Query 013388
Match_columns 444
No_of_seqs 175 out of 802
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 03:21:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013388.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013388hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2880 SMAD6 interacting prot 100.0 5.9E-61 1.3E-65 478.8 13.3 364 3-444 39-424 (424)
2 cd08066 MPN_AMSH_like Mov34/MP 100.0 1.4E-43 3.1E-48 327.7 21.0 173 267-444 1-173 (173)
3 cd08069 MPN_RPN11_CSN5 Mov34/M 99.9 2.9E-26 6.3E-31 225.0 17.9 133 266-401 8-150 (268)
4 cd08058 MPN_euk_mb Mpr1p, Pad1 99.9 2.3E-26 5E-31 198.9 12.5 114 275-395 1-119 (119)
5 cd08067 MPN_2A_DUB Mov34/MPN/P 99.9 7.7E-26 1.7E-30 212.1 16.9 127 267-397 4-147 (187)
6 KOG1554 COP9 signalosome, subu 99.9 2.8E-26 6E-31 225.3 10.9 143 267-426 52-205 (347)
7 cd08068 MPN_BRCC36 Mov34/MPN/P 99.9 2.6E-25 5.5E-30 216.3 16.2 127 268-396 2-151 (244)
8 cd07767 MPN Mpr1p, Pad1p N-ter 99.9 2.9E-21 6.2E-26 162.7 12.2 113 278-392 2-116 (116)
9 smart00232 JAB_MPN JAB/MPN dom 99.9 1.2E-20 2.5E-25 162.2 16.2 125 270-396 2-134 (135)
10 cd08056 MPN_PRP8 Mpr1p, Pad1p 99.8 9.8E-21 2.1E-25 185.0 14.5 135 267-408 35-177 (252)
11 cd08065 MPN_eIF3h Mpr1p, Pad1p 99.8 1E-20 2.3E-25 185.3 14.5 138 269-413 2-149 (266)
12 cd08070 MPN_like Mpr1p, Pad1p 99.8 4.5E-20 9.8E-25 161.3 14.2 115 275-396 2-120 (128)
13 PF01398 JAB: JAB1/Mov34/MPN/P 99.8 3.3E-20 7.2E-25 158.0 9.8 106 267-374 3-114 (114)
14 cd08072 MPN_archaeal Mov34/MPN 99.7 2.4E-17 5.2E-22 143.8 13.6 109 272-396 1-109 (117)
15 KOG1560 Translation initiation 99.7 8.2E-18 1.8E-22 165.6 9.8 143 267-414 12-169 (339)
16 KOG1555 26S proteasome regulat 99.7 8.7E-18 1.9E-22 168.2 7.2 141 260-402 23-179 (316)
17 cd08073 MPN_NLPC_P60 Mpr1p, Pa 99.7 4.9E-16 1.1E-20 134.1 12.2 102 276-393 2-104 (108)
18 COG1310 Predicted metal-depend 99.6 1.5E-14 3.2E-19 127.7 11.9 103 270-383 2-107 (134)
19 cd08057 MPN_euk_non_mb Mpr1p, 99.5 1.8E-13 3.9E-18 124.0 15.1 126 270-396 1-136 (157)
20 PF14464 Prok-JAB: Prokaryotic 99.5 4.2E-14 9.1E-19 117.9 8.5 98 274-394 2-104 (104)
21 cd08062 MPN_RPN7_8 Mpr1p, Pad1 99.4 1.2E-11 2.6E-16 122.9 15.0 127 269-400 2-138 (280)
22 cd08064 MPN_eIF3f Mpr1p, Pad1p 99.3 1.5E-11 3.3E-16 120.6 14.7 127 270-400 1-134 (265)
23 cd08059 MPN_prok_mb Mpr1p, Pad 99.3 2.6E-11 5.6E-16 101.9 10.7 101 275-392 1-101 (101)
24 TIGR03735 PRTRC_A PRTRC system 99.3 4.5E-11 9.7E-16 113.4 11.7 111 271-396 74-184 (192)
25 cd08060 MPN_UPF0172 Mov34/MPN/ 99.2 1.6E-10 3.4E-15 108.6 13.0 107 272-385 1-115 (182)
26 cd08061 MPN_NPL4 Mov34/MPN/PAD 99.0 1.3E-08 2.7E-13 101.5 14.3 133 269-404 12-166 (274)
27 PLN03246 26S proteasome regula 98.9 3.2E-08 6.9E-13 99.8 14.6 126 267-396 5-140 (303)
28 TIGR02256 ICE_VC0181 integrati 98.9 2.2E-08 4.7E-13 90.1 11.8 106 276-382 2-114 (131)
29 cd08063 MPN_CSN6 Mpr1p, Pad1p 98.9 2.5E-08 5.5E-13 99.2 13.1 128 269-400 2-142 (288)
30 KOG1795 U5 snRNP spliceosome s 98.3 1.6E-06 3.4E-11 99.0 7.3 150 268-427 2095-2248(2321)
31 KOG1556 26S proteasome regulat 98.2 1.1E-05 2.4E-10 79.6 11.9 117 267-387 8-132 (309)
32 PF05021 NPL4: NPL4 family; I 98.2 1.1E-05 2.3E-10 81.9 11.4 109 295-404 2-149 (306)
33 PF03665 UPF0172: Uncharacteri 97.6 0.00065 1.4E-08 65.0 11.8 113 269-385 3-121 (196)
34 COG5178 PRP8 U5 snRNP spliceos 97.3 0.00032 7E-09 80.5 6.0 139 267-414 2133-2284(2365)
35 KOG2975 Translation initiation 97.3 0.0018 3.9E-08 64.8 10.4 129 267-400 20-154 (288)
36 KOG2834 Nuclear pore complex, 96.1 0.037 7.9E-07 59.2 10.3 128 273-404 181-347 (510)
37 KOG3289 Uncharacterized conser 94.8 0.49 1.1E-05 45.5 11.9 109 269-384 3-120 (199)
38 cd08071 MPN_DUF2466 Mov34/MPN/ 93.5 1.2 2.7E-05 38.9 11.1 73 291-368 15-87 (113)
39 KOG3050 COP9 signalosome, subu 90.8 0.8 1.7E-05 46.1 7.3 92 289-385 33-130 (299)
40 PF04002 RadC: RadC-like JAB d 89.6 2.9 6.3E-05 37.0 9.1 75 291-370 20-94 (123)
41 TIGR00608 radc DNA repair prot 82.9 15 0.00032 36.1 10.9 88 273-367 99-186 (218)
42 PRK00024 hypothetical protein; 82.6 17 0.00037 35.6 11.2 90 273-369 105-194 (224)
43 PF14220 DUF4329: Domain of un 80.6 9.3 0.0002 34.5 8.0 66 289-365 18-88 (123)
44 COG5100 NPL4 Nuclear pore prot 78.4 3.9 8.5E-05 43.9 5.6 128 273-404 240-406 (571)
45 PF08084 PROCT: PROCT (NUC072) 64.6 2.7 5.8E-05 38.3 0.6 33 375-408 1-33 (125)
46 PF15659 Toxin-JAB1: JAB-like 55.9 52 0.0011 31.3 7.5 40 337-378 112-151 (162)
47 PF14778 ODR4-like: Olfactory 41.1 1.4E+02 0.0031 31.2 8.8 57 296-352 1-74 (362)
48 COG2003 RadC DNA repair protei 23.2 76 0.0016 31.7 3.0 90 270-366 102-191 (224)
No 1
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=100.00 E-value=5.9e-61 Score=478.83 Aligned_cols=364 Identities=42% Similarity=0.670 Sum_probs=308.3
Q ss_pred ccccccccCcchHHHHHHHHHH-----------------HHHHhh----hhCHHHHHHHHHhhccccccccCccccCCCC
Q 013388 3 SRLSSIVQEPKTLFEKGIKLLN-----------------ALSELE----ELQPAVQQKINELNRKKTNQVTGWSHASQNS 61 (444)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~l~~-----------------~~~ele----~lkp~~~~~~~~~n~~~~~~~~~~~~~~~~~ 61 (444)
.|+||||.||+|+-..+.-++. +..|++ +||++++.+|+||-.+...+.|-..
T Consensus 39 ~rmA~VY~~EgN~enafvLy~ry~tLfiEkipkHrDy~s~k~ek~d~~~klk~~~~p~~deL~~~ll~rY~~ey------ 112 (424)
T KOG2880|consen 39 LRMANVYLEEGNVENAFVLYLRYITLFIEKIPKHRDYRSVKPEKEDIRKKLKEEAFPRIDELKAKLLKRYNVEY------ 112 (424)
T ss_pred HHHHHHHHhcCCcchhhhHHHHHHHHHHHhcccCcchhhhchhHHHHHHHHHHHhhhhHHHHHHHHHHHHhhHH------
Confidence 5899999999986544332222 444554 7899999999999887766554432
Q ss_pred CCCCCccccccCCcccccccccCCCccceecCCcccccccCcchHHHhhcccccCCCCCcccccccccccCCCCCCCCCC
Q 013388 62 TLEWPSLKKQTLTNYDVTKALRLPSRELAYQGSIPQQLAYTRPVDEQFRRMSLNFPRPNAETLSRHSLLGPNGLYGHWQP 141 (444)
Q Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~etlsrhs~lgp~~l~~~w~~ 141 (444)
+.|+.-|- +-.++.||+|.. .+.+||++.|++
T Consensus 113 ------------n~y~~~K~---------------------k~~~E~~k~le~---~~~~E~e~kr~a------------ 144 (424)
T KOG2880|consen 113 ------------NEYDHSKK---------------------KNLAERFKKLEV---QREEETERKRSA------------ 144 (424)
T ss_pred ------------HHHHHHHh---------------------hhHHHHHHHhhc---chhhHHHHHHHH------------
Confidence 23333221 116788999988 899999999988
Q ss_pred CCCCccccccCCCCCCcccCCCCCCCCCcccCCCCCCCCCCCCcccccccccCCCCccccCCcCCCCCCcccccCCCCcc
Q 013388 142 PKSDKLVKYPNNIDLTPIEIPSLRQPSESSIKIKTDSSNVEPEKSSVQSISTPNDEIEIHRTEEPCSMISFETSEAPNSA 221 (444)
Q Consensus 142 ~~~~~~~~yps~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (444)
..++||+++.++.+.+.++++|....+.+... .+.+.++.....+++-....+.....++....++++..++....
T Consensus 145 ---q~k~Q~l~~~~f~~~~~~~~~q~~~s~~m~s~-~~~gl~e~~~~~~~~p~~~~~~~~~s~~l~~~~s~ep~~s~~~n 220 (424)
T KOG2880|consen 145 ---QTKQQQLESSQFSPLEPPSFKQLLDSGPMPSN-QSNGLPEQPIGEPLVPSNESRSLNYSELLSVLSSPEPSDSCTTN 220 (424)
T ss_pred ---HHhhhcCCcccCCccCchHHHhhhcccCCCcC-CCCCCcCCCcCCCCcccccccccCCchhhhhccCCCcccccccc
Confidence 78999999999999999999999998887643 34455556777777766777788888888788888999999999
Q ss_pred cccccCCCCcceeeeccccccCCCCccCCcCCCCCCCCCCCCCCC-CeEEEECHHHHHHHHHHHhccCCCCcceEEEeee
Q 013388 222 DVIRQPSPPPVLTEVQDLIAAMSPQVTETECQVGNSLSDAFDRSE-PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAG 300 (444)
Q Consensus 222 ~~~~~~~p~p~~~~v~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~-~r~V~Is~~aL~kILkHA~snt~~P~EvCGLLlG 300 (444)
..+++|+++++|+.+- .+ .+..+....+. ++.|+|+..++..|++.|++||.++.|+||+|+|
T Consensus 221 ~~~k~p~~~r~l~p~a----------~~------n~~~~~~~~~k~lr~v~ip~~l~~~Fl~la~~NT~knlETCGiL~g 284 (424)
T KOG2880|consen 221 VTIKSPSVDRVLKPGA----------TD------NSNHGESSEGKILRDVHIPERLMEVFLQLAKSNTKKNLETCGILAG 284 (424)
T ss_pred ccccCCCCCccccccc----------cc------ccccccccCCccceEEEecHHHHHHHHHHHhhcccccchHHHHhhh
Confidence 9999999999988761 11 11111112222 8999999999999999999999999999999999
Q ss_pred eeCCCEEEEEEEEecCCCCCCCceecCChHHHHHHHhhCCCccEEEEeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEE
Q 013388 301 SLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVM 380 (444)
Q Consensus 301 ~~~~~~l~VT~lf~ppqegtsds~~a~deee~fe~q~~rgLeiVGWYHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIi 380 (444)
+...+.++||++++|+|++++++|.+++++++|.+|+.++|..+||+||||+++||+|++|||||++||.|+|+++||||
T Consensus 285 ~L~~n~f~IThliiPkQeatsd~C~t~neeelF~vQdq~~L~tlGWIHTHPTQt~FmSSVDlHTHcSYQiMlPEAiAIV~ 364 (424)
T KOG2880|consen 285 KLERNEFYITHLIIPKQEATSDSCNTMNEEELFEVQDQHELLTLGWIHTHPTQTCFMSSVDLHTHCSYQIMLPEAIAIVC 364 (424)
T ss_pred HhhcCcEEEEEEEeecccCCCccccccCHHHHheecccccceeeeeeecCCccchhheeccccccceeeeecchheeEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCceeEEEecCCCCchhhhhcccCCCcCCCCCCCCCCCccccCceEecCCCceEEeeCC
Q 013388 381 APQDATRKHGIFRLTSPGGMSVIRQCQQRGFHPHDPPPDGGPIYKPCTDVYMNPNLKFDVIDLR 444 (444)
Q Consensus 381 SP~~s~~~LrAFRLtdP~Gm~~ik~C~~~gFhPh~~~~~g~~iy~~~~hv~~~~~~~~~~~dlr 444 (444)
+|+.. ..|+|||++|+||.++..|+++|||||.. +|+|+|++|+||||+.+.+++|+|||
T Consensus 365 aPk~~--~tGiFrLt~~~Gm~~i~~C~~~GFHpH~~--~~~pl~~~~~~v~~~~~~k~~v~dLR 424 (424)
T KOG2880|consen 365 APKSK--TTGIFRLTDPGGMEVIRGCRKKGFHPHSE--KGPPLFEHCSHVYMHHNNKLCVIDLR 424 (424)
T ss_pred ccccC--CcceEEecCCcchHHHhhcccCCCCCCCC--CCCCceeecceeEEcCCcceeeeeCC
Confidence 99854 59999999999999999999999999975 79999999999999999999999998
No 2
>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=100.00 E-value=1.4e-43 Score=327.68 Aligned_cols=173 Identities=57% Similarity=1.017 Sum_probs=161.7
Q ss_pred CeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHHHHHHHhhCCCccEEE
Q 013388 267 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGW 346 (444)
Q Consensus 267 ~r~V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee~fe~q~~rgLeiVGW 346 (444)
++++.|+++++++|+.||+.++..|+|+||+|+|+..++.+.|++++.++|.+++.++++.++++.++.++.+|+++|||
T Consensus 1 ~~~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~~~~~~~~I~~i~~~~q~~~~~~~~~~~~~e~~~~~~~~gle~vGw 80 (173)
T cd08066 1 LRQVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSNNAFFITHLIIPKQSGTSDSCQTTNEEELFDFQDQHDLITLGW 80 (173)
T ss_pred CeEEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeEcCCCeEEEEEEEeccccCCCceecCCCHHHHHHHHHhCCCeeEEE
Confidence 36899999999999999999763579999999999888888999999999999999999888888888889999999999
Q ss_pred EeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCCCCceeEEEecCCCCchhhhhcccCCCcCCCCCCCCCCCccc
Q 013388 347 IHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLTSPGGMSVIRQCQQRGFHPHDPPPDGGPIYKP 426 (444)
Q Consensus 347 YHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~~~LrAFRLtdP~Gm~~ik~C~~~gFhPh~~~~~g~~iy~~ 426 (444)
|||||..+|+||.+|+++|++||+++|+++||||||. ...++||||++|+||+|+++|+++|||||+++ .++|++
T Consensus 81 yHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~--~~~l~afrl~~~~g~~~~~~~~~~~~h~~~~~---~~~~~~ 155 (173)
T cd08066 81 IHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK--YNEFGIFRLTDPPGLDEILNCKKTGFHPHPKD---PPLYED 155 (173)
T ss_pred EeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC--CcEEeEEEeecCCcceecccCCcCccCCCCCC---CCccee
Confidence 9999999999999999999999999999999999985 46799999996789999999999999999886 899999
Q ss_pred cCceEecCCCceEEeeCC
Q 013388 427 CTDVYMNPNLKFDVIDLR 444 (444)
Q Consensus 427 ~~hv~~~~~~~~~~~dlr 444 (444)
|+|||.+.+++|+|||||
T Consensus 156 ~~~~~~~~~~~~~~~~~~ 173 (173)
T cd08066 156 CGHVIWKDQLKVTVVDLR 173 (173)
T ss_pred eeEEEEcCCCceEEEeCC
Confidence 999999999999999998
No 3
>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=99.94 E-value=2.9e-26 Score=225.02 Aligned_cols=133 Identities=25% Similarity=0.398 Sum_probs=115.4
Q ss_pred CCeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChH--HHHH--H--HhhC
Q 013388 266 EPLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEE--EIFE--V--QDKR 339 (444)
Q Consensus 266 ~~r~V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~dee--e~fe--~--q~~r 339 (444)
.++.|.|+..++.+|++||++ +.|.||||+|+|..+++.++|+++|++|+.++++.+++.++. ++++ . +.++
T Consensus 8 ~~~~V~Is~~allkil~Ha~~--~~p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~~~~~ 85 (268)
T cd08069 8 YFEKVYISSLALLKMLKHARA--GGPIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQTGR 85 (268)
T ss_pred cccEEEECHHHHHHHHHHHhc--cCCceEEEEEEeeecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHHHhCC
Confidence 478999999999999999999 559999999999988889999999999998888888765431 2222 2 2468
Q ss_pred CCccEEEEeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCC-CC---ceeEEEecCCCCch
Q 013388 340 SLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDA-TR---KHGIFRLTSPGGMS 401 (444)
Q Consensus 340 gLeiVGWYHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s-~~---~LrAFRLtdP~Gm~ 401 (444)
++++||||||||+++||||.+|+++|..||++.+++|+||+||..+ .. .+||||+.+ .++.
T Consensus 86 ~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~-~~~~ 150 (268)
T cd08069 86 PENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIP-PGYK 150 (268)
T ss_pred CceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEEC-cccc
Confidence 9999999999999999999999999999999999999999999887 32 699999998 4654
No 4
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=99.94 E-value=2.3e-26 Score=198.92 Aligned_cols=114 Identities=39% Similarity=0.727 Sum_probs=93.2
Q ss_pred HHHHHHHHHHhccCCCCcceEEEeeeeeCC-----CEEEEEEEEecCCCCCCCceecCChHHHHHHHhhCCCccEEEEeC
Q 013388 275 TMMDNFMKLAKSNTDKNLETCGILAGSLKN-----RKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHT 349 (444)
Q Consensus 275 ~aL~kILkHA~snt~~P~EvCGLLlG~~~~-----~~l~VT~lf~ppqegtsds~~a~deee~fe~q~~rgLeiVGWYHS 349 (444)
+++++|++||++++ |.|+||+|+|...+ .++.|+++++.+... +..+....+..+.++|+++||||||
T Consensus 1 ~~~~~i~~ha~~~~--p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~-----~~~~~~~~~~~~~~~g~~~vG~YHS 73 (119)
T cd08058 1 DALLKMLQHAESNT--GIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSC-----TGENVEELFNVQTGRPLLVVGWYHS 73 (119)
T ss_pred CHHHHHHHHhcCCC--CeEEEEEeeeEEecCccceeEEEEeecCCCCCCc-----hhHHHHHHHHHHhCCCCeEEEEEec
Confidence 47899999999965 99999999998763 456777777655421 1111112333467999999999999
Q ss_pred CCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCCCCceeEEEec
Q 013388 350 HPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLT 395 (444)
Q Consensus 350 HP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~~~LrAFRLt 395 (444)
||.++++||.+|+++|+.||++.|+++|||+||.++...+|||||+
T Consensus 74 HP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~~~~~~a~rl~ 119 (119)
T cd08058 74 HPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHRNKDTGIFRLT 119 (119)
T ss_pred CCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCCCcccceEEeC
Confidence 9999999999999999999999999999999999976789999995
No 5
>cd08067 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase. This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it p
Probab=99.94 E-value=7.7e-26 Score=212.12 Aligned_cols=127 Identities=24% Similarity=0.362 Sum_probs=109.8
Q ss_pred CeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeeC--CCEEEEEEEEecCCCCCCCceecCChHHH---HHHHhhCCC
Q 013388 267 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK--NRKFYITALIIPKQESTSDSCQATNEEEI---FEVQDKRSL 341 (444)
Q Consensus 267 ~r~V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~--~~~l~VT~lf~ppqegtsds~~a~deee~---fe~q~~rgL 341 (444)
.-.|.|+..++.+|++||+. +. .|+||+|+|..+ ++.+.|+.+||+++..+++.+++ +++++ ++.++.+|+
T Consensus 4 pf~V~Is~~all~m~~Ha~~--~~-~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e~-dp~~q~e~~~~l~~~gl 79 (187)
T cd08067 4 PFKVTVSSNALLLMDFHCHL--TT-SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEM-DPVSETEIRESLESRGL 79 (187)
T ss_pred CEEEEECHHHHHHHHHHhcC--CC-cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCccccc-CHHHHHHHHHHHHHcCC
Confidence 45799999999999999998 33 999999999975 36889999999999877777764 55443 445679999
Q ss_pred ccEEEEeCCCCCCCCCCHHHHHhHHHHhhhCC-------CeEEEEEccCCCCC-----ceeEEEecCC
Q 013388 342 FPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLP-------ESVAIVMAPQDATR-----KHGIFRLTSP 397 (444)
Q Consensus 342 eiVGWYHSHP~~~afPSstDL~tQ~sYQ~~lP-------eaVaLIiSP~~s~~-----~LrAFRLtdP 397 (444)
.+||||||||.++|+||.+|+++|+.||.+++ ++|+|||||.++.. .++||++.++
T Consensus 80 ~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~ 147 (187)
T cd08067 80 SVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPP 147 (187)
T ss_pred EEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECC
Confidence 99999999999999999999999999999987 69999999998642 5999999975
No 6
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.93 E-value=2.8e-26 Score=225.25 Aligned_cols=143 Identities=27% Similarity=0.407 Sum_probs=124.8
Q ss_pred CeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHHHHHHH-------hhC
Q 013388 267 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQ-------DKR 339 (444)
Q Consensus 267 ~r~V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee~fe~q-------~~r 339 (444)
++.|+|++.++++|+.||++ +++.|+||+|.|+.+++++.|.++|.+|.+||++++++..++..+.++ .++
T Consensus 52 fk~vkISalAllKm~~hA~~--GgnlEiMGlm~Gkv~g~t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k~~gr 129 (347)
T KOG1554|consen 52 FKHVKISALALLKMVMHARS--GGNLEIMGLMQGKVDGDTIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEAKNVGR 129 (347)
T ss_pred hhhhhhHHHHHHHHHHHHhc--CCCeEEEeeecccccCCeEEEEeccccccccccceechHHHHHHHHHHHHHHHHHhhh
Confidence 78899999999999999999 779999999999999999999999999999999999887665433321 267
Q ss_pred CCccEEEEeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCCCC----ceeEEEecCCCCchhhhhcccCCCcCCC
Q 013388 340 SLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR----KHGIFRLTSPGGMSVIRQCQQRGFHPHD 415 (444)
Q Consensus 340 gLeiVGWYHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~~----~LrAFRLtdP~Gm~~ik~C~~~gFhPh~ 415 (444)
-+++||||||||+++||+|.+||.||...|++..+|||||+||.++-. .++|||..+ .||.|.
T Consensus 130 ~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRTyp------------~gyk~~- 196 (347)
T KOG1554|consen 130 LENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTYP------------KGYKPP- 196 (347)
T ss_pred hhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCccccccCceeeceeeccc------------CCCCCC-
Confidence 789999999999999999999999999999999999999999999853 599999996 356664
Q ss_pred CCCCCCCCccc
Q 013388 416 PPPDGGPIYKP 426 (444)
Q Consensus 416 ~~~~g~~iy~~ 426 (444)
++++..|+.
T Consensus 197 --d~~~seyqt 205 (347)
T KOG1554|consen 197 --DEPPSEYQT 205 (347)
T ss_pred --CCCchhhhc
Confidence 445777764
No 7
>cd08068 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex. BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-contai
Probab=99.93 E-value=2.6e-25 Score=216.30 Aligned_cols=127 Identities=22% Similarity=0.363 Sum_probs=105.3
Q ss_pred eEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeeC-------CCEEEEEEEEecCCCCCCCceecCChHHHHHHH---h
Q 013388 268 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK-------NRKFYITALIIPKQESTSDSCQATNEEEIFEVQ---D 337 (444)
Q Consensus 268 r~V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~-------~~~l~VT~lf~ppqegtsds~~a~deee~fe~q---~ 337 (444)
..|.|+++++++|+.||++.+ |+|+||||+|..+ ...+.|...+++.+...+...+.+|++++++++ +
T Consensus 2 ~~V~Is~~~l~~il~HA~~~~--P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea~ 79 (244)
T cd08068 2 SKVHLSADVYLVCLTHALSTE--KEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEAE 79 (244)
T ss_pred cEEEECHHHHHHHHHHHHhCC--CcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHHH
Confidence 579999999999999999955 9999999999875 244556566666565444444567888776652 3
Q ss_pred h------CCCccEEEEeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCCC-------CceeEEEecC
Q 013388 338 K------RSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDAT-------RKHGIFRLTS 396 (444)
Q Consensus 338 ~------rgLeiVGWYHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~-------~~LrAFRLtd 396 (444)
. +|+.+||||||||.++|+||.+|+.+|.+||++.|+++|||+|+.+.. ..++|||+.+
T Consensus 80 ~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~ 151 (244)
T cd08068 80 RLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQ 151 (244)
T ss_pred HHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecC
Confidence 4 999999999999999999999999999999999999999999987753 3699999986
No 8
>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. J
Probab=99.86 E-value=2.9e-21 Score=162.66 Aligned_cols=113 Identities=26% Similarity=0.352 Sum_probs=90.5
Q ss_pred HHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHHHHHHHhhCCCccEEEEeCCCCCCCCC
Q 013388 278 DNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQSCFM 357 (444)
Q Consensus 278 ~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee~fe~q~~rgLeiVGWYHSHP~~~afP 357 (444)
.+|++||+.++ +.|+||+|+|+..+++++|++++++++..+...+...........+...|+++||||||||..+++|
T Consensus 2 k~il~~a~~~~--~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iVGwyhshp~~~~~~ 79 (116)
T cd07767 2 KMFLDAAKSIN--GKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNAGLRIVGWYHTHPKPSCFL 79 (116)
T ss_pred HhHHHHHhcCC--CcEEEEEeEEEEcCCEEEEEEEEecccCCCCCccHHHHHHHHHHHHhcCCCeEEEEEEcCCCCCCcc
Confidence 68999999965 9999999999998889999999999986544332211101112235679999999999999999999
Q ss_pred CHHHHHhHHHHhhhCCCeEEEEEccCCCC--CceeEE
Q 013388 358 SSIDVHTHYSYQIMLPESVAIVMAPQDAT--RKHGIF 392 (444)
Q Consensus 358 SstDL~tQ~sYQ~~lPeaVaLIiSP~~s~--~~LrAF 392 (444)
|..|+.+|..||.+.+++++||+++.... ..++||
T Consensus 80 s~~dv~~~~~~q~~~~~~v~li~~~~~~~~~~~~~~~ 116 (116)
T cd07767 80 SPNDLATHELFQRYFPEKVMIIVDVKPKDLGNSWKCY 116 (116)
T ss_pred CHHHHHHHHHHHHhCCCCEEEEEECCCccCCCCcccC
Confidence 99999999999999999999999998863 234543
No 9
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=99.86 E-value=1.2e-20 Score=162.22 Aligned_cols=125 Identities=28% Similarity=0.451 Sum_probs=103.6
Q ss_pred EEECHHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCce--ecCChHHHHH-H--HhhCCCccE
Q 013388 270 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSC--QATNEEEIFE-V--QDKRSLFPL 344 (444)
Q Consensus 270 V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~--~a~deee~fe-~--q~~rgLeiV 344 (444)
|.|...++++|++||.++. +.|+||+|+|+..++.+.|+++|++++....+.+ +..+..+.+. . +...++.+|
T Consensus 2 v~i~~~v~~~i~~h~~~~~--p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v 79 (135)
T smart00232 2 VKVHPLVPLNILKHAIRDG--PEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQEYDEDYSHLMDEELKKVNKDLEIV 79 (135)
T ss_pred EEEcHHHHHHHHHHHhcCC--CcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchhhhhhhHHHHHHHHHHhhCCCceEE
Confidence 7899999999999999955 9999999999998888999999998886554443 2222222221 1 347899999
Q ss_pred EEEeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCCCC---ceeEEEecC
Q 013388 345 GWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR---KHGIFRLTS 396 (444)
Q Consensus 345 GWYHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~~---~LrAFRLtd 396 (444)
|||||||..+++||..|+.+|..|+..++.++.+++++..+.. .++||++++
T Consensus 80 Gwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~~g~~~~~af~~~~ 134 (135)
T smart00232 80 GWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLTP 134 (135)
T ss_pred EEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccccCcEEEEEEEecC
Confidence 9999999999999999999999999999999999999887652 589999875
No 10
>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=99.85 E-value=9.8e-21 Score=185.00 Aligned_cols=135 Identities=20% Similarity=0.300 Sum_probs=122.4
Q ss_pred CeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeeCC---CEEEEEEEEecCCCCCCCceecCChHHHHHHHhhCCCcc
Q 013388 267 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKN---RKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFP 343 (444)
Q Consensus 267 ~r~V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~---~~l~VT~lf~ppqegtsds~~a~deee~fe~q~~rgLei 343 (444)
..++.||++++.+|+..|+. +.|+||+|.|+... ++.+|++++++||.++.++|.+.+. ..+++...+|+.
T Consensus 35 ~~t~vlPknllkkFi~iaD~----rtQ~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~--~~~~~~l~~Le~ 108 (252)
T cd08056 35 GYTYILPKNLLKKFISISDL----RTQIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQ--LPQHEYLEDLEP 108 (252)
T ss_pred CCEEEeCHHHHHHHHHHhhh----cceEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCcc--CccchhhCCCEe
Confidence 35799999999999999998 45999999999764 7899999999999999999998764 356677899999
Q ss_pred EEEEeCCCCCCCCCCHHHHHhHHHHhhhCC-----CeEEEEEccCCCCCceeEEEecCCCCchhhhhccc
Q 013388 344 LGWIHTHPTQSCFMSSIDVHTHYSYQIMLP-----ESVAIVMAPQDATRKHGIFRLTSPGGMSVIRQCQQ 408 (444)
Q Consensus 344 VGWYHSHP~~~afPSstDL~tQ~sYQ~~lP-----eaVaLIiSP~~s~~~LrAFRLtdP~Gm~~ik~C~~ 408 (444)
|||+||||...+++|+.|+++|++||.+.| .+|+|+|+++.+..+++||+|++ +|++|+++=++
T Consensus 109 LGWIHTqp~e~~~Lss~Dv~tha~~~~~~~~w~~~~~V~it~SftpGs~sl~ay~LT~-~G~~wg~~n~d 177 (252)
T cd08056 109 LGWIHTQPNELPQLSPQDVTTHAKILADNPSWDGEKTVILTCSFTPGSCSLTAYKLTP-EGYEWGKQNKD 177 (252)
T ss_pred eEEEEcCCCCccccCHHHHHHHHHHHHhccccCCCcEEEEEEcCCCCceEEEEEecCH-HHHHHHHhCcc
Confidence 999999999999999999999999999998 79999999998888999999996 89999987664
No 11
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=99.85 E-value=1e-20 Score=185.27 Aligned_cols=138 Identities=19% Similarity=0.250 Sum_probs=110.2
Q ss_pred EEEECHHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCce--ecCChHHHHH---HHhhCCC--
Q 013388 269 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSC--QATNEEEIFE---VQDKRSL-- 341 (444)
Q Consensus 269 ~V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~--~a~deee~fe---~q~~rgL-- 341 (444)
.|.|++.++.+|++||.+.. |.||||+|+|...+++++|+++|++|+..+++.. ...+...+.+ ...+.+.
T Consensus 2 ~V~I~~~vllkIv~H~~~~~--p~~v~G~LLG~~~~~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~e 79 (266)
T cd08065 2 SVQIDGLVVLKIIKHCKEEL--PELVQGQLLGLDVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVDH 79 (266)
T ss_pred EEEEeHHHHHHHHHHHhcCC--CcEEEEEEeeeEcCCEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCCC
Confidence 58999999999999999955 9999999999999999999999999986554432 2222223323 3344444
Q ss_pred ccEEEEeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCC---CCceeEEEecCCCCchhhhhcccCCCcC
Q 013388 342 FPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDA---TRKHGIFRLTSPGGMSVIRQCQQRGFHP 413 (444)
Q Consensus 342 eiVGWYHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s---~~~LrAFRLtdP~Gm~~ik~C~~~gFhP 413 (444)
.+|||||||| .++|.|..+++++++||...+++|+||+|+..+ ...+||||+++ .||.. +++..|.+
T Consensus 80 ~iVGWY~S~p-~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s~~g~l~lkAyrl~~-~~~~~---~~~~~~~~ 149 (266)
T cd08065 80 NHVGWYQSTY-LGSFFTRDLIETQYNYQEAIEESVVLVYDPSKTSQGSLSLKAYRLSE-KFMEL---YKEGKFST 149 (266)
T ss_pred cEEEeEeecC-CCCcCCHHHHHHHHHHhccCCCCEEEEECCCcccccceeeEEEEEcH-HHHHH---hhcCCcCH
Confidence 9999999999 799999999999999999889999999999842 24699999996 78855 34455553
No 12
>cd08070 MPN_like Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding). This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.84 E-value=4.5e-20 Score=161.34 Aligned_cols=115 Identities=17% Similarity=0.254 Sum_probs=97.5
Q ss_pred HHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCC-ceecCChHHHHHH---HhhCCCccEEEEeCC
Q 013388 275 TMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSD-SCQATNEEEIFEV---QDKRSLFPLGWIHTH 350 (444)
Q Consensus 275 ~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsd-s~~a~deee~fe~---q~~rgLeiVGWYHSH 350 (444)
.++.+|++||++.+ |.|+||||+|+.+.....|+.+++++|...+. ..+.+|+++++++ ...+|+.+|||||||
T Consensus 2 ~~~~~il~ha~~~~--P~E~cGlL~G~~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~~~~~~~g~~~vG~~HSH 79 (128)
T cd08070 2 ELLEAILAHAEAEY--PEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEIDPAEQLAAQREARERGLEVVGIYHSH 79 (128)
T ss_pred HHHHHHHHHHHhCC--CCceEEEEEeecCCCCceEEEEEEccCCCCCCCceEEECHHHHHHHHHHHHHCCCeEEEEEeCC
Confidence 57899999999955 99999999999987666788999999976555 6667888777665 457899999999999
Q ss_pred CCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCCCCceeEEEecC
Q 013388 351 PTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLTS 396 (444)
Q Consensus 351 P~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~~~LrAFRLtd 396 (444)
|..+++||.+|+.++ ..++.++||++...+...+++|++.+
T Consensus 80 P~~~~~PS~~D~~~~-----~~~~~~~lIv~~~~~~~~~~~~~~~~ 120 (128)
T cd08070 80 PDGPARPSETDLRLA-----WPPGVSYLIVSLAGGAPELRAWRLEG 120 (128)
T ss_pred CCCCCCCCHHHHHhc-----cCCCCeEEEEECCCCCcEEEEEEEcC
Confidence 999999999999853 34579999999988766899999986
No 13
>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain [] and PAD-1-like domain []. It has been shown that this domain occurs in prokaryotes []. Mov34 proteins act as the regulatory subunit of the 26 proteasome, which is involved in the ATP-dependent degradation of ubiquitinated proteins. The function of this domain is unclear, but it is found in the N terminus of the proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. A number of the proteins associated with this family belong to MEROPS peptidase family M67 (clan M-). This includes the Poh1 peptidase of Saccharomyces cerevisiae (Baker's yeast) which is a component of the 19S proteasome regulatory particle.; GO: 0005515 protein binding; PDB: 2ZNV_D 2ZNR_A 4E0Q_A 2P87_A 2P8R_A 2O96_B 2O95_A 3RZU_F 3RZV_A.
Probab=99.82 E-value=3.3e-20 Score=158.02 Aligned_cols=106 Identities=26% Similarity=0.448 Sum_probs=86.6
Q ss_pred CeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeeCCC-EEEEEEEEecCCCCCCCceecCChHHH---HHHHh--hCC
Q 013388 267 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNR-KFYITALIIPKQESTSDSCQATNEEEI---FEVQD--KRS 340 (444)
Q Consensus 267 ~r~V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~-~l~VT~lf~ppqegtsds~~a~deee~---fe~q~--~rg 340 (444)
.+.|.|.+.++.+|++||.+.. +.|+||+|+|..+++ .++|+++|+++...+...+.+.+.... ++... ...
T Consensus 3 ~~~V~i~p~vll~i~~h~~r~~--~~~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (114)
T PF01398_consen 3 VQTVQIHPLVLLKIIDHATRSS--PNEVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVNPN 80 (114)
T ss_dssp CEEEEEEHHHHHHHHHHHHHHH--CTEEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCSTT
T ss_pred cEEEEECHHHHHHHHHHHhcCC--CCEEEEEEEEEecCceEEEEEEEEEeeEecCccccccchhhHHHHHHhhhcccccc
Confidence 6889999999999999999854 779999999999988 999999999998877776665554322 22222 245
Q ss_pred CccEEEEeCCCCCCCCCCHHHHHhHHHHhhhCCC
Q 013388 341 LFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPE 374 (444)
Q Consensus 341 LeiVGWYHSHP~~~afPSstDL~tQ~sYQ~~lPe 374 (444)
+.+||||||||..+||||..|+++|..||++.|+
T Consensus 81 ~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 81 LEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp SEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred ceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence 9999999999999999999999999999999874
No 14
>cd08072 MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme. This family contains only archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.74 E-value=2.4e-17 Score=143.80 Aligned_cols=109 Identities=20% Similarity=0.209 Sum_probs=87.6
Q ss_pred ECHHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHHHHHHHhhCCCccEEEEeCCC
Q 013388 272 ISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHP 351 (444)
Q Consensus 272 Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee~fe~q~~rgLeiVGWYHSHP 351 (444)
|++.+++.|++||++.+ |+|+||||+|+.+ .|++++++++...++..+..+. .+...|++++|.|||||
T Consensus 1 i~~~~~~~i~~ha~~~~--P~E~CGlL~G~~~----~v~~~~~~~n~~~~~~~~~f~~-----~~~~~g~~ivgi~HSHP 69 (117)
T cd08072 1 ISRDLLDSILEAAKSSH--PNEFAALLRGKDG----VITELLILPGTESGEVSAVFPL-----LMLPLDMSIVGSVHSHP 69 (117)
T ss_pred CCHHHHHHHHHHHhhcC--CceEEEEEEeecc----EEEEEEECCCCCCCCcceeech-----HHhcCCCeEEEEEEcCC
Confidence 57889999999999955 9999999999765 6888998887544333222221 25678999999999999
Q ss_pred CCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCCCCceeEEEecC
Q 013388 352 TQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLTS 396 (444)
Q Consensus 352 ~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~~~LrAFRLtd 396 (444)
+.+++||..|+.. +..++++++|+++......++||++..
T Consensus 70 ~~~~~PS~~D~~~-----~~~~~~~~lIvs~~~~~~~~~a~~~~g 109 (117)
T cd08072 70 SGSPRPSDADLSF-----FSKTGLVHIIVGYPYDEDDWRAYDSDG 109 (117)
T ss_pred CCCCCCCHHHHHh-----hhcCCCEEEEEECcCCCCCEEEEecCC
Confidence 9999999999863 356899999999766556799999875
No 15
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=99.73 E-value=8.2e-18 Score=165.56 Aligned_cols=143 Identities=19% Similarity=0.351 Sum_probs=113.6
Q ss_pred CeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCC--CCCcee--cCChH---HHHHHHh--
Q 013388 267 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQES--TSDSCQ--ATNEE---EIFEVQD-- 337 (444)
Q Consensus 267 ~r~V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqeg--tsds~~--a~dee---e~fe~q~-- 337 (444)
.+.|.|+..++++|++||++...+..-+.|+|+|...+++++||.|||.|+.- ..+.+. ..+++ +..+++.
T Consensus 12 vk~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~Glvvd~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~mlrrl 91 (339)
T KOG1560|consen 12 VKRVELDSLVVMKIIKHCREEFPNGDGTQGVLLGLVVDGRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLAMLRRL 91 (339)
T ss_pred cceeeehhHHHHHHHHHHHhhcCCcchhhheeeeeeecceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHHHHHHh
Confidence 78999999999999999999763323466999999999999999999987631 122211 12222 1122221
Q ss_pred ---hCCCccEEEEeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCCCCc---eeEEEecCCCCchhhhhcccCCC
Q 013388 338 ---KRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRK---HGIFRLTSPGGMSVIRQCQQRGF 411 (444)
Q Consensus 338 ---~rgLeiVGWYHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~~~---LrAFRLtdP~Gm~~ik~C~~~gF 411 (444)
+.+-..||||.||.. ++|+|..-+++|+.||++.|+.|++|+||.+++.+ +|||||++ +.| ..|+++.|
T Consensus 92 r~vnid~~hVGwYqs~~v-gs~lS~~lveSqy~YQ~a~pesVvliYD~~kssqG~L~lrAyrLTp-~am---~~~kekdw 166 (339)
T KOG1560|consen 92 RYVNIDHLHVGWYQSAYV-GSFLSPALVESQYAYQKAIPESVVLIYDPIKSSQGTLSLRAYRLTP-EAM---AAHKEKDW 166 (339)
T ss_pred hhcCccceeeeeeeeehh-ccccCHHHHHHHHHHHhcCCccEEEEeccccccCceEEeehhhcCH-HHH---HHHhcCCC
Confidence 456689999999987 79999888999999999999999999999999874 89999996 676 66999999
Q ss_pred cCC
Q 013388 412 HPH 414 (444)
Q Consensus 412 hPh 414 (444)
.|+
T Consensus 167 tpe 169 (339)
T KOG1560|consen 167 TPE 169 (339)
T ss_pred CHH
Confidence 986
No 16
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.71 E-value=8.7e-18 Score=168.19 Aligned_cols=141 Identities=23% Similarity=0.374 Sum_probs=110.6
Q ss_pred CCCCCCCCeEEEECHHHHHHHHHHHhccCCCCcc-eEEEe-ee---eeC-CCEEEEEEEEecCCCCCCCc--eecCChHH
Q 013388 260 DAFDRSEPLQLHISTTMMDNFMKLAKSNTDKNLE-TCGIL-AG---SLK-NRKFYITALIIPKQESTSDS--CQATNEEE 331 (444)
Q Consensus 260 ~~~~~~~~r~V~Is~~aL~kILkHA~snt~~P~E-vCGLL-lG---~~~-~~~l~VT~lf~ppqegtsds--~~a~deee 331 (444)
|.+.-.+.++++|...++.++++|++. +.+.| ++|+| +| .+. ..+..|.++|..++.++..+ .++.++.-
T Consensus 23 d~~~~~~~e~v~i~slall~m~rh~r~--~~p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg~~is~~~e~~d~V~ 100 (316)
T KOG1555|consen 23 DEPHSDEKETVYISSLALLKMLRHDRA--GSPEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAVDPVF 100 (316)
T ss_pred ccccccCcceeeeehhhhhhccccccc--CCchhhccceeecccccceeeecceeeeeeeccccccceecccchhccHHH
Confidence 344444578999999999999999999 55999 99999 89 333 46778888999999988887 44455422
Q ss_pred ---HHHH--HhhCCCccEEEEeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCCCC---ceeEEEecCCCCchh
Q 013388 332 ---IFEV--QDKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR---KHGIFRLTSPGGMSV 402 (444)
Q Consensus 332 ---~fe~--q~~rgLeiVGWYHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~~---~LrAFRLtdP~Gm~~ 402 (444)
.++. ++++.+.+||||||||+++|+||..|+.+|++||++.+.+++.+++|..+.. -+.||++.++..+..
T Consensus 101 q~q~~~~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~g~vv~d~f~~In~~~~~~ 179 (316)
T KOG1555|consen 101 QTQMMDLLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPYGKVVPDAFSSINPQWISP 179 (316)
T ss_pred HHHHHHHHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCCCCccCChhhhcCcccccC
Confidence 1222 4577789999999999999999999999999999998888888877766543 378999888654433
No 17
>cd08073 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains. This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.67 E-value=4.9e-16 Score=134.10 Aligned_cols=102 Identities=18% Similarity=0.194 Sum_probs=81.8
Q ss_pred HHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCC-ceecCChHHHHHHHhhCCCccEEEEeCCCCCC
Q 013388 276 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSD-SCQATNEEEIFEVQDKRSLFPLGWIHTHPTQS 354 (444)
Q Consensus 276 aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsd-s~~a~deee~fe~q~~rgLeiVGWYHSHP~~~ 354 (444)
+++.|++||++.+ |.|+||||+|+.. ++.+++.+|...+. ..+.+|+++++++++. + .+||.|||||+.+
T Consensus 2 i~~~i~~ha~~~~--P~E~CGll~g~~~-----~~~~~p~~N~~~~p~~~F~idp~e~~~a~~~-~-~ivgi~HSHP~~~ 72 (108)
T cd08073 2 LEDAILAHAKAEY--PREACGLVVRKGR-----KLRYIPCRNIAADPEEHFEISPEDYAAAEDE-G-EIVAVVHSHPDGS 72 (108)
T ss_pred HHHHHHHHHhHCC--CCcceEEEEecCC-----ceEEEECccCCCCccceEEeCHHHHHHHhcC-C-CEEEEEEcCCCCC
Confidence 6789999999955 9999999999762 56678888764433 5677899998887643 3 8999999999999
Q ss_pred CCCCHHHHHhHHHHhhhCCCeEEEEEccCCCCCceeEEE
Q 013388 355 CFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFR 393 (444)
Q Consensus 355 afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~~~LrAFR 393 (444)
++||..|+.. +..++..+||++...+ .+++|+
T Consensus 73 a~PS~~D~~~-----~~~~~~~~iIvs~~~~--~~~~~~ 104 (108)
T cd08073 73 PAPSEADRAQ-----QEATGLPWIIVSWPEG--DLRVFR 104 (108)
T ss_pred CCCCHHHHHH-----hhcCCCcEEEEEcCCC--CEEEEe
Confidence 9999999862 3568999999998644 366765
No 18
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=99.58 E-value=1.5e-14 Score=127.71 Aligned_cols=103 Identities=22% Similarity=0.346 Sum_probs=72.6
Q ss_pred EEECHHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCC-CceecCChHHH--HHHHhhCCCccEEE
Q 013388 270 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTS-DSCQATNEEEI--FEVQDKRSLFPLGW 346 (444)
Q Consensus 270 V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegts-ds~~a~deee~--fe~q~~rgLeiVGW 346 (444)
+.|+++++..|+.||+..+ |.|+||+|+|...+ ...+..++...+ ...++++++.. ...+...|+.+|||
T Consensus 2 ~~i~~~~l~~il~~a~~~~--p~E~~g~l~~~~~~-----~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~g~~vvg~ 74 (134)
T COG1310 2 LVIPKEVLGAILEHARREH--PREVCGLLAGTREG-----ERYFPLKNVSVEPVEYFEIDPEYSLFYLAAEDAGEVVVGW 74 (134)
T ss_pred ceecHHHHHHHHHHHHhcC--ChheEEEEEeeccc-----ceeeccccccCCcceeEeeCHHHHHHHHHHhhCCCEEEEE
Confidence 5789999999999999965 99999999999765 334444444333 22334444322 22356788999999
Q ss_pred EeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccC
Q 013388 347 IHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQ 383 (444)
Q Consensus 347 YHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~ 383 (444)
|||||+.+|+||..|+. +++..+-.+.||+.+.
T Consensus 75 yHSHP~~~~~pS~~D~~----~~~~~~~~~~iv~~~~ 107 (134)
T COG1310 75 YHSHPGGPPYPSEADRR----LSKLGPLPWLIVSVPP 107 (134)
T ss_pred EcCCCCCCCCcCHHHHh----hccccCCCEEEEEcCC
Confidence 99999999999999997 3444444344444443
No 19
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=99.54 E-value=1.8e-13 Score=123.96 Aligned_cols=126 Identities=13% Similarity=0.180 Sum_probs=96.6
Q ss_pred EEECHHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHHH---HHH--HhhCCCccE
Q 013388 270 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEI---FEV--QDKRSLFPL 344 (444)
Q Consensus 270 V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee~---fe~--q~~rgLeiV 344 (444)
|.|.+.++.+|++|+.+....+.+++|+|+|...++.+.|+++|++|...+.+.. ..+.+.+ ++. +-..+..+|
T Consensus 1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~~~~~~veV~nsF~lp~~~~~~~~-~~d~~y~~~m~~~~~~v~~~~~vV 79 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGDKIEVTNSFELPFDEEEESI-FIDTEYLEKRYNLHKKVYPQEKIV 79 (157)
T ss_pred CEEccHHHhhHHHHHHhccCCCCeEEEEEEeEEeCCEEEEEEeEEccccCCCcch-hhhHHHHHHHHHHHHHhCCCCCEE
Confidence 4688899999999998743337899999999999999999999999986555432 2332222 222 125778999
Q ss_pred EEEeCCCCCCCCCCHHHHHhHHHHhhh-CCCeEEEEEccCC----CCCceeEEEecC
Q 013388 345 GWIHTHPTQSCFMSSIDVHTHYSYQIM-LPESVAIVMAPQD----ATRKHGIFRLTS 396 (444)
Q Consensus 345 GWYHSHP~~~afPSstDL~tQ~sYQ~~-lPeaVaLIiSP~~----s~~~LrAFRLtd 396 (444)
||||+|+...+.++..|...|..|... .+..|+|++||.. +.-.++||++..
T Consensus 80 GWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~ 136 (157)
T cd08057 80 GWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQ 136 (157)
T ss_pred EEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEec
Confidence 999999998777888887666666554 6788999999965 223699999996
No 20
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=99.52 E-value=4.2e-14 Score=117.90 Aligned_cols=98 Identities=21% Similarity=0.409 Sum_probs=69.6
Q ss_pred HHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHHHHH----HHhhCCCccEEEEeC
Q 013388 274 TTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFE----VQDKRSLFPLGWIHT 349 (444)
Q Consensus 274 ~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee~fe----~q~~rgLeiVGWYHS 349 (444)
+.++.+|++||+.+. |.|+||+|+|......+.|+..+. .++.+.+. .+...++.+||+|||
T Consensus 2 ~~~~~~i~~~~~~~~--p~E~~G~L~g~~~~~~~~~~~~~~------------~~p~~~~~~~~~~~~~~~~~~vg~~HS 67 (104)
T PF14464_consen 2 EEVLEQIIAHARAAY--PNEACGLLLGRRDDQRFIVVPNVN------------PDPRDSFRRERFEARERGLEIVGIWHS 67 (104)
T ss_dssp -HHHHHHHHHHHHHT--TS-EEEEEEEEEECCEEEEEEEEE--------------HHCHHHHHH-HHHHHT-EEEEEEEE
T ss_pred HHHHHHHHHHHhhCC--CCeEEEEEEEEecCCEEEEEeCCC------------CCcHHHHHHHhhhhhcccceeeEEEEc
Confidence 468999999999965 999999999998666666666543 23333333 356899999999999
Q ss_pred CCCCCCCCCHHHHHhHHHHhhhCC-CeEEEEEccCCCCCceeEEEe
Q 013388 350 HPTQSCFMSSIDVHTHYSYQIMLP-ESVAIVMAPQDATRKHGIFRL 394 (444)
Q Consensus 350 HP~~~afPSstDL~tQ~sYQ~~lP-eaVaLIiSP~~s~~~LrAFRL 394 (444)
||...++||.+|+.+. ... ..++||++. .. .. +||+
T Consensus 68 HP~~~a~pS~~D~~~~-----~~~~~~~~iI~~~-~~--~~-~W~~ 104 (104)
T PF14464_consen 68 HPSGPAFPSSTDIRSM-----RDLAPPSYIIVGN-PE--DR-AWRL 104 (104)
T ss_dssp ESSSSSS--HHHHHTH-----CCS-SCEEEEEEE-CE--SC-CEEE
T ss_pred CCCCCCCCCHHHHHhh-----hccCCeEEEEEeC-CC--CC-eEEC
Confidence 9999999999999753 222 789999987 21 23 7765
No 21
>cd08062 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8. This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural.
Probab=99.36 E-value=1.2e-11 Score=122.86 Aligned_cols=127 Identities=11% Similarity=0.162 Sum_probs=97.1
Q ss_pred EEEECHHHHHHHHHHHhccC-CCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCce--ecCChHH---HHHH--HhhCC
Q 013388 269 QLHISTTMMDNFMKLAKSNT-DKNLETCGILAGSLKNRKFYITALIIPKQESTSDSC--QATNEEE---IFEV--QDKRS 340 (444)
Q Consensus 269 ~V~Is~~aL~kILkHA~snt-~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~--~a~deee---~fe~--q~~rg 340 (444)
.|.|.+.++.+|++|+.+.. +.+.+++|.|+|...++.++|+++|++|...+.+.. .+.|.+. .++. .-..+
T Consensus 2 ~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~~~~~~veItnsF~~p~~~~~~~~~~~~~d~~y~~~m~~~~kkv~~~ 81 (280)
T cd08062 2 KVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWKKGVLDVTNSFAVPFEEDEKDPSVWFLDHNYLENMYGMFKKVNAK 81 (280)
T ss_pred eEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEEEeCCEEEEEEeeecCccCCCCCcchhhhhHHHHHHHHHHHHHhCCC
Confidence 58899999999999987633 226789999999999999999999999886544432 2233222 2222 12677
Q ss_pred CccEEEEeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCCCC--ceeEEEecCCCCc
Q 013388 341 LFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR--KHGIFRLTSPGGM 400 (444)
Q Consensus 341 LeiVGWYHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~~--~LrAFRLtdP~Gm 400 (444)
..+||||||||. ++..|+..|..|+...+..|+|+++|..... .+++|.-.. ++.
T Consensus 82 e~vVGWY~tg~~----~~~~d~~ih~~~~~~~~~pv~l~vd~~~~~~~lpi~aY~s~~-~~~ 138 (280)
T cd08062 82 EKIVGWYSTGPK----LRPNDLDINELFRRYCPNPVLVIIDVRPKDLGLPTEAYIAVE-EVH 138 (280)
T ss_pred CCeEEEecCCCC----CCcchHHHHHHHHHhCCCCEEEEEecCCCCCCCceEEEEEee-ecc
Confidence 899999999997 5677888888899988999999999987433 589998875 444
No 22
>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f. Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and ap
Probab=99.35 E-value=1.5e-11 Score=120.64 Aligned_cols=127 Identities=13% Similarity=0.181 Sum_probs=94.1
Q ss_pred EEECHHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHH---HHHHH--hhCCCccE
Q 013388 270 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEE---IFEVQ--DKRSLFPL 344 (444)
Q Consensus 270 V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee---~fe~q--~~rgLeiV 344 (444)
|.|.+.++.+|++|+.+....+..++|.|+|...++.++|+++|++|...+.+.++ .|.+. .++.. -..+..+|
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~~~-~d~~y~~~m~~~~kkv~~~~~vV 79 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNESEDQVA-VDMEYHRTMYELHQKVNPKEVIV 79 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCCEEEEEeCeecceeCCCCeEE-EcHHHHHHHHHHHHHhCCCCcEE
Confidence 46888999999999977434578899999999999999999999998866555443 33222 22221 26788999
Q ss_pred EEEeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCCCC--ceeEEEecCCCCc
Q 013388 345 GWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR--KHGIFRLTSPGGM 400 (444)
Q Consensus 345 GWYHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~~--~LrAFRLtdP~Gm 400 (444)
|||||++. .-.+...++.++.++...+..|.|++|+..+.. .++||++.+ .|+
T Consensus 80 GWY~tg~~--~~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~~~~l~i~ay~~~~-~~~ 134 (265)
T cd08064 80 GWYATGSE--ITEHSALIHDYYSRECTSYNPIHLTVDTSLDDGKMSIKAYVSSP-LGV 134 (265)
T ss_pred eeeeCCCC--CCccHHHHHHHHHhhCCCCCCEEEEEeCCCCCCCcceEEEEEEe-ccc
Confidence 99999984 223455677776666554588999999976543 689999986 453
No 23
>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic. This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=99.29 E-value=2.6e-11 Score=101.87 Aligned_cols=101 Identities=20% Similarity=0.237 Sum_probs=74.6
Q ss_pred HHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHHHHHHHhhCCCccEEEEeCCCCCC
Q 013388 275 TMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQS 354 (444)
Q Consensus 275 ~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee~fe~q~~rgLeiVGWYHSHP~~~ 354 (444)
++++.|+.|++..+ |.|+||+|+|..++ .|..+...++.. ...++.. +..+...+..+||.|||||+..
T Consensus 1 ~~~~~i~~~~~~~~--p~E~~gll~~~~~~---~~~~~~~~~~~~-----~~~~~~~-~~~a~~~~~~~v~i~HsHP~g~ 69 (101)
T cd08059 1 DLLKTILVHAKDAH--PDEFCGFLSGSKDN---VMDELIFLPFVS-----GSVSAVI-DLAALEIGMKVVGLVHSHPSGS 69 (101)
T ss_pred CHHHHHHHHHHhcC--ChhhheeeecCCCC---eEEEEEeCCCcC-----CccChHH-HHHHhhCCCcEEEEEecCcCCC
Confidence 36788999999855 99999999997654 455666555522 1123322 5567788999999999999999
Q ss_pred CCCCHHHHHhHHHHhhhCCCeEEEEEccCCCCCceeEE
Q 013388 355 CFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIF 392 (444)
Q Consensus 355 afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~~~LrAF 392 (444)
+.||..|+... ..+...+||++... ...++||
T Consensus 70 ~~PS~~D~~~~-----~~~~~~~iIv~~~~-~~~~~~~ 101 (101)
T cd08059 70 CRPSEADLSLF-----TRFGLYHVIVCYPY-ENSWKCY 101 (101)
T ss_pred CCCCHHHHHHH-----HhcCCeEEEEECCC-cccEEEC
Confidence 99999999742 23588899998665 3457776
No 24
>TIGR03735 PRTRC_A PRTRC system protein A. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.
Probab=99.25 E-value=4.5e-11 Score=113.42 Aligned_cols=111 Identities=16% Similarity=0.141 Sum_probs=83.1
Q ss_pred EECHHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHHHHHHHhhCCCccEEEEeCC
Q 013388 271 HISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTH 350 (444)
Q Consensus 271 ~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee~fe~q~~rgLeiVGWYHSH 350 (444)
.|++.++.+|+.||++.. |+|+||+++|...++ +..++++.|...+...+.+++. +..+|+.+|+.||||
T Consensus 74 ~Ip~~l~~~ii~hAr~~~--P~EacG~Iag~~~~~---~~r~~p~~N~~~Sp~~~~~d~~-----~~~~ge~lV~iyHSH 143 (192)
T TIGR03735 74 PIPASLLEEFAEAARAAL--PNEVAAWIVWNSETG---SLRLAALESIEASPGHIDYRRP-----RLDDGEHLVVDLHSH 143 (192)
T ss_pred CCCHHHHHHHHHHHHhcC--CcceEEEEEEcCCCC---EEEEEeccccccCCceEEEcch-----HHhCCCeEEEEEcCC
Confidence 699999999999999955 999999999964433 3466888887666666666654 358999999999999
Q ss_pred CCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCCCCceeEEEecC
Q 013388 351 PTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATRKHGIFRLTS 396 (444)
Q Consensus 351 P~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~~~LrAFRLtd 396 (444)
|..++|||.+|+.-- .-.--++.|+.-.+....-=+|||.-
T Consensus 144 ~~spA~PS~tD~~Dd-----~~~~k~~~ViG~~~~~~p~~~~Rl~~ 184 (192)
T TIGR03735 144 GTGSAFFSETDDADD-----KGEVKISGVLGCLDQGTPQAVFRLCL 184 (192)
T ss_pred CCCCCCCCcccchhh-----cCceEEEEEEEecCCCCceEEEEEEe
Confidence 999999999998531 11134666666555543456677764
No 25
>cd08060 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p). This family includes Noc4p (neighbor of COX4; neighbor of Cytochrome c Oxidase 4; nucleolar complex associated 4 homolog) which belongs to the family of unknown function, UPF0172, with MPN/JAMM-like domains. Proteins in this family are homologs of the NOC4 gene which is conserved in eukaryotic members including human, dog, mouse, rat, chicken, zebrafish, fruit fly, mosquito, S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa, A.thaliana, and rice. NOC4 highly expressed in the pancreas and moderately in liver, heart, lung, kidney, brain, skeletal muscle, and placenta. This nucleolar protein forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=99.21 E-value=1.6e-10 Score=108.64 Aligned_cols=107 Identities=13% Similarity=0.112 Sum_probs=80.2
Q ss_pred ECHHHHHHHHHHHhccCCCCcceEEEeeeeeC-CCEEEEEEEEecCCCCCCCceecCChHH---HHHH---HhhCCCccE
Q 013388 272 ISTTMMDNFMKLAKSNTDKNLETCGILAGSLK-NRKFYITALIIPKQESTSDSCQATNEEE---IFEV---QDKRSLFPL 344 (444)
Q Consensus 272 Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~-~~~l~VT~lf~ppqegtsds~~a~deee---~fe~---q~~rgLeiV 344 (444)
|+..++.+|+.||.... +.||||+|+|+.. +....|++++|+.+. ++..+|.. ++++ ...+|+.+|
T Consensus 1 is~~ay~ki~~HA~k~p--~~evcGlLlG~~~~~~~~~V~d~vPl~h~-----~~~l~P~~Eval~~ve~~~~~~gl~Iv 73 (182)
T cd08060 1 LSTLAYVKMLLHAAKYP--HCAVNGLLLGKKSSGGSVEITDAVPLFHS-----CLALAPMLEVALALVDAYCKSSGLVIV 73 (182)
T ss_pred CCHHHHHHHHHHHHHcC--CchheEEEEeeecCCCCEEEEEEEEcCCC-----ccccCHHHHHHHHHHHHHHHHCCCEEE
Confidence 57889999999999944 7899999999987 677899999998773 34566653 3333 457999999
Q ss_pred EEEeCCCCCC-CCCCHHHHHhHHHHhhhCCCeEEEEEccCCC
Q 013388 345 GWIHTHPTQS-CFMSSIDVHTHYSYQIMLPESVAIVMAPQDA 385 (444)
Q Consensus 345 GWYHSHP~~~-afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s 385 (444)
|+|||||... ..|+..=..-.-..+..++.++.++++-..-
T Consensus 74 G~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~l 115 (182)
T cd08060 74 GYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEKL 115 (182)
T ss_pred EEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCccc
Confidence 9999999763 3455554333344455678999999886554
No 26
>cd08061 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain. Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=98.95 E-value=1.3e-08 Score=101.49 Aligned_cols=133 Identities=19% Similarity=0.353 Sum_probs=103.4
Q ss_pred EEEECH-HHHHHHHHHHhccCCCCcceEEEeeeeeCCC-------EEEEEEEEecCCCCCCCceecCCh---HHHHHHHh
Q 013388 269 QLHIST-TMMDNFMKLAKSNTDKNLETCGILAGSLKNR-------KFYITALIIPKQESTSDSCQATNE---EEIFEVQD 337 (444)
Q Consensus 269 ~V~Is~-~aL~kILkHA~snt~~P~EvCGLLlG~~~~~-------~l~VT~lf~ppqegtsds~~a~de---ee~fe~q~ 337 (444)
.|.+.. .+++.|+..+...+ ....||+|.|+.... ...|.+++.|||.++.+.+..... ...-+++.
T Consensus 12 ~vef~~~~~~~~f~~~~w~~~--~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~iA~ 89 (274)
T cd08061 12 HVEFDNPSIVEFFLYVFWRKT--GQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAIAA 89 (274)
T ss_pred EEEEecHHHHHHHHHHHHHhh--cceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhHHHHHHH
Confidence 355444 45555665466655 689999999998643 678888899999999988876643 22334567
Q ss_pred hCCCccEEEEeCCCCC----CCCCCHHHHHhHHHHhh------hCCCeEEEEEccCCCC-CceeEEEecCCCCchhhh
Q 013388 338 KRSLFPLGWIHTHPTQ----SCFMSSIDVHTHYSYQI------MLPESVAIVMAPQDAT-RKHGIFRLTSPGGMSVIR 404 (444)
Q Consensus 338 ~rgLeiVGWYHSHP~~----~afPSstDL~tQ~sYQ~------~lPeaVaLIiSP~~s~-~~LrAFRLtdP~Gm~~ik 404 (444)
..||+.|||++||+.. +.++|+.++.+.+.||. .-..+|.+|+++..+. ..+.||++++ .+|...+
T Consensus 90 ~lGL~~VG~IfT~l~~~~~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~~g~i~~~ayQvSd-q~~~lv~ 166 (274)
T cd08061 90 ALGLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDKDGQIHFEAYQVSD-QAMALVR 166 (274)
T ss_pred HcCCeEEEEEEecCCCCCCCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCCCCceeeeeeeecH-HHHHHHH
Confidence 8999999999999976 78999999999999996 4568999999997554 3799999998 5776654
No 27
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=98.89 E-value=3.2e-08 Score=99.79 Aligned_cols=126 Identities=13% Similarity=0.196 Sum_probs=91.4
Q ss_pred CeEEEECHHHHHHHHHHHhccCCC-CcceEEEeeeeeCCCEEEEEEEEecCCCCCCCc--eecCChH---HHHHH--Hhh
Q 013388 267 PLQLHISTTMMDNFMKLAKSNTDK-NLETCGILAGSLKNRKFYITALIIPKQESTSDS--CQATNEE---EIFEV--QDK 338 (444)
Q Consensus 267 ~r~V~Is~~aL~kILkHA~snt~~-P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds--~~a~dee---e~fe~--q~~ 338 (444)
...|.|.+.++.+|++|+.+.... ..-+.|.|+|...++.++|+++|++|.....+. ....|.+ ++++. .-.
T Consensus 5 ~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~~~~~~ieItnsF~~p~~e~~~~~~~~~~D~~y~~~m~~~~k~V~ 84 (303)
T PLN03246 5 IEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFRGRVDVTNSFAVPFEEDDKDPSIWFLDHNYLESMFGMFKRIN 84 (303)
T ss_pred CcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEeeecCCEEEEEeccccCcccCCCCccceeecHHHHHHHHHHHHHhC
Confidence 567999999999999999884311 233999999999989999999999886433221 1123322 22222 125
Q ss_pred CCCccEEEEeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCCC--CceeEEEecC
Q 013388 339 RSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDAT--RKHGIFRLTS 396 (444)
Q Consensus 339 rgLeiVGWYHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~--~~LrAFRLtd 396 (444)
.+..+||||+|-|. ++..|+.-|..|....+..|.|++++.... -.+++|....
T Consensus 85 ~~~~vVGWY~tg~~----i~~~d~~IH~~~~~~~~~Pv~L~vD~~~~~~~lpi~aY~s~~ 140 (303)
T PLN03246 85 AKEHVVGWYSTGPK----LRENDLDIHELFNDYVPNPVLVIIDVQPKELGIPTKAYYAVE 140 (303)
T ss_pred CCCcEEeeecCCCC----CCcchHHHHHHHHhhCCCCeEEEEecCCCCCCCceEEEEEEE
Confidence 77899999999765 556677777788888888999999976533 3589998764
No 28
>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family. This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize.
Probab=98.88 E-value=2.2e-08 Score=90.15 Aligned_cols=106 Identities=18% Similarity=0.141 Sum_probs=68.5
Q ss_pred HHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCC--CCCCceecCCh--HHHHH-HHh--hCCCccEEEEe
Q 013388 276 MMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQE--STSDSCQATNE--EEIFE-VQD--KRSLFPLGWIH 348 (444)
Q Consensus 276 aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqe--gtsds~~a~de--ee~fe-~q~--~rgLeiVGWYH 348 (444)
++..|.++.+.. ..+.|+||+|+|...+..+.|+.+..|... .+...+..... .+.+. +.. ...+..||-||
T Consensus 2 v~~~~~~~~Q~~-~~~~EtGGiLiG~~~~~~~ii~~~t~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylGeWH 80 (131)
T TIGR02256 2 VVAMLKSYRQWH-DLSTETGGVLIGERRGAHAVITKISEPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGEWH 80 (131)
T ss_pred HHHHHHHHHhCc-CCCCccceEEEEEEcCCcEEEEEEEcCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEEecC
Confidence 345555555543 468899999999988778888887755432 22333332222 12222 222 23489999999
Q ss_pred CCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEcc
Q 013388 349 THPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAP 382 (444)
Q Consensus 349 SHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP 382 (444)
|||...+.||.+|+.+....-......+.||+.-
T Consensus 81 tHP~~~p~PS~~D~~~~~~~~~~~~~~l~iIvG~ 114 (131)
T TIGR02256 81 THPEDQPEPSWTDRRSWRTIIRSPEAMLLLIVGR 114 (131)
T ss_pred cCCCCCCCCCHHHHHHHHHHHhCCCeeEEEEEcC
Confidence 9999999999999988765544333455565553
No 29
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=98.87 E-value=2.5e-08 Score=99.21 Aligned_cols=128 Identities=16% Similarity=0.184 Sum_probs=89.7
Q ss_pred EEEECHHHHHHHHHHHhccCCC----CcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHH---HHHH--HhhC
Q 013388 269 QLHISTTMMDNFMKLAKSNTDK----NLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEE---IFEV--QDKR 339 (444)
Q Consensus 269 ~V~Is~~aL~kILkHA~snt~~----P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee---~fe~--q~~r 339 (444)
.|.|-+.++.+|++|+.+.... +.-++|.|+|..+++.++|+++|++|...+++.....|.+. .++. .-..
T Consensus 2 ~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~id~~y~~~m~~~~kkV~~ 81 (288)
T cd08063 2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGREIEIENSFELKYDTNEDGEIVLDKEFLETRLEQFKQVFK 81 (288)
T ss_pred eEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEcCCEEEEEEEEecccccCCCCceeeCHHHHHHHHHHHHHhcc
Confidence 4778889999999999873211 46789999999988999999999988754431122234322 2222 1257
Q ss_pred CCccEEEEeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCC--C--CceeEEEecCCCCc
Q 013388 340 SLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDA--T--RKHGIFRLTSPGGM 400 (444)
Q Consensus 340 gLeiVGWYHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s--~--~~LrAFRLtdP~Gm 400 (444)
++.+||||++.+. + +...|+.-|..|....+..|+|+++|... . -.++||+-.. .+.
T Consensus 82 ~~~vVGWY~tg~~-~--~~~~~~~Ih~~~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~-~~~ 142 (288)
T cd08063 82 DLDFVGWYTTGPG-G--PTESDLPIHKQILEINESPVLLLLDPEANASGKDLPVTIYESVL-ELV 142 (288)
T ss_pred CCceEEEEecCCC-C--CCHHHHHHHHHHHhhCCCcEEEEEccccccCCCCCceeEEEEEE-ecc
Confidence 7899999999887 3 44555555555566677789999999773 2 2589998775 444
No 30
>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=98.26 E-value=1.6e-06 Score=99.02 Aligned_cols=150 Identities=18% Similarity=0.244 Sum_probs=119.4
Q ss_pred eEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeeC---CCEEEEEEEEecCCCCCCCceecCChHHHHHHHhhCCCccE
Q 013388 268 LQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK---NRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPL 344 (444)
Q Consensus 268 r~V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~---~~~l~VT~lf~ppqegtsds~~a~deee~fe~q~~rgLeiV 344 (444)
.+..||.+++.+|+..++. ...+.|++.|... ..+.+|.++..+||-++-..+....--. .+..-.+++.+
T Consensus 2095 ~tyilPkNllkkFi~isD~----r~qiag~~yG~s~~d~pqvkeIr~ivmvPQ~gs~~~v~lp~~lP--~~~~l~d~e~L 2168 (2321)
T KOG1795|consen 2095 YTYILPKNLLKKFITISDL----RTQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGSHQGVHLPSFLP--IHGVLEDLEPL 2168 (2321)
T ss_pred ceeeccHHHHhhheeecch----hhhhheeeeccCCCCCCccceEEEEEeccccccccccccCccCC--cchhccCCccc
Confidence 4568999999999999876 6699999999753 3577898888899977655443321101 23456789999
Q ss_pred EEEeCCCCCCCCCCHHHHHhHHHHhhhC-CCeEEEEEccCCCCCceeEEEecCCCCchhhhhcccCCCcCCCCCCCCCCC
Q 013388 345 GWIHTHPTQSCFMSSIDVHTHYSYQIML-PESVAIVMAPQDATRKHGIFRLTSPGGMSVIRQCQQRGFHPHDPPPDGGPI 423 (444)
Q Consensus 345 GWYHSHP~~~afPSstDL~tQ~sYQ~~l-PeaVaLIiSP~~s~~~LrAFRLtdP~Gm~~ik~C~~~gFhPh~~~~~g~~i 423 (444)
||+||.|.--.++|+.|+.+|...-... ..+|.|-|+.+.++.++.||.|++ .|.+|+..-...|=.|++.- +.-
T Consensus 2169 gw~hTq~~el~~lsp~dV~th~ki~~~~k~k~i~~t~~~tpgs~sl~ay~lt~-~G~eWg~~n~d~g~~~~gy~---pt~ 2244 (2321)
T KOG1795|consen 2169 GWIHTQPNELPQLSPQDVTTHAKILVDNKEKCIIITCSFTPGSCSLTAYKLTP-SGYEWGEVNKDKGNNPKGYL---PTH 2244 (2321)
T ss_pred chhhcCccccccCCHHHhhhhhhhhhcCccceEEEEeeccCCcceeeeeccCc-cccccchhcccccCCccccC---ccH
Confidence 9999999999999999999998655443 479999999999988999999997 89999998888777777663 567
Q ss_pred cccc
Q 013388 424 YKPC 427 (444)
Q Consensus 424 y~~~ 427 (444)
|++|
T Consensus 2245 ~e~~ 2248 (2321)
T KOG1795|consen 2245 YEKV 2248 (2321)
T ss_pred HHHH
Confidence 7777
No 31
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=98.24 E-value=1.1e-05 Score=79.61 Aligned_cols=117 Identities=16% Similarity=0.228 Sum_probs=83.3
Q ss_pred CeEEEECHHHHHHHHHHHhccC-CCCcceEEEeeeeeCCCEEEEEEEEecCCCCCC--CceecCCh---HHHHHHHh--h
Q 013388 267 PLQLHISTTMMDNFMKLAKSNT-DKNLETCGILAGSLKNRKFYITALIIPKQESTS--DSCQATNE---EEIFEVQD--K 338 (444)
Q Consensus 267 ~r~V~Is~~aL~kILkHA~snt-~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegts--ds~~a~de---ee~fe~q~--~ 338 (444)
...|.+-+.+++..+.|-.+-. ....-+.|+|+|..++.++.|++.|++|-+... .++-+.|- +.+|.+.. .
T Consensus 8 ~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~~~~~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~mfkKvN 87 (309)
T KOG1556|consen 8 VEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGSWNGDVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGMFKKVN 87 (309)
T ss_pred cceeeeehhHHHHHHHHHhhhccCcCceEEEEEEecCCCCeEEeecceeccccccCCCCceEEeccHHHHHHHHHHHHhc
Confidence 5678888899999999986622 223668999999999899999999998875322 22323332 23344433 5
Q ss_pred CCCccEEEEeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCCCC
Q 013388 339 RSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDATR 387 (444)
Q Consensus 339 rgLeiVGWYHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~~ 387 (444)
....+||||||-|. +-..||.-...+..+.|..+.+|++.....-
T Consensus 88 akekivGWYhTGPk----l~~nDl~In~l~k~y~pnpvLvIIdvkpk~~ 132 (309)
T KOG1556|consen 88 AKEKVVGWYHTGPK----LRENDLDINELLKRYVPNPVLVIIDVKPKEL 132 (309)
T ss_pred chhheeeeeccCCc----cccchhhHHHHHhhcCCCceEEEEecccccC
Confidence 67789999999665 4445555555566788999999999877654
No 32
>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=98.21 E-value=1.1e-05 Score=81.89 Aligned_cols=109 Identities=24% Similarity=0.383 Sum_probs=85.8
Q ss_pred EEEeeeeeCC-C------EEEEEEEEecCCCCCCCceecCCh--HH-HHHHHhhCCCccEEEEeCCCC------------
Q 013388 295 CGILAGSLKN-R------KFYITALIIPKQESTSDSCQATNE--EE-IFEVQDKRSLFPLGWIHTHPT------------ 352 (444)
Q Consensus 295 CGLLlG~~~~-~------~l~VT~lf~ppqegtsds~~a~de--ee-~fe~q~~rgLeiVGWYHSHP~------------ 352 (444)
+|+|.|..+. . ...|..++.|||+++.+.+...+. ++ .=+++..-||+.|||+=||+.
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~lGL~rVG~IfTdl~~~~~~~g~v~~~ 81 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASALGLERVGWIFTDLTDDGSGDGTVKCK 81 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHHCCCEEEEEEEecCcccccCCCceeec
Confidence 7999999863 2 467888889999998888766432 12 223467889999999999997
Q ss_pred ---CCCCCCHHHHHhHHHHhhhCC-------------CeEEEEEccCCCCC-ceeEEEecCCCCchhhh
Q 013388 353 ---QSCFMSSIDVHTHYSYQIMLP-------------ESVAIVMAPQDATR-KHGIFRLTSPGGMSVIR 404 (444)
Q Consensus 353 ---~~afPSstDL~tQ~sYQ~~lP-------------eaVaLIiSP~~s~~-~LrAFRLtdP~Gm~~ik 404 (444)
.+.|+|+..+...+.||...| .+|.+|+++..+.. .+.||++++ .+|...+
T Consensus 82 r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~~~g~i~~~ayQvS~-q~~~Lv~ 149 (306)
T PF05021_consen 82 RHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGDEEGEIHFEAYQVSN-QCVALVR 149 (306)
T ss_pred cccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCCCCCceeeEEeeehH-HHHHHHH
Confidence 788999999999999998653 48999999866543 699999998 6776544
No 33
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=97.63 E-value=0.00065 Score=64.98 Aligned_cols=113 Identities=11% Similarity=0.091 Sum_probs=74.2
Q ss_pred EEEECHHHHHHHHHHHhccCCCCcceEEEeeeeeCCC--EEEEEEEEecCCCCCCCceecCChHH---HHHHHhhCCCcc
Q 013388 269 QLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNR--KFYITALIIPKQESTSDSCQATNEEE---IFEVQDKRSLFP 343 (444)
Q Consensus 269 ~V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~--~l~VT~lf~ppqegtsds~~a~deee---~fe~q~~rgLei 343 (444)
.|.|+..++.||+-||-..- -.-|+|+|+|+..++ .+.|++++|+==.... ...+-+.. +-.+....|+.+
T Consensus 3 ~v~is~~AY~K~~LHaaKyP--~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~~--L~PmlEvAL~qvd~~~~~~gl~I 78 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAKYP--HCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWLS--LSPMLEVALAQVDAYAKSNGLVI 78 (196)
T ss_pred eEEEcHHHHHHHHHHhccCC--CCceeeEEEeccCCCCceEEEeeceeccccccC--cchHHHHHHHHHHHHHhhCCCEE
Confidence 58899999999999998732 456899999998753 3999999987221110 00011111 111245789999
Q ss_pred EEEEeCCCCC-CCCCCHHHHHhHHHHhhhCCCeEEEEEccCCC
Q 013388 344 LGWIHTHPTQ-SCFMSSIDVHTHYSYQIMLPESVAIVMAPQDA 385 (444)
Q Consensus 344 VGWYHSHP~~-~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s 385 (444)
||+||..-.. ..-|+..=..-.......++.++.|+++-.+=
T Consensus 79 vGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~kl 121 (196)
T PF03665_consen 79 VGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKKL 121 (196)
T ss_pred EEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECccc
Confidence 9999987632 34466664333333444679999999986543
No 34
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=97.31 E-value=0.00032 Score=80.51 Aligned_cols=139 Identities=17% Similarity=0.298 Sum_probs=98.9
Q ss_pred CeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeeC---CCEEEEEEEEecCCCCCCCceecCC--hHHHHHHHhhCCC
Q 013388 267 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLK---NRKFYITALIIPKQESTSDSCQATN--EEEIFEVQDKRSL 341 (444)
Q Consensus 267 ~r~V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~---~~~l~VT~lf~ppqegtsds~~a~d--eee~fe~q~~rgL 341 (444)
.++..||.+++++|+...+- ...+.|++.|+.. .....|.++..+||-++-..+.... +.. .-...|+
T Consensus 2133 q~~y~lP~NLl~kF~~isD~----~vqvag~vyG~s~~d~p~ikeI~~~~lVPQlgs~~~vq~~s~vP~d---lp~~e~l 2205 (2365)
T COG5178 2133 QQMYRLPLNLLEKFMRISDP----HVQVAGLVYGKSGSDNPQIKEILSFGLVPQLGSLSGVQSSSFVPHD---LPGDEDL 2205 (2365)
T ss_pred hccccccHHHHHhhheeccc----ceeeEEEEeccCCccCcchhheeEEEeeccccccccccccccCCCC---CCCcccc
Confidence 45677999999999999876 6799999999764 2556777777788865433332111 100 1124689
Q ss_pred ccEEEEeCCCCCCCCCCHHHHHhHHHHhhhCC--CeEEEEEccCCCCCceeEEEecCCCCchhhhhcc------cCCCcC
Q 013388 342 FPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLP--ESVAIVMAPQDATRKHGIFRLTSPGGMSVIRQCQ------QRGFHP 413 (444)
Q Consensus 342 eiVGWYHSHP~~~afPSstDL~tQ~sYQ~~lP--eaVaLIiSP~~s~~~LrAFRLtdP~Gm~~ik~C~------~~gFhP 413 (444)
++|||+|+.-..-+|++..++.+|. +-...| .+|.|-++-..+.-+++||.+++ +|.+|+..-. .-||||
T Consensus 2206 e~lGwihtq~~el~~l~~~~v~th~-k~~~d~~~d~v~ltv~~~pgsiSl~ay~v~k-eG~~Wg~~n~di~~~~a~g~ep 2283 (2365)
T COG5178 2206 EILGWIHTQDDELPYLEVAGVLTHR-KKIVDPEWDAVTLTVSYLPGSISLRAYVVKK-EGCNWGSKNMDINSDEAIGVEP 2283 (2365)
T ss_pred eeeEEEecCCcccchhhhhhhhhhh-hcccCccccceeeeeeeccceeeeeeeeehh-cccccccccccccccccccccc
Confidence 9999999999999999999999885 333455 45666666555555799999998 8999974332 237876
Q ss_pred C
Q 013388 414 H 414 (444)
Q Consensus 414 h 414 (444)
-
T Consensus 2284 ~ 2284 (2365)
T COG5178 2284 V 2284 (2365)
T ss_pred c
Confidence 4
No 35
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=97.29 E-value=0.0018 Score=64.78 Aligned_cols=129 Identities=14% Similarity=0.229 Sum_probs=89.2
Q ss_pred CeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCCh--HHHHHHHh--hCCCc
Q 013388 267 PLQLHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNE--EEIFEVQD--KRSLF 342 (444)
Q Consensus 267 ~r~V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~de--ee~fe~q~--~rgLe 342 (444)
...|+|-+.++..|+.+-.+..++..-++|-|+|..+++.++|++||.+|-..+++.++...+ .+.++.-. .-...
T Consensus 20 ~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g~ieitNCFaVPhnEssdqvevdm~y~~~M~~l~~k~npnE~ 99 (288)
T KOG2975|consen 20 NLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKGSVEVTNCFAVPHNESSDQVEVDMEYAKNMYELHKKVNPNEL 99 (288)
T ss_pred CceEEEcceEEeEeehhhhcCCccchhhhhheeecccCCeEEEEEeeeccCccccccceeeHHHHHHHHHHhcccCCCce
Confidence 577888888888888888776666777999999999999999999998775444455442211 12222222 45678
Q ss_pred cEEEEeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEEEEccCCCC--CceeEEEecCCCCc
Q 013388 343 PLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAIVMAPQDAT--RKHGIFRLTSPGGM 400 (444)
Q Consensus 343 iVGWYHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~s~--~~LrAFRLtdP~Gm 400 (444)
+||||-|-++-..+-|. + |--|-.-.++.|-|-+|-.-.. -.+|||--+. -|+
T Consensus 100 vvGWyaTg~dvt~~ssl--i--hdyYare~~~pvhLtVDT~~~n~rm~ikaYvss~-~Gv 154 (288)
T KOG2975|consen 100 VVGWYATGHDVTEHSSL--I--HDYYAREAPNPVHLTVDTSLQNGRMSIKAYVSSL-MGV 154 (288)
T ss_pred eEEEEecCCCcccchhH--H--HHHhhccCCCCeEEEEeccccCCccceeEEEEec-cCC
Confidence 99999987775554433 2 3345555678888888765442 2589997775 455
No 36
>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=96.12 E-value=0.037 Score=59.23 Aligned_cols=128 Identities=18% Similarity=0.340 Sum_probs=95.4
Q ss_pred CHHHHHHHHHHHhccCCCCcceEEEeeeeeCC-CEE------EEEEEEecCCCCCCCceecCCh--HHHHH-HHhhCCCc
Q 013388 273 STTMMDNFMKLAKSNTDKNLETCGILAGSLKN-RKF------YITALIIPKQESTSDSCQATNE--EEIFE-VQDKRSLF 342 (444)
Q Consensus 273 s~~aL~kILkHA~snt~~P~EvCGLLlG~~~~-~~l------~VT~lf~ppqegtsds~~a~de--ee~fe-~q~~rgLe 342 (444)
...+++.|+..-+.. .....|+|.|...+ +.+ .|..++-|||.+..+....++. +..++ ...+-||.
T Consensus 181 ~~~~v~~Fl~~wr~s---g~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~~~~dgl~l~~~~e~~~vD~~a~~lGLr 257 (510)
T KOG2834|consen 181 NAELVNHFLNEWRAS---GVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQHGEEDGLELLEDDEAKRVDAIAEGLGLR 257 (510)
T ss_pred chHHHHHHHHHHHHh---hhhhcceEEEeecccccccccceeeEEEEecCCccCCcCCeEEeccchhhhHHHHHHhcCce
Confidence 468999999998862 67889999999863 333 7788889999999888776532 22233 35689999
Q ss_pred cEEEEeCCC---------------CCCCCCCHHHHHhHHHHhhhCCC-------------eEEEEEccCCCC-CceeEEE
Q 013388 343 PLGWIHTHP---------------TQSCFMSSIDVHTHYSYQIMLPE-------------SVAIVMAPQDAT-RKHGIFR 393 (444)
Q Consensus 343 iVGWYHSHP---------------~~~afPSstDL~tQ~sYQ~~lPe-------------aVaLIiSP~~s~-~~LrAFR 393 (444)
-||||-+-- .-+.|+|+.++.+.+.+|.+.|. +|-+|++-..+. -.+-.|+
T Consensus 258 RVG~IFTDl~~~~s~egtV~~~rhkdsyFLSseE~~~aa~~Q~~hpn~~~~s~~~~fgSkfVT~visg~~~~~V~f~~YQ 337 (510)
T KOG2834|consen 258 RVGWIFTDLVTADSAEGTVHYKRHKDSYFLSSEECITAAMFQNKHPNICEWSRDGHFGSKFVTLVISGDLDGEVHFEGYQ 337 (510)
T ss_pred eeEEEEeeeecccCccceEEeeeccchhcccHHHHHHHhhhhhcCCchheeeccccccceeEEEEEecCCCcceeeeeee
Confidence 999997642 13689999999999999987663 566777654443 2689999
Q ss_pred ecCCCCchhhh
Q 013388 394 LTSPGGMSVIR 404 (444)
Q Consensus 394 LtdP~Gm~~ik 404 (444)
.++ ..|...+
T Consensus 338 VSn-qc~alv~ 347 (510)
T KOG2834|consen 338 VSN-QCMALVE 347 (510)
T ss_pred hhH-HHHHHhh
Confidence 998 6877533
No 37
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=94.79 E-value=0.49 Score=45.50 Aligned_cols=109 Identities=12% Similarity=0.123 Sum_probs=70.9
Q ss_pred EEEECHHHHHHHHHHHhccCCCCcc-eEEEeeeeeC--CCEEEEEEEEecCCCCCCCceecCChHHHHHH-----HhhCC
Q 013388 269 QLHISTTMMDNFMKLAKSNTDKNLE-TCGILAGSLK--NRKFYITALIIPKQESTSDSCQATNEEEIFEV-----QDKRS 340 (444)
Q Consensus 269 ~V~Is~~aL~kILkHA~snt~~P~E-vCGLLlG~~~--~~~l~VT~lf~ppqegtsds~~a~deee~fe~-----q~~rg 340 (444)
.+.|+..++.+|+-||... |.- +-|+|+|... ++.+.|++++|+--.. .....+.|+.-+ -...|
T Consensus 3 ~veis~~aY~kmiLH~aky---ph~aVnGLLla~~~~kg~~v~itdcVPLfH~~----laLaPmlEvAl~lId~~~~~~G 75 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKY---PHAAVNGLLLAPATGKGECVEITDCVPLFHSH----LALAPMLEVALNLIDVWGAQAG 75 (199)
T ss_pred ceeehhhHHHHHHHHhccC---cccceeeEEEeccCCCCCeEEEEecchhhccc----cccccHHHHHHHHHHHHHHhcC
Confidence 4789999999999999862 444 6799999554 5789999999873321 111223332111 23789
Q ss_pred CccEEEEeCCCCCC-CCCCHHHHHhHHHHhhhCCCeEEEEEccCC
Q 013388 341 LFPLGWIHTHPTQS-CFMSSIDVHTHYSYQIMLPESVAIVMAPQD 384 (444)
Q Consensus 341 LeiVGWYHSHP~~~-afPSstDL~tQ~sYQ~~lPeaVaLIiSP~~ 384 (444)
+.++|+||+--.+. ..|-..=....-..+..+|.+..|+.+-+.
T Consensus 76 lviaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~~ 120 (199)
T KOG3289|consen 76 LVIAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNKK 120 (199)
T ss_pred eEEEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEeccc
Confidence 99999999864321 223333222233345578999888888654
No 38
>cd08071 MPN_DUF2466 Mov34/MPN/PAD-1 family. Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. However, to date, the name RadC has been misleading and no function has been determined.
Probab=93.51 E-value=1.2 Score=38.93 Aligned_cols=73 Identities=21% Similarity=0.191 Sum_probs=50.2
Q ss_pred CcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHHHHHHHhhCCCccEEEEeCCCCCCCCCCHHHHHhHHHH
Q 013388 291 NLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSY 368 (444)
Q Consensus 291 P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee~fe~q~~rgLeiVGWYHSHP~~~afPSstDL~tQ~sY 368 (444)
+.|.+.+|.=...++.+....++ .|+-+.+ ..++.++|+.....+..-+...|.||++.+.||..|++.-...
T Consensus 15 ~~E~~~vl~Ld~~~~li~~~~l~----~G~~~~~-~v~~R~i~~~aL~~~A~~vil~HNHPsG~~~PS~~D~~~T~~l 87 (113)
T cd08071 15 DQEEFVVLLLDTKNRLIAVETIS----VGTLNSS-LVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIELTKRL 87 (113)
T ss_pred CceEEEEEEecCCCCEEEEEEEe----ecCCcce-ecCHHHHHHHHHHHhhheEEEEeeCCCCCCCCCHHHHHHHHHH
Confidence 67777766643333444333332 2333333 3567888888888888899999999999999999999764443
No 39
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=90.81 E-value=0.8 Score=46.07 Aligned_cols=92 Identities=20% Similarity=0.297 Sum_probs=60.0
Q ss_pred CCCc-ceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHHHHHH-----HhhCCCccEEEEeCCCCCCCCCCHHHH
Q 013388 289 DKNL-ETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEV-----QDKRSLFPLGWIHTHPTQSCFMSSIDV 362 (444)
Q Consensus 289 ~~P~-EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee~fe~-----q~~rgLeiVGWYHSHP~~~afPSstDL 362 (444)
+.|. .+.|-|+|+..++.++|.+.|.+.-....+. ...+-+.+.+- +-=.++.++|||-+ +.-|...|+
T Consensus 33 gpp~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~~~-~~~dke~l~kk~eqykqVFpdl~vlGwYtt----G~d~t~sd~ 107 (299)
T KOG3050|consen 33 GPPVKQVYGALIGKQRGRNVEIMNSFELKMDTEEDT-ETIDKEYLEKKEEQYKQVFPDLYVLGWYTT----GSDPTPSDI 107 (299)
T ss_pred CCcHHHhhhhheecccCceEEEeeeeEEEecchhhh-hhccHHHHHHHHHHHHHhcccceEEEEeec----CCCCChhhh
Confidence 4466 7899999999999999999997754322111 12232221111 12478899999987 344677888
Q ss_pred HhHHHHhhhCCCeEEEEEccCCC
Q 013388 363 HTHYSYQIMLPESVAIVMAPQDA 385 (444)
Q Consensus 363 ~tQ~sYQ~~lPeaVaLIiSP~~s 385 (444)
+.|...-.....-++|-..|...
T Consensus 108 ~i~k~l~~i~esplflkLNp~t~ 130 (299)
T KOG3050|consen 108 HIHKQLMDINESPLFLKLNPATN 130 (299)
T ss_pred HHHHHHHhhhcCceEEEecchhc
Confidence 88776555566667777776443
No 40
>PF04002 RadC: RadC-like JAB domain; InterPro: IPR001405 This family was named initially with reference to the Escherichia coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions []. However the relevant mutation has subsequently been shown to be in recG, not radC []. In addition all attempts to characterise a radiation-related function for RadC in Streptococcus pneumoniae failed, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair [].; PDB: 2QLC_A.
Probab=89.56 E-value=2.9 Score=36.98 Aligned_cols=75 Identities=23% Similarity=0.168 Sum_probs=42.3
Q ss_pred CcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHHHHHHHhhCCCccEEEEeCCCCCCCCCCHHHHHhHHHHhh
Q 013388 291 NLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQI 370 (444)
Q Consensus 291 P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee~fe~q~~rgLeiVGWYHSHP~~~afPSstDL~tQ~sYQ~ 370 (444)
+.|.+-+++=...++.+.+..++ .|+.+.+ ..++.++|+.....+..-|-..|=||++.+.||..|+..-...+.
T Consensus 20 ~~E~~~~l~Ld~~~~li~~~~v~----~G~~~~~-~v~~R~I~~~al~~~A~~vIl~HNHPsG~~~PS~~D~~~T~~L~~ 94 (123)
T PF04002_consen 20 DQEQFRVLYLDSKNRLIGDEVVS----EGTIDSA-PVDPREIFRRALRLNASSVILAHNHPSGDPEPSDADIALTRRLKK 94 (123)
T ss_dssp TS-EEEEEEE-TTSBEEEEEEEE----ESTT-GG-GCSHHHHHHHHHHTT-SEEEEEEE-TTS--S--HHHHHHHHHHHH
T ss_pred CCeEEEEEEECCCCcEEEEEEec----ccCCCcc-cccHHHHHHHHHhhCCceEEEEEEcCCCCCCCCHhHHHHHHHHHH
Confidence 56766655533333444443333 2444444 356888888877777788888999999999999999965444333
No 41
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=82.94 E-value=15 Score=36.07 Aligned_cols=88 Identities=22% Similarity=0.153 Sum_probs=55.7
Q ss_pred CHHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHHHHHHHhhCCCccEEEEeCCCC
Q 013388 273 STTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPT 352 (444)
Q Consensus 273 s~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee~fe~q~~rgLeiVGWYHSHP~ 352 (444)
+...+..+++..-. ..+.|.+.+|+=...++.+....++ .|+-+.+ ..++.++|...-..+..-|=.-|=||+
T Consensus 99 s~~~v~~~l~~~l~--~~~~E~f~vl~Ld~~n~li~~~~i~----~Gt~~~~-~v~pReI~~~Al~~~A~~vIlaHNHPS 171 (218)
T TIGR00608 99 SPEAAAEFLHTDLA--HETREHFMVLFLDRKNRLIAKEVVF----IGTVNHV-PVHPREIFKEALKLSASALILAHNHPS 171 (218)
T ss_pred CHHHHHHHHHHHhc--CCCceEEEEEEECCCCcEEEEEEee----cCCCCeE-EEcHHHHHHHHHHhhCCeEEEEeecCC
Confidence 44455555555544 3367776665522223333333332 3554544 367889998877777777778899999
Q ss_pred CCCCCCHHHHHhHHH
Q 013388 353 QSCFMSSIDVHTHYS 367 (444)
Q Consensus 353 ~~afPSstDL~tQ~s 367 (444)
+.+.||..|+..=..
T Consensus 172 G~~~PS~~Di~~T~~ 186 (218)
T TIGR00608 172 GEPSPSQEDILITER 186 (218)
T ss_pred CCCCCCHHHHHHHHH
Confidence 999999999865433
No 42
>PRK00024 hypothetical protein; Reviewed
Probab=82.56 E-value=17 Score=35.59 Aligned_cols=90 Identities=21% Similarity=0.148 Sum_probs=57.5
Q ss_pred CHHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHHHHHHHhhCCCccEEEEeCCCC
Q 013388 273 STTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPT 352 (444)
Q Consensus 273 s~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee~fe~q~~rgLeiVGWYHSHP~ 352 (444)
+...+.++++..-. ..+.|.+.+|+=...++.+....++ .|+-+.+ ..++.++|...-..+..-|-.-|=||+
T Consensus 105 ~~~~~~~~l~~~l~--~~~~E~f~vl~Ld~~~~li~~~~i~----~Gt~~~~-~v~pRei~~~Al~~~A~~iIl~HNHPS 177 (224)
T PRK00024 105 SPEDVADYLMAELR--DEEQEHFVVLFLDTKNRVIADEELF----IGTLNSS-IVHPREIVKRALKLNAAALILAHNHPS 177 (224)
T ss_pred CHHHHHHHHHHHcc--CCCceEEEEEEECCCCCEeeEEEee----eecCCeE-EEcHHHHHHHHHHhhccceEEEecCCC
Confidence 44445555544444 2367877766643333444333332 2444444 366889998877777777888899999
Q ss_pred CCCCCCHHHHHhHHHHh
Q 013388 353 QSCFMSSIDVHTHYSYQ 369 (444)
Q Consensus 353 ~~afPSstDL~tQ~sYQ 369 (444)
+.+.||..|+..-...+
T Consensus 178 G~~~PS~~D~~~T~~l~ 194 (224)
T PRK00024 178 GDPEPSQADILITKRLK 194 (224)
T ss_pred CCCCCCHHHHHHHHHHH
Confidence 99999999986544333
No 43
>PF14220 DUF4329: Domain of unknown function (DUF4329)
Probab=80.58 E-value=9.3 Score=34.50 Aligned_cols=66 Identities=21% Similarity=0.346 Sum_probs=40.9
Q ss_pred CCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHHHHHHHhhCCCccEEEEeCCCC-----CCCCCCHHHHH
Q 013388 289 DKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHTHPT-----QSCFMSSIDVH 363 (444)
Q Consensus 289 ~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee~fe~q~~rgLeiVGWYHSHP~-----~~afPSstDL~ 363 (444)
..+.|.||+++ +..++.+.-+. +..+..+.|..... ....+...|+-||||.. .+..||..|+.
T Consensus 18 ~~nrEy~G~I~-~~~~G~y~~t~----p~~G~~~~~~~~~~------~~p~g~~~vA~yHTHG~~~~~y~~evfS~~D~~ 86 (123)
T PF14220_consen 18 RENREYCGYIG-KDEDGKYFATE----PRRGENASCYPSNP------PCPNGSTIVASYHTHGAYSDGYDNEVFSPQDIR 86 (123)
T ss_pred cCCcEEEEEEE-EcCCCcEEeec----CccCCCCCcCCCCc------ccccccceeeEeecccccCCCccccCCCHHHhh
Confidence 35899999865 44344433221 23344444443221 22457899999999986 35679999997
Q ss_pred hH
Q 013388 364 TH 365 (444)
Q Consensus 364 tQ 365 (444)
.-
T Consensus 87 ~~ 88 (123)
T PF14220_consen 87 GD 88 (123)
T ss_pred hh
Confidence 64
No 44
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=78.42 E-value=3.9 Score=43.89 Aligned_cols=128 Identities=22% Similarity=0.338 Sum_probs=88.9
Q ss_pred CHHHHHHHHHHHhccCCCCcceEEEeeeeeCC------C-EEEEEEEEecCCCCCCCceecCC--hHHHHHH-HhhCCCc
Q 013388 273 STTMMDNFMKLAKSNTDKNLETCGILAGSLKN------R-KFYITALIIPKQESTSDSCQATN--EEEIFEV-QDKRSLF 342 (444)
Q Consensus 273 s~~aL~kILkHA~snt~~P~EvCGLLlG~~~~------~-~l~VT~lf~ppqegtsds~~a~d--eee~fe~-q~~rgLe 342 (444)
.+.+++.|++.=+. ......|+|.|...+ + .-.|.+++.|||++..+.+-+.. .+..++. +..-||+
T Consensus 240 ~~~iv~~Fi~~WR~---sG~QRfGy~yG~y~~y~n~PLGiKaVveaIyEPpQ~de~DG~t~ee~~de~l~d~~a~~~GL~ 316 (571)
T COG5100 240 GKHIVENFIRNWRE---SGRQRFGYLYGRYMDYENIPLGIKAVVEAIYEPPQEDEPDGFTIEEWADEGLMDAPASGTGLE 316 (571)
T ss_pred CchHHHHHHHHHHH---hhhhhheeeeeehhhccCCcchhHHHhhhhcCCccccCCCceEeeeecccccccccccccCce
Confidence 45789999988875 367889999998753 1 12455667789986666553311 1111221 3477889
Q ss_pred cEEEEeCCCC---------------CCCCCCHHHHHhHHHHhhhCC-------------CeEEEEEccCCCC-CceeEEE
Q 013388 343 PLGWIHTHPT---------------QSCFMSSIDVHTHYSYQIMLP-------------ESVAIVMAPQDAT-RKHGIFR 393 (444)
Q Consensus 343 iVGWYHSHP~---------------~~afPSstDL~tQ~sYQ~~lP-------------eaVaLIiSP~~s~-~~LrAFR 393 (444)
.+|.+-|--. -+-|+|+..+...+.+|.+.| .++.+|++-.-.. -++..|+
T Consensus 317 riG~IfTDl~d~gs~~GsV~ckrh~dsyFLSSLEv~~~A~~Qt~hpn~~k~sr~g~FgSkfvT~Visgnl~GeI~~~sYQ 396 (571)
T COG5100 317 RIGMIFTDLLDEGSNRGSVTCKRHADSYFLSSLEVEFIAKMQTMHPNTVKDSREGEFGSKFVTIVISGNLDGEIGLQSYQ 396 (571)
T ss_pred eeeeeeeehhhccCCCCceeeeccccceehhhhhhHHHhhhhhcCCCcccccccccccceeEEEEEecccCceeeeeEEe
Confidence 9998876421 256899999999999998876 3678888765544 4799999
Q ss_pred ecCCCCchhhh
Q 013388 394 LTSPGGMSVIR 404 (444)
Q Consensus 394 LtdP~Gm~~ik 404 (444)
.++ .+|...+
T Consensus 397 VSn-~~~ALv~ 406 (571)
T COG5100 397 VSN-QCMALVK 406 (571)
T ss_pred ehh-hhhHHhh
Confidence 998 6876654
No 45
>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=64.62 E-value=2.7 Score=38.26 Aligned_cols=33 Identities=18% Similarity=0.245 Sum_probs=27.2
Q ss_pred eEEEEEccCCCCCceeEEEecCCCCchhhhhccc
Q 013388 375 SVAIVMAPQDATRKHGIFRLTSPGGMSVIRQCQQ 408 (444)
Q Consensus 375 aVaLIiSP~~s~~~LrAFRLtdP~Gm~~ik~C~~ 408 (444)
+|.|.|+.+.++..|.||+|++ +|.+|+++-++
T Consensus 1 ~i~it~sftpGSvsL~Ay~LT~-~G~eWg~~nkD 33 (125)
T PF08084_consen 1 TITITCSFTPGSVSLSAYKLTP-EGYEWGRQNKD 33 (125)
T ss_dssp -EEEEEEEETTEEEEEEEEE-H-HHHHHHHCTTT
T ss_pred CEEEEEeccCCceEEEEEecCH-HHHHHHhhccc
Confidence 4788999988888999999997 89999996655
No 46
>PF15659 Toxin-JAB1: JAB-like toxin 1
Probab=55.90 E-value=52 Score=31.27 Aligned_cols=40 Identities=20% Similarity=0.207 Sum_probs=27.2
Q ss_pred hhCCCccEEEEeCCCCCCCCCCHHHHHhHHHHhhhCCCeEEE
Q 013388 337 DKRSLFPLGWIHTHPTQSCFMSSIDVHTHYSYQIMLPESVAI 378 (444)
Q Consensus 337 ~~rgLeiVGWYHSHP~~~afPSstDL~tQ~sYQ~~lPeaVaL 378 (444)
...+-.++. +||||..+.+||..|..+..... -.|.++|+
T Consensus 112 ~~~~~~iid-iHSHP~~~~~~S~~D~~~~~~~~-~i~~a~y~ 151 (162)
T PF15659_consen 112 KNNGNKIID-IHSHPENSNGPSGNDMKNAKPRK-NIPYAIYS 151 (162)
T ss_pred ccCCceEEE-eccCCCCCCCCCcchhhhhhhcc-cccceeeE
Confidence 346667777 99999988899999986543221 23445544
No 47
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=41.14 E-value=1.4e+02 Score=31.16 Aligned_cols=57 Identities=26% Similarity=0.319 Sum_probs=36.0
Q ss_pred EEeeeee-CCCEEEEEEEEecCCCCCCCc----------eecCChHHHHHH------HhhCCCccEEEEeCCCC
Q 013388 296 GILAGSL-KNRKFYITALIIPKQESTSDS----------CQATNEEEIFEV------QDKRSLFPLGWIHTHPT 352 (444)
Q Consensus 296 GLLlG~~-~~~~l~VT~lf~ppqegtsds----------~~a~deee~fe~------q~~rgLeiVGWYHSHP~ 352 (444)
|||+|+. ..+.-+|.++++.|...+... ....|++.+.++ |-..|+.+||.|=.+|.
T Consensus 1 GLlIGq~~s~~kd~Vv~l~~tP~~d~~~~~~~~~~~~~~~~~id~~WVaeHA~qVsRMLPGGi~VlGifvv~~~ 74 (362)
T PF14778_consen 1 GLLIGQSSSSQKDYVVHLARTPPEDTDDEESDVRTSDSSIKDIDEEWVAEHARQVSRMLPGGISVLGIFVVAPD 74 (362)
T ss_pred CeEeccccCCCcceEEEecCCCCccccccccccccccccccccCHHHHHHHHHHHHhhCCCCcEEEEEEEEcCH
Confidence 8999998 555557777776554322211 223444444444 34799999999987754
No 48
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=23.20 E-value=76 Score=31.70 Aligned_cols=90 Identities=19% Similarity=0.179 Sum_probs=51.0
Q ss_pred EEECHHHHHHHHHHHhccCCCCcceEEEeeeeeCCCEEEEEEEEecCCCCCCCceecCChHHHHHHHhhCCCccEEEEeC
Q 013388 270 LHISTTMMDNFMKLAKSNTDKNLETCGILAGSLKNRKFYITALIIPKQESTSDSCQATNEEEIFEVQDKRSLFPLGWIHT 349 (444)
Q Consensus 270 V~Is~~aL~kILkHA~snt~~P~EvCGLLlG~~~~~~l~VT~lf~ppqegtsds~~a~deee~fe~q~~rgLeiVGWYHS 349 (444)
+.-+...+.++++....+. ..|.--+|+=...++.+....+|. ||-+. ....|.|++...-..+..-|=..|=
T Consensus 102 ~i~sp~~~~~~l~~~l~~~--~~E~f~vL~Ld~qnrlI~~e~lf~----GTi~~-s~V~PREI~k~Al~~nAaavIlaHN 174 (224)
T COG2003 102 VITSPEAVAEYLRAELGGE--EREHFVVLYLDSQNRLIATETLFI----GTLNV-SEVHPREIFKEALKYNAAAVILAHN 174 (224)
T ss_pred ccCCHHHHHHHHHHHhhhh--HHHHHHHHHhcCcCceecceeEEe----eeccc-ceecHHHHHHHHHHhcchhhheecc
Confidence 3345556666665444422 444433332112223333333432 22222 2345788888776666666667899
Q ss_pred CCCCCCCCCHHHHHhHH
Q 013388 350 HPTQSCFMSSIDVHTHY 366 (444)
Q Consensus 350 HP~~~afPSstDL~tQ~ 366 (444)
||++.+-||..|+.-..
T Consensus 175 HPSGd~~PS~aD~~iT~ 191 (224)
T COG2003 175 HPSGDPTPSRADILITE 191 (224)
T ss_pred CCCCCCCcCHHHHHHHH
Confidence 99999999999986443
Done!