       100       110
                ....*....|....*....|....*....|.
gi 41152289 106 EetglELSELIDE-ENLCGVPVLIFANKQDL 135
Cdd:cd01892  94 S----YCAEVYKKyFMLGEIPCLFVAAKADL 120
Rab14 cd04122
Rab GTPase family 14 (Rab14); Rab14 GTPases are localized to biosynthetic compartments, ...
 34-173 3.35e-03

Rab GTPase family 14 (Rab14); Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles. Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments. Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation. In addition, Rab14 is believed to play a role in the regulation of phagocytosis. 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: 133322 [Multi-domain]  Cd Length: 166  Bit Score: 36.74  E-value: 3.35e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  34 GKTTLL-----KSLASEDVNTITPTQGFNIKTVASRGMKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKKRFEET 108
Cdd:cd04122  14 GKSCLLhqfteKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHL 93

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 41152289 109 GlelSELIDEENLCGVPVLIF--ANKQDLG-----TAAPASEIAEGLNLhtyrdrvwQIQACSAITGEGVQD 173
Cdd:cd04122  94 S---SWLTDARNLTNPNTVIFliGNKADLEaqrdvTYEEAKQFADENGL--------LFLECSAKTGENVED 154
Rab19 cd01864
Rab GTPase family 19 (Rab19); Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. ...
 32-135 4.42e-03

Rab GTPase family 19 (Rab19); Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet characterized. 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: 133267 [Multi-domain]  Cd Length: 165  Bit Score: 36.26  E-value: 4.42e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  32 NAGKTTLLKSLASedvNTITPTQG------FNIKTVASRG--MKLNVWDIGGQRKIRPFWKKYLENTDLLVYVIDSADKK 103
Cdd:cd01864  13 NVGKTCVVQRFKS---GTFSERQGntigvdFTMKTLEIQGkrVKLQIWDTAGQERFRTITQSYYRSANGAIIAYDITRRS 89

                        90       100       110
                ....*....|....*....|....*....|....*
gi 41152289 104 RFEetglELSELIDEENLCGVP---VLIFANKQDL 135
Cdd:cd01864  90 SFE----SVPHWIEEVEKYGASnvvLLLIGNKCDL 120
Rho2 cd04129
Ras homology family 2 (Rho2) of small guanosine triphosphatases (GTPases); Rho2 is a fungal ...
 33-173 5.77e-03

Ras homology family 2 (Rho2) of small guanosine triphosphatases (GTPases); Rho2 is a fungal GTPase that plays a role in cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction. Rho2 activates the protein kinase C homolog Pck2, and Pck2 controls Mok1, the major (1-3) alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2 regulates the construction of the cell wall. Unlike Rho1, Rho2 is not an essential protein, but its overexpression is lethal. 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 proper intracellular localization via membrane attachment. As with other Rho family GTPases, the GDP/GTP cycling is regulated by GEFs (guanine nucleotide exchange factors), GAPs (GTPase-activating proteins) and GDIs (guanine nucleotide dissociation inhibitors).


Pssm-ID: 206702 [Multi-domain]  Cd Length: 190  Bit Score: 35.96  E-value: 5.77e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41152289  33 AGKTTLLKSLA-SEDVNTITPTQGFNIKT---VASRGMKLNVWDIGGQR---KIRPFwkKYLENTDLLV-YVIDSADKKR 104
Cdd:cd04129  12 CGKTSLLYVFTlGEFPEEYHPTVFENYVTdcrVDGKPVQLALWDTAGQEeyeRLRPL--SYSKAHVILIgFAIDTPDSLE 89

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41152289 105 FEETglelsELIDEEN-LCG-VPVLIFANKQDLGTAAPASEIA---EGLNLHTYRDRVWQIQA-----CSAITGEGVQD 173
Cdd:cd04129  90 NVRT-----KWIEEVRrYCPnVPVILVGLKKDLRQEAVAKGNYatdEFVPIQQAKLVARAIGAkkymeCSALTGEGVDD 163
 
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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