Query 030279
Match_columns 180
No_of_seqs 191 out of 1128
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 11:19:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030279.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030279hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd03775 MATH_Ubp21p Ubiquitin- 99.9 6.2E-24 1.4E-28 158.1 12.2 123 22-169 2-132 (134)
2 cd03774 MATH_SPOP Speckle-type 99.9 4.7E-22 1E-26 148.7 10.0 121 19-161 3-126 (139)
3 cd03772 MATH_HAUSP Herpesvirus 99.9 1.8E-21 3.8E-26 145.3 11.4 125 20-167 2-127 (137)
4 cd00270 MATH_TRAF_C Tumor Necr 99.9 1.2E-21 2.6E-26 147.8 8.9 135 21-167 1-145 (149)
5 cd03780 MATH_TRAF5 Tumor Necro 99.9 2.3E-21 4.9E-26 146.9 10.3 131 21-162 1-140 (148)
6 cd03776 MATH_TRAF6 Tumor Necro 99.9 3E-21 6.6E-26 145.8 9.7 136 21-167 1-143 (147)
7 cd03773 MATH_TRIM37 Tripartite 99.8 7E-21 1.5E-25 140.8 10.5 118 18-161 2-121 (132)
8 cd03781 MATH_TRAF4 Tumor Necro 99.8 1.7E-20 3.7E-25 142.9 9.3 130 21-162 1-146 (154)
9 cd03771 MATH_Meprin Meprin fam 99.8 5.8E-20 1.3E-24 141.4 11.6 137 21-161 2-158 (167)
10 cd03777 MATH_TRAF3 Tumor Necro 99.8 4.4E-20 9.6E-25 144.6 11.1 133 18-163 36-177 (186)
11 cd03779 MATH_TRAF1 Tumor Necro 99.8 1.6E-19 3.6E-24 136.4 9.1 130 21-162 1-139 (147)
12 cd03778 MATH_TRAF2 Tumor Necro 99.8 2.8E-18 6.1E-23 131.5 12.0 132 17-161 15-155 (164)
13 cd00121 MATH MATH (meprin and 99.7 3E-17 6.4E-22 118.0 11.0 117 21-161 1-117 (126)
14 smart00061 MATH meprin and TRA 99.7 1E-16 2.2E-21 110.7 10.2 74 23-105 2-75 (95)
15 PF00917 MATH: MATH domain; I 99.5 1.8E-14 3.9E-19 103.4 6.6 112 27-166 1-113 (119)
16 cd03782 MATH_Meprin_Beta Mepri 99.5 5.3E-14 1.1E-18 107.5 8.7 138 21-165 2-162 (167)
17 COG5077 Ubiquitin carboxyl-ter 99.5 1.1E-14 2.4E-19 131.3 4.2 127 18-169 36-167 (1089)
18 cd03783 MATH_Meprin_Alpha Mepr 99.4 4E-13 8.6E-18 103.0 8.4 138 21-164 2-161 (167)
19 cd03773 MATH_TRIM37 Tripartite 98.9 2E-09 4.4E-14 79.2 5.1 45 132-176 2-48 (132)
20 cd03775 MATH_Ubp21p Ubiquitin- 98.9 2.9E-09 6.3E-14 79.0 5.3 39 136-175 2-40 (134)
21 KOG1987 Speckle-type POZ prote 98.8 2.9E-09 6.3E-14 88.5 3.5 137 23-174 6-199 (297)
22 cd03772 MATH_HAUSP Herpesvirus 98.6 4.6E-08 1E-12 72.7 5.0 41 134-175 2-42 (137)
23 cd03774 MATH_SPOP Speckle-type 98.5 1.3E-07 2.8E-12 70.4 4.8 41 135-175 5-51 (139)
24 cd03777 MATH_TRAF3 Tumor Necro 98.1 2.1E-06 4.6E-11 67.4 3.8 45 133-177 37-90 (186)
25 smart00061 MATH meprin and TRA 98.1 2.8E-06 6E-11 58.0 3.2 36 137-172 2-38 (95)
26 cd00121 MATH MATH (meprin and 98.1 9.5E-06 2.1E-10 57.6 5.5 40 136-175 2-41 (126)
27 COG5077 Ubiquitin carboxyl-ter 97.9 5.1E-06 1.1E-10 76.2 2.7 43 133-176 37-79 (1089)
28 cd03778 MATH_TRAF2 Tumor Necro 97.7 2.3E-05 5.1E-10 60.3 2.1 45 133-177 17-70 (164)
29 KOG0297 TNF receptor-associate 97.5 7.6E-05 1.7E-09 64.9 3.1 81 19-100 278-365 (391)
30 PF00917 MATH: MATH domain; I 97.1 6.4E-05 1.4E-09 53.4 -1.3 33 141-173 1-35 (119)
31 cd00270 MATH_TRAF_C Tumor Necr 97.0 0.00058 1.3E-08 51.0 3.3 27 150-176 23-51 (149)
32 cd03776 MATH_TRAF6 Tumor Necro 96.6 0.0016 3.6E-08 48.7 3.0 26 152-177 25-52 (147)
33 cd03780 MATH_TRAF5 Tumor Necro 96.6 0.0018 3.8E-08 49.1 3.0 27 151-177 24-52 (148)
34 cd03781 MATH_TRAF4 Tumor Necro 96.6 0.0023 5E-08 48.5 3.6 27 151-177 24-52 (154)
35 KOG1863 Ubiquitin carboxyl-ter 96.3 0.0037 8E-08 61.0 3.5 115 21-161 27-141 (1093)
36 cd03779 MATH_TRAF1 Tumor Necro 94.8 0.029 6.3E-07 42.4 3.0 26 152-177 25-52 (147)
37 KOG1987 Speckle-type POZ prote 53.4 0.28 6E-06 40.6 -7.2 58 21-79 156-214 (297)
38 KOG1863 Ubiquitin carboxyl-ter 41.8 14 0.00031 36.6 1.5 41 132-173 24-64 (1093)
39 PF08922 DUF1905: Domain of un 38.6 34 0.00074 22.8 2.6 17 46-62 37-53 (80)
40 PF00976 ACTH_domain: Corticot 27.9 23 0.0005 20.4 0.3 15 161-175 14-29 (39)
41 PF06943 zf-LSD1: LSD1 zinc fi 27.3 36 0.00077 17.8 0.9 11 164-174 5-15 (25)
42 COG4680 Uncharacterized protei 26.6 59 0.0013 22.6 2.1 16 45-60 58-73 (98)
43 KOG4003 Pyrazinamidase/nicotin 26.1 31 0.00067 27.2 0.8 56 1-76 9-64 (223)
No 1
>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=99.91 E-value=6.2e-24 Score=158.14 Aligned_cols=123 Identities=20% Similarity=0.434 Sum_probs=96.4
Q ss_pred EEEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC----CCCCcEEEEEEEEEE
Q 030279 22 HFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS----LGLGWEVYVIFRLFV 97 (180)
Q Consensus 22 ~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~----~~~~~~~~a~f~~~l 97 (180)
+|+|+|+|||++ ++.+.|++|.||||+|+|.+||+|+.. .+||||||++.+... ++.+|.++|+|+|.|
T Consensus 2 ~f~w~I~~fS~~----~~~~~S~~F~vGG~~W~l~~yP~G~~~---~~~iSlyL~l~~~~~~~~~~~~~~~v~a~f~~~l 74 (134)
T cd03775 2 SFTWRIKNWSEL----EKKVHSPKFKCGGFEWRILLFPQGNSQ---TGGVSIYLEPHPEEEEKAPLDEDWSVCAQFALVI 74 (134)
T ss_pred cEEEEECCcccC----CcceeCCCEEECCeeEEEEEeCCCCCC---CCeEEEEEEecCcccccccCCCCCeEEEEEEEEE
Confidence 699999999997 589999999999999999999999862 789999999976553 367899999999999
Q ss_pred EeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCc----cCCCcEEeCCeEEEEEEe
Q 030279 98 LDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNI----YESEVFVAGDQKWYVYFL 169 (180)
Q Consensus 98 lnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~----~~S~~F~vg~~~w~i~~y 169 (180)
+||.++..... .... +.|......||+..|+++.++. ....+|+++| ...|.+|
T Consensus 75 ~n~~~~~~~~~-----------~~~~------~~F~~~~~~wG~~~fi~~~~L~~~~~~~~~g~l~nD-~l~I~~~ 132 (134)
T cd03775 75 SNPGDPSIQLS-----------NVAH------HRFNAEDKDWGFTRFIELRKLAHRTPDKPSPFLENG-ELNITVY 132 (134)
T ss_pred EcCCCCccceE-----------ccce------eEeCCCCCCCChhHcccHHHHcccccCCCCceeECC-EEEEEEE
Confidence 99986543331 1111 1233345689999999987654 2356899999 6667665
No 2
>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=99.87 E-value=4.7e-22 Score=148.65 Aligned_cols=121 Identities=26% Similarity=0.357 Sum_probs=93.1
Q ss_pred CCcEEEEEEcCccccccCCCCeEEccceeecCe---EEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEEE
Q 030279 19 PPAHFLLKIEAFSSLVENDVENYKSLEFDAGGY---KWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRL 95 (180)
Q Consensus 19 ~~~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~---~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~ 95 (180)
..-+|+|+|+|||++++..++.+.|++|.+||| +|+|.+||+|+.. +..+||||||++++.. .++++|+|+|
T Consensus 3 ~~~~~~w~I~~fS~~~~~~~~~i~S~~F~vgg~~~~~W~l~~yP~G~~~-~~~~~iSlyL~l~~~~----~~~v~a~f~~ 77 (139)
T cd03774 3 VKFCYMWTISNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDE-ESKDYLSLYLLLVSCP----KSEVRAKFKF 77 (139)
T ss_pred eEEEEEEEECCchhhhhcCCCEEECCCeecCCcCCceEEEEEeCCCCCC-CCCCeEEEEEEEccCC----CCcEEEEEEE
Confidence 456899999999998755578999999999995 9999999999863 4578999999997643 2579999999
Q ss_pred EEEeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCC
Q 030279 96 FVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGD 161 (180)
Q Consensus 96 ~llnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~ 161 (180)
.|+||.+++.... ...... .+.. ...||+.+|.++.++.....+|+++|
T Consensus 78 ~l~n~~~~~~~~~----------~~~~~~------~f~~-~~~wG~~~fi~~~~L~~~~~g~l~dD 126 (139)
T cd03774 78 SILNAKGEETKAM----------ESQRAY------RFVQ-GKDWGFKKFIRRDFLLDEANGLLPDD 126 (139)
T ss_pred EEEecCCCeeeee----------cccCcE------eCCC-CCccCHHHeeeHHHhhhhhcccccCC
Confidence 9999998764331 111111 1222 35899999999887644456799988
No 3
>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=99.87 E-value=1.8e-21 Score=145.31 Aligned_cols=125 Identities=19% Similarity=0.255 Sum_probs=94.8
Q ss_pred CcEEEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCC-CCCCcEEEEEEeecCCCCCCCcEEEEEEEEEEE
Q 030279 20 PAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNE-NVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVL 98 (180)
Q Consensus 20 ~~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~-~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~~ll 98 (180)
.++|+|+|.|||++ ++.+.|+.|.+|||.|+|.+||+|+... +..+||||||++.+.. ...+|.+.|+|+|.|+
T Consensus 2 ~~~~~~~I~~~S~l----~e~~~S~~f~vgG~~W~i~~~P~g~~~~~~~~~~lsvyL~~~~~~-~~~~w~i~a~~~~~l~ 76 (137)
T cd03772 2 EATFSFTVERFSRL----SESVLSPPCFVRNLPWKIMVMPRNYPDRNPHQKSVGFFLQCNAES-DSTSWSCHAQAVLRII 76 (137)
T ss_pred CcEEEEEECCcccC----CCcEECCCEEECCcceEEEEEeCCCCCCCCCCCeEEEEEeeCCcC-CCCCCeEEEEEEEEEE
Confidence 57899999999998 5789999999999999999999996531 2358999999997654 3347999999999999
Q ss_pred eCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCeEEEEE
Q 030279 99 DQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVY 167 (180)
Q Consensus 99 nq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~ 167 (180)
||.+......+ .... .+......||+.+|++++++...+.+|+++|+ ..|.
T Consensus 77 ~~~~~~~~~~~----------~~~~-------~f~~~~~~~G~~~fi~~~~L~~~~sgyl~~D~-l~Ie 127 (137)
T cd03772 77 NYKDDEPSFSR----------RISH-------LFFSKENDWGFSNFMTWSEVTDPEKGFIEDDT-ITLE 127 (137)
T ss_pred cCCCCcccEEE----------eeee-------EEcCCCCCccchheeEHHHhcCCCCCcEECCE-EEEE
Confidence 99854332211 0111 12223347999999999887666788999994 3443
No 4
>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=99.86 E-value=1.2e-21 Score=147.81 Aligned_cols=135 Identities=21% Similarity=0.324 Sum_probs=94.6
Q ss_pred cEEEEEEcCcccccc----CCCCeEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEEEEEE
Q 030279 21 AHFLLKIEAFSSLVE----NDVENYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEVYVIF 93 (180)
Q Consensus 21 ~~~~w~I~~fS~l~~----~~~~~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~~a~f 93 (180)
|+|+|+|++||++++ ..++.++|++|.+| ||+|+|.+||+|+.. +..+||||||++++... .+.+|++.|+|
T Consensus 1 g~~~w~I~~fs~~~~~~~~~~~~~~~S~~F~vg~~G~~w~i~~yP~G~~~-~~~~~lsl~L~l~~~~~d~~~~w~~~~~~ 79 (149)
T cd00270 1 GVLIWKIKDYSRKLQEAVAGSNTVLYSPPFYTSRYGYKLCLRLYLNGDGT-GKGTHLSLFVHVMKGEYDALLEWPFRGKI 79 (149)
T ss_pred CEEEEEECCHHHHHHHHhcCCCceEECCCcccCCCCceEEEEEEeCCCCC-CCCCEEEEEEEEeccCCCccccCCccceE
Confidence 689999999999865 24679999999999 999999999999863 35689999999987643 24679999999
Q ss_pred EEEEEeCCCC--ceeEEeeEE-eccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCeEEEEE
Q 030279 94 RLFVLDQKKD--EFLILQEVF-VKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVY 167 (180)
Q Consensus 94 ~~~llnq~~~--~~~~~~dvF-~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~ 167 (180)
+|+|+||.++ .... .+.| ..+ +...|.. .......-.||+..|.++.++. +.+|+++|+ ..|.
T Consensus 80 ~~~l~d~~~~~~~~~~-~~~~~~~~------~~~~f~~-~~~~~~~~~~G~~~fi~~~~L~--~~gfl~dD~-l~I~ 145 (149)
T cd00270 80 TLTLLDQSDDSKRKHI-TETFMPDP------NSSAFQR-PPTGENNIGFGYPEFVPLEKLE--SRGYVKDDT-LFIK 145 (149)
T ss_pred EEEEECCCCccccCce-EEEEEcCC------chHhhcC-CCcccCCCCcCcceEeEHHHhc--cCCCEeCCE-EEEE
Confidence 9999999874 1111 0011 000 0000100 0001234579999999988763 457999994 4443
No 5
>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=99.86 E-value=2.3e-21 Score=146.86 Aligned_cols=131 Identities=19% Similarity=0.276 Sum_probs=94.4
Q ss_pred cEEEEEEcCcccccc--CCCC--eEEccce--eecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCC-CCCcEEEEEE
Q 030279 21 AHFLLKIEAFSSLVE--NDVE--NYKSLEF--DAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSL-GLGWEVYVIF 93 (180)
Q Consensus 21 ~~~~w~I~~fS~l~~--~~~~--~~~S~~F--~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~-~~~~~~~a~f 93 (180)
|+|+|+|++||++++ ..|+ .+.|++| .+|||+|+|.+||||+.. +..+||||||+|+..+.- -..|++.+++
T Consensus 1 g~~vwkI~~ys~~~~~~~~g~~~~i~S~~Fyt~~~Gy~w~i~~ypnG~~~-~~~~~iSv~l~l~~g~~D~~l~wp~~~~~ 79 (148)
T cd03780 1 GKLIWKVTDYKMKKKEAVDGHTVSIFSQPFYTSRCGYRLCARAYLNGDGS-GKGTHLSLYFVVMRGEFDSLLQWPFRQRV 79 (148)
T ss_pred CEEEEEECCHHHHHHhhcCCCccEEECCCcccCCCCeeEEEEEEcCCCCC-CCCCEEEEEEEEecCccccccCcceEEEE
Confidence 689999999999974 3566 8999999 999999999999999984 467899999999975321 2469999999
Q ss_pred EEEEEeCCCCceeEEeeEE-eccccccccceEeceecccCC-CcceEEEeccccCCCCCccCCCcEEeCCe
Q 030279 94 RLFVLDQKKDEFLILQEVF-VKETKKCTGECLSMKKLTSAS-NYKHVWKIKNFSKLPDNIYESEVFVAGDQ 162 (180)
Q Consensus 94 ~~~llnq~~~~~~~~~dvF-~~~~~~~~~e~~s~~~~~~~~-~~~~tW~i~nFs~l~~~~~~S~~F~vg~~ 162 (180)
+|+|+||.+.+..+. +++ .++ +...|.+ +. .....||..+|+.++.+.-.+..|+.+|+
T Consensus 80 tfsLlDq~~~~~~~~-~~~~~~~------~~~~F~r---p~~~~n~~~G~~~Fi~~~~Le~s~~~ylkdD~ 140 (148)
T cd03780 80 TLMLLDQSGKKNHIM-ETFKADP------NSSSFKR---PDGEMNIASGCPRFVAHSVLENAKNTYIKDDT 140 (148)
T ss_pred EEEEECCCCCCCCcc-eeeecCC------ccccccC---CCCCCCCCcChhheeEHHHhhcccCCcCcCCE
Confidence 999999986543211 122 111 0111211 11 11346999999998877444468888884
No 6
>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=99.85 E-value=3e-21 Score=145.77 Aligned_cols=136 Identities=21% Similarity=0.271 Sum_probs=92.5
Q ss_pred cEEEEEEcCcccccc--CCCC--eEEccceee--cCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEEEEEE
Q 030279 21 AHFLLKIEAFSSLVE--NDVE--NYKSLEFDA--GGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEVYVIF 93 (180)
Q Consensus 21 ~~~~w~I~~fS~l~~--~~~~--~~~S~~F~v--gG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~~a~f 93 (180)
|+|+|+|.+||++++ ..++ .+.|++|.+ |||+|+|.+||+|... +..+|||+||+|++... ...+|++.|+|
T Consensus 1 g~h~~~I~~yS~~~~~~~~g~~~~i~S~~F~~~~gGy~W~i~~yP~G~~~-~~~~~lS~~L~l~~~~~d~~l~wpv~a~~ 79 (147)
T cd03776 1 GIYVWKIKNFSNLRRSMEAGSPVVIHSPGFYTSPPGYKLCARLNLSLPEA-RCPNYISLFVHLMQGENDSHLDWPFQGTI 79 (147)
T ss_pred CEEEEEECCHHHHHHHHhcCCCceEECCCcccCCCCceEEEEEEeCCCCC-CCCCEEEEEEEEeccCCCcccCCccccee
Confidence 689999999998654 2455 488999985 7999999999999874 46789999999987543 24579999999
Q ss_pred EEEEEeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCeEEEEE
Q 030279 94 RLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVY 167 (180)
Q Consensus 94 ~~~llnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~ 167 (180)
+|.|+||.++..... +.+. ...+...|.+..+ ....-.||+.+|.+++.+ .+.+|+++|+ ..|.
T Consensus 80 ~~~lldq~~~~~~~~-~~~~-----~~~~~~~F~~p~~-~~~~~~~G~~~fi~~~~L--e~~~yl~dD~-l~I~ 143 (147)
T cd03776 80 TLTLLDQSEPRQNIH-ETMM-----SKPELLAFQRPTT-DRNPKGFGYVEFAHIEDL--LQRGFVKNDT-LLIK 143 (147)
T ss_pred EEEEECCCcccCccE-EEEE-----cCCChHhhcCCCc-CCCCCCeeEceeeEHHHh--hhCCCccCCE-EEEE
Confidence 999999986433211 0010 0000000111000 012346999999998766 3457999984 4443
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=99.85 E-value=7e-21 Score=140.77 Aligned_cols=118 Identities=21% Similarity=0.320 Sum_probs=89.6
Q ss_pred CCCcEEEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEEEEE
Q 030279 18 VPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFV 97 (180)
Q Consensus 18 ~~~~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~~l 97 (180)
+..++++|+|.|||++++ .++++.|++|.+|||+|+|.+||+|+.. +..+||||||++.+.. ++.+.++|+|.|
T Consensus 2 ~~~~~~~~~I~~fS~~~~-~~~~~~S~~F~vgG~~W~i~~yP~G~~~-~~~~~lSl~L~l~~~~----~~~~~~~~~l~l 75 (132)
T cd03773 2 PPYDSATFTLENFSTLRQ-SADPVYSDPLNVDGLCWRLKVYPDGNGE-VRGNFLSVFLELCSGL----GEASKYEYRVEM 75 (132)
T ss_pred CCCcccEEEECChhhhhc-CCcceeCCCeEeCCccEEEEEECCCCCC-CCCCEEEEEEEeecCC----CCceeEEEEEEE
Confidence 356789999999999864 4689999999999999999999999874 4578999999987642 367889999999
Q ss_pred EeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeC--C
Q 030279 98 LDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAG--D 161 (180)
Q Consensus 98 lnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg--~ 161 (180)
+||.++.....+ ... ..+.. ...||+.+|.+++.+ ...+|+++ |
T Consensus 76 lnq~~~~~~~~~----------~~~-------~~f~~-~~~wG~~~Fi~~~~L--~~~gfl~~~~D 121 (132)
T cd03773 76 VHQANPTKNIKR----------EFA-------SDFEV-GECWGYNRFFRLDLL--INEGYLLPEND 121 (132)
T ss_pred EcCCCCccceEE----------ecc-------ccccC-CCCcCHHHhccHHHH--hhCCCcCCCCC
Confidence 999644332211 000 01222 346999999998765 34689998 7
No 8
>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=99.83 E-value=1.7e-20 Score=142.93 Aligned_cols=130 Identities=22% Similarity=0.316 Sum_probs=92.8
Q ss_pred cEEEEEEcCcccccc---C-CCCeEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCC-CCcEEEEEE
Q 030279 21 AHFLLKIEAFSSLVE---N-DVENYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLG-LGWEVYVIF 93 (180)
Q Consensus 21 ~~~~w~I~~fS~l~~---~-~~~~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~-~~~~~~a~f 93 (180)
|+|.|+|.+||++++ . .++.+.|++|.+| ||+|+|.+||+|... +..+|||+||+|++.+... ..|++.|++
T Consensus 1 g~~~~~I~gys~~~~~~~~~~~~~i~S~~F~vg~~Gy~w~i~~yPnG~~~-~~~~~vs~~l~l~~ge~d~~l~wp~~a~~ 79 (154)
T cd03781 1 GTLLWKITDYSRKLQEAKGRDNLELFSPPFYTHRYGYKLQVSAFLNGNGS-GEGSHLSVYIRVLPGEYDNLLEWPFSHRI 79 (154)
T ss_pred CEEEEEECCHHHHHHHhhcCCCceEECCCeecCCCCEEEEEEEECCCCCC-CCCCEEEEEEEEecCCcccccCCceeeEE
Confidence 689999999999875 2 3589999999999 999999999999874 4678999999999854322 479999999
Q ss_pred EEEEEeCCCCc--eeE-EeeEE-eccccccccceEeceecccCC-----CcceEEEeccccCCCCCccCCCcEEeCCe
Q 030279 94 RLFVLDQKKDE--FLI-LQEVF-VKETKKCTGECLSMKKLTSAS-----NYKHVWKIKNFSKLPDNIYESEVFVAGDQ 162 (180)
Q Consensus 94 ~~~llnq~~~~--~~~-~~dvF-~~~~~~~~~e~~s~~~~~~~~-----~~~~tW~i~nFs~l~~~~~~S~~F~vg~~ 162 (180)
+|+|+||.+.. ... ..+.| ..+. ...|. .|. ...-.||+..|.+++.+ .+..|+.+|+
T Consensus 80 ~~~llDq~~~~~~~~~~~~~~~~~~~~------~~~F~---rp~~~~~~~~~~~~G~~~fi~~~~L--e~~~yl~dD~ 146 (154)
T cd03781 80 TFTLLDQSDPSLSKPQHITETFTPDPT------WKNFQ---KPSASRLDESTLGFGYPKFISHEDL--KKRNYIKDDA 146 (154)
T ss_pred EEEEECCCCCccccCcceEEEEEcCCc------hhhhc---CCcccccCCCCCccchhHeeEHHHH--hhCCcccCCE
Confidence 99999998751 111 11122 1000 00011 111 12346999999998765 4457999884
No 9
>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=99.83 E-value=5.8e-20 Score=141.45 Aligned_cols=137 Identities=18% Similarity=0.276 Sum_probs=93.6
Q ss_pred cEEEEEEcCccccc-c-CCCCeEEccce-eecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcE-EEEEEEE
Q 030279 21 AHFLLKIEAFSSLV-E-NDVENYKSLEF-DAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWE-VYVIFRL 95 (180)
Q Consensus 21 ~~~~w~I~~fS~l~-~-~~~~~~~S~~F-~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~-~~a~f~~ 95 (180)
.+|+|+|.|||+++ + ..++.++|++| .+|||+|+|.+||+|+.. ..+||||||+|++.+. ..++|+ +.|+++|
T Consensus 2 p~hvwkI~~yS~~~~~~~~g~~i~S~~FysvgGy~w~I~~YPnG~~~--~~~~lSlyL~L~~g~~d~~L~WP~v~a~~t~ 79 (167)
T cd03771 2 PEAVWRVRNFSQLLETTPKGTKIYSPRFYSPEGYAFQVGLYPNGTES--YPGYTGLYFHLCSGENDDVLEWPCPNRQATM 79 (167)
T ss_pred CeEEEEEcCchhhhhcCCCCCEEECCCCCccCCeEEEEEEEeCCCCC--CCCcceEEEEEecCCccccccCcceeEEEEE
Confidence 57999999999996 3 35789999999 999999999999999974 5789999999987543 346799 6899999
Q ss_pred EEEeCCCC--ceeEEeeEE-eccccccc-cceEeceec------ccC-----CCcceEEEeccccCCCCCccCCCcEEeC
Q 030279 96 FVLDQKKD--EFLILQEVF-VKETKKCT-GECLSMKKL------TSA-----SNYKHVWKIKNFSKLPDNIYESEVFVAG 160 (180)
Q Consensus 96 ~llnq~~~--~~~~~~dvF-~~~~~~~~-~e~~s~~~~------~~~-----~~~~~tW~i~nFs~l~~~~~~S~~F~vg 160 (180)
+|+||..+ +..-..+.| .+|..... .+.+-+.+. ... -...-.||...|.++.++ .+..|+.+
T Consensus 80 ~LlDQ~~~~~~r~~~~~~~~~dp~~~~~~~~~~~~~rP~~~~~~~~~~~~~~~~~~~g~G~~~Fis~~~L--~~r~ylk~ 157 (167)
T cd03771 80 TLLDQDPDIQQRMSNQRSFTTDPSMTSSDNGEYFWDRPSKVGSYDTDTNGCTCYRGPGYGWSTFISHSRL--RRRDFLKG 157 (167)
T ss_pred EEECCCCcccccCcceEEEecCCcccccccccccccCCccccccccccccccccccCccccccceeHHHh--ccCCCCcC
Confidence 99999731 111112344 33321000 000000000 000 013457999999999976 34669998
Q ss_pred C
Q 030279 161 D 161 (180)
Q Consensus 161 ~ 161 (180)
|
T Consensus 158 d 158 (167)
T cd03771 158 D 158 (167)
T ss_pred C
Confidence 8
No 10
>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=99.83 E-value=4.4e-20 Score=144.60 Aligned_cols=133 Identities=20% Similarity=0.256 Sum_probs=95.4
Q ss_pred CCCcEEEEEEcCcccccc--CCCC--eEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEEE
Q 030279 18 VPPAHFLLKIEAFSSLVE--NDVE--NYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEVY 90 (180)
Q Consensus 18 ~~~~~~~w~I~~fS~l~~--~~~~--~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~~ 90 (180)
...|+|.|+|.+||.+++ ..|+ .+.|++|.+| ||+|+|.+||||+.. +..+|||+||+++..+. .-..|++.
T Consensus 36 ~~~G~hvwkI~~yS~~~~~~~~g~~~~i~S~~Fyvg~~GY~w~i~~ypnG~g~-~~~~~iSvyl~L~~ge~D~~L~WP~~ 114 (186)
T cd03777 36 SYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGM-GKGTHLSLFFVIMRGEYDALLPWPFK 114 (186)
T ss_pred ccceEEEEEECChhHHHHhhccCCCcEEECCCeEeCCCCeeEEEEEEcCCCCC-CCCCEEEEEEEEecCCcccccCCcee
Confidence 347999999999999864 3455 8999999999 999999999999984 46789999999997542 12469999
Q ss_pred EEEEEEEEeCCCCceeEEeeEE-eccccccccceEeceecccCC-CcceEEEeccccCCCCCccCCCcEEeCCeE
Q 030279 91 VIFRLFVLDQKKDEFLILQEVF-VKETKKCTGECLSMKKLTSAS-NYKHVWKIKNFSKLPDNIYESEVFVAGDQK 163 (180)
Q Consensus 91 a~f~~~llnq~~~~~~~~~dvF-~~~~~~~~~e~~s~~~~~~~~-~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~ 163 (180)
++++|+|+||.+..... .+.| ..|. . ..|.+ +. .....||...|.+++.+ .+..|+.+|+-
T Consensus 115 ~~~tfsLlDQ~~~~~~~-~~~~~p~p~---~---~~F~r---p~~~~n~~~G~~~Fi~~~~L--e~~~ylkdD~l 177 (186)
T cd03777 115 QKVTLMLMDQGSSRRHL-GDAFKPDPN---S---SSFKK---PTGEMNIASGCPVFVAQTVL--ENGTYIKDDTI 177 (186)
T ss_pred EEEEEEEEcCCCccccc-cceeccCCc---c---ccccC---CccCCCCCCCchheeEHHHh--ccCCcEeCCEE
Confidence 99999999997532211 1223 1111 0 11221 11 11345899999988765 55678988853
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=99.80 E-value=1.6e-19 Score=136.44 Aligned_cols=130 Identities=22% Similarity=0.297 Sum_probs=91.6
Q ss_pred cEEEEEEcCcccccc-C-C--CCeEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEEEEEE
Q 030279 21 AHFLLKIEAFSSLVE-N-D--VENYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEVYVIF 93 (180)
Q Consensus 21 ~~~~w~I~~fS~l~~-~-~--~~~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~~a~f 93 (180)
|+|+|+|.||+++.+ . . ...++||+|..+ ||+|+|.+||||+.. +..+||||||+|++.+. .-+.|++.|++
T Consensus 1 g~~~W~i~~f~~~~~~a~~~~~~~~~S~~Fyt~~~Gy~w~i~~ypnG~~~-~~~~~iSv~l~l~~g~~D~~l~wpv~~~~ 79 (147)
T cd03779 1 GTFLWKITDVSQKQRESSHGRDVSLCSPAFYTAKYGYKVCLRLYLNGDGA-GKGTHISLFFVIMKGEYDALLPWPFRHKV 79 (147)
T ss_pred CeEEEEECcHHHHHHHHhcCCCceEECCCcccCCCCceEEEEEEcCCCCC-CCCCEEEEEEEEecCCcccccCcceEEEE
Confidence 689999999997654 2 2 348999999987 999999999999984 46789999999987531 12469999999
Q ss_pred EEEEEeCCCCceeEEeeEEeccccccccceEeceecccCC-CcceEEEeccccCCCCCccCC-CcEEeCCe
Q 030279 94 RLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSAS-NYKHVWKIKNFSKLPDNIYES-EVFVAGDQ 162 (180)
Q Consensus 94 ~~~llnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~-~~~~tW~i~nFs~l~~~~~~S-~~F~vg~~ 162 (180)
+|+|+||.+.+.... ++ ++. .....|.+ |. .....||..+|++++++ ..| .+|+.+|+
T Consensus 80 tfsLlDq~~~~~~~~--~~-~~~----~~~~~F~r---P~~~~n~~~G~~~Fi~~~~L-e~s~~~ylkDD~ 139 (147)
T cd03779 80 TFMLLDQNNREHVID--AF-RPD----LSSASFQR---PVSDMNVASGCPLFFPLKKL-QSPKHAYCKDDT 139 (147)
T ss_pred EEEEECCCCCCCCcE--ee-cCC----cccccccC---cccCCCCCcchhheeEHHHh-cccCCCcEeCCE
Confidence 999999986554221 11 000 00011221 11 22346999999998876 223 48888884
No 12
>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=99.78 E-value=2.8e-18 Score=131.51 Aligned_cols=132 Identities=22% Similarity=0.343 Sum_probs=98.7
Q ss_pred cCCCcEEEEEEcCccccccC--C--CCeEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCC-CCcEE
Q 030279 17 HVPPAHFLLKIEAFSSLVEN--D--VENYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLG-LGWEV 89 (180)
Q Consensus 17 ~~~~~~~~w~I~~fS~l~~~--~--~~~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~-~~~~~ 89 (180)
....|+|+|+|.||+++++. . ...++||+|..+ ||+|+|.+||+|++. +.+.||||||+++.++..+ ++|++
T Consensus 15 ~~~~g~fiWkI~~fs~~~~~a~~~~~~~i~Sp~Fyt~~~GYk~~l~~ylnG~g~-~~g~~LSly~~l~~Ge~D~~L~WPf 93 (164)
T cd03778 15 STYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGT-GRGTHLSLFFVVMKGPNDALLRWPF 93 (164)
T ss_pred cccCCEEEEEECcHHHHHHHHhcCCCceEECCCcccCCCCeEEEEEEEeCCCCC-CCCCEEEEEEEEecCCcCcccCCce
Confidence 34579999999999998652 2 358999999764 899999999999985 4567999999999987655 78999
Q ss_pred EEEEEEEEEeCCCCceeEEeeEE-eccccccccceEeceecccC-CCcceEEEeccccCCCCCccCCCcEEeCC
Q 030279 90 YVIFRLFVLDQKKDEFLILQEVF-VKETKKCTGECLSMKKLTSA-SNYKHVWKIKNFSKLPDNIYESEVFVAGD 161 (180)
Q Consensus 90 ~a~f~~~llnq~~~~~~~~~dvF-~~~~~~~~~e~~s~~~~~~~-~~~~~tW~i~nFs~l~~~~~~S~~F~vg~ 161 (180)
..+++|+|+||.+.++.+. .| .++. + . .|. .| ......||...|..+.++.. +.+|+.+|
T Consensus 94 ~~~itl~llDQ~~r~hi~~--~~~pd~~---~-~--~f~---RP~~~~n~~~G~~~Fv~l~~l~~-~~~Yv~dD 155 (164)
T cd03778 94 NQKVTLMLLDQNNREHVID--AFRPDVT---S-S--SFQ---RPVNDMNIASGCPLFCPVSKXEA-KNSYVRDD 155 (164)
T ss_pred eeEEEEEEECCCCCCccee--EEEcCcc---h-H--hcC---CCCcccccCcCcceEEEhhHccc-cCCcccCC
Confidence 9999999999987555432 22 1221 0 0 111 23 22344699999999987743 36899988
No 13
>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=99.74 E-value=3e-17 Score=118.02 Aligned_cols=117 Identities=28% Similarity=0.442 Sum_probs=89.3
Q ss_pred cEEEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEEEEEEeC
Q 030279 21 AHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQ 100 (180)
Q Consensus 21 ~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~~llnq 100 (180)
++|+|+|.+|+.. .++.+.|+.|.++|+.|+|.+||+|... ..+||||||++......+..|.+.|+|+|.|+||
T Consensus 1 ~~~~~~i~~~~~~---~~~~~~S~~f~~~g~~W~l~~~p~~~~~--~~~~lsv~L~~~~~~~~~~~~~~~~~~~~~l~~~ 75 (126)
T cd00121 1 GKHTWKIVNFSEL---EGESIYSPPFEVGGYKWRIRIYPNGDGE--SGDYLSLYLELDKGESDLEKWSVRAEFTLKLVNQ 75 (126)
T ss_pred CEEEEEECCCCCC---CCcEEECCCEEEcCEeEEEEEEcCCCCC--CCCEEEEEEEecCCCCCCCCCcEEEEEEEEEECC
Confidence 4799999999993 3789999999999999999999999863 5789999999987765456799999999999999
Q ss_pred CCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCC
Q 030279 101 KKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGD 161 (180)
Q Consensus 101 ~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~ 161 (180)
.+.+..... .... -+......||+.+|..++++. .+.++++|
T Consensus 76 ~~~~~~~~~----------~~~~-------~~~~~~~~~G~~~fi~~~~l~--~~~~~~~d 117 (126)
T cd00121 76 NGGKSLSKS----------FTHV-------FFSEKGSGWGFPKFISWDDLE--DSYYLVDD 117 (126)
T ss_pred CCCccceEe----------ccCC-------cCCCCCCCCChHHeeEHHHhc--cCCcEECC
Confidence 854443320 1111 012345789999999988663 23336666
No 14
>smart00061 MATH meprin and TRAF homology.
Probab=99.71 E-value=1e-16 Score=110.66 Aligned_cols=74 Identities=20% Similarity=0.335 Sum_probs=65.2
Q ss_pred EEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEEEEEEeCCC
Q 030279 23 FLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKK 102 (180)
Q Consensus 23 ~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~~llnq~~ 102 (180)
++|+|.+|+.+. .++.+.|++|.+||+.|+|.+||+ .+||||||.+.+....+.+|.+.|+|+|.|+||.+
T Consensus 2 ~~~~~~~~~~~~--~~~~~~S~~f~~~g~~W~i~~~p~-------~~~lsl~L~~~~~~~~~~~w~v~a~~~~~l~~~~~ 72 (95)
T smart00061 2 LSHTFKNVSRLE--EGESYFSPSEEHFNIPWRLKIYRK-------NGFLSLYLHCEKEECDSRKWSIEAEFTLKLVSQNG 72 (95)
T ss_pred ceeEEEchhhcc--cCceEeCChhEEcCceeEEEEEEc-------CCEEEEEEEeCCCcCCCCCeEEEEEEEEEEEeCCC
Confidence 579999999984 378999999999999999999998 36999999998776555589999999999999998
Q ss_pred Cce
Q 030279 103 DEF 105 (180)
Q Consensus 103 ~~~ 105 (180)
.++
T Consensus 73 ~~~ 75 (95)
T smart00061 73 KSL 75 (95)
T ss_pred CEE
Confidence 665
No 15
>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=99.53 E-value=1.8e-14 Score=103.41 Aligned_cols=112 Identities=29% Similarity=0.477 Sum_probs=82.1
Q ss_pred EcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCC-CCcEEEEEEEEEEEeCCCCce
Q 030279 27 IEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLG-LGWEVYVIFRLFVLDQKKDEF 105 (180)
Q Consensus 27 I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~-~~~~~~a~f~~~llnq~~~~~ 105 (180)
|+|||+++. .+..+.|+.|.+||+.|+|.+||+|+ .+++|+||++....... .+|++.|++++.|+++.+...
T Consensus 1 i~nfs~l~~-~~~~~~s~~~~~~g~~W~l~~~~~~~-----~~~l~~~L~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~ 74 (119)
T PF00917_consen 1 IKNFSKLKE-GEEYSSSFVFSHGGYPWRLKVYPKGN-----GKYLSVYLHCDKGENDSDLEWSIEAEFRFRLLNQNGKSI 74 (119)
T ss_dssp ETTGGGHHT-SEEEEEEEESSTTSEEEEEEEETTES-----TTEEEEEEEEECSTTGGGSSSSEEEEEEEEEE-TTSCEE
T ss_pred CcccceEeC-CCcEECCCeEEECCEEEEEEEEeCCC-----cCcEEEEEEEeecccccccceeeeEEEEEEEecCCCCcc
Confidence 789999972 24455669999999999999999986 57999999999886543 689999999999999999874
Q ss_pred eEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCeEEEE
Q 030279 106 LILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYV 166 (180)
Q Consensus 106 ~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i 166 (180)
... .+...|. ....||+..|++++++.. +.|+++| +..|
T Consensus 75 ~~~------------~~~~~F~-------~~~~~g~~~fi~~~~l~~--~~fl~dd-~l~i 113 (119)
T PF00917_consen 75 SKR------------IKSHSFN-------NPSSWGWSSFISWEDLED--PYFLVDD-SLTI 113 (119)
T ss_dssp EEE------------EECEEEC-------TTSEEEEEEEEEHHHHTT--CTTSBTT-EEEE
T ss_pred eee------------eeeeEEe-------eecccchhheeEHHHhCc--cCCeECC-EEEE
Confidence 332 0111111 237899999999886532 3378887 4433
No 16
>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=99.52 E-value=5.3e-14 Score=107.46 Aligned_cols=138 Identities=18% Similarity=0.290 Sum_probs=94.6
Q ss_pred cEEEEEEcCcccccc--CCCCeEEccceeec-CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEEE-EEEEE
Q 030279 21 AHFLLKIEAFSSLVE--NDVENYKSLEFDAG-GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEVY-VIFRL 95 (180)
Q Consensus 21 ~~~~w~I~~fS~l~~--~~~~~~~S~~F~vg-G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~~-a~f~~ 95 (180)
..|+|+|.||+++++ ..+..++||+|... ||+.++.+||||++. + ++|||||++++.++. .-+.|++. -+++|
T Consensus 2 p~~iWkI~~fs~~~~~~~~~~~i~Sp~FYt~~GYkl~l~~ylnG~g~-~-~~~lsl~~~lm~Ge~D~~L~WPf~~~qit~ 79 (167)
T cd03782 2 PEHIWHIRNFTQLLATTPPNGKIYSPPFLSSTGYSFQVGLYLNGTDD-Y-PGNLAIYLHLTSGPNDDQLQWPCPWQQATM 79 (167)
T ss_pred CcEEEEeCcHHHHHHhcCCCceEECCCCcCccCceeEEEEEecCCCC-C-CCEEEEEEEEeccCCCccccCCCcCCeEEE
Confidence 469999999999876 24689999999754 999999999999984 3 679999999998764 23679999 89999
Q ss_pred EEEeCCCC--ceeEEeeEE-eccccccccceEece-ecccC-------CC-------cceEEEeccccCCCCCccCCCcE
Q 030279 96 FVLDQKKD--EFLILQEVF-VKETKKCTGECLSMK-KLTSA-------SN-------YKHVWKIKNFSKLPDNIYESEVF 157 (180)
Q Consensus 96 ~llnq~~~--~~~~~~dvF-~~~~~~~~~e~~s~~-~~~~~-------~~-------~~~tW~i~nFs~l~~~~~~S~~F 157 (180)
.|+||..+ +..-+.++| .+|.. ...+--++. + +| .. ....||...|.++.++ .+..|
T Consensus 80 ~LlDQ~~d~~~r~~~~~~~t~~P~~-~s~~n~~f~w~--rP~kvg~~~~~~~~~~~~r~~~~G~~~Fish~~L--~~r~y 154 (167)
T cd03782 80 MLLDQHPDIRQRMSNQRSVTTDPNM-TSTDSDEYFWD--DPRKVGSEVTDTDGSTFYRGPGYGTSAFITHLRL--RSRDF 154 (167)
T ss_pred EEEcCCCchhhccceeeeEEecCCc-ccccCccceec--CCcccCcccccccccccccccccCccceeeHHHH--hhcCc
Confidence 99999641 211123334 33310 000000010 0 11 11 1467888999998866 45778
Q ss_pred EeCCeEEE
Q 030279 158 VAGDQKWY 165 (180)
Q Consensus 158 ~vg~~~w~ 165 (180)
+.||.-.-
T Consensus 155 ikdD~ifi 162 (167)
T cd03782 155 IKGDDVIF 162 (167)
T ss_pred ccCCeEEE
Confidence 88885443
No 17
>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=99.50 E-value=1.1e-14 Score=131.29 Aligned_cols=127 Identities=20% Similarity=0.324 Sum_probs=96.7
Q ss_pred CCCcEEEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC--CC-CCcEEEEEEE
Q 030279 18 VPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS--LG-LGWEVYVIFR 94 (180)
Q Consensus 18 ~~~~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~--~~-~~~~~~a~f~ 94 (180)
....+|+|+|.+||.+. +++.||+|.|||+.|+|.++|+|+.+ .+ +|+||++...+. +. ..|.+||+|.
T Consensus 36 ~~~~sftW~vk~wsel~----~k~~Sp~F~vg~~twki~lfPqG~nq---~~-~sVyLe~~pqe~e~~~gk~~~ccaqFa 107 (1089)
T COG5077 36 LLEMSFTWKVKRWSELA----KKVESPPFSVGGHTWKIILFPQGNNQ---CN-VSVYLEYEPQELEETGGKYYDCCAQFA 107 (1089)
T ss_pred HhhcccceecCChhhhh----hhccCCcccccCeeEEEEEecccCCc---cc-cEEEEEeccchhhhhcCcchhhhhhee
Confidence 44578999999999994 68999999999999999999999974 33 999999875431 22 3499999999
Q ss_pred EEEEeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEE--eCCeEEEEEEe
Q 030279 95 LFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFV--AGDQKWYVYFL 169 (180)
Q Consensus 95 ~~llnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~--vg~~~w~i~~y 169 (180)
|.|.|+..+....+ ++. ++.|......||+.||..|++...+++++. +.+....|.+|
T Consensus 108 f~Is~p~~pti~~i----------N~s-------HhrFs~~~tDwGFt~f~dL~kl~~psp~~Ppfleeg~l~Itvy 167 (1089)
T COG5077 108 FDISNPKYPTIEYI----------NKS-------HHRFSMESTDWGFTNFIDLNKLIEPSPGRPPFLEEGTLVITVY 167 (1089)
T ss_pred eecCCCCCCchhhh----------hcc-------cccccccccccchhhhhhhhhhcCCCCCCCCcccCCeEEEEEE
Confidence 99999988655442 222 335777888999999999998877777654 23334444444
No 18
>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=99.44 E-value=4e-13 Score=103.01 Aligned_cols=138 Identities=17% Similarity=0.270 Sum_probs=93.5
Q ss_pred cEEEEEEcCccccccC--CCCeEEccceeec-CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEE-EEEEEE
Q 030279 21 AHFLLKIEAFSSLVEN--DVENYKSLEFDAG-GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEV-YVIFRL 95 (180)
Q Consensus 21 ~~~~w~I~~fS~l~~~--~~~~~~S~~F~vg-G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~-~a~f~~ 95 (180)
..++|+|.||+++++. .+..++||+|... ||+.+|.+||+|+...+.+.|||||++++.++. .-+.|++ .-+++|
T Consensus 2 p~~iWkI~nfs~~~~~a~~~~~i~Sp~Fyt~~GYk~~l~~~lng~~~~~~g~~lSl~~~lm~Ge~D~~L~WP~~~~~itl 81 (167)
T cd03783 2 PNAVWRVRNFSQILENTTKGDVLQSPRFYSPEGYGYGVSLYPLSNESDYSGNYTGLYFHLCSGENDAVLEWPALNRQAII 81 (167)
T ss_pred CceeEEECcHHHHHHhCcCCCeEECCCCccCCCceEEEEEEecCCCCCCCCCEEEEEEEEecccCCCcccCCCcCCEEEE
Confidence 4689999999997652 5689999999885 999999999999874345789999999998764 2367995 569999
Q ss_pred EEEeCCCC--ceeEEeeEE-eccccccccceE---eceecccC-----------CCcceEEEeccccCCCCCccCCCcEE
Q 030279 96 FVLDQKKD--EFLILQEVF-VKETKKCTGECL---SMKKLTSA-----------SNYKHVWKIKNFSKLPDNIYESEVFV 158 (180)
Q Consensus 96 ~llnq~~~--~~~~~~dvF-~~~~~~~~~e~~---s~~~~~~~-----------~~~~~tW~i~nFs~l~~~~~~S~~F~ 158 (180)
+|+||..+ +..-+.+.| ..+.. ..+.+ ..-+ +| ......+|...|.++..+ .+..|+
T Consensus 82 ~llDQ~~~~~~r~~~~~sf~~d~~~--~~~~~~~~~~f~--rP~~~~~~~~~~~~~~~~gfG~~~Fish~~L--~~r~yi 155 (167)
T cd03783 82 TVLDQDPDVRLRMSSSRSFTTDKSQ--TSSAINGTLRWD--RPSRVGTYDTSCDCFRGIDFGWSTFISHSQL--RRRSFL 155 (167)
T ss_pred EEEcCCcchhhccccceeeecCCCc--cccccccccccc--CCcccccccccccccCCcccccccceeHHHH--hhCCcc
Confidence 99999631 111111223 22110 00000 0001 12 124557888999999876 457899
Q ss_pred eCCeEE
Q 030279 159 AGDQKW 164 (180)
Q Consensus 159 vg~~~w 164 (180)
.+|.-.
T Consensus 156 kdDtlf 161 (167)
T cd03783 156 KNDDLI 161 (167)
T ss_pred cCCeEE
Confidence 888543
No 19
>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=98.90 E-value=2e-09 Score=79.23 Aligned_cols=45 Identities=13% Similarity=0.128 Sum_probs=39.3
Q ss_pred CCCcceEEEeccccCCC--CCccCCCcEEeCCeEEEEEEecCCCCCC
Q 030279 132 ASNYKHVWKIKNFSKLP--DNIYESEVFVAGDQKWYVYFLKWCSNPN 176 (180)
Q Consensus 132 ~~~~~~tW~i~nFs~l~--~~~~~S~~F~vg~~~w~i~~yp~g~~~~ 176 (180)
|...+++|.|.+||.+. ...+.|+.|.|||++|+|.+||+|+..+
T Consensus 2 ~~~~~~~~~I~~fS~~~~~~~~~~S~~F~vgG~~W~i~~yP~G~~~~ 48 (132)
T cd03773 2 PPYDSATFTLENFSTLRQSADPVYSDPLNVDGLCWRLKVYPDGNGEV 48 (132)
T ss_pred CCCcccEEEECChhhhhcCCcceeCCCeEeCCccEEEEEECCCCCCC
Confidence 45678999999999984 3578899999999999999999998653
No 20
>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=98.88 E-value=2.9e-09 Score=79.00 Aligned_cols=39 Identities=26% Similarity=0.542 Sum_probs=35.4
Q ss_pred ceEEEeccccCCCCCccCCCcEEeCCeEEEEEEecCCCCC
Q 030279 136 KHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCSNP 175 (180)
Q Consensus 136 ~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~~yp~g~~~ 175 (180)
+|+|.|.|||++. .++.|+.|.|||++|||.+||+|+..
T Consensus 2 ~f~w~I~~fS~~~-~~~~S~~F~vGG~~W~l~~yP~G~~~ 40 (134)
T cd03775 2 SFTWRIKNWSELE-KKVHSPKFKCGGFEWRILLFPQGNSQ 40 (134)
T ss_pred cEEEEECCcccCC-cceeCCCEEECCeeEEEEEeCCCCCC
Confidence 6999999999986 46889999999999999999999864
No 21
>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=98.81 E-value=2.9e-09 Score=88.49 Aligned_cols=137 Identities=23% Similarity=0.314 Sum_probs=100.4
Q ss_pred EEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEEEEEEeCCC
Q 030279 23 FLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKK 102 (180)
Q Consensus 23 ~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~~llnq~~ 102 (180)
+.|.|.+|+.. +..++|..|..||+.|++.+||.|+ ++|+|+.+.... +|.++|.++|.+.||..
T Consensus 6 ~~~~~~~~~~~----~l~~ys~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~----~~~~~~~~~l~v~n~~~ 70 (297)
T KOG1987|consen 6 FTWVISNFSSV----GLVIYSNGFVKGGCKWRLSAYPKGN-------YLSLTLSVSDSP----GWERYAKLRLTVVNQKS 70 (297)
T ss_pred cceeeccCcch----hhhccccceeecCceEEEEEecCCC-------EEEEEEEeccCC----CcceeEEEEEEEccCCC
Confidence 33899999888 3789999999999999999999875 789999887653 69999999999999999
Q ss_pred Cce-eEE-ee--EE-ec--ccccc------------------------------------ccceEecee------cccCC
Q 030279 103 DEF-LIL-QE--VF-VK--ETKKC------------------------------------TGECLSMKK------LTSAS 133 (180)
Q Consensus 103 ~~~-~~~-~d--vF-~~--~~~~~------------------------------------~~e~~s~~~------~~~~~ 133 (180)
.++ ... .+ +| .+ ...++ +.+...... ..++.
T Consensus 71 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~g~~~~~~~~~~a~~~V~~~~~~~d~~~~~~~~~~~~d~~~~ 150 (297)
T KOG1987|consen 71 EKYLSTVEEGFSWFRFNKVLKEWGFGKMLPLTLLIDCSNGFLVAHKLVLVARSEVFEAMGKSDVFKESSKLITLLEEKPE 150 (297)
T ss_pred cceeeeeeeeEEeccccccccccCcccccChHHhhcccCcEEEcCceEEEeeecceeeecccccchhccccccccccchh
Confidence 876 555 23 22 11 11111 111111100 11233
Q ss_pred C----cceEEEeccccCCCCC----ccCCCcEEeCCeEEEEEEecCCCC
Q 030279 134 N----YKHVWKIKNFSKLPDN----IYESEVFVAGDQKWYVYFLKWCSN 174 (180)
Q Consensus 134 ~----~~~tW~i~nFs~l~~~----~~~S~~F~vg~~~w~i~~yp~g~~ 174 (180)
. ..|+|.+.+|+.++.. .+.+..|.++++.||+.++|.|.+
T Consensus 151 ~~~~~~~F~~~~s~~~~~~~~~~~~~~~a~~f~~~~~~lk~~~~~~l~~ 199 (297)
T KOG1987|consen 151 VLEALNGFQVLPSQVSSVERIFEKHPDLAAAFKYKNRHLKLACMPVLLS 199 (297)
T ss_pred hHhhhceEEEeccchHHHHHhhcCChhhhhccccccHHHHHHHHHHHHH
Confidence 3 7899999999998853 556789999999999999998753
No 22
>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=98.63 E-value=4.6e-08 Score=72.72 Aligned_cols=41 Identities=12% Similarity=0.215 Sum_probs=36.3
Q ss_pred CcceEEEeccccCCCCCccCCCcEEeCCeEEEEEEecCCCCC
Q 030279 134 NYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCSNP 175 (180)
Q Consensus 134 ~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~~yp~g~~~ 175 (180)
.+.++|.|.||+.|. ..+.|+.|.|||+.|+|.+||+|...
T Consensus 2 ~~~~~~~I~~~S~l~-e~~~S~~f~vgG~~W~i~~~P~g~~~ 42 (137)
T cd03772 2 EATFSFTVERFSRLS-ESVLSPPCFVRNLPWKIMVMPRNYPD 42 (137)
T ss_pred CcEEEEEECCcccCC-CcEECCCEEECCcceEEEEEeCCCCC
Confidence 368999999999994 56889999999999999999999643
No 23
>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=98.53 E-value=1.3e-07 Score=70.43 Aligned_cols=41 Identities=24% Similarity=0.456 Sum_probs=35.5
Q ss_pred cceEEEeccccCCC---CCccCCCcEEeCCe---EEEEEEecCCCCC
Q 030279 135 YKHVWKIKNFSKLP---DNIYESEVFVAGDQ---KWYVYFLKWCSNP 175 (180)
Q Consensus 135 ~~~tW~i~nFs~l~---~~~~~S~~F~vg~~---~w~i~~yp~g~~~ 175 (180)
-+|+|.|.+||++. ...+.|+.|.|||+ +|+|.+||+|...
T Consensus 5 ~~~~w~I~~fS~~~~~~~~~i~S~~F~vgg~~~~~W~l~~yP~G~~~ 51 (139)
T cd03774 5 FCYMWTISNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDE 51 (139)
T ss_pred EEEEEEECCchhhhhcCCCEEECCCeecCCcCCceEEEEEeCCCCCC
Confidence 47999999999874 45788999999995 9999999999754
No 24
>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=98.14 E-value=2.1e-06 Score=67.39 Aligned_cols=45 Identities=18% Similarity=0.215 Sum_probs=38.4
Q ss_pred CCcceEEEeccccCCCC-----C--ccCCCcEEeC--CeEEEEEEecCCCCCCC
Q 030279 133 SNYKHVWKIKNFSKLPD-----N--IYESEVFVAG--DQKWYVYFLKWCSNPNI 177 (180)
Q Consensus 133 ~~~~~tW~i~nFs~l~~-----~--~~~S~~F~vg--~~~w~i~~yp~g~~~~~ 177 (180)
..+.|.|+|.+|+.+.+ . ...|+.|.+| |++|+|.+||+|++.+.
T Consensus 37 ~~G~hvwkI~~yS~~~~~~~~g~~~~i~S~~Fyvg~~GY~w~i~~ypnG~g~~~ 90 (186)
T cd03777 37 YNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGK 90 (186)
T ss_pred cceEEEEEECChhHHHHhhccCCCcEEECCCeEeCCCCeeEEEEEEcCCCCCCC
Confidence 35889999999998752 2 5789999999 99999999999987654
No 25
>smart00061 MATH meprin and TRAF homology.
Probab=98.09 E-value=2.8e-06 Score=58.00 Aligned_cols=36 Identities=19% Similarity=0.142 Sum_probs=32.3
Q ss_pred eEEEeccccCCC-CCccCCCcEEeCCeEEEEEEecCC
Q 030279 137 HVWKIKNFSKLP-DNIYESEVFVAGDQKWYVYFLKWC 172 (180)
Q Consensus 137 ~tW~i~nFs~l~-~~~~~S~~F~vg~~~w~i~~yp~g 172 (180)
++|.|+||+++. +..+.|+.|.++|+.|||.+||++
T Consensus 2 ~~~~~~~~~~~~~~~~~~S~~f~~~g~~W~i~~~p~~ 38 (95)
T smart00061 2 LSHTFKNVSRLEEGESYFSPSEEHFNIPWRLKIYRKN 38 (95)
T ss_pred ceeEEEchhhcccCceEeCChhEEcCceeEEEEEEcC
Confidence 589999999984 467889999999999999999984
No 26
>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=98.05 E-value=9.5e-06 Score=57.64 Aligned_cols=40 Identities=35% Similarity=0.539 Sum_probs=35.9
Q ss_pred ceEEEeccccCCCCCccCCCcEEeCCeEEEEEEecCCCCC
Q 030279 136 KHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCSNP 175 (180)
Q Consensus 136 ~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~~yp~g~~~ 175 (180)
.++|.|.+|+......+.|+.|.++|..|||.+||+|...
T Consensus 2 ~~~~~i~~~~~~~~~~~~S~~f~~~g~~W~l~~~p~~~~~ 41 (126)
T cd00121 2 KHTWKIVNFSELEGESIYSPPFEVGGYKWRIRIYPNGDGE 41 (126)
T ss_pred EEEEEECCCCCCCCcEEECCCEEEcCEeEEEEEEcCCCCC
Confidence 5899999999966667889999999999999999999854
No 27
>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=97.94 E-value=5.1e-06 Score=76.22 Aligned_cols=43 Identities=26% Similarity=0.502 Sum_probs=38.7
Q ss_pred CCcceEEEeccccCCCCCccCCCcEEeCCeEEEEEEecCCCCCC
Q 030279 133 SNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCSNPN 176 (180)
Q Consensus 133 ~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~~yp~g~~~~ 176 (180)
...+|+|.|++|++|.+ ++.||.|.|||+.|+|.+||+|+++-
T Consensus 37 ~~~sftW~vk~wsel~~-k~~Sp~F~vg~~twki~lfPqG~nq~ 79 (1089)
T COG5077 37 LEMSFTWKVKRWSELAK-KVESPPFSVGGHTWKIILFPQGNNQC 79 (1089)
T ss_pred hhcccceecCChhhhhh-hccCCcccccCeeEEEEEecccCCcc
Confidence 44689999999999997 58899999999999999999998764
No 28
>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=97.66 E-value=2.3e-05 Score=60.27 Aligned_cols=45 Identities=16% Similarity=0.199 Sum_probs=36.2
Q ss_pred CCcceEEEeccccCCCCC-------ccCCCcEEeC--CeEEEEEEecCCCCCCC
Q 030279 133 SNYKHVWKIKNFSKLPDN-------IYESEVFVAG--DQKWYVYFLKWCSNPNI 177 (180)
Q Consensus 133 ~~~~~tW~i~nFs~l~~~-------~~~S~~F~vg--~~~w~i~~yp~g~~~~~ 177 (180)
.++.|.|+|+||+.+.+. ...|+.|..+ |++|+|.+||+|++.+.
T Consensus 17 ~~g~fiWkI~~fs~~~~~a~~~~~~~i~Sp~Fyt~~~GYk~~l~~ylnG~g~~~ 70 (164)
T cd03778 17 YDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGR 70 (164)
T ss_pred cCCEEEEEECcHHHHHHHHhcCCCceEECCCcccCCCCeEEEEEEEeCCCCCCC
Confidence 468999999999986532 4567888764 89999999999987654
No 29
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=97.48 E-value=7.6e-05 Score=64.93 Aligned_cols=81 Identities=23% Similarity=0.329 Sum_probs=67.8
Q ss_pred CCcEEEEEEcCcccccc----CCCCeEEccceee--cCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCC-CCCcEEEE
Q 030279 19 PPAHFLLKIEAFSSLVE----NDVENYKSLEFDA--GGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSL-GLGWEVYV 91 (180)
Q Consensus 19 ~~~~~~w~I~~fS~l~~----~~~~~~~S~~F~v--gG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~-~~~~~~~a 91 (180)
..|..+|+|.+|...+. +....++|+.|.. .||+.+..+|-+|+.. +.+.++|+|+.++..+.. .+.|+.+-
T Consensus 278 ~~g~~iwki~~~~~~~~e~~~~~~~~~~S~~f~t~~~Gyk~~~~~~lng~g~-~~~~~~s~~~~~~~ge~d~~l~wpf~~ 356 (391)
T KOG0297|consen 278 YDGTLIWKIPDYGRKKQEAVAGATLSLFSPAFYTSKYGYKLCARIYLNGDGT-GKGTHLSLYFVVMRGEYDALLPWPFRQ 356 (391)
T ss_pred cCCEEEEEecchhhhhHHHHhccCccccccccccccccHHHHhHhhhcCCCC-CCcceeeeeeeecccCcccccccCCCC
Confidence 46899999999965543 3568999999986 5999999999999985 467799999999987643 35799999
Q ss_pred EEEEEEEeC
Q 030279 92 IFRLFVLDQ 100 (180)
Q Consensus 92 ~f~~~llnq 100 (180)
+.+|.+++|
T Consensus 357 ~v~~~l~dq 365 (391)
T KOG0297|consen 357 KVTLMLLDQ 365 (391)
T ss_pred ceEEEEecc
Confidence 999999999
No 30
>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=97.12 E-value=6.4e-05 Score=53.36 Aligned_cols=33 Identities=36% Similarity=0.469 Sum_probs=27.9
Q ss_pred eccccCCC--CCccCCCcEEeCCeEEEEEEecCCC
Q 030279 141 IKNFSKLP--DNIYESEVFVAGDQKWYVYFLKWCS 173 (180)
Q Consensus 141 i~nFs~l~--~~~~~S~~F~vg~~~w~i~~yp~g~ 173 (180)
|+||++|+ +..+.|+.|.++|+.|+|.+||+|+
T Consensus 1 i~nfs~l~~~~~~~~s~~~~~~g~~W~l~~~~~~~ 35 (119)
T PF00917_consen 1 IKNFSKLKEGEEYSSSFVFSHGGYPWRLKVYPKGN 35 (119)
T ss_dssp ETTGGGHHTSEEEEEEEESSTTSEEEEEEEETTES
T ss_pred CcccceEeCCCcEECCCeEEECCEEEEEEEEeCCC
Confidence 68999997 3345558889999999999999998
No 31
>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=97.04 E-value=0.00058 Score=51.04 Aligned_cols=27 Identities=11% Similarity=0.049 Sum_probs=23.5
Q ss_pred CccCCCcEEeC--CeEEEEEEecCCCCCC
Q 030279 150 NIYESEVFVAG--DQKWYVYFLKWCSNPN 176 (180)
Q Consensus 150 ~~~~S~~F~vg--~~~w~i~~yp~g~~~~ 176 (180)
..+.|+.|.|| |++|+|.+||+|...+
T Consensus 23 ~~~~S~~F~vg~~G~~w~i~~yP~G~~~~ 51 (149)
T cd00270 23 TVLYSPPFYTSRYGYKLCLRLYLNGDGTG 51 (149)
T ss_pred ceEECCCcccCCCCceEEEEEEeCCCCCC
Confidence 45789999999 9999999999998543
No 32
>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=96.64 E-value=0.0016 Score=48.75 Aligned_cols=26 Identities=12% Similarity=-0.067 Sum_probs=22.2
Q ss_pred cCCCcEEe--CCeEEEEEEecCCCCCCC
Q 030279 152 YESEVFVA--GDQKWYVYFLKWCSNPNI 177 (180)
Q Consensus 152 ~~S~~F~v--g~~~w~i~~yp~g~~~~~ 177 (180)
+.|+.|.+ ||++|+|.+||+|...+.
T Consensus 25 i~S~~F~~~~gGy~W~i~~yP~G~~~~~ 52 (147)
T cd03776 25 IHSPGFYTSPPGYKLCARLNLSLPEARC 52 (147)
T ss_pred EECCCcccCCCCceEEEEEEeCCCCCCC
Confidence 56899985 799999999999987654
No 33
>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=96.61 E-value=0.0018 Score=49.06 Aligned_cols=27 Identities=7% Similarity=-0.159 Sum_probs=23.8
Q ss_pred ccCCCcE--EeCCeEEEEEEecCCCCCCC
Q 030279 151 IYESEVF--VAGDQKWYVYFLKWCSNPNI 177 (180)
Q Consensus 151 ~~~S~~F--~vg~~~w~i~~yp~g~~~~~ 177 (180)
...|+.| .++|++|+|.+||+|.+.+.
T Consensus 24 ~i~S~~Fyt~~~Gy~w~i~~ypnG~~~~~ 52 (148)
T cd03780 24 SIFSQPFYTSRCGYRLCARAYLNGDGSGK 52 (148)
T ss_pred EEECCCcccCCCCeeEEEEEEcCCCCCCC
Confidence 4679999 99999999999999997654
No 34
>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=96.61 E-value=0.0023 Score=48.51 Aligned_cols=27 Identities=15% Similarity=-0.114 Sum_probs=23.4
Q ss_pred ccCCCcEEeC--CeEEEEEEecCCCCCCC
Q 030279 151 IYESEVFVAG--DQKWYVYFLKWCSNPNI 177 (180)
Q Consensus 151 ~~~S~~F~vg--~~~w~i~~yp~g~~~~~ 177 (180)
...|+.|.|| |++|+|.+||+|...+.
T Consensus 24 ~i~S~~F~vg~~Gy~w~i~~yPnG~~~~~ 52 (154)
T cd03781 24 ELFSPPFYTHRYGYKLQVSAFLNGNGSGE 52 (154)
T ss_pred eEECCCeecCCCCEEEEEEEECCCCCCCC
Confidence 4678999999 99999999999976543
No 35
>KOG1863 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=96.25 E-value=0.0037 Score=60.99 Aligned_cols=115 Identities=19% Similarity=0.158 Sum_probs=84.9
Q ss_pred cEEEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEEEEEEeC
Q 030279 21 AHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQ 100 (180)
Q Consensus 21 ~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~~llnq 100 (180)
..++|.+.+...+. ....|+.|..|+..|++.+.|+|+. ...+++|+........ ..|.+++++.+.+.|.
T Consensus 27 ~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~-~~~s~~~~~~~~v~~~ 97 (1093)
T KOG1863|consen 27 QSTTIDGIDDKSLL----YRALSSNFGAGATKWKILIAPKVNS----LQSTRKKLEVMPSQSL-KSWSCGAQAVLRVKNT 97 (1093)
T ss_pred ccccccCcCcchhh----hHhcCccccccccceeeeeccccCc----ccceeEEeeeccCCCC-cceEecchhhhccccC
Confidence 44556665555543 3788999999999999999999984 4679999998877665 4499999999999993
Q ss_pred CCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCC
Q 030279 101 KKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGD 161 (180)
Q Consensus 101 ~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~ 161 (180)
.++..... +.. .+-+......|+..+|+.+.+.+.+..+|...|
T Consensus 98 ~~~~~~~~-----------~~~------~h~~~~~~~dwg~~~~~~~~~~~~~~~~~~~~~ 141 (1093)
T KOG1863|consen 98 IDNLPDPE-----------KAI------HHVFTADERDWGFSCFSTSSDIRKPEDGYVRNG 141 (1093)
T ss_pred CCCchhhh-----------hhh------hhcccccccchhhccchhHhhccCccccccccc
Confidence 33332221 111 113456678899889998888777778888877
No 36
>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=94.78 E-value=0.029 Score=42.41 Aligned_cols=26 Identities=12% Similarity=-0.022 Sum_probs=22.0
Q ss_pred cCCCcEEeC--CeEEEEEEecCCCCCCC
Q 030279 152 YESEVFVAG--DQKWYVYFLKWCSNPNI 177 (180)
Q Consensus 152 ~~S~~F~vg--~~~w~i~~yp~g~~~~~ 177 (180)
..|+.|..+ |++|+|.+||+|.+.+.
T Consensus 25 ~~S~~Fyt~~~Gy~w~i~~ypnG~~~~~ 52 (147)
T cd03779 25 LCSPAFYTAKYGYKVCLRLYLNGDGAGK 52 (147)
T ss_pred EECCCcccCCCCceEEEEEEcCCCCCCC
Confidence 568888876 99999999999987653
No 37
>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=53.39 E-value=0.28 Score=40.59 Aligned_cols=58 Identities=16% Similarity=0.001 Sum_probs=46.6
Q ss_pred cEEEEEEcCccccccC-CCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeec
Q 030279 21 AHFLLKIEAFSSLVEN-DVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVD 79 (180)
Q Consensus 21 ~~~~w~I~~fS~l~~~-~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~ 79 (180)
..|+|.+.+++..... ....+.+..|.+++..|++.++|.|... .....++.||.+.+
T Consensus 156 ~~F~~~~s~~~~~~~~~~~~~~~a~~f~~~~~~lk~~~~~~l~~~-~~~~~~~~~l~~~~ 214 (297)
T KOG1987|consen 156 NGFQVLPSQVSSVERIFEKHPDLAAAFKYKNRHLKLACMPVLLSL-IETLNVSQSLQEAS 214 (297)
T ss_pred ceEEEeccchHHHHHhhcCChhhhhccccccHHHHHHHHHHHHHH-HHhhhhcccHHHhc
Confidence 7899999999988642 2247788999999999999999999873 23557888888665
No 38
>KOG1863 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=41.84 E-value=14 Score=36.64 Aligned_cols=41 Identities=20% Similarity=0.084 Sum_probs=34.4
Q ss_pred CCCcceEEEeccccCCCCCccCCCcEEeCCeEEEEEEecCCC
Q 030279 132 ASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCS 173 (180)
Q Consensus 132 ~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~~yp~g~ 173 (180)
+.+...+|...+...+.. ...++.|..|+.+|+|.+.|+|+
T Consensus 24 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 64 (1093)
T KOG1863|consen 24 SLNQSTTIDGIDDKSLLY-RALSSNFGAGATKWKILIAPKVN 64 (1093)
T ss_pred hhcccccccCcCcchhhh-HhcCccccccccceeeeeccccC
Confidence 455677788777777776 67899999999999999999987
No 39
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=38.61 E-value=34 Score=22.80 Aligned_cols=17 Identities=29% Similarity=0.690 Sum_probs=14.7
Q ss_pred eeecCeEEEEEEeeCCC
Q 030279 46 FDAGGYKWKLVVYPNGN 62 (180)
Q Consensus 46 F~vgG~~Wrl~~yP~G~ 62 (180)
=.++|+.|+-.++|.|+
T Consensus 37 ~tI~g~~~~~sl~p~g~ 53 (80)
T PF08922_consen 37 GTIDGHPWRTSLFPMGN 53 (80)
T ss_dssp EEETTEEEEEEEEESST
T ss_pred EEECCEEEEEEEEECCC
Confidence 36899999999999765
No 40
>PF00976 ACTH_domain: Corticotropin ACTH domain; InterPro: IPR013531 Pro-opiomelanocortin is present in high levels in the pituitary and is processed into 3 major peptide families: adrenocorticotrophin (ACTH); alpha-, beta- and gamma-melanocyte- stimulating hormones (MSH); and beta-endorphin []. ACTH regulates the synthesis and release of glucocorticoids and, to some extent, aldosterone in the adrenal cortex. It is synthesised and released in response to corticotrophin-releasing factor at times of stress (i.e. heat, cold, infection, etc.), its release leading to increased metabolism. The action of MSH in man is poorly understood, but it may be involved in temperature regulation []. Full activity of ACTH resides in the first 20 N-terminal amino acids, the first 13 of which are identical to alpha-MSH [, ]. The function of this region is not known, though it is found near the centre of these proteins.
Probab=27.95 E-value=23 Score=20.38 Aligned_cols=15 Identities=13% Similarity=-0.039 Sum_probs=11.1
Q ss_pred CeEEE-EEEecCCCCC
Q 030279 161 DQKWY-VYFLKWCSNP 175 (180)
Q Consensus 161 ~~~w~-i~~yp~g~~~ 175 (180)
|+++| |.|||+|...
T Consensus 14 g~KRRPvKVypn~~Ee 29 (39)
T PF00976_consen 14 GRKRRPVKVYPNGAEE 29 (39)
T ss_pred CcccCcceeCCCCccc
Confidence 56666 8899998743
No 41
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=27.25 E-value=36 Score=17.81 Aligned_cols=11 Identities=0% Similarity=-0.121 Sum_probs=8.5
Q ss_pred EEEEEecCCCC
Q 030279 164 WYVYFLKWCSN 174 (180)
Q Consensus 164 w~i~~yp~g~~ 174 (180)
-.+++||.|-.
T Consensus 5 r~~L~yp~GA~ 15 (25)
T PF06943_consen 5 RTLLMYPRGAP 15 (25)
T ss_pred CceEEcCCCCC
Confidence 36889999963
No 42
>COG4680 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.61 E-value=59 Score=22.65 Aligned_cols=16 Identities=44% Similarity=0.771 Sum_probs=13.3
Q ss_pred ceeecCeEEEEEEeeC
Q 030279 45 EFDAGGYKWKLVVYPN 60 (180)
Q Consensus 45 ~F~vgG~~Wrl~~yP~ 60 (180)
.|.|||++-||.++-.
T Consensus 58 Vfdi~GN~yRLIvhv~ 73 (98)
T COG4680 58 VFDIGGNKYRLIVHVA 73 (98)
T ss_pred EEEcCCCEEEEEEEEE
Confidence 4899999999988753
No 43
>KOG4003 consensus Pyrazinamidase/nicotinamidase PNC1 [Defense mechanisms]
Probab=26.10 E-value=31 Score=27.24 Aligned_cols=56 Identities=23% Similarity=0.294 Sum_probs=33.8
Q ss_pred CCCCcccCceeeEEEecCCCcEEEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEE
Q 030279 1 MENDFVDQVAISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLA 76 (180)
Q Consensus 1 ~~~~~~~~~~~s~~~~~~~~~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~ 76 (180)
|.||||+.+.-.+...+... -|.-- ++...-..++|.+.+|-+.-- ..+|||+--.
T Consensus 9 ~qndfi~~~~~~~s~~E~~~-----~i~Pi------------~~lLq~~d~dw~~Vv~TKDwH---P~~HiSF~~~ 64 (223)
T KOG4003|consen 9 MQNDFISPLGSLTSVPEGEE-----LINPI------------SDLLQDADRDWHRVVVTKDWH---PSRHISFAKN 64 (223)
T ss_pred ccccccccccccccCCCchh-----hhccH------------HHHHHhcccccceEEEecccC---cccceehhhh
Confidence 78999987765553332211 11111 222355678999999987654 4678986443
Done!