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Conserved domains on  [gi|1207184600|ref|XP_021334293|]
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E3 ubiquitin-protein ligase MYCBP2 isoform X13 [Danio rerio]

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 ...
 1228-1378 7.23e-57

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: 195.15  E-value: 7.23e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600 1228 NRFESHGGGWGYSAHSVEAIRFCADADILLGGLG---LFGGRGEYTAKIKLfelgPDGGDHETDGDLLAETDVLAYDCAA 1304
Cdd:pfam08005    1 NRFQSTGGGWGYSGGSPDAIRFSVDRDIFLVGFGlygSIGGPADYSVKIEL----IDGERWESLGEVLGENDTTFSSDGS 76

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1207184600 1305 REKYAMMFDEPVLLQLGWWYVAWARVSGPSSDCGSHGQATITTDDGVVFQFKSSKKSNNGTDVNAGQIPQLLYR 1378
Cdd:pfam08005   77 NDIFRVLFDEPVEIEPNVKYTASAKIKGPSSYYGTNGLREVTCDGGVTFQFSSSSLSNNGTSVNRGQIPELLYY 150
PHR pfam08005
PHR domain; This domain is called PHR as it was original found in the proteins PAM, highwire ...
 1719-1878 2.69e-53

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: 184.75  E-value: 2.69e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600 1719 NRFTKTSQGrsWNTGNGSPDAICFTVDKpGVVLVGFCVYGG-GGIHEYELEV-LAddaqtehpgdsaHSHRWTSLELVKG 1796
Cdd:pfam08005    1 NRFQSTGGG--WGYSGGSPDAIRFSVDR-DIFLVGFGLYGSiGGPADYSVKIeLI------------DGERWESLGEVLG 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600 1797 TYCTD---DSPSDIAEIRLDKAVPLKENVKYAVRLRNYGSRTANGDGGITTVQCSDGVAFTFSTCSLSSNGTNQTRGQIP 1873
Cdd:pfam08005   66 ENDTTfssDGSNDIFRVLFDEPVEIEPNVKYTASAKIKGPSSYYGTNGLREVTCDGGVTFQFSSSSLSNNGTSVNRGQIP 145


                   ....*
gi 1207184600 1874 QILYY 1878
Cdd:pfam08005  146 ELLYY 150
RING-H2_PHR cd16463
RING finger, H2 subclass, found in the PHR (Pam/Highwire/RPM-1) protein family; The PHR ...
 4455-4509 3.93e-34

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: 126.30  E-value: 3.93e-34
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1207184600 4455 DDMCMICFTEALSAAPAIQLDCSHVFHLQCTRRVLENRWLGPRITFGFMSCPICK 4509
Cdd:cd16463      1 DDMCMICFTEALSAAPAIQLDCGHVFHLHCCRRVLENRWPGPRITFGFLKCPICK 55
Bbox2_MYCBP2 cd19799
B-box-type 2 zinc finger found in Myc-binding protein 2 (MYCBP2) and similar proteins; MYCBP2, ...
 4289-4337 2.50e-25

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: 101.32  E-value: 2.50e-25
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1207184600 4289 PMCDNHDDGETAAIILCNACGN-LCTDCDRFLHLHRRTRTHQRQVFKEEE 4337
Cdd:cd19799      1 PTCDNHDDGETAAIIFCCDCGNyLCAECDRFLHLHRKNRSHQRQVFKEEE 50
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 574-1018 1.22e-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: 99.67  E-value: 1.22e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  574 VQFSVGhdGSHALLVAEDGSVFFTGSASKGEDGESTKSRRqpkpYKPKKMIKLETKMAVytACNNGSSSIVTKDGELYMF 653
Cdd:COG5184      1 TQVAAG--GSHSCALKSDGTVWCWGDNSYGQLGDGTTTDR----STPVRVPGLSNVVAV--AAGGDHTCALKADGTVWCW 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  654 GK-------DAIYSDST--CQVSDLKGhfVTQVAMGKAHTCVLTKSGEVWTFGVNNKGQCGRDTGAMSQA-----GKAFG 719
Cdd:COG5184     73 GNnsygqlgDGTTTDRTtpVKVPGLTG--VVAVAAGYYHSCALKSDGTVWCWGDNSSGQLGDGTTTNRLTpvqvdAGLSG 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  720 VENMATAmdedledeldekeeksmmcqpGMHkwkldqcmVCTVCGD----CTGYGA-------SCVSSGRPDRVPG--GI 786
Cdd:COG5184    151 VVAIAAG---------------------GYH--------TCALKSDgtvwCWGANSygqlgdgTTTDRPTPVQVGGlsGV 201

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  787 CGCGSGESGcsscgcckACARELDGQearqrgifdaVKEMipldlllavpvppppGVNieehiqirqeekrqrinrrhrl 866
Cdd:COG5184    202 VAVAAGGDH--------SCALKSDGT----------VWCW---------------GSN---------------------- 226

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  867 eeGRGPLVFPGPLfmnqreqvlARLRPLQAVKLMReklkdgssergdkdaskittyppgavrfdcelrAVQVSCGFHHSV 946
Cdd:COG5184    227 --SSGQLGDGTTT---------DRATPVQVAGLTG---------------------------------VVAIAAGGSHTC 262

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207184600  947 VLMENGDVYTFGYGQHGQLGHGDVNSRGSPTLVQALPGPsTQVTAGSNHTAVLLMDGQVFTFGSFSKGQLGR 1018
Cdd:COG5184    263 ALKSDGTVWCWGDNSYGQLGDGTTTDRSTPVKVPGLSGV-VAVAAGSSHTCALLTDGTVWCWGDNAYGQLGD 333
IG_FLMN super family cl42963
Filamin-type immunoglobulin domains; These form a rod-like structure in the actin-binding ...
 2385-2436 2.45e-05

Filamin-type immunoglobulin domains; These form a rod-like structure in the actin-binding cytoskeleton protein, filamin. The C-terminal repeats of filamin bind beta1-integrin (CD29).


The actual alignment was detected with superfamily member smart00557:

Pssm-ID: 214720 [Multi-domain]  Cd Length: 93  Bit Score: 45.67  E-value: 2.45e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|...
gi 1207184600  2385 PKRPSENMLIRANTDGTYSANWTPGAVGLYTIHVTIDGIEIDAG-LEVEVKDP 2436
Cdd:smart00557   41 PSGKKVPVEVKDNGDGTYTVSYTPTEPGDYTVTVKFGGEHIPGSpFTVKVGPA 93
SH3_3 pfam08239
Bacterial SH3 domain;
2468-2530 6.20e-04

Bacterial SH3 domain;


:

Pssm-ID: 462405 [Multi-domain]  Cd Length: 54  Bit Score: 40.69  E-value: 6.20e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1207184600 2468 AGLRVRSHPSLQSEQIGIVQVNGTITFIDEihnDDGVWLRLNDEtvkkyvpnmNGYTeAWCLS 2530
Cdd:pfam08239    1 SGLNVRSGPSTSSEVVGTLPKGEKVEVLEE---QGGGWYKVRTY---------DGYE-GWVSS 50
 
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 ...
 1228-1378 7.23e-57

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: 195.15  E-value: 7.23e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600 1228 NRFESHGGGWGYSAHSVEAIRFCADADILLGGLG---LFGGRGEYTAKIKLfelgPDGGDHETDGDLLAETDVLAYDCAA 1304
Cdd:pfam08005    1 NRFQSTGGGWGYSGGSPDAIRFSVDRDIFLVGFGlygSIGGPADYSVKIEL----IDGERWESLGEVLGENDTTFSSDGS 76

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1207184600 1305 REKYAMMFDEPVLLQLGWWYVAWARVSGPSSDCGSHGQATITTDDGVVFQFKSSKKSNNGTDVNAGQIPQLLYR 1378
Cdd:pfam08005   77 NDIFRVLFDEPVEIEPNVKYTASAKIKGPSSYYGTNGLREVTCDGGVTFQFSSSSLSNNGTSVNRGQIPELLYY 150
PHR pfam08005
PHR domain; This domain is called PHR as it was original found in the proteins PAM, highwire ...
 1719-1878 2.69e-53

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: 184.75  E-value: 2.69e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600 1719 NRFTKTSQGrsWNTGNGSPDAICFTVDKpGVVLVGFCVYGG-GGIHEYELEV-LAddaqtehpgdsaHSHRWTSLELVKG 1796
Cdd:pfam08005    1 NRFQSTGGG--WGYSGGSPDAIRFSVDR-DIFLVGFGLYGSiGGPADYSVKIeLI------------DGERWESLGEVLG 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600 1797 TYCTD---DSPSDIAEIRLDKAVPLKENVKYAVRLRNYGSRTANGDGGITTVQCSDGVAFTFSTCSLSSNGTNQTRGQIP 1873
Cdd:pfam08005   66 ENDTTfssDGSNDIFRVLFDEPVEIEPNVKYTASAKIKGPSSYYGTNGLREVTCDGGVTFQFSSSSLSNNGTSVNRGQIP 145


                   ....*
gi 1207184600 1874 QILYY 1878
Cdd:pfam08005  146 ELLYY 150
RING-H2_PHR cd16463
RING finger, H2 subclass, found in the PHR (Pam/Highwire/RPM-1) protein family; The PHR ...
 4455-4509 3.93e-34

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: 126.30  E-value: 3.93e-34
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1207184600 4455 DDMCMICFTEALSAAPAIQLDCSHVFHLQCTRRVLENRWLGPRITFGFMSCPICK 4509
Cdd:cd16463      1 DDMCMICFTEALSAAPAIQLDCGHVFHLHCCRRVLENRWPGPRITFGFLKCPICK 55
Bbox2_MYCBP2 cd19799
B-box-type 2 zinc finger found in Myc-binding protein 2 (MYCBP2) and similar proteins; MYCBP2, ...
 4289-4337 2.50e-25

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: 101.32  E-value: 2.50e-25
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1207184600 4289 PMCDNHDDGETAAIILCNACGN-LCTDCDRFLHLHRRTRTHQRQVFKEEE 4337
Cdd:cd19799      1 PTCDNHDDGETAAIIFCCDCGNyLCAECDRFLHLHRKNRSHQRQVFKEEE 50
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 574-1018 1.22e-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: 99.67  E-value: 1.22e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  574 VQFSVGhdGSHALLVAEDGSVFFTGSASKGEDGESTKSRRqpkpYKPKKMIKLETKMAVytACNNGSSSIVTKDGELYMF 653
Cdd:COG5184      1 TQVAAG--GSHSCALKSDGTVWCWGDNSYGQLGDGTTTDR----STPVRVPGLSNVVAV--AAGGDHTCALKADGTVWCW 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  654 GK-------DAIYSDST--CQVSDLKGhfVTQVAMGKAHTCVLTKSGEVWTFGVNNKGQCGRDTGAMSQA-----GKAFG 719
Cdd:COG5184     73 GNnsygqlgDGTTTDRTtpVKVPGLTG--VVAVAAGYYHSCALKSDGTVWCWGDNSSGQLGDGTTTNRLTpvqvdAGLSG 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  720 VENMATAmdedledeldekeeksmmcqpGMHkwkldqcmVCTVCGD----CTGYGA-------SCVSSGRPDRVPG--GI 786
Cdd:COG5184    151 VVAIAAG---------------------GYH--------TCALKSDgtvwCWGANSygqlgdgTTTDRPTPVQVGGlsGV 201

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  787 CGCGSGESGcsscgcckACARELDGQearqrgifdaVKEMipldlllavpvppppGVNieehiqirqeekrqrinrrhrl 866
Cdd:COG5184    202 VAVAAGGDH--------SCALKSDGT----------VWCW---------------GSN---------------------- 226

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  867 eeGRGPLVFPGPLfmnqreqvlARLRPLQAVKLMReklkdgssergdkdaskittyppgavrfdcelrAVQVSCGFHHSV 946
Cdd:COG5184    227 --SSGQLGDGTTT---------DRATPVQVAGLTG---------------------------------VVAIAAGGSHTC 262

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207184600  947 VLMENGDVYTFGYGQHGQLGHGDVNSRGSPTLVQALPGPsTQVTAGSNHTAVLLMDGQVFTFGSFSKGQLGR 1018
Cdd:COG5184    263 ALKSDGTVWCWGDNSYGQLGDGTTTDRSTPVKVPGLSGV-VAVAAGSSHTCALLTDGTVWCWGDNAYGQLGD 333
RCC1 pfam00415
Regulator of chromosome condensation (RCC1) repeat;
951-999 1.39e-13

Regulator of chromosome condensation (RCC1) repeat;


Pssm-ID: 395335 [Multi-domain]  Cd Length: 50  Bit Score: 67.54  E-value: 1.39e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1207184600  951 NGDVYTFGYGQHGQLGHGDVNSRGSPTLVQALPG-PSTQVTAGSNHTAVL 999
Cdd:pfam00415    1 DGRVYTWGRNDYGQLGLGTTENVLVPQKVEGLSGnKVVQVACGGDHTVAL 50
IG_FLMN smart00557
Filamin-type immunoglobulin domains; These form a rod-like structure in the actin-binding ...
 2385-2436 2.45e-05

Filamin-type immunoglobulin domains; These form a rod-like structure in the actin-binding cytoskeleton protein, filamin. The C-terminal repeats of filamin bind beta1-integrin (CD29).


Pssm-ID: 214720 [Multi-domain]  Cd Length: 93  Bit Score: 45.67  E-value: 2.45e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|...
gi 1207184600  2385 PKRPSENMLIRANTDGTYSANWTPGAVGLYTIHVTIDGIEIDAG-LEVEVKDP 2436
Cdd:smart00557   41 PSGKKVPVEVKDNGDGTYTVSYTPTEPGDYTVTVKFGGEHIPGSpFTVKVGPA 93
zf-RING_2 pfam13639
Ring finger domain;
4456-4509 4.37e-05

Ring finger domain;


Pssm-ID: 433370 [Multi-domain]  Cd Length: 44  Bit Score: 43.55  E-value: 4.37e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1207184600 4456 DMCMICFTEALSAAPAIQLDCSHVFHLQCTRRVLENRwlgpritfgfMSCPICK 4509
Cdd:pfam13639    1 DECPICLEEFEEGDKVVVLPCGHHFHRECLDKWLRSS----------NTCPLCR 44
Filamin pfam00630
Filamin/ABP280 repeat;
2384-2425 5.13e-04

Filamin/ABP280 repeat;


Pssm-ID: 395505  Cd Length: 89  Bit Score: 41.89  E-value: 5.13e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1207184600 2384 TPKRPSENMLIRANTDGTYSANWTPGAVGLYTIHVTIDGIEI 2425
Cdd:pfam00630   42 GPDGSPVPVEVTDNGDGTYTVSYTPTEPGDYTVSVKFNGQHI 83
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
 4458-4508 5.58e-04

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: 40.18  E-value: 5.58e-04
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1207184600  4458 CMICFTEALSaaPAIQLDCSHVFHLQCTRRVLENrwlgpritfGFMSCPIC 4508
Cdd:smart00184    1 CPICLEEYLK--DPVILPCGHTFCRSCIRKWLES---------GNNTCPIC 40
SH3_3 pfam08239
Bacterial SH3 domain;
2468-2530 6.20e-04

Bacterial SH3 domain;


Pssm-ID: 462405 [Multi-domain]  Cd Length: 54  Bit Score: 40.69  E-value: 6.20e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1207184600 2468 AGLRVRSHPSLQSEQIGIVQVNGTITFIDEihnDDGVWLRLNDEtvkkyvpnmNGYTeAWCLS 2530
Cdd:pfam08239    1 SGLNVRSGPSTSSEVVGTLPKGEKVEVLEE---QGGGWYKVRTY---------DGYE-GWVSS 50
 
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 ...
 1228-1378 7.23e-57

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: 195.15  E-value: 7.23e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600 1228 NRFESHGGGWGYSAHSVEAIRFCADADILLGGLG---LFGGRGEYTAKIKLfelgPDGGDHETDGDLLAETDVLAYDCAA 1304
Cdd:pfam08005    1 NRFQSTGGGWGYSGGSPDAIRFSVDRDIFLVGFGlygSIGGPADYSVKIEL----IDGERWESLGEVLGENDTTFSSDGS 76

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1207184600 1305 REKYAMMFDEPVLLQLGWWYVAWARVSGPSSDCGSHGQATITTDDGVVFQFKSSKKSNNGTDVNAGQIPQLLYR 1378
Cdd:pfam08005   77 NDIFRVLFDEPVEIEPNVKYTASAKIKGPSSYYGTNGLREVTCDGGVTFQFSSSSLSNNGTSVNRGQIPELLYY 150
PHR pfam08005
PHR domain; This domain is called PHR as it was original found in the proteins PAM, highwire ...
 1719-1878 2.69e-53

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: 184.75  E-value: 2.69e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600 1719 NRFTKTSQGrsWNTGNGSPDAICFTVDKpGVVLVGFCVYGG-GGIHEYELEV-LAddaqtehpgdsaHSHRWTSLELVKG 1796
Cdd:pfam08005    1 NRFQSTGGG--WGYSGGSPDAIRFSVDR-DIFLVGFGLYGSiGGPADYSVKIeLI------------DGERWESLGEVLG 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600 1797 TYCTD---DSPSDIAEIRLDKAVPLKENVKYAVRLRNYGSRTANGDGGITTVQCSDGVAFTFSTCSLSSNGTNQTRGQIP 1873
Cdd:pfam08005   66 ENDTTfssDGSNDIFRVLFDEPVEIEPNVKYTASAKIKGPSSYYGTNGLREVTCDGGVTFQFSSSSLSNNGTSVNRGQIP 145


                   ....*
gi 1207184600 1874 QILYY 1878
Cdd:pfam08005  146 ELLYY 150
RING-H2_PHR cd16463
RING finger, H2 subclass, found in the PHR (Pam/Highwire/RPM-1) protein family; The PHR ...
 4455-4509 3.93e-34

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: 126.30  E-value: 3.93e-34
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1207184600 4455 DDMCMICFTEALSAAPAIQLDCSHVFHLQCTRRVLENRWLGPRITFGFMSCPICK 4509
Cdd:cd16463      1 DDMCMICFTEALSAAPAIQLDCGHVFHLHCCRRVLENRWPGPRITFGFLKCPICK 55
Bbox2_MYCBP2 cd19799
B-box-type 2 zinc finger found in Myc-binding protein 2 (MYCBP2) and similar proteins; MYCBP2, ...
 4289-4337 2.50e-25

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: 101.32  E-value: 2.50e-25
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1207184600 4289 PMCDNHDDGETAAIILCNACGN-LCTDCDRFLHLHRRTRTHQRQVFKEEE 4337
Cdd:cd19799      1 PTCDNHDDGETAAIIFCCDCGNyLCAECDRFLHLHRKNRSHQRQVFKEEE 50
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 574-1018 1.22e-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: 99.67  E-value: 1.22e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  574 VQFSVGhdGSHALLVAEDGSVFFTGSASKGEDGESTKSRRqpkpYKPKKMIKLETKMAVytACNNGSSSIVTKDGELYMF 653
Cdd:COG5184      1 TQVAAG--GSHSCALKSDGTVWCWGDNSYGQLGDGTTTDR----STPVRVPGLSNVVAV--AAGGDHTCALKADGTVWCW 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  654 GK-------DAIYSDST--CQVSDLKGhfVTQVAMGKAHTCVLTKSGEVWTFGVNNKGQCGRDTGAMSQA-----GKAFG 719
Cdd:COG5184     73 GNnsygqlgDGTTTDRTtpVKVPGLTG--VVAVAAGYYHSCALKSDGTVWCWGDNSSGQLGDGTTTNRLTpvqvdAGLSG 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  720 VENMATAmdedledeldekeeksmmcqpGMHkwkldqcmVCTVCGD----CTGYGA-------SCVSSGRPDRVPG--GI 786
Cdd:COG5184    151 VVAIAAG---------------------GYH--------TCALKSDgtvwCWGANSygqlgdgTTTDRPTPVQVGGlsGV 201

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  787 CGCGSGESGcsscgcckACARELDGQearqrgifdaVKEMipldlllavpvppppGVNieehiqirqeekrqrinrrhrl 866
Cdd:COG5184    202 VAVAAGGDH--------SCALKSDGT----------VWCW---------------GSN---------------------- 226

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  867 eeGRGPLVFPGPLfmnqreqvlARLRPLQAVKLMReklkdgssergdkdaskittyppgavrfdcelrAVQVSCGFHHSV 946
Cdd:COG5184    227 --SSGQLGDGTTT---------DRATPVQVAGLTG---------------------------------VVAIAAGGSHTC 262

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207184600  947 VLMENGDVYTFGYGQHGQLGHGDVNSRGSPTLVQALPGPsTQVTAGSNHTAVLLMDGQVFTFGSFSKGQLGR 1018
Cdd:COG5184    263 ALKSDGTVWCWGDNSYGQLGDGTTTDRSTPVKVPGLSGV-VAVAAGSSHTCALLTDGTVWCWGDNAYGQLGD 333
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 936-1019 3.39e-18

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: 89.65  E-value: 3.39e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  936 VQVSCGFHHSVVLMENGDVYTFGYGQHGQLGHGDVNSRGSPTLVQALPGpSTQVTAGSNHTAVLLMDGQVFTFGSFSKGQ 1015
Cdd:COG5184      1 TQVAAGGSHSCALKSDGTVWCWGDNSYGQLGDGTTTDRSTPVRVPGLSN-VVAVAAGGDHTCALKADGTVWCWGNNSYGQ 79


                   ....
gi 1207184600 1016 LGRP 1019
Cdd:COG5184     80 LGDG 83
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 934-1019 3.36e-17

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: 86.57  E-value: 3.36e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  934 RAVQVSCGFHHSVVLMENGDVYTFGYGQHGQLGHGDVNSRGSPTLVQALpGPSTQVTAGSNHTAVLLMDGQVFTFGSFSK 1013
Cdd:COG5184     49 NVVAVAAGGDHTCALKADGTVWCWGNNSYGQLGDGTTTDRTTPVKVPGL-TGVVAVAAGYYHSCALKSDGTVWCWGDNSS 127


                   ....*.
gi 1207184600 1014 GQLGRP 1019
Cdd:COG5184    128 GQLGDG 133
RCC1 pfam00415
Regulator of chromosome condensation (RCC1) repeat;
951-999 1.39e-13

Regulator of chromosome condensation (RCC1) repeat;


Pssm-ID: 395335 [Multi-domain]  Cd Length: 50  Bit Score: 67.54  E-value: 1.39e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1207184600  951 NGDVYTFGYGQHGQLGHGDVNSRGSPTLVQALPG-PSTQVTAGSNHTAVL 999
Cdd:pfam00415    1 DGRVYTWGRNDYGQLGLGTTENVLVPQKVEGLSGnKVVQVACGGDHTVAL 50
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 525-708 1.65e-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: 72.32  E-value: 1.65e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  525 IGAGREFALMKTASGKIYYTGK--YQSLGIkqgGPSSGKWVELPVTKSPKIVQFSVGhdGSHALLVAEDGSVFFTGSASK 602
Cdd:COG5184    154 IAAGGYHTCALKSDGTVWCWGAnsYGQLGD---GTTTDRPTPVQVGGLSGVVAVAAG--GDHSCALKSDGTVWCWGSNSS 228

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  603 GEDGESTKSRRqpkpYKPKKMIKLETKMAVytACNNGSSSIVTKDGELYMFGK---------DAIYSDSTCQVSDLKGhf 673
Cdd:COG5184    229 GQLGDGTTTDR----ATPVQVAGLTGVVAI--AAGGSHTCALKSDGTVWCWGDnsygqlgdgTTTDRSTPVKVPGLSG-- 300

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 1207184600  674 VTQVAMGKAHTCVLTKSGEVWTFGVNNKGQCGRDT 708
Cdd:COG5184    301 VVAVAAGSSHTCALLTDGTVWCWGDNAYGQLGDGT 335
ATS1 COG5184
Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, ...
 525-710 6.56e-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: 6.56e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  525 IGAGREFALMKTASGKIY---YTGKYQsLGIkqgGPSSGKWVELPVTKSP-KIVQFSVGhdGSHALLVAEDGSVFFTGSA 600
Cdd:COG5184    103 VAAGYYHSCALKSDGTVWcwgDNSSGQ-LGD---GTTTNRLTPVQVDAGLsGVVAIAAG--GYHTCALKSDGTVWCWGAN 176

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184600  601 SKGEDGESTKSRRqpkpYKPKKMIKLETKMAVytACNNGSSSIVTKDGELYMFGK-------DAIYSDSTC--QVSDLKG 671
Cdd:COG5184    177 SYGQLGDGTTTDR----PTPVQVGGLSGVVAV--AAGGDHSCALKSDGTVWCWGSnssgqlgDGTTTDRATpvQVAGLTG 250

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 1207184600  672 hfVTQVAMGKAHTCVLTKSGEVWTFGVNNKGQCGRDTGA 710
Cdd:COG5184    251 --VVAIAAGGSHTCALKSDGTVWCWGDNSYGQLGDGTTT 287
RCC1_2 pfam13540
Regulator of chromosome condensation (RCC1) repeat;
936-964 2.60e-07

Regulator of chromosome condensation (RCC1) repeat;


Pssm-ID: 463914 [Multi-domain]  Cd Length: 30  Bit Score: 49.34  E-value: 2.60e-07
                           10        20
                   ....*....|....*....|....*....
gi 1207184600  936 VQVSCGFHHSVVLMENGDVYTFGYGQHGQ 964
Cdd:pfam13540    2 VSVAAGDNHTLALTSDGRVYCWGDNSYGQ 30
RING-H2 cd16448
H2 subclass of RING (RING-H2) fingers and its variants; The RING finger is a specialized type ...
 4458-4509 3.17e-07

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: 49.71  E-value: 3.17e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1207184600 4458 CMICFTEALSAAPAIQLDCSHVFHLQCTRRVLENrwlgpritfGFMSCPICK 4509
Cdd:cd16448      1 CVICLEEFEEGDVVRLLPCGHVFHLACILRWLES---------GNNTCPLCR 43
RCC1_2 pfam13540
Regulator of chromosome condensation (RCC1) repeat;
674-703 4.28e-07

Regulator of chromosome condensation (RCC1) repeat;


Pssm-ID: 463914 [Multi-domain]  Cd Length: 30  Bit Score: 48.96  E-value: 4.28e-07
                           10        20        30
                   ....*....|....*....|....*....|
gi 1207184600  674 VTQVAMGKAHTCVLTKSGEVWTFGVNNKGQ 703
Cdd:pfam13540    1 VVSVAAGDNHTLALTSDGRVYCWGDNSYGQ 30
IG_FLMN smart00557
Filamin-type immunoglobulin domains; These form a rod-like structure in the actin-binding ...
 2385-2436 2.45e-05

Filamin-type immunoglobulin domains; These form a rod-like structure in the actin-binding cytoskeleton protein, filamin. The C-terminal repeats of filamin bind beta1-integrin (CD29).


Pssm-ID: 214720 [Multi-domain]  Cd Length: 93  Bit Score: 45.67  E-value: 2.45e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|...
gi 1207184600  2385 PKRPSENMLIRANTDGTYSANWTPGAVGLYTIHVTIDGIEIDAG-LEVEVKDP 2436
Cdd:smart00557   41 PSGKKVPVEVKDNGDGTYTVSYTPTEPGDYTVTVKFGGEHIPGSpFTVKVGPA 93
zf-RING_2 pfam13639
Ring finger domain;
4456-4509 4.37e-05

Ring finger domain;


Pssm-ID: 433370 [Multi-domain]  Cd Length: 44  Bit Score: 43.55  E-value: 4.37e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1207184600 4456 DMCMICFTEALSAAPAIQLDCSHVFHLQCTRRVLENRwlgpritfgfMSCPICK 4509
Cdd:pfam13639    1 DECPICLEEFEEGDKVVVLPCGHHFHRECLDKWLRSS----------NTCPLCR 44
RING-H2_RHA1-like cd23121
RING finger, H2 subclass, found in Arabidopsis thaliana RING-H2 finger A1a (RHA1A), A1b (RHA1B) ...
 4455-4510 1.00e-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: 42.86  E-value: 1.00e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1207184600 4455 DDMCMICFTEALSAAPAIQL-DCSHVFHLQCTrrvleNRWlgprITFGFMSCPICKN 4510
Cdd:cd23121      1 DDCCAICLSDFNSDEKLRQLpKCGHIFHHHCL-----DRW----IRYNKITCPLCRA 48
RCC1_2 pfam13540
Regulator of chromosome condensation (RCC1) repeat;
987-1015 3.01e-04

Regulator of chromosome condensation (RCC1) repeat;


Pssm-ID: 463914 [Multi-domain]  Cd Length: 30  Bit Score: 40.87  E-value: 3.01e-04
                           10        20
                   ....*....|....*....|....*....
gi 1207184600  987 TQVTAGSNHTAVLLMDGQVFTFGSFSKGQ 1015
Cdd:pfam13540    2 VSVAAGDNHTLALTSDGRVYCWGDNSYGQ 30
RING-H2_RNF32_rpt1 cd16677
first RING finger, H2 subclass, found in RING finger protein 32 (RNF32) and similar proteins; ...
 4458-4511 4.16e-04

first RING finger, H2 subclass, found in RING finger protein 32 (RNF32) and similar proteins; RNF32 is mainly expressed in testis spermatogenesis, most likely in spermatocytes and/or in spermatids, suggesting a possible role in sperm formation. RNF32 contains two C3H2C3-type RING-H2 fingers separated by an IQ domain of unknown function. Although the biological function of RNF32 remains unclear, proteins with double RING-H2 fingers may act as scaffolds for binding several proteins that function in the same pathway. This model corresponds to the first RING-H2 finger.


Pssm-ID: 438339 [Multi-domain]  Cd Length: 49  Bit Score: 40.75  E-value: 4.16e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1207184600 4458 CMICfTEALSAAPAIQLDCSHVFHLQCtrrvLEN--RWLGPRitfgfmSCPICKNK 4511
Cdd:cd16677      2 CPIC-LEDFGLQQQVLLSCSHVFHRAC----LESfeRFSGKK------TCPMCRKE 46
Filamin pfam00630
Filamin/ABP280 repeat;
2384-2425 5.13e-04

Filamin/ABP280 repeat;


Pssm-ID: 395505  Cd Length: 89  Bit Score: 41.89  E-value: 5.13e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1207184600 2384 TPKRPSENMLIRANTDGTYSANWTPGAVGLYTIHVTIDGIEI 2425
Cdd:pfam00630   42 GPDGSPVPVEVTDNGDGTYTVSYTPTEPGDYTVSVKFNGQHI 83
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
 4458-4508 5.58e-04

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: 40.18  E-value: 5.58e-04
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1207184600  4458 CMICFTEALSaaPAIQLDCSHVFHLQCTRRVLENrwlgpritfGFMSCPIC 4508
Cdd:smart00184    1 CPICLEEYLK--DPVILPCGHTFCRSCIRKWLES---------GNNTCPIC 40
SH3_3 pfam08239
Bacterial SH3 domain;
2468-2530 6.20e-04

Bacterial SH3 domain;


Pssm-ID: 462405 [Multi-domain]  Cd Length: 54  Bit Score: 40.69  E-value: 6.20e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1207184600 2468 AGLRVRSHPSLQSEQIGIVQVNGTITFIDEihnDDGVWLRLNDEtvkkyvpnmNGYTeAWCLS 2530
Cdd:pfam08239    1 SGLNVRSGPSTSSEVVGTLPKGEKVEVLEE---QGGGWYKVRTY---------DGYE-GWVSS 50
RING-H2_WAVH2 cd23114
RING finger, H2 subclass, found in Arabidopsis thaliana protein WAV3 homolog 2 (WAVH2) and ...
 4458-4514 8.40e-04

RING finger, H2 subclass, found in Arabidopsis thaliana protein WAV3 homolog 2 (WAVH2) and similar proteins; WAVH2, also known as RING-type E3 ubiquitin transferase WAVH2, is a probable E3 ubiquitin-protein ligase involved in the regulation of root growth. It acts as a positive regulator of root gravitropism. WAVH2 contains a C3H2C3-type RING-H2 finger.


Pssm-ID: 438476 [Multi-domain]  Cd Length: 56  Bit Score: 40.26  E-value: 8.40e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207184600 4458 CMICF--TEALSAAPAIQLDCSHVFHLQCTRRVLENRWLgpritfgfmSCPICKNKINH 4514
Cdd:cd23114      7 CSICLetMKPGSGHAIFTAECSHSFHFECIAGNVRHGNL---------RCPVCRAKWKE 56
RING-H2_RNF139 cd16683
RING finger, H2 subclass, found in RING finger protein 139 (RNF139) and similar proteins; ...
 4452-4512 1.77e-03

RING finger, H2 subclass, found in RING finger protein 139 (RNF139) and similar proteins; RNF139, also known as translocation in renal carcinoma on chromosome 8 protein (TRC8), is an endoplasmic reticulum (ER)-resident multi-transmembrane protein that functions as a potent growth suppressor in mammalian cells, inducing G2/M arrest, decreased DNA synthesis and increased apoptosis. It is a tumor suppressor that has been implicated in a novel regulatory relationship linking the cholesterol/lipid biosynthetic pathway with cellular growth control. A mutation in RNF139 has been identified in families with hereditary renal (RCC) and thyroid cancers. RNF139 physically and functionally interacts with von Hippel-Lindau (VHL), which is part of an SCF related E3-ubiquitin ligase complex with "gatekeeper" function in renal carcinoma and is defective in most sporadic clear-cell renal cell carcinomas (ccRCC). It suppresses growth and functions with VHL in a common pathway. RNF139 also suppresses tumorigenesis by targeting heme oxygenase-1 for ubiquitination and degradation. Moreover, RNF139 is a target of Translin (TSN), a posttranscriptional regulator of genes transcribed by the transcription factor CREM-tau in postmeiotic male germ cells, suggesting a role of RNF139 in dysgerminoma. In addition, RNF139 forms an integral part of a novel multi-protein ER complex, containing MHC I, US2, and signal peptide peptidase, which is associated with the ER-associated degradation (ERAD) pathway. It is required for the ubiquitination of MHC class I molecules before dislocation from the ER. As a novel sterol-sensing ER membrane protein, RNF139 hinders sterol regulatory element-binding protein-2 (SREBP-2) processing through interaction with SREBP-2 and SREBP cleavage-activated protein (SCAP), regulating its own turnover rate via its E3 ubiquitin ligase activity. RNF139 shows two regions of similarity with the receptor for sonic hedgehog (SHH), Patched. The first region corresponds to the second extracellular domain of Patched, which is involved in binding SHH. The second region is a putative sterol-sensing domain (SSD). The C-terminal half of RNF139 contains a C3H2C3-type RING-H2 finger with E3-ubiquitin ligase activity in vitro.


Pssm-ID: 438345 [Multi-domain]  Cd Length: 54  Bit Score: 39.17  E-value: 1.77e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1207184600 4452 QDADDMCMICFTEALSAAPAIQldCSHVFHLQCTRrvlenRWLGPRITfgfmsCPICKNKI 4512
Cdd:cd16683      1 REIDDVCAICYQEFTTSARITP--CNHYFHALCLR-----KWLYIQDT-----CPMCHQKV 49
RING-HC_RNF213 cd16561
RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; ...
 4457-4513 1.93e-03

RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; RNF213, also known as ALK lymphoma oligomerization partner on chromosome 17 or Moyamoya steno-occlusive disease-associated AAA+ and RING finger protein (mysterin), is an intracellular soluble protein that functions as an E3 ubiquitin-protein ligase and AAA+ ATPase, which possibly contributes to vascular development through mechanical processes in the cell. It plays a unique role in endothelial cells for proper gene expression in response to inflammatory signals from the environment. Mutations in RNF213 may be associated with Moyamoya disease (MMD), an idiopathic cerebrovascular occlusive disorder prevalent in East Asia. It also acts as a nuclear marker for acanthomorph phylogeny. RNF213 contains two tandem enzymatically active AAA+ ATPase modules and a C3HC4-type RING-HC finger. It can form a huge ring-shaped oligomeric complex.


Pssm-ID: 438223 [Multi-domain]  Cd Length: 50  Bit Score: 39.18  E-value: 1.93e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1207184600 4457 MCMICFTEALSAapaIQLDCSHVFHLQCTRRVLENRwlgpritfgfMSCPICKNKIN 4513
Cdd:cd16561      4 ECSICLEDLNDP---VKLPCDHVFCEECIRQWLPGQ----------MSCPLCRTELP 47
RING-H2_RNF6 cd16673
RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6 and similar proteins; RNF6 ...
 4458-4512 3.07e-03

RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6 and similar proteins; RNF6 is an androgen receptor (AR)-associated protein that induces AR ubiquitination and promotes AR transcriptional activity. RNF6-induced ubiquitination may regulate AR transcriptional activity and specificity by modulating cofactor recruitment. RNF6 is overexpressed in hormone-refractory human prostate cancer tissues and required for prostate cancer cell growth under androgen-depleted conditions. Moreover, RNF6 regulates local serine/threonine kinase LIM kinase 1 (LIMK1) levels in axonal growth cones. RNF6-induced LIMK1 polyubiquitination is mediated via K48 of ubiquitin and leads to proteasomal degradation of the kinase. RNF6 also binds and upregulates the Inha promoter, and functions as a transcription regulatory protein in the mouse sertoli cell. RNF6 also acts as a potential tumor suppressor gene involved in the pathogenesis of esophageal squamous cell carcinoma (ESCC). RNF6 contains an N-terminal coiled-coil domain, a Lys-X-X-Leu/Ile-X-X-Leu/Ile (KIL) motif, and a C-terminal C3H2C3-type RING-H2 finger which is responsible for its ubiquitin ligase activity. The KIL motif is present in a subset of RING-H2 proteins from organisms as evolutionarily diverse as human, mouse, chicken, Drosophila, Caenorhabditis elegans, and Arabidopsis thaliana.


Pssm-ID: 438335 [Multi-domain]  Cd Length: 52  Bit Score: 38.78  E-value: 3.07e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1207184600 4458 CMICFTEALSAAPAIQLDCSHVFHLQCTrrvleNRWLGPRITfgfmsCPICKNKI 4512
Cdd:cd16673      3 CSVCINEYATGNKLRRLPCAHEFHIHCI-----DRWLSENST-----CPICRQPV 47
RING-H2_RNF12 cd16674
RING finger, H2 subclass, found in RING finger protein 12 (RNF12) and similar proteins; RNF12, ...
 4458-4512 3.88e-03

RING finger, H2 subclass, found in RING finger protein 12 (RNF12) and similar proteins; RNF12, also known as LIM domain-interacting RING finger protein or RING finger LIM domain-binding protein (R-LIM), is an E3 ubiquitin-protein ligase encoded by gene RLIM that is crucial for normal embryonic development in some species and for normal X inactivation in mice. It thus functions as a major sex-specific epigenetic regulator of female mouse nurturing tissues. RNF12 is widely expressed during embryogenesis, and mainly localizes to the cell nucleus, where it regulates the levels of many proteins, including CLIM, LMO, HDAC2, TRF1, SMAD7, and REX1, by proteasomal degradation. Its functional activity is regulated by phosphorylation-dependent nucleocytoplasmic shuttling. It is negatively regulated by pluripotency factors in embryonic stem cells. p53 represses its transcription through Sp1. RNF12 is the primary factor responsible for X chromosome inactivation (XCI) in female placental mammals. It is an indispensable factor in up-regulation of Xist transcription, thereby leading to initiation of random XCI. It also targets REX1, an inhibitor of XCI, for proteasomal degradation. RNF12 also acts as a co-regulator for a range of transcription factors, particularly those containing a LIM homeodomain, and modulates the formation of transcriptional multiprotein complexes. It is a negative regulator of Smad7, which in turn negatively regulates the signaling of type I receptors from the transforming growth factor beta (TGF-beta) superfamily. In addition, paternal RNF12 is a critical survival factor for milk-producing alveolar cells. RNF12 contains an nuclear localization signal (NLS) and a C3H2C3-type RING-H2 finger.


Pssm-ID: 438336 [Multi-domain]  Cd Length: 51  Bit Score: 38.16  E-value: 3.88e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1207184600 4458 CMICFTEALSAAPAIQLDCSHVFHLQCTrrvleNRWLGPRITfgfmsCPICKNKI 4512
Cdd:cd16674      3 CSVCITEYTEGNKLRKLPCSHEYHVHCI-----DRWLSENST-----CPICRRAV 47
RING-H2_synoviolin cd16479
RING finger, H2 subclass, found in synoviolin and similar proteins; Synoviolin, also known as ...
 4455-4509 4.36e-03

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: 37.72  E-value: 4.36e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1207184600 4455 DDMCMICFTEALSAAPaiQLDCSHVFHLQCTRRVLENRwlgpritfgfMSCPICK 4509
Cdd:cd16479      1 DNTCIICREEMTVGAK--KLPCGHIFHLSCLRSWLQRQ----------QTCPTCR 43
RING-H2_RNF13 cd16796
RING finger, H2 subclass, found in RING finger protein 13 (RNF13) and similar proteins; RNF13 ...
 4451-4512 4.42e-03

RING finger, H2 subclass, found in RING finger protein 13 (RNF13) and similar proteins; RNF13 is a widely expressed membrane-associated E3 ubiquitin-protein ligase that is functionally significant in the regulation of cancer development, muscle cell growth, and neuronal development. Its expression is developmentally regulated during myogenesis and is upregulated in various tumors. RNF13 negatively regulates cell proliferation through its E3 ligase activity. It functions as an important regulator of inositol-requiring transmembrane kinase/endonuclease IRE1alpha, mediating endoplasmic reticulum (ER) stress-induced apoptosis through the activation of the IRE1alpha-TRAF2-JNK signaling pathway. Moreover, RNF13 is involved in the regulation of the soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor (SNARE) complex via the ubiquitination of snapin, a SNAP25-interacting protein, which thereby controls synaptic function. In addition, RNF13 participates in regulating the function of satellite cells by modulating cytokine composition. RNF13 is evolutionarily conserved among many metazoans and contains an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C-terminal C3H2C3-type RING-H2 finger domain followed by a putative PEST sequence.


Pssm-ID: 438450 [Multi-domain]  Cd Length: 59  Bit Score: 38.49  E-value: 4.42e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207184600 4451 KQDADDMCMICFTEALSAAPAIQLDCSHVFHLQCtrrvlenrwLGPRITFGFMSCPICKNKI 4512
Cdd:cd16796      4 KGDEYDVCAICLDEYEEGDKLRILPCSHAYHCKC---------VDPWLTKTKKTCPVCKQKV 56
Bbox1_HOIP cd19815
B-box-type 1 zinc finger found in HOIL-1-interacting protein (HOIP) and similar proteins; HOIP, ...
 4297-4331 4.70e-03

B-box-type 1 zinc finger found in HOIL-1-interacting protein (HOIP) and similar proteins; HOIP, also termed RING finger protein 31 (RNF31), or zinc in-between-RING-finger ubiquitin-associated domain protein, together with HOIL-1 and SHARPIN, forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis. It also interacts with the atypical mammalian orphan receptor DAX-1, trigger DAX-1 ubiquitination and stabilization, and participate in repressing steroidogenic gene expression. HOIP contains a B-box motif that shows high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs). The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.


Pssm-ID: 380873  Cd Length: 43  Bit Score: 37.70  E-value: 4.70e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1207184600 4297 GETAAIILCNACGN-LCTDCDRFLHLHRRTRTHQRQ 4331
Cdd:cd19815      6 GEAAASVFCASCEDkLCLSCDDLYHKHPARRSHHRQ 41
 
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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