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 148689291   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 148689291   6 LCTICSDFFDHSRDVAAIHCGHTFHLQCLIQWFETapSRTCPQCR 50
Cdd:cd16480    1 YCTICSDFFDNSRDVAAIHCGHTFHYDCLLQWFDT--SRTCPQCR 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 148689291    73 VLDAEFLKNELDSVKAQLSQK-------DREKRDSQAIIDTLRDTLEERNATVESLQNALNKAEMLCSTLKKQMKFLEQR 145
Cdd:TIGR02168  231 VLRLEELREELEELQEELKEAeeeleelTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRER 310

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291   146 --QDETKQAREEAHRLKCKMKTMEQIELLLQSQrsevEEMIRDMGVGQSAVEQLAvycvSLKKEYENLKEARKATGELAD 223
Cdd:TIGR02168  311 laNLERQLEELEAQLEELESKLDELAEELAELE----EKLEELKEELESLEAELE----ELEAELEELESRLEELEEQLE 382

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 148689291   224 RLKKDLVSSRSKLKTLNTELDQAKLELRSAQKDLQSADQEITSLRKKL 271
Cdd:TIGR02168  383 TLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQEIEELLKKL 430

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 148689291     7 CTICSDFFdhSRDVAAIHCGHTFHLQCLIQWFETApSRTCPQC 49
Cdd:smart00184   1 CPICLEEY--LKDPVILPCGHTFCRSCIRKWLESG-NNTCPIC 40

Coiled-coil domain-containing protein 158; CCDC158 is a family of proteins found in eukaryotes. The function is not known.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291    70 EENVLDAEFLKNELDSVKAQLSQKDRE-KRDSQAIIDTLRDTLEERNATVESLQ----NALNKAEMLCSTLKKQMKFLEQ 144
Cdd:pfam15921  624 EARVSDLELEKVKLVNAGSERLRAVKDiKQERDQLLNEVKTSRNELNSLSEDYEvlkrNFRNKSEEMETTTNKLKMQLKS 703

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291   145 RQDETKQARE--------EAHRLKCKMKTMEQIelllQSQRSEVEEMirdmgvgQSAVEQLAVYCVSLKKEYENLKEAR- 215
Cdd:pfam15921  704 AQSELEQTRNtlksmegsDGHAMKVAMGMQKQI----TAKRGQIDAL-------QSKIQFLEEAMTNANKEKHFLKEEKn 772

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291   216 KATGELA------DRLKKDLVSSRS-----KLKTLNTE--LDQAKLELRSAQKDLQSADQEitSLRKKlmiLQGTLSlpp 282
Cdd:pfam15921  773 KLSQELStvatekNKMAGELEVLRSqerrlKEKVANMEvaLDKASLQFAECQDIIQRQEQE--SVRLK---LQHTLD--- 844

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291   283 atnetVSRLVFESPAPVEMMNPRLHQPPfgdeidLNTTFDVNTPPTQTSG---SQHCLPKKLCLERARSPMQNVLKKVHK 359
Cdd:pfam15921  845 -----VKELQGPGYTSNSSMKPRLLQPA------SFTRTHSNVPSSQSTAsflSHHSRKTNALKEDPTRDLKQLLQELRS 913

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|.
gi 148689291   360 VSKPESQLSLGGQRCVGELDEelAGAFPLFIRNAVLGQKQPNRTTAESRCS 410
Cdd:pfam15921  914 VINEEPTVQLSKAEDKGRAPS--LGALDDRVRDCIIESSLRSDICHSSSNS 962

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 148689291   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 148689291   7 CTICSDFFDHSRDVAAIHCGHTFHLQCLIQWFETaPSRTCPQCR 50
Cdd:cd16448    1 CVICLEEFEEGDVVRLLPCGHVFHLACILRWLES-GNNTCPLCR 43

Ring finger domain;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 148689291    7 CTICSDFFDHSRDVAAIHCGHTFHLQCLIQWFETapSRTCPQCR 50
Cdd:pfam13639   3 CPICLEEFEEGDKVVVLPCGHHFHRECLDKWLRS--SNTCPLCR 44

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 148689291   6 LCTICSDFFdHSRDVAAIHCGHTFHLQCLIQWFETapSRTCPQCRIQV 53
Cdd:cd16481    1 PCIICHDDL-KPDQLAKLECGHIFHKECIKQWLKE--QSTCPTCRVHV 45

RING finger, H2 subclass, found in the PA-TM-RING ubiquitin ligase family; The PA-TM-RING family represents a group of transmembrane-type E3 ubiquitin ligases, which has been characterized by an N-terminal transient signal peptide, a PA (protease-associated) domain, a TM (transmembrane) domain, as well as a C-terminal C3H2C3-type RING-H2 finger domain. It includes RNF13, RNF167, ZNRF4 (zinc and RING finger 4), GRAIL (gene related to anergy in lymphocytes)/RNF128, RNF130, RNF133, RNF148, RNF149 and RNF150 (which are more closely related), as well as RNF43 and ZNRF3, which have substantially longer C-terminal tail extensions compared with the others. PA-TM-RING proteins are expressed at low levels in all mammalian tissues and species, but they are not present in yeast. They play a common regulatory role in intracellular trafficking/sorting, suggesting that abrogation of their function may result in dysregulation of cellular signaling events in cancer.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 148689291   7 CTICSDFFDHSRDVAAIHCGHTFHLQCLIQWFETapSRTCPQCR 50
Cdd:cd16454    2 CAICLEEFKEGEKVRVLPCNHLFHKDCIDPWLEQ--HNTCPLCR 43

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 148689291   6 LCTICSDFFDHSRDVAAIHCGHTFHLQCLIQWFETapSRTCPQCRIQV 53
Cdd:cd16460    2 PCVICHEAFSDGDRLLVLPCAHKFHTQCIGPWLDG--QQTCPTCRLHV 47

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 148689291   7 CTICSDFFdhSRDVAAIHCGHTFHLQCLIQWFETApSRTCPQCRIQV 53
Cdd:cd16503    5 CSICQDLL--HDCVSLQPCMHNFCAACYSDWMERS-NTECPTCRATV 48

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 148689291   7 CTICSDFFdhsRDVAAIHCGHTFHLQCLIQ-WFETAPSRTCPQCRIQVGKK 56
Cdd:cd16594    8 CPICLDYF---TDPVTLDCGHSFCRACIARcWEEPETSASCPQCRETCPQR 55

RING finger, HC subclass, found in RING finger protein 5 (RNF5) and similar proteins; RNF5, also known as protein G16 or Ram1, is an E3 ubiquitin-protein ligase anchored to the outer membrane of the endoplasmic reticulum (ER). It acts at early stages of cystic fibrosis (CF) transmembrane conductance regulator (CFTR) biosynthesis and functions as a target for therapeutic modalities to antagonize mutant CFTR proteins in CF patients carrying the F508del allele. It also regulates the turnover of specific G protein-coupled receptors by ubiquitinating JNK-associated membrane protein (JAMP) and preventing proteasome recruitment. RNF5 limits basal levels of autophagy and influences susceptibility to bacterial infection through the regulation of ATG4B stability. It is also involved in the degradation of Pendrin, a transmembrane chloride/anion exchanger highly expressed in thyroid, kidney, and inner ear. RNF5 plays an important role in cell adhesion and migration. It can modulate cell migration by ubiquitinating paxillin. Furthermore, RNF5 interacts with virus-induced signaling adaptor (VISA) at mitochondria in a viral infection-dependent manner, and further targets VISA at K362 and K461 for K48-linked ubiquitination and degradation after viral infection. It also negatively regulates virus-triggered signaling by targeting MITA, also known as STING, for ubiquitination and degradation at the mitochondria. In addition, RNF5 determines breast cancer response to ER stress-inducing chemotherapies through the regulation of the L-glutamine carrier proteins SLC1A5 and SLC38A2 (SLC1A5/38A2). It also has been implicated in muscle organization and in recognition and processing of misfolded proteins. RNF5 contains a C3HC4-type RING-HC finger.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 148689291   7 CTICsdfFDHSRDVAAIHCGHTFHLQCLIQWFETAPSR-TCPQCRIQVGKKTII 59
Cdd:cd16743    3 CNIC---LETARDAVVSLCGHLFCWPCLHQWLETRPERqECPVCKAGISRDKVI 53

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 148689291   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 148689291   89 QLSQKDREKRDSQAIIDTLRDTLE--ERNATVESLQNALNKAEMLCSTLKKQMKFLEQRQDETKQAREEAH--RLKCKMK 164
Cdd:COG4913   259 ELAERYAAARERLAELEYLRAALRlwFAQRRLELLEAELEELRAELARLEAELERLEARLDALREELDELEaqIRGNGGD 338

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291  165 TMEQIELLLQSQRSEVEEMIRDMGVGQSAVEQLAVycvSLKKEYENLKEARKATGELADRLKkdlvssrSKLKTLNTELD 244
Cdd:COG4913   339 RLEQLEREIERLERELEERERRRARLEALLAALGL---PLPASAEEFAALRAEAAALLEALE-------EELEALEEALA 408

                         170       180
                  ....*....|....*....|....*.
gi 148689291  245 QAKLELRSAQKDLQSADQEITSLRKK 270
Cdd:COG4913   409 EAEAALRDLRRELRELEAEIASLERR 434

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291  67 AQEEENVLDAEFLKNELDSVKAQLSQKDREKRDSQAIIDTLRDTLEERNATVESLQNALNKAEmlcSTLKKQMKFLeQRQ 146
Cdd:COG3883   23 KELSELQAELEAAQAELDALQAELEELNEEYNELQAELEALQAEIDKLQAEIAEAEAEIEERR---EELGERARAL-YRS 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291 147 DetkqareeahrlkckmKTMEQIELLLQSQrsEVEEMIRDMGV-------GQSAVEQLAvycvSLKKEYENLKEARKATG 219
Cdd:COG3883   99 G----------------GSVSYLDVLLGSE--SFSDFLDRLSAlskiadaDADLLEELK----ADKAELEAKKAELEAKL 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291 220 ELADRLKKDLvssRSKLKTLNTELDQAKLELRSAQKDLQSADQEITSLRKKLMILQGTLSLPPATNETVSRLVFESPAPV 299
Cdd:COG3883  157 AELEALKAEL---EAAKAELEAQQAEQEALLAQLSAEEAAAEAQLAELEAELAAAEAAAAAAAAAAAAAAAAAAAAAAAA 233

                 .
gi 148689291 300 E 300
Cdd:COG3883  234 A 234

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291  68 QEEENVLD----AEFLKNELDSVKAQLSQKDREKRDSQAIIDTLRDTLEERNATVESLQNALNKAEmlcstLKKQMKFLE 143
Cdd:COG3206  202 RQKNGLVDlseeAKLLLQQLSELESQLAEARAELAEAEARLAALRAQLGSGPDALPELLQSPVIQQ-----LRAQLAELE 276

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291 144 QRQDETKQAREEAHRlkcKMKTM-EQIELLLQSQRSEVEEMIRDMgvgQSAVEQLAVYCVSLKKEYENLKEARKATGELA 222
Cdd:COG3206  277 AELAELSARYTPNHP---DVIALrAQIAALRAQLQQEAQRILASL---EAELEALQAREASLQAQLAQLEARLAELPELE 350

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 148689291 223 D---RLKKDLVSSRSKLKTLNTELDQAKLELRSAQKDLQ-----SADQEITSLRKKLMILQGTL 278
Cdd:COG3206  351 AelrRLEREVEVARELYESLLQRLEEARLAEALTVGNVRvidpaVVPLKPVSPKKLLILALGLL 414

DNA double-strand break repair Rad50 ATPase;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291  50 RIQVGKKTIINKLFFDLAQEEENVLDAEF--LKNELDSVKAQLSQKDREKRDSQAIIDTLRDTL---EERNATVESLQNA 124
Cdd:PRK02224 180 RVLSDQRGSLDQLKAQIEEKEEKDLHERLngLESELAELDEEIERYEEQREQARETRDEADEVLeehEERREELETLEAE 259

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291 125 LNKAEM-----------LCSTLKKQMKFLEQRQDETKQAREEAHRLKCKMKTMEQIELLLQSQRSEVEEMIRDMGVGQSA 193
Cdd:PRK02224 260 IEDLREtiaeterereeLAEEVRDLRERLEELEEERDDLLAEAGLDDADAEAVEARREELEDRDEELRDRLEECRVAAQA 339

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 148689291 194 veqlavycvsLKKEYENLKEARKATGELADRLkkdlvssRSKLKTLNTELDQAKLELRSAQKDLQSADQEITSLRKKL 271
Cdd:PRK02224 340 ----------HNEEAESLREDADDLEERAEEL-------REEAAELESELEEAREAVEDRREEIEELEEEIEELRERF 400

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 148689291    75 DAEFLKNELDSVKAQLSQKDREKRDSQAIIDTLRDTLEERNATVESLQNALNKAEM------------LCSTLKKQMKFL 142
Cdd:TIGR02169  731 EEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEArlshsripeiqaELSKLEEEVSRI 810

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291   143 EQRQDETKQAREEAHRLKC----KMKTMEQIELLLQSQRSEVEEMIRDMGVG-----------QSAVEQLAVYCVSLKKE 207
Cdd:TIGR02169  811 EARLREIEQKLNRLTLEKEylekEIQELQEQRIDLKEQIKSIEKEIENLNGKkeeleeeleelEAALRDLESRLGDLKKE 890

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291   208 YenlkearkatgelaDRLKKDLVSSRSKLKTLNTELDQAKLELRSAQKDLQSADQEITSL 267
Cdd:TIGR02169  891 R--------------DELEAQLRELERKIEELEAQIEKKRKRLSELKAKLEALEEELSEI 936

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

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 148689291   7 CTIC-SDFFDHSRDVAAIHCGHTFHLQCLIQWFETAPSrTCPQCR 50
Cdd:cd23121    4 CAIClSDFNSDEKLRQLPKCGHIFHHHCLDRWIRYNKI-TCPLCR 47

Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins; RFWD3, also known as RING finger protein 201 (RNF201) or FLJ10520, is an E3 ubiquitin-protein ligase that forms a complex with Mdm2 and p53 to synergistically ubiquitinate p53 and acts as a positive regulator of p53 stability in response to DNA damage. It is phosphorylated by checkpoint kinase ATM/ATR and the phosphorylation mutant fails to stimulate p53 ubiquitination. RFWD3 also functions as a novel replication protein A (RPA)-associated protein involved in DNA replication checkpoint control. RFWD3 contains an N-terminal SQ-rich region followed by a RING finger domain that exhibits robust E3 ubiquitin ligase activity toward p53, a coiled-coil domain and three WD40 repeats in the C-terminus, the latter two of which may be responsible for protein-protein interaction. The RING finger in this family is a modified C3HGC3-type RING finger, but not a canonical C3H2C3-type RING-H2 finger or C3HC4-type RING-HC finger.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 148689291   7 CTICSDFFDHSRD--VAAIHCGHTFHLQCLIQWFETApSRTCPQCRIQVGKKTIIN 60
Cdd:cd16450    5 CPICFEPWTSSGEhrLVSLKCGHLFGYSCIEKWLKGK-GKKCPQCNKKAKRSDIRP 59

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 148689291   25 CGHTFHLQCLIQWFETapSRTCPQCR 50
Cdd:pfam12678  32 CGHAFHLHCISRWLKT--NNTCPLCR 55

RING finger, H2 subclass, found in RING finger proteins RNF24, RNF122, and similar proteins; This subfamily includes RNF24, RNF122, and similar proteins. RNF24 is an intrinsic membrane protein localized in the Golgi apparatus. It specifically interacts with the ankyrin-repeats domains (ARDs) of TRPC1, -3, -4, -5, -6, and -7, and affects TRPC intracellular trafficking without affecting their activity. RNF122 is a RING finger protein associated with HEK 293T cell viability. It is localized to the endoplasmic reticulum (ER) and the Golgi apparatus, and overexpressed in anaplastic thyroid cancer cells. RNF122 functions as an E3 ubiquitin ligase that can ubiquitinate itself and undergo degradation through its RING finger in a proteasome-dependent manner. Both RNF24 and RNF122 contain an N-terminal transmembrane domain and a C-terminal C3H2C3-type RING-H2 finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 148689291   5 ALCTICSDFFDHSRDVAAIHCGHTFHLQCLIQWFETAPSrtCPQCRIQV 53
Cdd:cd16469    1 DTCAVCLEEFKLKEELGVCPCGHAFHTKCLKKWLEVRNS--CPICKSPV 47

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 148689291   7 CTICSDFFDHSRDvaAIHCGHTFHLQCLIQWFETapSRTCPQCR 50
Cdd:cd16479    4 CIICREEMTVGAK--KLPCGHIFHLSCLRSWLQR--QQTCPTCR 43

RING finger, H2 subclass, found in RING finger protein 111 (RNF111) 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 acts as an amplifier of Nodal signals, and enhances the dorsalizing activity of limiting amounts of Xnr1, a Nodal homolog, and requires Nodal signaling for its function. The loss of RNF111 results in early embryonic lethality, with defects attributed to compromised Nodal signaling. RNF111 also regulates tumor metastasis by modulation of the TGF-beta pathway. Its ubiquitination can be modulated by the four and a half LIM-only protein 2 (FHL2) that activates TGF-beta signal transduction. Furthermore, RNF111 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. In addition, RNF111 has been identified as a small ubiquitin-like modifier (SUMO)-binding protein with clustered SUMO-interacting motifs (SIMs) that together form a SUMO-binding domain (SBD). 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). The N-terminal half of RNF111 harbors three SIMs. Its C-terminal half show high sequence similarity with RING finger protein 165 (RNF165), where it contains two serine rich domains, two nuclear localization signals, an NRG-TIER domain, and a C-terminal C3H2C3-type RING-H2 finger that is required for polyubiqutination and proteasome-dependent degradation of phosphorylated forms of Smad2/3 and three major negative regulators of TGF-beta signaling, Smad7, SnoN and c-Ski.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 148689291   7 CTICSDFFDHSRDVAAIHCGHTFHLQCLIQWFETapSRTCPQCRIQV 53
Cdd:cd16681   13 CTICLSILEEGEDVRRLPCMHLFHQVCVDQWLIT--NKKCPICRVDI 57

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291  118 VESLQNALNKAEMLCSTLKKQMKFLEQRQDETKQAREEAHRLKckMKTMEQIELL-LQSQRSEVEEMIRDMGVGQSAVEQ 196
Cdd:COG4913   612 LAALEAELAELEEELAEAEERLEALEAELDALQERREALQRLA--EYSWDEIDVAsAEREIAELEAELERLDASSDDLAA 689

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 148689291  197 LavycvslKKEYENLKEARKATGELADRLKKDLVSSRSKLKTLNTELDQAKLELRSAQKDLQSADQE 263
Cdd:COG4913   690 L-------EEQLEELEAELEELEEELDELKGEIGRLEKELEQAEEELDELQDRLEAAEDLARLELRA 749

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and similar proteins; TRIM41 and TRIM52, two closely related tripartite motif-containing proteins, have dramatically expanded RING domains compared with the rest of the TRIM family proteins. TRIM41 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. In contrast, TRIM52 lacks the putative viral recognition SPRY/B30.2 domain, and thus has been classified to the C-V subclass of the TRIM family that contains only RBCC domains. TRIM41, also known as RING finger-interacting protein with C kinase (RINCK), is an E3 ubiquitin-protein ligase that promotes the ubiquitination of protein kinase C (PKC) isozymes in cells. It specifically recognizes the C1 domain of PKC isozymes. It controls the amplitude of PKC signaling by controlling the amount of PKC in the cell. TRIM52, also known as RING finger protein 102 (RNF102), is encoded by a novel, noncanonical antiviral TRIM52 gene in primate genomes with unique specificity determined by the rapidly evolving RING domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 148689291   5 ALCTICSDFFdhsRDVAAIHCGHTFHLQCLIQWFetapSRTCPQCR 50
Cdd:cd16602    4 AVCAICLDYF---KDPVSIGCGHNFCRVCVTQLW----GFTCPQCR 42

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291  65 DLAQEEENVLDAEFLKNELDSVKAQLSQKDREKR----DSQAIIDTLRDTLEERNATVESLQNALNKAEMLCSTLKKQMK 140
Cdd:COG1196  296 ELARLEQDIARLEERRRELEERLEELEEELAELEeeleELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELA 375

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148689291 141 FLEQRQDETKQAREEAhrlkckmktmEQIELLLQSQRSEVEEMIrdmgvgQSAVEQLAvycvSLKKEYENLKEARKATGE 220
Cdd:COG1196  376 EAEEELEELAEELLEA----------LRAAAELAAQLEELEEAE------EALLERLE----RLEEELEELEEALAELEE 435

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 148689291 221 LADRLKKDLVSSRSKLKTLNTELDQAKLELRSAQKDLQSADQEITSLRKKL 271
Cdd:COG1196  436 EEEEEEEALEEAAEEEAELEEEEEALLELLAELLEEAALLEAALAELLEEL 486