RUN domain; RUN domain, named after RPIP8 (Rap2 interacting protein 8), UNC-14 and NESCA (new ...
3-227
2.40e-116
RUN domain; RUN domain, named after RPIP8 (Rap2 interacting protein 8), UNC-14 and NESCA (new molecule containing SH3 at the carboxyl-terminus), is a less conserved protein motif that comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases. RUN domains are often found in proteins linked particularly to the functions of GTPases in the Rap and Rab families, suggesting the RUN domain may be involved in Rab-mediated membrane trafficking, possibly as a Rab-binding site. RUN domain-containing proteins could hence play important roles in multiple Ras-like GTPase signalling pathways.
The actual alignment was detected with superfamily member cd17704:
Pssm-ID: 459241 Cd Length: 180 Bit Score: 356.55 E-value: 2.40e-116
Rab-binding Pleckstrin homology domain (PH) of small G-protein signaling modulator 1 and ...
286-454
1.92e-98
Rab-binding Pleckstrin homology domain (PH) of small G-protein signaling modulator 1 and similar proteins; Small G-protein signaling modulator 1, or RUN and TBC1 domain containing 2 (RUTBC2), as well as RUTBC1, bind to Rab9A via their Pleckstrin homology (PH) domain. They do not seem to act as GAP proteins that stimulate GTP hydrolysis by Rab9A, and RUTBC2 has been shown to also interact with Rab9B, most likely in a similar manner. RUTBC1 does stimulate GTP hydrolysis by Rab32 and Rab33B, however, while RUTBC2 appears to be a GAP for Rab36. Rab9A and associated proteins control the recycling of mannose-6-phosphate receptors from late endosomes to the trans-Golgi.
:
Pssm-ID: 275431 Cd Length: 176 Bit Score: 308.49 E-value: 1.92e-98
Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs; Widespread domain present in Gyp6 and ...
869-1037
7.68e-43
Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs; Widespread domain present in Gyp6 and Gyp7, thereby giving rise to the notion that it performs a GTP-activator activity on Rab-like GTPases.
:
Pssm-ID: 214540 [Multi-domain] Cd Length: 216 Bit Score: 155.54 E-value: 7.68e-43
RUN domain found in small G protein signaling modulator 2 (SGSM2) and similar proteins; SGSM2, ...
3-227
2.40e-116
RUN domain found in small G protein signaling modulator 2 (SGSM2) and similar proteins; SGSM2, also called RUN and TBC1 domain-containing protein 1 (RUTBC1), is a GTPase-activating protein for Rab32/38, and regulates melanogenic enzyme trafficking in melanocytes. It also acts as a Rab9A effector that activates GTP hydrolysis by Rab32 and Rab33B proteins. This model contains the RUN domain of SGSM2.
Pssm-ID: 439066 Cd Length: 180 Bit Score: 356.55 E-value: 2.40e-116
Rab-binding Pleckstrin homology domain (PH) of small G-protein signaling modulator 1 and ...
286-454
1.92e-98
Rab-binding Pleckstrin homology domain (PH) of small G-protein signaling modulator 1 and similar proteins; Small G-protein signaling modulator 1, or RUN and TBC1 domain containing 2 (RUTBC2), as well as RUTBC1, bind to Rab9A via their Pleckstrin homology (PH) domain. They do not seem to act as GAP proteins that stimulate GTP hydrolysis by Rab9A, and RUTBC2 has been shown to also interact with Rab9B, most likely in a similar manner. RUTBC1 does stimulate GTP hydrolysis by Rab32 and Rab33B, however, while RUTBC2 appears to be a GAP for Rab36. Rab9A and associated proteins control the recycling of mannose-6-phosphate receptors from late endosomes to the trans-Golgi.
Pssm-ID: 275431 Cd Length: 176 Bit Score: 308.49 E-value: 1.92e-98
Rab-binding domain (RBD); This domain has been called the Rab-binding domain (RBD). The domain ...
287-422
1.15e-50
Rab-binding domain (RBD); This domain has been called the Rab-binding domain (RBD). The domain adopts a Ph-like fold. This domain is found associated with pfam00566.
Pssm-ID: 432305 Cd Length: 149 Bit Score: 175.39 E-value: 1.15e-50
Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs; Widespread domain present in Gyp6 and ...
869-1037
7.68e-43
Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs; Widespread domain present in Gyp6 and Gyp7, thereby giving rise to the notion that it performs a GTP-activator activity on Rab-like GTPases.
Pssm-ID: 214540 [Multi-domain] Cd Length: 216 Bit Score: 155.54 E-value: 7.68e-43
RUN domain; This domain is present in several proteins that are linked to the functions of ...
74-219
6.49e-31
RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases.
Pssm-ID: 460679 Cd Length: 134 Bit Score: 118.15 E-value: 6.49e-31
Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are ...
870-1037
1.33e-29
Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases.
Pssm-ID: 459855 Cd Length: 178 Bit Score: 116.20 E-value: 1.33e-29
RUN domain found in small G protein signaling modulator 2 (SGSM2) and similar proteins; SGSM2, ...
3-227
2.40e-116
RUN domain found in small G protein signaling modulator 2 (SGSM2) and similar proteins; SGSM2, also called RUN and TBC1 domain-containing protein 1 (RUTBC1), is a GTPase-activating protein for Rab32/38, and regulates melanogenic enzyme trafficking in melanocytes. It also acts as a Rab9A effector that activates GTP hydrolysis by Rab32 and Rab33B proteins. This model contains the RUN domain of SGSM2.
Pssm-ID: 439066 Cd Length: 180 Bit Score: 356.55 E-value: 2.40e-116
Rab-binding Pleckstrin homology domain (PH) of small G-protein signaling modulator 1 and ...
286-454
1.92e-98
Rab-binding Pleckstrin homology domain (PH) of small G-protein signaling modulator 1 and similar proteins; Small G-protein signaling modulator 1, or RUN and TBC1 domain containing 2 (RUTBC2), as well as RUTBC1, bind to Rab9A via their Pleckstrin homology (PH) domain. They do not seem to act as GAP proteins that stimulate GTP hydrolysis by Rab9A, and RUTBC2 has been shown to also interact with Rab9B, most likely in a similar manner. RUTBC1 does stimulate GTP hydrolysis by Rab32 and Rab33B, however, while RUTBC2 appears to be a GAP for Rab36. Rab9A and associated proteins control the recycling of mannose-6-phosphate receptors from late endosomes to the trans-Golgi.
Pssm-ID: 275431 Cd Length: 176 Bit Score: 308.49 E-value: 1.92e-98
RUN domain found in small G protein signaling modulator 1 (SGSM1) and similar proteins; SGSM1, ...
3-227
4.99e-91
RUN domain found in small G protein signaling modulator 1 (SGSM1) and similar proteins; SGSM1, also called RUN and TBC1 domain-containing protein 2 (RUTBC2), interacts with numerous Rab family members, functioning as Rab effector for some, and as GTPase activator for others. It is a Rab9A effector and GTPase-activating protein for Rab36, and links Rab9A function to Rab36 function in the endosomal system. This model contains the RUN domain of SGSM1.
Pssm-ID: 439065 Cd Length: 177 Bit Score: 288.83 E-value: 4.99e-91
RUN domain found in small G protein signaling modulators, SGSM1, SGSM2, and similar proteins; ...
3-215
3.15e-73
RUN domain found in small G protein signaling modulators, SGSM1, SGSM2, and similar proteins; SGSM1, also called RUN and TBC1 domain-containing protein 2 (RUTBC2), interacts with numerous Rab family members, functioning as Rab effector for some, and as GTPase activator for others. It is a Rab9A effector and GTPase-activating protein for Rab36, and links Rab9A function to Rab36 function in the endosomal system. SGSM2, also called RUN and TBC1 domain-containing protein 1 (RUTBC1), is a GTPase-activating protein for Rab32/38, and regulates melanogenic enzyme trafficking in melanocytes. It also acts as a Rab9A effector that activates GTP hydrolysis by Rab32 and Rab33B proteins. This model contains the RUN domain of SGSM1 and SGSM2.
Pssm-ID: 439049 Cd Length: 161 Bit Score: 239.50 E-value: 3.15e-73
Rab-binding domain (RBD); This domain has been called the Rab-binding domain (RBD). The domain ...
287-422
1.15e-50
Rab-binding domain (RBD); This domain has been called the Rab-binding domain (RBD). The domain adopts a Ph-like fold. This domain is found associated with pfam00566.
Pssm-ID: 432305 Cd Length: 149 Bit Score: 175.39 E-value: 1.15e-50
Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs; Widespread domain present in Gyp6 and ...
869-1037
7.68e-43
Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs; Widespread domain present in Gyp6 and Gyp7, thereby giving rise to the notion that it performs a GTP-activator activity on Rab-like GTPases.
Pssm-ID: 214540 [Multi-domain] Cd Length: 216 Bit Score: 155.54 E-value: 7.68e-43
RUN domain; This domain is present in several proteins that are linked to the functions of ...
74-219
6.49e-31
RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases.
Pssm-ID: 460679 Cd Length: 134 Bit Score: 118.15 E-value: 6.49e-31
Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are ...
870-1037
1.33e-29
Rab-GTPase-TBC domain; Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases.
Pssm-ID: 459855 Cd Length: 178 Bit Score: 116.20 E-value: 1.33e-29
RUN domain; RUN domain, named after RPIP8 (Rap2 interacting protein 8), UNC-14 and NESCA (new ...
75-211
5.90e-12
RUN domain; RUN domain, named after RPIP8 (Rap2 interacting protein 8), UNC-14 and NESCA (new molecule containing SH3 at the carboxyl-terminus), is a less conserved protein motif that comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases. RUN domains are often found in proteins linked particularly to the functions of GTPases in the Rap and Rab families, suggesting the RUN domain may be involved in Rab-mediated membrane trafficking, possibly as a Rab-binding site. RUN domain-containing proteins could hence play important roles in multiple Ras-like GTPase signalling pathways.
Pssm-ID: 439038 Cd Length: 154 Bit Score: 64.75 E-value: 5.90e-12
Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like ...
292-397
6.20e-07
Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins.
Pssm-ID: 275390 Cd Length: 89 Bit Score: 48.55 E-value: 6.20e-07
RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; ...
77-207
2.62e-03
RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; RUFY3, also called Rap2-interacting protein x (RIPx or RPIPx), or single axon-regulated protein (singar), is an N-terminal RUN domain and a C-terminal FYVE domain containing protein predominantly expressed in the brain. It suppresses formation of surplus axons for neuronal polarity. Unlike other RUFY proteins, RUFY3 can associate with the GTP-bound active form of Rab5. This model represents the RUN domain of RUFY3.
Pssm-ID: 439058 Cd Length: 156 Bit Score: 39.59 E-value: 2.62e-03
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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