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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193208549   1 MRTLAFIENFISTVPFAMGQSMTKLKKGLEG---QSNLISKLMKKHEANIPFIEDTMATDIEKVLETNQKLQLAFAELDE 77
Cdd:COG4942    1 MRKLLLLALLLALAAAAQADAAAEAEAELEQlqqEIAELEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELAA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193208549  78 QSEKINSLETQQHKLVAELSKMEIERS-----------NSAIEIMKKDKQLRTTEEQLIMMANLGEELGNDAKRYRSELE 146
Cdd:COG4942   81 LEAELAELEKEIAELRAELEAQKEELAellralyrlgrQPPLALLLSPEDFLDAVRRLQYLKYLAPARREQAEELRADLA 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 193208549 147 saheELYQTYTIFDKEKSDLCELIEEQTKKLTESNAKQESRKE 189
Cdd:COG4942  161 ----ELAALRAELEAERAELEALLAELEEERAALEALKAERQK 199

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 193208549   190 CPICCWNYDNEdrlPRVMDCGHTMCHTCIISTI-NESDTEPIC 231
Cdd:smart00184   1 CPICLEEYLKD---PVILPCGHTFCRSCIRKWLeSGNNTCPIC 40

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193208549   1 MRTLAFIENFISTVPFAMGQSMTKLKKGLEG---QSNLISKLMKKHEANIPFIEDTMATDIEKVLETNQKLQLAFAELDE 77
Cdd:COG4942    1 MRKLLLLALLLALAAAAQADAAAEAEAELEQlqqEIAELEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELAA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193208549  78 QSEKINSLETQQHKLVAELSKMEIERS-----------NSAIEIMKKDKQLRTTEEQLIMMANLGEELGNDAKRYRSELE 146
Cdd:COG4942   81 LEAELAELEKEIAELRAELEAQKEELAellralyrlgrQPPLALLLSPEDFLDAVRRLQYLKYLAPARREQAEELRADLA 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 193208549 147 saheELYQTYTIFDKEKSDLCELIEEQTKKLTESNAKQESRKE 189
Cdd:COG4942  161 ----ELAALRAELEAERAELEALLAELEEERAALEALKAERQK 199

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 193208549    29 LEGQSNLISKLMKKHEANIPFIEDTMATDIEKVLETNQKLQLAFAELDEQSEKINSLETQQHKLVAELSKMEIERSNSAI 108
Cdd:TIGR02168  759 LEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRERLESLERRIAATER 838

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193208549   109 EIMKKDKQLRTTEEQLIMMANLGEELGNDAKRYRSELESAHEELYQTYTIFDKEKSDLCELIEEQTKKLTESNAKQESRK 188
Cdd:TIGR02168  839 RLEDLEEQIEELSEDIESLAAEIEELEELIEELESELEALLNERASLEEALALLRSELEELSEELRELESKRSELRRELE 918

                   ..
gi 193208549   189 EC 190
Cdd:TIGR02168  919 EL 920

Modified RING finger, HC subclass (C3HC3D-type), found in Caenorhabditis elegans putative GTP-binding protein trim-23 homolog (arc-1) and similar proteins; arc-1, also called RING-type E3 ubiquitin transferase arc-1, is an E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination. arc-1 contains a modified C3HC3D-type RING-HC finger.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 193208549 189 ECPICCWNY--DNEDRLPRVM-DCGHTMCHTCIISTINESDTEPICPFDREP 237
Cdd:cd23124    3 ECGICQQEYsaDDPLLIPRILtECGHTICTNCAGTILGQSSGSIFCPFDRIV 54

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 193208549   190 CPICCWNYDNEdrlPRVMDCGHTMCHTCIISTI-NESDTEPIC 231
Cdd:smart00184   1 CPICLEEYLKD---PVILPCGHTFCRSCIRKWLeSGNNTCPIC 40

Modified RING finger, HC subclass (C3HC3D-type), found in Roquin-1, Roquin-2, and similar proteins; The ROQUIN family includes Roquin-1, Roquin-2, and similar proteins, which localize to the cytoplasm and upon stress, are concentrated in stress granules. They may play essential roles in preventing T-cell-mediated autoimmune disease and in microRNA-mediated repression of inducible costimulator (Icos) mRNA. They function as E3 ubiquitin ligases consisting of an N-terminal modified C3HC3D-type RING-HC finger with a potential E3 activity, a highly conserved ROQ domain required for RNA binding and localization to stress granules, and a CCCH-type zinc finger involved in RNA recognition.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 193208549 190 CPICCWNYDNEDRLPRVMDCGHTMCHTCIISTINesdtePICPFD 234
Cdd:cd16638    4 CPVCTNEFDGTQRKPISLGCGHTVCKTCLSKLHR-----KQCPFD 43

Modified RING finger, HC subclass (C3HC3D-type), found in Roquin-1; Roquin-1, also known as RING finger and C3H zinc finger protein 1 (RC3H1), or RING finger protein 198 (RNF198), is a ubiquitously expressed RNA-binding protein essential for degradation of inflammation-related mRNAs and maintenance of immune homeostasis. It is localized in cytoplasmic granules and binds to the 3' untranslated region (3'UTR) of inducible costimulator (Icos) mRNA to post-transcriptionally repress its expression. Roquin-1 interacts with the 3'UTR of tumor necrosis factor receptor superfamily member 4 (TNFRSF4) and tumor-necrosis factor-alpha (TNFalpha), and post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-kappaB pathway. Moreover, Roquin-1 shares functions with its paralog Roquin-2 in the repression of mRNAs controlling T follicular helper cells and systemic inflammation. Roquin-1 contains an N-terminal modified C3HC3D-type RING-HC finger with a potential E3 ubiquitin-ligase function, a highly conserved ROQ domain required for RNA binding and localization to stress granules, and a CCCH-type zinc finger that is involved in RNA recognition, typically contacting AU-rich elements. In addition, both N- and C-terminal to the ROQ domain are combined to form a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain that is highly likely to function as an RNA-binding domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 193208549 190 CPICCWNYDNEDRLPRVMDCGHTMCHTCIISTINESdtepiCPFDR 235
Cdd:cd16781    9 CPICTQTFDETIRKPISLGCGHTVCKMCLNKLHRKA-----CPFDQ 49

Modified RING finger, HC subclass (C3HC3D-type), found in tripartite motif-containing protein 23 (TRIM23) and similar proteins; TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a modified C3HC3D-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 193208549 189 ECPICCWNYDNE-DRLPRVMDCGHTMCHTCIISTINEsDTEPICPFDRE 236
Cdd:cd16645    3 ECGVCEDVFSLQgDKVPRLLLCGHTVCHDCLTRLPLH-GRAVRCPFDRQ 50

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 193208549 189 ECPICCWNYDNedrlPRVMDCGHTMCHTCIISTINESDTE-PIC 231
Cdd:cd16449    2 ECPICLERLKD----PVLLPCGHVFCRECIRRLLESGSIKcPIC 41

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 5 (TRAF5) and similar proteins; TRAF5, also known as RING finger protein 84 (RNF84), is an important signal transducer for a wide range of TNF receptor superfamily members, including tumor necrosis factor receptor 1 (TNFR1), TNFR2, CD40, and other lymphocyte costimulatory receptors, RANK/TRANCE-R, ectodysplasin-A Receptor (EDAR), lymphotoxin-beta receptor (LT-betaR), latent membrane protein 1 (LMP1), and IRE1. It functions as an activator of NF-kappaB, MAPK, and JNK, and is involved in both RANKL- and TNFalpha-induced osteoclastogenesis. It mediates CD40 signaling by associating with the cytoplasmic tail of CD40. It also negatively regulates Toll-like receptor (TLR) signaling and functions as a negative regulator of the interleukin 6 (IL-6) receptor signaling pathway that limits the differentiation of inflammatory CD4(+) T cells. TRAF5 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and several zinc fingers, and a C-terminal TRAF domain that comprises a coiled coil domain and a conserved TRAF-C domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 193208549 185 ESRKECPICCWNYDNedrlPRVMDCGHTMCHTCIISTINESDTePICPFDRE 236
Cdd:cd16642    2 EDRYKCATCHFVLHN----PHQTGCGHRFCQHCILSLLELNTT-PICPIDKE 48

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193208549   1 MRTLAFIENFISTVPFAMGQSMTKLKKGLEG---QSNLISKLMKKHEANIPFIEDTMATDIEKVLETNQKLQLAFAELDE 77
Cdd:COG4942    1 MRKLLLLALLLALAAAAQADAAAEAEAELEQlqqEIAELEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELAA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193208549  78 QSEKINSLETQQHKLVAELSKMEIERS-----------NSAIEIMKKDKQLRTTEEQLIMMANLGEELGNDAKRYRSELE 146
Cdd:COG4942   81 LEAELAELEKEIAELRAELEAQKEELAellralyrlgrQPPLALLLSPEDFLDAVRRLQYLKYLAPARREQAEELRADLA 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 193208549 147 saheELYQTYTIFDKEKSDLCELIEEQTKKLTESNAKQESRKE 189
Cdd:COG4942  161 ----ELAALRAELEAERAELEALLAELEEERAALEALKAERQK 199

Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining Golgi structure. They stimulate the formation of Golgi stacks and ribbons, and are involved in intra-Golgi retrograde transport. Two main interactions have been characterized: one with RAB1A that has been activated by GTP-binding and another with isoform CASP of CUTL1.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193208549   74 ELDEQSEKINSLETQQHKLVAELSKMEIERSNsaiEIMKKDKQLRTTEEQLIMMANLGEELGNDAKRYRSELESAHEELY 153
Cdd:pfam09787  55 ERDLLREEIQKLRGQIQQLRTELQELEAQQQE---EAESSREQLQELEEQLATERSARREAEAELERLQEELRYLEEELR 131

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 193208549  154 QTYTIFDKEKSDLCELIEEQTKKLTESNAKQESRKE 189
Cdd:pfam09787 132 RSKATLQSRIKDREAEIEKLRNQLTSKSQSSSSQSE 167

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 7 (TRAF7) and similar proteins; TRAF7, also known as RING finger and WD repeat-containing protein 1 or RING finger protein 119 (RNF119), is an E3 ubiquitin-protein ligase involved in signal transduction pathways that lead either to activation or repression of NF-kappaB transcription factor by promoting K29-linked ubiquitination of several cellular targets, including the NF-kappaB essential modulator (NEMO) and the p65 subunit of NF-kappaB transcription factor. It is also involved in K29-linked polyubiquitination that has been implicated in lysosomal degradation of proteins. Moreover, TRAF7 is required for K48-linked ubiquitination of p53, a key tumor suppressor and a master regulator of various signaling pathways, such as those related to apoptosis, cell cycle and DNA repair. It is also required for tumor necrosis factor alpha (TNFalpha)-induced Jun N-terminal kinase activation and promotes cell death by regulating polyubiquitination and lysosomal degradation of c-FLIP protein. Furthermore, TRAF7 functions as small ubiquitin-like modifier (SUMO) E3 ligase involved in other post-translational modification, such as sumoylation. It binds to and stimulates sumoylation of the proto-oncogene product c-Myb, a transcription factor regulating proliferation and differentiation of hematopoietic cells. It potentiates MEKK3-induced AP1 and CHOP activation and induces apoptosis. Meanwhile, TRAF7 mediates MyoD1 regulation of the pathway and cell-cycle progression in myoblasts. It also plays a role in Toll-like receptors (TLR) signaling. TRAF7 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and an adjacent zinc finger, and a unique C-terminal domain that comprises a coiled coil domain and seven WD40 repeats.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 193208549 190 CPICCWNYDNedrlPRVMDCGHTMCHTCIISTINEsdtepICPFDREPM 238
Cdd:cd16644    8 CPLCQRVFKD----PVITSCGHTFCRRCALTAPGE-----KCPVDNMKL 47

RING finger, HC subclass, found in RING finger protein 186 (RNF186) and similar proteins; RNF186 is an E3 ubiquitin-protein ligase with an N-terminal C3HC4-type RING-HC finger and two putative C-terminal transmembrane domains which enable it to localize in a certain organelle. It regulates RING-dependent self-ubiquitination, as well as endoplasmic reticulum (ER) stress-mediated apoptosis through interaction with the Bcl-2 family protein BNip1.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 193208549 189 ECPICCWNYDNEDRLPRVMDCGHTMCHTCIISTINESD-----TEPIC 231
Cdd:cd16557    3 ECLVCRNPYSCFVRKPKLLACQHAFCAICLKLILCEQDgtwsvTCPLC 50

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193208549  71 AFAE--LDEQSEKINSLETQQHKLVAELSKM--EIERSNSAIEimKKDKQLRTTEEQLimmanlgEELGNDAKRYRSELE 146
Cdd:COG3883   12 AFADpqIQAKQKELSELQAELEAAQAELDALqaELEELNEEYN--ELQAELEALQAEI-------DKLQAEIAEAEAEIE 82

                 ....*.
gi 193208549 147 SAHEEL 152
Cdd:COG3883   83 ERREEL 88

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 193208549    29 LEGQSNLISKLMKKHEANIPFIEDTMATDIEKVLETNQKLQLAFAELDEQSEKINSLETQQHKLVAELSKMEIERSNSAI 108
Cdd:TIGR02168  759 LEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRERLESLERRIAATER 838

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193208549   109 EIMKKDKQLRTTEEQLIMMANLGEELGNDAKRYRSELESAHEELYQTYTIFDKEKSDLCELIEEQTKKLTESNAKQESRK 188
Cdd:TIGR02168  839 RLEDLEEQIEELSEDIESLAAEIEELEELIEELESELEALLNERASLEEALALLRSELEELSEELRELESKRSELRRELE 918

                   ..
gi 193208549   189 EC 190
Cdd:TIGR02168  919 EL 920

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
                 ....*....|....*....|....*....|....*.
gi 193208549 190 CPICCWNYDNedrlPRVMDCGHTMCHTCIISTINES 225
Cdd:cd16581    5 CSICYNIFDD----PKILPCSHTFCKNCLEKLLAAS 36

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193208549  59 EKVLETNQKLQLAFAELDEQSEKINSLETQQHKLVAELSKMEIERSNSAIEIMKKDKQLRTTEEQLIMMA---------- 128
Cdd:COG3883   23 KELSELQAELEAAQAELDALQAELEELNEEYNELQAELEALQAEIDKLQAEIAEAEAEIEERREELGERAralyrsggsv 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193208549 129 ----------NLGE----------------ELGNDAKRYRSELESAHEELyqtytifDKEKSDLCELIEEQTKKLTESNA 182
Cdd:COG3883  103 syldvllgseSFSDfldrlsalskiadadaDLLEELKADKAELEAKKAEL-------EAKLAELEALKAELEAAKAELEA 175

                 ....*..
gi 193208549 183 KQESRKE 189
Cdd:COG3883  176 QQAEQEA 182

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193208549  67 KLQLAFAELDEQSEKINSLETQQHKLVAELSKMEIERSNSAIEIMKKDKQLRTTEEQLIMMANLGEELGNDAKRYRSELE 146
Cdd:COG1196  233 KLRELEAELEELEAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRR 312

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 193208549 147 SAHEELYQTytifDKEKSDLCELIEEQTKKLTESNAKQESRKE 189
Cdd:COG1196  313 ELEERLEEL----EEELAELEEELEELEEELEELEEELEEAEE 351

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 193208549    57 DIEKVLETNQKLQLAFAELDEQSEKINSLETQQHKLVAELSKMEIERsNSAIEIMKKDKQLRTTEEQLImmANLGEELGN 136
Cdd:TIGR02169  161 EIAGVAEFDRKKEKALEELEEVEENIERLDLIIDEKRQQLERLRRER-EKAERYQALLKEKREYEGYEL--LKEKEALER 237

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 193208549   137 DAKRYRSELESAHEELYQtytiFDKEKSDLCELIEEQTKKLTESNAK 183
Cdd:TIGR02169  238 QKEAIERQLASLEEELEK----LTEEISELEKRLEEIEQLLEELNKK 280

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.

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gi 193208549 190 CPICCWNYdnedRLPRVMDCGHTMCHTCIISTINESDTEPICPFDREP 237
Cdd:cd16594    8 CPICLDYF----TDPVTLDCGHSFCRACIARCWEEPETSASCPQCRET 51

RING finger, H2 subclass, found in RING finger protein 126 (RNF126) and similar proteins; RNF126 is a Bag6-dependent E3 ubiquitin ligase that is involved in the mislocalized protein (MLP) pathway of quality control. It regulates the retrograde sorting of the cation-independent mannose 6-phosphate receptor (CI-MPR). Moreover, RNF126 promotes cancer cell proliferation by targeting the tumor suppressor p21 for ubiquitin-mediated degradation, and could be a novel therapeutic target in breast and prostate cancers. It is also able to ubiquitylate cytidine deaminase (AID), a poorly soluble protein that is essential for antibody diversification. In addition, RNF126 and the related protein, RNF115 associate with the epidermal growth factor receptor (EGFR) and promote ubiquitylation of EGFR, suggesting they play a role in the ubiquitin-dependent sorting and downregulation of membrane receptors. RNF126 contains an N-terminal BCA2 Zinc-finger domain (BZF), the AKT-phosphorylation sites, and the C-terminal C3H2C3-type RING-H2 finger.

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                 ....*....|....*....|....*....|....*....|...
gi 193208549 189 ECPICCWNYDNEDRLpRVMDCGHTMCHTCIISTINESDTEPIC 231
Cdd:cd16801    1 ECPVCKEDYTVGENV-RQLPCNHLFHNDCIVPWLEQHDTCPVC 42

Modified RING finger, HC subclass (C3HC3D-type), found in uncharacterized proteins similar to tumor necrosis factor (TNF) receptor-associated factor 4 (TRAF4); This subfamily corresponds to a group of uncharacterized proteins that shows high sequence similarity with tumor necrosis factor (TNF) receptor-associated factor 4 (TRAF4). TRAF4, also known as cysteine-rich domain associated with RING and Traf domains protein 1, or metastatic lymph node gene 62 protein (MLN 62), or RING finger protein 83 (RNF83), is a member of TRAF protein family, which mainly function in the immune system, where they mediate signaling through tumor necrosis factor receptors (TNFRs) and interleukin-1/Toll-like receptors (IL-1/TLRs). It also plays a critical role in the nervous system, as well as in carcinogenesis. Like TRAF4, members of this subfamily contain a modified C3HC3D-type RING-HC finger.

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                 ....*....|....*....|....*....|....*....|....*....|....
gi 193208549 185 ESRKECPICCwnydNEDRLP-RVMDCGHTMCHTCIISTINesdTEPICPFDREP 237
Cdd:cd23126    2 DKKYECPVCC----QVLRYPvQFEECGHRVCSSCLPELLR---VEPRCPIDQGP 48

RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar proteins; TRIM25, also known as estrogen-responsive finger protein (EFP), RING finger protein 147 (RNF147), or RING-type E3 ubiquitin transferase, is an E3 ubiquitin/ISG15 ligase that is induced by estrogen and is therefore particularly abundant in placenta and uterus. TRIM25 regulates various cellular processes through E3 ubiquitin ligase activity, transferring ubiquitin and ISG15 to target proteins. It mediates K63-linked polyubiquitination of retinoic acid inducible gene I (RIG-I) that is crucial for downstream antiviral interferon signaling. It is also required for melanoma differentiation-associated gene 5 (MDA5) and mitochondrial antiviral signaling (MAVS, also known as IPS-1, VISA, Cardiff) mediated activation of nuclear factor-kappaB (NF-kappaB) and interferon production. Upon UV irradiation, TRIM25 interacts with mono-ubiquitinated PCNA and promotes its ISG15 modification (ISGylation), suggesting a crucial role in termination of error-prone translesion DNA synthesis. TRIM25 also functions as a novel regulator of p53 and Mdm2. It enhances p53 and Mdm2 abundance by inhibiting their ubiquitination and degradation in 26S proteasomes. Meanwhile, it inhibits p53's transcriptional activity and dampens the response to DNA damage, and is essential for medaka development and this dependence is rescued by silencing of p53. Moreover, TRIM25 is involved in the host cellular innate immune response against retroviral infection. It interferes with the late stage of feline leukemia virus (FeLV) replication. Furthermore, TRIM25 acts as an oncogene in gastric cancer. Its blockade by RNA interference inhibits migration and invasion of gastric cancer cells through transforming growth factor-beta (TGF-beta) signaling, suggesting it presents a novel target for the detection and treatment of gastric cancer. In addition, TRIM25 acts as an RNA-specific activator for Lin28a/TuT4-mediated uridylation. TRIM25 belongs to the C-IV 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 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.

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                 ....*....|....*....|....*....|....*....|....*....
gi 193208549 190 CPICCWNYDNEDRLPrvmdCGHTMCHTCIISTINES-DTEPICPFDREP 237
Cdd:cd16597    8 CSICLELFKDPVTLP----CGHNFCGVCIEKTWDSQhGSEYSCPQCRAT 52

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]

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193208549    73 AELDEQSEKINSLETQQHKLVAELSKMEIERSNSAIEIMKKDKQLRTTEEQLIMMANLGEELGNDAKRYRSELESAHEEL 152
Cdd:TIGR02168  677 REIEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKEL 756

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 193208549   153 yqtyTIFDKEKSDLCELIEEQTKKLTESNAKQESRKE 189
Cdd:TIGR02168  757 ----TELEAEIEELEERLEEAEEELAEAEAEIEELEA 789

RING finger, HC subclass, found in tripartite motif-containing protein 68 (TRIM68) and similar proteins; TRIM68, also known as RING finger protein 137 (RNF137) or SSA protein SS-56 (SS-56), is an E3 ubiquitin-protein ligase that negatively regulates Toll-like receptor (TLR)- and RIG-I-like receptor (RLR)-driven type I interferon production by degrading TRK fused gene (TFG), a novel driver of IFN-beta downstream of anti-viral detection systems. It also functions as a cofactor for androgen receptor-mediated transcription by regulating ligand-dependent transcription of androgen receptor in prostate cancer cells. Moreover, TRIM68 is a cellular target of autoantibody responses in Sjogre's syndrome (SS), as well as systemic lupus erythematosus (SLE). It is also an auto-antigen for T cells in SS and SLE. TRIM68 belongs 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.

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gi 193208549 190 CPICCWNYdnedRLPRVMDCGHTMCHTCI 218
Cdd:cd16610    4 CPICMTFL----REPVSIDCGHSFCHSCL 28