ADP-ribosylation factor-like protein 3 isoform X2 [Gallus gallus]
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
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 ... |
3-176 | 4.48e-123 | ||||
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: 343.99 E-value: 4.48e-123
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| 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 ... |
3-176 | 4.48e-123 | ||||
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: 343.99 E-value: 4.48e-123
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| Arf | pfam00025 | ADP-ribosylation factor family; Pfam combines a number of different Prosite families together |
18-177 | 8.90e-92 | ||||
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together Pssm-ID: 459636 [Multi-domain] Cd Length: 160 Bit Score: 264.47 E-value: 8.90e-92
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| ARF | smart00177 | ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ... |
15-176 | 9.97e-62 | ||||
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: 188.98 E-value: 9.97e-62
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| PLN00223 | PLN00223 | ADP-ribosylation factor; Provisional |
16-180 | 3.23e-61 | ||||
ADP-ribosylation factor; Provisional Pssm-ID: 165788 Cd Length: 181 Bit Score: 187.87 E-value: 3.23e-61
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| Gem1 | COG1100 | GTPase SAR1 family domain [General function prediction only]; |
17-168 | 1.59e-19 | ||||
GTPase SAR1 family domain [General function prediction only]; Pssm-ID: 440717 [Multi-domain] Cd Length: 177 Bit Score: 80.80 E-value: 1.59e-19
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| small_GTP | TIGR00231 | small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ... |
17-133 | 1.82e-15 | ||||
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: 70.09 E-value: 1.82e-15
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| 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 ... |
3-176 | 4.48e-123 | ||||
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: 343.99 E-value: 4.48e-123
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| Arf | pfam00025 | ADP-ribosylation factor family; Pfam combines a number of different Prosite families together |
18-177 | 8.90e-92 | ||||
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together Pssm-ID: 459636 [Multi-domain] Cd Length: 160 Bit Score: 264.47 E-value: 8.90e-92
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| Arl2 | cd04154 | Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind ... |
3-176 | 4.47e-86 | ||||
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: 250.32 E-value: 4.47e-86
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| Arf_Arl | cd00878 | ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ... |
19-176 | 3.88e-85 | ||||
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: 247.49 E-value: 3.88e-85
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| Arl1 | cd04151 | ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi ... |
19-173 | 4.97e-68 | ||||
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: 204.18 E-value: 4.97e-68
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| Arl5_Arl8 | cd04153 | Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like ... |
14-176 | 9.12e-62 | ||||
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: 189.10 E-value: 9.12e-62
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| ARF | smart00177 | ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ... |
15-176 | 9.97e-62 | ||||
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: 188.98 E-value: 9.97e-62
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| PLN00223 | PLN00223 | ADP-ribosylation factor; Provisional |
16-180 | 3.23e-61 | ||||
ADP-ribosylation factor; Provisional Pssm-ID: 165788 Cd Length: 181 Bit Score: 187.87 E-value: 3.23e-61
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| PTZ00133 | PTZ00133 | ADP-ribosylation factor; Provisional |
16-182 | 2.32e-60 | ||||
ADP-ribosylation factor; Provisional Pssm-ID: 173423 Cd Length: 182 Bit Score: 185.82 E-value: 2.32e-60
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| Arf6 | cd04149 | ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins ... |
15-176 | 3.18e-60 | ||||
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: 184.98 E-value: 3.18e-60
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| Arf1_5_like | cd04150 | ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like ... |
18-176 | 5.91e-59 | ||||
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: 181.45 E-value: 5.91e-59
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| ARLTS1 | cd04156 | Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), ... |
19-170 | 5.12e-56 | ||||
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: 173.76 E-value: 5.12e-56
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| Arfrp1 | cd04160 | Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a ... |
20-172 | 2.63e-52 | ||||
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: 164.82 E-value: 2.63e-52
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| Arl6 | cd04157 | Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small ... |
20-172 | 3.95e-47 | ||||
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: 151.43 E-value: 3.95e-47
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| Arl4_Arl7 | cd04152 | Arf-like 4 (Arl4) and 7 (Arl7) GTPases; Arl4 (Arf-like 4) is highly expressed in testicular ... |
16-170 | 5.90e-45 | ||||
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: 146.48 E-value: 5.90e-45
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| ARD1 | cd04158 | (ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein ... |
19-179 | 6.81e-45 | ||||
(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: 145.94 E-value: 6.81e-45
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| Arl10_like | cd04159 | Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from ... |
20-176 | 4.35e-43 | ||||
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: 140.92 E-value: 4.35e-43
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| Arl9_Arfrp2_like | cd04162 | Arf-like 9 (Arl9)/Arfrp2-like GTPase; Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first ... |
20-160 | 8.40e-43 | ||||
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: 140.28 E-value: 8.40e-43
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| Sar1 | cd00879 | Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII ... |
17-177 | 4.23e-42 | ||||
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: 139.34 E-value: 4.23e-42
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| Arl2l1_Arl13_like | cd04161 | Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ... |
20-172 | 3.77e-34 | ||||
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: 118.26 E-value: 3.77e-34
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| SAR | smart00178 | Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene ... |
15-177 | 1.53e-29 | ||||
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: 107.33 E-value: 1.53e-29
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| Ras_like_GTPase | cd00882 | Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ... |
21-175 | 1.69e-21 | ||||
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: 85.59 E-value: 1.69e-21
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| Gem1 | COG1100 | GTPase SAR1 family domain [General function prediction only]; |
17-168 | 1.59e-19 | ||||
GTPase SAR1 family domain [General function prediction only]; Pssm-ID: 440717 [Multi-domain] Cd Length: 177 Bit Score: 80.80 E-value: 1.59e-19
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| SR_beta | cd04105 | Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ... |
20-169 | 4.41e-18 | ||||
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: 77.75 E-value: 4.41e-18
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| small_GTP | TIGR00231 | small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ... |
17-133 | 1.82e-15 | ||||
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: 70.09 E-value: 1.82e-15
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| SRPRB | pfam09439 | Signal recognition particle receptor beta subunit; The beta subunit of the signal recognition ... |
19-151 | 1.16e-12 | ||||
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: 62.85 E-value: 1.16e-12
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| Rab | cd00154 | Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ... |
18-168 | 2.49e-12 | ||||
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: 61.32 E-value: 2.49e-12
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| PLN03118 | PLN03118 | Rab family protein; Provisional |
15-100 | 1.17e-10 | ||||
Rab family protein; Provisional Pssm-ID: 215587 [Multi-domain] Cd Length: 211 Bit Score: 58.14 E-value: 1.17e-10
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| trmE | cd04164 | trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in ... |
18-168 | 1.60e-10 | ||||
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: 56.73 E-value: 1.60e-10
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| RocCOR | cd09914 | Ras of complex proteins (Roc) C-terminal of Roc (COR) domain family; RocCOR (or Roco) protein ... |
17-175 | 4.43e-10 | ||||
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: 55.42 E-value: 4.43e-10
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| Roc | pfam08477 | Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial ... |
19-129 | 4.74e-10 | ||||
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: 54.44 E-value: 4.74e-10
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| Ras | pfam00071 | Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ... |
19-168 | 5.70e-10 | ||||
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: 55.21 E-value: 5.70e-10
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| Era_like | cd00880 | E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ... |
22-168 | 1.31e-08 | ||||
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: 51.48 E-value: 1.31e-08
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| Rab4 | cd04113 | Rab GTPase family 4 (Rab4); Rab4 subfamily. Rab4 has been implicated in numerous functions ... |
18-168 | 3.15e-08 | ||||
Rab GTPase family 4 (Rab4); Rab4 subfamily. Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. 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: 206696 [Multi-domain] Cd Length: 161 Bit Score: 50.51 E-value: 3.15e-08
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| MMR_HSR1 | pfam01926 | 50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ... |
19-127 | 6.45e-08 | ||||
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotide. Pssm-ID: 460387 [Multi-domain] Cd Length: 113 Bit Score: 48.77 E-value: 6.45e-08
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| RAB | smart00175 | Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking. |
18-130 | 1.76e-07 | ||||
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking. Pssm-ID: 197555 [Multi-domain] Cd Length: 164 Bit Score: 48.66 E-value: 1.76e-07
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| G-alpha | pfam00503 | G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular ... |
40-131 | 1.89e-07 | ||||
G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular signaling pathways. The G protein alpha subunit binds guanyl nucleotide and is a weak GTPase. A set of residues that are unique to G-alpha as compared to its ancestor the Arf-like family form a ring of residues centered on the nucleotide binding site. A Ggamma is found fused to an inactive Galpha in the Dictyostelium protein gbqA. Pssm-ID: 459835 [Multi-domain] Cd Length: 316 Bit Score: 49.51 E-value: 1.89e-07
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| Rab18 | cd01863 | Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic ... |
18-168 | 2.55e-07 | ||||
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: 48.08 E-value: 2.55e-07
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| Gtr1_RagA | pfam04670 | Gtr1/RagA G protein conserved region; GTR1 was first identified in S. cerevisiae as a ... |
19-160 | 3.69e-07 | ||||
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: 48.35 E-value: 3.69e-07
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| HflX | cd01878 | HflX GTPase family; HflX subfamily. A distinct conserved domain with a glycine-rich segment ... |
86-168 | 1.28e-06 | ||||
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: 46.68 E-value: 1.28e-06
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| Rab39 | cd04111 | Rab GTPase family 39 (Rab39); Found in eukaryotes, Rab39 is mainly found in epithelial cell ... |
19-101 | 1.82e-06 | ||||
Rab GTPase family 39 (Rab39); Found in eukaryotes, Rab39 is mainly found in epithelial cell lines, but is distributed widely in various human tissues and cell lines. It is believed to be a novel Rab protein involved in regulating Golgi-associated vesicular transport during cellular endocytosis. 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: 133311 [Multi-domain] Cd Length: 211 Bit Score: 46.29 E-value: 1.82e-06
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| RabL4 | cd04101 | Rab GTPase-like family 4 (Rab-like4); RabL4 (Rab-like4) subfamily. RabL4s are novel proteins ... |
19-167 | 2.01e-06 | ||||
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: 45.60 E-value: 2.01e-06
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| Rab8_Rab10_Rab13_like | cd01867 | Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13); Rab8/Sec4/Ypt2 are known or suspected to ... |
15-130 | 2.55e-06 | ||||
Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13); Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. 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: 206659 [Multi-domain] Cd Length: 167 Bit Score: 45.34 E-value: 2.55e-06
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| Rab6 | cd01861 | Rab GTPase family 6 (Rab6); Rab6 is involved in microtubule-dependent transport pathways ... |
19-168 | 4.19e-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: 4.19e-06
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| MnmE | COG0486 | tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal ... |
18-168 | 6.42e-06 | ||||
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: 45.44 E-value: 6.42e-06
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| Rab15 | cd04117 | Rab GTPase family 15 (Rab15); Rab15 colocalizes with the transferrin receptor in early ... |
19-129 | 6.83e-06 | ||||
Rab GTPase family 15 (Rab15); Rab15 colocalizes with the transferrin receptor in early endosome compartments, but not with late endosomal markers. It codistributes with Rab4 and Rab5 on early/sorting endosomes, and with Rab11 on pericentriolar recycling endosomes. It is believed to function as an inhibitory GTPase that regulates distinct steps in early endocytic 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: 206698 [Multi-domain] Cd Length: 164 Bit Score: 44.20 E-value: 6.83e-06
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| MnmE_helical | pfam12631 | MnmE helical domain; The tRNA modification GTPase MnmE consists of three domains. An ... |
3-168 | 7.68e-06 | ||||
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: 44.78 E-value: 7.68e-06
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| Rab14 | cd04122 | Rab GTPase family 14 (Rab14); Rab14 GTPases are localized to biosynthetic compartments, ... |
21-168 | 8.02e-06 | ||||
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: 44.06 E-value: 8.02e-06
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| RERG_RasL11_like | cd04146 | Ras-related and Estrogen-Regulated Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like ... |
20-131 | 1.21e-05 | ||||
Ras-related and Estrogen-Regulated Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like families; RERG (Ras-related and Estrogen- Regulated Growth inhibitor) and Ras-like 11 are members of a novel subfamily of Ras that were identified based on their behavior in breast and prostate tumors, respectively. RERG expression was decreased or lost in a significant fraction of primary human breast tumors that lack estrogen receptor and are correlated with poor clinical prognosis. Elevated RERG expression correlated with favorable patient outcome in a breast tumor subtype that is positive for estrogen receptor expression. In contrast to most Ras proteins, RERG overexpression inhibited the growth of breast tumor cells in vitro and in vivo. RasL11 was found to be ubiquitously expressed in human tissue, but down-regulated in prostate tumors. Both RERG and RasL11 lack the C-terminal CaaX prenylation motif, where a = an aliphatic amino acid and X = any amino acid, and are localized primarily in the cytoplasm. Both are believed to have tumor suppressor activity. Pssm-ID: 206713 [Multi-domain] Cd Length: 166 Bit Score: 43.42 E-value: 1.21e-05
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| Rab28 | cd04109 | Rab GTPase family 28 (Rab28); Rab28 subfamily. First identified in maize, Rab28 has been shown ... |
18-130 | 2.13e-05 | ||||
Rab GTPase family 28 (Rab28); Rab28 subfamily. First identified in maize, Rab28 has been shown to be a late embryogenesis-abundant (Lea) protein that is regulated by the plant hormone abcisic acid (ABA). In Arabidopsis, Rab28 is expressed during embryo development and is generally restricted to provascular tissues in mature embryos. Unlike maize Rab28, it is not ABA-inducible. Characterization of the human Rab28 homolog revealed two isoforms, which differ by a 95-base pair insertion, producing an alternative sequence for the 30 amino acids at the C-terminus. The two human isoforms are presumably the result of alternative splicing. Since they differ at the C-terminus but not in the GTP-binding region, they are predicted to be targeted to different cellular locations. 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: 206694 [Multi-domain] Cd Length: 213 Bit Score: 43.25 E-value: 2.13e-05
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| Rab19 | cd01864 | Rab GTPase family 19 (Rab19); Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. ... |
19-130 | 3.39e-05 | ||||
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: 42.04 E-value: 3.39e-05
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| Obg | cd01898 | Obg GTPase; The Obg nucleotide binding protein subfamily has been implicated in stress ... |
83-168 | 4.30e-05 | ||||
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: 42.03 E-value: 4.30e-05
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| Rab5_related | cd01860 | Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The ... |
17-168 | 4.50e-05 | ||||
Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The Rab5-related subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. 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: 206653 [Multi-domain] Cd Length: 163 Bit Score: 41.77 E-value: 4.50e-05
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| Era | cd04163 | E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ... |
22-175 | 6.20e-05 | ||||
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: 41.29 E-value: 6.20e-05
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| Rab12 | cd04120 | Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was ... |
19-129 | 1.61e-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: 40.77 E-value: 1.61e-04
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| PTZ00099 | PTZ00099 | rab6; Provisional |
62-130 | 2.65e-04 | ||||
rab6; Provisional Pssm-ID: 185444 [Multi-domain] Cd Length: 176 Bit Score: 39.73 E-value: 2.65e-04
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| Rab40 | cd04121 | Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c; The Rab40 subfamily contains ... |
15-145 | 3.43e-04 | ||||
Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c; The Rab40 subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous. In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle. Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components. Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. 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: 133321 [Multi-domain] Cd Length: 189 Bit Score: 39.53 E-value: 3.43e-04
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| DO-GTPase1 | pfam19975 | Double-GTPase 1; GTPase of a GTPase-centric, NTP-dependent ternary systems. The domain belongs ... |
21-121 | 7.36e-04 | ||||
Double-GTPase 1; GTPase of a GTPase-centric, NTP-dependent ternary systems. The domain belongs to a previously unrecognized family of the TRAFAC clade with a conserved glutamate in its Walker B motif. Pssm-ID: 466245 Cd Length: 271 Bit Score: 39.16 E-value: 7.36e-04
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| RagA_like | cd11384 | Rag GTPase, subfamily of Ras-related GTPases, includes Ras-related GTP-binding proteins A and ... |
60-131 | 8.05e-04 | ||||
Rag GTPase, subfamily of Ras-related GTPases, includes Ras-related GTP-binding proteins A and B; RagA and RagB are closely related Rag GTPases (ras-related GTP-binding protein A and B) that constitute a unique subgroup of the Ras superfamily, and are functional homologs of Saccharomyces cerevisiae Gtr1. These domains function by forming heterodimers with RagC or RagD, and similarly, Gtr1 dimerizes with Gtr2, through the carboxy-terminal segments. They play an essential role in regulating amino acid-induced target of rapamycin complex 1 (TORC1) kinase signaling, exocytic cargo sorting at endosomes, and epigenetic control of gene expression. In response to amino acids, the Rag GTPases guide the TORC1 complex to activate the platform containing Rheb proto-oncogene by driving the relocalization of mTORC1 from discrete locations in the cytoplasm to a late endosomal and/or lysosomal compartment that is Rheb-enriched and contains Rab-7. Pssm-ID: 206744 Cd Length: 286 Bit Score: 38.73 E-value: 8.05e-04
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| RalA_RalB | cd04139 | Ral (Ras-like) family containing highly homologous RalA and RalB; The Ral (Ras-like) subfamily ... |
18-145 | 9.75e-04 | ||||
Ral (Ras-like) family containing highly homologous RalA and RalB; The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (>80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exocyst and for localizing the exocyst to the leading edge of migrating cells. In human cancer cells, RalA is required to support anchorage-independent proliferation and RalB is required to suppress apoptosis. RalA has been shown to localize to the plasma membrane while RalB is localized to the intracellular vesicles. Most Ras 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 Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Pssm-ID: 206710 [Multi-domain] Cd Length: 163 Bit Score: 38.18 E-value: 9.75e-04
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| Rab3 | cd01865 | Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D; The Rab3 subfamily contains Rab3A, ... |
19-130 | 1.99e-03 | ||||
Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D; The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D. All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression. Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules. Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. 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: 206657 [Multi-domain] Cd Length: 165 Bit Score: 37.20 E-value: 1.99e-03
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| PLN03108 | PLN03108 | Rab family protein; Provisional |
19-130 | 2.66e-03 | ||||
Rab family protein; Provisional Pssm-ID: 178655 [Multi-domain] Cd Length: 210 Bit Score: 37.23 E-value: 2.66e-03
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| G_alpha | smart00275 | G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding ... |
40-131 | 2.80e-03 | ||||
G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding site Pssm-ID: 214595 [Multi-domain] Cd Length: 342 Bit Score: 37.56 E-value: 2.80e-03
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| RagC_like | cd11385 | Rag GTPase, subfamily of Ras-related GTPases, includes Ras-related GTP-binding proteins C and ... |
19-96 | 3.17e-03 | ||||
Rag GTPase, subfamily of Ras-related GTPases, includes Ras-related GTP-binding proteins C and D; RagC and RagD are closely related Rag GTPases (ras-related GTP-binding protein C and D) that constitute a unique subgroup of the Ras superfamily, and are functional homologs of Saccharomyces cerevisiae Gtr2. These domains form heterodimers with RagA or RagB, and similarly, Gtr2 dimerizes with Gtr1 in order to function. They play an essential role in regulating amino acid-induced target of rapamycin complex 1 (TORC1) kinase signaling, exocytic cargo sorting at endosomes, and epigenetic control of gene expression. In response to amino acids, the Rag GTPases guide the TORC1 complex to activate the platform containing Rheb proto-oncogene by driving the relocalization of mTORC1 from discrete locations in the cytoplasm to a late endosomal and/or lysosomal compartment that is Rheb-enriched and contains Rab-7. Pssm-ID: 206745 [Multi-domain] Cd Length: 175 Bit Score: 36.43 E-value: 3.17e-03
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| ABC_NatA_like | cd03267 | ATP-binding cassette domain of an uncharacterized transporter similar in sequence to NatA; ... |
22-121 | 3.43e-03 | ||||
ATP-binding cassette domain of an uncharacterized transporter similar in sequence to NatA; NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake. NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the proton-motive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunorubicin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single integral membrane protein. Pssm-ID: 213234 [Multi-domain] Cd Length: 236 Bit Score: 36.93 E-value: 3.43e-03
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| Rag | cd09915 | Rag GTPase subfamily of Ras-related GTPases; Rag GTPases (ras-related GTP-binding proteins) ... |
19-96 | 3.54e-03 | ||||
Rag GTPase subfamily of Ras-related GTPases; Rag GTPases (ras-related GTP-binding proteins) constitute a unique subgroup of the Ras superfamily, playing an essential role in regulating amino acid-induced target of rapamycin complex 1 (TORC1) kinase signaling, exocytic cargo sorting at endosomes, and epigenetic control of gene expression. This subfamily consists of RagA and RagB as well as RagC and RagD that are closely related. Saccharomyces cerevisiae encodes single orthologs of metazoan RagA/B and RagC/D, Gtr1 and Gtr2, respectively. Dimer formation is important for their cellular function; these domains form heterodimers, as RagA or RagB dimerizes with RagC or RagD, and similarly, Gtr1 dimerizes with Gtr2. In response to amino acids, the Rag GTPases guide the TORC1 complex to activate the platform containing Rheb proto-oncogene by driving the relocalization of mTORC1 from discrete locations in the cytoplasm to a late endosomal and/or lysosomal compartment that is Rheb-enriched and contains Rab-7. Pssm-ID: 206742 [Multi-domain] Cd Length: 175 Bit Score: 36.39 E-value: 3.54e-03
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| AAA | pfam00004 | ATPase family associated with various cellular activities (AAA); AAA family proteins often ... |
20-134 | 3.74e-03 | ||||
ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. Pssm-ID: 459627 [Multi-domain] Cd Length: 130 Bit Score: 36.03 E-value: 3.74e-03
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| Era | COG1159 | GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis]; |
82-176 | 7.42e-03 | ||||
GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440773 [Multi-domain] Cd Length: 290 Bit Score: 36.12 E-value: 7.42e-03
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