Query psy9085
Match_columns 394
No_of_seqs 408 out of 1310
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 18:28:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9085.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9085hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1554|consensus 100.0 1.3E-97 3E-102 707.9 22.1 323 57-382 4-328 (347)
2 cd08069 MPN_RPN11_CSN5 Mov34/M 100.0 9.9E-59 2.2E-63 449.8 28.0 262 97-364 1-267 (268)
3 cd08065 MPN_eIF3h Mpr1p, Pad1p 100.0 7.7E-37 1.7E-41 296.5 21.4 218 106-330 1-227 (266)
4 cd08064 MPN_eIF3f Mpr1p, Pad1p 100.0 2.1E-30 4.5E-35 251.3 23.6 244 108-379 1-247 (265)
5 cd08067 MPN_2A_DUB Mov34/MPN/P 100.0 1.2E-30 2.7E-35 241.3 18.3 132 107-244 6-147 (187)
6 KOG1560|consensus 100.0 3E-28 6.4E-33 232.7 13.6 219 102-327 9-245 (339)
7 cd08062 MPN_RPN7_8 Mpr1p, Pad1 100.0 8.8E-27 1.9E-31 227.8 22.5 201 106-333 1-205 (280)
8 KOG1555|consensus 100.0 1.3E-27 2.9E-32 233.8 15.5 193 104-301 29-236 (316)
9 cd08068 MPN_BRCC36 Mov34/MPN/P 99.9 3.7E-27 8E-32 225.6 17.4 138 105-244 1-152 (244)
10 cd08058 MPN_euk_mb Mpr1p, Pad1 99.9 1.2E-27 2.5E-32 205.5 12.2 114 113-242 1-119 (119)
11 smart00232 JAB_MPN JAB/MPN dom 99.9 7.5E-26 1.6E-30 194.7 17.9 134 107-243 1-134 (135)
12 cd08057 MPN_euk_non_mb Mpr1p, 99.9 1.8E-25 4E-30 200.6 16.5 134 108-244 1-137 (157)
13 PF01398 JAB: JAB1/Mov34/MPN/P 99.9 4E-26 8.7E-31 193.5 11.2 111 104-216 2-113 (114)
14 KOG2975|consensus 99.9 3.6E-24 7.8E-29 203.6 18.3 197 105-330 20-218 (288)
15 cd08066 MPN_AMSH_like Mov34/MP 99.9 2E-23 4.3E-28 191.2 17.1 131 106-249 2-135 (173)
16 PLN03246 26S proteasome regula 99.9 1.2E-22 2.7E-27 200.5 23.7 207 101-332 1-210 (303)
17 cd08063 MPN_CSN6 Mpr1p, Pad1p 99.9 2.3E-22 5E-27 197.3 19.6 202 107-333 2-209 (288)
18 cd07767 MPN Mpr1p, Pad1p N-ter 99.9 1.2E-21 2.6E-26 164.9 12.8 115 116-239 2-116 (116)
19 cd08070 MPN_like Mpr1p, Pad1p 99.8 9.4E-19 2E-23 151.9 14.7 120 113-244 2-121 (128)
20 KOG1556|consensus 99.7 1.6E-16 3.4E-21 150.5 16.2 179 103-306 6-191 (309)
21 COG1310 Predicted metal-depend 99.6 9.1E-15 2E-19 128.0 12.8 105 108-225 2-107 (134)
22 cd08072 MPN_archaeal Mov34/MPN 99.6 1.1E-14 2.4E-19 125.4 13.0 109 110-243 1-109 (117)
23 cd08073 MPN_NLPC_P60 Mpr1p, Pa 99.5 5.4E-13 1.2E-17 113.5 11.9 95 114-226 2-96 (108)
24 cd08060 MPN_UPF0172 Mov34/MPN/ 99.4 5.6E-12 1.2E-16 116.6 13.2 111 110-227 1-114 (182)
25 PF14464 Prok-JAB: Prokaryotic 99.3 1E-11 2.2E-16 103.1 10.8 95 112-225 2-96 (104)
26 KOG2880|consensus 99.3 5E-12 1.1E-16 125.4 7.0 129 102-243 248-378 (424)
27 cd08056 MPN_PRP8 Mpr1p, Pad1p 99.1 1.4E-09 3.1E-14 105.1 12.3 127 107-248 37-171 (252)
28 PTZ00196 60S ribosomal protein 99.0 4.5E-11 9.8E-16 99.5 0.3 41 3-55 1-41 (98)
29 cd08059 MPN_prok_mb Mpr1p, Pad 99.0 3.2E-09 6.9E-14 88.4 10.1 91 114-225 2-92 (101)
30 TIGR03735 PRTRC_A PRTRC system 99.0 3.7E-09 8.1E-14 98.4 11.5 113 109-245 74-186 (192)
31 TIGR02256 ICE_VC0181 integrati 99.0 6.2E-09 1.3E-13 91.7 12.2 109 116-225 3-114 (131)
32 PF01158 Ribosomal_L36e: Ribos 98.9 8.2E-11 1.8E-15 98.2 -3.1 41 3-55 1-41 (98)
33 KOG3452|consensus 98.9 2.9E-10 6.2E-15 94.0 -0.5 43 1-55 1-43 (102)
34 PF03665 UPF0172: Uncharacteri 98.8 1.5E-07 3.1E-12 88.3 13.9 114 106-227 2-120 (196)
35 KOG3050|consensus 98.5 7.9E-07 1.7E-11 85.0 10.0 161 106-295 9-176 (299)
36 cd08061 MPN_NPL4 Mov34/MPN/PAD 98.2 5.1E-05 1.1E-09 74.7 15.6 135 103-244 8-160 (274)
37 KOG3289|consensus 98.1 4E-05 8.6E-10 70.5 12.2 114 107-226 3-119 (199)
38 COG5051 RPL36A Ribosomal prote 97.6 7.1E-06 1.5E-10 67.0 -1.7 43 1-55 1-43 (97)
39 PF05021 NPL4: NPL4 family; I 97.3 0.0024 5.3E-08 63.9 11.4 107 131-244 2-143 (306)
40 KOG2834|consensus 90.0 3.1 6.7E-05 43.9 11.1 130 107-244 176-341 (510)
41 KOG1795|consensus 84.1 2.3 4.9E-05 49.8 6.5 112 124-248 2111-2226(2321)
42 cd08071 MPN_DUF2466 Mov34/MPN/ 84.0 13 0.00028 31.8 9.9 30 183-212 59-89 (113)
43 PF04002 RadC: RadC-like JAB d 77.2 20 0.00043 31.0 8.9 89 112-212 5-94 (123)
44 PRK00024 hypothetical protein; 63.5 81 0.0018 30.2 10.5 105 109-225 103-212 (224)
45 TIGR00608 radc DNA repair prot 59.7 1.3E+02 0.0028 28.9 11.1 103 110-225 98-206 (218)
46 PF14220 DUF4329: Domain of un 39.6 25 0.00054 30.9 2.5 64 126-207 19-87 (123)
47 PF14778 ODR4-like: Olfactory 37.1 52 0.0011 33.8 4.8 61 132-195 1-74 (362)
48 PF15659 Toxin-JAB1: JAB-like 35.2 43 0.00094 30.9 3.5 28 181-209 113-140 (162)
49 COG5178 PRP8 U5 snRNP spliceos 30.6 68 0.0015 38.2 4.7 111 124-248 2150-2266(2365)
No 1
>KOG1554|consensus
Probab=100.00 E-value=1.3e-97 Score=707.95 Aligned_cols=323 Identities=70% Similarity=1.167 Sum_probs=310.8
Q ss_pred ccchhhhhhhhhccCccccccccccccCCHHHHHHHHhcCCCCCCCCCeeEEEECHHHHHHHHHHHhcCCCceEEEEEee
Q psy9085 57 CTIIFQNKTWIMENNIETLSATDEIFKYDRKRQQDMIAAKPWEKDPHFFKDIKISALALLKMVMHARSGGTLEVMGLLLG 136 (394)
Q Consensus 57 ~~~~~~~~~~~~~n~~~~~~~~d~~~~~d~~~~~~~~~~~pw~~dp~~~~~V~Is~~aLlkIl~Hars~~p~EVmGlLLG 136 (394)
+.+.+|+++||++||++.++..|+||+||.+.|.++..++||..||+||+.|+||+++|+||++||++|++.||||+|+|
T Consensus 4 ~~s~~~~k~we~en~~~~~~~~deif~yd~~sq~~~~~~kpw~~Dp~~fk~vkISalAllKm~~hA~~GgnlEiMGlm~G 83 (347)
T KOG1554|consen 4 SSSYTAQKTWELENNIQSVESEDEIFRYDQKSQRKIILEKPWSTDPHYFKHVKISALALLKMVMHARSGGNLEIMGLMQG 83 (347)
T ss_pred ccccchhHHHHHhhhhccCccchhhhhcCHHHHHHHHhcCcccCCCchhhhhhhHHHHHHHHHHHHhcCCCeEEEeeecc
Confidence 44668999999999999998899999999999999999999999999999999999999999999999999999999999
Q ss_pred EEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceEEEEecCCCCCCcccHhhHHhHHhhhccCC
Q psy9085 137 KIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQE 216 (394)
Q Consensus 137 ~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~ 216 (394)
++++++++|+|||+||++|||+|||++.+++|||.+|.+.++.+||.+++||||||||+|+||+|+|||.||.++|++++
T Consensus 84 kv~g~t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k~~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQe 163 (347)
T KOG1554|consen 84 KVDGDTIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEAKNVGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQE 163 (347)
T ss_pred cccCCeEEEEeccccccccccceechHHHHHHHHHHHHHHHHHhhhhhceeeeeecCCCCCccccCcchhHHHHhhhhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeEEEEEcCCCCCCCCceEEEEEEEccCCCCCCCCCCCcccccccchhccccccceeEEeeeeEEecCHHHHHHHHhhhh
Q psy9085 217 PFVAIVIDPVRTISAGKVCLGSFRTYPKGYKPANEEPSEYQTIPLNKIEDFGVHCKQYYSLDVSYFKSSLDRRLLDSLWN 296 (394)
Q Consensus 217 p~VaLVvDp~~t~~~Gkv~i~AFR~~p~~~~~~~~~~~e~~~iPl~ki~d~g~~~~~yy~L~V~~~~S~ld~~~L~~L~~ 296 (394)
||||+||||.||.++|++.|+|||++|.||+||++.|++||+||++||+|||+||.+||+|+|+||+|.+|.++|+.||+
T Consensus 164 PfvAvViDP~Rtlsagkv~iGAFRTyp~gyk~~d~~~seyqtipl~kied~gvHck~yysl~isyfks~ld~kll~~Lwn 243 (347)
T KOG1554|consen 164 PFVAVVIDPTRTLSAGKVNIGAFRTYPKGYKPPDEPPSEYQTIPLNKIEDFGVHCKQYYSLEISYFKSSLDMKLLELLWN 243 (347)
T ss_pred CeEEEEecCccccccCceeeceeecccCCCCCCCCCchhhhccchhhhhhcccceEEeeccchhhhhhhhhHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhccccccccHHHHHHHHHHHHHHHHHHHHhhcccccccccccCc--chhhHHHHhhhhhHHHHHHHhhhHHHHH
Q psy9085 297 KYWVNTLSSSSLLTNADYLTGQMCDLSDKLEQAESALVRNFLISESQERR--PETKLMKATKDCCKTTIECIHGLMAQMI 374 (394)
Q Consensus 297 ~~w~~~Ls~s~l~~n~~~~~~~i~dl~~k~~~~~~~~~~~~~~~~~~~~~--~~~~~~k~~~~~~~~~~e~~~g~~~~~~ 374 (394)
+||++||+++|+++|.+|+++|+.||++||.+.+++++++. ..++++ ++.+|+|+++|+++...|++||+|+|++
T Consensus 244 kywv~Tlsss~ll~N~dy~~~qi~d~~ekl~q~~~~l~~s~---~~~d~~~ed~~~l~k~~~Ds~~~~~e~~~gl~s~vv 320 (347)
T KOG1554|consen 244 KYWVRTLSSSPLLKNIDYLNGQIRDLSEKLEQREDSLETSD---NTHDRKSEDENLLAKATRDSSKCTNELIHGLMSQVV 320 (347)
T ss_pred hhhhcccccccccccchhhcchhhhHHHHHHhhhhhcccCc---ccccccccchhhhhhhhhhhhhhhhcchhHHHHHHH
Confidence 99999999999999999999999999999999999998862 233333 3455999999999999999999999999
Q ss_pred HHHHcCCC
Q psy9085 375 KQQLFNHN 382 (394)
Q Consensus 375 k~~~f~~~ 382 (394)
|+.|||..
T Consensus 321 kd~lf~~~ 328 (347)
T KOG1554|consen 321 KDKLFNDN 328 (347)
T ss_pred HHHHHHhh
Confidence 99999964
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=9.9e-59 Score=449.84 Aligned_cols=262 Identities=58% Similarity=0.998 Sum_probs=236.2
Q ss_pred CCCCCCCCeeEEEECHHHHHHHHHHHhcCCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHH-
Q psy9085 97 PWEKDPHFFKDIKISALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIE- 175 (394)
Q Consensus 97 pw~~dp~~~~~V~Is~~aLlkIl~Hars~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle- 175 (394)
||+.||+||++|+|++.|+++|++||+++.|.||||+|+|.+++++++|++|||+|+.++++++++.. +|+..|++
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 89999999999999999999999999999999999999999999999999999999999998887743 56666676
Q ss_pred -HHHHhCCCCceEEEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEccCCCCC--CCCC
Q psy9085 176 -AAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYPKGYKP--ANEE 252 (394)
Q Consensus 176 -~~~kvgr~e~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~~~~~--~~~~ 252 (394)
+++++++++++||||||||+++||||++|+.+|..||.+.+|+|+|||||.++.+.|++.|+|||++|.++.+ +.+.
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 9999999999999999999999999999999999999999999999999999866999999999999999886 5666
Q ss_pred CCcccccccchhccccccceeEEeeeeEEecCHHHHHHHHhhhhhhhhhhhccccccccH-HHHHHHHHHHHHHHHHHHH
Q psy9085 253 PSEYQTIPLNKIEDFGVHCKQYYSLDVSYFKSSLDRRLLDSLWNKYWVNTLSSSSLLTNA-DYLTGQMCDLSDKLEQAES 331 (394)
Q Consensus 253 ~~e~~~iPl~ki~d~g~~~~~yy~L~V~~~~S~ld~~~L~~L~~~~w~~~Ls~s~l~~n~-~~~~~~i~dl~~k~~~~~~ 331 (394)
.++++.+|..+++++|.+++.||+|||+|++|++|+.+|..||++||+++|+++++.+|+ ++..++|.+|++++.++..
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 677889999999999999999999999999999999999999999999999999999998 9999999999999999887
Q ss_pred hhcccccccccccCcchhhHHHHhhhhhHHHHH
Q psy9085 332 ALVRNFLISESQERRPETKLMKATKDCCKTTIE 364 (394)
Q Consensus 332 ~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~e 364 (394)
...+.. +.....+..+++.|+ +|+.|++.|
T Consensus 238 ~~~~~~--~~~~~~~~~~~~~~~-~~~~~~~~~ 267 (268)
T cd08069 238 QEERLT--GEELDIANVGKLDKA-RDSSKIHLE 267 (268)
T ss_pred hhhccC--hhhhcccchhhhhhc-cccchhhhc
Confidence 765431 112234455667777 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=7.7e-37 Score=296.47 Aligned_cols=218 Identities=24% Similarity=0.330 Sum_probs=177.0
Q ss_pred eEEEECHHHHHHHHHHHhcCCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCc
Q psy9085 106 KDIKISALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLEN 185 (394)
Q Consensus 106 ~~V~Is~~aLlkIl~Hars~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~ 185 (394)
++|+|+++|+++|++||.++.|.+|||+|+|...+++++||||||+|+.+++++..+...+.+|+.+|+++++++|.+++
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 47999999999999999999999999999999999999999999999987766543334466899999999999999999
Q ss_pred eEEEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEccCCCCCCCCCCCcccccccchhc
Q psy9085 186 AIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYPKGYKPANEEPSEYQTIPLNKIE 265 (394)
Q Consensus 186 iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~~~~~~~~~~~e~~~iPl~ki~ 265 (394)
+|||||||| +++|.+..++++|..||...+++|+||+||.++ +.|++.++|||++|.+.....++ .+.. ..++
T Consensus 81 iVGWY~S~p-~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s-~~g~l~lkAyrl~~~~~~~~~~~--~~~~---~~l~ 153 (266)
T cd08065 81 HVGWYQSTY-LGSFFTRDLIETQYNYQEAIEESVVLVYDPSKT-SQGSLSLKAYRLSEKFMELYKEG--KFST---ESLR 153 (266)
T ss_pred EEEeEeecC-CCCcCCHHHHHHHHHHhccCCCCEEEEECCCcc-cccceeeEEEEEcHHHHHHhhcC--CcCH---HHHH
Confidence 999999999 999989999999999998888899999999986 47899999999999754322211 1111 1223
Q ss_pred ccccc-ceeEEeeeeEEecCHHHHHHHHhhhhhh-------hhhhhcccccc-ccHHHHHHHHHHHHHHHHHHH
Q psy9085 266 DFGVH-CKQYYSLDVSYFKSSLDRRLLDSLWNKY-------WVNTLSSSSLL-TNADYLTGQMCDLSDKLEQAE 330 (394)
Q Consensus 266 d~g~~-~~~yy~L~V~~~~S~ld~~~L~~L~~~~-------w~~~Ls~s~l~-~n~~~~~~~i~dl~~k~~~~~ 330 (394)
..+.. .+.|++|||+++++.+++.+|..|.... -...|+..+++ .|.+.+.++|++|.....++.
T Consensus 154 ~~~~~~~~if~eiPv~i~n~~l~~~~L~~l~~~~~~~~~~~~~l~l~~~~~le~~l~~l~~~id~l~~e~~~~~ 227 (266)
T cd08065 154 EANLTFSNIFEEIPVVIRNSHLVNALLSELEEDSPSSQSDFDRLDLSTNSFLEKNLELLMESVDELSQEQGKFN 227 (266)
T ss_pred HhcCchhcEEEEEEEEEEchHHHHHHHHhcccCCCcccCCcccccccCchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33332 6889999999999999999999996532 22445556655 777888888888877766554
No 4
>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=99.97 E-value=2.1e-30 Score=251.30 Aligned_cols=244 Identities=17% Similarity=0.259 Sum_probs=191.5
Q ss_pred EEECHHHHHHHHHHHhc--CCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCc
Q psy9085 108 IKISALALLKMVMHARS--GGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLEN 185 (394)
Q Consensus 108 V~Is~~aLlkIl~Hars--~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~ 185 (394)
|+|+|+|+++|++|+.+ ..+.+|+|+|+|...+++++|||||++|+..+++++.. +.+|+.+|+++++++++++.
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~---d~~y~~~m~~~~kkv~~~~~ 77 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNESEDQVAV---DMEYHRTMYELHQKVNPKEV 77 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCCEEEEEeCeecceeCCCCeEEE---cHHHHHHHHHHHHHhCCCCc
Confidence 68999999999999854 67899999999999999999999999999877665433 46899999999999999999
Q ss_pred eEEEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEccCCCCCCCCCCCcccccccchhc
Q psy9085 186 AIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYPKGYKPANEEPSEYQTIPLNKIE 265 (394)
Q Consensus 186 iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~~~~~~~~~~~e~~~iPl~ki~ 265 (394)
+||||||+|... ++...|+.|..+|...++.|+|++||..+ .+++.++||++.+.+....
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 999999999543 33455666655554323669999999875 4589999999999752210
Q ss_pred cccccceeEEeeeeEEecCHHHHHHHHhhhhhhhhhhhccccccccHHHHHHHHHHHHHHHHHHHHhhcccccccc-ccc
Q psy9085 266 DFGVHCKQYYSLDVSYFKSSLDRRLLDSLWNKYWVNTLSSSSLLTNADYLTGQMCDLSDKLEQAESALVRNFLISE-SQE 344 (394)
Q Consensus 266 d~g~~~~~yy~L~V~~~~S~ld~~~L~~L~~~~w~~~Ls~s~l~~n~~~~~~~i~dl~~k~~~~~~~~~~~~~~~~-~~~ 344 (394)
.....|.++|+++..++.|+..++.|++.+|..+ ..+++.++.+++.+.+.+|..+++.+..-+..-. .|. ..+
T Consensus 138 ---~~~~~F~~ip~~i~~~eaE~i~v~~l~~~~~~~~-~~~~~~~~l~~~~~al~~L~~~l~~i~~Yl~~V~-~g~~~~d 212 (265)
T cd08064 138 ---TLGSMFVPIPLELLYSEAERVALDLLAKTLASPS-RSAPLTSDLEQLEASLEKLQEMLDRVLRYVEDVL-AGKVKAD 212 (265)
T ss_pred ---CcceEEEEcceeeecCcHHHHHHHHHHhhccCCc-ccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCC
Confidence 1246799999999999999999999999999766 5566779999999999999999999887664310 011 111
Q ss_pred CcchhhHHHHhhhhhHHHHHHHhhhHHHHHHHHHc
Q psy9085 345 RRPETKLMKATKDCCKTTIECIHGLMAQMIKQQLF 379 (394)
Q Consensus 345 ~~~~~~~~k~~~~~~~~~~e~~~g~~~~~~k~~~f 379 (394)
.+-...|.+++...-++..|+....+...+++.|+
T Consensus 213 ~~i~r~l~~~~~~lp~~~~~~f~~~~~~~~~D~lm 247 (265)
T cd08064 213 NAIGRYLMDALTSVPKLDPEEFEKMFNSSLQDLLM 247 (265)
T ss_pred HHHHHHHHHHHhhCCCCCHHHHHHHHHhhcchHHH
Confidence 22234467777777777788888888888777765
No 5
>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=1.2e-30 Score=241.31 Aligned_cols=132 Identities=27% Similarity=0.336 Sum_probs=114.2
Q ss_pred EEEECHHHHHHHHHHHhcCCCceEEEEEeeEEc--CCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCC
Q psy9085 107 DIKISALALLKMVMHARSGGTLEVMGLLLGKID--ANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLE 184 (394)
Q Consensus 107 ~V~Is~~aLlkIl~Hars~~p~EVmGlLLG~~d--~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e 184 (394)
+|+|++.||++|++||+++. .||||+|+|..+ +..++|+++||+|+..+..++++ +.+++.+|++.+++. ++
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---DPVSETEIRESLESR--GL 79 (187)
T ss_pred EEEECHHHHHHHHHHhcCCC-cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCccccc---CHHHHHHHHHHHHHc--CC
Confidence 69999999999999999987 999999999975 46899999999999776666654 345678899999874 58
Q ss_pred ceEEEEecCCCCCCcccHhhHHhHHhhhccC-------CCeEEEEEcCCCCCCC-CceEEEEEEEccC
Q psy9085 185 NAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQ-------EPFVAIVIDPVRTISA-GKVCLGSFRTYPK 244 (394)
Q Consensus 185 ~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~-------~p~VaLVvDp~~t~~~-Gkv~i~AFR~~p~ 244 (394)
++||||||||.++||||.+||+||..||.+. +|||+|||||..+... ....|+||++.|.
T Consensus 80 ~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~ 147 (187)
T cd08067 80 SVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPP 147 (187)
T ss_pred EEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECC
Confidence 9999999999999999999999999999864 4899999999876433 4468999999994
No 6
>KOG1560|consensus
Probab=99.95 E-value=3e-28 Score=232.74 Aligned_cols=219 Identities=22% Similarity=0.352 Sum_probs=170.4
Q ss_pred CCCeeEEEECHHHHHHHHHHHhcCCCc--eEEEEEeeEEcCCeEEEEEEEecCccC--CCCccccc--ccH-HHHHHHHH
Q psy9085 102 PHFFKDIKISALALLKMVMHARSGGTL--EVMGLLLGKIDANSMIVMDAFALPVEG--TETRVNAQ--AQA-YEYMTAYI 174 (394)
Q Consensus 102 p~~~~~V~Is~~aLlkIl~Hars~~p~--EVmGlLLG~~d~~tl~Vtd~F~lP~~~--te~rv~a~--~ea-~ey~~~ml 174 (394)
..++++|.|++++++||++||++..+. -+.|.|+|.+.+++++||+|||.|... .++.++.+ +++ ..|+.+|+
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 346899999999999999999987665 578999999989999999999999732 33444433 222 36899999
Q ss_pred HHHHHhCCCCceEEEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEccCCCCCCCCCCC
Q psy9085 175 EAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYPKGYKPANEEPS 254 (394)
Q Consensus 175 e~~~kvgr~e~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~~~~~~~~~~~ 254 (394)
+.+|.+|.+...||||+||- +|.++|..-+++|+.||...+..|.+|+||.+|. +|.+.++|||++|+....-++.
T Consensus 89 rrlr~vnid~~hVGwYqs~~-vgs~lS~~lveSqy~YQ~a~pesVvliYD~~kss-qG~L~lrAyrLTp~am~~~kek-- 164 (339)
T KOG1560|consen 89 RRLRYVNIDHLHVGWYQSAY-VGSFLSPALVESQYAYQKAIPESVVLIYDPIKSS-QGTLSLRAYRLTPEAMAAHKEK-- 164 (339)
T ss_pred HHhhhcCccceeeeeeeeeh-hccccCHHHHHHHHHHHhcCCccEEEEecccccc-CceEEeehhhcCHHHHHHHhcC--
Confidence 99999999999999999998 7789999999999999999999999999999985 9999999999999543322111
Q ss_pred cccccccchhcccccc-ceeEEeeeeEEecCHHHHHHHHhhh-------hhhhhh--hhccc-cccccHHHHHHHHHHHH
Q psy9085 255 EYQTIPLNKIEDFGVH-CKQYYSLDVSYFKSSLDRRLLDSLW-------NKYWVN--TLSSS-SLLTNADYLTGQMCDLS 323 (394)
Q Consensus 255 e~~~iPl~ki~d~g~~-~~~yy~L~V~~~~S~ld~~~L~~L~-------~~~w~~--~Ls~s-~l~~n~~~~~~~i~dl~ 323 (394)
++. | +-++..++. .+.|.+|||.|++|.|.++++.+|. +++-.+ .|++. .|-.|.+-+.+.+++|.
T Consensus 165 dwt--p-ealk~~nltyenmfeElPIVIknS~L~nvlmseLs~~e~c~sdk~~~~~fdlgs~t~leknir~lme~vDEl~ 241 (339)
T KOG1560|consen 165 DWT--P-EALKSANLTYENMFEELPIVIKNSHLANVLMSELSEPEDCESDKPLHSNFDLGSGTRLEKNIRLLMERVDELH 241 (339)
T ss_pred CCC--H-HHHHhcCCCHHHHHhhcCeeeeccHHHHHHHHhccccccccccccccccccccchhhHHHHHHHHHHHHHHHH
Confidence 111 2 223333444 5789999999999999999999997 223222 33333 34477778888888776
Q ss_pred HHHH
Q psy9085 324 DKLE 327 (394)
Q Consensus 324 ~k~~ 327 (394)
+.+.
T Consensus 242 qe~~ 245 (339)
T KOG1560|consen 242 QEIV 245 (339)
T ss_pred HHHH
Confidence 6653
No 7
>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=99.95 E-value=8.8e-27 Score=227.80 Aligned_cols=201 Identities=20% Similarity=0.283 Sum_probs=163.5
Q ss_pred eEEEECHHHHHHHHHHHhc---CCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCC
Q psy9085 106 KDIKISALALLKMVMHARS---GGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGR 182 (394)
Q Consensus 106 ~~V~Is~~aLlkIl~Hars---~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr 182 (394)
++|.|+|+||++|++|+.+ +.+.+|+|+|||...+++++|+|||++|++.++++.+....+.+|+.+|+++++++++
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 4799999999999999953 4578999999999999999999999999987777665544568999999999999999
Q ss_pred CCceEEEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEccCCCCCCCCCCCcccccccc
Q psy9085 183 LENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYPKGYKPANEEPSEYQTIPLN 262 (394)
Q Consensus 183 ~e~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~~~~~~~~~~~e~~~iPl~ 262 (394)
++.+||||||||+. +..|+..+..|+.+.+++|+|++||... .+++.++||...+.+...
T Consensus 81 ~e~vVGWY~tg~~~----~~~d~~ih~~~~~~~~~pv~l~vd~~~~--~~~lpi~aY~s~~~~~~~-------------- 140 (280)
T cd08062 81 KEKIVGWYSTGPKL----RPNDLDINELFRRYCPNPVLVIIDVRPK--DLGLPTEAYIAVEEVHDD-------------- 140 (280)
T ss_pred CCCeEEEecCCCCC----CcchHHHHHHHHHhCCCCEEEEEecCCC--CCCCceEEEEEeeeccCC--------------
Confidence 99999999999974 4567777888898888889999999763 577999999998855321
Q ss_pred hhccccc-cceeEEeeeeEEecCHHHHHHHHhhhhhhhhhhhccccccccHHHHHHHHHHHHHHHHHHHHhh
Q psy9085 263 KIEDFGV-HCKQYYSLDVSYFKSSLDRRLLDSLWNKYWVNTLSSSSLLTNADYLTGQMCDLSDKLEQAESAL 333 (394)
Q Consensus 263 ki~d~g~-~~~~yy~L~V~~~~S~ld~~~L~~L~~~~w~~~Ls~s~l~~n~~~~~~~i~dl~~k~~~~~~~~ 333 (394)
|. ....|.++|+++-.++.|+..++.|.+.- ..-+.+.+.++.....+.+..|..+|+....-+
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 24679999999999999999999997631 122344454577777888888888887776543
No 8
>KOG1555|consensus
Probab=99.95 E-value=1.3e-27 Score=233.76 Aligned_cols=193 Identities=35% Similarity=0.623 Sum_probs=162.7
Q ss_pred CeeEEEECHHHHHHHHHHHhcCCCce-EEEEE-ee---E-EcCCeEEEEEEEecCccCCCCc--ccccccHHHHHHHHHH
Q psy9085 104 FFKDIKISALALLKMVMHARSGGTLE-VMGLL-LG---K-IDANSMIVMDAFALPVEGTETR--VNAQAQAYEYMTAYIE 175 (394)
Q Consensus 104 ~~~~V~Is~~aLlkIl~Hars~~p~E-VmGlL-LG---~-~d~~tl~Vtd~F~lP~~~te~r--v~a~~ea~ey~~~mle 175 (394)
.-.+|.|+.+++++|++|.|.+.|.| +||+| +| . ++..++.|.+.|+.|..++.-. +... +.-++.+|++
T Consensus 29 ~~e~v~i~slall~m~rh~r~~~p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg~~is~~~e~~--d~V~q~q~~~ 106 (316)
T KOG1555|consen 29 EKETVYISSLALLKMLRHDRAGSPEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAV--DPVFQTQMMD 106 (316)
T ss_pred CcceeeeehhhhhhcccccccCCchhhccceeecccccceeeecceeeeeeeccccccceecccchhc--cHHHHHHHHH
Confidence 35689999999999999999999999 99999 99 3 4678899999999999887654 3332 3457889999
Q ss_pred HHHHhCCCCceEEEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEccCCCCCCCCCCCc
Q psy9085 176 AAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYPKGYKPANEEPSE 255 (394)
Q Consensus 176 ~~~kvgr~e~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~~~~~~~~~~~e 255 (394)
+++..|+.+.+||||||||+++||||..||+||+.||...+..++.+|||..+. .|++.+.|||+.......+..+|+.
T Consensus 107 ~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~-~g~vv~d~f~~In~~~~~~~~eprq 185 (316)
T KOG1555|consen 107 LLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSP-YGKVVPDAFSSINPQWISPGGEPRQ 185 (316)
T ss_pred HHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCC-CCCccCChhhhcCcccccCCCCCcc
Confidence 999999999999999999999999999999999999999889999999999876 8999999999988655555555654
Q ss_pred ccc--cccch----hcc-ccccceeEEeeeeEEecCHHHHHHHHhhhhhhhhh
Q psy9085 256 YQT--IPLNK----IED-FGVHCKQYYSLDVSYFKSSLDRRLLDSLWNKYWVN 301 (394)
Q Consensus 256 ~~~--iPl~k----i~d-~g~~~~~yy~L~V~~~~S~ld~~~L~~L~~~~w~~ 301 (394)
..+ .|+++ .++ +|. +.||.++|.+++.+.++.++..+..+.|.+
T Consensus 186 tts~~~~m~~~~s~q~~~~g~--n~y~~~ei~~~v~~~~~~~~~nv~~~s~~~ 236 (316)
T KOG1555|consen 186 TTSNGGHMDMQESLQEDIHGL--NRYYRIEIPLHVLPYEQLMLLNVPLKSWKS 236 (316)
T ss_pred ccccccccccchhHHhHhhcc--CceEEEEeeEEechhhhhchhccchhhhhh
Confidence 332 35555 333 443 279999999999999999999999998865
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=99.95 E-value=3.7e-27 Score=225.59 Aligned_cols=138 Identities=29% Similarity=0.460 Sum_probs=109.0
Q ss_pred eeEEEECHHHHHHHHHHHhcCCCceEEEEEeeEEc-------CCeEEEEEEEecCcc-CCCCcccccccHHHH---HHHH
Q psy9085 105 FKDIKISALALLKMVMHARSGGTLEVMGLLLGKID-------ANSMIVMDAFALPVE-GTETRVNAQAQAYEY---MTAY 173 (394)
Q Consensus 105 ~~~V~Is~~aLlkIl~Hars~~p~EVmGlLLG~~d-------~~tl~Vtd~F~lP~~-~te~rv~a~~ea~ey---~~~m 173 (394)
+++|+|++.++.+|+.||+++.|+||||+|+|..+ ...+.|...+++++. .+.+++.+ ++.++ +.++
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 36899999999999999999999999999999975 334444455544443 23455554 23332 3344
Q ss_pred HHHHHHhCCCCceEEEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCC---CCCCCceEEEEEEEccC
Q psy9085 174 IEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVR---TISAGKVCLGSFRTYPK 244 (394)
Q Consensus 174 le~~~kvgr~e~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~---t~~~Gkv~i~AFR~~p~ 244 (394)
.++.+..|+++.+||||||||+++||||.+|+.+|..||.+.+++++||+|+.. +...|++.++|||+.+.
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 455566789999999999999999999999999999999999999999998753 33468899999999884
No 10
>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=99.95 E-value=1.2e-27 Score=205.49 Aligned_cols=114 Identities=38% Similarity=0.519 Sum_probs=95.8
Q ss_pred HHHHHHHHHHhcCCCceEEEEEeeEEc-----CCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceE
Q psy9085 113 LALLKMVMHARSGGTLEVMGLLLGKID-----ANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAI 187 (394)
Q Consensus 113 ~aLlkIl~Hars~~p~EVmGlLLG~~d-----~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iV 187 (394)
.|+++|+.||+++.|.||||+|+|..+ ..+++|+++|+.|...+ ..+ .|....+..++++++|
T Consensus 1 ~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~~---------~~~---~~~~~~~~~~~g~~~v 68 (119)
T cd08058 1 DALLKMLQHAESNTGIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCT---------GEN---VEELFNVQTGRPLLVV 68 (119)
T ss_pred CHHHHHHHHhcCCCCeEEEEEeeeEEecCccceeEEEEeecCCCCCCch---------hHH---HHHHHHHHhCCCCeEE
Confidence 379999999999999999999999865 34589999998876321 222 2333445577899999
Q ss_pred EEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEc
Q psy9085 188 GWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTY 242 (394)
Q Consensus 188 GWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~ 242 (394)
|||||||+++++||..|+++|..||.+.+++++||+||.++ ++.++|||++
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 99999999999999999999999999999999999999762 7899999984
No 11
>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=99.94 E-value=7.5e-26 Score=194.70 Aligned_cols=134 Identities=32% Similarity=0.528 Sum_probs=120.1
Q ss_pred EEEECHHHHHHHHHHHhcCCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCce
Q psy9085 107 DIKISALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENA 186 (394)
Q Consensus 107 ~V~Is~~aLlkIl~Hars~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~i 186 (394)
.|.|++.++++|++||.+..|.|+||+|+|..++++++|+++|++|+.....+... .+.+|+..|.+..++.++++++
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 37899999999999999999999999999999888999999999998765554322 2457888888899999999999
Q ss_pred EEEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEcc
Q psy9085 187 IGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYP 243 (394)
Q Consensus 187 VGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p 243 (394)
||||||||..+++||..|+.+|..+|.....++++++||.++. .|++.++||++.+
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 9999999999999999999999999999888999999999875 5999999999975
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=99.93 E-value=1.8e-25 Score=200.62 Aligned_cols=134 Identities=23% Similarity=0.377 Sum_probs=114.1
Q ss_pred EEECHHHHHHHHHHHhcCC--CceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCc
Q psy9085 108 IKISALALLKMVMHARSGG--TLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLEN 185 (394)
Q Consensus 108 V~Is~~aLlkIl~Hars~~--p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~ 185 (394)
|+|+|+|+++|++|+.+.. +.+|+|+|+|..++++++|+|||++|.+.+++.. ..+.+|+.+|++++++++++++
T Consensus 1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~~~~~~veV~nsF~lp~~~~~~~~---~~d~~y~~~m~~~~~~v~~~~~ 77 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGDKIEVTNSFELPFDEEEESI---FIDTEYLEKRYNLHKKVYPQEK 77 (157)
T ss_pred CEEccHHHhhHHHHHHhccCCCCeEEEEEEeEEeCCEEEEEEeEEccccCCCcch---hhhHHHHHHHHHHHHHhCCCCC
Confidence 6899999999999996655 8999999999999999999999999997766542 2367899999999999999999
Q ss_pred eEEEEecCCCCCCcccHhhHHhHHhhhcc-CCCeEEEEEcCCCCCCCCceEEEEEEEccC
Q psy9085 186 AIGWYHSHPGYGCWLSGIDVSTQMLNQNF-QEPFVAIVIDPVRTISAGKVCLGSFRTYPK 244 (394)
Q Consensus 186 iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~-~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~ 244 (394)
+|||||||+.++++++..|..-+..+... .+++|+|++||.++...|++.|+|||+.+.
T Consensus 78 vVGWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~ 137 (157)
T cd08057 78 IVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQR 137 (157)
T ss_pred EEEEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEecC
Confidence 99999999998877777776654444443 567799999998754579999999999973
No 13
>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=99.93 E-value=4e-26 Score=193.49 Aligned_cols=111 Identities=32% Similarity=0.582 Sum_probs=95.8
Q ss_pred CeeEEEECHHHHHHHHHHHhcCCCceEEEEEeeEEcCC-eEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCC
Q psy9085 104 FFKDIKISALALLKMVMHARSGGTLEVMGLLLGKIDAN-SMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGR 182 (394)
Q Consensus 104 ~~~~V~Is~~aLlkIl~Hars~~p~EVmGlLLG~~d~~-tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr 182 (394)
++.+|.|+++|+++|++||.+..+.||||+|+|..+++ +++|++||++|+.+++........ ++..+|+++++++++
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 57899999999999999998877889999999999998 999999999999877776544333 334688899999988
Q ss_pred CCceEEEEecCCCCCCcccHhhHHhHHhhhccCC
Q psy9085 183 LENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQE 216 (394)
Q Consensus 183 ~e~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~ 216 (394)
++.+||||||||.++||||..|+++|..||++.+
T Consensus 80 ~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~ 113 (114)
T PF01398_consen 80 NLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNP 113 (114)
T ss_dssp TSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTT
T ss_pred cceEEEEEEccCCccccCCHHHHHHHHHHHHhCC
Confidence 8999999999999999999999999999998875
No 14
>KOG2975|consensus
Probab=99.92 E-value=3.6e-24 Score=203.58 Aligned_cols=197 Identities=21% Similarity=0.272 Sum_probs=165.6
Q ss_pred eeEEEECHHHHHHHHHHH--hcCCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCC
Q psy9085 105 FKDIKISALALLKMVMHA--RSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGR 182 (394)
Q Consensus 105 ~~~V~Is~~aLlkIl~Ha--rs~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr 182 (394)
.-.|+|+|.++++|++|. |..+..+|||+|||.++++.++||+||++|+.+.+++++. +.+|..+|+++++++++
T Consensus 20 ~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g~ieitNCFaVPhnEssdqvev---dm~y~~~M~~l~~k~np 96 (288)
T KOG2975|consen 20 NLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKGSVEVTNCFAVPHNESSDQVEV---DMEYAKNMYELHKKVNP 96 (288)
T ss_pred CceEEEcceEEeEeehhhhcCCccchhhhhheeecccCCeEEEEEeeeccCcccccccee---eHHHHHHHHHHhcccCC
Confidence 448999999999999998 4568899999999999999999999999999988888876 67899999999999999
Q ss_pred CCceEEEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEccCCCCCCCCCCCcccccccc
Q psy9085 183 LENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYPKGYKPANEEPSEYQTIPLN 262 (394)
Q Consensus 183 ~e~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~~~~~~~~~~~e~~~iPl~ 262 (394)
+|.+||||.+.++.+...|.| |..|-+..+++|+|.||+..+ .|++.|+||..++-|....
T Consensus 97 nE~vvGWyaTg~dvt~~ssli----hdyYare~~~pvhLtVDT~~~--n~rm~ikaYvss~~Gvpg~------------- 157 (288)
T KOG2975|consen 97 NELVVGWYATGHDVTEHSSLI----HDYYAREAPNPVHLTVDTSLQ--NGRMSIKAYVSSLMGVPGR------------- 157 (288)
T ss_pred CceeEEEEecCCCcccchhHH----HHHhhccCCCCeEEEEecccc--CCccceeEEEEeccCCCCc-------------
Confidence 999999999999999887777 677888788899999999874 6999999999999663221
Q ss_pred hhccccccceeEEeeeeEEecCHHHHHHHHhhhhhhhhhhhccccccccHHHHHHHHHHHHHHHHHHH
Q psy9085 263 KIEDFGVHCKQYYSLDVSYFKSSLDRRLLDSLWNKYWVNTLSSSSLLTNADYLTGQMCDLSDKLEQAE 330 (394)
Q Consensus 263 ki~d~g~~~~~yy~L~V~~~~S~ld~~~L~~L~~~~w~~~Ls~s~l~~n~~~~~~~i~dl~~k~~~~~ 330 (394)
.....|.+|||++..-+.|+..|+.+.+.. ...-...+|...++.+.....+|...|+..-
T Consensus 158 ------~~~~mF~plpvel~~~~~ervgl~li~kt~-~sp~r~~~l~~dLqQv~~at~~l~~~L~~Vl 218 (288)
T KOG2975|consen 158 ------TMGVMFTPLPVELAYYDAERVGLDLIEKTS-FSPSRVAGLSSDLQQVEGATARLQSLLERVL 218 (288)
T ss_pred ------ccceeeeeeeeEEeecchhhhHHHHHHHhc-cChhhhccccchHHHHHHHHHHHHHHHHHHH
Confidence 113489999999999999999999997664 2333445777888877777777766666543
No 15
>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=99.91 E-value=2e-23 Score=191.17 Aligned_cols=131 Identities=25% Similarity=0.406 Sum_probs=111.2
Q ss_pred eEEEECHHHHHHHHHHHhcC--CCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCC
Q psy9085 106 KDIKISALALLKMVMHARSG--GTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRL 183 (394)
Q Consensus 106 ~~V~Is~~aLlkIl~Hars~--~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~ 183 (394)
+.+.|+..++.+|+.||+.. .|.||||+|+|...++..+|++++..|..+++..++..+ ..+ +++.++. ++
T Consensus 2 ~~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~~~~~~~~I~~i~~~~q~~~~~~~~~~~-~~e----~~~~~~~--~g 74 (173)
T cd08066 2 RQVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSNNAFFITHLIIPKQSGTSDSCQTTN-EEE----LFDFQDQ--HD 74 (173)
T ss_pred eEEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeEcCCCeEEEEEEEeccccCCCceecCCC-HHH----HHHHHHh--CC
Confidence 57899999999999999987 469999999999888888999998888888777665532 222 4444544 67
Q ss_pred CceEEEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEc-cCCCCCC
Q psy9085 184 ENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTY-PKGYKPA 249 (394)
Q Consensus 184 e~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~-p~~~~~~ 249 (394)
+.+||||||||..+||||.+|+.||..||.+.+++++|||+|. .++++|||+. ++|+.-.
T Consensus 75 le~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~------~~~l~afrl~~~~g~~~~ 135 (173)
T cd08066 75 LITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK------YNEFGIFRLTDPPGLDEI 135 (173)
T ss_pred CeeEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC------CcEEeEEEeecCCcceec
Confidence 9999999999999999999999999999999999999999983 5789999999 7777654
No 16
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=99.91 E-value=1.2e-22 Score=200.49 Aligned_cols=207 Identities=17% Similarity=0.226 Sum_probs=157.3
Q ss_pred CCCCeeEEEECHHHHHHHHHHHhcCC---CceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHH
Q psy9085 101 DPHFFKDIKISALALLKMVMHARSGG---TLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAA 177 (394)
Q Consensus 101 dp~~~~~V~Is~~aLlkIl~Hars~~---p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~ 177 (394)
.|.++.+|.|+|+|+++|++||.+.. +..|+|.|||..+++.++|+|||++|+...++.......+.+|+.+|++++
T Consensus 1 ~~~~~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~~~~~~ieItnsF~~p~~e~~~~~~~~~~D~~y~~~m~~~~ 80 (303)
T PLN03246 1 SPRGIEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFRGRVDVTNSFAVPFEEDDKDPSIWFLDHNYLESMFGMF 80 (303)
T ss_pred CCCCCcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEeeecCCEEEEEeccccCcccCCCCccceeecHHHHHHHHHHH
Confidence 37788999999999999999996543 567999999999999999999999998654443222223578999999999
Q ss_pred HHhCCCCceEEEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEccCCCCCCCCCCCccc
Q psy9085 178 KEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYPKGYKPANEEPSEYQ 257 (394)
Q Consensus 178 ~kvgr~e~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~~~~~~~~~~~e~~ 257 (394)
+++++++.+||||+|.|... ..|+.-+..|..+.+..|+|++|+... .+.+.++||...+.+... ..
T Consensus 81 k~V~~~~~vVGWY~tg~~i~----~~d~~IH~~~~~~~~~Pv~L~vD~~~~--~~~lpi~aY~s~~~~~~~--~~----- 147 (303)
T PLN03246 81 KRINAKEHVVGWYSTGPKLR----ENDLDIHELFNDYVPNPVLVIIDVQPK--ELGIPTKAYYAVEEVKEN--AT----- 147 (303)
T ss_pred HHhCCCCcEEeeecCCCCCC----cchHHHHHHHHhhCCCCeEEEEecCCC--CCCCceEEEEEEEeccCC--CC-----
Confidence 99999999999999999754 334454567777777789999998653 577999999998865311 00
Q ss_pred ccccchhccccccceeEEeeeeEEecCHHHHHHHHhhhhhhhhhhhccccccccHHHHHHHHHHHHHHHHHHHHh
Q psy9085 258 TIPLNKIEDFGVHCKQYYSLDVSYFKSSLDRRLLDSLWNKYWVNTLSSSSLLTNADYLTGQMCDLSDKLEQAESA 332 (394)
Q Consensus 258 ~iPl~ki~d~g~~~~~yy~L~V~~~~S~ld~~~L~~L~~~~w~~~Ls~s~l~~n~~~~~~~i~dl~~k~~~~~~~ 332 (394)
+.....|.++|+++-..+.|+..++.|.+.. ..-+.+.+........+.+..|..+|+....-
T Consensus 148 ----------~~~~~~F~~vp~~i~~~EaE~Igve~l~r~~--~~~~~s~l~~~l~~~~~al~~L~~rl~~i~~Y 210 (303)
T PLN03246 148 ----------QKSQKVFVHVPSEIGAHEAEEIGVEHLLRDV--KDTTVSTLATEVTGKLTALKGLDARLREIRSY 210 (303)
T ss_pred ----------cccccEEEECCeeeeecCHHHHHHHHHHhcc--cCCccchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0124679999999999999999999997532 11122334446666677777777777766643
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=99.90 E-value=2.3e-22 Score=197.31 Aligned_cols=202 Identities=18% Similarity=0.245 Sum_probs=152.6
Q ss_pred EEEECHHHHHHHHHHHhc----CC--CceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHh
Q psy9085 107 DIKISALALLKMVMHARS----GG--TLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEV 180 (394)
Q Consensus 107 ~V~Is~~aLlkIl~Hars----~~--p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kv 180 (394)
+|.|+|+||++|++|+.+ .. +..|+|.|||..++++++|+|||++|+..++... ...+.+|+.+|+++++++
T Consensus 2 ~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~~~~veItnsF~~p~~~~~~~~--~~id~~y~~~m~~~~kkV 79 (288)
T cd08063 2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGREIEIENSFELKYDTNEDGE--IVLDKEFLETRLEQFKQV 79 (288)
T ss_pred eEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEcCCEEEEEEEEecccccCCCCc--eeeCHHHHHHHHHHHHHh
Confidence 689999999999999954 22 6899999999999999999999999997655221 112578999999999999
Q ss_pred CCCCceEEEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEccCCCCCCCCCCCcccccc
Q psy9085 181 GRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYPKGYKPANEEPSEYQTIP 260 (394)
Q Consensus 181 gr~e~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~~~~~~~~~~~e~~~iP 260 (394)
++++.+||||++++. +...+...|+.| |....+..|+|++||..+.+.|.+.++||+..+.+...
T Consensus 80 ~~~~~vVGWY~tg~~-~~~~~~~~Ih~~--~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~~~~~~------------ 144 (288)
T cd08063 80 FKDLDFVGWYTTGPG-GPTESDLPIHKQ--ILEINESPVLLLLDPEANASGKDLPVTIYESVLELVDG------------ 144 (288)
T ss_pred ccCCceEEEEecCCC-CCCHHHHHHHHH--HHhhCCCcEEEEEccccccCCCCCceeEEEEEEeccCC------------
Confidence 999999999999998 444444445543 44556667999999987534788999999998854211
Q ss_pred cchhccccccceeEEeeeeEEecCHHHHHHHHhhhhhhhhhhhccccccccHHHHHHHHHHHHHHHHHHHHhh
Q psy9085 261 LNKIEDFGVHCKQYYSLDVSYFKSSLDRRLLDSLWNKYWVNTLSSSSLLTNADYLTGQMCDLSDKLEQAESAL 333 (394)
Q Consensus 261 l~ki~d~g~~~~~yy~L~V~~~~S~ld~~~L~~L~~~~w~~~Ls~s~l~~n~~~~~~~i~dl~~k~~~~~~~~ 333 (394)
.....|.++|.++-.++.|+..++.+.+..=...-+.+.+.+..+.+.+.+..|..+++....-+
T Consensus 145 --------~~~~~F~~i~~~i~~~eaErIgv~~l~~~~~~~~~~~~~~~~~l~~~~~al~~L~~rl~~i~~Yl 209 (288)
T cd08063 145 --------EATLRFRELPYTIETGEAERIGVDHVARGGASGSSEKSTVAAHLQAQHNAIKMLNSRVELILEYL 209 (288)
T ss_pred --------ccccEEEeeeeEEEeccCceeeHHHHHhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 12467999999999999999999999765311111222344566667777777777777666543
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=99.87 E-value=1.2e-21 Score=164.91 Aligned_cols=115 Identities=25% Similarity=0.355 Sum_probs=92.4
Q ss_pred HHHHHHHhcCCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceEEEEecCCC
Q psy9085 116 LKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYHSHPG 195 (394)
Q Consensus 116 lkIl~Hars~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVGWYHSHP~ 195 (394)
.+|++||+...|.||||+|+|+.++++++|+++|++|+..++.... ..++ |+......+.++++||||||||.
T Consensus 2 k~il~~a~~~~~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~~----~~~~---~~~~~~~~~~~~~iVGwyhshp~ 74 (116)
T cd07767 2 KMFLDAAKSINGKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDN----VWFL---MYLDFKKLNAGLRIVGWYHTHPK 74 (116)
T ss_pred HhHHHHHhcCCCcEEEEEeEEEEcCCEEEEEEEEecccCCCCCccH----HHHH---HHHHHHHhcCCCeEEEEEEcCCC
Confidence 5789999998899999999999988899999999999865443321 1222 33344556789999999999999
Q ss_pred CCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEE
Q psy9085 196 YGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSF 239 (394)
Q Consensus 196 ~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AF 239 (394)
++++||..|+.+|..||...+++++||+|+... ...+.++||
T Consensus 75 ~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~~--~~~~~~~~~ 116 (116)
T cd07767 75 PSCFLSPNDLATHELFQRYFPEKVMIIVDVKPK--DLGNSWKCY 116 (116)
T ss_pred CCCccCHHHHHHHHHHHHhCCCCEEEEEECCCc--cCCCCcccC
Confidence 999999999999999998888899999999763 224556654
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=99.80 E-value=9.4e-19 Score=151.92 Aligned_cols=120 Identities=24% Similarity=0.252 Sum_probs=95.7
Q ss_pred HHHHHHHHHHhcCCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceEEEEec
Q psy9085 113 LALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYHS 192 (394)
Q Consensus 113 ~aLlkIl~Hars~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVGWYHS 192 (394)
.++.+|+.||+.+.|.|+||+|+|..++....|++++++|+...+.+..+..++.+ +..+.+.+++ +++.+||||||
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 46789999999999999999999998877778899999999765553333344544 4456667766 46999999999
Q ss_pred CCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEccC
Q psy9085 193 HPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYPK 244 (394)
Q Consensus 193 HP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~ 244 (394)
||..+++||..|+.++. ..+.++||+++.. +...++||++...
T Consensus 79 HP~~~~~PS~~D~~~~~-----~~~~~~lIv~~~~----~~~~~~~~~~~~~ 121 (128)
T cd08070 79 HPDGPARPSETDLRLAW-----PPGVSYLIVSLAG----GAPELRAWRLEGG 121 (128)
T ss_pred CCCCCCCCCHHHHHhcc-----CCCCeEEEEECCC----CCcEEEEEEEcCC
Confidence 99999999999998643 3468999999853 3568999999763
No 20
>KOG1556|consensus
Probab=99.72 E-value=1.6e-16 Score=150.46 Aligned_cols=179 Identities=21% Similarity=0.326 Sum_probs=132.3
Q ss_pred CCeeEEEECHHHHHHHHHHHhcC---CCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHH
Q psy9085 103 HFFKDIKISALALLKMVMHARSG---GTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKE 179 (394)
Q Consensus 103 ~~~~~V~Is~~aLlkIl~Hars~---~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~k 179 (394)
..+.+|.|+|+||+..++|+... ...+|.|+|||..+++++.|+++|++|.++.+..-..+.-+..|+..|.+++++
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 35789999999999999999643 458999999999999999999999999988776655555677899999999999
Q ss_pred hCCCCceEEEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEccCCCCCCCCCCCccccc
Q psy9085 180 VGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYPKGYKPANEEPSEYQTI 259 (394)
Q Consensus 180 vgr~e~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~~~~~~~~~~~e~~~i 259 (394)
++..|.+||||||+|.. ..+-+||+. +.-.+.|..|.+|||..... -| +--.||-...+
T Consensus 86 vNakekivGWYhTGPkl--~~nDl~In~--l~k~y~pnpvLvIIdvkpk~-~g-LPT~AY~aVee--------------- 144 (309)
T KOG1556|consen 86 VNAKEKVVGWYHTGPKL--RENDLDINE--LLKRYVPNPVLVIIDVKPKE-LG-LPTEAYIAVEE--------------- 144 (309)
T ss_pred hcchhheeeeeccCCcc--ccchhhHHH--HHhhcCCCceEEEEeccccc-CC-CCchheeeeee---------------
Confidence 99999999999999975 356666664 34567777799999964211 11 12224433331
Q ss_pred ccchhcccccc-ceeEEeeeeEEecCHHHHHHHHhhhhh---hhhhhhccc
Q psy9085 260 PLNKIEDFGVH-CKQYYSLDVSYFKSSLDRRLLDSLWNK---YWVNTLSSS 306 (394)
Q Consensus 260 Pl~ki~d~g~~-~~~yy~L~V~~~~S~ld~~~L~~L~~~---~w~~~Ls~s 306 (394)
++|-|.. ...|.-+|.++---+.|....+.|.+. .-+.+|++.
T Consensus 145 ----v~dDgt~t~ktF~Hvps~I~AeEAEEvGVEHLlRDikd~t~gtla~r 191 (309)
T KOG1556|consen 145 ----VKDDGTPTSKTFVHVPSEIEAEEAEEVGVEHLLRDIKDTTVGTLATR 191 (309)
T ss_pred ----eecCCCCccceeEecCcccchhHHHHhhHHHHHHHHHhhhhhHHHHH
Confidence 1222221 356888999998888888888888654 234555543
No 21
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=99.60 E-value=9.1e-15 Score=128.02 Aligned_cols=105 Identities=30% Similarity=0.416 Sum_probs=74.9
Q ss_pred EEECHHHHHHHHHHHhcCCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceE
Q psy9085 108 IKISALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAI 187 (394)
Q Consensus 108 V~Is~~aLlkIl~Hars~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iV 187 (394)
+.|...++..|+.||+...|.|+||+|+|...+ ...|.+++...+.. ..+..+.++.. +...++. .++.+|
T Consensus 2 ~~i~~~~l~~il~~a~~~~p~E~~g~l~~~~~~-----~~~~~~~n~~~~~~-~~~~~~~~~~~-~~~~~~~--~g~~vv 72 (134)
T COG1310 2 LVIPKEVLGAILEHARREHPREVCGLLAGTREG-----ERYFPLKNVSVEPV-EYFEIDPEYSL-FYLAAED--AGEVVV 72 (134)
T ss_pred ceecHHHHHHHHHHHHhcCChheEEEEEeeccc-----ceeeccccccCCcc-eeEeeCHHHHH-HHHHHhh--CCCEEE
Confidence 568899999999999999999999999999766 55677777554432 22222334433 3444444 459999
Q ss_pred EEEecCCCCCCcccHhhHHhHHhhhccCC-CeEEEEEcC
Q psy9085 188 GWYHSHPGYGCWLSGIDVSTQMLNQNFQE-PFVAIVIDP 225 (394)
Q Consensus 188 GWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~-p~VaLVvDp 225 (394)
|||||||+++||||..|+.. |.+.+ +|+.++.+|
T Consensus 73 g~yHSHP~~~~~pS~~D~~~----~~~~~~~~~iv~~~~ 107 (134)
T COG1310 73 GWYHSHPGGPPYPSEADRRL----SKLGPLPWLIVSVPP 107 (134)
T ss_pred EEEcCCCCCCCCcCHHHHhh----ccccCCCEEEEEcCC
Confidence 99999999999999999983 33333 344444444
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=99.60 E-value=1.1e-14 Score=125.40 Aligned_cols=109 Identities=20% Similarity=0.130 Sum_probs=82.5
Q ss_pred ECHHHHHHHHHHHhcCCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceEEE
Q psy9085 110 ISALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGW 189 (394)
Q Consensus 110 Is~~aLlkIl~Hars~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVGW 189 (394)
|+..++..|+.||++..|+|+||+|+|+.+ .|++++++|+....+....+. .+ +.+ .++.+||.
T Consensus 1 i~~~~~~~i~~ha~~~~P~E~CGlL~G~~~----~v~~~~~~~n~~~~~~~~~f~------~~----~~~--~g~~ivgi 64 (117)
T cd08072 1 ISRDLLDSILEAAKSSHPNEFAALLRGKDG----VITELLILPGTESGEVSAVFP------LL----MLP--LDMSIVGS 64 (117)
T ss_pred CCHHHHHHHHHHHhhcCCceEEEEEEeecc----EEEEEEECCCCCCCCcceeec------hH----Hhc--CCCeEEEE
Confidence 456789999999999999999999999764 689999999865433222111 11 222 56999999
Q ss_pred EecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEcc
Q psy9085 190 YHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYP 243 (394)
Q Consensus 190 YHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p 243 (394)
|||||+.+++||..|+..+ ..+++++||+++-. +.-.++||+...
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 9999999999999998742 34678999999642 224588998865
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=99.47 E-value=5.4e-13 Score=113.49 Aligned_cols=95 Identities=17% Similarity=0.102 Sum_probs=70.3
Q ss_pred HHHHHHHHHhcCCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceEEEEecC
Q psy9085 114 ALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYHSH 193 (394)
Q Consensus 114 aLlkIl~Hars~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVGWYHSH 193 (394)
++..|+.||++..|.|+||+|+|.. .++..+++.|...+.+..+..++.++... . + ...+||.||||
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-----RKLRYIPCRNIAADPEEHFEISPEDYAAA----E-D---EGEIVAVVHSH 68 (108)
T ss_pred HHHHHHHHHhHCCCCcceEEEEecC-----CceEEEECccCCCCccceEEeCHHHHHHH----h-c---CCCEEEEEEcC
Confidence 4678999999999999999999965 24566888876544433343455555432 1 2 23899999999
Q ss_pred CCCCCcccHhhHHhHHhhhccCCCeEEEEEcCC
Q psy9085 194 PGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPV 226 (394)
Q Consensus 194 P~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~ 226 (394)
|+..+.||..|+..+ ..++.++||++..
T Consensus 69 P~~~a~PS~~D~~~~-----~~~~~~~iIvs~~ 96 (108)
T cd08073 69 PDGSPAPSEADRAQQ-----EATGLPWIIVSWP 96 (108)
T ss_pred CCCCCCCCHHHHHHh-----hcCCCcEEEEEcC
Confidence 999999999998732 3467889999863
No 24
>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=99.38 E-value=5.6e-12 Score=116.63 Aligned_cols=111 Identities=23% Similarity=0.268 Sum_probs=76.0
Q ss_pred ECHHHHHHHHHHHhcCCCceEEEEEeeEEc-CCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceEE
Q psy9085 110 ISALALLKMVMHARSGGTLEVMGLLLGKID-ANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIG 188 (394)
Q Consensus 110 Is~~aLlkIl~Hars~~p~EVmGlLLG~~d-~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVG 188 (394)
|+..++.||+.||....+.||||+|+|+.+ ++++.|++++|+.|.... ..... ...+ ....+.+++ .++.|||
T Consensus 1 is~~ay~ki~~HA~k~p~~evcGlLlG~~~~~~~~~V~d~vPl~h~~~~--l~P~~-Eval-~~ve~~~~~--~gl~IvG 74 (182)
T cd08060 1 LSTLAYVKMLLHAAKYPHCAVNGLLLGKKSSGGSVEITDAVPLFHSCLA--LAPML-EVAL-ALVDAYCKS--SGLVIVG 74 (182)
T ss_pred CCHHHHHHHHHHHHHcCCchheEEEEeeecCCCCEEEEEEEEcCCCccc--cCHHH-HHHH-HHHHHHHHH--CCCEEEE
Confidence 578899999999999888899999999987 778999999999984211 11111 1122 234456666 5699999
Q ss_pred EEecCCCCC-CcccHhhHH-hHHhhhccCCCeEEEEEcCCC
Q psy9085 189 WYHSHPGYG-CWLSGIDVS-TQMLNQNFQEPFVAIVIDPVR 227 (394)
Q Consensus 189 WYHSHP~~~-~~pS~iDV~-tQ~~yQ~~~~p~VaLVvDp~~ 227 (394)
+|||||... .-|+.+-.. .....+.+ +.++.++||-.+
T Consensus 75 ~Yhsh~~~~d~~~~~~a~kIadki~~~~-~~a~ll~vdn~~ 114 (182)
T cd08060 75 YYQANERLDDSSPSPVAKKIADKIAENF-SNACLLMVDNEK 114 (182)
T ss_pred EEecCCcccCCCCcHHHHHHHHHHHHhC-CCCEEEEEeCcc
Confidence 999999775 244444222 12333333 456778888654
No 25
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=99.33 E-value=1e-11 Score=103.06 Aligned_cols=95 Identities=25% Similarity=0.307 Sum_probs=63.3
Q ss_pred HHHHHHHHHHHhcCCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceEEEEe
Q psy9085 112 ALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYH 191 (394)
Q Consensus 112 ~~aLlkIl~Hars~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVGWYH 191 (394)
..++..|+.|++...|.|+||+|+|......+.|+...... ..++......... ..+..+||+||
T Consensus 2 ~~~~~~i~~~~~~~~p~E~~G~L~g~~~~~~~~~~~~~~~~-------------p~~~~~~~~~~~~--~~~~~~vg~~H 66 (104)
T PF14464_consen 2 EEVLEQIIAHARAAYPNEACGLLLGRRDDQRFIVVPNVNPD-------------PRDSFRRERFEAR--ERGLEIVGIWH 66 (104)
T ss_dssp -HHHHHHHHHHHHHTTS-EEEEEEEEEECCEEEEEEEEE---------------HHCHHHHHH-HHH--HHT-EEEEEEE
T ss_pred HHHHHHHHHHHhhCCCCeEEEEEEEEecCCEEEEEeCCCCC-------------cHHHHHHHhhhhh--cccceeeEEEE
Confidence 35789999999999999999999999876777777666411 1111111110222 25699999999
Q ss_pred cCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcC
Q psy9085 192 SHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDP 225 (394)
Q Consensus 192 SHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp 225 (394)
|||+.+++||.+|+...... .++++||+..
T Consensus 67 SHP~~~a~pS~~D~~~~~~~----~~~~~iI~~~ 96 (104)
T PF14464_consen 67 SHPSGPAFPSSTDIRSMRDL----APPSYIIVGN 96 (104)
T ss_dssp EESSSSSS--HHHHHTHCCS-----SCEEEEEEE
T ss_pred cCCCCCCCCCHHHHHhhhcc----CCeEEEEEeC
Confidence 99999999999999864311 1568888775
No 26
>KOG2880|consensus
Probab=99.28 E-value=5e-12 Score=125.36 Aligned_cols=129 Identities=24% Similarity=0.380 Sum_probs=104.3
Q ss_pred CCCeeEEEECHHHHHHHHHHHhcC--CCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHH
Q psy9085 102 PHFFKDIKISALALLKMVMHARSG--GTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKE 179 (394)
Q Consensus 102 p~~~~~V~Is~~aLlkIl~Hars~--~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~k 179 (394)
...++.|.|+....-..++-|++. -..|-||+|.|+-..+.+.||+.+.--.+++.+.+++..+..-| +..
T Consensus 248 ~k~lr~v~ip~~l~~~Fl~la~~NT~knlETCGiL~g~L~~n~f~IThliiPkQeatsd~C~t~neeelF--~vQ----- 320 (424)
T KOG2880|consen 248 GKILRDVHIPERLMEVFLQLAKSNTKKNLETCGILAGKLERNEFYITHLIIPKQEATSDSCNTMNEEELF--EVQ----- 320 (424)
T ss_pred CccceEEEecHHHHHHHHHHHhhcccccchHHHHhhhHhhcCcEEEEEEEeecccCCCccccccCHHHHh--eec-----
Confidence 344789999999999999998753 46899999999998899999998855567777777765443222 111
Q ss_pred hCCCCceEEEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEcc
Q psy9085 180 VGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYP 243 (394)
Q Consensus 180 vgr~e~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p 243 (394)
-.+++-.+||-|+||.-+||+|.+|+.|+..||.+.|.+||||+.|.... -|-||+.+
T Consensus 321 dq~~L~tlGWIHTHPTQt~FmSSVDlHTHcSYQiMlPEAiAIV~aPk~~~------tGiFrLt~ 378 (424)
T KOG2880|consen 321 DQHELLTLGWIHTHPTQTCFMSSVDLHTHCSYQIMLPEAIAIVCAPKSKT------TGIFRLTD 378 (424)
T ss_pred ccccceeeeeeecCCccchhheeccccccceeeeecchheeEEeccccCC------cceEEecC
Confidence 12568899999999999999999999999999999999999999997432 45699985
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=99.06 E-value=1.4e-09 Score=105.08 Aligned_cols=127 Identities=21% Similarity=0.247 Sum_probs=103.1
Q ss_pred EEEECHHHHHHHHHHHhcCCCceEEEEEeeEEcC---CeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCC
Q psy9085 107 DIKISALALLKMVMHARSGGTLEVMGLLLGKIDA---NSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRL 183 (394)
Q Consensus 107 ~V~Is~~aLlkIl~Hars~~p~EVmGlLLG~~d~---~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~ 183 (394)
.+.|+..++.|.+.-|.. ..++||+|.|.... +..+|+-+...|+.++...+....+..++ ++ + .+
T Consensus 37 t~vlPknllkkFi~iaD~--rtQ~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~~~~~--~~---l----~~ 105 (252)
T cd08056 37 TYILPKNLLKKFISISDL--RTQIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQLPQH--EY---L----ED 105 (252)
T ss_pred EEEeCHHHHHHHHHHhhh--cceEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCccCccc--hh---h----CC
Confidence 788999999999988853 56999999998543 67788888888898888877654332221 11 1 46
Q ss_pred CceEEEEecCCCCCCcccHhhHHhHHhhhccCC-----CeEEEEEcCCCCCCCCceEEEEEEEccCCCCC
Q psy9085 184 ENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQE-----PFVAIVIDPVRTISAGKVCLGSFRTYPKGYKP 248 (394)
Q Consensus 184 e~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~-----p~VaLVvDp~~t~~~Gkv~i~AFR~~p~~~~~ 248 (394)
+..+||-|+||.-.|++|..|+.++..+|...+ .+|.++|++. .|.++++||+++++|+.-
T Consensus 106 Le~LGWIHTqp~e~~~Lss~Dv~tha~~~~~~~~w~~~~~V~it~Sft----pGs~sl~ay~LT~~G~~w 171 (252)
T cd08056 106 LEPLGWIHTQPNELPQLSPQDVTTHAKILADNPSWDGEKTVILTCSFT----PGSCSLTAYKLTPEGYEW 171 (252)
T ss_pred CEeeEEEEcCCCCccccCHHHHHHHHHHHHhccccCCCcEEEEEEcCC----CCceEEEEEecCHHHHHH
Confidence 899999999999999999999999999998776 6899999985 699999999999977653
No 28
>PTZ00196 60S ribosomal protein L36; Provisional
Probab=99.03 E-value=4.5e-11 Score=99.47 Aligned_cols=41 Identities=41% Similarity=0.442 Sum_probs=38.5
Q ss_pred CCccceeecCCCccccccccccchhhcccccccCCCCcccCCCCCcceEEEec
Q psy9085 3 PRYELAVGLKKGHRNTKIKWANSLAQKTSKIVKMRPSRLKGNGSQLVNIFLIL 55 (394)
Q Consensus 3 ~~~~~~~g~~kg~~~t~~~~~~~~~~~~~~~~~~~~~~~kg~~~~~~~~~~~~ 55 (394)
++|||||||||||+||++.. ++|||++||.+|+|++|||..
T Consensus 1 ~~~g~avGlnKGh~vtk~~~------------~~r~s~rkg~~tkr~~fVr~v 41 (98)
T PTZ00196 1 PRTGIAVGLNKGHIVTKRAR------------KPSPSKRKGLLSKRKRLVKDV 41 (98)
T ss_pred CCCceeeecCCCcccCcCCC------------CCCcccccCCCCchhHHHHHH
Confidence 57999999999999999999 999999999999999999854
No 29
>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=98.99 E-value=3.2e-09 Score=88.35 Aligned_cols=91 Identities=25% Similarity=0.273 Sum_probs=65.4
Q ss_pred HHHHHHHHHhcCCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceEEEEecC
Q psy9085 114 ALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYHSH 193 (394)
Q Consensus 114 aLlkIl~Hars~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVGWYHSH 193 (394)
++..|+.|++...|.|+||+|+|..++ .++++..+|+.. .+. .... .+.+.+ .+..+||.||||
T Consensus 2 ~~~~i~~~~~~~~p~E~~gll~~~~~~---~~~~~~~~~~~~----~~~--~~~~-----~~~a~~--~~~~~v~i~HsH 65 (101)
T cd08059 2 LLKTILVHAKDAHPDEFCGFLSGSKDN---VMDELIFLPFVS----GSV--SAVI-----DLAALE--IGMKVVGLVHSH 65 (101)
T ss_pred HHHHHHHHHHhcCChhhheeeecCCCC---eEEEEEeCCCcC----Ccc--ChHH-----HHHHhh--CCCcEEEEEecC
Confidence 567889999998999999999996543 577778788532 111 1111 223333 468999999999
Q ss_pred CCCCCcccHhhHHhHHhhhccCCCeEEEEEcC
Q psy9085 194 PGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDP 225 (394)
Q Consensus 194 P~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp 225 (394)
|++.+.||..|+.... .....++||..
T Consensus 66 P~g~~~PS~~D~~~~~-----~~~~~~iIv~~ 92 (101)
T cd08059 66 PSGSCRPSEADLSLFT-----RFGLYHVIVCY 92 (101)
T ss_pred cCCCCCCCHHHHHHHH-----hcCCeEEEEEC
Confidence 9999999999998432 12568888864
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=98.99 E-value=3.7e-09 Score=98.38 Aligned_cols=113 Identities=19% Similarity=0.123 Sum_probs=79.5
Q ss_pred EECHHHHHHHHHHHhcCCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceEE
Q psy9085 109 KISALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIG 188 (394)
Q Consensus 109 ~Is~~aLlkIl~Hars~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVG 188 (394)
+|....+.+|+.||+++.|.|+||++.|..++.. ..++++.+...... ....+. .+ ..+++.+|+
T Consensus 74 ~Ip~~l~~~ii~hAr~~~P~EacG~Iag~~~~~~---~r~~p~~N~~~Sp~-~~~~d~-----~~------~~~ge~lV~ 138 (192)
T TIGR03735 74 PIPASLLEEFAEAARAALPNEVAAWIVWNSETGS---LRLAALESIEASPG-HIDYRR-----PR------LDDGEHLVV 138 (192)
T ss_pred CCCHHHHHHHHHHHHhcCCcceEEEEEEcCCCCE---EEEEeccccccCCc-eEEEcc-----hH------HhCCCeEEE
Confidence 8999999999999999999999999999643333 35588887543332 111111 11 137899999
Q ss_pred EEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCCCCceEEEEEEEccCC
Q psy9085 189 WYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYPKG 245 (394)
Q Consensus 189 WYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~~ 245 (394)
.|||||..+++||.+|+..- ..+--++.|+.... ++.+++ +||+.=.|
T Consensus 139 iyHSH~~spA~PS~tD~~Dd-----~~~~k~~~ViG~~~---~~~p~~-~~Rl~~~G 186 (192)
T TIGR03735 139 DLHSHGTGSAFFSETDDADD-----KGEVKISGVLGCLD---QGTPQA-VFRLCLLG 186 (192)
T ss_pred EEcCCCCCCCCCCcccchhh-----cCceEEEEEEEecC---CCCceE-EEEEEecc
Confidence 99999999999999998742 12235888887652 344444 47775543
No 31
>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=98.99 E-value=6.2e-09 Score=91.69 Aligned_cols=109 Identities=17% Similarity=0.153 Sum_probs=71.5
Q ss_pred HHHHHHHh--cCCCceEEEEEeeEEcCCeEEEEEEEecCcc-CCCCcccccccHHHHHHHHHHHHHHhCCCCceEEEEec
Q psy9085 116 LKMVMHAR--SGGTLEVMGLLLGKIDANSMIVMDAFALPVE-GTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYHS 192 (394)
Q Consensus 116 lkIl~Har--s~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~-~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVGWYHS 192 (394)
++++..++ ...+.|.+|+|+|..++..++|+++. .|.. ...++..+.......+...-+..++.+.....||-|||
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 34444443 34578999999999888888888866 3332 22333333322323334444455555656899999999
Q ss_pred CCCCCCcccHhhHHhHHhhhccCCCeEEEEEcC
Q psy9085 193 HPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDP 225 (394)
Q Consensus 193 HP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp 225 (394)
||...+.||.+|..+....=....+.+.|||..
T Consensus 82 HP~~~p~PS~~D~~~~~~~~~~~~~~l~iIvG~ 114 (131)
T TIGR02256 82 HPEDQPEPSWTDRRSWRTIIRSPEAMLLLIVGR 114 (131)
T ss_pred CCCCCCCCCHHHHHHHHHHHhCCCeeEEEEEcC
Confidence 999999999999987543323345567777764
No 32
>PF01158 Ribosomal_L36e: Ribosomal protein L36e; InterPro: IPR000509 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. The L36E ribosomal family consists of mammalian, Caenorhabditis elegans and Drosophila L36, Candida albicans L39, and yeast YL39 ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1B_Q 4A1D_Q 4A19_Q 4A18_Q 3IZS_k 3IZR_k.
Probab=98.89 E-value=8.2e-11 Score=98.24 Aligned_cols=41 Identities=46% Similarity=0.614 Sum_probs=27.1
Q ss_pred CCccceeecCCCccccccccccchhhcccccccCCCCcccCCCCCcceEEEec
Q psy9085 3 PRYELAVGLKKGHRNTKIKWANSLAQKTSKIVKMRPSRLKGNGSQLVNIFLIL 55 (394)
Q Consensus 3 ~~~~~~~g~~kg~~~t~~~~~~~~~~~~~~~~~~~~~~~kg~~~~~~~~~~~~ 55 (394)
|+|+|||||||||+||++.. ++|||+++|.+|++++|||..
T Consensus 1 ~~~~iavGlnkGh~vtk~~~------------~~r~s~~kg~~tk~~kfvr~v 41 (98)
T PF01158_consen 1 PRYGIAVGLNKGHKVTKNVS------------KPRPSRRKGRLTKRTKFVRDV 41 (98)
T ss_dssp --TTSTTSSS-S-----TTS---------------STTS-SHHCHHHHHHHHH
T ss_pred CCCceeeeCCCCcccCCCCC------------CCCcccccCccchhHHHHHHH
Confidence 58999999999999999999 999999999999999998753
No 33
>KOG3452|consensus
Probab=98.87 E-value=2.9e-10 Score=93.99 Aligned_cols=43 Identities=49% Similarity=0.516 Sum_probs=41.0
Q ss_pred CCCCccceeecCCCccccccccccchhhcccccccCCCCcccCCCCCcceEEEec
Q psy9085 1 MAPRYELAVGLKKGHRNTKIKWANSLAQKTSKIVKMRPSRLKGNGSQLVNIFLIL 55 (394)
Q Consensus 1 m~~~~~~~~g~~kg~~~t~~~~~~~~~~~~~~~~~~~~~~~kg~~~~~~~~~~~~ 55 (394)
|+.+|++||||||||++||+.. ++|+||+||..|++++|||..
T Consensus 1 m~~~~~~~vglnkgh~~tk~~~------------~pr~s~~kg~~sk~tkfvr~l 43 (102)
T KOG3452|consen 1 MAVCYGLAVGLNKGHKVTKRVS------------KPRQSRRKGETSKRTKFVRDL 43 (102)
T ss_pred CCcccceeecccccchhhcccC------------CCCcCccccchhhhHHHHHHH
Confidence 8899999999999999999999 999999999999999999864
No 34
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=98.77 E-value=1.5e-07 Score=88.32 Aligned_cols=114 Identities=22% Similarity=0.220 Sum_probs=77.0
Q ss_pred eEEEECHHHHHHHHHHHhcCCCceEEEEEeeEEcCCe--EEEEEEEecCccCCCCccccccc-HHHHHHHHHHHHHHhCC
Q psy9085 106 KDIKISALALLKMVMHARSGGTLEVMGLLLGKIDANS--MIVMDAFALPVEGTETRVNAQAQ-AYEYMTAYIEAAKEVGR 182 (394)
Q Consensus 106 ~~V~Is~~aLlkIl~Hars~~p~EVmGlLLG~~d~~t--l~Vtd~F~lP~~~te~rv~a~~e-a~ey~~~mle~~~kvgr 182 (394)
.+|.|+..++.||+.||.......|+|+|+|...++. +.|+||+||-|... .+....| +... .-..++. .
T Consensus 2 ~~v~is~~AY~K~~LHaaKyP~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~--~L~PmlEvAL~q---vd~~~~~--~ 74 (196)
T PF03665_consen 2 SSVEISSRAYAKMILHAAKYPHCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWL--SLSPMLEVALAQ---VDAYAKS--N 74 (196)
T ss_pred ceEEEcHHHHHHHHHHhccCCCCceeeEEEeccCCCCceEEEeeceecccccc--CcchHHHHHHHH---HHHHHhh--C
Confidence 4789999999999999998777899999999976444 99999999998532 2222222 2221 1123443 4
Q ss_pred CCceEEEEecCCCCC-CcccHhhHHh-HHhhhccCCCeEEEEEcCCC
Q psy9085 183 LENAIGWYHSHPGYG-CWLSGIDVST-QMLNQNFQEPFVAIVIDPVR 227 (394)
Q Consensus 183 ~e~iVGWYHSHP~~~-~~pS~iDV~t-Q~~yQ~~~~p~VaLVvDp~~ 227 (394)
++.|||+||...... .-|+.+-..- ..... ..+.++.|+||-.+
T Consensus 75 gl~IvGyY~Ane~~~d~~~~~~a~kiad~I~~-~~~~a~ll~idn~k 120 (196)
T PF03665_consen 75 GLVIVGYYQANERLDDNSPSPVAEKIADKIAE-NFSDACLLMIDNKK 120 (196)
T ss_pred CCEEEEEEEeccccccCCCCHHHHHHHHHHHh-hCCCcEEEEEECcc
Confidence 699999999988653 3455552221 12222 34556888888754
No 35
>KOG3050|consensus
Probab=98.48 E-value=7.9e-07 Score=85.04 Aligned_cols=161 Identities=20% Similarity=0.310 Sum_probs=107.2
Q ss_pred eEEEECHHHHHHHHHHHh-----cCCCc-eEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHH
Q psy9085 106 KDIKISALALLKMVMHAR-----SGGTL-EVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKE 179 (394)
Q Consensus 106 ~~V~Is~~aLlkIl~Har-----s~~p~-EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~k 179 (394)
-+|.++|+|+++|-+|.. .+.|. .|.|.|+|+..|.+++|.|+|-+-.+-.+... . .+.+|...-.+..++
T Consensus 9 ~tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~~~~-~--~dke~l~kk~eqykq 85 (299)
T KOG3050|consen 9 VTVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGKQRGRNVEIMNSFELKMDTEEDTE-T--IDKEYLEKKEEQYKQ 85 (299)
T ss_pred eeEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheecccCceEEEeeeeEEEecchhhhh-h--ccHHHHHHHHHHHHH
Confidence 478999999999999973 46666 89999999999999999999988764322221 1 245677777788899
Q ss_pred hCCCCceEEEEecCCCCCCcccHhhHHhHHhhhccCCCeEEEEEcCCCCCC-CCceEEEEEEEccCCCCCCCCCCCcccc
Q psy9085 180 VGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVRTIS-AGKVCLGSFRTYPKGYKPANEEPSEYQT 258 (394)
Q Consensus 180 vgr~e~iVGWYHSHP~~~~~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~~t~~-~Gkv~i~AFR~~p~~~~~~~~~~~e~~~ 258 (394)
+-+++.++|||.++.+ +.||-+-|..|.. ...+-.+.|-..|..... ...+.+-+|-+
T Consensus 86 VFpdl~vlGwYttG~d--~t~sd~~i~k~l~--~i~esplflkLNp~t~~t~~~pv~lfese~----------------- 144 (299)
T KOG3050|consen 86 VFPDLYVLGWYTTGSD--PTPSDIHIHKQLM--DINESPLFLKLNPATNHTDKDPVTLFESEI----------------- 144 (299)
T ss_pred hcccceEEEEeecCCC--CChhhhHHHHHHH--hhhcCceEEEecchhccccCCCceeeeeeh-----------------
Confidence 9999999999998754 3456555544432 234555888888864221 11233322222
Q ss_pred cccchhccccccceeEEeeeeEEecCHHHHHHHHhhh
Q psy9085 259 IPLNKIEDFGVHCKQYYSLDVSYFKSSLDRRLLDSLW 295 (394)
Q Consensus 259 iPl~ki~d~g~~~~~yy~L~V~~~~S~ld~~~L~~L~ 295 (394)
+++. |..-..|.++.-.+-.-+.|+...+...
T Consensus 145 ---dvid--g~~q~~f~~~tytl~teEaERIgVdHVA 176 (299)
T KOG3050|consen 145 ---DVID--GEAQMLFVPLTYTLATEEAERIGVDHVA 176 (299)
T ss_pred ---eeec--CcceeeeeeeEEEEeehhhhhccchhhe
Confidence 1111 1112347777777777777777777653
No 36
>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=98.20 E-value=5.1e-05 Score=74.68 Aligned_cols=135 Identities=16% Similarity=0.285 Sum_probs=101.2
Q ss_pred CCeeEEEECHHHHHHHHHH-HhcCCCceEEEEEeeEEcCC-------eEEEEEEEecCccCCCCcccccccHHHHHHHHH
Q psy9085 103 HFFKDIKISALALLKMVMH-ARSGGTLEVMGLLLGKIDAN-------SMIVMDAFALPVEGTETRVNAQAQAYEYMTAYI 174 (394)
Q Consensus 103 ~~~~~V~Is~~aLlkIl~H-ars~~p~EVmGlLLG~~d~~-------tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~ml 174 (394)
+.+..|.+....+..-... +.......-||+|.|+.+.. .++|.-.+--|..++.+.+....+.. ....-
T Consensus 8 r~Vd~vef~~~~~~~~f~~~~w~~~~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~--~~~vd 85 (274)
T cd08061 8 RHVDHVEFDNPSIVEFFLYVFWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPN--ADTVD 85 (274)
T ss_pred CCcCEEEEecHHHHHHHHHHHHHhhcceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchh--hhHHH
Confidence 3466777776666655555 54445678899999997654 57777777778888877776554322 22233
Q ss_pred HHHHHhCCCCceEEEEecCCCC----CCcccHhhHHhHHhhhc------cCCCeEEEEEcCCCCCCCCceEEEEEEEccC
Q psy9085 175 EAAKEVGRLENAIGWYHSHPGY----GCWLSGIDVSTQMLNQN------FQEPFVAIVIDPVRTISAGKVCLGSFRTYPK 244 (394)
Q Consensus 175 e~~~kvgr~e~iVGWYHSHP~~----~~~pS~iDV~tQ~~yQ~------~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~ 244 (394)
+.+.. .++..|||-.||+.- ++++|..++.+...+|. +...||-+|+++.. .|.+.+.||++++.
T Consensus 86 ~iA~~--lGL~~VG~IfT~l~~~~~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~---~g~i~~~ayQvSdq 160 (274)
T cd08061 86 AIAAA--LGLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDK---DGQIHFEAYQVSDQ 160 (274)
T ss_pred HHHHH--cCCeEEEEEEecCCCCCCCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCC---CCceeeeeeeecHH
Confidence 44544 459999999999976 78999999999888884 67889999999975 59999999999984
No 37
>KOG3289|consensus
Probab=98.13 E-value=4e-05 Score=70.51 Aligned_cols=114 Identities=23% Similarity=0.248 Sum_probs=75.5
Q ss_pred EEEECHHHHHHHHHHHhcCCCceEEEEEeeEE--cCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCC
Q psy9085 107 DIKISALALLKMVMHARSGGTLEVMGLLLGKI--DANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLE 184 (394)
Q Consensus 107 ~V~Is~~aLlkIl~Hars~~p~EVmGlLLG~~--d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e 184 (394)
.|+|+..++.||+-||......-|.|+|+|.. .|+.++|+||.|+-++..- + ....|-...+++..-. ..+.
T Consensus 3 ~veis~~aY~kmiLH~akyph~aVnGLLla~~~~kg~~v~itdcVPLfH~~la--L---aPmlEvAl~lId~~~~-~~Gl 76 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYPHAAVNGLLLAPATGKGECVEITDCVPLFHSHLA--L---APMLEVALNLIDVWGA-QAGL 76 (199)
T ss_pred ceeehhhHHHHHHHHhccCcccceeeEEEeccCCCCCeEEEEecchhhccccc--c---ccHHHHHHHHHHHHHH-hcCe
Confidence 58999999999999999877778999999964 4788999999999986421 1 2234444445544322 2569
Q ss_pred ceEEEEecCCCCCC-cccHhhHHhHHhhhccCCCeEEEEEcCC
Q psy9085 185 NAIGWYHSHPGYGC-WLSGIDVSTQMLNQNFQEPFVAIVIDPV 226 (394)
Q Consensus 185 ~iVGWYHSHP~~~~-~pS~iDV~tQ~~yQ~~~~p~VaLVvDp~ 226 (394)
.|+|+||+.-.+.- -|-..-..-...-+.+-+.+..|++|..
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 99999999886542 1222211111112234455677777764
No 38
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=97.59 E-value=7.1e-06 Score=66.95 Aligned_cols=43 Identities=35% Similarity=0.335 Sum_probs=38.4
Q ss_pred CCCCccceeecCCCccccccccccchhhcccccccCCCCcccCCCCCcceEEEec
Q psy9085 1 MAPRYELAVGLKKGHRNTKIKWANSLAQKTSKIVKMRPSRLKGNGSQLVNIFLIL 55 (394)
Q Consensus 1 m~~~~~~~~g~~kg~~~t~~~~~~~~~~~~~~~~~~~~~~~kg~~~~~~~~~~~~ 55 (394)
|+..++++||||||.++|++.. .+|||++||..++|+.|+++.
T Consensus 1 ri~~~g~~~glNkgKkvt~r~p------------~~rps~kkgq~s~Rt~fvrsi 43 (97)
T COG5051 1 RIMAPGLVVGLNKGKKVTKRQP------------PERPSRKKGQLSKRTEFVRSI 43 (97)
T ss_pred CCcccchhhhhcccceeeeccC------------CCCcchhhhccccHHHHHHHH
Confidence 4556799999999999999999 999999999999999988753
No 39
>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=97.28 E-value=0.0024 Score=63.91 Aligned_cols=107 Identities=17% Similarity=0.283 Sum_probs=80.6
Q ss_pred EEEEeeEEcCC-------eEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceEEEEecCCC--------
Q psy9085 131 MGLLLGKIDAN-------SMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYHSHPG-------- 195 (394)
Q Consensus 131 mGlLLG~~d~~-------tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVGWYHSHP~-------- 195 (394)
+|+|.|+.+.. ..+|.-.+--|++++.+.+....++. ....-+.++.. +++.|||-=||+.
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~--~~~vd~iA~~l--GL~rVG~IfTdl~~~~~~~g~ 77 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDEN--EERVDAIASAL--GLERVGWIFTDLTDDGSGDGT 77 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCcc--HHHHHHHHHHC--CCEEEEEEEecCcccccCCCc
Confidence 79999997543 46777778888888877776643332 23333445554 5999999999997
Q ss_pred -------CCCcccHhhHHhHHhhhcc-------------CCCeEEEEEcCCCCCCCCceEEEEEEEccC
Q psy9085 196 -------YGCWLSGIDVSTQMLNQNF-------------QEPFVAIVIDPVRTISAGKVCLGSFRTYPK 244 (394)
Q Consensus 196 -------~~~~pS~iDV~tQ~~yQ~~-------------~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~ 244 (394)
-+.++|...+.....+|.. ...||-+|+++.. .|.+.+.||++++.
T Consensus 78 v~~~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~~---~g~i~~~ayQvS~q 143 (306)
T PF05021_consen 78 VKCKRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGDE---EGEIHFEAYQVSNQ 143 (306)
T ss_pred eeeccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCCC---CCceeeEEeeehHH
Confidence 5678999999877777752 3568999999963 79999999999984
No 40
>KOG2834|consensus
Probab=90.04 E-value=3.1 Score=43.89 Aligned_cols=130 Identities=19% Similarity=0.286 Sum_probs=83.1
Q ss_pred EEEEC-HHHHHHHHHHHhcCCCceEEEEEeeEEcC-CeE------EEEEEEecCccCCCCcccccccHHHHHHHHHHHHH
Q psy9085 107 DIKIS-ALALLKMVMHARSGGTLEVMGLLLGKIDA-NSM------IVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAK 178 (394)
Q Consensus 107 ~V~Is-~~aLlkIl~Hars~~p~EVmGlLLG~~d~-~tl------~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~ 178 (394)
.|.+. +.++...++..|.. ...-.|+|.|...+ +.+ +|.-.+--|+.++++.+.... +.+ +..+-+.+.
T Consensus 176 ~VeFd~~~~v~~Fl~~wr~s-g~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~~~~dgl~l~~-~~e-~~~vD~~a~ 252 (510)
T KOG2834|consen 176 HVEFDNAELVNHFLNEWRAS-GVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQHGEEDGLELLE-DDE-AKRVDAIAE 252 (510)
T ss_pred eEeecchHHHHHHHHHHHHh-hhhhcceEEEeecccccccccceeeEEEEecCCccCCcCCeEEec-cch-hhhHHHHHH
Confidence 34443 44445555555543 34456999999743 333 788888888888888876542 222 222223333
Q ss_pred HhCCCCceEEEEecCCC---------------CCCcccHhhHHhHHhhhcc-------------CCCeEEEEEcCCCCCC
Q psy9085 179 EVGRLENAIGWYHSHPG---------------YGCWLSGIDVSTQMLNQNF-------------QEPFVAIVIDPVRTIS 230 (394)
Q Consensus 179 kvgr~e~iVGWYHSHP~---------------~~~~pS~iDV~tQ~~yQ~~-------------~~p~VaLVvDp~~t~~ 230 (394)
+-+++.|||--+--- -+.|+|...+.+...+|.. ...+|-+||.-..
T Consensus 253 --~lGLrRVG~IFTDl~~~~s~egtV~~~rhkdsyFLSseE~~~aa~~Q~~hpn~~~~s~~~~fgSkfVT~visg~~--- 327 (510)
T KOG2834|consen 253 --GLGLRRVGWIFTDLVTADSAEGTVHYKRHKDSYFLSSEECITAAMFQNKHPNICEWSRDGHFGSKFVTLVISGDL--- 327 (510)
T ss_pred --hcCceeeEEEEeeeecccCccceEEeeeccchhcccHHHHHHHhhhhhcCCchheeeccccccceeEEEEEecCC---
Confidence 356999999754331 2358999988887777753 2347778886553
Q ss_pred CCceEEEEEEEccC
Q psy9085 231 AGKVCLGSFRTYPK 244 (394)
Q Consensus 231 ~Gkv~i~AFR~~p~ 244 (394)
.|.+.+-+|+++..
T Consensus 328 ~~~V~f~~YQVSnq 341 (510)
T KOG2834|consen 328 DGEVHFEGYQVSNQ 341 (510)
T ss_pred CcceeeeeeehhHH
Confidence 68899999999874
No 41
>KOG1795|consensus
Probab=84.10 E-value=2.3 Score=49.81 Aligned_cols=112 Identities=21% Similarity=0.249 Sum_probs=74.8
Q ss_pred cCCCceEEEEEeeEE---cCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceEEEEecCCCCCCcc
Q psy9085 124 SGGTLEVMGLLLGKI---DANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWL 200 (394)
Q Consensus 124 s~~p~EVmGlLLG~~---d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVGWYHSHP~~~~~p 200 (394)
++....+.|+|.|.- ++..-+|.-..-+|.-++...++....-.+ .. +=.+...+||-|+-|.--..+
T Consensus 2111 sD~r~qiag~~yG~s~~d~pqvkeIr~ivmvPQ~gs~~~v~lp~~lP~--~~-------~l~d~e~Lgw~hTq~~el~~l 2181 (2321)
T KOG1795|consen 2111 SDLRTQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGSHQGVHLPSFLPI--HG-------VLEDLEPLGWIHTQPNELPQL 2181 (2321)
T ss_pred cchhhhhheeeeccCCCCCCccceEEEEEeccccccccccccCccCCc--ch-------hccCCcccchhhcCccccccC
Confidence 344567889999964 233446665566787776665543111001 11 114688999999999888899
Q ss_pred cHhhHHhHHh-hhccCCCeEEEEEcCCCCCCCCceEEEEEEEccCCCCC
Q psy9085 201 SGIDVSTQML-NQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYPKGYKP 248 (394)
Q Consensus 201 S~iDV~tQ~~-yQ~~~~p~VaLVvDp~~t~~~Gkv~i~AFR~~p~~~~~ 248 (394)
|..||.++.- .+.-...+|.|.|+-. .|.+++.||.++|.||.=
T Consensus 2182 sp~dV~th~ki~~~~k~k~i~~t~~~t----pgs~sl~ay~lt~~G~eW 2226 (2321)
T KOG1795|consen 2182 SPQDVTTHAKILVDNKEKCIIITCSFT----PGSCSLTAYKLTPSGYEW 2226 (2321)
T ss_pred CHHHhhhhhhhhhcCccceEEEEeecc----CCcceeeeeccCcccccc
Confidence 9999987542 2222345676666643 699999999999988764
No 42
>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=83.96 E-value=13 Score=31.78 Aligned_cols=30 Identities=30% Similarity=0.214 Sum_probs=24.6
Q ss_pred CCceEEEEecCCCCCCcccHhhHH-hHHhhh
Q psy9085 183 LENAIGWYHSHPGYGCWLSGIDVS-TQMLNQ 212 (394)
Q Consensus 183 ~e~iVGWYHSHP~~~~~pS~iDV~-tQ~~yQ 212 (394)
+-.-|..-|.||.+.+.||..|+. |....+
T Consensus 59 ~A~~vil~HNHPsG~~~PS~~D~~~T~~l~~ 89 (113)
T cd08071 59 NAAAIILAHNHPSGDPTPSREDIELTKRLKE 89 (113)
T ss_pred hhheEEEEeeCCCCCCCCCHHHHHHHHHHHH
Confidence 477899999999999999999998 444333
No 43
>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=77.23 E-value=20 Score=30.98 Aligned_cols=89 Identities=16% Similarity=0.069 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHhcCCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceEEEEe
Q psy9085 112 ALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYH 191 (394)
Q Consensus 112 ~~aLlkIl~Hars~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVGWYH 191 (394)
+..+...++....+.+.|++-++.=......+.+...+ .|+-+++.+ .. .++++.+-.. +-.-|=..|
T Consensus 5 ~~~v~~~l~~~l~~~~~E~~~~l~Ld~~~~li~~~~v~----~G~~~~~~v--~~----R~I~~~al~~--~A~~vIl~H 72 (123)
T PF04002_consen 5 PEDVADYLRPKLQGLDQEQFRVLYLDSKNRLIGDEVVS----EGTIDSAPV--DP----REIFRRALRL--NASSVILAH 72 (123)
T ss_dssp HHHHHHHHTTTSS-TTS-EEEEEEE-TTSBEEEEEEEE----ESTT-GGGC--SH----HHHHHHHHHT--T-SEEEEEE
T ss_pred HHHHHHHHHHHhCCCCCeEEEEEEECCCCcEEEEEEec----ccCCCcccc--cH----HHHHHHHHhh--CCceEEEEE
Confidence 34445555544445566766665422222222232222 344444333 22 2333333332 355666789
Q ss_pred cCCCCCCcccHhhHH-hHHhhh
Q psy9085 192 SHPGYGCWLSGIDVS-TQMLNQ 212 (394)
Q Consensus 192 SHP~~~~~pS~iDV~-tQ~~yQ 212 (394)
-||.+.+.||.-|+. |....+
T Consensus 73 NHPsG~~~PS~~D~~~T~~L~~ 94 (123)
T PF04002_consen 73 NHPSGDPEPSDADIALTRRLKK 94 (123)
T ss_dssp E-TTS--S--HHHHHHHHHHHH
T ss_pred EcCCCCCCCCHhHHHHHHHHHH
Confidence 999999999999997 544444
No 44
>PRK00024 hypothetical protein; Reviewed
Probab=63.52 E-value=81 Score=30.24 Aligned_cols=105 Identities=18% Similarity=0.127 Sum_probs=58.7
Q ss_pred EECHHHHHHHHHHHhcCCCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceEE
Q psy9085 109 KISALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIG 188 (394)
Q Consensus 109 ~Is~~aLlkIl~Hars~~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVG 188 (394)
.-++..+...+.....+.+.|+..+|.=.....-+.....| .|+-+++.+ .+.+ .++.+-+. +-.-|=
T Consensus 103 i~~~~~~~~~l~~~l~~~~~E~f~vl~Ld~~~~li~~~~i~----~Gt~~~~~v--~pRe----i~~~Al~~--~A~~iI 170 (224)
T PRK00024 103 LLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELF----IGTLNSSIV--HPRE----IVKRALKL--NAAALI 170 (224)
T ss_pred CCCHHHHHHHHHHHccCCCceEEEEEEECCCCCEeeEEEee----eecCCeEEE--cHHH----HHHHHHHh--hccceE
Confidence 34677777777766667778887776532222222322222 344333322 1222 33333222 245556
Q ss_pred EEecCCCCCCcccHhhHH-hHHhhhcc---CCCeE-EEEEcC
Q psy9085 189 WYHSHPGYGCWLSGIDVS-TQMLNQNF---QEPFV-AIVIDP 225 (394)
Q Consensus 189 WYHSHP~~~~~pS~iDV~-tQ~~yQ~~---~~p~V-aLVvDp 225 (394)
.-|-||.+.+.||.-|+. |....+.. .=+.+ |+||..
T Consensus 171 l~HNHPSG~~~PS~~D~~~T~~l~~a~~~l~I~llDHiIv~~ 212 (224)
T PRK00024 171 LAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGD 212 (224)
T ss_pred EEecCCCCCCCCCHHHHHHHHHHHHHHHhCCCEEeeEEEEcC
Confidence 679999999999999998 55544432 22334 777753
No 45
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=59.70 E-value=1.3e+02 Score=28.90 Aligned_cols=103 Identities=20% Similarity=0.131 Sum_probs=57.3
Q ss_pred ECHHHHHHHHHHHhcCCCceEEEEEeeEEcCCe-EEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceEE
Q psy9085 110 ISALALLKMVMHARSGGTLEVMGLLLGKIDANS-MIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIG 188 (394)
Q Consensus 110 Is~~aLlkIl~Hars~~p~EVmGlLLG~~d~~t-l~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVG 188 (394)
-++..+...++....+.+.|.+-+|.= ...+. +.....| .|+-+.+.. .+.+ .++.+-+. +-.-|=
T Consensus 98 ~s~~~v~~~l~~~l~~~~~E~f~vl~L-d~~n~li~~~~i~----~Gt~~~~~v--~pRe----I~~~Al~~--~A~~vI 164 (218)
T TIGR00608 98 RSPEAAAEFLHTDLAHETREHFMVLFL-DRKNRLIAKEVVF----IGTVNHVPV--HPRE----IFKEALKL--SASALI 164 (218)
T ss_pred CCHHHHHHHHHHHhcCCCceEEEEEEE-CCCCcEEEEEEee----cCCCCeEEE--cHHH----HHHHHHHh--hCCeEE
Confidence 356677777777666677787776642 22222 2222222 344343322 1222 33332222 245555
Q ss_pred EEecCCCCCCcccHhhHH-hHHhhhcc---CCCeE-EEEEcC
Q psy9085 189 WYHSHPGYGCWLSGIDVS-TQMLNQNF---QEPFV-AIVIDP 225 (394)
Q Consensus 189 WYHSHP~~~~~pS~iDV~-tQ~~yQ~~---~~p~V-aLVvDp 225 (394)
.-|-||.+.+.||.-|+. |....+.. .=+.+ |+||..
T Consensus 165 laHNHPSG~~~PS~~Di~~T~~l~~a~~~lgI~llDHiIvg~ 206 (218)
T TIGR00608 165 LAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGK 206 (218)
T ss_pred EEeecCCCCCCCCHHHHHHHHHHHHHHHhCCCEEeeEEEEcC
Confidence 679999999999999998 65554432 22334 777754
No 46
>PF14220 DUF4329: Domain of unknown function (DUF4329)
Probab=39.57 E-value=25 Score=30.88 Aligned_cols=64 Identities=17% Similarity=0.212 Sum_probs=37.0
Q ss_pred CCceEEEEEeeEEcCCeEEEEEEEecCccCCCCcccccccHHHHHHHHHHHHHHhCCCCceEEEEecCCCCC-----Ccc
Q psy9085 126 GTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYHSHPGYG-----CWL 200 (394)
Q Consensus 126 ~p~EVmGlLLG~~d~~tl~Vtd~F~lP~~~te~rv~a~~ea~ey~~~mle~~~kvgr~e~iVGWYHSHP~~~-----~~p 200 (394)
...|.||++. +..++.+.-| -|..+....+..... ....+..+|+-||||..+. -.|
T Consensus 19 ~nrEy~G~I~-~~~~G~y~~t----~p~~G~~~~~~~~~~-------------~~p~g~~~vA~yHTHG~~~~~y~~evf 80 (123)
T PF14220_consen 19 ENREYCGYIG-KDEDGKYFAT----EPRRGENASCYPSNP-------------PCPNGSTIVASYHTHGAYSDGYDNEVF 80 (123)
T ss_pred CCcEEEEEEE-EcCCCcEEee----cCccCCCCCcCCCCc-------------ccccccceeeEeecccccCCCccccCC
Confidence 5789999765 4444444332 244443332221100 0112468999999999755 468
Q ss_pred cHhhHHh
Q psy9085 201 SGIDVST 207 (394)
Q Consensus 201 S~iDV~t 207 (394)
|..|+..
T Consensus 81 S~~D~~~ 87 (123)
T PF14220_consen 81 SPQDIRG 87 (123)
T ss_pred CHHHhhh
Confidence 8888874
No 47
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=37.13 E-value=52 Score=33.75 Aligned_cols=61 Identities=23% Similarity=0.291 Sum_probs=38.1
Q ss_pred EEEeeEE-cCCeEEEEEEEecCccCCCCcc--------cccccHHHHHHHHHHHHHHhC----CCCceEEEEecCCC
Q psy9085 132 GLLLGKI-DANSMIVMDAFALPVEGTETRV--------NAQAQAYEYMTAYIEAAKEVG----RLENAIGWYHSHPG 195 (394)
Q Consensus 132 GlLLG~~-d~~tl~Vtd~F~lP~~~te~rv--------~a~~ea~ey~~~mle~~~kvg----r~e~iVGWYHSHP~ 195 (394)
|+|+|.. .++.-.|.+..+.|...++... ...+.+.+ .+.+.++++. -+..|||.|=.+|.
T Consensus 1 GLlIGq~~s~~kd~Vv~l~~tP~~d~~~~~~~~~~~~~~~~~id~~---WVaeHA~qVsRMLPGGi~VlGifvv~~~ 74 (362)
T PF14778_consen 1 GLLIGQSSSSQKDYVVHLARTPPEDTDDEESDVRTSDSSIKDIDEE---WVAEHARQVSRMLPGGISVLGIFVVAPD 74 (362)
T ss_pred CeEeccccCCCcceEEEecCCCCccccccccccccccccccccCHH---HHHHHHHHHHhhCCCCcEEEEEEEEcCH
Confidence 8999997 6666678888988876544330 00011222 2334555553 36899999988864
No 48
>PF15659 Toxin-JAB1: JAB-like toxin 1
Probab=35.17 E-value=43 Score=30.86 Aligned_cols=28 Identities=29% Similarity=0.285 Sum_probs=23.0
Q ss_pred CCCCceEEEEecCCCCCCcccHhhHHhHH
Q psy9085 181 GRLENAIGWYHSHPGYGCWLSGIDVSTQM 209 (394)
Q Consensus 181 gr~e~iVGWYHSHP~~~~~pS~iDV~tQ~ 209 (394)
+....++. .||||.....||.-|.....
T Consensus 113 ~~~~~iid-iHSHP~~~~~~S~~D~~~~~ 140 (162)
T PF15659_consen 113 NNGNKIID-IHSHPENSNGPSGNDMKNAK 140 (162)
T ss_pred cCCceEEE-eccCCCCCCCCCcchhhhhh
Confidence 45678888 99999888899999987643
No 49
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=30.64 E-value=68 Score=38.20 Aligned_cols=111 Identities=17% Similarity=0.225 Sum_probs=68.0
Q ss_pred cCCCceEEEEEeeEEc---CCeEEEEEEEecCccCCCCccccc-ccHHHHHHHHHHHHHHhCCCCceEEEEecCCCCCCc
Q psy9085 124 SGGTLEVMGLLLGKID---ANSMIVMDAFALPVEGTETRVNAQ-AQAYEYMTAYIEAAKEVGRLENAIGWYHSHPGYGCW 199 (394)
Q Consensus 124 s~~p~EVmGlLLG~~d---~~tl~Vtd~F~lP~~~te~rv~a~-~ea~ey~~~mle~~~kvgr~e~iVGWYHSHP~~~~~ 199 (394)
++....|.|++.|+-. ...-+|...--+|+-++-..+... ..+.+ + -...++.++||-|+..+--.+
T Consensus 2150 sD~~vqvag~vyG~s~~d~p~ikeI~~~~lVPQlgs~~~vq~~s~vP~d-------l--p~~e~le~lGwihtq~~el~~ 2220 (2365)
T COG5178 2150 SDPHVQVAGLVYGKSGSDNPQIKEILSFGLVPQLGSLSGVQSSSFVPHD-------L--PGDEDLEILGWIHTQDDELPY 2220 (2365)
T ss_pred cccceeeEEEEeccCCccCcchhheeEEEeeccccccccccccccCCCC-------C--CCcccceeeEEEecCCcccch
Confidence 3456789999999743 223355544457776544433221 00100 0 011357899999999987778
Q ss_pred ccHhhHHhHHhhhccCCC--eEEEEEcCCCCCCCCceEEEEEEEccCCCCC
Q psy9085 200 LSGIDVSTQMLNQNFQEP--FVAIVIDPVRTISAGKVCLGSFRTYPKGYKP 248 (394)
Q Consensus 200 pS~iDV~tQ~~yQ~~~~p--~VaLVvDp~~t~~~Gkv~i~AFR~~p~~~~~ 248 (394)
++..++.|+. +-...+. +|-|.|.-. .|.++++||.+..+|+.=
T Consensus 2221 l~~~~v~th~-k~~~d~~~d~v~ltv~~~----pgsiSl~ay~v~keG~~W 2266 (2365)
T COG5178 2221 LEVAGVLTHR-KKIVDPEWDAVTLTVSYL----PGSISLRAYVVKKEGCNW 2266 (2365)
T ss_pred hhhhhhhhhh-hcccCccccceeeeeeec----cceeeeeeeeehhccccc
Confidence 8888888753 2222333 344444432 699999999999988654
Done!