Query 046357
Match_columns 137
No_of_seqs 172 out of 329
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 11:17:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046357.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046357hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd03772 MATH_HAUSP Herpesvirus 99.5 6.3E-14 1.4E-18 102.2 7.5 71 1-75 52-134 (137)
2 cd03775 MATH_Ubp21p Ubiquitin- 99.5 1.1E-13 2.3E-18 100.9 6.8 68 1-71 46-133 (134)
3 cd03774 MATH_SPOP Speckle-type 99.3 7.7E-12 1.7E-16 91.2 6.4 68 1-76 59-139 (139)
4 PF00917 MATH: MATH domain; I 99.1 1E-10 2.2E-15 81.2 5.0 67 1-73 41-119 (119)
5 cd00121 MATH MATH (meprin and 99.0 2.5E-09 5.4E-14 73.7 7.3 66 1-71 48-125 (126)
6 cd00270 MATH_TRAF_C Tumor Necr 98.9 3.3E-09 7.2E-14 77.8 5.4 66 1-71 58-148 (149)
7 cd03773 MATH_TRIM37 Tripartite 98.7 1.9E-08 4.1E-13 72.3 5.5 62 1-72 55-130 (132)
8 cd03776 MATH_TRAF6 Tumor Necro 98.5 1.1E-07 2.5E-12 70.0 4.8 66 1-71 58-146 (147)
9 KOG1987 Speckle-type POZ prote 98.5 4.3E-08 9.3E-13 79.1 1.4 64 14-80 54-132 (297)
10 cd03778 MATH_TRAF2 Tumor Necro 98.3 1.6E-06 3.5E-11 66.2 6.7 65 1-66 76-161 (164)
11 cd03779 MATH_TRAF1 Tumor Necro 98.3 2.5E-06 5.5E-11 63.9 6.6 68 1-71 58-146 (147)
12 COG5077 Ubiquitin carboxyl-ter 98.2 7.9E-07 1.7E-11 81.1 3.4 74 1-77 83-174 (1089)
13 cd03781 MATH_TRAF4 Tumor Necro 98.2 2.7E-06 5.8E-11 63.5 5.7 66 1-71 58-153 (154)
14 cd03780 MATH_TRAF5 Tumor Necro 98.2 4.5E-06 9.8E-11 62.5 6.1 66 1-66 58-145 (148)
15 cd03772 MATH_HAUSP Herpesvirus 98.0 4.4E-06 9.4E-11 60.7 3.4 63 61-130 66-133 (137)
16 smart00061 MATH meprin and TRA 97.9 1.5E-05 3.2E-10 52.8 4.5 43 1-44 43-95 (95)
17 cd03777 MATH_TRAF3 Tumor Necro 97.9 3.7E-05 7.9E-10 59.7 6.7 67 1-72 96-184 (186)
18 cd03771 MATH_Meprin Meprin fam 97.8 4.3E-05 9.4E-10 58.5 5.7 64 1-66 55-164 (167)
19 cd03774 MATH_SPOP Speckle-type 97.6 4.6E-05 1E-09 55.3 2.2 34 98-131 105-138 (139)
20 cd03778 MATH_TRAF2 Tumor Necro 97.3 0.00022 4.7E-09 54.5 3.8 29 98-127 135-163 (164)
21 KOG1863 Ubiquitin carboxyl-ter 97.3 0.00024 5.2E-09 67.6 3.7 74 2-79 72-157 (1093)
22 PF00917 MATH: MATH domain; I 97.2 0.00027 5.8E-09 48.6 2.6 30 98-129 90-119 (119)
23 cd03775 MATH_Ubp21p Ubiquitin- 97.1 0.00028 6.1E-09 51.1 2.4 30 98-127 100-133 (134)
24 cd00270 MATH_TRAF_C Tumor Necr 96.6 0.0015 3.3E-08 47.6 2.7 29 98-128 121-149 (149)
25 cd03771 MATH_Meprin Meprin fam 95.3 0.0098 2.1E-07 45.5 1.9 29 98-128 139-167 (167)
26 cd03780 MATH_TRAF5 Tumor Necro 95.2 0.014 3E-07 43.6 2.2 30 98-127 118-147 (148)
27 cd03773 MATH_TRIM37 Tripartite 95.2 0.0091 2E-07 42.5 1.2 29 98-128 100-130 (132)
28 cd03776 MATH_TRAF6 Tumor Necro 94.9 0.019 4.1E-07 42.1 2.3 28 98-127 119-146 (147)
29 cd00121 MATH MATH (meprin and 94.6 0.03 6.4E-07 38.0 2.5 29 98-128 98-126 (126)
30 cd03783 MATH_Meprin_Alpha Mepr 94.4 0.023 5.1E-07 43.6 1.8 29 36-66 136-164 (167)
31 cd03779 MATH_TRAF1 Tumor Necro 93.6 0.064 1.4E-06 40.1 2.8 30 98-127 117-146 (147)
32 cd03781 MATH_TRAF4 Tumor Necro 92.9 0.067 1.4E-06 39.7 1.9 28 98-127 126-153 (154)
33 cd03782 MATH_Meprin_Beta Mepri 91.3 0.13 2.8E-06 39.6 1.9 30 35-66 135-164 (167)
34 cd03783 MATH_Meprin_Alpha Mepr 89.7 0.18 3.8E-06 38.8 1.3 29 98-128 139-167 (167)
35 cd03777 MATH_TRAF3 Tumor Necro 89.6 0.34 7.4E-06 37.5 2.9 29 98-128 156-184 (186)
36 cd03782 MATH_Meprin_Beta Mepri 78.7 1.2 2.7E-05 34.2 1.6 29 98-128 139-167 (167)
37 KOG1863 Ubiquitin carboxyl-ter 43.3 15 0.00032 35.8 1.8 36 99-134 121-156 (1093)
38 COG5077 Ubiquitin carboxyl-ter 25.5 55 0.0012 31.4 2.4 42 91-132 127-173 (1089)
39 KOG1987 Speckle-type POZ prote 20.2 98 0.0021 24.6 2.6 34 98-131 94-127 (297)
No 1
>cd03772 MATH_HAUSP Herpesvirus-associated ubiquitin-specific protease (HAUSP, also known as USP7) family, N-terminal MATH (TRAF-like) domain; composed of proteins similar to human HAUSP, an enzyme that specifically catalyzes the deubiquitylation of p53 and MDM2, hence playing an important role in the p53-MDM2 pathway. It contains an N-terminal TRAF-like domain and a C-terminal catalytic protease (C19 family) domain. The tumor suppressor p53 protein is a transcription factor that responds to many cellular stress signals and is regulated primarily through ubiquitylation and subsequent degradation. MDM2 is a RING-finger E3 ubiquitin ligase that promotes p53 ubiquitinylation. p53 and MDM2 bind to the same site in the N-terminal TRAF-like domain of HAUSP in a mutually exclusive manner. HAUSP also interacts with the Epstein-Barr nuclear antigen 1 (EBNA1) protein of the Epstein-Barr virus (EBV), which efficiently immortalizes infected cells predisposing the host to a variety of cancers. EBNA1
Probab=99.50 E-value=6.3e-14 Score=102.17 Aligned_cols=71 Identities=15% Similarity=0.242 Sum_probs=61.1
Q ss_pred CeEEecCCCCCCCCCEEEEEEEEEEEe------------CcccccccccccccceeccccccccCCceEeCCeEEEEEee
Q 046357 1 MTLQKSETSSLPTGWEVNAIINFFFYC------------EKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVC 68 (137)
Q Consensus 1 lYL~~~~~~~l~~~w~v~a~fkl~i~N------------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~~ 68 (137)
|||++.+.. ..++|++.|+|+|+|+| .++|+.....|||++||++++|.++++|||+||+++|+|
T Consensus 52 vyL~~~~~~-~~~~w~i~a~~~~~l~~~~~~~~~~~~~~~~~f~~~~~~~G~~~fi~~~~L~~~~sgyl~~D~l~Ie~-- 128 (137)
T cd03772 52 FFLQCNAES-DSTSWSCHAQAVLRIINYKDDEPSFSRRISHLFFSKENDWGFSNFMTWSEVTDPEKGFIEDDTITLEV-- 128 (137)
T ss_pred EEEeeCCcC-CCCCCeEEEEEEEEEEcCCCCcccEEEeeeeEEcCCCCCccchheeEHHHhcCCCCCcEECCEEEEEE--
Confidence 589987644 44599999999999999 346877778999999999999999999999999999999
Q ss_pred eeEEEEc
Q 046357 69 EEVFVVK 75 (137)
Q Consensus 69 ~eV~vv~ 75 (137)
+|.|=.
T Consensus 129 -~V~~~~ 134 (137)
T cd03772 129 -YVQADA 134 (137)
T ss_pred -EEEeeC
Confidence 997643
No 2
>cd03775 MATH_Ubp21p Ubiquitin-specific protease 21 (Ubp21p) family, MATH domain; composed of fungal proteins with similarity to Ubp21p of fission yeast. Ubp21p is a deubiquitinating enzyme that may be involved in the regulation of the protein kinase Prp4p, which controls the formation of active spliceosomes. Members of this family are similar to human HAUSP (Herpesvirus-associated ubiquitin-specific protease) in that they contain an N-terminal MATH domain and a C-terminal catalytic protease (C19 family) domain. HAUSP is also an ubiquitin-specific protease that specifically catalyzes the deubiquitylation of p53 and MDM2. The MATH domain of HAUSP contains the binding site for p53 and MDM2. Similarly, the MATH domain of members in this family may be involved in substrate binding.
Probab=99.47 E-value=1.1e-13 Score=100.87 Aligned_cols=68 Identities=24% Similarity=0.392 Sum_probs=59.3
Q ss_pred CeEEecCCCC----CCCCCEEEEEEEEEEEe------------Ccccccccccccccceecccccccc----CCceEeCC
Q 046357 1 MTLQKSETSS----LPTGWEVNAIINFFFYC------------EKHFRAVKTKWCITKFIDLETLSNT----LNEYLIND 60 (137)
Q Consensus 1 lYL~~~~~~~----l~~~w~v~a~fkl~i~N------------~~~F~~~~~~wG~~~fi~l~~l~d~----~~GyLv~D 60 (137)
+||++.+.+. ++++|.++|+|+|+++| .++|+.....|||.+||++++|.+| .+|||+||
T Consensus 46 lyL~l~~~~~~~~~~~~~~~v~a~f~~~l~n~~~~~~~~~~~~~~~F~~~~~~wG~~~fi~~~~L~~~~~~~~~g~l~nD 125 (134)
T cd03775 46 IYLEPHPEEEEKAPLDEDWSVCAQFALVISNPGDPSIQLSNVAHHRFNAEDKDWGFTRFIELRKLAHRTPDKPSPFLENG 125 (134)
T ss_pred EEEEecCcccccccCCCCCeEEEEEEEEEEcCCCCccceEccceeEeCCCCCCCChhHcccHHHHcccccCCCCceeECC
Confidence 5888876554 47899999999999999 4688877789999999999999965 68999999
Q ss_pred eEEEEEeeeeE
Q 046357 61 VCVCGCVCEEV 71 (137)
Q Consensus 61 ~~v~~a~~~eV 71 (137)
+++|.| +|
T Consensus 126 ~l~I~~---~~ 133 (134)
T cd03775 126 ELNITV---YV 133 (134)
T ss_pred EEEEEE---EE
Confidence 999999 76
No 3
>cd03774 MATH_SPOP Speckle-type POZ protein (SPOP) family, MATH domain; composed of proteins with similarity to human SPOP. SPOP was isolated as a novel antigen recognized by serum from a scleroderma patient, whose overexpression in COS cells results in a discrete speckled pattern in the nuclei. It contains an N-terminal MATH domain and a C-terminal BTB (also called POZ) domain. Together with Cul3, SPOP constitutes an ubiquitin E3 ligase which is able to ubiquitinate the PcG protein BMI1, the variant histone macroH2A1 and the death domain-associated protein Daxx. Therefore, SPOP may be involved in the regulation of these proteins and may play a role in transcriptional regulation, apoptosis and X-chromosome inactivation. Cul3 binds to the BTB domain of SPOP whereas Daxx and the macroH2A1 nonhistone region have been shown to bind to the MATH domain. Both MATH and BTB domains are necessary for the nuclear speckled accumulation of SPOP. There are many proteins, mostly uncharacterized, conta
Probab=99.28 E-value=7.7e-12 Score=91.23 Aligned_cols=68 Identities=28% Similarity=0.332 Sum_probs=57.0
Q ss_pred CeEEecCCCCCCCCCEEEEEEEEEEEe-------------CcccccccccccccceeccccccccCCceEeCCeEEEEEe
Q 046357 1 MTLQKSETSSLPTGWEVNAIINFFFYC-------------EKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCV 67 (137)
Q Consensus 1 lYL~~~~~~~l~~~w~v~a~fkl~i~N-------------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~ 67 (137)
|||++.+.+ .+.+.|+|+|+++| .++|+. ...|||.+||++++|.++.+|||+||+++|++
T Consensus 59 lyL~l~~~~----~~~v~a~f~~~l~n~~~~~~~~~~~~~~~~f~~-~~~wG~~~fi~~~~L~~~~~g~l~dD~l~I~c- 132 (139)
T cd03774 59 LYLLLVSCP----KSEVRAKFKFSILNAKGEETKAMESQRAYRFVQ-GKDWGFKKFIRRDFLLDEANGLLPDDKLTLFC- 132 (139)
T ss_pred EEEEEccCC----CCcEEEEEEEEEEecCCCeeeeecccCcEeCCC-CCccCHHHeeeHHHhhhhhcccccCCEEEEEE-
Confidence 588876532 46899999999999 245654 46899999999999998889999999999999
Q ss_pred eeeEEEEcc
Q 046357 68 CEEVFVVKN 76 (137)
Q Consensus 68 ~~eV~vv~~ 76 (137)
+|.|+++
T Consensus 133 --~I~V~~~ 139 (139)
T cd03774 133 --EVSVVQD 139 (139)
T ss_pred --EEEEEcC
Confidence 9999853
No 4
>PF00917 MATH: MATH domain; InterPro: IPR002083 Although apparently functionally unrelated, intracellular TRAFs and extracellular meprins share a conserved region of about 180 residues, the meprin and TRAF homology (MATH) domain []. Meprins are mammalian tissue-specific metalloendopeptidases of the astacin family implicated in developmental, normal and pathological processes by hydrolysing a variety of proteins. Various growth factors, cytokines, and extracellular matrix proteins are substrates for meprins. They are composed of five structural domains: an N-terminal endopeptidase domain, a MAM domain (see PDOC00604 from PROSITEDOC), a MATH domain, an EGF-like domain (see PDOC00021 from PROSITEDOC) and a C-terminal transmembrane region. Meprin A and B form membrane bound homotetramer whereas homooligomers of meprin A are secreted. A proteolitic site adjacent to the MATH domain, only present in meprin A, allows the release of the protein from the membrane []. TRAF proteins were first isolated by their ability to interact with TNF receptors []. They promote cell survival by the activation of downstream protein kinases and, finally, transcription factors of the NF-kB and AP-1 family. The TRAF proteins are composed of 3 structural domains: a RING finger (see PDOC00449 from PROSITEDOC) in the N-terminal part of the protein, one to seven TRAF zinc fingers (see PDOC50145 from PROSITEDOC) in the middle and the MATH domain in the C-terminal part []. The MATH domain is necessary and sufficient for self-association and receptor interaction. From the structural analysis two consensus sequence recognised by the TRAF domain have been defined: a major one, [PSAT]x[QE]E and a minor one, PxQxxD []. The structure of the TRAF2 protein reveals a trimeric self-association of the MATH domain []. The domain forms a new, light-stranded antiparallel beta sandwich structure. A coiled-coil region adjacent to the MATH domain is also important for the trimerisation. The oligomerisation is essential for establishing appropriate connections to form signalling complexes with TNF receptor-1. The ligand binding surface of TRAF proteins is located in beta-strands 6 and 7 [].; GO: 0005515 protein binding; PDB: 1D00_E 1CZY_A 1D01_F 1CA9_A 1D0J_D 1F3V_B 1CA4_C 1D0A_A 1QSC_C 1CZZ_C ....
Probab=99.11 E-value=1e-10 Score=81.20 Aligned_cols=67 Identities=21% Similarity=0.416 Sum_probs=56.9
Q ss_pred CeEEecCCCCCC-CCCEEEEEEEEEEEe-----------CcccccccccccccceeccccccccCCceEeCCeEEEEEee
Q 046357 1 MTLQKSETSSLP-TGWEVNAIINFFFYC-----------EKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVC 68 (137)
Q Consensus 1 lYL~~~~~~~l~-~~w~v~a~fkl~i~N-----------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~~ 68 (137)
+||.+..++... .+|.+.|++++.++| .+.|+.. ..|||.+||++++|.++. |+.||+++|+|
T Consensus 41 ~~L~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~F~~~-~~~g~~~fi~~~~l~~~~--fl~dd~l~ie~-- 115 (119)
T PF00917_consen 41 VYLHCDKGENDSDLEWSIEAEFRFRLLNQNGKSISKRIKSHSFNNP-SSWGWSSFISWEDLEDPY--FLVDDSLTIEV-- 115 (119)
T ss_dssp EEEEEECSTTGGGSSSSEEEEEEEEEE-TTSCEEEEEEECEEECTT-SEEEEEEEEEHHHHTTCT--TSBTTEEEEEE--
T ss_pred EEEEEeecccccccceeeeEEEEEEEecCCCCcceeeeeeeEEeee-cccchhheeEHHHhCccC--CeECCEEEEEE--
Confidence 589998887665 799999999999998 2567444 799999999999999765 99999999999
Q ss_pred eeEEE
Q 046357 69 EEVFV 73 (137)
Q Consensus 69 ~eV~v 73 (137)
+|.|
T Consensus 116 -~v~I 119 (119)
T PF00917_consen 116 -EVKI 119 (119)
T ss_dssp -EEEE
T ss_pred -EEEC
Confidence 9976
No 5
>cd00121 MATH 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 doma
Probab=98.97 E-value=2.5e-09 Score=73.75 Aligned_cols=66 Identities=24% Similarity=0.402 Sum_probs=54.4
Q ss_pred CeEEecCCCCCCCCCEEEEEEEEEEEe-----------Ccccc-cccccccccceeccccccccCCceEeCCeEEEEEee
Q 046357 1 MTLQKSETSSLPTGWEVNAIINFFFYC-----------EKHFR-AVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVC 68 (137)
Q Consensus 1 lYL~~~~~~~l~~~w~v~a~fkl~i~N-----------~~~F~-~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~~ 68 (137)
+||.+.+....+..|.+.|+++|.|+| ..+|. .....|||.+||++++|.++. +++||+++|+|
T Consensus 48 v~L~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~G~~~fi~~~~l~~~~--~~~~d~l~i~~-- 123 (126)
T cd00121 48 LYLELDKGESDLEKWSVRAEFTLKLVNQNGGKSLSKSFTHVFFSEKGSGWGFPKFISWDDLEDSY--YLVDDSLTIEV-- 123 (126)
T ss_pred EEEEecCCCCCCCCCcEEEEEEEEEECCCCCccceEeccCCcCCCCCCCCChHHeeEHHHhccCC--cEECCEEEEEE--
Confidence 488887776667889999999999998 22443 556799999999999999643 39999999999
Q ss_pred eeE
Q 046357 69 EEV 71 (137)
Q Consensus 69 ~eV 71 (137)
+|
T Consensus 124 -~v 125 (126)
T cd00121 124 -EV 125 (126)
T ss_pred -EE
Confidence 77
No 6
>cd00270 MATH_TRAF_C 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-ter
Probab=98.88 E-value=3.3e-09 Score=77.79 Aligned_cols=66 Identities=17% Similarity=0.289 Sum_probs=52.0
Q ss_pred CeEEecCCCC-CCCCCEEEEEEEEEEEeCc-------------------ccc-----cccccccccceeccccccccCCc
Q 046357 1 MTLQKSETSS-LPTGWEVNAIINFFFYCEK-------------------HFR-----AVKTKWCITKFIDLETLSNTLNE 55 (137)
Q Consensus 1 lYL~~~~~~~-l~~~w~v~a~fkl~i~N~~-------------------~F~-----~~~~~wG~~~fi~l~~l~d~~~G 55 (137)
|||.+.+.+. .+.+|.+.|+|+|+|+|+. .|. .....|||.+||++++|.+ .|
T Consensus 58 l~L~l~~~~~d~~~~w~~~~~~~~~l~d~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~fi~~~~L~~--~g 135 (149)
T cd00270 58 LFVHVMKGEYDALLEWPFRGKITLTLLDQSDDSKRKHITETFMPDPNSSAFQRPPTGENNIGFGYPEFVPLEKLES--RG 135 (149)
T ss_pred EEEEEeccCCCccccCCccceEEEEEECCCCccccCceEEEEEcCCchHhhcCCCcccCCCCcCcceEeEHHHhcc--CC
Confidence 5888766543 3568999999999999921 122 1346799999999999985 49
Q ss_pred eEeCCeEEEEEeeeeE
Q 046357 56 YLINDVCVCGCVCEEV 71 (137)
Q Consensus 56 yLv~D~~v~~a~~~eV 71 (137)
||+||+|+|++ +|
T Consensus 136 fl~dD~l~I~~---~v 148 (149)
T cd00270 136 YVKDDTLFIKV---EV 148 (149)
T ss_pred CEeCCEEEEEE---EE
Confidence 99999999999 76
No 7
>cd03773 MATH_TRIM37 Tripartite motif containing protein 37 (TRIM37) family, MATH domain; TRIM37 is a peroxisomal protein and is a member of the tripartite motif (TRIM) protein subfamily, also known as the RING-B-box-coiled-coil (RBCC) subfamily of zinc-finger proteins. Mutations in the human TRIM37 gene (also known as MUL) cause Mulibrey (muscle-liver-brain-eye) nanism, a rare growth disorder of prenatal onset characterized by dysmorphic features, pericardial constriction and hepatomegaly. TRIM37, similar to other TRIMs, contains a cysteine-rich, zinc-binding RING-finger domain followed by another cysteine-rich zinc-binding domain, the B-box, and a coiled-coil domain. TRIM37 is autoubiquitinated in a RING domain-dependent manner, indicating that it functions as an ubiquitin E3 ligase. In addition to the tripartite motif, TRIM37 also contains a MATH domain C-terminal to the coiled-coil domain. The MATH domain of TRIM37 has been shown to interact with the TRAF domain of six known TRAFs i
Probab=98.74 E-value=1.9e-08 Score=72.28 Aligned_cols=62 Identities=19% Similarity=0.260 Sum_probs=49.3
Q ss_pred CeEEecCCCCCCCCCEEEEEEEEEEEe------------CcccccccccccccceeccccccccCCceEeC--CeEEEEE
Q 046357 1 MTLQKSETSSLPTGWEVNAIINFFFYC------------EKHFRAVKTKWCITKFIDLETLSNTLNEYLIN--DVCVCGC 66 (137)
Q Consensus 1 lYL~~~~~~~l~~~w~v~a~fkl~i~N------------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~--D~~v~~a 66 (137)
+||++.+. .+|.+.++|+|+|+| .++|.. ...|||.+||++++|.+ +|||.| |+++|++
T Consensus 55 l~L~l~~~----~~~~~~~~~~l~llnq~~~~~~~~~~~~~~f~~-~~~wG~~~Fi~~~~L~~--~gfl~~~~D~l~i~~ 127 (132)
T cd03773 55 VFLELCSG----LGEASKYEYRVEMVHQANPTKNIKREFASDFEV-GECWGYNRFFRLDLLIN--EGYLLPENDTLILRF 127 (132)
T ss_pred EEEEeecC----CCCceeEEEEEEEEcCCCCccceEEeccccccC-CCCcCHHHhccHHHHhh--CCCcCCCCCEEEEEE
Confidence 47776543 247789999999998 346654 46799999999999974 799999 9999999
Q ss_pred eeeeEE
Q 046357 67 VCEEVF 72 (137)
Q Consensus 67 ~~~eV~ 72 (137)
+|+
T Consensus 128 ---~v~ 130 (132)
T cd03773 128 ---SVR 130 (132)
T ss_pred ---EEe
Confidence 664
No 8
>cd03776 MATH_TRAF6 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-kapp
Probab=98.54 E-value=1.1e-07 Score=70.03 Aligned_cols=66 Identities=15% Similarity=0.277 Sum_probs=50.9
Q ss_pred CeEEecCCCC-CCCCCEEEEEEEEEEEeCc-----------------cccc-----ccccccccceeccccccccCCceE
Q 046357 1 MTLQKSETSS-LPTGWEVNAIINFFFYCEK-----------------HFRA-----VKTKWCITKFIDLETLSNTLNEYL 57 (137)
Q Consensus 1 lYL~~~~~~~-l~~~w~v~a~fkl~i~N~~-----------------~F~~-----~~~~wG~~~fi~l~~l~d~~~GyL 57 (137)
+||.+.+... ...+|.+.|+++|++.|+. .|.. ....|||++||++++|.. .|||
T Consensus 58 ~~L~l~~~~~d~~l~wpv~a~~~~~lldq~~~~~~~~~~~~~~~~~~~F~~p~~~~~~~~~G~~~fi~~~~Le~--~~yl 135 (147)
T cd03776 58 LFVHLMQGENDSHLDWPFQGTITLTLLDQSEPRQNIHETMMSKPELLAFQRPTTDRNPKGFGYVEFAHIEDLLQ--RGFV 135 (147)
T ss_pred EEEEEeccCCCcccCCcccceeEEEEECCCcccCccEEEEEcCCChHhhcCCCcCCCCCCeeEceeeEHHHhhh--CCCc
Confidence 4788765432 3457999999999999921 2431 235799999999999974 5899
Q ss_pred eCCeEEEEEeeeeE
Q 046357 58 INDVCVCGCVCEEV 71 (137)
Q Consensus 58 v~D~~v~~a~~~eV 71 (137)
.||+++|++ +|
T Consensus 136 ~dD~l~I~c---~V 146 (147)
T cd03776 136 KNDTLLIKI---EV 146 (147)
T ss_pred cCCEEEEEE---EE
Confidence 999999999 76
No 9
>KOG1987 consensus Speckle-type POZ protein SPOP and related proteins with TRAF, MATH and BTB/POZ domains [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=98.48 E-value=4.3e-08 Score=79.09 Aligned_cols=64 Identities=25% Similarity=0.355 Sum_probs=49.8
Q ss_pred CCEEEEEEEEEEEeCcc---------------cccccccccccceeccccccccCCceEeCCeEEEEEeeeeEEEEccCC
Q 046357 14 GWEVNAIINFFFYCEKH---------------FRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVCEEVFVVKNTF 78 (137)
Q Consensus 14 ~w~v~a~fkl~i~N~~~---------------F~~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~~~eV~vv~~~~ 78 (137)
+|+++|+++|+++|+.. |+...+.||+.+++|+..+.++..||+++..+++.| .+.|.++..
T Consensus 54 ~~~~~~~~~l~v~n~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~g~~~~~~~~~~a---~~~V~~~~~ 130 (297)
T KOG1987|consen 54 GWERYAKLRLTVVNQKSEKYLSTVEEGFSWFRFNKVLKEWGFGKMLPLTLLIDCSNGFLVAHKLVLVA---RSEVFEAMG 130 (297)
T ss_pred CcceeEEEEEEEccCCCcceeeeeeeeEEeccccccccccCcccccChHHhhcccCcEEEcCceEEEe---eecceeeec
Confidence 99999999999999321 222357899999999999999999999996666666 455666554
Q ss_pred CC
Q 046357 79 KG 80 (137)
Q Consensus 79 ~~ 80 (137)
+.
T Consensus 131 ~~ 132 (297)
T KOG1987|consen 131 KS 132 (297)
T ss_pred cc
Confidence 43
No 10
>cd03778 MATH_TRAF2 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 z
Probab=98.33 E-value=1.6e-06 Score=66.22 Aligned_cols=65 Identities=11% Similarity=0.204 Sum_probs=53.0
Q ss_pred CeEEecCCCCCC-CCCEEEEEEEEEEEeCc----------------cc----ccccccccccceeccccccccCCceEeC
Q 046357 1 MTLQKSETSSLP-TGWEVNAIINFFFYCEK----------------HF----RAVKTKWCITKFIDLETLSNTLNEYLIN 59 (137)
Q Consensus 1 lYL~~~~~~~l~-~~w~v~a~fkl~i~N~~----------------~F----~~~~~~wG~~~fi~l~~l~d~~~GyLv~ 59 (137)
+|+.+...+..+ .+|-...+++|.|.||. .| +.....||+++|+|+++|.++ .|||.|
T Consensus 76 ly~~l~~Ge~D~~L~WPf~~~itl~llDQ~~r~hi~~~~~pd~~~~~f~RP~~~~n~~~G~~~Fv~l~~l~~~-~~Yv~d 154 (164)
T cd03778 76 LFFVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKXEAK-NSYVRD 154 (164)
T ss_pred EEEEEecCCcCcccCCceeeEEEEEEECCCCCCcceeEEEcCcchHhcCCCCcccccCcCcceEEEhhHcccc-CCcccC
Confidence 578888877776 89999999999999821 24 223346999999999999864 599999
Q ss_pred CeEEEEE
Q 046357 60 DVCVCGC 66 (137)
Q Consensus 60 D~~v~~a 66 (137)
|++.++|
T Consensus 155 DtlfIk~ 161 (164)
T cd03778 155 DAIFIKA 161 (164)
T ss_pred CeEEEEE
Confidence 9999998
No 11
>cd03779 MATH_TRAF1 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-mediat
Probab=98.28 E-value=2.5e-06 Score=63.91 Aligned_cols=68 Identities=15% Similarity=0.253 Sum_probs=51.2
Q ss_pred CeEEecCCCC-CCCCCEEEEEEEEEEEeC----------------cccc----cccccccccceeccccccccCCceEeC
Q 046357 1 MTLQKSETSS-LPTGWEVNAIINFFFYCE----------------KHFR----AVKTKWCITKFIDLETLSNTLNEYLIN 59 (137)
Q Consensus 1 lYL~~~~~~~-l~~~w~v~a~fkl~i~N~----------------~~F~----~~~~~wG~~~fi~l~~l~d~~~GyLv~ 59 (137)
+||.+...+. --..|.+.|+++|.++|+ +.|+ .....||+++||++++|..+..+||.|
T Consensus 58 v~l~l~~g~~D~~l~wpv~~~~tfsLlDq~~~~~~~~~~~~~~~~~~F~rP~~~~n~~~G~~~Fi~~~~Le~s~~~ylkD 137 (147)
T cd03779 58 LFFVIMKGEYDALLPWPFRHKVTFMLLDQNNREHVIDAFRPDLSSASFQRPVSDMNVASGCPLFFPLKKLQSPKHAYCKD 137 (147)
T ss_pred EEEEEecCCcccccCcceEEEEEEEEECCCCCCCCcEeecCCcccccccCcccCCCCCcchhheeEHHHhcccCCCcEeC
Confidence 4677764221 123689999999999981 3465 333479999999999997544599999
Q ss_pred CeEEEEEeeeeE
Q 046357 60 DVCVCGCVCEEV 71 (137)
Q Consensus 60 D~~v~~a~~~eV 71 (137)
|++.|.| +|
T Consensus 138 D~~~Irc---~V 146 (147)
T cd03779 138 DTIYIKC---VV 146 (147)
T ss_pred CEEEEEE---EE
Confidence 9999999 76
No 12
>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=98.23 E-value=7.9e-07 Score=81.13 Aligned_cols=74 Identities=23% Similarity=0.287 Sum_probs=62.8
Q ss_pred CeEEecCCC--CCC-CCCEEEEEEEEEEEe------------CcccccccccccccceeccccccccCCc---eEeCCeE
Q 046357 1 MTLQKSETS--SLP-TGWEVNAIINFFFYC------------EKHFRAVKTKWCITKFIDLETLSNTLNE---YLINDVC 62 (137)
Q Consensus 1 lYL~~~~~~--~l~-~~w~v~a~fkl~i~N------------~~~F~~~~~~wG~~~fi~l~~l~d~~~G---yLv~D~~ 62 (137)
+||+..-.+ .+. ..|.++|+|.|.|-| +|||+...++|||++|+.|..+..|+.| |+.++++
T Consensus 83 VyLe~~pqe~e~~~gk~~~ccaqFaf~Is~p~~pti~~iN~sHhrFs~~~tDwGFt~f~dL~kl~~psp~~Ppfleeg~l 162 (1089)
T COG5077 83 VYLEYEPQELEETGGKYYDCCAQFAFDISNPKYPTIEYINKSHHRFSMESTDWGFTNFIDLNKLIEPSPGRPPFLEEGTL 162 (1089)
T ss_pred EEEEeccchhhhhcCcchhhhhheeeecCCCCCCchhhhhcccccccccccccchhhhhhhhhhcCCCCCCCCcccCCeE
Confidence 366654332 222 459999999999977 7999999999999999999999998888 7899999
Q ss_pred EEEEeeeeEEEEccC
Q 046357 63 VCGCVCEEVFVVKNT 77 (137)
Q Consensus 63 v~~a~~~eV~vv~~~ 77 (137)
++.| .|.|++++
T Consensus 163 ~Itv---yVRvlkdP 174 (1089)
T COG5077 163 VITV---YVRVLKDP 174 (1089)
T ss_pred EEEE---EEEEEeCC
Confidence 9999 99999985
No 13
>cd03781 MATH_TRAF4 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 TR
Probab=98.23 E-value=2.7e-06 Score=63.52 Aligned_cols=66 Identities=18% Similarity=0.269 Sum_probs=49.9
Q ss_pred CeEEecCCCCCC-CCCEEEEEEEEEEEeCc------------c---------cc--------cccccccccceecccccc
Q 046357 1 MTLQKSETSSLP-TGWEVNAIINFFFYCEK------------H---------FR--------AVKTKWCITKFIDLETLS 50 (137)
Q Consensus 1 lYL~~~~~~~l~-~~w~v~a~fkl~i~N~~------------~---------F~--------~~~~~wG~~~fi~l~~l~ 50 (137)
+||.+...+.-+ ..|.+.|+++|++.|+. . |+ .....||+.+||++++|.
T Consensus 58 ~~l~l~~ge~d~~l~wp~~a~~~~~llDq~~~~~~~~~~~~~~~~~~~~~~~F~rp~~~~~~~~~~~~G~~~fi~~~~Le 137 (154)
T cd03781 58 VYIRVLPGEYDNLLEWPFSHRITFTLLDQSDPSLSKPQHITETFTPDPTWKNFQKPSASRLDESTLGFGYPKFISHEDLK 137 (154)
T ss_pred EEEEEecCCcccccCCceeeEEEEEEECCCCCccccCcceEEEEEcCCchhhhcCCcccccCCCCCccchhHeeEHHHHh
Confidence 477776644333 48999999999999831 1 11 122359999999999997
Q ss_pred ccCCceEeCCeEEEEEeeeeE
Q 046357 51 NTLNEYLINDVCVCGCVCEEV 71 (137)
Q Consensus 51 d~~~GyLv~D~~v~~a~~~eV 71 (137)
++|||.||+++|++ +|
T Consensus 138 --~~~yl~dD~l~Irc---~v 153 (154)
T cd03781 138 --KRNYIKDDAIFLRA---SV 153 (154)
T ss_pred --hCCcccCCEEEEEE---Ee
Confidence 47899999999999 76
No 14
>cd03780 MATH_TRAF5 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 dive
Probab=98.18 E-value=4.5e-06 Score=62.47 Aligned_cols=66 Identities=12% Similarity=0.197 Sum_probs=50.2
Q ss_pred CeEEecCCCCC-CCCCEEEEEEEEEEEeC-----------------cccccc----cccccccceeccccccccCCceEe
Q 046357 1 MTLQKSETSSL-PTGWEVNAIINFFFYCE-----------------KHFRAV----KTKWCITKFIDLETLSNTLNEYLI 58 (137)
Q Consensus 1 lYL~~~~~~~l-~~~w~v~a~fkl~i~N~-----------------~~F~~~----~~~wG~~~fi~l~~l~d~~~GyLv 58 (137)
+||.+...+.- -..|.+.++++|.++++ +.|+.. ...||+++||++++|..++.+||.
T Consensus 58 v~l~l~~g~~D~~l~wp~~~~~tfsLlDq~~~~~~~~~~~~~~~~~~~F~rp~~~~n~~~G~~~Fi~~~~Le~s~~~ylk 137 (148)
T cd03780 58 LYFVVMRGEFDSLLQWPFRQRVTLMLLDQSGKKNHIMETFKADPNSSSFKRPDGEMNIASGCPRFVAHSVLENAKNTYIK 137 (148)
T ss_pred EEEEEecCccccccCcceEEEEEEEEECCCCCCCCcceeeecCCccccccCCCCCCCCCcChhheeEHHHhhcccCCcCc
Confidence 46776643211 14699999999999881 236443 346999999999999866679999
Q ss_pred CCeEEEEE
Q 046357 59 NDVCVCGC 66 (137)
Q Consensus 59 ~D~~v~~a 66 (137)
||++.|.|
T Consensus 138 dD~~~Ik~ 145 (148)
T cd03780 138 DDTLFLKV 145 (148)
T ss_pred CCEEEEEE
Confidence 99999998
No 15
>cd03772 MATH_HAUSP Herpesvirus-associated ubiquitin-specific protease (HAUSP, also known as USP7) family, N-terminal MATH (TRAF-like) domain; composed of proteins similar to human HAUSP, an enzyme that specifically catalyzes the deubiquitylation of p53 and MDM2, hence playing an important role in the p53-MDM2 pathway. It contains an N-terminal TRAF-like domain and a C-terminal catalytic protease (C19 family) domain. The tumor suppressor p53 protein is a transcription factor that responds to many cellular stress signals and is regulated primarily through ubiquitylation and subsequent degradation. MDM2 is a RING-finger E3 ubiquitin ligase that promotes p53 ubiquitinylation. p53 and MDM2 bind to the same site in the N-terminal TRAF-like domain of HAUSP in a mutually exclusive manner. HAUSP also interacts with the Epstein-Barr nuclear antigen 1 (EBNA1) protein of the Epstein-Barr virus (EBV), which efficiently immortalizes infected cells predisposing the host to a variety of cancers. EBNA1
Probab=98.03 E-value=4.4e-06 Score=60.71 Aligned_cols=63 Identities=13% Similarity=0.280 Sum_probs=43.3
Q ss_pred eEEEEEeeeeEEEEccCCCCccceeeeCCCeeeeeec-----ccceeeecccccCCCCCeEEcCeEEEEEEEEEE
Q 046357 61 VCVCGCVCEEVFVVKNTFKGERSSMMHEPPHLLPYLE-----SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLL 130 (137)
Q Consensus 61 ~~v~~a~~~eV~vv~~~~~~e~~s~ik~~~~lslyL~-----d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~ 130 (137)
++.... ++.++........++ +...+ .|-. +|++||++++|.++++|||+||+|+||++|+|=
T Consensus 66 ~i~a~~---~~~l~~~~~~~~~~~--~~~~~--~f~~~~~~~G~~~fi~~~~L~~~~sgyl~~D~l~Ie~~V~~~ 133 (137)
T cd03772 66 SCHAQA---VLRIINYKDDEPSFS--RRISH--LFFSKENDWGFSNFMTWSEVTDPEKGFIEDDTITLEVYVQAD 133 (137)
T ss_pred eEEEEE---EEEEEcCCCCcccEE--Eeeee--EEcCCCCCccchheeEHHHhcCCCCCcEECCEEEEEEEEEee
Confidence 466666 777776653222222 11111 2311 499999999999999999999999999999763
No 16
>smart00061 MATH meprin and TRAF homology.
Probab=97.95 E-value=1.5e-05 Score=52.78 Aligned_cols=43 Identities=19% Similarity=0.426 Sum_probs=35.8
Q ss_pred CeEEecCCCCCCCCCEEEEEEEEEEEe----------Cccccccccccccccee
Q 046357 1 MTLQKSETSSLPTGWEVNAIINFFFYC----------EKHFRAVKTKWCITKFI 44 (137)
Q Consensus 1 lYL~~~~~~~l~~~w~v~a~fkl~i~N----------~~~F~~~~~~wG~~~fi 44 (137)
+||.+.+....+.+|.+.|+++|+|.| .++|.. ...|||++||
T Consensus 43 l~L~~~~~~~~~~~w~v~a~~~~~l~~~~~~~~~~~~~~~F~~-~~~~G~~~fi 95 (95)
T smart00061 43 LYLHCEKEECDSRKWSIEAEFTLKLVSQNGKSLSKKDKHVFEK-PSGWGFSKFI 95 (95)
T ss_pred EEEEeCCCcCCCCCeEEEEEEEEEEEeCCCCEEeeeeeEEEcC-CCccceeeEC
Confidence 588888877677799999999999998 356765 6789999885
No 17
>cd03777 MATH_TRAF3 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 al
Probab=97.91 E-value=3.7e-05 Score=59.68 Aligned_cols=67 Identities=10% Similarity=0.137 Sum_probs=50.5
Q ss_pred CeEEecCCCC-CCCCCEEEEEEEEEEEeCc-----------------ccc-cc---cccccccceeccccccccCCceEe
Q 046357 1 MTLQKSETSS-LPTGWEVNAIINFFFYCEK-----------------HFR-AV---KTKWCITKFIDLETLSNTLNEYLI 58 (137)
Q Consensus 1 lYL~~~~~~~-l~~~w~v~a~fkl~i~N~~-----------------~F~-~~---~~~wG~~~fi~l~~l~d~~~GyLv 58 (137)
+||.+...+. --..|.+.++++|.+.++. .|+ .. ...||+++||++++|. +.+||.
T Consensus 96 vyl~L~~ge~D~~L~WP~~~~~tfsLlDQ~~~~~~~~~~~~p~p~~~~F~rp~~~~n~~~G~~~Fi~~~~Le--~~~ylk 173 (186)
T cd03777 96 LFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLE--NGTYIK 173 (186)
T ss_pred EEEEEecCCcccccCCceeEEEEEEEEcCCCccccccceeccCCccccccCCccCCCCCCCchheeEHHHhc--cCCcEe
Confidence 4677654321 1236999999999999832 275 22 3479999999999997 478999
Q ss_pred CCeEEEEEeeeeEE
Q 046357 59 NDVCVCGCVCEEVF 72 (137)
Q Consensus 59 ~D~~v~~a~~~eV~ 72 (137)
||++.|.| .|.
T Consensus 174 dD~l~Irv---~v~ 184 (186)
T cd03777 174 DDTIFIKV---IVD 184 (186)
T ss_pred CCEEEEEE---EEe
Confidence 99999999 664
No 18
>cd03771 MATH_Meprin 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 co
Probab=97.82 E-value=4.3e-05 Score=58.45 Aligned_cols=64 Identities=11% Similarity=0.156 Sum_probs=48.0
Q ss_pred CeEEecCCCC-CCCCCE-EEEEEEEEEEeCc----------c-----------------cccc-----------------
Q 046357 1 MTLQKSETSS-LPTGWE-VNAIINFFFYCEK----------H-----------------FRAV----------------- 34 (137)
Q Consensus 1 lYL~~~~~~~-l~~~w~-v~a~fkl~i~N~~----------~-----------------F~~~----------------- 34 (137)
+||.+.+.+. ....|- +.|+++|+++++. + |+..
T Consensus 55 lyL~L~~g~~d~~L~WP~v~a~~t~~LlDQ~~~~~~r~~~~~~~~~dp~~~~~~~~~~~~~rP~~~~~~~~~~~~~~~~~ 134 (167)
T cd03771 55 LYFHLCSGENDDVLEWPCPNRQATMTLLDQDPDIQQRMSNQRSFTTDPSMTSSDNGEYFWDRPSKVGSYDTDTNGCTCYR 134 (167)
T ss_pred EEEEEecCCccccccCcceeEEEEEEEECCCCcccccCcceEEEecCCcccccccccccccCCccccccccccccccccc
Confidence 5788765433 356788 6899999999821 1 2221
Q ss_pred cccccccceeccccccccCCceEeCCeEEEEE
Q 046357 35 KTKWCITKFIDLETLSNTLNEYLINDVCVCGC 66 (137)
Q Consensus 35 ~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a 66 (137)
...|||++|||++.|.. .+||.||++.|.+
T Consensus 135 ~~g~G~~~Fis~~~L~~--r~ylk~dtl~i~~ 164 (167)
T cd03771 135 GPGYGWSTFISHSRLRR--RDFLKGDDLIILL 164 (167)
T ss_pred cCccccccceeHHHhcc--CCCCcCCEEEEEE
Confidence 13699999999999985 4599999999999
No 19
>cd03774 MATH_SPOP Speckle-type POZ protein (SPOP) family, MATH domain; composed of proteins with similarity to human SPOP. SPOP was isolated as a novel antigen recognized by serum from a scleroderma patient, whose overexpression in COS cells results in a discrete speckled pattern in the nuclei. It contains an N-terminal MATH domain and a C-terminal BTB (also called POZ) domain. Together with Cul3, SPOP constitutes an ubiquitin E3 ligase which is able to ubiquitinate the PcG protein BMI1, the variant histone macroH2A1 and the death domain-associated protein Daxx. Therefore, SPOP may be involved in the regulation of these proteins and may play a role in transcriptional regulation, apoptosis and X-chromosome inactivation. Cul3 binds to the BTB domain of SPOP whereas Daxx and the macroH2A1 nonhistone region have been shown to bind to the MATH domain. Both MATH and BTB domains are necessary for the nuclear speckled accumulation of SPOP. There are many proteins, mostly uncharacterized, conta
Probab=97.55 E-value=4.6e-05 Score=55.33 Aligned_cols=34 Identities=15% Similarity=0.212 Sum_probs=31.7
Q ss_pred ccceeeecccccCCCCCeEEcCeEEEEEEEEEEE
Q 046357 98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLG 131 (137)
Q Consensus 98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~~ 131 (137)
+|.+||++++|.++.+|||+||++.|+++|+|++
T Consensus 105 G~~~fi~~~~L~~~~~g~l~dD~l~I~c~I~V~~ 138 (139)
T cd03774 105 GFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQ 138 (139)
T ss_pred CHHHeeeHHHhhhhhcccccCCEEEEEEEEEEEc
Confidence 5899999999998889999999999999999975
No 20
>cd03778 MATH_TRAF2 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 z
Probab=97.35 E-value=0.00022 Score=54.54 Aligned_cols=29 Identities=24% Similarity=0.430 Sum_probs=26.0
Q ss_pred ccceeeecccccCCCCCeEEcCeEEEEEEE
Q 046357 98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEF 127 (137)
Q Consensus 98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev 127 (137)
++++|+|+++|.++ .|||++|++.|+|.|
T Consensus 135 G~~~Fv~l~~l~~~-~~Yv~dDtlfIk~~V 163 (164)
T cd03778 135 GCPLFCPVSKXEAK-NSYVRDDAIFIKAIV 163 (164)
T ss_pred CcceEEEhhHcccc-CCcccCCeEEEEEEE
Confidence 49999999999764 699999999999987
No 21
>KOG1863 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=97.25 E-value=0.00024 Score=67.62 Aligned_cols=74 Identities=19% Similarity=0.206 Sum_probs=66.2
Q ss_pred eEEecCCCCCCCCCEEEEEEEEEEEe------------CcccccccccccccceeccccccccCCceEeCCeEEEEEeee
Q 046357 2 TLQKSETSSLPTGWEVNAIINFFFYC------------EKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVCE 69 (137)
Q Consensus 2 YL~~~~~~~l~~~w~v~a~fkl~i~N------------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~~~ 69 (137)
|+++..+... +.|.+++++.+.+.| +|+|.+..++||+.+|+.++++.++..||+.+|++.+.+
T Consensus 72 ~~~~~~~~~~-~~~s~~~~~~~~v~~~~~~~~~~~~~~~h~~~~~~~dwg~~~~~~~~~~~~~~~~~~~~~~~~~~~--- 147 (1093)
T KOG1863|consen 72 KLEVMPSQSL-KSWSCGAQAVLRVKNTIDNLPDPEKAIHHVFTADERDWGFSCFSTSSDIRKPEDGYVRNGLEKLEK--- 147 (1093)
T ss_pred EeeeccCCCC-cceEecchhhhccccCCCCchhhhhhhhhcccccccchhhccchhHhhccCcccccccccceeeee---
Confidence 5666666666 559999999999988 889999999999999999999999999999999999999
Q ss_pred eEEEEccCCC
Q 046357 70 EVFVVKNTFK 79 (137)
Q Consensus 70 eV~vv~~~~~ 79 (137)
+|.+-.++..
T Consensus 148 ~v~v~~~~~~ 157 (1093)
T KOG1863|consen 148 RVRVEQPTSL 157 (1093)
T ss_pred eeeeecCCcc
Confidence 9999887754
No 22
>PF00917 MATH: MATH domain; InterPro: IPR002083 Although apparently functionally unrelated, intracellular TRAFs and extracellular meprins share a conserved region of about 180 residues, the meprin and TRAF homology (MATH) domain []. Meprins are mammalian tissue-specific metalloendopeptidases of the astacin family implicated in developmental, normal and pathological processes by hydrolysing a variety of proteins. Various growth factors, cytokines, and extracellular matrix proteins are substrates for meprins. They are composed of five structural domains: an N-terminal endopeptidase domain, a MAM domain (see PDOC00604 from PROSITEDOC), a MATH domain, an EGF-like domain (see PDOC00021 from PROSITEDOC) and a C-terminal transmembrane region. Meprin A and B form membrane bound homotetramer whereas homooligomers of meprin A are secreted. A proteolitic site adjacent to the MATH domain, only present in meprin A, allows the release of the protein from the membrane []. TRAF proteins were first isolated by their ability to interact with TNF receptors []. They promote cell survival by the activation of downstream protein kinases and, finally, transcription factors of the NF-kB and AP-1 family. The TRAF proteins are composed of 3 structural domains: a RING finger (see PDOC00449 from PROSITEDOC) in the N-terminal part of the protein, one to seven TRAF zinc fingers (see PDOC50145 from PROSITEDOC) in the middle and the MATH domain in the C-terminal part []. The MATH domain is necessary and sufficient for self-association and receptor interaction. From the structural analysis two consensus sequence recognised by the TRAF domain have been defined: a major one, [PSAT]x[QE]E and a minor one, PxQxxD []. The structure of the TRAF2 protein reveals a trimeric self-association of the MATH domain []. The domain forms a new, light-stranded antiparallel beta sandwich structure. A coiled-coil region adjacent to the MATH domain is also important for the trimerisation. The oligomerisation is essential for establishing appropriate connections to form signalling complexes with TNF receptor-1. The ligand binding surface of TRAF proteins is located in beta-strands 6 and 7 [].; GO: 0005515 protein binding; PDB: 1D00_E 1CZY_A 1D01_F 1CA9_A 1D0J_D 1F3V_B 1CA4_C 1D0A_A 1QSC_C 1CZZ_C ....
Probab=97.20 E-value=0.00027 Score=48.63 Aligned_cols=30 Identities=27% Similarity=0.515 Sum_probs=27.4
Q ss_pred ccceeeecccccCCCCCeEEcCeEEEEEEEEE
Q 046357 98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTL 129 (137)
Q Consensus 98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i 129 (137)
+|.+||++++|.++. |++||+++|||+|+|
T Consensus 90 g~~~fi~~~~l~~~~--fl~dd~l~ie~~v~I 119 (119)
T PF00917_consen 90 GWSSFISWEDLEDPY--FLVDDSLTIEVEVKI 119 (119)
T ss_dssp EEEEEEEHHHHTTCT--TSBTTEEEEEEEEEE
T ss_pred chhheeEHHHhCccC--CeECCEEEEEEEEEC
Confidence 489999999999875 899999999999986
No 23
>cd03775 MATH_Ubp21p Ubiquitin-specific protease 21 (Ubp21p) family, MATH domain; composed of fungal proteins with similarity to Ubp21p of fission yeast. Ubp21p is a deubiquitinating enzyme that may be involved in the regulation of the protein kinase Prp4p, which controls the formation of active spliceosomes. Members of this family are similar to human HAUSP (Herpesvirus-associated ubiquitin-specific protease) in that they contain an N-terminal MATH domain and a C-terminal catalytic protease (C19 family) domain. HAUSP is also an ubiquitin-specific protease that specifically catalyzes the deubiquitylation of p53 and MDM2. The MATH domain of HAUSP contains the binding site for p53 and MDM2. Similarly, the MATH domain of members in this family may be involved in substrate binding.
Probab=97.15 E-value=0.00028 Score=51.08 Aligned_cols=30 Identities=13% Similarity=0.170 Sum_probs=27.1
Q ss_pred ccceeeecccccCC----CCCeEEcCeEEEEEEE
Q 046357 98 SCAQLMSLAKLKDP----KEGYMVRDICIIKAEF 127 (137)
Q Consensus 98 d~~~fi~l~~l~~~----~~gylv~D~~~ieaev 127 (137)
+|.+||++++|.++ ..|||+||+++|+++|
T Consensus 100 G~~~fi~~~~L~~~~~~~~~g~l~nD~l~I~~~~ 133 (134)
T cd03775 100 GFTRFIELRKLAHRTPDKPSPFLENGELNITVYV 133 (134)
T ss_pred ChhHcccHHHHcccccCCCCceeECCEEEEEEEE
Confidence 48999999999955 6799999999999987
No 24
>cd00270 MATH_TRAF_C 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-ter
Probab=96.64 E-value=0.0015 Score=47.60 Aligned_cols=29 Identities=31% Similarity=0.535 Sum_probs=25.8
Q ss_pred ccceeeecccccCCCCCeEEcCeEEEEEEEE
Q 046357 98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFT 128 (137)
Q Consensus 98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~ 128 (137)
+|.+||++++|.++ |||+||+|+|+++|.
T Consensus 121 G~~~fi~~~~L~~~--gfl~dD~l~I~~~v~ 149 (149)
T cd00270 121 GYPEFVPLEKLESR--GYVKDDTLFIKVEVD 149 (149)
T ss_pred CcceEeEHHHhccC--CCEeCCEEEEEEEEC
Confidence 59999999999754 999999999999873
No 25
>cd03771 MATH_Meprin 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 co
Probab=95.34 E-value=0.0098 Score=45.52 Aligned_cols=29 Identities=21% Similarity=0.402 Sum_probs=26.0
Q ss_pred ccceeeecccccCCCCCeEEcCeEEEEEEEE
Q 046357 98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFT 128 (137)
Q Consensus 98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~ 128 (137)
+|++||++++|+. ++||++|+++|+++++
T Consensus 139 G~~~Fis~~~L~~--r~ylk~dtl~i~~~~~ 167 (167)
T cd03771 139 GWSTFISHSRLRR--RDFLKGDDLIILLDFE 167 (167)
T ss_pred ccccceeHHHhcc--CCCCcCCEEEEEEEeC
Confidence 4999999999986 5699999999999974
No 26
>cd03780 MATH_TRAF5 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 dive
Probab=95.18 E-value=0.014 Score=43.62 Aligned_cols=30 Identities=20% Similarity=0.497 Sum_probs=27.3
Q ss_pred ccceeeecccccCCCCCeEEcCeEEEEEEE
Q 046357 98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEF 127 (137)
Q Consensus 98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev 127 (137)
++++||+.++|..++.|||.+|++.|+|+|
T Consensus 118 G~~~Fi~~~~Le~s~~~ylkdD~~~Ik~~v 147 (148)
T cd03780 118 GCPRFVAHSVLENAKNTYIKDDTLFLKVAV 147 (148)
T ss_pred ChhheeEHHHhhcccCCcCcCCEEEEEEEE
Confidence 589999999997777899999999999976
No 27
>cd03773 MATH_TRIM37 Tripartite motif containing protein 37 (TRIM37) family, MATH domain; TRIM37 is a peroxisomal protein and is a member of the tripartite motif (TRIM) protein subfamily, also known as the RING-B-box-coiled-coil (RBCC) subfamily of zinc-finger proteins. Mutations in the human TRIM37 gene (also known as MUL) cause Mulibrey (muscle-liver-brain-eye) nanism, a rare growth disorder of prenatal onset characterized by dysmorphic features, pericardial constriction and hepatomegaly. TRIM37, similar to other TRIMs, contains a cysteine-rich, zinc-binding RING-finger domain followed by another cysteine-rich zinc-binding domain, the B-box, and a coiled-coil domain. TRIM37 is autoubiquitinated in a RING domain-dependent manner, indicating that it functions as an ubiquitin E3 ligase. In addition to the tripartite motif, TRIM37 also contains a MATH domain C-terminal to the coiled-coil domain. The MATH domain of TRIM37 has been shown to interact with the TRAF domain of six known TRAFs i
Probab=95.16 E-value=0.0091 Score=42.51 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=25.7
Q ss_pred ccceeeecccccCCCCCeEEc--CeEEEEEEEE
Q 046357 98 SCAQLMSLAKLKDPKEGYMVR--DICIIKAEFT 128 (137)
Q Consensus 98 d~~~fi~l~~l~~~~~gylv~--D~~~ieaev~ 128 (137)
+|.+||++++|.+ +|||+| |++.||+.|.
T Consensus 100 G~~~Fi~~~~L~~--~gfl~~~~D~l~i~~~v~ 130 (132)
T cd03773 100 GYNRFFRLDLLIN--EGYLLPENDTLILRFSVR 130 (132)
T ss_pred CHHHhccHHHHhh--CCCcCCCCCEEEEEEEEe
Confidence 5999999999964 699999 9999999874
No 28
>cd03776 MATH_TRAF6 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-kapp
Probab=94.90 E-value=0.019 Score=42.06 Aligned_cols=28 Identities=21% Similarity=0.438 Sum_probs=25.1
Q ss_pred ccceeeecccccCCCCCeEEcCeEEEEEEE
Q 046357 98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEF 127 (137)
Q Consensus 98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev 127 (137)
+|++||+.++|.. .|||+||++.|+++|
T Consensus 119 G~~~fi~~~~Le~--~~yl~dD~l~I~c~V 146 (147)
T cd03776 119 GYVEFAHIEDLLQ--RGFVKNDTLLIKIEV 146 (147)
T ss_pred eEceeeEHHHhhh--CCCccCCEEEEEEEE
Confidence 4899999999965 489999999999987
No 29
>cd00121 MATH 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 doma
Probab=94.58 E-value=0.03 Score=38.00 Aligned_cols=29 Identities=28% Similarity=0.432 Sum_probs=25.0
Q ss_pred ccceeeecccccCCCCCeEEcCeEEEEEEEE
Q 046357 98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFT 128 (137)
Q Consensus 98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~ 128 (137)
+|++||++++|.++ +++++|++.|+++|.
T Consensus 98 G~~~fi~~~~l~~~--~~~~~d~l~i~~~v~ 126 (126)
T cd00121 98 GFPKFISWDDLEDS--YYLVDDSLTIEVEVK 126 (126)
T ss_pred ChHHeeEHHHhccC--CcEECCEEEEEEEEC
Confidence 58999999999886 239999999999983
No 30
>cd03783 MATH_Meprin_Alpha 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
Probab=94.45 E-value=0.023 Score=43.62 Aligned_cols=29 Identities=21% Similarity=0.273 Sum_probs=26.5
Q ss_pred ccccccceeccccccccCCceEeCCeEEEEE
Q 046357 36 TKWCITKFIDLETLSNTLNEYLINDVCVCGC 66 (137)
Q Consensus 36 ~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a 66 (137)
..+||+.|||++.|.. .+||.||++.|-+
T Consensus 136 ~gfG~~~Fish~~L~~--r~yikdDtlfI~~ 164 (167)
T cd03783 136 IDFGWSTFISHSQLRR--RSFLKNDDLIIFV 164 (167)
T ss_pred cccccccceeHHHHhh--CCcccCCeEEEEE
Confidence 3799999999999984 7899999999988
No 31
>cd03779 MATH_TRAF1 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-mediat
Probab=93.58 E-value=0.064 Score=40.12 Aligned_cols=30 Identities=33% Similarity=0.580 Sum_probs=26.3
Q ss_pred ccceeeecccccCCCCCeEEcCeEEEEEEE
Q 046357 98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEF 127 (137)
Q Consensus 98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev 127 (137)
++++||+.++|..+..|||.+|++.|+++|
T Consensus 117 G~~~Fi~~~~Le~s~~~ylkDD~~~Irc~V 146 (147)
T cd03779 117 GCPLFFPLKKLQSPKHAYCKDDTIYIKCVV 146 (147)
T ss_pred chhheeEHHHhcccCCCcEeCCEEEEEEEE
Confidence 589999999996544799999999999987
No 32
>cd03781 MATH_TRAF4 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 TR
Probab=92.89 E-value=0.067 Score=39.74 Aligned_cols=28 Identities=21% Similarity=0.427 Sum_probs=24.8
Q ss_pred ccceeeecccccCCCCCeEEcCeEEEEEEE
Q 046357 98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEF 127 (137)
Q Consensus 98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev 127 (137)
++.+||+.++|.. .|||+||+++|+++|
T Consensus 126 G~~~fi~~~~Le~--~~yl~dD~l~Irc~v 153 (154)
T cd03781 126 GYPKFISHEDLKK--RNYIKDDAIFLRASV 153 (154)
T ss_pred chhHeeEHHHHhh--CCcccCCEEEEEEEe
Confidence 4899999999953 689999999999987
No 33
>cd03782 MATH_Meprin_Beta 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 f
Probab=91.32 E-value=0.13 Score=39.58 Aligned_cols=30 Identities=13% Similarity=0.210 Sum_probs=26.7
Q ss_pred cccccccceeccccccccCCceEeCCeEEEEE
Q 046357 35 KTKWCITKFIDLETLSNTLNEYLINDVCVCGC 66 (137)
Q Consensus 35 ~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a 66 (137)
...+|++.|||++.|.. ..||.||.+.|-+
T Consensus 135 ~~~~G~~~Fish~~L~~--r~yikdD~ifi~~ 164 (167)
T cd03782 135 GPGYGTSAFITHLRLRS--RDFIKGDDVIFLL 164 (167)
T ss_pred ccccCccceeeHHHHhh--cCcccCCeEEEEE
Confidence 36799999999999985 7799999999877
No 34
>cd03783 MATH_Meprin_Alpha 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
Probab=89.67 E-value=0.18 Score=38.81 Aligned_cols=29 Identities=21% Similarity=0.408 Sum_probs=25.7
Q ss_pred ccceeeecccccCCCCCeEEcCeEEEEEEEE
Q 046357 98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFT 128 (137)
Q Consensus 98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~ 128 (137)
+|++||+++.|+. ++||.+|+++|-++++
T Consensus 139 G~~~Fish~~L~~--r~yikdDtlfI~~~~~ 167 (167)
T cd03783 139 GWSTFISHSQLRR--RSFLKNDDLIIFVDFE 167 (167)
T ss_pred ccccceeHHHHhh--CCcccCCeEEEEEecC
Confidence 3999999999975 8999999999988763
No 35
>cd03777 MATH_TRAF3 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 al
Probab=89.64 E-value=0.34 Score=37.54 Aligned_cols=29 Identities=21% Similarity=0.406 Sum_probs=25.8
Q ss_pred ccceeeecccccCCCCCeEEcCeEEEEEEEE
Q 046357 98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFT 128 (137)
Q Consensus 98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~ 128 (137)
++++||+.++|.. .+||.+|++.|+++|.
T Consensus 156 G~~~Fi~~~~Le~--~~ylkdD~l~Irv~v~ 184 (186)
T cd03777 156 GCPVFVAQTVLEN--GTYIKDDTIFIKVIVD 184 (186)
T ss_pred CchheeEHHHhcc--CCcEeCCEEEEEEEEe
Confidence 4899999999953 6999999999999885
No 36
>cd03782 MATH_Meprin_Beta 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 f
Probab=78.72 E-value=1.2 Score=34.19 Aligned_cols=29 Identities=10% Similarity=0.266 Sum_probs=25.0
Q ss_pred ccceeeecccccCCCCCeEEcCeEEEEEEEE
Q 046357 98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFT 128 (137)
Q Consensus 98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~ 128 (137)
+|+.||+.++|+. +.||.+|+++|-++++
T Consensus 139 G~~~Fish~~L~~--r~yikdD~ifi~~~~e 167 (167)
T cd03782 139 GTSAFITHLRLRS--RDFIKGDDVIFLLTME 167 (167)
T ss_pred CccceeeHHHHhh--cCcccCCeEEEEEecC
Confidence 4999999999975 8899999998877653
No 37
>KOG1863 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=43.34 E-value=15 Score=35.77 Aligned_cols=36 Identities=8% Similarity=0.253 Sum_probs=32.7
Q ss_pred cceeeecccccCCCCCeEEcCeEEEEEEEEEEEEee
Q 046357 99 CAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLGVVL 134 (137)
Q Consensus 99 ~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~~~t~ 134 (137)
+.+|+.++++.++..||+.+|++..+++|.+-.-+.
T Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~~~~ 156 (1093)
T KOG1863|consen 121 FSCFSTSSDIRKPEDGYVRNGLEKLEKRVRVEQPTS 156 (1093)
T ss_pred hccchhHhhccCcccccccccceeeeeeeeeecCCc
Confidence 789999999999999999999999999998876543
No 38
>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=25.50 E-value=55 Score=31.39 Aligned_cols=42 Identities=17% Similarity=0.225 Sum_probs=34.9
Q ss_pred eeeeeec--ccceeeecccccCCCCCe---EEcCeEEEEEEEEEEEE
Q 046357 91 HLLPYLE--SCAQLMSLAKLKDPKEGY---MVRDICIIKAEFTLLGV 132 (137)
Q Consensus 91 ~lslyL~--d~~~fi~l~~l~~~~~gy---lv~D~~~ieaev~i~~~ 132 (137)
.||..-. +|++|+.|.++..|+.|. +.+++++|.|.|.|++-
T Consensus 127 rFs~~~tDwGFt~f~dL~kl~~psp~~Ppfleeg~l~ItvyVRvlkd 173 (1089)
T COG5077 127 RFSMESTDWGFTNFIDLNKLIEPSPGRPPFLEEGTLVITVYVRVLKD 173 (1089)
T ss_pred cccccccccchhhhhhhhhhcCCCCCCCCcccCCeEEEEEEEEEEeC
Confidence 5666666 489999999999987764 78889999999999873
No 39
>KOG1987 consensus Speckle-type POZ protein SPOP and related proteins with TRAF, MATH and BTB/POZ domains [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=20.19 E-value=98 Score=24.61 Aligned_cols=34 Identities=18% Similarity=0.352 Sum_probs=28.1
Q ss_pred ccceeeecccccCCCCCeEEcCeEEEEEEEEEEE
Q 046357 98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLG 131 (137)
Q Consensus 98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~~ 131 (137)
++.+.+++..+.+...||+++..+++-|+..|..
T Consensus 94 g~~~~~~~~~~~~~~~g~~~~~~~~~~a~~~V~~ 127 (297)
T KOG1987|consen 94 GFGKMLPLTLLIDCSNGFLVAHKLVLVARSEVFE 127 (297)
T ss_pred CcccccChHHhhcccCcEEEcCceEEEeeeccee
Confidence 4778899999999999999998777777766554
Done!