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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961  36 RLLDAVKQCQIRFGGRKEIASDSDSRVTCLCAQFEAVLQHGMKRSRGLALTAAAIKQA---AGFTSKTETEPVFWVYVKE 112
Cdd:cd17689     1 RLLDAVKQCQIRFGGKTELATESDSRVSCLCAQLEAVLQHGLKTSRSPNLVSSAVTQVsglAGSLGSAETEPTFWPFVKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961 113 VLSKHELQRFYSLHHITADVGRGRAWLRCALNEHSLERYLHMLLADRTRLSTFYEDWSFVMDEERSSMLPTMAAGLNSIL 192
Cdd:cd17689    81 HLTKHELERFELLKNIWTDIGRGRAWLRSALNEHSLERYLHILLSNENLLRQYYEDWAFLRDEERSSMLPNMAAGLGSIL 160

                  ....*.
gi 1958660961 193 FAINID 198
Cdd:cd17689   161 FALSID 166

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961  36 RLLDAVKQCQIRFGGRKEIASDSDSRVTCLCAQFEAVLQHGMKRSRGLALTAAAIKQA---AGFTSKTETEPVFWVYVKE 112
Cdd:cd17689     1 RLLDAVKQCQIRFGGKTELATESDSRVSCLCAQLEAVLQHGLKTSRSPNLVSSAVTQVsglAGSLGSAETEPTFWPFVKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961 113 VLSKHELQRFYSLHHITADVGRGRAWLRCALNEHSLERYLHMLLADRTRLSTFYEDWSFVMDEERSSMLPTMAAGLNSIL 192
Cdd:cd17689    81 HLTKHELERFELLKNIWTDIGRGRAWLRSALNEHSLERYLHILLSNENLLRQYYEDWAFLRDEERSSMLPNMAAGLGSIL 160

                  ....*.
gi 1958660961 193 FAINID 198
Cdd:cd17689   161 FALSID 166

domain involved in Ras-like GTPase signaling;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958660961  135 GRAWLRCALNEHSLERYLHMLLADRTRLSTFYEDWSFVMDEERSSMLPTMAAGLNSILFAINID 198
Cdd:smart00593   1 FRAWIRLALNEKLLSSWLNLLLSDEELLSKYYEPWAFLRDPEEGEQLLGLLVGLSALDFNLPVD 64

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961  36 RLLDAVKQCQIRFGGRKEIASDSDSRVTCLCAQFEAVLQHGMKRSRGLALTAAAIKQA---AGFTSKTETEPVFWVYVKE 112
Cdd:cd17689     1 RLLDAVKQCQIRFGGKTELATESDSRVSCLCAQLEAVLQHGLKTSRSPNLVSSAVTQVsglAGSLGSAETEPTFWPFVKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961 113 VLSKHELQRFYSLHHITADVGRGRAWLRCALNEHSLERYLHMLLADRTRLSTFYEDWSFVMDEERSSMLPTMAAGLNSIL 192
Cdd:cd17689    81 HLTKHELERFELLKNIWTDIGRGRAWLRSALNEHSLERYLHILLSNENLLRQYYEDWAFLRDEERSSMLPNMAAGLGSIL 160

                  ....*.
gi 1958660961 193 FAINID 198
Cdd:cd17689   161 FALSID 166

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961  40 AVKQCQIRFGGRKEIAS-------DSDSRVTCLCAQFEAVLQHGMKRSRGLaltaaaikqaagftsktETEPVFWVYVKE 112
Cdd:cd17671     2 AVKELLESFADNGEADDsaaltltDDDPVVGRLCAALEAILSHGLKPKRFG-----------------GGKVSFWDFLEA 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961 113 VL-------SKHELQRFYSLHHITADVGRGRAWLRCALNEHSLERYLHMLLADRTRLSTFYEDWSFVMDEERSSMLPTMA 185
Cdd:cd17671    65 LEkllpapsLKQAIRDINSLSNVKTDDGRGRAWIRLALNEKSLESYLAALLSDQSLLRKYYEPWALLRDPEEAELFLSLL 144

                         170
                  ....*....|
gi 1958660961 186 AGLNSILFAI 195
Cdd:cd17671   145 VGLSSLDFNL 154

RUN domain found in pleckstrin homology domain-containing family M member 2 (PLEKHM2) and similar proteins; PLEKHM2, also called PH domain-containing family M member 2, or Salmonella-induced filaments A (SifA) and Kinesin-Interacting Protein (SKIP), is the lysosome, melanosome and lytic granule cargo adaptor that controls lysosome positioning using a composite kinesin-1 heavy and light chain-binding domain. In addition to kinesin-1, it also interacts with several Rabs to affect endosomal trafficking. This model represents the RUN domain of PLEKHM2.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961  32 FLLERLLDAVKQCQIRFGGRKEIASDSDSR---VTCLCAQFEAVLQHGMKRSRGLaltaaaikqaagftsktetepvFWV 108
Cdd:cd17680     1 RILRNISEAIKSLQSYSSSQEEEDVLITNEnreLQRLCEALDHALLHGLRRGNRG----------------------YWP 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961 109 YVKEVLSKHELQRFYSLHHITADVGRGRAWLRCALNEHSLERYLHMLLADRTRLSTFYEDWSFVMDEERSSMLPTMAAGL 188
Cdd:cd17680    59 FVKEFTHKETIKQIENLPNVTTDLGRGRAWLYLALNEGSLESYLRSFLENRKLVKKFYHKHALLRDSQRLELLLTLLSGL 138

                  ....*.
gi 1958660961 189 NSILFA 194
Cdd:cd17680   139 EFVQFD 144

RUN domain found in RUN domain-containing protein 3 (RUNDC3) and similar proteins; RUNDC3 contains two isoforms, RUNDC3A and RUNDC3B. RUNDC3A, also called Rap2-interacting protein 8 (RPIP8), may act as an effector of Rap2A GTPase in neuronal cells. 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. Both RUNDC3A and RUNDC3B contain a RUN domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961  53 EIASDSDSRVTCLCAQFEAVLQHGMKrsrglaltaaAIKQAAGftskTETEPVFWVYVKEVLSK---HELQRFYSLHHIT 129
Cdd:cd17684    20 ETIDDSSEELINFAAILEQILSHRLK----------PVKPWYG----SEEPRTFWDYIRVACKKvpqNCIASIEQMENIK 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958660961 130 ADVGRGRAWLRCALNEHSLERYLHMLLADRTRLSTFYEDWSFVMDEErSSMLPTMAAGLNSILF 193
Cdd:cd17684    86 SPKAKGRAWIRVALMEKRLSEYLSTALKQTRLTRNFYQDGAIMLSED-ATVLCGMLIGLNAIDF 148

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961  65 LCAQFEAVLQHGMKRSRglaltaaaikqaagftSKTETEPVFWvYVKEVLSKH--ELQRFYS----LHHITADVGRGRAW 138
Cdd:cd17681    37 FFVILEHVLRHGLKVKK----------------SFLGPNKSFW-PVLEHVEKLvpEANEITAsvrdLPGIKTPLGRARAW 99

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1958660961 139 LRCALNEHSLERYLHMLLADRTRLSTFYEDWSFVMDEE 176
Cdd:cd17681   100 LRLALMQKKLADYFRALIENKDLLSEFYEPGALMMSEE 137

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961 132 VGRGRAWLRCALNEHSLERYLHMLLADRTRLSTFYEDWSFVMDEErSSMLPTMAAGLNSI 191
Cdd:cd17695    93 LGRARAWLRLALMQKKLADYLRCLIIRRDLLSEFYEYHALMMEEE-GAVIVGLLVGLNVI 151

RUN domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins; 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. RUFY1 contains an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between; this model represents the RUN domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961  68 QFEAVLQHGMKRsrGLALTAAAIKQAAGFTSKTEtepvfwvyVKEVLSKHELQRFYS---LHHITADVGRGRAWLRCALN 144
Cdd:cd17694    36 QFFVVLEHCLKH--GLKVKKSFIGQNKSFFGPLE--------LVEKLCPEASDIATSarnLPELKTAVGRGRAWLHLALM 105

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1958660961 145 EHSLERYLHMLLADRTRLSTFYEDWSFVMDEERSSMLpTMAAGLNSI 191
Cdd:cd17694   106 QKKLADYLKVLIDRKDLLSEFYEPGALMMEEEGAVIV-GLLVGLNVI 151

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961  65 LCAQFEAVLQHGMKRSRGLaltaaaikqaagFTSKTEtepvFWVYVKEVLSKHELqRFYSLHHITADV----------GR 134
Cdd:cd17682    27 FCETLEKILRKGLKEKVSL------------GGRRKD----YWDWLEELLKKLNK-IPKSLSDAVKFVksckkvktnqGR 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958660961 135 GRAWLRCALNEHSLERYLHMLLADRTRLSTFYEDWSFVMDEERSSMLPTMAAGLNSILFAI 195
Cdd:cd17682    90 GRLFIRYALNKKCLHDPVQQLVKNPKLLSDYYSPDSILGNEILSEILLSLLYQLNEINFDL 150

RUN1 domain found in DENN domain-containing protein 5 (DENND5) and similar proteins; DENND5 has been characterized as Rab6-interacting protein which is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. It functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. DENND5 has two isoforms, DENND5A and DENND5B. This model represents the first RUN domain of DENND5.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958660961 128 ITADVGRGRAWLRCALNEHSLERYLHMLLADRTRLSTFYEDWSFVM-DEERSSML 181
Cdd:cd17677   110 IKTDVGYARAWIRLALEKKLLSKHLKTLLSNQDLLRSLYKRYAFLRcEDEREQFL 164

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961  41 VKQCQIRFGGRKEIASDSdSRVTCLCAQFEAVLQHGM-KRSRGL---ALTAAAIKQAAgfTSKTETEPVFwVYVKEVLSK 116
Cdd:cd17687     3 VKQLMEEAVTRKFIHEDS-SSVTSLCGAVDACLLHGLrKRALGLfrsSSTFSLLQKVA--KSCPPAADIL-RKVQEIENL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961 117 HELQRFYSLH-------HITADVGRGRAWLRCALNEHSLERYLHMLLadrTRLSTFYEDWSFVMDEERSSMLPTMAAGLN 189
Cdd:cd17687    79 SENKRSSSSSgsnssnsHGNSSSNRKILWIRIALFEKVLDKIVDYLV---ENASKYYEKEALMADPVDGPLLASLLVGPC 155

                  ....
gi 1958660961 190 SILF 193
Cdd:cd17687   156 ALDY 159

Axonemal dynein light chain; Axonemal dynein light chain proteins play a dynamic role in flagellar and cilia motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organizms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958660961 485 ESMTVHELRQAIVAMMNRKD------ELEEENGSLRNLLdgemehsAALRQEVDALRRKVTEQQE----RHATKVQALAR 554
Cdd:pfam10211 104 ESSVAFGMRKALQAEQGKAElekkiaDLEEEKEELEKQV-------AELKAKCEAIEKREEERRQaeekKHAEEIAFLKK 176

                          90
                  ....*....|.
gi 1958660961 555 ENEVLKVQLKK 565
Cdd:pfam10211 177 TNQQLKAQLER 187