Query 023811
Match_columns 277
No_of_seqs 135 out of 720
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 06:49:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023811.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023811hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2975 Translation initiation 100.0 3.5E-59 7.5E-64 412.6 19.1 233 42-275 3-240 (288)
2 PLN03246 26S proteasome regula 100.0 1.5E-55 3.2E-60 407.1 23.3 219 56-275 2-230 (303)
3 cd08062 MPN_RPN7_8 Mpr1p, Pad1 100.0 1.1E-54 2.3E-59 398.2 22.7 214 61-275 2-224 (280)
4 cd08064 MPN_eIF3f Mpr1p, Pad1p 100.0 1.4E-54 2.9E-59 395.3 22.5 213 62-275 1-220 (265)
5 cd08063 MPN_CSN6 Mpr1p, Pad1p 100.0 2.2E-53 4.7E-58 391.6 18.8 214 60-275 1-228 (288)
6 KOG1556 26S proteasome regulat 100.0 2.5E-49 5.4E-54 347.0 17.3 219 55-274 4-231 (309)
7 KOG3050 COP9 signalosome, subu 100.0 7.7E-48 1.7E-52 337.1 13.0 221 53-275 2-233 (299)
8 cd08057 MPN_euk_non_mb Mpr1p, 100.0 8.6E-40 1.9E-44 276.3 15.8 150 62-219 1-157 (157)
9 cd08065 MPN_eIF3h Mpr1p, Pad1p 100.0 6E-35 1.3E-39 266.3 21.6 196 61-259 2-226 (266)
10 cd08069 MPN_RPN11_CSN5 Mov34/M 100.0 5.3E-29 1.2E-33 227.3 21.7 171 56-229 6-205 (268)
11 PF01398 JAB: JAB1/Mov34/MPN/P 99.9 3.4E-26 7.3E-31 182.8 9.8 107 58-167 2-114 (114)
12 KOG1560 Translation initiation 99.9 7.9E-25 1.7E-29 195.6 13.9 195 56-251 9-239 (339)
13 smart00232 JAB_MPN JAB/MPN dom 99.9 5.3E-22 1.1E-26 161.5 14.7 128 61-191 1-134 (135)
14 KOG1554 COP9 signalosome, subu 99.8 1E-17 2.2E-22 150.6 13.3 196 57-256 50-280 (347)
15 cd07767 MPN Mpr1p, Pad1p N-ter 99.7 9.8E-16 2.1E-20 121.6 11.8 111 70-187 2-116 (116)
16 cd08067 MPN_2A_DUB Mov34/MPN/P 99.6 3.7E-14 8E-19 123.3 15.1 146 59-213 4-164 (187)
17 cd08058 MPN_euk_mb Mpr1p, Pad1 99.6 2.5E-14 5.5E-19 115.4 10.7 110 68-190 2-119 (119)
18 cd08068 MPN_BRCC36 Mov34/MPN/P 99.3 3.1E-10 6.7E-15 102.3 17.3 148 60-212 2-169 (244)
19 KOG1555 26S proteasome regulat 99.1 2.4E-09 5.2E-14 98.9 13.7 135 56-192 27-174 (316)
20 cd08066 MPN_AMSH_like Mov34/MP 99.0 1E-08 2.2E-13 88.2 14.9 124 61-194 3-132 (173)
21 PF13012 MitMem_reg: Maintenan 98.8 1.3E-09 2.8E-14 87.1 1.5 63 213-275 1-67 (115)
22 cd08070 MPN_like Mpr1p, Pad1p 98.5 6.7E-06 1.4E-10 67.0 13.9 113 68-190 3-119 (128)
23 cd08060 MPN_UPF0172 Mov34/MPN/ 98.5 3.7E-06 8E-11 73.0 13.1 105 65-177 2-114 (182)
24 PF03665 UPF0172: Uncharacteri 98.4 7.5E-06 1.6E-10 71.8 13.0 124 61-189 3-135 (196)
25 COG1310 Predicted metal-depend 98.1 4.1E-05 9E-10 62.8 10.8 99 63-174 3-105 (134)
26 KOG3289 Uncharacterized conser 97.6 0.0012 2.6E-08 56.6 12.2 124 61-189 3-135 (199)
27 cd08056 MPN_PRP8 Mpr1p, Pad1p 96.7 0.01 2.2E-07 54.0 9.0 103 83-194 55-169 (252)
28 cd08072 MPN_archaeal Mov34/MPN 96.5 0.064 1.4E-06 43.1 11.7 98 69-190 6-108 (117)
29 TIGR02256 ICE_VC0181 integrati 96.5 0.058 1.3E-06 44.5 11.5 80 68-149 1-84 (131)
30 PF14464 Prok-JAB: Prokaryotic 96.1 0.055 1.2E-06 41.7 8.8 93 68-175 4-96 (104)
31 cd08073 MPN_NLPC_P60 Mpr1p, Pa 88.7 2.6 5.6E-05 33.3 7.5 64 70-149 4-70 (108)
32 cd08061 MPN_NPL4 Mov34/MPN/PAD 88.0 5.7 0.00012 36.7 10.3 109 83-193 33-161 (274)
33 PF05021 NPL4: NPL4 family; I 86.6 7.1 0.00015 36.7 10.2 105 87-193 2-144 (306)
34 cd08059 MPN_prok_mb Mpr1p, Pad 81.8 6.8 0.00015 30.0 6.7 63 71-149 5-67 (101)
35 PF06442 DHFR_2: R67 dihydrofo 70.7 2.2 4.8E-05 30.8 1.1 12 137-148 39-50 (78)
36 KOG2880 SMAD6 interacting prot 64.3 14 0.0003 35.5 5.3 96 83-190 275-377 (424)
37 TIGR03735 PRTRC_A PRTRC system 56.6 49 0.0011 29.1 7.0 71 63-149 74-145 (192)
38 PF14778 ODR4-like: Olfactory 53.7 84 0.0018 30.1 8.8 101 88-190 1-128 (362)
39 KOG2834 Nuclear pore complex, 49.4 23 0.00049 35.1 4.1 77 69-146 181-264 (510)
40 KOG1795 U5 snRNP spliceosome s 40.2 70 0.0015 35.9 6.3 117 70-195 2101-2225(2321)
41 PF09457 RBD-FIP: FIP domain ; 29.8 78 0.0017 21.5 3.2 37 237-273 11-47 (48)
42 PF07620 SLEI_Leptospira: SLEI 21.6 69 0.0015 16.8 1.3 12 94-105 4-15 (16)
43 COG4387 Mu-like prophage prote 20.7 1.3E+02 0.0029 24.6 3.5 26 241-266 82-107 (139)
No 1
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.5e-59 Score=412.55 Aligned_cols=233 Identities=43% Similarity=0.721 Sum_probs=222.4
Q ss_pred ccccceeeecCCCCCCCCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccH
Q 023811 42 ASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDI 121 (277)
Q Consensus 42 ~~~~~~~~~~~~~~~~~~~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~ 121 (277)
.....+.+.+.|++.++..+|.|||+|+++|+|||.||.+++.||||+|||+ .++|.|||||||++||+|.++++.+|+
T Consensus 3 ~~~~~v~~~~~~~~~ss~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~-~~~g~ieitNCFaVPhnEssdqvevdm 81 (288)
T KOG2975|consen 3 TPAPHVPGPALPSPFSSNLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGT-VDKGSVEVTNCFAVPHNESSDQVEVDM 81 (288)
T ss_pred CCcCcCCCcCCCCCCCCCceEEEcceEEeEeehhhhcCCccchhhhhheeec-ccCCeEEEEEeeeccCccccccceeeH
Confidence 3445667778888899999999999999999999999999999999999999 779999999999999999999999999
Q ss_pred HHHHHHHHHhhhcCCCCcEEEeeecCCCCCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEeeeeccCCccccc
Q 023811 122 EYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAA 201 (277)
Q Consensus 122 ~y~~~m~~l~kkv~p~e~iVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~~~~~~~~~~~~ 201 (277)
+|.+.|+++|+|+||+|.+||||+||++++.+++.||++|.+++++||||++|++.+++.+++|||.+++.++++++.+.
T Consensus 82 ~y~~~M~~l~~k~npnE~vvGWyaTg~dvt~~sslihdyYare~~~pvhLtVDT~~~n~rm~ikaYvss~~Gvpg~~~~~ 161 (288)
T KOG2975|consen 82 EYAKNMYELHKKVNPNELVVGWYATGHDVTEHSSLIHDYYAREAPNPVHLTVDTSLQNGRMSIKAYVSSLMGVPGRTMGV 161 (288)
T ss_pred HHHHHHHHHhcccCCCceeEEEEecCCCcccchhHHHHHhhccCCCCeEEEEeccccCCccceeEEEEeccCCCCcccce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999899
Q ss_pred ceEEeceEEEcChhhHHHHHHhhccCCC-----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeeec
Q 023811 202 QFQEIPLDLRMIEAERVGFDILKSTSVD-----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIV 275 (277)
Q Consensus 202 ~F~~ip~~I~~~eaErIav~~l~k~~~~-----~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~~ 275 (277)
.|.|+|++|.+.|+||+|++.|.|++.+ .+.++|+++..|..+|+++++.+++|+++|.+|++++|..++||+.
T Consensus 162 mF~plpvel~~~~~ervgl~li~kt~~sp~r~~~l~~dLqQv~~at~~l~~~L~~Vl~YVedVl~gk~~pdn~VGR~Lm 240 (288)
T KOG2975|consen 162 MFTPLPVELAYYDAERVGLDLIEKTSFSPSRVAGLSSDLQQVEGATARLQSLLERVLKYVEDVLAGKVKPDNAVGRFLM 240 (288)
T ss_pred eeeeeeeEEeecchhhhHHHHHHHhccChhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcchHHHHHH
Confidence 9999999999999999999999998843 5789999999999999999999999999999999999999999975
No 2
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=100.00 E-value=1.5e-55 Score=407.13 Aligned_cols=219 Identities=29% Similarity=0.443 Sum_probs=200.5
Q ss_pred CCCCcEEEEehhhHhHHHHHHhhcCCC-CceEEEEeeeeEecCCeEEEEeeeecccCCCCcc---eeccHHHHHHHHHHh
Q 023811 56 ATSNVTAKVHPLVIFNICDCYVRRPDQ-AERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSH 131 (277)
Q Consensus 56 ~~~~~~V~vhPlVlL~I~dH~~R~~~~-~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~---~~iD~~y~~~m~~l~ 131 (277)
.++..+|.|||+|||+|+|||+|+..+ +.+|+|+|||+ +.|+.|||+|||++|+++++++ |++|.+|+++|+++|
T Consensus 2 ~~~~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~-~~~~~ieItnsF~~p~~e~~~~~~~~~~D~~y~~~m~~~~ 80 (303)
T PLN03246 2 PRGIEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGS-SFRGRVDVTNSFAVPFEEDDKDPSIWFLDHNYLESMFGMF 80 (303)
T ss_pred CCCCcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEee-ecCCEEEEEeccccCcccCCCCccceeecHHHHHHHHHHH
Confidence 466789999999999999999999765 68999999998 7889999999999999876554 789999999999999
Q ss_pred hhcCCCCcEEEeeecCCCCCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEeeeeccCCcc--cccceEEeceE
Q 023811 132 LKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQ--LAAQFQEIPLD 209 (277)
Q Consensus 132 kkv~p~e~iVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~~~~~~~~~--~~~~F~~ip~~ 209 (277)
|+|||++.+||||+||++++++|+.||++|++++++||||++|+...++++|++||++...+.++++ .+..|.++|++
T Consensus 81 k~V~~~~~vVGWY~tg~~i~~~d~~IH~~~~~~~~~Pv~L~vD~~~~~~~lpi~aY~s~~~~~~~~~~~~~~~F~~vp~~ 160 (303)
T PLN03246 81 KRINAKEHVVGWYSTGPKLRENDLDIHELFNDYVPNPVLVIIDVQPKELGIPTKAYYAVEEVKENATQKSQKVFVHVPSE 160 (303)
T ss_pred HHhCCCCcEEeeecCCCCCCcchHHHHHHHHhhCCCCeEEEEecCCCCCCCceEEEEEEEeccCCCCcccccEEEECCee
Confidence 9999999999999999999999999999999999999999999998888899999999988775433 46789999999
Q ss_pred EEcChhhHHHHHHhhccCCC----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeeec
Q 023811 210 LRMIEAERVGFDILKSTSVD----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIV 275 (277)
Q Consensus 210 I~~~eaErIav~~l~k~~~~----~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~~ 275 (277)
|.++|+||||++|+++...+ .+..++.++.+|+++|.+|++.+++||++|.+|++++|+++||++-
T Consensus 161 i~~~EaE~Igve~l~r~~~~~~~s~l~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~g~~~~d~~IlR~l~ 230 (303)
T PLN03246 161 IGAHEAEEIGVEHLLRDVKDTTVSTLATEVTGKLTALKGLDARLREIRSYLDLVVEGKLPLNHEILYHLQ 230 (303)
T ss_pred eeecCHHHHHHHHHHhcccCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHH
Confidence 99999999999999985543 3556888999999999999999999999999999999999999874
No 3
>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=1.1e-54 Score=398.22 Aligned_cols=214 Identities=29% Similarity=0.449 Sum_probs=197.7
Q ss_pred EEEEehhhHhHHHHHHhhcCCC-CceEEEEeeeeEecCCeEEEEeeeecccCCCCcc---eeccHHHHHHHHHHhhhcCC
Q 023811 61 TAKVHPLVIFNICDCYVRRPDQ-AERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSHLKVNP 136 (277)
Q Consensus 61 ~V~vhPlVlL~I~dH~~R~~~~-~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~---~~iD~~y~~~m~~l~kkv~p 136 (277)
+|+|||+|||+|+|||+|+..+ +.+|+|+|||+ +.|+.|||+|||++|+++++++ +++|.+|+++|+++||+|||
T Consensus 2 ~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~-~~~~~veItnsF~~p~~~~~~~~~~~~~d~~y~~~m~~~~kkv~~ 80 (280)
T cd08062 2 KVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGS-WKKGVLDVTNSFAVPFEEDEKDPSVWFLDHNYLENMYGMFKKVNA 80 (280)
T ss_pred eEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEE-EeCCEEEEEEeeecCccCCCCCcchhhhhHHHHHHHHHHHHHhCC
Confidence 7999999999999999998755 78999999998 7889999999999999887665 58999999999999999999
Q ss_pred CCcEEEeeecCCCCCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEeeeeccCCcc-cccceEEeceEEEcChh
Q 023811 137 QEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQ-LAAQFQEIPLDLRMIEA 215 (277)
Q Consensus 137 ~e~iVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~~~~~~~~~-~~~~F~~ip~~I~~~ea 215 (277)
++.+||||+||++++.+|+.||++|++++++||+|++||...++++|++||++.+...++++ .+..|.++|++|.++|+
T Consensus 81 ~e~vVGWY~tg~~~~~~d~~ih~~~~~~~~~pv~l~vd~~~~~~~lpi~aY~s~~~~~~~g~~~~~~F~~vp~~i~~~ea 160 (280)
T cd08062 81 KEKIVGWYSTGPKLRPNDLDINELFRRYCPNPVLVIIDVRPKDLGLPTEAYIAVEEVHDDGTPTSKTFVHVPSEIGAEEA 160 (280)
T ss_pred CCCeEEEecCCCCCCcchHHHHHHHHHhCCCCEEEEEecCCCCCCCceEEEEEeeeccCCCCcceeEEEEcceEeeccch
Confidence 99999999999999999999999999999999999999999888999999999988775555 78899999999999999
Q ss_pred hHHHHHHhhccCCC----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeeec
Q 023811 216 ERVGFDILKSTSVD----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIV 275 (277)
Q Consensus 216 ErIav~~l~k~~~~----~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~~ 275 (277)
||||++|+++...+ .+..++.++.+|+++|+.|++.+.+||++|.+|++++|+++||++-
T Consensus 161 E~igve~l~r~~~~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~IlR~l~ 224 (280)
T cd08062 161 EEVGVEHLLRDIKDVTVSTLSTRVTNKLNSLKGLQSKLKEIKDYLQLVVEGKLPINHQIIYNLQ 224 (280)
T ss_pred HHHHHHHHHhhccCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH
Confidence 99999999974332 3556889999999999999999999999999999999999999874
No 4
>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=1.4e-54 Score=395.30 Aligned_cols=213 Identities=47% Similarity=0.786 Sum_probs=199.8
Q ss_pred EEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEE
Q 023811 62 AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIV 141 (277)
Q Consensus 62 V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iV 141 (277)
|.|||+|||+|+|||+|+..++.+|+|+|||+ +.++.+||||||++|++++++++.+|.+|+++|+++||+|||++.+|
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~-~~~~~veItnsF~~p~~~~~~~~~~d~~y~~~m~~~~kkv~~~~~vV 79 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGT-RSEGEVEITNCFAVPHNESEDQVAVDMEYHRTMYELHQKVNPKEVIV 79 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEE-EeCCEEEEEeCeecceeCCCCeEEEcHHHHHHHHHHHHHhCCCCcEE
Confidence 68999999999999999987789999999998 78899999999999999988889999999999999999999999999
Q ss_pred EeeecCCCCCCchhHHHHHHhhcCC--CcEEEEEecCCCCCcceeEEEEeeeeccCCcccccceEEeceEEEcChhhHHH
Q 023811 142 GWFSTGLGVTGGSALIHEFYCREVP--NPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219 (277)
Q Consensus 142 GWY~t~~~~~~~~~~ih~~~~~~~~--~PI~L~vD~~~~~~~l~ikay~~~~~~~~~~~~~~~F~~ip~~I~~~eaErIa 219 (277)
|||+||+.++.++..||++|+++++ +||+|++||...++++|++||++.+.++.+++....|.++|++|.++|+||||
T Consensus 80 GWY~tg~~~~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~~~~l~i~ay~~~~~~~~~~~~~~~F~~ip~~i~~~eaE~i~ 159 (265)
T cd08064 80 GWYATGSEITEHSALIHDYYSRECTSYNPIHLTVDTSLDDGKMSIKAYVSSPLGVPGKTLGSMFVPIPLELLYSEAERVA 159 (265)
T ss_pred eeeeCCCCCCccHHHHHHHHHhhCCCCCCEEEEEeCCCCCCCcceEEEEEEecccCCCCcceEEEEcceeeecCcHHHHH
Confidence 9999999999999999999999988 99999999998777999999999988877777889999999999999999999
Q ss_pred HHHhhccCCC-----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeeec
Q 023811 220 FDILKSTSVD-----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIV 275 (277)
Q Consensus 220 v~~l~k~~~~-----~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~~ 275 (277)
++++++...+ .+.++++.+.+++++|+++++.+.+||++|.+|+.++|++++|++.
T Consensus 160 v~~l~~~~~~~~~~~~~~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~i~r~l~ 220 (265)
T cd08064 160 LDLLAKTLASPSRSAPLTSDLEQLEASLEKLQEMLDRVLRYVEDVLAGKVKADNAIGRYLM 220 (265)
T ss_pred HHHHHhhccCCcccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 9999986553 2457899999999999999999999999999999999999999874
No 5
>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=2.2e-53 Score=391.59 Aligned_cols=214 Identities=27% Similarity=0.395 Sum_probs=197.0
Q ss_pred cEEEEehhhHhHHHHHHhhcCCC----CceEEEEeeeeEecCCeEEEEeeeecccCCCC-cceeccHHHHHHHHHHhhhc
Q 023811 60 VTAKVHPLVIFNICDCYVRRPDQ----AERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS-DQVALDIEYHHTMLKSHLKV 134 (277)
Q Consensus 60 ~~V~vhPlVlL~I~dH~~R~~~~----~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~-~~~~iD~~y~~~m~~l~kkv 134 (277)
.+|.|||+|||+|+|||+|+..+ +.+|+|+|||+ ++|+.|||+|||++|+++++ +++.+|.+|+++|+++||+|
T Consensus 1 ~~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~-~~~~~veItnsF~~p~~~~~~~~~~id~~y~~~m~~~~kkV 79 (288)
T cd08063 1 LSVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQ-QDGREIEIENSFELKYDTNEDGEIVLDKEFLETRLEQFKQV 79 (288)
T ss_pred CeEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEE-EcCCEEEEEEEEecccccCCCCceeeCHHHHHHHHHHHHHh
Confidence 37999999999999999998643 58999999998 88999999999999999877 67899999999999999999
Q ss_pred CCCCcEEEeeecCCC-CCCchhHHHHHHhhcCCCcEEEEEecCC--CCCcceeEEEEeeeeccCCcccccceEEeceEEE
Q 023811 135 NPQEVIVGWFSTGLG-VTGGSALIHEFYCREVPNPVHLTVDTGF--RNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLR 211 (277)
Q Consensus 135 ~p~e~iVGWY~t~~~-~~~~~~~ih~~~~~~~~~PI~L~vD~~~--~~~~l~ikay~~~~~~~~~~~~~~~F~~ip~~I~ 211 (277)
||++.+||||+||+. ++.++..||++|++.+++||+|++||.. .++++|++||++...+.++ .....|+|+|++|+
T Consensus 80 ~~~~~vVGWY~tg~~~~~~~~~~Ih~~~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~~~~~~-~~~~~F~~i~~~i~ 158 (288)
T cd08063 80 FKDLDFVGWYTTGPGGPTESDLPIHKQILEINESPVLLLLDPEANASGKDLPVTIYESVLELVDG-EATLRFRELPYTIE 158 (288)
T ss_pred ccCCceEEEEecCCCCCCHHHHHHHHHHHhhCCCcEEEEEccccccCCCCCceeEEEEEEeccCC-ccccEEEeeeeEEE
Confidence 999999999999998 9999999999999999999999999998 5789999999999887765 56688999999999
Q ss_pred cChhhHHHHHHhhccCC--C----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeeec
Q 023811 212 MIEAERVGFDILKSTSV--D----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIV 275 (277)
Q Consensus 212 ~~eaErIav~~l~k~~~--~----~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~~ 275 (277)
++|+||||++|+++... + .+.++++.+.+|+++|++|++.|++||++|.+|++++|+++||++.
T Consensus 159 ~~eaErIgv~~l~~~~~~~~~~~~~~~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~g~~~~d~~ilR~l~ 228 (288)
T cd08063 159 TGEAERIGVDHVARGGASGSSEKSTVAAHLQAQHNAIKMLNSRVELILEYLKAVPVGEVPPDHSILRSIS 228 (288)
T ss_pred eccCceeeHHHHHhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Confidence 99999999999998652 1 2467899999999999999999999999999999999999999874
No 6
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.5e-49 Score=346.97 Aligned_cols=219 Identities=28% Similarity=0.429 Sum_probs=200.9
Q ss_pred CCCCCcEEEEehhhHhHHHHHHhhcCC-CCceEEEEeeeeEecCCeEEEEeeeecccCCCCcc---eeccHHHHHHHHHH
Q 023811 55 AATSNVTAKVHPLVIFNICDCYVRRPD-QAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKS 130 (277)
Q Consensus 55 ~~~~~~~V~vhPlVlL~I~dH~~R~~~-~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~---~~iD~~y~~~m~~l 130 (277)
+.-+..+|.+||||||+++|||.|... +++||+|.|||. ..++++.|+|||++|++|++++ |++|.+|++.|++|
T Consensus 4 ~~~~~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~-~~~~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~m 82 (309)
T KOG1556|consen 4 SELTVEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGS-WNGDVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGM 82 (309)
T ss_pred cccccceeeeehhHHHHHHHHHhhhccCcCceEEEEEEec-CCCCeEEeecceeccccccCCCCceEEeccHHHHHHHHH
Confidence 355677999999999999999999863 468999999998 6777999999999999998876 89999999999999
Q ss_pred hhhcCCCCcEEEeeecCCCCCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEeeeeccC-CcccccceEEeceE
Q 023811 131 HLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLG-DRQLAAQFQEIPLD 209 (277)
Q Consensus 131 ~kkv~p~e~iVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~~~~~~-~~~~~~~F~~ip~~ 209 (277)
|+|+|.+|.+||||+|||.+.++|+.|++++.+++|+|+++++|..+.+-+||..||...++..+ +.+...+|+.+|++
T Consensus 83 fkKvNakekivGWYhTGPkl~~nDl~In~l~k~y~pnpvLvIIdvkpk~~gLPT~AY~aVeev~dDgt~t~ktF~Hvps~ 162 (309)
T KOG1556|consen 83 FKKVNAKEKVVGWYHTGPKLRENDLDINELLKRYVPNPVLVIIDVKPKELGLPTEAYIAVEEVKDDGTPTSKTFVHVPSE 162 (309)
T ss_pred HHHhcchhheeeeeccCCccccchhhHHHHHhhcCCCceEEEEecccccCCCCchheeeeeeeecCCCCccceeEecCcc
Confidence 99999999999999999999999999999999999999999999998888999999999887654 45567899999999
Q ss_pred EEcChhhHHHHHHhhccCCC----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeee
Q 023811 210 LRMIEAERVGFDILKSTSVD----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQI 274 (277)
Q Consensus 210 I~~~eaErIav~~l~k~~~~----~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~ 274 (277)
|++.|||+||++|+.+...+ .+...+.++..+++.|+.++..|.+||++|.+|++|.||+++-|.
T Consensus 163 I~AeEAEEvGVEHLlRDikd~t~gtla~rit~ql~sLkgl~~~L~eI~~YL~~Vi~g~lpiNh~Il~~l 231 (309)
T KOG1556|consen 163 IEAEEAEEVGVEHLLRDIKDTTVGTLATRITNQLMSLKGLQSRLREIRSYLDKVIDGKLPINHEILYQL 231 (309)
T ss_pred cchhHHHHhhHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHH
Confidence 99999999999999986543 467788899999999999999999999999999999999998764
No 7
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=7.7e-48 Score=337.08 Aligned_cols=221 Identities=24% Similarity=0.360 Sum_probs=197.8
Q ss_pred CCCCCCCcEEEEehhhHhHHHHHHhhcCCC--C--ceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHH
Q 023811 53 SSAATSNVTAKVHPLVIFNICDCYVRRPDQ--A--ERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTML 128 (277)
Q Consensus 53 ~~~~~~~~~V~vhPlVlL~I~dH~~R~~~~--~--~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~ 128 (277)
+++++++.+|.+||||++||+|||+|.+.+ + ++|+|+|+|. |.|++|||.|||++..+..++...+|.+|++++.
T Consensus 2 Aps~S~s~tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~-Q~GR~vEi~NSFeL~~d~~~~~~~~dke~l~kk~ 80 (299)
T KOG3050|consen 2 APSSSGSVTVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGK-QRGRNVEIMNSFELKMDTEEDTETIDKEYLEKKE 80 (299)
T ss_pred CCCCCCceeEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheec-ccCceEEEeeeeEEEecchhhhhhccHHHHHHHH
Confidence 355778899999999999999999999743 2 4899999998 9999999999999998877666689999999999
Q ss_pred HHhhhcCCCCcEEEeeecCCCCCCchhHHHHHHhhcCCCcEEEEEecCCC-CCcceeEEEEeeeeccCCcccccceEEec
Q 023811 129 KSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFR-NGEGTVKAYVSVNLSLGDRQLAAQFQEIP 207 (277)
Q Consensus 129 ~l~kkv~p~e~iVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~-~~~l~ikay~~~~~~~~~~~~~~~F~~ip 207 (277)
++||+|||+..++|||+||.+.++.|..||.+++..++.|++|.++|..+ ..+.|+..|++.--.++ +....+|.|+.
T Consensus 81 eqykqVFpdl~vlGwYttG~d~t~sd~~i~k~l~~i~esplflkLNp~t~~t~~~pv~lfese~dvid-g~~q~~f~~~t 159 (299)
T KOG3050|consen 81 EQYKQVFPDLYVLGWYTTGSDPTPSDIHIHKQLMDINESPLFLKLNPATNHTDKDPVTLFESEIDVID-GEAQMLFVPLT 159 (299)
T ss_pred HHHHHhcccceEEEEeecCCCCChhhhHHHHHHHhhhcCceEEEecchhccccCCCceeeeeeheeec-CcceeeeeeeE
Confidence 99999999999999999999999999999999999999999999999885 45569999988744443 45578999999
Q ss_pred eEEEcChhhHHHHHHhhccCCC------CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeeec
Q 023811 208 LDLRMIEAERVGFDILKSTSVD------KLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIV 275 (277)
Q Consensus 208 ~~I~~~eaErIav~~l~k~~~~------~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~~ 275 (277)
|++.+.|||||||||+++-+.. ....|++.+..|++||+.|++.|++|+++|.+|++++||++|||.-
T Consensus 160 ytl~teEaERIgVdHVA~lt~~~gge~s~VaeHl~AQdsA~~ml~~Rvklil~Y~k~~e~G~l~~N~eILrea~ 233 (299)
T KOG3050|consen 160 YTLATEEAERIGVDHVARLTPSDGGEGSSVAEHLEAQDSAIKMLDNRVKLILAYLKKVEAGTLQPNFEILREAY 233 (299)
T ss_pred EEEeehhhhhccchhheeeccCCCCCcchHHHHHhhHHHHHHHHhhHHHHHHHHHhhhhcCCcCccHHHHHHHH
Confidence 9999999999999999984331 3678999999999999999999999999999999999999999864
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=8.6e-40 Score=276.27 Aligned_cols=150 Identities=31% Similarity=0.551 Sum_probs=137.0
Q ss_pred EEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEE
Q 023811 62 AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIV 141 (277)
Q Consensus 62 V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iV 141 (277)
|+|||+|||||+|||+|+..++.+|+|+|||+ +.++.++|+|||++|++++++.+.+|.+|+++|+++|++|+|++.+|
T Consensus 1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~-~~~~~veV~nsF~lp~~~~~~~~~~d~~y~~~m~~~~~~v~~~~~vV 79 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGY-VDGDKIEVTNSFELPFDEEEESIFIDTEYLEKRYNLHKKVYPQEKIV 79 (157)
T ss_pred CEEccHHHhhHHHHHHhccCCCCeEEEEEEeE-EeCCEEEEEEeEEccccCCCcchhhhHHHHHHHHHHHHHhCCCCCEE
Confidence 68999999999999999876678999999998 77999999999999998887778899999999999999999999999
Q ss_pred EeeecCCC----CCCchhHHHHHHhhc-CCCcEEEEEecCC--CCCcceeEEEEeeeeccCCcccccceEEeceEEEcCh
Q 023811 142 GWFSTGLG----VTGGSALIHEFYCRE-VPNPVHLTVDTGF--RNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIE 214 (277)
Q Consensus 142 GWY~t~~~----~~~~~~~ih~~~~~~-~~~PI~L~vD~~~--~~~~l~ikay~~~~~~~~~~~~~~~F~~ip~~I~~~e 214 (277)
|||++++. ++..+..||++|+++ .++||+|++||.. .+++++++||++.+.... +.++|+++.+.|
T Consensus 80 GWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~~~~-------~~~~~~~i~~~e 152 (157)
T cd08057 80 GWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQREEN-------GAEITYEIGTEE 152 (157)
T ss_pred EEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEecCCCC-------CceeeeEEeccc
Confidence 99999987 889999999999998 8889999999987 478999999999854321 339999999999
Q ss_pred hhHHH
Q 023811 215 AERVG 219 (277)
Q Consensus 215 aErIa 219 (277)
+||||
T Consensus 153 ~E~I~ 157 (157)
T cd08057 153 TERIA 157 (157)
T ss_pred ccccC
Confidence 99985
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=100.00 E-value=6e-35 Score=266.32 Aligned_cols=196 Identities=22% Similarity=0.277 Sum_probs=160.4
Q ss_pred EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcc---eeccHHHHHHHHHHhhhcCCC
Q 023811 61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSHLKVNPQ 137 (277)
Q Consensus 61 ~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~---~~iD~~y~~~m~~l~kkv~p~ 137 (277)
+|+|||+|+++|+|||.|+. +.+|+|+|||. ..|+.+||||||++|+.+++++ ...|.+|+.+|++++++++++
T Consensus 2 ~V~I~~~vllkIv~H~~~~~--p~~v~G~LLG~-~~~~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~ 78 (266)
T cd08065 2 SVQIDGLVVLKIIKHCKEEL--PELVQGQLLGL-DVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVD 78 (266)
T ss_pred EEEEeHHHHHHHHHHHhcCC--CcEEEEEEeee-EcCCEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCC
Confidence 69999999999999998874 89999999998 6789999999999999887665 466789999999999999999
Q ss_pred CcEEEeeecCC-CCCCchhHHHHHHhhcC--CCcEEEEEecCC-CCCcceeEEEEeeeeccC---------------Ccc
Q 023811 138 EVIVGWFSTGL-GVTGGSALIHEFYCREV--PNPVHLTVDTGF-RNGEGTVKAYVSVNLSLG---------------DRQ 198 (277)
Q Consensus 138 e~iVGWY~t~~-~~~~~~~~ih~~~~~~~--~~PI~L~vD~~~-~~~~l~ikay~~~~~~~~---------------~~~ 198 (277)
+.+||||+|++ +...+...||.++..+. +++|+|++||.. .+|.++++||++++.+++ +.+
T Consensus 79 e~iVGWY~S~p~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s~~g~l~lkAyrl~~~~~~~~~~~~~~~~~l~~~~~~ 158 (266)
T cd08065 79 HNHVGWYQSTYLGSFFTRDLIETQYNYQEAIEESVVLVYDPSKTSQGSLSLKAYRLSEKFMELYKEGKFSTESLREANLT 158 (266)
T ss_pred CcEEEeEeecCCCCcCCHHHHHHHHHHhccCCCCEEEEECCCcccccceeeEEEEEcHHHHHHhhcCCcCHHHHHHhcCc
Confidence 99999999999 55666788999988874 778999999997 578899999999988764 456
Q ss_pred cccceEEeceEEEcChhhHHHHHHhhccCCCC-------CcccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023811 199 LAAQFQEIPLDLRMIEAERVGFDILKSTSVDK-------LPSDLEGMEVLMERLLTLINDIYKYVDDT 259 (277)
Q Consensus 199 ~~~~F~~ip~~I~~~eaErIav~~l~k~~~~~-------l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V 259 (277)
.+.+|.|||++|++++.+++.+..+....... ..+....+...++.|.+.++.+..+.++.
T Consensus 159 ~~~if~eiPv~i~n~~l~~~~L~~l~~~~~~~~~~~~~l~l~~~~~le~~l~~l~~~id~l~~e~~~~ 226 (266)
T cd08065 159 FSNIFEEIPVVIRNSHLVNALLSELEEDSPSSQSDFDRLDLSTNSFLEKNLELLMESVDELSQEQGKF 226 (266)
T ss_pred hhcEEEEEEEEEEchHHHHHHHHhcccCCCcccCCcccccccCchhHHHHHHHHHHHHHHHHHHHHHH
Confidence 78999999999999999999999886533221 12233455555555555555555554443
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=99.97 E-value=5.3e-29 Score=227.31 Aligned_cols=171 Identities=15% Similarity=0.204 Sum_probs=151.8
Q ss_pred CCCCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHHH--Hhhh
Q 023811 56 ATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLK--SHLK 133 (277)
Q Consensus 56 ~~~~~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~--l~kk 133 (277)
.....+|.|+|+|+++|++|+.|. .+.+|+|+|+|. .+++.++|++||++|+.++++.+..+.+|++.|.+ ++++
T Consensus 6 ~~~~~~V~Is~~allkil~Ha~~~--~p~Ev~GlLlG~-~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~~ 82 (268)
T cd08069 6 PDYFEKVYISSLALLKMLKHARAG--GPIEVMGLMLGK-VDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQ 82 (268)
T ss_pred CCcccEEEECHHHHHHHHHHHhcc--CCceEEEEEEee-ecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHHH
Confidence 355678999999999999999874 578999999998 67889999999999998887777777899999999 9999
Q ss_pred cCCCCcEEEeeecCCC----CCCchhHHHHHHhhcCCCcEEEEEecCCC--CCcceeEEEEeeeeccC----Cc------
Q 023811 134 VNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR--NGEGTVKAYVSVNLSLG----DR------ 197 (277)
Q Consensus 134 v~p~e~iVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~--~~~l~ikay~~~~~~~~----~~------ 197 (277)
+++++.+||||||+++ ++..|+.+|..|++..+.+|+|++||..+ .|++.++||++.+.+.. +.
T Consensus 83 ~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~~~~~~~~~~~~~s~~~ 162 (268)
T cd08069 83 TGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIPPGYKPLEPRQTTSNIG 162 (268)
T ss_pred hCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEECccccccCcccCccccC
Confidence 9999999999999997 88999999999999888899999998764 78899999999987753 12
Q ss_pred -----------ccccceEEeceEEEcChhhHHHHHHhhccCCC
Q 023811 198 -----------QLAAQFQEIPLDLRMIEAERVGFDILKSTSVD 229 (277)
Q Consensus 198 -----------~~~~~F~~ip~~I~~~eaErIav~~l~k~~~~ 229 (277)
.....|++||+++.+++.|+..++.+.+..|.
T Consensus 163 ~~~~~~~~~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~~w~ 205 (268)
T cd08069 163 HLPKPKIEDFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNKYWV 205 (268)
T ss_pred ccCcHHHHHhCchhcEEEEeeeEEecCHHHHHHHHHHHHHhHH
Confidence 25689999999999999999999999887663
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=3.4e-26 Score=182.79 Aligned_cols=107 Identities=36% Similarity=0.579 Sum_probs=94.0
Q ss_pred CCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCC-eEEEEeeeecccCCCCcce-eccHHHHHHHHHHhhhcC
Q 023811 58 SNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDG-TVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKVN 135 (277)
Q Consensus 58 ~~~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~-~VeVtnsF~vp~~e~~~~~-~iD~~y~~~m~~l~kkv~ 135 (277)
+..+|.|||+|+++|+||+.|+. +.+|+|+|+|+ .+++ .++|+|||++|+.+++++. ..+.++.++|++++++++
T Consensus 2 s~~~V~i~p~vll~i~~h~~r~~--~~~v~G~LlG~-~~~~~~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (114)
T PF01398_consen 2 SVQTVQIHPLVLLKIIDHATRSS--PNEVIGLLLGT-QDGDNTVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVN 78 (114)
T ss_dssp SCEEEEEEHHHHHHHHHHHHHHH--CTEEEEEEEEE-EETT-EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCS
T ss_pred CcEEEEECHHHHHHHHHHHhcCC--CCEEEEEEEEE-ecCceEEEEEEEEEeeEecCccccccchhhHHHHHHhhhcccc
Confidence 46799999999999999999985 35999999998 6777 9999999999999877654 456677799999999999
Q ss_pred CCCcEEEeeecCCCC----CCchhHHHHHHhhcCCC
Q 023811 136 PQEVIVGWFSTGLGV----TGGSALIHEFYCREVPN 167 (277)
Q Consensus 136 p~e~iVGWY~t~~~~----~~~~~~ih~~~~~~~~~ 167 (277)
|++.+||||+|++.. +..|+.+|.+|++.+++
T Consensus 79 ~~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 79 PNLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp TTSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred ccceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence 999999999999876 89999999999987664
No 12
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=7.9e-25 Score=195.63 Aligned_cols=195 Identities=22% Similarity=0.350 Sum_probs=150.8
Q ss_pred CCCCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCC--CCcce---eccH---HHHHHH
Q 023811 56 ATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNE--FSDQV---ALDI---EYHHTM 127 (277)
Q Consensus 56 ~~~~~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e--~~~~~---~iD~---~y~~~m 127 (277)
+++...|.+..||+++|++||.....+..-+.|+|+|. .-++.+|||||||.|... +++.+ ..|. .|+..|
T Consensus 9 ~p~vk~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~Gl-vvd~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~m 87 (339)
T KOG1560|consen 9 SPPVKRVELDSLVVMKIIKHCREEFPNGDGTQGVLLGL-VVDGRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLAM 87 (339)
T ss_pred CCccceeeehhHHHHHHHHHHHhhcCCcchhhheeeee-eecceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHHH
Confidence 67788999999999999999987765557899999998 668899999999999754 22322 2332 599999
Q ss_pred HHHhhhcCCCCcEEEeeecCC-CCCCchhHHHHHHhhc--CCCcEEEEEecCC-CCCcceeEEEEeeeeccC--------
Q 023811 128 LKSHLKVNPQEVIVGWFSTGL-GVTGGSALIHEFYCRE--VPNPVHLTVDTGF-RNGEGTVKAYVSVNLSLG-------- 195 (277)
Q Consensus 128 ~~l~kkv~p~e~iVGWY~t~~-~~~~~~~~ih~~~~~~--~~~PI~L~vD~~~-~~~~l~ikay~~~~~~~~-------- 195 (277)
+..++.+|.+..+||||++.- +..-+...+..+|.++ +++.|+|++||.+ ++|.|.++||++.+..+.
T Consensus 88 lrrlr~vnid~~hVGwYqs~~vgs~lS~~lveSqy~YQ~a~pesVvliYD~~kssqG~L~lrAyrLTp~am~~~kekdwt 167 (339)
T KOG1560|consen 88 LRRLRYVNIDHLHVGWYQSAYVGSFLSPALVESQYAYQKAIPESVVLIYDPIKSSQGTLSLRAYRLTPEAMAAHKEKDWT 167 (339)
T ss_pred HHHhhhcCccceeeeeeeeehhccccCHHHHHHHHHHHhcCCccEEEEeccccccCceEEeehhhcCHHHHHHHhcCCCC
Confidence 999999999999999999652 3333356778888777 5677999999999 589999999999987642
Q ss_pred -------CcccccceEEeceEEEcChhhHHHHHHhh--ccCCCC--CcccH-----HHHHHHHHHHHHHHHH
Q 023811 196 -------DRQLAAQFQEIPLDLRMIEAERVGFDILK--STSVDK--LPSDL-----EGMEVLMERLLTLIND 251 (277)
Q Consensus 196 -------~~~~~~~F~~ip~~I~~~eaErIav~~l~--k~~~~~--l~~~l-----~~l~~sl~~L~~~l~~ 251 (277)
+.++.+.|.|+|+.|+++..-.+-+..+. +.+.+. +.+++ ..+++.++.|.++++.
T Consensus 168 pealk~~nltyenmfeElPIVIknS~L~nvlmseLs~~e~c~sdk~~~~~fdlgs~t~leknir~lme~vDE 239 (339)
T KOG1560|consen 168 PEALKSANLTYENMFEELPIVIKNSHLANVLMSELSEPEDCESDKPLHSNFDLGSGTRLEKNIRLLMERVDE 239 (339)
T ss_pred HHHHHhcCCCHHHHHhhcCeeeeccHHHHHHHHhccccccccccccccccccccchhhHHHHHHHHHHHHHH
Confidence 35678999999999999999999988887 433321 11111 2555666666666554
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=99.88 E-value=5.3e-22 Score=161.48 Aligned_cols=128 Identities=31% Similarity=0.442 Sum_probs=112.7
Q ss_pred EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcce-eccHHHHHHHHHHhhhcCCCCc
Q 023811 61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKVNPQEV 139 (277)
Q Consensus 61 ~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~-~iD~~y~~~m~~l~kkv~p~e~ 139 (277)
.|.|||+|+++|++|+.|. .+.+++|.|+|. ..++.++|+++|++|...+++.. ..+.+|++.|.++++++++++.
T Consensus 1 ~v~i~~~v~~~i~~h~~~~--~p~e~~G~L~G~-~~~~~~~i~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (135)
T smart00232 1 EVKVHPLVPLNILKHAIRD--GPEEVCGVLLGK-SNKDRPEVKEVFAVPNEPQDDSVQEYDEDYSHLMDEELKKVNKDLE 77 (135)
T ss_pred CEEEcHHHHHHHHHHHhcC--CCcEEEEEEEEE-EcCCEEEEEEEEecCcCCCCcchhhhhhhHHHHHHHHHHhhCCCce
Confidence 4789999999999999886 578999999998 67889999999999987765554 6789999999999999999999
Q ss_pred EEEeeecCCC----CCCchhHHHHHHhhcCCCcEEEEEecCCC-CCcceeEEEEeee
Q 023811 140 IVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR-NGEGTVKAYVSVN 191 (277)
Q Consensus 140 iVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~-~~~l~ikay~~~~ 191 (277)
+||||+|++. ++..|..+|..+......++++++|+..+ .++++++||++..
T Consensus 78 ~vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~~g~~~~~af~~~~ 134 (135)
T smart00232 78 IVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLTP 134 (135)
T ss_pred EEEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccccCcEEEEEEEecC
Confidence 9999999873 56678888988888888899999999985 4889999999863
No 14
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.76 E-value=1e-17 Score=150.63 Aligned_cols=196 Identities=14% Similarity=0.213 Sum_probs=146.9
Q ss_pred CCCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcce---eccHHHHHHHHHHhhh
Q 023811 57 TSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV---ALDIEYHHTMLKSHLK 133 (277)
Q Consensus 57 ~~~~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~---~iD~~y~~~m~~l~kk 133 (277)
..-..|.|..|++|+|.-|..|. ++-.|+|.++|+ .+|+++.|.+||++|.+.++..+ .--.+|+....+.-+.
T Consensus 50 ~~fk~vkISalAllKm~~hA~~G--gnlEiMGlm~Gk-v~g~t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k~ 126 (347)
T KOG1554|consen 50 HYFKHVKISALALLKMVMHARSG--GNLEIMGLMQGK-VDGDTIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEAKN 126 (347)
T ss_pred chhhhhhhHHHHHHHHHHHHhcC--CCeEEEeeeccc-ccCCeEEEEeccccccccccceechHHHHHHHHHHHHHHHHH
Confidence 34558999999999999998553 688999999998 88999999999999999988765 2236788888999999
Q ss_pred cCCCCcEEEeeecCCC----CCCchhHHHHHHhhcCCCc-EEEEEecCC--CCCcceeEEEEeeeeccCC----------
Q 023811 134 VNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNP-VHLTVDTGF--RNGEGTVKAYVSVNLSLGD---------- 196 (277)
Q Consensus 134 v~p~e~iVGWY~t~~~----~~~~~~~ih~~~~~~~~~P-I~L~vD~~~--~~~~l~ikay~~~~~~~~~---------- 196 (277)
++..+.+||||+++|+ ++..|+..|.+ .+.+..| +++++||.. +.|++.|.|||+-+.+...
T Consensus 127 ~gr~envVGWyHSHPgYgCWLSgIDVsTQ~l-NQ~fQePfvAvViDP~Rtlsagkv~iGAFRTyp~gyk~~d~~~seyqt 205 (347)
T KOG1554|consen 127 VGRLENVVGWYHSHPGYGCWLSGIDVSTQML-NQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTYPKGYKPPDEPPSEYQT 205 (347)
T ss_pred hhhhhceeeeeecCCCCCccccCcchhHHHH-hhhhcCCeEEEEecCccccccCceeeceeecccCCCCCCCCCchhhhc
Confidence 9999999999999997 34555555543 4446778 899999988 4789999999998876421
Q ss_pred ---------cccccceEEeceEEEcChhhHHHHHHhhccCC------CCCcccHHHHHHHHHHHHHHHHHHHHHH
Q 023811 197 ---------RQLAAQFQEIPLDLRMIEAERVGFDILKSTSV------DKLPSDLEGMEVLMERLLTLINDIYKYV 256 (277)
Q Consensus 197 ---------~~~~~~F~~ip~~I~~~eaErIav~~l~k~~~------~~l~~~l~~l~~sl~~L~~~l~~i~~Yl 256 (277)
+-.+..+..+++.+--+-.++--++.+-+..+ +++..+.+.+...+..|.+++++.-+.+
T Consensus 206 ipl~kied~gvHck~yysl~isyfks~ld~kll~~Lwnkywv~Tlsss~ll~N~dy~~~qi~d~~ekl~q~~~~l 280 (347)
T KOG1554|consen 206 IPLNKIEDFGVHCKQYYSLEISYFKSSLDMKLLELLWNKYWVRTLSSSPLLKNIDYLNGQIRDLSEKLEQREDSL 280 (347)
T ss_pred cchhhhhhcccceEEeeccchhhhhhhhhHHHHHHHHhhhhhcccccccccccchhhcchhhhHHHHHHhhhhhc
Confidence 11234455555555555566666666654333 2466677777777777777777655544
No 15
>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=99.66 E-value=9.8e-16 Score=121.64 Aligned_cols=111 Identities=25% Similarity=0.355 Sum_probs=88.1
Q ss_pred hHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEEEeeecCCC
Q 023811 70 FNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG 149 (277)
Q Consensus 70 L~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iVGWY~t~~~ 149 (277)
.+|++|+.+. .+.+|+|.|+|+ ..++.++|+++|++|...++.. .+... -|....+.+..++.+||||+|++.
T Consensus 2 k~il~~a~~~--~~~ev~G~L~G~-~~~~~~~i~~~~~~~~~~~~~~--~~~~~--~~~~~~~~~~~~~~iVGwyhshp~ 74 (116)
T cd07767 2 KMFLDAAKSI--NGKEVIGLLYGS-KTKKVLDVDEVIAVPFDEGDKD--DNVWF--LMYLDFKKLNAGLRIVGWYHTHPK 74 (116)
T ss_pred HhHHHHHhcC--CCcEEEEEeEEE-EcCCEEEEEEEEecccCCCCCc--cHHHH--HHHHHHHHhcCCCeEEEEEEcCCC
Confidence 4678888663 468999999998 6777899999999998765432 22222 266667778899999999999975
Q ss_pred ----CCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEE
Q 023811 150 ----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAY 187 (277)
Q Consensus 150 ----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay 187 (277)
++..|+..|..+++..+++++|++|+...+.+++++||
T Consensus 75 ~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~~~~~~~~~~~ 116 (116)
T cd07767 75 PSCFLSPNDLATHELFQRYFPEKVMIIVDVKPKDLGNSWKCY 116 (116)
T ss_pred CCCccCHHHHHHHHHHHHhCCCCEEEEEECCCccCCCCcccC
Confidence 67888888888888788899999999887667888886
No 16
>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=99.59 E-value=3.7e-14 Score=123.30 Aligned_cols=146 Identities=14% Similarity=0.095 Sum_probs=107.2
Q ss_pred CcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEec-CCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCC
Q 023811 59 NVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLP-DGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQ 137 (277)
Q Consensus 59 ~~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~-~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~ 137 (277)
..+|+|+++|+|+|..|+... ...|+|.|+|.+.. ++.++|+++|++|.....++..+|.+++.+|.+..++.+
T Consensus 4 pf~V~Is~~all~m~~Ha~~~---~~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e~dp~~q~e~~~~l~~~g-- 78 (187)
T cd08067 4 PFKVTVSSNALLLMDFHCHLT---TSEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEMDPVSETEIRESLESRG-- 78 (187)
T ss_pred CEEEEECHHHHHHHHHHhcCC---CcEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccccCHHHHHHHHHHHHHcC--
Confidence 578999999999999999653 28899999998433 468999999999987765666789999999999988766
Q ss_pred CcEEEeeecCCC----CCCchhHHHHHHhhcCC------Cc-EEEEEecCCC---CCcceeEEEEeeeeccCCcccccce
Q 023811 138 EVIVGWFSTGLG----VTGGSALIHEFYCREVP------NP-VHLTVDTGFR---NGEGTVKAYVSVNLSLGDRQLAAQF 203 (277)
Q Consensus 138 e~iVGWY~t~~~----~~~~~~~ih~~~~~~~~------~P-I~L~vD~~~~---~~~l~ikay~~~~~~~~~~~~~~~F 203 (277)
+.+|||||+++. ++..|+..|..|+...+ .| |.++++|-.. ...-.|++|...+..-.+ ..-
T Consensus 79 l~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~~~~~----~~~ 154 (187)
T cd08067 79 LSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPPPENR----PNE 154 (187)
T ss_pred CEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECCCCCC----Ccc
Confidence 699999999984 33444544444544433 24 9999999763 235679999998653221 122
Q ss_pred EEeceEEEcC
Q 023811 204 QEIPLDLRMI 213 (277)
Q Consensus 204 ~~ip~~I~~~ 213 (277)
..+|+.+.+.
T Consensus 155 ~~~p~~~~~~ 164 (187)
T cd08067 155 YGVPMLMSYT 164 (187)
T ss_pred CCcCeEEEec
Confidence 3356655554
No 17
>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=99.56 E-value=2.5e-14 Score=115.38 Aligned_cols=110 Identities=13% Similarity=0.209 Sum_probs=83.4
Q ss_pred hHhHHHHHHhhcCCCCceEEEEeeeeEec----CCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEEEe
Q 023811 68 VIFNICDCYVRRPDQAERVIGTLLGSVLP----DGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGW 143 (277)
Q Consensus 68 VlL~I~dH~~R~~~~~~~ViG~LLG~~~~----~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iVGW 143 (277)
|+++|++|+.+. .+..++|.|+|...+ ++.++|+++|+.|...+. .+.|..+.+....++.+|||
T Consensus 2 ~~~~i~~ha~~~--~p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~~~---------~~~~~~~~~~~~~g~~~vG~ 70 (119)
T cd08058 2 ALLKMLQHAESN--TGIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCTG---------ENVEELFNVQTGRPLLVVGW 70 (119)
T ss_pred HHHHHHHHhcCC--CCeEEEEEeeeEEecCccceeEEEEeecCCCCCCchh---------HHHHHHHHHHhCCCCeEEEE
Confidence 789999999774 478999999998432 346899999999875432 22455556678899999999
Q ss_pred eecCCC----CCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEee
Q 023811 144 FSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV 190 (277)
Q Consensus 144 Y~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~ 190 (277)
||++++ ++..|+..|.+|....++.++|++||..+ .++++||+++
T Consensus 71 YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~--~~~~~a~rl~ 119 (119)
T cd08058 71 YHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHR--NKDTGIFRLT 119 (119)
T ss_pred EecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCC--CcccceEEeC
Confidence 999983 45566555555555567779999999663 7899999874
No 18
>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=99.27 E-value=3.1e-10 Score=102.25 Aligned_cols=148 Identities=17% Similarity=0.185 Sum_probs=99.9
Q ss_pred cEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEe------cCCeEEEEeeeecccCC-CCcceeccHH----HHHHHH
Q 023811 60 VTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVL------PDGTVDIRNSYVVPHNE-FSDQVALDIE----YHHTML 128 (277)
Q Consensus 60 ~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~------~~~~VeVtnsF~vp~~e-~~~~~~iD~~----y~~~m~ 128 (277)
.+|.|.+.++..|++|..+. .+..++|.|+|.+. .++.+.|..-++.+..+ ..+.+.+|.+ ..+.+.
T Consensus 2 ~~V~Is~~~l~~il~HA~~~--~P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea~ 79 (244)
T cd08068 2 SKVHLSADVYLVCLTHALST--EKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEAE 79 (244)
T ss_pred cEEEECHHHHHHHHHHHHhC--CCcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHHH
Confidence 37999999999999999775 58899999999832 13445555555544333 2344677854 335566
Q ss_pred HHhhhcCCCCcEEEeeecCCC----CCCchhHHHHHHhhcCCCcEEEEEecCC-----CCCcceeEEEEeeeeccCCccc
Q 023811 129 KSHLKVNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGF-----RNGEGTVKAYVSVNLSLGDRQL 199 (277)
Q Consensus 129 ~l~kkv~p~e~iVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~-----~~~~l~ikay~~~~~~~~~~~~ 199 (277)
++.+.+..++.+|||||++++ ++..|...+..|....+.-++|++.+.. ..++..+++|+..+.. ...
T Consensus 80 ~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~g~---~~~ 156 (244)
T cd08068 80 RLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQGN---KAG 156 (244)
T ss_pred HHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecCCC---CCC
Confidence 777788999999999999985 3445544433343333555899887543 2367889999997431 122
Q ss_pred ccceEEeceEEEc
Q 023811 200 AAQFQEIPLDLRM 212 (277)
Q Consensus 200 ~~~F~~ip~~I~~ 212 (277)
.....++|+.|..
T Consensus 157 ~~~~~e~pl~i~~ 169 (244)
T cd08068 157 QYERIEVPLEIVP 169 (244)
T ss_pred cceEEEeeeEEec
Confidence 3456788887774
No 19
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.07 E-value=2.4e-09 Score=98.94 Aligned_cols=135 Identities=21% Similarity=0.321 Sum_probs=110.2
Q ss_pred CCCCcEEEEehhhHhHHHHHHhhcCCCCc-eEEEEe-ee---eEecCCeEEEEeeeecccCCCCcc--e-eccHHHHHHH
Q 023811 56 ATSNVTAKVHPLVIFNICDCYVRRPDQAE-RVIGTL-LG---SVLPDGTVDIRNSYVVPHNEFSDQ--V-ALDIEYHHTM 127 (277)
Q Consensus 56 ~~~~~~V~vhPlVlL~I~dH~~R~~~~~~-~ViG~L-LG---~~~~~~~VeVtnsF~vp~~e~~~~--~-~iD~~y~~~m 127 (277)
+....+|.++.++++.+++|- |.. .+. .++|.+ +| .+.+..++.|.+.|+.|+...+=. + +.|.-|+.+|
T Consensus 27 ~~~~e~v~i~slall~m~rh~-r~~-~p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg~~is~~~e~~d~V~q~q~ 104 (316)
T KOG1555|consen 27 SDEKETVYISSLALLKMLRHD-RAG-SPEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAVDPVFQTQM 104 (316)
T ss_pred ccCcceeeeehhhhhhccccc-ccC-CchhhccceeecccccceeeecceeeeeeeccccccceecccchhccHHHHHHH
Confidence 466789999999999999987 442 233 489999 99 666788999999999998875432 2 6889999999
Q ss_pred HHHhhhcCCCCcEEEeeecCCC----CCCchhHHHHHHhhcCCCcEEEEEecCCC-CCcceeEEEEeeee
Q 023811 128 LKSHLKVNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR-NGEGTVKAYVSVNL 192 (277)
Q Consensus 128 ~~l~kkv~p~e~iVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~-~~~l~ikay~~~~~ 192 (277)
.++.++....+.+|||||++++ ++..|+..|+-|+...+..+..++||..+ .|+..+.||+....
T Consensus 105 ~~~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~g~vv~d~f~~In~ 174 (316)
T KOG1555|consen 105 MDLLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPYGKVVPDAFSSINP 174 (316)
T ss_pred HHHHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCCCCccCChhhhcCc
Confidence 9999999988999999999986 45677777777877778889999999884 56666778887654
No 20
>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al
Probab=99.03 E-value=1e-08 Score=88.24 Aligned_cols=124 Identities=13% Similarity=0.143 Sum_probs=90.0
Q ss_pred EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCccee-ccHHHHHHHHHHhhhcCCCCc
Q 023811 61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVA-LDIEYHHTMLKSHLKVNPQEV 139 (277)
Q Consensus 61 ~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~-iD~~y~~~m~~l~kkv~p~e~ 139 (277)
.+.|-.-.+-+|+.|..++...+..+.|.|+|. ..++..+|++.+-.|...++..+. .|.. ++++. .-..++.
T Consensus 3 ~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~-~~~~~~~I~~i~~~~q~~~~~~~~~~~~~---e~~~~--~~~~gle 76 (173)
T cd08066 3 QVVVPADLMDKFLQLAEPNTSRNLETCGILCGK-LSNNAFFITHLIIPKQSGTSDSCQTTNEE---ELFDF--QDQHDLI 76 (173)
T ss_pred EEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeE-cCCCeEEEEEEEeccccCCCceecCCCHH---HHHHH--HHhCCCe
Confidence 355666678889999977532357999999998 667788999998778776654432 3321 12211 1235899
Q ss_pred EEEeeecCCC----CCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEee-eecc
Q 023811 140 IVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV-NLSL 194 (277)
Q Consensus 140 iVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~-~~~~ 194 (277)
+||||+|+++ ++..|+..|..|....+..++|+++|. ...++||+.. +.++
T Consensus 77 ~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~----~~~l~afrl~~~~g~ 132 (173)
T cd08066 77 TLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK----YNEFGIFRLTDPPGL 132 (173)
T ss_pred eEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC----CcEEeEEEeecCCcc
Confidence 9999999874 567888888877776777899999973 6789999998 6654
No 21
>PF13012 MitMem_reg: Maintenance of mitochondrial structure and function; PDB: 2O96_B 2O95_A.
Probab=98.81 E-value=1.3e-09 Score=87.13 Aligned_cols=63 Identities=27% Similarity=0.283 Sum_probs=12.6
Q ss_pred ChhhHHHHHHhhccCC----CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeeec
Q 023811 213 IEAERVGFDILKSTSV----DKLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIV 275 (277)
Q Consensus 213 ~eaErIav~~l~k~~~----~~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~~ 275 (277)
.||||||++|+++... +.+.++++.+.+++.+|+++++.+.+||++|.+|++++|++++||+-
T Consensus 1 eEaErigv~~l~~~~~~~~~s~~~~~l~~~~~al~~L~~~l~~i~~Yl~~v~~g~~~~d~~i~r~l~ 67 (115)
T PF13012_consen 1 EEAERIGVDHLARGLGDHYYSSLSSQLENEQNALKMLHKRLWQILDYLEDVISGEIPPDHEILRQLQ 67 (115)
T ss_dssp SHHHHHHHHHHHHH--S--------------------------------------------------
T ss_pred CchHHHHHHHHHccCCCccccHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcCCCchhHHHHHH
Confidence 4899999999998543 25678899999999999999999999999999999999999999984
No 22
>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=98.47 E-value=6.7e-06 Score=66.95 Aligned_cols=113 Identities=15% Similarity=0.067 Sum_probs=78.4
Q ss_pred hHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCc--ceeccHHHHHHHHHHhhhcCCCCcEEEeee
Q 023811 68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSD--QVALDIEYHHTMLKSHLKVNPQEVIVGWFS 145 (277)
Q Consensus 68 VlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~--~~~iD~~y~~~m~~l~kkv~p~e~iVGWY~ 145 (277)
++-+|++|+.+. .+..+.|.|+|. .++....|+..+++|....+. ...+|.+.+.++.+..++. ++.+|||||
T Consensus 3 ~~~~il~ha~~~--~P~E~cGlL~G~-~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~~~~~~~--g~~~vG~~H 77 (128)
T cd08070 3 LLEAILAHAEAE--YPEECCGLLLGK-GGGVTAIVTEVYPVRNVAESPRRRFEIDPAEQLAAQREARER--GLEVVGIYH 77 (128)
T ss_pred HHHHHHHHHHhC--CCCceEEEEEee-cCCCCceEEEEEEccCCCCCCCceEEECHHHHHHHHHHHHHC--CCeEEEEEe
Confidence 456889999774 478999999998 656555678999998765443 4568887777776666544 699999999
Q ss_pred cCCC--CCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEee
Q 023811 146 TGLG--VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV 190 (277)
Q Consensus 146 t~~~--~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~ 190 (277)
|+++ ...+...+..+ . ....++|++..... ...+++|...
T Consensus 78 SHP~~~~~PS~~D~~~~--~-~~~~~~lIv~~~~~--~~~~~~~~~~ 119 (128)
T cd08070 78 SHPDGPARPSETDLRLA--W-PPGVSYLIVSLAGG--APELRAWRLE 119 (128)
T ss_pred CCCCCCCCCCHHHHHhc--c-CCCCeEEEEECCCC--CcEEEEEEEc
Confidence 9985 23333222222 1 12457888886433 4678999886
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=98.47 E-value=3.7e-06 Score=72.99 Aligned_cols=105 Identities=22% Similarity=0.248 Sum_probs=74.3
Q ss_pred ehhhHhHHHHHHhhcCCCCceEEEEeeeeEec-CCeEEEEeeeecccCCCCcceeccHHH--HHHHHHHhhhcCCCCcEE
Q 023811 65 HPLVIFNICDCYVRRPDQAERVIGTLLGSVLP-DGTVDIRNSYVVPHNEFSDQVALDIEY--HHTMLKSHLKVNPQEVIV 141 (277)
Q Consensus 65 hPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~-~~~VeVtnsF~vp~~e~~~~~~iD~~y--~~~m~~l~kkv~p~e~iV 141 (277)
.+.+..+|..|..+.. +..|.|.|+|+ .. ++.+.|++++|+.+.. ..++... ...+.+.+-+. .+..||
T Consensus 2 s~~ay~ki~~HA~k~p--~~evcGlLlG~-~~~~~~~~V~d~vPl~h~~----~~l~P~~Eval~~ve~~~~~-~gl~Iv 73 (182)
T cd08060 2 STLAYVKMLLHAAKYP--HCAVNGLLLGK-KSSGGSVEITDAVPLFHSC----LALAPMLEVALALVDAYCKS-SGLVIV 73 (182)
T ss_pred CHHHHHHHHHHHHHcC--CchheEEEEee-ecCCCCEEEEEEEEcCCCc----cccCHHHHHHHHHHHHHHHH-CCCEEE
Confidence 3567889999998853 56999999998 55 7789999999999852 3455442 22233333333 389999
Q ss_pred EeeecCCCCC-----CchhHHHHHHhhcCCCcEEEEEecCC
Q 023811 142 GWFSTGLGVT-----GGSALIHEFYCREVPNPVHLTVDTGF 177 (277)
Q Consensus 142 GWY~t~~~~~-----~~~~~ih~~~~~~~~~PI~L~vD~~~ 177 (277)
|+|++++... .....|=+.+.+.++++++|++|-.+
T Consensus 74 G~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~ 114 (182)
T cd08060 74 GYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEK 114 (182)
T ss_pred EEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCcc
Confidence 9999998543 23334455566677889999999765
No 24
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=98.38 E-value=7.5e-06 Score=71.85 Aligned_cols=124 Identities=16% Similarity=0.181 Sum_probs=86.8
Q ss_pred EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCe-EEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCc
Q 023811 61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT-VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEV 139 (277)
Q Consensus 61 ~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~-VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~ 139 (277)
+|.+.+.+..+|+=|..+.. ...|.|.|||....++. |+|++|.|+=|.... ..--.|-.-.+.+.|-+. .+..
T Consensus 3 ~v~is~~AY~K~~LHaaKyP--~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~~--L~PmlEvAL~qvd~~~~~-~gl~ 77 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAKYP--HCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWLS--LSPMLEVALAQVDAYAKS-NGLV 77 (196)
T ss_pred eEEEcHHHHHHHHHHhccCC--CCceeeEEEeccCCCCceEEEeeceeccccccC--cchHHHHHHHHHHHHHhh-CCCE
Confidence 68999999999999998874 46899999999433333 999999999995432 122234444556666643 5799
Q ss_pred EEEeeecCCC-----CCCchhHHHHHHhhcCCCcEEEEEecCC-C--CCcceeEEEEe
Q 023811 140 IVGWFSTGLG-----VTGGSALIHEFYCREVPNPVHLTVDTGF-R--NGEGTVKAYVS 189 (277)
Q Consensus 140 iVGWY~t~~~-----~~~~~~~ih~~~~~~~~~PI~L~vD~~~-~--~~~l~ikay~~ 189 (277)
|||+|++... ++..-..|=+...+.++++++|++|-.+ . .+...+.+|..
T Consensus 78 IvGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~kl~~~~~~~~~~~~~~ 135 (196)
T PF03665_consen 78 IVGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKKLSSDCKAPAISVYQR 135 (196)
T ss_pred EEEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcccccccCCCcceeeee
Confidence 9999998753 3333334555666678899999999765 2 23344567763
No 25
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=98.09 E-value=4.1e-05 Score=62.80 Aligned_cols=99 Identities=19% Similarity=0.251 Sum_probs=63.9
Q ss_pred EEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCC--cceeccHHHHHHHHHHhhhcCCCCcE
Q 023811 63 KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS--DQVALDIEYHHTMLKSHLKVNPQEVI 140 (277)
Q Consensus 63 ~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~--~~~~iD~~y~~~m~~l~kkv~p~e~i 140 (277)
.+-..++-.|+.|..|. .+.+++|.|+|+ ..+ ...|+++....+ +...++.++.. ++....+. ++.+
T Consensus 3 ~i~~~~l~~il~~a~~~--~p~E~~g~l~~~-~~~-----~~~~~~~n~~~~~~~~~~~~~~~~~-~~~~~~~~--g~~v 71 (134)
T COG1310 3 VIPKEVLGAILEHARRE--HPREVCGLLAGT-REG-----ERYFPLKNVSVEPVEYFEIDPEYSL-FYLAAEDA--GEVV 71 (134)
T ss_pred eecHHHHHHHHHHHHhc--CChheEEEEEee-ccc-----ceeeccccccCCcceeEeeCHHHHH-HHHHHhhC--CCEE
Confidence 45667888999999886 368999999998 545 344444433322 22355666555 44444333 3999
Q ss_pred EEeeecCCC--CCCchhHHHHHHhhcCCCcEEEEEe
Q 023811 141 VGWFSTGLG--VTGGSALIHEFYCREVPNPVHLTVD 174 (277)
Q Consensus 141 VGWY~t~~~--~~~~~~~ih~~~~~~~~~PI~L~vD 174 (277)
||||||+++ ...++..++ +++..+.|-+++..
T Consensus 72 vg~yHSHP~~~~~pS~~D~~--~~~~~~~~~~iv~~ 105 (134)
T COG1310 72 VGWYHSHPGGPPYPSEADRR--LSKLGPLPWLIVSV 105 (134)
T ss_pred EEEEcCCCCCCCCcCHHHHh--hccccCCCEEEEEc
Confidence 999999995 445555555 66666666566554
No 26
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=97.63 E-value=0.0012 Score=56.64 Aligned_cols=124 Identities=16% Similarity=0.164 Sum_probs=86.6
Q ss_pred EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeE-ecCCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCc
Q 023811 61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSV-LPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEV 139 (277)
Q Consensus 61 ~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~-~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~ 139 (277)
.|++..++..+|+=|+.|.+ ...|.|.|+|.. ..|+.|+|++|.|+=|+.-. +.--.|-.-.|++-+- +--+..
T Consensus 3 ~veis~~aY~kmiLH~akyp--h~aVnGLLla~~~~kg~~v~itdcVPLfH~~la--LaPmlEvAl~lId~~~-~~~Glv 77 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYP--HAAVNGLLLAPATGKGECVEITDCVPLFHSHLA--LAPMLEVALNLIDVWG-AQAGLV 77 (199)
T ss_pred ceeehhhHHHHHHHHhccCc--ccceeeEEEeccCCCCCeEEEEecchhhccccc--cccHHHHHHHHHHHHH-HhcCeE
Confidence 57889999999999999874 467999999932 45678999999999877531 1223344445555544 235899
Q ss_pred EEEeeecCCCCC-----CchhHHHHHHhhcCCCcEEEEEecCC-C--CCcceeEEEEe
Q 023811 140 IVGWFSTGLGVT-----GGSALIHEFYCREVPNPVHLTVDTGF-R--NGEGTVKAYVS 189 (277)
Q Consensus 140 iVGWY~t~~~~~-----~~~~~ih~~~~~~~~~PI~L~vD~~~-~--~~~l~ikay~~ 189 (277)
|+|.|++...+. ..-..|-+..++.+++..+|++|-.. . -..-++.+|+-
T Consensus 78 iaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~~l~~~~e~~~v~v~e~ 135 (199)
T KOG3289|consen 78 IAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNKKLVPQCERPPVIVLED 135 (199)
T ss_pred EEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEeccccccccCCCCEEEeec
Confidence 999999875432 23334556677788887777777554 2 23457888884
No 27
>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=96.70 E-value=0.01 Score=54.05 Aligned_cols=103 Identities=22% Similarity=0.298 Sum_probs=72.3
Q ss_pred CceEEEEeeeeEecC---CeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEEEeeecCCC----CCCchh
Q 023811 83 AERVIGTLLGSVLPD---GTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG----VTGGSA 155 (277)
Q Consensus 83 ~~~ViG~LLG~~~~~---~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iVGWY~t~~~----~~~~~~ 155 (277)
...+.|.|.|. ... +.-||+.-...|+..+.+.+.+..+- -.|. ---+++.|||=+|.+. ++..|+
T Consensus 55 rtQ~~GyLyG~-~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~~-----~~~~-~l~~Le~LGWIHTqp~e~~~Lss~Dv 127 (252)
T cd08056 55 RTQIAGYLYGK-SPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQL-----PQHE-YLEDLEPLGWIHTQPNELPQLSPQDV 127 (252)
T ss_pred cceEEEEEecc-CCCCCCCeEEEEEEEECCEeCCcCcEECCccC-----ccch-hhCCCEeeEEEEcCCCCccccCHHHH
Confidence 35899999998 554 56688888888888876665432110 1111 1247899999999863 567888
Q ss_pred HHHHHHhhcCC-----CcEEEEEecCCCCCcceeEEEEeeeecc
Q 023811 156 LIHEFYCREVP-----NPVHLTVDTGFRNGEGTVKAYVSVNLSL 194 (277)
Q Consensus 156 ~ih~~~~~~~~-----~PI~L~vD~~~~~~~l~ikay~~~~~~~ 194 (277)
..|..+...++ +.|.+++ +...|..++.||.+.+.++
T Consensus 128 ~tha~~~~~~~~w~~~~~V~it~--SftpGs~sl~ay~LT~~G~ 169 (252)
T cd08056 128 TTHAKILADNPSWDGEKTVILTC--SFTPGSCSLTAYKLTPEGY 169 (252)
T ss_pred HHHHHHHHhccccCCCcEEEEEE--cCCCCceEEEEEecCHHHH
Confidence 88988887766 3455544 4457789999999997764
No 28
>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=96.51 E-value=0.064 Score=43.10 Aligned_cols=98 Identities=18% Similarity=0.214 Sum_probs=62.2
Q ss_pred HhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcce-eccHHHHHHHHHHhhhcCCCCcEEEeeecC
Q 023811 69 IFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKVNPQEVIVGWFSTG 147 (277)
Q Consensus 69 lL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~-~iD~~y~~~m~~l~kkv~p~e~iVGWY~t~ 147 (277)
+-.|++|..+. .+..+.|.|+|+ . + .|++.+++|....++.. ..+.+ |. -.+.++||-||++
T Consensus 6 ~~~i~~ha~~~--~P~E~CGlL~G~-~-~---~v~~~~~~~n~~~~~~~~~f~~~----~~------~~g~~ivgi~HSH 68 (117)
T cd08072 6 LDSILEAAKSS--HPNEFAALLRGK-D-G---VITELLILPGTESGEVSAVFPLL----ML------PLDMSIVGSVHSH 68 (117)
T ss_pred HHHHHHHHhhc--CCceEEEEEEee-c-c---EEEEEEECCCCCCCCcceeechH----Hh------cCCCeEEEEEEcC
Confidence 45788888765 478999999997 3 2 58899999966543321 12221 21 2489999999999
Q ss_pred CC----CCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEee
Q 023811 148 LG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV 190 (277)
Q Consensus 148 ~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~ 190 (277)
++ ++..|. . ++.. +.-.+|++.... +.-.++||...
T Consensus 69 P~~~~~PS~~D~--~--~~~~-~~~~~lIvs~~~--~~~~~~a~~~~ 108 (117)
T cd08072 69 PSGSPRPSDADL--S--FFSK-TGLVHIIVGYPY--DEDDWRAYDSD 108 (117)
T ss_pred CCCCCCCCHHHH--H--hhhc-CCCEEEEEECcC--CCCCEEEEecC
Confidence 85 334442 2 2222 334778776433 22468898875
No 29
>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family. This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize.
Probab=96.50 E-value=0.058 Score=44.46 Aligned_cols=80 Identities=16% Similarity=0.160 Sum_probs=54.2
Q ss_pred hHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCC-Ccc--eeccHHHHHHHHH-HhhhcCCCCcEEEe
Q 023811 68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEF-SDQ--VALDIEYHHTMLK-SHLKVNPQEVIVGW 143 (277)
Q Consensus 68 VlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~-~~~--~~iD~~y~~~m~~-l~kkv~p~e~iVGW 143 (277)
++++++..|......+...-|.|+|. ..+..+.|+..- .|..++ ... ..-+.+.+++.++ .+++.+-....||=
T Consensus 1 ~v~~~~~~~~Q~~~~~~EtGGiLiG~-~~~~~~ii~~~t-~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylGe 78 (131)
T TIGR02256 1 VVVAMLKSYRQWHDLSTETGGVLIGE-RRGAHAVITKIS-EPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGE 78 (131)
T ss_pred CHHHHHHHHHhCcCCCCccceEEEEE-EcCCcEEEEEEE-cCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEEe
Confidence 46777778866655678999999998 556677777744 443332 111 2345666666655 55556566999999
Q ss_pred eecCCC
Q 023811 144 FSTGLG 149 (277)
Q Consensus 144 Y~t~~~ 149 (277)
+||+|.
T Consensus 79 WHtHP~ 84 (131)
T TIGR02256 79 WHTHPE 84 (131)
T ss_pred cCcCCC
Confidence 999985
No 30
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=96.07 E-value=0.055 Score=41.70 Aligned_cols=93 Identities=14% Similarity=0.028 Sum_probs=50.9
Q ss_pred hHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEEEeeecC
Q 023811 68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTG 147 (277)
Q Consensus 68 VlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iVGWY~t~ 147 (277)
++-.|+.|..+. .+....|.|+|. ..+..+.++........+ +...... +....+..+||+|||+
T Consensus 4 ~~~~i~~~~~~~--~p~E~~G~L~g~-~~~~~~~~~~~~~~~p~~----------~~~~~~~--~~~~~~~~~vg~~HSH 68 (104)
T PF14464_consen 4 VLEQIIAHARAA--YPNEACGLLLGR-RDDQRFIVVPNVNPDPRD----------SFRRERF--EARERGLEIVGIWHSH 68 (104)
T ss_dssp HHHHHHHHHHHH--TTS-EEEEEEEE-EECCEEEEEEEEE--HHC----------HHHHHH---HHHHHT-EEEEEEEEE
T ss_pred HHHHHHHHHhhC--CCCeEEEEEEEE-ecCCEEEEEeCCCCCcHH----------HHHHHhh--hhhcccceeeEEEEcC
Confidence 455678888775 478999999998 566666677666511111 1111110 4455799999999999
Q ss_pred CCCCCchhHHHHHHhhcCCCcEEEEEec
Q 023811 148 LGVTGGSALIHEFYCREVPNPVHLTVDT 175 (277)
Q Consensus 148 ~~~~~~~~~ih~~~~~~~~~PI~L~vD~ 175 (277)
++-...=+............+++|++..
T Consensus 69 P~~~a~pS~~D~~~~~~~~~~~~iI~~~ 96 (104)
T PF14464_consen 69 PSGPAFPSSTDIRSMRDLAPPSYIIVGN 96 (104)
T ss_dssp SSSSSS--HHHHHTHCCS-SCEEEEEEE
T ss_pred CCCCCCCCHHHHHhhhccCCeEEEEEeC
Confidence 8643222222222233222556666653
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=88.72 E-value=2.6 Score=33.29 Aligned_cols=64 Identities=8% Similarity=-0.046 Sum_probs=40.2
Q ss_pred hHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCC--cceeccH-HHHHHHHHHhhhcCCCCcEEEeeec
Q 023811 70 FNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS--DQVALDI-EYHHTMLKSHLKVNPQEVIVGWFST 146 (277)
Q Consensus 70 L~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~--~~~~iD~-~y~~~m~~l~kkv~p~e~iVGWY~t 146 (277)
-.|++|..+. .+....|.|+|. . + ++..++++....+ ....+|. ++++-+ + ...+||-|||
T Consensus 4 ~~i~~ha~~~--~P~E~CGll~g~-~--~---~~~~~p~~N~~~~p~~~F~idp~e~~~a~----~----~~~ivgi~HS 67 (108)
T cd08073 4 DAILAHAKAE--YPREACGLVVRK-G--R---KLRYIPCRNIAADPEEHFEISPEDYAAAE----D----EGEIVAVVHS 67 (108)
T ss_pred HHHHHHHhHC--CCCcceEEEEec-C--C---ceEEEECccCCCCccceEEeCHHHHHHHh----c----CCCEEEEEEc
Confidence 4678888665 478899999996 3 2 3344666533222 3356775 454432 1 2389999999
Q ss_pred CCC
Q 023811 147 GLG 149 (277)
Q Consensus 147 ~~~ 149 (277)
+++
T Consensus 68 HP~ 70 (108)
T cd08073 68 HPD 70 (108)
T ss_pred CCC
Confidence 974
No 32
>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=88.03 E-value=5.7 Score=36.72 Aligned_cols=109 Identities=17% Similarity=0.207 Sum_probs=68.7
Q ss_pred CceEEEEeeeeEecC------CeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEEEeeecCCC-------
Q 023811 83 AERVIGTLLGSVLPD------GTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG------- 149 (277)
Q Consensus 83 ~~~ViG~LLG~~~~~------~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iVGWY~t~~~------- 149 (277)
...-+|-|.|+..+. .++.|.--|+=|+..+.+.+.+..+-.++..+... ..-+...|||=-|...
T Consensus 33 ~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~iA-~~lGL~~VG~IfT~l~~~~~d~~ 111 (274)
T cd08061 33 GQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAIA-AALGLERVGWIFTDLPREDKDGY 111 (274)
T ss_pred cceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhHHHHHH-HHcCCeEEEEEEecCCCCCCCce
Confidence 356799999995443 37889889999988777766443333323233333 2348999999888752
Q ss_pred -CCCchhHHHHHHhh-----cCCCc-EEEEEecCCCCCcceeEEEEeeeec
Q 023811 150 -VTGGSALIHEFYCR-----EVPNP-VHLTVDTGFRNGEGTVKAYVSVNLS 193 (277)
Q Consensus 150 -~~~~~~~ih~~~~~-----~~~~P-I~L~vD~~~~~~~l~ikay~~~~~~ 193 (277)
++...+.....++. ...+. +-+++.+.. ++...+.||..++..
T Consensus 112 ~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~-~g~i~~~ayQvSdq~ 161 (274)
T cd08061 112 FLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDK-DGQIHFEAYQVSDQA 161 (274)
T ss_pred eECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCC-CCceeeeeeeecHHH
Confidence 22333333344442 23333 557777654 478999999998654
No 33
>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=86.62 E-value=7.1 Score=36.70 Aligned_cols=105 Identities=18% Similarity=0.167 Sum_probs=62.5
Q ss_pred EEEeeeeEecCC------eEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEEEeeecCCC-----------
Q 023811 87 IGTLLGSVLPDG------TVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG----------- 149 (277)
Q Consensus 87 iG~LLG~~~~~~------~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iVGWY~t~~~----------- 149 (277)
+|-|.|+..+.. ++.|.--|+=|+..+.+.+.+..+-.++..+...+. -+...|||=-|...
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~-lGL~rVG~IfTdl~~~~~~~g~v~~ 80 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASA-LGLERVGWIFTDLTDDGSGDGTVKC 80 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHH-CCCEEEEEEEecCcccccCCCceee
Confidence 799999844434 688999999999887776655322233333333322 28999999876532
Q ss_pred --------CCCchhHHHHHHhhcC------------CCc-EEEEEecCCCCCcceeEEEEeeeec
Q 023811 150 --------VTGGSALIHEFYCREV------------PNP-VHLTVDTGFRNGEGTVKAYVSVNLS 193 (277)
Q Consensus 150 --------~~~~~~~ih~~~~~~~------------~~P-I~L~vD~~~~~~~l~ikay~~~~~~ 193 (277)
++...+..=..++... .+. |-+++.+. .++.+.+.||..++..
T Consensus 81 ~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~-~~g~i~~~ayQvS~q~ 144 (306)
T PF05021_consen 81 KRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGD-EEGEIHFEAYQVSNQC 144 (306)
T ss_pred ccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCC-CCCceeeEEeeehHHH
Confidence 1222222212222222 222 55666654 5678999999998653
No 34
>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=81.80 E-value=6.8 Score=29.97 Aligned_cols=63 Identities=14% Similarity=0.098 Sum_probs=39.7
Q ss_pred HHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEEEeeecCCC
Q 023811 71 NICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG 149 (277)
Q Consensus 71 ~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iVGWY~t~~~ 149 (277)
.|.+|+.+. .+....|.|+|. . ++ .+.+..++|.... ..+..+ ......-+..+||-|+++++
T Consensus 5 ~i~~~~~~~--~p~E~~gll~~~-~-~~--~~~~~~~~~~~~~----~~~~~~------~~~a~~~~~~~v~i~HsHP~ 67 (101)
T cd08059 5 TILVHAKDA--HPDEFCGFLSGS-K-DN--VMDELIFLPFVSG----SVSAVI------DLAALEIGMKVVGLVHSHPS 67 (101)
T ss_pred HHHHHHHhc--CChhhheeeecC-C-CC--eEEEEEeCCCcCC----ccChHH------HHHHhhCCCcEEEEEecCcC
Confidence 455666543 367899999996 4 33 5778788875431 233333 22223357789999999974
No 35
>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=70.71 E-value=2.2 Score=30.83 Aligned_cols=12 Identities=50% Similarity=1.063 Sum_probs=7.8
Q ss_pred CCcEEEeeecCC
Q 023811 137 QEVIVGWFSTGL 148 (277)
Q Consensus 137 ~e~iVGWY~t~~ 148 (277)
+-.|||||+|.-
T Consensus 39 qg~vvgwy~t~l 50 (78)
T PF06442_consen 39 QGQVVGWYCTKL 50 (78)
T ss_dssp EEEEEEEE--SS
T ss_pred cceEeEEEeccc
Confidence 457999999864
No 36
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=64.32 E-value=14 Score=35.47 Aligned_cols=96 Identities=17% Similarity=0.234 Sum_probs=59.6
Q ss_pred CceEEEEeeeeEecCCeEEEEeeeecccCC-CCcce-eccHHHHHHHHHHhh-hcCCCCcEEEeeecCCCC--CCchhHH
Q 023811 83 AERVIGTLLGSVLPDGTVDIRNSYVVPHNE-FSDQV-ALDIEYHHTMLKSHL-KVNPQEVIVGWFSTGLGV--TGGSALI 157 (277)
Q Consensus 83 ~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e-~~~~~-~iD~~y~~~m~~l~k-kv~p~e~iVGWY~t~~~~--~~~~~~i 157 (277)
+-.-.|+|-|. -..|..-||+-. +|..+ +.|.. +.|.+- +|. +---++--+||-+|++.- +-+++.+
T Consensus 275 nlETCGiL~g~-L~~n~f~IThli-iPkQeatsd~C~t~neee------lF~vQdq~~L~tlGWIHTHPTQt~FmSSVDl 346 (424)
T KOG2880|consen 275 NLETCGILAGK-LERNEFYITHLI-IPKQEATSDSCNTMNEEE------LFEVQDQHELLTLGWIHTHPTQTCFMSSVDL 346 (424)
T ss_pred cchHHHHhhhH-hhcCcEEEEEEE-eecccCCCccccccCHHH------HheecccccceeeeeeecCCccchhheeccc
Confidence 34678999998 677888888765 45443 33311 222111 111 112367789999999853 3455566
Q ss_pred HHHHhhc--CCCcEEEEEecCCCCCcceeEEEEee
Q 023811 158 HEFYCRE--VPNPVHLTVDTGFRNGEGTVKAYVSV 190 (277)
Q Consensus 158 h~~~~~~--~~~PI~L~vD~~~~~~~l~ikay~~~ 190 (277)
|.-++++ .|.+|++++-|..++ -.+|++.
T Consensus 347 HTHcSYQiMlPEAiAIV~aPk~~~----tGiFrLt 377 (424)
T KOG2880|consen 347 HTHCSYQIMLPEAIAIVCAPKSKT----TGIFRLT 377 (424)
T ss_pred cccceeeeecchheeEEeccccCC----cceEEec
Confidence 7767776 577799999987532 3356666
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=56.55 E-value=49 Score=29.06 Aligned_cols=71 Identities=10% Similarity=0.018 Sum_probs=47.0
Q ss_pred EEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcc-eeccHHHHHHHHHHhhhcCCCCcEE
Q 023811 63 KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ-VALDIEYHHTMLKSHLKVNPQEVIV 141 (277)
Q Consensus 63 ~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~-~~iD~~y~~~m~~l~kkv~p~e~iV 141 (277)
+|..-.+=.|+.|+.+. -+..+.|.|.|. .+++.. ..+++...+.+.. ...|.. |. ..++.+|
T Consensus 74 ~Ip~~l~~~ii~hAr~~--~P~EacG~Iag~-~~~~~~---r~~p~~N~~~Sp~~~~~d~~----~~------~~ge~lV 137 (192)
T TIGR03735 74 PIPASLLEEFAEAARAA--LPNEVAAWIVWN-SETGSL---RLAALESIEASPGHIDYRRP----RL------DDGEHLV 137 (192)
T ss_pred CCCHHHHHHHHHHHHhc--CCcceEEEEEEc-CCCCEE---EEEeccccccCCceEEEcch----HH------hCCCeEE
Confidence 34455667889998665 378999999996 445443 4477765543322 234433 22 6799999
Q ss_pred EeeecCCC
Q 023811 142 GWFSTGLG 149 (277)
Q Consensus 142 GWY~t~~~ 149 (277)
+-||+++.
T Consensus 138 ~iyHSH~~ 145 (192)
T TIGR03735 138 VDLHSHGT 145 (192)
T ss_pred EEEcCCCC
Confidence 99999875
No 38
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=53.65 E-value=84 Score=30.05 Aligned_cols=101 Identities=15% Similarity=0.163 Sum_probs=62.4
Q ss_pred EEeeeeEe-cCCeEEEEeeeecccCCCCcc-----------eeccHHHHHHHHHHhhhcCC-CCcEEEeeecCCCC-CCc
Q 023811 88 GTLLGSVL-PDGTVDIRNSYVVPHNEFSDQ-----------VALDIEYHHTMLKSHLKVNP-QEVIVGWFSTGLGV-TGG 153 (277)
Q Consensus 88 G~LLG~~~-~~~~VeVtnsF~vp~~e~~~~-----------~~iD~~y~~~m~~l~kkv~p-~e~iVGWY~t~~~~-~~~ 153 (277)
|.|+|. . .++.--|.+..+-|.++++++ -.+|.++..+-..+-.+.-| +..|||-|..+++. ...
T Consensus 1 GLlIGq-~~s~~kd~Vv~l~~tP~~d~~~~~~~~~~~~~~~~~id~~WVaeHA~qVsRMLPGGi~VlGifvv~~~~~~~~ 79 (362)
T PF14778_consen 1 GLLIGQ-SSSSQKDYVVHLARTPPEDTDDEESDVRTSDSSIKDIDEEWVAEHARQVSRMLPGGISVLGIFVVAPDDAFKD 79 (362)
T ss_pred CeEecc-ccCCCcceEEEecCCCCccccccccccccccccccccCHHHHHHHHHHHHhhCCCCcEEEEEEEEcCHHHhcc
Confidence 789998 5 566567889999998776544 14788888777766666665 57899999977642 221
Q ss_pred h---hHHHHHHh--h-----cC---CCcEEEEEecCCCCCcceeEEEEee
Q 023811 154 S---ALIHEFYC--R-----EV---PNPVHLTVDTGFRNGEGTVKAYVSV 190 (277)
Q Consensus 154 ~---~~ih~~~~--~-----~~---~~PI~L~vD~~~~~~~l~ikay~~~ 190 (277)
. ..+...+. . .. ..-+.|.++.+.. .++.-|.|...
T Consensus 80 ~~~~~~l~~l~~~~~~~~~~~~~~~~e~~~l~i~~st~-kk~~Ck~~~~~ 128 (362)
T PF14778_consen 80 SSTLNKLKKLLFSSNSLWSVYNDDVSERLLLHICSSTS-KKLTCKSYDVA 128 (362)
T ss_pred chHHHHHHHHHhhhcccccccCCCcccceEEEEEcccC-ceEEEEEEEec
Confidence 1 12222222 1 11 1236777776543 35666666553
No 39
>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=49.43 E-value=23 Score=35.12 Aligned_cols=77 Identities=17% Similarity=0.193 Sum_probs=50.6
Q ss_pred HhHHHHHHhhcCCC-CceEEEEeeeeEecCCeE------EEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEE
Q 023811 69 IFNICDCYVRRPDQ-AERVIGTLLGSVLPDGTV------DIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIV 141 (277)
Q Consensus 69 lL~I~dH~~R~~~~-~~~ViG~LLG~~~~~~~V------eVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iV 141 (277)
=-+|.+||.+.+.. ...-+|-|.|..++.+.| +|---|+=|+...++.+.+.++=-....+.-. ..-+...|
T Consensus 181 ~~~~v~~Fl~~wr~sg~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~~~~dgl~l~~~~e~~~vD~~a-~~lGLrRV 259 (510)
T KOG2834|consen 181 NAELVNHFLNEWRASGVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQHGEEDGLELLEDDEAKRVDAIA-EGLGLRRV 259 (510)
T ss_pred chHHHHHHHHHHHHhhhhhcceEEEeecccccccccceeeEEEEecCCccCCcCCeEEeccchhhhHHHHH-HhcCceee
Confidence 34677888877532 345689999997677778 89999999988877776554222222222222 22478999
Q ss_pred Eeeec
Q 023811 142 GWFST 146 (277)
Q Consensus 142 GWY~t 146 (277)
||--|
T Consensus 260 G~IFT 264 (510)
T KOG2834|consen 260 GWIFT 264 (510)
T ss_pred EEEEe
Confidence 99754
No 40
>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=40.20 E-value=70 Score=35.94 Aligned_cols=117 Identities=20% Similarity=0.242 Sum_probs=71.7
Q ss_pred hHHHHHHhhcCCCCceEEEEeeeeEecC--CeE-EEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEEEeeec
Q 023811 70 FNICDCYVRRPDQAERVIGTLLGSVLPD--GTV-DIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFST 146 (277)
Q Consensus 70 L~I~dH~~R~~~~~~~ViG~LLG~~~~~--~~V-eVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iVGWY~t 146 (277)
.||++-+.+...-...+.|.+.|. ... .+| ||..---+|+-..-..+.+. .++- -..+--+.+.+||-+|
T Consensus 2101 kNllkkFi~isD~r~qiag~~yG~-s~~d~pqvkeIr~ivmvPQ~gs~~~v~lp-~~lP-----~~~~l~d~e~Lgw~hT 2173 (2321)
T KOG1795|consen 2101 KNLLKKFITISDLRTQIAGYLYGV-SPPDNPQVKEIRCIVMVPQWGSHQGVHLP-SFLP-----IHGVLEDLEPLGWIHT 2173 (2321)
T ss_pred HHHHhhheeecchhhhhheeeecc-CCCCCCccceEEEEEeccccccccccccC-ccCC-----cchhccCCcccchhhc
Confidence 456666766542235789999996 432 344 55544445654432222110 0000 1223468889999999
Q ss_pred CCC----CCCchhHHHHHHhhcCC-CcEEEEEecCCCCCcceeEEEEeeeeccC
Q 023811 147 GLG----VTGGSALIHEFYCREVP-NPVHLTVDTGFRNGEGTVKAYVSVNLSLG 195 (277)
Q Consensus 147 ~~~----~~~~~~~ih~~~~~~~~-~PI~L~vD~~~~~~~l~ikay~~~~~~~~ 195 (277)
.++ +.+.|+.+|.......+ ..|.+.+ +..-|..++.||..++++.+
T Consensus 2174 q~~el~~lsp~dV~th~ki~~~~k~k~i~~t~--~~tpgs~sl~ay~lt~~G~e 2225 (2321)
T KOG1795|consen 2174 QPNELPQLSPQDVTTHAKILVDNKEKCIIITC--SFTPGSCSLTAYKLTPSGYE 2225 (2321)
T ss_pred CccccccCCHHHhhhhhhhhhcCccceEEEEe--eccCCcceeeeeccCccccc
Confidence 864 57788899988766543 4455554 35567899999999988754
No 41
>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=29.76 E-value=78 Score=21.48 Aligned_cols=37 Identities=14% Similarity=0.110 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeee
Q 023811 237 GMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQ 273 (277)
Q Consensus 237 ~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~ 273 (277)
.++.-+..-..++..+.+|++++.---....|++|.+
T Consensus 11 ~~e~~~~~k~~~v~eLe~YiD~LL~rVmE~~P~ILe~ 47 (48)
T PF09457_consen 11 KQEEENARKDSRVRELEDYIDNLLVRVMEQTPSILEV 47 (48)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-GGGGBS
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcchhcC
Confidence 4444555556667779999999988777777777754
No 42
>PF07620 SLEI_Leptospira: SLEI; InterPro: IPR011512 This entry represents a highly conserved sequence motif found at the C-terminal of some hypothetical proteins from Leptospira interrogans.
Probab=21.64 E-value=69 Score=16.82 Aligned_cols=12 Identities=33% Similarity=0.540 Sum_probs=9.0
Q ss_pred EecCCeEEEEee
Q 023811 94 VLPDGTVDIRNS 105 (277)
Q Consensus 94 ~~~~~~VeVtns 105 (277)
+..++++||.|+
T Consensus 4 ~~rdNsLeIsn~ 15 (16)
T PF07620_consen 4 WLRDNSLEISNQ 15 (16)
T ss_pred cccCCeEEEeec
Confidence 346888999875
No 43
>COG4387 Mu-like prophage protein gp36 [Function unknown]
Probab=20.73 E-value=1.3e+02 Score=24.62 Aligned_cols=26 Identities=4% Similarity=0.190 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCccc
Q 023811 241 LMERLLTLINDIYKYVDDTVVSMIIF 266 (277)
Q Consensus 241 sl~~L~~~l~~i~~Yl~~V~~G~~~~ 266 (277)
+..+...+-+..+++|++|.+|+++.
T Consensus 82 ~Tdq~r~rYe~av~~L~~va~G~V~l 107 (139)
T COG4387 82 ATDQARQRYEDAVRFLEKVASGAVSL 107 (139)
T ss_pred hhHHHHHHHHHHHHHHHHHHcCCCcc
Confidence 77788899999999999999999874
Done!