Query 041233
Match_columns 240
No_of_seqs 164 out of 803
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 05:05:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041233.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041233hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2880 SMAD6 interacting prot 100.0 5.7E-57 1.2E-61 410.4 12.3 217 18-240 204-424 (424)
2 cd08066 MPN_AMSH_like Mov34/MP 100.0 4.5E-48 9.7E-53 327.7 21.4 173 63-240 1-173 (173)
3 cd08058 MPN_euk_mb Mpr1p, Pad1 100.0 9.6E-29 2.1E-33 196.6 12.2 114 71-191 1-119 (119)
4 cd08069 MPN_RPN11_CSN5 Mov34/M 100.0 6.5E-28 1.4E-32 217.0 17.7 139 57-198 3-151 (268)
5 cd08068 MPN_BRCC36 Mov34/MPN/P 100.0 1E-27 2.2E-32 212.7 16.0 127 64-192 2-151 (244)
6 cd08067 MPN_2A_DUB Mov34/MPN/P 100.0 3.4E-27 7.4E-32 202.4 17.4 128 62-193 3-147 (187)
7 cd08056 MPN_PRP8 Mpr1p, Pad1p 99.9 6.4E-26 1.4E-30 201.8 14.6 136 64-206 36-179 (252)
8 KOG1554 COP9 signalosome, subu 99.9 5.1E-24 1.1E-28 190.3 11.1 135 58-195 47-192 (347)
9 cd07767 MPN Mpr1p, Pad1p N-ter 99.9 4.3E-23 9.2E-28 160.9 11.8 106 74-181 2-107 (116)
10 smart00232 JAB_MPN JAB/MPN dom 99.9 2.4E-22 5.2E-27 160.0 16.0 125 66-192 2-134 (135)
11 cd08065 MPN_eIF3h Mpr1p, Pad1p 99.9 1.7E-22 3.6E-27 181.6 13.9 139 65-210 2-150 (266)
12 cd08070 MPN_like Mpr1p, Pad1p 99.9 3.9E-22 8.4E-27 160.3 14.2 115 71-192 2-120 (128)
13 PF01398 JAB: JAB1/Mov34/MPN/P 99.8 4.6E-21 9.9E-26 150.5 9.9 107 62-170 2-114 (114)
14 KOG1560 Translation initiation 99.8 6.8E-21 1.5E-25 169.9 9.9 148 59-211 8-170 (339)
15 cd08072 MPN_archaeal Mov34/MPN 99.8 3.6E-19 7.8E-24 142.0 13.1 109 68-192 1-109 (117)
16 cd08073 MPN_NLPC_P60 Mpr1p, Pa 99.8 6.5E-18 1.4E-22 133.1 11.8 102 72-189 2-104 (108)
17 KOG1555 26S proteasome regulat 99.8 1E-18 2.2E-23 159.2 6.8 139 52-194 19-175 (316)
18 COG1310 Predicted metal-depend 99.7 6.9E-16 1.5E-20 125.0 12.0 113 66-192 2-117 (134)
19 PF14464 Prok-JAB: Prokaryotic 99.6 1.9E-15 4E-20 116.2 8.9 98 70-190 2-104 (104)
20 cd08057 MPN_euk_non_mb Mpr1p, 99.6 5.3E-14 1.2E-18 116.9 15.0 126 66-192 1-136 (157)
21 TIGR03735 PRTRC_A PRTRC system 99.4 1.2E-12 2.6E-17 112.7 12.0 114 67-196 74-187 (192)
22 cd08059 MPN_prok_mb Mpr1p, Pad 99.4 1.3E-12 2.8E-17 100.7 10.1 101 71-188 1-101 (101)
23 cd08064 MPN_eIF3f Mpr1p, Pad1p 99.4 5.9E-12 1.3E-16 113.2 14.8 127 66-196 1-134 (265)
24 cd08062 MPN_RPN7_8 Mpr1p, Pad1 99.4 9.4E-12 2E-16 113.0 14.9 127 65-196 2-138 (280)
25 cd08060 MPN_UPF0172 Mov34/MPN/ 99.4 8E-12 1.7E-16 107.0 12.5 107 68-181 1-115 (182)
26 cd08061 MPN_NPL4 Mov34/MPN/PAD 99.3 5.3E-11 1.1E-15 107.8 13.3 133 66-201 13-167 (274)
27 TIGR02256 ICE_VC0181 integrati 99.1 3E-09 6.5E-14 86.7 12.2 105 72-177 2-113 (131)
28 PLN03246 26S proteasome regula 99.0 1.4E-08 3.1E-13 93.3 14.2 131 61-196 3-143 (303)
29 KOG1795 U5 snRNP spliceosome s 98.9 1.5E-09 3.2E-14 112.2 7.3 150 64-223 2095-2248(2321)
30 cd08063 MPN_CSN6 Mpr1p, Pad1p 98.9 1.7E-08 3.6E-13 92.0 12.9 129 65-197 2-143 (288)
31 PF05021 NPL4: NPL4 family; I 98.6 4.4E-07 9.5E-12 83.6 11.5 110 91-201 2-150 (306)
32 COG5178 PRP8 U5 snRNP spliceos 98.2 2.2E-06 4.8E-11 88.9 7.5 138 64-210 2134-2284(2365)
33 KOG1556 26S proteasome regulat 98.2 2.6E-05 5.6E-10 69.7 12.1 125 61-189 6-140 (309)
34 PF03665 UPF0172: Uncharacteri 97.8 0.00033 7.2E-09 60.8 12.0 112 65-180 3-120 (196)
35 KOG2834 Nuclear pore complex, 97.6 0.00042 9E-09 66.6 10.3 128 69-200 181-347 (510)
36 KOG2975 Translation initiation 97.4 0.0011 2.5E-08 59.7 10.0 130 64-198 21-156 (288)
37 KOG3289 Uncharacterized conser 94.8 0.5 1.1E-05 40.7 10.9 124 65-198 3-140 (199)
38 cd08071 MPN_DUF2466 Mov34/MPN/ 94.5 0.53 1.1E-05 37.2 9.9 72 87-163 15-86 (113)
39 PF14220 DUF4329: Domain of un 93.8 0.52 1.1E-05 38.2 8.6 65 86-161 19-88 (123)
40 KOG3050 COP9 signalosome, subu 92.9 0.4 8.6E-06 43.3 7.1 90 87-181 35-130 (299)
41 PF08084 PROCT: PROCT (NUC072) 92.7 0.092 2E-06 42.7 2.6 33 171-204 1-33 (125)
42 COG5100 NPL4 Nuclear pore prot 92.2 0.35 7.6E-06 46.5 6.1 128 69-200 240-406 (571)
43 PF04002 RadC: RadC-like JAB d 90.7 2.3 5.1E-05 33.9 8.8 74 87-165 20-93 (123)
44 PRK00024 hypothetical protein; 85.5 9.5 0.00021 33.7 10.0 89 69-164 105-193 (224)
45 TIGR00608 radc DNA repair prot 83.5 17 0.00036 32.1 10.6 88 69-163 99-186 (218)
46 PF15659 Toxin-JAB1: JAB-like 74.0 11 0.00023 32.1 6.0 28 133-161 112-139 (162)
47 PF14778 ODR4-like: Olfactory 65.7 44 0.00096 31.5 9.0 101 92-192 1-129 (362)
48 PF09935 DUF2167: Protein of u 44.1 1.2E+02 0.0026 27.4 7.6 80 62-143 20-113 (239)
49 COG2003 RadC DNA repair protei 37.2 37 0.00079 30.3 3.2 87 67-160 103-189 (224)
50 TIGR02867 spore_II_P stage II 26.4 40 0.00087 29.3 1.6 15 140-154 1-15 (196)
51 PF07454 SpoIIP: Stage II spor 22.0 60 0.0013 29.6 2.0 21 134-154 70-90 (268)
No 1
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=100.00 E-value=5.7e-57 Score=410.41 Aligned_cols=217 Identities=52% Similarity=0.928 Sum_probs=193.1
Q ss_pred eeeeccCCCcceeeeeccCC-CCcccccccCCCC---CCCCCCCCCCCceeEEEECHHHHHHHHHHHhccCCCCcceEEE
Q 041233 18 HAVTLSSPSPVLFLTAKAPQ-GALVTHVSVADSD---KQSNTEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGV 93 (240)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~---~~~~~~~~~~~~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGl 93 (240)
+...-.||.|..+++..... .+.+++ +..++ ....+.+...+.++.|+||..+++.|++.|++|+.++.|+||+
T Consensus 204 ~l~~~~s~ep~~s~~~n~~~k~p~~~r--~l~p~a~~n~~~~~~~~~k~lr~v~ip~~l~~~Fl~la~~NT~knlETCGi 281 (424)
T KOG2880|consen 204 LLSVLSSPEPSDSCTTNVTIKSPSVDR--VLKPGATDNSNHGESSEGKILRDVHIPERLMEVFLQLAKSNTKKNLETCGI 281 (424)
T ss_pred hhhhccCCCccccccccccccCCCCCc--ccccccccccccccccCCccceEEEecHHHHHHHHHHHhhcccccchHHHH
Confidence 35566778888887776542 233333 33332 3333444555569999999999999999999999999999999
Q ss_pred eeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEE
Q 041233 94 LGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFA 173 (240)
Q Consensus 94 L~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~va 173 (240)
|+|++..+.++||++++|+|++++++|.+++++|+|.+|++++|..|||+||||+++||||++||||||+||.|+||++|
T Consensus 282 L~g~L~~n~f~IThliiPkQeatsd~C~t~neeelF~vQdq~~L~tlGWIHTHPTQt~FmSSVDlHTHcSYQiMlPEAiA 361 (424)
T KOG2880|consen 282 LAGKLERNEFYITHLIIPKQEATSDSCNTMNEEELFEVQDQHELLTLGWIHTHPTQTCFMSSVDLHTHCSYQIMLPEAIA 361 (424)
T ss_pred hhhHhhcCcEEEEEEEeecccCCCccccccCHHHHheecccccceeeeeeecCCccchhheeccccccceeeeecchhee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEccCCCCceeEEEEeeCCCCcchhhcccCCCcccCCCCCCCCCcccccCceEecCCceeEEeeCC
Q 041233 174 IVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEHCSHVYTNSNLRFEIFDLR 240 (240)
Q Consensus 174 IVisP~~~~~~l~aFrLt~p~gm~~~~~c~~~~fhph~~~~~~~~~y~~~~hv~~~~~~~~~~~dlr 240 (240)
|||+|+.. ..|+|||++|+||+++++|+++|||||+. +|+|||++|+||||+.+.+++|+|||
T Consensus 362 IV~aPk~~--~tGiFrLt~~~Gm~~i~~C~~~GFHpH~~--~~~pl~~~~~~v~~~~~~k~~v~dLR 424 (424)
T KOG2880|consen 362 IVCAPKSK--TTGIFRLTDPGGMEVIRGCRKKGFHPHSE--KGPPLFEHCSHVYMHHNNKLCVIDLR 424 (424)
T ss_pred EEeccccC--CcceEEecCCcchHHHhhcccCCCCCCCC--CCCCceeecceeEEcCCcceeeeeCC
Confidence 99999954 79999999999999999999999999997 68999999999999999999999998
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=4.5e-48 Score=327.71 Aligned_cols=173 Identities=53% Similarity=1.009 Sum_probs=162.4
Q ss_pred eeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEE
Q 041233 63 LQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGW 142 (240)
Q Consensus 63 ~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGW 142 (240)
++++.||++++++|++||+.++..|+|+||+|+|+..++.++|++++.++|.+++.++++.++++.++.++.+|+++|||
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 36899999999999999999874579999999999877888999999999999999999989888888889999999999
Q ss_pred EecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEeeCCCCcchhhcccCCCcccCCCCCCCCCcccc
Q 041233 143 IHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPIYEH 222 (240)
Q Consensus 143 YHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrLt~p~gm~~~~~c~~~~fhph~~~~~~~~~y~~ 222 (240)
|||||+.+++||.+|++||++||.++|+++|||+||. ...++||||++++|++|+++|+++|||||+++ .+||++
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 46899999996699999999999999999986 699999
Q ss_pred cCceEecCCceeEEeeCC
Q 041233 223 CSHVYTNSNLRFEIFDLR 240 (240)
Q Consensus 223 ~~hv~~~~~~~~~~~dlr 240 (240)
|+||+++++++|+|+|||
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=99.96 E-value=9.6e-29 Score=196.61 Aligned_cols=114 Identities=38% Similarity=0.642 Sum_probs=93.6
Q ss_pred HHHHHHHHHHhccCCCCcceEEEeeeeecC-----CEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEec
Q 041233 71 QLMEDFLELAKENTDKDLETCGVLGAFLEN-----GTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHT 145 (240)
Q Consensus 71 ~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~-----~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHS 145 (240)
+++++|++||++++ |+|+||+|+|+.+. ..++|+.+++.+.... ..+..+.+..+.++|+++||||||
T Consensus 1 ~~~~~i~~ha~~~~--p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~~-----~~~~~~~~~~~~~~g~~~vG~YHS 73 (119)
T cd08058 1 DALLKMLQHAESNT--GIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCT-----GENVEELFNVQTGRPLLVVGWYHS 73 (119)
T ss_pred CHHHHHHHHhcCCC--CeEEEEEeeeEEecCccceeEEEEeecCCCCCCch-----hHHHHHHHHHHhCCCCeEEEEEec
Confidence 47899999999988 99999999998753 3467777776654221 111112333467899999999999
Q ss_pred CCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEee
Q 041233 146 HPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLT 191 (240)
Q Consensus 146 HP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrLt 191 (240)
||+++++||.+|+++|++||++.|++++||+||.++...+|||||+
T Consensus 74 HP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~~~~~~a~rl~ 119 (119)
T cd08058 74 HPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHRNKDTGIFRLT 119 (119)
T ss_pred CCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCCCcccceEEeC
Confidence 9999999999999999999999999999999999876789999996
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=99.96 E-value=6.5e-28 Score=217.02 Aligned_cols=139 Identities=23% Similarity=0.374 Sum_probs=118.9
Q ss_pred CCCCCceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccCh--HHHHH--H-
Q 041233 57 PSVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNE--EDVFA--I- 131 (240)
Q Consensus 57 ~~~~~~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de--~e~~~--~- 131 (240)
...+..++.|.|+..++.+|++||+++. |.|+||+|+|+.++++++|+++|++|+.+++..++..++ +++.+ .
T Consensus 3 ~~~~~~~~~V~Is~~allkil~Ha~~~~--p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~ 80 (268)
T cd08069 3 KPDPDYFEKVYISSLALLKMLKHARAGG--PIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEML 80 (268)
T ss_pred CCCCCcccEEEECHHHHHHHHHHHhccC--CceEEEEEEeeecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHH
Confidence 3456788899999999999999999976 999999999998888999999999999888777666442 12333 2
Q ss_pred -hhhCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCC-C---ceeEEEEeeCCCCcch
Q 041233 132 -QNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDS-S---RSYGIFQLTEPSGMSV 198 (240)
Q Consensus 132 -~~~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~-~---~~l~aFrLt~p~gm~~ 198 (240)
+..+++.+||||||||.++||||.+|+++|..||.+.+++|+||++|..+ . ..+||||+++ .++..
T Consensus 81 ~~~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~-~~~~~ 151 (268)
T cd08069 81 KQTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIP-PGYKP 151 (268)
T ss_pred HHhCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEEC-ccccc
Confidence 24588999999999999999999999999999999999999999999876 3 3699999996 66653
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=99.95 E-value=1e-27 Score=212.69 Aligned_cols=127 Identities=24% Similarity=0.347 Sum_probs=109.2
Q ss_pred eEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeec-------CCEEEEEEEEecCCCCCCCceeccChHHHHHHh---h
Q 041233 64 QDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLE-------NGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQ---N 133 (240)
Q Consensus 64 ~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~-------~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~---~ 133 (240)
..|.|+++++++|+.||+..+ |+|+||||+|+.+ ...+.|...+++++...+...+.+|++++++++ +
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 579999999999999999988 9999999999874 234566566666666666677899999888763 4
Q ss_pred h------CCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCC-------ceeEEEEeeC
Q 041233 134 E------RSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS-------RSYGIFQLTE 192 (240)
Q Consensus 134 ~------~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~-------~~l~aFrLt~ 192 (240)
. +|+.+||||||||+++++||.+|+++|.+||++.|+++|||+|+..+. ..++|||+.+
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 5 999999999999999999999999999999999999999999987752 4699999986
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=99.95 E-value=3.4e-27 Score=202.37 Aligned_cols=128 Identities=20% Similarity=0.285 Sum_probs=109.4
Q ss_pred ceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeec--CCEEEEEEEEecCCCCCCCceeccChHH---HHHHhhhCC
Q 041233 62 VLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLE--NGTFYVTTLIIPKQDSTSSSCQALNEED---VFAIQNERS 136 (240)
Q Consensus 62 ~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~--~~~~~Vt~l~~ppq~~ts~~~~~~de~e---~~~~~~~~g 136 (240)
....|.|+..++.+|++||+.. ..|+||+|+|+.+ .+.++|+.++|+++..+++.++ +|+++ +++.++++|
T Consensus 3 ~pf~V~Is~~all~m~~Ha~~~---~~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e-~dp~~q~e~~~~l~~~g 78 (187)
T cd08067 3 QPFKVTVSSNALLLMDFHCHLT---TSEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCE-MDPVSETEIRESLESRG 78 (187)
T ss_pred CCEEEEECHHHHHHHHHHhcCC---CcEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccc-cCHHHHHHHHHHHHHcC
Confidence 3467999999999999999985 3999999999964 4678999999999977766644 46654 444568899
Q ss_pred CcceEEEecCCCCCCCCCHHHHHHHHhhhhcCC-------CEEEEEEccCCCC-----ceeEEEEeeCC
Q 041233 137 LFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVP-------EAFAIVLAPTDSS-----RSYGIFQLTEP 193 (240)
Q Consensus 137 l~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~p-------e~vaIVisP~~~~-----~~l~aFrLt~p 193 (240)
+++||||||||.++++||.+|++||++||.+++ ++|+|||||++.. ..+++|++.++
T Consensus 79 l~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~ 147 (187)
T cd08067 79 LSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPP 147 (187)
T ss_pred CEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECC
Confidence 999999999999999999999999999999987 6999999999853 24999999964
No 7
>cd08056 MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8. Members of this family are found in pre-mRNA-processing factor 8 (Prp8) which is a critical splicing factor, interacting with several other spliceosomal proteins, snRNAs, and the pre-mRNA, thus organizing and stabilizing the spliceosome catalytic core. Prp8 is one of the largest and most highly conserved of nuclear proteins, occupying a central position in the catalytic core of the spliceosome. Its C-terminal domain exhibits a JAB1/MPN-like core similar to deubiquitinating enzymes, but does not show catalytic isopeptidase activity, possibly because the putative isopeptidase center is covered by insertions and terminal appendices that are grafted onto this core, thus impairing the metal binding site. It is proposed that this domain is a protein interaction domain instead of a Zn(2+)-dependent metalloenzyme as proposed for some MPN proteins. The DEAD-box protein Brr2 and t
Probab=99.94 E-value=6.4e-26 Score=201.76 Aligned_cols=136 Identities=21% Similarity=0.272 Sum_probs=124.9
Q ss_pred eEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecC---CEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcce
Q 041233 64 QDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLEN---GTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPM 140 (240)
Q Consensus 64 ~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~---~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iV 140 (240)
..++||++++++|+..|+.++ |+||+|+|+... +..+|+++++|||.++.++|.+.+. +.+++...||+.|
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 589999999999999999955 999999999743 6789999999999999999998764 5777888999999
Q ss_pred EEEecCCCCCCCCCHHHHHHHHhhhhcCC-----CEEEEEEccCCCCceeEEEEeeCCCCcchhhcccCCC
Q 041233 141 GWIHTHPSQSCFMSSVDLHTHYSYQMMVP-----EAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETG 206 (240)
Q Consensus 141 GWYHSHP~~~~fpSs~Dl~tq~syQ~~~p-----e~vaIVisP~~~~~~l~aFrLt~p~gm~~~~~c~~~~ 206 (240)
||+||||..++|||+.|+++|++||.+.| ++|+++||++.++.+++||+||+ +|++|++++++..
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 89999999998888999999995 8999999999754
No 8
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.91 E-value=5.1e-24 Score=190.31 Aligned_cols=135 Identities=24% Similarity=0.390 Sum_probs=117.4
Q ss_pred CCCCceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHh-----
Q 041233 58 SVSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQ----- 132 (240)
Q Consensus 58 ~~~~~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~----- 132 (240)
..+..++.|.|+.-+++||+.||+++. ++|++|+|.|+.+++++.|..+|..|.++|+.++++..++.-+.++
T Consensus 47 ~Dp~~fk~vkISalAllKm~~hA~~Gg--nlEiMGlm~Gkv~g~t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~ 124 (347)
T KOG1554|consen 47 TDPHYFKHVKISALALLKMVMHARSGG--NLEIMGLMQGKVDGDTIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEA 124 (347)
T ss_pred CCCchhhhhhhHHHHHHHHHHHHhcCC--CeEEEeeecccccCCeEEEEeccccccccccceechHHHHHHHHHHHHHHH
Confidence 455577889999999999999999987 9999999999999999999999999999999998876654333221
Q ss_pred h--hCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCc----eeEEEEeeCCCC
Q 041233 133 N--ERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSR----SYGIFQLTEPSG 195 (240)
Q Consensus 133 ~--~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~----~l~aFrLt~p~g 195 (240)
. .+-+.+||||||||+.+||+|.+|+.||.--|....+++|||++|.++-. .+||||.-+ +|
T Consensus 125 k~~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRTyp-~g 192 (347)
T KOG1554|consen 125 KNVGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTYP-KG 192 (347)
T ss_pred HHhhhhhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCccccccCceeeceeeccc-CC
Confidence 2 35588999999999999999999999999999999999999999998732 499999994 77
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=99.90 E-value=4.3e-23 Score=160.86 Aligned_cols=106 Identities=27% Similarity=0.328 Sum_probs=88.1
Q ss_pred HHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCCCCCCC
Q 041233 74 EDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFM 153 (240)
Q Consensus 74 ~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~~~~fp 153 (240)
++|++||+.++ +.|+||+|+|+.+++.++|++++++++..+...............+...|+++||||||||..+++|
T Consensus 2 k~il~~a~~~~--~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iVGwyhshp~~~~~~ 79 (116)
T cd07767 2 KMFLDAAKSIN--GKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNAGLRIVGWYHTHPKPSCFL 79 (116)
T ss_pred HhHHHHHhcCC--CcEEEEEeEEEEcCCEEEEEEEEecccCCCCCccHHHHHHHHHHHHhcCCCeEEEEEEcCCCCCCcc
Confidence 68999999987 9999999999998888899999999986654332211101122235678999999999999999999
Q ss_pred CHHHHHHHHhhhhcCCCEEEEEEccCCC
Q 041233 154 SSVDLHTHYSYQMMVPEAFAIVLAPTDS 181 (240)
Q Consensus 154 Ss~Dl~tq~syQ~~~pe~vaIVisP~~~ 181 (240)
|..|+.+|..||.+.+++++||+++...
T Consensus 80 s~~dv~~~~~~q~~~~~~v~li~~~~~~ 107 (116)
T cd07767 80 SPNDLATHELFQRYFPEKVMIIVDVKPK 107 (116)
T ss_pred CHHHHHHHHHHHHhCCCCEEEEEECCCc
Confidence 9999999999999999999999999886
No 10
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=99.90 E-value=2.4e-22 Score=160.05 Aligned_cols=125 Identities=26% Similarity=0.360 Sum_probs=105.0
Q ss_pred EEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCce--eccChHHHHHH---hhhCCCcce
Q 041233 66 VHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSC--QALNEEDVFAI---QNERSLFPM 140 (240)
Q Consensus 66 V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~--~~~de~e~~~~---~~~~gl~iV 140 (240)
|.|...++++|++||.++. +.|+||+|+|+..++.+.|+++++.|+...++.+ +..++.+.... +...++++|
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 6889999999999999987 9999999999998888999999999887665553 33333322221 346889999
Q ss_pred EEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCC---ceeEEEEeeC
Q 041233 141 GWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS---RSYGIFQLTE 192 (240)
Q Consensus 141 GWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~---~~l~aFrLt~ 192 (240)
|||||||..+++||..|+.+|..||..++.++.+++++..+. ..++||++++
T Consensus 80 Gwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~~g~~~~~af~~~~ 134 (135)
T smart00232 80 GWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLTP 134 (135)
T ss_pred EEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccccCcEEEEEEEecC
Confidence 999999999999999999999999999999999999988764 2599999974
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=99.89 E-value=1.7e-22 Score=181.65 Aligned_cols=139 Identities=21% Similarity=0.301 Sum_probs=113.0
Q ss_pred EEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCce-eccCh-H---HHHHHhhhCCC--
Q 041233 65 DVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSC-QALNE-E---DVFAIQNERSL-- 137 (240)
Q Consensus 65 ~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~-~~~de-~---e~~~~~~~~gl-- 137 (240)
.|.|+..++.+|++||.++. |.|+||+|+|...+++++||++|+.|+..+++.. +..++ . ++++..++.|.
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 58999999999999999988 9999999999998899999999999987664431 11222 2 23333455555
Q ss_pred cceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCC---CCceeEEEEeeCCCCcchhhcccCCCcccC
Q 041233 138 FPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTD---SSRSYGIFQLTEPSGMSVLKECQETGFHPH 210 (240)
Q Consensus 138 ~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~---~~~~l~aFrLt~p~gm~~~~~c~~~~fhph 210 (240)
.+|||||||| .++|.|..+++++++||...+++|+||+||.. +...+||||+++ .||... ++..|.+.
T Consensus 80 ~iVGWY~S~p-~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s~~g~l~lkAyrl~~-~~~~~~---~~~~~~~~ 150 (266)
T cd08065 80 NHVGWYQSTY-LGSFFTRDLIETQYNYQEAIEESVVLVYDPSKTSQGSLSLKAYRLSE-KFMELY---KEGKFSTE 150 (266)
T ss_pred cEEEeEeecC-CCCcCCHHHHHHHHHHhccCCCCEEEEECCCcccccceeeEEEEEcH-HHHHHh---hcCCcCHH
Confidence 9999999999 89999999999999999988999999999984 235799999995 898774 44556653
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=99.89 E-value=3.9e-22 Score=160.35 Aligned_cols=115 Identities=22% Similarity=0.256 Sum_probs=99.7
Q ss_pred HHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCC-ceeccChHHHHHH---hhhCCCcceEEEecC
Q 041233 71 QLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSS-SCQALNEEDVFAI---QNERSLFPMGWIHTH 146 (240)
Q Consensus 71 ~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~-~~~~~de~e~~~~---~~~~gl~iVGWYHSH 146 (240)
.++++|++||+.+. |.|+||+|+|+.+.....|+.+++++|...+. ..+.+|++++.++ .++.|+.+|||||||
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 57899999999988 99999999999876666788999999987776 7888999887776 356899999999999
Q ss_pred CCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEeeC
Q 041233 147 PSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTE 192 (240)
Q Consensus 147 P~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrLt~ 192 (240)
|+.+++||.+|+.++ ..++.+++|++...+...+++|++.+
T Consensus 80 P~~~~~PS~~D~~~~-----~~~~~~~lIv~~~~~~~~~~~~~~~~ 120 (128)
T cd08070 80 PDGPARPSETDLRLA-----WPPGVSYLIVSLAGGAPELRAWRLEG 120 (128)
T ss_pred CCCCCCCCHHHHHhc-----cCCCCeEEEEECCCCCcEEEEEEEcC
Confidence 999999999999864 34578999999887656899999985
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=99.85 E-value=4.6e-21 Score=150.49 Aligned_cols=107 Identities=25% Similarity=0.429 Sum_probs=86.8
Q ss_pred ceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCC-EEEEEEEEecCCCCCCCceeccChHHH---HHHhh--hC
Q 041233 62 VLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENG-TFYVTTLIIPKQDSTSSSCQALNEEDV---FAIQN--ER 135 (240)
Q Consensus 62 ~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~-~~~Vt~l~~ppq~~ts~~~~~~de~e~---~~~~~--~~ 135 (240)
..+.|.|...++.+|++||.+.. +.|+||+|+|..+++ .++|+++|+.|...+...+...+.... ++..+ ..
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 35789999999999999999976 779999999999888 999999999998877776665554322 22222 14
Q ss_pred CCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCC
Q 041233 136 SLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPE 170 (240)
Q Consensus 136 gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe 170 (240)
.+.+||||||||..++|||..|+++|..||.+.|+
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=99.84 E-value=6.8e-21 Score=169.95 Aligned_cols=148 Identities=19% Similarity=0.364 Sum_probs=117.6
Q ss_pred CCCceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCC-C-Ccee--ccChH-HHHHH--
Q 041233 59 VSNVLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDST-S-SSCQ--ALNEE-DVFAI-- 131 (240)
Q Consensus 59 ~~~~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~t-s-~~~~--~~de~-e~~~~-- 131 (240)
.+.+.+.|.|+..++.+|++||+++.-+..=+.|+|+|.+.+++++||++||.|+... + +... ..+++ +.++.
T Consensus 8 ~~p~vk~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~Glvvd~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~m 87 (339)
T KOG1560|consen 8 ESPPVKRVELDSLVVMKIIKHCREEFPNGDGTQGVLLGLVVDGRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLAM 87 (339)
T ss_pred CCCccceeeehhHHHHHHHHHHHhhcCCcchhhheeeeeeecceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHHH
Confidence 4456789999999999999999998722233579999999899999999999887432 1 1111 12222 12222
Q ss_pred h-----hhCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCce---eEEEEeeCCCCcchhhccc
Q 041233 132 Q-----NERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRS---YGIFQLTEPSGMSVLKECQ 203 (240)
Q Consensus 132 ~-----~~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~---l~aFrLt~p~gm~~~~~c~ 203 (240)
+ ...+...||||.||- .++|+|..-+++||.||.+.|++|++|+||.+++++ +|||||| |+.|++ |+
T Consensus 88 lrrlr~vnid~~hVGwYqs~~-vgs~lS~~lveSqy~YQ~a~pesVvliYD~~kssqG~L~lrAyrLT-p~am~~---~k 162 (339)
T KOG1560|consen 88 LRRLRYVNIDHLHVGWYQSAY-VGSFLSPALVESQYAYQKAIPESVVLIYDPIKSSQGTLSLRAYRLT-PEAMAA---HK 162 (339)
T ss_pred HHHhhhcCccceeeeeeeeeh-hccccCHHHHHHHHHHHhcCCccEEEEeccccccCceEEeehhhcC-HHHHHH---Hh
Confidence 1 135788999999995 789999888999999999999999999999998764 9999999 588887 99
Q ss_pred CCCcccCC
Q 041233 204 ETGFHPHK 211 (240)
Q Consensus 204 ~~~fhph~ 211 (240)
+++|.|+.
T Consensus 163 ekdwtpea 170 (339)
T KOG1560|consen 163 EKDWTPEA 170 (339)
T ss_pred cCCCCHHH
Confidence 99999984
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=99.81 E-value=3.6e-19 Score=142.00 Aligned_cols=109 Identities=20% Similarity=0.215 Sum_probs=88.7
Q ss_pred ECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCC
Q 041233 68 ISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHP 147 (240)
Q Consensus 68 I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP 147 (240)
|++++++.|++||++.+ |+|+||+|+|+.+ .|+.++++++...++..+..+. .+.+.|++++|.|||||
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 57899999999999988 9999999999775 6889999887655443332222 24578999999999999
Q ss_pred CCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEeeC
Q 041233 148 SQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTE 192 (240)
Q Consensus 148 ~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrLt~ 192 (240)
+.++.||..|++. +..|+.+++|+|+......++||++..
T Consensus 70 ~~~~~PS~~D~~~-----~~~~~~~~lIvs~~~~~~~~~a~~~~g 109 (117)
T cd08072 70 SGSPRPSDADLSF-----FSKTGLVHIIVGYPYDEDDWRAYDSDG 109 (117)
T ss_pred CCCCCCCHHHHHh-----hhcCCCEEEEEECcCCCCCEEEEecCC
Confidence 9999999999874 346899999999755446799999874
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=99.76 E-value=6.5e-18 Score=133.12 Aligned_cols=102 Identities=19% Similarity=0.172 Sum_probs=83.9
Q ss_pred HHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCC-ceeccChHHHHHHhhhCCCcceEEEecCCCCC
Q 041233 72 LMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSS-SCQALNEEDVFAIQNERSLFPMGWIHTHPSQS 150 (240)
Q Consensus 72 ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~-~~~~~de~e~~~~~~~~gl~iVGWYHSHP~~~ 150 (240)
+++.|++||+..+ |.|+||||+|+. .++.+++.+|...+. ..|.+|+++++++++ .+ ++||.|||||+.+
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-----RKLRYIPCRNIAADPEEHFEISPEDYAAAED-EG-EIVAVVHSHPDGS 72 (108)
T ss_pred HHHHHHHHHhHCC--CCcceEEEEecC-----CceEEEECccCCCCccceEEeCHHHHHHHhc-CC-CEEEEEEcCCCCC
Confidence 6789999999988 999999999966 256678888876554 678999999998774 33 8999999999999
Q ss_pred CCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEE
Q 041233 151 CFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQ 189 (240)
Q Consensus 151 ~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFr 189 (240)
+.||..|+.. +..++..+||+|...+ .+++|+
T Consensus 73 a~PS~~D~~~-----~~~~~~~~iIvs~~~~--~~~~~~ 104 (108)
T cd08073 73 PAPSEADRAQ-----QEATGLPWIIVSWPEG--DLRVFR 104 (108)
T ss_pred CCCCHHHHHH-----hhcCCCcEEEEEcCCC--CEEEEe
Confidence 9999999963 3568899999997644 466765
No 17
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.75 E-value=1e-18 Score=159.23 Aligned_cols=139 Identities=27% Similarity=0.390 Sum_probs=112.6
Q ss_pred CCCCCCCCCCceeEEEECHHHHHHHHHHHhccCCCCcc-eEEEe-ee---ee-cCCEEEEEEEEecCCCCCCCc--eecc
Q 041233 52 QSNTEPSVSNVLQDVHISAQLMEDFLELAKENTDKDLE-TCGVL-GA---FL-ENGTFYVTTLIIPKQDSTSSS--CQAL 123 (240)
Q Consensus 52 ~~~~~~~~~~~~~~V~I~~~ll~k~l~hA~~~~~~p~E-vcGlL-~G---~~-~~~~~~Vt~l~~ppq~~ts~~--~~~~ 123 (240)
.-.++.+..+..++++|...++.+|++|++... +.| +.|++ +| .+ +..++.|.+++..++.++.-+ .+..
T Consensus 19 ~~~~d~~~~~~~e~v~i~slall~m~rh~r~~~--p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg~~is~~~e~~ 96 (316)
T KOG1555|consen 19 ELLGDEPHSDEKETVYISSLALLKMLRHDRAGS--PEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAV 96 (316)
T ss_pred cccCccccccCcceeeeehhhhhhcccccccCC--chhhccceeecccccceeeecceeeeeeeccccccceecccchhc
Confidence 344567777888999999999999999999977 999 89999 88 32 456778888999999998887 4555
Q ss_pred ChHHHHHH-------hhhCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCc---eeEEEEeeCC
Q 041233 124 NEEDVFAI-------QNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSR---SYGIFQLTEP 193 (240)
Q Consensus 124 de~e~~~~-------~~~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~---~l~aFrLt~p 193 (240)
|+ .++. +..+.+.+||||||||.++|+||..|+.||.+||+..+.+++.+++|..+.. -..+|++.++
T Consensus 97 d~--V~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 97 DP--VFQTQMMDLLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPYGKVVPDAFSSINP 174 (316)
T ss_pred cH--HHHHHHHHHHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCCCCccCChhhhcCc
Confidence 55 3333 3446688999999999999999999999999999998888888877766532 3778888875
Q ss_pred C
Q 041233 194 S 194 (240)
Q Consensus 194 ~ 194 (240)
.
T Consensus 175 ~ 175 (316)
T KOG1555|consen 175 Q 175 (316)
T ss_pred c
Confidence 3
No 18
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=99.67 E-value=6.9e-16 Score=125.02 Aligned_cols=113 Identities=20% Similarity=0.317 Sum_probs=79.1
Q ss_pred EEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCce-eccChHH--HHHHhhhCCCcceEE
Q 041233 66 VHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSC-QALNEED--VFAIQNERSLFPMGW 142 (240)
Q Consensus 66 V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~-~~~de~e--~~~~~~~~gl~iVGW 142 (240)
+.|+++++..|+.||+.++ |.|+||+|+|...+ ...+..++...+... +..+++. .+..++..|+.+|||
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 5689999999999999988 99999999998754 344455554444332 3344332 333467788999999
Q ss_pred EecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEeeC
Q 041233 143 IHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTE 192 (240)
Q Consensus 143 YHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrLt~ 192 (240)
|||||+.+++||..|++ .|...+-.+.||+.+... ...|+..+
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 334444444555554433 44444443
No 19
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=99.62 E-value=1.9e-15 Score=116.18 Aligned_cols=98 Identities=24% Similarity=0.351 Sum_probs=70.2
Q ss_pred HHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHH----HhhhCCCcceEEEec
Q 041233 70 AQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFA----IQNERSLFPMGWIHT 145 (240)
Q Consensus 70 ~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~----~~~~~gl~iVGWYHS 145 (240)
++++++|++|++.+. |.|+||+|+|......+.++.... .++.+.++ .+.+.++.+||+|||
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 578999999999988 999999999998666666666553 23333333 356789999999999
Q ss_pred CCCCCCCCCHHHHHHHHhhhhcCC-CEEEEEEccCCCCceeEEEEe
Q 041233 146 HPSQSCFMSSVDLHTHYSYQMMVP-EAFAIVLAPTDSSRSYGIFQL 190 (240)
Q Consensus 146 HP~~~~fpSs~Dl~tq~syQ~~~p-e~vaIVisP~~~~~~l~aFrL 190 (240)
||+..++||.+|+.+.. .. ..++||++. .+ +. +|||
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 99999999999998642 22 778999987 21 23 7765
No 20
>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=99.59 E-value=5.3e-14 Score=116.92 Aligned_cols=126 Identities=14% Similarity=0.190 Sum_probs=93.6
Q ss_pred EEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHH---HHHHh--hhCCCcce
Q 041233 66 VHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEED---VFAIQ--NERSLFPM 140 (240)
Q Consensus 66 V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e---~~~~~--~~~gl~iV 140 (240)
|.|.+.++.+|++|+.+....+.+++|+|+|...++.++|+++|+.|...+++. ...|.+. +++.. -..++.+|
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 467888999999999875434788999999999999999999999998765544 2333321 22211 23678999
Q ss_pred EEEecCCCCCCCCCHHHHHHHHhhhhc-CCCEEEEEEccCC----CCceeEEEEeeC
Q 041233 141 GWIHTHPSQSCFMSSVDLHTHYSYQMM-VPEAFAIVLAPTD----SSRSYGIFQLTE 192 (240)
Q Consensus 141 GWYHSHP~~~~fpSs~Dl~tq~syQ~~-~pe~vaIVisP~~----~~~~l~aFrLt~ 192 (240)
||||+++...+.++..|...|..|... .+..++++++|.. +...++||++..
T Consensus 80 GWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~ 136 (157)
T cd08057 80 GWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQ 136 (157)
T ss_pred EEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEec
Confidence 999999987766777775555544443 6778999999965 234699999995
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=99.44 E-value=1.2e-12 Score=112.68 Aligned_cols=114 Identities=21% Similarity=0.180 Sum_probs=87.6
Q ss_pred EECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecC
Q 041233 67 HISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTH 146 (240)
Q Consensus 67 ~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSH 146 (240)
.|+++++++|+.||+++. |+|+||+|+|..+++ +..++++.|...+...+.+++. +..+|+.+|+.||||
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 799999999999999988 999999999964333 4467888888888888888875 348899999999999
Q ss_pred CCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEEEeeCCCCc
Q 041233 147 PSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIFQLTEPSGM 196 (240)
Q Consensus 147 P~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aFrLt~p~gm 196 (240)
|..++|||.+|+.-- ...--++.|+.-.+....--+|||-- .|+
T Consensus 144 ~~spA~PS~tD~~Dd-----~~~~k~~~ViG~~~~~~p~~~~Rl~~-~G~ 187 (192)
T TIGR03735 144 GTGSAFFSETDDADD-----KGEVKISGVLGCLDQGTPQAVFRLCL-LGV 187 (192)
T ss_pred CCCCCCCCcccchhh-----cCceEEEEEEEecCCCCceEEEEEEe-cce
Confidence 999999999998631 11124566666555433345778873 454
No 22
>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=99.42 E-value=1.3e-12 Score=100.72 Aligned_cols=101 Identities=24% Similarity=0.292 Sum_probs=75.2
Q ss_pred HHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCCCC
Q 041233 71 QLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQS 150 (240)
Q Consensus 71 ~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~~~ 150 (240)
++++.|+.+++..+ |.|+||+|+|..++ .+.++.+.++.. +..++.+ ++.+.+.+...||.|||||+..
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 36788999999987 99999999997654 566666665532 2233433 5667788999999999999999
Q ss_pred CCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCceeEEE
Q 041233 151 CFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRSYGIF 188 (240)
Q Consensus 151 ~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~l~aF 188 (240)
+.||..|+... ..+...+||++... ...++||
T Consensus 70 ~~PS~~D~~~~-----~~~~~~~iIv~~~~-~~~~~~~ 101 (101)
T cd08059 70 CRPSEADLSLF-----TRFGLYHVIVCYPY-ENSWKCY 101 (101)
T ss_pred CCCCHHHHHHH-----HhcCCeEEEEECCC-cccEEEC
Confidence 99999999743 23467788887654 3456665
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=99.41 E-value=5.9e-12 Score=113.21 Aligned_cols=127 Identities=13% Similarity=0.208 Sum_probs=94.3
Q ss_pred EEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChH---HHHHHhh--hCCCcce
Q 041233 66 VHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEE---DVFAIQN--ERSLFPM 140 (240)
Q Consensus 66 V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~---e~~~~~~--~~gl~iV 140 (240)
|.|.+-++.+|++|+.+....+..++|.|+|...++.++|+++|+.|...+++.. ..|.+ ++++... ..+..+|
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~~-~~d~~y~~~m~~~~kkv~~~~~vV 79 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNESEDQV-AVDMEYHRTMYELHQKVNPKEVIV 79 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCCEEEEEeCeecceeCCCCeE-EEcHHHHHHHHHHHHHhCCCCcEE
Confidence 4677889999999987744447889999999998899999999999886655543 33432 2222222 4678999
Q ss_pred EEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCC--ceeEEEEeeCCCCc
Q 041233 141 GWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS--RSYGIFQLTEPSGM 196 (240)
Q Consensus 141 GWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~--~~l~aFrLt~p~gm 196 (240)
|||||+|. .-.+...++.++++|...+..|.++++|..++ ..++||++.+ .|+
T Consensus 80 GWY~tg~~--~~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~~~~l~i~ay~~~~-~~~ 134 (265)
T cd08064 80 GWYATGSE--ITEHSALIHDYYSRECTSYNPIHLTVDTSLDDGKMSIKAYVSSP-LGV 134 (265)
T ss_pred eeeeCCCC--CCccHHHHHHHHHhhCCCCCCEEEEEeCCCCCCCcceEEEEEEe-ccc
Confidence 99999983 22346668888888766557799999997654 4699999995 563
No 24
>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=99.39 E-value=9.4e-12 Score=113.02 Aligned_cols=127 Identities=13% Similarity=0.191 Sum_probs=95.6
Q ss_pred EEEECHHHHHHHHHHHhccCC-CCcceEEEeeeeecCCEEEEEEEEecCCCCCCCce--eccChH---HHHHHh--hhCC
Q 041233 65 DVHISAQLMEDFLELAKENTD-KDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSC--QALNEE---DVFAIQ--NERS 136 (240)
Q Consensus 65 ~V~I~~~ll~k~l~hA~~~~~-~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~--~~~de~---e~~~~~--~~~g 136 (240)
.|.|.+.++.+|+.|+.+... .+.+++|.|+|...++.++|+++|+.|...+++.. ...|.+ ++++.. -..+
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 588999999999999876431 26789999999998899999999999886554432 233432 122221 2367
Q ss_pred CcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCC--ceeEEEEeeCCCCc
Q 041233 137 LFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS--RSYGIFQLTEPSGM 196 (240)
Q Consensus 137 l~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~--~~l~aFrLt~p~gm 196 (240)
+.+||||||+|. ++..|+..|..|+...+..|+++++|..+. ..+++|.-.+ ++.
T Consensus 82 e~vVGWY~tg~~----~~~~d~~ih~~~~~~~~~pv~l~vd~~~~~~~lpi~aY~s~~-~~~ 138 (280)
T cd08062 82 EKIVGWYSTGPK----LRPNDLDINELFRRYCPNPVLVIIDVRPKDLGLPTEAYIAVE-EVH 138 (280)
T ss_pred CCeEEEecCCCC----CCcchHHHHHHHHHhCCCCEEEEEecCCCCCCCceEEEEEee-ecc
Confidence 899999999986 566788888888888888899999998743 3589998874 554
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=99.37 E-value=8e-12 Score=107.01 Aligned_cols=107 Identities=14% Similarity=0.097 Sum_probs=82.0
Q ss_pred ECHHHHHHHHHHHhccCCCCcceEEEeeeeec-CCEEEEEEEEecCCCCCCCceeccChHH---HHHH---hhhCCCcce
Q 041233 68 ISAQLMEDFLELAKENTDKDLETCGVLGAFLE-NGTFYVTTLIIPKQDSTSSSCQALNEED---VFAI---QNERSLFPM 140 (240)
Q Consensus 68 I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~-~~~~~Vt~l~~ppq~~ts~~~~~~de~e---~~~~---~~~~gl~iV 140 (240)
|+..++.+|+.||.... +.|+||+|+|+.. ++...|+.++|..+. ++.++|.+ +.++ .+.+|+.+|
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 57789999999999966 8899999999986 667899999998773 46677753 5544 467899999
Q ss_pred EEEecCCCCC-CCCCHHHHHHHHhhhhcCCCEEEEEEccCCC
Q 041233 141 GWIHTHPSQS-CFMSSVDLHTHYSYQMMVPEAFAIVLAPTDS 181 (240)
Q Consensus 141 GWYHSHP~~~-~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~ 181 (240)
|+|||||... ..|+..=..-.-.-+...+.++.++++-..-
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 3466555444444556778899888886554
No 26
>cd08061 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain. Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=99.28 E-value=5.3e-11 Score=107.83 Aligned_cols=133 Identities=20% Similarity=0.347 Sum_probs=104.8
Q ss_pred EEEC-HHHHHHHHHHHhccCCCCcceEEEeeeeecCC-------EEEEEEEEecCCCCCCCceeccCh---HHHHHHhhh
Q 041233 66 VHIS-AQLMEDFLELAKENTDKDLETCGVLGAFLENG-------TFYVTTLIIPKQDSTSSSCQALNE---EDVFAIQNE 134 (240)
Q Consensus 66 V~I~-~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~-------~~~Vt~l~~ppq~~ts~~~~~~de---~e~~~~~~~ 134 (240)
|.+. ..+++.|+......+ ..+.||+|+|+.+.. ...|..++.|||.++.+.+..... +.+-+.+..
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 3443 346666666566666 788999999998543 579999999999999888776542 234445778
Q ss_pred CCCcceEEEecCCCC----CCCCCHHHHHHHHhhhh------cCCCEEEEEEccCCC-CceeEEEEeeCCCCcchhhc
Q 041233 135 RSLFPMGWIHTHPSQ----SCFMSSVDLHTHYSYQM------MVPEAFAIVLAPTDS-SRSYGIFQLTEPSGMSVLKE 201 (240)
Q Consensus 135 ~gl~iVGWYHSHP~~----~~fpSs~Dl~tq~syQ~------~~pe~vaIVisP~~~-~~~l~aFrLt~p~gm~~~~~ 201 (240)
.||+.|||+.||+.. +.|||+.++.+.+.||. ....++.+|+++..+ ...+.||++++ .+|+.+++
T Consensus 91 lGL~~VG~IfT~l~~~~~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~~g~i~~~ayQvSd-q~~~lv~~ 167 (274)
T cd08061 91 LGLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDKDGQIHFEAYQVSD-QAMALVRD 167 (274)
T ss_pred cCCeEEEEEEecCCCCCCCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCCCCceeeeeeeecH-HHHHHHHc
Confidence 999999999999977 78999999999999996 456888999999754 35799999998 58887663
No 27
>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=99.06 E-value=3e-09 Score=86.75 Aligned_cols=105 Identities=15% Similarity=0.063 Sum_probs=66.8
Q ss_pred HHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCC-CCCCCceeccCh---HHHHH-Hhhh--CCCcceEEEe
Q 041233 72 LMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQ-DSTSSSCQALNE---EDVFA-IQNE--RSLFPMGWIH 144 (240)
Q Consensus 72 ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq-~~ts~~~~~~de---~e~~~-~~~~--~gl~iVGWYH 144 (240)
++..|.++.+.. ..+.|+||+|+|...++.+.|+.+..|.. ...+...+.-+. ++.++ +.++ ..+..||-+|
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 445556666554 36889999999998777888888775432 322233333221 22222 2222 3388999999
Q ss_pred cCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEc
Q 041233 145 THPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLA 177 (240)
Q Consensus 145 SHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVis 177 (240)
|||...+.||.+|+.+....-......+.||+.
T Consensus 81 tHP~~~p~PS~~D~~~~~~~~~~~~~~l~iIvG 113 (131)
T TIGR02256 81 THPEDQPEPSWTDRRSWRTIIRSPEAMLLLIVG 113 (131)
T ss_pred cCCCCCCCCCHHHHHHHHHHHhCCCeeEEEEEc
Confidence 999999999999998866543322234455554
No 28
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=98.97 E-value=1.4e-08 Score=93.32 Aligned_cols=131 Identities=15% Similarity=0.205 Sum_probs=91.9
Q ss_pred CceeEEEECHHHHHHHHHHHhccCCC-CcceEEEeeeeecCCEEEEEEEEecCCCCCCCc--eeccChH---HHHHHhh-
Q 041233 61 NVLQDVHISAQLMEDFLELAKENTDK-DLETCGVLGAFLENGTFYVTTLIIPKQDSTSSS--CQALNEE---DVFAIQN- 133 (240)
Q Consensus 61 ~~~~~V~I~~~ll~k~l~hA~~~~~~-p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~--~~~~de~---e~~~~~~- 133 (240)
.+...|.|...++.+|+.|+.+.... ..-+.|.|+|...++.++|+++|+.|....++. ....|.+ ++++...
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 35577999999999999999886411 233899999999889999999999886433322 1223321 2222222
Q ss_pred -hCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCC--ceeEEEEeeCCCCc
Q 041233 134 -ERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSS--RSYGIFQLTEPSGM 196 (240)
Q Consensus 134 -~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~--~~l~aFrLt~p~gm 196 (240)
..+..+||||+|-|. ++..|+.-|..|....+..+.+++++..+. ..++||.... .|.
T Consensus 83 V~~~~~vVGWY~tg~~----i~~~d~~IH~~~~~~~~~Pv~L~vD~~~~~~~lpi~aY~s~~-~~~ 143 (303)
T PLN03246 83 INAKEHVVGWYSTGPK----LRENDLDIHELFNDYVPNPVLVIIDVQPKELGIPTKAYYAVE-EVK 143 (303)
T ss_pred hCCCCcEEeeecCCCC----CCcchHHHHHHHHhhCCCCeEEEEecCCCCCCCceEEEEEEE-ecc
Confidence 367899999999765 455666666667777788888999876532 4589998763 444
No 29
>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=98.94 E-value=1.5e-09 Score=112.17 Aligned_cols=150 Identities=20% Similarity=0.239 Sum_probs=120.2
Q ss_pred eEEEECHHHHHHHHHHHhccCCCCcceEEEeeeee--cC-CEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcce
Q 041233 64 QDVHISAQLMEDFLELAKENTDKDLETCGVLGAFL--EN-GTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPM 140 (240)
Q Consensus 64 ~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~--~~-~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iV 140 (240)
-...+|.+++++|+..++. ...+.|++.|.. ++ ..-+|.++.-+||-++-..+.... .+.....-.+++.+
T Consensus 2095 ~tyilPkNllkkFi~isD~----r~qiag~~yG~s~~d~pqvkeIr~ivmvPQ~gs~~~v~lp~--~lP~~~~l~d~e~L 2168 (2321)
T KOG1795|consen 2095 YTYILPKNLLKKFITISDL----RTQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGSHQGVHLPS--FLPIHGVLEDLEPL 2168 (2321)
T ss_pred ceeeccHHHHhhheeecch----hhhhheeeeccCCCCCCccceEEEEEeccccccccccccCc--cCCcchhccCCccc
Confidence 4578999999999999988 569999999975 33 345899999999976543333211 12233456799999
Q ss_pred EEEecCCCCCCCCCHHHHHHHHhhhhcC-CCEEEEEEccCCCCceeEEEEeeCCCCcchhhcccCCCcccCCCCCCCCCc
Q 041233 141 GWIHTHPSQSCFMSSVDLHTHYSYQMMV-PEAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQETGFHPHKEPADGSPI 219 (240)
Q Consensus 141 GWYHSHP~~~~fpSs~Dl~tq~syQ~~~-pe~vaIVisP~~~~~~l~aFrLt~p~gm~~~~~c~~~~fhph~~~~~~~~~ 219 (240)
||+||.|+.-.++|+.|+.+|...-... ..+|.|.|+.+.++.++.||.|++ +|.+|+..+++.|=.|+.. .+.-
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-SGYEWGEVNKDKGNNPKGY---LPTH 2244 (2321)
T ss_pred chhhcCccccccCCHHHhhhhhhhhhcCccceEEEEeeccCCcceeeeeccCc-cccccchhcccccCCcccc---CccH
Confidence 9999999999999999999998665544 478999999999999999999995 9999999999998888875 3566
Q ss_pred cccc
Q 041233 220 YEHC 223 (240)
Q Consensus 220 y~~~ 223 (240)
|++|
T Consensus 2245 ~e~~ 2248 (2321)
T KOG1795|consen 2245 YEKV 2248 (2321)
T ss_pred HHHH
Confidence 7777
No 30
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=98.92 E-value=1.7e-08 Score=91.95 Aligned_cols=129 Identities=13% Similarity=0.150 Sum_probs=87.6
Q ss_pred EEEECHHHHHHHHHHHhccCCC----CcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHH---HHHHh--hhC
Q 041233 65 DVHISAQLMEDFLELAKENTDK----DLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEED---VFAIQ--NER 135 (240)
Q Consensus 65 ~V~I~~~ll~k~l~hA~~~~~~----p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e---~~~~~--~~~ 135 (240)
.|.|.+.++.+|+.|+.+...+ +.-++|.|+|..+++.++|+++|+.|...+++.....|.+. +++.. -..
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 4677888889999998874321 45689999999988899999999988755442222344321 22211 235
Q ss_pred CCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCC--C--ceeEEEEeeCCCCcc
Q 041233 136 SLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDS--S--RSYGIFQLTEPSGMS 197 (240)
Q Consensus 136 gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~--~--~~l~aFrLt~p~gm~ 197 (240)
++.+||||+|.+. +.+.+...++.+ |....+..|+++++|... . ..++||+-.. .|..
T Consensus 82 ~~~vVGWY~tg~~-~~~~~~~~Ih~~--~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~-~~~~ 143 (288)
T cd08063 82 DLDFVGWYTTGPG-GPTESDLPIHKQ--ILEINESPVLLLLDPEANASGKDLPVTIYESVL-ELVD 143 (288)
T ss_pred CCceEEEEecCCC-CCCHHHHHHHHH--HHhhCCCcEEEEEccccccCCCCCceeEEEEEE-eccC
Confidence 7899999999876 344444445544 445556679999999773 2 3599998774 4543
No 31
>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=98.60 E-value=4.4e-07 Score=83.62 Aligned_cols=110 Identities=22% Similarity=0.331 Sum_probs=87.3
Q ss_pred EEEeeeeecC-C------EEEEEEEEecCCCCCCCceeccCh---HHHHHHhhhCCCcceEEEecCCC------------
Q 041233 91 CGVLGAFLEN-G------TFYVTTLIIPKQDSTSSSCQALNE---EDVFAIQNERSLFPMGWIHTHPS------------ 148 (240)
Q Consensus 91 cGlL~G~~~~-~------~~~Vt~l~~ppq~~ts~~~~~~de---~e~~~~~~~~gl~iVGWYHSHP~------------ 148 (240)
+|+|+|+.+. . ...|..++.|||.++.+.....+. +.+=+.+..-||+.|||+=||+.
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 7999999753 2 478999999999998887665432 22333467789999999999997
Q ss_pred ---CCCCCCHHHHHHHHhhhhcCC-------------CEEEEEEccCCCC-ceeEEEEeeCCCCcchhhc
Q 041233 149 ---QSCFMSSVDLHTHYSYQMMVP-------------EAFAIVLAPTDSS-RSYGIFQLTEPSGMSVLKE 201 (240)
Q Consensus 149 ---~~~fpSs~Dl~tq~syQ~~~p-------------e~vaIVisP~~~~-~~l~aFrLt~p~gm~~~~~ 201 (240)
.+.|+|+..+...+.+|...| .+|.+|+++..+. ..+.||+.++ .+|+.+++
T Consensus 82 r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~~~g~i~~~ayQvS~-q~~~Lv~~ 150 (306)
T PF05021_consen 82 RHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGDEEGEIHFEAYQVSN-QCVALVRA 150 (306)
T ss_pred cccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCCCCCceeeEEeeehH-HHHHHHHC
Confidence 789999999999999999653 5789999986553 4699999997 68887653
No 32
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=98.25 E-value=2.2e-06 Score=88.92 Aligned_cols=138 Identities=18% Similarity=0.288 Sum_probs=101.7
Q ss_pred eEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeec--C-CEEEEEEEEecCCCCCCCceecc--ChHHHHHHhhhCCCc
Q 041233 64 QDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLE--N-GTFYVTTLIIPKQDSTSSSCQAL--NEEDVFAIQNERSLF 138 (240)
Q Consensus 64 ~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~--~-~~~~Vt~l~~ppq~~ts~~~~~~--de~e~~~~~~~~gl~ 138 (240)
.+..||.+++++|++..+. ...+.|++.|+.. + ..-+|.++...||.+.-..+... -+.++ -...||+
T Consensus 2134 ~~y~lP~NLl~kF~~isD~----~vqvag~vyG~s~~d~p~ikeI~~~~lVPQlgs~~~vq~~s~vP~dl---p~~e~le 2206 (2365)
T COG5178 2134 QMYRLPLNLLEKFMRISDP----HVQVAGLVYGKSGSDNPQIKEILSFGLVPQLGSLSGVQSSSFVPHDL---PGDEDLE 2206 (2365)
T ss_pred ccccccHHHHHhhheeccc----ceeeEEEEeccCCccCcchhheeEEEeeccccccccccccccCCCCC---CCcccce
Confidence 4578999999999999988 6699999999763 2 23478888888887643322221 11111 1236899
Q ss_pred ceEEEecCCCCCCCCCHHHHHHHHhhhhcCC--CEEEEEEccCCCCceeEEEEeeCCCCcchhhcccCC------CcccC
Q 041233 139 PMGWIHTHPSQSCFMSSVDLHTHYSYQMMVP--EAFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQET------GFHPH 210 (240)
Q Consensus 139 iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~p--e~vaIVisP~~~~~~l~aFrLt~p~gm~~~~~c~~~------~fhph 210 (240)
+|||+|+..+.-.|++..++.+|..- ...| ++|.|.++-..++.+++||.++. +|.+|...+++- ||||-
T Consensus 2207 ~lGwihtq~~el~~l~~~~v~th~k~-~~d~~~d~v~ltv~~~pgsiSl~ay~v~k-eG~~Wg~~n~di~~~~a~g~ep~ 2284 (2365)
T COG5178 2207 ILGWIHTQDDELPYLEVAGVLTHRKK-IVDPEWDAVTLTVSYLPGSISLRAYVVKK-EGCNWGSKNMDINSDEAIGVEPV 2284 (2365)
T ss_pred eeEEEecCCcccchhhhhhhhhhhhc-ccCccccceeeeeeeccceeeeeeeeehh-ccccccccccccccccccccccc
Confidence 99999999988899999999988633 3444 56777777677777899999997 899998766532 66654
No 33
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=98.19 E-value=2.6e-05 Score=69.69 Aligned_cols=125 Identities=15% Similarity=0.215 Sum_probs=85.3
Q ss_pred CceeEEEECHHHHHHHHHHHhccCC-CCcceEEEeeeeecCCEEEEEEEEecCCCCCC--CceeccCh---HHHHHHhh-
Q 041233 61 NVLQDVHISAQLMEDFLELAKENTD-KDLETCGVLGAFLENGTFYVTTLIIPKQDSTS--SSCQALNE---EDVFAIQN- 133 (240)
Q Consensus 61 ~~~~~V~I~~~ll~k~l~hA~~~~~-~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts--~~~~~~de---~e~~~~~~- 133 (240)
.....|.+-+.+++..+.|-..-.+ ..--+.|+|+|....+++.|++.|..|-+... .++-..|. +.+|....
T Consensus 6 ~~~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~~~~~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~mfkK 85 (309)
T KOG1556|consen 6 LTVEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGSWNGDVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGMFKK 85 (309)
T ss_pred cccceeeeehhHHHHHHHHHhhhccCcCceEEEEEEecCCCCeEEeecceeccccccCCCCceEEeccHHHHHHHHHHHH
Confidence 3456788888899999999776442 23457899999998889999999998875432 23333342 22444333
Q ss_pred -hCCCcceEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCce--eEEEE
Q 041233 134 -ERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSRS--YGIFQ 189 (240)
Q Consensus 134 -~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~~--l~aFr 189 (240)
.....+||||||-|. +-..||.-...+-...|..+-+|++.+....+ ..||-
T Consensus 86 vNakekivGWYhTGPk----l~~nDl~In~l~k~y~pnpvLvIIdvkpk~~gLPT~AY~ 140 (309)
T KOG1556|consen 86 VNAKEKVVGWYHTGPK----LRENDLDINELLKRYVPNPVLVIIDVKPKELGLPTEAYI 140 (309)
T ss_pred hcchhheeeeeccCCc----cccchhhHHHHHhhcCCCceEEEEecccccCCCCchhee
Confidence 356789999999764 55556655555566788899999998776433 44443
No 34
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=97.82 E-value=0.00033 Score=60.79 Aligned_cols=112 Identities=13% Similarity=0.075 Sum_probs=75.0
Q ss_pred EEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCC--EEEEEEEEecCCCCCCCceeccChHHHHH---HhhhCCCcc
Q 041233 65 DVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENG--TFYVTTLIIPKQDSTSSSCQALNEEDVFA---IQNERSLFP 139 (240)
Q Consensus 65 ~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~--~~~Vt~l~~ppq~~ts~~~~~~de~e~~~---~~~~~gl~i 139 (240)
.+.|+..++.||+-||-.-. -.-++|+|+|+..++ .+.|+.++|.-=....- ..+-|-.+.+ +....|+.+
T Consensus 3 ~v~is~~AY~K~~LHaaKyP--~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~~L--~PmlEvAL~qvd~~~~~~gl~I 78 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAKYP--HCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWLSL--SPMLEVALAQVDAYAKSNGLVI 78 (196)
T ss_pred eEEEcHHHHHHHHHHhccCC--CCceeeEEEeccCCCCceEEEeeceeccccccCc--chHHHHHHHHHHHHHhhCCCEE
Confidence 58899999999999998853 466899999997543 39999999863211111 1111111222 245789999
Q ss_pred eEEEecCCC-CCCCCCHHHHHHHHhhhhcCCCEEEEEEccCC
Q 041233 140 MGWIHTHPS-QSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTD 180 (240)
Q Consensus 140 VGWYHSHP~-~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~ 180 (240)
||+||..-. ...-|+..-..-.-.-....+.++.|+++-++
T Consensus 79 vGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~k 120 (196)
T PF03665_consen 79 VGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKK 120 (196)
T ss_pred EEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcc
Confidence 999998653 23446666444444444568899999998654
No 35
>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=97.62 E-value=0.00042 Score=66.61 Aligned_cols=128 Identities=21% Similarity=0.343 Sum_probs=97.0
Q ss_pred CHHHHHHHHHHHhccCCCCcceEEEeeeeec-CCEE------EEEEEEecCCCCCCCceeccChH--HHHH-HhhhCCCc
Q 041233 69 SAQLMEDFLELAKENTDKDLETCGVLGAFLE-NGTF------YVTTLIIPKQDSTSSSCQALNEE--DVFA-IQNERSLF 138 (240)
Q Consensus 69 ~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~-~~~~------~Vt~l~~ppq~~ts~~~~~~de~--e~~~-~~~~~gl~ 138 (240)
..++++.|++.-+.. .....|+|+|... ++.+ +|..++.|||.++.+.....+.. ...+ .+..-||+
T Consensus 181 ~~~~v~~Fl~~wr~s---g~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~~~~dgl~l~~~~e~~~vD~~a~~lGLr 257 (510)
T KOG2834|consen 181 NAELVNHFLNEWRAS---GVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQHGEEDGLELLEDDEAKRVDAIAEGLGLR 257 (510)
T ss_pred chHHHHHHHHHHHHh---hhhhcceEEEeecccccccccceeeEEEEecCCccCCcCCeEEeccchhhhHHHHHHhcCce
Confidence 457999999998885 6888999999974 3444 88999999999998877665322 2233 35788999
Q ss_pred ceEEEecCC---------------CCCCCCCHHHHHHHHhhhhcCCC-------------EEEEEEccCCC-CceeEEEE
Q 041233 139 PMGWIHTHP---------------SQSCFMSSVDLHTHYSYQMMVPE-------------AFAIVLAPTDS-SRSYGIFQ 189 (240)
Q Consensus 139 iVGWYHSHP---------------~~~~fpSs~Dl~tq~syQ~~~pe-------------~vaIVisP~~~-~~~l~aFr 189 (240)
-||||-|-- ..+.|+|+.+..+.+.+|.+.|. +|.+|++-..+ ...+-.|+
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 999997643 24689999999999999987763 56677765444 34699999
Q ss_pred eeCCCCcchhh
Q 041233 190 LTEPSGMSVLK 200 (240)
Q Consensus 190 Lt~p~gm~~~~ 200 (240)
.++ .+|..+.
T Consensus 338 VSn-qc~alv~ 347 (510)
T KOG2834|consen 338 VSN-QCMALVE 347 (510)
T ss_pred hhH-HHHHHhh
Confidence 998 6887533
No 36
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=97.44 E-value=0.0011 Score=59.74 Aligned_cols=130 Identities=12% Similarity=0.203 Sum_probs=84.0
Q ss_pred eEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccC--hHHHHHHhhh--CCCcc
Q 041233 64 QDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALN--EEDVFAIQNE--RSLFP 139 (240)
Q Consensus 64 ~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~d--e~e~~~~~~~--~gl~i 139 (240)
..|.|-.-++-.++.+.....++..-++|-|+|..+++.++||++|..|-...++.++.-. ..++++.-.+ -+..+
T Consensus 21 ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g~ieitNCFaVPhnEssdqvevdm~y~~~M~~l~~k~npnE~v 100 (288)
T KOG2975|consen 21 LTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKGSVEVTNCFAVPHNESSDQVEVDMEYAKNMYELHKKVNPNELV 100 (288)
T ss_pred ceEEEcceEEeEeehhhhcCCccchhhhhheeecccCCeEEEEEeeeccCccccccceeeHHHHHHHHHHhcccCCCcee
Confidence 4566666666677777666554556689999999999999999999877554445433211 1234443333 46789
Q ss_pred eEEEecCCCCCCCCCHHHHHHHHhhhhcCCCEEEEEEccCCC--CceeEEEEeeCCCCcch
Q 041233 140 MGWIHTHPSQSCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDS--SRSYGIFQLTEPSGMSV 198 (240)
Q Consensus 140 VGWYHSHP~~~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~--~~~l~aFrLt~p~gm~~ 198 (240)
||||=|-++-+.+ +.=+|.- |-.-.++.+-+.++-.-. .-.+|||--+. -|+..
T Consensus 101 vGWyaTg~dvt~~--sslihdy--Yare~~~pvhLtVDT~~~n~rm~ikaYvss~-~Gvpg 156 (288)
T KOG2975|consen 101 VGWYATGHDVTEH--SSLIHDY--YAREAPNPVHLTVDTSLQNGRMSIKAYVSSL-MGVPG 156 (288)
T ss_pred EEEEecCCCcccc--hhHHHHH--hhccCCCCeEEEEeccccCCccceeEEEEec-cCCCC
Confidence 9999887765553 3334443 444567777777775433 23599998774 56543
No 37
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=94.81 E-value=0.5 Score=40.74 Aligned_cols=124 Identities=17% Similarity=0.145 Sum_probs=76.9
Q ss_pred EEEECHHHHHHHHHHHhccCCCCcc-eEEEeeeee--cCCEEEEEEEEecCCCCCCCceeccChHHHH--HH---hhhCC
Q 041233 65 DVHISAQLMEDFLELAKENTDKDLE-TCGVLGAFL--ENGTFYVTTLIIPKQDSTSSSCQALNEEDVF--AI---QNERS 136 (240)
Q Consensus 65 ~V~I~~~ll~k~l~hA~~~~~~p~E-vcGlL~G~~--~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~--~~---~~~~g 136 (240)
.+.|+..++-+|+-||..- |.- +-|+|+|.. +++.++|+.++|.--+.. ....+.|+. .+ ....|
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 4789999999999999874 444 579999965 457899999998633221 111122221 11 34789
Q ss_pred CcceEEEecCCCC-CCCCCHHHHHHHHhhhhcCCCEEEEEEccCCCCc-----eeEEEEeeCCCCcch
Q 041233 137 LFPMGWIHTHPSQ-SCFMSSVDLHTHYSYQMMVPEAFAIVLAPTDSSR-----SYGIFQLTEPSGMSV 198 (240)
Q Consensus 137 l~iVGWYHSHP~~-~~fpSs~Dl~tq~syQ~~~pe~vaIVisP~~~~~-----~l~aFrLt~p~gm~~ 198 (240)
+.++|.||+--.. ...|...-....-.-+...|.+..|+.+-+.-.. .+-.|- + .|..|
T Consensus 76 lviaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~~l~~~~e~~~v~v~e--~-~g~rW 140 (199)
T KOG3289|consen 76 LVIAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNKKLVPQCERPPVIVLE--D-QGLRW 140 (199)
T ss_pred eEEEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEeccccccccCCCCEEEee--c-cCcce
Confidence 9999999985431 1223333333333345567888888887654321 244443 3 57777
No 38
>cd08071 MPN_DUF2466 Mov34/MPN/PAD-1 family. Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. However, to date, the name RadC has been misleading and no function has been determined.
Probab=94.54 E-value=0.53 Score=37.19 Aligned_cols=72 Identities=21% Similarity=0.157 Sum_probs=49.9
Q ss_pred CcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCCCCCCCCHHHHHHHHh
Q 041233 87 DLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYS 163 (240)
Q Consensus 87 p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~s 163 (240)
+.|...+|+=...++.+....+.. ++-+ ....++.++++.+...+..-+..-|.||+..+.||..|++.-..
T Consensus 15 ~~E~~~vl~Ld~~~~li~~~~l~~----G~~~-~~~v~~R~i~~~aL~~~A~~vil~HNHPsG~~~PS~~D~~~T~~ 86 (113)
T cd08071 15 DQEEFVVLLLDTKNRLIAVETISV----GTLN-SSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIELTKR 86 (113)
T ss_pred CceEEEEEEecCCCCEEEEEEEee----cCCc-ceecCHHHHHHHHHHHhhheEEEEeeCCCCCCCCCHHHHHHHHH
Confidence 678777665333333333333332 2222 24557889998888888899999999999999999999876543
No 39
>PF14220 DUF4329: Domain of unknown function (DUF4329)
Probab=93.81 E-value=0.52 Score=38.16 Aligned_cols=65 Identities=22% Similarity=0.360 Sum_probs=41.3
Q ss_pred CCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCC-----CCCCCCHHHHHH
Q 041233 86 KDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPS-----QSCFMSSVDLHT 160 (240)
Q Consensus 86 ~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~-----~~~fpSs~Dl~t 160 (240)
++.|.||++ ++..++.+.-+. |..+..+.|..... ....+...|+-||||.. ..-.||..|+..
T Consensus 19 ~nrEy~G~I-~~~~~G~y~~t~----p~~G~~~~~~~~~~------~~p~g~~~vA~yHTHG~~~~~y~~evfS~~D~~~ 87 (123)
T PF14220_consen 19 ENREYCGYI-GKDEDGKYFATE----PRRGENASCYPSNP------PCPNGSTIVASYHTHGAYSDGYDNEVFSPQDIRG 87 (123)
T ss_pred CCcEEEEEE-EEcCCCcEEeec----CccCCCCCcCCCCc------ccccccceeeEeecccccCCCccccCCCHHHhhh
Confidence 588999976 455555544332 23334444443332 12358899999999985 345699999875
Q ss_pred H
Q 041233 161 H 161 (240)
Q Consensus 161 q 161 (240)
-
T Consensus 88 ~ 88 (123)
T PF14220_consen 88 D 88 (123)
T ss_pred h
Confidence 3
No 40
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=92.93 E-value=0.4 Score=43.32 Aligned_cols=90 Identities=16% Similarity=0.258 Sum_probs=56.3
Q ss_pred Cc-ceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhh-----hCCCcceEEEecCCCCCCCCCHHHHHH
Q 041233 87 DL-ETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQN-----ERSLFPMGWIHTHPSQSCFMSSVDLHT 160 (240)
Q Consensus 87 p~-EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~-----~~gl~iVGWYHSHP~~~~fpSs~Dl~t 160 (240)
|. .+-|-|+|+..++.++|.+.|...-....+. ..+|-+-+.+-++ =.++.++|||-+- .. +...|++.
T Consensus 35 p~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~~~-~~~dke~l~kk~eqykqVFpdl~vlGwYttG--~d--~t~sd~~i 109 (299)
T KOG3050|consen 35 PVKQVYGALIGKQRGRNVEIMNSFELKMDTEEDT-ETIDKEYLEKKEEQYKQVFPDLYVLGWYTTG--SD--PTPSDIHI 109 (299)
T ss_pred cHHHhhhhheecccCceEEEeeeeEEEecchhhh-hhccHHHHHHHHHHHHHhcccceEEEEeecC--CC--CChhhhHH
Confidence 66 7889999999999999999987754433222 1334322222221 2689999999763 23 46677777
Q ss_pred HHhhhhcCCCEEEEEEccCCC
Q 041233 161 HYSYQMMVPEAFAIVLAPTDS 181 (240)
Q Consensus 161 q~syQ~~~pe~vaIVisP~~~ 181 (240)
|...-....--+++-..|...
T Consensus 110 ~k~l~~i~esplflkLNp~t~ 130 (299)
T KOG3050|consen 110 HKQLMDINESPLFLKLNPATN 130 (299)
T ss_pred HHHHHhhhcCceEEEecchhc
Confidence 664444444456666666443
No 41
>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=92.67 E-value=0.092 Score=42.67 Aligned_cols=33 Identities=21% Similarity=0.258 Sum_probs=28.3
Q ss_pred EEEEEEccCCCCceeEEEEeeCCCCcchhhcccC
Q 041233 171 AFAIVLAPTDSSRSYGIFQLTEPSGMSVLKECQE 204 (240)
Q Consensus 171 ~vaIVisP~~~~~~l~aFrLt~p~gm~~~~~c~~ 204 (240)
.|.|.|+.+.++.++.||+||+ +|.+|++++++
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 3788999999988999999995 99999999887
No 42
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=92.17 E-value=0.35 Score=46.55 Aligned_cols=128 Identities=20% Similarity=0.289 Sum_probs=91.3
Q ss_pred CHHHHHHHHHHHhccCCCCcceEEEeeeeecC--C-----EEEEEEEEecCCCCCCCceec--cChHHHHHH-hhhCCCc
Q 041233 69 SAQLMEDFLELAKENTDKDLETCGVLGAFLEN--G-----TFYVTTLIIPKQDSTSSSCQA--LNEEDVFAI-QNERSLF 138 (240)
Q Consensus 69 ~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~--~-----~~~Vt~l~~ppq~~ts~~~~~--~de~e~~~~-~~~~gl~ 138 (240)
.+.+++.|++.=+.. +.+..|+|.|.... + .-.|..++.|||....+-... -..+.+.+. +..-||+
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 457899999887774 67889999998632 1 126677888999877665332 111123322 3567899
Q ss_pred ceEEEecCC---------------CCCCCCCHHHHHHHHhhhhcCC-------------CEEEEEEccCCC-CceeEEEE
Q 041233 139 PMGWIHTHP---------------SQSCFMSSVDLHTHYSYQMMVP-------------EAFAIVLAPTDS-SRSYGIFQ 189 (240)
Q Consensus 139 iVGWYHSHP---------------~~~~fpSs~Dl~tq~syQ~~~p-------------e~vaIVisP~~~-~~~l~aFr 189 (240)
.+|.+-|-- .-+-|+|+..+...+.+|.+.| .++.+|++-..+ +.++..|+
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 999987643 2357899999999999999876 457788876554 46799999
Q ss_pred eeCCCCcchhh
Q 041233 190 LTEPSGMSVLK 200 (240)
Q Consensus 190 Lt~p~gm~~~~ 200 (240)
.++ .+|+.++
T Consensus 397 VSn-~~~ALv~ 406 (571)
T COG5100 397 VSN-QCMALVK 406 (571)
T ss_pred ehh-hhhHHhh
Confidence 997 7887654
No 43
>PF04002 RadC: RadC-like JAB domain; InterPro: IPR001405 This family was named initially with reference to the Escherichia coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions []. However the relevant mutation has subsequently been shown to be in recG, not radC []. In addition all attempts to characterise a radiation-related function for RadC in Streptococcus pneumoniae failed, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair [].; PDB: 2QLC_A.
Probab=90.71 E-value=2.3 Score=33.86 Aligned_cols=74 Identities=19% Similarity=0.116 Sum_probs=41.5
Q ss_pred CcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCCCCCCCCHHHHHHHHhhh
Q 041233 87 DLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPSQSCFMSSVDLHTHYSYQ 165 (240)
Q Consensus 87 p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~~~~fpSs~Dl~tq~syQ 165 (240)
+.|...+|+=...++.+....+. .++.+. -..+++++++.+-..+-.-|-..|-||+..+.||..|+..-...+
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 DQEQFRVLYLDSKNRLIGDEVVS----EGTIDS-APVDPREIFRRALRLNASSVILAHNHPSGDPEPSDADIALTRRLK 93 (123)
T ss_dssp TS-EEEEEEE-TTSBEEEEEEEE----ESTT-G-GGCSHHHHHHHHHHTT-SEEEEEEE-TTS--S--HHHHHHHHHHH
T ss_pred CCeEEEEEEECCCCcEEEEEEec----ccCCCc-ccccHHHHHHHHHhhCCceEEEEEEcCCCCCCCCHhHHHHHHHHH
Confidence 55776655432233334444443 233333 345788999988777777788889999999999999986544333
No 44
>PRK00024 hypothetical protein; Reviewed
Probab=85.46 E-value=9.5 Score=33.68 Aligned_cols=89 Identities=18% Similarity=0.100 Sum_probs=55.4
Q ss_pred CHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCC
Q 041233 69 SAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPS 148 (240)
Q Consensus 69 ~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~ 148 (240)
+.+.+.++++..-... +.|...+|+=...++.+....++ .++-+. ...++.++|+.+-..+-.-|=.-|=||+
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----IGTLNS-SIVHPREIVKRALKLNAAALILAHNHPS 177 (224)
T ss_pred CHHHHHHHHHHHccCC--CceEEEEEEECCCCCEeeEEEee----eecCCe-EEEcHHHHHHHHHHhhccceEEEecCCC
Confidence 3334445554433333 67877776533333333433332 233233 4567899999877777777777899999
Q ss_pred CCCCCCHHHHHHHHhh
Q 041233 149 QSCFMSSVDLHTHYSY 164 (240)
Q Consensus 149 ~~~fpSs~Dl~tq~sy 164 (240)
..+.||..|+..-...
T Consensus 178 G~~~PS~~D~~~T~~l 193 (224)
T PRK00024 178 GDPEPSQADILITKRL 193 (224)
T ss_pred CCCCCCHHHHHHHHHH
Confidence 9999999998764433
No 45
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.50 E-value=17 Score=32.10 Aligned_cols=88 Identities=18% Similarity=0.094 Sum_probs=54.3
Q ss_pred CHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecCCC
Q 041233 69 SAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTHPS 148 (240)
Q Consensus 69 ~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSHP~ 148 (240)
+.+.+.+++...-... +.|...+|+=...++.+....++ .++-+. -..++.++|+.+-..+-.-|=.-|=||+
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----IGTVNH-VPVHPREIFKEALKLSASALILAHNHPS 171 (218)
T ss_pred CHHHHHHHHHHHhcCC--CceEEEEEEECCCCcEEEEEEee----cCCCCe-EEEcHHHHHHHHHHhhCCeEEEEeecCC
Confidence 3444445555444433 67777666422223333333332 233333 4567899998877766666667799999
Q ss_pred CCCCCCHHHHHHHHh
Q 041233 149 QSCFMSSVDLHTHYS 163 (240)
Q Consensus 149 ~~~fpSs~Dl~tq~s 163 (240)
..+.||..|+..-..
T Consensus 172 G~~~PS~~Di~~T~~ 186 (218)
T TIGR00608 172 GEPSPSQEDILITER 186 (218)
T ss_pred CCCCCCHHHHHHHHH
Confidence 999999999875433
No 46
>PF15659 Toxin-JAB1: JAB-like toxin 1
Probab=73.96 E-value=11 Score=32.10 Aligned_cols=28 Identities=25% Similarity=0.277 Sum_probs=22.7
Q ss_pred hhCCCcceEEEecCCCCCCCCCHHHHHHH
Q 041233 133 NERSLFPMGWIHTHPSQSCFMSSVDLHTH 161 (240)
Q Consensus 133 ~~~gl~iVGWYHSHP~~~~fpSs~Dl~tq 161 (240)
...+-.++. +||||..+.++|..|..+.
T Consensus 112 ~~~~~~iid-iHSHP~~~~~~S~~D~~~~ 139 (162)
T PF15659_consen 112 KNNGNKIID-IHSHPENSNGPSGNDMKNA 139 (162)
T ss_pred ccCCceEEE-eccCCCCCCCCCcchhhhh
Confidence 346677777 9999998889999998754
No 47
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=65.70 E-value=44 Score=31.51 Aligned_cols=101 Identities=17% Similarity=0.171 Sum_probs=52.8
Q ss_pred EEeeeee-cCCEEEEEEEEecCCCCCCCc----------eeccChHHHHHH------hhhCCCcceEEEecCCCCCCCCC
Q 041233 92 GVLGAFL-ENGTFYVTTLIIPKQDSTSSS----------CQALNEEDVFAI------QNERSLFPMGWIHTHPSQSCFMS 154 (240)
Q Consensus 92 GlL~G~~-~~~~~~Vt~l~~ppq~~ts~~----------~~~~de~e~~~~------~~~~gl~iVGWYHSHP~~~~fpS 154 (240)
|||+|+. ..+.-+|.++.+.|...+... ...+|++-+.++ +...|+.+||+|=.+|....--+
T Consensus 1 GLlIGq~~s~~kd~Vv~l~~tP~~d~~~~~~~~~~~~~~~~~id~~WVaeHA~qVsRMLPGGi~VlGifvv~~~~~~~~~ 80 (362)
T PF14778_consen 1 GLLIGQSSSSQKDYVVHLARTPPEDTDDEESDVRTSDSSIKDIDEEWVAEHARQVSRMLPGGISVLGIFVVAPDDAFKDS 80 (362)
T ss_pred CeEeccccCCCcceEEEecCCCCccccccccccccccccccccCHHHHHHHHHHHHhhCCCCcEEEEEEEEcCHHHhccc
Confidence 8999998 555557777777554332222 223454434444 23579999999977653211111
Q ss_pred H--HHHHHHHh--------hhhcCCCEEEEEEccCC-CCceeEEEEeeC
Q 041233 155 S--VDLHTHYS--------YQMMVPEAFAIVLAPTD-SSRSYGIFQLTE 192 (240)
Q Consensus 155 s--~Dl~tq~s--------yQ~~~pe~vaIVisP~~-~~~~l~aFrLt~ 192 (240)
. .-+..... |.....+.+.|.++... .....|.|.+.+
T Consensus 81 ~~~~~l~~l~~~~~~~~~~~~~~~~e~~~l~i~~st~kk~~Ck~~~~~~ 129 (362)
T PF14778_consen 81 STLNKLKKLLFSSNSLWSVYNDDVSERLLLHICSSTSKKLTCKSYDVAD 129 (362)
T ss_pred hHHHHHHHHHhhhcccccccCCCcccceEEEEEcccCceEEEEEEEecC
Confidence 1 01111111 11123456666666554 234577777754
No 48
>PF09935 DUF2167: Protein of unknown function (DUF2167); InterPro: IPR018682 This family of various hypothetical membrane-anchored prokaryotic proteins has no known function.
Probab=44.05 E-value=1.2e+02 Score=27.38 Aligned_cols=80 Identities=13% Similarity=0.158 Sum_probs=48.9
Q ss_pred ceeEEEECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhh--------
Q 041233 62 VLQDVHISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQN-------- 133 (240)
Q Consensus 62 ~~~~V~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~-------- 133 (240)
+...++++..--.++++.. -|...+.+ +|+++...++..+.|+--+...-....+.....|..++++-++
T Consensus 20 P~g~~fL~~~~a~~~l~~~-GN~~~~~~-~Gli~P~~~~~~W~v~~~y~~~GyVkDdda~~id~d~LL~~~k~~t~e~N~ 97 (239)
T PF09935_consen 20 PAGFRFLNPEDARKVLEEW-GNPPSPAE-LGLIFPDDDDEDWFVVFEYEDSGYVKDDDAKNIDYDELLKSMKEGTEESNK 97 (239)
T ss_pred CCCcEEcCHHHHHHHHHHh-CCCCCcce-EEEEeccCCCCCEEEEEEEcCCCceecchhhhCCHHHHHHHHHHhHHhhhH
Confidence 3345889999999999544 34422334 8999877655555554444443333445555677777776421
Q ss_pred ---hC---CCcceEEE
Q 041233 134 ---ER---SLFPMGWI 143 (240)
Q Consensus 134 ---~~---gl~iVGWY 143 (240)
++ .+.++||.
T Consensus 98 eR~~~G~~~l~l~GW~ 113 (239)
T PF09935_consen 98 ERKKRGYPPLHLVGWA 113 (239)
T ss_pred HHHhcCCCceEEeccc
Confidence 22 37899995
No 49
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=37.19 E-value=37 Score=30.34 Aligned_cols=87 Identities=20% Similarity=0.163 Sum_probs=48.8
Q ss_pred EECHHHHHHHHHHHhccCCCCcceEEEeeeeecCCEEEEEEEEecCCCCCCCceeccChHHHHHHhhhCCCcceEEEecC
Q 041233 67 HISAQLMEDFLELAKENTDKDLETCGVLGAFLENGTFYVTTLIIPKQDSTSSSCQALNEEDVFAIQNERSLFPMGWIHTH 146 (240)
Q Consensus 67 ~I~~~ll~k~l~hA~~~~~~p~EvcGlL~G~~~~~~~~Vt~l~~ppq~~ts~~~~~~de~e~~~~~~~~gl~iVGWYHSH 146 (240)
.-+.+.+.+++.-...+. ..|.--+|+=...++.+....++.- |- +.....|.|+++.+-..+..=|=..|=|
T Consensus 103 i~sp~~~~~~l~~~l~~~--~~E~f~vL~Ld~qnrlI~~e~lf~G----Ti-~~s~V~PREI~k~Al~~nAaavIlaHNH 175 (224)
T COG2003 103 ITSPEAVAEYLRAELGGE--EREHFVVLYLDSQNRLIATETLFIG----TL-NVSEVHPREIFKEALKYNAAAVILAHNH 175 (224)
T ss_pred cCCHHHHHHHHHHHhhhh--HHHHHHHHHhcCcCceecceeEEee----ec-ccceecHHHHHHHHHHhcchhhheeccC
Confidence 334455555555444433 4454333332222333344444422 21 1233458888887766555555557999
Q ss_pred CCCCCCCCHHHHHH
Q 041233 147 PSQSCFMSSVDLHT 160 (240)
Q Consensus 147 P~~~~fpSs~Dl~t 160 (240)
|+..+-||..|+.-
T Consensus 176 PSGd~~PS~aD~~i 189 (224)
T COG2003 176 PSGDPTPSRADILI 189 (224)
T ss_pred CCCCCCcCHHHHHH
Confidence 99999999999764
No 50
>TIGR02867 spore_II_P stage II sporulation protein P. Stage II sporulation protein P is a protein of the endospore formation program in a number of lineages in the Firmicutes (low-GC Gram-positive bacteria). It is expressed in the mother cell compartment, under control of Sigma-E. SpoIIP, along with SpoIIM and SpoIID, is one of three major proteins involved in engulfment of the forespore by the mother cell. This protein family is named for the single member in Bacillus subtilis, although most sporulating bacteria have two members.
Probab=26.44 E-value=40 Score=29.32 Aligned_cols=15 Identities=27% Similarity=0.301 Sum_probs=11.1
Q ss_pred eEEEecCCCCCCCCC
Q 041233 140 MGWIHTHPSQSCFMS 154 (240)
Q Consensus 140 VGWYHSHP~~~~fpS 154 (240)
|++||||...+-.|+
T Consensus 1 V~IYhTH~~Esy~p~ 15 (196)
T TIGR02867 1 VFIYHTHSTESYLPE 15 (196)
T ss_pred CEEEeCCCcccccCC
Confidence 689999986555555
No 51
>PF07454 SpoIIP: Stage II sporulation protein P (SpoIIP); InterPro: IPR010897 This family contains the bacterial stage II sporulation protein P (SpoIIP) (approximately 350 residues long). It has been shown that a block in polar cytokinesis in Bacillus subtilis is mediated partly by transcription of spoIID, spoIIM and spoIIP. This inhibition of polar division is involved in the locking in of asymmetry after the formation of a polar septum during sporulation []. SpoIIP is one of the three genes (spoIID, spoIIM and spoIIP, [, , ]), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan and mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the stage of engulfment. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers [].
Probab=22.01 E-value=60 Score=29.59 Aligned_cols=21 Identities=24% Similarity=0.165 Sum_probs=15.3
Q ss_pred hCCCcceEEEecCCCCCCCCC
Q 041233 134 ERSLFPMGWIHTHPSQSCFMS 154 (240)
Q Consensus 134 ~~gl~iVGWYHSHP~~~~fpS 154 (240)
..+.-.|++||||...+-.|+
T Consensus 70 ~~~~~~V~IYhTH~~EsY~p~ 90 (268)
T PF07454_consen 70 TSGKPQVLIYHTHSTESYLPS 90 (268)
T ss_pred CCCCCEEEEEeCCCccccccc
Confidence 455678999999986544455
Done!