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Conserved domains on  [gi|392892359|ref|NP_001254408|]
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RUN domain-containing protein [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
zf-RING_9 pfam13901
Putative zinc-RING and/or ribbon; This is a family of cysteine-rich proteins. Many members ...
 725-925 6.13e-79

Putative zinc-RING and/or ribbon; This is a family of cysteine-rich proteins. Many members also carry a pleckstrin-homology domain, pfam00169


:

Pssm-ID: 464030  Cd Length: 205  Bit Score: 255.23  E-value: 6.13e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  725 CAIDSKYYCTECMkSGGKVSIPARVVMDWDWRERAVSDRGRAWYEANQEKALINIKTTNSRLYAHAPALEETRKLREKLQ 804
Cdd:pfam13901   3 CDYTGKYYCSGCH-WNDTSVIPARILHNWDFKKYPVSKFAKQLLDSIYSQPLLNLSDLNPSLYSKVKELAKVRELREQLK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  805 LVSMYLFTCRESVSEDFRR--RLWPKEYLRSEIDVYSFADLIDVKSGALQRRLNSLLKHSINHVMTCTLCKQKGFCCELC 882
Cdd:pfam13901  82 LLKDYLKTCRFAAEEELLKlfRLRPRHHLLEDSHLYSLQDLVDIKNGSLLPFLEELVQFAEKHVTNCELCQGKGFICELC 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 392892359  883 TVNEVIYPFNTESTHRCLVCFSAFHVECWR-TSGDCPKCVRRQN 925
Cdd:pfam13901 162 NSDDIIFPFDIDTTSRCEKCKAVFHKSCFRsGASPCPKCERLQK 205
RUN_PLEKHM1 cd17679
RUN domain found in pleckstrin homology domain-containing family M member 1 (PLEKHM1) and ...
 20-186 2.32e-68

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.


:

Pssm-ID: 439041 [Multi-domain]  Cd Length: 171  Bit Score: 225.16  E-value: 2.32e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  20 RADLQKELDNVVKAAIASPHSKRENVPS--EITQNLCNSIEAIFIHGLRDPFFLK-----GTRYAKYPEPNFWPFVSKFS 92
Cdd:cd17679    1 KKSLTKELSSSVKELQLEYVSSDEVVTSsdDGANTLCCVLEAIFLHGLKDKFISKvssvfSGDVDKLPEPNFWPLLLKFS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  93 HRSITSQIACLGQIRSEIGKSRAWIRIVLNENALGQYLDLLAAEATAIQQFYSDDAFLRllsDGDQSERIRGLLKPLSSL 172
Cdd:cd17679   81 HRDVIDQIEHLSQITTDVGRCRAWIRLALNDGLLESYLEAILKDKSALKSYYNPSAFLR---DPEQLDILKSLLQGLESF 157

                        170
                 ....*....|....
gi 392892359 173 PISAATNSSFLNTW 186
Cdd:cd17679  158 QFELPYNSSLLNTW 171
LIM super family cl02475
LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains ...
 699-738 2.30e-03

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).


The actual alignment was detected with superfamily member cd09429:

Pssm-ID: 413332  Cd Length: 53  Bit Score: 37.10  E-value: 2.30e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 392892359 699 GLDAQD-------FRCAMCRKTIGGSTFSkfetcAIDSKYYCTECMK 738
Cdd:cd09429   12 GVTYQDqpwhsecFVCSSCSKKLAGQRFT-----AVEDQYYCVDCYK 53
 
Name Accession Description Interval E-value
zf-RING_9 pfam13901
Putative zinc-RING and/or ribbon; This is a family of cysteine-rich proteins. Many members ...
 725-925 6.13e-79

Putative zinc-RING and/or ribbon; This is a family of cysteine-rich proteins. Many members also carry a pleckstrin-homology domain, pfam00169


Pssm-ID: 464030  Cd Length: 205  Bit Score: 255.23  E-value: 6.13e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  725 CAIDSKYYCTECMkSGGKVSIPARVVMDWDWRERAVSDRGRAWYEANQEKALINIKTTNSRLYAHAPALEETRKLREKLQ 804
Cdd:pfam13901   3 CDYTGKYYCSGCH-WNDTSVIPARILHNWDFKKYPVSKFAKQLLDSIYSQPLLNLSDLNPSLYSKVKELAKVRELREQLK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  805 LVSMYLFTCRESVSEDFRR--RLWPKEYLRSEIDVYSFADLIDVKSGALQRRLNSLLKHSINHVMTCTLCKQKGFCCELC 882
Cdd:pfam13901  82 LLKDYLKTCRFAAEEELLKlfRLRPRHHLLEDSHLYSLQDLVDIKNGSLLPFLEELVQFAEKHVTNCELCQGKGFICELC 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 392892359  883 TVNEVIYPFNTESTHRCLVCFSAFHVECWR-TSGDCPKCVRRQN 925
Cdd:pfam13901 162 NSDDIIFPFDIDTTSRCEKCKAVFHKSCFRsGASPCPKCERLQK 205
RUN_PLEKHM1 cd17679
RUN domain found in pleckstrin homology domain-containing family M member 1 (PLEKHM1) and ...
 20-186 2.32e-68

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.


Pssm-ID: 439041 [Multi-domain]  Cd Length: 171  Bit Score: 225.16  E-value: 2.32e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  20 RADLQKELDNVVKAAIASPHSKRENVPS--EITQNLCNSIEAIFIHGLRDPFFLK-----GTRYAKYPEPNFWPFVSKFS 92
Cdd:cd17679    1 KKSLTKELSSSVKELQLEYVSSDEVVTSsdDGANTLCCVLEAIFLHGLKDKFISKvssvfSGDVDKLPEPNFWPLLLKFS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  93 HRSITSQIACLGQIRSEIGKSRAWIRIVLNENALGQYLDLLAAEATAIQQFYSDDAFLRllsDGDQSERIRGLLKPLSSL 172
Cdd:cd17679   81 HRDVIDQIEHLSQITTDVGRCRAWIRLALNDGLLESYLEAILKDKSALKSYYNPSAFLR---DPEQLDILKSLLQGLESF 157

                        170
                 ....*....|....
gi 392892359 173 PISAATNSSFLNTW 186
Cdd:cd17679  158 QFELPYNSSLLNTW 171
RUN pfam02759
RUN domain; This domain is present in several proteins that are linked to the functions of ...
 52-175 4.65e-22

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: 92.72  E-value: 4.65e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359   52 NLCNSIEAIFIHGLRDPFFLKGTRYAKYPEPNFWPFVSKF-----SHRSITSQIACLGQIRSEI---GKSRAWIRIVLNE 123
Cdd:pfam02759   1 QLCAALEALLSHGLKRSSLLILRAAGLLPERSFWALLERVgklvpPAEELLSSVQELEQIHTPYspdGRGRAWIRLALNE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 392892359  124 NALGQYLDLLAAEATAIQQFYSDDAFLRLLSDGDQserIRGLLKPLSSLPIS 175
Cdd:pfam02759  81 KLLDQWLKLLLSNKELLSEYYEPWALLADPEFGEI---LLGLLVGLSALDFN 129
RUN smart00593
domain involved in Ras-like GTPase signaling;
113-179 1.51e-14

domain involved in Ras-like GTPase signaling;


Pssm-ID: 214736 [Multi-domain]  Cd Length: 64  Bit Score: 68.79  E-value: 1.51e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392892359   113 SRAWIRIVLNENALGQYLDLLAAEATAIQQFYSDDAFLRllsDGDQSERIRGLLKPLSSLPISAATN 179
Cdd:smart00593   1 FRAWIRLALNEKLLSSWLNLLLSDEELLSKYYEPWAFLR---DPEEGEQLLGLLVGLSALDFNLPVD 64
RING-HC_PCGF5 cd16737
RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, ...
 864-920 2.23e-03

RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, also known as RING finger protein 159 (RNF159), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) and serves as the core component of a Polycomb repressive complex 1 (PRC1). Like other PCGF homologs, PCGF5 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. PCGF5 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438395 [Multi-domain]  Cd Length: 95  Bit Score: 38.20  E-value: 2.23e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 392892359 864 NHVMTCTLCkqKGFCCELCTVNEVIYPFntesthrCLVCFsafhVECWRTSGDCPKC 920
Cdd:cd16737    8 NPYITCRIC--KGYLIKPTTVTECLHTF-------CKSCI----VQHFEDSNDCPEC 51
LIM3_FHL1 cd09429
The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of ...
 699-738 2.30e-03

The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188813  Cd Length: 53  Bit Score: 37.10  E-value: 2.30e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 392892359 699 GLDAQD-------FRCAMCRKTIGGSTFSkfetcAIDSKYYCTECMK 738
Cdd:cd09429   12 GVTYQDqpwhsecFVCSSCSKKLAGQRFT-----AVEDQYYCVDCYK 53
 
Name Accession Description Interval E-value
zf-RING_9 pfam13901
Putative zinc-RING and/or ribbon; This is a family of cysteine-rich proteins. Many members ...
 725-925 6.13e-79

Putative zinc-RING and/or ribbon; This is a family of cysteine-rich proteins. Many members also carry a pleckstrin-homology domain, pfam00169


Pssm-ID: 464030  Cd Length: 205  Bit Score: 255.23  E-value: 6.13e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  725 CAIDSKYYCTECMkSGGKVSIPARVVMDWDWRERAVSDRGRAWYEANQEKALINIKTTNSRLYAHAPALEETRKLREKLQ 804
Cdd:pfam13901   3 CDYTGKYYCSGCH-WNDTSVIPARILHNWDFKKYPVSKFAKQLLDSIYSQPLLNLSDLNPSLYSKVKELAKVRELREQLK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  805 LVSMYLFTCRESVSEDFRR--RLWPKEYLRSEIDVYSFADLIDVKSGALQRRLNSLLKHSINHVMTCTLCKQKGFCCELC 882
Cdd:pfam13901  82 LLKDYLKTCRFAAEEELLKlfRLRPRHHLLEDSHLYSLQDLVDIKNGSLLPFLEELVQFAEKHVTNCELCQGKGFICELC 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 392892359  883 TVNEVIYPFNTESTHRCLVCFSAFHVECWR-TSGDCPKCVRRQN 925
Cdd:pfam13901 162 NSDDIIFPFDIDTTSRCEKCKAVFHKSCFRsGASPCPKCERLQK 205
RUN_PLEKHM1 cd17679
RUN domain found in pleckstrin homology domain-containing family M member 1 (PLEKHM1) and ...
 20-186 2.32e-68

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.


Pssm-ID: 439041 [Multi-domain]  Cd Length: 171  Bit Score: 225.16  E-value: 2.32e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  20 RADLQKELDNVVKAAIASPHSKRENVPS--EITQNLCNSIEAIFIHGLRDPFFLK-----GTRYAKYPEPNFWPFVSKFS 92
Cdd:cd17679    1 KKSLTKELSSSVKELQLEYVSSDEVVTSsdDGANTLCCVLEAIFLHGLKDKFISKvssvfSGDVDKLPEPNFWPLLLKFS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  93 HRSITSQIACLGQIRSEIGKSRAWIRIVLNENALGQYLDLLAAEATAIQQFYSDDAFLRllsDGDQSERIRGLLKPLSSL 172
Cdd:cd17679   81 HRDVIDQIEHLSQITTDVGRCRAWIRLALNDGLLESYLEAILKDKSALKSYYNPSAFLR---DPEQLDILKSLLQGLESF 157

                        170
                 ....*....|....
gi 392892359 173 PISAATNSSFLNTW 186
Cdd:cd17679  158 QFELPYNSSLLNTW 171
RUN cd17671
RUN domain; RUN domain, named after RPIP8 (Rap2 interacting protein 8), UNC-14 and NESCA (new ...
 51-175 9.07e-26

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: 104.04  E-value: 9.07e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  51 QNLCNSIEAIFIHGLRDPFFLKGTryakypePNFWPFVSKFSHRSITSQ-------IACLGQIRSEIGKSRAWIRIVLNE 123
Cdd:cd17671   32 GRLCAALEAILSHGLKPKRFGGGK-------VSFWDFLEALEKLLPAPSlkqairdINSLSNVKTDDGRGRAWIRLALNE 104

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 392892359 124 NALGQYLDLLAAEATAIQQFYSDDAFLRllsDGDQSERIRGLLKPLSSLPIS 175
Cdd:cd17671  105 KSLESYLAALLSDQSLLRKYYEPWALLR---DPEEAELFLSLLVGLSSLDFN 153
RUN pfam02759
RUN domain; This domain is present in several proteins that are linked to the functions of ...
 52-175 4.65e-22

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: 92.72  E-value: 4.65e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359   52 NLCNSIEAIFIHGLRDPFFLKGTRYAKYPEPNFWPFVSKF-----SHRSITSQIACLGQIRSEI---GKSRAWIRIVLNE 123
Cdd:pfam02759   1 QLCAALEALLSHGLKRSSLLILRAAGLLPERSFWALLERVgklvpPAEELLSSVQELEQIHTPYspdGRGRAWIRLALNE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 392892359  124 NALGQYLDLLAAEATAIQQFYSDDAFLRLLSDGDQserIRGLLKPLSSLPIS 175
Cdd:pfam02759  81 KLLDQWLKLLLSNKELLSEYYEPWALLADPEFGEI---LLGLLVGLSALDFN 129
RUN_PLEKHM2 cd17680
RUN domain found in pleckstrin homology domain-containing family M member 2 (PLEKHM2) and ...
 27-166 7.22e-21

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.


Pssm-ID: 439042  Cd Length: 145  Bit Score: 89.61  E-value: 7.22e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  27 LDNVVKA--AIASPHSKRENVPSEIT------QNLCNSIEAIFIHGLRDPffLKGtryakypepnFWPFVSKFSHRSITS 98
Cdd:cd17680    3 LRNISEAikSLQSYSSSQEEEDVLITnenrelQRLCEALDHALLHGLRRG--NRG----------YWPFVKEFTHKETIK 70

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 392892359  99 QIACLGQIRSEIGKSRAWIRIVLNENALGQYLDLLAAEATAIQQFYSDDAFLRllsDGDQSERIRGLL 166
Cdd:cd17680   71 QIENLPNVTTDLGRGRAWLYLALNEGSLESYLRSFLENRKLVKKFYHKHALLR---DSQRLELLLTLL 135
RUN_SNX29 cd17689
RUN domain found in sorting nexin-29 (SNX29) and similar proteins; SNX29, also called RUN ...
 52-171 1.43e-18

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.


Pssm-ID: 439051  Cd Length: 166  Bit Score: 83.82  E-value: 1.43e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  52 NLCNSIEAIFIHGLRDPFFLK-------------GTRYAKYPEPNFWPFVSKFSHRSITSQIACLGQIRSEIGKSRAWIR 118
Cdd:cd17689   29 CLCAQLEAVLQHGLKTSRSPNlvssavtqvsglaGSLGSAETEPTFWPFVKEHLTKHELERFELLKNIWTDIGRGRAWLR 108

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 392892359 119 IVLNENALGQYLDLLAAEATAIQQFYSDDAFLRllsDGDQSERIRGLLKPLSS 171
Cdd:cd17689  109 SALNEHSLERYLHILLSNENLLRQYYEDWAFLR---DEERSSMLPNMAAGLGS 158
RUN smart00593
domain involved in Ras-like GTPase signaling;
113-179 1.51e-14

domain involved in Ras-like GTPase signaling;


Pssm-ID: 214736 [Multi-domain]  Cd Length: 64  Bit Score: 68.79  E-value: 1.51e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392892359   113 SRAWIRIVLNENALGQYLDLLAAEATAIQQFYSDDAFLRllsDGDQSERIRGLLKPLSSLPISAATN 179
Cdd:smart00593   1 FRAWIRLALNEKLLSSWLNLLLSDEELLSKYYEPWAFLR---DPEEGEQLLGLLVGLSALDFNLPVD 64
RUN_RUFY1_like cd17681
RUN domain found in RUN and FYVE domain-containing proteins, RUFY1, RUFY2, RUFY3 and similar ...
 51-172 2.25e-12

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.


Pssm-ID: 439043  Cd Length: 155  Bit Score: 65.67  E-value: 2.25e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  51 QNLCNSIEAIFIHGLrdpfflKGTRYAKYPEPNFWPFVSKFSHRS-----ITSQIACLGQIRSEIGKSRAWIRIVLNENA 125
Cdd:cd17681   35 QQFFVILEHVLRHGL------KVKKSFLGPNKSFWPVLEHVEKLVpeaneITASVRDLPGIKTPLGRARAWLRLALMQKK 108

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 392892359 126 LGQYLDLLAAEATAIQQFYSDDAFLRllsdGDQSERIRGLLKPLSSL 172
Cdd:cd17681  109 LADYFRALIENKDLLSEFYEPGALMM----SEEAVVIAGLLVGLNVI 151
RUN_RUBCN cd17686
RUN domain found in Run domain Beclin-1-interacting and cysteine-rich domain-containing ...
 51-151 1.27e-10

RUN domain found in Run domain Beclin-1-interacting and cysteine-rich domain-containing protein (RUBCN) and similar proteins; RUBCN, also called rubicon, or beclin-1 associated RUN domain containing protein (Baron), is part of a Beclin-1-Vps34-containing autophagy complex. It negatively regulates endosome maturation and degradative endocytic trafficking and impairs autophagosome maturation process. It is also an important negative regulator of the innate immune response, enhances viral replication and may play a role in viral immune evasion. This model contains the RUN domain of RUBCN.


Pssm-ID: 439048  Cd Length: 151  Bit Score: 60.74  E-value: 1.27e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  51 QNLCNSIEAIFIHGLRDPFFLKGtryakypEPNFWPFV--SKFSH----RSITSQIACLGQIRSEIGKSRAWIRIVLNEN 124
Cdd:cd17686   22 QRLCRAVENILQHGLKEFQGLNK-------EIDDWEFVqgLRWLQptlaPSIEQQSRSSPSESEVSDKGRLWLRQSLQQH 94

                         90       100
                 ....*....|....*....|....*..
gi 392892359 125 ALGQYLDLLAAEATAIQQFYSDDAFLR 151
Cdd:cd17686   95 CLSSQLQWLVSDKELLRKYYEDEAFLR 121
RUN_RUNDC3 cd17684
RUN domain found in RUN domain-containing protein 3 (RUNDC3) and similar proteins; RUNDC3 ...
 47-175 1.12e-09

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.


Pssm-ID: 439046  Cd Length: 150  Bit Score: 57.79  E-value: 1.12e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  47 SEITQNLCNSIEAIFIHGLRdpfflKGTRYAKYPEP-NFWPFV----SKFSHRSITSqIACLGQIRSEIGKSRAWIRIVL 121
Cdd:cd17684   26 SEELINFAAILEQILSHRLK-----PVKPWYGSEEPrTFWDYIrvacKKVPQNCIAS-IEQMENIKSPKAKGRAWIRVAL 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 392892359 122 NENALGQYLDLLAAEATAIQQFYSDDAFlrLLSdgDQSERIRGLLKPLSSLPIS 175
Cdd:cd17684  100 MEKRLSEYLSTALKQTRLTRNFYQDGAI--MLS--EDATVLCGMLIGLNAIDFS 149
RUN_RUSC cd17685
RUN domain found in RUN and SH3 domain-containing proteins, RUSC1, RUSC2 and similar proteins; ...
 8-173 3.30e-08

RUN domain found in RUN and SH3 domain-containing proteins, RUSC1, RUSC2 and similar proteins; RUSC1, also called new molecule containing SH3 at the carboxy-terminus (NESCA), may acts as a signaling adapter that translocates to the nuclear envelope and regulates neurotrophin-induced neurite outgrowth. RUSC2, also called iporin, or interacting protein of Rab1, is a novel interacting molecule for the active GTP-bound conformation of Rab1. It may function as a link between the targeting of endoplasmic reticulum derived vesicles, triggered by the Rab1 GTPase and a signaling pathway regulated by molecules containing SH3 and/or poly-proline regions. This model contains the RUN domain of RUSC1 and RUSC2.


Pssm-ID: 439047  Cd Length: 178  Bit Score: 54.21  E-value: 3.30e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359   8 LTPAQKLKQEKIRADLQKELDNVVKAAIASPhSKRENVPSEITQNLCNSIEAIFIHGLRdPFFLKGTRYAKYpepNFWPF 87
Cdd:cd17685    5 LVKAVIAAVDKIVAHFSQSRDPSDKAKLGNS-AVSPEVGHLVLKYLCPALYALLSDGLK-PYVLTLFGQVKN---SVWSV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  88 VSKFSH--------RSITSQIACLGQIRSEIGKSRAWIRIVLNENALGQYLDLLAAEATAIQQFYSDDAFLRLLSDGDQS 159
Cdd:cd17685   80 VEASTQpgpstkalNELVNKLNSEEKLTSGTLKFNAFIFGLLNLRSLDAWLSYLVTKENLLSKHYNPNAFLLLASSAYRP 159

                        170
                 ....*....|....*.
gi 392892359 160 --ERIRGLLKPLSSLP 173
Cdd:cd17685  160 lfDELLLALQPLSVLP 175
RUN_RUNDC3B cd17700
RUN domain found in RUN domain-containing protein 3B (RUNDC3B) and similar proteins; RUN ...
 52-175 1.61e-07

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.


Pssm-ID: 439062  Cd Length: 151  Bit Score: 51.51  E-value: 1.61e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  52 NLCNSIEAIFIHGLRDPFFLKGtryakYPEP-NFWPFV----SKFSHRSITSqIACLGQIRSEIGKSRAWIRIVLNENAL 126
Cdd:cd17700   31 NFAAILEQILSHRLKGQVTWFG-----YESPrSFWDYIrvacSKVPHNCICS-IENMENVSSSRAKGRAWIRVALMEKRL 104

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 392892359 127 GQYLDLLAAEATAIQQFYSDDAFLRllsdGDQSERIRGLLKPLSSLPIS 175
Cdd:cd17700  105 SEYISTALRDFKTTRRFYEDGAIVL----GEEANMLAGMLLGLNAIDFS 149
RUN1_DENND5 cd17677
RUN1 domain found in DENN domain-containing protein 5 (DENND5) and similar proteins; DENND5 ...
 53-151 3.02e-06

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.


Pssm-ID: 439039  Cd Length: 183  Bit Score: 48.55  E-value: 3.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  53 LCNSIEAIFIHGLRD------------PFFLKGTRYAKYPEPNFwpfvskFSHRSITSqiacLGQIRSEIGKSRAWIRIV 120
Cdd:cd17677   55 LCDLLERIWSHGLQTkqgksalwshllAYQENEERLKPLPESLL------FDMKNVQN----MKEIKTDVGYARAWIRLA 124

                         90       100       110
                 ....*....|....*....|....*....|.
gi 392892359 121 LNENALGQYLDLLAAEATAIQQFYSDDAFLR 151
Cdd:cd17677  125 LEKKLLSKHLKTLLSNQDLLRSLYKRYAFLR 155
RUN_RUNDC3A cd17699
RUN domain found in RUN domain-containing protein 3A (RUNDC3A) and similar proteins; RUN ...
 47-175 5.39e-06

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.


Pssm-ID: 439061  Cd Length: 151  Bit Score: 47.33  E-value: 5.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  47 SEITQNLCNSIEAIFIHGLRDP---FFLKGTRyakypepNFWPFV----SKFSHRSITSqIACLGQIRSEIGKSRAWIRI 119
Cdd:cd17699   26 SEEFVNFAAILEQILSHRFKGPvswFSSDGQR-------GFWDYIrlacSKVPNNCISS-IENMENISTSRAKGRAWIRV 97

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 392892359 120 VLNENALGQYLDLLAAEATAIQQFYSDDA-FLRllsdgDQSERIRGLLKPLSSLPIS 175
Cdd:cd17699   98 ALMEKRLSEYIATALRDTRTTRRFYDDGAiMLR-----EESTVLTGMLIGLSAIDFS 149
RUN1_DENND5B cd17691
RUN1 domain found in DENN domain-containing protein 5B (DENND5B) and similar proteins; DENND5B, ...
 103-158 2.08e-05

RUN1 domain found in DENN domain-containing protein 5B (DENND5B) and similar proteins; DENND5B, also called Rab6-interacting protein 1 (Rab6IP1)-like protein, functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. It 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. This model represents the first RUN domain of DENND5B.


Pssm-ID: 439053 [Multi-domain]  Cd Length: 206  Bit Score: 46.59  E-value: 2.08e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 392892359 103 LGQIRSEIGKSRAWIRIVLNENALGQYLDLLAAEATAIQQFYSDDAFLRLLSDGDQ 158
Cdd:cd17691  130 MSEIKTDVGRARAWIRLSLEKKLLSQHLKQLLSNQALTKKLYKRYAFLRCEEEKEQ 185
RUN_RUFY4_like cd17682
RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4), FYVE and coiled-coil ...
 53-170 3.89e-05

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.


Pssm-ID: 439044  Cd Length: 150  Bit Score: 44.52  E-value: 3.89e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  53 LCNSIEAIFIHGLRDPFFLKGTRyakypePNFWPFVSKFSHR---------SITSQIACLGQIRSEIGKSRAWIRIVLNE 123
Cdd:cd17682   27 FCETLEKILRKGLKEKVSLGGRR------KDYWDWLEELLKKlnkipkslsDAVKFVKSCKKVKTNQGRGRLFIRYALNK 100

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 392892359 124 NALGQYLDLLAAEATAIQQFYSDDAFLRllsDGDQSERIRGLLKPLS 170
Cdd:cd17682  101 KCLHDPVQQLVKNPKLLSDYYSPDSILG---NEILSEILLSLLYQLN 144
RUN1_DENND5A cd17690
RUN1 domain found in DENN domain-containing protein 5A (DENND5A) and similar proteins; DENND5A, ...
 99-158 1.71e-04

RUN1 domain found in DENN domain-containing protein 5A (DENND5A) and similar proteins; DENND5A, also called Rab6-interacting protein 1 (Rab6IP1), is present predominantly in developing neuronal tissue, and functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. It 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. This model represents the first RUN domain of DENND5A.


Pssm-ID: 439052 [Multi-domain]  Cd Length: 209  Bit Score: 43.84  E-value: 1.71e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 392892359  99 QIACLGQIRSEIGKSRAWIRIVLNENALGQYLDLLAAEATAIQQFYSDDAFLRLLSDGDQ 158
Cdd:cd17690  129 HIQNIGEIKTDVGKARAWVRLSMEKKLLSRHLKQLLSDHELTKKLYKRYAFLRCDDEKEQ 188
RING-HC_PCGF5 cd16737
RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, ...
 864-920 2.23e-03

RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, also known as RING finger protein 159 (RNF159), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) and serves as the core component of a Polycomb repressive complex 1 (PRC1). Like other PCGF homologs, PCGF5 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. PCGF5 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438395 [Multi-domain]  Cd Length: 95  Bit Score: 38.20  E-value: 2.23e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 392892359 864 NHVMTCTLCkqKGFCCELCTVNEVIYPFntesthrCLVCFsafhVECWRTSGDCPKC 920
Cdd:cd16737    8 NPYITCRIC--KGYLIKPTTVTECLHTF-------CKSCI----VQHFEDSNDCPEC 51
LIM3_FHL1 cd09429
The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of ...
 699-738 2.30e-03

The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188813  Cd Length: 53  Bit Score: 37.10  E-value: 2.30e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 392892359 699 GLDAQD-------FRCAMCRKTIGGSTFSkfetcAIDSKYYCTECMK 738
Cdd:cd09429   12 GVTYQDqpwhsecFVCSSCSKKLAGQRFT-----AVEDQYYCVDCYK 53
RUN_RUFY2 cd17695
RUN domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins; ...
 96-150 5.03e-03

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.


Pssm-ID: 439057  Cd Length: 156  Bit Score: 38.81  E-value: 5.03e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 392892359  96 ITSQIACLGQIRSEIGKSRAWIRIVLNENALGQYLDLLAAEATAIQQFYSDDAFL 150
Cdd:cd17695   79 IAASVRDLPGLKTPLGRARAWLRLALMQKKLADYLRCLIIRRDLLSEFYEYHALM 133
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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