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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62087480   243 LDAMTQALQEQDSAFGAVHAQMHAAVGQLGRARAETEELIRERVRQVVAHVRAQERELLEAVDARYQRDYEEMASRLGRL 322
Cdd:pfam12126   1 LDTMTQALQEQDGAFGAAHAQMRSAISQLGRARADTEELIRARVRQVVAHVQAQERELLEAVNARYQRDYEEMAGQLGRL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62087480   323 DAVLQRIRTGSALVQRMKCYASDQEVLDMHGFLRQALCRLRQEEPQSLQAAVRTDGFDEFKVRLQDLSSCITQGKDAAVS 402
Cdd:pfam12126  81 DAVLQRIRTGGALVQRMKRYASDQEVLDMHGFLREALCRLRQEEPQNLQAAVRTDGFDEFKVRLQDLVSCITQGTDAAVS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62087480   403 KKASPEAASTPRDPIDVDL----------------------------------------------DVSNTTTAQKRKCSQ 436
Cdd:pfam12126 161 RRASPEAASTPRDPSDVDLpeevqrvqaqalglaetqpvavvqsvpgahpvpvyafsikdpsyreEVSNTVTPQKRKSCQ 240

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62087480   437 TQCPRKVIKMESEEGKEARLARSSPEQPRPSTSKAVSPPHLDGPPSPRSPVIGSEVFLPNSNHVASGAGEA 507
Cdd:pfam12126 241 TECPRKVIKMESEEEKEARLARSSPEQPRPSTSKAVSPPHLDGPPSPESPIVGKEVLLPNSNHVTSDPGEA 311

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 62087480  54 EFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASG--------MQCPICQAP 97
Cdd:cd16579   1 EFKFLRCPGCKAEYKCPKLLPCLHTVCSGCLEALAeqasetteFQCPICKAS 52

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62087480   243 LDAMTQALQEQDSAFGAVHAQMHAAVGQLGRARAETEELIRERVRQVVAHVRAQERELLEAVDARYQRDYEEMASRLGRL 322
Cdd:pfam12126   1 LDTMTQALQEQDGAFGAAHAQMRSAISQLGRARADTEELIRARVRQVVAHVQAQERELLEAVNARYQRDYEEMAGQLGRL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62087480   323 DAVLQRIRTGSALVQRMKCYASDQEVLDMHGFLRQALCRLRQEEPQSLQAAVRTDGFDEFKVRLQDLSSCITQGKDAAVS 402
Cdd:pfam12126  81 DAVLQRIRTGGALVQRMKRYASDQEVLDMHGFLREALCRLRQEEPQNLQAAVRTDGFDEFKVRLQDLVSCITQGTDAAVS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62087480   403 KKASPEAASTPRDPIDVDL----------------------------------------------DVSNTTTAQKRKCSQ 436
Cdd:pfam12126 161 RRASPEAASTPRDPSDVDLpeevqrvqaqalglaetqpvavvqsvpgahpvpvyafsikdpsyreEVSNTVTPQKRKSCQ 240

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62087480   437 TQCPRKVIKMESEEGKEARLARSSPEQPRPSTSKAVSPPHLDGPPSPRSPVIGSEVFLPNSNHVASGAGEA 507
Cdd:pfam12126 241 TECPRKVIKMESEEEKEARLARSSPEQPRPSTSKAVSPPHLDGPPSPESPIVGKEVLLPNSNHVTSDPGEA 311

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 62087480  54 EFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASG--------MQCPICQAP 97
Cdd:cd16579   1 EFKFLRCPGCKAEYKCPKLLPCLHTVCSGCLEALAeqasetteFQCPICKAS 52

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62087480 233 SAEIQQRQEELDAMTQALQEQDSAFGAVHAQMHAAVGQLgrarAETEELIRERVRQVVAHVRAqERELLEAVDARYQRDY 312
Cdd:COG3206 262 SPVIQQLRAQLAELEAELAELSARYTPNHPDVIALRAQI----AALRAQLQQEAQRILASLEA-ELEALQAREASLQAQL 336

                        90
                ....*....|....*...
gi 62087480 313 EEMASRLGRLDAVLQRIR 330
Cdd:COG3206 337 AQLEARLAELPELEAELR 354

B-Box-type zinc finger;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 62087480    127 DAQAVCTRCK-ESADFWCFECEQLLCAKCFEA-HQwflKHEARPL 169
Cdd:smart00336   1 QRAPKCDSHGdEPAEFFCEECGALLCRTCDEAeHR---GHTVVLL 42

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)

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 62087480     60 CQQC-QAEAKCPKLLPCLHTLCSGC----LEASGMQCPIC 94
Cdd:smart00184   1 CPIClEEYLKDPVILPCGHTFCRSCirkwLESGNNTCPIC 40

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62087480   243 LDAMTQALQEQDSAFGAVHAQMHAAVGQLGRARAETEELIRERVRQVVAHVRAQERELLEAVDARYQRDYEEMASRLGRL 322
Cdd:pfam12126   1 LDTMTQALQEQDGAFGAAHAQMRSAISQLGRARADTEELIRARVRQVVAHVQAQERELLEAVNARYQRDYEEMAGQLGRL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62087480   323 DAVLQRIRTGSALVQRMKCYASDQEVLDMHGFLRQALCRLRQEEPQSLQAAVRTDGFDEFKVRLQDLSSCITQGKDAAVS 402
Cdd:pfam12126  81 DAVLQRIRTGGALVQRMKRYASDQEVLDMHGFLREALCRLRQEEPQNLQAAVRTDGFDEFKVRLQDLVSCITQGTDAAVS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62087480   403 KKASPEAASTPRDPIDVDL----------------------------------------------DVSNTTTAQKRKCSQ 436
Cdd:pfam12126 161 RRASPEAASTPRDPSDVDLpeevqrvqaqalglaetqpvavvqsvpgahpvpvyafsikdpsyreEVSNTVTPQKRKSCQ 240

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62087480   437 TQCPRKVIKMESEEGKEARLARSSPEQPRPSTSKAVSPPHLDGPPSPRSPVIGSEVFLPNSNHVASGAGEA 507
Cdd:pfam12126 241 TECPRKVIKMESEEEKEARLARSSPEQPRPSTSKAVSPPHLDGPPSPESPIVGKEVLLPNSNHVTSDPGEA 311

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 62087480  54 EFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASG--------MQCPICQAP 97
Cdd:cd16579   1 EFKFLRCPGCKAEYKCPKLLPCLHTVCSGCLEALAeqasetteFQCPICKAS 52

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).

                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 62087480 131 VCTRCKES-ADFWCFECEQLLCAKCFE--AHQWflkHEARPL 169
Cdd:cd00021   1 MCQEHDEEkANKYCVTCEVLYCALCKKsgAHPD---HEVAPL 39

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.

                        10        20
                ....*....|....*....|....*..
gi 62087480  59 RCQQCQAEAKCPKLLPCLHTLCSGCLE 85
Cdd:cd16588   2 RCPVCGKLFQEPRLLPCLHTLCSPCLR 28

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 62087480  57 FLRCQQCQAEAKCPKLLPCLHTLCSGCL------EASGMQCPICQ 95
Cdd:cd16586   1 FLSCGICLERYKNPKVLPCLHTFCERCLqnyipaESLSLSCPVCR 45

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 62087480  58 LRCQQCQAEAKCPKLLPCLHTLCSGCL----EASGMQCPIC 94
Cdd:cd16449   1 LECPICLERLKDPVLLPCGHVFCRECIrrllESGSIKCPIC 41

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 62087480  57 FLRCQQCQAEAKCPKLLPCLHTLCSGC----LEASGMQCPICQ 95
Cdd:cd16584   1 FLACKICLEQLRAPKTLPCLHTYCQDClaqlADGGRVRCPECR 43

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 62087480  56 QFLRCQQCQAEAKCPKLLPCLHTLCSGCLE------ASGMQCPICQ 95
Cdd:cd16767   5 QFLICSICLDRYKNPKVLPCLHTFCERCLQnyipahSLTLSCPVCR 50

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62087480 231 DISAEIQQRQEELDAMTQALQEQDSAFGAVHAQMHAAVGQLGRARAE---TEELIRERVRQVVAHVRAQERE-------- 299
Cdd:COG3883  27 ELQAELEAAQAELDALQAELEELNEEYNELQAELEALQAEIDKLQAEiaeAEAEIEERREELGERARALYRSggsvsyld 106

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62087480 300 -LLEAvdaryqRDYEEMASRLGRLDAV-------LQRIRTGSALVQRMKCYASDQEVLdmhgfLRQALCRLRQEEpQSLQ 371
Cdd:COG3883 107 vLLGS------ESFSDFLDRLSALSKIadadadlLEELKADKAELEAKKAELEAKLAE-----LEALKAELEAAK-AELE 174

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62087480 372 AAVrtdgfDEFKVRLQDLSSCITQGKDAAVSKKASPEAASTPRDPIDVDLDVSNTTTAQKRKCSQTQCPRKVIKMESEEG 451
Cdd:COG3883 175 AQQ-----AEQEALLAQLSAEEAAAEAQLAELEAELAAAEAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAASAAGA 249

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62087480 452 KEARLARSSPEQPRPSTSKAVSPPHLDGPPSP-RSPVIGSEVFLPNSNHVASGAGEAGREVGRAVAWVLPARVWAV 526
Cdd:COG3883 250 GAAGAAGAAAGSAGAAGAAAGAAGAGAAAASAaGGGAGGAGGGGGGGGAASGGSGGGSGGAGGVGSGGGAGAVVGG 325

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.

                        10        20        30
                ....*....|....*....|....*....|.
gi 62087480 131 VCTRCK--ESADFWCFECEQLLCAKCFEAHQ 159
Cdd:cd19813   1 HCTGCKskETAVARCFDCQVLLCANCVTAHQ 31

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 62087480  56 QFLRCQQCQAEAKCPKLLPCLHTLCSGCLEA----------SGMQCPIC 94
Cdd:cd16581   1 EELTCSICYNIFDDPKILPCSHTFCKNCLEKllaasgyyllASLKCPTC 49

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).

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 62087480 131 VCTRCKE-SADFWCFECEQLLCAKCFEA-HQW---FLKHEARPL 169
Cdd:cd19757   1 LCDECEErEATVYCLECEEFLCDDCSDAiHRRgklTRSHKLVPL 44

Centrosome localization domain of PPC89; The N-terminal region of the fission yeast spindle pole body protein PPC89 has low similarity to the human Cep57 protein. The CLD or centrosome localization domain of Cep57 and PPC89 is found at the N-terminus. This region localizes to the centrosome internally to gamma-tubulin, suggesting that it is either on both centrioles or on a centromatrix component. This N-terminal region can also multimerize with the N-terminus of other Cep57 molecules. The C-terminal part, Family Cep57_MT_bd, pfam06657, is the microtubule-binding region of Cep57 and PPC89.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62087480   234 AEIQQRQEELDAMTQALQEQDSAFGAVHAQMHAAVGQLGRARAETEELIRErvrqvVAHVRAQERELLEA 303
Cdd:pfam14197   3 AENLTLQNRLDSLTRKVAVHEIELKRLRRERDSAVRQLGVAYLEIQELKAE-----NEALRKELKEQRAQ 67

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)

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 62087480     60 CQQC-QAEAKCPKLLPCLHTLCSGC----LEASGMQCPIC 94
Cdd:smart00184   1 CPIClEEYLKDPVILPCGHTFCRSCirkwLESGNNTCPIC 40

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 62087480  56 QFLRCQQCQAEAKCPKLLPCLHTLC-SGCLEASGM------QCPICQA 96
Cdd:cd16524   4 QLLTCPICLDRYRRPKLLPCQHTFClSPCLEGLVDyvtrklKCPECRA 51

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.

                        10        20        30
                ....*....|....*....|....*....|....*
gi 62087480 127 DAQAVCTRCKES--ADFWCFECEQLLCAKCFEAHQ 159
Cdd:cd19846   1 ETIQCCTSCEDNapATSYCVECSEPLCETCVEAHQ 35

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 62087480  58 LRCQQCQAEAKCPKLLPCLHTLCSGCLEA-------SGMQCPICQAPWP 99
Cdd:cd16604   1 LSCPICLDLLKDPVTLPCGHSFCMGCLGAlwgagrgGRASCPLCRQTFP 49

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62087480  39 SPSPSPTERAPASEEEFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEAS-GMQ--CPICQAPwplgadtpaldnvFFESL 115
Cdd:COG5432   7 DPSDWNQTKIPSLKGLDSMLRCRICDCRISIPCETTCGHTFCSLCIRRHlGTQpfCPVCRED-------------PCESR 73

                        90
                ....*....|....*.
gi 62087480 116 QRRLSVYRQIVDAQAV 131
Cdd:COG5432  74 LRGSSGSREINESHAR 89

Zinc finger, C3HC4 type (RING finger);

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 62087480    60 CQQCQAEAKCPKLLPCLHT-LCSGC---LEASGMQCPICQAP 97
Cdd:pfam13920   5 CVICLDRPRNVVLLPCGHLcLCEECaerLLRKKKKCPICRQP 46