Query 018085
Match_columns 361
No_of_seqs 327 out of 1071
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 06:01:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018085.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018085hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1554 COP9 signalosome, subu 100.0 3E-95 7E-100 682.2 23.3 342 2-360 5-346 (347)
2 cd08069 MPN_RPN11_CSN5 Mov34/M 100.0 1.1E-58 2.4E-63 443.7 26.5 262 52-324 1-267 (268)
3 cd08065 MPN_eIF3h Mpr1p, Pad1p 100.0 1E-42 2.2E-47 333.3 21.8 219 61-286 1-228 (266)
4 KOG1560 Translation initiation 100.0 6.1E-37 1.3E-41 288.0 13.2 222 57-285 9-248 (339)
5 cd08064 MPN_eIF3f Mpr1p, Pad1p 100.0 1.1E-31 2.3E-36 257.0 23.9 245 63-339 1-247 (265)
6 cd08067 MPN_2A_DUB Mov34/MPN/P 100.0 3.1E-31 6.7E-36 242.0 17.3 133 62-200 6-148 (187)
7 cd08058 MPN_euk_mb Mpr1p, Pad1 100.0 6.8E-29 1.5E-33 210.4 12.5 114 68-197 1-119 (119)
8 cd08062 MPN_RPN7_8 Mpr1p, Pad1 100.0 1.1E-27 2.4E-32 231.0 22.5 201 61-288 1-205 (280)
9 cd08068 MPN_BRCC36 Mov34/MPN/P 100.0 4.3E-28 9.3E-33 228.8 18.5 138 60-199 1-152 (244)
10 smart00232 JAB_MPN JAB/MPN dom 99.9 1.7E-26 3.6E-31 196.5 17.7 134 62-198 1-134 (135)
11 PF01398 JAB: JAB1/Mov34/MPN/P 99.9 4E-27 8.6E-32 197.2 11.4 112 59-172 2-114 (114)
12 cd08057 MPN_euk_non_mb Mpr1p, 99.9 2.2E-26 4.9E-31 203.9 15.9 134 63-199 1-137 (157)
13 KOG1555 26S proteasome regulat 99.9 1E-25 2.2E-30 217.5 14.8 192 60-256 30-236 (316)
14 PLN03246 26S proteasome regula 99.9 3.4E-24 7.4E-29 208.7 22.1 203 57-285 2-208 (303)
15 KOG2975 Translation initiation 99.9 7.4E-25 1.6E-29 205.3 15.2 199 60-288 20-224 (288)
16 cd08066 MPN_AMSH_like Mov34/MP 99.9 5.2E-24 1.1E-28 192.4 17.1 130 61-203 2-134 (173)
17 cd08063 MPN_CSN6 Mpr1p, Pad1p 99.9 1.9E-23 4.2E-28 202.3 20.8 200 62-287 2-208 (288)
18 cd07767 MPN Mpr1p, Pad1p N-ter 99.9 1.9E-22 4E-27 167.8 13.2 115 71-194 2-116 (116)
19 cd08070 MPN_like Mpr1p, Pad1p 99.8 2.2E-19 4.8E-24 153.9 14.1 119 68-198 2-120 (128)
20 KOG1556 26S proteasome regulat 99.8 5E-18 1.1E-22 158.2 13.6 168 58-252 6-179 (309)
21 COG1310 Predicted metal-depend 99.6 6.5E-15 1.4E-19 127.2 11.2 90 63-161 2-91 (134)
22 cd08072 MPN_archaeal Mov34/MPN 99.6 1.2E-14 2.5E-19 123.6 12.0 109 65-198 1-109 (117)
23 cd08073 MPN_NLPC_P60 Mpr1p, Pa 99.5 1.6E-13 3.4E-18 115.1 11.6 94 69-180 2-95 (108)
24 KOG2880 SMAD6 interacting prot 99.4 2E-13 4.3E-18 133.3 6.5 132 55-199 246-379 (424)
25 cd08060 MPN_UPF0172 Mov34/MPN/ 99.3 1.4E-11 2.9E-16 112.5 13.1 110 65-182 1-114 (182)
26 PF14464 Prok-JAB: Prokaryotic 99.3 7E-12 1.5E-16 102.7 9.4 93 67-180 2-96 (104)
27 cd08056 MPN_PRP8 Mpr1p, Pad1p 99.2 4.2E-10 9.1E-15 107.2 12.7 126 62-202 37-170 (252)
28 cd08059 MPN_prok_mb Mpr1p, Pad 99.0 2.7E-09 5.9E-14 87.6 10.6 91 69-180 2-92 (101)
29 TIGR02256 ICE_VC0181 integrati 99.0 9.6E-09 2.1E-13 89.2 12.1 108 71-179 3-113 (131)
30 TIGR03735 PRTRC_A PRTRC system 98.9 7.1E-09 1.5E-13 95.1 10.7 113 63-200 73-186 (192)
31 KOG3050 COP9 signalosome, subu 98.5 2.4E-07 5.2E-12 87.2 6.4 161 61-250 9-176 (299)
32 cd08061 MPN_NPL4 Mov34/MPN/PAD 98.3 2E-05 4.4E-10 76.4 15.6 137 57-200 7-161 (274)
33 PF03665 UPF0172: Uncharacteri 98.3 1.3E-05 2.9E-10 74.1 13.2 115 62-182 3-120 (196)
34 PF05021 NPL4: NPL4 family; I 97.4 0.0021 4.5E-08 63.5 12.4 108 86-200 2-144 (306)
35 KOG3289 Uncharacterized conser 97.4 0.003 6.4E-08 57.5 12.1 114 62-181 3-119 (199)
36 KOG1795 U5 snRNP spliceosome s 85.0 2.2 4.9E-05 49.1 6.9 110 80-202 2112-2225(2321)
37 KOG2834 Nuclear pore complex, 72.9 41 0.00089 35.3 11.1 132 60-199 174-341 (510)
38 cd08071 MPN_DUF2466 Mov34/MPN/ 46.8 1.7E+02 0.0037 24.4 9.8 25 138-162 59-83 (113)
39 COG1029 FwdB Formylmethanofura 45.1 66 0.0014 33.0 6.7 57 135-198 138-202 (429)
40 PF14220 DUF4329: Domain of un 36.6 30 0.00064 29.9 2.5 25 138-162 58-87 (123)
41 COG5178 PRP8 U5 snRNP spliceos 36.2 49 0.0011 38.7 4.6 110 80-203 2151-2266(2365)
42 PF15659 Toxin-JAB1: JAB-like 34.7 42 0.00091 30.4 3.3 27 136-163 113-139 (162)
43 PF14778 ODR4-like: Olfactory 33.8 57 0.0012 33.0 4.4 61 87-150 1-74 (362)
44 PF04002 RadC: RadC-like JAB d 26.3 4E+02 0.0086 22.5 9.2 24 139-162 65-88 (123)
45 PF06442 DHFR_2: R67 dihydrofo 26.2 34 0.00074 26.5 1.0 11 139-149 40-50 (78)
No 1
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=3e-95 Score=682.21 Aligned_cols=342 Identities=73% Similarity=1.133 Sum_probs=324.8
Q ss_pred ChhHHhhhhhhcccceecCCCCCCCCCCCCCCcccccCChHHhhHHHhcCCCCCCCCCeeEEEECHHHHHHHHHHHhcCC
Q 018085 2 DSSIAQKTWELENNIVSMETPPTNSTADTSASDAIFFYDEGAQTKFQQEKPWVNDPHYFKRVKISALALLKMVVHARSGG 81 (361)
Q Consensus 2 ~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~d~~~~~d~~~~~~~~~~~pw~~~~~~~~~V~Is~~vLlkIl~Ha~~~~ 81 (361)
++.+|+++||++|||+.+++. |.||+||.+.+.++..++||..||++|+.|+|++++|+||++||++|+
T Consensus 5 ~s~~~~k~we~en~~~~~~~~-----------deif~yd~~sq~~~~~~kpw~~Dp~~fk~vkISalAllKm~~hA~~Gg 73 (347)
T KOG1554|consen 5 SSYTAQKTWELENNIQSVESE-----------DEIFRYDQKSQRKIILEKPWSTDPHYFKHVKISALALLKMVMHARSGG 73 (347)
T ss_pred cccchhHHHHHhhhhccCccc-----------hhhhhcCHHHHHHHHhcCcccCCCchhhhhhhHHHHHHHHHHHHhcCC
Confidence 556899999999999999875 999999999999999999999999999999999999999999999999
Q ss_pred CceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCCceEEEEecCCCCCCccCHHhHH
Q 018085 82 TIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHSHPGYGCWLSGIDVS 161 (361)
Q Consensus 82 p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e~vVGWYHSHP~~~~~pS~~DV~ 161 (361)
+.||||+|+|++++++++|+|||++|++|||+|||++.+++|||.++.+.++.+||.+++||||||||+||||+|++||.
T Consensus 74 nlEiMGlm~Gkv~g~t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k~~gr~envVGWyHSHPgYgCWLSgIDVs 153 (347)
T KOG1554|consen 74 NLEIMGLMQGKVDGDTIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEAKNVGRLENVVGWYHSHPGYGCWLSGIDVS 153 (347)
T ss_pred CeEEEeeecccccCCeEEEEeccccccccccceechHHHHHHHHHHHHHHHHHhhhhhceeeeeecCCCCCccccCcchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCCcccccChhhhhhhCCccceeEEeeEEEecChh
Q 018085 162 TQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPISEYQTIPLNKIEDFGVHCKQYYSLDITYFKSSL 241 (361)
Q Consensus 162 tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p~~~~~~~~~~~e~~~ip~~ki~d~g~~~~~fyeLpV~i~~s~l 241 (361)
||..+|++++|||++||||.||++.|++.|+|||++|.+|+++.+++++|+.+|+.||+|||+||.+||+|+|++|+|.+
T Consensus 154 TQ~lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRTyp~gyk~~d~~~seyqtipl~kied~gvHck~yysl~isyfks~l 233 (347)
T KOG1554|consen 154 TQMLNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTYPKGYKPPDEPPSEYQTIPLNKIEDFGVHCKQYYSLEISYFKSSL 233 (347)
T ss_pred HHHHhhhhcCCeEEEEecCccccccCceeeceeecccCCCCCCCCCchhhhccchhhhhhcccceEEeeccchhhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhccccccccCCCcCccChHHHHHHHHHHHHHHHHHHHhcccCCCCCCCCCCCCCcchhhhHHHHHHhhHhHH
Q 018085 242 DCHLLDLLWNKYWVNTLSSSPLLGNGDYVAGQISDLAEKLEQAENQLSHSRYGPLIAPPPRRKEQEDSQLAKITRDSAKI 321 (361)
Q Consensus 242 ~~~~L~~L~~~~w~~~Ls~s~~l~n~~~l~~~i~dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 321 (361)
+.++|+.||++||+++|+++|+++|.+|+.+||.||++|+.+.+.++.++. ....++-.++.+|+|+++|++++
T Consensus 234 d~kll~~Lwnkywv~Tlsss~ll~N~dy~~~qi~d~~ekl~q~~~~l~~s~------~~~d~~~ed~~~l~k~~~Ds~~~ 307 (347)
T KOG1554|consen 234 DMKLLELLWNKYWVRTLSSSPLLKNIDYLNGQIRDLSEKLEQREDSLETSD------NTHDRKSEDENLLAKATRDSSKC 307 (347)
T ss_pred hHHHHHHHHhhhhhcccccccccccchhhcchhhhHHHHHHhhhhhcccCc------ccccccccchhhhhhhhhhhhhh
Confidence 999999999999999999999999999999999999999999999987651 11222224567799999999999
Q ss_pred HHHHHHhHHHHHHHHHhcCCCCCCCcCCCCCCCCCCCCC
Q 018085 322 TVEQVHGLMSQVIKDILFNSVRQSTKTHAEPSDPEPMIE 360 (361)
Q Consensus 322 ~~e~~~g~~~~~~k~~~f~~~~~~~~~~~~~~~~~~~~~ 360 (361)
..|+.||+|+|++|+.||+....+++...++..+.+|+.
T Consensus 308 ~~e~~~gl~s~vvkd~lf~~~~~~~k~~~~s~~~~~di~ 346 (347)
T KOG1554|consen 308 TNELIHGLMSQVVKDKLFNDNFHSSKRMNSSQERCHDIG 346 (347)
T ss_pred hhcchhHHHHHHHHHHHHHhhccccCCCCcCCCCCcccc
Confidence 999999999999999999998887788888888888764
No 2
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i
Probab=100.00 E-value=1.1e-58 Score=443.70 Aligned_cols=262 Identities=64% Similarity=0.987 Sum_probs=233.4
Q ss_pred CCCCCCCCeeEEEECHHHHHHHHHHHhcCCCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHH-
Q 018085 52 PWVNDPHYFKRVKISALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQ- 130 (361)
Q Consensus 52 pw~~~~~~~~~V~Is~~vLlkIl~Ha~~~~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~- 130 (361)
||+.+|++|++|+|++.|+++|++||+++.|.||||+|+|.+++++++|++|||+|+.++++++++.. +|+..|++
T Consensus 1 ~~~~~~~~~~~V~Is~~allkil~Ha~~~~p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~~---e~~~~m~~~ 77 (268)
T cd08069 1 PWKPDPDYFEKVYISSLALLKMLKHARAGGPIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQD---EFQEYMVQY 77 (268)
T ss_pred CCCCCCCcccEEEECHHHHHHHHHHHhccCCceEEEEEEeeecCCeEEEEEEEECCcCCCCCceeccH---HHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999998887754 45666666
Q ss_pred -HHHHhCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCC--CCCC
Q 018085 131 -TNKQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKP--PDEP 207 (361)
Q Consensus 131 -~~r~v~~~e~vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p~~~~~--~~~~ 207 (361)
+++++++++++||||||||++|||||++||++|..||++.+|+|+|||||.++..+|++.|+|||++|.++.+ +.+.
T Consensus 78 ~~~~~~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~~~~~~~~~~~~ 157 (268)
T cd08069 78 EMLKQTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIPPGYKPLEPRQT 157 (268)
T ss_pred HHHHHhCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEECccccccCcccC
Confidence 9999999999999999999999999999999999999999999999999999867999999999999999885 4445
Q ss_pred CCcccccChhhhhhhCCccceeEEeeEEEecChhHHHHHHHHhccccccccCCCcCccCh-HHHHHHHHHHHHHHHHHHH
Q 018085 208 ISEYQTIPLNKIEDFGVHCKQYYSLDITYFKSSLDCHLLDLLWNKYWVNTLSSSPLLGNG-DYVAGQISDLAEKLEQAEN 286 (361)
Q Consensus 208 ~~e~~~ip~~ki~d~g~~~~~fyeLpV~i~~s~l~~~~L~~L~~~~w~~~Ls~s~~l~n~-~~l~~~i~dl~~~~~~~~~ 286 (361)
.++++.+|.+++++++.++++||+|||+|++|.+++.+|..||++||+.+|+++++.+|. ++..++|.+|++++.+...
T Consensus 158 ~s~~~~~~~~~~~~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~~w~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 237 (268)
T cd08069 158 TSNIGHLPKPKIEDFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNKYWVNTLSLSPLLENSNEYTIKQILDLAEKLEKAEQ 237 (268)
T ss_pred ccccCccCcHHHHHhCchhcEEEEeeeEEecCHHHHHHHHHHHHHhHHHHhhCCchhhhhhHHHHHHHHHHHHHHHHHHh
Confidence 567789999999999999999999999999999999999999999999999999999998 9999999999999999887
Q ss_pred hcccCCCCCCCCCCCCCcchhhhHHHHHHhhHhHHHHH
Q 018085 287 QLSHSRYGPLIAPPPRRKEQEDSQLAKITRDSAKITVE 324 (361)
Q Consensus 287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 324 (361)
...+.... .. +.....++.|+ +|+.++++|
T Consensus 238 ~~~~~~~~------~~-~~~~~~~~~~~-~~~~~~~~~ 267 (268)
T cd08069 238 QEERLTGE------EL-DIANVGKLDKA-RDSSKIHLE 267 (268)
T ss_pred hhhccChh------hh-cccchhhhhhc-cccchhhhc
Confidence 76543100 00 11245566666 888888776
No 3
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=100.00 E-value=1e-42 Score=333.27 Aligned_cols=219 Identities=21% Similarity=0.307 Sum_probs=190.4
Q ss_pred eEEEECHHHHHHHHHHHhcCCCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCCc
Q 018085 61 KRVKISALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLEN 140 (361)
Q Consensus 61 ~~V~Is~~vLlkIl~Ha~~~~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e~ 140 (361)
++|+|++.|+++|++||+++.|.+|||+|||...+++++||||||+|+.++++...+..+..+|+.+|+++++++|.+++
T Consensus 1 ~~V~I~~~vllkIv~H~~~~~p~~v~G~LLG~~~~~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~e~ 80 (266)
T cd08065 1 TSVQIDGLVVLKIIKHCKEELPELVQGQLLGLDVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVDHN 80 (266)
T ss_pred CEEEEeHHHHHHHHHHHhcCCCcEEEEEEeeeEcCCEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCCCc
Confidence 47999999999999999999999999999999999999999999999987765533344456899999999999999999
Q ss_pred eEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCCcccccChhhhh
Q 018085 141 AVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPISEYQTIPLNKIE 220 (361)
Q Consensus 141 vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p~~~~~~~~~~~e~~~ip~~ki~ 220 (361)
+|||||||| +|+|.+..+|++|+.||...+++|+||+||.++ ..|++.++|||+.|.+....++ ..+..+.++
T Consensus 81 iVGWY~S~p-~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s-~~g~l~lkAyrl~~~~~~~~~~-----~~~~~~~l~ 153 (266)
T cd08065 81 HVGWYQSTY-LGSFFTRDLIETQYNYQEAIEESVVLVYDPSKT-SQGSLSLKAYRLSEKFMELYKE-----GKFSTESLR 153 (266)
T ss_pred EEEeEeecC-CCCcCCHHHHHHHHHHhccCCCCEEEEECCCcc-cccceeeEEEEEcHHHHHHhhc-----CCcCHHHHH
Confidence 999999999 999999999999999998888999999999985 3788999999999876432111 234445666
Q ss_pred hhC-CccceeEEeeEEEecChhHHHHHHHHh-------ccccccccCCCcCc-cChHHHHHHHHHHHHHHHHHHH
Q 018085 221 DFG-VHCKQYYSLDITYFKSSLDCHLLDLLW-------NKYWVNTLSSSPLL-GNGDYVAGQISDLAEKLEQAEN 286 (361)
Q Consensus 221 d~g-~~~~~fyeLpV~i~~s~l~~~~L~~L~-------~~~w~~~Ls~s~~l-~n~~~l~~~i~dl~~~~~~~~~ 286 (361)
+.+ .+.++|+||||+|+++.|++.+|..|. ..|..++|+..++| +|++.++++||+|++++.++..
T Consensus 154 ~~~~~~~~if~eiPv~i~n~~l~~~~L~~l~~~~~~~~~~~~~l~l~~~~~le~~l~~l~~~id~l~~e~~~~~~ 228 (266)
T cd08065 154 EANLTFSNIFEEIPVVIRNSHLVNALLSELEEDSPSSQSDFDRLDLSTNSFLEKNLELLMESVDELSQEQGKFNY 228 (266)
T ss_pred HhcCchhcEEEEEEEEEEchHHHHHHHHhcccCCCcccCCcccccccCchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666 478999999999999999999999995 35778999999988 9999999999999999887663
No 4
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.1e-37 Score=287.96 Aligned_cols=222 Identities=21% Similarity=0.282 Sum_probs=188.1
Q ss_pred CCCeeEEEECHHHHHHHHHHHhcCCCc--eeEEEeceeecCCeEEEEEEEeCCCcc--CCccccc-ccCh--HHHHHHHH
Q 018085 57 PHYFKRVKISALALLKMVVHARSGGTI--EVMGLMQGKTDGDAIIVMDAFALPVEG--TETRVNA-QADA--YEYMVDYS 129 (361)
Q Consensus 57 ~~~~~~V~Is~~vLlkIl~Ha~~~~p~--EV~GlLlG~~~~~tl~Vtd~F~lP~~~--te~rv~~-~~e~--~eY~~~ml 129 (361)
..++++|.|++++++||++||+++.+. -+.|.|+|.+.+++++||||||+|... .++.++. +.+. ..||.+|+
T Consensus 9 ~p~vk~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~Glvvd~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~ml 88 (339)
T KOG1560|consen 9 SPPVKRVELDSLVVMKIIKHCREEFPNGDGTQGVLLGLVVDGRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLAML 88 (339)
T ss_pred CCccceeeehhHHHHHHHHHHHhhcCCcchhhheeeeeeecceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHHHH
Confidence 347999999999999999999987664 677999999999999999999999732 2333333 2222 36899999
Q ss_pred HHHHHhCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCC
Q 018085 130 QTNKQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPIS 209 (361)
Q Consensus 130 ~~~r~v~~~e~vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p~~~~~~~~~~~ 209 (361)
|.+|.+|.+..+||||+||. +|.++|...+++|+.||.+.|+.|++|+||.+|. +|.+.+||||++|+....-++
T Consensus 89 rrlr~vnid~~hVGwYqs~~-vgs~lS~~lveSqy~YQ~a~pesVvliYD~~kss-qG~L~lrAyrLTp~am~~~ke--- 163 (339)
T KOG1560|consen 89 RRLRYVNIDHLHVGWYQSAY-VGSFLSPALVESQYAYQKAIPESVVLIYDPIKSS-QGTLSLRAYRLTPEAMAAHKE--- 163 (339)
T ss_pred HHhhhcCccceeeeeeeeeh-hccccCHHHHHHHHHHHhcCCccEEEEecccccc-CceEEeehhhcCHHHHHHHhc---
Confidence 99999999999999999999 8999999999999999999999999999999985 999999999999976322111
Q ss_pred cccccChhhhhhhCC-ccceeEEeeEEEecChhHHHHHHHHh-------cc--ccccccCCCcCc-cChHHHHHHHHHHH
Q 018085 210 EYQTIPLNKIEDFGV-HCKQYYSLDITYFKSSLDCHLLDLLW-------NK--YWVNTLSSSPLL-GNGDYVAGQISDLA 278 (361)
Q Consensus 210 e~~~ip~~ki~d~g~-~~~~fyeLpV~i~~s~l~~~~L~~L~-------~~--~w~~~Ls~s~~l-~n~~~l~~~i~dl~ 278 (361)
..+..+.++..|+ +.++|.||||.|+||+|.+.++.+|. ++ +-..+|++...+ +|++.|++.+|+|.
T Consensus 164 --kdwtpealk~~nltyenmfeElPIVIknS~L~nvlmseLs~~e~c~sdk~~~~~fdlgs~t~leknir~lme~vDEl~ 241 (339)
T KOG1560|consen 164 --KDWTPEALKSANLTYENMFEELPIVIKNSHLANVLMSELSEPEDCESDKPLHSNFDLGSGTRLEKNIRLLMERVDELH 241 (339)
T ss_pred --CCCCHHHHHhcCCCHHHHHhhcCeeeeccHHHHHHHHhccccccccccccccccccccchhhHHHHHHHHHHHHHHHH
Confidence 3577788888884 89999999999999999999999996 12 345677777766 99999999999999
Q ss_pred HHHHHHH
Q 018085 279 EKLEQAE 285 (361)
Q Consensus 279 ~~~~~~~ 285 (361)
+++.++.
T Consensus 242 qe~~~l~ 248 (339)
T KOG1560|consen 242 QEIVNLN 248 (339)
T ss_pred HHHHHHH
Confidence 9886554
No 5
>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f. Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and ap
Probab=100.00 E-value=1.1e-31 Score=257.00 Aligned_cols=245 Identities=17% Similarity=0.279 Sum_probs=195.2
Q ss_pred EEECHHHHHHHHHHHhc--CCCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCCc
Q 018085 63 VKISALALLKMVVHARS--GGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLEN 140 (361)
Q Consensus 63 V~Is~~vLlkIl~Ha~~--~~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e~ 140 (361)
|+|+|+|+++|++|+.+ ..+.+|+|+|||...+++++|||||++|+..+++++..+ .+|+.+|+++++++++++.
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~d---~~y~~~m~~~~kkv~~~~~ 77 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNESEDQVAVD---MEYHRTMYELHQKVNPKEV 77 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCCEEEEEeCeecceeCCCCeEEEc---HHHHHHHHHHHHHhCCCCc
Confidence 68999999999999965 678999999999999999999999999998777665543 4799999999999999999
Q ss_pred eEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCCcccccChhhhh
Q 018085 141 AVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPISEYQTIPLNKIE 220 (361)
Q Consensus 141 vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p~~~~~~~~~~~e~~~ip~~ki~ 220 (361)
+||||||+|... ++...|+.|+.+|...+++|+|++||..+ .+++.++||++.+.+....
T Consensus 78 vVGWY~tg~~~~--~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~--~~~l~i~ay~~~~~~~~~~---------------- 137 (265)
T cd08064 78 IVGWYATGSEIT--EHSALIHDYYSRECTSYNPIHLTVDTSLD--DGKMSIKAYVSSPLGVPGK---------------- 137 (265)
T ss_pred EEeeeeCCCCCC--ccHHHHHHHHHhhCCCCCCEEEEEeCCCC--CCCcceEEEEEEecccCCC----------------
Confidence 999999999533 34555666666554434779999999875 4589999999998653211
Q ss_pred hhCCccceeEEeeEEEecChhHHHHHHHHhccccccccCCCcCccChHHHHHHHHHHHHHHHHHHHhcccCCCCCCCCCC
Q 018085 221 DFGVHCKQYYSLDITYFKSSLDCHLLDLLWNKYWVNTLSSSPLLGNGDYVAGQISDLAEKLEQAENQLSHSRYGPLIAPP 300 (361)
Q Consensus 221 d~g~~~~~fyeLpV~i~~s~l~~~~L~~L~~~~w~~~Ls~s~~l~n~~~l~~~i~dl~~~~~~~~~~~~~~~~~~~~~~~ 300 (361)
....+|.+||++|.++..|+..++.|++..|..+ .+.++.++++++..++..|..+++++..-+..-..|.. +.
T Consensus 138 ---~~~~~F~~ip~~i~~~eaE~i~v~~l~~~~~~~~-~~~~~~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~--~~ 211 (265)
T cd08064 138 ---TLGSMFVPIPLELLYSEAERVALDLLAKTLASPS-RSAPLTSDLEQLEASLEKLQEMLDRVLRYVEDVLAGKV--KA 211 (265)
T ss_pred ---CcceEEEEcceeeecCcHHHHHHHHHHhhccCCc-ccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC--CC
Confidence 2457999999999999999999999999999887 55566699999999999999999888766643211110 00
Q ss_pred CCCcchhhhHHHHHHhhHhHHHHHHHHhHHHHHHHHHhc
Q 018085 301 PRRKEQEDSQLAKITRDSAKITVEQVHGLMSQVIKDILF 339 (361)
Q Consensus 301 ~~~~~~~~~~~~~~~~~~~~~~~e~~~g~~~~~~k~~~f 339 (361)
..+-...|.+++...-++..|+-.+.+...+++.|+
T Consensus 212 ---d~~i~r~l~~~~~~lp~~~~~~f~~~~~~~~~D~lm 247 (265)
T cd08064 212 ---DNAIGRYLMDALTSVPKLDPEEFEKMFNSSLQDLLM 247 (265)
T ss_pred ---CHHHHHHHHHHHhhCCCCCHHHHHHHHHhhcchHHH
Confidence 112345677788878888888888888888888776
No 6
>cd08067 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase. This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it p
Probab=99.97 E-value=3.1e-31 Score=242.01 Aligned_cols=133 Identities=26% Similarity=0.364 Sum_probs=115.2
Q ss_pred EEEECHHHHHHHHHHHhcCCCceeEEEeceeecC--CeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCC
Q 018085 62 RVKISALALLKMVVHARSGGTIEVMGLMQGKTDG--DAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLE 139 (361)
Q Consensus 62 ~V~Is~~vLlkIl~Ha~~~~p~EV~GlLlG~~~~--~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e 139 (361)
+|+|++.||++|++||+.+. .||||+|+|..++ ..++|+++||+|+..+++++++ ++ +++.+|++.+++ +++
T Consensus 6 ~V~Is~~all~m~~Ha~~~~-~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e~--dp-~~q~e~~~~l~~--~gl 79 (187)
T cd08067 6 KVTVSSNALLLMDFHCHLTT-SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEM--DP-VSETEIRESLES--RGL 79 (187)
T ss_pred EEEECHHHHHHHHHHhcCCC-cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCccccc--CH-HHHHHHHHHHHH--cCC
Confidence 79999999999999999987 9999999999764 5799999999999777666665 33 568889999986 457
Q ss_pred ceEEEEecCCCCCCccCHHhHHHHHhhhhcCC-------CeEEEEEcCCCCcc-CCeeeEEEEEEccCC
Q 018085 140 NAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQE-------PFLAVVIDPTRTVS-AGKVEIGAFRTYPEG 200 (361)
Q Consensus 140 ~vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~-------p~V~LIvDP~~t~~-~Gk~~ikAFRl~p~~ 200 (361)
++||||||||.++|+||.+||++|+.||.+.+ |||+|||||..+.. .....|+||++.|+.
T Consensus 80 ~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~~ 148 (187)
T cd08067 80 SVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPPP 148 (187)
T ss_pred EEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECCC
Confidence 99999999999999999999999999998754 89999999987543 334789999999854
No 7
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=99.96 E-value=6.8e-29 Score=210.39 Aligned_cols=114 Identities=39% Similarity=0.548 Sum_probs=96.7
Q ss_pred HHHHHHHHHHhcCCCceeEEEeceeec-----CCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCCceE
Q 018085 68 LALLKMVVHARSGGTIEVMGLMQGKTD-----GDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAV 142 (361)
Q Consensus 68 ~vLlkIl~Ha~~~~p~EV~GlLlG~~~-----~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e~vV 142 (361)
.|+++|++||+++.|.||||+|+|... ..+++|+++|+.|... ++.+ .|....+..++++++|
T Consensus 1 ~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~---------~~~~---~~~~~~~~~~~g~~~v 68 (119)
T cd08058 1 DALLKMLQHAESNTGIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSC---------TGEN---VEELFNVQTGRPLLVV 68 (119)
T ss_pred CHHHHHHHHhcCCCCeEEEEEeeeEEecCccceeEEEEeecCCCCCCc---------hhHH---HHHHHHHHhCCCCeEE
Confidence 379999999999999999999999976 3457999999988632 1222 3344455678999999
Q ss_pred EEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEc
Q 018085 143 GWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTY 197 (361)
Q Consensus 143 GWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~ 197 (361)
|||||||++++|||..||++|+.||.+.+++++||+||.++ ++++||||++
T Consensus 69 G~YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~----~~~~~a~rl~ 119 (119)
T cd08058 69 GWYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHR----NKDTGIFRLT 119 (119)
T ss_pred EEEecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCC----CcccceEEeC
Confidence 99999999999999999999999999999999999999763 6789999984
No 8
>cd08062 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8. This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural.
Probab=99.96 E-value=1.1e-27 Score=230.99 Aligned_cols=201 Identities=21% Similarity=0.268 Sum_probs=160.1
Q ss_pred eEEEECHHHHHHHHHHHhc---CCCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCC
Q 018085 61 KRVKISALALLKMVVHARS---GGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGR 137 (361)
Q Consensus 61 ~~V~Is~~vLlkIl~Ha~~---~~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~ 137 (361)
++|.|+|+||++|++|+.+ +.+.+|+|+|||...+++++|||||++|.+.++++.+...-..+|+.+|+++++++++
T Consensus 1 ~~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~~~~~~veItnsF~~p~~~~~~~~~~~~~d~~y~~~m~~~~kkv~~ 80 (280)
T cd08062 1 KKVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWKKGVLDVTNSFAVPFEEDEKDPSVWFLDHNYLENMYGMFKKVNA 80 (280)
T ss_pred CeEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEEEeCCEEEEEEeeecCccCCCCCcchhhhhHHHHHHHHHHHHHhCC
Confidence 4799999999999999965 3478999999999999999999999999987666543222235899999999999999
Q ss_pred CCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCCcccccChh
Q 018085 138 LENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPISEYQTIPLN 217 (361)
Q Consensus 138 ~e~vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p~~~~~~~~~~~e~~~ip~~ 217 (361)
++.+||||||||+ ++..|+..|..|+++.+++|+|++||... .+++.++||...+.+...
T Consensus 81 ~e~vVGWY~tg~~----~~~~d~~ih~~~~~~~~~pv~l~vd~~~~--~~~lpi~aY~s~~~~~~~-------------- 140 (280)
T cd08062 81 KEKIVGWYSTGPK----LRPNDLDINELFRRYCPNPVLVIIDVRPK--DLGLPTEAYIAVEEVHDD-------------- 140 (280)
T ss_pred CCCeEEEecCCCC----CCcchHHHHHHHHHhCCCCEEEEEecCCC--CCCCceEEEEEeeeccCC--------------
Confidence 9999999999997 45567788888999988999999999763 567999999988755321
Q ss_pred hhhhhCC-ccceeEEeeEEEecChhHHHHHHHHhccccccccCCCcCccChHHHHHHHHHHHHHHHHHHHhc
Q 018085 218 KIEDFGV-HCKQYYSLDITYFKSSLDCHLLDLLWNKYWVNTLSSSPLLGNGDYVAGQISDLAEKLEQAENQL 288 (361)
Q Consensus 218 ki~d~g~-~~~~fyeLpV~i~~s~l~~~~L~~L~~~~w~~~Ls~s~~l~n~~~l~~~i~dl~~~~~~~~~~~ 288 (361)
|. .+..|.+||.++.....|+..++.|...- .+-+.+.+...+......|..|..+++.+..=+
T Consensus 141 -----g~~~~~~F~~vp~~i~~~eaE~igve~l~r~~--~~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Yl 205 (280)
T cd08062 141 -----GTPTSKTFVHVPSEIGAEEAEEVGVEHLLRDI--KDVTVSTLSTRVTNKLNSLKGLQSKLKEIKDYL 205 (280)
T ss_pred -----CCcceeEEEEcceEeeccchHHHHHHHHHhhc--cCcccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11 35789999999999999999999997531 122334444577777777777777776655433
No 9
>cd08068 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex. BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-contai
Probab=99.96 E-value=4.3e-28 Score=228.83 Aligned_cols=138 Identities=27% Similarity=0.456 Sum_probs=109.8
Q ss_pred eeEEEECHHHHHHHHHHHhcCCCceeEEEeceeecC-------CeEEEEEEEeCCCc-cCCcccccccChHHH---HHHH
Q 018085 60 FKRVKISALALLKMVVHARSGGTIEVMGLMQGKTDG-------DAIIVMDAFALPVE-GTETRVNAQADAYEY---MVDY 128 (361)
Q Consensus 60 ~~~V~Is~~vLlkIl~Ha~~~~p~EV~GlLlG~~~~-------~tl~Vtd~F~lP~~-~te~rv~~~~e~~eY---~~~m 128 (361)
+++|+|++.++.+|+.||++++|+||||+|+|..++ ..+.|...++.++. .+.+++++ ++.++ +.++
T Consensus 1 l~~V~Is~~~l~~il~HA~~~~P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~ei--dPee~~~a~~ea 78 (244)
T cd08068 1 LSKVHLSADVYLVCLTHALSTEKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVEI--SPEQLSAASTEA 78 (244)
T ss_pred CcEEEECHHHHHHHHHHHHhCCCcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEEe--CHHHHHHHHHHH
Confidence 468999999999999999999999999999999853 23444444444442 24456655 44443 2344
Q ss_pred HHHHHHhCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCC---CccCCeeeEEEEEEccC
Q 018085 129 SQTNKQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTR---TVSAGKVEIGAFRTYPE 199 (361)
Q Consensus 129 l~~~r~v~~~e~vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~---t~~~Gk~~ikAFRl~p~ 199 (361)
-++.+..|+++.+||||||||+++||||.+|+.+|..||.+.+++++||+++.. +...|++.++|||+.+.
T Consensus 79 ~~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~g 152 (244)
T cd08068 79 ERLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQG 152 (244)
T ss_pred HHHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecCC
Confidence 555667889999999999999999999999999999999999999999998643 33468899999999884
No 10
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=99.95 E-value=1.7e-26 Score=196.51 Aligned_cols=134 Identities=31% Similarity=0.480 Sum_probs=119.6
Q ss_pred EEEECHHHHHHHHHHHhcCCCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCCce
Q 018085 62 RVKISALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENA 141 (361)
Q Consensus 62 ~V~Is~~vLlkIl~Ha~~~~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e~v 141 (361)
.|+|++.++++|++||.+..|.|+||+|+|+..+++++|+++|++|+....+++.. ...+|+.+|.+..++++.++.+
T Consensus 1 ~v~i~~~v~~~i~~h~~~~~p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 78 (135)
T smart00232 1 EVKVHPLVPLNILKHAIRDGPEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQE--YDEDYSHLMDEELKKVNKDLEI 78 (135)
T ss_pred CEEEcHHHHHHHHHHHhcCCCcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchhh--hhhhHHHHHHHHHHhhCCCceE
Confidence 37899999999999999999999999999999988999999999998765554311 2346788888888899999999
Q ss_pred EEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEcc
Q 018085 142 VGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYP 198 (361)
Q Consensus 142 VGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p 198 (361)
||||||||..+++||..|+.+|..+|.....++++++||.++. .|++.++||++.+
T Consensus 79 vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~-~g~~~~~af~~~~ 134 (135)
T smart00232 79 VGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSF-QGRLSLRAFRLTP 134 (135)
T ss_pred EEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccc-cCcEEEEEEEecC
Confidence 9999999999999999999999999999999999999999975 5999999999875
No 11
>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain [] and PAD-1-like domain []. It has been shown that this domain occurs in prokaryotes []. Mov34 proteins act as the regulatory subunit of the 26 proteasome, which is involved in the ATP-dependent degradation of ubiquitinated proteins. The function of this domain is unclear, but it is found in the N terminus of the proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. A number of the proteins associated with this family belong to MEROPS peptidase family M67 (clan M-). This includes the Poh1 peptidase of Saccharomyces cerevisiae (Baker's yeast) which is a component of the 19S proteasome regulatory particle.; GO: 0005515 protein binding; PDB: 2ZNV_D 2ZNR_A 4E0Q_A 2P87_A 2P8R_A 2O96_B 2O95_A 3RZU_F 3RZV_A.
Probab=99.94 E-value=4e-27 Score=197.17 Aligned_cols=112 Identities=30% Similarity=0.558 Sum_probs=96.8
Q ss_pred CeeEEEECHHHHHHHHHHHhcCCCceeEEEeceeecCC-eEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCC
Q 018085 59 YFKRVKISALALLKMVVHARSGGTIEVMGLMQGKTDGD-AIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGR 137 (361)
Q Consensus 59 ~~~~V~Is~~vLlkIl~Ha~~~~p~EV~GlLlG~~~~~-tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~ 137 (361)
.+++|+|+|+|+++|++||.+..+.||||+|+|..+++ +++|++||++|+.++++.+..... ++..+|+++++++++
T Consensus 2 s~~~V~i~p~vll~i~~h~~r~~~~~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~~~~--~~~~~~~~~~~~~~~ 79 (114)
T PF01398_consen 2 SVQTVQIHPLVLLKIIDHATRSSPNEVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDMDDE--DFQKKMIELLKKVNP 79 (114)
T ss_dssp SCEEEEEEHHHHHHHHHHHHHHHCTEEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEEECC--HHHHHHHHHHHHCST
T ss_pred CcEEEEECHHHHHHHHHHHhcCCCCEEEEEEEEEecCceEEEEEEEEEeeEecCccccccchh--hHHHHHHhhhccccc
Confidence 57899999999999999999877889999999999999 999999999999877766544332 344788999999988
Q ss_pred CCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCC
Q 018085 138 LENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEP 172 (361)
Q Consensus 138 ~e~vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p 172 (361)
++.+||||||||.++||||..||++|..||++.++
T Consensus 80 ~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 80 NLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp TSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred cceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence 99999999999999999999999999999998753
No 12
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=99.94 E-value=2.2e-26 Score=203.93 Aligned_cols=134 Identities=27% Similarity=0.397 Sum_probs=113.5
Q ss_pred EEECHHHHHHHHHHHhcCC--CceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCCc
Q 018085 63 VKISALALLKMVVHARSGG--TIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLEN 140 (361)
Q Consensus 63 V~Is~~vLlkIl~Ha~~~~--p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e~ 140 (361)
|+|+|+|+++|++|+.+.. +.+|+|+|+|...+++++|+|||++|.+.+++.... ..+|+.+|+++++++++++.
T Consensus 1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~~~~~~veV~nsF~lp~~~~~~~~~~---d~~y~~~m~~~~~~v~~~~~ 77 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGDKIEVTNSFELPFDEEEESIFI---DTEYLEKRYNLHKKVYPQEK 77 (157)
T ss_pred CEEccHHHhhHHHHHHhccCCCCeEEEEEEeEEeCCEEEEEEeEEccccCCCcchhh---hHHHHHHHHHHHHHhCCCCC
Confidence 6899999999999997766 899999999999999999999999999776654322 35899999999999999999
Q ss_pred eEEEEecCCCCCCccCHHhHHHHHhhhhc-CCCeEEEEEcCCCCccCCeeeEEEEEEccC
Q 018085 141 AVGWYHSHPGYGCWLSGIDVSTQMLNQQF-QEPFLAVVIDPTRTVSAGKVEIGAFRTYPE 199 (361)
Q Consensus 141 vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~-~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p~ 199 (361)
+|||||+|+..+++++..|...+..|... .+++|+|++||.++...|++.|+|||+.+.
T Consensus 78 vVGWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~ 137 (157)
T cd08057 78 IVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQR 137 (157)
T ss_pred EEEEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEecC
Confidence 99999999987767777666655555443 678899999998744478899999999863
No 13
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=1e-25 Score=217.47 Aligned_cols=192 Identities=38% Similarity=0.581 Sum_probs=152.3
Q ss_pred eeEEEECHHHHHHHHHHHhcCCCce-eEEEe-ce---e-ecCCeEEEEEEEeCCCccCCcc--cccccChHHHHHHHHHH
Q 018085 60 FKRVKISALALLKMVVHARSGGTIE-VMGLM-QG---K-TDGDAIIVMDAFALPVEGTETR--VNAQADAYEYMVDYSQT 131 (361)
Q Consensus 60 ~~~V~Is~~vLlkIl~Ha~~~~p~E-V~GlL-lG---~-~~~~tl~Vtd~F~lP~~~te~r--v~~~~e~~eY~~~ml~~ 131 (361)
-.+|.|+.+++++|++|.|.+.|.| |||+| +| . ++..++.|.+.|+.|..++.-. +++. ++ -|+.+|+++
T Consensus 30 ~e~v~i~slall~m~rh~r~~~p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg~~is~~~e~~-d~-V~q~q~~~~ 107 (316)
T KOG1555|consen 30 KETVYISSLALLKMLRHDRAGSPEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAV-DP-VFQTQMMDL 107 (316)
T ss_pred cceeeeehhhhhhcccccccCCchhhccceeecccccceeeecceeeeeeeccccccceecccchhc-cH-HHHHHHHHH
Confidence 4589999999999999999999999 99999 99 3 3567889999999999876543 3222 22 478999999
Q ss_pred HHHhCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCC-CCCCCCCCCc
Q 018085 132 NKQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEG-YKPPDEPISE 210 (361)
Q Consensus 132 ~r~v~~~e~vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p~~-~~~~~~~~~e 210 (361)
++..|+.+.|||||||||+++||||..||.||+.||...+..++.++||..+. .|++.+.|||+.... ..++.+++..
T Consensus 108 l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~-~g~vv~d~f~~In~~~~~~~~eprqt 186 (316)
T KOG1555|consen 108 LKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSP-YGKVVPDAFSSINPQWISPGGEPRQT 186 (316)
T ss_pred HHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCC-CCCccCChhhhcCcccccCCCCCccc
Confidence 99999999999999999999999999999999999999899999999999876 888888999985432 2222221111
Q ss_pred c-cccChhh----h-hhhCCccceeEEeeEEEecChhHHHHHHHHhcccccc
Q 018085 211 Y-QTIPLNK----I-EDFGVHCKQYYSLDITYFKSSLDCHLLDLLWNKYWVN 256 (361)
Q Consensus 211 ~-~~ip~~k----i-~d~g~~~~~fyeLpV~i~~s~l~~~~L~~L~~~~w~~ 256 (361)
. ...+.++ . .-+|. +.||.++|.++..++++.++..+..+.|..
T Consensus 187 ts~~~~m~~~~s~q~~~~g~--n~y~~~ei~~~v~~~~~~~~~nv~~~s~~~ 236 (316)
T KOG1555|consen 187 TSNGGHMDMQESLQEDIHGL--NRYYRIEIPLHVLPYEQLMLLNVPLKSWKS 236 (316)
T ss_pred cccccccccchhHHhHhhcc--CceEEEEeeEEechhhhhchhccchhhhhh
Confidence 0 0012211 1 22443 389999999999999999999998777765
No 14
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=99.93 E-value=3.4e-24 Score=208.74 Aligned_cols=203 Identities=18% Similarity=0.207 Sum_probs=154.2
Q ss_pred CCCeeEEEECHHHHHHHHHHHhcCC---CceeEEEeceeecCCeEEEEEEEeCCCccCCcccc-cccChHHHHHHHHHHH
Q 018085 57 PHYFKRVKISALALLKMVVHARSGG---TIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVN-AQADAYEYMVDYSQTN 132 (361)
Q Consensus 57 ~~~~~~V~Is~~vLlkIl~Ha~~~~---p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~-~~~e~~eY~~~ml~~~ 132 (361)
|.++.+|.|+|+||++|++||.+.. +.+|+|.|||...++.++|||||++|....++.-. ...| .+|+.+|++++
T Consensus 2 ~~~~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~~~~~~ieItnsF~~p~~e~~~~~~~~~~D-~~y~~~m~~~~ 80 (303)
T PLN03246 2 PRGIEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFRGRVDVTNSFAVPFEEDDKDPSIWFLD-HNYLESMFGMF 80 (303)
T ss_pred CCCCcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEeeecCCEEEEEeccccCcccCCCCccceeec-HHHHHHHHHHH
Confidence 7889999999999999999997643 56799999999999999999999999864433211 1112 58999999999
Q ss_pred HHhCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCCccc
Q 018085 133 KQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPISEYQ 212 (361)
Q Consensus 133 r~v~~~e~vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p~~~~~~~~~~~e~~ 212 (361)
+++++++.+||||+|.|... ..|+..|..|.++.+.+|+|++|+... .+++.++||...+.+...+.
T Consensus 81 k~V~~~~~vVGWY~tg~~i~----~~d~~IH~~~~~~~~~Pv~L~vD~~~~--~~~lpi~aY~s~~~~~~~~~------- 147 (303)
T PLN03246 81 KRINAKEHVVGWYSTGPKLR----ENDLDIHELFNDYVPNPVLVIIDVQPK--ELGIPTKAYYAVEEVKENAT------- 147 (303)
T ss_pred HHhCCCCcEEeeecCCCCCC----cchHHHHHHHHhhCCCCeEEEEecCCC--CCCCceEEEEEEEeccCCCC-------
Confidence 99999999999999999743 345666777888888899999998653 56799999998775532110
Q ss_pred ccChhhhhhhCCccceeEEeeEEEecChhHHHHHHHHhccccccccCCCcCccChHHHHHHHHHHHHHHHHHH
Q 018085 213 TIPLNKIEDFGVHCKQYYSLDITYFKSSLDCHLLDLLWNKYWVNTLSSSPLLGNGDYVAGQISDLAEKLEQAE 285 (361)
Q Consensus 213 ~ip~~ki~d~g~~~~~fyeLpV~i~~s~l~~~~L~~L~~~~w~~~Ls~s~~l~n~~~l~~~i~dl~~~~~~~~ 285 (361)
+..+..|.+||.++.....++..++.|...-- +=+.+.+...+......|..|..+++.+.
T Consensus 148 ----------~~~~~~F~~vp~~i~~~EaE~Igve~l~r~~~--~~~~s~l~~~l~~~~~al~~L~~rl~~i~ 208 (303)
T PLN03246 148 ----------QKSQKVFVHVPSEIGAHEAEEIGVEHLLRDVK--DTTVSTLATEVTGKLTALKGLDARLREIR 208 (303)
T ss_pred ----------cccccEEEECCeeeeecCHHHHHHHHHHhccc--CCccchhHHHHHHHHHHHHHHHHHHHHHH
Confidence 11347899999999999999999999975322 11223333456666666666666665544
No 15
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=7.4e-25 Score=205.27 Aligned_cols=199 Identities=19% Similarity=0.224 Sum_probs=158.8
Q ss_pred eeEEEECHHHHHHHHHHHh--cCCCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCC
Q 018085 60 FKRVKISALALLKMVVHAR--SGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGR 137 (361)
Q Consensus 60 ~~~V~Is~~vLlkIl~Ha~--~~~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~ 137 (361)
--+|+|+|.|+++|++|.. ..+.++|||.|||.++++.++|||||++|+.+.+++++.++ +|..+|+++++++++
T Consensus 20 ~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g~ieitNCFaVPhnEssdqvevdm---~y~~~M~~l~~k~np 96 (288)
T KOG2975|consen 20 NLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKGSVEVTNCFAVPHNESSDQVEVDM---EYAKNMYELHKKVNP 96 (288)
T ss_pred CceEEEcceEEeEeehhhhcCCccchhhhhheeecccCCeEEEEEeeeccCccccccceeeH---HHHHHHHHHhcccCC
Confidence 3479999999999999884 35789999999999999999999999999999889988866 799999999999999
Q ss_pred CCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCCcccccChh
Q 018085 138 LENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPISEYQTIPLN 217 (361)
Q Consensus 138 ~e~vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p~~~~~~~~~~~e~~~ip~~ 217 (361)
+|.+||||.+.++.....|.+ |..|-+-.+++|+|.||+.. +.|++.||||..++.|.-.+.
T Consensus 97 nE~vvGWyaTg~dvt~~ssli----hdyYare~~~pvhLtVDT~~--~n~rm~ikaYvss~~Gvpg~~------------ 158 (288)
T KOG2975|consen 97 NELVVGWYATGHDVTEHSSLI----HDYYAREAPNPVHLTVDTSL--QNGRMSIKAYVSSLMGVPGRT------------ 158 (288)
T ss_pred CceeEEEEecCCCcccchhHH----HHHhhccCCCCeEEEEeccc--cCCccceeEEEEeccCCCCcc------------
Confidence 999999999999988877654 56777778899999999875 379999999999886643221
Q ss_pred hhhhhCCccceeEEeeEEEecChhHHHHHHHHhccc-cccccCCCcCccChHHHHHHHHHHHHHH---HHHHHhc
Q 018085 218 KIEDFGVHCKQYYSLDITYFKSSLDCHLLDLLWNKY-WVNTLSSSPLLGNGDYVAGQISDLAEKL---EQAENQL 288 (361)
Q Consensus 218 ki~d~g~~~~~fyeLpV~i~~s~l~~~~L~~L~~~~-w~~~Ls~s~~l~n~~~l~~~i~dl~~~~---~~~~~~~ 288 (361)
-..+|.+|||+|..-+.++..|+.+.... ... -..+++..++.+.....+|...| -+|...+
T Consensus 159 -------~~~mF~plpvel~~~~~ervgl~li~kt~~sp~--r~~~l~~dLqQv~~at~~l~~~L~~Vl~YVedV 224 (288)
T KOG2975|consen 159 -------MGVMFTPLPVELAYYDAERVGLDLIEKTSFSPS--RVAGLSSDLQQVEGATARLQSLLERVLKYVEDV 224 (288)
T ss_pred -------cceeeeeeeeEEeecchhhhHHHHHHHhccChh--hhccccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 12499999999999999999999997553 222 23445566665554444444444 4444443
No 16
>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al
Probab=99.92 E-value=5.2e-24 Score=192.36 Aligned_cols=130 Identities=25% Similarity=0.407 Sum_probs=110.5
Q ss_pred eEEEECHHHHHHHHHHHhcC--CCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCC
Q 018085 61 KRVKISALALLKMVVHARSG--GTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRL 138 (361)
Q Consensus 61 ~~V~Is~~vLlkIl~Ha~~~--~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~ 138 (361)
+.+.|+..++.+|+.||+.. .|.||||+|+|+..++..+|++++..|+.+++..+.+. ++. ++++.++. ++
T Consensus 2 ~~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~~~~~~~~I~~i~~~~q~~~~~~~~~~-~~~----e~~~~~~~--~g 74 (173)
T cd08066 2 RQVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSNNAFFITHLIIPKQSGTSDSCQTT-NEE----ELFDFQDQ--HD 74 (173)
T ss_pred eEEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeEcCCCeEEEEEEEeccccCCCceecCC-CHH----HHHHHHHh--CC
Confidence 57899999999999999998 46999999999988888899999888888877766553 222 24444543 67
Q ss_pred CceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEc-cCCCCC
Q 018085 139 ENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTY-PEGYKP 203 (361)
Q Consensus 139 e~vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~-p~~~~~ 203 (361)
+.+||||||||+.+||||..|+.+|..||.+.+++++||++|. ..+++|||+. |+|+.-
T Consensus 75 le~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~------~~~l~afrl~~~~g~~~ 134 (173)
T cd08066 75 LITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK------YNEFGIFRLTDPPGLDE 134 (173)
T ss_pred CeeEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC------CcEEeEEEeecCCccee
Confidence 9999999999999999999999999999999999999999973 5789999999 777653
No 17
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=99.91 E-value=1.9e-23 Score=202.28 Aligned_cols=200 Identities=19% Similarity=0.235 Sum_probs=152.5
Q ss_pred EEEECHHHHHHHHHHHhc----CC--CceeEEEeceeecCCeEEEEEEEeCCCccCC-cccccccChHHHHHHHHHHHHH
Q 018085 62 RVKISALALLKMVVHARS----GG--TIEVMGLMQGKTDGDAIIVMDAFALPVEGTE-TRVNAQADAYEYMVDYSQTNKQ 134 (361)
Q Consensus 62 ~V~Is~~vLlkIl~Ha~~----~~--p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te-~rv~~~~e~~eY~~~ml~~~r~ 134 (361)
+|.|+|+||++|++|+.+ .. +..|+|.|||..++++++|+|||++|...++ .....+ .+|+.+|++++++
T Consensus 2 ~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~id---~~y~~~m~~~~kk 78 (288)
T cd08063 2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGREIEIENSFELKYDTNEDGEIVLD---KEFLETRLEQFKQ 78 (288)
T ss_pred eEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEcCCEEEEEEEEecccccCCCCceeeC---HHHHHHHHHHHHH
Confidence 689999999999999976 23 6899999999999999999999999997655 223232 4899999999999
Q ss_pred hCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCCCCCCCCCccccc
Q 018085 135 AGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYKPPDEPISEYQTI 214 (361)
Q Consensus 135 v~~~e~vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p~~~~~~~~~~~e~~~i 214 (361)
+++++.+||||++++. +...+...|+.| |....+..|+|++||..+...|++.++||+..+.+-..
T Consensus 79 V~~~~~vVGWY~tg~~-~~~~~~~~Ih~~--~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~~~~~~----------- 144 (288)
T cd08063 79 VFKDLDFVGWYTTGPG-GPTESDLPIHKQ--ILEINESPVLLLLDPEANASGKDLPVTIYESVLELVDG----------- 144 (288)
T ss_pred hccCCceEEEEecCCC-CCCHHHHHHHHH--HHhhCCCcEEEEEccccccCCCCCceeEEEEEEeccCC-----------
Confidence 9999999999999996 555555555544 44566778999999987423678999999988754211
Q ss_pred ChhhhhhhCCccceeEEeeEEEecChhHHHHHHHHhccccccccCCCcCccChHHHHHHHHHHHHHHHHHHHh
Q 018085 215 PLNKIEDFGVHCKQYYSLDITYFKSSLDCHLLDLLWNKYWVNTLSSSPLLGNGDYVAGQISDLAEKLEQAENQ 287 (361)
Q Consensus 215 p~~ki~d~g~~~~~fyeLpV~i~~s~l~~~~L~~L~~~~w~~~Ls~s~~l~n~~~l~~~i~dl~~~~~~~~~~ 287 (361)
.....|.++|.++..+..++..++.|....-..+=+.+.+...+..+...+..|..+++....-
T Consensus 145 ---------~~~~~F~~i~~~i~~~eaErIgv~~l~~~~~~~~~~~~~~~~~l~~~~~al~~L~~rl~~i~~Y 208 (288)
T cd08063 145 ---------EATLRFRELPYTIETGEAERIGVDHVARGGASGSSEKSTVAAHLQAQHNAIKMLNSRVELILEY 208 (288)
T ss_pred ---------ccccEEEeeeeEEEeccCceeeHHHHHhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1246899999999999999999999986542222222334456666666666666666554433
No 18
>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. J
Probab=99.89 E-value=1.9e-22 Score=167.78 Aligned_cols=115 Identities=23% Similarity=0.340 Sum_probs=93.4
Q ss_pred HHHHHHHhcCCCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCCceEEEEecCCC
Q 018085 71 LKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHSHPG 150 (361)
Q Consensus 71 lkIl~Ha~~~~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e~vVGWYHSHP~ 150 (361)
.+|++||+...|.||||+|+|+..+++++|+++|++|+..++... +..++ |....+..+.++.+||||||||.
T Consensus 2 k~il~~a~~~~~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~----~~~~~---~~~~~~~~~~~~~iVGwyhshp~ 74 (116)
T cd07767 2 KMFLDAAKSINGKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDD----NVWFL---MYLDFKKLNAGLRIVGWYHTHPK 74 (116)
T ss_pred HhHHHHHhcCCCcEEEEEeEEEEcCCEEEEEEEEecccCCCCCcc----HHHHH---HHHHHHHhcCCCeEEEEEEcCCC
Confidence 578999999899999999999999889999999999986543321 11122 33444566789999999999999
Q ss_pred CCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEE
Q 018085 151 YGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAF 194 (361)
Q Consensus 151 ~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAF 194 (361)
.+++||..|+.+|..||+..++.++||+|+... ...+.++||
T Consensus 75 ~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~~--~~~~~~~~~ 116 (116)
T cd07767 75 PSCFLSPNDLATHELFQRYFPEKVMIIVDVKPK--DLGNSWKCY 116 (116)
T ss_pred CCCccCHHHHHHHHHHHHhCCCCEEEEEECCCc--cCCCCcccC
Confidence 999999999999999999888999999999763 224667765
No 19
>cd08070 MPN_like Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding). This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.82 E-value=2.2e-19 Score=153.86 Aligned_cols=119 Identities=24% Similarity=0.285 Sum_probs=96.5
Q ss_pred HHHHHHHHHHhcCCCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCCceEEEEec
Q 018085 68 LALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHS 147 (361)
Q Consensus 68 ~vLlkIl~Ha~~~~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e~vVGWYHS 147 (361)
.++.+|+.||+++.|.|+||+|+|..++....|+.++++|+...+.+..+..++.+ +.++.+.+++ .++.+||||||
T Consensus 2 ~~~~~il~ha~~~~P~E~cGlL~G~~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~-~~~~~~~~~~--~g~~~vG~~HS 78 (128)
T cd08070 2 ELLEAILAHAEAEYPEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEIDPAE-QLAAQREARE--RGLEVVGIYHS 78 (128)
T ss_pred HHHHHHHHHHHhCCCCceEEEEEeecCCCCceEEEEEEccCCCCCCCceEEECHHH-HHHHHHHHHH--CCCeEEEEEeC
Confidence 36789999999999999999999999887778899999999766553455566655 4556666665 46999999999
Q ss_pred CCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEcc
Q 018085 148 HPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYP 198 (361)
Q Consensus 148 HP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p 198 (361)
||+.+++||..|+..+. ..+.++||+++.. +...++||++..
T Consensus 79 HP~~~~~PS~~D~~~~~-----~~~~~~lIv~~~~----~~~~~~~~~~~~ 120 (128)
T cd08070 79 HPDGPARPSETDLRLAW-----PPGVSYLIVSLAG----GAPELRAWRLEG 120 (128)
T ss_pred CCCCCCCCCHHHHHhcc-----CCCCeEEEEECCC----CCcEEEEEEEcC
Confidence 99999999999998642 3478999999753 256899999865
No 20
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=99.77 E-value=5e-18 Score=158.24 Aligned_cols=168 Identities=21% Similarity=0.318 Sum_probs=127.0
Q ss_pred CCeeEEEECHHHHHHHHHHHhcC---CCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHH
Q 018085 58 HYFKRVKISALALLKMVVHARSG---GTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQ 134 (361)
Q Consensus 58 ~~~~~V~Is~~vLlkIl~Ha~~~---~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~ 134 (361)
.++.+|.|+|+||+..++|+.+. ...+|.|+|||..+++++.|+|+|++|.++.+..-....-...|+..|..++++
T Consensus 6 ~~~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~~~~~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~mfkK 85 (309)
T KOG1556|consen 6 LTVEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGSWNGDVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGMFKK 85 (309)
T ss_pred cccceeeeehhHHHHHHHHHhhhccCcCceEEEEEEecCCCCeEEeecceeccccccCCCCceEEeccHHHHHHHHHHHH
Confidence 46789999999999999999764 348999999999999999999999999987664422111123799999999999
Q ss_pred hCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCe--eeEEEEEEccCCCCCCCCCCCccc
Q 018085 135 AGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGK--VEIGAFRTYPEGYKPPDEPISEYQ 212 (361)
Q Consensus 135 v~~~e~vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk--~~ikAFRl~p~~~~~~~~~~~e~~ 212 (361)
+|..+.+||||||+|.. ..+.+||. ..+-++.|..|.+|||.. .+. +...||-..
T Consensus 86 vNakekivGWYhTGPkl--~~nDl~In--~l~k~y~pnpvLvIIdvk----pk~~gLPT~AY~aV--------------- 142 (309)
T KOG1556|consen 86 VNAKEKVVGWYHTGPKL--RENDLDIN--ELLKRYVPNPVLVIIDVK----PKELGLPTEAYIAV--------------- 142 (309)
T ss_pred hcchhheeeeeccCCcc--ccchhhHH--HHHhhcCCCceEEEEecc----cccCCCCchheeee---------------
Confidence 99999999999999974 34555555 455667888999999953 222 233455332
Q ss_pred ccChhhhhhhCC-ccceeEEeeEEEecChhHHHHHHHHhcc
Q 018085 213 TIPLNKIEDFGV-HCKQYYSLDITYFKSSLDCHLLDLLWNK 252 (361)
Q Consensus 213 ~ip~~ki~d~g~-~~~~fyeLpV~i~~s~l~~~~L~~L~~~ 252 (361)
+-+++-|. ...-|.-+|.+|---..+....+-|-.+
T Consensus 143 ----eev~dDgt~t~ktF~Hvps~I~AeEAEEvGVEHLlRD 179 (309)
T KOG1556|consen 143 ----EEVKDDGTPTSKTFVHVPSEIEAEEAEEVGVEHLLRD 179 (309)
T ss_pred ----eeeecCCCCccceeEecCcccchhHHHHhhHHHHHHH
Confidence 23344443 3467999999998888888888877543
No 21
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=99.60 E-value=6.5e-15 Score=127.25 Aligned_cols=90 Identities=32% Similarity=0.430 Sum_probs=68.0
Q ss_pred EEECHHHHHHHHHHHhcCCCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCCceE
Q 018085 63 VKISALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAV 142 (361)
Q Consensus 63 V~Is~~vLlkIl~Ha~~~~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e~vV 142 (361)
+.|...++-.|+.||+++.|.|+||+|+|...+ ...|.+++...+.......+ .++.. +...++ ..++.+|
T Consensus 2 ~~i~~~~l~~il~~a~~~~p~E~~g~l~~~~~~-----~~~~~~~n~~~~~~~~~~~~-~~~~~-~~~~~~--~~g~~vv 72 (134)
T COG1310 2 LVIPKEVLGAILEHARREHPREVCGLLAGTREG-----ERYFPLKNVSVEPVEYFEID-PEYSL-FYLAAE--DAGEVVV 72 (134)
T ss_pred ceecHHHHHHHHHHHHhcCChheEEEEEeeccc-----ceeeccccccCCcceeEeeC-HHHHH-HHHHHh--hCCCEEE
Confidence 568899999999999999999999999999876 56677776544432111122 23333 444444 3559999
Q ss_pred EEEecCCCCCCccCHHhHH
Q 018085 143 GWYHSHPGYGCWLSGIDVS 161 (361)
Q Consensus 143 GWYHSHP~~~~~pS~~DV~ 161 (361)
|||||||+.+||||..|+.
T Consensus 73 g~yHSHP~~~~~pS~~D~~ 91 (134)
T COG1310 73 GWYHSHPGGPPYPSEADRR 91 (134)
T ss_pred EEEcCCCCCCCCcCHHHHh
Confidence 9999999999999999997
No 22
>cd08072 MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme. This family contains only archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.59 E-value=1.2e-14 Score=123.56 Aligned_cols=109 Identities=20% Similarity=0.179 Sum_probs=81.5
Q ss_pred ECHHHHHHHHHHHhcCCCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCCceEEE
Q 018085 65 ISALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGW 144 (361)
Q Consensus 65 Is~~vLlkIl~Ha~~~~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e~vVGW 144 (361)
|+..++..|+.||++++|.|+||+|+|+.. .|++++++|+....+.. .. |-.+ ++ ..++.+||.
T Consensus 1 i~~~~~~~i~~ha~~~~P~E~CGlL~G~~~----~v~~~~~~~n~~~~~~~-~~-----f~~~----~~--~~g~~ivgi 64 (117)
T cd08072 1 ISRDLLDSILEAAKSSHPNEFAALLRGKDG----VITELLILPGTESGEVS-AV-----FPLL----ML--PLDMSIVGS 64 (117)
T ss_pred CCHHHHHHHHHHHhhcCCceEEEEEEeecc----EEEEEEECCCCCCCCcc-ee-----echH----Hh--cCCCeEEEE
Confidence 456788999999999999999999999764 69999999986443221 11 1111 22 257899999
Q ss_pred EecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEcc
Q 018085 145 YHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYP 198 (361)
Q Consensus 145 YHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p 198 (361)
|||||+.+++||..|+... ..++.+++|+++-. ..-.++||+..-
T Consensus 65 ~HSHP~~~~~PS~~D~~~~-----~~~~~~~lIvs~~~----~~~~~~a~~~~g 109 (117)
T cd08072 65 VHSHPSGSPRPSDADLSFF-----SKTGLVHIIVGYPY----DEDDWRAYDSDG 109 (117)
T ss_pred EEcCCCCCCCCCHHHHHhh-----hcCCCEEEEEECcC----CCCCEEEEecCC
Confidence 9999999999999998632 34789999999532 123688998653
No 23
>cd08073 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains. This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.51 E-value=1.6e-13 Score=115.13 Aligned_cols=94 Identities=16% Similarity=0.095 Sum_probs=71.8
Q ss_pred HHHHHHHHHhcCCCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCCceEEEEecC
Q 018085 69 ALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHSH 148 (361)
Q Consensus 69 vLlkIl~Ha~~~~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e~vVGWYHSH 148 (361)
++..|+.||+++.|.|+||+|+|+. .++..++++|...+.+..+..++.+|.. ..+ ...+||.||||
T Consensus 2 i~~~i~~ha~~~~P~E~CGll~g~~-----~~~~~~p~~N~~~~p~~~F~idp~e~~~----a~~----~~~ivgi~HSH 68 (108)
T cd08073 2 LEDAILAHAKAEYPREACGLVVRKG-----RKLRYIPCRNIAADPEEHFEISPEDYAA----AED----EGEIVAVVHSH 68 (108)
T ss_pred HHHHHHHHHhHCCCCcceEEEEecC-----CceEEEECccCCCCccceEEeCHHHHHH----Hhc----CCCEEEEEEcC
Confidence 4668999999999999999999965 2456788887655444456667766533 222 22899999999
Q ss_pred CCCCCccCHHhHHHHHhhhhcCCCeEEEEEcC
Q 018085 149 PGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDP 180 (361)
Q Consensus 149 P~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP 180 (361)
|+..+.||..|+..+ ..++.++||++.
T Consensus 69 P~~~a~PS~~D~~~~-----~~~~~~~iIvs~ 95 (108)
T cd08073 69 PDGSPAPSEADRAQQ-----EATGLPWIIVSW 95 (108)
T ss_pred CCCCCCCCHHHHHHh-----hcCCCcEEEEEc
Confidence 999999999998632 347889999994
No 24
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=99.42 E-value=2e-13 Score=133.30 Aligned_cols=132 Identities=20% Similarity=0.370 Sum_probs=106.9
Q ss_pred CCCCCeeEEEECHHHHHHHHHHHhcC--CCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHH
Q 018085 55 NDPHYFKRVKISALALLKMVVHARSG--GTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTN 132 (361)
Q Consensus 55 ~~~~~~~~V~Is~~vLlkIl~Ha~~~--~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~ 132 (361)
.....++.|+|.....-+.++-|++. ...|.||+|.|+...+.+.||+...--++++.+.|++..+.. ..+..
T Consensus 246 ~~~k~lr~v~ip~~l~~~Fl~la~~NT~knlETCGiL~g~L~~n~f~IThliiPkQeatsd~C~t~neee--lF~vQ--- 320 (424)
T KOG2880|consen 246 SEGKILRDVHIPERLMEVFLQLAKSNTKKNLETCGILAGKLERNEFYITHLIIPKQEATSDSCNTMNEEE--LFEVQ--- 320 (424)
T ss_pred cCCccceEEEecHHHHHHHHHHHhhcccccchHHHHhhhHhhcCcEEEEEEEeecccCCCccccccCHHH--Hheec---
Confidence 34566899999999999999998863 568999999999999999999987555677888787755432 12211
Q ss_pred HHhCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccC
Q 018085 133 KQAGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPE 199 (361)
Q Consensus 133 r~v~~~e~vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p~ 199 (361)
...++-.+||-|+||.-+||+|.+|++|+++||.+.|.+||||+.|... .-+-||+.+.
T Consensus 321 --dq~~L~tlGWIHTHPTQt~FmSSVDlHTHcSYQiMlPEAiAIV~aPk~~------~tGiFrLt~~ 379 (424)
T KOG2880|consen 321 --DQHELLTLGWIHTHPTQTCFMSSVDLHTHCSYQIMLPEAIAIVCAPKSK------TTGIFRLTDP 379 (424)
T ss_pred --ccccceeeeeeecCCccchhheeccccccceeeeecchheeEEeccccC------CcceEEecCC
Confidence 1356789999999999999999999999999999999999999999642 3556999843
No 25
>cd08060 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p). This family includes Noc4p (neighbor of COX4; neighbor of Cytochrome c Oxidase 4; nucleolar complex associated 4 homolog) which belongs to the family of unknown function, UPF0172, with MPN/JAMM-like domains. Proteins in this family are homologs of the NOC4 gene which is conserved in eukaryotic members including human, dog, mouse, rat, chicken, zebrafish, fruit fly, mosquito, S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa, A.thaliana, and rice. NOC4 highly expressed in the pancreas and moderately in liver, heart, lung, kidney, brain, skeletal muscle, and placenta. This nucleolar protein forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=99.34 E-value=1.4e-11 Score=112.52 Aligned_cols=110 Identities=20% Similarity=0.186 Sum_probs=76.0
Q ss_pred ECHHHHHHHHHHHhcCCCceeEEEeceeec-CCeEEEEEEEeCCCccCCcccccccChHH--HHHHHHHHHHHhCCCCce
Q 018085 65 ISALALLKMVVHARSGGTIEVMGLMQGKTD-GDAIIVMDAFALPVEGTETRVNAQADAYE--YMVDYSQTNKQAGRLENA 141 (361)
Q Consensus 65 Is~~vLlkIl~Ha~~~~p~EV~GlLlG~~~-~~tl~Vtd~F~lP~~~te~rv~~~~e~~e--Y~~~ml~~~r~v~~~e~v 141 (361)
|+..++.||+.||....+.||||+|+|+.. ++++.|++++|+.+. +... ++.. -+....+.+++ .++.|
T Consensus 1 is~~ay~ki~~HA~k~p~~evcGlLlG~~~~~~~~~V~d~vPl~h~----~~~l--~P~~Eval~~ve~~~~~--~gl~I 72 (182)
T cd08060 1 LSTLAYVKMLLHAAKYPHCAVNGLLLGKKSSGGSVEITDAVPLFHS----CLAL--APMLEVALALVDAYCKS--SGLVI 72 (182)
T ss_pred CCHHHHHHHHHHHHHcCCchheEEEEeeecCCCCEEEEEEEEcCCC----cccc--CHHHHHHHHHHHHHHHH--CCCEE
Confidence 467899999999999777899999999987 778999999999984 2222 3332 13344556665 57899
Q ss_pred EEEEecCCCCC-CccCHHhHHHHHhhhhcCCCeEEEEEcCCC
Q 018085 142 VGWYHSHPGYG-CWLSGIDVSTQMLNQQFQEPFLAVVIDPTR 182 (361)
Q Consensus 142 VGWYHSHP~~~-~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~ 182 (361)
||+|||||.+. .-|+.+=...-..-+...+..+.+++|-.+
T Consensus 73 vG~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~ 114 (182)
T cd08060 73 VGYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEK 114 (182)
T ss_pred EEEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCcc
Confidence 99999999764 234333111111122334677888888544
No 26
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=99.33 E-value=7e-12 Score=102.67 Aligned_cols=93 Identities=23% Similarity=0.323 Sum_probs=63.3
Q ss_pred HHHHHHHHHHHhcCCCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHH-HHHHhCCCCceEEEE
Q 018085 67 ALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQ-TNKQAGRLENAVGWY 145 (361)
Q Consensus 67 ~~vLlkIl~Ha~~~~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~-~~r~v~~~e~vVGWY 145 (361)
..++.+|+.|++...|.|+||+|+|......+.++...... +.++. .+.. .. ...+..+||+|
T Consensus 2 ~~~~~~i~~~~~~~~p~E~~G~L~g~~~~~~~~~~~~~~~~-------------p~~~~-~~~~~~~--~~~~~~~vg~~ 65 (104)
T PF14464_consen 2 EEVLEQIIAHARAAYPNEACGLLLGRRDDQRFIVVPNVNPD-------------PRDSF-RRERFEA--RERGLEIVGIW 65 (104)
T ss_dssp -HHHHHHHHHHHHHTTS-EEEEEEEEEECCEEEEEEEEE---------------HHCHH-HHHH-HH--HHHT-EEEEEE
T ss_pred HHHHHHHHHHHhhCCCCeEEEEEEEEecCCEEEEEeCCCCC-------------cHHHH-HHHhhhh--hcccceeeEEE
Confidence 35788999999999999999999999966677777665411 11111 1111 22 23568999999
Q ss_pred ecCCCCCCccCHHhHHHHHhhhhcCC-CeEEEEEcC
Q 018085 146 HSHPGYGCWLSGIDVSTQMLNQQFQE-PFLAVVIDP 180 (361)
Q Consensus 146 HSHP~~~~~pS~~DV~tQ~~yQ~~~~-p~V~LIvDP 180 (361)
||||+.+++||..|+.... .. ++++||+..
T Consensus 66 HSHP~~~a~pS~~D~~~~~-----~~~~~~~iI~~~ 96 (104)
T PF14464_consen 66 HSHPSGPAFPSSTDIRSMR-----DLAPPSYIIVGN 96 (104)
T ss_dssp EEESSSSSS--HHHHHTHC-----CS-SCEEEEEEE
T ss_pred EcCCCCCCCCCHHHHHhhh-----ccCCeEEEEEeC
Confidence 9999999999999987642 22 678888874
No 27
>cd08056 MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8. Members of this family are found in pre-mRNA-processing factor 8 (Prp8) which is a critical splicing factor, interacting with several other spliceosomal proteins, snRNAs, and the pre-mRNA, thus organizing and stabilizing the spliceosome catalytic core. Prp8 is one of the largest and most highly conserved of nuclear proteins, occupying a central position in the catalytic core of the spliceosome. Its C-terminal domain exhibits a JAB1/MPN-like core similar to deubiquitinating enzymes, but does not show catalytic isopeptidase activity, possibly because the putative isopeptidase center is covered by insertions and terminal appendices that are grafted onto this core, thus impairing the metal binding site. It is proposed that this domain is a protein interaction domain instead of a Zn(2+)-dependent metalloenzyme as proposed for some MPN proteins. The DEAD-box protein Brr2 and t
Probab=99.15 E-value=4.2e-10 Score=107.21 Aligned_cols=126 Identities=21% Similarity=0.264 Sum_probs=103.7
Q ss_pred EEEECHHHHHHHHHHHhcCCCceeEEEeceeecC---CeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCC
Q 018085 62 RVKISALALLKMVVHARSGGTIEVMGLMQGKTDG---DAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRL 138 (361)
Q Consensus 62 ~V~Is~~vLlkIl~Ha~~~~p~EV~GlLlG~~~~---~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~ 138 (361)
++.|+...|.|.+.-|.. ..++||.|.|+... +..+|+-..-.|+.++.+.|.+..+..+ .+. + .+
T Consensus 37 t~vlPknllkkFi~iaD~--rtQ~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~~~~--~~~---l----~~ 105 (252)
T cd08056 37 TYILPKNLLKKFISISDL--RTQIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQLPQ--HEY---L----ED 105 (252)
T ss_pred EEEeCHHHHHHHHHHhhh--cceEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCccCcc--chh---h----CC
Confidence 788999999999988864 46999999999754 6789998888899998888776433212 111 1 46
Q ss_pred CceEEEEecCCCCCCccCHHhHHHHHhhhhcCC-----CeEEEEEcCCCCccCCeeeEEEEEEccCCCC
Q 018085 139 ENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQE-----PFLAVVIDPTRTVSAGKVEIGAFRTYPEGYK 202 (361)
Q Consensus 139 e~vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~-----p~V~LIvDP~~t~~~Gk~~ikAFRl~p~~~~ 202 (361)
+..+||-||||.-.+++|..||.++..+|...+ .+|.+++++. .|.++++||++++.|+.
T Consensus 106 Le~LGWIHTqp~e~~~Lss~Dv~tha~~~~~~~~w~~~~~V~it~Sft----pGs~sl~ay~LT~~G~~ 170 (252)
T cd08056 106 LEPLGWIHTQPNELPQLSPQDVTTHAKILADNPSWDGEKTVILTCSFT----PGSCSLTAYKLTPEGYE 170 (252)
T ss_pred CEeeEEEEcCCCCccccCHHHHHHHHHHHHhccccCCCcEEEEEEcCC----CCceEEEEEecCHHHHH
Confidence 889999999999899999999999999998876 6899999974 68899999999998764
No 28
>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic. This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.02 E-value=2.7e-09 Score=87.60 Aligned_cols=91 Identities=24% Similarity=0.290 Sum_probs=66.2
Q ss_pred HHHHHHHHHhcCCCceeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCCceEEEEecC
Q 018085 69 ALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHSH 148 (361)
Q Consensus 69 vLlkIl~Ha~~~~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e~vVGWYHSH 148 (361)
++..|..|++...|.|+||+|+|.... .|++...+|+.. .+. ++.. .+.+. ..+..+||.||||
T Consensus 2 ~~~~i~~~~~~~~p~E~~gll~~~~~~---~~~~~~~~~~~~----~~~--~~~~-----~~~a~--~~~~~~v~i~HsH 65 (101)
T cd08059 2 LLKTILVHAKDAHPDEFCGFLSGSKDN---VMDELIFLPFVS----GSV--SAVI-----DLAAL--EIGMKVVGLVHSH 65 (101)
T ss_pred HHHHHHHHHHhcCChhhheeeecCCCC---eEEEEEeCCCcC----Ccc--ChHH-----HHHHh--hCCCcEEEEEecC
Confidence 567889999999999999999997543 678888888632 111 2221 22222 2567899999999
Q ss_pred CCCCCccCHHhHHHHHhhhhcCCCeEEEEEcC
Q 018085 149 PGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDP 180 (361)
Q Consensus 149 P~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP 180 (361)
|+..+.||..|+.... .....++|+..
T Consensus 66 P~g~~~PS~~D~~~~~-----~~~~~~iIv~~ 92 (101)
T cd08059 66 PSGSCRPSEADLSLFT-----RFGLYHVIVCY 92 (101)
T ss_pred cCCCCCCCHHHHHHHH-----hcCCeEEEEEC
Confidence 9999999999987422 23778899964
No 29
>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family. This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize.
Probab=98.96 E-value=9.6e-09 Score=89.17 Aligned_cols=108 Identities=18% Similarity=0.185 Sum_probs=72.1
Q ss_pred HHHHHHHh-c-CCCceeEEEeceeecCCeEEEEEEEeCCCc-cCCcccccccChHHHHHHHHHHHHHhCCCCceEEEEec
Q 018085 71 LKMVVHAR-S-GGTIEVMGLMQGKTDGDAIIVMDAFALPVE-GTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHS 147 (361)
Q Consensus 71 lkIl~Ha~-~-~~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~-~te~rv~~~~e~~eY~~~ml~~~r~v~~~e~vVGWYHS 147 (361)
++++..++ . ..+.|.+|+|+|...+..+.|+++. .|.. ...++..+..+....+...-+..++.+.....||=|||
T Consensus 3 ~~~~~~~~Q~~~~~~EtGGiLiG~~~~~~~ii~~~t-~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylGeWHt 81 (131)
T TIGR02256 3 VAMLKSYRQWHDLSTETGGVLIGERRGAHAVITKIS-EPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGEWHT 81 (131)
T ss_pred HHHHHHHHhCcCCCCccceEEEEEEcCCcEEEEEEE-cCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEEecCc
Confidence 44444443 3 4578999999999988888888865 3332 22344455444333344555556666666899999999
Q ss_pred CCCCCCccCHHhHHHHHhhhhcCCCeEEEEEc
Q 018085 148 HPGYGCWLSGIDVSTQMLNQQFQEPFLAVVID 179 (361)
Q Consensus 148 HP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvD 179 (361)
||...+.||.+|+.+-...=....+.+.||+-
T Consensus 82 HP~~~p~PS~~D~~~~~~~~~~~~~~l~iIvG 113 (131)
T TIGR02256 82 HPEDQPEPSWTDRRSWRTIIRSPEAMLLLIVG 113 (131)
T ss_pred CCCCCCCCCHHHHHHHHHHHhCCCeeEEEEEc
Confidence 99988899999998754332234456667765
No 30
>TIGR03735 PRTRC_A PRTRC system protein A. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.
Probab=98.93 E-value=7.1e-09 Score=95.15 Aligned_cols=113 Identities=19% Similarity=0.095 Sum_probs=79.7
Q ss_pred EEECHHHHHHHHHHHhcCCCceeEEEeceeecCCeEEEEEEEeCCCccCC-cccccccChHHHHHHHHHHHHHhCCCCce
Q 018085 63 VKISALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTE-TRVNAQADAYEYMVDYSQTNKQAGRLENA 141 (361)
Q Consensus 63 V~Is~~vLlkIl~Ha~~~~p~EV~GlLlG~~~~~tl~Vtd~F~lP~~~te-~rv~~~~e~~eY~~~ml~~~r~v~~~e~v 141 (361)
=+|....+-+|+.||+++.|.|+||++.|...+. +..++++.+.... +.+.+ +.. | ..+++.+
T Consensus 73 g~Ip~~l~~~ii~hAr~~~P~EacG~Iag~~~~~---~~r~~p~~N~~~Sp~~~~~--d~~-----~------~~~ge~l 136 (192)
T TIGR03735 73 GPIPASLLEEFAEAARAALPNEVAAWIVWNSETG---SLRLAALESIEASPGHIDY--RRP-----R------LDDGEHL 136 (192)
T ss_pred CCCCHHHHHHHHHHHHhcCCcceEEEEEEcCCCC---EEEEEeccccccCCceEEE--cch-----H------HhCCCeE
Confidence 3899999999999999999999999999963332 3466888875432 23332 221 1 1478999
Q ss_pred EEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCC
Q 018085 142 VGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEG 200 (361)
Q Consensus 142 VGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p~~ 200 (361)
|+.|||||..+++||.+|+..- ..+-.++.|+--.. ++.+++ +||+.-.|
T Consensus 137 V~iyHSH~~spA~PS~tD~~Dd-----~~~~k~~~ViG~~~---~~~p~~-~~Rl~~~G 186 (192)
T TIGR03735 137 VVDLHSHGTGSAFFSETDDADD-----KGEVKISGVLGCLD---QGTPQA-VFRLCLLG 186 (192)
T ss_pred EEEEcCCCCCCCCCCcccchhh-----cCceEEEEEEEecC---CCCceE-EEEEEecc
Confidence 9999999999999999998641 12356888886432 334443 57776544
No 31
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=98.48 E-value=2.4e-07 Score=87.21 Aligned_cols=161 Identities=20% Similarity=0.295 Sum_probs=106.8
Q ss_pred eEEEECHHHHHHHHHHHhc-----CCCc-eeEEEeceeecCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHH
Q 018085 61 KRVKISALALLKMVVHARS-----GGTI-EVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQ 134 (361)
Q Consensus 61 ~~V~Is~~vLlkIl~Ha~~-----~~p~-EV~GlLlG~~~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~ 134 (361)
-+|.++|+|++.|-+|..+ +.|. .|.|.|+|+..|..+||.|+|-+-..-.++..-++ .+|...=.+..++
T Consensus 9 ~tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~~~~~~d---ke~l~kk~eqykq 85 (299)
T KOG3050|consen 9 VTVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGKQRGRNVEIMNSFELKMDTEEDTETID---KEYLEKKEEQYKQ 85 (299)
T ss_pred eeEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheecccCceEEEeeeeEEEecchhhhhhcc---HHHHHHHHHHHHH
Confidence 3789999999999999843 5566 89999999999999999999998754322221122 3566665677788
Q ss_pred hCCCCceEEEEecCCCCCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCc-cCCeeeEEEEEEccCCCCCCCCCCCcccc
Q 018085 135 AGRLENAVGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTV-SAGKVEIGAFRTYPEGYKPPDEPISEYQT 213 (361)
Q Consensus 135 v~~~e~vVGWYHSHP~~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~-~~Gk~~ikAFRl~p~~~~~~~~~~~e~~~ 213 (361)
|=+++.++|||.++.+ +-||.+-|..|... ..+..++|-..|...- ....+.+=+|-+.-
T Consensus 86 VFpdl~vlGwYttG~d--~t~sd~~i~k~l~~--i~esplflkLNp~t~~t~~~pv~lfese~dv--------------- 146 (299)
T KOG3050|consen 86 VFPDLYVLGWYTTGSD--PTPSDIHIHKQLMD--INESPLFLKLNPATNHTDKDPVTLFESEIDV--------------- 146 (299)
T ss_pred hcccceEEEEeecCCC--CChhhhHHHHHHHh--hhcCceEEEecchhccccCCCceeeeeehee---------------
Confidence 9999999999998763 45666655554432 3567788888885321 11123333322211
Q ss_pred cChhhhhhhCCccceeEEeeEEEecChhHHHHHHHHh
Q 018085 214 IPLNKIEDFGVHCKQYYSLDITYFKSSLDCHLLDLLW 250 (361)
Q Consensus 214 ip~~ki~d~g~~~~~fyeLpV~i~~s~l~~~~L~~L~ 250 (361)
+. |...-.|.++.-.+-.-..+|...+-..
T Consensus 147 -----id--g~~q~~f~~~tytl~teEaERIgVdHVA 176 (299)
T KOG3050|consen 147 -----ID--GEAQMLFVPLTYTLATEEAERIGVDHVA 176 (299)
T ss_pred -----ec--CcceeeeeeeEEEEeehhhhhccchhhe
Confidence 00 1113467777777777777777776653
No 32
>cd08061 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain. Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=98.32 E-value=2e-05 Score=76.42 Aligned_cols=137 Identities=18% Similarity=0.279 Sum_probs=104.4
Q ss_pred CCCeeEEEECHHHHHHHHHH-HhcCCCceeEEEeceeecCC-------eEEEEEEEeCCCccCCcccccccChHHHHHHH
Q 018085 57 PHYFKRVKISALALLKMVVH-ARSGGTIEVMGLMQGKTDGD-------AIIVMDAFALPVEGTETRVNAQADAYEYMVDY 128 (361)
Q Consensus 57 ~~~~~~V~Is~~vLlkIl~H-a~~~~p~EV~GlLlG~~~~~-------tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~m 128 (361)
-+.+.+|.+....++.-..+ +.+.....-||+|.|+.... ..+|.-.+--|++++.+.+.+..+.. ....
T Consensus 7 ~r~Vd~vef~~~~~~~~f~~~~w~~~~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~--~~~v 84 (274)
T cd08061 7 YRHVDHVEFDNPSIVEFFLYVFWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPN--ADTV 84 (274)
T ss_pred CCCcCEEEEecHHHHHHHHHHHHHhhcceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchh--hhHH
Confidence 34577888888777766655 54445688899999999755 56777778888888877776544332 2333
Q ss_pred HHHHHHhCCCCceEEEEecCCCC----CCccCHHhHHHHHhhhh------cCCCeEEEEEcCCCCccCCeeeEEEEEEcc
Q 018085 129 SQTNKQAGRLENAVGWYHSHPGY----GCWLSGIDVSTQMLNQQ------FQEPFLAVVIDPTRTVSAGKVEIGAFRTYP 198 (361)
Q Consensus 129 l~~~r~v~~~e~vVGWYHSHP~~----~~~pS~~DV~tQ~~yQ~------~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p 198 (361)
.+.+. ..++..|||-.||+.- ++++|...|...+.+|. +...||-+|++|.. .|.+.+.||+++.
T Consensus 85 d~iA~--~lGL~~VG~IfT~l~~~~~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~---~g~i~~~ayQvSd 159 (274)
T cd08061 85 DAIAA--ALGLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDK---DGQIHFEAYQVSD 159 (274)
T ss_pred HHHHH--HcCCeEEEEEEecCCCCCCCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCC---CCceeeeeeeecH
Confidence 33344 3679999999999966 78999999999899994 67899999999975 5889999999987
Q ss_pred CC
Q 018085 199 EG 200 (361)
Q Consensus 199 ~~ 200 (361)
.+
T Consensus 160 q~ 161 (274)
T cd08061 160 QA 161 (274)
T ss_pred HH
Confidence 54
No 33
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=98.30 E-value=1.3e-05 Score=74.13 Aligned_cols=115 Identities=19% Similarity=0.175 Sum_probs=73.6
Q ss_pred EEEECHHHHHHHHHHHhcCCCceeEEEeceeecCCe--EEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCC
Q 018085 62 RVKISALALLKMVVHARSGGTIEVMGLMQGKTDGDA--IIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLE 139 (361)
Q Consensus 62 ~V~Is~~vLlkIl~Ha~~~~p~EV~GlLlG~~~~~t--l~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e 139 (361)
.|.|+..|+.||+-||-.-...-|+|+|+|...++. +.|+||.|+=+....- ..-.|.. +...-..++ ..++
T Consensus 3 ~v~is~~AY~K~~LHaaKyP~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~~L--~PmlEvA--L~qvd~~~~--~~gl 76 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAKYPHCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWLSL--SPMLEVA--LAQVDAYAK--SNGL 76 (196)
T ss_pred eEEEcHHHHHHHHHHhccCCCCceeeEEEeccCCCCceEEEeeceeccccccCc--chHHHHH--HHHHHHHHh--hCCC
Confidence 689999999999999998656899999999987554 9999999987743221 1101111 111122333 2569
Q ss_pred ceEEEEecCCCCC-CccCHHhHHHHHhhhhcCCCeEEEEEcCCC
Q 018085 140 NAVGWYHSHPGYG-CWLSGIDVSTQMLNQQFQEPFLAVVIDPTR 182 (361)
Q Consensus 140 ~vVGWYHSHP~~~-~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~ 182 (361)
.|||+||....+. .-|+.+-...-..-....+..+.|++|-.+
T Consensus 77 ~IvGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~k 120 (196)
T PF03665_consen 77 VIVGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKK 120 (196)
T ss_pred EEEEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcc
Confidence 9999999987442 234443111111112245778889998543
No 34
>PF05021 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation following ubiquitination of target proteins but preceding their recognition by the 26S proteasome []. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing [].
Probab=97.41 E-value=0.0021 Score=63.46 Aligned_cols=108 Identities=16% Similarity=0.258 Sum_probs=82.1
Q ss_pred EEEeceeecCC-------eEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCCceEEEEecCCC--------
Q 018085 86 MGLMQGKTDGD-------AIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHSHPG-------- 150 (361)
Q Consensus 86 ~GlLlG~~~~~-------tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e~vVGWYHSHP~-------- 150 (361)
+|+|.|+.+.. +.+|.-.|--|++++.+.+....++. ....-+.++. -|+..|||-=||+.
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~--~~~vd~iA~~--lGL~rVG~IfTdl~~~~~~~g~ 77 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDEN--EERVDAIASA--LGLERVGWIFTDLTDDGSGDGT 77 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCcc--HHHHHHHHHH--CCCEEEEEEEecCcccccCCCc
Confidence 79999998643 46777778888988888776644332 2333444443 57999999999986
Q ss_pred -------CCCccCHHhHHHHHhhhhc-------------CCCeEEEEEcCCCCccCCeeeEEEEEEccCC
Q 018085 151 -------YGCWLSGIDVSTQMLNQQF-------------QEPFLAVVIDPTRTVSAGKVEIGAFRTYPEG 200 (361)
Q Consensus 151 -------~~~~pS~~DV~tQ~~yQ~~-------------~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p~~ 200 (361)
-..++|...|-..+.+|.. ...||-+|+++.. .|.+.+.||+++..+
T Consensus 78 v~~~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~~---~g~i~~~ayQvS~q~ 144 (306)
T PF05021_consen 78 VKCKRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGDE---EGEIHFEAYQVSNQC 144 (306)
T ss_pred eeeccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCCC---CCceeeEEeeehHHH
Confidence 5689999999888888863 3568999999864 789999999998754
No 35
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=97.39 E-value=0.003 Score=57.49 Aligned_cols=114 Identities=23% Similarity=0.250 Sum_probs=73.7
Q ss_pred EEEECHHHHHHHHHHHhcCCCceeEEEeceee--cCCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCC
Q 018085 62 RVKISALALLKMVVHARSGGTIEVMGLMQGKT--DGDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLE 139 (361)
Q Consensus 62 ~V~Is~~vLlkIl~Ha~~~~p~EV~GlLlG~~--~~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e 139 (361)
.|+|+..++.||+-||.+-...-|-|+|+|.. .|+.++|++|.|+=++..- . ....|-...+++..- ...+.
T Consensus 3 ~veis~~aY~kmiLH~akyph~aVnGLLla~~~~kg~~v~itdcVPLfH~~la----L-aPmlEvAl~lId~~~-~~~Gl 76 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYPHAAVNGLLLAPATGKGECVEITDCVPLFHSHLA----L-APMLEVALNLIDVWG-AQAGL 76 (199)
T ss_pred ceeehhhHHHHHHHHhccCcccceeeEEEeccCCCCCeEEEEecchhhccccc----c-ccHHHHHHHHHHHHH-HhcCe
Confidence 58999999999999999865568999999965 3678999999998765321 1 112333333444322 24679
Q ss_pred ceEEEEecCCCCC-CccCHHhHHHHHhhhhcCCCeEEEEEcCC
Q 018085 140 NAVGWYHSHPGYG-CWLSGIDVSTQMLNQQFQEPFLAVVIDPT 181 (361)
Q Consensus 140 ~vVGWYHSHP~~~-~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~ 181 (361)
.|+|.||+--.+. .-|.+.-...--.-+.+.+....|++|-.
T Consensus 77 viaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~ 119 (199)
T KOG3289|consen 77 VIAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNK 119 (199)
T ss_pred EEEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEecc
Confidence 9999999986532 22222211111223445677777888854
No 36
>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=84.96 E-value=2.2 Score=49.14 Aligned_cols=110 Identities=18% Similarity=0.225 Sum_probs=75.6
Q ss_pred CCCceeEEEeceeec---CCeEEEEEEEeCCCccCCcccccccChHHHHHHHHHHHHHhCCCCceEEEEecCCCCCCccC
Q 018085 80 GGTIEVMGLMQGKTD---GDAIIVMDAFALPVEGTETRVNAQADAYEYMVDYSQTNKQAGRLENAVGWYHSHPGYGCWLS 156 (361)
Q Consensus 80 ~~p~EV~GlLlG~~~---~~tl~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~~r~v~~~e~vVGWYHSHP~~~~~pS 156 (361)
.....+.|+|.|.-- +...+|.-..-+|+-++-..++....--. .. +-.+...+||-|+-|.--.++|
T Consensus 2112 D~r~qiag~~yG~s~~d~pqvkeIr~ivmvPQ~gs~~~v~lp~~lP~--~~-------~l~d~e~Lgw~hTq~~el~~ls 2182 (2321)
T KOG1795|consen 2112 DLRTQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGSHQGVHLPSFLPI--HG-------VLEDLEPLGWIHTQPNELPQLS 2182 (2321)
T ss_pred chhhhhheeeeccCCCCCCccceEEEEEeccccccccccccCccCCc--ch-------hccCCcccchhhcCccccccCC
Confidence 345678899999653 33457776666787666555543210000 11 1246789999999998889999
Q ss_pred HHhHHHHHh-hhhcCCCeEEEEEcCCCCccCCeeeEEEEEEccCCCC
Q 018085 157 GIDVSTQML-NQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYPEGYK 202 (361)
Q Consensus 157 ~~DV~tQ~~-yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p~~~~ 202 (361)
..||.++.. .+.....+|.|.++- ..|.+++.||.++|.||.
T Consensus 2183 p~dV~th~ki~~~~k~k~i~~t~~~----tpgs~sl~ay~lt~~G~e 2225 (2321)
T KOG1795|consen 2183 PQDVTTHAKILVDNKEKCIIITCSF----TPGSCSLTAYKLTPSGYE 2225 (2321)
T ss_pred HHHhhhhhhhhhcCccceEEEEeec----cCCcceeeeeccCccccc
Confidence 999998753 233345677777763 379999999999999985
No 37
>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=72.95 E-value=41 Score=35.27 Aligned_cols=132 Identities=18% Similarity=0.293 Sum_probs=84.5
Q ss_pred eeEEEEC-HHHHHHHHHHHhcCCCceeEEEeceeecCC-eE------EEEEEEeCCCccCCcccccccChHHHHHHHHHH
Q 018085 60 FKRVKIS-ALALLKMVVHARSGGTIEVMGLMQGKTDGD-AI------IVMDAFALPVEGTETRVNAQADAYEYMVDYSQT 131 (361)
Q Consensus 60 ~~~V~Is-~~vLlkIl~Ha~~~~p~EV~GlLlG~~~~~-tl------~Vtd~F~lP~~~te~rv~~~~e~~eY~~~ml~~ 131 (361)
+.+|.++ +.++...++-.|.. ...-.|.|.|...+. .+ +|.-.|--|+.++++.+.+..+ .+ +..+-+.
T Consensus 174 vD~VeFd~~~~v~~Fl~~wr~s-g~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~~~~dgl~l~~~-~e-~~~vD~~ 250 (510)
T KOG2834|consen 174 VDHVEFDNAELVNHFLNEWRAS-GVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQHGEEDGLELLED-DE-AKRVDAI 250 (510)
T ss_pred cceEeecchHHHHHHHHHHHHh-hhhhcceEEEeecccccccccceeeEEEEecCCccCCcCCeEEecc-ch-hhhHHHH
Confidence 4445554 23444444444543 355679999998533 23 7777888899988887766422 22 2223233
Q ss_pred HHHhCCCCceEEEEecCC---------------CCCCccCHHhHHHHHhhhhcC-------------CCeEEEEEcCCCC
Q 018085 132 NKQAGRLENAVGWYHSHP---------------GYGCWLSGIDVSTQMLNQQFQ-------------EPFLAVVIDPTRT 183 (361)
Q Consensus 132 ~r~v~~~e~vVGWYHSHP---------------~~~~~pS~~DV~tQ~~yQ~~~-------------~p~V~LIvDP~~t 183 (361)
+ .+.++..|||--+-- .-+.|+|...+.+-+.+|..- ..+|-+|+.-..
T Consensus 251 a--~~lGLrRVG~IFTDl~~~~s~egtV~~~rhkdsyFLSseE~~~aa~~Q~~hpn~~~~s~~~~fgSkfVT~visg~~- 327 (510)
T KOG2834|consen 251 A--EGLGLRRVGWIFTDLVTADSAEGTVHYKRHKDSYFLSSEECITAAMFQNKHPNICEWSRDGHFGSKFVTLVISGDL- 327 (510)
T ss_pred H--HhcCceeeEEEEeeeecccCccceEEeeeccchhcccHHHHHHHhhhhhcCCchheeeccccccceeEEEEEecCC-
Confidence 3 357799999953321 125689999998888888653 246778887543
Q ss_pred ccCCeeeEEEEEEccC
Q 018085 184 VSAGKVEIGAFRTYPE 199 (361)
Q Consensus 184 ~~~Gk~~ikAFRl~p~ 199 (361)
.|.+.+-.|+.+..
T Consensus 328 --~~~V~f~~YQVSnq 341 (510)
T KOG2834|consen 328 --DGEVHFEGYQVSNQ 341 (510)
T ss_pred --CcceeeeeeehhHH
Confidence 67899999998653
No 38
>cd08071 MPN_DUF2466 Mov34/MPN/PAD-1 family. Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. However, to date, the name RadC has been misleading and no function has been determined.
Probab=46.81 E-value=1.7e+02 Score=24.43 Aligned_cols=25 Identities=24% Similarity=0.110 Sum_probs=22.0
Q ss_pred CCceEEEEecCCCCCCccCHHhHHH
Q 018085 138 LENAVGWYHSHPGYGCWLSGIDVST 162 (361)
Q Consensus 138 ~e~vVGWYHSHP~~~~~pS~~DV~t 162 (361)
+..-|..-|.||...+.||..|+..
T Consensus 59 ~A~~vil~HNHPsG~~~PS~~D~~~ 83 (113)
T cd08071 59 NAAAIILAHNHPSGDPTPSREDIEL 83 (113)
T ss_pred hhheEEEEeeCCCCCCCCCHHHHHH
Confidence 4578899999999999999999875
No 39
>COG1029 FwdB Formylmethanofuran dehydrogenase subunit B [Energy production and conversion]
Probab=45.13 E-value=66 Score=33.05 Aligned_cols=57 Identities=28% Similarity=0.465 Sum_probs=34.6
Q ss_pred hCCCCceEEE----EecCCC----CCCccCHHhHHHHHhhhhcCCCeEEEEEcCCCCccCCeeeEEEEEEcc
Q 018085 135 AGRLENAVGW----YHSHPG----YGCWLSGIDVSTQMLNQQFQEPFLAVVIDPTRTVSAGKVEIGAFRTYP 198 (361)
Q Consensus 135 v~~~e~vVGW----YHSHP~----~~~~pS~~DV~tQ~~yQ~~~~p~V~LIvDP~~t~~~Gk~~ikAFRl~p 198 (361)
.||...+|=| +||||. |+.||-+.-. ++....--.++|||.+|. .-++.=-.+++-|
T Consensus 138 KNraDviVyWGtNP~~shPRhmSRYs~f~RG~~~------~rGr~dRtvIvVD~RkT~-TAklad~~~qi~p 202 (429)
T COG1029 138 KNRADVIVYWGTNPMHSHPRHMSRYSVFPRGFFR------PRGREDRTVIVVDPRKTA-TAKLADNHVQIKP 202 (429)
T ss_pred cccccEEEEeCCCcccccchhhhhcccccccccc------cCCcccceEEEEecCcCc-hhhhhhheEecCC
Confidence 3677889989 899995 4555555421 122234477999999875 3444433344444
No 40
>PF14220 DUF4329: Domain of unknown function (DUF4329)
Probab=36.62 E-value=30 Score=29.90 Aligned_cols=25 Identities=28% Similarity=0.349 Sum_probs=19.4
Q ss_pred CCceEEEEecCCCC-----CCccCHHhHHH
Q 018085 138 LENAVGWYHSHPGY-----GCWLSGIDVST 162 (361)
Q Consensus 138 ~e~vVGWYHSHP~~-----~~~pS~~DV~t 162 (361)
+..+|+-||||..+ +-.||..|+..
T Consensus 58 g~~~vA~yHTHG~~~~~y~~evfS~~D~~~ 87 (123)
T PF14220_consen 58 GSTIVASYHTHGAYSDGYDNEVFSPQDIRG 87 (123)
T ss_pred ccceeeEeecccccCCCccccCCCHHHhhh
Confidence 46899999999865 34778888764
No 41
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=36.18 E-value=49 Score=38.73 Aligned_cols=110 Identities=16% Similarity=0.222 Sum_probs=67.6
Q ss_pred CCCceeEEEeceeecC---CeEEEEEEEeCCCccCCccccccc-ChHHHHHHHHHHHHHhCCCCceEEEEecCCCCCCcc
Q 018085 80 GGTIEVMGLMQGKTDG---DAIIVMDAFALPVEGTETRVNAQA-DAYEYMVDYSQTNKQAGRLENAVGWYHSHPGYGCWL 155 (361)
Q Consensus 80 ~~p~EV~GlLlG~~~~---~tl~Vtd~F~lP~~~te~rv~~~~-e~~eY~~~ml~~~r~v~~~e~vVGWYHSHP~~~~~p 155 (361)
.....|.|++.|+-.. ...+|...--+|+-+.-..|.... -+.+ +- -..++.++||-|+..+--+++
T Consensus 2151 D~~vqvag~vyG~s~~d~p~ikeI~~~~lVPQlgs~~~vq~~s~vP~d--------lp-~~e~le~lGwihtq~~el~~l 2221 (2365)
T COG5178 2151 DPHVQVAGLVYGKSGSDNPQIKEILSFGLVPQLGSLSGVQSSSFVPHD--------LP-GDEDLEILGWIHTQDDELPYL 2221 (2365)
T ss_pred ccceeeEEEEeccCCccCcchhheeEEEeeccccccccccccccCCCC--------CC-CcccceeeEEEecCCcccchh
Confidence 3457899999997542 234565444567755433332210 0000 00 114578999999999877889
Q ss_pred CHHhHHHHHhhhhcCCC--eEEEEEcCCCCccCCeeeEEEEEEccCCCCC
Q 018085 156 SGIDVSTQMLNQQFQEP--FLAVVIDPTRTVSAGKVEIGAFRTYPEGYKP 203 (361)
Q Consensus 156 S~~DV~tQ~~yQ~~~~p--~V~LIvDP~~t~~~Gk~~ikAFRl~p~~~~~ 203 (361)
+..++.++.. --..+. +|-|.|.- ..|.++++||.+..+|+.=
T Consensus 2222 ~~~~v~th~k-~~~d~~~d~v~ltv~~----~pgsiSl~ay~v~keG~~W 2266 (2365)
T COG5178 2222 EVAGVLTHRK-KIVDPEWDAVTLTVSY----LPGSISLRAYVVKKEGCNW 2266 (2365)
T ss_pred hhhhhhhhhh-cccCccccceeeeeee----ccceeeeeeeeehhccccc
Confidence 9998887642 112233 34444442 2789999999999988753
No 42
>PF15659 Toxin-JAB1: JAB-like toxin 1
Probab=34.71 E-value=42 Score=30.44 Aligned_cols=27 Identities=26% Similarity=0.302 Sum_probs=22.0
Q ss_pred CCCCceEEEEecCCCCCCccCHHhHHHH
Q 018085 136 GRLENAVGWYHSHPGYGCWLSGIDVSTQ 163 (361)
Q Consensus 136 ~~~e~vVGWYHSHP~~~~~pS~~DV~tQ 163 (361)
+.+..++. .||||.....||..|...-
T Consensus 113 ~~~~~iid-iHSHP~~~~~~S~~D~~~~ 139 (162)
T PF15659_consen 113 NNGNKIID-IHSHPENSNGPSGNDMKNA 139 (162)
T ss_pred cCCceEEE-eccCCCCCCCCCcchhhhh
Confidence 56678888 9999977779999987653
No 43
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=33.83 E-value=57 Score=32.95 Aligned_cols=61 Identities=20% Similarity=0.237 Sum_probs=38.9
Q ss_pred EEeceee-cCCeEEEEEEEeCCCccCCcc---cc--------cccC-hHHHHHHHHHHHHHhCCCCceEEEEecCCC
Q 018085 87 GLMQGKT-DGDAIIVMDAFALPVEGTETR---VN--------AQAD-AYEYMVDYSQTNKQAGRLENAVGWYHSHPG 150 (361)
Q Consensus 87 GlLlG~~-~~~tl~Vtd~F~lP~~~te~r---v~--------~~~e-~~eY~~~ml~~~r~v~~~e~vVGWYHSHP~ 150 (361)
|+|+|.. ..+.-.|.+..+.|.+.++.. +. ++.+ ..++..+..|++ --|..|||.|=.+|.
T Consensus 1 GLlIGq~~s~~kd~Vv~l~~tP~~d~~~~~~~~~~~~~~~~~id~~WVaeHA~qVsRML---PGGi~VlGifvv~~~ 74 (362)
T PF14778_consen 1 GLLIGQSSSSQKDYVVHLARTPPEDTDDEESDVRTSDSSIKDIDEEWVAEHARQVSRML---PGGISVLGIFVVAPD 74 (362)
T ss_pred CeEeccccCCCcceEEEecCCCCccccccccccccccccccccCHHHHHHHHHHHHhhC---CCCcEEEEEEEEcCH
Confidence 8999998 666567888888887654433 00 1111 124445555554 347899999988764
No 44
>PF04002 RadC: RadC-like JAB domain; InterPro: IPR001405 This family was named initially with reference to the Escherichia coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions []. However the relevant mutation has subsequently been shown to be in recG, not radC []. In addition all attempts to characterise a radiation-related function for RadC in Streptococcus pneumoniae failed, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair [].; PDB: 2QLC_A.
Probab=26.28 E-value=4e+02 Score=22.47 Aligned_cols=24 Identities=25% Similarity=0.202 Sum_probs=14.6
Q ss_pred CceEEEEecCCCCCCccCHHhHHH
Q 018085 139 ENAVGWYHSHPGYGCWLSGIDVST 162 (361)
Q Consensus 139 e~vVGWYHSHP~~~~~pS~~DV~t 162 (361)
..-|=..|-||...+.||.-|+..
T Consensus 65 A~~vIl~HNHPsG~~~PS~~D~~~ 88 (123)
T PF04002_consen 65 ASSVILAHNHPSGDPEPSDADIAL 88 (123)
T ss_dssp -SEEEEEEE-TTS--S--HHHHHH
T ss_pred CceEEEEEEcCCCCCCCCHhHHHH
Confidence 455667899999999999999864
No 45
>PF06442 DHFR_2: R67 dihydrofolate reductase; InterPro: IPR009159 Dihydrofolate reductase (DHFR) (1.5.1.3 from EC) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate, an essential step in de novo synthesis both of glycine and of purines and deoxythymidine phosphate (the precursors of DNA synthesis) [], and important also in the conversion of deoxyuridine monophosphate to deoxythymidine monophosphate. Although DHFR is found ubiquitously in prokaryotes and eukaryotes, and is found in all dividing cells, maintaining levels of fully reduced folate coenzymes, the catabolic steps are still not well understood []. Bacterial species possesses distinct DHFR enzymes (based on their pattern of binding diaminoheterocyclic molecules), but mammalian DHFRs are highly similar []. The active site is situated in the N-terminal half of the sequence, which includes a conserved Pro-Trp dipeptide; the tryptophan has been shown [] to be involved in the binding of substrate by the enzyme. Its central role in DNA precursor synthesis, coupled with its inhibition by antagonists such as trimethoprim and methotrexate, which are used as anti-bacterial or anti-cancer agents, has made DHFR a target of anticancer chemotherapy. However, resistance has developed against some drugs, as a result of changes in DHFR itself []. This entry represents a plasmid-encoded DHFR which shows a high level of resistance to the antibiotic trimethoprim. It is a homotetramer with an unusual pore, which contains the active site, passing through the middle of the molecule []. Its structure is unrelated to that of chromosomal DHFRs.; GO: 0004146 dihydrofolate reductase activity, 0042493 response to drug, 0055114 oxidation-reduction process; PDB: 1VIF_A 3SFM_A 2P4T_A 2GQV_A 2RK2_A 2RH2_A 2RK1_A 1VIE_A.
Probab=26.21 E-value=34 Score=26.51 Aligned_cols=11 Identities=36% Similarity=0.924 Sum_probs=7.0
Q ss_pred CceEEEEecCC
Q 018085 139 ENAVGWYHSHP 149 (361)
Q Consensus 139 e~vVGWYHSHP 149 (361)
-.|||||.+.-
T Consensus 40 g~vvgwy~t~l 50 (78)
T PF06442_consen 40 GQVVGWYCTKL 50 (78)
T ss_dssp EEEEEEE--SS
T ss_pred ceEeEEEeccc
Confidence 47999997653
Done!