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Conserved domains on  [gi|568979512|ref|XP_006515863|]
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TNF receptor-associated factor 3 isoform X1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
MATH_TRAF3 cd03777
Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF ...
377-562 1.99e-141

Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF3 was first described as a molecule that binds the cytoplasmic tail of CD40. However, it is not required for CD40 signaling. More recently, TRAF3 has been identified as a key regulator of type I interferon (IFN) production and the mammalian innate antiviral immunity. It mediates IFN responses in Toll-like receptor (TLR)-dependent as well as TLR-independent viral recognition pathways. It is also a key element in immunological homeostasis through its regulation of the anti-inflammatory cytokine interleukin-10. TRAF3 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors.


:

Pssm-ID: 239746  Cd Length: 186  Bit Score: 406.64  E-value: 1.99e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 377 TGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCAR 456
Cdd:cd03777    1 TGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCAR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 457 VYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVF 536
Cdd:cd03777   81 VYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVF 160
                        170       180
                 ....*....|....*....|....*.
gi 568979512 537 VAQTVLENGTYIKDDTIFIKVIVDTS 562
Cdd:cd03777  161 VAQTVLENGTYIKDDTIFIKVIVDTS 186
RING-HC_TRAF3 cd16640
RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 3 ...
50-91 1.74e-21

RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 3 (TRAF3) and similar proteins; TRAF3, also known as CAP-1, CD40 receptor-associated factor 1 (CRAF1), CD40-binding protein (CD40BP), or LMP1-associated protein 1 (LAP1), is a member of the TRAF protein family, which mainly functions in the immune system, where it mediates signaling through tumor necrosis factor receptors (TNFRs) and interleukin-1/Toll-like receptors (IL-1/TLRs). It also plays a unique cell type-specific and critical role in the restraint of B-cell homeostatic survival, a role with important implications for both B-cell differentiation and the pathogenesis of B-cell malignancies. TRAF3 differentially regulates differentiation of specific T cell subsets. It is required for iNKT cell development, restrains Treg cell development in the thymus, and plays an essential role in the homeostasis of central memory CD8+ T cells. TRAF3 contains an N-terminal domain with a typical C3HC4-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.


:

Pssm-ID: 438302 [Multi-domain]  Cd Length: 42  Bit Score: 87.26  E-value: 1.74e-21
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 568979512  50 YKCEKCRLVLCNPKQTECGHRFCESCMAALLSSSSPKCTACQ 91
Cdd:cd16640    1 YKCEKCRLVLCNPKQTECGHRFCESCMNALLSSSNPQCPACE 42
zf-TRAF pfam02176
TRAF-type zinc finger;
135-191 4.23e-14

TRAF-type zinc finger;


:

Pssm-ID: 280357 [Multi-domain]  Cd Length: 60  Bit Score: 67.10  E-value: 4.23e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568979512  135 HLKNeCQFEELPCLRADCKEKVLRKDLRDHVEKACKYREATCSH----CKSQVPMIKLQKH 191
Cdd:pfam02176   1 HLET-CPFFPIPCPNGCCKKKILREDLPDHLELDCPKAEVPCPFkvfgCKEDVKREALQRH 60
Cast super family cl37807
RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part ...
243-389 8.08e-07

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.


The actual alignment was detected with superfamily member pfam10174:

Pssm-ID: 431111 [Multi-domain]  Cd Length: 766  Bit Score: 52.13  E-value: 8.08e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  243 TNQQikaheaSSAVQHVNLLKEWSNSLEKKVSLLQNES--------------VEKNKSIQSLHNQICSFEIEIERQKEML 308
Cdd:pfam10174 316 TNQN------SDCKQHIEVLKESLTAKEQRAAILQTEVdalrlrleekesflNKKTKQLQDLTEEKSTLAGEIRDLKDML 389
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  309 RNNESKILHLQRVIDSQAEKLKELDKEIrpfrqnweeaDSMKSSVESLQ----NRVTELESVDKSAGQAARNTGLLESQL 384
Cdd:pfam10174 390 DVKERKINVLQKKIENLQEQLRDKDKQL----------AGLKERVKSLQtdssNTDTALTTLEEALSEKERIIERLKEQR 459

                  ....*
gi 568979512  385 SRHDQ 389
Cdd:pfam10174 460 EREDR 464
zf-TRAF super family cl44369
TRAF-type zinc finger;
196-246 9.66e-06

TRAF-type zinc finger;


The actual alignment was detected with superfamily member pfam02176:

Pssm-ID: 280357 [Multi-domain]  Cd Length: 60  Bit Score: 43.21  E-value: 9.66e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568979512  196 CPCVVVSCPHKCSVQTLLRSELSAHLSE-CVNAPSTCSFKRYGC--VFQGTNQQ 246
Cdd:pfam02176   5 CPFFPIPCPNGCCKKKILREDLPDHLELdCPKAEVPCPFKVFGCkeDVKREALQ 58
 
Name Accession Description Interval E-value
MATH_TRAF3 cd03777
Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF ...
377-562 1.99e-141

Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF3 was first described as a molecule that binds the cytoplasmic tail of CD40. However, it is not required for CD40 signaling. More recently, TRAF3 has been identified as a key regulator of type I interferon (IFN) production and the mammalian innate antiviral immunity. It mediates IFN responses in Toll-like receptor (TLR)-dependent as well as TLR-independent viral recognition pathways. It is also a key element in immunological homeostasis through its regulation of the anti-inflammatory cytokine interleukin-10. TRAF3 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors.


Pssm-ID: 239746  Cd Length: 186  Bit Score: 406.64  E-value: 1.99e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 377 TGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCAR 456
Cdd:cd03777    1 TGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCAR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 457 VYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVF 536
Cdd:cd03777   81 VYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVF 160
                        170       180
                 ....*....|....*....|....*.
gi 568979512 537 VAQTVLENGTYIKDDTIFIKVIVDTS 562
Cdd:cd03777  161 VAQTVLENGTYIKDDTIFIKVIVDTS 186
RING-HC_TRAF3 cd16640
RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 3 ...
50-91 1.74e-21

RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 3 (TRAF3) and similar proteins; TRAF3, also known as CAP-1, CD40 receptor-associated factor 1 (CRAF1), CD40-binding protein (CD40BP), or LMP1-associated protein 1 (LAP1), is a member of the TRAF protein family, which mainly functions in the immune system, where it mediates signaling through tumor necrosis factor receptors (TNFRs) and interleukin-1/Toll-like receptors (IL-1/TLRs). It also plays a unique cell type-specific and critical role in the restraint of B-cell homeostatic survival, a role with important implications for both B-cell differentiation and the pathogenesis of B-cell malignancies. TRAF3 differentially regulates differentiation of specific T cell subsets. It is required for iNKT cell development, restrains Treg cell development in the thymus, and plays an essential role in the homeostasis of central memory CD8+ T cells. TRAF3 contains an N-terminal domain with a typical C3HC4-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.


Pssm-ID: 438302 [Multi-domain]  Cd Length: 42  Bit Score: 87.26  E-value: 1.74e-21
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 568979512  50 YKCEKCRLVLCNPKQTECGHRFCESCMAALLSSSSPKCTACQ 91
Cdd:cd16640    1 YKCEKCRLVLCNPKQTECGHRFCESCMNALLSSSNPQCPACE 42
zf-TRAF pfam02176
TRAF-type zinc finger;
135-191 4.23e-14

TRAF-type zinc finger;


Pssm-ID: 280357 [Multi-domain]  Cd Length: 60  Bit Score: 67.10  E-value: 4.23e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568979512  135 HLKNeCQFEELPCLRADCKEKVLRKDLRDHVEKACKYREATCSH----CKSQVPMIKLQKH 191
Cdd:pfam02176   1 HLET-CPFFPIPCPNGCCKKKILREDLPDHLELDCPKAEVPCPFkvfgCKEDVKREALQRH 60
MATH smart00061
meprin and TRAF homology;
416-537 4.82e-12

meprin and TRAF homology;


Pssm-ID: 214496 [Multi-domain]  Cd Length: 95  Bit Score: 62.32  E-value: 4.82e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512   416 VLIWKIRDYKRrkqeavMGKTLSLYSQPFYTgyFGYKMCARVYLNGDgmgkgtHLSLFFVIMRGEYDALlPWPFKQKVTL 495
Cdd:smart00061   1 VLSHTFKNVSR------LEEGESYFSPSEEH--FNIPWRLKIYRKNG------FLSLYLHCEKEECDSR-KWSIEAEFTL 65
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 568979512   496 MLMDQGSSRRhlgdafkPDPNSSSFKKPTGemniaSGCPVFV 537
Cdd:smart00061  66 KLVSQNGKSL-------SKKDKHVFEKPSG-----WGFSKFI 95
Cast pfam10174
RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part ...
243-389 8.08e-07

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.


Pssm-ID: 431111 [Multi-domain]  Cd Length: 766  Bit Score: 52.13  E-value: 8.08e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  243 TNQQikaheaSSAVQHVNLLKEWSNSLEKKVSLLQNES--------------VEKNKSIQSLHNQICSFEIEIERQKEML 308
Cdd:pfam10174 316 TNQN------SDCKQHIEVLKESLTAKEQRAAILQTEVdalrlrleekesflNKKTKQLQDLTEEKSTLAGEIRDLKDML 389
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  309 RNNESKILHLQRVIDSQAEKLKELDKEIrpfrqnweeaDSMKSSVESLQ----NRVTELESVDKSAGQAARNTGLLESQL 384
Cdd:pfam10174 390 DVKERKINVLQKKIENLQEQLRDKDKQL----------AGLKERVKSLQtdssNTDTALTTLEEALSEKERIIERLKEQR 459

                  ....*
gi 568979512  385 SRHDQ 389
Cdd:pfam10174 460 EREDR 464
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
257-367 1.00e-06

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.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 51.56  E-value: 1.00e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  257 QHVNLLKEWSNSLEKKVSLLQNESVEKNKSIQSLHNQICSFEIEIERQKEMLRNNESKILHLQRVIDSQAEKLKELDKEI 336
Cdd:TIGR04523 335 KIISQLNEQISQLKKELTNSESENSEKQRELEEKQNEIEKLKKENQSYKQEIKNLESQINDLESKIQNQEKLNQQKDEQI 414
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 568979512  337 RPFRQNWE----EADSMKSSVESLQNRVTELESVD 367
Cdd:TIGR04523 415 KKLQQEKEllekEIERLKETIIKNNSEIKDLTNQD 449
zf-TRAF pfam02176
TRAF-type zinc finger;
196-246 9.66e-06

TRAF-type zinc finger;


Pssm-ID: 280357 [Multi-domain]  Cd Length: 60  Bit Score: 43.21  E-value: 9.66e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568979512  196 CPCVVVSCPHKCSVQTLLRSELSAHLSE-CVNAPSTCSFKRYGC--VFQGTNQQ 246
Cdd:pfam02176   5 CPFFPIPCPNGCCKKKILREDLPDHLELdCPKAEVPCPFKVFGCkeDVKREALQ 58
HEC1 COG5185
Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell ...
244-411 2.88e-05

Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 444066 [Multi-domain]  Cd Length: 594  Bit Score: 46.87  E-value: 2.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 244 NQQIKAHEASSAVQHVNLLKEWSNSLEKKVSLLQ---NESVEKN---KSIQSLHNQICSFEI--EIERQKemlRNNESKI 315
Cdd:COG5185  262 NTDLRLEKLGENAESSKRLNENANNLIKQFENTKekiAEYTKSIdikKATESLEEQLAAAEAeqELEESK---RETETGI 338
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 316 LHLQRVIDSQAEKLKELDKEIRPFRQNWEEADSMKSSVESLQNRVTELESVDKSAGQAARN----TGLLESQLSRHdqmL 391
Cdd:COG5185  339 QNLTAEIEQGQESLTENLEAIKEEIENIVGEVELSKSSEELDSFKDTIESTKESLDEIPQNqrgyAQEILATLEDT---L 415
                        170       180
                 ....*....|....*....|..
gi 568979512 392 SVHDIRLADM--DLRFQVLETA 411
Cdd:COG5185  416 KAADRQIEELqrQIEQATSSNE 437
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
51-230 7.04e-04

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


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 42.00  E-value: 7.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  51 KCEKCRLVLCNPKQTECGHRFCESCMAALLsSSSPKCTACQESiIKDKVFKDNCCKREIlaLQVYCRNEGRgcaeqltlg 130
Cdd:COG5432   27 RCRICDCRISIPCETTCGHTFCSLCIRRHL-GTQPFCPVCRED-PCESRLRGSSGSREI--NESHARNRDL--------- 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 131 hLLVHLKNECQFEELPCLRADCKEKVLRKDLRDHVEKACKYREATCSH----CKSQVPMIKLQKHED-TDCPCVVVSCPH 205
Cdd:COG5432   94 -LRKVLESLCRLPRPIKEERPCRWETVIAQDSASGDEEWEDDLASNSSpasiAKKTSRDSKKRKREDlVHCPACSNLVPH 172
                        170       180
                 ....*....|....*....|....*
gi 568979512 206 KcsvqtllrsELSAHLSECVNAPST 230
Cdd:COG5432  173 N---------QINQHLDSCLNSPSS 188
COG5222 COG5222
Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];
51-109 7.07e-04

Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];


Pssm-ID: 227547 [Multi-domain]  Cd Length: 427  Bit Score: 42.43  E-value: 7.07e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568979512  51 KCEKCRLVLCNPKQTE-CGHRFCESCMAALLSSSSPKCTACQ-ESIIKDKVFKDNCCKREI 109
Cdd:COG5222  276 KCPLCHCLLRNPMKTPcCGHTFCDECIGTALLDSDFKCPNCSrKDVLLDGLTPDIDKKLEV 336
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
55-90 1.05e-03

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


Pssm-ID: 395049 [Multi-domain]  Cd Length: 40  Bit Score: 36.95  E-value: 1.05e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 568979512   55 CRLVLCNPKQ----TECGHRFCESCMAALLSSSSPKCTAC 90
Cdd:pfam00097   1 CPICLEEPKDpvtlLPCGHLFCSKCIRSWLESGNVTCPLC 40
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
52-87 1.46e-03

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 36.72  E-value: 1.46e-03
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 568979512    52 CEKCR-LVLCNPKQTECGHRFCESCMAALLSSSSPKC 87
Cdd:smart00184   1 CPICLeEYLKDPVILPCGHTFCRSCIRKWLESGNNTC 37
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
43-96 2.57e-03

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


Pssm-ID: 273165 [Multi-domain]  Cd Length: 397  Bit Score: 40.37  E-value: 2.57e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568979512   43 VKTVEDKYKCEKCRLVLCNPKQTECGHRFCESCMAALLsSSSPKCTAC----QESIIK 96
Cdd:TIGR00599  20 LYPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCL-SNQPKCPLCraedQESKLR 76
MukF_N cd16335
bacterial condensin complex subunit MukF, N-terminal domain; MukF is part of the MukBEF ...
276-402 5.53e-03

bacterial condensin complex subunit MukF, N-terminal domain; MukF is part of the MukBEF condensin complex that is mainly found in proteobacteria and is involved in chromosome organization and condensation. The complex is believed to serve as a part of the chromosome scaffold rather than a bulk DNA packing protein. MukE and MukF form a stable complex with each other and dynamically associate with MukB, a member of the SMC protein family. MukEF does not bind DNA on its own but modulates MukB-DNA activity. The stoichiometry of the MukEF complex is MukE4F2.


Pssm-ID: 319981  Cd Length: 315  Bit Score: 39.17  E-value: 5.53e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 276 LQNESVEKNksIQSLHNQicSFEIEIERQKEMLRNNESKILHLQRVIDSQAEKLKELDKEIRPFRQNwEEADSMKSSVES 355
Cdd:cd16335  168 AQQQQLRAE--IASLLSQ--DWFAAIDQCEELLQETAGTLRDLQDLLLASADKLLALLLEIQEAAEQ-AGPEEAQNAVQD 242
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 568979512 356 LQNRvteLESVDKSAGQAARntgllesQLSRHDQMlsVHD-IRLA-DMD 402
Cdd:cd16335  243 LQDQ---LDRIRAWGNQRLR-------DWSEYHRR--VHRfIRTViRLD 279
 
Name Accession Description Interval E-value
MATH_TRAF3 cd03777
Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF ...
377-562 1.99e-141

Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF3 was first described as a molecule that binds the cytoplasmic tail of CD40. However, it is not required for CD40 signaling. More recently, TRAF3 has been identified as a key regulator of type I interferon (IFN) production and the mammalian innate antiviral immunity. It mediates IFN responses in Toll-like receptor (TLR)-dependent as well as TLR-independent viral recognition pathways. It is also a key element in immunological homeostasis through its regulation of the anti-inflammatory cytokine interleukin-10. TRAF3 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors.


Pssm-ID: 239746  Cd Length: 186  Bit Score: 406.64  E-value: 1.99e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 377 TGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCAR 456
Cdd:cd03777    1 TGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCAR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 457 VYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVF 536
Cdd:cd03777   81 VYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVF 160
                        170       180
                 ....*....|....*....|....*.
gi 568979512 537 VAQTVLENGTYIKDDTIFIKVIVDTS 562
Cdd:cd03777  161 VAQTVLENGTYIKDDTIFIKVIVDTS 186
MATH_TRAF_C cd00270
Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF domain, C-terminal ...
415-560 3.16e-84

Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link cell surface TNFRs and receptors of the interleukin-1/Toll-like family to downstream kinase signaling cascades which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. There are at least six mammalian and three Drosophila proteins containing TRAF domains. The mammalian TRAFs display varying expression profiles, indicating independent and cell type-specific regulation. They display distinct, as well as overlapping functions and interactions with receptors. Most TRAFs, except TRAF1, share N-terminal homology and contain a RING domain, multiple zinc finger domains, and a TRAF domain. TRAFs form homo- and heterotrimers through its TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors.


Pssm-ID: 238168  Cd Length: 149  Bit Score: 258.69  E-value: 3.16e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 415 GVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVT 494
Cdd:cd00270    1 GVLIWKIKDYSRKLQEAVAGSNTVLYSPPFYTSRYGYKLCLRLYLNGDGTGKGTHLSLFVHVMKGEYDALLEWPFRGKIT 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568979512 495 LMLMDQG--SSRRHLGDAFKPDPNSSSFKK-PTGEMNIASGCPVFVAQTVLENGTYIKDDTIFIKVIVD 560
Cdd:cd00270   81 LTLLDQSddSKRKHITETFMPDPNSSAFQRpPTGENNIGFGYPEFVPLEKLESRGYVKDDTLFIKVEVD 149
MATH_TRAF5 cd03780
Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF5 subfamily, TRAF ...
415-560 1.16e-81

Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF5 subfamily, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF5 was identified as an activator of nuclear factor-kappaB and a regulator of lymphotoxin-beta receptor and CD40 signaling. Its interaction with CD40 is indirect, involving hetero-oligomerization with TRAF3. In addition, TRAF5 has been shown to associate with other TNFRs including CD27, CD30, OX40 and GITR (glucocorticoid-induced TNFR). It plays a role in modulating Th2 immune responses (driven by OX40 costimulation) and T-cell activation (triggered by GITR). It is also involved in osteoclastogenesis. TRAF5 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors.


Pssm-ID: 239749 [Multi-domain]  Cd Length: 148  Bit Score: 252.25  E-value: 1.16e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 415 GVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVT 494
Cdd:cd03780    1 GKLIWKVTDYKMKKKEAVDGHTVSIFSQPFYTSRCGYRLCARAYLNGDGSGKGTHLSLYFVVMRGEFDSLLQWPFRQRVT 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568979512 495 LMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLENG--TYIKDDTIFIKVIVD 560
Cdd:cd03780   81 LMLLDQSGKKNHIMETFKADPNSSSFKRPDGEMNIASGCPRFVAHSVLENAknTYIKDDTLFLKVAVD 148
MATH_TRAF2 cd03778
Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF2 subfamily, TRAF ...
399-560 5.70e-71

Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF2 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF2 associates with the receptors TNFR-1, TNFR-2, RANK (which mediates differentiation and maturation of osteoclasts) and CD40 (which is important for the proliferation and activation of B cells), among others. It regulates distinct pathways that lead to the activation of nuclear factor-kappaB and Jun NH2-terminal kinases. TRAF2 also indirectly associates with death receptors through its interaction with TRADD (TNFR-associated death domain protein). It is involved in regulating oxidative stress or ROS-induced cell death and in the preconditioning of cells by sublethal stress for protection from subsequent injury. TRAF2 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors.


Pssm-ID: 239747  Cd Length: 164  Bit Score: 224.88  E-value: 5.70e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 399 ADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMR 478
Cdd:cd03778    3 ADLEQKVLE*EASTYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVVMK 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 479 GEYDALLPWPFKQKVTLMLMDQgSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVF--VAQTVLENgTYIKDDTIFIK 556
Cdd:cd03778   83 GPNDALLRWPFNQKVTLMLLDQ-NNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFcpVSK*EAKN-SYVRDDAIFIK 160

                 ....
gi 568979512 557 VIVD 560
Cdd:cd03778  161 AIVD 164
MATH_TRAF1 cd03779
Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF1 subfamily, TRAF ...
415-560 7.23e-66

Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF1 subfamily, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF1 expression is the most restricted among the TRAFs. It is found exclusively in activated lymphocytes, dendritic cells and certain epithelia. TRAF1 associates, directly or indirectly through heterodimerization with TRAF2, with the TNFR family receptors TNFR-2, CD30, RANK, CD40 and LMP1, among others. It also binds the intracellular proteins TRADD, TANK, TRIP, RIP1, RIP2 and FLIP. TRAF1 is unique among the TRAFs in that it lacks a RING domain, which is critical for the activation of nuclear factor-kappaB and Jun NH2-terminal kinase. Studies on TRAF1-deficient mice suggest that TRAF1 has a negative regulatory role in TNFR-mediated signaling events. TRAF1 contains one zinc finger and one TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors.


Pssm-ID: 239748  Cd Length: 147  Bit Score: 210.90  E-value: 7.23e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 415 GVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVT 494
Cdd:cd03779    1 GTFLWKITDVSQKQRESSHGRDVSLCSPAFYTAKYGYKVCLRLYLNGDGAGKGTHISLFFVIMKGEYDALLPWPFRHKVT 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568979512 495 LMLMDQgSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLEN--GTYIKDDTIFIKVIVD 560
Cdd:cd03779   81 FMLLDQ-NNREHVIDAFRPDLSSASFQRPVSDMNVASGCPLFFPLKKLQSpkHAYCKDDTIYIKCVVD 147
MATH_TRAF4 cd03781
Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF4 subfamily, TRAF ...
415-560 2.62e-46

Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF4 subfamily, TRAF domain, C-terminal MATH subdomain; composed of proteins with similarity to human TRAF4, including the Drosophila protein DTRAF1. TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF4 is highly expressed during embryogenesis, especially in the central and peripheral nervous system. Studies using TRAF4-deficient mice show that TRAF4 is required for neurogenesis, as well as the development of the trachea and the axial skeleton. In addition, TRAF4 augments nuclear factor-kappaB activation triggered by GITR (glucocorticoid-induced TNFR), a receptor expressed in T-cells, B-cells and macrophages. It also participates in counteracting the signaling mediated by Toll-like receptors through its association with TRAF6 and TRIF. DTRAF1 plays a pivotal role in the development of eye imaginal discs and photosensory neuron arrays in Drosophila. TRAF4 contains a RING finger domain, seven zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors.


Pssm-ID: 239750  Cd Length: 154  Bit Score: 159.59  E-value: 2.62e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 415 GVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVT 494
Cdd:cd03781    1 GTLLWKITDYSRKLQEAKGRDNLELFSPPFYTHRYGYKLQVSAFLNGNGSGEGSHLSVYIRVLPGEYDNLLEWPFSHRIT 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568979512 495 LMLMDQG----SSRRHLGDAFKPDPNSSSFKKPTG----EMNIASGCPVFVAQTVLENGTYIKDDTIFIKVIVD 560
Cdd:cd03781   81 FTLLDQSdpslSKPQHITETFTPDPTWKNFQKPSAsrldESTLGFGYPKFISHEDLKKRNYIKDDAIFLRASVE 154
MATH_TRAF6 cd03776
Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF6 subfamily, TRAF ...
415-559 1.40e-38

Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF6 subfamily, TRAF domain, C-terminal MATH subdomain; composed of proteins with similarity to human TRAF6, including the Drosophila protein DTRAF2. TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF6 is the most divergent in its TRAF domain among the mammalian TRAFs. In addition to mediating TNFR family signaling, it is also an essential signaling molecule of the interleukin-1/Toll-like receptor superfamily. Whereas other TRAF molecules display similar and overlapping TNFR-binding specificities, TRAF6 binds completely different sites on receptors such as CD40 and RANK. TRAF6 serves as a molecular bridge between innate and adaptive immunity and plays a central role in osteoimmunology. DTRAF2, as an activator of nuclear factor-kappaB, plays a pivotal role in Drosophila development and innate immunity. TRAF6 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors.


Pssm-ID: 239745  Cd Length: 147  Bit Score: 138.61  E-value: 1.40e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 415 GVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVT 494
Cdd:cd03776    1 GIYVWKIKNFSNLRRSMEAGSPVVIHSPGFYTSPPGYKLCARLNLSLPEARCPNYISLFVHLMQGENDSHLDWPFQGTIT 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568979512 495 LMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIAS-GCPVFVAQTVLENGTYIKDDTIFIKVIV 559
Cdd:cd03776   81 LTLLDQSEPRQNIHETMMSKPELLAFQRPTTDRNPKGfGYVEFAHIEDLLQRGFVKNDTLLIKIEV 146
RING-HC_TRAF3 cd16640
RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 3 ...
50-91 1.74e-21

RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 3 (TRAF3) and similar proteins; TRAF3, also known as CAP-1, CD40 receptor-associated factor 1 (CRAF1), CD40-binding protein (CD40BP), or LMP1-associated protein 1 (LAP1), is a member of the TRAF protein family, which mainly functions in the immune system, where it mediates signaling through tumor necrosis factor receptors (TNFRs) and interleukin-1/Toll-like receptors (IL-1/TLRs). It also plays a unique cell type-specific and critical role in the restraint of B-cell homeostatic survival, a role with important implications for both B-cell differentiation and the pathogenesis of B-cell malignancies. TRAF3 differentially regulates differentiation of specific T cell subsets. It is required for iNKT cell development, restrains Treg cell development in the thymus, and plays an essential role in the homeostasis of central memory CD8+ T cells. TRAF3 contains an N-terminal domain with a typical C3HC4-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.


Pssm-ID: 438302 [Multi-domain]  Cd Length: 42  Bit Score: 87.26  E-value: 1.74e-21
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 568979512  50 YKCEKCRLVLCNPKQTECGHRFCESCMAALLSSSSPKCTACQ 91
Cdd:cd16640    1 YKCEKCRLVLCNPKQTECGHRFCESCMNALLSSSNPQCPACE 42
MATH cd00121
MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded ...
415-560 1.02e-19

MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains.


Pssm-ID: 238068  Cd Length: 126  Bit Score: 85.12  E-value: 1.02e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 415 GVLIWKIRDYKRRKQEavmgktlSLYSQPFYTGyfGYKMCARVYLNGDGmGKGTHLSLFFVIMRGEYDaLLPWPFKQKVT 494
Cdd:cd00121    1 GKHTWKIVNFSELEGE-------SIYSPPFEVG--GYKWRIRIYPNGDG-ESGDYLSLYLELDKGESD-LEKWSVRAEFT 69
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568979512 495 LMLMDQgSSRRHLGDAFKPDPNSssfkkptgEMNIASGCPVFVAQTVLENGTYIKDDTIFIKVIVD 560
Cdd:cd00121   70 LKLVNQ-NGGKSLSKSFTHVFFS--------EKGSGWGFPKFISWDDLEDSYYLVDDSLTIEVEVK 126
zf-TRAF pfam02176
TRAF-type zinc finger;
135-191 4.23e-14

TRAF-type zinc finger;


Pssm-ID: 280357 [Multi-domain]  Cd Length: 60  Bit Score: 67.10  E-value: 4.23e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568979512  135 HLKNeCQFEELPCLRADCKEKVLRKDLRDHVEKACKYREATCSH----CKSQVPMIKLQKH 191
Cdd:pfam02176   1 HLET-CPFFPIPCPNGCCKKKILREDLPDHLELDCPKAEVPCPFkvfgCKEDVKREALQRH 60
mRING-HC-C3HC3D_TRAF5 cd16642
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
47-100 2.45e-13

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.


Pssm-ID: 438304 [Multi-domain]  Cd Length: 56  Bit Score: 64.77  E-value: 2.45e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 568979512  47 EDKYKCEKCRLVLCNPKQTECGHRFCESCMAALLS-SSSPKCTACQESIIKDKVF 100
Cdd:cd16642    2 EDRYKCATCHFVLHNPHQTGCGHRFCQHCILSLLElNTTPICPIDKETIKSDEVF 56
MATH smart00061
meprin and TRAF homology;
416-537 4.82e-12

meprin and TRAF homology;


Pssm-ID: 214496 [Multi-domain]  Cd Length: 95  Bit Score: 62.32  E-value: 4.82e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512   416 VLIWKIRDYKRrkqeavMGKTLSLYSQPFYTgyFGYKMCARVYLNGDgmgkgtHLSLFFVIMRGEYDALlPWPFKQKVTL 495
Cdd:smart00061   1 VLSHTFKNVSR------LEEGESYFSPSEEH--FNIPWRLKIYRKNG------FLSLYLHCEKEECDSR-KWSIEAEFTL 65
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 568979512   496 MLMDQGSSRRhlgdafkPDPNSSSFKKPTGemniaSGCPVFV 537
Cdd:smart00061  66 KLVSQNGKSL-------SKKDKHVFEKPSG-----WGFSKFI 95
mRING-HC-C3HC3D_TRAF6 cd16643
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
49-106 6.05e-12

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) and similar proteins; TRAF6, also known as interleukin-1 signal transducer or RING finger protein 85 (RNF85), is a cytoplasmic adapter protein that mediates signals induced by the tumor necrosis factor receptor (TNFR) superfamily and Toll-like receptor (TLR)/interleukin-1 receptor (IL-1R) family. It functions as a mediator involved in the activation of mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase (PI3K), and interferon regulatory factor pathways, as well as in IL-1R-mediated activation of NF-kappaB. TRAF6 is also an oncogene that plays a vital role in K-RAS-mediated oncogenesis. TRAF6 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.


Pssm-ID: 438305 [Multi-domain]  Cd Length: 58  Bit Score: 60.86  E-value: 6.05e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 568979512  49 KYKCEKCRLVLCNPKQTECGHRFCESCMAALLSSSSPKCTACQESIIKDKVFKDNCCK 106
Cdd:cd16643    1 KYECPICLMALREPVQTPCGHRFCKACILKSIREAGHKCPVDNEPLLENQLFPDNFAK 58
MATH_Meprin cd03771
Meprin family, MATH domain; Meprins are multidomain, highly glycosylated extracellular ...
418-554 2.10e-09

Meprin family, MATH domain; Meprins are multidomain, highly glycosylated extracellular metalloproteases, which are either anchored to the membrane or secreted into extracellular spaces. They are expressed in renal and intestinal brush border membranes, leukocytes, and cancer cells, and are capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. Meprin proteases are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. Despite their similarity, the two subunits differ in their ability to self-associate, in proteolytic processing during biosynthesis and in substrate specificity. Both subunits are synthesized as membrane spanning proteins, however, the alpha subunit is cleaved during biosynthesis and loses its transmembrane domain. Meprin beta forms homodimers or heterotetramers while meprin alpha oligomerizes into large complexes containing 10-100 subunits. Both alpha and beta subunits contain a catalytic astacin (M12 family) protease domain followed by the adhesion or interaction domains MAM, MATH and AM. The MATH and MAM domains provide symmetrical intersubunit disulfide bonds necessary for the dimerization of meprin subunits. The MATH domain may also be required for folding of an activable zymogen.


Pssm-ID: 239740  Cd Length: 167  Bit Score: 56.64  E-value: 2.10e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 418 IWKIRDYKRRKQEAvmGKTLSLYSQPFY--TGYfGYKMcaRVYLNGdGMGKGTHLSLFFVIMRGEYDALLPWP-FKQKVT 494
Cdd:cd03771    5 VWRVRNFSQLLETT--PKGTKIYSPRFYspEGY-AFQV--GLYPNG-TESYPGYTGLYFHLCSGENDDVLEWPcPNRQAT 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 495 LMLMDQGSS-RRHLGDA--FKPDPNSSS-----------------FKKPTGEM---NIASGCPVFVAQTVLENGTYIK-D 550
Cdd:cd03771   79 MTLLDQDPDiQQRMSNQrsFTTDPSMTSsdngeyfwdrpskvgsyDTDTNGCTcyrGPGYGWSTFISHSRLRRRDFLKgD 158

                 ....
gi 568979512 551 DTIF 554
Cdd:cd03771  159 DLII 162
RING-HC_TRAF2 cd16639
RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 2 ...
49-90 1.37e-08

RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 2 (TRAF2) and similar proteins; TRAF2, also known as tumor necrosis factor type 2 receptor-associated protein 3, is an E3 ubiquitin-protein ligase that was identified as a 75 kDa tumor necrosis factor receptor (TNF-R2)-associated signaling protein. It interacts with members of the TNF receptor superfamily and connects the receptors to downstream signaling proteins. It also mediates K63-linked polyubiquitination of RIP1, a kinase pivotal in TNFalpha-induced NF-kappaB activation. Moreover, TRAF2 regulates peripheral CD8(+) T-cell and NKT-cell homeostasis by modulating sensitivity to IL-15. It also acts as an important biological suppressor of necroptosis. It inhibits TNF-related apoptosis inducing ligand (TRAIL)- and CD95L-induced apoptosis and necroptosis. TRAF2 contains an N-terminal domain with a typical C3HC4-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.


Pssm-ID: 438301 [Multi-domain]  Cd Length: 43  Bit Score: 50.92  E-value: 1.37e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 568979512  49 KYKCEKCRLVLCNPKQTECGHRFCESCMAALLSSSSPKCTAC 90
Cdd:cd16639    1 KYLCSDCRNILRRPFQAQCGHRYCSYCLKKILSSGPQKCAAC 42
mRING-HC-C3HC3D_TRAF4-like cd23126
Modified RING finger, HC subclass (C3HC3D-type), found in uncharacterized proteins similar to ...
46-97 7.92e-07

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.


Pssm-ID: 438488 [Multi-domain]  Cd Length: 52  Bit Score: 46.18  E-value: 7.92e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 568979512  46 VEDKYKCEKCRLVLCNPKQ-TECGHRFCESCMAALLsSSSPKCTACQESIIKD 97
Cdd:cd23126    1 LDKKYECPVCCQVLRYPVQfEECGHRVCSSCLPELL-RVEPRCPIDQGPIDRD 52
Cast pfam10174
RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part ...
243-389 8.08e-07

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.


Pssm-ID: 431111 [Multi-domain]  Cd Length: 766  Bit Score: 52.13  E-value: 8.08e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  243 TNQQikaheaSSAVQHVNLLKEWSNSLEKKVSLLQNES--------------VEKNKSIQSLHNQICSFEIEIERQKEML 308
Cdd:pfam10174 316 TNQN------SDCKQHIEVLKESLTAKEQRAAILQTEVdalrlrleekesflNKKTKQLQDLTEEKSTLAGEIRDLKDML 389
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  309 RNNESKILHLQRVIDSQAEKLKELDKEIrpfrqnweeaDSMKSSVESLQ----NRVTELESVDKSAGQAARNTGLLESQL 384
Cdd:pfam10174 390 DVKERKINVLQKKIENLQEQLRDKDKQL----------AGLKERVKSLQtdssNTDTALTTLEEALSEKERIIERLKEQR 459

                  ....*
gi 568979512  385 SRHDQ 389
Cdd:pfam10174 460 EREDR 464
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
257-367 1.00e-06

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.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 51.56  E-value: 1.00e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  257 QHVNLLKEWSNSLEKKVSLLQNESVEKNKSIQSLHNQICSFEIEIERQKEMLRNNESKILHLQRVIDSQAEKLKELDKEI 336
Cdd:TIGR04523 335 KIISQLNEQISQLKKELTNSESENSEKQRELEEKQNEIEKLKKENQSYKQEIKNLESQINDLESKIQNQEKLNQQKDEQI 414
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 568979512  337 RPFRQNWE----EADSMKSSVESLQNRVTELESVD 367
Cdd:TIGR04523 415 KKLQQEKEllekEIERLKETIIKNNSEIKDLTNQD 449
MATH_Meprin_Beta cd03782
Meprin family, Beta subunit, MATH domain; Meprins are multidomain extracellular ...
418-555 2.51e-06

Meprin family, Beta subunit, MATH domain; Meprins are multidomain extracellular metalloproteases capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. They are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. The beta subunit is a type I membrane protein, which forms homodimers or heterotetramers (alpha2beta2 or alpha3beta). Meprin beta shows preference for acidic residues at the P1 and P1' sites of its substrate. Among its best substrates are growth factors and chemokines such as gastrin and osteopontin. Both alpha and beta subunits contain a catalytic astacin (M12 family) protease domain followed by the adhesion or interaction domains MAM, MATH and AM. The MATH and MAM domains provide symmetrical intersubunit disulfide bonds necessary for the dimerization of meprin subunits. The MATH domain may also be required for folding of an activable zymogen.


Pssm-ID: 239751  Cd Length: 167  Bit Score: 47.93  E-value: 2.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 418 IWKIRDYKRrkqeaVMGKTL---SLYSQPFYTGYfGYKMCARVYLNGDGMGKGtHLSLFFVIMRGEYDALLPWPFK-QKV 493
Cdd:cd03782    5 IWHIRNFTQ-----LLATTPpngKIYSPPFLSST-GYSFQVGLYLNGTDDYPG-NLAIYLHLTSGPNDDQLQWPCPwQQA 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 494 TLMLMDQGSS-RRHLG-------DAFK--------------------PDPNSSSFKKPTGemniaSGCPVFVAQTVLENG 545
Cdd:cd03782   78 TMMLLDQHPDiRQRMSnqrsvttDPNMtstdsdeyfwddprkvgsevTDTDGSTFYRGPG-----YGTSAFITHLRLRSR 152
                        170
                 ....*....|
gi 568979512 546 TYIKDDTIFI 555
Cdd:cd03782  153 DFIKGDDVIF 162
RING-HC_TRAF1-like cd23125
RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 1 ...
47-92 2.51e-06

RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 1 (TRAF1)-like and similar proteins; TRAF1, also known as Epstein-Barr virus-induced protein 6 (EBI6), is an adapter molecule that regulates the activation of NF-kappa-B and JNK. It plays a role in the regulation of cell survival and apoptosis. The heterotrimer formed by TRAF1 and TRAF2 is part of an E3 ubiquitin-protein ligase complex that promotes ubiquitination of target proteins, such as MAP3K14. The TRAF1/TRAF2 complex recruits the antiapoptotic E3 protein-ubiquitin ligases BIRC2 and BIRC3 to TNFRSF1B/TNFR2. This subfamily corresponds a group of TRAF1-like proteins that contains an N-terminal domain with a typical C3HC4-type RING-HC finger.


Pssm-ID: 438487 [Multi-domain]  Cd Length: 51  Bit Score: 44.82  E-value: 2.51e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 568979512  47 EDKYKCEKCRLVLCNPKQTECGHRFCESCMAALL-SSSSPKCTACQE 92
Cdd:cd23125    2 EEKYLCCNCKNVLKKAQQTLCGHRYCLACLSWIVrNNKNPICQKCKE 48
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
50-90 4.47e-06

HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers. Some have a different Cys/His pattern. Some lack a single Cys or His residue at typical Zn ligand positions, especially, the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can chelate Zn in a RING finger as well. This family corresponds to the HC subclass of RING (RING-HC) fingers that are characterized by containing C3HC4-type canonical RING-HC fingers or noncanonical RING-HC finger variants, including C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type modified RING-HC fingers. The canonical RING-HC finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-HC fingers can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle, and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates.


Pssm-ID: 438113 [Multi-domain]  Cd Length: 41  Bit Score: 43.63  E-value: 4.47e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 568979512  50 YKCEKCRLVLCNPKQTECGHRFCESCMAALLSSSSPKCTAC 90
Cdd:cd16449    1 LECPICLERLKDPVLLPCGHVFCRECIRRLLESGSIKCPIC 41
zf-TRAF pfam02176
TRAF-type zinc finger;
196-246 9.66e-06

TRAF-type zinc finger;


Pssm-ID: 280357 [Multi-domain]  Cd Length: 60  Bit Score: 43.21  E-value: 9.66e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568979512  196 CPCVVVSCPHKCSVQTLLRSELSAHLSE-CVNAPSTCSFKRYGC--VFQGTNQQ 246
Cdd:pfam02176   5 CPFFPIPCPNGCCKKKILREDLPDHLELdCPKAEVPCPFKVFGCkeDVKREALQ 58
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
267-364 1.37e-05

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.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 48.09  E-value: 1.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  267 NSLEKKVSLLQNESVEKNKSIQSLHNQICSFEIEIERqkemlrnneskilhLQRVIDSQAEKLKELDKEIRPFRQNWE-- 344
Cdd:TIGR04523 422 ELLEKEIERLKETIIKNNSEIKDLTNQDSVKELIIKN--------------LDNTRESLETQLKVLSRSINKIKQNLEqk 487
                          90       100
                  ....*....|....*....|..
gi 568979512  345 --EADSMKSSVESLQNRVTELE 364
Cdd:TIGR04523 488 qkELKSKEKELKKLNEEKKELE 509
HEC1 COG5185
Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell ...
244-411 2.88e-05

Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 444066 [Multi-domain]  Cd Length: 594  Bit Score: 46.87  E-value: 2.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 244 NQQIKAHEASSAVQHVNLLKEWSNSLEKKVSLLQ---NESVEKN---KSIQSLHNQICSFEI--EIERQKemlRNNESKI 315
Cdd:COG5185  262 NTDLRLEKLGENAESSKRLNENANNLIKQFENTKekiAEYTKSIdikKATESLEEQLAAAEAeqELEESK---RETETGI 338
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 316 LHLQRVIDSQAEKLKELDKEIRPFRQNWEEADSMKSSVESLQNRVTELESVDKSAGQAARN----TGLLESQLSRHdqmL 391
Cdd:COG5185  339 QNLTAEIEQGQESLTENLEAIKEEIENIVGEVELSKSSEELDSFKDTIESTKESLDEIPQNqrgyAQEILATLEDT---L 415
                        170       180
                 ....*....|....*....|..
gi 568979512 392 SVHDIRLADM--DLRFQVLETA 411
Cdd:COG5185  416 KAADRQIEELqrQIEQATSSNE 437
RING-HC_RNF125 cd16542
RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as ...
50-91 8.79e-05

RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as T-cell RING activation protein 1 (TRAC-1), is an E3 ubiquitin-protein ligase that is predominantly expressed in lymphoid cells, and functions as a positive regulator of T cell activation. It also down-modulates HIV replication and inhibits pathogen-induced cytokine production. It negatively regulates type I interferon signaling, which conjugates Lys(48)-linked ubiquitination to retinoic acid-inducible gene-I (RIG-I) and subsequently leads to the proteasome-dependent degradation of RIG-I. Further, RNF125 conjugates ubiquitin to melanoma differentiation-associated gene 5 (MDA5), a family protein of RIG-I. It thus acts as a negative regulator of RIG-I signaling, and is a direct target of miR-15b in the context of Japanese encephalitis virus (JEV) infection. Moreover, RNF125 binds to and ubiquitinates JAK1, prompting its degradation and inhibition of receptor tyrosine kinase (RTK) expression. It also negatively regulates p53 function through physical interaction and ubiquitin-mediated proteasome degradation. Mutations in RNF125 may lead to overgrowth syndromes (OGS). RNF125, together with three closely related proteins: RNF114, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM). The UIM of RNF125 binds K48-linked poly-ubiquitin chains and is, together with the RING domain, required for auto-ubiquitination.


Pssm-ID: 438204 [Multi-domain]  Cd Length: 50  Bit Score: 40.25  E-value: 8.79e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 568979512  50 YKCEKCRLVLCNPKQTECGHRFCESCMAALLSSSSPKCTACQ 91
Cdd:cd16542    2 FDCAVCLEVLHQPVRTRCGHVFCRPCIATSLRNNTWTCPYCR 43
RING-HC_LONFs_rpt2 cd16514
second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
52-94 1.02e-04

second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family; The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the second RING-HC finger.


Pssm-ID: 438177 [Multi-domain]  Cd Length: 45  Bit Score: 39.94  E-value: 1.02e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 568979512  52 CEKCRLVLCNPKQTECGHRFCESCMAALLsSSSPKCTACQESI 94
Cdd:cd16514    4 CSLCLRLLYEPVTTPCGHTFCRACLERCL-DHSPKCPLCRTSL 45
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
245-365 1.48e-04

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.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 44.63  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  245 QQIKAhEASSAVQHVNLLKEWSNSLEKKVSLLQNESVEKNKSIQSLHNQICSFEIEIERQKEMLRNNESKILHLQrvIDS 324
Cdd:TIGR04523 242 NEKTT-EISNTQTQLNQLKDEQNKIKKQLSEKQKELEQNNKKIKELEKQLNQLKSEISDLNNQKEQDWNKELKSE--LKN 318
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 568979512  325 QAEKLKELDKEIrpfRQNWEEADSMKSSVESLQNRVTELES 365
Cdd:TIGR04523 319 QEKKLEEIQNQI---SQNNKIISQLNEQISQLKKELTNSES 356
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
259-365 1.51e-04

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.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 44.63  E-value: 1.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  259 VNLLKEWSNSLEKKVSLLQNESVEKNKSIQSLHNQICSFEIEIERQKEMLRNNESKILHLQRVIDSQAEKLKELDKEIRP 338
Cdd:TIGR04523 220 ISELKKQNNQLKDNIEKKQQEINEKTTEISNTQTQLNQLKDEQNKIKKQLSEKQKELEQNNKKIKELEKQLNQLKSEISD 299
                          90       100       110
                  ....*....|....*....|....*....|.
gi 568979512  339 FR----QNWEEadSMKSSVESLQNRVTELES 365
Cdd:TIGR04523 300 LNnqkeQDWNK--ELKSELKNQEKKLEEIQN 328
vRING-HC-C4C4_RBBP6 cd16620
Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) ...
48-99 2.22e-04

Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) and similar proteins; RBBP6, also known as proliferation potential-related protein, protein P2P-R, retinoblastoma-binding Q protein 1 (RBQ-1), or p53-associated cellular protein of testis (PACT), is a nuclear E3 ubiquitin-protein ligase involved in multiple processes, such as the control of gene expression, mitosis, cell differentiation, and cell apoptosis. It plays a role in both promoting and inhibiting apoptosis in many human cancers, including esophageal, lung, hepatocellular, and colon cancers, familial myeloproliferative neoplasms, as well as in human immunodeficiency virus-associated nephropathy (HIVAN). It functions as an Rb- and p53-binding protein that plays an important role in chaperone-mediated ubiquitination and possibly in protein quality control. It acts as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in an increase of MDM2-mediated ubiquitination and degradation of p53/TP53, and leading to both apoptosis and cell growth. It is also a double-stranded RNA-binding protein that plays a role in mRNA processing by regulating the human polyadenylation machinery and modulating expression of mRNAs with AU-rich 3' untranslated regions (UTRs). Moreover, RBBP6 ubiquitinates and destabilizes the transcriptional repressor ZBTB38 that negatively regulates transcription and levels of the MCM10 replication factor on chromatin. Furthermore, RBBP6 is involved in tunicamycin-induced apoptosis by mediating protein kinase (PKR) activation. RBBP6 contains an N-terminal ubiquitin-like domain and a C4C4-type RING finger, whose overall folding is similar to that of the typical C3HC4-type RING-HC finger. RBBP6 interacts with chaperones Hsp70 and Hsp40 through its N-terminal ubiquitin-like domain. It promotes the ubiquitination of p53 by Hdm2 in an E4-like manner through its RING finger. It also interacts directly with the pro-proliferative transcription factor Y-box-binding protein-1 (YB-1) via its RING finger.


Pssm-ID: 438282 [Multi-domain]  Cd Length: 55  Bit Score: 39.31  E-value: 2.22e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 568979512  48 DKYKCEKCRLVLCNPKQTEC-GHRFCESCMAALLSSSSPKCTACQESIIKDKV 99
Cdd:cd16620    2 DELKCPICKDLMKDAVLTPCcGNSFCDECIRTALLEEDFTCPTCKEPDVSPDA 54
RING-HC_RAD5 cd23131
RING finger, HC subclass, found in radiation sensitivity protein 5 (RAD5) and similar proteins; ...
65-101 3.09e-04

RING finger, HC subclass, found in radiation sensitivity protein 5 (RAD5) and similar proteins; RAD5, also known as revertibility protein 2 (REV2), or DNA repair protein RAD5, is a probable helicase, and a member of the UBC2/RAD6 epistasis group. It functions with the DNA repair protein RAD18 in error-free postreplication DNA repair. It is involved in the maintenance of wild-type rates of instability of simple repetitive sequences such as poly(GT) repeats. It may also be involved in maintaining a balance which acts in favor of error-prone non-homologous joining during DNA double-strand breaks repairs. It recruits the UBC13-MMS2 dimer to chromatin for DNA repair. RAD5 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438493 [Multi-domain]  Cd Length: 65  Bit Score: 39.35  E-value: 3.09e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 568979512  65 TECGHRFCESCMAALL-----SSSSPKCTACQESIIKDKVFK 101
Cdd:cd23131   22 TECGHSFCEDCLLEYIefqnkKKLDLKCPNCREPISKYRLLK 63
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
260-365 3.12e-04

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.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 43.86  E-value: 3.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  260 NLLKEWSNSLEKKVSLLQNESVEKNKSIQSLHNQICSfeieIERQKEMLRNNESKIlhlQRVIdsqAEKLKELDKEIRpf 339
Cdd:TIGR04523 310 KELKSELKNQEKKLEEIQNQISQNNKIISQLNEQISQ----LKKELTNSESENSEK---QREL---EEKQNEIEKLKK-- 377
                          90       100
                  ....*....|....*....|....*.
gi 568979512  340 rqnweEADSMKSSVESLQNRVTELES 365
Cdd:TIGR04523 378 -----ENQSYKQEIKNLESQINDLES 398
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
233-439 4.11e-04

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 43.22  E-value: 4.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 233 FKRYGCVFQGTNQQIKA-----HEASSAVQHVNLLKEWSNSLEKKVSLLQNESVEKNKSIQSLHNQICSFEIEIERQKem 307
Cdd:COG4717   59 FKPQGRKPELNLKELKEleeelKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKLLQLLPLYQELEA-- 136
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 308 lrnneskilhLQRVIDSQAEKLKELDKEIRPFRQNWEEADSMKSSVESLQNRVTELE-----SVDKSAGQAARNTGLLES 382
Cdd:COG4717  137 ----------LEAELAELPERLEELEERLEELRELEEELEELEAELAELQEELEELLeqlslATEEELQDLAEELEELQQ 206
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 568979512 383 QLSRHDQMLSVHDIRLADMDLRFQVLETASyngvliWKIRDYKRRKQEAVMGKTLSL 439
Cdd:COG4717  207 RLAELEEELEEAQEELEELEEELEQLENEL------EAAALEERLKEARLLLLIAAA 257
MATH_Meprin_Alpha cd03783
Meprin family, Alpha subunit, MATH domain; Meprins are multidomain extracellular ...
418-557 5.08e-04

Meprin family, Alpha subunit, MATH domain; Meprins are multidomain extracellular metalloproteases capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. They are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. The alpha subunit is synthesized as a membrane spanning protein, however, it is cleaved during biosynthesis and loses its transmembrane domain. It oligomerizes into large complexes, containing 10-100 subunits (dimers that associate noncovalently), which are secreted as latent proteases and can move through extracellular spaces in a nondestructive manner. This allows delivery of the concentrated protease to sites containing activating enzymes, such as sites of inflammation, infection or cancerous growth. Meprin alpha shows preference for small or hydrophobic residues at the P1 and P1' sites of its substrate. Both alpha and beta subunits contain a catalytic astacin (M12 family) protease domain followed by the adhesion or interaction domains MAM, MATH and AM. The MATH and MAM domains provide symmetrical intersubunit disulfide bonds necessary for the dimerization of meprin subunits. The MATH domain may also be required for folding of an activable zymogen.


Pssm-ID: 239752  Cd Length: 167  Bit Score: 41.00  E-value: 5.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 418 IWKIRDYKRRKQEAVmgKTLSLYSQPFYTGYfGYKMCARVY-LNGDGMGKGTHLSLFFVIMRGEYDALLPWP-FKQKVTL 495
Cdd:cd03783    5 VWRVRNFSQILENTT--KGDVLQSPRFYSPE-GYGYGVSLYpLSNESDYSGNYTGLYFHLCSGENDAVLEWPaLNRQAII 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 496 MLMDQ--------GSSRRHLGDAFKPDP---NSSSFKKPT--GEMNIASGC--------PVFVAQTVLENGTYIKDDTIF 554
Cdd:cd03783   82 TVLDQdpdvrlrmSSSRSFTTDKSQTSSainGTLRWDRPSrvGTYDTSCDCfrgidfgwSTFISHSQLRRRSFLKNDDLI 161

                 ...
gi 568979512 555 IKV 557
Cdd:cd03783  162 IFV 164
RING-HC_BRCA1 cd16498
RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and ...
52-96 5.30e-04

RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and similar proteins; BRCA1, also known as RING finger protein 53 (RNF53), is a RING finger protein encoded by the tumor suppressor gene BRCA1 that regulates all DNA double-strand break (DSB) repair pathways. BRCA1 is frequently mutated in patients with hereditary breast and ovarian cancer (HBOC). Its mutation is also associated with an increased risk of pancreatic, stomach, laryngeal, fallopian tube, and prostate cancer. It plays an important role in the DNA damage response signaling and has been implicated in various cellular processes such as cell cycle regulation, transcriptional regulation, chromatin remodeling, DNA DSBs, and apoptosis. BRCA1 contains an N-terminal C3HC4-type RING-HC finger, and two BRCT (BRCA1 C-terminus domain) repeats at the C-terminus.


Pssm-ID: 438161 [Multi-domain]  Cd Length: 94  Bit Score: 39.20  E-value: 5.30e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 568979512  52 CEKCRLVLCNPKQTECGHRFCESCMAALLSSSSPK--CTACQESIIK 96
Cdd:cd16498   19 CPICLELLKEPVSTKCDHQFCRFCILKLLQKKKKPapCPLCKKSVTK 65
RING-HC_RNF138 cd16544
RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; ...
48-98 5.50e-04

RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; RNF138, also known as Nemo-like kinase-associated RING finger protein (NARF) or NLK-associated RING finger protein, is an E3 ubiquitin-protein ligase that plays an important role in glioma cell proliferation, apoptosis, and cell cycle. It specifically cooperates with the E2 conjugating enzyme E2-25K (Hip-2/UbcH1), regulates the ubiquitylation and degradation of T cell factor/lymphoid enhancer factor (TCF/LEF), and further suppresses Wnt-beta-catenin signaling. RNF138, together with three closely related proteins: RNF114, RNF125 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).


Pssm-ID: 438206 [Multi-domain]  Cd Length: 53  Bit Score: 38.15  E-value: 5.50e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 568979512  48 DKYKCEKCRLVLCNPKQTE-CGHRFCESCMAALLSSSSPKCTACQESIIKDK 98
Cdd:cd16544    1 AELTCPVCQEVLKDPVELPpCRHIFCKACILLALRSSGARCPLCRGPVGKTE 52
mRING-HC-C3HC3D_TRAF4 cd16641
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
49-87 6.07e-04

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 4 (TRAF4) and similar proteins; TRAF4, also known as cysteine-rich domain associated with RING and Traf domains protein 1, metastatic lymph node gene 62 protein (MLN 62), or RING finger protein 83 (RNF83), is a member of the 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 nervous system, as well as in carcinogenesis. TRAF4 promotes the growth and invasion of colon cancer through the Wnt/beta-catenin pathway. It contributes to the TNFalpha-induced activation of the 70 kDa ribosomal protein S6 kinase (p70s6k) signaling pathway, and activation of transforming growth factor beta (TGF-beta)-induced SMAD-dependent signaling and non-SMAD signaling in breast cancer. It also enhances osteosarcoma cell proliferation and invasion by the Akt signaling pathway. Moreover, TRAF4 is a novel phosphoinositide-binding protein modulating tight junctions and favoring cell migration. TRAF4 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.


Pssm-ID: 438303 [Multi-domain]  Cd Length: 45  Bit Score: 37.82  E-value: 6.07e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 568979512  49 KYKCEKCRLVLCNPKQ-TECGHRFCESCMAALLSSSSPKC 87
Cdd:cd16641    1 RLLCPLCRLPMREPVQiSTCGHRFCDTCLQEFLSEGVFKC 40
RING-HC_RNF113A_B cd16539
RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; ...
51-92 6.72e-04

RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; RNF113A, also known as zinc finger protein 183 (ZNF183), is an E3 ubiquitin-protein ligase that physically interacts with the E2 protein, UBE2U. A nonsense mutation in RNF113A is associated with an X-linked trichothiodystrophy (TTD). Its yeast ortholog Cwc24p is predicted to have a spliceosome function and acts in a complex with Cef1p to participate in pre-U3 snoRNA splicing, indirectly affecting pre-rRNA processing. It is also important for the U2 snRNP binding to primary transcripts and co-migrates with spliceosomes. Moreover, the ortholog of RNF113A in fruit flies may also act as a spliceosome and is hypothesized to be involved in splicing, namely within the central nervous system. The ortholog in Caenorhabditis elegans is involved in DNA repair of inter-strand crosslinks. RNF113B, also known as zinc finger protein 183-like 1, shows high sequence similarity with RNF113A. Both RNF113A and RNF113B contain a CCCH-type zinc finger, which is commonly found in RNA-binding proteins involved in splicing, and a C3HC4-type RING-HC finger, which is frequently found in E3 ubiquitin ligases.


Pssm-ID: 438201 [Multi-domain]  Cd Length: 54  Bit Score: 37.96  E-value: 6.72e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 568979512  51 KCEKCRLVLCNPKQTECGHRFCESCmAALLSSSSPKCTACQE 92
Cdd:cd16539    7 ACFICRKPFKNPVVTKCGHYFCEKC-ALKHYRKSKKCFVCGK 47
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
51-230 7.04e-04

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


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 42.00  E-value: 7.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  51 KCEKCRLVLCNPKQTECGHRFCESCMAALLsSSSPKCTACQESiIKDKVFKDNCCKREIlaLQVYCRNEGRgcaeqltlg 130
Cdd:COG5432   27 RCRICDCRISIPCETTCGHTFCSLCIRRHL-GTQPFCPVCRED-PCESRLRGSSGSREI--NESHARNRDL--------- 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 131 hLLVHLKNECQFEELPCLRADCKEKVLRKDLRDHVEKACKYREATCSH----CKSQVPMIKLQKHED-TDCPCVVVSCPH 205
Cdd:COG5432   94 -LRKVLESLCRLPRPIKEERPCRWETVIAQDSASGDEEWEDDLASNSSpasiAKKTSRDSKKRKREDlVHCPACSNLVPH 172
                        170       180
                 ....*....|....*....|....*
gi 568979512 206 KcsvqtllrsELSAHLSECVNAPST 230
Cdd:COG5432  173 N---------QINQHLDSCLNSPSS 188
COG5222 COG5222
Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];
51-109 7.07e-04

Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];


Pssm-ID: 227547 [Multi-domain]  Cd Length: 427  Bit Score: 42.43  E-value: 7.07e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568979512  51 KCEKCRLVLCNPKQTE-CGHRFCESCMAALLSSSSPKCTACQ-ESIIKDKVFKDNCCKREI 109
Cdd:COG5222  276 KCPLCHCLLRNPMKTPcCGHTFCDECIGTALLDSDFKCPNCSrKDVLLDGLTPDIDKKLEV 336
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
55-90 1.05e-03

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


Pssm-ID: 395049 [Multi-domain]  Cd Length: 40  Bit Score: 36.95  E-value: 1.05e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 568979512   55 CRLVLCNPKQ----TECGHRFCESCMAALLSSSSPKCTAC 90
Cdd:pfam00097   1 CPICLEEPKDpvtlLPCGHLFCSKCIRSWLESGNVTCPLC 40
RING-HC_RNF114 cd16540
RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; ...
49-91 1.09e-03

RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; RNF114, also known as zinc finger protein 228 (ZNF228) or zinc finger protein 313 (ZNF313), is a p21(WAF1)-targeting ubiquitin E3 ligase that interacts with X-linked inhibitor of apoptosis (XIAP)-associated factor 1 (XAF1) and may play a role in p53-mediated cell-fate decisions. It is involved in the immune response to double-stranded RNA in disease pathogenesis. Moreover, RNF114 interacts with A20 and modulates its ubiquitylation. It negatively regulates nuclear factor-kappaB (NF-kappaB)-dependent transcription and positively regulates T-cell activation. RNF114 may play a putative role in the regulation of immune responses, since it corresponds to a novel psoriasis susceptibility gene, ZNF313. RNF114, together with three closely related proteins: RNF125, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).


Pssm-ID: 438202 [Multi-domain]  Cd Length: 46  Bit Score: 37.05  E-value: 1.09e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 568979512  49 KYKCEKCRLVLCNPKQTECGHRFCESCMAALLSSSSPKCTACQ 91
Cdd:cd16540    1 RFTCPVCLEIFETPVRVPCGHVFCNACLQECLKPKKPVCAVCR 43
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
52-87 1.46e-03

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 36.72  E-value: 1.46e-03
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 568979512    52 CEKCR-LVLCNPKQTECGHRFCESCMAALLSSSSPKC 87
Cdd:smart00184   1 CPICLeEYLKDPVILPCGHTFCRSCIRKWLESGNNTC 37
Cast pfam10174
RIM-binding protein of the cytomatrix active zone; This is a family of proteins that form part ...
269-398 1.75e-03

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.


Pssm-ID: 431111 [Multi-domain]  Cd Length: 766  Bit Score: 41.35  E-value: 1.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  269 LEKKVSLLQNESVEKNKSIQSLHNQ--------------ICSFEIEIERQKEMLRNNESKILHLQRVIDSQ------AEK 328
Cdd:pfam10174 480 LKEKVSALQPELTEKESSLIDLKEHasslassglkkdskLKSLEIAVEQKKEECSKLENQLKKAHNAEEAVrtnpeiNDR 559
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568979512  329 LKELDKEIRPFRqnwEEADSMKSSVESLQN--RVTELESVDKSAGQAArntglLESQLSRH--DQMLSVHDIRL 398
Cdd:pfam10174 560 IRLLEQEVARYK---EESGKAQAEVERLLGilREVENEKNDKDKKIAE-----LESLTLRQmkEQNKKVANIKH 625
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
270-363 2.41e-03

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.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 40.77  E-value: 2.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  270 EKKVSLLQNESVEKNKSIQSLHNQICSFEIEIERQKEMLRNNESKILHLQRVIDSQAEKLKELDKEIRPFRQNWEEADSM 349
Cdd:TIGR04523 553 ELKKENLEKEIDEKNKEIEELKQTQKSLKKKQEEKQELIDQKEKEKKDLIKEIEEKEKKISSLEKELEKAKKENEKLSSI 632
                          90
                  ....*....|....
gi 568979512  350 KSSVESLQNRVTEL 363
Cdd:TIGR04523 633 IKNIKSKKNKLKQE 646
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
268-365 2.51e-03

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.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 40.77  E-value: 2.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512  268 SLEKKVSLLQNESVEKNKSIQSLHNQICSFEIEI-------ERQKEMLRNNESKILHLQRVIDSQAEKLKELDKEIrpfr 340
Cdd:TIGR04523 444 DLTNQDSVKELIIKNLDNTRESLETQLKVLSRSInkikqnlEQKQKELKSKEKELKKLNEEKKELEEKVKDLTKKI---- 519
                          90       100
                  ....*....|....*....|....*
gi 568979512  341 qnweeaDSMKSSVESLQNRVTELES 365
Cdd:TIGR04523 520 ------SSLKEKIEKLESEKKEKES 538
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
43-96 2.57e-03

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


Pssm-ID: 273165 [Multi-domain]  Cd Length: 397  Bit Score: 40.37  E-value: 2.57e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568979512   43 VKTVEDKYKCEKCRLVLCNPKQTECGHRFCESCMAALLsSSSPKCTAC----QESIIK 96
Cdd:TIGR00599  20 LYPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCL-SNQPKCPLCraedQESKLR 76
RING-HC_UHRF1 cd16769
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
41-103 2.98e-03

RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1, also known as inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1, is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 can acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also a N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET and RING finger associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintenance DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD domain targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-HC finger exhibits both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 438425 [Multi-domain]  Cd Length: 84  Bit Score: 36.95  E-value: 2.98e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568979512  41 KFVKTVEDKYKCEKCRLVLCNPKQTECGHRFCESCMAALLSSSSPKCTACQESIIKDKVFKDN 103
Cdd:cd16769    4 LFLSKVEETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGRSYAMQVN 66
DR0291 COG1579
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ...
269-365 3.26e-03

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];


Pssm-ID: 441187 [Multi-domain]  Cd Length: 236  Bit Score: 39.52  E-value: 3.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 269 LEKKVSLLQNESVEKNKSIQSLHNQICSFEIEIERQKEMLRNNESKILH---------LQRVIDSQAEKLKELDKEIRPF 339
Cdd:COG1579   36 LEDELAALEARLEAAKTELEDLEKEIKRLELEIEEVEARIKKYEEQLGNvrnnkeyeaLQKEIESLKRRISDLEDEILEL 115
                         90       100
                 ....*....|....*....|....*.
gi 568979512 340 rqnWEEADSMKSSVESLQNRVTELES 365
Cdd:COG1579  116 ---MERIEELEEELAELEAELAELEA 138
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
270-390 4.28e-03

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]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 40.05  E-value: 4.28e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512   270 EKKVSLLQNESVEKNKSIQSLHNQICSFEIEIERQKEMLRNNESKILHLQRVIDSQAEKLKEL-DKEIRPFRqnwEEADS 348
Cdd:TIGR02169  222 EYEGYELLKEKEALERQKEAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLgEEEQLRVK---EKIGE 298
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 568979512   349 MKSSVESLQNRVTELES-VDKSAGQAARNTGLLESQLSRHDQM 390
Cdd:TIGR02169  299 LEAEIASLERSIAEKEReLEDAEERLAKLEAEIDKLLAEIEEL 341
RING-HC_LNX3 cd16718
RING finger, HC subclass, found in ligand of numb protein X 3 (LNX3); LNX3, also known as PDZ ...
46-76 5.20e-03

RING finger, HC subclass, found in ligand of numb protein X 3 (LNX3); LNX3, also known as PDZ domain-containing RING finger protein 3 (PDZRN3), or Semaphorin cytoplasmic domain-associated protein 3 (SEMACAP3), is an E3 ubiquitin-protein ligase that was first identified as a Semaphorin-binding partner. It is also responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. LNX3 acts as a negative regulator of osteoblast differentiation by inhibiting Wnt-beta-catenin signaling. LNX3 also plays an important role in neuromuscular junction formation. It interacts with and ubiquitinates the muscle specific tyrosine kinase (MuSK), thus promoting its endocytosis and negatively regulating the cell surface expression of this key regulator of postsynaptic assembly. LNX3 contains an N-terminal C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain.


Pssm-ID: 438378 [Multi-domain]  Cd Length: 47  Bit Score: 35.35  E-value: 5.20e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 568979512  46 VEDKYKCEKCRLVLCNPKQTECGHRFCESCM 76
Cdd:cd16718    1 VDPDFKCNLCNKVLEDPLTTPCGHVFCAGCV 31
MukF_N cd16335
bacterial condensin complex subunit MukF, N-terminal domain; MukF is part of the MukBEF ...
276-402 5.53e-03

bacterial condensin complex subunit MukF, N-terminal domain; MukF is part of the MukBEF condensin complex that is mainly found in proteobacteria and is involved in chromosome organization and condensation. The complex is believed to serve as a part of the chromosome scaffold rather than a bulk DNA packing protein. MukE and MukF form a stable complex with each other and dynamically associate with MukB, a member of the SMC protein family. MukEF does not bind DNA on its own but modulates MukB-DNA activity. The stoichiometry of the MukEF complex is MukE4F2.


Pssm-ID: 319981  Cd Length: 315  Bit Score: 39.17  E-value: 5.53e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 276 LQNESVEKNksIQSLHNQicSFEIEIERQKEMLRNNESKILHLQRVIDSQAEKLKELDKEIRPFRQNwEEADSMKSSVES 355
Cdd:cd16335  168 AQQQQLRAE--IASLLSQ--DWFAAIDQCEELLQETAGTLRDLQDLLLASADKLLALLLEIQEAAEQ-AGPEEAQNAVQD 242
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 568979512 356 LQNRvteLESVDKSAGQAARntgllesQLSRHDQMlsVHD-IRLA-DMD 402
Cdd:cd16335  243 LQDQ---LDRIRAWGNQRLR-------DWSEYHRR--VHRfIRTViRLD 279
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
262-406 6.39e-03

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]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 39.65  E-value: 6.39e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512   262 LKEWSNSLEKKVSLLQNESVEKNKSIQSLHNQICSFEIEIERQKEMLRNNESKILHLQRVIDSQaeKLKELDKEIRPFRQ 341
Cdd:TIGR02168  370 LESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQEIEELLKKLEEA--ELKELQAELEELEE 447
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568979512   342 NWEEAdsmkssVESLQNRVTELESVDKSAGQAARNTGLLESQLSRHDQMLSVhdirLADMDLRFQ 406
Cdd:TIGR02168  448 ELEEL------QEELERLEEALEELREELEEAEQALDAAERELAQLQARLDS----LERLQENLE 502
COG2433 COG2433
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
269-344 7.59e-03

Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];


Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 39.07  E-value: 7.59e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568979512 269 LEKKVSLLQNESVEKNKSIQSLHNQIcsFEIEIERQKEMLRNNESKIL-----HLQRVIDSQAEKLKELDKEIRPFRQNW 343
Cdd:COG2433  425 LEAEVEELEAELEEKDERIERLEREL--SEARSEERREIRKDREISRLdreieRLERELEEERERIEELKRKLERLKELW 502

                 .
gi 568979512 344 E 344
Cdd:COG2433  503 K 503
RING-HC_ORTHRUS_rpt2 cd23139
second RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; ...
50-78 8.18e-03

second RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; This subfamily includes Arabidopsis thaliana ORTHRUS 1-5. They are E3 ubiquitin-protein ligases that may participate in CpG methylation-dependent transcriptional regulation and/or epigenetic transcriptional silencing. ORTHRUS 1 mediates ubiquitination with the E2 ubiquitin-conjugating enzymes UBC11, UBC8 and UBC8 homologs (e.g. UBC10, UBC11, UBC28 and UBC29) but not with UBC27, UBC30, UBC32, UBC34 and UBC36. ORTHRUS 2 and 5 mediate ubiquitination with the E2 ubiquitin-conjugating enzyme UBC11. ORTHRUS 1 and 2 promote methylation-mediated gene silencing leading, for example, to early flowering. They can bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong preference for methylated forms, and with highest affinity for CpG substrates. Members of this subfamily contain two typical C3HC4-type RING-HC fingers. This model corresponds to the second one.


Pssm-ID: 438501 [Multi-domain]  Cd Length: 72  Bit Score: 35.51  E-value: 8.18e-03
                         10        20
                 ....*....|....*....|....*....
gi 568979512  50 YKCEKCRLVLCNPKQTECGHRFCESCMAA 78
Cdd:cd23139    6 FGCQICKKVLSLPVSTPCGHNFCKACLEA 34
RING-HC_RNF166 cd16549
RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins; ...
49-91 9.23e-03

RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins; RNF166 is encoded by the gene RNF166 targeted by thyroid hormone receptor alpha1 (TRalpha1), which is important in brain development. It plays an important role in RNA virus-induced interferon-beta production by enhancing the ubiquitination of TRAF3 and TRAF6. RNF166, together with three closely related proteins: RNF114, RNF125 and RNF138, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).


Pssm-ID: 438211 [Multi-domain]  Cd Length: 47  Bit Score: 34.40  E-value: 9.23e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 568979512  49 KYKCEKCRLVLCNPKQT-ECGHRFCESCMAALLSSSSPKCTACQ 91
Cdd:cd16549    1 QFSCPICLEVYHKPVVItSCGHTFCGECLQPCLQVASPLCPLCR 44
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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