RING finger, H2 subclass, found in TRAF-interacting protein (TRAIP) and similar proteins; TRAIP, also known as RING finger protein 206 (RNF206) or TRIP, is a ubiquitously expressed nucleolar E3 ubiquitin ligase important for cellular proliferation and differentiation. It is found near mitotic chromosomes and functions as a regulator of the spindle assembly checkpoint. TRAIP interacts with tumor necrosis factor (TNF)-receptor-associated factor (TRAF) proteins and inhibits TNF-alpha-mediated nuclear factor (NF)-kappaB activation. It also interacts with two tumor suppressors CYLD and spleen tyrosine kinase (Syk), and DNA polymerase eta, which facilitates translesional synthesis after DNA damage. TRAIP contains an N-terminal C3H2C2-type RING-H2 finger and an extended coiled-coil domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 157823719   6 LCTICSDFFDHSRDVAAIHCGHTFHLQCLIQWFETapSRTCPQCR 50
Cdd:cd16480    1 YCTICSDFFDNSRDVAAIHCGHTFHYDCLLQWFDT--SRTCPQCR 43

RING finger, H2 subclass, found in TRAF-interacting protein (TRAIP) and similar proteins; TRAIP, also known as RING finger protein 206 (RNF206) or TRIP, is a ubiquitously expressed nucleolar E3 ubiquitin ligase important for cellular proliferation and differentiation. It is found near mitotic chromosomes and functions as a regulator of the spindle assembly checkpoint. TRAIP interacts with tumor necrosis factor (TNF)-receptor-associated factor (TRAF) proteins and inhibits TNF-alpha-mediated nuclear factor (NF)-kappaB activation. It also interacts with two tumor suppressors CYLD and spleen tyrosine kinase (Syk), and DNA polymerase eta, which facilitates translesional synthesis after DNA damage. TRAIP contains an N-terminal C3H2C2-type RING-H2 finger and an extended coiled-coil domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 157823719   6 LCTICSDFFDHSRDVAAIHCGHTFHLQCLIQWFETapSRTCPQCR 50
Cdd:cd16480    1 YCTICSDFFDNSRDVAAIHCGHTFHYDCLLQWFDT--SRTCPQCR 43

Ring finger domain;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 157823719    7 CTICSDFFDHSRDVAAIHCGHTFHLQCLIQWFETapSRTCPQCR 50
Cdd:pfam13639   3 CPICLEEFEEGDKVVVLPCGHHFHRECLDKWLRS--SNTCPLCR 44

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 157823719     7 CTICSDFFdhSRDVAAIHCGHTFHLQCLIQWFETApSRTCPQC 49
Cdd:smart00184   1 CPICLEEY--LKDPVILPCGHTFCRSCIRKWLESG-NNTCPIC 40

RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719   79 LKNELDSIKAQLSQKD------REKRDSQA--------IIDTLRDTLEERNATVESLQNALNKA------EMLCSTLKKQ 138
Cdd:pfam10174 480 LKEKVSALQPELTEKEsslidlKEHASSLAssglkkdsKLKSLEIAVEQKKEECSKLENQLKKAhnaeeaVRTNPEINDR 559

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719  139 MKFLEQQ----RDETKHAQEEARQLKSKMKTMEQIELLLQSQRSEVEEMIRDMGVGQS-AVEQL-AVYCISLKKEYENLK 212
Cdd:pfam10174 560 IRLLEQEvaryKEESGKAQAEVERLLGILREVENEKNDKDKKIAELESLTLRQMKEQNkKVANIkHGQQEMKKKGAQLLE 639

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 157823719  213 EARKASGELADR-LRKDLASSRSKLKTVNTELDQAKLELRSAQKDLQSADKEITSLR 268
Cdd:pfam10174 640 EARRREDNLADNsQQLQLEELMGALEKTRQELDATKARLSSTQQSLAEKDGHLTNLR 696

Bacillus thuringiensis crystal 6Aa (Cry6Aa) toxin, and similar proteins; This model includes pesticidal Cry6Aa toxin from Bacillus thuringiensis, one of the many parasporal crystal (Cry) toxins produced during the sporulation phase of growth. Many of these proteins are toxic to numerous insect species and have been effectively used as proteinaceous insecticides to directly kill insect pests; some have been used to control insect growth on transgenic agricultural plants. Cry6Aa exists as a protoxin, which is activated by cleavage using trypsin. Structure studies for Cry6Aa support a mechanism of action by pore formation, similar to cytolysin A (ClyA)-type alpha pore-forming toxins (alpha-PFTs) such as HblB, and bioassay and mutation studies show that Cry6Aa is an active pore-forming toxin. Cry6Aa shows atypical features compared to other members of alpha-PFTs, including internal repeat sequences and small loop regions within major alpha helices.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719  79 LKNELDSIKAQLSQKDRE--KRDSQAIIDTLRDTLEERNATVESLQNALNKAEMLCSTLKKQMKFLEQQRDEtKHAQEEA 156
Cdd:cd22656   96 ILELIDDLADATDDEELEeaKKTIKALLDDLLKEAKKYQDKAAKVVDKLTDFENQTEKDQTALETLEKALKD-LLTDEGG 174

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719 157 RQLKSKMKTMEQielllqsqrsEVEEMIRDmgvgqsaveqlavYCISLKKEYENLKEA-RKASGELAD--RLRKDLASSR 233
Cdd:cd22656  175 AIARKEIKDLQK----------ELEKLNEE-------------YAAKLKAKIDELKALiADDEAKLAAalRLIADLTAAD 231

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 157823719 234 SKLKTVNTELDQAKLELRSAQKDLQSADKEITSLRKKLTILQGTLSLPPVTSETVSRLV 292
Cdd:cd22656  232 TDLDNLLALIGPAIPALEKLQGAWQAIATDLDSLKDLLEDDISKIPAAILAKLELEKAI 290

RING finger, H2 subclass, found in TRAF-interacting protein (TRAIP) and similar proteins; TRAIP, also known as RING finger protein 206 (RNF206) or TRIP, is a ubiquitously expressed nucleolar E3 ubiquitin ligase important for cellular proliferation and differentiation. It is found near mitotic chromosomes and functions as a regulator of the spindle assembly checkpoint. TRAIP interacts with tumor necrosis factor (TNF)-receptor-associated factor (TRAF) proteins and inhibits TNF-alpha-mediated nuclear factor (NF)-kappaB activation. It also interacts with two tumor suppressors CYLD and spleen tyrosine kinase (Syk), and DNA polymerase eta, which facilitates translesional synthesis after DNA damage. TRAIP contains an N-terminal C3H2C2-type RING-H2 finger and an extended coiled-coil domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 157823719   6 LCTICSDFFDHSRDVAAIHCGHTFHLQCLIQWFETapSRTCPQCR 50
Cdd:cd16480    1 YCTICSDFFDNSRDVAAIHCGHTFHYDCLLQWFDT--SRTCPQCR 43

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

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 157823719   7 CTICSDFFDHSRDVAAIHCGHTFHLQCLIQWFETaPSRTCPQCR 50
Cdd:cd16448    1 CVICLEEFEEGDVVRLLPCGHVFHLACILRWLES-GNNTCPLCR 43

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719    72 SVLDAEFLKNELDSIKAQLSQK-------DREKRDSQAIIDTLRDTLEERNATVESLQNALNKAEMLCSTLKKQMKFLEQ 144
Cdd:TIGR02168  230 LVLRLEELREELEELQEELKEAeeeleelTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRE 309

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719   145 QRD----ETKHAQEEARQLKSKMKTMEQIELLLQSQRSEVEEMIrdmgvgQSAVEQLAvyciSLKKEYENLKEARKASGE 220
Cdd:TIGR02168  310 RLAnlerQLEELEAQLEELESKLDELAEELAELEEKLEELKEEL------ESLEAELE----ELEAELEELESRLEELEE 379

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 157823719   221 LADRLRKDLASSRSKLKTVNTELDQAKLELRSAQKDLQSADKEITSLRKKLTILQ 275
Cdd:TIGR02168  380 QLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQEIEELLKKLEEAE 434

RING finger, H2 subclass, found in Tetratricopeptide repeat protein 3 (TTC3) and similar proteins; TTC3, also known as protein DCRR1, TPR repeat protein D, TPR repeat protein 3, or RING finger protein 105 (RNF105), is an E3 ubiquitin-protein ligase encoded by a gene within the Down syndrome (DS) critical region on chromosome 21. It affects differentiation and Golgi compactness in neurons through specific actin-regulating pathways. It inhibits the neuronal-like differentiation of pheocromocytoma cells by activating RhoA and by binding to Citron proteins. TTC3 is an Akt-specific E3 ligase that binds to phosphorylated Akt and facilitates its ubiquitination and degradation within the nucleus. It contains four N-terminal TPR motifs, a potential coiled-coil region and a Citron binding region in the central part, and a C-terminal C3H2C2-type RING-H2 finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 157823719   6 LCTICSDFFdHSRDVAAIHCGHTFHLQCLIQWFETapSRTCPQCRIQV 53
Cdd:cd16481    1 PCIICHDDL-KPDQLAKLECGHIFHKECIKQWLKE--QSTCPTCRVHV 45

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719  67 AQEEESVLDAEF--LKNELDSIKAQLSQKDREKRDSQAIIDTLRDTLEERNATVESLQNALNKAEMLCSTLKKQMKFLEQ 144
Cdd:COG1196  258 LEAELAELEAELeeLRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAELEEELEELEE 337

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719 145 QRDETKHAQEEAR-QLKSKMKTMEQIELLLQSQRSEVEEMIRDMGVGQSAVEQLAVYCISLKKEYENLKEARKASGELAD 223
Cdd:COG1196  338 ELEELEEELEEAEeELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLE 417

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 157823719 224 RLRKDLASSRSKLKTVNTELDQAKLELRSAQKDLQSADKEITSLRKKLTILQ 275
Cdd:COG1196  418 RLEEELEELEEALAELEEEEEEEEEALEEAAEEEAELEEEEEALLELLAELL 469

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 157823719     7 CTICSDFFdhSRDVAAIHCGHTFHLQCLIQWFETApSRTCPQC 49
Cdd:smart00184   1 CPICLEEY--LKDPVILPCGHTFCRSCIRKWLESG-NNTCPIC 40

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719    55 KKTIINKLFFDLAQE------EESVLDA--EFLKNELDSIKAQLSQKDREKRDSQAIIDTLRDTLEERNATVESLQNALN 126
Cdd:TIGR02168  282 EIEELQKELYALANEisrleqQKQILRErlANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELE 361

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719   127 KAEmlcstlkKQMKFLEQQRDEtkhAQEEARQLKSKMKTMEQIELLLQSQRSEVEEMIRDMgvgQSAVEQLAVYCISLKK 206
Cdd:TIGR02168  362 ELE-------AELEELESRLEE---LEEQLETLRSKVAQLELQIASLNNEIERLEARLERL---EDRRERLQQEIEELLK 428

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157823719   207 EYENlKEARKASGELADrLRKDLASSRSKLKTVNTELDQAKLELRSAQKDLQSADKEITSLRKKLTILQ 275
Cdd:TIGR02168  429 KLEE-AELKELQAELEE-LEEELEELQEELERLEEALEELREELEEAEQALDAAERELAQLQARLDSLE 495

RING finger, H2 subclass, found in DAZ (deleted in azoospermia)-interacting protein 3 (DZIP3) and similar proteins; DZIP3, also known as RNA-binding ubiquitin ligase of 138 kDa (RUL138) or 2A-HUB protein, is an RNA-binding E3 ubiquitin-protein ligase that interacts with coactivator-associated arginine methyltransferase 1 (CARM1) and acts as a transcriptional coactivator of estrogen receptor (ER) alpha. It is also a histone H2A ubiquitin ligase that catalyzes monoubiquitination of H2A at lysine 119, functioning as a combinatorial component of the repression machinery required for repressing a specific chemokine gene expression program, critically modulating migratory responses to Toll-like receptors (TLR) activation. DZIP3 contains a C3H2C3-type RING-H2 finger at the C-terminus.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 157823719   6 LCTICSDFFDHSRDVAAIHCGHTFHLQCLIQWFETapSRTCPQCRIQV 53
Cdd:cd16460    2 PCVICHEAFSDGDRLLVLPCAHKFHTQCIGPWLDG--QQTCPTCRLHV 47

RING finger, H2 subclass, found in RING finger proteins RNF111, RNF165, and similar proteins; The family includes RING finger proteins RNF111, RNF165, and similar proteins. RNF111, also known as Arkadia, is a nuclear E3 ubiquitin-protein ligase that targets intracellular effectors and modulators of transforming growth factor beta (TGF-beta)/Nodal-related signaling for polyubiquitination and proteasome-dependent degradation. It also interacts with the clathrin-adaptor 2 (AP2) complex and regulates endocytosis of certain cell surface receptors, leading to modulation of epidermal growth factor (EGF) and possibly other signaling pathways. The N-terminal half of RNF111 harbors three SUMO-interacting motifs (SIMs). It thus functions as a SUMO-targeted ubiquitin ligase (STUbL) that directly links nonproteolytic ubiquitylation and SUMOylation in the DNA damage response, as well as triggers degradation of signal-induced polysumoylated proteins, such as the promyelocytic leukemia protein (PML). RNF165, also known as Arkadia-like 2, Arkadia2, or Ark2C, is an E3 ubiquitin ligase with homology to the C-terminal half of RNF111. It is expressed specifically in the nervous system, and can serve to amplify neuronal responses to specific signals. It acts as a positive regulator of bone morphogenetic protein (BMP)-Smad signaling that is involved in motor neuron (MN) axon elongation. Both RNF165 and RNF111 contain a C-terminal C3H2C3-type RING-H2 finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 157823719   7 CTICSDFFDHSRDVAAIHCGHTFHLQCLIQWFETapSRTCPQCRI 51
Cdd:cd16474    3 CTICLSDFEEGEDVRRLPCMHLFHQECVDQWLST--NKRCPICRV 45

RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and TRIM27, and similar proteins; TRIM7, TRIM11 and TRIM27, closely related tripartite motif-containing proteins, belong 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, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM7, also known as glycogenin-interacting protein (GNIP) or RING finger protein 90 (RNF90), is an E3 ubiquitin-protein ligase that mediates c-Jun/AP-1 activation by Ras signalling. Its phosphorylation and activation by MSK1 in response to direct activation by the Ras-Raf-MEK-ERK pathway can stimulate TRIM7 E3 ubiquitin ligase activity in mediating Lys63-linked ubiquitination of the AP-1 coactivator RACO-1, leading to RACO-1 protein stabilization. Moreover, TRIM7 binds and activates glycogenin, the self-glucosylating initiator of glycogen biosynthesis. TRIM11, also known as protein BIA1, or RING finger protein 92 (RNF92), is an E3 ubiquitin-protein ligase involved in the development of the central nervous system. It is overexpressed in high-grade gliomas and promotes proliferation, invasion, migration and glial tumor growth. TRIM11 acts as a potential therapeutic target for congenital central hypoventilation syndrome (CCHS) by mediating the degradation of CCHS-associated polyalanine-expanded Phox2b. TRIM11 modulates the function of neurogenic transcription factor Pax6 through the ubiquitin-proteosome system, and thus plays an essential role for Pax6-dependent neurogenesis. It also binds to and destabilizes a key component of the activator-mediated cofactor complex (ARC105), humanin, a neuroprotective peptide against Alzheimer's disease-relevant insults, and further regulates ARC105 function in transforming growth factor beta (TGFbeta) signaling. Moreover, TRIM11 negatively regulates retinoic acid-inducible gene-I (RIG-I)-mediated interferon-beta (IFNbeta) production and antiviral activity by targeting TANK-binding kinase-1 (TBK1). It may contribute to the endogenous restriction of retroviruses in cells. It enhances N-tropic murine leukemia virus (N-MLV) entry by interfering with Ref1 restriction. It also suppresses the early steps of human immunodeficiency virus HIV-1 transduction, resulting in decreased reverse transcripts. TRIM27, also known as RING finger protein 76 (RNF76), RET finger protein (RFP), or zinc finger protein RFP, is a nuclear E3 ubiquitin-protein ligase that is highly expressed in testis and in various tumor cell lines. Expression of TRIM27 is associated with prognosis of colon and endometrial cancers. TRIM27 was first identified as a fusion partner of the RET receptor tyrosine kinase. It functions as a transcriptional repressor and associates with several proteins involved in transcriptional activity, such as enhancer of polycomb 1 (Epc1), a member of the Polycomb group proteins, and Mi-2beta, a main component of the nucleosome remodeling and deacetylase (NuRD) complex, and the cell cycle regulator retinoblastoma protein (RB1). It also interacts with HDAC1, leading to downregulation of thioredoxin binding protein 2 (TBP-2), which inhibits the function of thioredoxin. Moreover, TRIM27 mediates Pax7-induced ubiquitination of MyoD in skeletal muscle atrophy. In addition, it inhibits muscle differentiation by modulating serum response factor (SRF) and Epc1. TRIM27 promotes a non-canonical polyubiquitination of PTEN, a lipid phosphatase that catalyzes PtdIns(3,4,5)P3 (PIP3) to PtdIns(4,5)P2 (PIP2). It is an IKKepsilon-interacting protein that regulates IkappaB kinase (IKK) function and negatively regulates signaling involved in the antiviral response and inflammation. TRIM27 also forms a protein complex with MBD4 or MBD2 or MBD3, and thus plays an important role in the enhancement of transcriptional repression through MBD proteins in tumorigenesis, spermatogenesis, and embryogenesis. It is a component of an estrogen receptor 1 (ESR1) regulatory complex that is involved in estrogen receptor-mediated transcription in MCF-7 cells.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 157823719   7 CTICSDFFdhsRDVAAIHCGHTFHLQCLIQ-WFETAPSRTCPQCRIQVGKK 56
Cdd:cd16594    8 CPICLDYF---TDPVTLDCGHSFCRACIARcWEEPETSASCPQCRETCPQR 55

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719  79 LKNELDSIKAQLSQKDREKRDSQAIIDTLRDTLEERNATVESLQNALNKAEmlcstlkkqmKFLEQQRDETKhaqEEARQ 158
Cdd:COG3883   28 LQAELEAAQAELDALQAELEELNEEYNELQAELEALQAEIDKLQAEIAEAE----------AEIEERREELG---ERARA 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719 159 LKSKMKTMEQIELLLQSQrsEVEEMIRDMGVGQSAVEQLAVYCISLKKEYENLKEARKASGELADRLRKDLASSRSKLKT 238
Cdd:COG3883   95 LYRSGGSVSYLDVLLGSE--SFSDFLDRLSALSKIADADADLLEELKADKAELEAKKAELEAKLAELEALKAELEAAKAE 172

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157823719 239 VNTELDQAKLELRSAQKDLQSADKEITSLRKKLTILQGTLSLPPVTSETVSRLVFESPAPVE 300
Cdd:COG3883  173 LEAQQAEQEALLAQLSAEEAAAEAQLAELEAELAAAEAAAAAAAAAAAAAAAAAAAAAAAAA 234

RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar proteins; TRIM69, also known as RFP-like domain-containing protein trimless or RING finger protein 36 (RNF36), is a testis E3 ubiquitin-protein ligase that plays a specific role in apoptosis and may also play an important role in germ cell homeostasis during spermatogenesis. TRIM69 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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 157823719   7 CTICSDFFdhsRDVAAIHCGHTFHLQCLIQWFET-APSRTCPQCR 50
Cdd:cd16611    7 CPLCLDFF---RDPVMLSCGHNFCQSCITGFWELqAEDTTCPECR 48

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719   89 QLSQKDREKRDSQAIIDTLRDTLE--ERNATVESLQNALNKAEMLCSTLKKQMKFLEQQRDEtkhAQEEARQLKSKM--- 163
Cdd:COG4913   259 ELAERYAAARERLAELEYLRAALRlwFAQRRLELLEAELEELRAELARLEAELERLEARLDA---LREELDELEAQIrgn 335

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719  164 --KTMEQIELLLQSQRSEVEEMIRdmgvgqsAVEQLAVYCISLKkeyENLKEARKASGELADRLRKDLASSRSKLKTVNT 241
Cdd:COG4913   336 ggDRLEQLEREIERLERELEERER-------RRARLEALLAALG---LPLPASAEEFAALRAEAAALLEALEEELEALEE 405

                         170       180
                  ....*....|....*....|....*....
gi 157823719  242 ELDQAKLELRSAQKDLQSADKEITSLRKK 270
Cdd:COG4913   406 ALAEAEAALRDLRRELRELEAEIASLERR 434

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719   79 LKNELDSIKAQLSQKDREKRDSQAIIDTLRDTLEERNATVESLQNalNKAEMLCSTLKKQMKFLEQQRDETKHAQEEARQ 158
Cdd:TIGR04523 258 LKDEQNKIKKQLSEKQKELEQNNKKIKELEKQLNQLKSEISDLNN--QKEQDWNKELKSELKNQEKKLEEIQNQISQNNK 335

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719  159 LKSKMK-TMEQIELLLQSQRSEVEEMIRDMGVGQSAVEQLAVYCISLKKEYENLKEArkasgeladrlRKDLASSRSKLK 237
Cdd:TIGR04523 336 IISQLNeQISQLKKELTNSESENSEKQRELEEKQNEIEKLKKENQSYKQEIKNLESQ-----------INDLESKIQNQE 404

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 157823719  238 TVNTELDQaklELRSAQKDLQSADKEITSLRKKLTILQGTLS 279
Cdd:TIGR04523 405 KLNQQKDE---QIKKLQQEKELLEKEIERLKETIIKNNSEIK 443

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719    67 AQEEESVLDAEFLKNELDSIKAQLSQKDREKRDSQAIIDTLRDTLEERNATVESLQNALNKAEmlcSTLKKQMKFLEQQR 146
Cdd:TIGR02169  756 VKSELKELEARIEELEEDLHKLEEALNDLEARLSHSRIPEIQAELSKLEEEVSRIEARLREIE---QKLNRLTLEKEYLE 832

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719   147 DETKHAQEEARQLKSKMKTMEQIELLLQSQRSEVEEMIRDMgvgQSAVEQLAVYCISLKKEYENLK----EARKASGELA 222
Cdd:TIGR02169  833 KEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEEL---EAALRDLESRLGDLKKERDELEaqlrELERKIEELE 909

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 157823719   223 ---DRLRKDLASSRSKLKTVNTELDqaklELRSAQKDLQSADKEITSLRK 269
Cdd:TIGR02169  910 aqiEKKRKRLSELKAKLEALEEELS----EIEDPKGEDEEIPEEELSLED 955

RING finger, H2 subclass, found in Saccharomyces cerevisiae alcohol-sensitive RING finger protein 1 (ASR1) and similar proteins; ASR1 is required for tolerance to alcohol. It signals alcohol stress to the nucleus. ASR1 contains a C3H2C3-type RING-H2 finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 157823719   7 CTICSDFfDHSRDVAAIHCGHTFHLQCLIQWFETAPSRTCPQCRIQ 52
Cdd:cd23120    4 CPICLEE-MNSGTGYLADCGHEFHLTCIREWHNKSGNLDCPICRVE 48

DNA double-strand break repair Rad50 ATPase;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719  59 INKLFFDLAQEEESVLDAEFLKNELDSIKAQLSQKDR--EKR-DSQAIIDTLRDTLEERNATVESLQNalNKAEmlcstL 135
Cdd:PRK02224 477 VEELEAELEDLEEEVEEVEERLERAEDLVEAEDRIERleERReDLEELIAERRETIEEKRERAEELRE--RAAE-----L 549

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719 136 KKQMkflEQQRDETKHAQEEARQLKSKMKTMEQielllqsQRSEVEEMIRDMGVGQSAVEQLAVYcislKKEYENLKEAR 215
Cdd:PRK02224 550 EAEA---EEKREAAAEAEEEAEEAREEVAELNS-------KLAELKERIESLERIRTLLAAIADA----EDEIERLREKR 615

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 157823719 216 KASGELADRLRKDLASSRSKLKTVNTELDQAKLELRSAQKD-----LQSADKEITSLRKKLTILQGTL 278
Cdd:PRK02224 616 EALAELNDERRERLAEKRERKRELEAEFDEARIEEAREDKEraeeyLEQVEEKLDELREERDDLQAEI 683

chromosome segregation protein; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719  73 VLDAEFLKNELDSIKAQLSQKDREKRDSQAIidtLRDTLEERNATVESLQNALNKAEMLCSTLKKqmkfLEQQRDETKHA 152
Cdd:PRK01156 182 ISNIDYLEEKLKSSNLELENIKKQIADDEKS---HSITLKEIERLSIEYNNAMDDYNNLKSALNE----LSSLEDMKNRY 254

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719 153 QEEARQLKSKMKTMEQIELLLQSQRSEVEEMIRDMGVGQSavEQLAVYcISLKKEYENLKE------ARKASGELADRLR 226
Cdd:PRK01156 255 ESEIKTAESDLSMELEKNNYYKELEERHMKIINDPVYKNR--NYINDY-FKYKNDIENKKQilsnidAEINKYHAIIKKL 331

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 157823719 227 KDLASSRS---KLKTVNTELDQAKLELRSAQKDLQSADKEITSLRKKL 271
Cdd:PRK01156 332 SVLQKDYNdyiKKKSRYDDLNNQILELEGYEMDYNSYLKSIESLKKKI 379

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

                          10        20
                  ....*....|....*....|....*.
gi 157823719   25 CGHTFHLQCLIQWFETapSRTCPQCR 50
Cdd:pfam12678  32 CGHAFHLHCISRWLKT--NNTCPLCR 55

RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar proteins; TRIM77 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 two consecutive zinc-binding domains, a C3HC4-type RING-HC finger and Bbox2, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 157823719   7 CTICSDFFdhsRDVAAIHCGHTFHLQCLIQ-WFETAPSRTCPQCR 50
Cdd:cd16543    6 CSICLDLL---KDPVTIPCGHSFCMNCITLlWDRKQGVPSCPQCR 47

RING finger, HC subclass, found in bifunctional apoptosis regulator (BAR); BAR, also known as RING finger protein 47, was originally identified as an inhibitor of Bax-induced apoptosis. It participates in the block of apoptosis induced by TNF-family death receptors (extrinsic pathway) and mitochondria-dependent apoptosis (intrinsic pathway). BAR is predominantly expressed by neurons in the central nervous system and is involved in the regulation of neuronal survival. It is an endoplasmic reticulum (ER)-associated RING-type E3 ubiquitin ligase that interacts with BI-1 protein and post-translationally regulates its stability, as well as functioning in ER stress. BAR contains an N-terminal C3HC4-type RING-HC finger, a SAM domain, a coiled-coil domain, and a C-terminal transmembrane (TM) domain. This model corresponds to the RING-HC finger responsible for the binding of ubiquitin conjugating enzymes (E2s).

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 157823719   6 LCTICsdfFDHSRDVAAIHCGHTFHLQCLIQWFETAPSRTCPQCR 50
Cdd:cd16497    3 LCHCC---YDLLVNPTTLNCGHSFCRHCLALWWKSSKKTECPECR 44

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

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 157823719   7 CTICSDFFDHSRDvaAIHCGHTFHLQCLIQWFETapSRTCPQCR 50
Cdd:cd16479    4 CIICREEMTVGAK--KLPCGHIFHLSCLRSWLQR--QQTCPTCR 43

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719  76 AEFLKNELDSIKAQLSQKDREKRD--SQAIIDTLRDTLEERNATVESLQNALNKAEMLCSTLKKQMKFLEQQRDETKHAQ 153
Cdd:COG3206  177 LEFLEEQLPELRKELEEAEAALEEfrQKNGLVDLSEEAKLLLQQLSELESQLAEARAELAEAEARLAALRAQLGSGPDAL 256

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157823719 154 EEARQLKSKMKTMEQiellLQSQRSEVEEMIRDMGVGQSAVeqlavycISLKKEYENLKEA-RKASGELADRLRKDLASS 232
Cdd:COG3206  257 PELLQSPVIQQLRAQ----LAELEAELAELSARYTPNHPDV-------IALRAQIAALRAQlQQEAQRILASLEAELEAL 325

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 157823719 233 RSKLKTVNTELDQakleLRSAQKDLQSADKEITSLRKKLTILQGTL 278
Cdd:COG3206  326 QAREASLQAQLAQ----LEARLAELPELEAELRRLEREVEVARELY 367