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Conserved domains on  [gi|67089149|ref|NP_150241|]
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protein PML isoform 1 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
DUF3583 pfam12126
Protein of unknown function (DUF3583); This domain is found in eukaryotes, and is typically ...
240-570 0e+00

Protein of unknown function (DUF3583); This domain is found in eukaryotes, and is typically between 302 and 338 amino acids in length. It is found in association with pfam00097 and pfam00643. Most members are promyelocytic leukemia proteins, and this family lies towards the C-terminus.


:

Pssm-ID: 432347 [Multi-domain]  Cd Length: 329  Bit Score: 662.28  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149   240 LDAMTQALQEQDSAFGAVHAQMHAAVGQLGRARAETEELIRERVRQVVAHVRAQERELLEAVDARYQRDYEEMASRLGRL 319
Cdd:pfam12126   1 LDTMTQALQEQDGAFGAAHAQMRSAISQLGRARADTEELIRARVRQVVAHVQAQERELLEAVNARYQRDYEEMAGQLGRL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149   320 DAVLQRIRTGSALVQRMKCYASDQEVLDMHGFLRQALCRLRQEEPQSLQAAVRTDGFDEFKVRLQDLSSCITQGKDAAVS 399
Cdd:pfam12126  81 DAVLQRIRTGGALVQRMKRYASDQEVLDMHGFLREALCRLRQEEPQNLQAAVRTDGFDEFKVRLQDLVSCITQGTDAAVS 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149   400 KKASPEAASTPRDPIDVDLPEEAERVKAqvQALGLAEAQPMAVVQSVPGAHPVPVYAFSIKGPSYGEDVSNTTTAQKRKC 479
Cdd:pfam12126 161 RRASPEAASTPRDPSDVDLPEEVQRVQA--QALGLAETQPVAVVQSVPGAHPVPVYAFSIKDPSYREEVSNTVTPQKRKS 238
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149   480 SQTQCPRKVIKMESEEGKEARLARSSPEQPRPSTSKAVSPPHLDGPPSPRSPVIGSEVFLPNSNHVASGAGEAEERVVVI 559
Cdd:pfam12126 239 CQTECPRKVIKMESEEEKEARLARSSPEQPRPSTSKAVSPPHLDGPPSPESPIVGKEVLLPNSNHVTSDPGEAEERIVVI 318
                         330
                  ....*....|.
gi 67089149   560 SSSEDSDAENS 570
Cdd:pfam12126 319 SSSEDSDAENS 329
Bbox2_TRIM19_C-V cd19770
B-box-type 2 zinc finger found in tripartite motif-containing protein 19, also called ...
187-237 3.58e-21

B-box-type 2 zinc finger found in tripartite motif-containing protein 19, also called promyelocytic leukemia protein (PML), and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


:

Pssm-ID: 380828  Cd Length: 50  Bit Score: 87.22  E-value: 3.58e-21
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 67089149 187 IFCSNPNHRTPTLtSIYCRGCSKPLCCSCALLDSSHSELKCDISAEIQQRQ 237
Cdd:cd19770   1 PFCPSPNHETQMI-SIYCRQCSKSVCCTCALLDSSHKGQHCDIKAEIQRRQ 50
RING-HC_PML_C-V cd16579
RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; ...
51-94 4.32e-18

RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


:

Pssm-ID: 438241 [Multi-domain]  Cd Length: 52  Bit Score: 78.75  E-value: 4.32e-18
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 67089149  51 EFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASG--------MQCPICQAP 94
Cdd:cd16579   1 EFKFLRCPGCKAEYKCPKLLPCLHTVCSGCLEALAeqasetteFQCPICKAS 52
Bbox1_TRIM19_C-V cd19804
B-box-type 1 zinc finger found in promyelocytic leukemia protein (PML) and similar proteins; ...
126-168 1.87e-15

B-box-type 1 zinc finger found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cellular processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites, and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.


:

Pssm-ID: 380862 [Multi-domain]  Cd Length: 47  Bit Score: 70.95  E-value: 1.87e-15
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 67089149 126 QAVCTRCKES-ADFWCFECEQLLCAKCFEAHQWF---LKHEARPLAE 168
Cdd:cd19804   1 ELMCNRCSESeAEFWCSECEEFLCRKCFEAHQRFkkrKKHEALRLAE 47
DnaQ_like_exo super family cl10012
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ...
610-758 7.28e-05

DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer.


The actual alignment was detected with superfamily member smart00479:

Pssm-ID: 447876 [Multi-domain]  Cd Length: 169  Bit Score: 44.21  E-value: 7.28e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149    610 LVFFDLK---IDNETQKISQLAAVN-----RESKFRVVIQPEAFFSIYSKAVS------------LEVGLQHFLSFLSsm 669
Cdd:smart00479   2 LVVIDCEttgLDPGKDEIIEIAAVDvdggeIIEVFDTYVKPDRPITDYATEIHgitpemlddaptFEEVLEELLEFLR-- 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149    670 RRPILACYklwgpGLPNFFRALE-DINRLWEFQEAISGFLAALPLIRERVPGASSFKLKNLAQTYLARNMSER-SAMA-A 746
Cdd:smart00479  80 GRILVAGN-----SAHFDLRFLKlEHPRLGIKQPPKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQRAhRALDdA 154
                          170
                   ....*....|..
gi 67089149    747 VLAMRDLCRLLE 758
Cdd:smart00479 155 RATAKLFKKLLE 166
 
Name Accession Description Interval E-value
DUF3583 pfam12126
Protein of unknown function (DUF3583); This domain is found in eukaryotes, and is typically ...
240-570 0e+00

Protein of unknown function (DUF3583); This domain is found in eukaryotes, and is typically between 302 and 338 amino acids in length. It is found in association with pfam00097 and pfam00643. Most members are promyelocytic leukemia proteins, and this family lies towards the C-terminus.


Pssm-ID: 432347 [Multi-domain]  Cd Length: 329  Bit Score: 662.28  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149   240 LDAMTQALQEQDSAFGAVHAQMHAAVGQLGRARAETEELIRERVRQVVAHVRAQERELLEAVDARYQRDYEEMASRLGRL 319
Cdd:pfam12126   1 LDTMTQALQEQDGAFGAAHAQMRSAISQLGRARADTEELIRARVRQVVAHVQAQERELLEAVNARYQRDYEEMAGQLGRL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149   320 DAVLQRIRTGSALVQRMKCYASDQEVLDMHGFLRQALCRLRQEEPQSLQAAVRTDGFDEFKVRLQDLSSCITQGKDAAVS 399
Cdd:pfam12126  81 DAVLQRIRTGGALVQRMKRYASDQEVLDMHGFLREALCRLRQEEPQNLQAAVRTDGFDEFKVRLQDLVSCITQGTDAAVS 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149   400 KKASPEAASTPRDPIDVDLPEEAERVKAqvQALGLAEAQPMAVVQSVPGAHPVPVYAFSIKGPSYGEDVSNTTTAQKRKC 479
Cdd:pfam12126 161 RRASPEAASTPRDPSDVDLPEEVQRVQA--QALGLAETQPVAVVQSVPGAHPVPVYAFSIKDPSYREEVSNTVTPQKRKS 238
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149   480 SQTQCPRKVIKMESEEGKEARLARSSPEQPRPSTSKAVSPPHLDGPPSPRSPVIGSEVFLPNSNHVASGAGEAEERVVVI 559
Cdd:pfam12126 239 CQTECPRKVIKMESEEEKEARLARSSPEQPRPSTSKAVSPPHLDGPPSPESPIVGKEVLLPNSNHVTSDPGEAEERIVVI 318
                         330
                  ....*....|.
gi 67089149   560 SSSEDSDAENS 570
Cdd:pfam12126 319 SSSEDSDAENS 329
Bbox2_TRIM19_C-V cd19770
B-box-type 2 zinc finger found in tripartite motif-containing protein 19, also called ...
187-237 3.58e-21

B-box-type 2 zinc finger found in tripartite motif-containing protein 19, also called promyelocytic leukemia protein (PML), and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380828  Cd Length: 50  Bit Score: 87.22  E-value: 3.58e-21
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 67089149 187 IFCSNPNHRTPTLtSIYCRGCSKPLCCSCALLDSSHSELKCDISAEIQQRQ 237
Cdd:cd19770   1 PFCPSPNHETQMI-SIYCRQCSKSVCCTCALLDSSHKGQHCDIKAEIQRRQ 50
RING-HC_PML_C-V cd16579
RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; ...
51-94 4.32e-18

RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438241 [Multi-domain]  Cd Length: 52  Bit Score: 78.75  E-value: 4.32e-18
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 67089149  51 EFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASG--------MQCPICQAP 94
Cdd:cd16579   1 EFKFLRCPGCKAEYKCPKLLPCLHTVCSGCLEALAeqasetteFQCPICKAS 52
Bbox1_TRIM19_C-V cd19804
B-box-type 1 zinc finger found in promyelocytic leukemia protein (PML) and similar proteins; ...
126-168 1.87e-15

B-box-type 1 zinc finger found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cellular processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites, and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.


Pssm-ID: 380862 [Multi-domain]  Cd Length: 47  Bit Score: 70.95  E-value: 1.87e-15
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 67089149 126 QAVCTRCKES-ADFWCFECEQLLCAKCFEAHQWF---LKHEARPLAE 168
Cdd:cd19804   1 ELMCNRCSESeAEFWCSECEEFLCRKCFEAHQRFkkrKKHEALRLAE 47
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
57-91 8.29e-06

Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway.


Pssm-ID: 395049 [Multi-domain]  Cd Length: 40  Bit Score: 43.50  E-value: 8.29e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 67089149    57 CQQCQAEAKCP-KLLPCLHTLCSGCLEASGM----QCPIC 91
Cdd:pfam00097   1 CPICLEEPKDPvTLLPCGHLFCSKCIRSWLEsgnvTCPLC 40
BBOX smart00336
B-Box-type zinc finger;
124-166 2.19e-05

B-Box-type zinc finger;


Pssm-ID: 197662 [Multi-domain]  Cd Length: 42  Bit Score: 42.32  E-value: 2.19e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 67089149    124 DAQAVCTRCK-ESADFWCFECEQLLCAKCFEA-HQwflKHEARPL 166
Cdd:smart00336   1 QRAPKCDSHGdEPAEFFCEECGALLCRTCDEAeHR---GHTVVLL 42
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
610-758 7.28e-05

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 44.21  E-value: 7.28e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149    610 LVFFDLK---IDNETQKISQLAAVN-----RESKFRVVIQPEAFFSIYSKAVS------------LEVGLQHFLSFLSsm 669
Cdd:smart00479   2 LVVIDCEttgLDPGKDEIIEIAAVDvdggeIIEVFDTYVKPDRPITDYATEIHgitpemlddaptFEEVLEELLEFLR-- 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149    670 RRPILACYklwgpGLPNFFRALE-DINRLWEFQEAISGFLAALPLIRERVPGASSFKLKNLAQTYLARNMSER-SAMA-A 746
Cdd:smart00479  80 GRILVAGN-----SAHFDLRFLKlEHPRLGIKQPPKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQRAhRALDdA 154
                          170
                   ....*....|..
gi 67089149    747 VLAMRDLCRLLE 758
Cdd:smart00479 155 RATAKLFKKLLE 166
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
57-91 1.52e-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: 39.80  E-value: 1.52e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 67089149     57 CQQC-QAEAKCPKLLPCLHTLCSGC----LEASGMQCPIC 91
Cdd:smart00184   1 CPIClEEYLKDPVILPCGHTFCRSCirkwLESGNNTCPIC 40
GumC COG3206
Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];
230-327 2.18e-04

Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442439 [Multi-domain]  Cd Length: 687  Bit Score: 45.01  E-value: 2.18e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149 230 SAEIQQRQEELDAMTQALQEQDSAFGAVHAQMHAAVGQLgrarAETEELIRERVRQVVAHVRAqERELLEAVDARYQRDY 309
Cdd:COG3206 262 SPVIQQLRAQLAELEAELAELSARYTPNHPDVIALRAQI----AALRAQLQQEAQRILASLEA-ELEALQAREASLQAQL 336
                        90
                ....*....|....*...
gi 67089149 310 EEMASRLGRLDAVLQRIR 327
Cdd:COG3206 337 AQLEARLAELPELEAELR 354
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
53-125 4.38e-04

DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273165 [Multi-domain]  Cd Length: 397  Bit Score: 43.45  E-value: 4.38e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 67089149    53 QFLRCQQCQAEAKCPKLLPCLHTLCSGC----LEASGMqCPICQAPwplgadtpaldnvFFESLQRRLSVYRQIVDA 125
Cdd:TIGR00599  25 TSLRCHICKDFFDVPVLTSCSHTFCSLCirrcLSNQPK-CPLCRAE-------------DQESKLRSNWLVSEIVES 87
zf-B_box pfam00643
B-box zinc finger;
128-166 5.26e-04

B-box zinc finger;


Pssm-ID: 459886 [Multi-domain]  Cd Length: 42  Bit Score: 38.22  E-value: 5.26e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 67089149   128 VCTRCKES-ADFWCFECEQLLCAKCF-EAHQwflKHEARPL 166
Cdd:pfam00643   5 LCPEHEEEpLTLYCNDCQELLCEECSvGEHR---GHTVVPL 42
 
Name Accession Description Interval E-value
DUF3583 pfam12126
Protein of unknown function (DUF3583); This domain is found in eukaryotes, and is typically ...
240-570 0e+00

Protein of unknown function (DUF3583); This domain is found in eukaryotes, and is typically between 302 and 338 amino acids in length. It is found in association with pfam00097 and pfam00643. Most members are promyelocytic leukemia proteins, and this family lies towards the C-terminus.


Pssm-ID: 432347 [Multi-domain]  Cd Length: 329  Bit Score: 662.28  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149   240 LDAMTQALQEQDSAFGAVHAQMHAAVGQLGRARAETEELIRERVRQVVAHVRAQERELLEAVDARYQRDYEEMASRLGRL 319
Cdd:pfam12126   1 LDTMTQALQEQDGAFGAAHAQMRSAISQLGRARADTEELIRARVRQVVAHVQAQERELLEAVNARYQRDYEEMAGQLGRL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149   320 DAVLQRIRTGSALVQRMKCYASDQEVLDMHGFLRQALCRLRQEEPQSLQAAVRTDGFDEFKVRLQDLSSCITQGKDAAVS 399
Cdd:pfam12126  81 DAVLQRIRTGGALVQRMKRYASDQEVLDMHGFLREALCRLRQEEPQNLQAAVRTDGFDEFKVRLQDLVSCITQGTDAAVS 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149   400 KKASPEAASTPRDPIDVDLPEEAERVKAqvQALGLAEAQPMAVVQSVPGAHPVPVYAFSIKGPSYGEDVSNTTTAQKRKC 479
Cdd:pfam12126 161 RRASPEAASTPRDPSDVDLPEEVQRVQA--QALGLAETQPVAVVQSVPGAHPVPVYAFSIKDPSYREEVSNTVTPQKRKS 238
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149   480 SQTQCPRKVIKMESEEGKEARLARSSPEQPRPSTSKAVSPPHLDGPPSPRSPVIGSEVFLPNSNHVASGAGEAEERVVVI 559
Cdd:pfam12126 239 CQTECPRKVIKMESEEEKEARLARSSPEQPRPSTSKAVSPPHLDGPPSPESPIVGKEVLLPNSNHVTSDPGEAEERIVVI 318
                         330
                  ....*....|.
gi 67089149   560 SSSEDSDAENS 570
Cdd:pfam12126 319 SSSEDSDAENS 329
Bbox2_TRIM19_C-V cd19770
B-box-type 2 zinc finger found in tripartite motif-containing protein 19, also called ...
187-237 3.58e-21

B-box-type 2 zinc finger found in tripartite motif-containing protein 19, also called promyelocytic leukemia protein (PML), and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380828  Cd Length: 50  Bit Score: 87.22  E-value: 3.58e-21
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 67089149 187 IFCSNPNHRTPTLtSIYCRGCSKPLCCSCALLDSSHSELKCDISAEIQQRQ 237
Cdd:cd19770   1 PFCPSPNHETQMI-SIYCRQCSKSVCCTCALLDSSHKGQHCDIKAEIQRRQ 50
RING-HC_PML_C-V cd16579
RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; ...
51-94 4.32e-18

RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438241 [Multi-domain]  Cd Length: 52  Bit Score: 78.75  E-value: 4.32e-18
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 67089149  51 EFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASG--------MQCPICQAP 94
Cdd:cd16579   1 EFKFLRCPGCKAEYKCPKLLPCLHTVCSGCLEALAeqasetteFQCPICKAS 52
Bbox1_TRIM19_C-V cd19804
B-box-type 1 zinc finger found in promyelocytic leukemia protein (PML) and similar proteins; ...
126-168 1.87e-15

B-box-type 1 zinc finger found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cellular processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites, and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.


Pssm-ID: 380862 [Multi-domain]  Cd Length: 47  Bit Score: 70.95  E-value: 1.87e-15
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 67089149 126 QAVCTRCKES-ADFWCFECEQLLCAKCFEAHQWF---LKHEARPLAE 168
Cdd:cd19804   1 ELMCNRCSESeAEFWCSECEEFLCRKCFEAHQRFkkrKKHEALRLAE 47
Bbox_SF cd00021
B-box-type zinc finger superfamily; The B-box-type zinc finger is a short zinc binding domain ...
128-166 4.19e-09

B-box-type zinc finger superfamily; 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, B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2).


Pssm-ID: 380813 [Multi-domain]  Cd Length: 39  Bit Score: 52.60  E-value: 4.19e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 67089149 128 VCTRCKES-ADFWCFECEQLLCAKCFE--AHQWflkHEARPL 166
Cdd:cd00021   1 MCQEHDEEkANKYCVTCEVLYCALCKKsgAHPD---HEVAPL 39
RING-HC_TRIM45_C-VII cd16588
RING finger, HC subclass, found in tripartite motif-containing protein 45 (TRIM45) and similar ...
56-82 2.25e-06

RING finger, HC subclass, found in tripartite motif-containing protein 45 (TRIM45) and similar proteins; TRIM45, also known as RING finger protein 99 (RNF99), is a novel receptor for activated C-kinase (RACK1)-interacting protein that suppresses transcriptional activities of Elk-1 and AP-1 and downregulates mitogen-activated protein kinase (MAPK) signal transduction through inhibiting RACK1/PKC (protein kinase C) complex formation. It also negatively regulates tumor necrosis factor alpha (TNFalpha)-induced nuclear factor-kappaB (NF-kappa B)-mediated transcription and suppresses cell proliferation. TRIM45 belongs to the C-VII subclass of the TRIM (tripartite motif) family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a filamin-type immunoglobulin (IG-FLMN) domain and NHL repeats positioned C-terminal to the RBCC domain.


Pssm-ID: 438250 [Multi-domain]  Cd Length: 59  Bit Score: 45.59  E-value: 2.25e-06
                        10        20
                ....*....|....*....|....*..
gi 67089149  56 RCQQCQAEAKCPKLLPCLHTLCSGCLE 82
Cdd:cd16588   2 RCPVCGKLFQEPRLLPCLHTLCSPCLR 28
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
55-91 2.58e-06

HC subclass of RING (RING-HC) finger 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 a different Cys/His pattern. Some lack a single Cys or His residue at typical Zn ligand positions, especially, the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can chelate Zn in a RING finger as well. This family corresponds to the HC subclass of RING (RING-HC) fingers that are characterized by containing C3HC4-type canonical RING-HC fingers or noncanonical RING-HC finger variants, including C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type modified RING-HC fingers. The canonical RING-HC finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-HC fingers 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 serve as scaffolds 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: 438113 [Multi-domain]  Cd Length: 41  Bit Score: 44.78  E-value: 2.58e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 67089149  55 LRCQQCQAEAKCPKLLPCLHTLCSGCL----EASGMQCPIC 91
Cdd:cd16449   1 LECPICLERLKDPVLLPCGHVFCRECIrrllESGSIKCPIC 41
RING-HC_TRIM3 cd16768
RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also ...
53-92 2.93e-06

RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It functions as a tumor suppressor that regulates asymmetric cell division in glioblastoma. It binds to the cdk inhibitor p21(WAF1/CIP1) and regulates its availability that promotes cyclin D1-cdk4 nuclear accumulation. Moreover, TRIM3 plays an important role in the central nervous system (CNS). It is encoded by the gene BERP (brain-expressed RING finger protein), a unique p53-regulated gene that modulates seizure susceptibility and GABAAR cell surface expression. Furthermore, TRIM3 mediates activity-dependent turnover of postsynaptic density (PSD) scaffold proteins GKAP/SAPAP1 and is a negative regulator of dendritic spine morphology. In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. It also regulates the motility of the kinesin superfamily protein KIF21B. TRIM3 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438424 [Multi-domain]  Cd Length: 48  Bit Score: 44.99  E-value: 2.93e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 67089149  53 QFLRCQQCQAEAKCPKLLPCLHTLCSGCL------EASGMQCPICQ 92
Cdd:cd16768   3 QFLVCSICLDRYHNPKVLPCLHTFCERCLqnyippQSLTLSCPVCR 48
RING-HC_TRIM9-like_C-I cd16576
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM9, TRIM67, and ...
49-91 3.55e-06

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM9, TRIM67, and similar proteins; Tripartite motif-containing proteins TRIM9 and TRIM67 belong to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, consisting of three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. TRIM9 (the human ortholog of rat Spring), also known as RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. TRIM9 plays an important role in the regulation of neuronal functions and participates in neurodegenerative disorders through its ligase activity. TRIM67, also known as TRIM9-like protein (TNL), is a protein selectively expressed in the cerebellum. It interacts with PRG-1, an important molecule in the control of hippocampal excitability dependent on presynaptic LPA2 receptor signaling, and 80K-H, also known as glucosidase II beta, a protein kinase C substrate.


Pssm-ID: 438238 [Multi-domain]  Cd Length: 42  Bit Score: 44.32  E-value: 3.55e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 67089149  49 EEEfqfLRCQQCQAEAKCPKLLPCLHTLCSGCLEASGMQCPIC 91
Cdd:cd16576   1 EEE---LKCPVCGSLFTEPVILPCSHNLCLGCALNIQLTCPIC 40
RING-HC_TRIM2_like_C-VII cd16586
RING finger, HC subclass, found in tripartite motif-containing protein TRIM2, TRIM3, and ...
54-92 3.67e-06

RING finger, HC subclass, found in tripartite motif-containing protein TRIM2, TRIM3, and similar proteins; TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It also plays an important role in the central nervous system (CNS). In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. Both TRIM2 and TRIM3 belong to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438248 [Multi-domain]  Cd Length: 45  Bit Score: 44.36  E-value: 3.67e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 67089149  54 FLRCQQCQAEAKCPKLLPCLHTLCSGCL------EASGMQCPICQ 92
Cdd:cd16586   1 FLSCGICLERYKNPKVLPCLHTFCERCLqnyipaESLSLSCPVCR 45
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
57-91 8.29e-06

Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway.


Pssm-ID: 395049 [Multi-domain]  Cd Length: 40  Bit Score: 43.50  E-value: 8.29e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 67089149    57 CQQCQAEAKCP-KLLPCLHTLCSGCLEASGM----QCPIC 91
Cdd:pfam00097   1 CPICLEEPKDPvTLLPCGHLFCSKCIRSWLEsgnvTCPLC 40
RING-HC_TRIM56_C-V cd16584
RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar ...
54-92 2.16e-05

RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar proteins; TRIM56, also known as RING finger protein 109 (RNF109), is a virus-inducible E3 ubiquitin ligase that restricts pestivirus infection. It positively regulates the Toll-like receptor 3 (TLR3) antiviral signaling pathway, and possesses antiviral activity against bovine viral diarrhea virus (BVDV), a ruminant pestivirus classified within the family Flaviviridae shared by tick-borne encephalitis virus (TBEV). It also possesses antiviral activity against two classical flaviviruses, yellow fever virus (YFV) and dengue virus (DENV), as well as a human coronavirus, HCoV-OC43, which is responsible for a significant share of common cold cases. It may not act on positive-strand RNA viruses indiscriminately. Moreover, TRIM56 is an interferon-inducible E3 ubiquitin ligase that modulates STING to confer double-stranded DNA-mediated innate immune responses. TRIM56 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438246 [Multi-domain]  Cd Length: 56  Bit Score: 42.67  E-value: 2.16e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 67089149  54 FLRCQQCQAEAKCPKLLPCLHTLCSGC----LEASGMQCPICQ 92
Cdd:cd16584   1 FLACKICLEQLRAPKTLPCLHTYCQDClaqlADGGRVRCPECR 43
BBOX smart00336
B-Box-type zinc finger;
124-166 2.19e-05

B-Box-type zinc finger;


Pssm-ID: 197662 [Multi-domain]  Cd Length: 42  Bit Score: 42.32  E-value: 2.19e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 67089149    124 DAQAVCTRCK-ESADFWCFECEQLLCAKCFEA-HQwflKHEARPL 166
Cdd:smart00336   1 QRAPKCDSHGdEPAEFFCEECGALLCRTCDEAeHR---GHTVVLL 42
RING-HC_TRIM2 cd16767
RING finger, HC subclass, found in tripartite motif-containing protein 2 (TRIM2); TRIM2, also ...
53-92 4.74e-05

RING finger, HC subclass, found in tripartite motif-containing protein 2 (TRIM2); TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM2 also plays a role in mediating the p42/p44 MAPK-dependent ubiquitination of the cell death-promoting protein Bcl-2-interacting mediator of cell death (Bim) in rapid ischemic tolerance. TRIM2 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438423 [Multi-domain]  Cd Length: 51  Bit Score: 41.54  E-value: 4.74e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 67089149  53 QFLRCQQCQAEAKCPKLLPCLHTLCSGCLE------ASGMQCPICQ 92
Cdd:cd16767   5 QFLICSICLDRYKNPKVLPCLHTFCERCLQnyipahSLTLSCPVCR 50
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
610-758 7.28e-05

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 44.21  E-value: 7.28e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149    610 LVFFDLK---IDNETQKISQLAAVN-----RESKFRVVIQPEAFFSIYSKAVS------------LEVGLQHFLSFLSsm 669
Cdd:smart00479   2 LVVIDCEttgLDPGKDEIIEIAAVDvdggeIIEVFDTYVKPDRPITDYATEIHgitpemlddaptFEEVLEELLEFLR-- 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149    670 RRPILACYklwgpGLPNFFRALE-DINRLWEFQEAISGFLAALPLIRERVPGASSFKLKNLAQTYLARNMSER-SAMA-A 746
Cdd:smart00479  80 GRILVAGN-----SAHFDLRFLKlEHPRLGIKQPPKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQRAhRALDdA 154
                          170
                   ....*....|..
gi 67089149    747 VLAMRDLCRLLE 758
Cdd:smart00479 155 RATAKLFKKLLE 166
RING-HC_RNF169 cd16551
RING finger, HC subclass, found in RING finger protein 169 (RNF169) and similar proteins; ...
55-99 9.70e-05

RING finger, HC subclass, found in RING finger protein 169 (RNF169) and similar proteins; RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to regulation of the DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. RNF169 contains an N-terminal C3HC4-type RING-HC finger and a C-terminal MIU (motif interacting with ubiquitin) domain.


Pssm-ID: 438213 [Multi-domain]  Cd Length: 55  Bit Score: 40.99  E-value: 9.70e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 67089149  55 LRCQQCQAEAKCPKLLPCLHTLCSGCLE------ASGMQCPICQAPWPLGA 99
Cdd:cd16551   2 LTCAGCLEVPVEPATLPCGHTLCRGCANraldaaEAGPTCPRCRAPLPGWA 52
Bbox1 cd19757
B-box-type 1 zinc finger (Bbox1); The B-box-type zinc finger is a short zinc binding domain of ...
128-166 1.19e-04

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: 40.17  E-value: 1.19e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 67089149 128 VCTRCKE-SADFWCFECEQLLCAKCFEA-HQW---FLKHEARPL 166
Cdd:cd19757   1 LCDECEErEATVYCLECEEFLCDDCSDAiHRRgklTRSHKLVPL 44
Bbox1_BRAT-like cd19813
B-box-type 1 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and ...
128-156 1.47e-04

B-box-type 1 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and similar proteins; BRAT is a NHL-domain family protein that functions as a translational repressor to inhibit cell proliferation. The family also contains Caenorhabditis elegans B-box type zinc finger protein ncl-1, a C. elegans Brat homolog which functions as a translational repressor that inhibits protein synthesis. BRAT contains Bbox1 and Bbox2 zinc fingers and NHL repeats. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.


Pssm-ID: 380871  Cd Length: 44  Bit Score: 40.08  E-value: 1.47e-04
                        10        20        30
                ....*....|....*....|....*....|.
gi 67089149 128 VCTRCK--ESADFWCFECEQLLCAKCFEAHQ 156
Cdd:cd19813   1 HCTGCKskETAVARCFDCQVLLCANCVTAHQ 31
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
57-91 1.52e-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: 39.80  E-value: 1.52e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 67089149     57 CQQC-QAEAKCPKLLPCLHTLCSGC----LEASGMQCPIC 91
Cdd:smart00184   1 CPIClEEYLKDPVILPCGHTFCRSCirkwLESGNNTCPIC 40
RING-HC_TRIM13_like_C-V cd16581
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and ...
53-91 1.68e-04

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and similar proteins; TRIM13 and TRIM59, two closely related tripartite motif-containing proteins, belong to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, followed by a C-terminal transmembrane domain. TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). TRIM59, also known as RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis.


Pssm-ID: 438243 [Multi-domain]  Cd Length: 50  Bit Score: 40.19  E-value: 1.68e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 67089149  53 QFLRCQQCQAEAKCPKLLPCLHTLCSGCLEA----------SGMQCPIC 91
Cdd:cd16581   1 EELTCSICYNIFDDPKILPCSHTFCKNCLEKllaasgyyllASLKCPTC 49
GumC COG3206
Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];
230-327 2.18e-04

Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442439 [Multi-domain]  Cd Length: 687  Bit Score: 45.01  E-value: 2.18e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149 230 SAEIQQRQEELDAMTQALQEQDSAFGAVHAQMHAAVGQLgrarAETEELIRERVRQVVAHVRAqERELLEAVDARYQRDY 309
Cdd:COG3206 262 SPVIQQLRAQLAELEAELAELSARYTPNHPDVIALRAQI----AALRAQLQQEAQRILASLEA-ELEALQAREASLQAQL 336
                        90
                ....*....|....*...
gi 67089149 310 EEMASRLGRLDAVLQRIR 327
Cdd:COG3206 337 AQLEARLAELPELEAELR 354
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
53-125 4.38e-04

DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273165 [Multi-domain]  Cd Length: 397  Bit Score: 43.45  E-value: 4.38e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 67089149    53 QFLRCQQCQAEAKCPKLLPCLHTLCSGC----LEASGMqCPICQAPwplgadtpaldnvFFESLQRRLSVYRQIVDA 125
Cdd:TIGR00599  25 TSLRCHICKDFFDVPVLTSCSHTFCSLCirrcLSNQPK-CPLCRAE-------------DQESKLRSNWLVSEIVES 87
zf-B_box pfam00643
B-box zinc finger;
128-166 5.26e-04

B-box zinc finger;


Pssm-ID: 459886 [Multi-domain]  Cd Length: 42  Bit Score: 38.22  E-value: 5.26e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 67089149   128 VCTRCKES-ADFWCFECEQLLCAKCF-EAHQwflKHEARPL 166
Cdd:pfam00643   5 LCPEHEEEpLTLYCNDCQELLCEECSvGEHR---GHTVVPL 42
zf-C3HC4_3 pfam13920
Zinc finger, C3HC4 type (RING finger);
57-94 6.31e-04

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 464042 [Multi-domain]  Cd Length: 50  Bit Score: 38.51  E-value: 6.31e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 67089149    57 CQQCQAEAKCPKLLPCLHT-LCSGC---LEASGMQCPICQAP 94
Cdd:pfam13920   5 CVICLDRPRNVVLLPCGHLcLCEECaerLLRKKKKCPICRQP 46
RING-HC_CHFR cd16503
RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein ...
55-94 8.58e-04

RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR); CHFR, also known as RING finger protein 196 (RNF196), is a checkpoint protein that delays entry into mitosis in response to stress. It functions as an E3 ubiquitin ligase that ubiquitinates and degrades its target proteins, such as Aurora-A, Plk1, Kif22, and PARP-1, which are critical for proper mitotic transitions. It also plays an important role in cell cycle progression and tumor suppression, and is negatively regulated by SUMOylation-mediated proteasomal ubiquitylation. Moreover, CHFR is involved in the early stage of the DNA damage response, which mediates the crosstalk between ubiquitination and poly-ADP-ribosylation. CHFR contains a fork head associated (FHA) domain and a C3HC4-type RING-HC finger.


Pssm-ID: 438166 [Multi-domain]  Cd Length: 55  Bit Score: 38.12  E-value: 8.58e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 67089149  55 LRCQQCQAE-AKCPKLLPCLHTLCSGCL----EASGMQCPICQAP 94
Cdd:cd16503   3 LTCSICQDLlHDCVSLQPCMHNFCAACYsdwmERSNTECPTCRAT 47
Bbox1_TIF1b_C-VI cd19846
B-box-type 1 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta); ...
124-156 9.61e-04

B-box-type 1 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), KRAB-interacting protein 1 (KRIP-1), nuclear co-repressor KAP-1, RING finger protein 96, tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-beta/KAP-1 acts as a nuclear co-repressor that plays a role in transcription and in the DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during the DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. Moreover, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. The N-terminal RBCC domains of TIF1-beta are responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 380904  Cd Length: 52  Bit Score: 38.14  E-value: 9.61e-04
                        10        20        30
                ....*....|....*....|....*....|....*
gi 67089149 124 DAQAVCTRCKES--ADFWCFECEQLLCAKCFEAHQ 156
Cdd:cd19846   1 ETIQCCTSCEDNapATSYCVECSEPLCETCVEAHQ 35
zf-RING_5 pfam14634
zinc-RING finger domain;
56-92 9.65e-04

zinc-RING finger domain;


Pssm-ID: 434085 [Multi-domain]  Cd Length: 43  Bit Score: 37.79  E-value: 9.65e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 67089149    56 RCQQCQ---AEAKCPKLLPCLHTLCSGCL--EASGMQCPICQ 92
Cdd:pfam14634   1 HCNKCFkelSKTRPFYLTSCGHIFCEECLtrLLQERQCPICK 42
RING-HC_NHL-1-like cd16524
RING finger, HC subclass, found in Caenorhabditis elegans RING finger protein NHL-1 and ...
53-93 1.02e-03

RING finger, HC subclass, found in Caenorhabditis elegans RING finger protein NHL-1 and similar proteins; NHL-1 functions as an E3 ubiquitin-protein ligase in the presence of both UBC-13 and UBC-1 within the ubiquitin pathway of Caenorhabditis elegans. It acts in chemosensory neurons to promote stress resistance in distal tissues by the transcription factor DAF-16 activation but is dispensable for the activation of heat shock factor 1 (HSF-1). NHL-1 belongs to the TRIM (tripartite motif)-NHL family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as an NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438187 [Multi-domain]  Cd Length: 53  Bit Score: 37.79  E-value: 1.02e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 67089149  53 QFLRCQQCQAEAKCPKLLPCLHTLC-SGCLEASGM------QCPICQA 93
Cdd:cd16524   4 QLLTCPICLDRYRRPKLLPCQHTFClSPCLEGLVDyvtrklKCPECRA 51
RING-HC_TRIM47-like_C-IV cd16604
RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar ...
55-96 1.02e-03

RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar proteins; TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. It plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. This subfamily also includes RING finger protein 135 (RNF135). RNF135, also known as RIG-I E3 ubiquitin ligase (REUL) or Riplet, is a widely expressed E3 ubiquitin-protein ligase that consists of an N-terminal C3HC4-type RING-HC finger and C-terminal B30.2/SPRY and PRY motifs, but lacks the B-box and coiled-coil domains that are also typically present in TRIM proteins. RNF135 serves as a specific retinoic acid-inducible gene-I (RIG-I)-interacting protein that ubiquitinates RIG-I and specifically stimulates RIG-I-mediated innate antiviral activity to produce antiviral type-I interferon (IFN) during the early phase of viral infection. It also has been identified as a bio-marker and therapy target of glioblastoma. It associates with the ERK signal transduction pathway and plays a role in glioblastoma cell proliferation, migration and cell cycle.


Pssm-ID: 438266 [Multi-domain]  Cd Length: 49  Bit Score: 37.79  E-value: 1.02e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 67089149  55 LRCQQCQAEAKCPKLLPCLHTLCSGCLEA-------SGMQCPICQAPWP 96
Cdd:cd16604   1 LSCPICLDLLKDPVTLPCGHSFCMGCLGAlwgagrgGRASCPLCRQTFP 49
mRING-HC-C3HC5_CGRF1-like cd16649
Modified RING finger, HC subclass (C3HC5-type), found in RING finger proteins, RNF26, RNF197 ...
57-91 1.24e-03

Modified RING finger, HC subclass (C3HC5-type), found in RING finger proteins, RNF26, RNF197 (CGRRF1), RNF156 (MGRN1), RNF157 and similar proteins; This subfamily corresponds to a group of RING finger proteins containing a modified C3HC5-type RING-HC finger, which is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain. Cell growth regulator with RING finger domain protein 1 (CGRRF1), also known as cell growth regulatory gene 19 protein (CGR19) or RING finger protein 197 (RNF197), functions as a novel biomarker to monitor endometrial sensitivity and response to insulin-sensitizing drugs, such as metformin, in the context of obesity. RNF26 is an E3 ubiquitin ligase that temporally regulates virus-triggered type I interferon induction by increasing the stability of Mediator of IRF3 activation, MITA, also known as STING, through K11-linked polyubiquitination after viral infection and promoting degradation of IRF3, another important component required for virus-triggered interferon induction. Mahogunin ring finger-1 (MGRN1), also known as RING finger protein 156 (RNF156), is a cytosolic E3 ubiquitin-protein ligase that inhibits signaling through the G protein-coupled melanocortin receptors-1 (MC1R), -2 (MC2R) and -4 (MC4R) via ubiquitylation-dependent and -independent processes. It suppresses chaperone-associated misfolded protein aggregation and toxicity. RNF157 is a cytoplasmic E3 ubiquitin ligase predominantly expressed in the brain. It is a homolog of the E3 ligase MGRN1. In cultured neurons, it promotes neuronal survival in an E3 ligase-dependent manner. In contrast, it supports growth and maintenance of dendrites independent of its E3 ligase activity. RNF157 interacts with and ubiquitinates the adaptor protein APBB1 (amyloid beta precursor protein-binding, family B, member 1 or Fe65), which regulates neuronal survival, but not dendritic growth downstream of RNF157. The nuclear localization of APBB1 together with its interaction partner RNA-binding protein SART3 (squamous cell carcinoma antigen recognized by T cells 3 or Tip110) is crucial to trigger apoptosis.


Pssm-ID: 438311 [Multi-domain]  Cd Length: 40  Bit Score: 37.30  E-value: 1.24e-03
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 67089149  57 CQQCQAEAKCPKLLPCLHT-LCSGCLEA-SGMQCPIC 91
Cdd:cd16649   3 CVVCLENPASVLLLPCRHLcLCEVCAKGlRGKTCPIC 39
Bbox1_TIF1a_C-VI cd19845
B-box-type 1 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); ...
128-156 1.27e-03

B-box-type 1 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-alpha interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoic X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development.


Pssm-ID: 380903  Cd Length: 45  Bit Score: 37.35  E-value: 1.27e-03
                        10        20        30
                ....*....|....*....|....*....|.
gi 67089149 128 VCTRCKESADF--WCFECEQLLCAKCFEAHQ 156
Cdd:cd19845   2 VCTSCEDNAEAngFCVECVEWLCKTCIEAHQ 32
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
230-446 1.64e-03

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 41.67  E-value: 1.64e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149 230 SAEIQQRQEELDAMTQALQEQDSAFGAVHAQMHAAVGQLGRARAETEELiRERVRQVVAHVRAQEREL--LEAVDARYQR 307
Cdd:COG4942  19 ADAAAEAEAELEQLQQEIAELEKELAALKKEEKALLKQLAALERRIAAL-ARRIRALEQELAALEAELaeLEKEIAELRA 97
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149 308 DYEEMASRLGRLDAVLQRirtgSALVQRMKCYASDQEVLDMHGFLR--QALCRLRQEEPQSLQAavRTDGFDEFKVRLQD 385
Cdd:COG4942  98 ELEAQKEELAELLRALYR----LGRQPPLALLLSPEDFLDAVRRLQylKYLAPARREQAEELRA--DLAELAALRAELEA 171
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 67089149 386 LSSCITQGKDAAVSKKASPEAASTPRDPIDVDLPEEAERVKAQVQALGLAEAQPMAVVQSV 446
Cdd:COG4942 172 ERAELEALLAELEEERAALEALKAERQKLLARLEKELAELAAELAELQQEAEELEALIARL 232
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
218-386 1.85e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 41.43  E-value: 1.85e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149 218 LDSSHSELKcDISAEIQQRQEELDAMTQALQEQDSAFGAVHAQMHAAVGQLGRARAETEELIRERVRQvvahvrAQEREL 297
Cdd:COG4372  61 LEQLEEELE-QARSELEQLEEELEELNEQLQAAQAELAQAQEELESLQEEAEELQEELEELQKERQDL------EQQRKQ 133
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149 298 LEAVDARYQRDYEEMASRLGRLDAVLQRIRTGSALVQRMKCYASDQEVL-DMHGFLRQALCRLRQEEPQSLQAAVRTDGF 376
Cdd:COG4372 134 LEAQIAELQSEIAEREEELKELEEQLESLQEELAALEQELQALSEAEAEqALDELLKEANRNAEKEEELAEAEKLIESLP 213
                       170
                ....*....|
gi 67089149 377 DEFKVRLQDL 386
Cdd:COG4372 214 RELAEELLEA 223
Bbox1_TIF1 cd19805
B-box-type 1 zinc finger found in transcription intermediary factor 1 (TIF1) family; This ...
128-156 2.31e-03

B-box-type 1 zinc finger found in transcription intermediary factor 1 (TIF1) family; This family corresponds to the TIF1 family of transcriptional cofactors including TIF1-alpha (TRIM24), TIF1-beta (TRIM28), and TIF1-gamma (TRIM33), which belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1-alpha and TIF1-beta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. They bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. TIF1-gamma is structurally closely related to TIF1-alpha and TIF1-beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta and gamma. It cannot bind to nuclear receptors (NRs).


Pssm-ID: 380863  Cd Length: 44  Bit Score: 36.59  E-value: 2.31e-03
                        10        20        30
                ....*....|....*....|....*....|.
gi 67089149 128 VCTRCKE--SADFWCFECEQLLCAKCFEAHQ 156
Cdd:cd19805   1 VCTSCEDnaPATSFCVECSEWLCDTCVQAHQ 31
RING-HC_TRIM65_C-IV cd16609
RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar ...
49-99 2.40e-03

RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar proteins; TRIM65 is an E3 ubiquitin-protein ligase that interacts with the innate immune receptor MDA5, enhancing its ability to stimulate interferon-beta signaling. It functions as a potential oncogenic protein that negatively regulates p53 through ubiquitination, providing insight into the development of novel approaches targeting TRIM65 for non-small cell lung carcinoma (NSCLC) treatment, and also overcoming chemotherapy resistance. Moreover, TRIM65 negatively regulates microRNA-driven suppression of mRNA translation by targeting TNRC6 proteins for ubiquitination and degradation. TRIM65 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438271 [Multi-domain]  Cd Length: 58  Bit Score: 36.97  E-value: 2.40e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 67089149  49 EEEfqfLRCQQCQAEAKCPKLLPCLHTLCSGCLE-------ASGMQCPICQAPWPLGA 99
Cdd:cd16609   1 EEE---LTCSICLGLYQDPVTLPCQHSFCRACIEdhwrqkdEGSFSCPECRAPFPEGP 55
RING-HC_AtBARD1-like cd23146
RING finger, HC subclass, found in Arabidopsis thaliana BRCA1-associated RING domain protein 1 ...
55-96 2.61e-03

RING finger, HC subclass, found in Arabidopsis thaliana BRCA1-associated RING domain protein 1 (AtBARD1) and similar proteins; AtBARD1, also called protein REPRESSOR OF WUSCHEL 1, binds specifically to H3K4me3 regions of target gene (e.g. WUS and WOX5) promoters to repress their transcription via chromatin remodeling. It is required for the shoot apical meristem (SAM) organization and maintenance, by confining WUS expression to the organizing center, and for the quiescent center (QC) development in the root apical meristem (RAM), by repressing WOX5 expression in the root proximal meristem. AtBARD1 plays a role in DNA repair and in cell-cycle control. It is required for the repair of DNA double-strand breaks (DSBs), both natural and induced by genotoxic stress, by homologous recombination (HR). AtBARD1 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438508 [Multi-domain]  Cd Length: 54  Bit Score: 36.68  E-value: 2.61e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 67089149  55 LRCQQCQAEAKCPKLLPCLHTLCSGCLEAS---GMQCPICQAPWP 96
Cdd:cd23146   5 LKCPICLKLLNRPVLLPCDHIFCSSCITDStkvGSDCPVCKLPYH 49
mRING-HC-C3HC5_CGRF1 cd16787
Modified RING finger, HC subclass (C3HC5-type), found in cell growth regulator with RING ...
57-92 4.21e-03

Modified RING finger, HC subclass (C3HC5-type), found in cell growth regulator with RING finger domain protein 1 (CGRRF1) and similar proteins; CGRRF1, also known as cell growth regulatory gene 19 protein (CGR19) or RING finger protein 197 (RNF197), functions as a novel biomarker to monitor endometrial sensitivity and response to insulin-sensitizing drugs, such as metformin, in the context of obesity. CGRRF1 contains a C-terminal modified C3HC5-type RING-HC finger, which is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain.


Pssm-ID: 438441 [Multi-domain]  Cd Length: 38  Bit Score: 35.81  E-value: 4.21e-03
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 67089149  57 CQQCQAEAKCPKLLPCLHT-LCSGCLEASgMQCPICQ 92
Cdd:cd16787   3 CVVCQNAPVNRVLLPCRHAcVCDECFKRL-QRCPMCR 38
EzrA pfam06160
Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like ...
228-363 7.76e-03

Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation. The structure contains 5 spectrin like alpha helical repeats.


Pssm-ID: 428797 [Multi-domain]  Cd Length: 542  Bit Score: 39.84  E-value: 7.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149   228 DISAEIQQRQEELDAMTQALQEQD-----SAFGAVHAQMHAAVGQLGR---ARAETEELIRErVRQVVAHVRAQEREL-- 297
Cdd:pfam06160 234 NVDKEIQQLEEQLEENLALLENLEldeaeEALEEIEERIDQLYDLLEKevdAKKYVEKNLPE-IEDYLEHAEEQNKELke 312
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67089149   298 -LEAVDARY---------QRDYEEMASRL-GRLDAVLQRIRTG----SALVQRMK-CYASDQEVLDMHGFLRQALCRLRQ 361
Cdd:pfam06160 313 eLERVQQSYtlnenelerVRGLEKQLEELeKRYDEIVERLEEKevaySELQEELEeILEQLEEIEEEQEEFKESLQSLRK 392

                  ..
gi 67089149   362 EE 363
Cdd:pfam06160 393 DE 394
RING-HC_ScPSH1-like cd16568
RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated ...
57-94 8.06e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated protein 1 (ScPSH1) and similar proteins; ScPSH1 is a Cse4-specific E3 ubiquitin ligase that interacts with the kinetochore protein Pat1 and targets the degradation of budding yeast centromeric histone H3 variant, CENP-ACse4, which is essential for faithful chromosome segregation. ScPSH1 contains a C3HC4-type RING-HC finger and a DNA directed RNA polymerase domain.


Pssm-ID: 438230 [Multi-domain]  Cd Length: 54  Bit Score: 35.42  E-value: 8.06e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 67089149  57 CQQCQAEAKCPKLLPCLHTLCSGCLEA-----SGMQCPICQAP 94
Cdd:cd16568   7 CIICHEYLYEPMVTTCGHTYCYTCLNTwfksnRSLSCPDCRTK 49
 
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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