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Conserved domains on  [gi|767910370|ref|XP_011508261|]
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TNF receptor-associated factor 5 isoform X2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
MATH super family cl02446
MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded ...
415-561 3.85e-112

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.


The actual alignment was detected with superfamily member cd03780:

Pssm-ID: 445786 [Multi-domain]  Cd Length: 148  Bit Score: 330.44  E-value: 3.85e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 415 GKLIWKVTDYKMKKREAVDGHTVSIFSQSFYTSRCGYRLCARAYLNGDGSGRGSHLSLYFVVMRGEFDSLLQWPFRQRVT 494
Cdd:cd03780    1 GKLIWKVTDYKMKKKEAVDGHTVSIFSQPFYTSRCGYRLCARAYLNGDGSGKGTHLSLYFVVMRGEFDSLLQWPFRQRVT 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767910370 495 LMLLDQSGKKN-IMETFKPDPNSSSFKRPDGEMNIASGCPRFVAHSVLENAKNAYIKDDTLFLKVAVD 561
Cdd:cd03780   81 LMLLDQSGKKNhIMETFKADPNSSSFKRPDGEMNIASGCPRFVAHSVLENAKNTYIKDDTLFLKVAVD 148
mRING-HC-C3HC3D_TRAF5 cd16642
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
39-94 1.26e-29

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: 110.60  E-value: 1.26e-29
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 767910370  39 LEERYKCAFCHSVLHNPHQTGCGHRFCQHCILSLRELNTVPICPVDKEVIKSQEVF 94
Cdd:cd16642    1 LEDRYKCATCHFVLHNPHQTGCGHRFCQHCILSLLELNTTPICPIDKETIKSDEVF 56
zf-TRAF pfam02176
TRAF-type zinc finger;
194-252 3.95e-16

TRAF-type zinc finger;


:

Pssm-ID: 280357 [Multi-domain]  Cd Length: 60  Bit Score: 72.87  E-value: 3.95e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767910370  194 HEENlCPEYPVFCPNNCA-KIILKTEVDEHL-AVCPEAEQDCPFKHYGCAVTDKRRNLQQH 252
Cdd:pfam02176   1 HLET-CPFFPIPCPNGCCkKKILREDLPDHLeLDCPKAEVPCPFKVFGCKEDVKREALQRH 60
zf-TRAF super family cl44369
TRAF-type zinc finger;
139-194 8.73e-13

TRAF-type zinc finger;


The actual alignment was detected with superfamily member pfam02176:

Pssm-ID: 280357 [Multi-domain]  Cd Length: 60  Bit Score: 63.24  E-value: 8.73e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  139 HLQQCLFQPVQCSNEKCREPVLRKDLKEHLSASCQFRKEKCLY----CKKDVVVINLQNH 194
Cdd:pfam02176   1 HLETCPFFPIPCPNGCCKKKILREDLPDHLELDCPKAEVPCPFkvfgCKEDVKREALQRH 60
EnvC super family cl34844
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
243-409 3.80e-05

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


The actual alignment was detected with superfamily member COG4942:

Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 46.30  E-value: 3.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 243 TDKRRNLQQHEHSALREHMRLVLEKNVQLEEQISDLHKSLEQKESKIQQLAETIKKLEKEFKQFAQLFGKNGS-----FL 317
Cdd:COG4942   46 LKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEIAELRAELEAQKEELAELLRALYRLGRqpplaLL 125
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 318 PNIQVFASHIDKSAWLEAQVHQLLQMVNQ-QQNKFDLRPLMEAVDTVKQKI-TLLENNDQRLAVLEEETNKHDTHINIHK 395
Cdd:COG4942  126 LSPEDFLDAVRRLQYLKYLAPARREQAEElRADLAELAALRAELEAERAELeALLAELEEERAALEALKAERQKLLARLE 205
                        170
                 ....*....|....
gi 767910370 396 AQLSKNEERFKLLE 409
Cdd:COG4942  206 KELAELAAELAELQ 219
 
Name Accession Description Interval E-value
MATH_TRAF5 cd03780
Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF5 subfamily, TRAF ...
415-561 3.85e-112

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: 330.44  E-value: 3.85e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 415 GKLIWKVTDYKMKKREAVDGHTVSIFSQSFYTSRCGYRLCARAYLNGDGSGRGSHLSLYFVVMRGEFDSLLQWPFRQRVT 494
Cdd:cd03780    1 GKLIWKVTDYKMKKKEAVDGHTVSIFSQPFYTSRCGYRLCARAYLNGDGSGKGTHLSLYFVVMRGEFDSLLQWPFRQRVT 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767910370 495 LMLLDQSGKKN-IMETFKPDPNSSSFKRPDGEMNIASGCPRFVAHSVLENAKNAYIKDDTLFLKVAVD 561
Cdd:cd03780   81 LMLLDQSGKKNhIMETFKADPNSSSFKRPDGEMNIASGCPRFVAHSVLENAKNTYIKDDTLFLKVAVD 148
mRING-HC-C3HC3D_TRAF5 cd16642
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
39-94 1.26e-29

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: 110.60  E-value: 1.26e-29
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 767910370  39 LEERYKCAFCHSVLHNPHQTGCGHRFCQHCILSLRELNTVPICPVDKEVIKSQEVF 94
Cdd:cd16642    1 LEDRYKCATCHFVLHNPHQTGCGHRFCQHCILSLLELNTTPICPIDKETIKSDEVF 56
zf-TRAF pfam02176
TRAF-type zinc finger;
194-252 3.95e-16

TRAF-type zinc finger;


Pssm-ID: 280357 [Multi-domain]  Cd Length: 60  Bit Score: 72.87  E-value: 3.95e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767910370  194 HEENlCPEYPVFCPNNCA-KIILKTEVDEHL-AVCPEAEQDCPFKHYGCAVTDKRRNLQQH 252
Cdd:pfam02176   1 HLET-CPFFPIPCPNGCCkKKILREDLPDHLeLDCPKAEVPCPFKVFGCKEDVKREALQRH 60
zf-TRAF pfam02176
TRAF-type zinc finger;
139-194 8.73e-13

TRAF-type zinc finger;


Pssm-ID: 280357 [Multi-domain]  Cd Length: 60  Bit Score: 63.24  E-value: 8.73e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  139 HLQQCLFQPVQCSNEKCREPVLRKDLKEHLSASCQFRKEKCLY----CKKDVVVINLQNH 194
Cdd:pfam02176   1 HLETCPFFPIPCPNGCCKKKILREDLPDHLELDCPKAEVPCPFkvfgCKEDVKREALQRH 60
MATH smart00061
meprin and TRAF homology;
417-536 7.96e-09

meprin and TRAF homology;


Pssm-ID: 214496 [Multi-domain]  Cd Length: 95  Bit Score: 53.07  E-value: 7.96e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370   417 LIWKVTDykMKKREavdgHTVSIFSQSFYtsRCGYRLCARAYLNGDgsgrgsHLSLYFVVMRGEFDSLlQWPFRQRVTLM 496
Cdd:smart00061   2 LSHTFKN--VSRLE----EGESYFSPSEE--HFNIPWRLKIYRKNG------FLSLYLHCEKEECDSR-KWSIEAEFTLK 66
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 767910370   497 LLDQSGKKnimetfKPDPNSSSFKRPDGemniaSGCPRFV 536
Cdd:smart00061  67 LVSQNGKS------LSKKDKHVFEKPSG-----WGFSKFI 95
PEX10 COG5574
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
40-83 2.13e-06

RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 49.51  E-value: 2.13e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 767910370  40 EERYKCAFCHSVLHNPHQTGCGHRFCQHCILSLRELNTVPICPV 83
Cdd:COG5574  213 LADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPL 256
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
243-409 3.80e-05

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


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 46.30  E-value: 3.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 243 TDKRRNLQQHEHSALREHMRLVLEKNVQLEEQISDLHKSLEQKESKIQQLAETIKKLEKEFKQFAQLFGKNGS-----FL 317
Cdd:COG4942   46 LKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEIAELRAELEAQKEELAELLRALYRLGRqpplaLL 125
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 318 PNIQVFASHIDKSAWLEAQVHQLLQMVNQ-QQNKFDLRPLMEAVDTVKQKI-TLLENNDQRLAVLEEETNKHDTHINIHK 395
Cdd:COG4942  126 LSPEDFLDAVRRLQYLKYLAPARREQAEElRADLAELAALRAELEAERAELeALLAELEEERAALEALKAERQKLLARLE 205
                        170
                 ....*....|....
gi 767910370 396 AQLSKNEERFKLLE 409
Cdd:COG4942  206 KELAELAAELAELQ 219
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
39-82 5.71e-05

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: 45.76  E-value: 5.71e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767910370   39 LEERYKCAFCHSVLHNPHQTGCGHRFCQHCIlsLRELNTVPICP 82
Cdd:TIGR00599  23 LDTSLRCHICKDFFDVPVLTSCSHTFCSLCI--RRCLSNQPKCP 64
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
247-407 1.94e-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: 44.24  E-value: 1.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  247 RNLQQHEHSALREHMRLvLEKNVQLEEQISDLHKSLEQKESKIQQLAETIKKLEKEFKQFAQLFGKNGSFLPNIQvfash 326
Cdd:TIGR04523 415 KKLQQEKELLEKEIERL-KETIIKNNSEIKDLTNQDSVKELIIKNLDNTRESLETQLKVLSRSINKIKQNLEQKQ----- 488
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  327 idksAWLEAQVHQLLQMVNQQQNkfdlrpLMEAVDTVKQKITLLENN-----------DQRLAVLEEETNKHD---THIN 392
Cdd:TIGR04523 489 ----KELKSKEKELKKLNEEKKE------LEEKVKDLTKKISSLKEKieklesekkekESKISDLEDELNKDDfelKKEN 558
                         170
                  ....*....|....*
gi 767910370  393 IHKAQLSKNEERFKL 407
Cdd:TIGR04523 559 LEKEIDEKNKEIEEL 573
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
45-81 6.23e-04

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: 37.49  E-value: 6.23e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 767910370    45 CAFCHSV-LHNPHQTGCGHRFCQHCILSLRELNTV--PIC 81
Cdd:smart00184   1 CPICLEEyLKDPVILPCGHTFCRSCIRKWLESGNNtcPIC 40
zf-C3HC4_2 pfam13923
Zinc finger, C3HC4 type (RING finger);
44-81 2.01e-03

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 404756 [Multi-domain]  Cd Length: 40  Bit Score: 36.26  E-value: 2.01e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 767910370   44 KCAFCHSVLHNPHQ-TGCGHRFCQHCIL-SLRELNTVPIC 81
Cdd:pfam13923   1 MCPICMDMLKDPSTtTPCGHVFCQDCILrALRAGNECPLC 40
Dynamitin pfam04912
Dynamitin; Dynamitin is a subunit of the microtubule-dependent motor complex and in implicated ...
266-408 2.52e-03

Dynamitin; Dynamitin is a subunit of the microtubule-dependent motor complex and in implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS).


Pssm-ID: 461477 [Multi-domain]  Cd Length: 390  Bit Score: 40.40  E-value: 2.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  266 EKNVQLEEQISDLHKSLEQ-----------KESKIQQLAETIKKLEKEFKQFAQLFGKNGSFLPNIQVFAS-HID----- 328
Cdd:pfam04912 124 ADPVELAAQLASLQKQLDElkleellgpdvAIGLTDPQGALSKRLLSQLEAFKQTSAPSGKKEPSASEPPSnHVTyelyy 203
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  329 -----------KSAWLEAQVHQLLQMVNQQQNKFD-------LRPLMEAVDTVKQKITLLENN-----DQRLAVLEEETN 385
Cdd:pfam04912 204 rpeqaksqqlaKIAELEKRLAELEKLVGIDSDLLDelsanlgPAPLLETLSRLQAKLSLLDPAhldaiERRLKSLLAEMD 283
                         170       180
                  ....*....|....*....|....
gi 767910370  386 KHDTHINIHKA-QLSKNEERFKLL 408
Cdd:pfam04912 284 ELAEKREKADAtQEAKINELYELL 307
mukB PRK04863
chromosome partition protein MukB;
272-383 5.19e-03

chromosome partition protein MukB;


Pssm-ID: 235316 [Multi-domain]  Cd Length: 1486  Bit Score: 39.94  E-value: 5.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  272 EEQISDLHKSLEQKESKIQQLAETIKKLEKEFKQFAQLFGKNGS--FLPNIQV-FASHIDKSAWLEAQVHQLLQMVNQQQ 348
Cdd:PRK04863  785 EKRIEQLRAEREELAERYATLSFDVQKLQRLHQAFSRFIGSHLAvaFEADPEAeLRQLNRRRVELERALADHESQEQQQR 864
                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 767910370  349 NKFD-LRPLMEAVDTVKQKITLLENN--DQRLAVLEEE 383
Cdd:PRK04863  865 SQLEqAKEGLSALNRLLPRLNLLADEtlADRVEEIREQ 902
Prefoldin_alpha_GimC cd23160
Prefoldin alpha subunit, archaeal; Archaeal alpha subunit of prefoldin (GimC), a hexameric ...
264-305 9.19e-03

Prefoldin alpha subunit, archaeal; Archaeal alpha subunit of prefoldin (GimC), a hexameric molecular chaperone complex, found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.


Pssm-ID: 467476 [Multi-domain]  Cd Length: 127  Bit Score: 36.70  E-value: 9.19e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 767910370 264 VLEKNVQ-----LEEQISDLHKSLEQKESKIQQLAETIKKLEKEFKQ 305
Cdd:cd23160   81 VVEKTIDeaieiLEKRIKELEKALEKLQEQLQQIAQRLEELEAELQE 127
 
Name Accession Description Interval E-value
MATH_TRAF5 cd03780
Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF5 subfamily, TRAF ...
415-561 3.85e-112

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: 330.44  E-value: 3.85e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 415 GKLIWKVTDYKMKKREAVDGHTVSIFSQSFYTSRCGYRLCARAYLNGDGSGRGSHLSLYFVVMRGEFDSLLQWPFRQRVT 494
Cdd:cd03780    1 GKLIWKVTDYKMKKKEAVDGHTVSIFSQPFYTSRCGYRLCARAYLNGDGSGKGTHLSLYFVVMRGEFDSLLQWPFRQRVT 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767910370 495 LMLLDQSGKKN-IMETFKPDPNSSSFKRPDGEMNIASGCPRFVAHSVLENAKNAYIKDDTLFLKVAVD 561
Cdd:cd03780   81 LMLLDQSGKKNhIMETFKADPNSSSFKRPDGEMNIASGCPRFVAHSVLENAKNTYIKDDTLFLKVAVD 148
MATH_TRAF3 cd03777
Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF ...
377-563 9.27e-92

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: 279.53  E-value: 9.27e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 377 LAVLEEETNKHDTHINIHKAQLSKNEERFKLLEGTCYNGKLIWKVTDYKMKKREAVDGHTVSIFSQSFYTSRCGYRLCAR 456
Cdd:cd03777    1 TGLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCAR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 457 AYLNGDGSGRGSHLSLYFVVMRGEFDSLLQWPFRQRVTLMLLDQ-SGKKNIMETFKPDPNSSSFKRPDGEMNIASGCPRF 535
Cdd:cd03777   81 VYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQgSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVF 160
                        170       180
                 ....*....|....*....|....*...
gi 767910370 536 VAHSVLENAknAYIKDDTLFLKVAVDLT 563
Cdd:cd03777  161 VAQTVLENG--TYIKDDTIFIKVIVDTS 186
MATH_TRAF_C cd00270
Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF domain, C-terminal ...
415-561 1.20e-78

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: 244.44  E-value: 1.20e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 415 GKLIWKVTDYKMKKREAVDGHTVSIFSQSFYTSRCGYRLCARAYLNGDGSGRGSHLSLYFVVMRGEFDSLLQWPFRQRVT 494
Cdd:cd00270    1 GVLIWKIKDYSRKLQEAVAGSNTVLYSPPFYTSRYGYKLCLRLYLNGDGTGKGTHLSLFVHVMKGEYDALLEWPFRGKIT 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767910370 495 LMLLDQSGK---KNIMETFKPDPNSSSF-KRPDGEMNIASGCPRFVAHSVLENakNAYIKDDTLFLKVAVD 561
Cdd:cd00270   81 LTLLDQSDDskrKHITETFMPDPNSSAFqRPPTGENNIGFGYPEFVPLEKLES--RGYVKDDTLFIKVEVD 149
MATH_TRAF2 cd03778
Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF2 subfamily, TRAF ...
397-561 5.99e-67

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: 214.48  E-value: 5.99e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 397 QLSKNEERFKLLEGTCYNGKLIWKVTDYKMKKREAVDGHTVSIFSQSFYTSRCGYRLCARAYLNGDGSGRGSHLSLYFVV 476
Cdd:cd03778    1 A*ADLEQKVLE*EASTYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 477 MRGEFDSLLQWPFRQRVTLMLLDQSGKKNIMETFKPDPNSSSFKRPDGEMNIASGCPRFVAHSVLEnAKNAYIKDDTLFL 556
Cdd:cd03778   81 MKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSK*E-AKNSYVRDDAIFI 159

                 ....*
gi 767910370 557 KVAVD 561
Cdd:cd03778  160 KAIVD 164
MATH_TRAF1 cd03779
Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF1 subfamily, TRAF ...
415-561 1.21e-61

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: 200.12  E-value: 1.21e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 415 GKLIWKVTDYKMKKREAVDGHTVSIFSQSFYTSRCGYRLCARAYLNGDGSGRGSHLSLYFVVMRGEFDSLLQWPFRQRVT 494
Cdd:cd03779    1 GTFLWKITDVSQKQRESSHGRDVSLCSPAFYTAKYGYKVCLRLYLNGDGAGKGTHISLFFVIMKGEYDALLPWPFRHKVT 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767910370 495 LMLLDQSGKKNIMETFKPDPNSSSFKRPDGEMNIASGCPRFVAHSVLENAKNAYIKDDTLFLKVAVD 561
Cdd:cd03779   81 FMLLDQNNREHVIDAFRPDLSSASFQRPVSDMNVASGCPLFFPLKKLQSPKHAYCKDDTIYIKCVVD 147
MATH_TRAF4 cd03781
Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF4 subfamily, TRAF ...
415-561 1.14e-49

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: 168.83  E-value: 1.14e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 415 GKLIWKVTDYKMKKREAVDGHTVSIFSQSFYTSRCGYRLCARAYLNGDGSGRGSHLSLYFVVMRGEFDSLLQWPFRQRVT 494
Cdd:cd03781    1 GTLLWKITDYSRKLQEAKGRDNLELFSPPFYTHRYGYKLQVSAFLNGNGSGEGSHLSVYIRVLPGEYDNLLEWPFSHRIT 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767910370 495 LMLLDQ-----SGKKNIMETFKPDPNSSSFKRP----DGEMNIASGCPRFVAHSVLEnaKNAYIKDDTLFLKVAVD 561
Cdd:cd03781   81 FTLLDQsdpslSKPQHITETFTPDPTWKNFQKPsasrLDESTLGFGYPKFISHEDLK--KRNYIKDDAIFLRASVE 154
MATH_TRAF6 cd03776
Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF6 subfamily, TRAF ...
415-560 1.34e-33

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: 124.74  E-value: 1.34e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 415 GKLIWKVTDYKMKKREAVDGHTVSIFSQSFYTSRCGYRLCARAYLNGDGSGRGSHLSLYFVVMRGEFDSLLQWPFRQRVT 494
Cdd:cd03776    1 GIYVWKIKNFSNLRRSMEAGSPVVIHSPGFYTSPPGYKLCARLNLSLPEARCPNYISLFVHLMQGENDSHLDWPFQGTIT 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767910370 495 LMLLDQSGK-KNIMETFKPDPNSSSFKRPDGEMNIAS-GCPRFVAHSVLENAKnaYIKDDTLFLKVAV 560
Cdd:cd03776   81 LTLLDQSEPrQNIHETMMSKPELLAFQRPTTDRNPKGfGYVEFAHIEDLLQRG--FVKNDTLLIKIEV 146
mRING-HC-C3HC3D_TRAF5 cd16642
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
39-94 1.26e-29

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: 110.60  E-value: 1.26e-29
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 767910370  39 LEERYKCAFCHSVLHNPHQTGCGHRFCQHCILSLRELNTVPICPVDKEVIKSQEVF 94
Cdd:cd16642    1 LEDRYKCATCHFVLHNPHQTGCGHRFCQHCILSLLELNTTPICPIDKETIKSDEVF 56
MATH cd00121
MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded ...
415-561 2.51e-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: 83.97  E-value: 2.51e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 415 GKLIWKVTDYKMKKREavdghtvSIFSQSFYtsRCGYRLCARAYLNGDGSgRGSHLSLYFVVMRGEFDSLlQWPFRQRVT 494
Cdd:cd00121    1 GKHTWKIVNFSELEGE-------SIYSPPFE--VGGYKWRIRIYPNGDGE-SGDYLSLYLELDKGESDLE-KWSVRAEFT 69
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767910370 495 LMLLDQSGKKNIMETFKPDPNSssfkrpdgEMNIASGCPRFVAHSVLEnaKNAYIKDDTLFLKVAVD 561
Cdd:cd00121   70 LKLVNQNGGKSLSKSFTHVFFS--------EKGSGWGFPKFISWDDLE--DSYYLVDDSLTIEVEVK 126
zf-TRAF pfam02176
TRAF-type zinc finger;
194-252 3.95e-16

TRAF-type zinc finger;


Pssm-ID: 280357 [Multi-domain]  Cd Length: 60  Bit Score: 72.87  E-value: 3.95e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767910370  194 HEENlCPEYPVFCPNNCA-KIILKTEVDEHL-AVCPEAEQDCPFKHYGCAVTDKRRNLQQH 252
Cdd:pfam02176   1 HLET-CPFFPIPCPNGCCkKKILREDLPDHLeLDCPKAEVPCPFKVFGCKEDVKREALQRH 60
mRING-HC-C3HC3D_TRAF6 cd16643
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
42-100 1.09e-14

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: 68.56  E-value: 1.09e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  42 RYKCAFCHSVLHNPHQTGCGHRFCQHCIL-SLRElnTVPICPVDKEVIKSQEVFKDNCCK 100
Cdd:cd16643    1 KYECPICLMALREPVQTPCGHRFCKACILkSIRE--AGHKCPVDNEPLLENQLFPDNFAK 58
zf-TRAF pfam02176
TRAF-type zinc finger;
139-194 8.73e-13

TRAF-type zinc finger;


Pssm-ID: 280357 [Multi-domain]  Cd Length: 60  Bit Score: 63.24  E-value: 8.73e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  139 HLQQCLFQPVQCSNEKCREPVLRKDLKEHLSASCQFRKEKCLY----CKKDVVVINLQNH 194
Cdd:pfam02176   1 HLETCPFFPIPCPNGCCKKKILREDLPDHLELDCPKAEVPCPFkvfgCKEDVKREALQRH 60
MATH smart00061
meprin and TRAF homology;
417-536 7.96e-09

meprin and TRAF homology;


Pssm-ID: 214496 [Multi-domain]  Cd Length: 95  Bit Score: 53.07  E-value: 7.96e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370   417 LIWKVTDykMKKREavdgHTVSIFSQSFYtsRCGYRLCARAYLNGDgsgrgsHLSLYFVVMRGEFDSLlQWPFRQRVTLM 496
Cdd:smart00061   2 LSHTFKN--VSRLE----EGESYFSPSEE--HFNIPWRLKIYRKNG------FLSLYLHCEKEECDSR-KWSIEAEFTLK 66
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 767910370   497 LLDQSGKKnimetfKPDPNSSSFKRPDGemniaSGCPRFV 536
Cdd:smart00061  67 LVSQNGKS------LSKKDKHVFEKPSG-----WGFSKFI 95
RING-HC_TRAF3 cd16640
RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 3 ...
43-84 4.60e-08

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: 49.12  E-value: 4.60e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 767910370  43 YKCAFCHSVLHNPHQTGCGHRFCQHCILSLRElNTVPICPVD 84
Cdd:cd16640    1 YKCEKCRLVLCNPKQTECGHRFCESCMNALLS-SSNPQCPAC 41
RING-HC_TRAF1-like cd23125
RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 1 ...
40-86 1.08e-07

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: 48.67  E-value: 1.08e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 767910370  40 EERYKCAFCHSVLHNPHQTGCGHRFCQHCILSLRELNTVPICPVDKE 86
Cdd:cd23125    2 EEKYLCCNCKNVLKKAQQTLCGHRYCLACLSWIVRNNKNPICQKCKE 48
MATH_Meprin cd03771
Meprin family, MATH domain; Meprins are multidomain, highly glycosylated extracellular ...
438-501 7.98e-07

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: 49.32  E-value: 7.98e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767910370 438 SIFSQSFYTSRcGYRLCARAYLNGdGSGRGSHLSLYFVVMRGEFDSLLQWP-FRQRVTLMLLDQS 501
Cdd:cd03771   23 KIYSPRFYSPE-GYAFQVGLYPNG-TESYPGYTGLYFHLCSGENDDVLEWPcPNRQATMTLLDQD 85
mRING-HC-C3HC3D_TRAF4-like cd23126
Modified RING finger, HC subclass (C3HC3D-type), found in uncharacterized proteins similar to ...
39-89 1.17e-06

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: 45.41  E-value: 1.17e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 767910370  39 LEERYKCAFCHSVLHNPHQ-TGCGHRFCQHCILSLreLNTVPICPVDKEVIK 89
Cdd:cd23126    1 LDKKYECPVCCQVLRYPVQfEECGHRVCSSCLPEL--LRVEPRCPIDQGPID 50
PEX10 COG5574
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
40-83 2.13e-06

RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 49.51  E-value: 2.13e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 767910370  40 EERYKCAFCHSVLHNPHQTGCGHRFCQHCILSLRELNTVPICPV 83
Cdd:COG5574  213 LADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPL 256
MATH_Meprin_Alpha cd03783
Meprin family, Alpha subunit, MATH domain; Meprins are multidomain extracellular ...
412-558 2.49e-06

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: 47.94  E-value: 2.49e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 412 CYNGklIWKVTDYKmKKREAVDGHTVsIFSQSFYTSRcGYRLCARAY-LNGDGSGRGSHLSLYFVVMRGEFDSLLQWPFR 490
Cdd:cd03783    1 CPNA--VWRVRNFS-QILENTTKGDV-LQSPRFYSPE-GYGYGVSLYpLSNESDYSGNYTGLYFHLCSGENDAVLEWPAL 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 491 QR-VTLMLLDQSGK-KNIMET---FKPDPNSSS--------FKRPD--GEMNIASGCPR--------FVAHSVLEnaKNA 547
Cdd:cd03783   76 NRqAIITVLDQDPDvRLRMSSsrsFTTDKSQTSsaingtlrWDRPSrvGTYDTSCDCFRgidfgwstFISHSQLR--RRS 153
                        170
                 ....*....|.
gi 767910370 548 YIKDDTLFLKV 558
Cdd:cd03783  154 FLKNDDLIIFV 164
MATH_Meprin_Beta cd03782
Meprin family, Beta subunit, MATH domain; Meprins are multidomain extracellular ...
418-556 1.25e-05

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: 45.62  E-value: 1.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 418 IWKVTDYKmkKREAVDGHTVSIFSQSFYTSRcGYRLCARAYLNGDGSGRGsHLSLYFVVMRGEFDSLLQWPFR-QRVTLM 496
Cdd:cd03782    5 IWHIRNFT--QLLATTPPNGKIYSPPFLSST-GYSFQVGLYLNGTDDYPG-NLAIYLHLTSGPNDDQLQWPCPwQQATMM 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 497 LLDQ--------SGKKNIM-----------ETFKPDPNS--SSFKRPDGEMNI---ASGCPRFVAHSVLENakNAYIK-D 551
Cdd:cd03782   81 LLDQhpdirqrmSNQRSVTtdpnmtstdsdEYFWDDPRKvgSEVTDTDGSTFYrgpGYGTSAFITHLRLRS--RDFIKgD 158

                 ....*
gi 767910370 552 DTLFL 556
Cdd:cd03782  159 DVIFL 163
RING-HC_RNF125 cd16542
RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as ...
43-91 1.32e-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: 42.56  E-value: 1.32e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 767910370  43 YKCAFCHSVLHNPHQTGCGHRFCQHCI-LSLRelNTVPICPVDKEVIKSQ 91
Cdd:cd16542    2 FDCAVCLEVLHQPVRTRCGHVFCRPCIaTSLR--NNTWTCPYCRAYLSSE 49
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
243-409 3.80e-05

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


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 46.30  E-value: 3.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 243 TDKRRNLQQHEHSALREHMRLVLEKNVQLEEQISDLHKSLEQKESKIQQLAETIKKLEKEFKQFAQLFGKNGS-----FL 317
Cdd:COG4942   46 LKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEIAELRAELEAQKEELAELLRALYRLGRqpplaLL 125
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 318 PNIQVFASHIDKSAWLEAQVHQLLQMVNQ-QQNKFDLRPLMEAVDTVKQKI-TLLENNDQRLAVLEEETNKHDTHINIHK 395
Cdd:COG4942  126 LSPEDFLDAVRRLQYLKYLAPARREQAEElRADLAELAALRAELEAERAELeALLAELEEERAALEALKAERQKLLARLE 205
                        170
                 ....*....|....
gi 767910370 396 AQLSKNEERFKLLE 409
Cdd:COG4942  206 KELAELAAELAELQ 219
mRING-HC-C3HC3D_LNX1-like cd16637
Modified RING finger, HC subclass (C3HC3D-type), found in ligand of Numb protein LNX1, LNX2, ...
42-85 4.99e-05

Modified RING finger, HC subclass (C3HC3D-type), found in ligand of Numb protein LNX1, LNX2, and similar proteins; The ligand of Numb protein X (LNX) family, also known as PDZ and RING (PDZRN) family, includes LNX1-5, which can interact with Numb, a key regulator of neurogenesis and neuronal differentiation. LNX5 (also known as PDZK4 or PDZRN4L) shows high sequence homology to LNX3 and LNX4, but it lacks the RING domain. LNX1-4 proteins function as E3 ubiquitin ligases and have a unique domain architecture consisting of an N-terminal RING-HC finger for E3 ubiquitin ligase activity and either two or four PDZ domains necessary for substrate-binding. LNX1/LNX2-like proteins contain a modified C3HC3D-type RING-HC finger and four PDZ domains. This model corresponds to the RING finger.


Pssm-ID: 438299 [Multi-domain]  Cd Length: 42  Bit Score: 40.84  E-value: 4.99e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 767910370  42 RYKCAFCHSVLHNPHQTGCGHRFCQHCILSLreLNTVPICPVDK 85
Cdd:cd16637    1 DLTCHICLQPLVEPLDTPCGHTFCYKCLTNY--LKIQQCCPLDR 42
RING-HC_LNX3 cd16718
RING finger, HC subclass, found in ligand of numb protein X 3 (LNX3); LNX3, also known as PDZ ...
43-70 4.99e-05

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: 40.74  E-value: 4.99e-05
                         10        20
                 ....*....|....*....|....*...
gi 767910370  43 YKCAFCHSVLHNPHQTGCGHRFCQHCIL 70
Cdd:cd16718    5 FKCNLCNKVLEDPLTTPCGHVFCAGCVL 32
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
39-82 5.71e-05

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: 45.76  E-value: 5.71e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 767910370   39 LEERYKCAFCHSVLHNPHQTGCGHRFCQHCIlsLRELNTVPICP 82
Cdd:TIGR00599  23 LDTSLRCHICKDFFDVPVLTSCSHTFCSLCI--RRCLSNQPKCP 64
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
43-84 5.87e-05

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: 40.55  E-value: 5.87e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 767910370  43 YKCAFCHSVLHNPHQTGCGHRFCQHCILSLRELNTVPiCPVD 84
Cdd:cd16449    1 LECPICLERLKDPVLLPCGHVFCRECIRRLLESGSIK-CPIC 41
mRING-HC-C3HC3D_TRAF7 cd16644
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
45-85 6.63e-05

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


Pssm-ID: 438306 [Multi-domain]  Cd Length: 47  Bit Score: 40.41  E-value: 6.63e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 767910370  45 CAFCHSVLHNPHQTGCGHRFCQHCILSlrelNTVPICPVDK 85
Cdd:cd16644    8 CPLCQRVFKDPVITSCGHTFCRRCALT----APGEKCPVDN 44
RING-HC_PEX2 cd16526
RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins; PEX2, also known as ...
44-71 1.23e-04

RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins; PEX2, also known as peroxisome biogenesis factor 2, 35 kDa peroxisomal membrane protein, peroxisomal membrane protein 3, peroxisome assembly factor 1 (PAF-1), or RING finger protein 72 (RNF72), is an integral peroxisomal membrane protein with two transmembrane regions and a C3HC4-type RING-HC finger within its cytoplasmically exposed C-terminus. It may be involved in the biogenesis of peroxisomes, as well as in peroxisomal matrix protein import. Mutations in the PEX2 gene are the primary defect in a subset of patients with Zellweger syndrome and related peroxisome biogenesis disorders. Moreover, PEX2 functions as an E3-ubiquitin ligase that mediates the UBC4-dependent polyubiquitination of PEX5, a key player in peroxisomal matrix protein import, to control PEX5 receptor recycling or degradation.


Pssm-ID: 438189 [Multi-domain]  Cd Length: 49  Bit Score: 39.68  E-value: 1.23e-04
                         10        20
                 ....*....|....*....|....*....
gi 767910370  44 KCAFCHSV-LHNPHQTGCGHRFCQHCILS 71
Cdd:cd16526    3 ECAICGEWpTNNPYSTGCGHVYCYYCIKS 31
RING-HC_LNX3-like cd16512
RING finger, HC subclass, found in ligand of Numb protein LNX3, LNX4, and similar proteins; ...
44-70 1.24e-04

RING finger, HC subclass, found in ligand of Numb protein LNX3, LNX4, and similar proteins; The ligand of Numb protein X (LNX) family, also known as PDZ and RING (PDZRN) family, includes LNX1-5, which can interact with Numb, a key regulator of neurogenesis and neuronal differentiation. LNX5 (also known as PDZK4, or PDZRN4L) shows high sequence homology to LNX3 and LNX4, but it lacks the RING domain. LNX1-4 proteins function as E3 ubiquitin ligases and have a unique domain architecture consisting of an N-terminal RING-HC finger for E3 ubiquitin ligase activity and either two or four PDZ domains necessary for the substrate-binding. This family corresponds to LNX3/LNX4-like proteins, which contains a C3HC4-type RING-HC finger and two PDZ domains.


Pssm-ID: 438175 [Multi-domain]  Cd Length: 43  Bit Score: 39.70  E-value: 1.24e-04
                         10        20
                 ....*....|....*....|....*..
gi 767910370  44 KCAFCHSVLHNPHQTGCGHRFCQHCIL 70
Cdd:cd16512    2 KCKLCLGVLEEPLATPCGHVFCAGCVL 28
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
39-83 1.64e-04

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


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 44.31  E-value: 1.64e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 767910370  39 LEERYKCAFCHSVLHNPHQTGCGHRFCQHCIlsLRELNTVPICPV 83
Cdd:COG5432   22 LDSMLRCRICDCRISIPCETTCGHTFCSLCI--RRHLGTQPFCPV 64
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
247-407 1.94e-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: 44.24  E-value: 1.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  247 RNLQQHEHSALREHMRLvLEKNVQLEEQISDLHKSLEQKESKIQQLAETIKKLEKEFKQFAQLFGKNGSFLPNIQvfash 326
Cdd:TIGR04523 415 KKLQQEKELLEKEIERL-KETIIKNNSEIKDLTNQDSVKELIIKNLDNTRESLETQLKVLSRSINKIKQNLEQKQ----- 488
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  327 idksAWLEAQVHQLLQMVNQQQNkfdlrpLMEAVDTVKQKITLLENN-----------DQRLAVLEEETNKHD---THIN 392
Cdd:TIGR04523 489 ----KELKSKEKELKKLNEEKKE------LEEKVKDLTKKISSLKEKieklesekkekESKISDLEDELNKDDfelKKEN 558
                         170
                  ....*....|....*
gi 767910370  393 IHKAQLSKNEERFKL 407
Cdd:TIGR04523 559 LEKEIDEKNKEIEEL 573
RING-HC_BRCA1 cd16498
RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and ...
45-88 2.06e-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: 40.36  E-value: 2.06e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 767910370  45 CAFCHSVLHNPHQTGCGHRFCQHCILSLRELNTVPI-CPVDKEVI 88
Cdd:cd16498   19 CPICLELLKEPVSTKCDHQFCRFCILKLLQKKKKPApCPLCKKSV 63
RING-HC_LONFs_rpt2 cd16514
second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
45-88 2.19e-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: 38.79  E-value: 2.19e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 767910370  45 CAFCHSVLHNPHQTGCGHRFCQHCIlsLRELNTVPICPVDKEVI 88
Cdd:cd16514    4 CSLCLRLLYEPVTTPCGHTFCRACL--ERCLDHSPKCPLCRTSL 45
HemX COG2959
Proteobacterial HemX domain, involved in 2-ketogluconate production (unrelated to B. subtilis ...
270-378 2.53e-04

Proteobacterial HemX domain, involved in 2-ketogluconate production (unrelated to B. subtilis HemX, COG0755, no evidence of involvement in heme biosynthesis) [General function prediction only];


Pssm-ID: 442199 [Multi-domain]  Cd Length: 361  Bit Score: 43.41  E-value: 2.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 270 QLEEQISDLHKSLEQKESKIQQLAETIKKLEKefkQFAQLfgkngsflpniqvfaSHIDKSAWLEAQVHQLLQMVNQQ-- 347
Cdd:COG2959   85 QLQELLQQLAARLAQLEQRLAELQQQLAALQQ---LLQSL---------------SGSSRDDWLLAEAEYLLRLAGQQlq 146
                         90       100       110
                 ....*....|....*....|....*....|...
gi 767910370 348 --QNkfdlrplmeaVDTVkqkITLLENNDQRLA 378
Cdd:COG2959  147 leGD----------VKTA---LAALQSADARLA 166
RING-HC_PEX10 cd16527
RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins; PEX10, also known ...
44-93 3.53e-04

RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins; PEX10, also known as peroxisome biogenesis factor 10, peroxisomal biogenesis factor 10, peroxisome assembly protein 10, or RING finger protein 69 (RNF69), is an integral peroxisomal membrane protein with two transmembrane regions and a C3HC4-type RING-HC finger within its cytoplasmically exposed C-terminus. It plays an essential role in peroxisome assembly, import of target substrates, and recycling or degradation of protein complexes and amino acids. It is an essential component of the spinal locomotor circuit, and thus its mutations may be involved in peroxisomal biogenesis disorders (PBD). Mutations in human PEX10 also result in autosomal recessive ataxia. Moreover, PEX10 functions as an E3-ubiquitin ligase with an E2, UBCH5C. It mono- or poly-ubiquitinates PEX5, a key player in peroxisomal matrix protein import, in a UBC4-dependent manner, to control PEX5 receptor recycling or degradation. It also links the E2 ubiquitin conjugating enzyme PEX4 to the protein import machinery of the peroxisome.


Pssm-ID: 438190 [Multi-domain]  Cd Length: 52  Bit Score: 38.75  E-value: 3.53e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 767910370  44 KCAFCHSVLHNPHQTGCGHRFCQHCILSLreLNTVPICPVDKEVIKSQEV 93
Cdd:cd16527    2 KCSLCLEERRHPTATPCGHLFCWSCITEW--CNEKPECPLCREPFQPQRL 49
RING-HC_TRIM26_C-IV cd16598
RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar ...
39-83 4.34e-04

RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar proteins; TRIM26, also known as acid finger protein (AFP), RING finger protein 95 (RNF95), or zinc finger protein 173 (ZNF173), is an E3 ubiquitin-protein ligase that negatively regulates interferon-beta production and antiviral response through polyubiquitination and degradation of nuclear transcription factor IRF3. It functions as an important regulator for RNA virus-triggered innate immune response by bridging TBK1 to NEMO (NF-kappaB essential modulator, also known as IKKgamma) and mediating TBK1 activation. It also acts as a novel tumor suppressor of hepatocellular carcinoma by regulating cancer cell proliferation, colony forming ability, migration, and invasion. TRIM26 belongs the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438260 [Multi-domain]  Cd Length: 64  Bit Score: 38.61  E-value: 4.34e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 767910370  39 LEERYKCAFCHSVLHNPHQTGCGHRFCQHCILSLREL---NTVPICPV 83
Cdd:cd16598    1 LEEEVTCSICLDYLRDPVTIDCGHNFCRSCITDYCPIsggHERPVCPL 48
RING-HC_TRAF2 cd16639
RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 2 ...
42-69 4.66e-04

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: 37.82  E-value: 4.66e-04
                         10        20
                 ....*....|....*....|....*...
gi 767910370  42 RYKCAFCHSVLHNPHQTGCGHRFCQHCI 69
Cdd:cd16639    1 KYLCSDCRNILRRPFQAQCGHRYCSYCL 28
vRING-HC-C4C4_RBBP6 cd16620
Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) ...
41-90 5.61e-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: 38.15  E-value: 5.61e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 767910370  41 ERYKCAFCHSVLHNPHQTGC-GHRFCQHCILSLReLNTVPICPVDKEVIKS 90
Cdd:cd16620    2 DELKCPICKDLMKDAVLTPCcGNSFCDECIRTAL-LEEDFTCPTCKEPDVS 51
RING-HC_TRIM35_C-IV cd16599
RING finger, HC subclass, found in tripartite motif-containing protein 35 (TRIM35) and similar ...
39-92 5.71e-04

RING finger, HC subclass, found in tripartite motif-containing protein 35 (TRIM35) and similar proteins; TRIM35, also known as hemopoietic lineage switch protein 5 (HLS5), is a putative hepatocellular carcinoma (HCC) suppressor that inhibits phosphorylation of pyruvate kinase isoform M2 (PKM2), which is involved in aerobic glycolysis of cancer cells and further suppresses the Warburg effect and tumorigenicity in HCC. It also negatively regulates Toll-like receptor 7 (TLR7)- and TLR9-mediated type I interferon production by suppressing the stability of interferon regulatory factor 7 (IRF7). Moreover, TRIM35 regulates erythroid differentiation by modulating globin transcription factor 1 (GATA-1) activity. TRIM35 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438261 [Multi-domain]  Cd Length: 66  Bit Score: 38.60  E-value: 5.71e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 767910370  39 LEERYKCAFCHSVLHNPHQTGCGHRFCQHCILSLRELNTVPICPVDKEVIKSQE 92
Cdd:cd16599    1 FKEELLCPICYEPFREAVTLRCGHNFCKGCVSRSWERQPRAPCPVCKEASSSDD 54
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
45-81 6.23e-04

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: 37.49  E-value: 6.23e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 767910370    45 CAFCHSV-LHNPHQTGCGHRFCQHCILSLRELNTV--PIC 81
Cdd:smart00184   1 CPICLEEyLKDPVILPCGHTFCRSCIRKWLESGNNtcPIC 40
RING-HC_TRIM62_C-IV cd16608
RING finger, HC subclass, found in tripartite motif-containing protein 62 (TRIM62) and similar ...
38-81 7.02e-04

RING finger, HC subclass, found in tripartite motif-containing protein 62 (TRIM62) and similar proteins; TRIM62, also known as Ductal Epithelium Associated Ring Chromosome 1 (DEAR1), is a cytoplasmic E3 ubiquitin-protein ligase that was identified as a dominant regulator of acinar morphogenesis in the mammary gland. It is implicated in the inflammatory response of immune cells by regulating the Toll-like receptor 4 (TLR4) signaling pathway, leading to increased activity of the activator protein 1 (AP-1) transcription factor in primary macrophages. It is also involved in muscular protein homeostasis, especially during inflammation-induced atrophy, and may play a role in the pathogenesis of ICU-acquired weakness (ICUAW) by activating and maintaining inflammation in myocytes. Moreover, TRIM62 facilitates K27-linked poly-ubiquitination of CARD9 and also regulates CARD9-mediated anti-fungal immunity and intestinal inflammation. It also functions as a chromosome 1p35 tumor suppressor and negatively regulates transforming growth factor beta (TGFbeta)-driven epithelial-mesenchymal transition (EMT) by binding to and promoting the ubiquitination of SMAD3, a major effector of TGFbeta-mediated EMT. TRIM62 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438270 [Multi-domain]  Cd Length: 52  Bit Score: 37.87  E-value: 7.02e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 767910370  38 RLEERYKCAFCHSVLHNPHQTGCGHRFCQHCIL---SLRELNTVPIC 81
Cdd:cd16608    2 SLKDELLCSICLSIYQDPVSLGCEHYFCRQCITehwSRSEHRDCPEC 48
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
255-409 1.53e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 41.04  E-value: 1.53e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 255 SALREHMRLVLEKNVQLEEQISDLHKSLEQKESKIQQLAETIKKLEKEFKQFAQlfgkngsflpNIQVFASHIDKSAWLE 334
Cdd:COG4372   27 AALSEQLRKALFELDKLQEELEQLREELEQAREELEQLEEELEQARSELEQLEE----------ELEELNEQLQAAQAEL 96
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767910370 335 AQVHQLLQMVNQQQNKfdlrpLMEAVDTVKQKITLLEnndQRLAVLEEETNKHDTHINIHKAQLSKNEERFKLLE 409
Cdd:COG4372   97 AQAQEELESLQEEAEE-----LQEELEELQKERQDLE---QQRKQLEAQIAELQSEIAEREEELKELEEQLESLQ 163
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
219-412 1.55e-03

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


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 41.44  E-value: 1.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  219 VDEHLA-----VCPEAEQDcpFKHYGCAVTDK---RRNLQQHEH---SALREhmRLVLEKNVqlEEQISDLHKSLEQKES 287
Cdd:COG4913   551 LEAELGrrfdyVCVDSPEE--LRRHPRAITRAgqvKGNGTRHEKddrRRIRS--RYVLGFDN--RAKLAALEAELAELEE 624
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  288 KIQQLAETIKKLEKEFKQfaqlfgkngsflpniqvfashidksawLEAQVHQLLQMVNQQQNKFDLRPLMEAVDTVKQKI 367
Cdd:COG4913   625 ELAEAEERLEALEAELDA---------------------------LQERREALQRLAEYSWDEIDVASAEREIAELEAEL 677
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 767910370  368 TLLENNDQRLAVLEEEtnkhdthINIHKAQLSKNEERFKLLEGTC 412
Cdd:COG4913   678 ERLDASSDDLAALEEQ-------LEELEAELEELEEELDELKGEI 715
RING-HC_IRC20-like cd23135
RING finger, HC subclass, found in Saccharomyces cerevisiae increased recombination centers ...
43-81 1.60e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae increased recombination centers protein 20 (IRC20) and similar proteins; IRC20 is an uncharacterized ATP-dependent helicase that is probably involved in a pathway contributing to genomic integrity. IRC20 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438497 [Multi-domain]  Cd Length: 44  Bit Score: 36.72  E-value: 1.60e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 767910370  43 YKCAFCHSVLHNPHQTGCGHRFCQHCILS-LRELNTVPIC 81
Cdd:cd23135    4 LSCSICFSEIRSGAILKCGHFFCLSCIASwLREKSTCPLC 43
zf-C3HC4_2 pfam13923
Zinc finger, C3HC4 type (RING finger);
44-81 2.01e-03

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 404756 [Multi-domain]  Cd Length: 40  Bit Score: 36.26  E-value: 2.01e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 767910370   44 KCAFCHSVLHNPHQ-TGCGHRFCQHCIL-SLRELNTVPIC 81
Cdd:pfam13923   1 MCPICMDMLKDPSTtTPCGHVFCQDCILrALRAGNECPLC 40
Dynamitin pfam04912
Dynamitin; Dynamitin is a subunit of the microtubule-dependent motor complex and in implicated ...
266-408 2.52e-03

Dynamitin; Dynamitin is a subunit of the microtubule-dependent motor complex and in implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS).


Pssm-ID: 461477 [Multi-domain]  Cd Length: 390  Bit Score: 40.40  E-value: 2.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  266 EKNVQLEEQISDLHKSLEQ-----------KESKIQQLAETIKKLEKEFKQFAQLFGKNGSFLPNIQVFAS-HID----- 328
Cdd:pfam04912 124 ADPVELAAQLASLQKQLDElkleellgpdvAIGLTDPQGALSKRLLSQLEAFKQTSAPSGKKEPSASEPPSnHVTyelyy 203
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  329 -----------KSAWLEAQVHQLLQMVNQQQNKFD-------LRPLMEAVDTVKQKITLLENN-----DQRLAVLEEETN 385
Cdd:pfam04912 204 rpeqaksqqlaKIAELEKRLAELEKLVGIDSDLLDelsanlgPAPLLETLSRLQAKLSLLDPAhldaiERRLKSLLAEMD 283
                         170       180
                  ....*....|....*....|....
gi 767910370  386 KHDTHINIHKA-QLSKNEERFKLL 408
Cdd:pfam04912 284 ELAEKREKADAtQEAKINELYELL 307
RING-HC_TRIM77_C-IV cd16543
RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar ...
40-86 2.62e-03

RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar proteins; TRIM77 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including two consecutive zinc-binding domains, a C3HC4-type RING-HC finger and Bbox2, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438205 [Multi-domain]  Cd Length: 54  Bit Score: 36.22  E-value: 2.62e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 767910370  40 EERYKCAFCHSVLHNPHQTGCGHRFCQHCILSLRE-LNTVPICPVDKE 86
Cdd:cd16543    1 EDQLTCSICLDLLKDPVTIPCGHSFCMNCITLLWDrKQGVPSCPQCRE 48
RING-HC_ORTHRUS_rpt2 cd23139
second RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; ...
38-69 2.89e-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: 36.67  E-value: 2.89e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 767910370  38 RLEERYKCAFCHSVLHNPHQTGCGHRFCQHCI 69
Cdd:cd23139    1 RLLKEFGCQICKKVLSLPVSTPCGHNFCKACL 32
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
270-430 3.87e-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: 40.00  E-value: 3.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  270 QLEEQISDLHKSLEQKESKIQQLAETIKKLEKEfkqfaqlfgKNGSFLPNiqvfaSHIDKSawLEAQVHQLLQMVNQQQN 349
Cdd:TIGR04523 318 NQEKKLEEIQNQISQNNKIISQLNEQISQLKKE---------LTNSESEN-----SEKQRE--LEEKQNEIEKLKKENQS 381
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  350 KFD-LRPLMEAVDTVKQKIT----LLENNDQRLAVLEEETNKHDTHINIHKAQLSKNEERFKLLEGTCYNGKLIWKVTDY 424
Cdd:TIGR04523 382 YKQeIKNLESQINDLESKIQnqekLNQQKDEQIKKLQQEKELLEKEIERLKETIIKNNSEIKDLTNQDSVKELIIKNLDN 461

                  ....*.
gi 767910370  425 KMKKRE 430
Cdd:TIGR04523 462 TRESLE 467
RING-HC_LNX4 cd16719
RING finger, HC subclass, found in ligand of numb protein X 4 (LNX4); LNX4, also known as PDZ ...
44-70 4.31e-03

RING finger, HC subclass, found in ligand of numb protein X 4 (LNX4); LNX4, also known as PDZ domain-containing RING finger protein 4 (PDZRN4), or SEMACAP3-like protein (SEMCAP3L), is an E3 ubiquitin-protein ligase 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. LNX4 contains an N-terminal C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain.


Pssm-ID: 438379 [Multi-domain]  Cd Length: 53  Bit Score: 35.67  E-value: 4.31e-03
                         10        20
                 ....*....|....*....|....*..
gi 767910370  44 KCAFCHSVLHNPHQTGCGHRFCQHCIL 70
Cdd:cd16719    6 KCKLCGKVLEEPLSTPCGHVFCAGCLL 32
RING-HC_HLTF cd16509
RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar ...
45-81 4.76e-03

RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins; HLTF, also known as DNA-binding protein/plasminogen activator inhibitor 1 regulator, HIP116, RING finger protein 80, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3, or sucrose nonfermenting protein 2-like 3, is a yeast RAD5 homolog found in mammals. It has both E3 ubiquitin ligase and DNA helicase activities, and plays a pivotal role in the template-switching pathway of DNA damage tolerance. It is involved in Lys-63-linked poly-ubiquitination of proliferating cell nuclear antigen (PCNA) at Lys-164 and in the regulation of DNA damage tolerance. It shows double-stranded DNA translocase activity with 3'-5' polarity, thereby facilitating regression of the replication fork. HLTF contains an N-terminal HIRAN (HIP116 and RAD5 N-terminal) domain, a SWI/SNF helicase domain that is divided into N- and C-terminal parts by an insertion of a C3HC4-type RING-HC finger involved in the poly-ubiquitination of PCNA.


Pssm-ID: 438172 [Multi-domain]  Cd Length: 53  Bit Score: 35.36  E-value: 4.76e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 767910370  45 CAFCHSVLHNPHQTGCGHRFCQHCILS--LRELNTVPIC 81
Cdd:cd16509    6 CAICLDSLTNPVITPCAHVFCRRCICEviQREKAKCPMC 44
mukB PRK04863
chromosome partition protein MukB;
272-383 5.19e-03

chromosome partition protein MukB;


Pssm-ID: 235316 [Multi-domain]  Cd Length: 1486  Bit Score: 39.94  E-value: 5.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370  272 EEQISDLHKSLEQKESKIQQLAETIKKLEKEFKQFAQLFGKNGS--FLPNIQV-FASHIDKSAWLEAQVHQLLQMVNQQQ 348
Cdd:PRK04863  785 EKRIEQLRAEREELAERYATLSFDVQKLQRLHQAFSRFIGSHLAvaFEADPEAeLRQLNRRRVELERALADHESQEQQQR 864
                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 767910370  349 NKFD-LRPLMEAVDTVKQKITLLENN--DQRLAVLEEE 383
Cdd:PRK04863  865 SQLEqAKEGLSALNRLLPRLNLLADEtlADRVEEIREQ 902
RING-HC_TRIM39_C-IV cd16601
RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar ...
45-83 5.28e-03

RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins; TRIM39, also known as RING finger protein 23 (RNF23) or testis-abundant finger protein, is an E3 ubiquitin-protein ligase that plays a role in controlling DNA damage-induced apoptosis through inhibition of the anaphase promoting complex (APC/C), a multiprotein ubiquitin ligase that controls multiple cell cycle regulators, including cyclins, geminin, and others. TRIM39 also functions as a regulator of several key processes in the proliferative cycle. It directly regulates p53 stability. It modulates cell cycle progression and DNA damage responses via stabilizing p21. Moreover, TRIM39 negatively regulates the nuclear factor kappaB (NFkappaB)-mediated signaling pathway through stabilization of Cactin, an inhibitor of NFkappaB- and Toll-like receptor (TLR)-mediated transcription, which is induced by inflammatory stimulants such as tumor necrosis factor alpha. Furthermore, TRIM39 is a MOAP-1-binding protein that can promote apoptosis signaling through stabilization of MOAP-1 via the inhibition of its poly-ubiquitination process. TRIM39 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438263 [Multi-domain]  Cd Length: 44  Bit Score: 35.15  E-value: 5.28e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 767910370  45 CAFCHSVLHNPHQTGCGHRFCQHCILSL-RELNTVPICPV 83
Cdd:cd16601    4 CSLCKEYLKDPVIIECGHNFCRACITRFwEELDGDFPCPQ 43
RING-HC_MmTRIM43-like cd23133
RING finger, HC subclass, found in Mus musculus tripartite motif-containing protein 43 (TRIM43) ...
40-93 6.09e-03

RING finger, HC subclass, found in Mus musculus tripartite motif-containing protein 43 (TRIM43) and similar propteins; This subfamily includes TRIM43A, TRIM43B and TRIM43C, which are expressed specifically in mouse preimplantation embryos. They contain a typical C3HC4-type RING-HC finger.


Pssm-ID: 438495 [Multi-domain]  Cd Length: 57  Bit Score: 35.27  E-value: 6.09e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 767910370  40 EERYKCAFCHSVLHNPHQTGCGHRFCQHCILSLRELNTVP-ICPVDKEVIKSQEV 93
Cdd:cd23133    1 EETLTCSICQGIFMNPVYLRCGHKFCEACLLLFQEDIKFPaYCPMCRQPFNQEYI 55
RING-HC_ScRAD18-like cd23148
RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 ...
44-85 6.12e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 (RAD18) and similar proteins; RAD18, also called RING-type E3 ubiquitin transferase RAD18, acts as a postreplication repair E3 ubiquitin-protein ligase that associates with the E2 ubiquitin conjugating enzyme UBC2/RAD6 to form the UBC2-RAD18 ubiquitin ligase complex involved in postreplicative repair (PRR) of damaged DNA. The UBC2-RAD18 complex cooperates with RAD5 and the UBC13-MMS2 dimer to attach mono-ubiquitin chains on 'Lys-164' of POL30, which is necessary for PRR. The UBC2-RAD18 complex is also involved in prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine. RAD18 is an E3 RING-finger protein belonging to the UBC2/RAD6 epistasis group. It contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438510 [Multi-domain]  Cd Length: 52  Bit Score: 35.20  E-value: 6.12e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 767910370  44 KCAFCHSVLHNPHQTGCGHRFCQHCIlsLRELNTVPICPVDK 85
Cdd:cd23148    5 RCHICKDLLKAPMRTPCNHTFCSFCI--RTHLNNDARCPLCK 44
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
245-409 6.30e-03

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 39.37  E-value: 6.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 245 KRRNLQQ-HEHSALREHMRLVLEKNVQLEEQISDLHKSLEQKESKIQQLAETIKKLEKEfKQFAQLFGKNGSFLPNIQVF 323
Cdd:COG4717   66 PELNLKElKELEEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKL-LQLLPLYQELEALEAELAEL 144
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 324 ASHIDKsawLEAQVHQLLQMVNQQQNKF-DLRPLMEAVDTVKQKITL-----LENNDQRLAVLEEETNKHDTHINIHKAQ 397
Cdd:COG4717  145 PERLEE---LEERLEELRELEEELEELEaELAELQEELEELLEQLSLateeeLQDLAEELEELQQRLAELEEELEEAQEE 221
                        170
                 ....*....|..
gi 767910370 398 LSKNEERFKLLE 409
Cdd:COG4717  222 LEELEEELEQLE 233
RING-HC_BARD1 cd16496
RING finger, HC subclass, found in BRCA1-associated RING domain protein 1 (BARD-1) and similar ...
37-81 6.48e-03

RING finger, HC subclass, found in BRCA1-associated RING domain protein 1 (BARD-1) and similar proteins; BARD-1 is a critical factor in BRCA1-mediated tumor suppression and may also serve as a target for tumorigenic lesions in some human cancers. It associates with BRCA1 (breast cancer-1) to form a heterodimeric BRCA1/BARD1 complex that is responsible for maintaining genomic stability through nuclear functions involving DNA damage signaling and repair, transcriptional regulation, and cell cycle control. The BRCA1/BARD1 complex catalyzes autoubiquitination of BRCA1 and trans ubiquitination of other protein substrates. Its E3 ligase activity is dramatically reduced in the presence of UBX domain protein 1 (UBXN1). BARD-1 contains an C3HC4-type RING-HC finger that binds BRCA1 at its N-terminus and three tandem ankyrin repeats and tandem BRCT repeat domains at its C-terminus. The BRCT repeats bind CstF-50 (cleavage stimulation factor) to modulate mRNA processing and RNAP II stability in response to DNA damage.


Pssm-ID: 438159 [Multi-domain]  Cd Length: 86  Bit Score: 36.16  E-value: 6.48e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 767910370  37 ERLEERYKCAFCHSVLHNPHQTG-CGHRFCQHCILSlRELNTVPIC 81
Cdd:cd16496   10 DELENLLRCSRCASILKEPVTLGgCEHVFCRSCVGD-RLGNGCPVC 54
RING-HC_RNF151 cd16547
RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; ...
45-81 7.02e-03

RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; RNF151 is a testis-specific RING finger protein that interacts with dysbindin, a synaptic and microtubular protein that binds brain snapin, a SNARE-binding protein that mediates intracellular membrane fusion in both neuronal and non-neuronal cells. Thus, it may be involved in acrosome formation of spermatids by interacting with multiple proteins participating in membrane biogenesis and microtubule organization. RNF151 contains a C3HC4-type RING finger domain, a putative nuclear localization signal (NLS), and a TNF receptor associated factor (TRAF)-type zinc finger domain.


Pssm-ID: 438209 [Multi-domain]  Cd Length: 49  Bit Score: 34.74  E-value: 7.02e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 767910370  45 CAFCHSVLHNPHQTGCGHRFCQHCILS-LRELNTVPIC 81
Cdd:cd16547    6 CSICHGVLRCPVRLSCSHIFCKKCILQwLKRQETCPCC 43
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
241-411 7.32e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 38.73  E-value: 7.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 241 AVTDKRRNLQQHEHSALREHMRLVLEKNvQLEEQISDLHKSLEQKESKIQQLAETIKKLEKEFKQFAQLFGKngsflpni 320
Cdd:COG4372  105 SLQEEAEELQEELEELQKERQDLEQQRK-QLEAQIAELQSEIAEREEELKELEEQLESLQEELAALEQELQA-------- 175
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 321 qvfashiDKSAWLEAQVHQLLQMVNQQQNKFDLRPLMEAVDTVKQKITLLENNDQRLAVLEEETNKHDTHINIHKAQLSK 400
Cdd:COG4372  176 -------LSEAEAEQALDELLKEANRNAEKEEELAEAEKLIESLPRELAEELLEAKDSLEAKLGLALSALLDALELEEDK 248
                        170
                 ....*....|.
gi 767910370 401 NEERFKLLEGT 411
Cdd:COG4372  249 EELLEEVILKE 259
RING-HC_RNF113A_B cd16539
RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; ...
44-70 7.68e-03

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: 34.87  E-value: 7.68e-03
                         10        20
                 ....*....|....*....|....*..
gi 767910370  44 KCAFCHSVLHNPHQTGCGHRFCQHCIL 70
Cdd:cd16539    7 ACFICRKPFKNPVVTKCGHYFCEKCAL 33
RING-HC_TRY3-like cd23137
RING finger, HC subclass, found in Candida albicans transcriptional regulator of yeast form ...
41-90 7.84e-03

RING finger, HC subclass, found in Candida albicans transcriptional regulator of yeast form adherence 3 (TRY3) and similar proteins; TRY3 acts as a transcription factor required for yeast cell adherence to silicone substrate. It contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438499 [Multi-domain]  Cd Length: 53  Bit Score: 34.75  E-value: 7.84e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 767910370  41 ERYKCAFCHSVLHNPHQTGCGHRFCQHCILSL--RELNTVPICPvDKEVIKS 90
Cdd:cd23137    1 DDYACPICMNVAWKPVRLECSHVFCLRCLVKAqkQKKDNCPLCR-AKGAVKA 51
RING-HC_RNF180 cd16554
RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins; ...
41-90 8.39e-03

RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins; RNF180, also known as Rines, is a membrane-bound E3 ubiquitin-protein ligase well conserved among vertebrates. It is a critical regulator of the monoaminergic system, as well as emotional and social behavior. It interacts with brain monoamine oxidase A (MAO-A) and targets it for ubiquitination and degradation. It also functions as a novel tumor suppressor in gastric carcinogenesis. The hypermethylated CpG site count of the RNF180 DNA promoter can be used to predict survival of gastric cancer. RNF180 contains a novel conserved dual specificity protein phosphatase Rines conserved (DSPRC) domain, a basic coiled-coil domain, a C3HC4-type RING-HC finger, and a C-terminal hydrophobic region that is predicted to be a transmembrane domain.


Pssm-ID: 438216 [Multi-domain]  Cd Length: 59  Bit Score: 34.98  E-value: 8.39e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 767910370  41 ERYKCAFCHSVLHNPHQ-TGCGHRFCQHCilsLRELN----TVPICPVDKEVIKS 90
Cdd:cd16554    1 ESLTCPVCLDLYYDPYMcYPCGHIFCEPC---LRQLAksspKNTPCPLCRTTIRR 52
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
262-406 8.92e-03

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. 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: 129705 [Multi-domain]  Cd Length: 1042  Bit Score: 39.18  E-value: 8.92e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370   262 RLVLEKNVQ-LEEQISDLHKSLEQKESKIQQLAETIKKLEKEFKQFAQLFGKNGSFLPNIQVFASHIDKSAwLEAQVHQL 340
Cdd:TIGR00618  678 RQLALQKMQsEKEQLTYWKEMLAQCQTLLRELETHIEEYDREFNEIENASSSLGSDLAAREDALNQSLKEL-MHQARTVL 756
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767910370   341 LQMVNQQQNKFDLRPLMEAVDT--------VKQKITLLENNDQRLAVLEEETNKHDTH----INIHKAQLSKNEERFK 406
Cdd:TIGR00618  757 KARTEAHFNNNEEVTAALQTGAelshlaaeIQFFNRLREEDTHLLKTLEAEIGQEIPSdediLNLQCETLVQEEEQFL 834
Prefoldin_alpha_GimC cd23160
Prefoldin alpha subunit, archaeal; Archaeal alpha subunit of prefoldin (GimC), a hexameric ...
264-305 9.19e-03

Prefoldin alpha subunit, archaeal; Archaeal alpha subunit of prefoldin (GimC), a hexameric molecular chaperone complex, found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.


Pssm-ID: 467476 [Multi-domain]  Cd Length: 127  Bit Score: 36.70  E-value: 9.19e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 767910370 264 VLEKNVQ-----LEEQISDLHKSLEQKESKIQQLAETIKKLEKEFKQ 305
Cdd:cd23160   81 VVEKTIDeaieiLEKRIKELEKALEKLQEQLQQIAQRLEELEAELQE 127
RING-HC_TRIM41-like_C-IV cd16602
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and ...
40-81 9.22e-03

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and similar proteins; TRIM41 and TRIM52, two closely related tripartite motif-containing proteins, have dramatically expanded RING domains compared with the rest of the TRIM family proteins. TRIM41 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM52 lacks the putative viral recognition SPRY/B30.2 domain, and thus has been classified to the C-V subclass of the TRIM family that contains only RBCC domains. TRIM41, also known as RING finger-interacting protein with C kinase (RINCK), is an E3 ubiquitin-protein ligase that promotes the ubiquitination of protein kinase C (PKC) isozymes in cells. It specifically recognizes the C1 domain of PKC isozymes. It controls the amplitude of PKC signaling by controlling the amount of PKC in the cell. TRIM52, also known as RING finger protein 102 (RNF102), is encoded by a novel, noncanonical antiviral TRIM52 gene in primate genomes with unique specificity determined by the rapidly evolving RING domain.


Pssm-ID: 438264 [Multi-domain]  Cd Length: 53  Bit Score: 34.52  E-value: 9.22e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 767910370  40 EERYKCAFCHSVLHNPHQTGCGHRFCQHCILSLRELnTVPIC 81
Cdd:cd16602    1 QEEAVCAICLDYFKDPVSIGCGHNFCRVCVTQLWGF-TCPQC 41
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
270-411 9.50e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 38.73  E-value: 9.50e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767910370 270 QLEEQISDLHKSLEQKESKIQQLAETIKKLEKEFK----QFAQLFGKNGSFLPNIQVFASHIDKSAWLEAQVHQLLQMVN 345
Cdd:COG4372   77 QLEEELEELNEQLQAAQAELAQAQEELESLQEEAEelqeELEELQKERQDLEQQRKQLEAQIAELQSEIAEREEELKELE 156
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767910370 346 QQQNKfdLRPLMEAVDTVKQKITlLENNDQRLAVLEEETNKHDTHINIHKAQLSKNEERFKLLEGT 411
Cdd:COG4372  157 EQLES--LQEELAALEQELQALS-EAEAEQALDELLKEANRNAEKEEELAEAEKLIESLPRELAEE 219
mRING-HC-C3HC3D_Nrdp1 cd16634
Modified RING finger, HC subclass (C3HC3D-type), found in neuregulin receptor degradation ...
45-85 9.74e-03

Modified RING finger, HC subclass (C3HC3D-type), found in neuregulin receptor degradation protein-1 (Nrdp1) and similar proteins; Nrdp1 (referred to as FLRF in mice), also known as RING finger protein 41 (RNF41), is an E3 ubiquitin-protein ligase that plays a critical role in the regulation of cell growth and apoptosis, inflammation and production of reactive oxygen species (ROS), as well as in doxorubicin (DOX)-induced cardiac injury. It promotes the degradation of the epidermal growth factor receptor (EGFR/ErbB) family member, ErbB3, which is independent of growth factor stimulation. It also promotes M2 macrophage polarization by ubiquitinating and activating transcription factor CCAAT/enhancer-binding protein beta (C/EBPbeta) via Lys-63-linked ubiquitination. Moreover, Nrdp1 interacts with and modulates the activity of Parkin, a causative protein for early onset recessive juvenile parkinsonism (AR-JP). It also interacts with ubiquitin-specific protease 8 (USP8), which is involved in trafficking of various transmembrane proteins. Furthermore, Nrdp1 inhibits basal lysosomal degradation and enhances ectodomain shedding of JAK2-associated cytokine receptors. Its phosphorylation by the kinase Par-1b (also known as MARK2) is required for epithelial cell polarity. Nrdp1 contains an N-terminal modified C3HC3D-type RING-HC finger required for enhancing ErbB3 degradation, a B-box, a coiled-coil domain responsible for Nrdp1 oligomerization, and a C-terminal ErbB3-binding domain.


Pssm-ID: 438296 [Multi-domain]  Cd Length: 43  Bit Score: 34.32  E-value: 9.74e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 767910370  45 CAFCHSVLHNPHQT-GCGHRFCQHCILSLreLNTVPICPVDK 85
Cdd:cd16634    4 CPICSGVLEEPLQApHCEHAFCNACITEW--LSRQQTCPVDR 43
RING-HC_TRIM10_C-IV cd16593
RING finger, HC subclass, found in tripartite motif-containing protein 10 (TRIM10) and similar ...
39-86 9.79e-03

RING finger, HC subclass, found in tripartite motif-containing protein 10 (TRIM10) and similar proteins; TRIM10, also known as B30-RING finger protein (RFB30), RING finger protein 9 (RNF9), or hematopoietic RING finger 1 (HERF1), is a novel hematopoiesis-specific RING finger protein required for terminal differentiation of erythroid cells. TRIM10 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438255 [Multi-domain]  Cd Length: 61  Bit Score: 34.88  E-value: 9.79e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 767910370  39 LEERYKCAFCHSVLHNPHQTGCGHRFCQHCILSLRE-----LNTVPICPVDKE 86
Cdd:cd16593    2 LADEVNCPICQGTLREPVTIDCGHNFCRACLTRYCEipgpdLEEPPTCPLCKE 54
zf-TRAF_2 pfam15965
TRAF-like zinc-finger;
206-252 9.85e-03

TRAF-like zinc-finger;


Pssm-ID: 464957  Cd Length: 92  Bit Score: 35.77  E-value: 9.85e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 767910370  206 CPNNCAKIILKTEVDEHLAVCPEAEQDCPFKHYGCAVTDKRRNLQQH 252
Cdd:pfam15965  27 CPLGCGAVFHSCKLEEHQLLCPNEKVPCLNASYGCPFTLPRKQLAKH 73
RING-HC_TRIM21_C-IV cd16596
RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar ...
36-83 9.96e-03

RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar proteins; TRIM21, also known as 52 kDa Ro protein, 52 kDa ribonucleoprotein autoantigen Ro/SS-A, Ro(SS-A), RING finger protein 81 (RNF81), or Sjoegren syndrome type A antigen (SS-A), is a ubiquitously expressed E3 ubiquitin-protein ligase and a high affinity antibody receptor uniquely expressed in the cytosol of mammalian cells. As a cytosolic Fc receptor, TRIM21 binds the Fc of virus-associated antibodies and targets the complex in the cytosol for proteasomal degradation in a process known as antibody-dependent intracellular neutralization (ADIN), and provides an intracellular immune response to protect host defense against pathogen infection. It shows remarkably broad isotype specificity as it does not only bind IgG, but also IgM and IgA. Moreover, TRIM21 promotes the cytosolic DNA sensor cGAS and the cytosolic RNA sensor RIG-I sensing of viral genomes during infection by antibody-opsonized virus. It stimulates inflammatory signaling and activates innate transcription factors, such as nuclear factor-kappaB (NF-kappaB). TRIM21 also plays an essential role in p62-regulated redox homeostasis, suggesting it may be a viable target for treating pathological conditions resulting from oxidative damage. Furthermore, TRIM21 may have implications for various autoimmune diseases associated with uncontrolled antiviral signaling through the regulation of Nmi-IFI35 complex-mediated inhibition of innate antiviral response. TRIM21 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438258 [Multi-domain]  Cd Length: 77  Bit Score: 35.26  E-value: 9.96e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 767910370  36 VERLEERYKCAFCHSVLHNPHQTGCGHRFCQHCILSLRElNTVPICPV 83
Cdd:cd16596    3 LTMMWEEVTCPICLDPFVEPVSIECGHSFCQECISQVGK-GGGSVCPV 49
 
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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