Query 021476
Match_columns 312
No_of_seqs 151 out of 681
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 03:15:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021476.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021476hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3050 COP9 signalosome, subu 100.0 1.6E-74 3.4E-79 501.7 26.2 296 1-312 1-299 (299)
2 cd08063 MPN_CSN6 Mpr1p, Pad1p 100.0 1.5E-70 3.2E-75 509.2 32.5 278 9-301 1-282 (288)
3 PLN03246 26S proteasome regula 100.0 2.6E-68 5.7E-73 493.8 33.3 270 5-296 2-279 (303)
4 cd08062 MPN_RPN7_8 Mpr1p, Pad1 100.0 2.3E-67 5.1E-72 484.1 33.6 265 10-296 2-273 (280)
5 KOG2975 Translation initiation 100.0 4.9E-68 1.1E-72 466.5 26.5 269 1-291 13-284 (288)
6 cd08064 MPN_eIF3f Mpr1p, Pad1p 100.0 6.1E-65 1.3E-69 466.6 31.0 259 11-291 1-264 (265)
7 KOG1556 26S proteasome regulat 100.0 1E-57 2.2E-62 397.2 23.5 272 2-295 2-280 (309)
8 cd08057 MPN_euk_non_mb Mpr1p, 100.0 8.3E-39 1.8E-43 272.1 16.7 150 11-184 1-157 (157)
9 cd08065 MPN_eIF3h Mpr1p, Pad1p 100.0 2E-30 4.4E-35 238.1 21.3 200 10-230 2-225 (266)
10 cd08069 MPN_RPN11_CSN5 Mov34/M 99.9 2.6E-25 5.5E-30 204.2 22.4 167 5-191 6-202 (268)
11 PF01398 JAB: JAB1/Mov34/MPN/P 99.9 1E-25 2.2E-30 181.4 11.2 105 7-131 2-114 (114)
12 PF13012 MitMem_reg: Maintenan 99.9 1.3E-23 2.8E-28 169.6 1.2 114 178-294 1-114 (115)
13 smart00232 JAB_MPN JAB/MPN dom 99.9 2.3E-20 5E-25 153.7 15.4 126 10-156 1-133 (135)
14 KOG1560 Translation initiation 99.8 1.1E-19 2.4E-24 161.9 19.0 237 4-265 8-292 (339)
15 KOG1554 COP9 signalosome, subu 99.7 1.2E-15 2.6E-20 136.6 12.9 201 9-230 53-282 (347)
16 cd07767 MPN Mpr1p, Pad1p N-ter 99.6 6.1E-15 1.3E-19 118.3 12.7 100 50-153 13-116 (116)
17 cd08067 MPN_2A_DUB Mov34/MPN/P 99.5 2.8E-12 6.1E-17 111.8 16.9 146 7-178 3-164 (187)
18 cd08058 MPN_euk_mb Mpr1p, Pad1 99.4 1.6E-12 3.4E-17 105.5 11.0 108 17-155 2-118 (119)
19 cd08068 MPN_BRCC36 Mov34/MPN/P 99.2 2.2E-09 4.7E-14 96.9 16.7 148 9-178 2-170 (244)
20 KOG1555 26S proteasome regulat 98.8 1.7E-07 3.7E-12 86.7 16.8 131 5-156 27-172 (316)
21 cd08066 MPN_AMSH_like Mov34/MP 98.7 2.2E-07 4.8E-12 80.2 12.9 116 11-156 4-127 (173)
22 PF03665 UPF0172: Uncharacteri 98.4 2E-05 4.3E-10 69.4 16.1 124 10-154 3-134 (196)
23 cd08060 MPN_UPF0172 Mov34/MPN/ 98.4 5.3E-06 1.1E-10 72.2 11.7 104 15-141 3-114 (182)
24 cd08070 MPN_like Mpr1p, Pad1p 98.2 2.6E-05 5.7E-10 63.8 11.3 110 17-155 3-118 (128)
25 COG1310 Predicted metal-depend 98.0 7.1E-05 1.5E-09 61.8 10.1 98 12-139 3-106 (134)
26 KOG3289 Uncharacterized conser 97.8 0.00061 1.3E-08 58.0 12.2 124 10-154 3-134 (199)
27 TIGR02256 ICE_VC0181 integrati 96.8 0.024 5.1E-07 46.7 10.8 87 50-137 16-112 (131)
28 PF14464 Prok-JAB: Prokaryotic 96.0 0.091 2E-06 40.7 9.7 54 50-113 17-70 (104)
29 cd08072 MPN_archaeal Mov34/MPN 95.8 0.096 2.1E-06 42.2 9.2 83 50-155 18-107 (117)
30 cd08056 MPN_PRP8 Mpr1p, Pad1p 94.8 0.12 2.7E-06 47.1 7.8 98 51-156 56-165 (252)
31 cd08073 MPN_NLPC_P60 Mpr1p, Pa 87.1 1.4 3.1E-05 34.8 5.2 51 50-113 15-70 (108)
32 cd08059 MPN_prok_mb Mpr1p, Pad 81.4 6.2 0.00013 30.4 6.4 60 50-120 15-78 (101)
33 PF06442 DHFR_2: R67 dihydrofo 73.2 1.9 4.1E-05 30.8 1.2 12 102-113 40-51 (78)
34 KOG2880 SMAD6 interacting prot 70.2 2.7 5.8E-05 40.1 1.8 90 50-142 275-369 (424)
35 PF14778 ODR4-like: Olfactory 63.2 42 0.00091 32.3 8.6 59 55-113 1-74 (362)
36 cd08061 MPN_NPL4 Mov34/MPN/PAD 59.0 1.2E+02 0.0026 28.2 10.4 101 51-156 34-158 (274)
37 TIGR03735 PRTRC_A PRTRC system 56.1 46 0.001 29.2 6.8 65 16-113 78-145 (192)
38 PF03127 GAT: GAT domain; Int 40.7 1.6E+02 0.0036 22.5 8.5 86 209-302 8-94 (100)
39 PF11430 EGL-1: Programmed cel 38.7 55 0.0012 18.0 2.8 11 240-250 1-11 (21)
40 PF12408 DUF3666: Ribose-5-pho 35.9 1.1E+02 0.0023 20.7 4.5 33 238-279 14-46 (48)
41 PF10073 DUF2312: Uncharacteri 34.9 1.9E+02 0.004 21.4 8.7 64 203-281 9-72 (74)
42 PF04740 LXG: LXG domain of WX 32.1 3.3E+02 0.0071 23.4 8.9 44 207-250 63-108 (204)
43 KOG3684 Ca2+-activated K+ chan 31.6 1.9E+02 0.0041 28.9 7.3 80 210-301 362-445 (489)
44 PF05021 NPL4: NPL4 family; I 30.9 4.6E+02 0.01 24.7 10.8 57 54-112 2-68 (306)
45 PF05377 FlaC_arch: Flagella a 29.8 1.8E+02 0.004 20.1 5.0 34 201-234 17-50 (55)
46 PF09457 RBD-FIP: FIP domain ; 28.1 85 0.0018 21.1 3.1 41 203-243 5-45 (48)
47 PF14071 YlbD_coat: Putative c 27.4 1.3E+02 0.0027 24.6 4.5 27 274-300 82-108 (124)
48 KOG0756 Mitochondrial tricarbo 26.8 36 0.00078 31.8 1.5 49 51-111 13-73 (299)
49 PF05184 SapB_1: Saposin-like 25.0 94 0.002 19.0 2.8 17 238-254 23-39 (39)
50 PF10224 DUF2205: Predicted co 24.6 3E+02 0.0066 20.6 5.9 47 202-252 20-66 (80)
51 KOG3650 Predicted coiled-coil 21.7 2.7E+02 0.0059 21.7 5.2 46 209-254 60-108 (120)
52 PF01381 HTH_3: Helix-turn-hel 21.0 2E+02 0.0043 18.7 4.0 37 215-251 13-49 (55)
No 1
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=1.6e-74 Score=501.70 Aligned_cols=296 Identities=55% Similarity=0.908 Sum_probs=276.0
Q ss_pred CCCCCCCCceEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCCCc
Q 021476 1 MASSSSSGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPST 80 (312)
Q Consensus 1 ~~~~~~~~~~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~ 80 (312)
||.+++++.+|.+|||||+||+|||+|.+.+. ++..++|+|+|+|.|.|+.|||.|||++..+..+
T Consensus 1 ~Aps~S~s~tv~LHPLVImniSdH~tR~k~Q~--------------gpp~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~ 66 (299)
T KOG3050|consen 1 MAPSSSGSVTVKLHPLVIMNISDHYTRVKTQL--------------GPPVKQVYGALIGKQRGRNVEIMNSFELKMDTEE 66 (299)
T ss_pred CCCCCCCceeEEeccEEEEehhHHHHHHHhhc--------------CCcHHHhhhhheecccCceEEEeeeeEEEecchh
Confidence 68889999999999999999999999999773 1123489999999999999999999999987644
Q ss_pred --ccccHHHHHHHHHHHhhhCCCCceEEEEecCCCCCcchHHHHHHHHhhCCCCEEEEEcCCCCCCCCCcceEEEEeeec
Q 021476 81 --HSLDRAFLEKKQELYKKVFPHFYILGWYSTGSDAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESELH 158 (312)
Q Consensus 81 --~~iD~~~~~~m~~l~~~V~p~~~iVGWY~tg~~~~~~d~~i~~~~~~~~~~pi~L~vD~~~~~~~~~lpi~ay~~~~~ 158 (312)
..+|.+|+.++.+||++|||++.++|||++|+++++.|+.||++++..+++|++|.++|..+. ..+.|+..|++..+
T Consensus 67 ~~~~~dke~l~kk~eqykqVFpdl~vlGwYttG~d~t~sd~~i~k~l~~i~esplflkLNp~t~~-t~~~pv~lfese~d 145 (299)
T KOG3050|consen 67 DTETIDKEYLEKKEEQYKQVFPDLYVLGWYTTGSDPTPSDIHIHKQLMDINESPLFLKLNPATNH-TDKDPVTLFESEID 145 (299)
T ss_pred hhhhccHHHHHHHHHHHHHhcccceEEEEeecCCCCChhhhHHHHHHHhhhcCceEEEecchhcc-ccCCCceeeeeehe
Confidence 369999999999999999999999999999999999999999999999999999999998765 34559999999989
Q ss_pred cccCCceeeeEeeceEEecchhhHHHHHHHhhcCCCCCCchhhHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCC
Q 021476 159 VIEGIPQLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPC 238 (312)
Q Consensus 159 ~~~g~~~~~f~~i~~~i~~~eaErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~ 238 (312)
+.+|.+...|.|+.|+++++|||||||||+++.++++++.. +.+..++..+..|++||+.|++.|++|+++|.+|++++
T Consensus 146 vidg~~q~~f~~~tytl~teEaERIgVdHVA~lt~~~gge~-s~VaeHl~AQdsA~~ml~~Rvklil~Y~k~~e~G~l~~ 224 (299)
T KOG3050|consen 146 VIDGEAQMLFVPLTYTLATEEAERIGVDHVARLTPSDGGEG-SSVAEHLEAQDSAIKMLDNRVKLILAYLKKVEAGTLQP 224 (299)
T ss_pred eecCcceeeeeeeEEEEeehhhhhccchhheeeccCCCCCc-chHHHHHhhHHHHHHHHhhHHHHHHHHHhhhhcCCcCc
Confidence 99999999999999999999999999999999988876533 45689999999999999999999999999999999999
Q ss_pred ChHHHHHHHHHHhcCCCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHhHhhhccc-CCCCCccCC
Q 021476 239 ENSLLRQVSSLLRRLPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDKFNTAYDRHS-RRGGRTAFI 312 (312)
Q Consensus 239 d~~ilR~i~~l~~~lP~~~~~~f~~~~~~~~~D~lmi~yLs~ltk~~~~l~~l~~K~~~~~~~~~-~~~~~~~~~ 312 (312)
|.+|||+...+|.+||.+++++|.+.|..++||+.+++||+.+|++++.||++|+|||++|||+| +||||++|.
T Consensus 225 N~eILrea~~L~~~Lp~~~~~~F~d~F~~e~nd~~l~syl~~iT~~~~nMn~~vnKfn~~ydr~gt~R~~r~~~f 299 (299)
T KOG3050|consen 225 NFEILREAYALCHRLPVMESEKFQDNFYMECNDVGLISYLGTITKCCNNMNEVVNKFNTLYDRQGTRRRMRGLFF 299 (299)
T ss_pred cHHHHHHHHHHHhhccccchHHHhHHHHHhcchhhHHHHHHHHHHhhccHHHHHHHHHHHHHhhhhhccccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999995 999999984
No 2
>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=100.00 E-value=1.5e-70 Score=509.16 Aligned_cols=278 Identities=53% Similarity=0.847 Sum_probs=254.8
Q ss_pred ceEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCCC---cccccH
Q 021476 9 LTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPS---THSLDR 85 (312)
Q Consensus 9 ~~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~---~~~iD~ 85 (312)
++|.|||+|||+|+|||+|+..+. ...+.+|+|+|||+++|++|||+|||++|++++ .+.+|.
T Consensus 1 ~~V~lHPlVll~I~dH~~R~~~~~--------------~~~~~~v~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~id~ 66 (288)
T cd08063 1 LSVKLHPLVILNISDHITRHRAQS--------------QSEPPRVVGALLGQQDGREIEIENSFELKYDTNEDGEIVLDK 66 (288)
T ss_pred CeEEEecceeeeHHhhHhHHhccC--------------CCCCCcEEEEEEEEEcCCEEEEEEEEecccccCCCCceeeCH
Confidence 479999999999999999998642 001479999999999999999999999999764 479999
Q ss_pred HHHHHHHHHHhhhCCCCceEEEEecCCC-CCcchHHHHHHHHhhCCCCEEEEEcCCCCCCCCCcceEEEEeeeccccCCc
Q 021476 86 AFLEKKQELYKKVFPHFYILGWYSTGSD-AQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESELHVIEGIP 164 (312)
Q Consensus 86 ~~~~~m~~l~~~V~p~~~iVGWY~tg~~-~~~~d~~i~~~~~~~~~~pi~L~vD~~~~~~~~~lpi~ay~~~~~~~~g~~ 164 (312)
+|+++|+++||+|||++.+||||++|+. ++..|+.||++|++++++||+|++||.....+++||++||++.....+|..
T Consensus 67 ~y~~~m~~~~kkV~~~~~vVGWY~tg~~~~~~~~~~Ih~~~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~~~~~~~~ 146 (288)
T cd08063 67 EFLETRLEQFKQVFKDLDFVGWYTTGPGGPTESDLPIHKQILEINESPVLLLLDPEANASGKDLPVTIYESVLELVDGEA 146 (288)
T ss_pred HHHHHHHHHHHHhccCCceEEEEecCCCCCCHHHHHHHHHHHhhCCCcEEEEEccccccCCCCCceeEEEEEEeccCCcc
Confidence 9999999999999999999999999998 999999999999999999999999998753468899999999776666767
Q ss_pred eeeeEeeceEEecchhhHHHHHHHhhcCCCCCCchhhHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCChHHHH
Q 021476 165 QLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLR 244 (312)
Q Consensus 165 ~~~f~~i~~~i~~~eaErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~ilR 244 (312)
...|+|+||+|+++|+||||++|+++..+..+ ...+.+..+++.+.+|+++|+.||+.|++||++|.+|++|+|++|||
T Consensus 147 ~~~F~~i~~~i~~~eaErIgv~~l~~~~~~~~-~~~~~~~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~g~~~~d~~ilR 225 (288)
T cd08063 147 TLRFRELPYTIETGEAERIGVDHVARGGASGS-SEKSTVAAHLQAQHNAIKMLNSRVELILEYLKAVPVGEVPPDHSILR 225 (288)
T ss_pred ccEEEeeeeEEEeccCceeeHHHHHhcCCCCC-CcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHH
Confidence 78899999999999999999999998764332 33456788999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHhHhhhc
Q 021476 245 QVSSLLRRLPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDKFNTAYDR 301 (312)
Q Consensus 245 ~i~~l~~~lP~~~~~~f~~~~~~~~~D~lmi~yLs~ltk~~~~l~~l~~K~~~~~~~ 301 (312)
+|+++|+++|.++.++|+++|++++||++|++|||++||++.+|+++++||+.++++
T Consensus 226 ~l~~~~~~lP~~~~~~~~~~~~~~~~D~lmv~yLs~lt~~~~~l~~~~~k~~~~~~~ 282 (288)
T cd08063 226 SISALCSRLPVLKSEAFREELLAEYNDVLLVAYLATLTKGCNTLNELVDKFNVVYDR 282 (288)
T ss_pred HHHHHHHhCccCChHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 999999999999999999999999999999999999999999999999999999986
No 3
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=100.00 E-value=2.6e-68 Score=493.85 Aligned_cols=270 Identities=27% Similarity=0.502 Sum_probs=244.5
Q ss_pred CCCCceEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCCCc----
Q 021476 5 SSSGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPST---- 80 (312)
Q Consensus 5 ~~~~~~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~---- 80 (312)
+.+..+|.|||+|||+|+|||+|+..+ .+.||+|+|||++.++.|||+|||++|+++++
T Consensus 2 ~~~~~~V~vhPlVll~I~dh~~R~~~~-----------------~~~rviG~LLG~~~~~~ieItnsF~~p~~e~~~~~~ 64 (303)
T PLN03246 2 PRGIEKVVVHPLVLLSIVDHYNRVAKD-----------------TRKRVVGVLLGSSFRGRVDVTNSFAVPFEEDDKDPS 64 (303)
T ss_pred CCCCcEEEECcHHHHHHHHHHHhccCC-----------------CCCeeEEEEEeeecCCEEEEEeccccCcccCCCCcc
Confidence 467789999999999999999998643 24799999999999999999999999996531
Q ss_pred -ccccHHHHHHHHHHHhhhCCCCceEEEEecCCCCCcchHHHHHHHHhhCCCCEEEEEcCCCCCCCCCcceEEEEeeecc
Q 021476 81 -HSLDRAFLEKKQELYKKVFPHFYILGWYSTGSDAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESELHV 159 (312)
Q Consensus 81 -~~iD~~~~~~m~~l~~~V~p~~~iVGWY~tg~~~~~~d~~i~~~~~~~~~~pi~L~vD~~~~~~~~~lpi~ay~~~~~~ 159 (312)
|++|.+|+++|+++|++|||++.+||||++|+.+++.|+.||++|++++++||||+||+.+. +++||++||++....
T Consensus 65 ~~~~D~~y~~~m~~~~k~V~~~~~vVGWY~tg~~i~~~d~~IH~~~~~~~~~Pv~L~vD~~~~--~~~lpi~aY~s~~~~ 142 (303)
T PLN03246 65 IWFLDHNYLESMFGMFKRINAKEHVVGWYSTGPKLRENDLDIHELFNDYVPNPVLVIIDVQPK--ELGIPTKAYYAVEEV 142 (303)
T ss_pred ceeecHHHHHHHHHHHHHhCCCCcEEeeecCCCCCCcchHHHHHHHHhhCCCCeEEEEecCCC--CCCCceEEEEEEEec
Confidence 67999999999999999999999999999999999999999999999999999999999864 468999999986554
Q ss_pred ccC-C--ceeeeEeeceEEecchhhHHHHHHHhhcCCCCCCchhhHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC
Q 021476 160 IEG-I--PQLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEI 236 (312)
Q Consensus 160 ~~g-~--~~~~f~~i~~~i~~~eaErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~ 236 (312)
..| . .+..|.++|++|.++|+|||||+|+++.... .+.+.+..++..+.+|+++|..||+.|++||++|.+|+.
T Consensus 143 ~~~~~~~~~~~F~~vp~~i~~~EaE~Igve~l~r~~~~---~~~s~l~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~g~~ 219 (303)
T PLN03246 143 KENATQKSQKVFVHVPSEIGAHEAEEIGVEHLLRDVKD---TTVSTLATEVTGKLTALKGLDARLREIRSYLDLVVEGKL 219 (303)
T ss_pred cCCCCcccccEEEECCeeeeecCHHHHHHHHHHhcccC---CccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 432 2 3578999999999999999999999985432 123467778999999999999999999999999999999
Q ss_pred CCChHHHHHHHHHHhcCCCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHh
Q 021476 237 PCENSLLRQVSSLLRRLPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDKFN 296 (312)
Q Consensus 237 ~~d~~ilR~i~~l~~~lP~~~~~~f~~~~~~~~~D~lmi~yLs~ltk~~~~l~~l~~K~~ 296 (312)
|+|++|||+|+++|+++|.+++++|+++|+++.||++|++|||+|||+|.+|+++++...
T Consensus 220 ~~d~~IlR~l~~l~~~lP~l~~~~f~~~f~~~~nD~lmv~YLa~l~kt~~~l~e~l~~~~ 279 (303)
T PLN03246 220 PLNHEILYHLQDVFNLLPNLNVEELVKAFAVKTNDMMLVIYLSSLIRSVIALHNLINNKI 279 (303)
T ss_pred CCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 999999999999999999999999999999999999999999999999999999988774
No 4
>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=100.00 E-value=2.3e-67 Score=484.10 Aligned_cols=265 Identities=25% Similarity=0.475 Sum_probs=241.1
Q ss_pred eEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCCC-----ccccc
Q 021476 10 TFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPS-----THSLD 84 (312)
Q Consensus 10 ~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~-----~~~iD 84 (312)
+|.|||+|||+|+|||+|+..+ .+.+|+|+|||++.++.+||+|||++|++++ .|++|
T Consensus 2 ~V~ihplVLl~I~dh~~R~~~~-----------------~~~~ViG~LLG~~~~~~veItnsF~~p~~~~~~~~~~~~~d 64 (280)
T cd08062 2 KVVVHPLVLLSVVDHYNRVAKG-----------------TSKRVVGVLLGSWKKGVLDVTNSFAVPFEEDEKDPSVWFLD 64 (280)
T ss_pred eEEEehHHHHHHHHHHhhhcCC-----------------CCceEEEEEEEEEeCCEEEEEEeeecCccCCCCCcchhhhh
Confidence 6999999999999999998743 2479999999999999999999999999753 26799
Q ss_pred HHHHHHHHHHHhhhCCCCceEEEEecCCCCCcchHHHHHHHHhhCCCCEEEEEcCCCCCCCCCcceEEEEeeeccc-cCC
Q 021476 85 RAFLEKKQELYKKVFPHFYILGWYSTGSDAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESELHVI-EGI 163 (312)
Q Consensus 85 ~~~~~~m~~l~~~V~p~~~iVGWY~tg~~~~~~d~~i~~~~~~~~~~pi~L~vD~~~~~~~~~lpi~ay~~~~~~~-~g~ 163 (312)
.+|+++|+++|++|||++.+||||++|+++++.|+.||++|++++++||+|++||... +++||++||++..+.. +|.
T Consensus 65 ~~y~~~m~~~~kkv~~~e~vVGWY~tg~~~~~~d~~ih~~~~~~~~~pv~l~vd~~~~--~~~lpi~aY~s~~~~~~~g~ 142 (280)
T cd08062 65 HNYLENMYGMFKKVNAKEKIVGWYSTGPKLRPNDLDINELFRRYCPNPVLVIIDVRPK--DLGLPTEAYIAVEEVHDDGT 142 (280)
T ss_pred HHHHHHHHHHHHHhCCCCCeEEEecCCCCCCcchHHHHHHHHHhCCCCEEEEEecCCC--CCCCceEEEEEeeeccCCCC
Confidence 9999999999999999999999999999999999999999999999999999999864 5789999999865443 555
Q ss_pred -ceeeeEeeceEEecchhhHHHHHHHhhcCCCCCCchhhHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCChHH
Q 021476 164 -PQLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSL 242 (312)
Q Consensus 164 -~~~~f~~i~~~i~~~eaErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~i 242 (312)
....|.++|++|+++|+|||||+|++|..... +.+.+..++..+.+|+++|+.||+.|++||++|.+|+.|+|++|
T Consensus 143 ~~~~~F~~vp~~i~~~eaE~igve~l~r~~~~~---~~~~l~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~I 219 (280)
T cd08062 143 PTSKTFVHVPSEIGAEEAEEVGVEHLLRDIKDV---TVSTLSTRVTNKLNSLKGLQSKLKEIKDYLQLVVEGKLPINHQI 219 (280)
T ss_pred cceeEEEEcceEeeccchHHHHHHHHHhhccCc---ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH
Confidence 67899999999999999999999999843311 23467779999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHh
Q 021476 243 LRQVSSLLRRLPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDKFN 296 (312)
Q Consensus 243 lR~i~~l~~~lP~~~~~~f~~~~~~~~~D~lmi~yLs~ltk~~~~l~~l~~K~~ 296 (312)
||.|+++|+++|.++.++|+++|+++.||++|++|||+|+|+|.+|+++++...
T Consensus 220 lR~l~~~~~~lP~l~~~~f~~~~~~~~nD~lmv~yLs~l~k~~~~l~~~~~~~~ 273 (280)
T cd08062 220 IYNLQDIFNLLPNLNLPELVKAFAVKTNDQMLVIYLSSLIRSVIALHNLINNKI 273 (280)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999998876553
No 5
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.9e-68 Score=466.46 Aligned_cols=269 Identities=26% Similarity=0.419 Sum_probs=247.5
Q ss_pred CCCCCCCCceEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCCC-
Q 021476 1 MASSSSSGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPS- 79 (312)
Q Consensus 1 ~~~~~~~~~~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~- 79 (312)
++++.++.++|.|||+|+|+|+|+|+||..+ ..||||+|||+.++|.|||+|||++||+|+
T Consensus 13 ~~~~~ss~ltv~ihP~Vlf~ivD~~~RR~~~------------------~~rviGTLLG~~~~g~ieitNCFaVPhnEss 74 (288)
T KOG2975|consen 13 LPSPFSSNLTVRLHPVVLFSIVDAYERRNKG------------------AERVIGTLLGTVDKGSVEVTNCFAVPHNESS 74 (288)
T ss_pred CCCCCCCCceEEEcceEEeEeehhhhcCCcc------------------chhhhhheeecccCCeEEEEEeeeccCcccc
Confidence 4677889999999999999999999999865 369999999999999999999999999885
Q ss_pred -cccccHHHHHHHHHHHhhhCCCCceEEEEecCCCCCcchHHHHHHHHhhCCCCEEEEEcCCCCCCCCCcceEEEEee-e
Q 021476 80 -THSLDRAFLEKKQELYKKVFPHFYILGWYSTGSDAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESE-L 157 (312)
Q Consensus 80 -~~~iD~~~~~~m~~l~~~V~p~~~iVGWY~tg~~~~~~d~~i~~~~~~~~~~pi~L~vD~~~~~~~~~lpi~ay~~~-~ 157 (312)
...+|++|++.|+++++|+||+|.+||||+||.+++.+...||++|.+.+++||||+||++++ ++.++|+||.+. .
T Consensus 75 dqvevdm~y~~~M~~l~~k~npnE~vvGWyaTg~dvt~~sslihdyYare~~~pvhLtVDT~~~--n~rm~ikaYvss~~ 152 (288)
T KOG2975|consen 75 DQVEVDMEYAKNMYELHKKVNPNELVVGWYATGHDVTEHSSLIHDYYAREAPNPVHLTVDTSLQ--NGRMSIKAYVSSLM 152 (288)
T ss_pred ccceeeHHHHHHHHHHhcccCCCceeEEEEecCCCcccchhHHHHHhhccCCCCeEEEEecccc--CCccceeEEEEecc
Confidence 468999999999999999999999999999999999999999999999999999999999976 689999999975 3
Q ss_pred ccccCCceeeeEeeceEEecchhhHHHHHHHhhcCCCCCCchhhHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCC
Q 021476 158 HVIEGIPQLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIP 237 (312)
Q Consensus 158 ~~~~g~~~~~f~~i~~~i~~~eaErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~ 237 (312)
.+.++....+|.|+|+++.+.|+||+|++.|.|... +.+....+.++|+++..|...|+.+|+.+++|+++|.+|+.+
T Consensus 153 Gvpg~~~~~mF~plpvel~~~~~ervgl~li~kt~~--sp~r~~~l~~dLqQv~~at~~l~~~L~~Vl~YVedVl~gk~~ 230 (288)
T KOG2975|consen 153 GVPGRTMGVMFTPLPVELAYYDAERVGLDLIEKTSF--SPSRVAGLSSDLQQVEGATARLQSLLERVLKYVEDVLAGKVK 230 (288)
T ss_pred CCCCcccceeeeeeeeEEeecchhhhHHHHHHHhcc--ChhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 334444567999999999999999999999998652 223556788999999999999999999999999999999999
Q ss_pred CChHHHHHHHHHHhcCCCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHH
Q 021476 238 CENSLLRQVSSLLRRLPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNEL 291 (312)
Q Consensus 238 ~d~~ilR~i~~l~~~lP~~~~~~f~~~~~~~~~D~lmi~yLs~ltk~~~~l~~l 291 (312)
+|..|||+|+++++++|.+.+++|+.+|+++.+|.||+.|||++||+|++|+|.
T Consensus 231 pdn~VGR~Lmd~v~~vP~l~p~~Fe~mfn~nLrD~Lmv~yLa~ltqTQl~l~EK 284 (288)
T KOG2975|consen 231 PDNAVGRFLMDLVTAVPKLVPDDFETMFNSNLRDLLMVIYLANLTQTQLALNEK 284 (288)
T ss_pred CcchHHHHHHHHHHhcCCCCHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999988844
No 6
>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=100.00 E-value=6.1e-65 Score=466.62 Aligned_cols=259 Identities=25% Similarity=0.422 Sum_probs=234.9
Q ss_pred EEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCCC--cccccHHHH
Q 021476 11 FKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPS--THSLDRAFL 88 (312)
Q Consensus 11 V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~--~~~iD~~~~ 88 (312)
|.|||+|||+|+|||+|+..+ +.+|+|+|||++.++.+||+|||++|++++ .+.+|.+|+
T Consensus 1 v~ihPlVll~I~dH~~R~~~~------------------~~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~d~~y~ 62 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEG------------------QERVIGTLLGTRSEGEVEITNCFAVPHNESEDQVAVDMEYH 62 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCC------------------CcEEEEEEEEEEeCCEEEEEeCeecceeCCCCeEEEcHHHH
Confidence 689999999999999998643 369999999999999999999999999754 578999999
Q ss_pred HHHHHHHhhhCCCCceEEEEecCCCCCcchHHHHHHHHhhCC--CCEEEEEcCCCCCCCCCcceEEEEeeeccc-cCCce
Q 021476 89 EKKQELYKKVFPHFYILGWYSTGSDAQESDMHIHKALMDINE--SPVYVLLNPSINPAQKDLPVTIFESELHVI-EGIPQ 165 (312)
Q Consensus 89 ~~m~~l~~~V~p~~~iVGWY~tg~~~~~~d~~i~~~~~~~~~--~pi~L~vD~~~~~~~~~lpi~ay~~~~~~~-~g~~~ 165 (312)
++|+++||+|||++.+||||++|+.+++.|..||++|++.++ +||+|++||.... +++|++||++..... ++...
T Consensus 63 ~~m~~~~kkv~~~~~vVGWY~tg~~~~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~~--~~l~i~ay~~~~~~~~~~~~~ 140 (265)
T cd08064 63 RTMYELHQKVNPKEVIVGWYATGSEITEHSALIHDYYSRECTSYNPIHLTVDTSLDD--GKMSIKAYVSSPLGVPGKTLG 140 (265)
T ss_pred HHHHHHHHHhCCCCcEEeeeeCCCCCCccHHHHHHHHHhhCCCCCCEEEEEeCCCCC--CCcceEEEEEEecccCCCCcc
Confidence 999999999999999999999999999999999999999888 9999999998653 489999999864332 33457
Q ss_pred eeeEeeceEEecchhhHHHHHHHhhcCCCCCCchhhHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCChHHHHH
Q 021476 166 LIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQ 245 (312)
Q Consensus 166 ~~f~~i~~~i~~~eaErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~ilR~ 245 (312)
..|.++|++|.++|+||||++++.+.....+ ....+.++++.+.+++++|..||+.|++||++|.+|+.++|++|||+
T Consensus 141 ~~F~~ip~~i~~~eaE~i~v~~l~~~~~~~~--~~~~~~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~i~r~ 218 (265)
T cd08064 141 SMFVPIPLELLYSEAERVALDLLAKTLASPS--RSAPLTSDLEQLEASLEKLQEMLDRVLRYVEDVLAGKVKADNAIGRY 218 (265)
T ss_pred eEEEEcceeeecCcHHHHHHHHHHhhccCCc--ccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHH
Confidence 8899999999999999999999999654432 22345688999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHH
Q 021476 246 VSSLLRRLPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNEL 291 (312)
Q Consensus 246 i~~l~~~lP~~~~~~f~~~~~~~~~D~lmi~yLs~ltk~~~~l~~l 291 (312)
|+++|+++|.++.++|+++|+++.||++|++|||+|||+|.+|+|.
T Consensus 219 l~~~~~~lp~~~~~~f~~~~~~~~~D~lmv~YLs~l~k~~~~l~ek 264 (265)
T cd08064 219 LMDALTSVPKLDPEEFEKMFNSSLQDLLMVTYLSNLTKTQLALAEK 264 (265)
T ss_pred HHHHHhhCCCCCHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHhhh
Confidence 9999999999999999999999999999999999999999999864
No 7
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1e-57 Score=397.18 Aligned_cols=272 Identities=26% Similarity=0.483 Sum_probs=247.5
Q ss_pred CCCCCCCceEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCCC--
Q 021476 2 ASSSSSGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPS-- 79 (312)
Q Consensus 2 ~~~~~~~~~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~-- 79 (312)
..++....+|.+||||||++.|||.|.... .++||+|+|||...++.+.|+|||++|++++
T Consensus 2 ~~~~~~~~kViVhPLVLLS~VDhynR~~k~-----------------~~KRvvGvLLG~~~~~~i~vtnSfAvpFeEDdk 64 (309)
T KOG1556|consen 2 PISELTVEKVIVHPLVLLSAVDHYNRVGKD-----------------TNKRVVGVLLGSWNGDVIDVTNSFAVPFEEDDK 64 (309)
T ss_pred CccccccceeeeehhHHHHHHHHHhhhccC-----------------cCceEEEEEEecCCCCeEEeecceeccccccCC
Confidence 456677789999999999999999998643 3589999999999999999999999999874
Q ss_pred ---cccccHHHHHHHHHHHhhhCCCCceEEEEecCCCCCcchHHHHHHHHhhCCCCEEEEEcCCCCCCCCCcceEEEEee
Q 021476 80 ---THSLDRAFLEKKQELYKKVFPHFYILGWYSTGSDAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESE 156 (312)
Q Consensus 80 ---~~~iD~~~~~~m~~l~~~V~p~~~iVGWY~tg~~~~~~d~~i~~~~~~~~~~pi~L~vD~~~~~~~~~lpi~ay~~~ 156 (312)
.|++|.+|++.|+++|++||.++.+||||+||+.+.++|+.|++.+.+++++|+.+++|..+. .-+||..||.+.
T Consensus 65 ~~svWFlDh~Y~esM~~mfkKvNakekivGWYhTGPkl~~nDl~In~l~k~y~pnpvLvIIdvkpk--~~gLPT~AY~aV 142 (309)
T KOG1556|consen 65 DKSVWFLDHNYIESMFGMFKKVNAKEKVVGWYHTGPKLRENDLDINELLKRYVPNPVLVIIDVKPK--ELGLPTEAYIAV 142 (309)
T ss_pred CCceEEeccHHHHHHHHHHHHhcchhheeeeeccCCccccchhhHHHHHhhcCCCceEEEEecccc--cCCCCchheeee
Confidence 399999999999999999999999999999999999999999999999999999999998764 468999999986
Q ss_pred eccc-cCC-ceeeeEeeceEEecchhhHHHHHHHhhcCCCCCCchhhHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 021476 157 LHVI-EGI-PQLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKG 234 (312)
Q Consensus 157 ~~~~-~g~-~~~~f~~i~~~i~~~eaErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G 234 (312)
.++. +|. ++.+|..+|++|+++|||.|||+|+.|.... .+.+.+...+..+..+++.|+.++..|..||++|.+|
T Consensus 143 eev~dDgt~t~ktF~Hvps~I~AeEAEEvGVEHLlRDikd---~t~gtla~rit~ql~sLkgl~~~L~eI~~YL~~Vi~g 219 (309)
T KOG1556|consen 143 EEVKDDGTPTSKTFVHVPSEIEAEEAEEVGVEHLLRDIKD---TTVGTLATRITNQLMSLKGLQSRLREIRSYLDKVIDG 219 (309)
T ss_pred eeeecCCCCccceeEecCcccchhHHHHhhHHHHHHHHHh---hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 6654 343 4678999999999999999999999984322 2345788889999999999999999999999999999
Q ss_pred CCCCChHHHHHHHHHHhcCCCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHH
Q 021476 235 EIPCENSLLRQVSSLLRRLPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDKF 295 (312)
Q Consensus 235 ~~~~d~~ilR~i~~l~~~lP~~~~~~f~~~~~~~~~D~lmi~yLs~ltk~~~~l~~l~~K~ 295 (312)
++|.||+|+.+++++++.+|.+...+|.+.|+-..||.||+.|+|+|+|+..+|++|++.-
T Consensus 220 ~lpiNh~Il~~lQdvfNllP~l~~~~~~~a~~vktndql~~iY~sslvrsViAlhdLi~Nk 280 (309)
T KOG1556|consen 220 KLPINHEILYQLQDVFNLLPNLTRNELVKAFNVKTNDQLMVIYLSSLVRSVIALHDLINNK 280 (309)
T ss_pred CCCCcHHHHHHHHHHHhhCccccchhhhhhhccccCceeeeeeHHHHHHHHHHHHHHHHhH
Confidence 9999999999999999999999999999999999999999999999999999999999754
No 8
>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=100.00 E-value=8.3e-39 Score=272.08 Aligned_cols=150 Identities=41% Similarity=0.680 Sum_probs=133.2
Q ss_pred EEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCCC--cccccHHHH
Q 021476 11 FKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPS--THSLDRAFL 88 (312)
Q Consensus 11 V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~--~~~iD~~~~ 88 (312)
|+|||+|||+|+|||+|+..+ +.+|+|+|||++.++.++|+|||++|++++ .+.+|.+|+
T Consensus 1 V~ihplvll~I~dh~~R~~~~------------------~~~v~G~LlG~~~~~~veV~nsF~lp~~~~~~~~~~d~~y~ 62 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYG------------------IKRVIGVLLGYVDGDKIEVTNSFELPFDEEEESIFIDTEYL 62 (157)
T ss_pred CEEccHHHhhHHHHHHhccCC------------------CCeEEEEEEeEEeCCEEEEEEeEEccccCCCcchhhhHHHH
Confidence 689999999999999998742 469999999999999999999999999764 358999999
Q ss_pred HHHHHHHhhhCCCCceEEEEecCCC----CCcchHHHHHHHHhh-CCCCEEEEEcCCCCCCCCCcceEEEEeeeccccCC
Q 021476 89 EKKQELYKKVFPHFYILGWYSTGSD----AQESDMHIHKALMDI-NESPVYVLLNPSINPAQKDLPVTIFESELHVIEGI 163 (312)
Q Consensus 89 ~~m~~l~~~V~p~~~iVGWY~tg~~----~~~~d~~i~~~~~~~-~~~pi~L~vD~~~~~~~~~lpi~ay~~~~~~~~g~ 163 (312)
++|+++|++|||++.+||||++++. ++..+..||++|+.. .++||+|++||.....++++|++||++......
T Consensus 63 ~~m~~~~~~v~~~~~vVGWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~~~~-- 140 (157)
T cd08057 63 EKRYNLHKKVYPQEKIVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQREEN-- 140 (157)
T ss_pred HHHHHHHHHhCCCCCEEEEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEecCCCC--
Confidence 9999999999999999999999987 789999999999987 889999999998644568999999998643332
Q ss_pred ceeeeEeeceEEecchhhHHH
Q 021476 164 PQLIFVRSSYTIETVEAERIS 184 (312)
Q Consensus 164 ~~~~f~~i~~~i~~~eaErI~ 184 (312)
+.++|+++.++|+||||
T Consensus 141 ----~~~~~~~i~~~e~E~I~ 157 (157)
T cd08057 141 ----GAEITYEIGTEETERIA 157 (157)
T ss_pred ----CceeeeEEecccccccC
Confidence 23999999999999985
No 9
>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=99.97 E-value=2e-30 Score=238.06 Aligned_cols=200 Identities=17% Similarity=0.198 Sum_probs=147.9
Q ss_pred eEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCCCc-----cccc
Q 021476 10 TFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPST-----HSLD 84 (312)
Q Consensus 10 ~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~-----~~iD 84 (312)
+|.|||+|+++|+|||.|+. +.+|+|+|||...++.+||+|||++|+.+++ +..|
T Consensus 2 ~V~I~~~vllkIv~H~~~~~--------------------p~~v~G~LLG~~~~~~leVtn~Fp~P~~~~~~~~~~~~~~ 61 (266)
T cd08065 2 SVQIDGLVVLKIIKHCKEEL--------------------PELVQGQLLGLDVGGTLEVTNCFPFPKSEEDDSDRADEDI 61 (266)
T ss_pred EEEEeHHHHHHHHHHHhcCC--------------------CcEEEEEEeeeEcCCEEEEEeccCCCCCCCCCcchhhhhH
Confidence 69999999999999998865 4699999999999999999999999996542 3567
Q ss_pred HHHHHHHHHHHhhhCCCCceEEEEecCC-CCCcchHHHHHHHHhh--CCCCEEEEEcCCCCCCCCCcceEEEEeeecccc
Q 021476 85 RAFLEKKQELYKKVFPHFYILGWYSTGS-DAQESDMHIHKALMDI--NESPVYVLLNPSINPAQKDLPVTIFESELHVIE 161 (312)
Q Consensus 85 ~~~~~~m~~l~~~V~p~~~iVGWY~tg~-~~~~~d~~i~~~~~~~--~~~pi~L~vD~~~~~~~~~lpi~ay~~~~~~~~ 161 (312)
.+|+.+|+++++++++++.+||||++++ +...+...|+.+|... .+++|+|++||... .++.++++||+.......
T Consensus 62 ~~yq~~m~~~~r~v~~~e~iVGWY~S~p~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s-~~g~l~lkAyrl~~~~~~ 140 (266)
T cd08065 62 ADYQLEMMRLLREVNVDHNHVGWYQSTYLGSFFTRDLIETQYNYQEAIEESVVLVYDPSKT-SQGSLSLKAYRLSEKFME 140 (266)
T ss_pred HHHHHHHHHHHHHhCCCCcEEEeEeecCCCCcCCHHHHHHHHHHhccCCCCEEEEECCCcc-cccceeeEEEEEcHHHHH
Confidence 7999999999999999999999999998 3333355688877654 47789999999863 367899999998543321
Q ss_pred ----C------------CceeeeEeeceEEecchhhHHHHHHHhhcCCCCCCchhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 021476 162 ----G------------IPQLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLH 225 (312)
Q Consensus 162 ----g------------~~~~~f~~i~~~i~~~eaErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~ 225 (312)
| ....+|.+||++|.++..+.+.+..+....+....+...-.......+...+..|.+.||.+.
T Consensus 141 ~~~~~~~~~~~l~~~~~~~~~if~eiPv~i~n~~l~~~~L~~l~~~~~~~~~~~~~l~l~~~~~le~~l~~l~~~id~l~ 220 (266)
T cd08065 141 LYKEGKFSTESLREANLTFSNIFEEIPVVIRNSHLVNALLSELEEDSPSSQSDFDRLDLSTNSFLEKNLELLMESVDELS 220 (266)
T ss_pred HhhcCCcCHHHHHHhcCchhcEEEEEEEEEEchHHHHHHHHhcccCCCcccCCcccccccCchhHHHHHHHHHHHHHHHH
Confidence 1 236789999999999999999999886644332000000001112334444555555555555
Q ss_pred HHHHh
Q 021476 226 HYLVA 230 (312)
Q Consensus 226 ~Yl~~ 230 (312)
.+.++
T Consensus 221 ~e~~~ 225 (266)
T cd08065 221 QEQGK 225 (266)
T ss_pred HHHHH
Confidence 54444
No 10
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i
Probab=99.94 E-value=2.6e-25 Score=204.18 Aligned_cols=167 Identities=12% Similarity=0.134 Sum_probs=143.0
Q ss_pred CCCCceEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCCCc--cc
Q 021476 5 SSSGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPST--HS 82 (312)
Q Consensus 5 ~~~~~~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~--~~ 82 (312)
.....+|.|+|+|+++|++|+.|.. +..|||+|+|..+++.++|++||++|+.+++ ..
T Consensus 6 ~~~~~~V~Is~~allkil~Ha~~~~--------------------p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~ 65 (268)
T cd08069 6 PDYFEKVYISSLALLKMLKHARAGG--------------------PIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVN 65 (268)
T ss_pred CCcccEEEECHHHHHHHHHHHhccC--------------------CceEEEEEEeeecCCeEEEEEEEECCcCCCCCcee
Confidence 4556789999999999999998843 4699999999999999999999999986543 34
Q ss_pred ccHHHHHHHHH--HHhhhCCCCceEEEEecCCC----CCcchHHHHHHHHhhCCCCEEEEEcCCCCCCCCCcceEEEEee
Q 021476 83 LDRAFLEKKQE--LYKKVFPHFYILGWYSTGSD----AQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESE 156 (312)
Q Consensus 83 iD~~~~~~m~~--l~~~V~p~~~iVGWY~tg~~----~~~~d~~i~~~~~~~~~~pi~L~vD~~~~~~~~~lpi~ay~~~ 156 (312)
.+.+|++.|.+ +++++++++.+||||++++. ++..|+.+|..|++..+++|+|++||..+...+++.|+||++.
T Consensus 66 ~~~e~~~~m~~~~~~~~~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~ 145 (268)
T cd08069 66 AQDEFQEYMVQYEMLKQTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTI 145 (268)
T ss_pred ccHHHHHHHHHHHHHHHhCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEE
Confidence 55689999999 99999999999999999986 8899999999999998899999999976535788999999985
Q ss_pred ecccc-----C-----------------CceeeeEeeceEEecchhhHHHHHHHhhc
Q 021476 157 LHVIE-----G-----------------IPQLIFVRSSYTIETVEAERISVDHVAHL 191 (312)
Q Consensus 157 ~~~~~-----g-----------------~~~~~f~~i~~~i~~~eaErI~v~~l~~~ 191 (312)
..... + .....|.++|+++..++.|+..++.+.+.
T Consensus 146 ~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~ 202 (268)
T cd08069 146 PPGYKPLEPRQTTSNIGHLPKPKIEDFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNK 202 (268)
T ss_pred CccccccCcccCccccCccCcHHHHHhCchhcEEEEeeeEEecCHHHHHHHHHHHHH
Confidence 33211 1 13568999999999999999999999873
No 11
>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=99.93 E-value=1e-25 Score=181.41 Aligned_cols=105 Identities=38% Similarity=0.573 Sum_probs=92.3
Q ss_pred CCceEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCC-EEEEEEEEEeecCCCc---cc
Q 021476 7 SGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGR-TVEIFNSFELLYDPST---HS 82 (312)
Q Consensus 7 ~~~~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~-~veI~nsF~vp~~~~~---~~ 82 (312)
+..+|.|||+|+|+|+||+.|+.. .+|+|+|+|+++++ .++|+|||++|+.++. ..
T Consensus 2 s~~~V~i~p~vll~i~~h~~r~~~--------------------~~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~ 61 (114)
T PF01398_consen 2 SVQTVQIHPLVLLKIIDHATRSSP--------------------NEVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDM 61 (114)
T ss_dssp SCEEEEEEHHHHHHHHHHHHHHHC--------------------TEEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEE
T ss_pred CcEEEEECHHHHHHHHHHHhcCCC--------------------CEEEEEEEEEecCceEEEEEEEEEeeEecCcccccc
Confidence 567999999999999999999863 39999999999999 9999999999996542 34
Q ss_pred ccHHHHHHHHHHHhhhCCCCceEEEEecCCCC----CcchHHHHHHHHhhCCC
Q 021476 83 LDRAFLEKKQELYKKVFPHFYILGWYSTGSDA----QESDMHIHKALMDINES 131 (312)
Q Consensus 83 iD~~~~~~m~~l~~~V~p~~~iVGWY~tg~~~----~~~d~~i~~~~~~~~~~ 131 (312)
.+.++..+|++++++++|++.+||||++++.. +..|+.+|.+|++.+++
T Consensus 62 ~~~~~~~~~~~~~~~~~~~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 62 DDEDFQKKMIELLKKVNPNLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp ECCHHHHHHHHHHHHCSTTSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred chhhHHHHHHhhhccccccceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence 56677799999999999999999999999876 89999999999988653
No 12
>PF13012 MitMem_reg: Maintenance of mitochondrial structure and function; PDB: 2O96_B 2O95_A.
Probab=99.87 E-value=1.3e-23 Score=169.58 Aligned_cols=114 Identities=38% Similarity=0.612 Sum_probs=12.9
Q ss_pred chhhHHHHHHHhhcCCCCCCchhhHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCChHHHHHHHHHHhcCCCCC
Q 021476 178 VEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRLPAIE 257 (312)
Q Consensus 178 ~eaErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~ilR~i~~l~~~lP~~~ 257 (312)
+|||||||+|+.+..... ..+.+.++++.+.+++.+|++|++.+..||++|.+|+.|+|+++||+|+++|+++|.++
T Consensus 1 eEaErigv~~l~~~~~~~---~~s~~~~~l~~~~~al~~L~~~l~~i~~Yl~~v~~g~~~~d~~i~r~l~~l~~~lp~~~ 77 (115)
T PF13012_consen 1 EEAERIGVDHLARGLGDH---YYSSLSSQLENEQNALKMLHKRLWQILDYLEDVISGEIPPDHEILRQLQDLLSSLPKYD 77 (115)
T ss_dssp SHHHHHHHHHHHHH--S---------------------------------------------------------------
T ss_pred CchHHHHHHHHHccCCCc---cccHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcCCCchhHHHHHHHHHHhccccc
Confidence 589999999999943222 22367789999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHH
Q 021476 258 SEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDK 294 (312)
Q Consensus 258 ~~~f~~~~~~~~~D~lmi~yLs~ltk~~~~l~~l~~K 294 (312)
+++|+++|.++.+|.+|+.||++++|++.+++++++|
T Consensus 78 ~~~~~~~~~~~~~D~l~v~yL~~l~k~~~~l~e~l~~ 114 (115)
T PF13012_consen 78 PEEFEEEFNSEINDVLMVSYLAKLTKKQHALNELLNN 114 (115)
T ss_dssp -------------------------------------
T ss_pred HHHHHHHHHhhchHHHHHHHHHHHhHHHHHHHHHHhc
Confidence 9999999999999999999999999999999998875
No 13
>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=99.85 E-value=2.3e-20 Score=153.66 Aligned_cols=126 Identities=25% Similarity=0.381 Sum_probs=110.0
Q ss_pred eEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCCCc---ccccHH
Q 021476 10 TFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPST---HSLDRA 86 (312)
Q Consensus 10 ~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~---~~iD~~ 86 (312)
.|.|||+|+++|++|+.|.. +..++|+|+|...++.++|+++|++|..... ..++.+
T Consensus 1 ~v~i~~~v~~~i~~h~~~~~--------------------p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~~~~~~ 60 (135)
T smart00232 1 EVKVHPLVPLNILKHAIRDG--------------------PEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQEYDED 60 (135)
T ss_pred CEEEcHHHHHHHHHHHhcCC--------------------CcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchhhhhhh
Confidence 47899999999999998753 4699999999999999999999999976432 267899
Q ss_pred HHHHHHHHHhhhCCCCceEEEEecCC----CCCcchHHHHHHHHhhCCCCEEEEEcCCCCCCCCCcceEEEEee
Q 021476 87 FLEKKQELYKKVFPHFYILGWYSTGS----DAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESE 156 (312)
Q Consensus 87 ~~~~m~~l~~~V~p~~~iVGWY~tg~----~~~~~d~~i~~~~~~~~~~pi~L~vD~~~~~~~~~lpi~ay~~~ 156 (312)
|.+.|.++++++++++.+||||++++ .++..|+.+|..+......++++.+|+.... .++++++||+..
T Consensus 61 ~~~~~~~~~~~~~~~~~~vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~-~g~~~~~af~~~ 133 (135)
T smart00232 61 YSHLMDEELKKVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSF-QGRLSLRAFRLT 133 (135)
T ss_pred HHHHHHHHHHhhCCCceEEEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccc-cCcEEEEEEEec
Confidence 99999999999999999999999987 4667799999988888888999999998754 478999999963
No 14
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=1.1e-19 Score=161.90 Aligned_cols=237 Identities=16% Similarity=0.213 Sum_probs=166.8
Q ss_pred CCCCCceEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCC----C
Q 021476 4 SSSSGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDP----S 79 (312)
Q Consensus 4 ~~~~~~~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~----~ 79 (312)
.+.+...|.+..||+++|++||.....+ ..-+.|+|+|...++.+|||||||.|... +
T Consensus 8 ~~p~vk~v~ldsLvVMkiiKHc~ee~~n------------------~d~~~GvL~Glvvd~~LeITncFp~p~~~~~edd 69 (339)
T KOG1560|consen 8 ESPPVKRVELDSLVVMKIIKHCREEFPN------------------GDGTQGVLLGLVVDGRLEITNCFPFPSVLENEDD 69 (339)
T ss_pred CCCccceeeehhHHHHHHHHHHHhhcCC------------------cchhhheeeeeeecceeEeecccCCCccCCCccc
Confidence 3455678999999999999999776532 25789999999999999999999999732 2
Q ss_pred c---ccccH---HHHHHHHHHHhhhCCCCceEEEEecC---CCCCcchHHHHHH--HHhhCCCCEEEEEcCCCCCCCCCc
Q 021476 80 T---HSLDR---AFLEKKQELYKKVFPHFYILGWYSTG---SDAQESDMHIHKA--LMDINESPVYVLLNPSINPAQKDL 148 (312)
Q Consensus 80 ~---~~iD~---~~~~~m~~l~~~V~p~~~iVGWY~tg---~~~~~~d~~i~~~--~~~~~~~pi~L~vD~~~~~~~~~l 148 (312)
. ...|. .|+..|+..++.||-+...||||.+. +.++. ..+..+ |++..+..|.|++||.. +.+|.|
T Consensus 70 a~~~~~~de~rq~~~l~mlrrlr~vnid~~hVGwYqs~~vgs~lS~--~lveSqy~YQ~a~pesVvliYD~~k-ssqG~L 146 (339)
T KOG1560|consen 70 AVNKSVSDEARQAYQLAMLRRLRYVNIDHLHVGWYQSAYVGSFLSP--ALVESQYAYQKAIPESVVLIYDPIK-SSQGTL 146 (339)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhhhcCccceeeeeeeeehhccccCH--HHHHHHHHHHhcCCccEEEEecccc-ccCceE
Confidence 1 12343 68899999999999999999999975 44552 245555 45667888999999985 458999
Q ss_pred ceEEEEeeeccc----cCC------------ceeeeEeeceEEecchhhHHHHHHHh--hcCCCCCC-------chhhHH
Q 021476 149 PVTIFESELHVI----EGI------------PQLIFVRSSYTIETVEAERISVDHVA--HLKPSDGG-------SAATQL 203 (312)
Q Consensus 149 pi~ay~~~~~~~----~g~------------~~~~f~~i~~~i~~~eaErI~v~~l~--~~~~~~~~-------~~~~~~ 203 (312)
.++||+...+.. ++. ...+|.++|+.|+.+---.+-+..+. +.-+++.. +....+
T Consensus 147 ~lrAyrLTp~am~~~kekdwtpealk~~nltyenmfeElPIVIknS~L~nvlmseLs~~e~c~sdk~~~~~fdlgs~t~l 226 (339)
T KOG1560|consen 147 SLRAYRLTPEAMAAHKEKDWTPEALKSANLTYENMFEELPIVIKNSHLANVLMSELSEPEDCESDKPLHSNFDLGSGTRL 226 (339)
T ss_pred EeehhhcCHHHHHHHhcCCCCHHHHHhcCCCHHHHHhhcCeeeeccHHHHHHHHhccccccccccccccccccccchhhH
Confidence 999999864431 221 24689999999999876666655554 21111111 123456
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCChHHHHHHHH--------HHhcCCCCChHHHHHHH
Q 021476 204 AAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSS--------LLRRLPAIESEKFQDDF 265 (312)
Q Consensus 204 ~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~ilR~i~~--------l~~~lP~~~~~~f~~~~ 265 (312)
.+++..+...+..|+..+..+-+|-+.+... |..+-+.+++ .-...|.++.+++.+.|
T Consensus 227 eknir~lme~vDEl~qe~~~l~kyqr~~~rq----q~~~~q~~aKrqaENa~R~argep~lP~dd~kr~f 292 (339)
T KOG1560|consen 227 EKNIRLLMERVDELHQEIVNLNKYQRQLARQ----QAKKHQWIAKRQAENANRAARGEPPLPEDDWKRIF 292 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHhhhhhhcCCCCCChHHHHHHh
Confidence 7777778888888888888888888776542 3333333222 23345667767776655
No 15
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.66 E-value=1.2e-15 Score=136.62 Aligned_cols=201 Identities=13% Similarity=0.175 Sum_probs=141.3
Q ss_pred ceEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCCCcccc-----
Q 021476 9 LTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPSTHSL----- 83 (312)
Q Consensus 9 ~~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~~i----- 83 (312)
..|+|..|++|+|.-|..|. .+-.|+|.++|+.+|+.+.|.+||++|..+.+..+
T Consensus 53 k~vkISalAllKm~~hA~~G--------------------gnlEiMGlm~Gkv~g~t~IvmD~FaLPVeGTETRVNAq~~ 112 (347)
T KOG1554|consen 53 KHVKISALALLKMVMHARSG--------------------GNLEIMGLMQGKVDGDTIIVMDSFALPVEGTETRVNAQAE 112 (347)
T ss_pred hhhhhHHHHHHHHHHHHhcC--------------------CCeEEEeeecccccCCeEEEEeccccccccccceechHHH
Confidence 47899999999999988664 25699999999999999999999999998765433
Q ss_pred cHHHHHHHHHHHhhhCCCCceEEEEecCCC----CCcchHHHHHHHHhhCCCCEEEEEcCCCCCCCCCcceEEEEeeecc
Q 021476 84 DRAFLEKKQELYKKVFPHFYILGWYSTGSD----AQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESELHV 159 (312)
Q Consensus 84 D~~~~~~m~~l~~~V~p~~~iVGWY~tg~~----~~~~d~~i~~~~~~~~~~pi~L~vD~~~~~~~~~lpi~ay~~~~~~ 159 (312)
-.+||-...+.-+.+...+.+||||+++++ ++..|+..+..-+++.++-+++++||..+.+.+++.|.||++-+..
T Consensus 113 AyEYmv~Y~e~~k~~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRTyp~g 192 (347)
T KOG1554|consen 113 AYEYMVQYIEEAKNVGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTYPKG 192 (347)
T ss_pred HHHHHHHHHHHHHHhhhhhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCccccccCceeeceeecccCC
Confidence 368898999999999999999999999986 4567777777667777777899999998888899999999974321
Q ss_pred c---c-----------------CCceeeeEeeceEEecchhhHHHHHHHhhcCCCCCCchhhHHHhhHHHHHHHHHHHHH
Q 021476 160 I---E-----------------GIPQLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNS 219 (312)
Q Consensus 160 ~---~-----------------g~~~~~f~~i~~~i~~~eaErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~ 219 (312)
. + |.....+..+++.+--+-.++--++.+-.-. .-.+-..+.+..+.+.+...+.-|..
T Consensus 193 yk~~d~~~seyqtipl~kied~gvHck~yysl~isyfks~ld~kll~~Lwnky-wv~Tlsss~ll~N~dy~~~qi~d~~e 271 (347)
T KOG1554|consen 193 YKPPDEPPSEYQTIPLNKIEDFGVHCKQYYSLEISYFKSSLDMKLLELLWNKY-WVRTLSSSPLLKNIDYLNGQIRDLSE 271 (347)
T ss_pred CCCCCCCchhhhccchhhhhhcccceEEeeccchhhhhhhhhHHHHHHHHhhh-hhcccccccccccchhhcchhhhHHH
Confidence 0 0 1112233333333333334444444333211 11111223455666677777777777
Q ss_pred HHHHHHHHHHh
Q 021476 220 RIRVLHHYLVA 230 (312)
Q Consensus 220 ~i~~i~~Yl~~ 230 (312)
.+.+.-+.+..
T Consensus 272 kl~q~~~~l~~ 282 (347)
T KOG1554|consen 272 KLEQREDSLET 282 (347)
T ss_pred HHHhhhhhccc
Confidence 66666665543
No 16
>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. J
Probab=99.62 E-value=6.1e-15 Score=118.27 Aligned_cols=100 Identities=16% Similarity=0.281 Sum_probs=79.9
Q ss_pred CCceEEEEeeEEeCCEEEEEEEEEeecCCCcccccHHHHHHHHHHHhhhCCCCceEEEEecCCC----CCcchHHHHHHH
Q 021476 50 QPRVYGCVIGIQRGRTVEIFNSFELLYDPSTHSLDRAFLEKKQELYKKVFPHFYILGWYSTGSD----AQESDMHIHKAL 125 (312)
Q Consensus 50 ~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~~iD~~~~~~m~~l~~~V~p~~~iVGWY~tg~~----~~~~d~~i~~~~ 125 (312)
+..|+|.|+|...++.++|+++|++|...+....+..++ |....+.+..++.+||||++++. ++..|+..|..|
T Consensus 13 ~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~iVGwyhshp~~~~~~s~~dv~~~~~~ 90 (116)
T cd07767 13 GKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWFL--MYLDFKKLNAGLRIVGWYHTHPKPSCFLSPNDLATHELF 90 (116)
T ss_pred CcEEEEEeEEEEcCCEEEEEEEEecccCCCCCccHHHHH--HHHHHHHhcCCCeEEEEEEcCCCCCCccCHHHHHHHHHH
Confidence 458999999999999999999999998654333333222 56666778899999999999875 678898889888
Q ss_pred HhhCCCCEEEEEcCCCCCCCCCcceEEE
Q 021476 126 MDINESPVYVLLNPSINPAQKDLPVTIF 153 (312)
Q Consensus 126 ~~~~~~pi~L~vD~~~~~~~~~lpi~ay 153 (312)
++..+++++|++|+... +.+++++||
T Consensus 91 q~~~~~~v~li~~~~~~--~~~~~~~~~ 116 (116)
T cd07767 91 QRYFPEKVMIIVDVKPK--DLGNSWKCY 116 (116)
T ss_pred HHhCCCCEEEEEECCCc--cCCCCcccC
Confidence 88777899999999753 346788876
No 17
>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=99.47 E-value=2.8e-12 Score=111.81 Aligned_cols=146 Identities=12% Similarity=0.082 Sum_probs=106.0
Q ss_pred CCceEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEe--CCEEEEEEEEEeecCC--Cccc
Q 021476 7 SGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQR--GRTVEIFNSFELLYDP--STHS 82 (312)
Q Consensus 7 ~~~~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~--~~~veI~nsF~vp~~~--~~~~ 82 (312)
.+.+|.|+++|+|.|..|+.... ..+||.|+|..+ ++.++|+++|+++... ....
T Consensus 3 ~pf~V~Is~~all~m~~Ha~~~~---------------------~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e 61 (187)
T cd08067 3 QPFKVTVSSNALLLMDFHCHLTT---------------------SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCE 61 (187)
T ss_pred CCEEEEECHHHHHHHHHHhcCCC---------------------cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccc
Confidence 46899999999999999996532 489999999975 5789999999998744 3456
Q ss_pred ccHHHHHHHHHHHhhhCCCCceEEEEecCCC----CCcchHHHHHHHHhhC-------CCCEEEEEcCCCCCC-CCCcce
Q 021476 83 LDRAFLEKKQELYKKVFPHFYILGWYSTGSD----AQESDMHIHKALMDIN-------ESPVYVLLNPSINPA-QKDLPV 150 (312)
Q Consensus 83 iD~~~~~~m~~l~~~V~p~~~iVGWY~tg~~----~~~~d~~i~~~~~~~~-------~~pi~L~vD~~~~~~-~~~lpi 150 (312)
+|.+++.+|.+..++.+ +.+||||++++. ++..|+.-|..|+... ++-|.++++|.-..+ ..+..|
T Consensus 62 ~dp~~q~e~~~~l~~~g--l~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i 139 (187)
T cd08067 62 MDPVSETEIRESLESRG--LSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQI 139 (187)
T ss_pred cCHHHHHHHHHHHHHcC--CEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcE
Confidence 78899999999888776 599999999873 5566766666677643 245999999975322 234569
Q ss_pred EEEEeeeccccCCceeeeEeeceEEecc
Q 021476 151 TIFESELHVIEGIPQLIFVRSSYTIETV 178 (312)
Q Consensus 151 ~ay~~~~~~~~g~~~~~f~~i~~~i~~~ 178 (312)
++|........ . ..-..+|+.+.+.
T Consensus 140 ~~f~~~~~~~~-~--~~~~~~p~~~~~~ 164 (187)
T cd08067 140 TCFWVMPPPEN-R--PNEYGVPMLMSYT 164 (187)
T ss_pred EEEEEECCCCC-C--CccCCcCeEEEec
Confidence 99987432211 1 1233466666544
No 18
>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=99.42 E-value=1.6e-12 Score=105.49 Aligned_cols=108 Identities=12% Similarity=0.178 Sum_probs=82.5
Q ss_pred hhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEe-----CCEEEEEEEEEeecCCCcccccHHHHHHH
Q 021476 17 VIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQR-----GRTVEIFNSFELLYDPSTHSLDRAFLEKK 91 (312)
Q Consensus 17 vll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~-----~~~veI~nsF~vp~~~~~~~iD~~~~~~m 91 (312)
|+++|++|+.+.. +..+||.|+|... ...++|+++|+.|...+ . .+.|
T Consensus 2 ~~~~i~~ha~~~~--------------------p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~~-----~--~~~~ 54 (119)
T cd08058 2 ALLKMLQHAESNT--------------------GIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCT-----G--ENVE 54 (119)
T ss_pred HHHHHHHHhcCCC--------------------CeEEEEEeeeEEecCccceeEEEEeecCCCCCCch-----h--HHHH
Confidence 7899999997743 4589999999876 45689999999886322 1 2244
Q ss_pred HHHHhhhCCCCceEEEEecCC----CCCcchHHHHHHHHhhCCCCEEEEEcCCCCCCCCCcceEEEEe
Q 021476 92 QELYKKVFPHFYILGWYSTGS----DAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFES 155 (312)
Q Consensus 92 ~~l~~~V~p~~~iVGWY~tg~----~~~~~d~~i~~~~~~~~~~pi~L~vD~~~~~~~~~lpi~ay~~ 155 (312)
..+.+...-++.+||||++++ .++..|+..|.+|+...+..++|++||.. ..+.+++|+.
T Consensus 55 ~~~~~~~~~g~~~vG~YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~----~~~~~~a~rl 118 (119)
T cd08058 55 ELFNVQTGRPLLVVGWYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKH----RNKDTGIFRL 118 (119)
T ss_pred HHHHHHhCCCCeEEEEEecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCC----CCcccceEEe
Confidence 555566888999999999987 36778877667677666777999999863 2677999985
No 19
>cd08068 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex. BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-contai
Probab=99.15 E-value=2.2e-09 Score=96.93 Aligned_cols=148 Identities=15% Similarity=0.142 Sum_probs=101.1
Q ss_pred ceEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEe-------CCEEEEEEEEEeecCC---
Q 021476 9 LTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQR-------GRTVEIFNSFELLYDP--- 78 (312)
Q Consensus 9 ~~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~-------~~~veI~nsF~vp~~~--- 78 (312)
.+|.|.+.++..|+.|..+.. +..+||.|+|... +..+.|..-++.+..+
T Consensus 2 ~~V~Is~~~l~~il~HA~~~~--------------------P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~ 61 (244)
T cd08068 2 SKVHLSADVYLVCLTHALSTE--------------------KEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRK 61 (244)
T ss_pred cEEEECHHHHHHHHHHHHhCC--------------------CcceeEEEEeecccccccccceeEEEeeeccccccCCCC
Confidence 378999999999999997754 5699999999875 3455554544443322
Q ss_pred CcccccHH----HHHHHHHHHhhhCCCCceEEEEecCCC----CCcchHHHHHHHHhhCCCCEEEEEcCCC---CCCCCC
Q 021476 79 STHSLDRA----FLEKKQELYKKVFPHFYILGWYSTGSD----AQESDMHIHKALMDINESPVYVLLNPSI---NPAQKD 147 (312)
Q Consensus 79 ~~~~iD~~----~~~~m~~l~~~V~p~~~iVGWY~tg~~----~~~~d~~i~~~~~~~~~~pi~L~vD~~~---~~~~~~ 147 (312)
+-..+|.+ ..+.+.++.+.+..++.+||||++++. ++..|+..+..|+...+.-++|++++.. +...++
T Consensus 62 ~r~eidPee~~~a~~ea~~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~ 141 (244)
T cd08068 62 DRVEISPEQLSAASTEAERLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGE 141 (244)
T ss_pred ceEEeCHHHHHHHHHHHHHHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCC
Confidence 22466754 335566677778899999999999974 5667766555665555666889986532 222356
Q ss_pred cceEEEEeeeccccCCceeeeEeeceEEecc
Q 021476 148 LPVTIFESELHVIEGIPQLIFVRSSYTIETV 178 (312)
Q Consensus 148 lpi~ay~~~~~~~~g~~~~~f~~i~~~i~~~ 178 (312)
..++||+.... ++.+.....++|+.|...
T Consensus 142 ~~i~aFr~~~g--~~~~~~~~~e~pl~i~~~ 170 (244)
T cd08068 142 VQVTCFQSVQG--NKAGQYERIEVPLEIVPT 170 (244)
T ss_pred EEEEEEEecCC--CCCCcceEEEeeeEEecC
Confidence 77999997421 112346678888888643
No 20
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=98.85 E-value=1.7e-07 Score=86.74 Aligned_cols=131 Identities=19% Similarity=0.337 Sum_probs=104.2
Q ss_pred CCCCceEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCC-ceEEEE-ee----EEeCCEEEEEEEEEeecCC
Q 021476 5 SSSGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQP-RVYGCV-IG----IQRGRTVEIFNSFELLYDP 78 (312)
Q Consensus 5 ~~~~~~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~-~v~G~L-LG----~~~~~~veI~nsF~vp~~~ 78 (312)
.....+|.++-++++..++|- |.. .+. .++|.+ +| +.+...+.|.+-|+.|...
T Consensus 27 ~~~~e~v~i~slall~m~rh~-r~~-------------------~p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg 86 (316)
T KOG1555|consen 27 SDEKETVYISSLALLKMLRHD-RAG-------------------SPEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSG 86 (316)
T ss_pred ccCcceeeeehhhhhhccccc-ccC-------------------Cchhhccceeecccccceeeecceeeeeeecccccc
Confidence 456789999999999999986 322 123 489999 89 3457788899999999866
Q ss_pred Cc-----ccccHHHHHHHHHHHhhhCCCCceEEEEecCCC----CCcchHHHHHHHHhhCCCCEEEEEcCCCCCCCCCcc
Q 021476 79 ST-----HSLDRAFLEKKQELYKKVFPHFYILGWYSTGSD----AQESDMHIHKALMDINESPVYVLLNPSINPAQKDLP 149 (312)
Q Consensus 79 ~~-----~~iD~~~~~~m~~l~~~V~p~~~iVGWY~tg~~----~~~~d~~i~~~~~~~~~~pi~L~vD~~~~~~~~~lp 149 (312)
.. ..+|.-|..+|.++.++..-.+.+||||+++++ ++..|+..|.-|+..++..+..++||..... ++.-
T Consensus 87 ~~is~~~e~~d~V~q~q~~~~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~-g~vv 165 (316)
T KOG1555|consen 87 TGISKFVEAVDPVFQTQMMDLLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPY-GKVV 165 (316)
T ss_pred ceecccchhccHHHHHHHHHHHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCC-CCcc
Confidence 32 368999999999999998877999999999875 5678888888899888899999999986554 4544
Q ss_pred eEEEEee
Q 021476 150 VTIFESE 156 (312)
Q Consensus 150 i~ay~~~ 156 (312)
+.||..+
T Consensus 166 ~d~f~~I 172 (316)
T KOG1555|consen 166 PDAFSSI 172 (316)
T ss_pred CChhhhc
Confidence 5588763
No 21
>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=98.74 E-value=2.2e-07 Score=80.21 Aligned_cols=116 Identities=14% Similarity=0.139 Sum_probs=82.1
Q ss_pred EEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCCCccc---ccHHH
Q 021476 11 FKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPSTHS---LDRAF 87 (312)
Q Consensus 11 V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~~---iD~~~ 87 (312)
+.|-.-.+-+|+.|..++.. .+..+||.|+|...++..+|++.|-.|....... .|..
T Consensus 4 l~Ipk~il~~~l~~A~~~~~------------------~p~E~cGlL~G~~~~~~~~I~~i~~~~q~~~~~~~~~~~~~- 64 (173)
T cd08066 4 VVVPADLMDKFLQLAEPNTS------------------RNLETCGILCGKLSNNAFFITHLIIPKQSGTSDSCQTTNEE- 64 (173)
T ss_pred EEECHHHHHHHHHHHHhCCC------------------CCCeEEEEEEeEcCCCeEEEEEEEeccccCCCceecCCCHH-
Confidence 44455566777888766521 1358999999998888889998877776543322 3321
Q ss_pred HHHHHHHHhhh-CCCCceEEEEecCCC----CCcchHHHHHHHHhhCCCCEEEEEcCCCCCCCCCcceEEEEee
Q 021476 88 LEKKQELYKKV-FPHFYILGWYSTGSD----AQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESE 156 (312)
Q Consensus 88 ~~~m~~l~~~V-~p~~~iVGWY~tg~~----~~~~d~~i~~~~~~~~~~pi~L~vD~~~~~~~~~lpi~ay~~~ 156 (312)
+ .++.. -.++.+||||+|.+. ++..|+..|..|....+..++|+++|. ...++||+..
T Consensus 65 --e---~~~~~~~~gle~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~------~~~l~afrl~ 127 (173)
T cd08066 65 --E---LFDFQDQHDLITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK------YNEFGIFRLT 127 (173)
T ss_pred --H---HHHHHHhCCCeeEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC------CcEEeEEEee
Confidence 1 22222 347899999999863 678999888888877778899999973 3569999875
No 22
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=98.40 E-value=2e-05 Score=69.38 Aligned_cols=124 Identities=13% Similarity=0.199 Sum_probs=85.9
Q ss_pred eEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCE--EEEEEEEEeecCCCcccccHHH
Q 021476 10 TFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRT--VEIFNSFELLYDPSTHSLDRAF 87 (312)
Q Consensus 10 ~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~--veI~nsF~vp~~~~~~~iD~~~ 87 (312)
+|.+.+.+..+|+=|..+.. ...|.|+|||...++. |+|++|.|+-|..-...--.+-
T Consensus 3 ~v~is~~AY~K~~LHaaKyP--------------------~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~~L~PmlEv 62 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAKYP--------------------HCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWLSLSPMLEV 62 (196)
T ss_pred eEEEcHHHHHHHHHHhccCC--------------------CCceeeEEEeccCCCCceEEEeeceeccccccCcchHHHH
Confidence 68899999999999998764 2489999999997443 9999999998843322223344
Q ss_pred HHHHHHHHhhhCCCCceEEEEecCCCC-----CcchHHHHHHHHhhCCCCEEEEEcCCCCC-CCCCcceEEEE
Q 021476 88 LEKKQELYKKVFPHFYILGWYSTGSDA-----QESDMHIHKALMDINESPVYVLLNPSINP-AQKDLPVTIFE 154 (312)
Q Consensus 88 ~~~m~~l~~~V~p~~~iVGWY~tg~~~-----~~~d~~i~~~~~~~~~~pi~L~vD~~~~~-~~~~lpi~ay~ 154 (312)
.-.+.+.|-+. .++.|||||+....+ ++.-..|-+.+.+.++.+++|++|-..-. ..+..++.+|.
T Consensus 63 AL~qvd~~~~~-~gl~IvGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~kl~~~~~~~~~~~~~ 134 (196)
T PF03665_consen 63 ALAQVDAYAKS-NGLVIVGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKKLSSDCKAPAISVYQ 134 (196)
T ss_pred HHHHHHHHHhh-CCCEEEEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcccccccCCCcceeee
Confidence 44555666543 479999999997633 33333455556667788999999855322 22333466776
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=98.37 E-value=5.3e-06 Score=72.17 Aligned_cols=104 Identities=17% Similarity=0.259 Sum_probs=72.3
Q ss_pred hhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEe-CCEEEEEEEEEeecCCCcccccHHH--HHHH
Q 021476 15 PLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQR-GRTVEIFNSFELLYDPSTHSLDRAF--LEKK 91 (312)
Q Consensus 15 Plvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~-~~~veI~nsF~vp~~~~~~~iD~~~--~~~m 91 (312)
+.+..+|..|..+.. +..|+|+|+|... ++.+.|++++|+.+.- ..++... ...+
T Consensus 3 ~~ay~ki~~HA~k~p--------------------~~evcGlLlG~~~~~~~~~V~d~vPl~h~~--~~l~P~~Eval~~ 60 (182)
T cd08060 3 TLAYVKMLLHAAKYP--------------------HCAVNGLLLGKKSSGGSVEITDAVPLFHSC--LALAPMLEVALAL 60 (182)
T ss_pred HHHHHHHHHHHHHcC--------------------CchheEEEEeeecCCCCEEEEEEEEcCCCc--cccCHHHHHHHHH
Confidence 456788999998743 3589999999998 8889999999998742 3455432 1223
Q ss_pred HHHHhhhCCCCceEEEEecCCCCC-----cchHHHHHHHHhhCCCCEEEEEcCCC
Q 021476 92 QELYKKVFPHFYILGWYSTGSDAQ-----ESDMHIHKALMDINESPVYVLLNPSI 141 (312)
Q Consensus 92 ~~l~~~V~p~~~iVGWY~tg~~~~-----~~d~~i~~~~~~~~~~pi~L~vD~~~ 141 (312)
.+.+-+- -++.|||+|++++... ..-..|-+-+.+..+++++|+||-..
T Consensus 61 ve~~~~~-~gl~IvG~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~ 114 (182)
T cd08060 61 VDAYCKS-SGLVIVGYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEK 114 (182)
T ss_pred HHHHHHH-CCCEEEEEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCcc
Confidence 3333333 3789999999997543 23334555566677889999998553
No 24
>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=98.18 E-value=2.6e-05 Score=63.81 Aligned_cols=110 Identities=15% Similarity=0.166 Sum_probs=73.6
Q ss_pred hhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCC----CcccccHHHHHHHH
Q 021476 17 VIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDP----STHSLDRAFLEKKQ 92 (312)
Q Consensus 17 vll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~----~~~~iD~~~~~~m~ 92 (312)
++-+|++|..+.. +..+||.|+|...+....|+..|++|... ..+.+|...+.+..
T Consensus 3 ~~~~il~ha~~~~--------------------P~E~cGlL~G~~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~ 62 (128)
T cd08070 3 LLEAILAHAEAEY--------------------PEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEIDPAEQLAAQ 62 (128)
T ss_pred HHHHHHHHHHhCC--------------------CCceEEEEEeecCCCCceEEEEEEccCCCCCCCceEEECHHHHHHHH
Confidence 4557788886643 56999999999987776778899998532 23567877766666
Q ss_pred HHHhhhCCCCceEEEEecCCC--CCcchHHHHHHHHhhCCCCEEEEEcCCCCCCCCCcceEEEEe
Q 021476 93 ELYKKVFPHFYILGWYSTGSD--AQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFES 155 (312)
Q Consensus 93 ~l~~~V~p~~~iVGWY~tg~~--~~~~d~~i~~~~~~~~~~pi~L~vD~~~~~~~~~lpi~ay~~ 155 (312)
+..++. ++.+||||+|++. +.++...+..+ .....++|++.... +...+++|..
T Consensus 63 ~~~~~~--g~~~vG~~HSHP~~~~~PS~~D~~~~---~~~~~~~lIv~~~~----~~~~~~~~~~ 118 (128)
T cd08070 63 REARER--GLEVVGIYHSHPDGPARPSETDLRLA---WPPGVSYLIVSLAG----GAPELRAWRL 118 (128)
T ss_pred HHHHHC--CCeEEEEEeCCCCCCCCCCHHHHHhc---cCCCCeEEEEECCC----CCcEEEEEEE
Confidence 666544 5899999999975 23332222222 11245788887542 2345899985
No 25
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=97.98 E-value=7.1e-05 Score=61.76 Aligned_cols=98 Identities=18% Similarity=0.248 Sum_probs=63.7
Q ss_pred EEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCCC----cccccHHH
Q 021476 12 KLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPS----THSLDRAF 87 (312)
Q Consensus 12 ~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~----~~~iD~~~ 87 (312)
.+-..++-.|+.|..|.. +..++|.|+|+..+ ...|+++.... ...++.++
T Consensus 3 ~i~~~~l~~il~~a~~~~--------------------p~E~~g~l~~~~~~-----~~~~~~~n~~~~~~~~~~~~~~~ 57 (134)
T COG1310 3 VIPKEVLGAILEHARREH--------------------PREVCGLLAGTREG-----ERYFPLKNVSVEPVEYFEIDPEY 57 (134)
T ss_pred eecHHHHHHHHHHHHhcC--------------------ChheEEEEEeeccc-----ceeeccccccCCcceeEeeCHHH
Confidence 455677888999998864 45999999999888 44555543221 13455554
Q ss_pred HHHHHHHHhhhCCCCceEEEEecCCC--CCcchHHHHHHHHhhCCCCEEEEEcC
Q 021476 88 LEKKQELYKKVFPHFYILGWYSTGSD--AQESDMHIHKALMDINESPVYVLLNP 139 (312)
Q Consensus 88 ~~~m~~l~~~V~p~~~iVGWY~tg~~--~~~~d~~i~~~~~~~~~~pi~L~vD~ 139 (312)
.. ++...+.. ++.+||||+|+++ +.+++..++ +++..+.|.+++..+
T Consensus 58 ~~-~~~~~~~~--g~~vvg~yHSHP~~~~~pS~~D~~--~~~~~~~~~~iv~~~ 106 (134)
T COG1310 58 SL-FYLAAEDA--GEVVVGWYHSHPGGPPYPSEADRR--LSKLGPLPWLIVSVP 106 (134)
T ss_pred HH-HHHHHhhC--CCEEEEEEcCCCCCCCCcCHHHHh--hccccCCCEEEEEcC
Confidence 44 44333333 3999999999984 445555555 666666666666553
No 26
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=97.76 E-value=0.00061 Score=58.04 Aligned_cols=124 Identities=15% Similarity=0.255 Sum_probs=84.8
Q ss_pred eEEEehhhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEee--EEeCCEEEEEEEEEeecCCCcccccHHH
Q 021476 10 TFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIG--IQRGRTVEIFNSFELLYDPSTHSLDRAF 87 (312)
Q Consensus 10 ~V~lhPlvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG--~~~~~~veI~nsF~vp~~~~~~~iD~~~ 87 (312)
.|.+..++..+|+=|+.|-.. .-|-|.|+| +..|+.|||++|.|+-|..-....-.|-
T Consensus 3 ~veis~~aY~kmiLH~akyph--------------------~aVnGLLla~~~~kg~~v~itdcVPLfH~~laLaPmlEv 62 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYPH--------------------AAVNGLLLAPATGKGECVEITDCVPLFHSHLALAPMLEV 62 (199)
T ss_pred ceeehhhHHHHHHHHhccCcc--------------------cceeeEEEeccCCCCCeEEEEecchhhccccccccHHHH
Confidence 577888999999999988653 389999999 5558999999999998764322333344
Q ss_pred HHHHHHHHhhhCCCCceEEEEecCCCCCc-----chHHHHHHHHhhCCCCEEEEEcCCC-CCCCCCcceEEEE
Q 021476 88 LEKKQELYKKVFPHFYILGWYSTGSDAQE-----SDMHIHKALMDINESPVYVLLNPSI-NPAQKDLPVTIFE 154 (312)
Q Consensus 88 ~~~m~~l~~~V~p~~~iVGWY~tg~~~~~-----~d~~i~~~~~~~~~~pi~L~vD~~~-~~~~~~lpi~ay~ 154 (312)
.-.|++-+-+ --.+.|+|.|+....++. .-..|-+-++++.+++.+|++|-.. ...-..-|+-+|+
T Consensus 63 Al~lId~~~~-~~GlviaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~~l~~~~e~~~v~v~e 134 (199)
T KOG3289|consen 63 ALNLIDVWGA-QAGLVIAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNKKLVPQCERPPVIVLE 134 (199)
T ss_pred HHHHHHHHHH-hcCeEEEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEeccccccccCCCCEEEee
Confidence 4445554442 347899999999865432 3335666677777776666666443 3333345688887
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=96.76 E-value=0.024 Score=46.71 Aligned_cols=87 Identities=15% Similarity=0.087 Sum_probs=53.7
Q ss_pred CCceEEEEeeEEeCCEEEEEEEEEeecCCC-----cccccHHHHHHHHHH-HhhhCCCCceEEEEecCCC--CCcchHHH
Q 021476 50 QPRVYGCVIGIQRGRTVEIFNSFELLYDPS-----THSLDRAFLEKKQEL-YKKVFPHFYILGWYSTGSD--AQESDMHI 121 (312)
Q Consensus 50 ~~~v~G~LLG~~~~~~veI~nsF~vp~~~~-----~~~iD~~~~~~m~~l-~~~V~p~~~iVGWY~tg~~--~~~~d~~i 121 (312)
+....|+|+|.+.+..+.|+..- .|..++ .+.-+.+.+++.++- +++.+-....||=++|++. +.++...+
T Consensus 16 ~~EtGGiLiG~~~~~~~ii~~~t-~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylGeWHtHP~~~p~PS~~D~ 94 (131)
T TIGR02256 16 STETGGVLIGERRGAHAVITKIS-EPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGEWHTHPEDQPEPSWTDR 94 (131)
T ss_pred CCccceEEEEEEcCCcEEEEEEE-cCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEEecCcCCCCCCCCCHHHH
Confidence 46889999999998888888754 333222 134466677666554 4555556899999999875 23333333
Q ss_pred HHH--HHhhCCCCEEEEE
Q 021476 122 HKA--LMDINESPVYVLL 137 (312)
Q Consensus 122 ~~~--~~~~~~~pi~L~v 137 (312)
... +.+.....+++++
T Consensus 95 ~~~~~~~~~~~~~l~iIv 112 (131)
T TIGR02256 95 RSWRTIIRSPEAMLLLIV 112 (131)
T ss_pred HHHHHHHhCCCeeEEEEE
Confidence 333 3344444445554
No 28
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=95.97 E-value=0.091 Score=40.73 Aligned_cols=54 Identities=7% Similarity=0.155 Sum_probs=33.7
Q ss_pred CCceEEEEeeEEeCCEEEEEEEEEeecCCCcccccHHHHHHHHHHHhhhCCCCceEEEEecCCC
Q 021476 50 QPRVYGCVIGIQRGRTVEIFNSFELLYDPSTHSLDRAFLEKKQELYKKVFPHFYILGWYSTGSD 113 (312)
Q Consensus 50 ~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~~iD~~~~~~m~~l~~~V~p~~~iVGWY~tg~~ 113 (312)
+...+|.|+|...+..+.++......-. . ++.... ++....+..+||+|+|++.
T Consensus 17 p~E~~G~L~g~~~~~~~~~~~~~~~~p~--~------~~~~~~--~~~~~~~~~~vg~~HSHP~ 70 (104)
T PF14464_consen 17 PNEACGLLLGRRDDQRFIVVPNVNPDPR--D------SFRRER--FEARERGLEIVGIWHSHPS 70 (104)
T ss_dssp TS-EEEEEEEEEECCEEEEEEEEE--HH--C------HHHHHH---HHHHHT-EEEEEEEEESS
T ss_pred CCeEEEEEEEEecCCEEEEEeCCCCCcH--H------HHHHHh--hhhhcccceeeEEEEcCCC
Confidence 4689999999998888888877762111 0 111000 0445568899999999875
No 29
>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=95.76 E-value=0.096 Score=42.19 Aligned_cols=83 Identities=11% Similarity=0.061 Sum_probs=50.8
Q ss_pred CCceEEEEeeEEeCCEEEEEEEEEeecCCCc---ccccHHHHHHHHHHHhhhCCCCceEEEEecCCC----CCcchHHHH
Q 021476 50 QPRVYGCVIGIQRGRTVEIFNSFELLYDPST---HSLDRAFLEKKQELYKKVFPHFYILGWYSTGSD----AQESDMHIH 122 (312)
Q Consensus 50 ~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~---~~iD~~~~~~m~~l~~~V~p~~~iVGWY~tg~~----~~~~d~~i~ 122 (312)
|..+||.|+|... .|++.+.+|..... ...+.+ |. -.++.+||-|+++++ ++..|. .
T Consensus 18 P~E~CGlL~G~~~----~v~~~~~~~n~~~~~~~~~f~~~----~~------~~g~~ivgi~HSHP~~~~~PS~~D~--~ 81 (117)
T cd08072 18 PNEFAALLRGKDG----VITELLILPGTESGEVSAVFPLL----ML------PLDMSIVGSVHSHPSGSPRPSDADL--S 81 (117)
T ss_pred CceEEEEEEeecc----EEEEEEECCCCCCCCcceeechH----Hh------cCCCeEEEEEEcCCCCCCCCCHHHH--H
Confidence 5699999999764 58888998854321 112221 11 247899999999874 455553 2
Q ss_pred HHHHhhCCCCEEEEEcCCCCCCCCCcceEEEEe
Q 021476 123 KALMDINESPVYVLLNPSINPAQKDLPVTIFES 155 (312)
Q Consensus 123 ~~~~~~~~~pi~L~vD~~~~~~~~~lpi~ay~~ 155 (312)
++.. ....++++.+.. +.=.++||..
T Consensus 82 --~~~~-~~~~~lIvs~~~----~~~~~~a~~~ 107 (117)
T cd08072 82 --FFSK-TGLVHIIVGYPY----DEDDWRAYDS 107 (117)
T ss_pred --hhhc-CCCEEEEEECcC----CCCCEEEEec
Confidence 2222 334677776421 1223899984
No 30
>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=94.83 E-value=0.12 Score=47.10 Aligned_cols=98 Identities=13% Similarity=0.143 Sum_probs=64.8
Q ss_pred CceEEEEeeEEeC---CEEEEEEEEEeecCCCcccccHHHHHHHHHHHhhhCCCCceEEEEecCC----CCCcchHHHHH
Q 021476 51 PRVYGCVIGIQRG---RTVEIFNSFELLYDPSTHSLDRAFLEKKQELYKKVFPHFYILGWYSTGS----DAQESDMHIHK 123 (312)
Q Consensus 51 ~~v~G~LLG~~~~---~~veI~nsF~vp~~~~~~~iD~~~~~~m~~l~~~V~p~~~iVGWY~tg~----~~~~~d~~i~~ 123 (312)
..++|.|.|.... +.-||+-....|...+...++..-. .-.+. ---++..|||=+|.+ .+++.|+..|.
T Consensus 56 tQ~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~---~~~~~-~l~~Le~LGWIHTqp~e~~~Lss~Dv~tha 131 (252)
T cd08056 56 TQIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQ---LPQHE-YLEDLEPLGWIHTQPNELPQLSPQDVTTHA 131 (252)
T ss_pred ceEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCcc---Cccch-hhCCCEeeEEEEcCCCCccccCHHHHHHHH
Confidence 4799999998764 6778888888887543222221000 01111 123689999999975 35789999998
Q ss_pred HHHhhCC-----CCEEEEEcCCCCCCCCCcceEEEEee
Q 021476 124 ALMDINE-----SPVYVLLNPSINPAQKDLPVTIFESE 156 (312)
Q Consensus 124 ~~~~~~~-----~pi~L~vD~~~~~~~~~lpi~ay~~~ 156 (312)
-++..++ +.|.+++-.. .|...+.||...
T Consensus 132 ~~~~~~~~w~~~~~V~it~Sft----pGs~sl~ay~LT 165 (252)
T cd08056 132 KILADNPSWDGEKTVILTCSFT----PGSCSLTAYKLT 165 (252)
T ss_pred HHHHhccccCCCcEEEEEEcCC----CCceEEEEEecC
Confidence 8887654 4566665433 467789999875
No 31
>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=87.14 E-value=1.4 Score=34.81 Aligned_cols=51 Identities=10% Similarity=0.059 Sum_probs=30.5
Q ss_pred CCceEEEEeeEEeCCEEEEEEEEEeecC-C---CcccccH-HHHHHHHHHHhhhCCCCceEEEEecCCC
Q 021476 50 QPRVYGCVIGIQRGRTVEIFNSFELLYD-P---STHSLDR-AFLEKKQELYKKVFPHFYILGWYSTGSD 113 (312)
Q Consensus 50 ~~~v~G~LLG~~~~~~veI~nsF~vp~~-~---~~~~iD~-~~~~~m~~l~~~V~p~~~iVGWY~tg~~ 113 (312)
+...||.|+|... ++..|++.-. + ..+.+|. ++++-+ + ...+||.|+++++
T Consensus 15 P~E~CGll~g~~~-----~~~~~p~~N~~~~p~~~F~idp~e~~~a~----~----~~~ivgi~HSHP~ 70 (108)
T cd08073 15 PREACGLVVRKGR-----KLRYIPCRNIAADPEEHFEISPEDYAAAE----D----EGEIVAVVHSHPD 70 (108)
T ss_pred CCcceEEEEecCC-----ceEEEECccCCCCccceEEeCHHHHHHHh----c----CCCEEEEEEcCCC
Confidence 5689999999662 2334555421 1 2356665 333322 1 2389999999863
No 32
>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=81.37 E-value=6.2 Score=30.35 Aligned_cols=60 Identities=12% Similarity=0.129 Sum_probs=37.8
Q ss_pred CCceEEEEeeEEeCCEEEEEEEEEeecCCCcccccHHHHHHHHHHHhhhCCCCceEEEEecCCC----CCcchHH
Q 021476 50 QPRVYGCVIGIQRGRTVEIFNSFELLYDPSTHSLDRAFLEKKQELYKKVFPHFYILGWYSTGSD----AQESDMH 120 (312)
Q Consensus 50 ~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~~iD~~~~~~m~~l~~~V~p~~~iVGWY~tg~~----~~~~d~~ 120 (312)
+...+|+|+|...+ .+.+..++|... ...+..+ ......-+..+||-|++++. ++..|..
T Consensus 15 p~E~~gll~~~~~~---~~~~~~~~~~~~--~~~~~~~------~~~a~~~~~~~v~i~HsHP~g~~~PS~~D~~ 78 (101)
T cd08059 15 PDEFCGFLSGSKDN---VMDELIFLPFVS--GSVSAVI------DLAALEIGMKVVGLVHSHPSGSCRPSEADLS 78 (101)
T ss_pred ChhhheeeecCCCC---eEEEEEeCCCcC--CccChHH------HHHHhhCCCcEEEEEecCcCCCCCCCHHHHH
Confidence 45899999997654 577777777432 2233332 22233446789999999863 4556643
No 33
>PF06442 DHFR_2: R67 dihydrofolate reductase; InterPro: IPR009159 Dihydrofolate reductase (DHFR) (1.5.1.3 from EC) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate, an essential step in de novo synthesis both of glycine and of purines and deoxythymidine phosphate (the precursors of DNA synthesis) [], and important also in the conversion of deoxyuridine monophosphate to deoxythymidine monophosphate. Although DHFR is found ubiquitously in prokaryotes and eukaryotes, and is found in all dividing cells, maintaining levels of fully reduced folate coenzymes, the catabolic steps are still not well understood []. Bacterial species possesses distinct DHFR enzymes (based on their pattern of binding diaminoheterocyclic molecules), but mammalian DHFRs are highly similar []. The active site is situated in the N-terminal half of the sequence, which includes a conserved Pro-Trp dipeptide; the tryptophan has been shown [] to be involved in the binding of substrate by the enzyme. Its central role in DNA precursor synthesis, coupled with its inhibition by antagonists such as trimethoprim and methotrexate, which are used as anti-bacterial or anti-cancer agents, has made DHFR a target of anticancer chemotherapy. However, resistance has developed against some drugs, as a result of changes in DHFR itself []. This entry represents a plasmid-encoded DHFR which shows a high level of resistance to the antibiotic trimethoprim. It is a homotetramer with an unusual pore, which contains the active site, passing through the middle of the molecule []. Its structure is unrelated to that of chromosomal DHFRs.; GO: 0004146 dihydrofolate reductase activity, 0042493 response to drug, 0055114 oxidation-reduction process; PDB: 1VIF_A 3SFM_A 2P4T_A 2GQV_A 2RK2_A 2RH2_A 2RK1_A 1VIE_A.
Probab=73.19 E-value=1.9 Score=30.77 Aligned_cols=12 Identities=33% Similarity=0.722 Sum_probs=7.2
Q ss_pred CceEEEEecCCC
Q 021476 102 FYILGWYSTGSD 113 (312)
Q Consensus 102 ~~iVGWY~tg~~ 113 (312)
-.|||||+|.-.
T Consensus 40 g~vvgwy~t~lt 51 (78)
T PF06442_consen 40 GQVVGWYCTKLT 51 (78)
T ss_dssp EEEEEEE--SS-
T ss_pred ceEeEEEecccc
Confidence 479999998643
No 34
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=70.15 E-value=2.7 Score=40.08 Aligned_cols=90 Identities=16% Similarity=0.200 Sum_probs=57.0
Q ss_pred CCceEEEEeeEEeCCEEEEEEEEEeecCCC-cccccHHHHHHHHHHHhhhCCCCceEEEEecCCC----CCcchHHHHHH
Q 021476 50 QPRVYGCVIGIQRGRTVEIFNSFELLYDPS-THSLDRAFLEKKQELYKKVFPHFYILGWYSTGSD----AQESDMHIHKA 124 (312)
Q Consensus 50 ~~~v~G~LLG~~~~~~veI~nsF~vp~~~~-~~~iD~~~~~~m~~l~~~V~p~~~iVGWY~tg~~----~~~~d~~i~~~ 124 (312)
+-..||+|-|.-..+..-||.-. +|..++ ....+..--++.++-.- --++-.|||-+|++. ++..|+..|=-
T Consensus 275 nlETCGiL~g~L~~n~f~IThli-iPkQeatsd~C~t~neeelF~vQd--q~~L~tlGWIHTHPTQt~FmSSVDlHTHcS 351 (424)
T KOG2880|consen 275 NLETCGILAGKLERNEFYITHLI-IPKQEATSDSCNTMNEEELFEVQD--QHELLTLGWIHTHPTQTCFMSSVDLHTHCS 351 (424)
T ss_pred cchHHHHhhhHhhcCcEEEEEEE-eecccCCCccccccCHHHHheecc--cccceeeeeeecCCccchhheeccccccce
Confidence 45789999999999999998754 454332 22222222222222111 136788999999874 45677666655
Q ss_pred HHhhCCCCEEEEEcCCCC
Q 021476 125 LMDINESPVYVLLNPSIN 142 (312)
Q Consensus 125 ~~~~~~~pi~L~vD~~~~ 142 (312)
|+-.-+.+|++++-|..+
T Consensus 352 YQiMlPEAiAIV~aPk~~ 369 (424)
T KOG2880|consen 352 YQIMLPEAIAIVCAPKSK 369 (424)
T ss_pred eeeecchheeEEeccccC
Confidence 665567779999888743
No 35
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=63.25 E-value=42 Score=32.34 Aligned_cols=59 Identities=14% Similarity=0.318 Sum_probs=45.9
Q ss_pred EEEeeEE-eCCEEEEEEEEEeecCCCcc-------------cccHHHHHHHHHHHhhhCCC-CceEEEEecCCC
Q 021476 55 GCVIGIQ-RGRTVEIFNSFELLYDPSTH-------------SLDRAFLEKKQELYKKVFPH-FYILGWYSTGSD 113 (312)
Q Consensus 55 G~LLG~~-~~~~veI~nsF~vp~~~~~~-------------~iD~~~~~~m~~l~~~V~p~-~~iVGWY~tg~~ 113 (312)
|.|+|.. .++.--|..-.+.|.+++.. .+|.++..+--.+-.+.-|. ..|||.|.+++.
T Consensus 1 GLlIGq~~s~~kd~Vv~l~~tP~~d~~~~~~~~~~~~~~~~~id~~WVaeHA~qVsRMLPGGi~VlGifvv~~~ 74 (362)
T PF14778_consen 1 GLLIGQSSSSQKDYVVHLARTPPEDTDDEESDVRTSDSSIKDIDEEWVAEHARQVSRMLPGGISVLGIFVVAPD 74 (362)
T ss_pred CeEeccccCCCcceEEEecCCCCccccccccccccccccccccCHHHHHHHHHHHHhhCCCCcEEEEEEEEcCH
Confidence 8899999 66667788888888754321 38999998888887777775 599999998864
No 36
>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=59.03 E-value=1.2e+02 Score=28.17 Aligned_cols=101 Identities=10% Similarity=0.082 Sum_probs=61.9
Q ss_pred CceEEEEeeEEeC-------CEEEEEEEEEeecCCC--cc-cccHHHHHHHHHHHhhhCCCCceEEEEecCCC-------
Q 021476 51 PRVYGCVIGIQRG-------RTVEIFNSFELLYDPS--TH-SLDRAFLEKKQELYKKVFPHFYILGWYSTGSD------- 113 (312)
Q Consensus 51 ~~v~G~LLG~~~~-------~~veI~nsF~vp~~~~--~~-~iD~~~~~~m~~l~~~V~p~~~iVGWY~tg~~------- 113 (312)
..-+|.|.|+... .++.|..-||=|.... .. .+++....+ .+... ..-.+..|||=-|...
T Consensus 34 ~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~-vd~iA-~~lGL~~VG~IfT~l~~~~~d~~ 111 (274)
T cd08061 34 QQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADT-VDAIA-AALGLERVGWIFTDLPREDKDGY 111 (274)
T ss_pred ceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhH-HHHHH-HHcCCeEEEEEEecCCCCCCCce
Confidence 3679999999973 4889999999987542 22 223333333 23322 2347999999988642
Q ss_pred -CCcchHHHHHHHHh-----hCCCC-EEEEEcCCCCCCCCCcceEEEEee
Q 021476 114 -AQESDMHIHKALMD-----INESP-VYVLLNPSINPAQKDLPVTIFESE 156 (312)
Q Consensus 114 -~~~~d~~i~~~~~~-----~~~~p-i~L~vD~~~~~~~~~lpi~ay~~~ 156 (312)
++..++.....++. ...+. +-+++.+.. .+.+.+.||...
T Consensus 112 ~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~---~g~i~~~ayQvS 158 (274)
T cd08061 112 FLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDK---DGQIHFEAYQVS 158 (274)
T ss_pred eECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCC---CCceeeeeeeec
Confidence 33445444455552 22333 346676653 367889999853
No 37
>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=56.11 E-value=46 Score=29.20 Aligned_cols=65 Identities=6% Similarity=-0.086 Sum_probs=41.6
Q ss_pred hhhhhHhHHHhhhcccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEEEEeecCC-Cc--ccccHHHHHHHH
Q 021476 16 LVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDP-ST--HSLDRAFLEKKQ 92 (312)
Q Consensus 16 lvll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~-~~--~~iD~~~~~~m~ 92 (312)
-.+=.|+.|+.+.. +..+||.|.|..+++.. ..+++...+ +. ...|.. |.
T Consensus 78 ~l~~~ii~hAr~~~--------------------P~EacG~Iag~~~~~~~---r~~p~~N~~~Sp~~~~~d~~----~~ 130 (192)
T TIGR03735 78 SLLEEFAEAARAAL--------------------PNEVAAWIVWNSETGSL---RLAALESIEASPGHIDYRRP----RL 130 (192)
T ss_pred HHHHHHHHHHHhcC--------------------CcceEEEEEEcCCCCEE---EEEeccccccCCceEEEcch----HH
Confidence 34556777776643 56999999998555554 346665322 22 233332 22
Q ss_pred HHHhhhCCCCceEEEEecCCC
Q 021476 93 ELYKKVFPHFYILGWYSTGSD 113 (312)
Q Consensus 93 ~l~~~V~p~~~iVGWY~tg~~ 113 (312)
..++.+|+-|++++.
T Consensus 131 ------~~ge~lV~iyHSH~~ 145 (192)
T TIGR03735 131 ------DDGEHLVVDLHSHGT 145 (192)
T ss_pred ------hCCCeEEEEEcCCCC
Confidence 668999999999864
No 38
>PF03127 GAT: GAT domain; InterPro: IPR004152 The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 [] and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins [].; GO: 0006886 intracellular protein transport, 0005622 intracellular; PDB: 1YD8_H 1WR6_C 1WRD_A 1O3X_A 1J2J_B 1NWM_X 1X79_A 1OXZ_A 1NAF_A.
Probab=40.67 E-value=1.6e+02 Score=22.45 Aligned_cols=86 Identities=10% Similarity=0.232 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCh-HHHHHHHHHHhcCCCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHH
Q 021476 209 GIHSAIKMLNSRIRVLHHYLVAMQKGEIPCEN-SLLRQVSSLLRRLPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCAST 287 (312)
Q Consensus 209 ~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~-~ilR~i~~l~~~lP~~~~~~f~~~~~~~~~D~lmi~yLs~ltk~~~~ 287 (312)
.....+......+..+.+-|.....|+...+. +++..+..-|..+. +.+.+.+..-.+|- +|+.+...-..
T Consensus 8 k~~~~l~~v~~~~~lL~emL~~~~~~~~~~~~~el~~eL~~~ck~~r----~~i~~li~~~~dee----~l~~lL~~ND~ 79 (100)
T PF03127_consen 8 KRRSELEKVKNNAKLLNEMLDNYDPGEESSSDNELIQELYESCKSMR----PRIQRLIEEVEDEE----LLGELLQANDE 79 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTTTTSTHHHHHHHHHHHHHHHHHH----HHHHHHHHTSTTCH----HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHH----HHHHHHHhhcCcHH----HHHHHHHHHHH
Confidence 34455666666666666777777777654433 78888888886532 23444443333332 66666677778
Q ss_pred HHHHHHHHhHhhhcc
Q 021476 288 MNELVDKFNTAYDRH 302 (312)
Q Consensus 288 l~~l~~K~~~~~~~~ 302 (312)
|+..+.||.....++
T Consensus 80 L~~~l~~Y~~l~~~~ 94 (100)
T PF03127_consen 80 LNQALERYDRLVKGQ 94 (100)
T ss_dssp HHHHHHHHHHHHCCC
T ss_pred HHHHHHHHHHHHcCc
Confidence 888888887654433
No 39
>PF11430 EGL-1: Programmed cell death activator EGL-1; InterPro: IPR021543 Initiation of programmed cell death in C.elegans occurs by the binding of EGL-1 to CED-9 which disrupts a complex involving CED-4/CED-9 and allows CED-4 to activate CED-3, a caspase. It is the C-terminal domain of EGL-1 which is involved in the formation of the complex with CED-9. The formation of the complex induces structural rearrangements in CED-9 and EGL-1 adopts an extended alpha-helical conformation []. ; PDB: 1TY4_D.
Probab=38.65 E-value=55 Score=17.98 Aligned_cols=11 Identities=0% Similarity=0.196 Sum_probs=9.0
Q ss_pred hHHHHHHHHHH
Q 021476 240 NSLLRQVSSLL 250 (312)
Q Consensus 240 ~~ilR~i~~l~ 250 (312)
++||.+++..|
T Consensus 1 ~~IG~kla~MC 11 (21)
T PF11430_consen 1 HEIGTKLAAMC 11 (21)
T ss_dssp HHHHHHHHHHH
T ss_pred CcHHHHHHHHH
Confidence 47888988888
No 40
>PF12408 DUF3666: Ribose-5-phosphate isomerase ; InterPro: IPR022133 This domain family is found in bacteria, and is approximately 50 amino acids in length. The family is found in association with PF02502 from PFAM. There are two completely conserved residues (D and F) that may be functionally important. ; PDB: 3ONO_A 3C5Y_N 2PPW_A.
Probab=35.93 E-value=1.1e+02 Score=20.70 Aligned_cols=33 Identities=27% Similarity=0.569 Sum_probs=22.5
Q ss_pred CChHHHHHHHHHHhcCCCCChHHHHHHHHHhhchHHHHHHHH
Q 021476 238 CENSLLRQVSSLLRRLPAIESEKFQDDFLMEYNDTLLIAYLA 279 (312)
Q Consensus 238 ~d~~ilR~i~~l~~~lP~~~~~~f~~~~~~~~~D~lmi~yLs 279 (312)
.|+++++-. ++.+.|.+-|..+++|--+..|+-
T Consensus 14 iDqdLvK~A---------isGe~Fqe~FF~ncqd~eI~~yvk 46 (48)
T PF12408_consen 14 IDQDLVKTA---------ISGERFQECFFANCQDEEIAAYVK 46 (48)
T ss_dssp S-HHHHHHH---------T-SHHHHHHHHHH---HHHHHHHH
T ss_pred hCHHHHHHH---------hccHHHHHHHHhcCCcHHHHHHHH
Confidence 577777642 567999999999999999888874
No 41
>PF10073 DUF2312: Uncharacterized protein conserved in bacteria (DUF2312); InterPro: IPR018753 This entry is represented by Azospirillum phage Cd, Gp10. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family of hypothetical bacterial proteins have no known function.
Probab=34.94 E-value=1.9e+02 Score=21.40 Aligned_cols=64 Identities=14% Similarity=0.274 Sum_probs=40.7
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCChHHHHHHHHHHhcCCCCChHHHHHHHHHhhchHHHHHHHHHH
Q 021476 203 LAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRLPAIESEKFQDDFLMEYNDTLLIAYLAMF 281 (312)
Q Consensus 203 ~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~ilR~i~~l~~~lP~~~~~~f~~~~~~~~~D~lmi~yLs~l 281 (312)
+...++.+..-.+.+...+..|..=.+. .| .|..++|+|-.+ ...++++.+ .+++++-.|++.|
T Consensus 9 ~ieRiErLEeEk~~i~~dikdVyaEAK~--~G---fD~K~lr~ii~l----Rk~d~~~r~------E~eail~~Y~~AL 72 (74)
T PF10073_consen 9 FIERIERLEEEKKAISDDIKDVYAEAKG--NG---FDTKALRQIIRL----RKKDPDERE------EEEAILDLYMSAL 72 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh--CC---CCHHHHHHHHHH----HcCCHhHHH------HHHHHHHHHHHHh
Confidence 3444555555666666666666554444 56 899999988765 334444433 3678888888765
No 42
>PF04740 LXG: LXG domain of WXG superfamily; InterPro: IPR006829 This group of putative transposases is found in Gram-positive bacteria, mostly Bacillus members and is thought to be a Cytosolic protein. However, we have also found a Bacillus subtilis bacteriophage SPbetac2 homologue (O64023 from SWISSPROT), possibly arising as a result of horizontal transfer. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=32.08 E-value=3.3e+02 Score=23.37 Aligned_cols=44 Identities=9% Similarity=0.286 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhc-CCCCCChHHHH-HHHHHH
Q 021476 207 LTGIHSAIKMLNSRIRVLHHYLVAMQK-GEIPCENSLLR-QVSSLL 250 (312)
Q Consensus 207 l~~~~~ai~~L~~~i~~i~~Yl~~V~~-G~~~~d~~ilR-~i~~l~ 250 (312)
+.....++..+...+..+.+|...|.. +..-.|.++|. .|..-+
T Consensus 63 l~~~~~~~~~~~~~l~~~~~~~~~vd~~~~a~i~e~~L~~el~~~l 108 (204)
T PF04740_consen 63 LQGLILLLEEYQEALKFIKDFQSEVDSSSNAIIDEDFLESELKKKL 108 (204)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHcccccccccHHHHHHHHHHHH
Confidence 567778888888888888888888853 33345677776 554433
No 43
>KOG3684 consensus Ca2+-activated K+ channel proteins (intermediate/small conductance classes) [Inorganic ion transport and metabolism]
Probab=31.56 E-value=1.9e+02 Score=28.93 Aligned_cols=80 Identities=13% Similarity=0.209 Sum_probs=46.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCCCCCChHHHHHHH----HHHhcCCCCChHHHHHHHHHhhchHHHHHHHHHHHHHH
Q 021476 210 IHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVS----SLLRRLPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCA 285 (312)
Q Consensus 210 ~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~ilR~i~----~l~~~lP~~~~~~f~~~~~~~~~D~lmi~yLs~ltk~~ 285 (312)
.++|.......--.|.++-+.|..+ |+.-+|+.+ ..++++.++..++ ..++.+.| -+..++|++
T Consensus 362 ~KnAAA~VLqeTW~i~K~trl~~k~----~~~rlR~hQRkfL~AI~~fR~Vk~~q--Rkl~e~~n------sl~d~aK~~ 429 (489)
T KOG3684|consen 362 HKNAAANVLQETWLIYKHTKLVSKG----DQARLRKHQRKFLQAIHQFRSVKWEQ--RKLSEQAN------SLVDLAKTQ 429 (489)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhccc----chHHHHHHHHHHHHHHHHHHHHHHHH--HHHHhhcc------cHHHHHHHH
Confidence 3444444445555677777777553 665555544 3334433333222 22333333 467888999
Q ss_pred HHHHHHHHHHhHhhhc
Q 021476 286 STMNELVDKFNTAYDR 301 (312)
Q Consensus 286 ~~l~~l~~K~~~~~~~ 301 (312)
..+.|++.+++..+|.
T Consensus 430 ~~myd~~~~l~~~q~~ 445 (489)
T KOG3684|consen 430 NDMYDLLQELHSRQEE 445 (489)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999888766553
No 44
>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=30.88 E-value=4.6e+02 Score=24.72 Aligned_cols=57 Identities=14% Similarity=0.156 Sum_probs=36.0
Q ss_pred EEEEeeEEeC-------CEEEEEEEEEeecCCC--cccc-cHHHHHHHHHHHhhhCCCCceEEEEecCC
Q 021476 54 YGCVIGIQRG-------RTVEIFNSFELLYDPS--THSL-DRAFLEKKQELYKKVFPHFYILGWYSTGS 112 (312)
Q Consensus 54 ~G~LLG~~~~-------~~veI~nsF~vp~~~~--~~~i-D~~~~~~m~~l~~~V~p~~~iVGWY~tg~ 112 (312)
+|.|.|+.+. -++.|..-||=|.... ...+ +++..+. .+...+- -.+..|||=-|..
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~-vd~iA~~-lGL~rVG~IfTdl 68 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEER-VDAIASA-LGLERVGWIFTDL 68 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHH-HHHHHHH-CCCEEEEEEEecC
Confidence 7999999972 3789999999997543 2222 3322222 2222211 2889999988764
No 45
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=29.79 E-value=1.8e+02 Score=20.15 Aligned_cols=34 Identities=6% Similarity=0.147 Sum_probs=21.9
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 021476 201 TQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKG 234 (312)
Q Consensus 201 ~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G 234 (312)
+.+.++.+.+..++.++...++.+++-=+-|..|
T Consensus 17 ~tvk~en~~i~~~ve~i~envk~ll~lYE~Vs~~ 50 (55)
T PF05377_consen 17 NTVKKENEEISESVEKIEENVKDLLSLYEVVSNQ 50 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 4455666667777777777777777666655544
No 46
>PF09457 RBD-FIP: FIP domain ; InterPro: IPR019018 The Rab11 GTPase regulates recycling of internalized plasma membrane receptors and is essential for completion of cytokinesis. A family of Rab11 interacting proteins (FIPs) that conserve a C-terminal Rab-binding domain (RBD) selectively recognise the active form of Rab11. FIPs are diverse in sequence length and composition toward their N-termini, presumably a feature that underpins their specific roles in Rab11-mediated vesicle trafficking. They have been divided into three subfamilies (classe I, II, and III)on the basis of domain architecture. Class I FIPs comprises a subfamily of three proteins (Rip11/pp75/FIP5, Rab-coupling protein (RCP), and FIP2) that possess an N- terminal C2 domain, localize to recycling endosomes, and regulate plasma membrane recycling. The class II subfamily consists of two proteins (FIP3/eferin/arfophilin and FIP4) with tandem EF hands and a proline-rich region. Class II FIPs localize to recycling endosomes, the trans-Golgi network, and have been implicated in the regulation of membrane trafficking during cytokinesis. The class III subfamily consists of a single protein, FIP1, which does not contain obvious homology domains or motifs other than the FIP-RBD [, , , ]. The FIP-RBD domain is also found in Rab6-interacting protein Erc1/Elks. Erc1 is the regulatory subunit of the IKK complex and probably recruits IkappaBalpha/NFKBIA to the complex []. It may be involved in the organisation of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. It may also be involved in vesicle trafficking at the CAZ, as well as in Rab-6 regulated endosomes to Golgi transport []. The FIB-RBD domain consists of an N-terminal long alpha-helix, followed by a 90 degrees bend at a conserved proline residue, a 3(10) helix and a C-terminal short beta-strand, adopting an "L" shape. The long alpha-helix forms a parallel coiled-coil homodimer that symmetrically interacts with two Rab11 molecules on both sides, forming a quaternary Rab11-(FIP)2-Rab11 complex. The Rab11-interacting region of FIP-RBD is confined to the C-terminal 24 amino acids, which cover the C-terminal half of the long alpha-helix and the short beta-strand [, , , ]. This entry represents the FIP-RBD domain.; PDB: 2HV8_E 2D7C_D 2K6S_B 2GZD_D 2GZH_B.
Probab=28.12 E-value=85 Score=21.13 Aligned_cols=41 Identities=22% Similarity=0.233 Sum_probs=25.1
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCChHHH
Q 021476 203 LAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLL 243 (312)
Q Consensus 203 ~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~il 243 (312)
+...+..++.-+..-..++..+.+|++++.--=+...|+||
T Consensus 5 L~~~l~~~e~~~~~k~~~v~eLe~YiD~LL~rVmE~~P~IL 45 (48)
T PF09457_consen 5 LISLLKKQEEENARKDSRVRELEDYIDNLLVRVMEQTPSIL 45 (48)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-GGGG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcchh
Confidence 44445566666677777778899999886532233445544
No 47
>PF14071 YlbD_coat: Putative coat protein
Probab=27.39 E-value=1.3e+02 Score=24.61 Aligned_cols=27 Identities=7% Similarity=0.206 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHhhh
Q 021476 274 LIAYLAMFTNCASTMNELVDKFNTAYD 300 (312)
Q Consensus 274 mi~yLs~ltk~~~~l~~l~~K~~~~~~ 300 (312)
|=.+|++++++..+++.++.+|.-.-.
T Consensus 82 ~q~hl~~~sqai~~vQ~~l~qFq~~~~ 108 (124)
T PF14071_consen 82 MQKHLNNVSQAIGSVQQVLSQFQGNGQ 108 (124)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 446788999999999999999975433
No 48
>KOG0756 consensus Mitochondrial tricarboxylate/dicarboxylate carrier proteins [Energy production and conversion]
Probab=26.77 E-value=36 Score=31.83 Aligned_cols=49 Identities=22% Similarity=0.287 Sum_probs=31.6
Q ss_pred CceEEEEeeEEeCCEEEEEEEEEeecCCCcccccHHHHHHHHHHHhhhC------C------CCceEEEEecC
Q 021476 51 PRVYGCVIGIQRGRTVEIFNSFELLYDPSTHSLDRAFLEKKQELYKKVF------P------HFYILGWYSTG 111 (312)
Q Consensus 51 ~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~~iD~~~~~~m~~l~~~V~------p------~~~iVGWY~tg 111 (312)
..+.|.++|-..| -+||+-+||. ||.+.++++++++. | .+-++|||.--
T Consensus 13 ~s~~~~~~Gg~~G-~~E~c~~~P~-----------E~vKT~LQldrr~a~~~~~~~~~~tv~~~G~lglYrGl 73 (299)
T KOG0756|consen 13 GSASGIVAGGIAG-GIEICITQPT-----------EYVKTQLQLDRRSATTKARGPPDCTVNGHGFLGLYRGL 73 (299)
T ss_pred Cchhhcccccccc-ceeeeecCch-----------hhhhheeehhhccccccccCCCceeeecCceeeEeecc
Confidence 3556666666555 6788888766 46667777766432 2 23499999753
No 49
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=25.00 E-value=94 Score=19.04 Aligned_cols=17 Identities=18% Similarity=0.421 Sum_probs=13.7
Q ss_pred CChHHHHHHHHHHhcCC
Q 021476 238 CENSLLRQVSSLLRRLP 254 (312)
Q Consensus 238 ~d~~ilR~i~~l~~~lP 254 (312)
...+|...+.++|+.+|
T Consensus 23 t~~~I~~~l~~~C~~lP 39 (39)
T PF05184_consen 23 TEEEIKKALEKACNKLP 39 (39)
T ss_dssp HHHHHHHHHHHHHTTSC
T ss_pred cHHHHHHHHHHHHhhCc
Confidence 35688888888888887
No 50
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=24.56 E-value=3e+02 Score=20.55 Aligned_cols=47 Identities=11% Similarity=0.270 Sum_probs=30.7
Q ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCChHHHHHHHHHHhc
Q 021476 202 QLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRR 252 (312)
Q Consensus 202 ~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~ilR~i~~l~~~ 252 (312)
.+..++..+++++..|..||+.+..=.++..+. |.-+.-+|..+.+.
T Consensus 20 ~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~E----N~~Lq~YI~nLm~~ 66 (80)
T PF10224_consen 20 ELIQEILELQDSLEALSDRVEEVKEENEKLESE----NEYLQQYIGNLMSS 66 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHh
Confidence 455666677778887777877777666665542 55666666666543
No 51
>KOG3650 consensus Predicted coiled-coil protein [General function prediction only]
Probab=21.75 E-value=2.7e+02 Score=21.71 Aligned_cols=46 Identities=9% Similarity=0.156 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcCCC---CCChHHHHHHHHHHhcCC
Q 021476 209 GIHSAIKMLNSRIRVLHHYLVAMQKGEI---PCENSLLRQVSSLLRRLP 254 (312)
Q Consensus 209 ~~~~ai~~L~~~i~~i~~Yl~~V~~G~~---~~d~~ilR~i~~l~~~lP 254 (312)
++.+.+-.|+.-++.+..-+++|...++ ..|..+|.+|..+.+.-.
T Consensus 60 RlItQVLELQnTLdDLSqRVdsVKEEnLKLrSENQVLGQYIeNLMSaSS 108 (120)
T KOG3650|consen 60 RLITQVLELQNTLDDLSQRVDSVKEENLKLRSENQVLGQYIENLMSASS 108 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhhh
Confidence 3344444455555555555555554442 347789999998887543
No 52
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=21.00 E-value=2e+02 Score=18.74 Aligned_cols=37 Identities=14% Similarity=0.249 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCCCChHHHHHHHHHHh
Q 021476 215 KMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLR 251 (312)
Q Consensus 215 ~~L~~~i~~i~~Yl~~V~~G~~~~d~~ilR~i~~l~~ 251 (312)
+.|-.++..=..++.+..+|+..++.+.+..|...+.
T Consensus 13 ~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~ 49 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENGKRNPSLDTLKKIAKALG 49 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHT
T ss_pred HHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHC
Confidence 4444555555667777788888899999999998886
Done!