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Conserved domains on  [gi|17563242|ref|NP_505267|]
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E3 ubiquitin-protein ligase rpm-1 [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PHR pfam08005
PHR domain; This domain is called PHR as it was original found in the proteins PAM, highwire ...
 1056-1203 4.41e-59

PHR domain; This domain is called PHR as it was original found in the proteins PAM, highwire and RPM. This domain can be duplicated in the highwire, PFAM and PRM sequence. The C-terminal region of the protein BTBD1 includes the PHR domain and is known to interact with Topoisomerase I, an enzyme which relaxes DNA supercoils.


:

Pssm-ID: 462339  Cd Length: 150  Bit Score: 201.31  E-value: 4.41e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242   1056 NRFDGTGGGWGYSANSVEAIQFKVSKEIRLVGVGLYGGRG---EYISKLKLyrqIGTEADELYVEQITETDETVYDCGAH 1132
Cdd:pfam08005    1 NRFQSTGGGWGYSGGSPDAIRFSVDRDIFLVGFGLYGSIGgpaDYSVKIEL---IDGERWESLGEVLGENDTTFSSDGSN 77

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17563242   1133 ETATLLFSQPIVIQPNHWHVVSAKISGPSSDCGANGKRHVECDG-VTFQFRKSAVSNNGTDVDVGQIPELYY 1203
Cdd:pfam08005   78 DIFRVLFDEPVEIEPNVKYTASAKIKGPSSYYGTNGLREVTCDGgVTFQFSSSSLSNNGTSVNRGQIPELLY 149
PHR pfam08005
PHR domain; This domain is called PHR as it was original found in the proteins PAM, highwire ...
 1503-1655 7.98e-37

PHR domain; This domain is called PHR as it was original found in the proteins PAM, highwire and RPM. This domain can be duplicated in the highwire, PFAM and PRM sequence. The C-terminal region of the protein BTBD1 includes the PHR domain and is known to interact with Topoisomerase I, an enzyme which relaxes DNA supercoils.


:

Pssm-ID: 462339  Cd Length: 150  Bit Score: 137.37  E-value: 7.98e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242   1503 SRFRRRSAQptWDMSDGCADAIAFRVDSeGIKLHGFGIYLPT-EPDRRNFVGEIMmlspdSSEKWTCLLRVTAEM----- 1576
Cdd:pfam08005    1 NRFQSTGGG--WGYSGGSPDAIRFSVDR-DIFLVGFGLYGSIgGPADYSVKIELI-----DGERWESLGEVLGENdttfs 72

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17563242   1577 SSEEKEVGIVRFPEYVLLSPGVTYAVKVNMMKNTkTFCGEGGVTQVHLLNGARLFFSGCSMSQNGTTVQRGQLPYLIYS 1655
Cdd:pfam08005   73 SDGSNDIFRVLFDEPVEIEPNVKYTASAKIKGPS-SYYGTNGLREVTCDGGVTFQFSSSSLSNNGTSVNRGQIPELLYY 150
RING-H2_PHR cd16463
RING finger, H2 subclass, found in the PHR (Pam/Highwire/RPM-1) protein family; The PHR ...
 3514-3567 5.43e-31

RING finger, H2 subclass, found in the PHR (Pam/Highwire/RPM-1) protein family; The PHR protein family represents an evolutionally conserved family of large proteins including human E3 ubiquitin ligase protein associated with Myc (Pam) and its homologs, Phr1 in mouse, Highwire (HIW) in Drosophila, RPM-1 (regulator of presynaptic morphology 1) in Caenorhabditis elegans, and Esrom in zebrafish. Those proteins are large E3 ubiquitin ligases containing regulator of chromosome condensation (RCC) homology domains (RHD-1 and RHD-2) with inferred guanine exchange factor (GEF) activity, a Myc-binding domain, a B-box zinc finger, and a C-terminal C3H2C3-type RING-H2 finger with E3 ubiquitin (Ub) ligase activity. They play an important role in axon guidance and synaptogenesis. They regulate synapse formation and growth in mammals, zebrafish, Drosophila, and Caenorhabditis elegans, and may control a variety of signaling pathways, including cAMP signaling in mammalian cells, JNK/p38 MAPK signaling in Drosophila and C. elegans, and bone morphogenetic protein signaling in Drosophila. Pam also known as Myc-binding protein 2 (MYCBP2), or Pam/highwire/rpm-1 protein (PHR1), negatively regulates neuronal growth, synaptogenesis and synaptic plasticity by modulating several signaling pathways including the p38 MAPK signaling cascade. It also participates in receptor and ion channel internalization, such as regulating internalization of transient receptor potential vanilloid receptor 1 (TRPV1) in peripheral sensory neurons, as well as duration of thermal hyperalgesia through p38 MAPK. It interacts with neuron-specific electroneutral potassium (K+) and chloride (Cl-) cotransporter KCC2 and modulates its function. Moreover, Pam genetically interacts with Robo2 to modulate axon guidance in the olfactory system. It also associates with tuberous sclerosis complex (TSC) proteins, ubiquitinating TSC2 and regulating mammalian/mechanistic target of rapamycin (mTOR) signaling. Furthermore, Pam is the longest lasting nontranscriptional regulator of adenylyl cyclase activity, and can mediate sustained inhibition of cAMP signaling by sphingosine-1-phosphate. It is also involved in spinal nociceptive processing. Phr1 is an essential regulator of retinal ganglion cell projection during both dorsal lateral geniculate nucleus (dLGN) and superior colliculus (SC) topographic map development. RPM-1 positively regulates a Rab GTPase pathway to promote vesicular trafficking via late endosomes, thereby regulating synapse formation and axon termination. Esrom has E3 ligase activity and modulates the amount of phosphorylated Tuberin, a tumor suppressor, in growth cones. It is required for the formation of the retinotectal projection.


:

Pssm-ID: 438126 [Multi-domain]  Cd Length: 55  Bit Score: 117.05  E-value: 5.43e-31
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 17563242 3514 DDVCVICFTERLGAAPCIRLGCGHMFHFHCVRMILERRWNGPRIVFRFMQCPLC 3567
Cdd:cd16463    1 DDMCMICFTEALSAAPAIQLDCGHVFHLHCCRRVLENRWPGPRITFGFLKCPIC 54
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 607-873 4.02e-23

Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton];


:

Pssm-ID: 444065 [Multi-domain]  Cd Length: 343  Bit Score: 103.90  E-value: 4.02e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  607 LNGLDNVmiSSLALGKSHGVAVTRNGHLFTWGLNNMNQCGRvESTSTTSSPRhsgrqeyQICPigehtwltdtpsvcaqc 686
Cdd:COG5184   94 VPGLTGV--VAVAAGYYHSCALKSDGTVWCWGDNSSGQLGD-GTTTNRLTPV-------QVDA----------------- 146

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  687 GLCSARGVACGRvprpkgtmCH-CGVGESTCLRCGlcrpcgevtepaqpGRAQHVQFSSTAAPQRSTlhPSRVILSQGph 765
Cdd:COG5184  147 GLSGVVAIAAGG--------YHtCALKSDGTVWCW--------------GANSYGQLGDGTTTDRPT--PVQVGGLSG-- 200

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  766 dvkVSSVSCGNFHTVLLASDRRVFTFGSNCHGQLGVGDTLSKNTPQQVILPSDtvIVQVAAGSNHTILRANDGSVFTFGA 845
Cdd:COG5184  201 ---VVAVAAGGDHSCALKSDGTVWCWGSNSSGQLGDGTTTDRATPVQVAGLTG--VVAIAAGGSHTCALKSDGTVWCWGD 275

                        250       260
                 ....*....|....*....|....*...
gi 17563242  846 FGKGQLARPAGEKAgwnAIPEKVSGFGP 873
Cdd:COG5184  276 NSYGQLGDGTTTDR---STPVKVPGLSG 300
Bbox2_MYCBP2 cd19799
B-box-type 2 zinc finger found in Myc-binding protein 2 (MYCBP2) and similar proteins; MYCBP2, ...
 3334-3383 2.33e-19

B-box-type 2 zinc finger found in Myc-binding protein 2 (MYCBP2) and similar proteins; MYCBP2, also termed protein associated with Myc (Pam), is an atypical E3 ubiquitin-protein ligase which specifically mediates ubiquitination of threonine and serine residues on target proteins, instead of ubiquitinating lysine residues. MYCBP2 harbors a B-box motif that shows high sequence similarity with B-Box-type zinc finger 2 found in tripartite motif-containing proteins (TRIMs). The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


:

Pssm-ID: 380857  Cd Length: 50  Bit Score: 83.98  E-value: 2.33e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 17563242 3334 LLCENHDDGHTVAQVFCVDCDVALCKECFTVMHLHKKNRNHGVKNLVQSS 3383
Cdd:cd19799    1 PTCDNHDDGETAAIIFCCDCGNYLCAECDRFLHLHRKNRSHQRQVFKEEE 50
APC10-like super family cl02148
APC10-like DOC1 domains in E3 ubiquitin ligases that mediate substrate ubiquitination; This ...
 2887-3049 4.33e-05

APC10-like DOC1 domains in E3 ubiquitin ligases that mediate substrate ubiquitination; This family contains the single domain protein, APC10, a subunit of the anaphase-promoting complex (APC), as well as the DOC1 domain of multi-domain proteins present in E3 ubiquitin ligases. E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. The APC, a multi-protein complex (or cyclosome), is a cell cycle-regulated, E3 ubiquitin ligase that controls important transitions in mitosis and the G1 phase by ubiquitinating regulatory proteins, thereby targeting them for degradation. APC10-like DOC1 domains such as those present in HECT (Homologous to the E6-AP Carboxyl Terminus) and Cullin-RING (Really Interesting New Gene) E3 ubiquitin ligase proteins, HECTD3, and CUL7, respectively, are also included in this hierarchy. CUL7 is a member of the Cullin-RING ligase family and functions as a molecular scaffold assembling a SCF-ROC1-like E3 ubiquitin ligase complex consisting of Skp1, CUL7, Fbx29 F-box protein, and ROC1 (RING-box protein 1) and promotes ubiquitination. CUL7 is a multi-domain protein with a C-terminal cullin domain that binds ROC1 and a centrally positioned APC10/DOC1 domain. HECTD3 contains a C-terminal HECT domain which contains the active site for ubiquitin transfer onto substrates, and an N-terminal APC10 domain which is responsible for substrate recognition and binding. An APC10/DOC1 domain homolog is also present in HERC2 (HECT domain and RLD2), a large multi-domain protein with three RCC1-like domains (RLDs), additional internal domains including zinc finger ZZ-type and Cyt-b5 (Cytochrome b5-like Heme/Steroid binding) domains, and a C-terminal HECT domain. Recent studies have shown that the protein complex HERC2-RNF8 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. Also included in this hierarchy is an uncharacterized APC10/DOC1-like domain found in a multi-domain protein, which also contains CUB, zinc finger ZZ-type, and EF-hand domains. The APC10/DOC1 domain forms a beta-sandwich structure that is related in architecture to the galactose-binding domain-like fold; their sequences are quite dissimilar, however, and are not included here.


The actual alignment was detected with superfamily member pfam03256:

Pssm-ID: 382862  Cd Length: 185  Bit Score: 47.05  E-value: 4.33e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242   2887 FVKEMKDITKFADITASSRQAM--VICLTDESGETFWESgeeDKNRSRSLSVQLDESAHGEILSLFIDNARDEGYRISSI 2964
Cdd:pfam03256   18 RVRHQREIGSQAVWSLSSCKPGfgVDLLRDDNLDTYWQS---DGSQPHLVNIQFRKKTPVKYVAIYLDYKLDESYTPSKI 94

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242   2965 AFKAILEDGRRKDLTSLTLESAyCGWLKCCIKD-------ISHIQI-----QFKGPNPasRIRQLMILGypakttgtPRL 3032
Cdd:pfam03256   95 SVRAGTGFNDLQEVRVVDLEEP-TGWVHIPLRDangkplrTFMLQIavlsnHQNGRDT--HVRQIKIYG--------PVE 163

                          170
                   ....*....|....*..
gi 17563242   3033 APSTSHHLFFSDTQRDA 3049
Cdd:pfam03256  164 ERSAVAARLGHFTTSDF 180
 
Name Accession Description Interval E-value
PHR pfam08005
PHR domain; This domain is called PHR as it was original found in the proteins PAM, highwire ...
 1056-1203 4.41e-59

PHR domain; This domain is called PHR as it was original found in the proteins PAM, highwire and RPM. This domain can be duplicated in the highwire, PFAM and PRM sequence. The C-terminal region of the protein BTBD1 includes the PHR domain and is known to interact with Topoisomerase I, an enzyme which relaxes DNA supercoils.


Pssm-ID: 462339  Cd Length: 150  Bit Score: 201.31  E-value: 4.41e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242   1056 NRFDGTGGGWGYSANSVEAIQFKVSKEIRLVGVGLYGGRG---EYISKLKLyrqIGTEADELYVEQITETDETVYDCGAH 1132
Cdd:pfam08005    1 NRFQSTGGGWGYSGGSPDAIRFSVDRDIFLVGFGLYGSIGgpaDYSVKIEL---IDGERWESLGEVLGENDTTFSSDGSN 77

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17563242   1133 ETATLLFSQPIVIQPNHWHVVSAKISGPSSDCGANGKRHVECDG-VTFQFRKSAVSNNGTDVDVGQIPELYY 1203
Cdd:pfam08005   78 DIFRVLFDEPVEIEPNVKYTASAKIKGPSSYYGTNGLREVTCDGgVTFQFSSSSLSNNGTSVNRGQIPELLY 149
PHR pfam08005
PHR domain; This domain is called PHR as it was original found in the proteins PAM, highwire ...
 1503-1655 7.98e-37

PHR domain; This domain is called PHR as it was original found in the proteins PAM, highwire and RPM. This domain can be duplicated in the highwire, PFAM and PRM sequence. The C-terminal region of the protein BTBD1 includes the PHR domain and is known to interact with Topoisomerase I, an enzyme which relaxes DNA supercoils.


Pssm-ID: 462339  Cd Length: 150  Bit Score: 137.37  E-value: 7.98e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242   1503 SRFRRRSAQptWDMSDGCADAIAFRVDSeGIKLHGFGIYLPT-EPDRRNFVGEIMmlspdSSEKWTCLLRVTAEM----- 1576
Cdd:pfam08005    1 NRFQSTGGG--WGYSGGSPDAIRFSVDR-DIFLVGFGLYGSIgGPADYSVKIELI-----DGERWESLGEVLGENdttfs 72

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17563242   1577 SSEEKEVGIVRFPEYVLLSPGVTYAVKVNMMKNTkTFCGEGGVTQVHLLNGARLFFSGCSMSQNGTTVQRGQLPYLIYS 1655
Cdd:pfam08005   73 SDGSNDIFRVLFDEPVEIEPNVKYTASAKIKGPS-SYYGTNGLREVTCDGGVTFQFSSSSLSNNGTSVNRGQIPELLYY 150
RING-H2_PHR cd16463
RING finger, H2 subclass, found in the PHR (Pam/Highwire/RPM-1) protein family; The PHR ...
 3514-3567 5.43e-31

RING finger, H2 subclass, found in the PHR (Pam/Highwire/RPM-1) protein family; The PHR protein family represents an evolutionally conserved family of large proteins including human E3 ubiquitin ligase protein associated with Myc (Pam) and its homologs, Phr1 in mouse, Highwire (HIW) in Drosophila, RPM-1 (regulator of presynaptic morphology 1) in Caenorhabditis elegans, and Esrom in zebrafish. Those proteins are large E3 ubiquitin ligases containing regulator of chromosome condensation (RCC) homology domains (RHD-1 and RHD-2) with inferred guanine exchange factor (GEF) activity, a Myc-binding domain, a B-box zinc finger, and a C-terminal C3H2C3-type RING-H2 finger with E3 ubiquitin (Ub) ligase activity. They play an important role in axon guidance and synaptogenesis. They regulate synapse formation and growth in mammals, zebrafish, Drosophila, and Caenorhabditis elegans, and may control a variety of signaling pathways, including cAMP signaling in mammalian cells, JNK/p38 MAPK signaling in Drosophila and C. elegans, and bone morphogenetic protein signaling in Drosophila. Pam also known as Myc-binding protein 2 (MYCBP2), or Pam/highwire/rpm-1 protein (PHR1), negatively regulates neuronal growth, synaptogenesis and synaptic plasticity by modulating several signaling pathways including the p38 MAPK signaling cascade. It also participates in receptor and ion channel internalization, such as regulating internalization of transient receptor potential vanilloid receptor 1 (TRPV1) in peripheral sensory neurons, as well as duration of thermal hyperalgesia through p38 MAPK. It interacts with neuron-specific electroneutral potassium (K+) and chloride (Cl-) cotransporter KCC2 and modulates its function. Moreover, Pam genetically interacts with Robo2 to modulate axon guidance in the olfactory system. It also associates with tuberous sclerosis complex (TSC) proteins, ubiquitinating TSC2 and regulating mammalian/mechanistic target of rapamycin (mTOR) signaling. Furthermore, Pam is the longest lasting nontranscriptional regulator of adenylyl cyclase activity, and can mediate sustained inhibition of cAMP signaling by sphingosine-1-phosphate. It is also involved in spinal nociceptive processing. Phr1 is an essential regulator of retinal ganglion cell projection during both dorsal lateral geniculate nucleus (dLGN) and superior colliculus (SC) topographic map development. RPM-1 positively regulates a Rab GTPase pathway to promote vesicular trafficking via late endosomes, thereby regulating synapse formation and axon termination. Esrom has E3 ligase activity and modulates the amount of phosphorylated Tuberin, a tumor suppressor, in growth cones. It is required for the formation of the retinotectal projection.


Pssm-ID: 438126 [Multi-domain]  Cd Length: 55  Bit Score: 117.05  E-value: 5.43e-31
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 17563242 3514 DDVCVICFTERLGAAPCIRLGCGHMFHFHCVRMILERRWNGPRIVFRFMQCPLC 3567
Cdd:cd16463    1 DDMCMICFTEALSAAPAIQLDCGHVFHLHCCRRVLENRWPGPRITFGFLKCPIC 54
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 607-873 4.02e-23

Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton];


Pssm-ID: 444065 [Multi-domain]  Cd Length: 343  Bit Score: 103.90  E-value: 4.02e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  607 LNGLDNVmiSSLALGKSHGVAVTRNGHLFTWGLNNMNQCGRvESTSTTSSPRhsgrqeyQICPigehtwltdtpsvcaqc 686
Cdd:COG5184   94 VPGLTGV--VAVAAGYYHSCALKSDGTVWCWGDNSSGQLGD-GTTTNRLTPV-------QVDA----------------- 146

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  687 GLCSARGVACGRvprpkgtmCH-CGVGESTCLRCGlcrpcgevtepaqpGRAQHVQFSSTAAPQRSTlhPSRVILSQGph 765
Cdd:COG5184  147 GLSGVVAIAAGG--------YHtCALKSDGTVWCW--------------GANSYGQLGDGTTTDRPT--PVQVGGLSG-- 200

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  766 dvkVSSVSCGNFHTVLLASDRRVFTFGSNCHGQLGVGDTLSKNTPQQVILPSDtvIVQVAAGSNHTILRANDGSVFTFGA 845
Cdd:COG5184  201 ---VVAVAAGGDHSCALKSDGTVWCWGSNSSGQLGDGTTTDRATPVQVAGLTG--VVAIAAGGSHTCALKSDGTVWCWGD 275

                        250       260
                 ....*....|....*....|....*...
gi 17563242  846 FGKGQLARPAGEKAgwnAIPEKVSGFGP 873
Cdd:COG5184  276 NSYGQLGDGTTTDR---STPVKVPGLSG 300
Bbox2_MYCBP2 cd19799
B-box-type 2 zinc finger found in Myc-binding protein 2 (MYCBP2) and similar proteins; MYCBP2, ...
 3334-3383 2.33e-19

B-box-type 2 zinc finger found in Myc-binding protein 2 (MYCBP2) and similar proteins; MYCBP2, also termed protein associated with Myc (Pam), is an atypical E3 ubiquitin-protein ligase which specifically mediates ubiquitination of threonine and serine residues on target proteins, instead of ubiquitinating lysine residues. MYCBP2 harbors a B-box motif that shows high sequence similarity with B-Box-type zinc finger 2 found in tripartite motif-containing proteins (TRIMs). The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380857  Cd Length: 50  Bit Score: 83.98  E-value: 2.33e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 17563242 3334 LLCENHDDGHTVAQVFCVDCDVALCKECFTVMHLHKKNRNHGVKNLVQSS 3383
Cdd:cd19799    1 PTCDNHDDGETAAIIFCCDCGNYLCAECDRFLHLHRKNRSHQRQVFKEEE 50
RCC1 pfam00415
Regulator of chromosome condensation (RCC1) repeat;
787-833 4.53e-13

Regulator of chromosome condensation (RCC1) repeat;


Pssm-ID: 395335 [Multi-domain]  Cd Length: 50  Bit Score: 66.00  E-value: 4.53e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 17563242    787 RVFTFGSNCHGQLGVGDTLSKNTPQQVILPSDTVIVQVAAGSNHTIL 833
Cdd:pfam00415    3 RVYTWGRNDYGQLGLGTTENVLVPQKVEGLSGNKVVQVACGGDHTVA 49
BBOX smart00336
B-Box-type zinc finger;
3331-3379 3.41e-07

B-Box-type zinc finger;


Pssm-ID: 197662 [Multi-domain]  Cd Length: 42  Bit Score: 49.26  E-value: 3.41e-07
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 17563242    3331 EPVLLCENHDDghTVAQVFCVDCDVALCKECFTVMHlhkknRNHGVKNL 3379
Cdd:smart00336    1 QRAPKCDSHGD--EPAEFFCEECGALLCRTCDEAEH-----RGHTVVLL 42
zf-RING_2 pfam13639
Ring finger domain;
3515-3567 4.19e-06

Ring finger domain;


Pssm-ID: 433370 [Multi-domain]  Cd Length: 44  Bit Score: 46.25  E-value: 4.19e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 17563242   3515 DVCVICFTERLGAAPCIRLGCGHMFHFHCVRMILERRwngprivfrfMQCPLC 3567
Cdd:pfam13639    1 DECPICLEEFEEGDKVVVLPCGHHFHRECLDKWLRSS----------NTCPLC 43
ANAPC10 pfam03256
Anaphase-promoting complex, subunit 10 (APC10);
2887-3049 4.33e-05

Anaphase-promoting complex, subunit 10 (APC10);


Pssm-ID: 367420  Cd Length: 185  Bit Score: 47.05  E-value: 4.33e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242   2887 FVKEMKDITKFADITASSRQAM--VICLTDESGETFWESgeeDKNRSRSLSVQLDESAHGEILSLFIDNARDEGYRISSI 2964
Cdd:pfam03256   18 RVRHQREIGSQAVWSLSSCKPGfgVDLLRDDNLDTYWQS---DGSQPHLVNIQFRKKTPVKYVAIYLDYKLDESYTPSKI 94

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242   2965 AFKAILEDGRRKDLTSLTLESAyCGWLKCCIKD-------ISHIQI-----QFKGPNPasRIRQLMILGypakttgtPRL 3032
Cdd:pfam03256   95 SVRAGTGFNDLQEVRVVDLEEP-TGWVHIPLRDangkplrTFMLQIavlsnHQNGRDT--HVRQIKIYG--------PVE 163

                          170
                   ....*....|....*..
gi 17563242   3033 APSTSHHLFFSDTQRDA 3049
Cdd:pfam03256  164 ERSAVAARLGHFTTSDF 180
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
 3517-3567 6.07e-05

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 42.88  E-value: 6.07e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 17563242    3517 CVICFTERLgaAPCIRLGCGHMFHFHCVRMILERrwngprivfRFMQCPLC 3567
Cdd:smart00184    1 CPICLEEYL--KDPVILPCGHTFCRSCIRKWLES---------GNNTCPIC 40
HRD1 COG5243
HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein ...
 3493-3571 6.30e-05

HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227568 [Multi-domain]  Cd Length: 491  Bit Score: 48.81  E-value: 6.30e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242 3493 RNEEECLPCMTckrEDAAQDGDDVCVICFTE----------RLGAAPCIRLGCGHMFHFHCVRMILERRwngprivfrfM 3562
Cdd:COG5243  269 KDLNAMYPTAT---EEQLTNSDRTCTICMDEmfhpdheplpRGLDMTPKRLPCGHILHLHCLKNWLERQ----------Q 335


                 ....*....
gi 17563242 3563 QCPLCIQPI 3571
Cdd:COG5243  336 TCPICRRPV 344
zf-B_box pfam00643
B-box zinc finger;
3332-3379 9.19e-04

B-box zinc finger;


Pssm-ID: 459886 [Multi-domain]  Cd Length: 42  Bit Score: 39.38  E-value: 9.19e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 17563242   3332 PVLLCENHddGHTVAQVFCVDCDVALCKECFTVMHlhkknRNHGVKNL 3379
Cdd:pfam00643    2 KERLCPEH--EEEPLTLYCNDCQELLCEECSVGEH-----RGHTVVPL 42
 
Name Accession Description Interval E-value
PHR pfam08005
PHR domain; This domain is called PHR as it was original found in the proteins PAM, highwire ...
 1056-1203 4.41e-59

PHR domain; This domain is called PHR as it was original found in the proteins PAM, highwire and RPM. This domain can be duplicated in the highwire, PFAM and PRM sequence. The C-terminal region of the protein BTBD1 includes the PHR domain and is known to interact with Topoisomerase I, an enzyme which relaxes DNA supercoils.


Pssm-ID: 462339  Cd Length: 150  Bit Score: 201.31  E-value: 4.41e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242   1056 NRFDGTGGGWGYSANSVEAIQFKVSKEIRLVGVGLYGGRG---EYISKLKLyrqIGTEADELYVEQITETDETVYDCGAH 1132
Cdd:pfam08005    1 NRFQSTGGGWGYSGGSPDAIRFSVDRDIFLVGFGLYGSIGgpaDYSVKIEL---IDGERWESLGEVLGENDTTFSSDGSN 77

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17563242   1133 ETATLLFSQPIVIQPNHWHVVSAKISGPSSDCGANGKRHVECDG-VTFQFRKSAVSNNGTDVDVGQIPELYY 1203
Cdd:pfam08005   78 DIFRVLFDEPVEIEPNVKYTASAKIKGPSSYYGTNGLREVTCDGgVTFQFSSSSLSNNGTSVNRGQIPELLY 149
PHR pfam08005
PHR domain; This domain is called PHR as it was original found in the proteins PAM, highwire ...
 1503-1655 7.98e-37

PHR domain; This domain is called PHR as it was original found in the proteins PAM, highwire and RPM. This domain can be duplicated in the highwire, PFAM and PRM sequence. The C-terminal region of the protein BTBD1 includes the PHR domain and is known to interact with Topoisomerase I, an enzyme which relaxes DNA supercoils.


Pssm-ID: 462339  Cd Length: 150  Bit Score: 137.37  E-value: 7.98e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242   1503 SRFRRRSAQptWDMSDGCADAIAFRVDSeGIKLHGFGIYLPT-EPDRRNFVGEIMmlspdSSEKWTCLLRVTAEM----- 1576
Cdd:pfam08005    1 NRFQSTGGG--WGYSGGSPDAIRFSVDR-DIFLVGFGLYGSIgGPADYSVKIELI-----DGERWESLGEVLGENdttfs 72

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17563242   1577 SSEEKEVGIVRFPEYVLLSPGVTYAVKVNMMKNTkTFCGEGGVTQVHLLNGARLFFSGCSMSQNGTTVQRGQLPYLIYS 1655
Cdd:pfam08005   73 SDGSNDIFRVLFDEPVEIEPNVKYTASAKIKGPS-SYYGTNGLREVTCDGGVTFQFSSSSLSNNGTSVNRGQIPELLYY 150
RING-H2_PHR cd16463
RING finger, H2 subclass, found in the PHR (Pam/Highwire/RPM-1) protein family; The PHR ...
 3514-3567 5.43e-31

RING finger, H2 subclass, found in the PHR (Pam/Highwire/RPM-1) protein family; The PHR protein family represents an evolutionally conserved family of large proteins including human E3 ubiquitin ligase protein associated with Myc (Pam) and its homologs, Phr1 in mouse, Highwire (HIW) in Drosophila, RPM-1 (regulator of presynaptic morphology 1) in Caenorhabditis elegans, and Esrom in zebrafish. Those proteins are large E3 ubiquitin ligases containing regulator of chromosome condensation (RCC) homology domains (RHD-1 and RHD-2) with inferred guanine exchange factor (GEF) activity, a Myc-binding domain, a B-box zinc finger, and a C-terminal C3H2C3-type RING-H2 finger with E3 ubiquitin (Ub) ligase activity. They play an important role in axon guidance and synaptogenesis. They regulate synapse formation and growth in mammals, zebrafish, Drosophila, and Caenorhabditis elegans, and may control a variety of signaling pathways, including cAMP signaling in mammalian cells, JNK/p38 MAPK signaling in Drosophila and C. elegans, and bone morphogenetic protein signaling in Drosophila. Pam also known as Myc-binding protein 2 (MYCBP2), or Pam/highwire/rpm-1 protein (PHR1), negatively regulates neuronal growth, synaptogenesis and synaptic plasticity by modulating several signaling pathways including the p38 MAPK signaling cascade. It also participates in receptor and ion channel internalization, such as regulating internalization of transient receptor potential vanilloid receptor 1 (TRPV1) in peripheral sensory neurons, as well as duration of thermal hyperalgesia through p38 MAPK. It interacts with neuron-specific electroneutral potassium (K+) and chloride (Cl-) cotransporter KCC2 and modulates its function. Moreover, Pam genetically interacts with Robo2 to modulate axon guidance in the olfactory system. It also associates with tuberous sclerosis complex (TSC) proteins, ubiquitinating TSC2 and regulating mammalian/mechanistic target of rapamycin (mTOR) signaling. Furthermore, Pam is the longest lasting nontranscriptional regulator of adenylyl cyclase activity, and can mediate sustained inhibition of cAMP signaling by sphingosine-1-phosphate. It is also involved in spinal nociceptive processing. Phr1 is an essential regulator of retinal ganglion cell projection during both dorsal lateral geniculate nucleus (dLGN) and superior colliculus (SC) topographic map development. RPM-1 positively regulates a Rab GTPase pathway to promote vesicular trafficking via late endosomes, thereby regulating synapse formation and axon termination. Esrom has E3 ligase activity and modulates the amount of phosphorylated Tuberin, a tumor suppressor, in growth cones. It is required for the formation of the retinotectal projection.


Pssm-ID: 438126 [Multi-domain]  Cd Length: 55  Bit Score: 117.05  E-value: 5.43e-31
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 17563242 3514 DDVCVICFTERLGAAPCIRLGCGHMFHFHCVRMILERRWNGPRIVFRFMQCPLC 3567
Cdd:cd16463    1 DDMCMICFTEALSAAPAIQLDCGHVFHLHCCRRVLENRWPGPRITFGFLKCPIC 54
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 607-873 4.02e-23

Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton];


Pssm-ID: 444065 [Multi-domain]  Cd Length: 343  Bit Score: 103.90  E-value: 4.02e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  607 LNGLDNVmiSSLALGKSHGVAVTRNGHLFTWGLNNMNQCGRvESTSTTSSPRhsgrqeyQICPigehtwltdtpsvcaqc 686
Cdd:COG5184   94 VPGLTGV--VAVAAGYYHSCALKSDGTVWCWGDNSSGQLGD-GTTTNRLTPV-------QVDA----------------- 146

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  687 GLCSARGVACGRvprpkgtmCH-CGVGESTCLRCGlcrpcgevtepaqpGRAQHVQFSSTAAPQRSTlhPSRVILSQGph 765
Cdd:COG5184  147 GLSGVVAIAAGG--------YHtCALKSDGTVWCW--------------GANSYGQLGDGTTTDRPT--PVQVGGLSG-- 200

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  766 dvkVSSVSCGNFHTVLLASDRRVFTFGSNCHGQLGVGDTLSKNTPQQVILPSDtvIVQVAAGSNHTILRANDGSVFTFGA 845
Cdd:COG5184  201 ---VVAVAAGGDHSCALKSDGTVWCWGSNSSGQLGDGTTTDRATPVQVAGLTG--VVAIAAGGSHTCALKSDGTVWCWGD 275

                        250       260
                 ....*....|....*....|....*...
gi 17563242  846 FGKGQLARPAGEKAgwnAIPEKVSGFGP 873
Cdd:COG5184  276 NSYGQLGDGTTTDR---STPVKVPGLSG 300
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 573-851 1.47e-22

Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton];


Pssm-ID: 444065 [Multi-domain]  Cd Length: 343  Bit Score: 102.36  E-value: 1.47e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  573 HVCA---SGHVY--GYvSENGKIfmGGLHTMRVNVSSQMLNGLDNVmiSSLALGKSHGVAVTRNGHLFTWGLNNMNQCGr 647
Cdd:COG5184  109 HSCAlksDGTVWcwGD-NSSGQL--GDGTTTNRLTPVQVDAGLSGV--VAIAAGGYHTCALKSDGTVWCWGANSYGQLG- 182

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  648 VESTSTTSSPRhsgrqeyqicPIGehtwltdtpsvcaqcGLCSARGVACGRVprpkgtmcH-CGVGESTCLRCGlcrpcg 726
Cdd:COG5184  183 DGTTTDRPTPV----------QVG---------------GLSGVVAVAAGGD--------HsCALKSDGTVWCW------ 223

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  727 evtepaqpGRAQHVQFSSTAAPQRSTlhPSRVILSQGphdvkVSSVSCGNFHTVLLASDRRVFTFGSNCHGQLGVGDTLS 806
Cdd:COG5184  224 --------GSNSSGQLGDGTTTDRAT--PVQVAGLTG-----VVAIAAGGSHTCALKSDGTVWCWGDNSYGQLGDGTTTD 288

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 17563242  807 KNTPQQVilPSDTVIVQVAAGSNHTILRANDGSVFTFGAFGKGQL 851
Cdd:COG5184  289 RSTPVKV--PGLSGVVAVAAGSSHTCALLTDGTVWCWGDNAYGQL 331
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 609-873 1.98e-21

Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton];


Pssm-ID: 444065 [Multi-domain]  Cd Length: 343  Bit Score: 98.90  E-value: 1.98e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  609 GLDNVmiSSLALGKSHGVAVTRNGHLFTWGLNNMNQCGRvesTSTTSSPrhsgrqeyqicpigehtwltdTPSVCAqcGL 688
Cdd:COG5184   46 GLSNV--VAVAAGGDHTCALKADGTVWCWGNNSYGQLGD---GTTTDRT---------------------TPVKVP--GL 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  689 CSARGVACGRVprpkgtmcH-CGVGESTCLRCglcrpcgevtepaqPGRAQHVQFSSTAAPQRSTlhPSRVILSQGPhdv 767
Cdd:COG5184   98 TGVVAVAAGYY--------HsCALKSDGTVWC--------------WGDNSSGQLGDGTTTNRLT--PVQVDAGLSG--- 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  768 kVSSVSCGNFHTVLLASDRRVFTFGSNCHGQLGVGDTLSKNTPQQVilPSDTVIVQVAAGSNHTILRANDGSVFTFGAFG 847
Cdd:COG5184  151 -VVAIAAGGYHTCALKSDGTVWCWGANSYGQLGDGTTTDRPTPVQV--GGLSGVVAVAAGGDHSCALKSDGTVWCWGSNS 227

                        250       260
                 ....*....|....*....|....*.
gi 17563242  848 KGQLARPAgekAGWNAIPEKVSGFGP 873
Cdd:COG5184  228 SGQLGDGT---TTDRATPVQVAGLTG 250
Bbox2_MYCBP2 cd19799
B-box-type 2 zinc finger found in Myc-binding protein 2 (MYCBP2) and similar proteins; MYCBP2, ...
 3334-3383 2.33e-19

B-box-type 2 zinc finger found in Myc-binding protein 2 (MYCBP2) and similar proteins; MYCBP2, also termed protein associated with Myc (Pam), is an atypical E3 ubiquitin-protein ligase which specifically mediates ubiquitination of threonine and serine residues on target proteins, instead of ubiquitinating lysine residues. MYCBP2 harbors a B-box motif that shows high sequence similarity with B-Box-type zinc finger 2 found in tripartite motif-containing proteins (TRIMs). The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380857  Cd Length: 50  Bit Score: 83.98  E-value: 2.33e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 17563242 3334 LLCENHDDGHTVAQVFCVDCDVALCKECFTVMHLHKKNRNHGVKNLVQSS 3383
Cdd:cd19799    1 PTCDNHDDGETAAIIFCCDCGNYLCAECDRFLHLHRKNRSHQRQVFKEEE 50
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 616-851 2.56e-19

Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton];


Pssm-ID: 444065 [Multi-domain]  Cd Length: 343  Bit Score: 92.73  E-value: 2.56e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  616 SSLALGKSHGVAVTRNGHLFTWGLNNMNQCGRvESTSTTSSPRhsgrqeyqicPIGehtwltdtpsvcaqcGLCSARGVA 695
Cdd:COG5184    1 TQVAAGGSHSCALKSDGTVWCWGDNSYGQLGD-GTTTDRSTPV----------RVP---------------GLSNVVAVA 54

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  696 CGRvprpkgtmCH-CGVGESTCLRCGlcrpcgevtepaqpGRAQHVQFSSTAAPQRSTlhPSRVilsqgPHDVKVSSVSC 774
Cdd:COG5184   55 AGG--------DHtCALKADGTVWCW--------------GNNSYGQLGDGTTTDRTT--PVKV-----PGLTGVVAVAA 105

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17563242  775 GNFHTVLLASDRRVFTFGSNCHGQLGVGDTLSKNTPQQVILPSDTViVQVAAGSNHTILRANDGSVFTFGAFGKGQL 851
Cdd:COG5184  106 GYYHSCALKSDGTVWCWGDNSSGQLGDGTTTNRLTPVQVDAGLSGV-VAIAAGGYHTCALKSDGTVWCWGANSYGQL 181
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 769-906 1.01e-16

Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton];


Pssm-ID: 444065 [Multi-domain]  Cd Length: 343  Bit Score: 84.64  E-value: 1.01e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  769 VSSVSCGNFHTVLLASDRRVFTFGSNCHGQLGVGDTLSKNTPQQVilPSDTVIVQVAAGSNHTILRANDGSVFTFGAFGK 848
Cdd:COG5184   50 VVAVAAGGDHTCALKADGTVWCWGNNSYGQLGDGTTTDRTTPVKV--PGLTGVVAVAAGYYHSCALKSDGTVWCWGDNSS 127

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 17563242  849 GQLARPAGEKAgwnAIPEKVSGFGPGFNAFAGwigadGDssiihSHTALLSSDNILKA 906
Cdd:COG5184  128 GQLGDGTTTNR---LTPVQVDAGLSGVVAIAA-----GG-----YHTCALKSDGTVWC 172
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 770-873 4.21e-16

Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton];


Pssm-ID: 444065 [Multi-domain]  Cd Length: 343  Bit Score: 82.72  E-value: 4.21e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  770 SSVSCGNFHTVLLASDRRVFTFGSNCHGQLGVGDTLSKNTPQQVilPSDTVIVQVAAGSNHTILRANDGSVFTFGAFGKG 849
Cdd:COG5184    1 TQVAAGGSHSCALKSDGTVWCWGDNSYGQLGDGTTTDRSTPVRV--PGLSNVVAVAAGGDHTCALKADGTVWCWGNNSYG 78

                         90       100
                 ....*....|....*....|....
gi 17563242  850 QLARPAGEKAgwnAIPEKVSGFGP 873
Cdd:COG5184   79 QLGDGTTTDR---TTPVKVPGLTG 99
RCC1 pfam00415
Regulator of chromosome condensation (RCC1) repeat;
787-833 4.53e-13

Regulator of chromosome condensation (RCC1) repeat;


Pssm-ID: 395335 [Multi-domain]  Cd Length: 50  Bit Score: 66.00  E-value: 4.53e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 17563242    787 RVFTFGSNCHGQLGVGDTLSKNTPQQVILPSDTVIVQVAAGSNHTIL 833
Cdd:pfam00415    3 RVYTWGRNDYGQLGLGTTENVLVPQKVEGLSGNKVVQVACGGDHTVA 49
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 609-811 5.83e-12

Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton];


Pssm-ID: 444065 [Multi-domain]  Cd Length: 343  Bit Score: 70.39  E-value: 5.83e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  609 GLDNVmiSSLALGKSHGVAVTRNGHLFTWGLNNMNQCGrVESTSTTSSPRhsgrqeyqicPIGehtwltdtpsvcaqcGL 688
Cdd:COG5184  197 GLSGV--VAVAAGGDHSCALKSDGTVWCWGSNSSGQLG-DGTTTDRATPV----------QVA---------------GL 248

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242  689 CSARGVACGRVprpkgtmcH-CGVGESTCLRCglcrpCGEVTEpAQPGRaqhvqfsSTAAPQRStlhPSRVilsqgPHDV 767
Cdd:COG5184  249 TGVVAIAAGGS--------HtCALKSDGTVWC-----WGDNSY-GQLGD-------GTTTDRST---PVKV-----PGLS 299

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 17563242  768 KVSSVSCGNFHTVLLASDRRVFTFGSNCHGQLGVGDTLSKNTPQ 811
Cdd:COG5184  300 GVVAVAAGSSHTCALLTDGTVWCWGDNAYGQLGDGTTTDRSTPV 343
BBOX smart00336
B-Box-type zinc finger;
3331-3379 3.41e-07

B-Box-type zinc finger;


Pssm-ID: 197662 [Multi-domain]  Cd Length: 42  Bit Score: 49.26  E-value: 3.41e-07
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 17563242    3331 EPVLLCENHDDghTVAQVFCVDCDVALCKECFTVMHlhkknRNHGVKNL 3379
Cdd:smart00336    1 QRAPKCDSHGD--EPAEFFCEECGALLCRTCDEAEH-----RGHTVVLL 42
RCC1_2 pfam13540
Regulator of chromosome condensation (RCC1) repeat;
769-798 3.52e-07

Regulator of chromosome condensation (RCC1) repeat;


Pssm-ID: 463914 [Multi-domain]  Cd Length: 30  Bit Score: 48.57  E-value: 3.52e-07
                           10        20        30
                   ....*....|....*....|....*....|
gi 17563242    769 VSSVSCGNFHTVLLASDRRVFTFGSNCHGQ 798
Cdd:pfam13540    1 VVSVAAGDNHTLALTSDGRVYCWGDNSYGQ 30
RING-H2_synoviolin cd16479
RING finger, H2 subclass, found in synoviolin and similar proteins; Synoviolin, also known as ...
 3514-3567 5.68e-07

RING finger, H2 subclass, found in synoviolin and similar proteins; Synoviolin, also known as synovial apoptosis inhibitor 1 (Syvn1), Hrd1, or Der3, is an endoplasmic reticulum (ER)-anchoring E3 ubiquitin ligase that functions as a suppressor of ER stress-induced apoptosis and plays a role in homeostasis maintenance. It also targets tumor suppressor gene p53 for proteasomal degradation, suggesting crosstalk between ER associated degradation (ERAD) and p53 mediated apoptotic pathway under ER stress. Moreover, synoviolin controls body weight and mitochondrial biogenesis through negative regulation of the thermogenic coactivator peroxisome proliferator-activated receptor coactivator (PGC)-1beta. It upregulates amyloid beta production by targeting a negative regulator of gamma-secretase, Retention in endoplasmic reticulum 1 (Rer1), for degradation. It is also involved in the degradation of endogenous immature nicastrin, and affects amyloid beta-protein generation. Moreover, synoviolin is highly expressed in rheumatoid synovial cells and may be involved in the pathogenesis of rheumatoid arthritis (RA). It functions as an anti-apoptotic factor that is responsible for the outgrowth of synovial cells during the development of RA. It promotes inositol-requiring enzyme 1 (IRE1) ubiquitination and degradation in synovial fibroblasts with collagen-induced arthritis. Furthermore, the upregulation of synoviolin may represent a protective response against neurodegeneration in Parkinson's disease (PD). In addition, synoviolin is involved in liver fibrogenesis. Synoviolin contains a C3H2C2-type RING-H2 finger.


Pssm-ID: 438142 [Multi-domain]  Cd Length: 43  Bit Score: 48.51  E-value: 5.68e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 17563242 3514 DDVCVICFTERlgAAPCIRLGCGHMFHFHCVRMILERRwngprivfrfMQCPLC 3567
Cdd:cd16479    1 DNTCIICREEM--TVGAKKLPCGHIFHLSCLRSWLQRQ----------QTCPTC 42
RING-H2 cd16448
H2 subclass of RING (RING-H2) fingers and its variants; The RING finger is a specialized type ...
 3517-3567 2.11e-06

H2 subclass of RING (RING-H2) fingers and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). This family corresponds to the H2 subclass of RING (RING-H2) finger proteins that are characterized by containing C3H2C3-type canonical RING-H2 fingers or noncanonical RING-H2 finger variants, including C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type modified RING-H2 fingers. The canonical RING-H2 finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-H-X2-C-X(4-48)-C-X2-C, X is any amino acid and the number of X residues varies in different fingers. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-H2 finger can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serves as a scaffold for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates.


Pssm-ID: 438112 [Multi-domain]  Cd Length: 43  Bit Score: 47.01  E-value: 2.11e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 17563242 3517 CVICFTERLGAAPCIRLGCGHMFHFHCVrmileRRWngprIVFRFMQCPLC 3567
Cdd:cd16448    1 CVICLEEFEEGDVVRLLPCGHVFHLACI-----LRW----LESGNNTCPLC 42
zf-RING_2 pfam13639
Ring finger domain;
3515-3567 4.19e-06

Ring finger domain;


Pssm-ID: 433370 [Multi-domain]  Cd Length: 44  Bit Score: 46.25  E-value: 4.19e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 17563242   3515 DVCVICFTERLGAAPCIRLGCGHMFHFHCVRMILERRwngprivfrfMQCPLC 3567
Cdd:pfam13639    1 DECPICLEEFEEGDKVVVLPCGHHFHRECLDKWLRSS----------NTCPLC 43
ANAPC10 pfam03256
Anaphase-promoting complex, subunit 10 (APC10);
2887-3049 4.33e-05

Anaphase-promoting complex, subunit 10 (APC10);


Pssm-ID: 367420  Cd Length: 185  Bit Score: 47.05  E-value: 4.33e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242   2887 FVKEMKDITKFADITASSRQAM--VICLTDESGETFWESgeeDKNRSRSLSVQLDESAHGEILSLFIDNARDEGYRISSI 2964
Cdd:pfam03256   18 RVRHQREIGSQAVWSLSSCKPGfgVDLLRDDNLDTYWQS---DGSQPHLVNIQFRKKTPVKYVAIYLDYKLDESYTPSKI 94

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242   2965 AFKAILEDGRRKDLTSLTLESAyCGWLKCCIKD-------ISHIQI-----QFKGPNPasRIRQLMILGypakttgtPRL 3032
Cdd:pfam03256   95 SVRAGTGFNDLQEVRVVDLEEP-TGWVHIPLRDangkplrTFMLQIavlsnHQNGRDT--HVRQIKIYG--------PVE 163

                          170
                   ....*....|....*..
gi 17563242   3033 APSTSHHLFFSDTQRDA 3049
Cdd:pfam03256  164 ERSAVAARLGHFTTSDF 180
RCC1_2 pfam13540
Regulator of chromosome condensation (RCC1) repeat;
821-850 4.68e-05

Regulator of chromosome condensation (RCC1) repeat;


Pssm-ID: 463914 [Multi-domain]  Cd Length: 30  Bit Score: 42.80  E-value: 4.68e-05
                           10        20        30
                   ....*....|....*....|....*....|
gi 17563242    821 IVQVAAGSNHTILRANDGSVFTFGAFGKGQ 850
Cdd:pfam13540    1 VVSVAAGDNHTLALTSDGRVYCWGDNSYGQ 30
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
 3517-3567 6.07e-05

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 42.88  E-value: 6.07e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 17563242    3517 CVICFTERLgaAPCIRLGCGHMFHFHCVRMILERrwngprivfRFMQCPLC 3567
Cdd:smart00184    1 CPICLEEYL--KDPVILPCGHTFCRSCIRKWLES---------GNNTCPIC 40
HRD1 COG5243
HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein ...
 3493-3571 6.30e-05

HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227568 [Multi-domain]  Cd Length: 491  Bit Score: 48.81  E-value: 6.30e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17563242 3493 RNEEECLPCMTckrEDAAQDGDDVCVICFTE----------RLGAAPCIRLGCGHMFHFHCVRMILERRwngprivfrfM 3562
Cdd:COG5243  269 KDLNAMYPTAT---EEQLTNSDRTCTICMDEmfhpdheplpRGLDMTPKRLPCGHILHLHCLKNWLERQ----------Q 335


                 ....*....
gi 17563242 3563 QCPLCIQPI 3571
Cdd:COG5243  336 TCPICRRPV 344
RCC1_2 pfam13540
Regulator of chromosome condensation (RCC1) repeat;
615-644 1.63e-04

Regulator of chromosome condensation (RCC1) repeat;


Pssm-ID: 463914 [Multi-domain]  Cd Length: 30  Bit Score: 41.26  E-value: 1.63e-04
                           10        20        30
                   ....*....|....*....|....*....|
gi 17563242    615 ISSLALGKSHGVAVTRNGHLFTWGLNNMNQ 644
Cdd:pfam13540    1 VVSVAAGDNHTLALTSDGRVYCWGDNSYGQ 30
zf-rbx1 pfam12678
RING-H2 zinc finger domain; There are 8 cysteine/ histidine residues which are proposed to be ...
 3489-3567 1.95e-04

RING-H2 zinc finger domain; There are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell cycle control.


Pssm-ID: 463669 [Multi-domain]  Cd Length: 55  Bit Score: 41.93  E-value: 1.95e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17563242   3489 CGGIRNEEEcLPCMTCKREdaaqdGDDVCVICFTErlgaapcirlgCGHMFHFHCVRMILERRwngprivfrfMQCPLC 3567
Cdd:pfam12678    3 CAICRNPFM-EPCPECQAP-----GDDECPVVWGE-----------CGHAFHLHCISRWLKTN----------NTCPLC 54
RING-H2_RHA1-like cd23121
RING finger, H2 subclass, found in Arabidopsis thaliana RING-H2 finger A1a (RHA1A), A1b (RHA1B) ...
 3514-3570 2.97e-04

RING finger, H2 subclass, found in Arabidopsis thaliana RING-H2 finger A1a (RHA1A), A1b (RHA1B) and similar proteins; This subfamily includes Arabidopsis thaliana RHA1A, RHA1B and XERICO. RHA1A is a probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro. RHA1B possesses E3 ubiquitin-protein ligase activity when associated with the E2 enzyme UBC8 in vitro. XERICO functions on abscisic acid homeostasis at post-translational level, probably through ubiquitin/proteasome-dependent substrate-specific degradation. Members of this subfamily contain a C3H2C3-type RING-H2 finger.


Pssm-ID: 438483 [Multi-domain]  Cd Length: 50  Bit Score: 40.93  E-value: 2.97e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 17563242 3514 DDVCVICFTERLGAAPCIRLG-CGHMFHFHCVrmileRRWngprIVFRFMQCPLCIQP 3570
Cdd:cd23121    1 DDCCAICLSDFNSDEKLRQLPkCGHIFHHHCL-----DRW----IRYNKITCPLCRAD 49
zf-B_box pfam00643
B-box zinc finger;
3332-3379 9.19e-04

B-box zinc finger;


Pssm-ID: 459886 [Multi-domain]  Cd Length: 42  Bit Score: 39.38  E-value: 9.19e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 17563242   3332 PVLLCENHddGHTVAQVFCVDCDVALCKECFTVMHlhkknRNHGVKNL 3379
Cdd:pfam00643    2 KERLCPEH--EEEPLTLYCNDCQELLCEECSVGEH-----RGHTVVPL 42
Bbox1 cd19757
B-box-type 1 zinc finger (Bbox1); The B-box-type zinc finger is a short zinc binding domain of ...
 3336-3379 1.26e-03

B-box-type 1 zinc finger (Bbox1); The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain, in functionally unrelated proteins, most likely mediating protein-protein interactions. Based on different consensus sequences and the spacing of the 7-8 zinc-binding residues, the B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2). This family corresponds to the type 1 B-box (Bbox1).


Pssm-ID: 380815 [Multi-domain]  Cd Length: 44  Bit Score: 39.02  E-value: 1.26e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 17563242 3336 CENHDdghtvAQVFCVDCDVALCKECFTVMHLHKKN-RNHGVKNL 3379
Cdd:cd19757    5 CEERE-----ATVYCLECEEFLCDDCSDAIHRRGKLtRSHKLVPL 44
RING-H2_RHF2A cd23122
RING finger, H2 subclass, found in Arabidopsis thaliana RING-H2 zinc finger protein RHF2A and ...
 3507-3571 4.44e-03

RING finger, H2 subclass, found in Arabidopsis thaliana RING-H2 zinc finger protein RHF2A and similar proteins; RHF2A is an E3 ubiquitin-protein ligase involved in the positive regulation of the gametogenesis progression. It is required for the degradation of KRP6, a cyclin-dependent kinase inhibitor which accumulates during meiosis and blocks the progression of subsequent mitoses during gametophytes development. It functions in association with RHF1A. Members of this subfamily contain a C3H2C3-type RING-H2 finger.


Pssm-ID: 438484 [Multi-domain]  Cd Length: 63  Bit Score: 38.04  E-value: 4.44e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17563242 3507 EDAAQDG-DDVCVICFTERLGAAPCIRLGCGHMFHFHCvrmILErrWNGprivfRFMQCPLCIQPI 3571
Cdd:cd23122    3 EGGIQDAcEDACSICLESFCEADPATVTSCKHEYHLQC---ILE--WSQ-----RSKECPMCWQAL 58
 
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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