Query 017219
Match_columns 375
No_of_seqs 175 out of 748
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 06:39:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017219.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017219hhsearch_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 9.6E-56 2.1E-60 433.1 14.4 301 39-375 122-424 (424)
2 cd08066 MPN_AMSH_like Mov34/MP 100.0 1.2E-44 2.6E-49 328.4 21.5 173 198-375 1-173 (173)
3 cd08058 MPN_euk_mb Mpr1p, Pad1 99.9 1.8E-27 3.9E-32 201.9 12.0 111 206-326 1-119 (119)
4 cd08069 MPN_RPN11_CSN5 Mov34/M 99.9 1.9E-26 4.1E-31 222.0 17.3 137 193-332 4-150 (268)
5 cd08068 MPN_BRCC36 Mov34/MPN/P 99.9 2.3E-26 5E-31 219.2 15.6 127 199-327 2-151 (244)
6 cd08067 MPN_2A_DUB Mov34/MPN/P 99.9 1.3E-25 2.8E-30 206.5 17.1 126 199-328 5-147 (187)
7 smart00232 JAB_MPN JAB/MPN dom 99.9 1.5E-21 3.2E-26 164.7 16.2 125 201-327 2-134 (135)
8 cd08056 MPN_PRP8 Mpr1p, Pad1p 99.9 3.1E-22 6.7E-27 191.6 12.8 136 199-341 36-179 (252)
9 cd07767 MPN Mpr1p, Pad1p N-ter 99.9 6.1E-22 1.3E-26 163.7 12.3 107 208-316 1-107 (116)
10 KOG1554 COP9 signalosome, subu 99.9 4.4E-22 9.6E-27 192.0 11.1 134 194-330 48-192 (347)
11 cd08065 MPN_eIF3h Mpr1p, Pad1p 99.9 1.1E-21 2.4E-26 188.4 13.5 138 200-344 2-149 (266)
12 cd08070 MPN_like Mpr1p, Pad1p 99.9 2.9E-21 6.2E-26 165.7 13.7 115 206-327 2-120 (128)
13 PF01398 JAB: JAB1/Mov34/MPN/P 99.8 1.3E-20 2.8E-25 157.6 9.7 107 197-305 2-114 (114)
14 KOG1560 Translation initiation 99.8 1.1E-20 2.4E-25 181.9 8.6 142 197-345 11-169 (339)
15 cd08072 MPN_archaeal Mov34/MPN 99.8 2.3E-18 4.9E-23 147.3 13.3 109 203-327 1-109 (117)
16 cd08073 MPN_NLPC_P60 Mpr1p, Pa 99.7 2E-17 4.3E-22 139.9 11.7 102 207-324 2-104 (108)
17 KOG1555 26S proteasome regulat 99.7 1.1E-17 2.3E-22 164.2 7.1 136 191-328 23-174 (316)
18 COG1310 Predicted metal-depend 99.6 5.7E-15 1.2E-19 127.8 11.5 113 201-327 2-117 (134)
19 cd08057 MPN_euk_non_mb Mpr1p, 99.6 4.9E-14 1.1E-18 125.1 15.3 127 201-328 1-137 (157)
20 PF14464 Prok-JAB: Prokaryotic 99.6 8.3E-15 1.8E-19 119.8 8.8 98 205-325 2-104 (104)
21 TIGR03735 PRTRC_A PRTRC system 99.4 1.1E-12 2.4E-17 121.7 11.4 111 202-327 74-184 (192)
22 cd08062 MPN_RPN7_8 Mpr1p, Pad1 99.4 4.8E-12 1E-16 123.2 15.0 124 200-327 2-135 (280)
23 cd08064 MPN_eIF3f Mpr1p, Pad1p 99.4 5.4E-12 1.2E-16 121.4 14.4 127 201-331 1-134 (265)
24 cd08059 MPN_prok_mb Mpr1p, Pad 99.4 4E-12 8.7E-17 104.7 10.5 101 206-323 1-101 (101)
25 cd08060 MPN_UPF0172 Mov34/MPN/ 99.3 3.2E-11 6.8E-16 111.0 14.3 107 203-316 1-115 (182)
26 PLN03246 26S proteasome regula 99.1 3.3E-09 7E-14 104.7 14.8 128 196-327 3-140 (303)
27 cd08061 MPN_NPL4 Mov34/MPN/PAD 99.0 3.8E-09 8.3E-14 103.0 12.7 132 201-335 13-166 (274)
28 cd08063 MPN_CSN6 Mpr1p, Pad1p 99.0 4.1E-09 8.8E-14 102.8 12.9 125 200-327 2-139 (288)
29 TIGR02256 ICE_VC0181 integrati 98.9 1.6E-08 3.4E-13 89.1 11.7 105 207-312 2-113 (131)
30 KOG1795 U5 snRNP spliceosome s 98.6 8.8E-08 1.9E-12 106.8 7.2 150 199-358 2095-2248(2321)
31 KOG1556 26S proteasome regulat 98.4 2.8E-06 6.1E-11 82.0 11.9 125 197-325 7-141 (309)
32 PF05021 NPL4: NPL4 family; I 98.2 7.4E-06 1.6E-10 81.3 10.2 109 226-335 2-149 (306)
33 PF03665 UPF0172: Uncharacteri 97.9 0.0002 4.3E-09 67.1 12.1 113 200-316 3-121 (196)
34 KOG2975 Translation initiation 97.5 0.00037 8E-09 68.0 8.9 130 197-332 19-155 (288)
35 COG5178 PRP8 U5 snRNP spliceos 97.5 0.00016 3.4E-09 81.4 6.8 130 198-336 2133-2269(2365)
36 KOG2834 Nuclear pore complex, 96.8 0.0052 1.1E-07 64.0 9.2 127 204-334 181-346 (510)
37 KOG3289 Uncharacterized conser 96.1 0.078 1.7E-06 49.6 11.0 109 200-315 3-120 (199)
38 KOG3050 COP9 signalosome, subu 94.7 0.097 2.1E-06 51.2 7.1 114 197-315 7-129 (299)
39 cd08071 MPN_DUF2466 Mov34/MPN/ 94.0 0.86 1.9E-05 39.0 10.8 73 222-299 15-87 (113)
40 PF14220 DUF4329: Domain of un 92.8 0.49 1.1E-05 41.6 7.5 65 221-296 19-88 (123)
41 PF04002 RadC: RadC-like JAB d 90.3 2.9 6.2E-05 36.2 9.5 74 222-300 20-93 (123)
42 PRK00024 hypothetical protein; 82.5 16 0.00034 35.0 10.7 89 204-299 105-193 (224)
43 COG5100 NPL4 Nuclear pore prot 82.2 2 4.4E-05 45.0 4.9 128 204-335 240-406 (571)
44 TIGR00608 radc DNA repair prot 82.0 16 0.00035 34.9 10.6 88 204-298 99-186 (218)
45 PF08084 PROCT: PROCT (NUC072) 68.2 1.2 2.6E-05 39.5 -0.9 33 306-339 1-33 (125)
46 PF15659 Toxin-JAB1: JAB-like 58.8 47 0.001 30.8 7.6 27 269-296 113-139 (162)
47 PF14778 ODR4-like: Olfactory 48.5 92 0.002 31.8 8.5 57 227-283 1-74 (362)
48 COG2003 RadC DNA repair protei 32.2 48 0.001 32.3 3.4 88 203-297 104-191 (224)
49 PF09935 DUF2167: Protein of u 20.1 4.8E+02 0.01 25.7 7.8 77 200-278 23-113 (239)
No 1
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=100.00 E-value=9.6e-56 Score=433.08 Aligned_cols=301 Identities=46% Similarity=0.743 Sum_probs=257.2
Q ss_pred hHHHHhhhcccccCCCCccccccccccCCCCCCCCCCCCcccceeecCCCCCCCccccCcccccCCCCCCCCCCCCCCCC
Q 017219 39 QIDKQFQKLSVNIPLPKKETLSRHSFLGPHGLRGQWLGPSAEIKVHYPSSTDLTTTEDISLNQAGQYGIVPIKDGDPGGA 118 (375)
Q Consensus 39 ~~~~~~~~~~~~~~~p~~~tl~~h~~~gp~~~~~~~~~~~~~~~~~yps~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 (375)
-.++.+|+|.. .+.+||++.|++ ..+.||+++.++.+.+.++++|....+.+.. .++.+.+
T Consensus 122 ~~~E~~k~le~---~~~~E~e~kr~a---------------q~k~Q~l~~~~f~~~~~~~~~q~~~s~~m~s-~~~~gl~ 182 (424)
T KOG2880|consen 122 NLAERFKKLEV---QREEETERKRSA---------------QTKQQQLESSQFSPLEPPSFKQLLDSGPMPS-NQSNGLP 182 (424)
T ss_pred hHHHHHHHhhc---chhhHHHHHHHH---------------HHhhhcCCcccCCccCchHHHhhhcccCCCc-CCCCCCc
Confidence 46788999988 899999999988 7899999999999999999999998877663 3333333
Q ss_pred -ccccccccccCCCCCccCCcCCCCCCccc-ccCCCcccccccCCCCCccccccccCCCCCCccCCCCCCCCCCCCCCCC
Q 017219 119 -ISTMESVLSLDDGRWLHPAEKSCPPMVHE-AREDPFQFVSTKQPSPPPVLAQVQQASIPPSRVADPRPGPAQDISLNTN 196 (375)
Q Consensus 119 -~~~~~s~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 (375)
+...++.+--.+.|.....++.. ..+++ ..++-.....+++|+++++|.... ...........++
T Consensus 183 e~~~~~~~~p~~~~~~~~~s~~l~-~~~s~ep~~s~~~n~~~k~p~~~r~l~p~a------------~~n~~~~~~~~~k 249 (424)
T KOG2880|consen 183 EQPIGEPLVPSNESRSLNYSELLS-VLSSPEPSDSCTTNVTIKSPSVDRVLKPGA------------TDNSNHGESSEGK 249 (424)
T ss_pred CCCcCCCCcccccccccCCchhhh-hccCCCccccccccccccCCCCCccccccc------------ccccccccccCCc
Confidence 45555555445555555555554 44443 455555566677777777665441 1111122456777
Q ss_pred CceEEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccEE
Q 017219 197 EYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLG 276 (375)
Q Consensus 197 ~~~~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiVG 276 (375)
.++.|+|+..++..|++.|+++++++.|+||+|+|+...+.++||.+++|+|++++++|.+++++|+|++|+.++|..||
T Consensus 250 ~lr~v~ip~~l~~~Fl~la~~NT~knlETCGiL~g~L~~n~f~IThliiPkQeatsd~C~t~neeelF~vQdq~~L~tlG 329 (424)
T KOG2880|consen 250 ILRDVHIPERLMEVFLQLAKSNTKKNLETCGILAGKLERNEFYITHLIIPKQEATSDSCNTMNEEELFEVQDQHELLTLG 329 (424)
T ss_pred cceEEEecHHHHHHHHHHHhhcccccchHHHHhhhHhhcCcEEEEEEEeecccCCCccccccCHHHHheecccccceeee
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCCceeEEEeeCCCCCceeecccccCCccCCCCCCCCCccc
Q 017219 277 WIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQQRGFHPHEEPEDGSPLYE 356 (375)
Q Consensus 277 WYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~~lrAFRLsdp~Gm~~~~~c~~~gFhph~~~~~~~~iy~ 356 (375)
|+||||+++||+|+.|+|||++||.|+|+++||||+|.. ...|+|||++|+||++|+.|+++|||||+. +|.|+|+
T Consensus 330 WIHTHPTQt~FmSSVDlHTHcSYQiMlPEAiAIV~aPk~--~~tGiFrLt~~~Gm~~i~~C~~~GFHpH~~--~~~pl~~ 405 (424)
T KOG2880|consen 330 WIHTHPTQTCFMSSVDLHTHCSYQIMLPEAIAIVCAPKS--KTTGIFRLTDPGGMEVIRGCRKKGFHPHSE--KGPPLFE 405 (424)
T ss_pred eeecCCccchhheeccccccceeeeecchheeEEecccc--CCcceEEecCCcchHHHhhcccCCCCCCCC--CCCCcee
Confidence 999999999999999999999999999999999999985 578999999999999999999999999987 7899999
Q ss_pred cccceEecCCCceeEeeCC
Q 017219 357 HCSHVFMNAKLQFDVVDLR 375 (375)
Q Consensus 357 ~~~~v~~~~~~~~~~~dlr 375 (375)
+|+||||+.|.+++|+|||
T Consensus 406 ~~~~v~~~~~~k~~v~dLR 424 (424)
T KOG2880|consen 406 HCSHVYMHHNNKLCVIDLR 424 (424)
T ss_pred ecceeEEcCCcceeeeeCC
Confidence 9999999999999999998
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=1.2e-44 Score=328.35 Aligned_cols=173 Identities=60% Similarity=1.058 Sum_probs=161.8
Q ss_pred ceEEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccEEE
Q 017219 198 YQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGW 277 (375)
Q Consensus 198 ~~~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiVGW 277 (375)
+++++|+++++++|++||+.++..|+|+||+|+|+..+++++|++++.++|.+++.+++++++++.++.++.+||++|||
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 36899999999999999999963469999999999887888999998999999988888899888888888999999999
Q ss_pred EeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCCceeEEEeeCCCCCceeecccccCCccCCCCCCCCCcccc
Q 017219 278 IHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQQRGFHPHEEPEDGSPLYEH 357 (375)
Q Consensus 278 YHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~~lrAFRLsdp~Gm~~~~~c~~~gFhph~~~~~~~~iy~~ 357 (375)
|||||..+|+||.+|+++|++||+++|+++||||||. ...++||||++++||+|++.|+++|||||+++ .+||++
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 47899999995679999999999999999987 799999
Q ss_pred ccceEecCCCceeEeeCC
Q 017219 358 CSHVFMNAKLQFDVVDLR 375 (375)
Q Consensus 358 ~~~v~~~~~~~~~~~dlr 375 (375)
|.|||++.+++|+|+|||
T Consensus 156 ~~~~~~~~~~~~~~~~~~ 173 (173)
T cd08066 156 CGHVIWKDQLKVTVVDLR 173 (173)
T ss_pred eeEEEEcCCCceEEEeCC
Confidence 999999999999999998
No 3
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=99.95 E-value=1.8e-27 Score=201.93 Aligned_cols=111 Identities=38% Similarity=0.687 Sum_probs=93.7
Q ss_pred HHHHHHHHHHHhcCCCCcceEEEeeeeeCC-----CeEEEEEEEecCCCCCCCcccccCHHH---HHHHHhhCCCccEEE
Q 017219 206 NMMQDFLRLAQANTEKNLETCGVLAGSLKN-----RVFHITTLIIPKQESTSDSCQTLNEEE---IFEVQDRLSLFPLGW 277 (375)
Q Consensus 206 ~ll~kILkHA~s~t~~P~EvCGLLlG~~~~-----~~l~VT~lfpppq~~ts~s~~~~DpeE---if~~q~~rgLeiVGW 277 (375)
+++++|++||++++ |+|+||+|+|...+ .+++|+++++.+... ++.+ .+..+..+|+++|||
T Consensus 1 ~~~~~i~~ha~~~~--p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~--------~~~~~~~~~~~~~~~g~~~vG~ 70 (119)
T cd08058 1 DALLKMLQHAESNT--GIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSC--------TGENVEELFNVQTGRPLLVVGW 70 (119)
T ss_pred CHHHHHHHHhcCCC--CeEEEEEeeeEEecCccceeEEEEeecCCCCCCc--------hhHHHHHHHHHHhCCCCeEEEE
Confidence 47899999999998 99999999998763 457788877665421 2222 333456799999999
Q ss_pred EeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCCceeEEEee
Q 017219 278 IHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLS 326 (375)
Q Consensus 278 YHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~~lrAFRLs 326 (375)
|||||.++++||.+|+++|++||++.|+++|||+||.++...+|||||+
T Consensus 71 YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~~~~~~a~rl~ 119 (119)
T cd08058 71 YHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHRNKDTGIFRLT 119 (119)
T ss_pred EecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCCCcccceEEeC
Confidence 9999999999999999999999999999999999999977789999995
No 4
>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=1.9e-26 Score=222.01 Aligned_cols=137 Identities=21% Similarity=0.396 Sum_probs=117.0
Q ss_pred CCCCCceEEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCH--HHHHH--H--
Q 017219 193 LNTNEYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNE--EEIFE--V-- 266 (375)
Q Consensus 193 ~~~~~~~~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~Dp--eEif~--~-- 266 (375)
.+++.++.|.|+..++.+|++||+++. |.|+||+|+|...+++++|+++|++|+.+++..+.+.++ +++.+ .
T Consensus 4 ~~~~~~~~V~Is~~allkil~Ha~~~~--p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~ 81 (268)
T cd08069 4 PDPDYFEKVYISSLALLKMLKHARAGG--PIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLK 81 (268)
T ss_pred CCCCcccEEEECHHHHHHHHHHHhccC--CceEEEEEEeeecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHH
Confidence 456788999999999999999999987 999999999998888999999999998877766655432 22233 2
Q ss_pred HhhCCCccEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCC-CC---ceeEEEeeCCCCCc
Q 017219 267 QDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDT-SS---PHGIFHLSDPGGVS 332 (375)
Q Consensus 267 q~~rgLeiVGWYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~t-s~---~lrAFRLsdp~Gm~ 332 (375)
+..+++++||||||||.++||||.+|+++|..||++.+++|+||+||.++ .. .++|||+.++ ++.
T Consensus 82 ~~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~~-~~~ 150 (268)
T cd08069 82 QTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIPP-GYK 150 (268)
T ss_pred HhCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEECc-ccc
Confidence 22488999999999999999999999999999999999999999999887 43 5799999985 765
No 5
>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=99.94 E-value=2.3e-26 Score=219.17 Aligned_cols=127 Identities=22% Similarity=0.391 Sum_probs=109.8
Q ss_pred eEEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeC-------CCeEEEEEEEecCCCCCCCcccccCHHHHHHH---Hh
Q 017219 199 QHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLK-------NRVFHITTLIIPKQESTSDSCQTLNEEEIFEV---QD 268 (375)
Q Consensus 199 ~~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~-------~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~---q~ 268 (375)
+.|.|+++++++|+.||+++. |+|+||||+|..+ .+.+.|...+++++...+...+.+|+++++++ ++
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 568999999999999999998 9999999999874 34456666677667666777899999998875 33
Q ss_pred h------CCCccEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCC-------CceeEEEeeC
Q 017219 269 R------LSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTS-------SPHGIFHLSD 327 (375)
Q Consensus 269 ~------rgLeiVGWYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts-------~~lrAFRLsd 327 (375)
. +++.+||||||||.++|+||.+|+++|.+||++.|+++|||+|+..+. ..++|||+.+
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 899999999999999999999999999999999999999999987752 4579999987
No 6
>cd08067 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase. This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it p
Probab=99.94 E-value=1.3e-25 Score=206.47 Aligned_cols=126 Identities=23% Similarity=0.285 Sum_probs=108.8
Q ss_pred eEEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeC--CCeEEEEEEEecCCCCCCCcccccCHHHHHH---HHhhCCCc
Q 017219 199 QHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLK--NRVFHITTLIIPKQESTSDSCQTLNEEEIFE---VQDRLSLF 273 (375)
Q Consensus 199 ~~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~--~~~l~VT~lfpppq~~ts~s~~~~DpeEif~---~q~~rgLe 273 (375)
-.|.|+..++++|++||+... .|+||+|+|..+ ++.++|+.+||+++..+... +.+|+++..+ .++++|++
T Consensus 5 f~V~Is~~all~m~~Ha~~~~---~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~-~e~dp~~q~e~~~~l~~~gl~ 80 (187)
T cd08067 5 FKVTVSSNALLLMDFHCHLTT---SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLD-CEMDPVSETEIRESLESRGLS 80 (187)
T ss_pred EEEEECHHHHHHHHHHhcCCC---cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcc-cccCHHHHHHHHHHHHHcCCE
Confidence 469999999999999999864 999999999975 36889999999999776555 4557655544 46789999
Q ss_pred cEEEEeCCCCCCCCCCHHHHHHHHHHhhcCC-------CeEEEEEcCCCCC-----CceeEEEeeCC
Q 017219 274 PLGWIHTHPSQTCFMSSVDLHTHYSYQIMLP-------EAVAIVMAPTDTS-----SPHGIFHLSDP 328 (375)
Q Consensus 274 iVGWYHSHP~~~afPSstDL~tq~sYQ~~~P-------eaVaLIvSP~~ts-----~~lrAFRLsdp 328 (375)
+||||||||.++++||.+|+++|+.||.+++ ++|+|||||.++. ..++||++.++
T Consensus 81 vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~ 147 (187)
T cd08067 81 VVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPP 147 (187)
T ss_pred EEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECC
Confidence 9999999999999999999999999999987 6999999999853 34799999986
No 7
>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=99.88 E-value=1.5e-21 Score=164.73 Aligned_cols=125 Identities=26% Similarity=0.396 Sum_probs=105.1
Q ss_pred EEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcc--cccCHHHHHHH---HhhCCCccE
Q 017219 201 LHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSC--QTLNEEEIFEV---QDRLSLFPL 275 (375)
Q Consensus 201 V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~--~~~DpeEif~~---q~~rgLeiV 275 (375)
|.|...++++|++||.++. |.|+||+|+|+..++.+.|+++|++++...+..+ +..++.+.... ....++++|
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 7899999999999999988 9999999999998888999999999987655543 33344333222 235799999
Q ss_pred EEEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCC---ceeEEEeeC
Q 017219 276 GWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSS---PHGIFHLSD 327 (375)
Q Consensus 276 GWYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~---~lrAFRLsd 327 (375)
|||||||..+++||..|+.+|..|+..++.++.+++++..+.. .++||++++
T Consensus 80 Gwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~~g~~~~~af~~~~ 134 (135)
T smart00232 80 GWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLTP 134 (135)
T ss_pred EEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccccCcEEEEEEEecC
Confidence 9999999999999999999999999999999999999988652 469999875
No 8
>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=99.88 E-value=3.1e-22 Score=191.60 Aligned_cols=136 Identities=23% Similarity=0.334 Sum_probs=124.0
Q ss_pred eEEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCC---CeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccE
Q 017219 199 QHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKN---RVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPL 275 (375)
Q Consensus 199 ~~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~---~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiV 275 (375)
.+++||++++++|+..|+.++ |+||+|+|+... ++.+|++++.+||.++.++|.+.+. +++++...||+.|
T Consensus 36 ~t~vlPknllkkFi~iaD~rt----Q~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~--~~~~~~l~~Le~L 109 (252)
T cd08056 36 YTYILPKNLLKKFISISDLRT----QIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQ--LPQHEYLEDLEPL 109 (252)
T ss_pred CEEEeCHHHHHHHHHHhhhcc----eEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCcc--CccchhhCCCEee
Confidence 479999999999999999875 999999999864 7899999999999999999988764 4777778999999
Q ss_pred EEEeCCCCCCCCCCHHHHHHHHHHhhcCC-----CeEEEEEcCCCCCCceeEEEeeCCCCCceeecccccC
Q 017219 276 GWIHTHPSQTCFMSSVDLHTHYSYQIMLP-----EAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQQRG 341 (375)
Q Consensus 276 GWYHSHP~~~afPSstDL~tq~sYQ~~~P-----eaVaLIvSP~~ts~~lrAFRLsdp~Gm~~~~~c~~~g 341 (375)
||+||||...+++|+.|+++|++||+++| ++|.++|+++.++..++||+|++ .|++|.+.=++..
T Consensus 110 GWIHTqp~e~~~Lss~Dv~tha~~~~~~~~w~~~~~V~it~SftpGs~sl~ay~LT~-~G~~wg~~n~d~~ 179 (252)
T cd08056 110 GWIHTQPNELPQLSPQDVTTHAKILADNPSWDGEKTVILTCSFTPGSCSLTAYKLTP-EGYEWGKQNKDLG 179 (252)
T ss_pred EEEEcCCCCccccCHHHHHHHHHHHHhccccCCCcEEEEEEcCCCCceEEEEEecCH-HHHHHHHhCcccc
Confidence 99999999999999999999999999998 79999999998888999999997 6999998866543
No 9
>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. J
Probab=99.87 E-value=6.1e-22 Score=163.71 Aligned_cols=107 Identities=27% Similarity=0.395 Sum_probs=88.2
Q ss_pred HHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccEEEEeCCCCCCCC
Q 017219 208 MQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIHTHPSQTCF 287 (375)
Q Consensus 208 l~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiVGWYHSHP~~~af 287 (375)
+++|++||+..+ +.|+||+|+|+..+++++|++++++++..+........-......+...|+++||||||||..+++
T Consensus 1 ~k~il~~a~~~~--~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iVGwyhshp~~~~~ 78 (116)
T cd07767 1 LKMFLDAAKSIN--GKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNAGLRIVGWYHTHPKPSCF 78 (116)
T ss_pred CHhHHHHHhcCC--CcEEEEEeEEEEcCCEEEEEEEEecccCCCCCccHHHHHHHHHHHHhcCCCeEEEEEEcCCCCCCc
Confidence 368999999988 999999999999888899999999998654333211111112223556899999999999999999
Q ss_pred CCHHHHHHHHHHhhcCCCeEEEEEcCCCC
Q 017219 288 MSSVDLHTHYSYQIMLPEAVAIVMAPTDT 316 (375)
Q Consensus 288 PSstDL~tq~sYQ~~~PeaVaLIvSP~~t 316 (375)
||..|+.+|..||.+++++++||+++...
T Consensus 79 ~s~~dv~~~~~~q~~~~~~v~li~~~~~~ 107 (116)
T cd07767 79 LSPNDLATHELFQRYFPEKVMIIVDVKPK 107 (116)
T ss_pred cCHHHHHHHHHHHHhCCCCEEEEEECCCc
Confidence 99999999999999999999999999886
No 10
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.87 E-value=4.4e-22 Score=191.97 Aligned_cols=134 Identities=22% Similarity=0.368 Sum_probs=114.2
Q ss_pred CCCCceEEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHH--HHHHHHh---
Q 017219 194 NTNEYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEE--EIFEVQD--- 268 (375)
Q Consensus 194 ~~~~~~~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~Dpe--Eif~~q~--- 268 (375)
++-.++.|.|++.+++||+.||+++. ++|+||+|.|+..++++.|.++|.+|.+++..++.+-.+. .+.++.+
T Consensus 48 Dp~~fk~vkISalAllKm~~hA~~Gg--nlEiMGlm~Gkv~g~t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k 125 (347)
T KOG1554|consen 48 DPHYFKHVKISALALLKMVMHARSGG--NLEIMGLMQGKVDGDTIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEAK 125 (347)
T ss_pred CCchhhhhhhHHHHHHHHHHHHhcCC--CeEEEeeecccccCCeEEEEeccccccccccceechHHHHHHHHHHHHHHHH
Confidence 34477889999999999999999988 9999999999999999999999999999988877654332 1222211
Q ss_pred --hCCCccEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCC----CceeEEEeeCCCC
Q 017219 269 --RLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTS----SPHGIFHLSDPGG 330 (375)
Q Consensus 269 --~rgLeiVGWYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts----~~lrAFRLsdp~G 330 (375)
.|-+++||||||||+.+||+|.+|+.||.--|+....+||||+||.++- -.++|||..+ .|
T Consensus 126 ~~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRTyp-~g 192 (347)
T KOG1554|consen 126 NVGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTYP-KG 192 (347)
T ss_pred HhhhhhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCccccccCceeeceeeccc-CC
Confidence 3678999999999999999999999999999998899999999999973 2369999997 46
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=99.87 E-value=1.1e-21 Score=188.40 Aligned_cols=138 Identities=17% Similarity=0.239 Sum_probs=111.6
Q ss_pred EEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCc--ccccCHHHHHHH---HhhCC--C
Q 017219 200 HLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDS--CQTLNEEEIFEV---QDRLS--L 272 (375)
Q Consensus 200 ~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s--~~~~DpeEif~~---q~~rg--L 272 (375)
.|.|+..++.+|++||.++. |.|+||+|+|...+++++||++|++|+..+.+. ....+.+.+.++ ..+.+ .
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 58999999999999999998 999999999999989999999999998665433 122222333333 33444 4
Q ss_pred ccEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCC---CCceeEEEeeCCCCCceeecccccCCcc
Q 017219 273 FPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDT---SSPHGIFHLSDPGGVSVIRNCQQRGFHP 344 (375)
Q Consensus 273 eiVGWYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~t---s~~lrAFRLsdp~Gm~~~~~c~~~gFhp 344 (375)
.+|||||||| .++|.+..+++++++||...+++|+||+||..+ ...++|||+++ .||.. .+++.|..
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 899999999999999999889999999999853 34679999998 58874 45555665
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=99.86 E-value=2.9e-21 Score=165.68 Aligned_cols=115 Identities=18% Similarity=0.240 Sum_probs=100.0
Q ss_pred HHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCC-cccccCHHHHHHH---HhhCCCccEEEEeCC
Q 017219 206 NMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSD-SCQTLNEEEIFEV---QDRLSLFPLGWIHTH 281 (375)
Q Consensus 206 ~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~-s~~~~DpeEif~~---q~~rgLeiVGWYHSH 281 (375)
.++.+|++||+++. |.|+||||+|...+....|+.+++++|...+. ..|.+|++++.++ ...+++.+|||||||
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 57899999999998 99999999999886656778999999987666 7889999888776 346899999999999
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCCceeEEEeeC
Q 017219 282 PSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSD 327 (375)
Q Consensus 282 P~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~~lrAFRLsd 327 (375)
|..+++||.+|+.+ +..++.++||+++..+...++||++..
T Consensus 80 P~~~~~PS~~D~~~-----~~~~~~~~lIv~~~~~~~~~~~~~~~~ 120 (128)
T cd08070 80 PDGPARPSETDLRL-----AWPPGVSYLIVSLAGGAPELRAWRLEG 120 (128)
T ss_pred CCCCCCCCHHHHHh-----ccCCCCeEEEEECCCCCcEEEEEEEcC
Confidence 99999999999985 335689999999987766899999986
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=99.83 E-value=1.3e-20 Score=157.55 Aligned_cols=107 Identities=25% Similarity=0.436 Sum_probs=86.9
Q ss_pred CceEEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCC-eEEEEEEEecCCCCCCCcccccCHHHH---HHHHh--hC
Q 017219 197 EYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNR-VFHITTLIIPKQESTSDSCQTLNEEEI---FEVQD--RL 270 (375)
Q Consensus 197 ~~~~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~-~l~VT~lfpppq~~ts~s~~~~DpeEi---f~~q~--~r 270 (375)
+.+.|.|...++.+|++||.+.. +.|+||+|+|...++ .++|+++|+.|...+...+...+.... ++... ..
T Consensus 2 s~~~V~i~p~vll~i~~h~~r~~--~~~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (114)
T PF01398_consen 2 SVQTVQIHPLVLLKIIDHATRSS--PNEVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVNP 79 (114)
T ss_dssp SCEEEEEEHHHHHHHHHHHHHHH--CTEEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCST
T ss_pred CcEEEEECHHHHHHHHHHHhcCC--CCEEEEEEEEEecCceEEEEEEEEEeeEecCccccccchhhHHHHHHhhhccccc
Confidence 46789999999999999999877 779999999999988 999999999998776666555544322 22222 14
Q ss_pred CCccEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCC
Q 017219 271 SLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPE 305 (375)
Q Consensus 271 gLeiVGWYHSHP~~~afPSstDL~tq~sYQ~~~Pe 305 (375)
.+.+||||||||..+||||..|+++|..||++.|+
T Consensus 80 ~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 80 NLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp TSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred cceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence 59999999999999999999999999999998874
No 14
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=99.83 E-value=1.1e-20 Score=181.93 Aligned_cols=142 Identities=15% Similarity=0.337 Sum_probs=114.8
Q ss_pred CceEEEECHHHHHHHHHHHHhcCCCCc-ceE-EEeeeeeCCCeEEEEEEEecCCCCC-C-Ccc--cccCHH-HHHHHHhh
Q 017219 197 EYQHLHVPVNMMQDFLRLAQANTEKNL-ETC-GVLAGSLKNRVFHITTLIIPKQEST-S-DSC--QTLNEE-EIFEVQDR 269 (375)
Q Consensus 197 ~~~~V~Ip~~ll~kILkHA~s~t~~P~-EvC-GLLlG~~~~~~l~VT~lfpppq~~t-s-~s~--~~~Dpe-Eif~~q~~ 269 (375)
+++.|.|+..++++|++||+++. ++ +.| |+|+|...+++++||+|||.|+... + +.+ ...|++ +.+...+.
T Consensus 11 ~vk~v~ldsLvVMkiiKHc~ee~--~n~d~~~GvL~Glvvd~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~ml 88 (339)
T KOG1560|consen 11 PVKRVELDSLVVMKIIKHCREEF--PNGDGTQGVLLGLVVDGRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLAML 88 (339)
T ss_pred ccceeeehhHHHHHHHHHHHhhc--CCcchhhheeeeeeecceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHHHH
Confidence 77889999999999999999988 55 655 9999999999999999999887431 1 111 122332 12222221
Q ss_pred -------CCCccEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCCc---eeEEEeeCCCCCceeecccc
Q 017219 270 -------LSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSP---HGIFHLSDPGGVSVIRNCQQ 339 (375)
Q Consensus 270 -------rgLeiVGWYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~~---lrAFRLsdp~Gm~~~~~c~~ 339 (375)
-+-..||||.||. .+.|+|..-+++||+||++.|+.|++|+||.++++| +|||||++ ..|. .|++
T Consensus 89 rrlr~vnid~~hVGwYqs~~-vgs~lS~~lveSqy~YQ~a~pesVvliYD~~kssqG~L~lrAyrLTp-~am~---~~ke 163 (339)
T KOG1560|consen 89 RRLRYVNIDHLHVGWYQSAY-VGSFLSPALVESQYAYQKAIPESVVLIYDPIKSSQGTLSLRAYRLTP-EAMA---AHKE 163 (339)
T ss_pred HHhhhcCccceeeeeeeeeh-hccccCHHHHHHHHHHHhcCCccEEEEeccccccCceEEeehhhcCH-HHHH---HHhc
Confidence 2568999999995 489999888999999999999999999999999876 59999998 4776 7999
Q ss_pred cCCccC
Q 017219 340 RGFHPH 345 (375)
Q Consensus 340 ~gFhph 345 (375)
++|.|+
T Consensus 164 kdwtpe 169 (339)
T KOG1560|consen 164 KDWTPE 169 (339)
T ss_pred CCCCHH
Confidence 999998
No 15
>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=99.78 E-value=2.3e-18 Score=147.26 Aligned_cols=109 Identities=18% Similarity=0.223 Sum_probs=89.5
Q ss_pred ECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccEEEEeCCC
Q 017219 203 VPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIHTHP 282 (375)
Q Consensus 203 Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiVGWYHSHP 282 (375)
|++.++..|++||++++ |+|+||+|+|+.. .|+.++++++...++..+.++. .+...|+++||.|||||
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 57899999999999999 9999999999765 6889999887655443332222 24568999999999999
Q ss_pred CCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCCceeEEEeeC
Q 017219 283 SQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSD 327 (375)
Q Consensus 283 ~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~~lrAFRLsd 327 (375)
+.+++||.+|++. +.+++.+++|+++......++||++..
T Consensus 70 ~~~~~PS~~D~~~-----~~~~~~~~lIvs~~~~~~~~~a~~~~g 109 (117)
T cd08072 70 SGSPRPSDADLSF-----FSKTGLVHIIVGYPYDEDDWRAYDSDG 109 (117)
T ss_pred CCCCCCCHHHHHh-----hhcCCCEEEEEECcCCCCCEEEEecCC
Confidence 9999999999873 457999999999766556799999975
No 16
>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=99.74 E-value=2e-17 Score=139.86 Aligned_cols=102 Identities=16% Similarity=0.166 Sum_probs=84.1
Q ss_pred HHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCC-cccccCHHHHHHHHhhCCCccEEEEeCCCCCC
Q 017219 207 MMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSD-SCQTLNEEEIFEVQDRLSLFPLGWIHTHPSQT 285 (375)
Q Consensus 207 ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~-s~~~~DpeEif~~q~~rgLeiVGWYHSHP~~~ 285 (375)
+++.|++||++++ |.|+||||+|+. .++.+++.+|...+. ..|.+|++++++++.. + ++||.|||||+.+
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--PREACGLVVRKG-----RKLRYIPCRNIAADPEEHFEISPEDYAAAEDE-G-EIVAVVHSHPDGS 72 (108)
T ss_pred HHHHHHHHHhHCC--CCcceEEEEecC-----CceEEEECccCCCCccceEEeCHHHHHHHhcC-C-CEEEEEEcCCCCC
Confidence 6789999999999 999999999976 256778888876544 7789999999987743 3 8999999999999
Q ss_pred CCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCCceeEEE
Q 017219 286 CFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFH 324 (375)
Q Consensus 286 afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~~lrAFR 324 (375)
+.||.+|+.. +.+++..+||++...+ ..++|+
T Consensus 73 a~PS~~D~~~-----~~~~~~~~iIvs~~~~--~~~~~~ 104 (108)
T cd08073 73 PAPSEADRAQ-----QEATGLPWIIVSWPEG--DLRVFR 104 (108)
T ss_pred CCCCHHHHHH-----hhcCCCcEEEEEcCCC--CEEEEe
Confidence 9999999962 4578999999998643 356654
No 17
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.71 E-value=1.1e-17 Score=164.22 Aligned_cols=136 Identities=23% Similarity=0.366 Sum_probs=112.0
Q ss_pred CCCCCCCceEEEECHHHHHHHHHHHHhcCCCCcc-eEEEe-ee---eeC-CCeEEEEEEEecCCCCCCCc--ccccCHHH
Q 017219 191 ISLNTNEYQHLHVPVNMMQDFLRLAQANTEKNLE-TCGVL-AG---SLK-NRVFHITTLIIPKQESTSDS--CQTLNEEE 262 (375)
Q Consensus 191 ~~~~~~~~~~V~Ip~~ll~kILkHA~s~t~~P~E-vCGLL-lG---~~~-~~~l~VT~lfpppq~~ts~s--~~~~DpeE 262 (375)
+.+..+.-++++|...++.++++|++... |.| ++|++ +| .+. +.++.|.++|..++.++..+ .+..|+.-
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 DEPHSDEKETVYISSLALLKMLRHDRAGS--PEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAVDPVF 100 (316)
T ss_pred ccccccCcceeeeehhhhhhcccccccCC--chhhccceeecccccceeeecceeeeeeeccccccceecccchhccHHH
Confidence 56677788899999999999999999988 999 99999 89 433 46788999999999988877 45566532
Q ss_pred HHHH-----HhhCCCccEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCCc---eeEEEeeCC
Q 017219 263 IFEV-----QDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSP---HGIFHLSDP 328 (375)
Q Consensus 263 if~~-----q~~rgLeiVGWYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~~---lrAFRLsdp 328 (375)
..++ +..+.+.+||||||||.|+|+||..|+.+|.+||++.+.+++.+++|..+..+ ..||++.++
T Consensus 101 q~q~~~~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~g~vv~d~f~~In~ 174 (316)
T KOG1555|consen 101 QTQMMDLLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPYGKVVPDAFSSINP 174 (316)
T ss_pred HHHHHHHHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCCCCccCChhhhcCc
Confidence 2222 22466889999999999999999999999999999988888888888776432 489998886
No 18
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=99.61 E-value=5.7e-15 Score=127.82 Aligned_cols=113 Identities=22% Similarity=0.316 Sum_probs=78.3
Q ss_pred EEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcc-cccCHHH--HHHHHhhCCCccEEE
Q 017219 201 LHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSC-QTLNEEE--IFEVQDRLSLFPLGW 277 (375)
Q Consensus 201 V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~-~~~DpeE--if~~q~~rgLeiVGW 277 (375)
+.|+++++..|+.||+.++ |.|+||+|+|...+ ...+..++....... ++++++. ....+...|+.+|||
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 5789999999999999999 99999999998764 344555555443333 4444432 223355678999999
Q ss_pred EeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCCceeEEEeeC
Q 017219 278 IHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSD 327 (375)
Q Consensus 278 YHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~~lrAFRLsd 327 (375)
|||||..+++||..|+. ++++.+-...||+.+... ...|+..+
T Consensus 75 yHSHP~~~~~pS~~D~~----~~~~~~~~~~iv~~~~~~---~~~~~~~~ 117 (134)
T COG1310 75 YHSHPGGPPYPSEADRR----LSKLGPLPWLIVSVPPGR---VHKGRAVD 117 (134)
T ss_pred EcCCCCCCCCcCHHHHh----hccccCCCEEEEEcCCCc---eeEEeeec
Confidence 99999999999999998 344444434444443332 44444444
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=99.58 E-value=4.9e-14 Score=125.14 Aligned_cols=127 Identities=11% Similarity=0.130 Sum_probs=97.5
Q ss_pred EEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHH---h--hCCCccE
Q 017219 201 LHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQ---D--RLSLFPL 275 (375)
Q Consensus 201 V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q---~--~rgLeiV 275 (375)
|.|...++.+|++|+.+....+.+++|+|+|...++.++|+++|++|...+... ...|.+.+-++. . ..++.+|
T Consensus 1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~~~~~~veV~nsF~lp~~~~~~~-~~~d~~y~~~m~~~~~~v~~~~~vV 79 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGDKIEVTNSFELPFDEEEES-IFIDTEYLEKRYNLHKKVYPQEKIV 79 (157)
T ss_pred CEEccHHHhhHHHHHHhccCCCCeEEEEEEeEEeCCEEEEEEeEEccccCCCcc-hhhhHHHHHHHHHHHHHhCCCCCEE
Confidence 467889999999999876544789999999999999999999999998665443 334443333321 1 3688999
Q ss_pred EEEeCCCCCCCCCCHHHHHHHHHHhhc-CCCeEEEEEcCCC----CCCceeEEEeeCC
Q 017219 276 GWIHTHPSQTCFMSSVDLHTHYSYQIM-LPEAVAIVMAPTD----TSSPHGIFHLSDP 328 (375)
Q Consensus 276 GWYHSHP~~~afPSstDL~tq~sYQ~~-~PeaVaLIvSP~~----ts~~lrAFRLsdp 328 (375)
||||+++...+.++..|...|..|... .+..|+|++||.. +.-.++||++...
T Consensus 80 GWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~ 137 (157)
T cd08057 80 GWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQR 137 (157)
T ss_pred EEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEecC
Confidence 999999987777888887666666554 6778999999965 2345799999963
No 20
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=99.57 E-value=8.3e-15 Score=119.81 Aligned_cols=98 Identities=21% Similarity=0.329 Sum_probs=70.2
Q ss_pred HHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHH----HHhhCCCccEEEEeC
Q 017219 205 VNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFE----VQDRLSLFPLGWIHT 280 (375)
Q Consensus 205 ~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~----~q~~rgLeiVGWYHS 280 (375)
+.++.+|++||+.+. |.|+||+|+|......+.|+..+. .++.+.++ .+..+++.+||+|||
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 578999999999998 999999999998655666665543 34444443 345689999999999
Q ss_pred CCCCCCCCCHHHHHHHHHHhhcCC-CeEEEEEcCCCCCCceeEEEe
Q 017219 281 HPSQTCFMSSVDLHTHYSYQIMLP-EAVAIVMAPTDTSSPHGIFHL 325 (375)
Q Consensus 281 HP~~~afPSstDL~tq~sYQ~~~P-eaVaLIvSP~~ts~~lrAFRL 325 (375)
||...++||.+|+..+. .. ..++||++. .. +. +|||
T Consensus 68 HP~~~a~pS~~D~~~~~-----~~~~~~~iI~~~-~~--~~-~W~~ 104 (104)
T PF14464_consen 68 HPSGPAFPSSTDIRSMR-----DLAPPSYIIVGN-PE--DR-AWRL 104 (104)
T ss_dssp ESSSSSS--HHHHHTHC-----CS-SCEEEEEEE-CE--SC-CEEE
T ss_pred CCCCCCCCCHHHHHhhh-----ccCCeEEEEEeC-CC--CC-eEEC
Confidence 99999999999998532 33 789999997 21 23 7775
No 21
>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=99.42 E-value=1.1e-12 Score=121.68 Aligned_cols=111 Identities=15% Similarity=0.159 Sum_probs=86.2
Q ss_pred EECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccEEEEeCC
Q 017219 202 HVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIHTH 281 (375)
Q Consensus 202 ~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiVGWYHSH 281 (375)
.|++.++.+|+.||+++. |+|+||+|+|...++ +..++++.|...+...+.+|+. +..+|+.+|+.||||
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 799999999999999999 999999999964433 4567899998888888888874 347899999999999
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCCceeEEEeeC
Q 017219 282 PSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSD 327 (375)
Q Consensus 282 P~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~~lrAFRLsd 327 (375)
|..++|||.+|+.-- .-.--++.|+.-......--+|||-=
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 999999999998621 11124566666555433345677754
No 22
>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=99.40 E-value=4.8e-12 Score=123.24 Aligned_cols=124 Identities=16% Similarity=0.228 Sum_probs=95.7
Q ss_pred EEEECHHHHHHHHHHHHhcCC-CCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCc--ccccCHHHHHHH---Hh--hCC
Q 017219 200 HLHVPVNMMQDFLRLAQANTE-KNLETCGVLAGSLKNRVFHITTLIIPKQESTSDS--CQTLNEEEIFEV---QD--RLS 271 (375)
Q Consensus 200 ~V~Ip~~ll~kILkHA~s~t~-~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s--~~~~DpeEif~~---q~--~rg 271 (375)
.|.|...++.+|++|+.+... .+.+++|.|+|...++.++|+++|+.|...+.+. ....|.+.+-++ .. ..+
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 588999999999999876532 2577999999999999999999999988654433 234454322222 11 367
Q ss_pred CccEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCC--ceeEEEeeC
Q 017219 272 LFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSS--PHGIFHLSD 327 (375)
Q Consensus 272 LeiVGWYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~--~lrAFRLsd 327 (375)
+.+||||||||. ++..|+..|..|+...+..|+|+++|..... .++||.-..
T Consensus 82 e~vVGWY~tg~~----~~~~d~~ih~~~~~~~~~pv~l~vd~~~~~~~lpi~aY~s~~ 135 (280)
T cd08062 82 EKIVGWYSTGPK----LRPNDLDINELFRRYCPNPVLVIIDVRPKDLGLPTEAYIAVE 135 (280)
T ss_pred CCeEEEecCCCC----CCcchHHHHHHHHHhCCCCEEEEEecCCCCCCCceEEEEEee
Confidence 999999999987 5778888888899888889999999987433 469998875
No 23
>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=99.39 E-value=5.4e-12 Score=121.36 Aligned_cols=127 Identities=16% Similarity=0.160 Sum_probs=93.3
Q ss_pred EEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHH---Hh--hCCCccE
Q 017219 201 LHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEV---QD--RLSLFPL 275 (375)
Q Consensus 201 V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~---q~--~rgLeiV 275 (375)
|.|...++.+|++|+.+....+..++|.|+|...++.++|+++|+.|...+.+. ...|.+.+-++ .. ..++.+|
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~-~~~d~~y~~~m~~~~kkv~~~~~vV 79 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNESEDQ-VAVDMEYHRTMYELHQKVNPKEVIV 79 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCCEEEEEeCeecceeCCCCe-EEEcHHHHHHHHHHHHHhCCCCcEE
Confidence 467889999999999875445788999999999999999999999998655443 33453333222 11 3688999
Q ss_pred EEEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCC--CceeEEEeeCCCCC
Q 017219 276 GWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTS--SPHGIFHLSDPGGV 331 (375)
Q Consensus 276 GWYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts--~~lrAFRLsdp~Gm 331 (375)
|||||++. ...+...|+.++.++...+..|.|++|+..+. -.++||++.+. |+
T Consensus 80 GWY~tg~~--~~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~~~~l~i~ay~~~~~-~~ 134 (265)
T cd08064 80 GWYATGSE--ITEHSALIHDYYSRECTSYNPIHLTVDTSLDDGKMSIKAYVSSPL-GV 134 (265)
T ss_pred eeeeCCCC--CCccHHHHHHHHHhhCCCCCCEEEEEeCCCCCCCcceEEEEEEec-cc
Confidence 99999974 22335556777766655457899999998664 35699999973 53
No 24
>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=99.37 E-value=4e-12 Score=104.66 Aligned_cols=101 Identities=21% Similarity=0.274 Sum_probs=76.1
Q ss_pred HHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccEEEEeCCCCCC
Q 017219 206 NMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIHTHPSQT 285 (375)
Q Consensus 206 ~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiVGWYHSHP~~~ 285 (375)
++++.|+.|++..+ |.|+||+|+|...+ .|.++...++.. +.+++.+ ++.+...+...||.|||||...
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 36788999999998 99999999997653 466666665432 2334433 5567778999999999999999
Q ss_pred CCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCCceeEE
Q 017219 286 CFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIF 323 (375)
Q Consensus 286 afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~~lrAF 323 (375)
+.||..|+... ..+...++|++... ...++||
T Consensus 70 ~~PS~~D~~~~-----~~~~~~~iIv~~~~-~~~~~~~ 101 (101)
T cd08059 70 CRPSEADLSLF-----TRFGLYHVIVCYPY-ENSWKCY 101 (101)
T ss_pred CCCCHHHHHHH-----HhcCCeEEEEECCC-cccEEEC
Confidence 99999999742 24588899998665 3456665
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=99.32 E-value=3.2e-11 Score=111.02 Aligned_cols=107 Identities=14% Similarity=0.100 Sum_probs=83.2
Q ss_pred ECHHHHHHHHHHHHhcCCCCcceEEEeeeeeC-CCeEEEEEEEecCCCCCCCcccccCHHH---HHHH---HhhCCCccE
Q 017219 203 VPVNMMQDFLRLAQANTEKNLETCGVLAGSLK-NRVFHITTLIIPKQESTSDSCQTLNEEE---IFEV---QDRLSLFPL 275 (375)
Q Consensus 203 Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~-~~~l~VT~lfpppq~~ts~s~~~~DpeE---if~~---q~~rgLeiV 275 (375)
|+..++.+|+.||.+.. +.|+||+|+|+.. ++.+.|++++|+.+. ++.++|.. +.++ ...+|+.+|
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 57889999999999976 7799999999987 667899999998862 46777764 4444 446899999
Q ss_pred EEEeCCCCCC-CCCCHHHHHHHHHHhhcCCCeEEEEEcCCCC
Q 017219 276 GWIHTHPSQT-CFMSSVDLHTHYSYQIMLPEAVAIVMAPTDT 316 (375)
Q Consensus 276 GWYHSHP~~~-afPSstDL~tq~sYQ~~~PeaVaLIvSP~~t 316 (375)
|+|||||... ..|+..=....-..+...+.++.++++=.+-
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 9999999753 3566554444445566788999999986654
No 26
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=99.06 E-value=3.3e-09 Score=104.72 Aligned_cols=128 Identities=15% Similarity=0.205 Sum_probs=93.8
Q ss_pred CCceEEEECHHHHHHHHHHHHhcCCC-CcceEEEeeeeeCCCeEEEEEEEecCCCCCCCc--ccccCHHHHHHH---Hh-
Q 017219 196 NEYQHLHVPVNMMQDFLRLAQANTEK-NLETCGVLAGSLKNRVFHITTLIIPKQESTSDS--CQTLNEEEIFEV---QD- 268 (375)
Q Consensus 196 ~~~~~V~Ip~~ll~kILkHA~s~t~~-P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s--~~~~DpeEif~~---q~- 268 (375)
.+...|.|...++.+|++|+.+.... ..-+.|.|+|...++.++|+++|++|.....+. ....|.+.+-++ ..
T Consensus 3 ~~~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~~~~~~ieItnsF~~p~~e~~~~~~~~~~D~~y~~~m~~~~k~ 82 (303)
T PLN03246 3 RGIEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFRGRVDVTNSFAVPFEEDDKDPSIWFLDHNYLESMFGMFKR 82 (303)
T ss_pred CCCcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEeeecCCEEEEEeccccCcccCCCCccceeecHHHHHHHHHHHHH
Confidence 46677999999999999999887521 233889999999889999999999886433222 233453222222 11
Q ss_pred -hCCCccEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCC--CceeEEEeeC
Q 017219 269 -RLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTS--SPHGIFHLSD 327 (375)
Q Consensus 269 -~rgLeiVGWYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts--~~lrAFRLsd 327 (375)
..+..+||||+|.|. ++..|+..|.-|....+..|.|++++..+. -.++||.-..
T Consensus 83 V~~~~~vVGWY~tg~~----i~~~d~~IH~~~~~~~~~Pv~L~vD~~~~~~~lpi~aY~s~~ 140 (303)
T PLN03246 83 INAKEHVVGWYSTGPK----LRENDLDIHELFNDYVPNPVLVIIDVQPKELGIPTKAYYAVE 140 (303)
T ss_pred hCCCCcEEeeecCCCC----CCcchHHHHHHHHhhCCCCeEEEEecCCCCCCCceEEEEEEE
Confidence 357899999999765 566778778778888888999999976543 3469998765
No 27
>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=99.00 E-value=3.8e-09 Score=102.98 Aligned_cols=132 Identities=20% Similarity=0.345 Sum_probs=102.3
Q ss_pred EEECH-HHHHHHHHHHHhcCCCCcceEEEeeeeeCCC-------eEEEEEEEecCCCCCCCcccccCH---HHHHHHHhh
Q 017219 201 LHVPV-NMMQDFLRLAQANTEKNLETCGVLAGSLKNR-------VFHITTLIIPKQESTSDSCQTLNE---EEIFEVQDR 269 (375)
Q Consensus 201 V~Ip~-~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~-------~l~VT~lfpppq~~ts~s~~~~Dp---eEif~~q~~ 269 (375)
|.+.. .++..|+..+...+ ..+.||+|+|..... ...|..++.|||.++.+.+..... +.+-+.+..
T Consensus 13 vef~~~~~~~~f~~~~w~~~--~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~iA~~ 90 (274)
T cd08061 13 VEFDNPSIVEFFLYVFWRKT--GQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAIAAA 90 (274)
T ss_pred EEEecHHHHHHHHHHHHHhh--cceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhHHHHHHHH
Confidence 45554 45555555366666 789999999998743 678999999999998877766532 233344677
Q ss_pred CCCccEEEEeCCCCC----CCCCCHHHHHHHHHHhh------cCCCeEEEEEcCCCC-CCceeEEEeeCCCCCceee
Q 017219 270 LSLFPLGWIHTHPSQ----TCFMSSVDLHTHYSYQI------MLPEAVAIVMAPTDT-SSPHGIFHLSDPGGVSVIR 335 (375)
Q Consensus 270 rgLeiVGWYHSHP~~----~afPSstDL~tq~sYQ~------~~PeaVaLIvSP~~t-s~~lrAFRLsdp~Gm~~~~ 335 (375)
.||+.|||++||+.. +.++|+.++.+.+.||+ .-..+|.+|+++... ...+.||++++ .+|..++
T Consensus 91 lGL~~VG~IfT~l~~~~~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~~g~i~~~ayQvSd-q~~~lv~ 166 (274)
T cd08061 91 LGLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDKDGQIHFEAYQVSD-QAMALVR 166 (274)
T ss_pred cCCeEEEEEEecCCCCCCCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCCCCceeeeeeeecH-HHHHHHH
Confidence 899999999999976 78999999999999996 345899999999754 35679999999 4887655
No 28
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=99.00 E-value=4.1e-09 Score=102.76 Aligned_cols=125 Identities=17% Similarity=0.199 Sum_probs=89.8
Q ss_pred EEEECHHHHHHHHHHHHhcCCC----CcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHh-----hC
Q 017219 200 HLHVPVNMMQDFLRLAQANTEK----NLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQD-----RL 270 (375)
Q Consensus 200 ~V~Ip~~ll~kILkHA~s~t~~----P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~-----~r 270 (375)
.|.|-..++.+|++|+.+.... +..++|.|+|...++.++|+++|+.|...+.......|.+.+-++.+ ..
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 4778889999999999885321 46789999999988899999999988755432223455433322211 25
Q ss_pred CCccEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCC--C--CceeEEEeeC
Q 017219 271 SLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDT--S--SPHGIFHLSD 327 (375)
Q Consensus 271 gLeiVGWYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~t--s--~~lrAFRLsd 327 (375)
++.+||||+|.+. + +...|+..|..|....+..|+|+++|... . -.++||+-..
T Consensus 82 ~~~vVGWY~tg~~-~--~~~~~~~Ih~~~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~ 139 (288)
T cd08063 82 DLDFVGWYTTGPG-G--PTESDLPIHKQILEINESPVLLLLDPEANASGKDLPVTIYESVL 139 (288)
T ss_pred CCceEEEEecCCC-C--CCHHHHHHHHHHHhhCCCcEEEEEccccccCCCCCceeEEEEEE
Confidence 7899999999877 3 44556555555666667789999999773 2 2469998775
No 29
>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family. This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize.
Probab=98.91 E-value=1.6e-08 Score=89.13 Aligned_cols=105 Identities=18% Similarity=0.095 Sum_probs=66.7
Q ss_pred HHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCC-CCcccccCH---HHHH-HHHhh--CCCccEEEEe
Q 017219 207 MMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQEST-SDSCQTLNE---EEIF-EVQDR--LSLFPLGWIH 279 (375)
Q Consensus 207 ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~t-s~s~~~~Dp---eEif-~~q~~--rgLeiVGWYH 279 (375)
++..|..+.+.. ..+.|+||+|+|...+..+.|+.+..|...+. +...|.-+. .+.+ ++..+ ..+..||-+|
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 344455555543 46789999999998877788888775443222 222233221 1222 22323 3489999999
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEc
Q 017219 280 THPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMA 312 (375)
Q Consensus 280 SHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvS 312 (375)
|||...+.||.+|+.+....-......+.||+.
T Consensus 81 tHP~~~p~PS~~D~~~~~~~~~~~~~~l~iIvG 113 (131)
T TIGR02256 81 THPEDQPEPSWTDRRSWRTIIRSPEAMLLLIVG 113 (131)
T ss_pred cCCCCCCCCCHHHHHHHHHHHhCCCeeEEEEEc
Confidence 999998999999998776554433345555554
No 30
>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=98.57 E-value=8.8e-08 Score=106.80 Aligned_cols=150 Identities=21% Similarity=0.277 Sum_probs=120.9
Q ss_pred eEEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeC---CCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccE
Q 017219 199 QHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLK---NRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPL 275 (375)
Q Consensus 199 ~~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~---~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiV 275 (375)
.+..||.+++++|+..++.. ..+.|++.|... ..+.+|.++..+||-++-..+.... .+..+....+++.+
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 YTYILPKNLLKKFITISDLR----TQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGSHQGVHLPS--FLPIHGVLEDLEPL 2168 (2321)
T ss_pred ceeeccHHHHhhheeecchh----hhhheeeeccCCCCCCccceEEEEEeccccccccccccCc--cCCcchhccCCccc
Confidence 45789999999999999875 499999999764 2567999999999976533332211 12233456899999
Q ss_pred EEEeCCCCCCCCCCHHHHHHHHHHhhcCC-CeEEEEEcCCCCCCceeEEEeeCCCCCceeecccccCCccCCCCCCCCCc
Q 017219 276 GWIHTHPSQTCFMSSVDLHTHYSYQIMLP-EAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQQRGFHPHEEPEDGSPL 354 (375)
Q Consensus 276 GWYHSHP~~~afPSstDL~tq~sYQ~~~P-eaVaLIvSP~~ts~~lrAFRLsdp~Gm~~~~~c~~~gFhph~~~~~~~~i 354 (375)
||+||.|..-.++|+.|+.+|........ .+|.|.|+.+.++..+.||.|++ .|.+|...-++.|-.|++.- ..-
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 99999999999999999999987766544 79999999999999999999998 59999998888888888763 456
Q ss_pred cccc
Q 017219 355 YEHC 358 (375)
Q Consensus 355 y~~~ 358 (375)
|++|
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=98.41 E-value=2.8e-06 Score=82.00 Aligned_cols=125 Identities=18% Similarity=0.240 Sum_probs=89.0
Q ss_pred CceEEEECHHHHHHHHHHHHhcCC-CCcceEEEeeeeeCCCeEEEEEEEecCCCC--CCCcccccCH---HHHHHHHh--
Q 017219 197 EYQHLHVPVNMMQDFLRLAQANTE-KNLETCGVLAGSLKNRVFHITTLIIPKQES--TSDSCQTLNE---EEIFEVQD-- 268 (375)
Q Consensus 197 ~~~~V~Ip~~ll~kILkHA~s~t~-~P~EvCGLLlG~~~~~~l~VT~lfpppq~~--ts~s~~~~Dp---eEif~~q~-- 268 (375)
....|.+-..+++..+.|..+-.+ ...-+.|+|+|.+.++++.|++.|..|-+. ...++-++|- +.+|.+..
T Consensus 7 ~~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~~~~~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~mfkKv 86 (309)
T KOG1556|consen 7 TVEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGSWNGDVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGMFKKV 86 (309)
T ss_pred ccceeeeehhHHHHHHHHHhhhccCcCceEEEEEEecCCCCeEEeecceeccccccCCCCceEEeccHHHHHHHHHHHHh
Confidence 456688899999999999876542 235577999999998899999999988753 2234445553 23444433
Q ss_pred hCCCccEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCCce--eEEEe
Q 017219 269 RLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPH--GIFHL 325 (375)
Q Consensus 269 ~rgLeiVGWYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~~l--rAFRL 325 (375)
...+.+||||||-|. +-..|+.....+-..-|+.+.+|++.....-++ .||--
T Consensus 87 NakekivGWYhTGPk----l~~nDl~In~l~k~y~pnpvLvIIdvkpk~~gLPT~AY~a 141 (309)
T KOG1556|consen 87 NAKEKVVGWYHTGPK----LRENDLDINELLKRYVPNPVLVIIDVKPKELGLPTEAYIA 141 (309)
T ss_pred cchhheeeeeccCCc----cccchhhHHHHHhhcCCCceEEEEecccccCCCCchheee
Confidence 256789999999665 556666655666667899999999998765543 45543
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=7.4e-06 Score=81.35 Aligned_cols=109 Identities=23% Similarity=0.374 Sum_probs=84.7
Q ss_pred EEEeeeeeCC-C------eEEEEEEEecCCCCCCCcccccCH---HHHHHHHhhCCCccEEEEeCCCC------------
Q 017219 226 CGVLAGSLKN-R------VFHITTLIIPKQESTSDSCQTLNE---EEIFEVQDRLSLFPLGWIHTHPS------------ 283 (375)
Q Consensus 226 CGLLlG~~~~-~------~l~VT~lfpppq~~ts~s~~~~Dp---eEif~~q~~rgLeiVGWYHSHP~------------ 283 (375)
+|+|+|.... . ...|..++.|||+++.+.....+. +.+-+.+..-||+.|||+=||+.
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 7999999874 2 478899999999988776655321 22233356789999999999997
Q ss_pred ---CCCCCCHHHHHHHHHHhhcCC-------------CeEEEEEcCCCCC-CceeEEEeeCCCCCceee
Q 017219 284 ---QTCFMSSVDLHTHYSYQIMLP-------------EAVAIVMAPTDTS-SPHGIFHLSDPGGVSVIR 335 (375)
Q Consensus 284 ---~~afPSstDL~tq~sYQ~~~P-------------eaVaLIvSP~~ts-~~lrAFRLsdp~Gm~~~~ 335 (375)
.+-|+|+..+.+.+.||...| .+|.+|+++..+. ..+.||++++ .+|..++
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 778999999999999999663 4799999986542 4579999998 5887544
No 33
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=97.87 E-value=0.0002 Score=67.06 Aligned_cols=113 Identities=12% Similarity=0.079 Sum_probs=77.0
Q ss_pred EEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCC--eEEEEEEEecCCCCCCCcccccCHHHH---HHHHhhCCCcc
Q 017219 200 HLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNR--VFHITTLIIPKQESTSDSCQTLNEEEI---FEVQDRLSLFP 274 (375)
Q Consensus 200 ~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~--~l~VT~lfpppq~~ts~s~~~~DpeEi---f~~q~~rgLei 274 (375)
.+.|+..++.||+-||.+-- -.-++|+|+|...++ .+.|++++|+=-.... ...+-+-.+ -.+....|+.+
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 58899999999999999864 466889999998753 3999999986432111 111111111 12244689999
Q ss_pred EEEEeCCCC-CCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCC
Q 017219 275 LGWIHTHPS-QTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDT 316 (375)
Q Consensus 275 VGWYHSHP~-~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~t 316 (375)
||+||..-. ....|+..=...........+.++.|+++-.+=
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 999999763 234567664444444455789999999986553
No 34
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=97.55 E-value=0.00037 Score=68.03 Aligned_cols=130 Identities=15% Similarity=0.223 Sum_probs=88.7
Q ss_pred CceEEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCH---HHHHHHHh--hCC
Q 017219 197 EYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNE---EEIFEVQD--RLS 271 (375)
Q Consensus 197 ~~~~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~Dp---eEif~~q~--~rg 271 (375)
....|.|-..++-.|+.+..+..+....++|-|+|...++.++||+||..|-...++.++ .|- .++++... ...
T Consensus 19 s~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g~ieitNCFaVPhnEssdqve-vdm~y~~~M~~l~~k~npn 97 (288)
T KOG2975|consen 19 SNLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKGSVEVTNCFAVPHNESSDQVE-VDMEYAKNMYELHKKVNPN 97 (288)
T ss_pred CCceEEEcceEEeEeehhhhcCCccchhhhhheeecccCCeEEEEEeeeccCccccccce-eeHHHHHHHHHHhcccCCC
Confidence 445688888888899988887766666788999999999999999999988765555442 232 22333322 257
Q ss_pred CccEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCC--CceeEEEeeCCCCCc
Q 017219 272 LFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTS--SPHGIFHLSDPGGVS 332 (375)
Q Consensus 272 LeiVGWYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts--~~lrAFRLsdp~Gm~ 332 (375)
..+||||-|-++-..+=| =||. -|..--++.|-|.+|-.-.. -.+|||--+.- |+-
T Consensus 98 E~vvGWyaTg~dvt~~ss--lihd--yYare~~~pvhLtVDT~~~n~rm~ikaYvss~~-Gvp 155 (288)
T KOG2975|consen 98 ELVVGWYATGHDVTEHSS--LIHD--YYAREAPNPVHLTVDTSLQNGRMSIKAYVSSLM-GVP 155 (288)
T ss_pred ceeEEEEecCCCcccchh--HHHH--HhhccCCCCeEEEEeccccCCccceeEEEEecc-CCC
Confidence 889999988776444322 2333 34445678888888865442 34689877763 553
No 35
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=97.53 E-value=0.00016 Score=81.37 Aligned_cols=130 Identities=18% Similarity=0.332 Sum_probs=96.9
Q ss_pred ceEEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeC---CCeEEEEEEEecCCCCCCCcccc--cCHHHHHHHHhhCCC
Q 017219 198 YQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLK---NRVFHITTLIIPKQESTSDSCQT--LNEEEIFEVQDRLSL 272 (375)
Q Consensus 198 ~~~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~---~~~l~VT~lfpppq~~ts~s~~~--~DpeEif~~q~~rgL 272 (375)
..+..||.+++++|++..+.. ..+.|++.|+.. ....+|.++..+||.+.-..+.. .-|.++ -...||
T Consensus 2133 q~~y~lP~NLl~kF~~isD~~----vqvag~vyG~s~~d~p~ikeI~~~~lVPQlgs~~~vq~~s~vP~dl---p~~e~l 2205 (2365)
T COG5178 2133 QQMYRLPLNLLEKFMRISDPH----VQVAGLVYGKSGSDNPQIKEILSFGLVPQLGSLSGVQSSSFVPHDL---PGDEDL 2205 (2365)
T ss_pred hccccccHHHHHhhheecccc----eeeEEEEeccCCccCcchhheeEEEeeccccccccccccccCCCCC---CCcccc
Confidence 446789999999999998764 699999999765 24668888888999754222221 111111 123689
Q ss_pred ccEEEEeCCCCCCCCCCHHHHHHHHHHhhcCC--CeEEEEEcCCCCCCceeEEEeeCCCCCceeec
Q 017219 273 FPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLP--EAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRN 336 (375)
Q Consensus 273 eiVGWYHSHP~~~afPSstDL~tq~sYQ~~~P--eaVaLIvSP~~ts~~lrAFRLsdp~Gm~~~~~ 336 (375)
++|||+|+.-..-.|++..++.+|..-. ..+ ++|.|.++-..++..++||.+++ +|.+|...
T Consensus 2206 e~lGwihtq~~el~~l~~~~v~th~k~~-~d~~~d~v~ltv~~~pgsiSl~ay~v~k-eG~~Wg~~ 2269 (2365)
T COG5178 2206 EILGWIHTQDDELPYLEVAGVLTHRKKI-VDPEWDAVTLTVSYLPGSISLRAYVVKK-EGCNWGSK 2269 (2365)
T ss_pred eeeEEEecCCcccchhhhhhhhhhhhcc-cCccccceeeeeeeccceeeeeeeeehh-cccccccc
Confidence 9999999999888999999998876433 344 67888887777777889999999 59999754
No 36
>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=96.84 E-value=0.0052 Score=64.03 Aligned_cols=127 Identities=20% Similarity=0.330 Sum_probs=95.4
Q ss_pred CHHHHHHHHHHHHhcCCCCcceEEEeeeeeCC-CeE------EEEEEEecCCCCCCCcccccC--HHHHHHH-HhhCCCc
Q 017219 204 PVNMMQDFLRLAQANTEKNLETCGVLAGSLKN-RVF------HITTLIIPKQESTSDSCQTLN--EEEIFEV-QDRLSLF 273 (375)
Q Consensus 204 p~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~-~~l------~VT~lfpppq~~ts~s~~~~D--peEif~~-q~~rgLe 273 (375)
..++++.|+..-+... ....|+|+|...+ +.+ +|..++.|||.+..+....++ ++..++. ...-||.
T Consensus 181 ~~~~v~~Fl~~wr~sg---~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~~~~dgl~l~~~~e~~~vD~~a~~lGLr 257 (510)
T KOG2834|consen 181 NAELVNHFLNEWRASG---VQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQHGEEDGLELLEDDEAKRVDAIAEGLGLR 257 (510)
T ss_pred chHHHHHHHHHHHHhh---hhhcceEEEeecccccccccceeeEEEEecCCccCCcCCeEEeccchhhhHHHHHHhcCce
Confidence 5799999999998764 8899999999874 333 888899999999888766553 2232333 5678999
Q ss_pred cEEEEeCCCC---------------CCCCCCHHHHHHHHHHhhcCCC-------------eEEEEEcCCCCC-CceeEEE
Q 017219 274 PLGWIHTHPS---------------QTCFMSSVDLHTHYSYQIMLPE-------------AVAIVMAPTDTS-SPHGIFH 324 (375)
Q Consensus 274 iVGWYHSHP~---------------~~afPSstDL~tq~sYQ~~~Pe-------------aVaLIvSP~~ts-~~lrAFR 324 (375)
-||||-|--. .+.|+|+.++.+.+.+|.+.|+ +|.+|++-..+. ..+.+|+
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 9999976432 2469999999999999987764 566666654432 4579999
Q ss_pred eeCCCCCcee
Q 017219 325 LSDPGGVSVI 334 (375)
Q Consensus 325 Lsdp~Gm~~~ 334 (375)
.++ .+|..+
T Consensus 338 VSn-qc~alv 346 (510)
T KOG2834|consen 338 VSN-QCMALV 346 (510)
T ss_pred hhH-HHHHHh
Confidence 998 588743
No 37
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=96.06 E-value=0.078 Score=49.64 Aligned_cols=109 Identities=13% Similarity=0.123 Sum_probs=72.3
Q ss_pred EEEECHHHHHHHHHHHHhcCCCCcce-EEEeeeeeC--CCeEEEEEEEecCCCCCCCcccccCHHHHHHH-----HhhCC
Q 017219 200 HLHVPVNMMQDFLRLAQANTEKNLET-CGVLAGSLK--NRVFHITTLIIPKQESTSDSCQTLNEEEIFEV-----QDRLS 271 (375)
Q Consensus 200 ~V~Ip~~ll~kILkHA~s~t~~P~Ev-CGLLlG~~~--~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~-----q~~rg 271 (375)
.+.|+..++-+|+-||.+- |.-+ -|+|+|... ++.++|++++|.--... ....+.|+.-+ ....|
T Consensus 3 ~veis~~aY~kmiLH~aky---ph~aVnGLLla~~~~kg~~v~itdcVPLfH~~l----aLaPmlEvAl~lId~~~~~~G 75 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKY---PHAAVNGLLLAPATGKGECVEITDCVPLFHSHL----ALAPMLEVALNLIDVWGAQAG 75 (199)
T ss_pred ceeehhhHHHHHHHHhccC---cccceeeEEEeccCCCCCeEEEEecchhhcccc----ccccHHHHHHHHHHHHHHhcC
Confidence 4789999999999999875 5554 499999654 57899999998643211 11222333221 33689
Q ss_pred CccEEEEeCCCCC-CCCCCHHHHHHHHHHhhcCCCeEEEEEcCCC
Q 017219 272 LFPLGWIHTHPSQ-TCFMSSVDLHTHYSYQIMLPEAVAIVMAPTD 315 (375)
Q Consensus 272 LeiVGWYHSHP~~-~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ 315 (375)
+.++|+||+--.+ ...+...=....-..+..+|.+..|+++-++
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 9999999997542 2223333333333445578998888888654
No 38
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=94.71 E-value=0.097 Score=51.21 Aligned_cols=114 Identities=16% Similarity=0.236 Sum_probs=71.3
Q ss_pred CceEEEECHHHHHHHHHHHHhc---CCCCc-ceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHh----
Q 017219 197 EYQHLHVPVNMMQDFLRLAQAN---TEKNL-ETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQD---- 268 (375)
Q Consensus 197 ~~~~V~Ip~~ll~kILkHA~s~---t~~P~-EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~---- 268 (375)
...+|.+-..+++.|-+|-.+- ...|. .+-|-|+|+..++.++|.+.|...-....+. ..+|-+.+.+-++
T Consensus 7 ~s~tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~~~-~~~dke~l~kk~eqykq 85 (299)
T KOG3050|consen 7 GSVTVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGKQRGRNVEIMNSFELKMDTEEDT-ETIDKEYLEKKEEQYKQ 85 (299)
T ss_pred CceeEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheecccCceEEEeeeeEEEecchhhh-hhccHHHHHHHHHHHHH
Confidence 3344566666666676663321 12366 6889999999999999999997654322221 2344333332222
Q ss_pred -hCCCccEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCC
Q 017219 269 -RLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTD 315 (375)
Q Consensus 269 -~rgLeiVGWYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ 315 (375)
=.++.++|||-+- .-+...|++.|...-..+.--++|-..|..
T Consensus 86 VFpdl~vlGwYttG----~d~t~sd~~i~k~l~~i~esplflkLNp~t 129 (299)
T KOG3050|consen 86 VFPDLYVLGWYTTG----SDPTPSDIHIHKQLMDINESPLFLKLNPAT 129 (299)
T ss_pred hcccceEEEEeecC----CCCChhhhHHHHHHHhhhcCceEEEecchh
Confidence 2689999999883 335777888877655545555666666654
No 39
>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=94.02 E-value=0.86 Score=38.99 Aligned_cols=73 Identities=25% Similarity=0.242 Sum_probs=51.0
Q ss_pred CcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccEEEEeCCCCCCCCCCHHHHHHHHHH
Q 017219 222 NLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYSY 299 (375)
Q Consensus 222 P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiVGWYHSHP~~~afPSstDL~tq~sY 299 (375)
+.|...+|+=...++.+....++. ++- .....++.++++.....+..-|..-|.||.+.+.||..|++.-...
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 DQEEFVVLLLDTKNRLIAVETISV----GTL-NSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIELTKRL 87 (113)
T ss_pred CceEEEEEEecCCCCEEEEEEEee----cCC-cceecCHHHHHHHHHHHhhheEEEEeeCCCCCCCCCHHHHHHHHHH
Confidence 578777666433344444333332 221 2345678999988888888999999999999999999999754433
No 40
>PF14220 DUF4329: Domain of unknown function (DUF4329)
Probab=92.81 E-value=0.49 Score=41.58 Aligned_cols=65 Identities=20% Similarity=0.249 Sum_probs=40.1
Q ss_pred CCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccEEEEeCCCCC-----CCCCCHHHHHH
Q 017219 221 KNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIHTHPSQ-----TCFMSSVDLHT 295 (375)
Q Consensus 221 ~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiVGWYHSHP~~-----~afPSstDL~t 295 (375)
++.|.||+++ +..++.+.-+. +..+..+.|..... ....+...|+-||||... +..||..|+..
T Consensus 19 ~nrEy~G~I~-~~~~G~y~~t~----p~~G~~~~~~~~~~------~~p~g~~~vA~yHTHG~~~~~y~~evfS~~D~~~ 87 (123)
T PF14220_consen 19 ENREYCGYIG-KDEDGKYFATE----PRRGENASCYPSNP------PCPNGSTIVASYHTHGAYSDGYDNEVFSPQDIRG 87 (123)
T ss_pred CCcEEEEEEE-EcCCCcEEeec----CccCCCCCcCCCCc------ccccccceeeEeecccccCCCccccCCCHHHhhh
Confidence 4789999766 44444433332 22333344433322 123588999999999864 45799999975
Q ss_pred H
Q 017219 296 H 296 (375)
Q Consensus 296 q 296 (375)
-
T Consensus 88 ~ 88 (123)
T PF14220_consen 88 D 88 (123)
T ss_pred h
Confidence 3
No 41
>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=90.25 E-value=2.9 Score=36.16 Aligned_cols=74 Identities=27% Similarity=0.226 Sum_probs=42.2
Q ss_pred CcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccEEEEeCCCCCCCCCCHHHHHHHHHHh
Q 017219 222 NLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQ 300 (375)
Q Consensus 222 P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiVGWYHSHP~~~afPSstDL~tq~sYQ 300 (375)
..|..-+|+=...++.+.+..++. ++... -..+++++++.....+..-|-..|=||++.+.||..|+..-...+
T Consensus 20 ~~E~~~~l~Ld~~~~li~~~~v~~----G~~~~-~~v~~R~I~~~al~~~A~~vIl~HNHPsG~~~PS~~D~~~T~~L~ 93 (123)
T PF04002_consen 20 DQEQFRVLYLDSKNRLIGDEVVSE----GTIDS-APVDPREIFRRALRLNASSVILAHNHPSGDPEPSDADIALTRRLK 93 (123)
T ss_dssp TS-EEEEEEE-TTSBEEEEEEEEE----STT-G-GGCSHHHHHHHHHHTT-SEEEEEEE-TTS--S--HHHHHHHHHHH
T ss_pred CCeEEEEEEECCCCcEEEEEEecc----cCCCc-ccccHHHHHHHHHhhCCceEEEEEEcCCCCCCCCHhHHHHHHHHH
Confidence 457666555333334444444432 33223 356889999988777777788899999999999999986544333
No 42
>PRK00024 hypothetical protein; Reviewed
Probab=82.49 E-value=16 Score=35.03 Aligned_cols=89 Identities=24% Similarity=0.170 Sum_probs=56.3
Q ss_pred CHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccEEEEeCCCC
Q 017219 204 PVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIHTHPS 283 (375)
Q Consensus 204 p~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiVGWYHSHP~ 283 (375)
+...+.++++..-... ..|...+|+=...++.+....++ .++ ...-..++.++|+..-..+-.-|=.-|=||+
T Consensus 105 ~~~~~~~~l~~~l~~~--~~E~f~vl~Ld~~~~li~~~~i~----~Gt-~~~~~v~pRei~~~Al~~~A~~iIl~HNHPS 177 (224)
T PRK00024 105 SPEDVADYLMAELRDE--EQEHFVVLFLDTKNRVIADEELF----IGT-LNSSIVHPREIVKRALKLNAAALILAHNHPS 177 (224)
T ss_pred CHHHHHHHHHHHccCC--CceEEEEEEECCCCCEeeEEEee----eec-CCeEEEcHHHHHHHHHHhhccceEEEecCCC
Confidence 3444444444433333 67877776643334444443333 122 2234568899999877777777778899999
Q ss_pred CCCCCCHHHHHHHHHH
Q 017219 284 QTCFMSSVDLHTHYSY 299 (375)
Q Consensus 284 ~~afPSstDL~tq~sY 299 (375)
+.+.||..|+..-...
T Consensus 178 G~~~PS~~D~~~T~~l 193 (224)
T PRK00024 178 GDPEPSQADILITKRL 193 (224)
T ss_pred CCCCCCHHHHHHHHHH
Confidence 9999999998754433
No 43
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=82.24 E-value=2 Score=44.97 Aligned_cols=128 Identities=19% Similarity=0.301 Sum_probs=88.8
Q ss_pred CHHHHHHHHHHHHhcCCCCcceEEEeeeeeCC------Ce-EEEEEEEecCCCCCCCcccccC--HHHHHHH-HhhCCCc
Q 017219 204 PVNMMQDFLRLAQANTEKNLETCGVLAGSLKN------RV-FHITTLIIPKQESTSDSCQTLN--EEEIFEV-QDRLSLF 273 (375)
Q Consensus 204 p~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~------~~-l~VT~lfpppq~~ts~s~~~~D--peEif~~-q~~rgLe 273 (375)
...+++.||+.=+.. .....|+|.|...+ +. -.|..++.|||++..+-..+.. -+.+++. +..-||+
T Consensus 240 ~~~iv~~Fi~~WR~s---G~QRfGy~yG~y~~y~n~PLGiKaVveaIyEPpQ~de~DG~t~ee~~de~l~d~~a~~~GL~ 316 (571)
T COG5100 240 GKHIVENFIRNWRES---GRQRFGYLYGRYMDYENIPLGIKAVVEAIYEPPQEDEPDGFTIEEWADEGLMDAPASGTGLE 316 (571)
T ss_pred CchHHHHHHHHHHHh---hhhhheeeeeehhhccCCcchhHHHhhhhcCCccccCCCceEeeeecccccccccccccCce
Confidence 468999999988876 48889999999863 22 2566778899987655432210 1112222 2346899
Q ss_pred cEEEEeCCCC---------------CCCCCCHHHHHHHHHHhhcCCC-------------eEEEEEcCCC-CCCceeEEE
Q 017219 274 PLGWIHTHPS---------------QTCFMSSVDLHTHYSYQIMLPE-------------AVAIVMAPTD-TSSPHGIFH 324 (375)
Q Consensus 274 iVGWYHSHP~---------------~~afPSstDL~tq~sYQ~~~Pe-------------aVaLIvSP~~-ts~~lrAFR 324 (375)
.+|.+-|--. -+-|+|+..+.+.+.+|.+.|+ +|.+|++-.. ++.++..|+
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 9999876432 1348999999999999998773 5666666543 457789999
Q ss_pred eeCCCCCceee
Q 017219 325 LSDPGGVSVIR 335 (375)
Q Consensus 325 Lsdp~Gm~~~~ 335 (375)
+++ .+|..++
T Consensus 397 VSn-~~~ALv~ 406 (571)
T COG5100 397 VSN-QCMALVK 406 (571)
T ss_pred ehh-hhhHHhh
Confidence 998 4887554
No 44
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=82.03 E-value=16 Score=34.93 Aligned_cols=88 Identities=25% Similarity=0.190 Sum_probs=54.5
Q ss_pred CHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccEEEEeCCCC
Q 017219 204 PVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIHTHPS 283 (375)
Q Consensus 204 p~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiVGWYHSHP~ 283 (375)
+...+..++....... ..|...+|+=...++.+....++ .++ .+.-..++.++|+..-..+-.-|=.-|=||+
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 SPEAAAEFLHTDLAHE--TREHFMVLFLDRKNRLIAKEVVF----IGT-VNHVPVHPREIFKEALKLSASALILAHNHPS 171 (218)
T ss_pred CHHHHHHHHHHHhcCC--CceEEEEEEECCCCcEEEEEEee----cCC-CCeEEEcHHHHHHHHHHhhCCeEEEEeecCC
Confidence 3444445554444443 67777665522223333333333 222 2334568899998877777777777899999
Q ss_pred CCCCCCHHHHHHHHH
Q 017219 284 QTCFMSSVDLHTHYS 298 (375)
Q Consensus 284 ~~afPSstDL~tq~s 298 (375)
+.+.||..|+..-..
T Consensus 172 G~~~PS~~Di~~T~~ 186 (218)
T TIGR00608 172 GEPSPSQEDILITER 186 (218)
T ss_pred CCCCCCHHHHHHHHH
Confidence 999999999864433
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=68.17 E-value=1.2 Score=39.47 Aligned_cols=33 Identities=18% Similarity=0.194 Sum_probs=27.2
Q ss_pred eEEEEEcCCCCCCceeEEEeeCCCCCceeecccc
Q 017219 306 AVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQQ 339 (375)
Q Consensus 306 aVaLIvSP~~ts~~lrAFRLsdp~Gm~~~~~c~~ 339 (375)
+|.|.|+.+.++..+.||+|++ +|++|.++=++
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 4788999999988999999998 69999996555
No 46
>PF15659 Toxin-JAB1: JAB-like toxin 1
Probab=58.78 E-value=47 Score=30.78 Aligned_cols=27 Identities=22% Similarity=0.224 Sum_probs=22.0
Q ss_pred hCCCccEEEEeCCCCCCCCCCHHHHHHH
Q 017219 269 RLSLFPLGWIHTHPSQTCFMSSVDLHTH 296 (375)
Q Consensus 269 ~rgLeiVGWYHSHP~~~afPSstDL~tq 296 (375)
..+-.++. +||||..+.++|..|..+.
T Consensus 113 ~~~~~iid-iHSHP~~~~~~S~~D~~~~ 139 (162)
T PF15659_consen 113 NNGNKIID-IHSHPENSNGPSGNDMKNA 139 (162)
T ss_pred cCCceEEE-eccCCCCCCCCCcchhhhh
Confidence 35667777 9999998889999998753
No 47
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=48.46 E-value=92 Score=31.81 Aligned_cols=57 Identities=23% Similarity=0.232 Sum_probs=35.9
Q ss_pred EEeeeee-CCCeEEEEEEEecCCCCCCCc----------ccccCHHHHHHH------HhhCCCccEEEEeCCCC
Q 017219 227 GVLAGSL-KNRVFHITTLIIPKQESTSDS----------CQTLNEEEIFEV------QDRLSLFPLGWIHTHPS 283 (375)
Q Consensus 227 GLLlG~~-~~~~l~VT~lfpppq~~ts~s----------~~~~DpeEif~~------q~~rgLeiVGWYHSHP~ 283 (375)
|||+|+. ....-+|..+++.|...+... ...+|.+-+.++ |...|+.+||+|=.+|.
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 444457777777665432222 223555444444 33579999999977754
No 48
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=32.17 E-value=48 Score=32.27 Aligned_cols=88 Identities=22% Similarity=0.216 Sum_probs=49.6
Q ss_pred ECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccEEEEeCCC
Q 017219 203 VPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIHTHP 282 (375)
Q Consensus 203 Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiVGWYHSHP 282 (375)
-+...+.+++....... ..|.--+|+=...++.+....+|.-. .+.....|.|+++..-..+..-|=..|=||
T Consensus 104 ~sp~~~~~~l~~~l~~~--~~E~f~vL~Ld~qnrlI~~e~lf~GT-----i~~s~V~PREI~k~Al~~nAaavIlaHNHP 176 (224)
T COG2003 104 TSPEAVAEYLRAELGGE--EREHFVVLYLDSQNRLIATETLFIGT-----LNVSEVHPREIFKEALKYNAAAVILAHNHP 176 (224)
T ss_pred CCHHHHHHHHHHHhhhh--HHHHHHHHHhcCcCceecceeEEeee-----cccceecHHHHHHHHHHhcchhhheeccCC
Confidence 34455555554333332 34443333322223344444444322 223345688999886665555555679999
Q ss_pred CCCCCCCHHHHHHHH
Q 017219 283 SQTCFMSSVDLHTHY 297 (375)
Q Consensus 283 ~~~afPSstDL~tq~ 297 (375)
++.+.||..|+....
T Consensus 177 SGd~~PS~aD~~iT~ 191 (224)
T COG2003 177 SGDPTPSRADILITE 191 (224)
T ss_pred CCCCCcCHHHHHHHH
Confidence 999999999986433
No 49
>PF09935 DUF2167: Protein of unknown function (DUF2167); InterPro: IPR018682 This family of various hypothetical membrane-anchored prokaryotic proteins has no known function.
Probab=20.09 E-value=4.8e+02 Score=25.68 Aligned_cols=77 Identities=10% Similarity=0.161 Sum_probs=45.2
Q ss_pred EEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHh-----------
Q 017219 200 HLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQD----------- 268 (375)
Q Consensus 200 ~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~----------- 268 (375)
...|+..-..+++++. -+...+. .+|+++....+....|+--|...-...-+....+|+.++++-+.
T Consensus 23 ~~fL~~~~a~~~l~~~-GN~~~~~-~~Gli~P~~~~~~W~v~~~y~~~GyVkDdda~~id~d~LL~~~k~~t~e~N~eR~ 100 (239)
T PF09935_consen 23 FRFLNPEDARKVLEEW-GNPPSPA-ELGLIFPDDDDEDWFVVFEYEDSGYVKDDDAKNIDYDELLKSMKEGTEESNKERK 100 (239)
T ss_pred cEEcCHHHHHHHHHHh-CCCCCcc-eEEEEeccCCCCCEEEEEEEcCCCceecchhhhCCHHHHHHHHHHhHHhhhHHHH
Confidence 4778999999999544 3432223 48999987754444444334332222334445677777765422
Q ss_pred h---CCCccEEEE
Q 017219 269 R---LSLFPLGWI 278 (375)
Q Consensus 269 ~---rgLeiVGWY 278 (375)
+ ..+.++||.
T Consensus 101 ~~G~~~l~l~GW~ 113 (239)
T PF09935_consen 101 KRGYPPLHLVGWA 113 (239)
T ss_pred hcCCCceEEeccc
Confidence 1 246899994
Done!