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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2022781872   1 MENVSSSRAKGRAWIRVALMEKHLSEYISTALRDFKTTRRFYEDGAIVLGEEANMLAGMLLGLNAIDFSFC 71
Cdd:cd17700    81 MENVSSSRAKGRAWIRVALMEKRLSEYISTALRDFKTTRRFYEDGAIVLGEEANMLAGMLLGLNAIDFSFC 151

RUN domain found in RUN domain-containing protein 3B (RUNDC3B) and similar proteins; RUN domain-containing protein 3B (RUNDC3B), also called Rap2-binding protein 9, or Rap2-interacting protein 9 (RPIP-9), contains a RUN domain in its N-terminal region that mediates interaction with Rap2, an important component of the Mitogen-Activated Protein Kinase (MAPK) cascade, which regulates cellular proliferation and differentiation. It also contains characteristic binding sites for MAPK intermediates. RUNDC3B contains a RUN domain.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2022781872   1 MENVSSSRAKGRAWIRVALMEKHLSEYISTALRDFKTTRRFYEDGAIVLGEEANMLAGMLLGLNAIDFSFC 71
Cdd:cd17700    81 MENVSSSRAKGRAWIRVALMEKRLSEYISTALRDFKTTRRFYEDGAIVLGEEANMLAGMLLGLNAIDFSFC 151

domain involved in Ras-like GTPase signaling;

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2022781872   11 GRAWIRVALMEKHLSEYISTALRDFKTTRRFYEDGAIVL-GEEANMLAGMLLGLNAIDFSFCLK 73
Cdd:smart00593   1 FRAWIRLALNEKLLSSWLNLLLSDEELLSKYYEPWAFLRdPEEGEQLLGLLVGLSALDFNLPVD 64

RUN domain found in RUN domain-containing protein 3B (RUNDC3B) and similar proteins; RUN domain-containing protein 3B (RUNDC3B), also called Rap2-binding protein 9, or Rap2-interacting protein 9 (RPIP-9), contains a RUN domain in its N-terminal region that mediates interaction with Rap2, an important component of the Mitogen-Activated Protein Kinase (MAPK) cascade, which regulates cellular proliferation and differentiation. It also contains characteristic binding sites for MAPK intermediates. RUNDC3B contains a RUN domain.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2022781872   1 MENVSSSRAKGRAWIRVALMEKHLSEYISTALRDFKTTRRFYEDGAIVLGEEANMLAGMLLGLNAIDFSFC 71
Cdd:cd17700    81 MENVSSSRAKGRAWIRVALMEKRLSEYISTALRDFKTTRRFYEDGAIVLGEEANMLAGMLLGLNAIDFSFC 151

RUN domain found in RUN domain-containing protein 3A (RUNDC3A) and similar proteins; RUN domain-containing protein 3A (RUNDC3A), also called Rap2-interacting protein 8 (RPIP8), may act as an effector of Rap2A GTPase in neuronal cells. It contains a RUN domain.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2022781872   1 MENVSSSRAKGRAWIRVALMEKHLSEYISTALRDFKTTRRFYEDGAIVLGEEANMLAGMLLGLNAIDFSFC 71
Cdd:cd17699    81 MENISTSRAKGRAWIRVALMEKRLSEYIATALRDTRTTRRFYDDGAIMLREESTVLTGMLIGLSAIDFSFC 151

RUN domain found in RUN and FYVE domain-containing proteins, RUFY1, RUFY2, RUFY3 and similar proteins; This family includes RUN and FYVE domain-containing protein RUFY1, RUFY2, and RUFY3. RUFY1, also called FYVE-finger protein EIP1, or La-binding protein 1, or Rab4-interacting protein (Rabip4), or Zinc finger FYVE domain-containing protein 12 (ZFY12), a human homolog of mouse Rabip4, an effector of Rab4 GTPase that regulates recycling of endocytosed cargo. RUFY1 is an endosomal protein that functions as a dual effector of Rab4 and Rab14 and is involved in efficient recycling of transferrin (Tfn). It is a downstream effector of Etk, a downstream tyrosine kinase of PI3-kinase that is involved in regulation of vesicle trafficking. RUFY2, also called Rab4-interacting protein related, is a novel embryonic factor that is present in the nucleus at early stages of embryonic development. It may have both endosomal functions in the cytoplasm and nuclear functions. 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. RUFY1, RUFY2, and RUFY3 contain an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between; this model represents the RUN domain.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2022781872   1 MENVSSSRAKGRAWIRVALMEKHLSEYIStALRDFKTTRR-FYEDGAIVLGEEANMLAGMLLGLNAIDFSF 70
Cdd:cd17681    86 LPGIKTPLGRARAWLRLALMQKKLADYFR-ALIENKDLLSeFYEPGALMMSEEAVVIAGLLVGLNVIDCNL 155

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2022781872   1 MENVSSSRAKGRAWIRVALMEKHLSEYISTALRDFKTTRRFYEDGAIVLG-EEANMLAGMLLGLNAIDFSF 70
Cdd:cd17671    84 LSNVKTDDGRGRAWIRLALNEKSLESYLAALLSDQSLLRKYYEPWALLRDpEEAELFLSLLVGLSSLDFNL 154

RUN domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins; RUFY2, also called Rab4-interacting protein related, is a novel embryonic factor that contains an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between. It is present in the nucleus at early stages of embryonic development. It may have both endosomal functions in the cytoplasm and nuclear functions. This model represents the RUN domain of RUFY2.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2022781872  10 KGRAWIRVALMEKHLSEYISTALRDFKTTRRFYEDGAIVLGEEANMLAGMLLGLNAIDFSFC 71
Cdd:cd17695    95 RARAWLRLALMQKKLADYLRCLIIRRDLLSEFYEYHALMMEEEGAVIVGLLVGLNVIDANLC 156

RUN domain found in sorting nexin-29 (SNX29) and similar proteins; SNX29, also called RUN domain-containing protein 2A (RUNDC2A), belongs to the sorting nexin family. Sorting nexins are a large group of proteins that are localized in the cytoplasm and have the potential for membrane association either through their lipid-binding PX domain, a phospholipid-binding motif, or through protein-protein interactions with membrane-associated protein complexes. Some sorting nexin family members have been shown to facilitate protein sorting. This model contains the RUN domain of SNX29.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2022781872   3 NVSSSRAKGRAWIRVALMEKHLSEYISTALRDFKTTRRFYEDGAIVLGEE-ANMLAGMLLGLNAIDFS 69
Cdd:cd17689    95 NIWTDIGRGRAWLRSALNEHSLERYLHILLSNENLLRQYYEDWAFLRDEErSSMLPNMAAGLGSILFA 162

RUN domain found in pleckstrin homology domain-containing family M member 1 (PLEKHM1) and similar proteins; PLEKHM1, also called PH domain-containing family M member 1, or 162 kDa adapter protein (AP162), may act as a multivalent adapter protein that regulates Rab7-dependent and HOPS complex-dependent fusion events in the endolysosomal system and couples autophagic and the endocytic trafficking pathways. This model represents the RUN domain of PLEKHM1.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2022781872  10 KGRAWIRVALMEKHLSEYISTALRDFKTTRRFYEDGAIVL-GEEANMLAGMLLGLNAIDFSF 70
Cdd:cd17679   100 RCRAWIRLALNDGLLESYLEAILKDKSALKSYYNPSAFLRdPEQLDILKSLLQGLESFQFEL 161

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2022781872  14 WIRVALMEKHLS---EYIStalrdfKTTRRFYEDGAIVL-GEEANMLAGMLLGLNAIDFS 69
Cdd:cd17687   107 WIRIALFEKVLDkivDYLV------ENASKYYEKEALMAdPVDGPLLASLLVGPCALDYT 160

RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4), FYVE and coiled-coil domain-containing protein 1 (FYCO1), and similar proteins; The family includes RUFY4 and FYCO1. RUFY4 acts as a positive regulator that enhances autophagy and lysosome tethering in response to Interleukin-4. It is expressed in a cell-specific manner or under specific immunological conditions associated with IL4 expression such as allergic asthma. FYCO1, also called zinc finger FYVE domain-containing protein 7 (ZFYVE7), is a multidomain autophagy adaptor protein that interacts with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7, and phosphatidylinositol 3-phosphate (PI3P), to mediate microtubule plus-end-directed autophagosome transport. Both RUFY4 and FYCO1 contain an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between; this model represents the RUN domain.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2022781872   2 ENVSSSRAKGRAWIRVALMEKHLSEYISTALRDFKTTRRFYEDGAIVLGEEANM-LAGMLLGLNAIDFSF 70
Cdd:cd17682    81 KKVKTNQGRGRLFIRYALNKKCLHDPVQQLVKNPKLLSDYYSPDSILGNEILSEiLLSLLYQLNEINFDL 150