Query 018450
Match_columns 355
No_of_seqs 165 out of 1126
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 09:07:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018450.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018450hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd08068 MPN_BRCC36 Mov34/MPN/P 100.0 8.2E-54 1.8E-58 404.0 24.8 227 3-351 1-243 (244)
2 KOG1555 26S proteasome regulat 100.0 1.4E-31 3E-36 259.3 12.6 245 4-350 31-286 (316)
3 cd08067 MPN_2A_DUB Mov34/MPN/P 100.0 5.1E-28 1.1E-32 221.0 19.2 148 5-164 6-163 (187)
4 cd08058 MPN_euk_mb Mpr1p, Pad1 99.9 2.1E-26 4.5E-31 194.5 13.8 119 11-149 1-119 (119)
5 cd08069 MPN_RPN11_CSN5 Mov34/M 99.9 7.6E-26 1.6E-30 216.6 18.8 140 2-153 8-149 (268)
6 cd08070 MPN_like Mpr1p, Pad1p 99.9 4.2E-24 9.1E-29 182.4 15.8 122 11-154 2-124 (128)
7 cd08066 MPN_AMSH_like Mov34/MP 99.9 2E-23 4.3E-28 188.6 18.0 123 3-149 1-127 (173)
8 smart00232 JAB_MPN JAB/MPN dom 99.9 1.1E-21 2.4E-26 165.1 16.9 132 5-150 1-134 (135)
9 KOG1554 COP9 signalosome, subu 99.9 6.8E-23 1.5E-27 195.7 9.9 142 3-153 52-193 (347)
10 cd08065 MPN_eIF3h Mpr1p, Pad1p 99.9 4.9E-21 1.1E-25 183.1 17.6 136 4-151 1-137 (266)
11 cd08073 MPN_NLPC_P60 Mpr1p, Pa 99.8 7.4E-20 1.6E-24 153.6 12.3 102 12-147 2-104 (108)
12 PF01398 JAB: JAB1/Mov34/MPN/P 99.8 4.5E-20 9.8E-25 153.6 10.2 114 1-122 1-114 (114)
13 cd08072 MPN_archaeal Mov34/MPN 99.8 2.9E-19 6.3E-24 151.8 14.3 114 8-156 1-114 (117)
14 cd07767 MPN Mpr1p, Pad1p N-ter 99.8 2.1E-18 4.6E-23 142.1 12.9 105 14-132 2-106 (116)
15 COG1310 Predicted metal-depend 99.7 4.9E-16 1.1E-20 133.8 13.7 104 6-131 2-106 (134)
16 cd08057 MPN_euk_non_mb Mpr1p, 99.7 3.3E-15 7.2E-20 132.0 17.3 145 6-162 1-148 (157)
17 PF14464 Prok-JAB: Prokaryotic 99.6 1.8E-15 4E-20 123.2 9.8 93 10-130 2-96 (104)
18 cd08062 MPN_RPN7_8 Mpr1p, Pad1 99.6 1.1E-13 2.3E-18 133.9 17.0 129 4-149 1-134 (280)
19 KOG1560 Translation initiation 99.6 2.6E-14 5.7E-19 136.9 11.8 139 2-150 11-155 (339)
20 KOG2880 SMAD6 interacting prot 99.5 3.2E-15 6.9E-20 147.0 4.9 167 2-203 250-424 (424)
21 cd08064 MPN_eIF3f Mpr1p, Pad1p 99.5 4.8E-13 1E-17 128.0 16.7 129 6-150 1-131 (265)
22 cd08059 MPN_prok_mb Mpr1p, Pad 99.5 1.2E-13 2.6E-18 113.2 9.9 92 11-130 1-92 (101)
23 cd08060 MPN_UPF0172 Mov34/MPN/ 99.5 5.8E-13 1.3E-17 121.6 13.5 130 8-153 1-134 (182)
24 TIGR03735 PRTRC_A PRTRC system 99.5 4.1E-13 8.9E-18 123.5 11.5 110 7-149 74-183 (192)
25 cd08063 MPN_CSN6 Mpr1p, Pad1p 99.3 4.8E-11 1E-15 115.6 16.6 131 5-149 2-138 (288)
26 PLN03246 26S proteasome regula 99.3 9.8E-11 2.1E-15 114.6 17.4 131 2-149 4-139 (303)
27 TIGR02256 ICE_VC0181 integrati 99.1 1.4E-09 3E-14 94.9 14.5 111 12-130 2-114 (131)
28 KOG1556 26S proteasome regulat 99.0 2.5E-09 5.3E-14 101.7 11.8 120 2-132 7-129 (309)
29 cd08056 MPN_PRP8 Mpr1p, Pad1p 98.8 5.2E-08 1.1E-12 93.4 13.8 124 5-151 37-167 (252)
30 PF03665 UPF0172: Uncharacteri 98.3 1.6E-05 3.6E-10 73.7 14.3 117 4-131 2-119 (196)
31 cd08061 MPN_NPL4 Mov34/MPN/PAD 97.9 0.00024 5.3E-09 69.1 14.3 133 4-151 11-160 (274)
32 KOG2975 Translation initiation 97.8 0.00017 3.6E-09 69.7 10.7 144 4-165 21-171 (288)
33 KOG3289 Uncharacterized conser 97.2 0.0073 1.6E-07 55.7 12.9 112 5-130 3-118 (199)
34 PF05021 NPL4: NPL4 family; I 96.7 0.024 5.2E-07 56.2 12.6 109 29-151 2-143 (306)
35 KOG3050 COP9 signalosome, subu 93.9 0.41 8.8E-06 46.5 9.4 144 5-163 10-161 (299)
36 cd08071 MPN_DUF2466 Mov34/MPN/ 92.1 1.5 3.3E-05 37.1 9.5 45 61-114 41-85 (113)
37 PF04002 RadC: RadC-like JAB d 81.0 7.2 0.00016 33.4 7.2 45 61-114 46-90 (123)
38 TIGR00608 radc DNA repair prot 76.6 29 0.00064 32.9 10.5 87 9-114 99-185 (218)
39 PRK00024 hypothetical protein; 76.0 30 0.00065 32.8 10.4 87 9-114 105-191 (224)
40 PF14220 DUF4329: Domain of un 66.6 5.4 0.00012 34.7 2.8 27 87-113 57-88 (123)
41 PF15659 Toxin-JAB1: JAB-like 57.9 7.9 0.00017 35.4 2.4 26 86-112 113-138 (162)
42 KOG2834 Nuclear pore complex, 57.7 1.6E+02 0.0035 31.4 12.0 127 10-153 182-343 (510)
43 PF14778 ODR4-like: Olfactory 43.7 45 0.00098 33.7 5.5 26 75-100 49-74 (362)
44 KOG1795 U5 snRNP spliceosome s 38.2 41 0.00089 40.0 4.5 123 7-154 2098-2225(2321)
45 cd07278 PX_RICS_like The phosp 27.2 15 0.00033 31.7 -0.8 11 335-345 103-113 (114)
46 cd07298 PX_RICS The phosphoino 26.8 15 0.00033 31.8 -0.9 11 335-345 104-114 (115)
47 cd07299 PX_TCGAP The phosphoin 25.8 16 0.00035 31.5 -0.9 11 335-345 102-112 (113)
48 KOG2332 Ferritin [Inorganic io 23.9 64 0.0014 30.0 2.5 43 310-354 61-104 (178)
49 COG2003 RadC DNA repair protei 21.8 63 0.0014 31.1 2.1 49 62-119 148-197 (224)
50 COG4138 BtuD ABC-type cobalami 20.5 95 0.0021 29.7 3.0 47 263-309 118-171 (248)
No 1
>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=100.00 E-value=8.2e-54 Score=404.00 Aligned_cols=227 Identities=52% Similarity=0.856 Sum_probs=199.8
Q ss_pred ccEEEECHHHHHHHHHHHccCCCceeEEEEeeeecCC---CCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHH
Q 018450 3 LTGVKMSEDVWLTCLTHALSTETEEIMGLLLGDIEHS---KNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQAD 79 (355)
Q Consensus 3 l~~V~Is~~vll~Il~HA~s~~P~EvcGLLlG~~~~~---~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae 79 (355)
+++|.|+++++++|+.||++++|+||||||+|..++. .... ...|...+|..+.+.++++|+|||+++.+|+++|+
T Consensus 1 l~~V~Is~~~l~~il~HA~~~~P~EvCGLL~G~~~~~~~~~~~~-~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea~ 79 (244)
T cd08068 1 LSKVHLSADVYLVCLTHALSTEKEEVMGLLIGEIEVSKKGEEVA-IVHISAVIILRRSDKRKDRVEISPEQLSAASTEAE 79 (244)
T ss_pred CcEEEECHHHHHHHHHHHHhCCCcceeEEEEeecccccccccce-eEEEeeeccccccCCCCceEEeCHHHHHHHHHHHH
Confidence 5789999999999999999999999999999987530 0011 11233556666777788999999999999999999
Q ss_pred HhhhhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCC-ccCCCceEEEEEEeeCCCceeEee
Q 018450 80 RMTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSED-ANKVGRIQVIAFQSSDGKQNHISK 158 (355)
Q Consensus 80 ~m~~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d-~s~~g~~~lrAFRl~dg~~~~i~i 158 (355)
++.+.+++|+++||||||||+++++||.+|+++|..||+++|+++|||+|+++++ .+..+++.++|||+.+|+.
T Consensus 80 ~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~g~~----- 154 (244)
T cd08068 80 RLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQGNK----- 154 (244)
T ss_pred HHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecCCCC-----
Confidence 9999999999999999999999999999999999999999999999999999876 4677889999999976433
Q ss_pred eeEEeecCCCccccccccccccccccccccccccCCCCCCCCcccccccccCCCCccccCCCcccccCCCCcccccCCCC
Q 018450 159 PIALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGN 238 (355)
Q Consensus 159 pi~v~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 (355)
T Consensus 155 -------------------------------------------------------------------------------- 154 (244)
T cd08068 155 -------------------------------------------------------------------------------- 154 (244)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCCCCCCCccCCCCCCCchHHHHHhhhcccCCCCCceeeeecceeeecCcccccccCCcchhhhHhHHHHHHHHHHHHH
Q 018450 239 YQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQ 318 (355)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~~~~~~ea~h~s~~~~s~~~y~r~e~pl~v~~~~~~~~~~~~~~~~~~~~~~~~~ee~~a~~~ 318 (355)
|++|.|+||||+|+|+.++.++ ||+|+++||||||+||++||||
T Consensus 155 ----------------------------------~~~~~~~e~pl~i~~~~~~~~~--~~~~~~~l~~~l~~e~~~a~~~ 198 (244)
T cd08068 155 ----------------------------------AGQYERIEVPLEIVPTSTISEA--CLESLVELPEILYQEEEDAYNK 198 (244)
T ss_pred ----------------------------------CCcceEEEeeeEEecCcccccc--CHHHHHHHHHHHHHHHHHHHHH
Confidence 5589999999999999999999 9999999999999999999999
Q ss_pred HHH-------HhhcCcceee----ehh-hhcchhHHHHHHHHHhh
Q 018450 319 AIM-------QNMSNCLQFY----SVM-EKCIPLLTFITHQLIRL 351 (355)
Q Consensus 319 ~~~-------~~~~~~~~~~----~~~-~~~~~~~~~~~~~~~~~ 351 (355)
|+. ..++|++||| .+| .+++|||||||+||+..
T Consensus 199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~l~~~~~~~ 243 (244)
T cd08068 199 ALQSCDLDPLTKIHNGSVYTKSLCHILETISGPLLQLLEARLEQN 243 (244)
T ss_pred HHhcccchHHHHHHhhHHHHHHHHHHHHHHHhhHHHHHHHHHHhc
Confidence 995 4566999999 367 89999999999999863
No 2
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=1.4e-31 Score=259.33 Aligned_cols=245 Identities=34% Similarity=0.448 Sum_probs=179.6
Q ss_pred cEEEECHHHHHHHHHHHccCCCce-eEEEE-ee---eecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHH
Q 018450 4 TGVKMSEDVWLTCLTHALSTETEE-IMGLL-LG---DIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQA 78 (355)
Q Consensus 4 ~~V~Is~~vll~Il~HA~s~~P~E-vcGLL-lG---~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~ea 78 (355)
+.|+|...+++++++|++.+.|.| ++|++ +| .+....+..++. +++.|..++.-+...-..||. -++++
T Consensus 31 e~v~i~slall~m~rh~r~~~p~e~v~Glm~lg~~~~fv~~~Tv~vv~--v~am~~sg~~is~~~e~~d~V----~q~q~ 104 (316)
T KOG1555|consen 31 ETVYISSLALLKMLRHDRAGSPEETVMGLMSLGRLPEFVDDYTVRVVD--VFAMPQSGTGISKFVEAVDPV----FQTQM 104 (316)
T ss_pred ceeeeehhhhhhcccccccCCchhhccceeecccccceeeecceeeee--eeccccccceecccchhccHH----HHHHH
Confidence 579999999999999999999999 99999 99 443332212111 223344433111112223443 23556
Q ss_pred HHhhhhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEeeCCCceeEee
Q 018450 79 DRMTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHISK 158 (355)
Q Consensus 79 e~m~~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~dg~~~~i~i 158 (355)
..+.+.+++.+.+||||||||++++|||..|+.||+.||...+..++.++++.. +..|+....||+..+....-
T Consensus 105 ~~~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~---S~~g~vv~d~f~~In~~~~~--- 178 (316)
T KOG1555|consen 105 MDLLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQ---SPYGKVVPDAFSSINPQWIS--- 178 (316)
T ss_pred HHHHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeeccc---CCCCCccCChhhhcCccccc---
Confidence 678888999999999999999999999999999999999887666656555542 34467777788876533310
Q ss_pred eeEEeecCCCccccccccccccccccccccccccCCCCCCCCcccccccccCCCCccccCCCcccccCCCCcccccCCCC
Q 018450 159 PIALLPVNKSTVIDLESSLSSSESLSARSGNVLAENPEQDTGDSKIVAGSWKGGGRTSELGGFFANVDANHPERARTGGN 238 (355)
Q Consensus 159 pi~v~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 (355)
| .+.
T Consensus 179 -----~----------------------------~~e------------------------------------------- 182 (316)
T KOG1555|consen 179 -----P----------------------------GGE------------------------------------------- 182 (316)
T ss_pred -----C----------------------------CCC-------------------------------------------
Confidence 0 000
Q ss_pred CCCCCCCCCccCCCCCCCchHHHHHhhhcccCCCCCceeeeecceeeecCcccccccCCcchhhhHhHHHHHHHHHHHHH
Q 018450 239 YQTGDLSNAIGDIDPMDMSESMQEAMHRSNLDMSGAEYVRKEIPLHVLPTSSLLKLDSPLTSFTDLQRVLYEEERAAYNQ 318 (355)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~~~~~~ea~h~s~~~~s~~~y~r~e~pl~v~~~~~~~~~~~~~~~~~~~~~~~~~ee~~a~~~ 318 (355)
-+..-..+++|||+++|||++|++| .|.|+|||+||.|...+.-++.|+.|+.++|+++|+||++||.+
T Consensus 183 -----prqtts~~~~m~~~~s~q~~~~g~n------~y~~~ei~~~v~~~~~~~~~nv~~~s~~~~~~~~y~e~~k~~~~ 251 (316)
T KOG1555|consen 183 -----PRQTTSNGGHMDMQESLQEDIHGLN------RYYRIEIPLHVLPYEQLMLLNVPLKSWKSLQDVLYEEKLKAYLQ 251 (316)
T ss_pred -----CccccccccccccchhHHhHhhccC------ceEEEEeeEEechhhhhchhccchhhhhhcchhhHHHHHHHhhh
Confidence 1111234678999999999999999 89999999999998888888889999999999999999999997
Q ss_pred HHHHhhcCcceee------ehhhhcchhHHHHHHHHHh
Q 018450 319 AIMQNMSNCLQFY------SVMEKCIPLLTFITHQLIR 350 (355)
Q Consensus 319 ~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~ 350 (355)
...+...-..++. .||. +-++||+|+.+-
T Consensus 252 ~~~~~~sL~~~~N~~~~~~k~~~---~~~~~i~d~~~~ 286 (316)
T KOG1555|consen 252 SVPSMKSLSKVYNKVCDVCKQMS---DFLLMIEDVGEQ 286 (316)
T ss_pred hhhHHHhHHHHHHHHHHHHhhcc---HHHHHHHHhhhh
Confidence 7766666555555 3442 338999998764
No 3
>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=99.96 E-value=5.1e-28 Score=220.96 Aligned_cols=148 Identities=26% Similarity=0.333 Sum_probs=120.8
Q ss_pred EEEECHHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHHhhhh
Q 018450 5 GVKMSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRMTVL 84 (355)
Q Consensus 5 ~V~Is~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~m~~~ 84 (355)
+|.|+..|+++|++||+.+. .||||+|+|..+.+. . +..|+.++|+++.. +.++|++||+++.++.+.+++
T Consensus 6 ~V~Is~~all~m~~Ha~~~~-~EvcGlL~G~~d~~~-~--~l~Vt~~~p~~~~~-~~~~~e~dp~~q~e~~~~l~~---- 76 (187)
T cd08067 6 KVTVSSNALLLMDFHCHLTT-SEVIGYLGGTWDPNT-Q--NLTILQAFPCRSRL-TGLDCEMDPVSETEIRESLES---- 76 (187)
T ss_pred EEEECHHHHHHHHHHhcCCC-cEEEEEEEeEEcCCC-C--eEEEEEEEecCCCC-CCcccccCHHHHHHHHHHHHH----
Confidence 68999999999999999987 999999999975421 1 23578888988853 467899999988888877765
Q ss_pred cCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCC-------CcEEEEEccCcCCccCCCceEEEEEEeeCCCce---
Q 018450 85 TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDT-------GFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQN--- 154 (355)
Q Consensus 85 ~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p-------~~V~LIvSp~~~d~s~~g~~~lrAFRl~dg~~~--- 154 (355)
+|+++||||||||.++++||..|++||..||.+.+ ++|+|||||++.++ ......++|||+.+..-.
T Consensus 77 --~gl~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~-~~~~s~i~~f~~~~~~~~~~~ 153 (187)
T cd08067 77 --RGLSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRN-STPESQITCFWVMPPPENRPN 153 (187)
T ss_pred --cCCEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCC-CCCCCcEEEEEEECCCCCCCc
Confidence 88999999999999999999999999999998876 69999999998643 344678999999865433
Q ss_pred eEeeeeEEee
Q 018450 155 HISKPIALLP 164 (355)
Q Consensus 155 ~i~ipi~v~p 164 (355)
.-.+|+.+..
T Consensus 154 ~~~~p~~~~~ 163 (187)
T cd08067 154 EYGVPMLMSY 163 (187)
T ss_pred cCCcCeEEEe
Confidence 3335555543
No 4
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=99.94 E-value=2.1e-26 Score=194.51 Aligned_cols=119 Identities=34% Similarity=0.465 Sum_probs=91.4
Q ss_pred HHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHHhhhhcCCCce
Q 018450 11 DVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRMTVLTGRTTR 90 (355)
Q Consensus 11 ~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~m~~~~~rgle 90 (355)
+++++|++||++++|.|+||+|+|....+.....+..|+.++|.+. ..++.++..+.. +..++|++
T Consensus 1 ~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~--------~~~~~~~~~~~~------~~~~~g~~ 66 (119)
T cd08058 1 DALLKMLQHAESNTGIEVMGLLCGELTHNEFTDKHVIVPKQSAGPD--------SCTGENVEELFN------VQTGRPLL 66 (119)
T ss_pred CHHHHHHHHhcCCCCeEEEEEeeeEEecCccceeEEEEeecCCCCC--------CchhHHHHHHHH------HHhCCCCe
Confidence 4789999999999999999999998764321111223444444332 334544333333 34569999
Q ss_pred EEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEee
Q 018450 91 VIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSS 149 (355)
Q Consensus 91 VVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~ 149 (355)
+||||||||+++++||..|+++|+.||.+.|++++||+||.+. ...++|||++
T Consensus 67 ~vG~YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~------~~~~~a~rl~ 119 (119)
T cd08058 67 VVGWYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHR------NKDTGIFRLT 119 (119)
T ss_pred EEEEEecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCC------CcccceEEeC
Confidence 9999999999999999999999999999999999999999752 6789999984
No 5
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i
Probab=99.94 E-value=7.6e-26 Score=216.65 Aligned_cols=140 Identities=28% Similarity=0.400 Sum_probs=115.7
Q ss_pred cccEEEECHHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHH-
Q 018450 2 SLTGVKMSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADR- 80 (355)
Q Consensus 2 sl~~V~Is~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~- 80 (355)
.+++|.|++.++++|++||+++.|.||||+|+|...++ +..|+.++|++.. .+.++++++++. +..|.+
T Consensus 8 ~~~~V~Is~~allkil~Ha~~~~p~Ev~GlLlG~~~~~-----~v~Vt~~fp~p~~-~t~~~v~~~~e~----~~~m~~~ 77 (268)
T cd08069 8 YFEKVYISSLALLKMLKHARAGGPIEVMGLMLGKVDDY-----TIIVVDVFALPVE-GTETRVNAQDEF----QEYMVQY 77 (268)
T ss_pred cccEEEECHHHHHHHHHHHhccCCceEEEEEEeeecCC-----eEEEEEEEECCcC-CCCCceeccHHH----HHHHHHH
Confidence 36789999999999999999999999999999996543 2356777777643 345778887643 233334
Q ss_pred -hhhhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEeeCCCc
Q 018450 81 -MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQ 153 (355)
Q Consensus 81 -m~~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~dg~~ 153 (355)
+.+..++++++||||||||++++|||..|+.||..||.+.+++|+||+||... .+.|+..++|||+.+...
T Consensus 78 ~~~~~~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t--~~~g~~~i~Afr~~~~~~ 149 (268)
T cd08069 78 EMLKQTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRS--LVKGKVVIGAFRTIPPGY 149 (268)
T ss_pred HHHHHhCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCcc--ccCCcceeeEEEEECccc
Confidence 66778999999999999999999999999999999999989999999999752 267889999999986544
No 6
>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=99.92 E-value=4.2e-24 Score=182.36 Aligned_cols=122 Identities=30% Similarity=0.386 Sum_probs=100.9
Q ss_pred HHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCC-CeeecCHHHHHHHHHHHHHhhhhcCCCc
Q 018450 11 DVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRK-DRVETNPEQLAAASAQADRMTVLTGRTT 89 (355)
Q Consensus 11 ~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~-~~feiDPeel~~A~~eae~m~~~~~rgl 89 (355)
.++.+|++||++++|+|+||||+|....... .|+.++|++|....+ ++|++||+++.++.+++++ .++
T Consensus 2 ~~~~~il~ha~~~~P~E~cGlL~G~~~~~~~-----~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~~~~~~------~g~ 70 (128)
T cd08070 2 ELLEAILAHAEAEYPEECCGLLLGKGGGVTA-----IVTEVYPVRNVAESPRRRFEIDPAEQLAAQREARE------RGL 70 (128)
T ss_pred HHHHHHHHHHHhCCCCceEEEEEeecCCCCc-----eEEEEEEccCCCCCCCceEEECHHHHHHHHHHHHH------CCC
Confidence 5788999999999999999999999875421 234557888875555 8999999999998888765 789
Q ss_pred eEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEeeCCCce
Q 018450 90 RVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQN 154 (355)
Q Consensus 90 eVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~dg~~~ 154 (355)
++||||||||+.+++||..|+.+ +..++.+|||+++.+ +...++||++.++...
T Consensus 71 ~~vG~~HSHP~~~~~PS~~D~~~-----~~~~~~~~lIv~~~~------~~~~~~~~~~~~~~~~ 124 (128)
T cd08070 71 EVVGIYHSHPDGPARPSETDLRL-----AWPPGVSYLIVSLAG------GAPELRAWRLEGGQFE 124 (128)
T ss_pred eEEEEEeCCCCCCCCCCHHHHHh-----ccCCCCeEEEEECCC------CCcEEEEEEEcCCCee
Confidence 99999999999999999999983 445589999999864 2578999999876443
No 7
>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al
Probab=99.91 E-value=2e-23 Score=188.63 Aligned_cols=123 Identities=25% Similarity=0.344 Sum_probs=95.5
Q ss_pred ccEEEECHHHHHHHHHHHccCC--CceeEEEEeeeecCCCCceeEEEEEee-ecCCCCCCCCCeee-cCHHHHHHHHHHH
Q 018450 3 LTGVKMSEDVWLTCLTHALSTE--TEEIMGLLLGDIEHSKNGNVTALIWGA-SPQSRSDRRKDRVE-TNPEQLAAASAQA 78 (355)
Q Consensus 3 l~~V~Is~~vll~Il~HA~s~~--P~EvcGLLlG~~~~~~~~~it~~V~~a-~P~~nsd~~~~~fe-iDPeel~~A~~ea 78 (355)
++++.|++.++.+|+.||.... |.|+||+|+|+..++ +..|... +|.++. ....+. +++.+ +.+++
T Consensus 1 ~~~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~~~~~-----~~~I~~i~~~~q~~--~~~~~~~~~~~e---~~~~~ 70 (173)
T cd08066 1 LRQVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSNN-----AFFITHLIIPKQSG--TSDSCQTTNEEE---LFDFQ 70 (173)
T ss_pred CeEEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeEcCCC-----eEEEEEEEeccccC--CCceecCCCHHH---HHHHH
Confidence 4689999999999999999984 699999999986542 1122222 333332 223333 45544 33344
Q ss_pred HHhhhhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEee
Q 018450 79 DRMTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSS 149 (355)
Q Consensus 79 e~m~~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~ 149 (355)
+. +|+++||||||||..+++||..|++||+.||.++|++++||+||. .+.++|||+.
T Consensus 71 ~~------~gle~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~--------~~~l~afrl~ 127 (173)
T cd08066 71 DQ------HDLITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK--------YNEFGIFRLT 127 (173)
T ss_pred Hh------CCCeeEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC--------CcEEeEEEee
Confidence 33 899999999999999999999999999999999999999999983 5799999999
No 8
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=99.88 E-value=1.1e-21 Score=165.09 Aligned_cols=132 Identities=27% Similarity=0.393 Sum_probs=102.5
Q ss_pred EEEECHHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCC--eeecCHHHHHHHHHHHHHhh
Q 018450 5 GVKMSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKD--RVETNPEQLAAASAQADRMT 82 (355)
Q Consensus 5 ~V~Is~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~--~feiDPeel~~A~~eae~m~ 82 (355)
+|.|.+.++++|++||.+.+|.|+||+|+|...++. ..|..++|+.+.....+ .+.+++.+. +.++.
T Consensus 1 ~v~i~~~v~~~i~~h~~~~~p~e~~G~L~G~~~~~~-----~~i~~~~~~p~~~~~~~~~~~~~~~~~~------~~~~~ 69 (135)
T smart00232 1 EVKVHPLVPLNILKHAIRDGPEEVCGVLLGKSNKDR-----PEVKEVFAVPNEPQDDSVQEYDEDYSHL------MDEEL 69 (135)
T ss_pred CEEEcHHHHHHHHHHHhcCCCcEEEEEEEEEEcCCE-----EEEEEEEecCcCCCCcchhhhhhhHHHH------HHHHH
Confidence 378999999999999999999999999999976541 23445555554322222 354455432 33334
Q ss_pred hhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEeeC
Q 018450 83 VLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSD 150 (355)
Q Consensus 83 ~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~d 150 (355)
++...++++||||||||..+++||..|+.+|..|+..++..+++++++.. +..|+..++||++.+
T Consensus 70 ~~~~~~~~~vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~---s~~g~~~~~af~~~~ 134 (135)
T smart00232 70 KKVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIK---SFQGRLSLRAFRLTP 134 (135)
T ss_pred HhhCCCceEEEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCc---cccCcEEEEEEEecC
Confidence 45679999999999999999999999999999999999999999999865 445889999999864
No 9
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.88 E-value=6.8e-23 Score=195.72 Aligned_cols=142 Identities=27% Similarity=0.380 Sum_probs=112.1
Q ss_pred ccEEEECHHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHHhh
Q 018450 3 LTGVKMSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRMT 82 (355)
Q Consensus 3 l~~V~Is~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~m~ 82 (355)
++.|.|++.++++|+.||+++.+.|+||||.|+.+++. ++.+=.|++|+..+ ++|+..-.+++. ++.+.-+..
T Consensus 52 fk~vkISalAllKm~~hA~~GgnlEiMGlm~Gkv~g~t---~IvmD~FaLPVeGT---ETRVNAq~~AyE-Ymv~Y~e~~ 124 (347)
T KOG1554|consen 52 FKHVKISALALLKMVMHARSGGNLEIMGLMQGKVDGDT---IIVMDSFALPVEGT---ETRVNAQAEAYE-YMVQYIEEA 124 (347)
T ss_pred hhhhhhHHHHHHHHHHHHhcCCCeEEEeeecccccCCe---EEEEeccccccccc---cceechHHHHHH-HHHHHHHHH
Confidence 56799999999999999999999999999999988752 22222456677764 466654333322 112222334
Q ss_pred hhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEeeCCCc
Q 018450 83 VLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQ 153 (355)
Q Consensus 83 ~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~dg~~ 153 (355)
+..++.+++||||||||+.+||.|..|+.||...|.+..+|++||+||.+. -..|++.++|||..+.+.
T Consensus 125 k~~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~Rt--lsagkv~iGAFRTyp~gy 193 (347)
T KOG1554|consen 125 KNVGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTRT--LSAGKVNIGAFRTYPKGY 193 (347)
T ss_pred HHhhhhhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCccc--cccCceeeceeecccCCC
Confidence 456899999999999999999999999999999999999999999999864 578999999999986543
No 10
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=99.87 E-value=4.9e-21 Score=183.08 Aligned_cols=136 Identities=21% Similarity=0.236 Sum_probs=110.8
Q ss_pred cEEEECHHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCC-CCCeeecCHHHHHHHHHHHHHhh
Q 018450 4 TGVKMSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDR-RKDRVETNPEQLAAASAQADRMT 82 (355)
Q Consensus 4 ~~V~Is~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~-~~~~feiDPeel~~A~~eae~m~ 82 (355)
+.|.|++.|+++|++||.++.|.||||+|+|...++ +..|+.+||.++.+. ...++.+++.. .+.+|.++.
T Consensus 1 ~~V~I~~~vllkIv~H~~~~~p~~v~G~LLG~~~~~-----~leVtn~Fp~P~~~~~~~~~~~~~~~~---yq~~m~~~~ 72 (266)
T cd08065 1 TSVQIDGLVVLKIIKHCKEELPELVQGQLLGLDVGG-----TLEVTNCFPFPKSEEDDSDRADEDIAD---YQLEMMRLL 72 (266)
T ss_pred CEEEEeHHHHHHHHHHHhcCCCcEEEEEEeeeEcCC-----EEEEEeccCCCCCCCCCcchhhhhHHH---HHHHHHHHH
Confidence 479999999999999999999999999999998653 346788888776422 12245555532 355666777
Q ss_pred hhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEeeCC
Q 018450 83 VLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDG 151 (355)
Q Consensus 83 ~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~dg 151 (355)
++.+.+..+|||||||| .+++.|..+++++..||...+++++||+|+.. +..|.+.++|||+.+.
T Consensus 73 r~v~~~e~iVGWY~S~p-~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~---s~~g~l~lkAyrl~~~ 137 (266)
T cd08065 73 REVNVDHNHVGWYQSTY-LGSFFTRDLIETQYNYQEAIEESVVLVYDPSK---TSQGSLSLKAYRLSEK 137 (266)
T ss_pred HHhCCCCcEEEeEeecC-CCCcCCHHHHHHHHHHhccCCCCEEEEECCCc---ccccceeeEEEEEcHH
Confidence 88899999999999999 88999999999999999888899999999963 3457899999999753
No 11
>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=99.82 E-value=7.4e-20 Score=153.61 Aligned_cols=102 Identities=25% Similarity=0.267 Sum_probs=81.5
Q ss_pred HHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCC-CCCeeecCHHHHHHHHHHHHHhhhhcCCCce
Q 018450 12 VWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDR-RKDRVETNPEQLAAASAQADRMTVLTGRTTR 90 (355)
Q Consensus 12 vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~-~~~~feiDPeel~~A~~eae~m~~~~~rgle 90 (355)
++..|++||++++|+|+||||+|+... ...+|+.|... +.++|+|||+++.+|.+ .+ +
T Consensus 2 i~~~i~~ha~~~~P~E~CGll~g~~~~----------~~~~p~~N~~~~p~~~F~idp~e~~~a~~----------~~-~ 60 (108)
T cd08073 2 LEDAILAHAKAEYPREACGLVVRKGRK----------LRYIPCRNIAADPEEHFEISPEDYAAAED----------EG-E 60 (108)
T ss_pred HHHHHHHHHhHCCCCcceEEEEecCCc----------eEEEECccCCCCccceEEeCHHHHHHHhc----------CC-C
Confidence 578999999999999999999997521 12368888643 45899999999876552 23 8
Q ss_pred EEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEE
Q 018450 91 VIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQ 147 (355)
Q Consensus 91 VVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFR 147 (355)
+||+|||||+.++.||..|+. ++..++..|||++... ..+++|+
T Consensus 61 ivgi~HSHP~~~a~PS~~D~~-----~~~~~~~~~iIvs~~~--------~~~~~~~ 104 (108)
T cd08073 61 IVAVVHSHPDGSPAPSEADRA-----QQEATGLPWIIVSWPE--------GDLRVFR 104 (108)
T ss_pred EEEEEEcCCCCCCCCCHHHHH-----HhhcCCCcEEEEEcCC--------CCEEEEe
Confidence 999999999999999999997 4566899999999853 2466665
No 12
>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain [] and PAD-1-like domain []. It has been shown that this domain occurs in prokaryotes []. Mov34 proteins act as the regulatory subunit of the 26 proteasome, which is involved in the ATP-dependent degradation of ubiquitinated proteins. The function of this domain is unclear, but it is found in the N terminus of the proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. A number of the proteins associated with this family belong to MEROPS peptidase family M67 (clan M-). This includes the Poh1 peptidase of Saccharomyces cerevisiae (Baker's yeast) which is a component of the 19S proteasome regulatory particle.; GO: 0005515 protein binding; PDB: 2ZNV_D 2ZNR_A 4E0Q_A 2P87_A 2P8R_A 2O96_B 2O95_A 3RZU_F 3RZV_A.
Probab=99.82 E-value=4.5e-20 Score=153.63 Aligned_cols=114 Identities=29% Similarity=0.520 Sum_probs=83.0
Q ss_pred CcccEEEECHHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHH
Q 018450 1 MSLTGVKMSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADR 80 (355)
Q Consensus 1 msl~~V~Is~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~ 80 (355)
.++++|.|++.|+++|++||.+..+.|+||+|+|...++. +..|+.++|+.... ....+.+...+.. ..+.+
T Consensus 1 ~s~~~V~i~p~vll~i~~h~~r~~~~~v~G~LlG~~~~~~----~v~I~~~f~~p~~~-~~~~~~~~~~~~~---~~~~~ 72 (114)
T PF01398_consen 1 QSVQTVQIHPLVLLKIIDHATRSSPNEVIGLLLGTQDGDN----TVEITNSFPVPHSE-SEDDCDMDDEDFQ---KKMIE 72 (114)
T ss_dssp -SCEEEEEEHHHHHHHHHHHHHHHCTEEEEEEEEEEETT-----EEEEEEEEEESEEE-ESSEEEEECCHHH---HHHHH
T ss_pred CCcEEEEECHHHHHHHHHHHhcCCCCEEEEEEEEEecCce----EEEEEEEEEeeEec-CccccccchhhHH---HHHHh
Confidence 3678999999999999999999888899999999998652 23566666665432 2234343332222 23344
Q ss_pred hhhhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCC
Q 018450 81 MTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTG 122 (355)
Q Consensus 81 m~~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~ 122 (355)
+.++....+.+||||||||.++++||..|+.+|+.||.+.|+
T Consensus 73 ~~~~~~~~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 73 LLKKVNPNLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp HHHHCSTTSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred hhccccccceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence 555565669999999999999999999999999999988764
No 13
>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=99.82 E-value=2.9e-19 Score=151.76 Aligned_cols=114 Identities=21% Similarity=0.195 Sum_probs=82.3
Q ss_pred ECHHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHHhhhhcCC
Q 018450 8 MSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRMTVLTGR 87 (355)
Q Consensus 8 Is~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~m~~~~~r 87 (355)
|+++++..|++||++++|+|+||||+|+.. . |+..+|..|.......+.++.+ +. ..
T Consensus 1 i~~~~~~~i~~ha~~~~P~E~CGlL~G~~~-----~----v~~~~~~~n~~~~~~~~~f~~~--------~~------~~ 57 (117)
T cd08072 1 ISRDLLDSILEAAKSSHPNEFAALLRGKDG-----V----ITELLILPGTESGEVSAVFPLL--------ML------PL 57 (117)
T ss_pred CCHHHHHHHHHHHhhcCCceEEEEEEeecc-----E----EEEEEECCCCCCCCcceeechH--------Hh------cC
Confidence 578899999999999999999999999753 1 2233444443222223333321 11 36
Q ss_pred CceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEeeCCCceeE
Q 018450 88 TTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHI 156 (355)
Q Consensus 88 gleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~dg~~~~i 156 (355)
|+++||.|||||+.++.||.+|++ ++.+++.+|+|+++-.+ ...++||++. |+..++
T Consensus 58 g~~ivgi~HSHP~~~~~PS~~D~~-----~~~~~~~~~lIvs~~~~------~~~~~a~~~~-g~~~~~ 114 (117)
T cd08072 58 DMSIVGSVHSHPSGSPRPSDADLS-----FFSKTGLVHIIVGYPYD------EDDWRAYDSD-GEPVEL 114 (117)
T ss_pred CCeEEEEEEcCCCCCCCCCHHHHH-----hhhcCCCEEEEEECcCC------CCCEEEEecC-CCEEee
Confidence 899999999999999999999997 45568999999996432 3579999885 444333
No 14
>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=99.78 E-value=2.1e-18 Score=142.14 Aligned_cols=105 Identities=21% Similarity=0.252 Sum_probs=77.2
Q ss_pred HHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHHhhhhcCCCceEEE
Q 018450 14 LTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRMTVLTGRTTRVIG 93 (355)
Q Consensus 14 l~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~m~~~~~rgleVVG 93 (355)
.+|++||+..+|.|+||+|+|+..++ +..|..+++..+... ....+..++..+.. .....|+++||
T Consensus 2 k~il~~a~~~~~~ev~G~L~G~~~~~-----~~~i~~~~~~~~~~~---~~~~~~~~~~~~~~------~~~~~~~~iVG 67 (116)
T cd07767 2 KMFLDAAKSINGKEVIGLLYGSKTKK-----VLDVDEVIAVPFDEG---DKDDNVWFLMYLDF------KKLNAGLRIVG 67 (116)
T ss_pred HhHHHHHhcCCCcEEEEEeEEEEcCC-----EEEEEEEEecccCCC---CCccHHHHHHHHHH------HHhcCCCeEEE
Confidence 57899999999999999999998754 223444444443211 11222222222222 23458999999
Q ss_pred EEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCc
Q 018450 94 WYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFS 132 (355)
Q Consensus 94 wYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~ 132 (355)
||||||..+++||..|+.+|..||...++.++||+++..
T Consensus 68 wyhshp~~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~ 106 (116)
T cd07767 68 WYHTHPKPSCFLSPNDLATHELFQRYFPEKVMIIVDVKP 106 (116)
T ss_pred EEEcCCCCCCccCHHHHHHHHHHHHhCCCCEEEEEECCC
Confidence 999999999999999999999999888999999999865
No 15
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=99.69 E-value=4.9e-16 Score=133.81 Aligned_cols=104 Identities=29% Similarity=0.332 Sum_probs=76.7
Q ss_pred EEECHHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCC-CCCeeecCHHHHHHHHHHHHHhhhh
Q 018450 6 VKMSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDR-RKDRVETNPEQLAAASAQADRMTVL 84 (355)
Q Consensus 6 V~Is~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~-~~~~feiDPeel~~A~~eae~m~~~ 84 (355)
+.|++.++..|+.||.+++|.|+||+|+|...+. . ..++.+... +...+.++++... +...++.
T Consensus 2 ~~i~~~~l~~il~~a~~~~p~E~~g~l~~~~~~~--------~--~~~~~n~~~~~~~~~~~~~~~~~-~~~~~~~---- 66 (134)
T COG1310 2 LVIPKEVLGAILEHARREHPREVCGLLAGTREGE--------R--YFPLKNVSVEPVEYFEIDPEYSL-FYLAAED---- 66 (134)
T ss_pred ceecHHHHHHHHHHHHhcCChheEEEEEeecccc--------e--eeccccccCCcceeEeeCHHHHH-HHHHHhh----
Confidence 5789999999999999999999999999987641 0 123334322 3456778887544 5555544
Q ss_pred cCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccC
Q 018450 85 TGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCF 131 (355)
Q Consensus 85 ~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~ 131 (355)
.|+.+||||||||+++++||..|+. ++. +.+..|+|++..
T Consensus 67 --~g~~vvg~yHSHP~~~~~pS~~D~~----~~~-~~~~~~~iv~~~ 106 (134)
T COG1310 67 --AGEVVVGWYHSHPGGPPYPSEADRR----LSK-LGPLPWLIVSVP 106 (134)
T ss_pred --CCCEEEEEEcCCCCCCCCcCHHHHh----hcc-ccCCCEEEEEcC
Confidence 7899999999999999999999997 223 345555666553
No 16
>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=99.67 E-value=3.3e-15 Score=131.98 Aligned_cols=145 Identities=14% Similarity=0.231 Sum_probs=108.2
Q ss_pred EEECHHHHHHHHHHHccCC--CceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHHhhh
Q 018450 6 VKMSEDVWLTCLTHALSTE--TEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRMTV 83 (355)
Q Consensus 6 V~Is~~vll~Il~HA~s~~--P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~m~~ 83 (355)
|.|++.|+++|++|+.+.. +.+++|+|+|...++ +..|+.+||+.... ..+.+.+|++ .+.++.++.+
T Consensus 1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~~~~~-----~veV~nsF~lp~~~-~~~~~~~d~~----y~~~m~~~~~ 70 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGD-----KIEVTNSFELPFDE-EEESIFIDTE----YLEKRYNLHK 70 (157)
T ss_pred CEEccHHHhhHHHHHHhccCCCCeEEEEEEeEEeCC-----EEEEEEeEEccccC-CCcchhhhHH----HHHHHHHHHH
Confidence 5799999999999998877 899999999998743 34567777766532 2233445554 4566777888
Q ss_pred hcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhc-CCCcEEEEEccCcCCccCCCceEEEEEEeeCCCceeEeeeeEE
Q 018450 84 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLL-DTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQNHISKPIAL 162 (355)
Q Consensus 84 ~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~-~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~dg~~~~i~ipi~v 162 (355)
+++.+..+|||||+||.....++..|...+..|... .+..++|++||... +..++..++||++..+.....++|..+
T Consensus 71 ~v~~~~~vVGWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~--~~~~~l~i~ay~~~~~~~~~~~~~~~i 148 (157)
T cd08057 71 KVYPQEKIVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQ--SDSEKLEISTFTSAQREENGAEITYEI 148 (157)
T ss_pred HhCCCCCEEEEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcc--cCCCcccEEEEEEecCCCCCceeeeEE
Confidence 899999999999999998777888888777766443 57789999999542 345789999999996554433444333
No 17
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=99.62 E-value=1.8e-15 Score=123.21 Aligned_cols=93 Identities=27% Similarity=0.430 Sum_probs=64.3
Q ss_pred HHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHH-HHHHhhhhcCCC
Q 018450 10 EDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASA-QADRMTVLTGRT 88 (355)
Q Consensus 10 ~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~-eae~m~~~~~rg 88 (355)
+.++..|+.|++...|.|+||+|+|..... ...++ ++. .++|.+..++.. .+.+ .+
T Consensus 2 ~~~~~~i~~~~~~~~p~E~~G~L~g~~~~~-----~~~~~---~~~---------~~~p~~~~~~~~~~~~~------~~ 58 (104)
T PF14464_consen 2 EEVLEQIIAHARAAYPNEACGLLLGRRDDQ-----RFIVV---PNV---------NPDPRDSFRRERFEARE------RG 58 (104)
T ss_dssp -HHHHHHHHHHHHHTTS-EEEEEEEEEECC-----EEEEE---EEE---------E--HHCHHHHHH-HHHH------HT
T ss_pred HHHHHHHHHHHhhCCCCeEEEEEEEEecCC-----EEEEE---eCC---------CCCcHHHHHHHhhhhhc------cc
Confidence 578999999999999999999999998332 11222 111 156666655554 3333 78
Q ss_pred ceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCC-CcEEEEEcc
Q 018450 89 TRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDT-GFIGLIFSC 130 (355)
Q Consensus 89 leVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p-~~V~LIvSp 130 (355)
..+||+|||||+.+++||.+|+.+ +... ++++||++.
T Consensus 59 ~~~vg~~HSHP~~~a~pS~~D~~~-----~~~~~~~~~iI~~~ 96 (104)
T PF14464_consen 59 LEIVGIWHSHPSGPAFPSSTDIRS-----MRDLAPPSYIIVGN 96 (104)
T ss_dssp -EEEEEEEEESSSSSS--HHHHHT-----HCCS-SCEEEEEEE
T ss_pred ceeeEEEEcCCCCCCCCCHHHHHh-----hhccCCeEEEEEeC
Confidence 999999999999999999999983 3333 889999986
No 18
>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=99.56 E-value=1.1e-13 Score=133.88 Aligned_cols=129 Identities=12% Similarity=0.164 Sum_probs=98.3
Q ss_pred cEEEECHHHHHHHHHHHccC---CCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCC--CCeeecCHHHHHHHHHHH
Q 018450 4 TGVKMSEDVWLTCLTHALST---ETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRR--KDRVETNPEQLAAASAQA 78 (355)
Q Consensus 4 ~~V~Is~~vll~Il~HA~s~---~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~--~~~feiDPeel~~A~~ea 78 (355)
++|.|.+.|+++|++|+.+. .+.+|+|.|+|...++ ...|+.+|++...+.. ...+.+|.+ ++.+|
T Consensus 1 ~~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~~~~~-----~veItnsF~~p~~~~~~~~~~~~~d~~----y~~~m 71 (280)
T cd08062 1 KKVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWKKG-----VLDVTNSFAVPFEEDEKDPSVWFLDHN----YLENM 71 (280)
T ss_pred CeEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEEEeCC-----EEEEEEeeecCccCCCCCcchhhhhHH----HHHHH
Confidence 47999999999999999864 3678999999998653 3456767666543211 112445643 45667
Q ss_pred HHhhhhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEee
Q 018450 79 DRMTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSS 149 (355)
Q Consensus 79 e~m~~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~ 149 (355)
.+++++++.++.+||||||||. ++..|+..|..|+...+..++|+++|... .+.+.++||...
T Consensus 72 ~~~~kkv~~~e~vVGWY~tg~~----~~~~d~~ih~~~~~~~~~pv~l~vd~~~~----~~~lpi~aY~s~ 134 (280)
T cd08062 72 YGMFKKVNAKEKIVGWYSTGPK----LRPNDLDINELFRRYCPNPVLVIIDVRPK----DLGLPTEAYIAV 134 (280)
T ss_pred HHHHHHhCCCCCeEEEecCCCC----CCcchHHHHHHHHHhCCCCEEEEEecCCC----CCCCceEEEEEe
Confidence 7888999999999999999997 45677888888888888889999998642 356889999886
No 19
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=99.55 E-value=2.6e-14 Score=136.87 Aligned_cols=139 Identities=19% Similarity=0.208 Sum_probs=108.7
Q ss_pred cccEEEECHHHHHHHHHHHccCCCc--eeEEEEeeeecCCCCceeEEEEEeeecCCCCC-CCCCee---ecCHHHHHHHH
Q 018450 2 SLTGVKMSEDVWLTCLTHALSTETE--EIMGLLLGDIEHSKNGNVTALIWGASPQSRSD-RRKDRV---ETNPEQLAAAS 75 (355)
Q Consensus 2 sl~~V~Is~~vll~Il~HA~s~~P~--EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd-~~~~~f---eiDPeel~~A~ 75 (355)
++++|.|+..++++|++||+...|+ -+.|+|+|-..++ ...|+.|||..... ...+.+ .++ ++....+
T Consensus 11 ~vk~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~Glvvd~-----~LeITncFp~p~~~~~edda~~~~~~d-e~rq~~~ 84 (339)
T KOG1560|consen 11 PVKRVELDSLVVMKIIKHCREEFPNGDGTQGVLLGLVVDG-----RLEITNCFPFPSVLENEDDAVNKSVSD-EARQAYQ 84 (339)
T ss_pred ccceeeehhHHHHHHHHHHHhhcCCcchhhheeeeeeecc-----eeEeecccCCCccCCCccchhhhhhhH-HHHHHHH
Confidence 5789999999999999999998886 4789999988754 35688888876531 111111 122 2222334
Q ss_pred HHHHHhhhhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEeeC
Q 018450 76 AQADRMTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSD 150 (355)
Q Consensus 76 ~eae~m~~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~d 150 (355)
.+|.+.++.++.+...||||.||- .+.+.|..=+++|+.||.+.|+.|.+|+||.. +.+|...+||||+++
T Consensus 85 l~mlrrlr~vnid~~hVGwYqs~~-vgs~lS~~lveSqy~YQ~a~pesVvliYD~~k---ssqG~L~lrAyrLTp 155 (339)
T KOG1560|consen 85 LAMLRRLRYVNIDHLHVGWYQSAY-VGSFLSPALVESQYAYQKAIPESVVLIYDPIK---SSQGTLSLRAYRLTP 155 (339)
T ss_pred HHHHHHhhhcCccceeeeeeeeeh-hccccCHHHHHHHHHHHhcCCccEEEEecccc---ccCceEEeehhhcCH
Confidence 445555677899999999999995 67899999999999999999999999999974 788999999999974
No 20
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=99.55 E-value=3.2e-15 Score=146.95 Aligned_cols=167 Identities=25% Similarity=0.341 Sum_probs=122.5
Q ss_pred cccEEEECHHHHHHHHHHHcc--CCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeec-CHHHHHHHHHHH
Q 018450 2 SLTGVKMSEDVWLTCLTHALS--TETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVET-NPEQLAAASAQA 78 (355)
Q Consensus 2 sl~~V~Is~~vll~Il~HA~s--~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~fei-DPeel~~A~~ea 78 (355)
+++.|+|+.......+.-|++ ....|.||+|+|+.... ...|+.+| +|.+.. +.+.+.. +.++++..|.
T Consensus 250 ~lr~v~ip~~l~~~Fl~la~~NT~knlETCGiL~g~L~~n-~f~IThli---iPkQea--tsd~C~t~neeelF~vQd-- 321 (424)
T KOG2880|consen 250 ILRDVHIPERLMEVFLQLAKSNTKKNLETCGILAGKLERN-EFYITHLI---IPKQEA--TSDSCNTMNEEELFEVQD-- 321 (424)
T ss_pred cceEEEecHHHHHHHHHHHhhcccccchHHHHhhhHhhcC-cEEEEEEE---eecccC--CCccccccCHHHHheecc--
Confidence 467899999999999998886 45689999999997643 23444333 477653 4565654 5555555543
Q ss_pred HHhhhhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEee-CCCceeEe
Q 018450 79 DRMTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSS-DGKQNHIS 157 (355)
Q Consensus 79 e~m~~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~-dg~~~~i~ 157 (355)
.+++-.+||.|+||..+||.|.+|++|+++||.|.|+.++||++|... ..+.||+. +|++..+.
T Consensus 322 -------q~~L~tlGWIHTHPTQt~FmSSVDlHTHcSYQiMlPEAiAIV~aPk~~--------~tGiFrLt~~~Gm~~i~ 386 (424)
T KOG2880|consen 322 -------QHELLTLGWIHTHPTQTCFMSSVDLHTHCSYQIMLPEAIAIVCAPKSK--------TTGIFRLTDPGGMEVIR 386 (424)
T ss_pred -------cccceeeeeeecCCccchhheeccccccceeeeecchheeEEeccccC--------CcceEEecCCcchHHHh
Confidence 367889999999999999999999999999999999999999999642 57889999 45554433
Q ss_pred --eeeEEeecC-CCccccccccccccccccccccccc-cCCCCCCCCccc
Q 018450 158 --KPIALLPVN-KSTVIDLESSLSSSESLSARSGNVL-AENPEQDTGDSK 203 (355)
Q Consensus 158 --ipi~v~p~~-~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 203 (355)
..-.++||. +.+.+. .+.++|+ .-+.-++..|+|
T Consensus 387 ~C~~~GFHpH~~~~~pl~------------~~~~~v~~~~~~k~~v~dLR 424 (424)
T KOG2880|consen 387 GCRKKGFHPHSEKGPPLF------------EHCSHVYMHHNNKLCVIDLR 424 (424)
T ss_pred hcccCCCCCCCCCCCCce------------eecceeEEcCCcceeeeeCC
Confidence 333499997 665554 4556666 334455555554
No 21
>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=99.51 E-value=4.8e-13 Score=127.97 Aligned_cols=129 Identities=17% Similarity=0.225 Sum_probs=95.0
Q ss_pred EEECHHHHHHHHHHHcc--CCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHHhhh
Q 018450 6 VKMSEDVWLTCLTHALS--TETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRMTV 83 (355)
Q Consensus 6 V~Is~~vll~Il~HA~s--~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~m~~ 83 (355)
|.|++.|+.+|++|+.+ ..+..|+|.|+|...++ ...|+.+||++..+ ..+.+.+|.+. +.+|.++++
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~-----~veItnsF~~p~~~-~~~~~~~d~~y----~~~m~~~~k 70 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEG-----EVEITNCFAVPHNE-SEDQVAVDMEY----HRTMYELHQ 70 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCC-----EEEEEeCeecceeC-CCCeEEEcHHH----HHHHHHHHH
Confidence 57999999999999887 57789999999998753 34577777776532 23467778653 456778889
Q ss_pred hcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEeeC
Q 018450 84 LTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSD 150 (355)
Q Consensus 84 ~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~d 150 (355)
+.+.+..+||||||+|.. .++...++.|..++...+..+.|++|+... .+...++||++..
T Consensus 71 kv~~~~~vVGWY~tg~~~--~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~----~~~l~i~ay~~~~ 131 (265)
T cd08064 71 KVNPKEVIVGWYATGSEI--TEHSALIHDYYSRECTSYNPIHLTVDTSLD----DGKMSIKAYVSSP 131 (265)
T ss_pred HhCCCCcEEeeeeCCCCC--CccHHHHHHHHHhhCCCCCCEEEEEeCCCC----CCCcceEEEEEEe
Confidence 999999999999999843 234555555554443323779999998642 2478999999874
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=99.50 E-value=1.2e-13 Score=113.18 Aligned_cols=92 Identities=23% Similarity=0.240 Sum_probs=68.3
Q ss_pred HHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHHhhhhcCCCce
Q 018450 11 DVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRMTVLTGRTTR 90 (355)
Q Consensus 11 ~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~m~~~~~rgle 90 (355)
+++..|+.|++..+|.|+||+|+|.... .+ ....+..+ ..++++|.. .+++.+ .+..
T Consensus 1 ~~~~~i~~~~~~~~p~E~~gll~~~~~~----~~----~~~~~~~~-----~~~~~~~~~----~~~a~~------~~~~ 57 (101)
T cd08059 1 DLLKTILVHAKDAHPDEFCGFLSGSKDN----VM----DELIFLPF-----VSGSVSAVI----DLAALE------IGMK 57 (101)
T ss_pred CHHHHHHHHHHhcCChhhheeeecCCCC----eE----EEEEeCCC-----cCCccChHH----HHHHhh------CCCc
Confidence 3678899999999999999999997542 11 22233433 246777764 233333 7889
Q ss_pred EEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEcc
Q 018450 91 VIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSC 130 (355)
Q Consensus 91 VVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp 130 (355)
+||.|||||++.+.||..|+.. ...++..|+|++.
T Consensus 58 ~v~i~HsHP~g~~~PS~~D~~~-----~~~~~~~~iIv~~ 92 (101)
T cd08059 58 VVGLVHSHPSGSCRPSEADLSL-----FTRFGLYHVIVCY 92 (101)
T ss_pred EEEEEecCcCCCCCCCHHHHHH-----HHhcCCeEEEEEC
Confidence 9999999999999999999982 2335889999986
No 23
>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=99.48 E-value=5.8e-13 Score=121.61 Aligned_cols=130 Identities=18% Similarity=0.194 Sum_probs=87.5
Q ss_pred ECHHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHH---HHHHHHHHHHhhhh
Q 018450 8 MSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQ---LAAASAQADRMTVL 84 (355)
Q Consensus 8 Is~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPee---l~~A~~eae~m~~~ 84 (355)
|++.++.+|+.||.+..|.||||+|+|+...+. ...|++++|+.+ .+|.++|.. +..+++++++
T Consensus 1 is~~ay~ki~~HA~k~p~~evcGlLlG~~~~~~----~~~V~d~vPl~h-----~~~~l~P~~Eval~~ve~~~~~---- 67 (182)
T cd08060 1 LSTLAYVKMLLHAAKYPHCAVNGLLLGKKSSGG----SVEITDAVPLFH-----SCLALAPMLEVALALVDAYCKS---- 67 (182)
T ss_pred CCHHHHHHHHHHHHHcCCchheEEEEeeecCCC----CEEEEEEEEcCC-----CccccCHHHHHHHHHHHHHHHH----
Confidence 578899999999999888899999999976221 135678889987 369999985 7778887765
Q ss_pred cCCCceEEEEEecCCCCCC-CCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEeeCCCc
Q 018450 85 TGRTTRVIGWYHSHPHITV-LPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQ 153 (355)
Q Consensus 85 ~~rgleVVGwYHSHP~~~a-~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~dg~~ 153 (355)
+|+.|||+|||||.... .|+..=...-..-+...+..+.++++-..-.. ......+..|...+++.
T Consensus 68 --~gl~IvG~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~l~~-~~~~~~~~~~~~~~~~W 134 (182)
T cd08060 68 --SGLVIVGYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEKLTL-DCKGNALVVYKDKGGRW 134 (182)
T ss_pred --CCCEEEEEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCccccc-cccCCceEEEEecCCCc
Confidence 79999999999997642 45544322222223445677777777533211 11122345555554443
No 24
>TIGR03735 PRTRC_A PRTRC system protein A. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.
Probab=99.46 E-value=4.1e-13 Score=123.51 Aligned_cols=110 Identities=12% Similarity=0.111 Sum_probs=83.0
Q ss_pred EECHHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHHhhhhcC
Q 018450 7 KMSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRMTVLTG 86 (355)
Q Consensus 7 ~Is~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~m~~~~~ 86 (355)
.|++.++.+|+.||+++.|+|+||++.|.... .++..+|.+|.+.++.+|.+|+..+ .
T Consensus 74 ~Ip~~l~~~ii~hAr~~~P~EacG~Iag~~~~--------~~~r~~p~~N~~~Sp~~~~~d~~~~--------------~ 131 (192)
T TIGR03735 74 PIPASLLEEFAEAARAALPNEVAAWIVWNSET--------GSLRLAALESIEASPGHIDYRRPRL--------------D 131 (192)
T ss_pred CCCHHHHHHHHHHHHhcCCcceEEEEEEcCCC--------CEEEEEeccccccCCceEEEcchHH--------------h
Confidence 58999999999999999999999999996322 1234579999888899999998631 3
Q ss_pred CCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEee
Q 018450 87 RTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSS 149 (355)
Q Consensus 87 rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~ 149 (355)
+|+.+|+.|||||..+|+||.+|++-- ...--++.|+...+. +.+ -.+||+.
T Consensus 132 ~ge~lV~iyHSH~~spA~PS~tD~~Dd-----~~~~k~~~ViG~~~~-----~~p-~~~~Rl~ 183 (192)
T TIGR03735 132 DGEHLVVDLHSHGTGSAFFSETDDADD-----KGEVKISGVLGCLDQ-----GTP-QAVFRLC 183 (192)
T ss_pred CCCeEEEEEcCCCCCCCCCCcccchhh-----cCceEEEEEEEecCC-----CCc-eEEEEEE
Confidence 789999999999999999999999721 121234555554432 223 3567775
No 25
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=99.33 E-value=4.8e-11 Score=115.60 Aligned_cols=131 Identities=15% Similarity=0.189 Sum_probs=96.6
Q ss_pred EEEECHHHHHHHHHHHccC----C--CceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHH
Q 018450 5 GVKMSEDVWLTCLTHALST----E--TEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQA 78 (355)
Q Consensus 5 ~V~Is~~vll~Il~HA~s~----~--P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~ea 78 (355)
.|.|.+.|+++|.+|+.+. . +..|+|.|+|...+. +..|+.+||+...+...+...+|.+. ++.|
T Consensus 2 ~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~~~-----~veItnsF~~p~~~~~~~~~~id~~y----~~~m 72 (288)
T cd08063 2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGR-----EIEIENSFELKYDTNEDGEIVLDKEF----LETR 72 (288)
T ss_pred eEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEcCC-----EEEEEEEEecccccCCCCceeeCHHH----HHHH
Confidence 6899999999999999983 3 678999999987543 23567777666532222456677653 4667
Q ss_pred HHhhhhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEee
Q 018450 79 DRMTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSS 149 (355)
Q Consensus 79 e~m~~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~ 149 (355)
.+++++++.++.+||||++.|. + |...|+..+..|....+..++|++||... .+.+...++||+..
T Consensus 73 ~~~~kkV~~~~~vVGWY~tg~~-~--~~~~~~~Ih~~~~~~~~~pv~L~~D~~~~--~~~~~lpi~ay~s~ 138 (288)
T cd08063 73 LEQFKQVFKDLDFVGWYTTGPG-G--PTESDLPIHKQILEINESPVLLLLDPEAN--ASGKDLPVTIYESV 138 (288)
T ss_pred HHHHHHhccCCceEEEEecCCC-C--CCHHHHHHHHHHHhhCCCcEEEEEccccc--cCCCCCceeEEEEE
Confidence 7888899999999999999987 3 45555555565555566779999998642 14577899999976
No 26
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=99.30 E-value=9.8e-11 Score=114.65 Aligned_cols=131 Identities=15% Similarity=0.174 Sum_probs=98.8
Q ss_pred cccEEEECHHHHHHHHHHHccCCC---ceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCC--CeeecCHHHHHHHHH
Q 018450 2 SLTGVKMSEDVWLTCLTHALSTET---EEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRK--DRVETNPEQLAAASA 76 (355)
Q Consensus 2 sl~~V~Is~~vll~Il~HA~s~~P---~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~--~~feiDPeel~~A~~ 76 (355)
++..|.|.+.|+++|++|+.+..+ ..|.|.|+|...+. +..|+.+||+...+... ..+.+|.+ ++.
T Consensus 4 ~~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~~~~~-----~ieItnsF~~p~~e~~~~~~~~~~D~~----y~~ 74 (303)
T PLN03246 4 GIEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFRG-----RVDVTNSFAVPFEEDDKDPSIWFLDHN----YLE 74 (303)
T ss_pred CCcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEeeecCC-----EEEEEeccccCcccCCCCccceeecHH----HHH
Confidence 567899999999999999998764 44999999998642 34577777776532222 23567743 456
Q ss_pred HHHHhhhhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEee
Q 018450 77 QADRMTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSS 149 (355)
Q Consensus 77 eae~m~~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~ 149 (355)
+|.+++++++.+..+||||+|.|.. +..|+..|..|....+..++|++++.. +.+.+.++||...
T Consensus 75 ~m~~~~k~V~~~~~vVGWY~tg~~i----~~~d~~IH~~~~~~~~~Pv~L~vD~~~----~~~~lpi~aY~s~ 139 (303)
T PLN03246 75 SMFGMFKRINAKEHVVGWYSTGPKL----RENDLDIHELFNDYVPNPVLVIIDVQP----KELGIPTKAYYAV 139 (303)
T ss_pred HHHHHHHHhCCCCcEEeeecCCCCC----CcchHHHHHHHHhhCCCCeEEEEecCC----CCCCCceEEEEEE
Confidence 7778899999999999999999764 445677777777777778889999753 2356889999975
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=99.14 E-value=1.4e-09 Score=94.92 Aligned_cols=111 Identities=21% Similarity=0.236 Sum_probs=72.2
Q ss_pred HHHHHHHHHcc-CCCceeEEEEeeeecCCCCceeEEEEEee-ecCCCCCCCCCeeecCHHHHHHHHHHHHHhhhhcCCCc
Q 018450 12 VWLTCLTHALS-TETEEIMGLLLGDIEHSKNGNVTALIWGA-SPQSRSDRRKDRVETNPEQLAAASAQADRMTVLTGRTT 89 (355)
Q Consensus 12 vll~Il~HA~s-~~P~EvcGLLlG~~~~~~~~~it~~V~~a-~P~~nsd~~~~~feiDPeel~~A~~eae~m~~~~~rgl 89 (355)
|+..|..|.+. ..|.|.||+|+|..... .. .|..+ .|....-.++.+|..+.... ++...+..+..+...
T Consensus 2 v~~~~~~~~Q~~~~~~EtGGiLiG~~~~~-~~----ii~~~t~P~p~d~~tr~~F~r~~~~~---q~~i~~~~~~s~g~~ 73 (131)
T TIGR02256 2 VVAMLKSYRQWHDLSTETGGVLIGERRGA-HA----VITKISEPGSGDIRTRKRFSRDGEHH---QSEVDEHFEVSGGVD 73 (131)
T ss_pred HHHHHHHHHhCcCCCCccceEEEEEEcCC-cE----EEEEEEcCCCCcccCceEEEeCcHHH---HHHHHHHHHHhCCce
Confidence 45556666664 45889999999998743 22 22323 24433223455666655543 333444555556668
Q ss_pred eEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEcc
Q 018450 90 RVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSC 130 (355)
Q Consensus 90 eVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp 130 (355)
..||-|||||...+.||..|+.+....-.....+++||+.-
T Consensus 74 ~ylGeWHtHP~~~p~PS~~D~~~~~~~~~~~~~~l~iIvG~ 114 (131)
T TIGR02256 74 TYLGEWHTHPEDQPEPSWTDRRSWRTIIRSPEAMLLLIVGR 114 (131)
T ss_pred EEEEecCcCCCCCCCCCHHHHHHHHHHHhCCCeeEEEEEcC
Confidence 99999999999999999999998775423334577777764
No 28
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=99.02 E-value=2.5e-09 Score=101.68 Aligned_cols=120 Identities=19% Similarity=0.259 Sum_probs=90.5
Q ss_pred cccEEEECHHHHHHHHHHHccCCC---ceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHH
Q 018450 2 SLTGVKMSEDVWLTCLTHALSTET---EEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQA 78 (355)
Q Consensus 2 sl~~V~Is~~vll~Il~HA~s~~P---~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~ea 78 (355)
.+++|.+.+.|++..++|..+... ..|.|+|+|....+ ...++. .+|+|+..-++...-+.+|... .+.|
T Consensus 7 ~~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~~~~~-~i~vtn--SfAvpFeEDdk~~svWFlDh~Y----~esM 79 (309)
T KOG1556|consen 7 TVEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGSWNGD-VIDVTN--SFAVPFEEDDKDKSVWFLDHNY----IESM 79 (309)
T ss_pred ccceeeeehhHHHHHHHHHhhhccCcCceEEEEEEecCCCC-eEEeec--ceeccccccCCCCceEEeccHH----HHHH
Confidence 467899999999999999998554 88999999998754 122222 4678887654444445567653 3556
Q ss_pred HHhhhhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCc
Q 018450 79 DRMTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFS 132 (355)
Q Consensus 79 e~m~~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~ 132 (355)
-.|+++++..+.+|||||+-|.. .++..||. ..+..+.|..+.+|++..-
T Consensus 80 ~~mfkKvNakekivGWYhTGPkl--~~nDl~In--~l~k~y~pnpvLvIIdvkp 129 (309)
T KOG1556|consen 80 FGMFKKVNAKEKVVGWYHTGPKL--RENDLDIN--ELLKRYVPNPVLVIIDVKP 129 (309)
T ss_pred HHHHHHhcchhheeeeeccCCcc--ccchhhHH--HHHhhcCCCceEEEEeccc
Confidence 68899999999999999999975 46666665 4555678889999999754
No 29
>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=98.84 E-value=5.2e-08 Score=93.37 Aligned_cols=124 Identities=16% Similarity=0.198 Sum_probs=90.9
Q ss_pred EEEECHHHHHHHHHHHccCCCceeEEEEeeeecCCCCc--eeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHHhh
Q 018450 5 GVKMSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNG--NVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRMT 82 (355)
Q Consensus 5 ~V~Is~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~--~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~m~ 82 (355)
.+.|+++++.+.+.-|.. ..++||+|.|+...+... .|..+| ..|+.. ..+.+.+..+. . ..+ .
T Consensus 37 t~vlPknllkkFi~iaD~--rtQ~~GyLyG~~~~d~~~vkeI~cIv--ipPQ~g---t~~sv~l~~~~-~--~~~--~-- 102 (252)
T cd08056 37 TYILPKNLLKKFISISDL--RTQIAGYLYGKSPPDNPQVKEIRCIV--LVPQLG---THQTVTLPQQL-P--QHE--Y-- 102 (252)
T ss_pred EEEeCHHHHHHHHHHhhh--cceEEEEEeccCCCCCCCeEEEEEEE--ECCEeC---CcCcEECCccC-c--cch--h--
Confidence 578999999999988865 469999999997654322 122222 124443 34556664321 1 111 1
Q ss_pred hhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCC-----CcEEEEEccCcCCccCCCceEEEEEEeeCC
Q 018450 83 VLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDT-----GFIGLIFSCFSEDANKVGRIQVIAFQSSDG 151 (355)
Q Consensus 83 ~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p-----~~V~LIvSp~~~d~s~~g~~~lrAFRl~dg 151 (355)
-.+++.+||.|+||.-.++.|..|+.+++.||.+.+ .+|.++|+.. .|...+.||++++.
T Consensus 103 ---l~~Le~LGWIHTqp~e~~~Lss~Dv~tha~~~~~~~~w~~~~~V~it~Sft------pGs~sl~ay~LT~~ 167 (252)
T cd08056 103 ---LEDLEPLGWIHTQPNELPQLSPQDVTTHAKILADNPSWDGEKTVILTCSFT------PGSCSLTAYKLTPE 167 (252)
T ss_pred ---hCCCEeeEEEEcCCCCccccCHHHHHHHHHHHHhccccCCCcEEEEEEcCC------CCceEEEEEecCHH
Confidence 168999999999999999999999999999998887 6888999874 37899999999853
No 30
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=98.32 E-value=1.6e-05 Score=73.66 Aligned_cols=117 Identities=21% Similarity=0.239 Sum_probs=78.2
Q ss_pred cEEEECHHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHHhhh
Q 018450 4 TGVKMSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRMTV 83 (355)
Q Consensus 4 ~~V~Is~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~m~~ 83 (355)
..|.|+..++.+|+-||..-...-|+|+|+|+...+.. ...|++++|+-+. ...+.|. +.-|...++.+.+
T Consensus 2 ~~v~is~~AY~K~~LHaaKyP~~aVnGvLlg~~~~~~~---~v~i~DaVPLfH~-----~~~L~Pm-lEvAL~qvd~~~~ 72 (196)
T PF03665_consen 2 SSVEISSRAYAKMILHAAKYPHCAVNGVLLGKSSKSSS---EVEIVDAVPLFHH-----WLSLSPM-LEVALAQVDAYAK 72 (196)
T ss_pred ceEEEcHHHHHHHHHHhccCCCCceeeEEEeccCCCCc---eEEEeeceecccc-----ccCcchH-HHHHHHHHHHHHh
Confidence 47899999999999999996668899999999765431 2457899999873 2344553 1123334444333
Q ss_pred hcCCCceEEEEEecCCCC-CCCCCHHHHHHHHHHhhcCCCcEEEEEccC
Q 018450 84 LTGRTTRVIGWYHSHPHI-TVLPSHVDVRTQAMYQLLDTGFIGLIFSCF 131 (355)
Q Consensus 84 ~~~rgleVVGwYHSHP~~-~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~ 131 (355)
..|+.|||+||..... ...|+..=.+.-..-....+..+.|+++-.
T Consensus 73 --~~gl~IvGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~ 119 (196)
T PF03665_consen 73 --SNGLVIVGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNK 119 (196)
T ss_pred --hCCCEEEEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECc
Confidence 3789999999998753 234666532222222235678888888754
No 31
>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=97.93 E-value=0.00024 Score=69.13 Aligned_cols=133 Identities=20% Similarity=0.270 Sum_probs=88.3
Q ss_pred cEEEECHHHHHHHHHH-HccCCCceeEEEEeeeecCCCC----cee-EEEEEeeecCCCCCCCCCeeecCHHHHH-HHHH
Q 018450 4 TGVKMSEDVWLTCLTH-ALSTETEEIMGLLLGDIEHSKN----GNV-TALIWGASPQSRSDRRKDRVETNPEQLA-AASA 76 (355)
Q Consensus 4 ~~V~Is~~vll~Il~H-A~s~~P~EvcGLLlG~~~~~~~----~~i-t~~V~~a~P~~nsd~~~~~feiDPeel~-~A~~ 76 (355)
..|.+.......-... ..+.....-||+|.|+...... +.+ +.-|+. -|+.+. .+.+++.++... ...+
T Consensus 11 d~vef~~~~~~~~f~~~~w~~~~~QR~G~LyG~y~~~~~~plgika~VeaIYE-PPQ~~~---~d~~~~l~d~~~~~vd~ 86 (274)
T cd08061 11 DHVEFDNPSIVEFFLYVFWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYE-PPQEGT---PDGFELLEDPNADTVDA 86 (274)
T ss_pred CEEEEecHHHHHHHHHHHHHhhcceeEEEEEEEeecccCCCCceEEEEEEEEC-CCccCC---CCCeEEccchhhhHHHH
Confidence 4455554444444434 5555668899999999875421 111 222322 255543 467777543221 1222
Q ss_pred HHHHhhhhcCCCceEEEEEecCCCC----CCCCCHHHHHHHHHHhh------cCCCcEEEEEccCcCCccCCCceEEEEE
Q 018450 77 QADRMTVLTGRTTRVIGWYHSHPHI----TVLPSHVDVRTQAMYQL------LDTGFIGLIFSCFSEDANKVGRIQVIAF 146 (355)
Q Consensus 77 eae~m~~~~~rgleVVGwYHSHP~~----~a~PS~~DI~TQ~~yQ~------~~p~~V~LIvSp~~~d~s~~g~~~lrAF 146 (355)
-|.. .|++.|||.+||+.. ..+.|..++.+.+.+|. ..+.|+-+|+++.. .|.+.+.||
T Consensus 87 iA~~------lGL~~VG~IfT~l~~~~~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~-----~g~i~~~ay 155 (274)
T cd08061 87 IAAA------LGLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDK-----DGQIHFEAY 155 (274)
T ss_pred HHHH------cCCeEEEEEEecCCCCCCCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCC-----CCceeeeee
Confidence 2322 789999999999976 67899999999999995 56789999999843 388999999
Q ss_pred EeeCC
Q 018450 147 QSSDG 151 (355)
Q Consensus 147 Rl~dg 151 (355)
|+++.
T Consensus 156 QvSdq 160 (274)
T cd08061 156 QVSDQ 160 (274)
T ss_pred eecHH
Confidence 99864
No 32
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=97.81 E-value=0.00017 Score=69.71 Aligned_cols=144 Identities=17% Similarity=0.251 Sum_probs=96.5
Q ss_pred cEEEECHHHHHHHHHHHcc--CCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHHh
Q 018450 4 TGVKMSEDVWLTCLTHALS--TETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRM 81 (355)
Q Consensus 4 ~~V~Is~~vll~Il~HA~s--~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~m 81 (355)
-.|.|.+.++-.|++|..+ ...+.|+|-|+|...+. . ..|+.||-++..+ ..+.+++|-+ +..+|.++
T Consensus 21 ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g---~--ieitNCFaVPhnE-ssdqvevdm~----y~~~M~~l 90 (288)
T KOG2975|consen 21 LTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKG---S--VEVTNCFAVPHNE-SSDQVEVDME----YAKNMYEL 90 (288)
T ss_pred ceEEEcceEEeEeehhhhcCCccchhhhhheeecccCC---e--EEEEEeeeccCcc-ccccceeeHH----HHHHHHHH
Confidence 3688999999999987765 34567999999998742 2 3456555443322 3467777754 23456667
Q ss_pred hhhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEEeeC-----CCceeE
Q 018450 82 TVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQSSD-----GKQNHI 156 (355)
Q Consensus 82 ~~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~d-----g~~~~i 156 (355)
.++.+..+.+||||-+-++.+..-|- .|-.|-.-.++.+.|.+|-- -+.|+..++||-.+. +..-.+
T Consensus 91 ~~k~npnE~vvGWyaTg~dvt~~ssl----ihdyYare~~~pvhLtVDT~----~~n~rm~ikaYvss~~Gvpg~~~~~m 162 (288)
T KOG2975|consen 91 HKKVNPNELVVGWYATGHDVTEHSSL----IHDYYAREAPNPVHLTVDTS----LQNGRMSIKAYVSSLMGVPGRTMGVM 162 (288)
T ss_pred hcccCCCceeEEEEecCCCcccchhH----HHHHhhccCCCCeEEEEecc----ccCCccceeEEEEeccCCCCccccee
Confidence 77889999999999988877654433 24455444577888888853 245789999998763 333335
Q ss_pred eeeeEEeec
Q 018450 157 SKPIALLPV 165 (355)
Q Consensus 157 ~ipi~v~p~ 165 (355)
+-|+++.-.
T Consensus 163 F~plpvel~ 171 (288)
T KOG2975|consen 163 FTPLPVELA 171 (288)
T ss_pred eeeeeeEEe
Confidence 555555433
No 33
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=97.23 E-value=0.0073 Score=55.71 Aligned_cols=112 Identities=16% Similarity=0.186 Sum_probs=72.0
Q ss_pred EEEECHHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCH-HHHHH--HHHHHHHh
Q 018450 5 GVKMSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNP-EQLAA--ASAQADRM 81 (355)
Q Consensus 5 ~V~Is~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDP-eel~~--A~~eae~m 81 (355)
.|+|+..++.+|+-||.+-...-|.|||+|...+.+ . ...|++|+|+-+. ...+.| -+++- ...++.
T Consensus 3 ~veis~~aY~kmiLH~akyph~aVnGLLla~~~~kg--~-~v~itdcVPLfH~-----~laLaPmlEvAl~lId~~~~-- 72 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYPHAAVNGLLLAPATGKG--E-CVEITDCVPLFHS-----HLALAPMLEVALNLIDVWGA-- 72 (199)
T ss_pred ceeehhhHHHHHHHHhccCcccceeeEEEeccCCCC--C-eEEEEecchhhcc-----ccccccHHHHHHHHHHHHHH--
Confidence 589999999999999999766889999999766543 2 2357899998764 233333 33322 222222
Q ss_pred hhhcCCCceEEEEEecCCCCCC-CCCHHHHHHHHHHhhcCCCcEEEEEcc
Q 018450 82 TVLTGRTTRVIGWYHSHPHITV-LPSHVDVRTQAMYQLLDTGFIGLIFSC 130 (355)
Q Consensus 82 ~~~~~rgleVVGwYHSHP~~~a-~PS~~DI~TQ~~yQ~~~p~~V~LIvSp 130 (355)
..|+-|+|+||+.-...- .|...=...-..-+.++|....|+++-
T Consensus 73 ----~~GlviaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn 118 (199)
T KOG3289|consen 73 ----QAGLVIAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDN 118 (199)
T ss_pred ----hcCeEEEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEec
Confidence 379999999999865332 233222221112234567777777774
No 34
>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=96.73 E-value=0.024 Score=56.24 Aligned_cols=109 Identities=21% Similarity=0.286 Sum_probs=73.2
Q ss_pred EEEEeeeecCCCCc--eeEEEEEee--ecCCCCCCCCCeeecCHHHH-HHHHHHHHHhhhhcCCCceEEEEEecCCC---
Q 018450 29 MGLLLGDIEHSKNG--NVTALIWGA--SPQSRSDRRKDRVETNPEQL-AAASAQADRMTVLTGRTTRVIGWYHSHPH--- 100 (355)
Q Consensus 29 cGLLlG~~~~~~~~--~it~~V~~a--~P~~nsd~~~~~feiDPeel-~~A~~eae~m~~~~~rgleVVGwYHSHP~--- 100 (355)
+|+|.|+....... -|.+.|... .|+.+ ..+.+.+.+..- .++.+-|.. .|++.|||.=||+.
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~---~~d~~~l~~d~~~~~vd~iA~~------lGL~rVG~IfTdl~~~~ 72 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEG---EPDGFTLLPDENEERVDAIASA------LGLERVGWIFTDLTDDG 72 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCC---CCCCEEEcCCccHHHHHHHHHH------CCCEEEEEEEecCcccc
Confidence 79999998754311 012222222 25544 356777743321 223322332 69999999999987
Q ss_pred ------------CCCCCCHHHHHHHHHHhhcC-------------CCcEEEEEccCcCCccCCCceEEEEEEeeCC
Q 018450 101 ------------ITVLPSHVDVRTQAMYQLLD-------------TGFIGLIFSCFSEDANKVGRIQVIAFQSSDG 151 (355)
Q Consensus 101 ------------~~a~PS~~DI~TQ~~yQ~~~-------------p~~V~LIvSp~~~d~s~~g~~~lrAFRl~dg 151 (355)
-.-+.|...+.+.+.+|... ..||.+|++.- ..|.+.+.|||.++.
T Consensus 73 ~~~g~v~~~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~-----~~g~i~~~ayQvS~q 143 (306)
T PF05021_consen 73 SGDGTVKCKRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGD-----EEGEIHFEAYQVSNQ 143 (306)
T ss_pred cCCCceeeccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCC-----CCCceeeEEeeehHH
Confidence 56689999999988999754 35889999873 458999999999863
No 35
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=93.93 E-value=0.41 Score=46.49 Aligned_cols=144 Identities=17% Similarity=0.209 Sum_probs=82.5
Q ss_pred EEEECHHHHHHHHHHHcc-----CCCc-eeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHH
Q 018450 5 GVKMSEDVWLTCLTHALS-----TETE-EIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQA 78 (355)
Q Consensus 5 ~V~Is~~vll~Il~HA~s-----~~P~-EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~ea 78 (355)
+|.+.+.|.+.|-+|.-+ +.|. .|.|-|+|+..+. + + .|...|.+.- +...+.-.+|-+.+..-+
T Consensus 10 tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~Q~GR---~-v-Ei~NSFeL~~-d~~~~~~~~dke~l~kk~--- 80 (299)
T KOG3050|consen 10 TVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGKQRGR---N-V-EIMNSFELKM-DTEEDTETIDKEYLEKKE--- 80 (299)
T ss_pred eEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheecccCc---e-E-EEeeeeEEEe-cchhhhhhccHHHHHHHH---
Confidence 678899999999998654 5666 7999999997653 1 2 2332222211 111122235555443222
Q ss_pred HHhhhhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhhcCCCcEEEEEccCcCCccCCCceEEEEEE--eeCCCceeE
Q 018450 79 DRMTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQLLDTGFIGLIFSCFSEDANKVGRIQVIAFQ--SSDGKQNHI 156 (355)
Q Consensus 79 e~m~~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~~~p~~V~LIvSp~~~d~s~~g~~~lrAFR--l~dg~~~~i 156 (355)
+.++++-.++.++|||-+-- .+.|| |+..+..--....-.++|-..|...- ....+..+-+|- +.||....+
T Consensus 81 -eqykqVFpdl~vlGwYttG~--d~t~s--d~~i~k~l~~i~esplflkLNp~t~~-t~~~pv~lfese~dvidg~~q~~ 154 (299)
T KOG3050|consen 81 -EQYKQVFPDLYVLGWYTTGS--DPTPS--DIHIHKQLMDINESPLFLKLNPATNH-TDKDPVTLFESEIDVIDGEAQML 154 (299)
T ss_pred -HHHHHhcccceEEEEeecCC--CCChh--hhHHHHHHHhhhcCceEEEecchhcc-ccCCCceeeeeeheeecCcceee
Confidence 34555668999999998763 33454 55544432224556677777775421 111134444443 358887777
Q ss_pred eeeeEEe
Q 018450 157 SKPIALL 163 (355)
Q Consensus 157 ~ipi~v~ 163 (355)
..|+.-.
T Consensus 155 f~~~tyt 161 (299)
T KOG3050|consen 155 FVPLTYT 161 (299)
T ss_pred eeeeEEE
Confidence 7776543
No 36
>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=92.13 E-value=1.5 Score=37.10 Aligned_cols=45 Identities=22% Similarity=0.279 Sum_probs=34.4
Q ss_pred CCeeecCHHHHHHHHHHHHHhhhhcCCCceEEEEEecCCCCCCCCCHHHHHHHH
Q 018450 61 KDRVETNPEQLAAASAQADRMTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQA 114 (355)
Q Consensus 61 ~~~feiDPeel~~A~~eae~m~~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~ 114 (355)
.++..++|.++.+ .|.. .+..-|...|.||.+.+.||..|+..-.
T Consensus 41 ~~~~~v~~R~i~~---~aL~------~~A~~vil~HNHPsG~~~PS~~D~~~T~ 85 (113)
T cd08071 41 LNSSLVHPREIFK---EALR------HNAAAIILAHNHPSGDPTPSREDIELTK 85 (113)
T ss_pred CcceecCHHHHHH---HHHH------HhhheEEEEeeCCCCCCCCCHHHHHHHH
Confidence 4678889987642 2222 4568899999999999999999998544
No 37
>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=81.03 E-value=7.2 Score=33.35 Aligned_cols=45 Identities=22% Similarity=0.287 Sum_probs=26.6
Q ss_pred CCeeecCHHHHHHHHHHHHHhhhhcCCCceEEEEEecCCCCCCCCCHHHHHHHH
Q 018450 61 KDRVETNPEQLAAASAQADRMTVLTGRTTRVIGWYHSHPHITVLPSHVDVRTQA 114 (355)
Q Consensus 61 ~~~feiDPeel~~A~~eae~m~~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~ 114 (355)
-+...++|++++ +.|.. .+..-|-..|=||++.+.||..|+..-.
T Consensus 46 ~~~~~v~~R~I~---~~al~------~~A~~vIl~HNHPsG~~~PS~~D~~~T~ 90 (123)
T PF04002_consen 46 IDSAPVDPREIF---RRALR------LNASSVILAHNHPSGDPEPSDADIALTR 90 (123)
T ss_dssp T-GGGCSHHHHH---HHHHH------TT-SEEEEEEE-TTS--S--HHHHHHHH
T ss_pred CCcccccHHHHH---HHHHh------hCCceEEEEEEcCCCCCCCCHhHHHHHH
Confidence 456778898764 23322 4556677889999999999999996443
No 38
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.64 E-value=29 Score=32.86 Aligned_cols=87 Identities=21% Similarity=0.182 Sum_probs=51.2
Q ss_pred CHHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHHhhhhcCCC
Q 018450 9 SEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRMTVLTGRT 88 (355)
Q Consensus 9 s~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~m~~~~~rg 88 (355)
+++.+...+.......+.|...+|+=... ..+.... .. ..++-+...++|.++. +.|.+ .+
T Consensus 99 s~~~v~~~l~~~l~~~~~E~f~vl~Ld~~----n~li~~~----~i--~~Gt~~~~~v~pReI~---~~Al~------~~ 159 (218)
T TIGR00608 99 SPEAAAEFLHTDLAHETREHFMVLFLDRK----NRLIAKE----VV--FIGTVNHVPVHPREIF---KEALK------LS 159 (218)
T ss_pred CHHHHHHHHHHHhcCCCceEEEEEEECCC----CcEEEEE----Ee--ecCCCCeEEEcHHHHH---HHHHH------hh
Confidence 44444455555555667776666542211 1222110 11 1234567889998764 23322 34
Q ss_pred ceEEEEEecCCCCCCCCCHHHHHHHH
Q 018450 89 TRVIGWYHSHPHITVLPSHVDVRTQA 114 (355)
Q Consensus 89 leVVGwYHSHP~~~a~PS~~DI~TQ~ 114 (355)
-.-|=..|=||++.+.||..|+..-.
T Consensus 160 A~~vIlaHNHPSG~~~PS~~Di~~T~ 185 (218)
T TIGR00608 160 ASALILAHNHPSGEPSPSQEDILITE 185 (218)
T ss_pred CCeEEEEeecCCCCCCCCHHHHHHHH
Confidence 46677789999999999999997544
No 39
>PRK00024 hypothetical protein; Reviewed
Probab=75.98 E-value=30 Score=32.81 Aligned_cols=87 Identities=20% Similarity=0.156 Sum_probs=51.3
Q ss_pred CHHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEEeeecCCCCCCCCCeeecCHHHHHHHHHHHHHhhhhcCCC
Q 018450 9 SEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIWGASPQSRSDRRKDRVETNPEQLAAASAQADRMTVLTGRT 88 (355)
Q Consensus 9 s~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~~a~P~~nsd~~~~~feiDPeel~~A~~eae~m~~~~~rg 88 (355)
++..+...+.......+.|...+|+=.... .+.... -.. .++-+...++|.++. +.|.+ .+
T Consensus 105 ~~~~~~~~l~~~l~~~~~E~f~vl~Ld~~~----~li~~~----~i~--~Gt~~~~~v~pRei~---~~Al~------~~ 165 (224)
T PRK00024 105 SPEDVADYLMAELRDEEQEHFVVLFLDTKN----RVIADE----ELF--IGTLNSSIVHPREIV---KRALK------LN 165 (224)
T ss_pred CHHHHHHHHHHHccCCCceEEEEEEECCCC----CEeeEE----Eee--eecCCeEEEcHHHHH---HHHHH------hh
Confidence 344444555555556677776666533221 122110 011 134567888998764 33322 34
Q ss_pred ceEEEEEecCCCCCCCCCHHHHHHHH
Q 018450 89 TRVIGWYHSHPHITVLPSHVDVRTQA 114 (355)
Q Consensus 89 leVVGwYHSHP~~~a~PS~~DI~TQ~ 114 (355)
-.-|-..|=||++.+.||..|+..-.
T Consensus 166 A~~iIl~HNHPSG~~~PS~~D~~~T~ 191 (224)
T PRK00024 166 AAALILAHNHPSGDPEPSQADILITK 191 (224)
T ss_pred ccceEEEecCCCCCCCCCHHHHHHHH
Confidence 46677789999999999999998544
No 40
>PF14220 DUF4329: Domain of unknown function (DUF4329)
Probab=66.64 E-value=5.4 Score=34.74 Aligned_cols=27 Identities=22% Similarity=0.379 Sum_probs=21.8
Q ss_pred CCceEEEEEecCCCC-----CCCCCHHHHHHH
Q 018450 87 RTTRVIGWYHSHPHI-----TVLPSHVDVRTQ 113 (355)
Q Consensus 87 rgleVVGwYHSHP~~-----~a~PS~~DI~TQ 113 (355)
.+..+|+.||+|... ...||..|+..-
T Consensus 57 ~g~~~vA~yHTHG~~~~~y~~evfS~~D~~~~ 88 (123)
T PF14220_consen 57 NGSTIVASYHTHGAYSDGYDNEVFSPQDIRGD 88 (123)
T ss_pred cccceeeEeecccccCCCccccCCCHHHhhhh
Confidence 478999999999864 347999999843
No 41
>PF15659 Toxin-JAB1: JAB-like toxin 1
Probab=57.87 E-value=7.9 Score=35.41 Aligned_cols=26 Identities=31% Similarity=0.505 Sum_probs=21.9
Q ss_pred CCCceEEEEEecCCCCCCCCCHHHHHH
Q 018450 86 GRTTRVIGWYHSHPHITVLPSHVDVRT 112 (355)
Q Consensus 86 ~rgleVVGwYHSHP~~~a~PS~~DI~T 112 (355)
..+.-++. .||||..+..||..|...
T Consensus 113 ~~~~~iid-iHSHP~~~~~~S~~D~~~ 138 (162)
T PF15659_consen 113 NNGNKIID-IHSHPENSNGPSGNDMKN 138 (162)
T ss_pred cCCceEEE-eccCCCCCCCCCcchhhh
Confidence 46667777 999999999999999973
No 42
>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=57.74 E-value=1.6e+02 Score=31.40 Aligned_cols=127 Identities=24% Similarity=0.301 Sum_probs=74.6
Q ss_pred HHHHHHHHHHHccCCCceeEEEEeeeecCCCCc--e---eEEEEEeeecCCCCCCCCCeeecC--HHHHHHHHHHHHHhh
Q 018450 10 EDVWLTCLTHALSTETEEIMGLLLGDIEHSKNG--N---VTALIWGASPQSRSDRRKDRVETN--PEQLAAASAQADRMT 82 (355)
Q Consensus 10 ~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~--~---it~~V~~a~P~~nsd~~~~~feiD--Peel~~A~~eae~m~ 82 (355)
+.++...++.-+.. ..--.|+|.|+....... - ++.-|+.+ |+.. .++.+++. +++. .+.+-|
T Consensus 182 ~~~v~~Fl~~wr~s-g~QR~GflyG~y~e~~~vPLGika~V~aIYEP-PQ~~---~~dgl~l~~~~e~~-~vD~~a---- 251 (510)
T KOG2834|consen 182 AELVNHFLNEWRAS-GVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEP-PQHG---EEDGLELLEDDEAK-RVDAIA---- 251 (510)
T ss_pred hHHHHHHHHHHHHh-hhhhcceEEEeecccccccccceeeEEEEecC-CccC---CcCCeEEeccchhh-hHHHHH----
Confidence 45566666655543 355679999998654321 1 12223321 4443 45677774 2222 111112
Q ss_pred hhcCCCceEEEEEecCC---------------CCCCCCCHHHHHHHHHHhhcCCC-------------cEEEEEccCcCC
Q 018450 83 VLTGRTTRVIGWYHSHP---------------HITVLPSHVDVRTQAMYQLLDTG-------------FIGLIFSCFSED 134 (355)
Q Consensus 83 ~~~~rgleVVGwYHSHP---------------~~~a~PS~~DI~TQ~~yQ~~~p~-------------~V~LIvSp~~~d 134 (355)
.+.|++.|||.-+-- .-+.+.|..++.+-+.||...|. +|-++++-
T Consensus 252 --~~lGLrRVG~IFTDl~~~~s~egtV~~~rhkdsyFLSseE~~~aa~~Q~~hpn~~~~s~~~~fgSkfVT~visg---- 325 (510)
T KOG2834|consen 252 --EGLGLRRVGWIFTDLVTADSAEGTVHYKRHKDSYFLSSEECITAAMFQNKHPNICEWSRDGHFGSKFVTLVISG---- 325 (510)
T ss_pred --HhcCceeeEEEEeeeecccCccceEEeeeccchhcccHHHHHHHhhhhhcCCchheeeccccccceeEEEEEec----
Confidence 247999999975432 12458999999998899877553 55555553
Q ss_pred ccCCCceEEEEEEeeCCCc
Q 018450 135 ANKVGRIQVIAFQSSDGKQ 153 (355)
Q Consensus 135 ~s~~g~~~lrAFRl~dg~~ 153 (355)
+..|.+.+-.||.++-..
T Consensus 326 -~~~~~V~f~~YQVSnqc~ 343 (510)
T KOG2834|consen 326 -DLDGEVHFEGYQVSNQCM 343 (510)
T ss_pred -CCCcceeeeeeehhHHHH
Confidence 234677888888775433
No 43
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=43.71 E-value=45 Score=33.73 Aligned_cols=26 Identities=15% Similarity=0.313 Sum_probs=20.7
Q ss_pred HHHHHHhhhhcCCCceEEEEEecCCC
Q 018450 75 SAQADRMTVLTGRTTRVIGWYHSHPH 100 (355)
Q Consensus 75 ~~eae~m~~~~~rgleVVGwYHSHP~ 100 (355)
...|+...|+.+-|..|||+|=.+|.
T Consensus 49 aeHA~qVsRMLPGGi~VlGifvv~~~ 74 (362)
T PF14778_consen 49 AEHARQVSRMLPGGISVLGIFVVAPD 74 (362)
T ss_pred HHHHHHHHhhCCCCcEEEEEEEEcCH
Confidence 34566777888999999999987764
No 44
>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=38.20 E-value=41 Score=39.96 Aligned_cols=123 Identities=19% Similarity=0.174 Sum_probs=73.4
Q ss_pred EECHHHHHHHHHHHccCCCceeEEEEeeeecCCCCceeEEEEE-eeecCCCCCC---CCCeeecCHHHHHHHHHHHHHhh
Q 018450 7 KMSEDVWLTCLTHALSTETEEIMGLLLGDIEHSKNGNVTALIW-GASPQSRSDR---RKDRVETNPEQLAAASAQADRMT 82 (355)
Q Consensus 7 ~Is~~vll~Il~HA~s~~P~EvcGLLlG~~~~~~~~~it~~V~-~a~P~~nsd~---~~~~feiDPeel~~A~~eae~m~ 82 (355)
.|+..++.+.+.- +....-+.|++.|....+. ..+..+-. -.+|+-.+.. .+...- ++..
T Consensus 2098 ilPkNllkkFi~i--sD~r~qiag~~yG~s~~d~-pqvkeIr~ivmvPQ~gs~~~v~lp~~lP-~~~~------------ 2161 (2321)
T KOG1795|consen 2098 ILPKNLLKKFITI--SDLRTQIAGYLYGVSPPDN-PQVKEIRCIVMVPQWGSHQGVHLPSFLP-IHGV------------ 2161 (2321)
T ss_pred eccHHHHhhheee--cchhhhhheeeeccCCCCC-CccceEEEEEeccccccccccccCccCC-cchh------------
Confidence 4566666665532 3445678899999765443 22211111 1245543211 011111 1111
Q ss_pred hhcCCCceEEEEEecCCCCCCCCCHHHHHHHHHHhh-cCCCcEEEEEccCcCCccCCCceEEEEEEeeCCCce
Q 018450 83 VLTGRTTRVIGWYHSHPHITVLPSHVDVRTQAMYQL-LDTGFIGLIFSCFSEDANKVGRIQVIAFQSSDGKQN 154 (355)
Q Consensus 83 ~~~~rgleVVGwYHSHP~~~a~PS~~DI~TQ~~yQ~-~~p~~V~LIvSp~~~d~s~~g~~~lrAFRl~dg~~~ 154 (355)
=.+++-+||.|+-|+--++.|+.|+.|++.-.. .-..++.|-|+. +.|..++.||.+++.+-.
T Consensus 2162 ---l~d~e~Lgw~hTq~~el~~lsp~dV~th~ki~~~~k~k~i~~t~~~------tpgs~sl~ay~lt~~G~e 2225 (2321)
T KOG1795|consen 2162 ---LEDLEPLGWIHTQPNELPQLSPQDVTTHAKILVDNKEKCIIITCSF------TPGSCSLTAYKLTPSGYE 2225 (2321)
T ss_pred ---ccCCcccchhhcCccccccCCHHHhhhhhhhhhcCccceEEEEeec------cCCcceeeeeccCccccc
Confidence 157899999999999999999999999885422 233566666653 458899999999864443
No 45
>cd07278 PX_RICS_like The phosphoinositide binding Phox Homology domain of PX-RICS-like proteins. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Members of this family include PX-RICS, TCGAP (Tc10/Cdc42 GTPase-activating protein), and similar proteins. They contain N-terminal PX and Src Homology 3 (SH3) domains, a central Rho GAP domain, and C-terminal extensions. They act as Rho GTPase-activating proteins. PX-RICS is the main isoform expressed during neural development. It is involved in neural functions including axon and dendrite extension, postnatal remodeling, and fine-tuning of neural circuits during early brain development. The PX domain of PX-RICS specifically binds phosphatidylinositol 3-phosphate (PI3P), PI4P, and PI5P. TCGAP is widely expressed in the brain where it is involved in regulating the outgrowth of axons and d
Probab=27.21 E-value=15 Score=31.70 Aligned_cols=11 Identities=27% Similarity=0.763 Sum_probs=9.1
Q ss_pred hhcchhHHHHH
Q 018450 335 EKCIPLLTFIT 345 (355)
Q Consensus 335 ~~~~~~~~~~~ 345 (355)
--|||.|+|||
T Consensus 103 inCGPvLtWle 113 (114)
T cd07278 103 LNCGPVLNWLE 113 (114)
T ss_pred ccchhcceeee
Confidence 45899999986
No 46
>cd07298 PX_RICS The phosphoinositide binding Phox Homology domain of PX-RICS. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. RICS is a Rho GTPase-activating protein for cdc42 and Rac1. It is implicated in the regulation of postsynaptic signaling and neurite outgrowth. An N-terminal splicing variant of RICS containing additional PX and Src Homology 3 (SH3) domains, also called PX-RICS, is the main isoform expressed during neural development. PX-RICS is involved in neural functions including axon and dendrite extension, postnatal remodeling, and fine-tuning of neural circuits during early brain development. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. The PX domain of PX-RICS specifically binds phosphatidylinositol 3-phosphate (PI3P), PI4P, and
Probab=26.85 E-value=15 Score=31.81 Aligned_cols=11 Identities=36% Similarity=0.727 Sum_probs=8.9
Q ss_pred hhcchhHHHHH
Q 018450 335 EKCIPLLTFIT 345 (355)
Q Consensus 335 ~~~~~~~~~~~ 345 (355)
--|||.|+|+|
T Consensus 104 ~nCGPvLtWle 114 (115)
T cd07298 104 INCGPALTWME 114 (115)
T ss_pred ccchhcceeee
Confidence 35899999986
No 47
>cd07299 PX_TCGAP The phosphoinositide binding Phox Homology domain of Tc10/Cdc42 GTPase-activating protein. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. TCGAP (Tc10/Cdc42 GTPase-activating protein) contains N-terminal PX and Src Homology 3 (SH3) domains, a central Rho GAP domain, and C-terminal proline-rich regions. It is widely expressed in the brain where it is involved in regulating the outgrowth of axons and dendrites and is regulated by the protein tyrosine kinase Fyn. It interacts with cdc42 and TC10beta through its GAP domain and with phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2] through its PX domain. It is translocated to the plasma membrane in adipocytes in response to insulin and may be involved in the regulation of insulin-stimulated glucose transport. TCGAP has also been named sorting nexins 26 (SNX26). SNXs
Probab=25.80 E-value=16 Score=31.50 Aligned_cols=11 Identities=36% Similarity=0.815 Sum_probs=9.0
Q ss_pred hhcchhHHHHH
Q 018450 335 EKCIPLLTFIT 345 (355)
Q Consensus 335 ~~~~~~~~~~~ 345 (355)
--|||.|+|+|
T Consensus 102 inCGPVLtWme 112 (113)
T cd07299 102 LNCGPVLTWME 112 (113)
T ss_pred ccccccceeee
Confidence 35899999986
No 48
>KOG2332 consensus Ferritin [Inorganic ion transport and metabolism]
Probab=23.87 E-value=64 Score=30.03 Aligned_cols=43 Identities=26% Similarity=0.169 Sum_probs=34.3
Q ss_pred HHHHHHHHHHH-HHhhcCcceeeehhhhcchhHHHHHHHHHhhhcc
Q 018450 310 EEERAAYNQAI-MQNMSNCLQFYSVMEKCIPLLTFITHQLIRLQCA 354 (355)
Q Consensus 310 ~ee~~a~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (355)
.|||+-..+.| .||+|+|.+... .|..|=.+-.++.|..|+||
T Consensus 61 ~eereha~klm~~~n~rgg~i~l~--~i~~P~~~ew~~~l~ale~a 104 (178)
T KOG2332|consen 61 QEEREHAEKLMKTQNMRGGRIELQ--DIKKPELDEWGKGLEALEAA 104 (178)
T ss_pred hhhhhhHHHHHHHHHHhCCccccc--cccccccchhHhHHHHHHHH
Confidence 68999999998 789999999842 34477777778888888876
No 49
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=21.80 E-value=63 Score=31.11 Aligned_cols=49 Identities=20% Similarity=0.276 Sum_probs=30.5
Q ss_pred CeeecCHHHHHHHHHHHHHhhhhcCCCceEEEEEecCCCCCCCCCHHHHH-HHHHHhhc
Q 018450 62 DRVETNPEQLAAASAQADRMTVLTGRTTRVIGWYHSHPHITVLPSHVDVR-TQAMYQLL 119 (355)
Q Consensus 62 ~~feiDPeel~~A~~eae~m~~~~~rgleVVGwYHSHP~~~a~PS~~DI~-TQ~~yQ~~ 119 (355)
++-.+-|.+.. ++|.+ ....-|=..|=||.+.+.||..|+. |+...++.
T Consensus 148 ~~s~V~PREI~---k~Al~------~nAaavIlaHNHPSGd~~PS~aD~~iT~rl~~a~ 197 (224)
T COG2003 148 NVSEVHPREIF---KEALK------YNAAAVILAHNHPSGDPTPSRADILITERLKEAG 197 (224)
T ss_pred ccceecHHHHH---HHHHH------hcchhhheeccCCCCCCCcCHHHHHHHHHHHHHH
Confidence 44556677653 23322 2223344579999999999999997 34444443
No 50
>COG4138 BtuD ABC-type cobalamin transport system, ATPase component [Coenzyme metabolism]
Probab=20.48 E-value=95 Score=29.68 Aligned_cols=47 Identities=32% Similarity=0.531 Sum_probs=37.8
Q ss_pred HhhhcccCCCCCceeeeecc---eeee----cCcccccccCCcchhhhHhHHHH
Q 018450 263 AMHRSNLDMSGAEYVRKEIP---LHVL----PTSSLLKLDSPLTSFTDLQRVLY 309 (355)
Q Consensus 263 a~h~s~~~~s~~~y~r~e~p---l~v~----~~~~~~~~~~~~~~~~~~~~~~~ 309 (355)
-+|||.=-.||+|+-|-... |+|- |...++-+|.|..++.--|+.+.
T Consensus 118 KL~Rs~~qLSGGEWQRVRLAav~LQv~Pd~NP~~~LLllDEP~~~LDvAQ~~aL 171 (248)
T COG4138 118 KLGRSTNQLSGGEWQRVRLAAVVLQITPDANPAGQLLLLDEPMNSLDVAQQSAL 171 (248)
T ss_pred hhhhhhhhcCcccceeeEEeEEEEEecCCCCccceeEEecCCCcchhHHHHHHH
Confidence 58999999999999997644 5555 45678999999999987776644
Done!