Query psy3344
Match_columns 1282
No_of_seqs 210 out of 266
Neff 3.1
Searched_HMMs 46136
Date Fri Aug 16 22:35:34 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3344.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3344hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1795|consensus 100.0 5E-282 1E-286 2416.2 41.3 565 27-690 1326-2195(2321)
2 COG5178 PRP8 U5 snRNP spliceos 100.0 2E-241 5E-246 2063.1 35.4 564 27-690 1362-2235(2365)
3 KOG1795|consensus 100.0 4E-162 9E-167 1411.0 3.3 469 703-1276 1219-1988(2321)
4 COG5178 PRP8 U5 snRNP spliceos 100.0 9E-142 2E-146 1233.4 -5.0 469 703-1276 1255-2024(2365)
5 cd08056 MPN_PRP8 Mpr1p, Pad1p 100.0 7.8E-86 1.7E-90 700.5 14.2 138 555-692 1-138 (252)
6 PF12134 PRP8_domainIV: PRP8 d 100.0 5.5E-64 1.2E-68 520.7 8.8 136 343-478 1-231 (231)
7 PF12134 PRP8_domainIV: PRP8 d 100.0 2.6E-57 5.7E-62 471.0 -10.8 213 1039-1271 3-231 (231)
8 PF08084 PROCT: PROCT (NUC072) 100.0 1.3E-49 2.9E-54 387.0 2.1 114 1118-1231 1-115 (125)
9 PF10596 U6-snRNA_bdg: U6-snRN 100.0 3E-36 6.6E-41 300.3 2.9 78 693-798 81-160 (160)
10 PF10597 U5_2-snRNA_bdg: U5-sn 100.0 1.4E-36 3.1E-41 296.4 -0.9 124 672-876 7-130 (135)
11 cd08056 MPN_PRP8 Mpr1p, Pad1p 99.9 5.3E-28 1.1E-32 258.9 6.2 236 958-1224 1-252 (252)
12 PF10598 RRM_4: RNA recognitio 99.9 1.6E-28 3.4E-33 228.0 1.8 62 137-198 32-93 (93)
13 cd08066 MPN_AMSH_like Mov34/MP 99.5 1.3E-14 2.8E-19 148.8 5.7 97 591-693 3-108 (173)
14 cd08066 MPN_AMSH_like Mov34/MP 99.3 2.3E-12 5E-17 132.4 4.8 141 994-1168 3-158 (173)
15 PF08084 PROCT: PROCT (NUC072) 98.7 6.9E-09 1.5E-13 103.1 1.3 44 696-739 76-119 (125)
16 cd07767 MPN Mpr1p, Pad1p N-ter 98.2 8.9E-07 1.9E-11 82.6 2.3 88 600-690 2-93 (116)
17 smart00232 JAB_MPN JAB/MPN dom 97.8 5.5E-06 1.2E-10 78.8 1.0 95 594-693 8-109 (135)
18 PF01398 JAB: JAB1/Mov34/MPN/P 96.5 0.00047 1E-08 65.5 -0.7 101 590-692 4-113 (114)
19 cd08061 MPN_NPL4 Mov34/MPN/PAD 95.4 0.026 5.6E-07 63.2 6.3 82 609-691 33-128 (274)
20 PF05021 NPL4: NPL4 family; I 95.4 0.041 8.8E-07 62.6 7.7 115 613-735 2-145 (306)
21 KOG2880|consensus 94.2 0.0086 1.9E-07 68.8 -1.5 91 590-686 252-351 (424)
22 cd08069 MPN_RPN11_CSN5 Mov34/M 87.9 0.56 1.2E-05 52.4 4.2 97 591-691 11-118 (268)
23 KOG2834|consensus 81.8 2.4 5.2E-05 51.0 5.9 108 595-706 181-315 (510)
24 cd08067 MPN_2A_DUB Mov34/MPN/P 80.3 2.3 5.1E-05 45.5 4.7 76 610-689 26-108 (187)
25 cd08058 MPN_euk_mb Mpr1p, Pad1 69.9 5.3 0.00011 39.1 3.8 86 607-700 13-105 (119)
26 PF05924 SAMP: SAMP Motif; In 67.6 2.5 5.5E-05 31.5 0.8 17 764-791 4-20 (20)
27 PF09816 EAF: RNA polymerase I 59.3 22 0.00048 35.1 5.8 50 360-409 40-100 (109)
28 cd08070 MPN_like Mpr1p, Pad1p 52.9 22 0.00047 35.3 4.7 70 609-684 16-94 (128)
29 cd07767 MPN Mpr1p, Pad1p N-ter 51.3 7.5 0.00016 36.7 1.2 23 1002-1024 1-25 (116)
30 cd08068 MPN_BRCC36 Mov34/MPN/P 40.6 48 0.001 37.6 5.4 38 658-695 87-124 (244)
31 COG3538 Uncharacterized conser 40.1 38 0.00083 40.5 4.7 85 290-390 212-315 (434)
32 KOG2199|consensus 31.6 33 0.00071 41.4 2.5 127 214-343 217-367 (462)
33 PF00367 PTS_EIIB: phosphotran 30.7 39 0.00084 28.0 2.1 17 265-281 2-18 (35)
34 PRK06046 alanine dehydrogenase 26.2 1.4E+02 0.0031 34.3 6.3 40 363-402 60-101 (326)
35 COG4713 Predicted membrane pro 25.5 54 0.0012 39.5 2.9 131 597-754 33-175 (489)
36 cd01646 RT_Bac_retron_I RT_Bac 23.2 85 0.0018 32.0 3.5 50 145-221 49-98 (158)
37 COG1310 Predicted metal-depend 22.7 39 0.00086 33.8 1.0 84 593-682 3-91 (134)
No 1
>KOG1795|consensus
Probab=100.00 E-value=4.9e-282 Score=2416.22 Aligned_cols=565 Identities=91% Similarity=1.402 Sum_probs=559.1
Q ss_pred hhcccccccccccccccceeeccCCCCCccccchhhhhccccchhhhhhhHHHHHHHHHHHHHHHHhccccccccccccc
Q psy3344 27 LRALHSDLRWSKQTDVGITHFRSGMSHDEDQLIPNLYRYIQPWESEFIDSQRVWAEYALKRQEANAQNRRLTLEDLEDSW 106 (1282)
Q Consensus 27 ~~~~~sdl~~skqtd~githfr~gmsh~ed~lIP~l~rYi~~We~Ef~dSqrvW~eya~kr~ea~~qnrrlt~edle~sw 106 (1282)
++.||||||||||||+|||||||||||||||||||+||||+|||+||+||||||||||+|||||.+||||||+|||||||
T Consensus 1326 ilip~sDl~wskqtd~githfrsgm~h~~~~lIP~l~rYiq~We~EF~dSqRVWaEYa~krqea~~qnrrltledle~sw 1405 (2321)
T KOG1795|consen 1326 ILIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQPWESEFIDSQRVWAEYALKRQEAPAQNRRLTLEDLEDSW 1405 (2321)
T ss_pred EeechhhcccccccCccceeecccCCcchhhhhhHHHHhcchhhhhhhhHHHHHHHHHhhhhhhhhhccccchhhhcccc
Confidence 45799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCcccccccccccccccccccceeeecccccccccCccccceeeccccchhhhhhHHHHHHHHhhhhcccccccCCCC
Q psy3344 107 DRGIPRINTLFQKDRHTLAYDKGWRIRTEFKQYQDMNHTNSYGIIRGLQFASFIVQYYGLVLDLLVLGLQRASEMAGPPQ 186 (1282)
Q Consensus 107 drGiPRInTLFqkdrhtlayDkG~Rvr~~fk~yKDM~h~n~yGlIrGlqFssFi~QyyglvlDlLvLGl~Ra~eiaGp~~ 186 (1282)
|||||||||||||||||||||||||||+|||+|+
T Consensus 1406 DrGIPRinTLfQkdRhtLaYDkG~RvrteFkqYq---------------------------------------------- 1439 (2321)
T KOG1795|consen 1406 DRGIPRINTLFQKDRHTLAYDKGWRVRTEFKQYQ---------------------------------------------- 1439 (2321)
T ss_pred ccCCchhhHHHhhcchhheecccchHHHHHHHHh----------------------------------------------
Confidence 9999999999999999999999999999999876
Q ss_pred CCCcccccccchhhhcCCccccccccceEEEEEEeeccccccccccchhhhhhhcccCCCCcccccCCCccccccchhhH
Q psy3344 187 MPNDFLTFQDTATELAHPIRLYCRYVDKVHLFLRHTLAYDKGWRIRTEFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTD 266 (1282)
Q Consensus 187 ~pn~fl~f~d~~~e~~hPIrly~Ry~d~i~ilfrf~~~~~~~~~~~~~~~~~~~~k~npfwwT~~~HDGKLWnln~yrtD 266 (1282)
++|+|||||||||||||||||||||+|
T Consensus 1440 -----------------------------------------------------~~k~npFWwT~qrHDGKLWnln~yrtD 1466 (2321)
T KOG1795|consen 1440 -----------------------------------------------------VLKQNPFWWTHQRHDGKLWNLNNYRTD 1466 (2321)
T ss_pred -----------------------------------------------------ccCCCCceecccccCcccccccchhHH
Confidence 899999999999999999999999999
Q ss_pred HHHhccCcceeeeeecccccccCCcccch---------------------------------------------------
Q psy3344 267 MIQALGGVEGILEHTLFKGTYFPTWEGLF--------------------------------------------------- 295 (1282)
Q Consensus 267 ~iqaLggve~ileHtlfkgt~f~sweglF--------------------------------------------------- 295 (1282)
|||||||||||||||||||||||+|||||
T Consensus 1467 ~iqALGGVegilehtlf~~t~f~s~e~Lfwekasgfees~k~KkltnaQr~gL~QipNrrftlwwspTinrAnvyvgfQv 1546 (2321)
T KOG1795|consen 1467 VIQALGGVEGILEHTLFKGTYFPSWEGLFWEKASGFEESMKYKKLTNAQRSGLNQIPNRRFTLWWSPTINRANVYVGFQV 1546 (2321)
T ss_pred HHHHhcCcchhhhcccccccCcHHHHHHHHHhhcCchhhhHHHHHHHHHHhcccCCCccceEEeecchhhhhhheeeeEE
Confidence 99999999999999999999999999999
Q ss_pred ----------------------------------------h---------------------------------------
Q psy3344 296 ----------------------------------------C--------------------------------------- 296 (1282)
Q Consensus 296 ----------------------------------------c--------------------------------------- 296 (1282)
|
T Consensus 1547 QldLTgi~mhgkIptlkIsLiqifRaHlwQKihesvv~~lc~v~D~ELDal~iEtV~ketih~rKsykm~SScAdIll~~ 1626 (2321)
T KOG1795|consen 1547 QLDLTGIYMHGKIPTLKISLIQIFRAHLWQKIHESVVNDLCQVFDQELDALSIETVQKETIHPRKSYKMNSSCADILLGA 1626 (2321)
T ss_pred eeccceeEEeccccceeeeHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhhhhhhcCcchhhhccchhHHHhhhc
Confidence 1
Q ss_pred --------------------------------------------------------------------------------
Q psy3344 297 -------------------------------------------------------------------------------- 296 (1282)
Q Consensus 297 -------------------------------------------------------------------------------- 296 (1282)
T Consensus 1627 ~~~~~vs~ps~i~~skd~~~~~~~~klw~dvqLr~gdyds~dv~rytrAkfLd~Ttd~~s~ypsptGv~i~iDL~YN~~s 1706 (2321)
T KOG1795|consen 1627 GVKWGVSNPSLIPESKDLWDPFFTAKLWIDVQLRWGDYDSHDVERYTRAKFLDYTTDNASQYPSPTGVLIGIDLAYNLHS 1706 (2321)
T ss_pred ceeecCCCccccccchhhccccchhhhhhhhhhhccchhhhhHHHHHHhhhhhhhccccccCCCCCceEEEeeehhhhhh
Confidence
Q ss_pred cccccCCCChHHHHHHHHHHHHhCchhHHHHHHHHhhhccccCCCCCCCcccccccccccCceEEEecCceeEEEEeeec
Q psy3344 297 AYGNWFPGSKPLIQQALAKIMKANPALYVLRERIRKALQLYSSEPTEPYLSSQNYGELFSNQIIWFVDDTNVYRVTIHKT 376 (1282)
Q Consensus 297 ayGnw~~glK~liq~aM~kImk~NpaL~vLRERIRKgLQLYsSe~~e~~l~s~Ny~ELF~n~~~wfVDdtnvYRvtihkt 376 (1282)
||||||||+|||||+||+||||+||||||||||||||||||+|+|+||||+|+||||||+||++||||||||||||||||
T Consensus 1707 ayGNw~~g~Kpli~qsM~kImkanpalyvLRERiRKgLQlYsSe~~e~~l~ssNygeLFsnqi~lfVDdtnvyRvtihkt 1786 (2321)
T KOG1795|consen 1707 AYGNWFPGLKPLIQQSMNKIMKANPALYVLRERIRKGLQLYSSEPTEPYLSSSNYGELFSNQIILFVDDTNVYRVTIHKT 1786 (2321)
T ss_pred hhcccccccHHHHHHHHHHHHhhCcHHHHHHHHHHHhhhhhccCCCCceeccccHHHhhhcceEEEEeccceEEEEeeec
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCccccccccceEEEEcCCCCceEEEEEeeccccccchhhHH-------------------------------------
Q psy3344 377 FEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQL------------------------------------- 419 (1282)
Q Consensus 377 ~egn~~tKpiNG~IFifNP~TGqLfLKIiHtsvWagQKRL~Ql------------------------------------- 419 (1282)
||||+||||||||||||||+||||||||||||||||||||||+
T Consensus 1787 fegnlttk~ingaiFi~nPrtG~LflKiihtsvwaGqkrl~qlaKwktAeeVaaLirslp~EEqpkqiIVtrk~MlDplE 1866 (2321)
T KOG1795|consen 1787 FEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLE 1866 (2321)
T ss_pred cccccccccccceEEEecCCCCceEEEEeecccccchhHHHHHHhHhhHHHHHHHHhcCChhhcCceEEEechhccChHH
Confidence 9999999999999999999999999999999999999999999
Q ss_pred ----------------------------------------------------------HHHHHHHHHHhcccCcccceee
Q psy3344 420 ----------------------------------------------------------AFSRLILILRALHVNTERTKVI 441 (1282)
Q Consensus 420 ----------------------------------------------------------AFsRLiLILRal~vn~~rtk~I 441 (1282)
|||||||||||||||+||||+|
T Consensus 1867 vhllDfPnI~ik~sel~lPFqa~m~i~k~~dlilkatEpqmvlfNlYddWl~tissyTaFsRliLilral~vn~e~~k~i 1946 (2321)
T KOG1795|consen 1867 VHLLDFPNIVIKGSELQLPFQACMKIEKFGDLILKATEPQMVLFNLYDDWLKTISSYTAFSRLILILRALHVNEERAKMI 1946 (2321)
T ss_pred HhhccCCceeeecccccccHHHHhhHHHHhhHHhhccCceEEEEehhhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHhhh
Confidence 9999999999999999999999
Q ss_pred ccCCCCccccccccCCCCCchhhhHHHHHHhHHHHHHhcccCCccccccchhhhhhhhhccccCCchHHHHHHHHHHHhh
Q psy3344 442 LKPDKSTITEPHHIWPSLSDDEWIKVEVQLKDLILADYGKKNNVNVASLTQSEIRDIILGMEISAPSAQRQQIAEIEKQT 521 (1282)
Q Consensus 442 L~p~~~~it~~hhiWPslsDeeWIkvEv~LkDLIL~dY~kknnVnvssLTQsEIRDIILG~eI~~ps~qrqqiaeiE~~~ 521 (1282)
|+|||+++|++||+||+|||+|||+||+|||||||+|||||||||++||||||||||||||+|+|||+|||||||||||.
T Consensus 1947 l~~d~t~i~~~~hiWP~~tD~qWikvE~qlkDLIl~dY~kk~nvn~s~LtqsEirDIilG~~isaps~qrqqiaeiekq~ 2026 (2321)
T KOG1795|consen 1947 LKPDKTTITEPHHIWPSLTDEQWIKVEVQLKDLILADYGKKNNVNVSSLTQSEIRDIILGMEISAPSQQRQQIAEIEKQT 2026 (2321)
T ss_pred cCCCcceeccccccCCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCcccccHHHHhhhheeeeecCcchhhHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccceeEEEEEecccCCeEEEEeccccccccccCchhHHHHHHHcccccccccceeeecccccccceeeeccchhhcc
Q psy3344 522 KEQSQLTATTTRTVNKHGDEIITSTTSNYETATFGSKTEWRVRAISATNLHLRTNHIYVSSDDIKETGYTYILPKNVLKK 601 (1282)
Q Consensus 522 ~~~~q~ta~tTkT~N~hGeeIvvtTtS~YEqqtFsSKtdWR~RAIsatnL~LR~~nIYVssdD~~e~~~tyViPKNlLkK 601 (1282)
+|++|+||++|+|+|+|||||+|+|+++||+++|+||++||+|||++++|+||++||||++||++|+++||+||||||||
T Consensus 2027 ~e~~q~ta~~t~t~n~~gde~i~~~ts~ye~~~f~sk~eWr~~ais~t~l~Lr~~~iyvnsddi~e~~~tyilPkNllkk 2106 (2321)
T KOG1795|consen 2027 KEQSQLTAVTTRTTNVHGDEIIVTTTSNYETQTFSSKTEWRVRAISATNLPLRTNHIYVNSDDIKETGYTYILPKNLLKK 2106 (2321)
T ss_pred hhhhhheeeceeeecccCceEEEEecccchhhhccchHHHHHHHHhccCcceecceeeecchhhhhcCceeeccHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceEeeeccceEEEEEEccCCCCCCcceeEEEEEcCCCccccceeecCCCCCCCCCcCCCCcceeeecCCCCCCCCChHhH
Q psy3344 602 FVTISDLRAQIAGYLYGVSPADNPQVKEIRCIVMPPQWGTHQTVHLPASLPGHPYLKEMEPLGWIHTQPNELPQLSPQDV 681 (1282)
Q Consensus 602 FI~ISDlRtQIaGyLYG~SP~Dnp~VKEIrCIVLvPQ~Gs~~sV~lp~~LP~h~~L~dLEpLGWIHTQ~~El~~Lsp~DV 681 (1282)
||+|||+|+|||||+||.||+||||||||+|||||||+|++++|++|.++|.|+.+.|||+|||||||++|+++|+|+||
T Consensus 2107 Fi~isD~r~qiag~~yG~s~~d~pqvkeIr~ivmvPQ~gs~~~v~lp~~lP~~~~l~d~e~Lgw~hTq~~el~~lsp~dV 2186 (2321)
T KOG1795|consen 2107 FITISDLRTQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGSHQGVHLPSFLPIHGVLEDLEPLGWIHTQPNELPQLSPQDV 2186 (2321)
T ss_pred heeecchhhhhheeeeccCCCCCCccceEEEEEeccccccccccccCccCCcchhccCCcccchhhcCccccccCCHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhc
Q psy3344 682 TSHAKIMAD 690 (1282)
Q Consensus 682 tthAkl~~d 690 (1282)
++|||++.+
T Consensus 2187 ~th~ki~~~ 2195 (2321)
T KOG1795|consen 2187 TTHAKILVD 2195 (2321)
T ss_pred hhhhhhhhc
Confidence 999999553
No 2
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=100.00 E-value=2.2e-241 Score=2063.13 Aligned_cols=564 Identities=64% Similarity=1.034 Sum_probs=550.4
Q ss_pred hhcccccccccccccccceeeccCCCCCccccchhhhhccccchhhhhhhHHHHHHHHHHHHHHHHhccccccccccccc
Q psy3344 27 LRALHSDLRWSKQTDVGITHFRSGMSHDEDQLIPNLYRYIQPWESEFIDSQRVWAEYALKRQEANAQNRRLTLEDLEDSW 106 (1282)
Q Consensus 27 ~~~~~sdl~~skqtd~githfr~gmsh~ed~lIP~l~rYi~~We~Ef~dSqrvW~eya~kr~ea~~qnrrlt~edle~sw 106 (1282)
++.|||||+||||||||||||||||+|+.|+|||++||||++||+||+||||||||||.|||||.+||||||+||||+||
T Consensus 1362 ilip~sDl~wSkqtdtgithfrsgmt~~~e~lIP~~~rYis~We~EF~dSqRVWaEYa~krqea~qqnrrl~~e~le~sw 1441 (2365)
T COG5178 1362 ILIPHSDLEWSKQTDTGITHFRSGMTTNGERLIPAAMRYISRWEYEFEDSQRVWAEYARKRQEAGQQNRRLTLEDLEMSW 1441 (2365)
T ss_pred EeeehhhcccccccCccceeeccccccCccccchHHHHhhhhhhhhhhhHHHHHHHHHHHHHHhhhhhhhcchhhhccCc
Confidence 45799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCcccccccccccccccccccceeeecccccccccCccccceeeccccchhhhhhHHHHHHHHhhhhcccccccCCCC
Q psy3344 107 DRGIPRINTLFQKDRHTLAYDKGWRIRTEFKQYQDMNHTNSYGIIRGLQFASFIVQYYGLVLDLLVLGLQRASEMAGPPQ 186 (1282)
Q Consensus 107 drGiPRInTLFqkdrhtlayDkG~Rvr~~fk~yKDM~h~n~yGlIrGlqFssFi~QyyglvlDlLvLGl~Ra~eiaGp~~ 186 (1282)
|||||||||||||||||||||||||||+|||+|.
T Consensus 1442 DrGIPRisTLfQrdRhtLaYDrG~R~r~eFkqYs---------------------------------------------- 1475 (2365)
T COG5178 1442 DRGIPRISTLFQRDRHTLAYDRGFRMRSEFKQYS---------------------------------------------- 1475 (2365)
T ss_pred ccCChhHHHHHhhcchhhhhccchHHHHHHHHhc----------------------------------------------
Confidence 9999999999999999999999999999999886
Q ss_pred CCCcccccccchhhhcCCccccccccceEEEEEEeeccccccccccchhhhhhhcccCCCCcccccCCCccccccchhhH
Q psy3344 187 MPNDFLTFQDTATELAHPIRLYCRYVDKVHLFLRHTLAYDKGWRIRTEFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTD 266 (1282)
Q Consensus 187 ~pn~fl~f~d~~~e~~hPIrly~Ry~d~i~ilfrf~~~~~~~~~~~~~~~~~~~~k~npfwwT~~~HDGKLWnln~yrtD 266 (1282)
+.++||||||+++||||||+||+||+|
T Consensus 1476 -----------------------------------------------------l~~n~pFWwT~~~HDGKLW~ln~yr~D 1502 (2365)
T COG5178 1476 -----------------------------------------------------LKPNNPFWWTDAKHDGKLWSLNRYRLD 1502 (2365)
T ss_pred -----------------------------------------------------cCCCCCceecccccCccccchhhhhHH
Confidence 678899999999999999999999999
Q ss_pred HHHhccCcceeeeeecccccccCCcccch---------------------------------------------------
Q psy3344 267 MIQALGGVEGILEHTLFKGTYFPTWEGLF--------------------------------------------------- 295 (1282)
Q Consensus 267 ~iqaLggve~ileHtlfkgt~f~sweglF--------------------------------------------------- 295 (1282)
+|||||||||||||||||||||+||||||
T Consensus 1503 viqALGGvegIleHTlFkaTgF~SweglFWEkasgfe~smkfkKLTnAQr~GLsQIPNRRFtLWWSPTINRaNVYVGfqV 1582 (2365)
T COG5178 1503 VIQALGGVEGILEHTLFKATGFRSWEGLFWEKASGFEESMKFKKLTNAQRMGLSQIPNRRFTLWWSPTINRANVYVGFQV 1582 (2365)
T ss_pred HHHHhcchhhhhhhhhhcccCcchhhhhhHhhhcchHHHHHHHHhhhhhhcccccCCCceeEEEecCcccccceEEEEEE
Confidence 99999999999999999999999999999
Q ss_pred ----------------------------------------h---------------------------------------
Q psy3344 296 ----------------------------------------C--------------------------------------- 296 (1282)
Q Consensus 296 ----------------------------------------c--------------------------------------- 296 (1282)
|
T Consensus 1583 QLDlTGI~mHGKiPTLKISlIQIFR~hLWqkIHESvV~dlCqvld~eldvlqiEtv~ketvHpRKSYkmnSScADIll~~ 1662 (2365)
T COG5178 1583 QLDLTGILMHGKIPTLKISLIQIFRNHLWQKIHESVVGDLCQVLDKELDVLQIETVQKETVHPRKSYKMNSSCADILLSG 1662 (2365)
T ss_pred EEechheeecCCCCceeehHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhheeeecccccccccccccccchHHHHHhhh
Confidence 1
Q ss_pred --------------------------------------------------------------------------------
Q psy3344 297 -------------------------------------------------------------------------------- 296 (1282)
Q Consensus 297 -------------------------------------------------------------------------------- 296 (1282)
T Consensus 1663 ~~~w~Vs~Psll~e~rD~~~~~~tnk~WiDVQLR~GDYDshdi~rY~RakFldyttD~qsmYPsptGv~igiDLcYNm~s 1742 (2365)
T COG5178 1663 AYDWCVSSPSLLLEERDGGSNVRTNKLWIDVQLRWGDYDSHDIHRYARAKFLDYTTDPQSMYPSPTGVVIGIDLCYNMWS 1742 (2365)
T ss_pred hhhhccCCchhhhhcccccccceeeeeEEEEEEeecCccccCHHHHHHhhhhhcccChhhcccCCCceEEEEeehhhhhh
Confidence
Q ss_pred cccccCCCChHHHHHHHHHHHHhCchhHHHHHHHHhhhccccCCCCCCCcccccccccccCceEEEecCceeEEEEeeec
Q psy3344 297 AYGNWFPGSKPLIQQALAKIMKANPALYVLRERIRKALQLYSSEPTEPYLSSQNYGELFSNQIIWFVDDTNVYRVTIHKT 376 (1282)
Q Consensus 297 ayGnw~~glK~liq~aM~kImk~NpaL~vLRERIRKgLQLYsSe~~e~~l~s~Ny~ELF~n~~~wfVDdtnvYRvtihkt 376 (1282)
|||||++|||||||++|++|||+||||||||||||||||||+|+|+|+||||+||+|||||++.+|||||||||||+|||
T Consensus 1743 aYGNw~~glKpliq~SM~~ImkanpaLyvLRERiRKgLQlY~S~~qe~~l~ssnyaElfsN~i~LFvddtnVyrvt~hkt 1822 (2365)
T COG5178 1743 AYGNWNEGLKPLIQSSMERIMKANPALYVLRERIRKGLQLYTSEPQEQYLSSSNYAELFSNSIDLFVDDTNVYRVTLHKT 1822 (2365)
T ss_pred hhcccchhhHHHHHHHHHHHHhhCcHHHHHHHHHHHhhhhhhcCcchhhccccchHHHhcCccceEecCceeeeeehhhh
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCccccccccceEEEEcCCCCceEEEEEeeccccccchhhHH-------------------------------------
Q psy3344 377 FEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQL------------------------------------- 419 (1282)
Q Consensus 377 ~egn~~tKpiNG~IFifNP~TGqLfLKIiHtsvWagQKRL~Ql------------------------------------- 419 (1282)
||||+||||||||||+|||+||||||||||||||||||||+|+
T Consensus 1823 fEgn~ttk~ing~iFvlnP~tG~LflKvihtsvwaGqkrl~qlaKwktAeeV~aL~rslp~EEqpkqiIVtrk~MlDplE 1902 (2365)
T COG5178 1823 FEGNLTTKPINGAIFVLNPATGNLFLKVIHTSVWAGQKRLIQLAKWKTAEEVFALGRSLPVEEQPKQIIVTRKSMLDPLE 1902 (2365)
T ss_pred hccccccccccceEEEecCCCCcEEEEEeecccccchhHHHHHHhHhhHHHHHHHhhcCChhhcCceeEEehhhhcChHH
Confidence 9999999999999999999999999999999999999999999
Q ss_pred ----------------------------------------------------------HHHHHHHHHHhcccCcccceee
Q psy3344 420 ----------------------------------------------------------AFSRLILILRALHVNTERTKVI 441 (1282)
Q Consensus 420 ----------------------------------------------------------AFsRLiLILRal~vn~~rtk~I 441 (1282)
|||||+||||||+||+||||+|
T Consensus 1903 vh~lDfPnIsir~~el~lPFsavm~idki~d~ilratEpqmvlfNlYddWl~~~SsyTaFsRL~Lvlral~vnee~~k~i 1982 (2365)
T COG5178 1903 VHILDFPNISIRTCELALPFSAVMGIDKIRDLILRATEPQMVLFNLYDDWLQETSSYTAFSRLLLVLRALDVNEERVKEI 1982 (2365)
T ss_pred hhhccCCCcceecccccCChHhhhchHHHHHHHHhccCceEEEEehhhhHHHhhhhHHHHHHHHHHHHHhccCHHHHHHh
Confidence 9999999999999999999999
Q ss_pred ccCCCCccccccccCCCCCchhhhHHHHHHhHHHHHHhcccCCccccccchhhhhhhhhccccCCchHHHHHHHHHHHhh
Q psy3344 442 LKPDKSTITEPHHIWPSLSDDEWIKVEVQLKDLILADYGKKNNVNVASLTQSEIRDIILGMEISAPSAQRQQIAEIEKQT 521 (1282)
Q Consensus 442 L~p~~~~it~~hhiWPslsDeeWIkvEv~LkDLIL~dY~kknnVnvssLTQsEIRDIILG~eI~~ps~qrqqiaeiE~~~ 521 (1282)
|+||++++|+.+|+||+|||+|||++|+|||||||++||+|||||+++|||||||||||||.|++||.+|||+||+|+|.
T Consensus 1983 l~~d~si~~k~nhlWP~f~D~qWi~~E~qlrDLIl~~Y~~k~nin~s~LtqsEvrDIilG~~i~aps~~rq~~ae~ekqn 2062 (2365)
T COG5178 1983 LRPDKSIITKINHLWPGFSDSQWIKKEIQLRDLILDRYCSKHNINPSGLTQSEVRDIILGFRISAPSGARQETAETEKQN 2062 (2365)
T ss_pred cCCCccceeeecccCCCCCHHHHhhhhhHHHHHHHHHHHHhcCCCccccchhHhhhhheeeeecCcccchhhhhhhhhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred hhcc--cceeEEEEEecccCCeEEEEeccccccccccCchhHHHHHHHcccccccccceeeeccccccc-ceeeeccchh
Q psy3344 522 KEQS--QLTATTTRTVNKHGDEIITSTTSNYETATFGSKTEWRVRAISATNLHLRTNHIYVSSDDIKET-GYTYILPKNV 598 (1282)
Q Consensus 522 ~~~~--q~ta~tTkT~N~hGeeIvvtTtS~YEqqtFsSKtdWR~RAIsatnL~LR~~nIYVssdD~~e~-~~tyViPKNl 598 (1282)
.|.. ..|+++|||+|++|+|+||++++-||.++|+||++||++||+++.|.+|++||||++||+.|+ .++|+||+|+
T Consensus 2063 ~e~a~~~~t~v~tktin~~g~e~Vv~~~~~ye~e~fssk~eWr~~ai~~~~L~lr~kniyv~ad~~~e~~q~~y~lP~NL 2142 (2365)
T COG5178 2063 SEKALSRPTNVSTKTINGWGREYVVLDGMIYEGEKFSSKEEWRSEAIRTGPLELRTKNIYVTADENEESIQQMYRLPLNL 2142 (2365)
T ss_pred chhhhcCCceeeeeeeccccceEEEeecccccccccchHHHHHHHHHhcCCcccccccceeccchhhhhhhccccccHHH
Confidence 7644 489999999999999999999999999999999999999999999999999999999999998 6899999999
Q ss_pred hccceEeeeccceEEEEEEccCCCCCCcceeEEEEEcCCCccccceeecCCCCCCCCC--cCCCCcceeeecCCCCCCCC
Q psy3344 599 LKKFVTISDLRAQIAGYLYGVSPADNPQVKEIRCIVMPPQWGTHQTVHLPASLPGHPY--LKEMEPLGWIHTQPNELPQL 676 (1282)
Q Consensus 599 LkKFI~ISDlRtQIaGyLYG~SP~Dnp~VKEIrCIVLvPQ~Gs~~sV~lp~~LP~h~~--L~dLEpLGWIHTQ~~El~~L 676 (1282)
|+|||+|||+++|+|||+||+|+.|||+||||+|++||||+|+..+|++|.++| |+. .+|||+|||||||..|+++|
T Consensus 2143 l~kF~~isD~~vqvag~vyG~s~~d~p~ikeI~~~~lVPQlgs~~~vq~~s~vP-~dlp~~e~le~lGwihtq~~el~~l 2221 (2365)
T COG5178 2143 LEKFMRISDPHVQVAGLVYGKSGSDNPQIKEILSFGLVPQLGSLSGVQSSSFVP-HDLPGDEDLEILGWIHTQDDELPYL 2221 (2365)
T ss_pred HHhhheecccceeeEEEEeccCCccCcchhheeEEEeeccccccccccccccCC-CCCCCcccceeeEEEecCCcccchh
Confidence 999999999999999999999999999999999999999999999999999999 543 48999999999999999999
Q ss_pred ChHhHHHHHHhhhc
Q psy3344 677 SPQDVTSHAKIMAD 690 (1282)
Q Consensus 677 sp~DVtthAkl~~d 690 (1282)
+..+|++|++++.+
T Consensus 2222 ~~~~v~th~k~~~d 2235 (2365)
T COG5178 2222 EVAGVLTHRKKIVD 2235 (2365)
T ss_pred hhhhhhhhhhcccC
Confidence 99999988887543
No 3
>KOG1795|consensus
Probab=100.00 E-value=4.4e-162 Score=1411.04 Aligned_cols=469 Identities=51% Similarity=0.718 Sum_probs=440.4
Q ss_pred cceeeeccCC-ccccccccCcceeeccccccccccccccchhhhHHHHHHHHHHhhhhHHHHHHHHHhhhccceeeeecc
Q psy3344 703 MKYDLQLANP-KEFYHEIHRPAHFLNFSSLEDGDGIVNKWNTALIGLMTYFRESVVNTQELLDLLVKCENKIQTRIKIGL 781 (1282)
Q Consensus 703 mkY~Lkld~P-~~FY~e~hRp~HFl~Fs~ied~~~I~~k~~t~~i~~~~~fr~~~~~~~~lld~l~k~e~~i~~~~~~~~ 781 (1282)
+...|++++. .++|+ +|++|+++.||+.+|+||++||||++||||||||||+|+||||||+|||||+|||||||+||
T Consensus 1219 a~a~l~V~ee~i~~F~--nrir~IlmsSGStTFtKia~kWNTali~l~TYfREaiv~T~~LldlLvk~E~kIq~rvKigl 1296 (2321)
T KOG1795|consen 1219 AQAFLRVDEEGIKMFE--NRIRQILMSSGSTTFTKIANKWNTALIGLMTYFREAIVNTQELLDLLVKCENKIQTRVKIGL 1296 (2321)
T ss_pred hheeeEecHHHHHHHH--HHHHHHhhccCchhHHHHHHHHhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhhhhhhc
Confidence 6677888887 89999 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCcch-------------------------------------------------------------------
Q psy3344 782 NSKMPSRFPPAVF------------------------------------------------------------------- 794 (1282)
Q Consensus 782 n~~mp~rf~~~~~------------------------------------------------------------------- 794 (1282)
||||||||||+||
T Consensus 1297 NSKMPsRFPPvvFYtPKElGGLGMlS~ghilip~sDl~wskqtd~githfrsgm~h~~~~lIP~l~rYiq~We~EF~dSq 1376 (2321)
T KOG1795|consen 1297 NSKMPSRFPPVVFYTPKELGGLGMLSMGHILIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQPWESEFIDSQ 1376 (2321)
T ss_pred ccCCCCCCCCeeeeChhhcCccceeecCcEeechhhcccccccCccceeecccCCcchhhhhhHHHHhcchhhhhhhhHH
Confidence 9999999999887
Q ss_pred --------------------------------------------------------------------------------
Q psy3344 795 -------------------------------------------------------------------------------- 794 (1282)
Q Consensus 795 -------------------------------------------------------------------------------- 794 (1282)
T Consensus 1377 RVWaEYa~krqea~~qnrrltledle~swDrGIPRinTLfQkdRhtLaYDkG~RvrteFkqYq~~k~npFWwT~qrHDGK 1456 (2321)
T KOG1795|consen 1377 RVWAEYALKRQEAPAQNRRLTLEDLEDSWDRGIPRINTLFQKDRHTLAYDKGWRVRTEFKQYQVLKQNPFWWTHQRHDGK 1456 (2321)
T ss_pred HHHHHHHhhhhhhhhhccccchhhhccccccCCchhhHHHhhcchhheecccchHHHHHHHHhccCCCCceecccccCcc
Confidence
Q ss_pred --------------------------------------------------------------------------------
Q psy3344 795 -------------------------------------------------------------------------------- 794 (1282)
Q Consensus 795 -------------------------------------------------------------------------------- 794 (1282)
T Consensus 1457 LWnln~yrtD~iqALGGVegilehtlf~~t~f~s~e~Lfwekasgfees~k~KkltnaQr~gL~QipNrrftlwwspTin 1536 (2321)
T KOG1795|consen 1457 LWNLNNYRTDVIQALGGVEGILEHTLFKGTYFPSWEGLFWEKASGFEESMKYKKLTNAQRSGLNQIPNRRFTLWWSPTIN 1536 (2321)
T ss_pred cccccchhHHHHHHhcCcchhhhcccccccCcHHHHHHHHHhhcCchhhhHHHHHHHHHHhcccCCCccceEEeecchhh
Confidence
Q ss_pred ------------------------------------------------------hhhhhhHhhhhhhhcccccccccccc
Q psy3344 795 ------------------------------------------------------DQELDALEIETVQKETIHPRKSYKMN 820 (1282)
Q Consensus 795 ------------------------------------------------------d~~~~~l~i~~vqke~ihprksy~~n 820 (1282)
||||||++||+|||||||||||||||
T Consensus 1537 rAnvyvgfQvQldLTgi~mhgkIptlkIsLiqifRaHlwQKihesvv~~lc~v~D~ELDal~iEtV~ketih~rKsykm~ 1616 (2321)
T KOG1795|consen 1537 RANVYVGFQVQLDLTGIYMHGKIPTLKISLIQIFRAHLWQKIHESVVNDLCQVFDQELDALSIETVQKETIHPRKSYKMN 1616 (2321)
T ss_pred hhhheeeeEEeeccceeEEeccccceeeeHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhhhhhhcCcchhhhcc
Confidence 99999999999999999999999999
Q ss_pred cchhhHHhhhhccccccCCcccccCCCCCCCccccCCcccccccccccCcccchhhhhhccccccceeeeecccccCccc
Q psy3344 821 SSCADVLLFAAYKWNVSRPSLLADSKGKFPPVVFYTPKELGGLGMLSMGHVLIPQVRELFKYNWGFIYTVSLDFYDNMSH 900 (1282)
Q Consensus 821 ~scadillf~~~~w~v~~p~ll~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~s~ 900 (1282)
||||||++++.++|+||+||++.+|||.++++ ...++|.|+||+||+|| ||
T Consensus 1617 SScAdIll~~~~~~~vs~ps~i~~skd~~~~~-------------------~~~klw~dvqLr~gdyd----------s~ 1667 (2321)
T KOG1795|consen 1617 SSCADILLGAGVKWGVSNPSLIPESKDLWDPF-------------------FTAKLWIDVQLRWGDYD----------SH 1667 (2321)
T ss_pred chhHHHhhhcceeecCCCccccccchhhcccc-------------------chhhhhhhhhhhccchh----------hh
Confidence 99999999999999999999999999966654 34567889999999988 88
Q ss_pred cccccccccchhHHHHHHHHHHHhhhhccceeeeeeeecccCceeeeeccccccccccCCchhHhHHHhhhcchhhhcCc
Q psy3344 901 YVNSMEISAPSAQRQQIAEIEKQTKEQSQLTATTTRTVNKHGDEIITSTTSNYETATFGSKTEWRVRAISATNLHLRTNH 980 (1282)
Q Consensus 901 ~~~gmeisaps~qrqq~AeIEkq~req~qltattt~T~NvhGeeiit~TtS~ye~~~F~SKt~wrirai~a~nL~~r~n~ 980 (1282)
+ +|+++|++ +|++|| ...| .|+|||+..|+++.|+|+|..++|
T Consensus 1668 d------------------v~rytrAk-fLd~Tt-------------d~~s-----~ypsptGv~i~iDL~YN~~sayGN 1710 (2321)
T KOG1795|consen 1668 D------------------VERYTRAK-FLDYTT-------------DNAS-----QYPSPTGVLIGIDLAYNLHSAYGN 1710 (2321)
T ss_pred h------------------HHHHHHhh-hhhhhc-------------cccc-----cCCCCCceEEEeeehhhhhhhhcc
Confidence 7 99999998 899984 3345 458999999999999999999999
Q ss_pred eeccCccccccceeeecccchhhhhhhhHhhhhhhccccccccccCccccccCCcccccccccCccceeeccceeeeecC
Q psy3344 981 IYVSSDDIKETGYTYILPKNVLKKFVTISDLRAQIAGYLYDHLVCGRHERVSSDHTQDIRRQSDHQTFIFHSQIIWFVDD 1060 (1282)
Q Consensus 981 Iyv~s~d~~~~~ytyimPkNiLkkfi~iadLR~qiagyLyg~s~~~~~~~~s~~~~kei~~~~~~~~~~f~~qi~wf~dd 1060 (1282)
+|.+.+++.++++..| |++++|.|++++++++++|+|+|+++++|.+ |+||+++|+|||+|||||
T Consensus 1711 w~~g~Kpli~qsM~kI--------------mkanpalyvLRERiRKgLQlYsSe~~e~~l~-ssNygeLFsnqi~lfVDd 1775 (2321)
T KOG1795|consen 1711 WFPGLKPLIQQSMNKI--------------MKANPALYVLRERIRKGLQLYSSEPTEPYLS-SSNYGELFSNQIILFVDD 1775 (2321)
T ss_pred cccccHHHHHHHHHHH--------------HhhCcHHHHHHHHHHHhhhhhccCCCCceec-cccHHHhhhcceEEEEec
Confidence 9988888766666555 7889999999999999999999999999996 999999999999999999
Q ss_pred CceeeeeecccccCCccccccCCcceeccCCcccceeeeEeeccccccccccccCcceEEEEeeeccCeeeeeccccCCC
Q psy3344 1061 TNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLGEKTVVITCSFTPGSCSLTAYKLTPS 1140 (1282)
Q Consensus 1061 tn~~rV~~h~t~~gnl~tkPingai~~f~p~tg~l~lkiIHt~~w~~~krl~q~~k~ti~~tvSftpgS~SL~A~~lT~~ 1140 (1282)
+|||||+||||||||++|||||||||+|||+|||+|||+||||||+|||||+|++||+.+++|+++.+|.+.
T Consensus 1776 tnvyRvtihktfegnlttk~ingaiFi~nPrtG~LflKiihtsvwaGqkrl~qlaKwktAeeVaaLirslp~-------- 1847 (2321)
T KOG1795|consen 1776 TNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPV-------- 1847 (2321)
T ss_pred cceEEEEeeeccccccccccccceEEEecCCCCceEEEEeecccccchhHHHHHHhHhhHHHHHHHHhcCCh--------
Confidence 999999999999999999999999999999999999999999999999999999999999999999997766
Q ss_pred cccccccccCCCCCCCCCCCchhhhhhhhccccccCc---------eeccCCCcccccccccccCCCcceeeecCCccch
Q psy3344 1141 GFEWGRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGF---------FMVPAQSSWNYNFMGVRHDPNMKYDLQLANPKEF 1211 (1282)
Q Consensus 1141 G~~wg~~nkd~~~~~~Gy~~~~~ekvQmLLsDrflGf---------fmVP~~~~WNy~fmG~~~~~~~ky~~~L~~P~~F 1211 (1282)
+++||+++++|+||++++ ++|+++| .++|+++|++.+.+|.....+.+.+|+|.|. |
T Consensus 1848 ----EEqpkqiIVtrk~MlDpl--------EvhllDfPnI~ik~sel~lPFqa~m~i~k~~dlilkatEpqmvlfNl--Y 1913 (2321)
T KOG1795|consen 1848 ----EEQPKQIIVTRKGMLDPL--------EVHLLDFPNIVIKGSELQLPFQACMKIEKFGDLILKATEPQMVLFNL--Y 1913 (2321)
T ss_pred ----hhcCceEEEechhccChH--------HHhhccCCceeeecccccccHHHHhhHHHHhhHHhhccCceEEEEeh--h
Confidence 999999999999999995 4466677 4999999999999999999999999999998 8
Q ss_pred hhcccCcccccccccC----------CCCCcccccCCCccccCccccCCCCCccceeeeehhhhhhhhhcccccc
Q psy3344 1212 YHEIHRPAHFLNFSSL----------EDGDGVILKPDKSTITEPHHIWPSLSDDEWIKVEVQLKDLILADYGKSR 1276 (1282)
Q Consensus 1212 y~elHRP~hF~~Fs~l----------ed~~~~~l~p~~~~~t~~hhiwp~l~~~~w~~ve~~l~d~il~dy~k~~ 1276 (1282)
.+|+.+.++|+||+|| |+.+++|||||||+|||||||||+|||+||||||+|||||||+||||+-
T Consensus 1914 ddWl~tissyTaFsRliLilral~vn~e~~k~il~~d~t~i~~~~hiWP~~tD~qWikvE~qlkDLIl~dY~kk~ 1988 (2321)
T KOG1795|consen 1914 DDWLKTISSYTAFSRLILILRALHVNEERAKMILKPDKTTITEPHHIWPSLTDEQWIKVEVQLKDLILADYGKKN 1988 (2321)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhcCCHHHHhhhcCCCcceeccccccCCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 8999999999999998 8999999999999999999999999999999999999999999999984
No 4
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=100.00 E-value=8.8e-142 Score=1233.42 Aligned_cols=469 Identities=40% Similarity=0.568 Sum_probs=433.4
Q ss_pred cceeeeccCC-ccccccccCcceeeccccccccccccccchhhhHHHHHHHHHHhhhhHHHHHHHHHhhhccceeeeecc
Q psy3344 703 MKYDLQLANP-KEFYHEIHRPAHFLNFSSLEDGDGIVNKWNTALIGLMTYFRESVVNTQELLDLLVKCENKIQTRIKIGL 781 (1282)
Q Consensus 703 mkY~Lkld~P-~~FY~e~hRp~HFl~Fs~ied~~~I~~k~~t~~i~~~~~fr~~~~~~~~lld~l~k~e~~i~~~~~~~~ 781 (1282)
+++.|++++. +++|+ +|++|+++.||+.+|+|+++||||++|+||||||||+|+|.+|||+|||||.+||+|||+||
T Consensus 1255 a~A~l~VsE~gI~~F~--srIr~IlmtSGStTFtKvA~kWNT~lial~TYyREai~~T~~Lld~Lvk~E~~IqnrVK~gl 1332 (2365)
T COG5178 1255 AHANLAVSEGGIEMFE--SRIRHILMTSGSTTFTKVATKWNTQLIALVTYYREAICDTKGLLDKLVKAERLIQNRVKKGL 1332 (2365)
T ss_pred hhhheeechhhHHHHH--hhhhHhhhccCchhHHHHHHHhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 6777888887 99999 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCcch-------------------------------------------------------------------
Q psy3344 782 NSKMPSRFPPAVF------------------------------------------------------------------- 794 (1282)
Q Consensus 782 n~~mp~rf~~~~~------------------------------------------------------------------- 794 (1282)
|||||+||||+||
T Consensus 1333 NSKMP~RFPPavFY~PKElGGLGMlS~ghilip~sDl~wSkqtdtgithfrsgmt~~~e~lIP~~~rYis~We~EF~dSq 1412 (2365)
T COG5178 1333 NSKMPVRFPPAVFYAPKELGGLGMLSVGHILIPHSDLEWSKQTDTGITHFRSGMTTNGERLIPAAMRYISRWEYEFEDSQ 1412 (2365)
T ss_pred ccCCCCCCCcceeeChhhcCCcceeecccEeeehhhcccccccCccceeeccccccCccccchHHHHhhhhhhhhhhhHH
Confidence 9999999999777
Q ss_pred --------------------------------------------------------------------------------
Q psy3344 795 -------------------------------------------------------------------------------- 794 (1282)
Q Consensus 795 -------------------------------------------------------------------------------- 794 (1282)
T Consensus 1413 RVWaEYa~krqea~qqnrrl~~e~le~swDrGIPRisTLfQrdRhtLaYDrG~R~r~eFkqYsl~~n~pFWwT~~~HDGK 1492 (2365)
T COG5178 1413 RVWAEYARKRQEAGQQNRRLTLEDLEMSWDRGIPRISTLFQRDRHTLAYDRGFRMRSEFKQYSLKPNNPFWWTDAKHDGK 1492 (2365)
T ss_pred HHHHHHHHHHHHhhhhhhhcchhhhccCcccCChhHHHHHhhcchhhhhccchHHHHHHHHhccCCCCCceecccccCcc
Confidence
Q ss_pred --------------------------------------------------------------------------------
Q psy3344 795 -------------------------------------------------------------------------------- 794 (1282)
Q Consensus 795 -------------------------------------------------------------------------------- 794 (1282)
T Consensus 1493 LW~ln~yr~DviqALGGvegIleHTlFkaTgF~SweglFWEkasgfe~smkfkKLTnAQr~GLsQIPNRRFtLWWSPTIN 1572 (2365)
T COG5178 1493 LWSLNRYRLDVIQALGGVEGILEHTLFKATGFRSWEGLFWEKASGFEESMKFKKLTNAQRMGLSQIPNRRFTLWWSPTIN 1572 (2365)
T ss_pred ccchhhhhHHHHHHhcchhhhhhhhhhcccCcchhhhhhHhhhcchHHHHHHHHhhhhhhcccccCCCceeEEEecCccc
Confidence
Q ss_pred ------------------------------------------------------hhhhhhHhhhhhhhcccccccccccc
Q psy3344 795 ------------------------------------------------------DQELDALEIETVQKETIHPRKSYKMN 820 (1282)
Q Consensus 795 ------------------------------------------------------d~~~~~l~i~~vqke~ihprksy~~n 820 (1282)
|+|||.|.||||||||+|||||||||
T Consensus 1573 RaNVYVGfqVQLDlTGI~mHGKiPTLKISlIQIFR~hLWqkIHESvV~dlCqvld~eldvlqiEtv~ketvHpRKSYkmn 1652 (2365)
T COG5178 1573 RANVYVGFQVQLDLTGILMHGKIPTLKISLIQIFRNHLWQKIHESVVGDLCQVLDKELDVLQIETVQKETVHPRKSYKMN 1652 (2365)
T ss_pred ccceEEEEEEEEechheeecCCCCceeehHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhheeeeccccccccccccccc
Confidence 99999999999999999999999999
Q ss_pred cchhhHHhhhhccccccCCcccccCCCCCCCccccCCcccccccccccCcccchhhhhhccccccceeeeecccccCccc
Q psy3344 821 SSCADVLLFAAYKWNVSRPSLLADSKGKFPPVVFYTPKELGGLGMLSMGHVLIPQVRELFKYNWGFIYTVSLDFYDNMSH 900 (1282)
Q Consensus 821 ~scadillf~~~~w~v~~p~ll~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~s~ 900 (1282)
||||||||-++|+|+||+||||.+.+|.+ +|+.+-++|.|+|||||+|| ||
T Consensus 1653 SScADIll~~~~~w~Vs~Psll~e~rD~~-------------------~~~~tnk~WiDVQLR~GDYD----------sh 1703 (2365)
T COG5178 1653 SSCADILLSGAYDWCVSSPSLLLEERDGG-------------------SNVRTNKLWIDVQLRWGDYD----------SH 1703 (2365)
T ss_pred chHHHHHhhhhhhhccCCchhhhhccccc-------------------ccceeeeeEEEEEEeecCcc----------cc
Confidence 99999999999999999999999999944 44556677888888888888 99
Q ss_pred cccccccccchhHHHHHHHHHHHhhhhccceeeeeeeecccCceeeeeccccccccccCCchhHhHHHhhhcchhhhcCc
Q psy3344 901 YVNSMEISAPSAQRQQIAEIEKQTKEQSQLTATTTRTVNKHGDEIITSTTSNYETATFGSKTEWRVRAISATNLHLRTNH 980 (1282)
Q Consensus 901 ~~~gmeisaps~qrqq~AeIEkq~req~qltattt~T~NvhGeeiit~TtS~ye~~~F~SKt~wrirai~a~nL~~r~n~ 980 (1282)
+ |+|++|++ +|+||| =.|+-|||||+..|+++.++|.+..++|
T Consensus 1704 d------------------i~rY~Rak-Fldytt------------------D~qsmYPsptGv~igiDLcYNm~saYGN 1746 (2365)
T COG5178 1704 D------------------IHRYARAK-FLDYTT------------------DPQSMYPSPTGVVIGIDLCYNMWSAYGN 1746 (2365)
T ss_pred C------------------HHHHHHhh-hhhccc------------------ChhhcccCCCceEEEEeehhhhhhhhcc
Confidence 9 99999999 999995 1466889999999999999999999999
Q ss_pred eeccCccccccceeeecccchhhhhhhhHhhhhhhccccccccccCccccccCCcccccccccCccceeeccceeeeecC
Q psy3344 981 IYVSSDDIKETGYTYILPKNVLKKFVTISDLRAQIAGYLYDHLVCGRHERVSSDHTQDIRRQSDHQTFIFHSQIIWFVDD 1060 (1282)
Q Consensus 981 Iyv~s~d~~~~~ytyimPkNiLkkfi~iadLR~qiagyLyg~s~~~~~~~~s~~~~kei~~~~~~~~~~f~~qi~wf~dd 1060 (1282)
++.+-+++-+..+ -..|++++|.|++++++++++|+|.+++-+.+++ |.||.++|+|+|..|+||
T Consensus 1747 w~~glKpliq~SM--------------~~ImkanpaLyvLRERiRKgLQlY~S~~qe~~l~-ssnyaElfsN~i~LFvdd 1811 (2365)
T COG5178 1747 WNEGLKPLIQSSM--------------ERIMKANPALYVLRERIRKGLQLYTSEPQEQYLS-SSNYAELFSNSIDLFVDD 1811 (2365)
T ss_pred cchhhHHHHHHHH--------------HHHHhhCcHHHHHHHHHHHhhhhhhcCcchhhcc-ccchHHHhcCccceEecC
Confidence 8854444332222 2238899999999999999999999999999996 999999999999999999
Q ss_pred CceeeeeecccccCCccccccCCcceeccCCcccceeeeEeeccccccccccccCcceEEEEeeeccCeeeeeccccCCC
Q psy3344 1061 TNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLGEKTVVITCSFTPGSCSLTAYKLTPS 1140 (1282)
Q Consensus 1061 tn~~rV~~h~t~~gnl~tkPingai~~f~p~tg~l~lkiIHt~~w~~~krl~q~~k~ti~~tvSftpgS~SL~A~~lT~~ 1140 (1282)
+|||||++|+|||||++|||||||||+|||.||++|+|+|||+||+|||||+|++|++.+++|+++.+|.+.
T Consensus 1812 tnVyrvt~hktfEgn~ttk~ing~iFvlnP~tG~LflKvihtsvwaGqkrl~qlaKwktAeeV~aL~rslp~-------- 1883 (2365)
T COG5178 1812 TNVYRVTLHKTFEGNLTTKPINGAIFVLNPATGNLFLKVIHTSVWAGQKRLIQLAKWKTAEEVFALGRSLPV-------- 1883 (2365)
T ss_pred ceeeeeehhhhhccccccccccceEEEecCCCCcEEEEEeecccccchhHHHHHHhHhhHHHHHHHhhcCCh--------
Confidence 999999999999999999999999999999999999999999999999999999999999999999997666
Q ss_pred cccccccccCCCCCCCCCCCchhhhhhhhccccccCc---------eeccCCCcccccccccccCCCcceeeecCCccch
Q psy3344 1141 GFEWGRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGF---------FMVPAQSSWNYNFMGVRHDPNMKYDLQLANPKEF 1211 (1282)
Q Consensus 1141 G~~wg~~nkd~~~~~~Gy~~~~~ekvQmLLsDrflGf---------fmVP~~~~WNy~fmG~~~~~~~ky~~~L~~P~~F 1211 (1282)
+++||+++++|+||++++ ++|+++| ..+|+++++....+......+.+.+|.|.|. |
T Consensus 1884 ----EEqpkqiIVtrk~MlDpl--------Evh~lDfPnIsir~~el~lPFsavm~idki~d~ilratEpqmvlfNl--Y 1949 (2365)
T COG5178 1884 ----EEQPKQIIVTRKSMLDPL--------EVHILDFPNISIRTCELALPFSAVMGIDKIRDLILRATEPQMVLFNL--Y 1949 (2365)
T ss_pred ----hhcCceeEEehhhhcChH--------HhhhccCCCcceecccccCChHhhhchHHHHHHHHhccCceEEEEeh--h
Confidence 999999999999999995 4466777 3789999999999988888888888889998 8
Q ss_pred hhcccCcccccccccC----------CCCCcccccCCCccccCccccCCCCCccceeeeehhhhhhhhhcccccc
Q psy3344 1212 YHEIHRPAHFLNFSSL----------EDGDGVILKPDKSTITEPHHIWPSLSDDEWIKVEVQLKDLILADYGKSR 1276 (1282)
Q Consensus 1212 y~elHRP~hF~~Fs~l----------ed~~~~~l~p~~~~~t~~hhiwp~l~~~~w~~ve~~l~d~il~dy~k~~ 1276 (1282)
.+|+.+.|.|+||++| |+..+.||+||||+||...|+||++||+|||++|.|||||||+||+++-
T Consensus 1950 ddWl~~~SsyTaFsRL~Lvlral~vnee~~k~il~~d~si~~k~nhlWP~f~D~qWi~~E~qlrDLIl~~Y~~k~ 2024 (2365)
T COG5178 1950 DDWLQETSSYTAFSRLLLVLRALDVNEERVKEILRPDKSIITKINHLWPGFSDSQWIKKEIQLRDLILDRYCSKH 2024 (2365)
T ss_pred hhHHHhhhhHHHHHHHHHHHHHhccCHHHHHHhcCCCccceeeecccCCCCCHHHHhhhhhHHHHHHHHHHHHhc
Confidence 8889999999999998 7889999999999999999999999999999999999999999999874
No 5
>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=100.00 E-value=7.8e-86 Score=700.46 Aligned_cols=138 Identities=82% Similarity=1.312 Sum_probs=135.6
Q ss_pred ccCchhHHHHHHHcccccccccceeeecccccccceeeeccchhhccceEeeeccceEEEEEEccCCCCCCcceeEEEEE
Q psy3344 555 FGSKTEWRVRAISATNLHLRTNHIYVSSDDIKETGYTYILPKNVLKKFVTISDLRAQIAGYLYGVSPADNPQVKEIRCIV 634 (1282)
Q Consensus 555 FsSKtdWR~RAIsatnL~LR~~nIYVssdD~~e~~~tyViPKNlLkKFI~ISDlRtQIaGyLYG~SP~Dnp~VKEIrCIV 634 (1282)
|+||||||+||||+++||+|++||||+++|++|++++||||||||||||+|||+|||+||||||++|+|||+||||+|||
T Consensus 1 F~Skt~WR~Raia~~~l~lr~~~Iyv~~~~~~~~~~t~vlPknllkkFi~iaD~rtQ~~GyLyG~~~~d~~~vkeI~cIv 80 (252)
T cd08056 1 FSSKTDWRVRAIAATNLHLRTKNIYVSSDDIKETGYTYILPKNLLKKFISISDLRTQIAGYLYGKSPPDNPQVKEIRCIV 80 (252)
T ss_pred CCccchHHHHHHHhhhhhhhhccEEEcccccccCCCEEEeCHHHHHHHHHHhhhcceEEEEEeccCCCCCCCeEEEEEEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCccccceeecCCCCCCCCCcCCCCcceeeecCCCCCCCCChHhHHHHHHhhhcCC
Q psy3344 635 MPPQWGTHQTVHLPASLPGHPYLKEMEPLGWIHTQPNELPQLSPQDVTSHAKIMADNA 692 (1282)
Q Consensus 635 LvPQ~Gs~~sV~lp~~LP~h~~L~dLEpLGWIHTQ~~El~~Lsp~DVtthAkl~~dN~ 692 (1282)
||||+|++++|++|..+|+|++|+|||+|||||||+.|+++|+|+||++||+++++|+
T Consensus 81 ipPQ~gt~~sv~l~~~~~~~~~l~~Le~LGWIHTqp~e~~~Lss~Dv~tha~~~~~~~ 138 (252)
T cd08056 81 LVPQLGTHQTVTLPQQLPQHEYLEDLEPLGWIHTQPNELPQLSPQDVTTHAKILADNP 138 (252)
T ss_pred ECCEeCCcCcEECCccCccchhhCCCEeeEEEEcCCCCccccCHHHHHHHHHHHHhcc
Confidence 9999999999999999999999999999999999999999999999999999988754
No 6
>PF12134 PRP8_domainIV: PRP8 domain IV core; InterPro: IPR021983 This domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with PF10597 from PFAM, PF10596 from PFAM, PF10598 from PFAM, PF08083 from PFAM, PF08082 from PFAM, PF01398 from PFAM, PF08084 from PFAM. There is a conserved LILR sequence motif. The domain is a selenomethionine domain in a subunit of the spliceosome. The function of PRP8 domain IV is believed to be interaction with the splicosomal core. ; PDB: 3E66_A 3E9P_A 3SBT_A 3E9O_A 3SBG_A 3LRU_A 3E9L_A 3ENB_A.
Probab=100.00 E-value=5.5e-64 Score=520.74 Aligned_cols=136 Identities=87% Similarity=1.369 Sum_probs=118.4
Q ss_pred CCCcccccccccccCceEEEecCceeEEEEeeecccCccccccccceEEEEcCCCCceEEEEEeeccccccchhhHH---
Q psy3344 343 EPYLSSQNYGELFSNQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQL--- 419 (1282)
Q Consensus 343 e~~l~s~Ny~ELF~n~~~wfVDdtnvYRvtihkt~egn~~tKpiNG~IFifNP~TGqLfLKIiHtsvWagQKRL~Ql--- 419 (1282)
||+|||+||||||+|+++||||||||||||+|+|||||++|||||||||||||+|||||||||||||||||||||||
T Consensus 1 e~~lns~Ny~eLF~n~~~~fVDDtnvYrvt~h~t~eGn~~tkpiNG~ifIfnP~TGqLflKiihtsvwaGQKRl~qlakw 80 (231)
T PF12134_consen 1 EPFLNSQNYAELFSNQTQWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLSQLAKW 80 (231)
T ss_dssp -EEE-TTTGGGGGSSS-EEEEEETTSSEEEEEE-TTS-EEEEEE-EEEEEE-TTT-EEEEEEE-GGGGCC-SSHHHHHHH
T ss_pred CCccccccHHHHhcCCeEEEEecCceEEEEEEeeccCCceeccccceEEEEeCCCCcEEEEEEeehhccchhHHHHHHHH
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred --------------------------------------------------------------------------------
Q psy3344 420 -------------------------------------------------------------------------------- 419 (1282)
Q Consensus 420 -------------------------------------------------------------------------------- 419 (1282)
T Consensus 81 KtAEEv~alirslP~eEqPkqiIVtrk~m~dple~~lldfPnI~I~~sel~lpF~~~lk~~k~~d~vl~a~e~~m~lfnl 160 (231)
T PF12134_consen 81 KTAEEVAALIRSLPKEEQPKQIIVTRKGMLDPLEVHLLDFPNISIKGSELHLPFQALLKIEKLKDLVLKATEPQMVLFNL 160 (231)
T ss_dssp HHHHHHHHHHHHS-CCCSGSEEEECSGGCHHHHHHHTTTTTTCEEEEESCTSTGGGGGGSHHHHHHHHH-SS-EEEEEET
T ss_pred hhHHHHHHHHHhCCHhhCCceEEEecHHHhhHHHHHhhhCCCeeEeccccccCHHHHhhHHHHHHHHHhccCCceEEEeh
Confidence
Q ss_pred ------------HHHHHHHHHHhcccCcccceeeccCCCCccccccccCCCCCchhhhHHHHHHhHHHHHH
Q psy3344 420 ------------AFSRLILILRALHVNTERTKVILKPDKSTITEPHHIWPSLSDDEWIKVEVQLKDLILAD 478 (1282)
Q Consensus 420 ------------AFsRLiLILRal~vn~~rtk~IL~p~~~~it~~hhiWPslsDeeWIkvEv~LkDLIL~d 478 (1282)
|||||||||||||||++|||+||+||+++++++||+||+|||+|||+||++||||||+|
T Consensus 161 YDdWL~siS~~TAFsRLiLILR~l~vn~~ktk~iL~p~~~~~~~~~h~WPtlsd~eWi~vEi~LkDLIl~D 231 (231)
T PF12134_consen 161 YDDWLKSISPYTAFSRLILILRALHVNNEKTKDILRPDKNVITQPHHIWPTLSDEEWIEVEIQLKDLILND 231 (231)
T ss_dssp TTTGGGTS-HHHHHHHHHHHHHHHHH-HHHHHHHCTSSTTS-B-TT-SSB---HHHHHHHHHHHHHHHHHH
T ss_pred hhhHHhhcchHHHHHHHHHHHHHhcCChHhhhhhccCCCCccccccccCCCCCHHHHHHHHHHHHHHhccC
Confidence 99999999999999999999999999999999999999999999999999999999997
No 7
>PF12134 PRP8_domainIV: PRP8 domain IV core; InterPro: IPR021983 This domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with PF10597 from PFAM, PF10596 from PFAM, PF10598 from PFAM, PF08083 from PFAM, PF08082 from PFAM, PF01398 from PFAM, PF08084 from PFAM. There is a conserved LILR sequence motif. The domain is a selenomethionine domain in a subunit of the spliceosome. The function of PRP8 domain IV is believed to be interaction with the splicosomal core. ; PDB: 3E66_A 3E9P_A 3SBT_A 3E9O_A 3SBG_A 3LRU_A 3E9L_A 3ENB_A.
Probab=100.00 E-value=2.6e-57 Score=471.00 Aligned_cols=213 Identities=50% Similarity=0.733 Sum_probs=181.2
Q ss_pred cccccCccceeeccceeeeecCCceeeeeecccccCCccccccCCcceeccCCcccceeeeEeeccccccccccccCcce
Q psy3344 1039 IRRQSDHQTFIFHSQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLGEKT 1118 (1282)
Q Consensus 1039 i~~~~~~~~~~f~~qi~wf~ddtn~~rV~~h~t~~gnl~tkPingai~~f~p~tg~l~lkiIHt~~w~~~krl~q~~k~t 1118 (1282)
+++ |+||+++|++++.||+||+|+|||++|+|+|||++|||+|||||||||+|||+||||||||+|+|||||+|++|++
T Consensus 3 ~ln-s~Ny~eLF~n~~~~fVDDtnvYrvt~h~t~eGn~~tkpiNG~ifIfnP~TGqLflKiihtsvwaGQKRl~qlakwK 81 (231)
T PF12134_consen 3 FLN-SQNYAELFSNQTQWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLSQLAKWK 81 (231)
T ss_dssp EE--TTTGGGGGSSS-EEEEEETTSSEEEEEE-TTS-EEEEEE-EEEEEE-TTT-EEEEEEE-GGGGCC-SSHHHHHHHH
T ss_pred ccc-cccHHHHhcCCeEEEEecCceEEEEEEeeccCCceeccccceEEEEeCCCCcEEEEEEeehhccchhHHHHHHHHh
Confidence 443 8999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeeeccCeeeeeccccCCCcccccccccCCCCCCCCCCCchhhhhhhhccccccCc------eeccCCCcccccccc
Q psy3344 1119 VVITCSFTPGSCSLTAYKLTPSGFEWGRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGF------FMVPAQSSWNYNFMG 1192 (1282)
Q Consensus 1119 i~~tvSftpgS~SL~A~~lT~~G~~wg~~nkd~~~~~~Gy~~~~~ekvQmLLsDrflGf------fmVP~~~~WNy~fmG 1192 (1282)
.++||++..+||+. +++||+++++++||.+++ +|.|| | |... +.+|++++++++.+|
T Consensus 82 tAEEv~alirslP~------------eEqPkqiIVtrk~m~dpl--e~~ll--d-fPnI~I~~sel~lpF~~~lk~~k~~ 144 (231)
T PF12134_consen 82 TAEEVAALIRSLPK------------EEQPKQIIVTRKGMLDPL--EVHLL--D-FPNISIKGSELHLPFQALLKIEKLK 144 (231)
T ss_dssp HHHHHHHHHHHS-C------------CCSGSEEEECSGGCHHHH--HHHTT--T-TTTCEEEEESCTSTGGGGGGSHHHH
T ss_pred hHHHHHHHHHhCCH------------hhCCceEEEecHHHhhHH--HHHhh--h-CCCeeEeccccccCHHHHhhHHHHH
Confidence 99999999998887 899999999999999995 35443 2 3222 589999999999999
Q ss_pred cccCCCcceeeecCCccchhhcccCcccccccccC----------CCCCcccccCCCccccCccccCCCCCccceeeeeh
Q psy3344 1193 VRHDPNMKYDLQLANPKEFYHEIHRPAHFLNFSSL----------EDGDGVILKPDKSTITEPHHIWPSLSDDEWIKVEV 1262 (1282)
Q Consensus 1193 ~~~~~~~ky~~~L~~P~~Fy~elHRP~hF~~Fs~l----------ed~~~~~l~p~~~~~t~~hhiwp~l~~~~w~~ve~ 1262 (1282)
.....+++.+|.|+|. |.+|+.+.|.|+||+|| +++++.+|+||++++|++|||||+|||+|||+||+
T Consensus 145 d~vl~a~e~~m~lfnl--YDdWL~siS~~TAFsRLiLILR~l~vn~~ktk~iL~p~~~~~~~~~h~WPtlsd~eWi~vEi 222 (231)
T PF12134_consen 145 DLVLKATEPQMVLFNL--YDDWLKSISPYTAFSRLILILRALHVNNEKTKDILRPDKNVITQPHHIWPTLSDEEWIEVEI 222 (231)
T ss_dssp HHHHH-SS-EEEEEET--TTTGGGTS-HHHHHHHHHHHHHHHHH-HHHHHHHCTSSTTS-B-TT-SSB---HHHHHHHHH
T ss_pred HHHHhccCCceEEEeh--hhhHHhhcchHHHHHHHHHHHHHhcCChHhhhhhccCCCCccccccccCCCCCHHHHHHHHH
Confidence 9999999999999997 78889999999999998 78999999999999999999999999999999999
Q ss_pred hhhhhhhhc
Q psy3344 1263 QLKDLILAD 1271 (1282)
Q Consensus 1263 ~l~d~il~d 1271 (1282)
+||||||+|
T Consensus 223 ~LkDLIl~D 231 (231)
T PF12134_consen 223 QLKDLILND 231 (231)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHhccC
Confidence 999999998
No 8
>PF08084 PROCT: PROCT (NUC072) domain; InterPro: IPR012984 The PROCT domain is the C-terminal domain in pre-mRNA splicing factors of PRO8 family [].; PDB: 2P87_A 2P8R_A 3SBG_A 2OG4_A.
Probab=100.00 E-value=1.3e-49 Score=386.97 Aligned_cols=114 Identities=68% Similarity=1.300 Sum_probs=75.6
Q ss_pred eEEEEeeeccCeeeeeccccCCCcccccccccCC-CCCCCCCCCchhhhhhhhccccccCceeccCCCcccccccccccC
Q psy3344 1118 TVVITCSFTPGSCSLTAYKLTPSGFEWGRQNTDK-GNNPKGYLPSHYERVQMLLSDRFLGFFMVPAQSSWNYNFMGVRHD 1196 (1282)
Q Consensus 1118 ti~~tvSftpgS~SL~A~~lT~~G~~wg~~nkd~-~~~~~Gy~~~~~ekvQmLLsDrflGffmVP~~~~WNy~fmG~~~~ 1196 (1282)
||++|||||||||||+||+|||+|||||++|||+ +.+|+||.|+|+|||||||||||+||||||++++|||+|||++|+
T Consensus 1 ~i~it~sftpGSvsL~Ay~LT~~G~eWg~~nkD~~~~~p~g~~p~~~ek~QllLSdr~~GfFlVP~~~~WNY~Fmg~~~~ 80 (125)
T PF08084_consen 1 TITITCSFTPGSVSLSAYKLTPEGYEWGRQNKDLISDNPQGFSPSFYEKVQLLLSDRILGFFLVPEDGVWNYNFMGAKFS 80 (125)
T ss_dssp -EEEEEEEETTEEEEEEEEE-HHHHHHHHCTTT--SS--TT--GGGEEEEEEEEETTS--EEEEETTS--B-TT-GGG--
T ss_pred CEEEEEeccCCceEEEEEecCHHHHHHHhhcccccccCCCCCCcchhheeeeeeecceeeEEEccCCCcccceecccccC
Confidence 6899999999999999999999999999999995 999999999999999999999999999999999999999999999
Q ss_pred CCcceeeecCCccchhhcccCcccccccccCCCCC
Q psy3344 1197 PNMKYDLQLANPKEFYHEIHRPAHFLNFSSLEDGD 1231 (1282)
Q Consensus 1197 ~~~ky~~~L~~P~~Fy~elHRP~hF~~Fs~led~~ 1231 (1282)
++|+|+|+||+|++||||+|||.||++|+++++++
T Consensus 81 ~~~~Y~lkld~P~~FY~e~HRP~HFl~F~~~~~~e 115 (125)
T PF08084_consen 81 PNMKYDLKLDIPKEFYHELHRPTHFLNFAELEEDE 115 (125)
T ss_dssp TT----EEE-----TT-CCCS-S------------
T ss_pred CCCeeEEEeCCchhhhCcccCHHHHHhHhhccccc
Confidence 99999999999999999999999999999996544
No 9
>PF10596 U6-snRNA_bdg: U6-snRNA interacting domain of PrP8; InterPro: IPR019580 This entry represents the interacting site for U6-snRNA, which is part of U4/U6. U5 tri-snRNPs complex of the spliceosome is a prime candidate for the role of cofactor in the spliceosome's RNA core. The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor [].
Probab=100.00 E-value=3e-36 Score=300.28 Aligned_cols=78 Identities=32% Similarity=0.476 Sum_probs=73.2
Q ss_pred CCCCCCCCCCcceeeeccCCccccccccCcceeecccccccccccc--ccchhhhHHHHHHHHHHhhhhHHHHHHHHHhh
Q psy3344 693 SWDGVRHDPNMKYDLQLANPKEFYHEIHRPAHFLNFSSLEDGDGIV--NKWNTALIGLMTYFRESVVNTQELLDLLVKCE 770 (1282)
Q Consensus 693 sWDg~~~d~nmkY~Lkld~P~~FY~e~hRp~HFl~Fs~ied~~~I~--~k~~t~~i~~~~~fr~~~~~~~~lld~l~k~e 770 (1282)
+..|+++.||++|+|||+ ++++|.+.+++|..+.|.+||+ +|++|++|||+++||+++|+
T Consensus 81 qrsgl~qiPNRrf~LWWs------PtINR~nvyvGfqvqldlTgIfmhGK~ptlkiS~i~ifr~~lwq------------ 142 (160)
T PF10596_consen 81 QRSGLNQIPNRRFTLWWS------PTINRANVYVGFQVQLDLTGIFMHGKIPTLKISLIQIFRAHLWQ------------ 142 (160)
T ss_pred cccCcccccccccccccC------CccccCCceEEEEeeccccceeccCcCchhhhhhhhcccccchh------------
Confidence 356777999999999999 9999999999999999999997 99999999999999999998
Q ss_pred hccceeeeecccCCCCCCCCCcchhhhh
Q psy3344 771 NKIQTRIKIGLNSKMPSRFPPAVFDQEL 798 (1282)
Q Consensus 771 ~~i~~~~~~~~n~~mp~rf~~~~~d~~~ 798 (1282)
|||++|+++| ||||||||
T Consensus 143 -kih~svv~dl---------~~~~~~~~ 160 (160)
T PF10596_consen 143 -KIHESVVMDL---------CQVFDQEL 160 (160)
T ss_pred -eehHHHHHHH---------HHHHHhcC
Confidence 7999999999 89999986
No 10
>PF10597 U5_2-snRNA_bdg: U5-snRNA binding site 2 of PrP8; InterPro: IPR019581 The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis []. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor [].
Probab=100.00 E-value=1.4e-36 Score=296.44 Aligned_cols=124 Identities=64% Similarity=0.974 Sum_probs=108.0
Q ss_pred CCCCCChHhHHHHHHhhhcCCCCCCCCCCCCcceeeeccCCccccccccCcceeeccccccccccccccchhhhHHHHHH
Q psy3344 672 ELPQLSPQDVTSHAKIMADNASWDGVRHDPNMKYDLQLANPKEFYHEIHRPAHFLNFSSLEDGDGIVNKWNTALIGLMTY 751 (1282)
Q Consensus 672 El~~Lsp~DVtthAkl~~dN~sWDg~~~d~nmkY~Lkld~P~~FY~e~hRp~HFl~Fs~ied~~~I~~k~~t~~i~~~~~ 751 (1282)
++..-+..+.+.+|.+...+.+.+ .|+ +|+.+++..+++.+|.+|++||||++||||+|
T Consensus 7 ~l~~~~tke~ta~a~l~vS~~~i~-------------------~F~--~rir~ilm~sgsttF~Ki~~KWNt~li~l~~Y 65 (135)
T PF10597_consen 7 DLQNESTKERTAQAFLRVSDESIK-------------------NFE--NRIRQILMSSGSTTFTKIANKWNTALIGLMTY 65 (135)
T ss_pred eccchhhhhhhhHHHhhcCHHHHH-------------------HHH--HHHHHHHHHhccchHHHHHHHHHHHHHHHHHH
Confidence 344445556666666655544444 444 99999999999999999999999999999999
Q ss_pred HHHHhhhhHHHHHHHHHhhhccceeeeecccCCCCCCCCCcchhhhhhhHhhhhhhhcccccccccccccchhhHHhhhh
Q psy3344 752 FRESVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPAVFDQELDALEIETVQKETIHPRKSYKMNSSCADVLLFAA 831 (1282)
Q Consensus 752 fr~~~~~~~~lld~l~k~e~~i~~~~~~~~n~~mp~rf~~~~~d~~~~~l~i~~vqke~ihprksy~~n~scadillf~~ 831 (1282)
||||+++|++|+|+|+|||+|||+|||+|||||||+||||+|
T Consensus 66 fREA~~~T~~lldil~k~E~kIq~RIK~gLNSkmPsRFPpvv-------------------------------------- 107 (135)
T PF10597_consen 66 FREAIVNTEELLDILVKCENKIQNRIKIGLNSKMPSRFPPVV-------------------------------------- 107 (135)
T ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhcccCCCCCCCee--------------------------------------
Confidence 999999999999999999999999999999999999996555
Q ss_pred ccccccCCcccccCCCCCCCccccCCcccccccccccCcccchhh
Q psy3344 832 YKWNVSRPSLLADSKGKFPPVVFYTPKELGGLGMLSMGHVLIPQV 876 (1282)
Q Consensus 832 ~~w~v~~p~ll~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 876 (1282)
||+|||+|||||||||+++||+-
T Consensus 108 ----------------------FYtPKElGGLGMLS~ghilip~s 130 (135)
T PF10597_consen 108 ----------------------FYTPKELGGLGMLSMGHILIPQS 130 (135)
T ss_pred ----------------------ecChhhccccceecccceeccch
Confidence 89999999999999999999974
No 11
>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=99.94 E-value=5.3e-28 Score=258.90 Aligned_cols=236 Identities=61% Similarity=1.025 Sum_probs=205.5
Q ss_pred cCCchhHhHHHhhhcchhhhcCceeccCccccccceeeecccchhhhhhhhHhhhhhhccccccccccCccccccCCccc
Q psy3344 958 FGSKTEWRVRAISATNLHLRTNHIYVSSDDIKETGYTYILPKNVLKKFVTISDLRAQIAGYLYDHLVCGRHERVSSDHTQ 1037 (1282)
Q Consensus 958 F~SKt~wrirai~a~nL~~r~n~Iyv~s~d~~~~~ytyimPkNiLkkfi~iadLR~qiagyLyg~s~~~~~~~~s~~~~k 1037 (1282)
|+||||||+|||||+|||+|+|||||+++|++++|++||+|||+|||||+|||+|+|++|||||.+|++ +++||
T Consensus 1 F~Skt~WR~Raia~~~l~lr~~~Iyv~~~~~~~~~~t~vlPknllkkFi~iaD~rtQ~~GyLyG~~~~d------~~~vk 74 (252)
T cd08056 1 FSSKTDWRVRAIAATNLHLRTKNIYVSSDDIKETGYTYILPKNLLKKFISISDLRTQIAGYLYGKSPPD------NPQVK 74 (252)
T ss_pred CCccchHHHHHHHhhhhhhhhccEEEcccccccCCCEEEeCHHHHHHHHHHhhhcceEEEEEeccCCCC------CCCeE
Confidence 899999999999999999999999999999999999999999999999999999999999999999984 67999
Q ss_pred ccccccCccceeeccceeeeecCCceeeeeecccccCCccccccCCcceeccCCcccceeeeEeecccc----------c
Q psy3344 1038 DIRRQSDHQTFIFHSQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWA----------G 1107 (1282)
Q Consensus 1038 ei~~~~~~~~~~f~~qi~wf~ddtn~~rV~~h~t~~gnl~tkPingai~~f~p~tg~l~lkiIHt~~w~----------~ 1107 (1282)
||+| |++.+|.|+.-.|++++.+. -...-.|+++||||||.+-. .
T Consensus 75 eI~c------------IvipPQ~gt~~sv~l~~~~~-------------~~~~l~~Le~LGWIHTqp~e~~~Lss~Dv~t 129 (252)
T cd08056 75 EIRC------------IVLVPQLGTHQTVTLPQQLP-------------QHEYLEDLEPLGWIHTQPNELPQLSPQDVTT 129 (252)
T ss_pred EEEE------------EEECCEeCCcCcEECCccCc-------------cchhhCCCEeeEEEEcCCCCccccCHHHHHH
Confidence 9997 33334445555555433321 11112356777777776542 3
Q ss_pred cccc----cccC-cceEEEEeeeccCeeeeeccccCCCcccccccccCC-CCCCCCCCCchhhhhhhhccccccCceecc
Q psy3344 1108 QKRL----GQLG-EKTVVITCSFTPGSCSLTAYKLTPSGFEWGRQNTDK-GNNPKGYLPSHYERVQMLLSDRFLGFFMVP 1181 (1282)
Q Consensus 1108 ~krl----~q~~-k~ti~~tvSftpgS~SL~A~~lT~~G~~wg~~nkd~-~~~~~Gy~~~~~ekvQmLLsDrflGffmVP 1181 (1282)
|+|+ ..|+ .++|+++||||||||||+||+||++||+||++|+|. +.+|+||.|+|+|||||||||||+||||||
T Consensus 130 ha~~~~~~~~w~~~~~V~it~SftpGs~sl~ay~LT~~G~~wg~~n~d~~~~~p~g~~~~~~ek~qllLSd~~~GfflVP 209 (252)
T cd08056 130 HAKILADNPSWDGEKTVILTCSFTPGSCSLTAYKLTPEGYEWGKQNKDLGNNTPKGYSPSFYEKVQLLLSDRFLGFFLVP 209 (252)
T ss_pred HHHHHHhccccCCCcEEEEEEcCCCCceEEEEEecCHHHHHHHHhCccccccCCCCCCccccceeEEEEEeeeeEEEEcc
Confidence 4444 3344 499999999999999999999999999999999998 556999999999999999999999999999
Q ss_pred CCCcccccccccccCCCcceeeecCCccchhhcccCccccccc
Q psy3344 1182 AQSSWNYNFMGVRHDPNMKYDLQLANPKEFYHEIHRPAHFLNF 1224 (1282)
Q Consensus 1182 ~~~~WNy~fmG~~~~~~~ky~~~L~~P~~Fy~elHRP~hF~~F 1224 (1282)
++++|||+|||++|+++|+|+++||+|++||||+|||.||++|
T Consensus 210 ~~~~WNY~f~g~~~~~~~~y~l~~~~P~~Fy~e~HRp~HFl~F 252 (252)
T cd08056 210 EDGVWNYNFMGAKHSPNMKYDLKLDIPKEFYHELHRPTHFLQF 252 (252)
T ss_pred CCCcccccccccccCCCCceeEEeCCchhhhccccCchhhhcC
Confidence 9999999999999999999999999999999999999999998
No 12
>PF10598 RRM_4: RNA recognition motif of the spliceosomal PrP8; InterPro: IPR019582 The large RNA-protein complex of the spliceosome catalyses pre-mRNA splicing. One of the most conserved core proteins is the pre-mRNA-processing-splicing factor 8 (PrP8) which occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molecular rearrangements that occur there, and has recently come under the spotlight for its role in the inherited human disease, Retinitis Pigmentosa []. The RNA-recognition motif of PrP8 is highly conserved and provides a possible RNA binding centre for the 5-prime SS, BP, or 3-prime SS of pre-mRNA which are known to contact with Prp8. The most conserved regions of an RNA- recognition-motif (RRM) are defined as the RNP1 and RNP2 sequences. Recognition of RNA targets can also be modulated by a number of other factors, most notably the two loops beta1-alpha1, beta2-beta3 and the amino acid residues C-terminal to the RNP2 domain [].
Probab=99.94 E-value=1.6e-28 Score=227.96 Aligned_cols=62 Identities=79% Similarity=1.343 Sum_probs=59.9
Q ss_pred cccccccCccccceeeccccchhhhhhHHHHHHHHhhhhcccccccCCCCCCCcccccccch
Q psy3344 137 KQYQDMNHTNSYGIIRGLQFASFIVQYYGLVLDLLVLGLQRASEMAGPPQMPNDFLTFQDTA 198 (1282)
Q Consensus 137 k~yKDM~h~n~yGlIrGlqFssFi~QyyglvlDlLvLGl~Ra~eiaGp~~~pn~fl~f~d~~ 198 (1282)
=+||||+|+|+||+||||||||||+||||||+|||+||++||+|+||||++||+||+|+|.+
T Consensus 32 i~yKDM~h~N~yGlirGlqFssFi~QyyglvlDLliLG~~ra~eiagp~~~pN~f~~f~~~~ 93 (93)
T PF10598_consen 32 INYKDMNHTNSYGLIRGLQFSSFIFQYYGLVLDLLILGLQRASEIAGPPQMPNEFLQFKDKE 93 (93)
T ss_pred EEEeccHHHhHhcccchhhHHHHHHHHHHHHHHHHHHccchHHHHcCCCCCCCchhcccccC
Confidence 36999999999999999999999999999999999999999999999999999999999864
No 13
>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=99.51 E-value=1.3e-14 Score=148.80 Aligned_cols=97 Identities=23% Similarity=0.429 Sum_probs=86.2
Q ss_pred eeeccchhhccceEeeeccc----eEEEEEEccCCCCCCcceeEEEEEcCCCccccceeecCCCCCCCCC-----cCCCC
Q psy3344 591 TYILPKNVLKKFVTISDLRA----QIAGYLYGVSPADNPQVKEIRCIVMPPQWGTHQTVHLPASLPGHPY-----LKEME 661 (1282)
Q Consensus 591 tyViPKNlLkKFI~ISDlRt----QIaGyLYG~SP~Dnp~VKEIrCIVLvPQ~Gs~~sV~lp~~LP~h~~-----L~dLE 661 (1282)
.++||+|++++|+++||.++ ++||||||+++. ++++|.|++++||.|+..++.++. +++. .++||
T Consensus 3 ~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~~~~---~~~~I~~i~~~~q~~~~~~~~~~~---~~e~~~~~~~~gle 76 (173)
T cd08066 3 QVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSN---NAFFITHLIIPKQSGTSDSCQTTN---EEELFDFQDQHDLI 76 (173)
T ss_pred EEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeEcCC---CeEEEEEEEeccccCCCceecCCC---HHHHHHHHHhCCCe
Confidence 68999999999999999996 899999998764 789999999999999999988754 2333 47999
Q ss_pred cceeeecCCCCCCCCChHhHHHHHHhhhcCCC
Q psy3344 662 PLGWIHTQPNELPQLSPQDVTSHAKIMADNAS 693 (1282)
Q Consensus 662 pLGWIHTQ~~El~~Lsp~DVtthAkl~~dN~s 693 (1282)
+|||+||.|.....+|+.|+.+|+++++..+.
T Consensus 77 ~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~ 108 (173)
T cd08066 77 TLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPE 108 (173)
T ss_pred eEEEEeccCCCCCccCHHHHHHHHHHHhcCCC
Confidence 99999999999999999999999999887543
No 14
>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=99.28 E-value=2.3e-12 Score=132.45 Aligned_cols=141 Identities=18% Similarity=0.311 Sum_probs=101.3
Q ss_pred eeecccchhhhhhhhHhhhh----hhccccccccccCccccccCCcccccccccCccceeeccceeeeecCCceeeeeec
Q psy3344 994 TYILPKNVLKKFVTISDLRA----QIAGYLYDHLVCGRHERVSSDHTQDIRRQSDHQTFIFHSQIIWFVDDTNVYRVTIH 1069 (1282)
Q Consensus 994 tyimPkNiLkkfi~iadLR~----qiagyLyg~s~~~~~~~~s~~~~kei~~~~~~~~~~f~~qi~wf~ddtn~~rV~~h 1069 (1282)
.+++|+|+|++|+.+|+.++ +++|||||..+ +++++|++ +.+. ++.++-.++...
T Consensus 3 ~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~~~---------~~~~~I~~------i~~~------~q~~~~~~~~~~ 61 (173)
T cd08066 3 QVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLS---------NNAFFITH------LIIP------KQSGTSDSCQTT 61 (173)
T ss_pred EEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeEcC---------CCeEEEEE------EEec------cccCCCceecCC
Confidence 47899999999999999995 89999999843 45677774 2232 223333333221
Q ss_pred ccccCCccccccCCcceeccCCcccceeeeEeecccc----------ccccccccCcceEEEEeeeccCeeeeeccccC-
Q psy3344 1070 KTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWA----------GQKRLGQLGEKTVVITCSFTPGSCSLTAYKLT- 1138 (1282)
Q Consensus 1070 ~t~~gnl~tkPingai~~f~p~tg~l~lkiIHt~~w~----------~~krl~q~~k~ti~~tvSftpgS~SL~A~~lT- 1138 (1282)
.. .+ ++-.--..|++.+||+||-+-. .|+++.......+.+.|| |+++++.||+||
T Consensus 62 ~~---------~e--~~~~~~~~gle~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvS--p~~~~l~afrl~~ 128 (173)
T cd08066 62 NE---------EE--LFDFQDQHDLITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCA--PKYNEFGIFRLTD 128 (173)
T ss_pred CH---------HH--HHHHHHhCCCeeEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEEC--CCCcEEeEEEeec
Confidence 11 00 1111123588999999986532 333333334578888899 899999999999
Q ss_pred CCcccccccccCCCCCCCCCCCchhhhhhh
Q psy3344 1139 PSGFEWGRQNTDKGNNPKGYLPSHYERVQM 1168 (1282)
Q Consensus 1139 ~~G~~wg~~nkd~~~~~~Gy~~~~~ekvQm 1168 (1282)
|.||+|+.++++.+..|+++.+++||+|+=
T Consensus 129 ~~g~~~~~~~~~~~~h~~~~~~~~~~~~~~ 158 (173)
T cd08066 129 PPGLDEILNCKKTGFHPHPKDPPLYEDCGH 158 (173)
T ss_pred CCcceecccCCcCccCCCCCCCCcceeeeE
Confidence 999999999999998999999999998854
No 15
>PF08084 PROCT: PROCT (NUC072) domain; InterPro: IPR012984 The PROCT domain is the C-terminal domain in pre-mRNA splicing factors of PRO8 family [].; PDB: 2P87_A 2P8R_A 3SBG_A 2OG4_A.
Probab=98.65 E-value=6.9e-09 Score=103.06 Aligned_cols=44 Identities=59% Similarity=1.136 Sum_probs=14.3
Q ss_pred CCCCCCCcceeeeccCCccccccccCcceeeccccccccccccc
Q psy3344 696 GVRHDPNMKYDLQLANPKEFYHEIHRPAHFLNFSSLEDGDGIVN 739 (1282)
Q Consensus 696 g~~~d~nmkY~Lkld~P~~FY~e~hRp~HFl~Fs~ied~~~I~~ 739 (1282)
|..|+++|+|+|+||+|++||||+|||.||++|+.+++.+.+.+
T Consensus 76 g~~~~~~~~Y~lkld~P~~FY~e~HRP~HFl~F~~~~~~e~~~a 119 (125)
T PF08084_consen 76 GAKFSPNMKYDLKLDIPKEFYHELHRPTHFLNFAELEEDEELEA 119 (125)
T ss_dssp GGG--TT----EEE-----TT-CCCS-S----------------
T ss_pred ccccCCCCeeEEEeCCchhhhCcccCHHHHHhHhhccccccccc
Confidence 67899999999999999999999999999999999976665543
No 16
>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=98.16 E-value=8.9e-07 Score=82.56 Aligned_cols=88 Identities=22% Similarity=0.320 Sum_probs=67.2
Q ss_pred ccceEeeec--cceEEEEEEccCCCCCCcceeEEEEEcCCCccccceeecCC--CCCCCCCcCCCCcceeeecCCCCCCC
Q psy3344 600 KKFVTISDL--RAQIAGYLYGVSPADNPQVKEIRCIVMPPQWGTHQTVHLPA--SLPGHPYLKEMEPLGWIHTQPNELPQ 675 (1282)
Q Consensus 600 kKFI~ISDl--RtQIaGyLYG~SP~Dnp~VKEIrCIVLvPQ~Gs~~sV~lp~--~LP~h~~L~dLEpLGWIHTQ~~El~~ 675 (1282)
|+|+..|+- ..+++|+|+|....+ +.+|.|+..+||..+........ ..+.+....+++++||.||.+...+.
T Consensus 2 k~il~~a~~~~~~ev~G~L~G~~~~~---~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iVGwyhshp~~~~~ 78 (116)
T cd07767 2 KMFLDAAKSINGKEVIGLLYGSKTKK---VLDVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNAGLRIVGWYHTHPKPSCF 78 (116)
T ss_pred HhHHHHHhcCCCcEEEEEeEEEEcCC---EEEEEEEEecccCCCCCccHHHHHHHHHHHHhcCCCeEEEEEEcCCCCCCc
Confidence 556666666 789999999996543 89999999999977654432211 12233344799999999999998889
Q ss_pred CChHhHHHHHHhhhc
Q psy3344 676 LSPQDVTSHAKIMAD 690 (1282)
Q Consensus 676 Lsp~DVtthAkl~~d 690 (1282)
+|+.|+.+|.++.+.
T Consensus 79 ~s~~dv~~~~~~q~~ 93 (116)
T cd07767 79 LSPNDLATHELFQRY 93 (116)
T ss_pred cCHHHHHHHHHHHHh
Confidence 999999999888764
No 17
>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=97.83 E-value=5.5e-06 Score=78.85 Aligned_cols=95 Identities=33% Similarity=0.467 Sum_probs=69.9
Q ss_pred ccchhhccceEeeeccceEEEEEEccCCCCCCcceeEEEEEcCCCccccceeecCCCCCCCCC-------cCCCCcceee
Q psy3344 594 LPKNVLKKFVTISDLRAQIAGYLYGVSPADNPQVKEIRCIVMPPQWGTHQTVHLPASLPGHPY-------LKEMEPLGWI 666 (1282)
Q Consensus 594 iPKNlLkKFI~ISDlRtQIaGyLYG~SP~Dnp~VKEIrCIVLvPQ~Gs~~sV~lp~~LP~h~~-------L~dLEpLGWI 666 (1282)
++.+++++.. ++...++||+|+|....++..|+++.++-.+++-++.. .++. -|.+.. ..+++++||.
T Consensus 8 v~~~i~~h~~--~~~p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~--~~~~-~~~~~~~~~~~~~~~~~~~vGwy 82 (135)
T smart00232 8 VPLNILKHAI--RDGPEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQ--EYDE-DYSHLMDEELKKVNKDLEIVGWY 82 (135)
T ss_pred HHHHHHHHHh--cCCCcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchh--hhhh-hHHHHHHHHHHhhCCCceEEEEE
Confidence 4678888876 57899999999999888877777766665555444321 2221 222222 3789999999
Q ss_pred ecCCCCCCCCChHhHHHHHHhhhcCCC
Q psy3344 667 HTQPNELPQLSPQDVTSHAKIMADNAS 693 (1282)
Q Consensus 667 HTQ~~El~~Lsp~DVtthAkl~~dN~s 693 (1282)
|+.+...+.+|..|+..|+.....+..
T Consensus 83 hshp~~~~~pS~~D~~~~~~~~~~~~~ 109 (135)
T smart00232 83 HSHPDESPFPSEVDVATHESYQAPWPI 109 (135)
T ss_pred EcCCCCCCCcCHHHHHHHHHHHhcCCc
Confidence 999999999999999999987766443
No 18
>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=96.54 E-value=0.00047 Score=65.46 Aligned_cols=101 Identities=22% Similarity=0.276 Sum_probs=72.2
Q ss_pred eeeeccchhhccceEeeec--cceEEEEEEccCCCCCCcceeEEEEEcCCCccccceeecCCCCCCCC---C----cCCC
Q psy3344 590 YTYILPKNVLKKFVTISDL--RAQIAGYLYGVSPADNPQVKEIRCIVMPPQWGTHQTVHLPASLPGHP---Y----LKEM 660 (1282)
Q Consensus 590 ~tyViPKNlLkKFI~ISDl--RtQIaGyLYG~SP~Dnp~VKEIrCIVLvPQ~Gs~~sV~lp~~LP~h~---~----L~dL 660 (1282)
.+..|...++-+++..+.- ...|+|+|.|....++ +.||.....+|+.++...+.........+ . -.++
T Consensus 4 ~~V~i~p~vll~i~~h~~r~~~~~v~G~LlG~~~~~~--~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (114)
T PF01398_consen 4 QTVQIHPLVLLKIIDHATRSSPNEVIGLLLGTQDGDN--TVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVNPNL 81 (114)
T ss_dssp EEEEEEHHHHHHHHHHHHHHHCTEEEEEEEEEEETT---EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCSTTS
T ss_pred EEEEECHHHHHHHHHHHhcCCCCEEEEEEEEEecCce--EEEEEEEEEeeEecCccccccchhhHHHHHHhhhccccccc
Confidence 4556666666666665433 3468999999976554 78999888999999988766554222201 1 1469
Q ss_pred CcceeeecCCCCCCCCChHhHHHHHHhhhcCC
Q psy3344 661 EPLGWIHTQPNELPQLSPQDVTSHAKIMADNA 692 (1282)
Q Consensus 661 EpLGWIHTQ~~El~~Lsp~DVtthAkl~~dN~ 692 (1282)
+++||-||.+.-...+|+.|+.+|+...+.++
T Consensus 82 ~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~ 113 (114)
T PF01398_consen 82 EIVGWYHSHPNISCFPSPTDIETQKQYQRMNP 113 (114)
T ss_dssp EEEEEEEEESSS-SS--HHHHHHHHHHHHHTT
T ss_pred eEEEEEEccCCccccCCHHHHHHHHHHHHhCC
Confidence 99999999999889999999999999988765
No 19
>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=95.42 E-value=0.026 Score=63.22 Aligned_cols=82 Identities=29% Similarity=0.368 Sum_probs=64.0
Q ss_pred cceEEEEEEccCCCCCC----cceeEEEEEcCCCccccceeecCCCCCCCCCc------CCCCcceeeecCCCC----CC
Q psy3344 609 RAQIAGYLYGVSPADNP----QVKEIRCIVMPPQWGTHQTVHLPASLPGHPYL------KEMEPLGWIHTQPNE----LP 674 (1282)
Q Consensus 609 RtQIaGyLYG~SP~Dnp----~VKEIrCIVLvPQ~Gs~~sV~lp~~LP~h~~L------~dLEpLGWIHTQ~~E----l~ 674 (1282)
..|=+|||||.-..+.. -.-.|.||--|||-|+..++++-. -|..+.. =+|+.+|||+|.... .-
T Consensus 33 ~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~-d~~~~~vd~iA~~lGL~~VG~IfT~l~~~~~d~~ 111 (274)
T cd08061 33 GQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLE-DPNADTVDAIAAALGLERVGWIFTDLPREDKDGY 111 (274)
T ss_pred cceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEcc-chhhhHHHHHHHHcCCeEEEEEEecCCCCCCCce
Confidence 47889999999765531 245789999999999999988763 2222211 489999999998865 55
Q ss_pred CCChHhHHHHHHhhhcC
Q psy3344 675 QLSPQDVTSHAKIMADN 691 (1282)
Q Consensus 675 ~Lsp~DVtthAkl~~dN 691 (1282)
.||+.||...|++-..|
T Consensus 112 ~LSs~Evi~aA~~Q~~~ 128 (274)
T cd08061 112 FLSAEEVILAAKFQLKH 128 (274)
T ss_pred eECHHHHHHHHHHhhhc
Confidence 79999999999998765
No 20
>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=95.40 E-value=0.041 Score=62.59 Aligned_cols=115 Identities=19% Similarity=0.265 Sum_probs=77.7
Q ss_pred EEEEEccCCCCCCc----ceeEEEEEcCCCccccceeecCCCCCCCCCc------CCCCcceeeecCCC-----------
Q psy3344 613 AGYLYGVSPADNPQ----VKEIRCIVMPPQWGTHQTVHLPASLPGHPYL------KEMEPLGWIHTQPN----------- 671 (1282)
Q Consensus 613 aGyLYG~SP~Dnp~----VKEIrCIVLvPQ~Gs~~sV~lp~~LP~h~~L------~dLEpLGWIHTQ~~----------- 671 (1282)
+|||||.=.++..- =-.|.+|--|||-|+..++++ ..-|+-+.. =+|+.+|||.|...
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l-~~d~~~~~vd~iA~~lGL~rVG~IfTdl~~~~~~~g~v~~ 80 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTL-LPDENEERVDAIASALGLERVGWIFTDLTDDGSGDGTVKC 80 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEE-cCCccHHHHHHHHHHCCCEEEEEEEecCcccccCCCceee
Confidence 59999996655420 146778889999999999999 333333322 38999999999987
Q ss_pred ----CCCCCChHhHHHHHHhhhcCCC---CCCCCCCCCcce-eeeccCCccccccccCcceeeccccccccc
Q psy3344 672 ----ELPQLSPQDVTSHAKIMADNAS---WDGVRHDPNMKY-DLQLANPKEFYHEIHRPAHFLNFSSLEDGD 735 (1282)
Q Consensus 672 ----El~~Lsp~DVtthAkl~~dN~s---WDg~~~d~nmkY-~Lkld~P~~FY~e~hRp~HFl~Fs~ied~~ 735 (1282)
+.-.||+.||..-|++-.++|+ |..--+ .+-+| ++.++ .+...-.||-.|+.+....
T Consensus 81 ~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~-fgSkFVT~vvs------g~~~g~i~~~ayQvS~q~~ 145 (306)
T PF05021_consen 81 KRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGY-FGSKFVTCVVS------GDEEGEIHFEAYQVSNQCV 145 (306)
T ss_pred ccccccccccHHHHHHHHHHHHhcCccccccCCCc-cCCeEEEEEEe------CCCCCceeeEEeeehHHHH
Confidence 7778999999999999988754 321111 12222 33444 2345566777777666543
No 21
>KOG2880|consensus
Probab=94.17 E-value=0.0086 Score=68.82 Aligned_cols=91 Identities=22% Similarity=0.404 Sum_probs=70.2
Q ss_pred eeeeccchhhccceEeeeccc----eEEEEEEccCCCCCCcceeEEEEEcCCCccccceeecCCCCCCCCCc-----CCC
Q psy3344 590 YTYILPKNVLKKFVTISDLRA----QIAGYLYGVSPADNPQVKEIRCIVMPPQWGTHQTVHLPASLPGHPYL-----KEM 660 (1282)
Q Consensus 590 ~tyViPKNlLkKFI~ISDlRt----QIaGyLYG~SP~Dnp~VKEIrCIVLvPQ~Gs~~sV~lp~~LP~h~~L-----~dL 660 (1282)
...+||+.+.+.|+++|-..| ..||.|.|+-. -+.-=|-.+++|-|=++..+...-+ +.+.. .+|
T Consensus 252 r~v~ip~~l~~~Fl~la~~NT~knlETCGiL~g~L~---~n~f~IThliiPkQeatsd~C~t~n---eeelF~vQdq~~L 325 (424)
T KOG2880|consen 252 RDVHIPERLMEVFLQLAKSNTKKNLETCGILAGKLE---RNEFYITHLIIPKQEATSDSCNTMN---EEELFEVQDQHEL 325 (424)
T ss_pred eEEEecHHHHHHHHHHHhhcccccchHHHHhhhHhh---cCcEEEEEEEeecccCCCccccccC---HHHHheecccccc
Confidence 578899999999999987665 57899999853 2345677778877988877654332 11211 579
Q ss_pred CcceeeecCCCCCCCCChHhHHHHHH
Q psy3344 661 EPLGWIHTQPNELPQLSPQDVTSHAK 686 (1282)
Q Consensus 661 EpLGWIHTQ~~El~~Lsp~DVtthAk 686 (1282)
=+||||||-|.-.-+||+.|+-||+.
T Consensus 326 ~tlGWIHTHPTQt~FmSSVDlHTHcS 351 (424)
T KOG2880|consen 326 LTLGWIHTHPTQTCFMSSVDLHTHCS 351 (424)
T ss_pred eeeeeeecCCccchhheeccccccce
Confidence 99999999999999999999999875
No 22
>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=87.87 E-value=0.56 Score=52.39 Aligned_cols=97 Identities=16% Similarity=0.158 Sum_probs=67.4
Q ss_pred eeeccchhhccceEe--eeccceEEEEEEccCCCCCCcceeEEEEEcCCCccccceeecCCCCCCCCCc---------CC
Q psy3344 591 TYILPKNVLKKFVTI--SDLRAQIAGYLYGVSPADNPQVKEIRCIVMPPQWGTHQTVHLPASLPGHPYL---------KE 659 (1282)
Q Consensus 591 tyViPKNlLkKFI~I--SDlRtQIaGyLYG~SP~Dnp~VKEIrCIVLvPQ~Gs~~sV~lp~~LP~h~~L---------~d 659 (1282)
...|+..+|.|.+.- +..-..|+|+|.|.. .....+|.-+.-+|+-++...+..-. -+....+ .+
T Consensus 11 ~V~Is~~allkil~Ha~~~~p~Ev~GlLlG~~---~~~~v~Vt~~fp~p~~~t~~~v~~~~-e~~~~m~~~~~~~~~~~~ 86 (268)
T cd08069 11 KVYISSLALLKMLKHARAGGPIEVMGLMLGKV---DDYTIIVVDVFALPVEGTETRVNAQD-EFQEYMVQYEMLKQTGRP 86 (268)
T ss_pred EEEECHHHHHHHHHHHhccCCceEEEEEEeee---cCCeEEEEEEEECCcCCCCCceeccH-HHHHHHHHHHHHHHhCCC
Confidence 456777777777743 355678999999983 23344655445557888877666532 1222211 46
Q ss_pred CCcceeeecCCCCCCCCChHhHHHHHHhhhcC
Q psy3344 660 MEPLGWIHTQPNELPQLSPQDVTSHAKIMADN 691 (1282)
Q Consensus 660 LEpLGWIHTQ~~El~~Lsp~DVtthAkl~~dN 691 (1282)
++.+||-|+-|.-...+|+.|+.+|....+.+
T Consensus 87 ~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~ 118 (268)
T cd08069 87 ENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQ 118 (268)
T ss_pred ceeEeeeccCCCcCCcCCHHHHHHHHHHHhcC
Confidence 99999999999888899999999998775543
No 23
>KOG2834|consensus
Probab=81.84 E-value=2.4 Score=50.97 Aligned_cols=108 Identities=19% Similarity=0.274 Sum_probs=76.5
Q ss_pred cchhhccceEeee-ccceEEEEEEccCCCCCCcc-----eeEEEEEcCCCccccceeecCCCCCCCCCc------CCCCc
Q psy3344 595 PKNVLKKFVTISD-LRAQIAGYLYGVSPADNPQV-----KEIRCIVMPPQWGTHQTVHLPASLPGHPYL------KEMEP 662 (1282)
Q Consensus 595 PKNlLkKFI~ISD-lRtQIaGyLYG~SP~Dnp~V-----KEIrCIVLvPQ~Gs~~sV~lp~~LP~h~~L------~dLEp 662 (1282)
-+|++..||.-+= .-.|=+|||||.-.+ +.+| -+|-.|-=|||.|...++.|= --++.... =+|+-
T Consensus 181 ~~~~v~~Fl~~wr~sg~QR~GflyG~y~e-~~~vPLGika~V~aIYEPPQ~~~~dgl~l~-~~~e~~~vD~~a~~lGLrR 258 (510)
T KOG2834|consen 181 NAELVNHFLNEWRASGVQRFGFLYGRYTE-HGNVPLGIKAVVAAIYEPPQHGEEDGLELL-EDDEAKRVDAIAEGLGLRR 258 (510)
T ss_pred chHHHHHHHHHHHHhhhhhcceEEEeecc-cccccccceeeEEEEecCCccCCcCCeEEe-ccchhhhHHHHHHhcCcee
Confidence 3677777765431 236788999999654 4455 477888889999999999887 22222212 37999
Q ss_pred ceeeecCCC---------------CCCCCChHhHHHHHHhhhcCCCCCCCCCCCCccee
Q psy3344 663 LGWIHTQPN---------------ELPQLSPQDVTSHAKIMADNASWDGVRHDPNMKYD 706 (1282)
Q Consensus 663 LGWIHTQ~~---------------El~~Lsp~DVtthAkl~~dN~sWDg~~~d~nmkY~ 706 (1282)
+|||.|+-. +.-+||+.++.+-|++...||+|- .|...++|+
T Consensus 259 VG~IFTDl~~~~s~egtV~~~rhkdsyFLSseE~~~aa~~Q~~hpn~~--~~s~~~~fg 315 (510)
T KOG2834|consen 259 VGWIFTDLVTADSAEGTVHYKRHKDSYFLSSEECITAAMFQNKHPNIC--EWSRDGHFG 315 (510)
T ss_pred eEEEEeeeecccCccceEEeeeccchhcccHHHHHHHhhhhhcCCchh--eeecccccc
Confidence 999999854 334599999999999999998875 244444444
No 24
>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=80.27 E-value=2.3 Score=45.54 Aligned_cols=76 Identities=21% Similarity=0.298 Sum_probs=54.8
Q ss_pred ceEEEEEEccCCCCCCcceeEEEEEcCCCccccceeecCCCCCCCC-----Cc--CCCCcceeeecCCCCCCCCChHhHH
Q psy3344 610 AQIAGYLYGVSPADNPQVKEIRCIVMPPQWGTHQTVHLPASLPGHP-----YL--KEMEPLGWIHTQPNELPQLSPQDVT 682 (1282)
Q Consensus 610 tQIaGyLYG~SP~Dnp~VKEIrCIVLvPQ~Gs~~sV~lp~~LP~h~-----~L--~dLEpLGWIHTQ~~El~~Lsp~DVt 682 (1282)
..+||+|-|.--.+ ..+.+|..+.-+|+..+...+++. |... .+ .+++++||.|+-|.-....|..||.
T Consensus 26 ~EvcGlL~G~~d~~-~~~l~Vt~~~p~~~~~~~~~~e~d---p~~q~e~~~~l~~~gl~vVGwYHSHP~~~~~pS~~Di~ 101 (187)
T cd08067 26 SEVIGYLGGTWDPN-TQNLTILQAFPCRSRLTGLDCEMD---PVSETEIRESLESRGLSVVGWYHSHPTFPPNPSLRDID 101 (187)
T ss_pred cEEEEEEEeEEcCC-CCeEEEEEEEecCCCCCCcccccC---HHHHHHHHHHHHHcCCEEEEEEecCCCCCcCCCHHHHH
Confidence 77999999984332 345577766777787765555542 3222 11 6899999999999888999999998
Q ss_pred HHHHhhh
Q psy3344 683 SHAKIMA 689 (1282)
Q Consensus 683 thAkl~~ 689 (1282)
++...-.
T Consensus 102 tQ~~yQ~ 108 (187)
T cd08067 102 TQLDYQI 108 (187)
T ss_pred HHHHHHh
Confidence 8877544
No 25
>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=69.94 E-value=5.3 Score=39.07 Aligned_cols=86 Identities=15% Similarity=0.187 Sum_probs=52.5
Q ss_pred eccceEEEEEEccCCCCCCcceeEEEEEcCCCccccceeecCCCCCCCCC-------cCCCCcceeeecCCCCCCCCChH
Q psy3344 607 DLRAQIAGYLYGVSPADNPQVKEIRCIVMPPQWGTHQTVHLPASLPGHPY-------LKEMEPLGWIHTQPNELPQLSPQ 679 (1282)
Q Consensus 607 DlRtQIaGyLYG~SP~Dnp~VKEIrCIVLvPQ~Gs~~sV~lp~~LP~h~~-------L~dLEpLGWIHTQ~~El~~Lsp~ 679 (1282)
+.-..+||+|-|.--.+ ...++++-++++.-...... |.... -.+++++||-|+-|.-....|+.
T Consensus 13 ~~p~E~cGlL~G~~~~~---~~~~~~~~v~~~~p~~~~~~-----~~~~~~~~~~~~~~g~~~vG~YHSHP~~~~~pS~~ 84 (119)
T cd08058 13 NTGIEVMGLLCGELTHN---EFTDKHVIVPKQSAGPDSCT-----GENVEELFNVQTGRPLLVVGWYHSHPTFTAWLSSV 84 (119)
T ss_pred CCCeEEEEEeeeEEecC---ccceeEEEEeecCCCCCCch-----hHHHHHHHHHHhCCCCeEEEEEecCCCCCCccCHH
Confidence 34567999999974322 22344444445543322110 11111 16899999999999888899999
Q ss_pred hHHHHHHhhhcCCCCCCCCCC
Q psy3344 680 DVTSHAKIMADNASWDGVRHD 700 (1282)
Q Consensus 680 DVtthAkl~~dN~sWDg~~~d 700 (1282)
|+.+++...+-.+.+-.+.++
T Consensus 85 Di~~~~~~q~~~p~~~~lI~s 105 (119)
T cd08058 85 DIHTQASYQLMLPEAIAIVVS 105 (119)
T ss_pred HHHHHHHHhccCCCeEEEEEC
Confidence 999988654433444433333
No 26
>PF05924 SAMP: SAMP Motif; InterPro: IPR009224 This short region is found repeated in the mid region of the adenomatous polyposis proteins (APCs). This motif binds axin [].; GO: 0008013 beta-catenin binding, 0016055 Wnt receptor signaling pathway; PDB: 1EMU_B 2RQU_B.
Probab=67.57 E-value=2.5 Score=31.47 Aligned_cols=17 Identities=35% Similarity=0.739 Sum_probs=10.2
Q ss_pred HHHHHhhhccceeeeecccCCCCCCCCC
Q psy3344 764 DLLVKCENKIQTRIKIGLNSKMPSRFPP 791 (1282)
Q Consensus 764 d~l~k~e~~i~~~~~~~~n~~mp~rf~~ 791 (1282)
|+|++| +||-||.|.++
T Consensus 4 eiL~~C-----------I~sAmPk~~~~ 20 (20)
T PF05924_consen 4 EILQEC-----------IGSAMPKRRRK 20 (20)
T ss_dssp HHHHHH-----------HHCTS------
T ss_pred HHHHHH-----------HHHhcccccCC
Confidence 889999 89999999863
No 27
>PF09816 EAF: RNA polymerase II transcription elongation factor; InterPro: IPR019194 This entry represents the N-terminal domain of ELL-associated factor (Eaf) proteins, which act as transcriptional transactivators of ELL and ELL2 RNA Polymerase II (Pol II) transcriptional elongation factors [, , , ]. Eaf proteins form a stable heterodimer complex with ELL proteins to facilitate the binding of RNA polymerase II to activate transcription elongation. ELL and EAF1 are components of Cajal bodies, which have a role in leukemogenesis []. EAF1 also has the capacity to interact with ELL1 and ELL2. The N terminus of approx 120 of EAF1 has a region of high serine, aspartic acid, and glutamic acid residues [, ].
Probab=59.35 E-value=22 Score=35.09 Aligned_cols=50 Identities=22% Similarity=0.553 Sum_probs=37.1
Q ss_pred EEEec-CceeEEEEe----------eecccCccccccccceEEEEcCCCCceEEEEEeecc
Q psy3344 360 IWFVD-DTNVYRVTI----------HKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSV 409 (1282)
Q Consensus 360 ~wfVD-dtnvYRvti----------hkt~egn~~tKpiNG~IFifNP~TGqLfLKIiHtsv 409 (1282)
.+.+. +.+-|.|++ ...|+|+....--.-||+||||.||..-|.=+++.+
T Consensus 40 ~l~~~~~~~~~~l~~~~~~~~~~~~~~~f~G~~~~~~~~ecVLifD~~~~~f~LErl~s~~ 100 (109)
T PF09816_consen 40 TLYVGSSNDEYTLTLPNPNGSGNNETYVFKGSQRPSKEKECVLIFDPETGEFVLERLSSTI 100 (109)
T ss_pred EEEecCCCCeEEEEEeCCCCCCCcccEEEEeccCCCCCcEEEEEEECCCCEEEEEEcceEE
Confidence 33455 677777777 257888744444458999999999999998887665
No 28
>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=52.93 E-value=22 Score=35.27 Aligned_cols=70 Identities=16% Similarity=0.218 Sum_probs=44.8
Q ss_pred cceEEEEEEccCCCCCCcceeEEEEEcCCCcccc--ceeecCCCCCCCC-----C--cCCCCcceeeecCCCCCCCCChH
Q psy3344 609 RAQIAGYLYGVSPADNPQVKEIRCIVMPPQWGTH--QTVHLPASLPGHP-----Y--LKEMEPLGWIHTQPNELPQLSPQ 679 (1282)
Q Consensus 609 RtQIaGyLYG~SP~Dnp~VKEIrCIVLvPQ~Gs~--~sV~lp~~LP~h~-----~--L~dLEpLGWIHTQ~~El~~Lsp~ 679 (1282)
-..+||+|.|....+...| --+.-+|..... ..+.+. |..- . -.+++++||.|+-|...+..|..
T Consensus 16 P~E~cGlL~G~~~~~~~~i---~~~~p~~n~~~~~~~~f~~d---~~~~~~~~~~~~~~g~~~vG~~HSHP~~~~~PS~~ 89 (128)
T cd08070 16 PEECCGLLLGKGGGVTAIV---TEVYPVRNVAESPRRRFEID---PAEQLAAQREARERGLEVVGIYHSHPDGPARPSET 89 (128)
T ss_pred CCceEEEEEeecCCCCceE---EEEEEccCCCCCCCceEEEC---HHHHHHHHHHHHHCCCeEEEEEeCCCCCCCCCCHH
Confidence 4578999999976665433 223334443332 222222 2110 0 15789999999999999999999
Q ss_pred hHHHH
Q psy3344 680 DVTSH 684 (1282)
Q Consensus 680 DVtth 684 (1282)
|+...
T Consensus 90 D~~~~ 94 (128)
T cd08070 90 DLRLA 94 (128)
T ss_pred HHHhc
Confidence 98764
No 29
>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=51.34 E-value=7.5 Score=36.65 Aligned_cols=23 Identities=26% Similarity=0.466 Sum_probs=17.8
Q ss_pred hhhhhhhHhh--hhhhccccccccc
Q psy3344 1002 LKKFVTISDL--RAQIAGYLYDHLV 1024 (1282)
Q Consensus 1002 Lkkfi~iadL--R~qiagyLyg~s~ 1024 (1282)
+|+++..++- ..++.|+|+|...
T Consensus 1 ~k~il~~a~~~~~~ev~G~L~G~~~ 25 (116)
T cd07767 1 LKMFLDAAKSINGKEVIGLLYGSKT 25 (116)
T ss_pred CHhHHHHHhcCCCcEEEEEeEEEEc
Confidence 3667767776 8899999999933
No 30
>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=40.64 E-value=48 Score=37.58 Aligned_cols=38 Identities=24% Similarity=0.386 Sum_probs=29.4
Q ss_pred CCCCcceeeecCCCCCCCCChHhHHHHHHhhhcCCCCC
Q psy3344 658 KEMEPLGWIHTQPNELPQLSPQDVTSHAKIMADNASWD 695 (1282)
Q Consensus 658 ~dLEpLGWIHTQ~~El~~Lsp~DVtthAkl~~dN~sWD 695 (1282)
.+++++||.|+-|.-....|..|+.++.....-++.+-
T Consensus 87 rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v 124 (244)
T cd08068 87 RPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFV 124 (244)
T ss_pred CCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcE
Confidence 68999999999999999999999987554433333443
No 31
>COG3538 Uncharacterized conserved protein [Function unknown]
Probab=40.09 E-value=38 Score=40.49 Aligned_cols=85 Identities=27% Similarity=0.478 Sum_probs=54.1
Q ss_pred Ccccch-----hcccccCCC-Ch-HHHHHHHHHHHHhCc---h----hHHHHHHHHhhhccccCCCCCCCcccccccccc
Q psy3344 290 TWEGLF-----CAYGNWFPG-SK-PLIQQALAKIMKANP---A----LYVLRERIRKALQLYSSEPTEPYLSSQNYGELF 355 (1282)
Q Consensus 290 sweglF-----cayGnw~~g-lK-~liq~aM~kImk~Np---a----L~vLRERIRKgLQLYsSe~~e~~l~s~Ny~ELF 355 (1282)
+|.|.= |.||+.+|. += -++-.-+++|..+-| . --+|++.|++|++=|.--.. .-|+|.+
T Consensus 212 ~wSgFRPSDDAC~YgYliPsNmFaVVvl~y~~ei~~~~~~~~~~a~~a~~L~~eIq~Gi~~~g~~~~------~~~~~iy 285 (434)
T COG3538 212 TWSGFRPSDDACEYGYLIPSNMFAVVVLSYLQEILEALPHDAEIARQAKELANEIQQGIEQFGKMDH------PKGGEIY 285 (434)
T ss_pred eecCcCCCccchhcccccccchhhhhhHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHhceecC------CCCCeeE
Confidence 477644 999999983 32 233444455544321 1 35799999999997765433 3456655
Q ss_pred -----cCceEEEecCceeEEEEeeecccCccccccccceE
Q psy3344 356 -----SNQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAI 390 (1282)
Q Consensus 356 -----~n~~~wfVDdtnvYRvtihkt~egn~~tKpiNG~I 390 (1282)
..+.+.|.||.||= .|-.-|.=|+.
T Consensus 286 AyEVDG~Gn~l~MDDaNvP----------SLLa~PYLG~c 315 (434)
T COG3538 286 AYEVDGLGNQLFMDDANVP----------SLLAAPYLGFC 315 (434)
T ss_pred EEEecCCCceeeccCCCch----------hhhhhhhhccc
Confidence 34568899999993 34555555555
No 32
>KOG2199|consensus
Probab=31.59 E-value=33 Score=41.43 Aligned_cols=127 Identities=25% Similarity=0.272 Sum_probs=70.7
Q ss_pred eEEEEEEeeccccccccccchhhhhhhcccCCCCcccccCCCc-cccccchhhHH----HHhc----cCcceeee-----
Q psy3344 214 KVHLFLRHTLAYDKGWRIRTEFKQYQVLKQNPFWWTHQRHDGK-LWNLNNYRTDM----IQAL----GGVEGILE----- 279 (1282)
Q Consensus 214 ~i~ilfrf~~~~~~~~~~~~~~~~~~~~k~npfwwT~~~HDGK-LWnln~yrtD~----iqaL----ggve~ile----- 279 (1282)
||--|+-|+++|.-.+--+-.---..+--.+|-||+..-|.|- |...|--.+|+ |.-. --.|-+..
T Consensus 217 kVRALYDFeAaE~nELsFkaGdIItVLd~s~~~WWKG~~~~~~GlFPsnfVT~~le~~~~ee~~~~~~~~E~~vfi~e~~ 296 (462)
T KOG2199|consen 217 KVRALYDFEAAEDNELSFKAGDIITVLDDSDPNWWKGENHRGIGLFPSNFVTADLEEPKIEEQEQKQKNKEAIVFIDEDK 296 (462)
T ss_pred hhhhhhcccccCCCccceecCcEEEEcccCCcchhccccCCcccccchhhhhhhhcccchhhhhhhhcCcceeeeccHHH
Confidence 5666788988887654222111111244579999998777764 55555444444 0000 01111100
Q ss_pred -----eecccccccCCcccch-----hcccccCCCChHHHHHHHHHHHHhCchhHHHHHHHHhhhccccCCCCC
Q psy3344 280 -----HTLFKGTYFPTWEGLF-----CAYGNWFPGSKPLIQQALAKIMKANPALYVLRERIRKALQLYSSEPTE 343 (1282)
Q Consensus 280 -----Htlfkgt~f~sweglF-----cayGnw~~glK~liq~aM~kImk~NpaL~vLRERIRKgLQLYsSe~~e 343 (1282)
|+| -+.=||=|-.= --||-- --+.|+|..-+++|=+..-.|--|+++++.+|.||..--.+
T Consensus 297 iDrlL~~L--~~~dPtd~~~D~~~l~~le~~~-~~mgPlid~~Le~idrk~~eL~~Ln~~l~~Al~lY~kLm~~ 367 (462)
T KOG2199|consen 297 IDRLLQVL--HEADPTDEVQDDDDLLDLEAAV-HQMGPLIDRKLEKIDRKHEELSQLNVKLLDALRLYNKLMNE 367 (462)
T ss_pred HHHHHHHH--hhcCCCCccCCCHHHHHHHHHH-HHhhhHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 000 00000000000 011111 45779999999999999999999999999999999764443
No 33
>PF00367 PTS_EIIB: phosphotransferase system, EIIB; InterPro: IPR018113 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to enzyme-I (EI) of PTS which in turn transfers it to a phosphoryl carrier protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease which consists of at least three structurally distinct domains (IIA, IIB, and IIC) [] which can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA) carries the first permease-specific phoshorylation site, a histidine, which is phosphorylated by phospho-HPr. The second domain (IIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the permease. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate in a process catalyzed by the IIC domain; this process is coupled to the transmembrane transport of the sugar. This entry covers the phosphorylation site of EIIB domains. ; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity; PDB: 3IPJ_B 3BP3_A 1O2F_B 3BP8_C 1IBA_A.
Probab=30.70 E-value=39 Score=27.97 Aligned_cols=17 Identities=41% Similarity=0.638 Sum_probs=14.3
Q ss_pred hHHHHhccCcceeeeee
Q psy3344 265 TDMIQALGGVEGILEHT 281 (1282)
Q Consensus 265 tD~iqaLggve~ileHt 281 (1282)
.++|+++||.|+|.+.+
T Consensus 2 ~~il~~lGG~~NI~~v~ 18 (35)
T PF00367_consen 2 KQILEALGGKENIKSVT 18 (35)
T ss_dssp HHHHHHCTTCCCEEEEE
T ss_pred hHHHHHhCCHHHHHHHh
Confidence 36899999999998765
No 34
>PRK06046 alanine dehydrogenase; Validated
Probab=26.18 E-value=1.4e+02 Score=34.27 Aligned_cols=40 Identities=23% Similarity=0.387 Sum_probs=31.7
Q ss_pred ecCceeEEEEeeecccCccc-ccc-ccceEEEEcCCCCceEE
Q psy3344 363 VDDTNVYRVTIHKTFEGNLT-TKP-INGAIFIFNPRTGQLFL 402 (1282)
Q Consensus 363 VDdtnvYRvtihkt~egn~~-tKp-iNG~IFifNP~TGqLfL 402 (1282)
+.+.+++-|++=..|-+|.. ..| ++|.|+.||++||++.-
T Consensus 60 ~~~~~~~g~K~~~~~p~N~~~glp~~~g~i~L~d~~tG~p~a 101 (326)
T PRK06046 60 LEELDIAGVKIVNVHPGNPDRGLPTVMAVIILNSPETGFPLA 101 (326)
T ss_pred eCCCCeEEEEEEeeCCCCcccCCCceeEEEEEEeCCCCceEE
Confidence 45667788888888888865 456 68999999999997754
No 35
>COG4713 Predicted membrane protein [Function unknown]
Probab=25.51 E-value=54 Score=39.50 Aligned_cols=131 Identities=23% Similarity=0.330 Sum_probs=81.8
Q ss_pred hhhccceEeeeccceEEEEEEccCCCCCCcceeE-----EEEEcCCCccccceeecCCCCCCCCCcCCCCcc-eeeecCC
Q psy3344 597 NVLKKFVTISDLRAQIAGYLYGVSPADNPQVKEI-----RCIVMPPQWGTHQTVHLPASLPGHPYLKEMEPL-GWIHTQP 670 (1282)
Q Consensus 597 NlLkKFI~ISDlRtQIaGyLYG~SP~Dnp~VKEI-----rCIVLvPQ~Gs~~sV~lp~~LP~h~~L~dLEpL-GWIHTQ~ 670 (1282)
|.=++||...=.---+...-||.+-.--.++-++ .+|..|-|++-..++|+.... +.+ |=|.|..
T Consensus 33 N~p~~fisl~fiv~~~~i~fl~~~~~~~~~~F~~i~~~gigii~Pvn~i~de~~h~~~Ti---------~~~~gdi~~~~ 103 (489)
T COG4713 33 NTPKLFISLVFIVGVVFILFLGNSEKLVKNTFFIILFLGIGIIKPVNFIVDEETHLRWTI---------RLADGDIFTRE 103 (489)
T ss_pred CCchhheeEEEEeccEEEEEechHHHHhhhhhhhhhccceeEeechhhccchhhhhhhhh---------hhcccccchhc
Confidence 5557777764333333455666654333333222 334344455555555544322 111 2233433
Q ss_pred CCCCCCChHhHHHHHHhhhcCCCCCCCC-----CCCCcceeeeccCCccccccccCcceeecccccccccccc-ccchhh
Q psy3344 671 NELPQLSPQDVTSHAKIMADNASWDGVR-----HDPNMKYDLQLANPKEFYHEIHRPAHFLNFSSLEDGDGIV-NKWNTA 744 (1282)
Q Consensus 671 ~El~~Lsp~DVtthAkl~~dN~sWDg~~-----~d~nmkY~Lkld~P~~FY~e~hRp~HFl~Fs~ied~~~I~-~k~~t~ 744 (1282)
+| +.++||.+. .++|.+.+ |=+.|.-||.++|-.+.+++++-+-...|+- ++.-|+
T Consensus 104 n~-----------------K~~D~dkv~k~~t~~~~nl~~~-Kn~~~~~~f~d~~~as~Ys~isyIPqalGi~ig~v~~~ 165 (489)
T COG4713 104 NE-----------------KQPDWDKVEKYDTLRNPNLEHA-KNGFPNKFFSDEHEASTYSNISYIPQALGIKIGMVTTS 165 (489)
T ss_pred cc-----------------cCcCHHHHhhhhccccCCchhh-hcCCcccccccccccceeeceeechHhhhhHHHHhhhH
Confidence 33 225688765 56776654 6688999999999999999999999999987 999999
Q ss_pred hHHHHHHHHH
Q psy3344 745 LIGLMTYFRE 754 (1282)
Q Consensus 745 ~i~~~~~fr~ 754 (1282)
-+.++.||-.
T Consensus 166 ~vl~~yYfGR 175 (489)
T COG4713 166 RVLVAYYFGR 175 (489)
T ss_pred HHHHHHHHHH
Confidence 9988888854
No 36
>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=23.24 E-value=85 Score=31.96 Aligned_cols=50 Identities=22% Similarity=0.271 Sum_probs=41.6
Q ss_pred ccccceeeccccchhhhhhHHHHHHHHhhhhcccccccCCCCCCCcccccccchhhhcCCccccccccceEEEEEEe
Q psy3344 145 TNSYGIIRGLQFASFIVQYYGLVLDLLVLGLQRASEMAGPPQMPNDFLTFQDTATELAHPIRLYCRYVDKVHLFLRH 221 (1282)
Q Consensus 145 ~n~yGlIrGlqFssFi~QyyglvlDlLvLGl~Ra~eiaGp~~~pn~fl~f~d~~~e~~hPIrly~Ry~d~i~ilfrf 221 (1282)
.+.-|+-.|...|+++.++|---+|..+-.. ++.-.|+||+|=+.|+.+-
T Consensus 49 ~~~~GlpqG~~lS~~L~~~~l~~~d~~i~~~---------------------------~~~~~~~RY~DD~~i~~~~ 98 (158)
T cd01646 49 GQTNGLPIGPLTSRFLANIYLNDVDHELKSK---------------------------LKGVDYVRYVDDIRIFADS 98 (158)
T ss_pred CCCceEccCcchHHHHHHHHHHHHHHHHHhc---------------------------cCCceEEEecCcEEEEcCC
Confidence 4556999999999999999998888877654 3457899999999998753
No 37
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=22.70 E-value=39 Score=33.78 Aligned_cols=84 Identities=17% Similarity=0.188 Sum_probs=46.9
Q ss_pred eccchhhccceEeeecc--ceEEEEEEccCCCCCCcceeEEEEEcCCCccccceeecCCC-CCCCCCc--CCCCcceeee
Q psy3344 593 ILPKNVLKKFVTISDLR--AQIAGYLYGVSPADNPQVKEIRCIVMPPQWGTHQTVHLPAS-LPGHPYL--KEMEPLGWIH 667 (1282)
Q Consensus 593 ViPKNlLkKFI~ISDlR--tQIaGyLYG~SP~Dnp~VKEIrCIVLvPQ~Gs~~sV~lp~~-LP~h~~L--~dLEpLGWIH 667 (1282)
+||+++++.-+.-|.=. ..+||++.|..-. .+..++..+=..- ......+.. .-..... .+++.+||.|
T Consensus 3 ~i~~~~l~~il~~a~~~~p~E~~g~l~~~~~~-----~~~~~~~n~~~~~-~~~~~~~~~~~~~~~~~~~~g~~vvg~yH 76 (134)
T COG1310 3 VIPKEVLGAILEHARREHPREVCGLLAGTREG-----ERYFPLKNVSVEP-VEYFEIDPEYSLFYLAAEDAGEVVVGWYH 76 (134)
T ss_pred eecHHHHHHHHHHHHhcCChheEEEEEeeccc-----ceeeccccccCCc-ceeEeeCHHHHHHHHHHhhCCCEEEEEEc
Confidence 56777777666655544 6789999998433 1111111111100 111111110 0000011 4599999999
Q ss_pred cCCCCCCCCChHhHH
Q psy3344 668 TQPNELPQLSPQDVT 682 (1282)
Q Consensus 668 TQ~~El~~Lsp~DVt 682 (1282)
+-|.-....|..|+.
T Consensus 77 SHP~~~~~pS~~D~~ 91 (134)
T COG1310 77 SHPGGPPYPSEADRR 91 (134)
T ss_pred CCCCCCCCcCHHHHh
Confidence 999999999999987
Done!