Query 026931
Match_columns 230
No_of_seqs 134 out of 634
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 02:37:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026931.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026931hhsearch_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 4.7E-53 1E-57 367.8 15.9 186 41-227 2-187 (288)
2 PLN03246 26S proteasome regula 100.0 1.7E-48 3.7E-53 351.9 20.5 171 56-227 2-178 (303)
3 cd08062 MPN_RPN7_8 Mpr1p, Pad1 100.0 1.3E-47 2.9E-52 343.0 20.0 165 61-226 2-171 (280)
4 cd08064 MPN_eIF3f Mpr1p, Pad1p 100.0 1.6E-47 3.5E-52 339.9 19.5 165 62-227 1-167 (265)
5 cd08063 MPN_CSN6 Mpr1p, Pad1p 100.0 1.9E-46 4.2E-51 336.6 16.7 166 60-227 1-174 (288)
6 KOG1556 26S proteasome regulat 100.0 3E-43 6.4E-48 304.4 16.1 171 56-227 5-180 (309)
7 cd08057 MPN_euk_non_mb Mpr1p, 100.0 1.9E-41 4.1E-46 279.2 15.5 150 62-219 1-157 (157)
8 KOG3050 COP9 signalosome, subu 100.0 1E-40 2.2E-45 288.2 10.3 172 52-225 1-177 (299)
9 cd08065 MPN_eIF3h Mpr1p, Pad1p 100.0 1.1E-33 2.5E-38 251.4 16.7 160 61-223 2-183 (266)
10 cd08069 MPN_RPN11_CSN5 Mov34/M 100.0 9.2E-30 2E-34 226.7 20.0 168 56-226 6-202 (268)
11 PF01398 JAB: JAB1/Mov34/MPN/P 99.9 1.4E-27 3E-32 185.9 10.9 107 58-167 2-114 (114)
12 KOG1560 Translation initiation 99.9 6.6E-25 1.4E-29 193.2 8.9 166 55-229 8-200 (339)
13 smart00232 JAB_MPN JAB/MPN dom 99.9 3.9E-23 8.4E-28 163.3 14.5 128 61-191 1-134 (135)
14 KOG1554 COP9 signalosome, subu 99.7 2.4E-17 5.1E-22 146.0 10.6 134 57-194 50-193 (347)
15 cd07767 MPN Mpr1p, Pad1p N-ter 99.7 8E-17 1.7E-21 124.3 11.7 111 70-187 2-116 (116)
16 cd08067 MPN_2A_DUB Mov34/MPN/P 99.7 4.2E-15 9E-20 126.4 15.1 129 59-192 4-147 (187)
17 cd08058 MPN_euk_mb Mpr1p, Pad1 99.6 2.1E-15 4.6E-20 118.7 10.2 110 68-190 2-119 (119)
18 cd08068 MPN_BRCC36 Mov34/MPN/P 99.4 4.1E-11 9E-16 105.6 17.2 148 60-213 2-170 (244)
19 cd08066 MPN_AMSH_like Mov34/MP 99.1 2E-09 4.4E-14 90.5 14.5 124 61-194 3-132 (173)
20 KOG1555 26S proteasome regulat 99.1 2.3E-10 5E-15 103.6 8.0 135 56-192 27-174 (316)
21 cd08070 MPN_like Mpr1p, Pad1p 98.5 5.7E-06 1.2E-10 65.7 13.6 113 68-190 3-119 (128)
22 cd08060 MPN_UPF0172 Mov34/MPN/ 98.5 2E-06 4.2E-11 73.1 11.2 106 65-178 2-115 (182)
23 PF03665 UPF0172: Uncharacteri 98.4 4.3E-06 9.4E-11 71.7 11.5 122 61-188 3-134 (196)
24 COG1310 Predicted metal-depend 98.1 2.6E-05 5.5E-10 62.5 10.3 100 63-175 3-106 (134)
25 KOG3289 Uncharacterized conser 97.7 0.0016 3.5E-08 55.1 13.5 123 61-189 3-135 (199)
26 cd08056 MPN_PRP8 Mpr1p, Pad1p 97.4 0.00084 1.8E-08 59.8 9.2 103 83-194 55-169 (252)
27 TIGR02256 ICE_VC0181 integrati 96.5 0.054 1.2E-06 43.8 11.2 80 68-149 1-84 (131)
28 cd08072 MPN_archaeal Mov34/MPN 96.5 0.069 1.5E-06 42.0 11.5 99 68-190 5-108 (117)
29 PF14464 Prok-JAB: Prokaryotic 96.0 0.056 1.2E-06 40.6 8.3 69 68-151 4-72 (104)
30 cd08061 MPN_NPL4 Mov34/MPN/PAD 92.5 1.4 2.9E-05 39.9 10.1 109 84-194 34-162 (274)
31 PF05021 NPL4: NPL4 family; I 90.4 2.4 5.2E-05 38.9 9.6 106 87-194 2-145 (306)
32 cd08073 MPN_NLPC_P60 Mpr1p, Pa 89.4 2.1 4.6E-05 33.1 7.3 65 69-149 3-70 (108)
33 cd08059 MPN_prok_mb Mpr1p, Pad 83.0 5.1 0.00011 29.9 6.3 63 71-149 5-67 (101)
34 KOG2880 SMAD6 interacting prot 81.8 2.4 5.3E-05 39.8 4.8 96 83-190 275-377 (424)
35 PF06442 DHFR_2: R67 dihydrofo 71.5 2.1 4.6E-05 30.6 1.1 10 138-147 40-49 (78)
36 TIGR03735 PRTRC_A PRTRC system 65.3 35 0.00077 29.3 7.5 71 63-149 74-145 (192)
37 KOG1795 U5 snRNP spliceosome s 57.4 18 0.00039 39.5 5.0 117 70-195 2101-2225(2321)
38 KOG2834 Nuclear pore complex, 44.7 29 0.00063 33.8 4.0 76 69-146 181-264 (510)
39 PF14778 ODR4-like: Olfactory 42.3 1.8E+02 0.0039 27.1 8.9 61 88-149 1-74 (362)
40 COG5178 PRP8 U5 snRNP spliceos 34.5 96 0.0021 34.1 6.1 126 61-194 2131-2264(2365)
No 1
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.7e-53 Score=367.85 Aligned_cols=186 Identities=46% Similarity=0.775 Sum_probs=177.2
Q ss_pred ecccccceeeccCCCCCCCcEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeec
Q 026931 41 AASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALD 120 (230)
Q Consensus 41 ~~~~~~~~~~~~~~~~~~~~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD 120 (230)
+.....+.+.+++++.++..+|.|||+|+++|+|||.||..++.||||+|||+ .++|.|||||||++||+|.+|++.+|
T Consensus 2 ~~~~~~v~~~~~~~~~ss~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~-~~~g~ieitNCFaVPhnEssdqvevd 80 (288)
T KOG2975|consen 2 QTPAPHVPGPALPSPFSSNLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGT-VDKGSVEVTNCFAVPHNESSDQVEVD 80 (288)
T ss_pred CCCcCcCCCcCCCCCCCCCceEEEcceEEeEeehhhhcCCccchhhhhheeec-ccCCeEEEEEeeeccCccccccceee
Confidence 34455666777888899999999999999999999999999999999999997 78999999999999999999999999
Q ss_pred HHHHHHHHHhhcccCCCCcEEEEeecCCCCCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeEeeecCCcccc
Q 026931 121 IEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLA 200 (230)
Q Consensus 121 ~~y~~~m~~l~kkV~p~e~iVGWY~tg~~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~~~~~~~~~~~ 200 (230)
++|+++|+++|+|+||+|.+||||+||+++++++..||++|.+++++||||++|++.+++.+++|||.+++.+++|++.+
T Consensus 81 m~y~~~M~~l~~k~npnE~vvGWyaTg~dvt~~sslihdyYare~~~pvhLtVDT~~~n~rm~ikaYvss~~Gvpg~~~~ 160 (288)
T KOG2975|consen 81 MEYAKNMYELHKKVNPNELVVGWYATGHDVTEHSSLIHDYYAREAPNPVHLTVDTSLQNGRMSIKAYVSSLMGVPGRTMG 160 (288)
T ss_pred HHHHHHHHHHhcccCCCceeEEEEecCCCcccchhHHHHHhhccCCCCeEEEEeccccCCccceeEEEEeccCCCCcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998888
Q ss_pred ccEEEeceEEecCchHHHHHHHHHHHh
Q 026931 201 AQFQEIPLDLRMIEAERVGCMYMLVIL 227 (230)
Q Consensus 201 ~~F~~lp~~I~~~eaErI~v~~i~k~~ 227 (230)
.+|.|+|++|.++|+||+|++.|.|..
T Consensus 161 ~mF~plpvel~~~~~ervgl~li~kt~ 187 (288)
T KOG2975|consen 161 VMFTPLPVELAYYDAERVGLDLIEKTS 187 (288)
T ss_pred eeeeeeeeEEeecchhhhHHHHHHHhc
Confidence 999999999999999999999999876
No 2
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=100.00 E-value=1.7e-48 Score=351.89 Aligned_cols=171 Identities=33% Similarity=0.497 Sum_probs=157.2
Q ss_pred CCCCcEEEEehhhHhhHhhhhhhccCC-CceEEEEEeeeEeeCCeEEEEEeeeecccCCCcc---eeecHHHHHHHHHhh
Q 026931 56 ATSNVTAKVHPLVIFNICDCYVRRPDQ-AERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSH 131 (230)
Q Consensus 56 ~~~~~~V~IhPlVlL~I~DH~~R~~~~-~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~---~~iD~~y~~~m~~l~ 131 (230)
+++..+|.|||+|||+|+|||+|+..+ +.||+|+|||+ +.|+.|||+|||++|+++++++ +++|.+|+++|+++|
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 467889999999999999999998765 68999999995 8899999999999999876543 789999999999999
Q ss_pred cccCCCCcEEEEeecCCCCCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeEeeecCCcc--ccccEEEeceE
Q 026931 132 LKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQ--LAAQFQEIPLD 209 (230)
Q Consensus 132 kkV~p~e~iVGWY~tg~~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~~~~~~~~~--~~~~F~~lp~~ 209 (230)
|+|||++.+||||+||++++++|+.||++|++++++||||++|+...+++||++||++...+..++. .+..|.++|++
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 9999999999999999999999999999999999999999999999888999999999988776543 56789999999
Q ss_pred EecCchHHHHHHHHHHHh
Q 026931 210 LRMIEAERVGCMYMLVIL 227 (230)
Q Consensus 210 I~~~eaErI~v~~i~k~~ 227 (230)
|+++|||||||+|+++..
T Consensus 161 i~~~EaE~Igve~l~r~~ 178 (303)
T PLN03246 161 IGAHEAEEIGVEHLLRDV 178 (303)
T ss_pred eeecCHHHHHHHHHHhcc
Confidence 999999999999999853
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=1.3e-47 Score=343.03 Aligned_cols=165 Identities=35% Similarity=0.535 Sum_probs=153.9
Q ss_pred EEEEehhhHhhHhhhhhhccCC-CceEEEEEeeeEeeCCeEEEEEeeeecccCCCcc---eeecHHHHHHHHHhhcccCC
Q 026931 61 TAKVHPLVIFNICDCYVRRPDQ-AERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSHLKVNP 136 (230)
Q Consensus 61 ~V~IhPlVlL~I~DH~~R~~~~-~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~---~~iD~~y~~~m~~l~kkV~p 136 (230)
+|+|||+|||+|+|||+|+..+ +.+|+|+|||+ +.|+++||+|||++|+++++++ +++|.+|+++|+++||+|||
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 7999999999999999998654 78999999995 8899999999999999887654 57999999999999999999
Q ss_pred CCcEEEEeecCCCCCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeEeeecCCcc-ccccEEEeceEEecCch
Q 026931 137 QEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQ-LAAQFQEIPLDLRMIEA 215 (230)
Q Consensus 137 ~e~iVGWY~tg~~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~~~~~~~~~-~~~~F~~lp~~I~~~ea 215 (230)
++.+||||+||++++++|+.+|++|++++++||+|++||..+++++|++||++.+....+++ .+..|.++|++|+++||
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 99999999999999999999999999999999999999999888999999999987775554 78899999999999999
Q ss_pred HHHHHHHHHHH
Q 026931 216 ERVGCMYMLVI 226 (230)
Q Consensus 216 ErI~v~~i~k~ 226 (230)
|||||+|+++.
T Consensus 161 E~igve~l~r~ 171 (280)
T cd08062 161 EEVGVEHLLRD 171 (280)
T ss_pred HHHHHHHHHhh
Confidence 99999999984
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=1.6e-47 Score=339.92 Aligned_cols=165 Identities=53% Similarity=0.872 Sum_probs=156.4
Q ss_pred EEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEE
Q 026931 62 AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIV 141 (230)
Q Consensus 62 V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iV 141 (230)
|+|||+|||+|+|||+|++.++.+|+|+|||+ +.|+++||+|||++|++++++++.+|.+|+++|+++||+|||++.+|
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 68999999999999999987889999999996 88999999999999999988889999999999999999999999999
Q ss_pred EEeecCCCCCcChHHHHHHHhhhCC--CcEEEEEeccCCCCceeEEEEEeEeeecCCccccccEEEeceEEecCchHHHH
Q 026931 142 GWFSTGLGVTGGSALIHEFYCREVP--NPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219 (230)
Q Consensus 142 GWY~tg~~~~~~~~~ih~~~~~~~~--~pI~L~vDp~~~~~~l~ikAY~~~~~~~~~~~~~~~F~~lp~~I~~~eaErI~ 219 (230)
|||+||+.++.++..||++|++.++ +||+|++||..+++++|++||++.+.++.+++.+.+|.++|++|.++|+||||
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 99999999998888999999999988887777889999999999999999999
Q ss_pred HHHHHHHh
Q 026931 220 CMYMLVIL 227 (230)
Q Consensus 220 v~~i~k~~ 227 (230)
|+|+++..
T Consensus 160 v~~l~~~~ 167 (265)
T cd08064 160 LDLLAKTL 167 (265)
T ss_pred HHHHHhhc
Confidence 99999853
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=1.9e-46 Score=336.58 Aligned_cols=166 Identities=31% Similarity=0.434 Sum_probs=153.6
Q ss_pred cEEEEehhhHhhHhhhhhhccCC----CceEEEEEeeeEeeCCeEEEEEeeeecccCCC-cceeecHHHHHHHHHhhccc
Q 026931 60 VTAKVHPLVIFNICDCYVRRPDQ----AERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS-DQVALDIEYHHTMLKSHLKV 134 (230)
Q Consensus 60 ~~V~IhPlVlL~I~DH~~R~~~~----~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e-~~~~iD~~y~~~m~~l~kkV 134 (230)
.+|.|||+|||+|+|||+|+..+ +.+|+|+|||+ ++|++|||+|||++|+.+++ +++.+|.+|+++|+++||+|
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 37999999999999999998653 58999999995 99999999999999999877 77899999999999999999
Q ss_pred CCCCcEEEEeecCCC-CCcChHHHHHHHhhhCCCcEEEEEeccC--CCCceeEEEEEeEeeecCCccccccEEEeceEEe
Q 026931 135 NPQEVIVGWFSTGLG-VTGGSALIHEFYCREVPNPVHLTVDTGF--RNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLR 211 (230)
Q Consensus 135 ~p~e~iVGWY~tg~~-~~~~~~~ih~~~~~~~~~pI~L~vDp~~--~~~~l~ikAY~~~~~~~~~~~~~~~F~~lp~~I~ 211 (230)
||++.+||||+||+. ++.+++.||++|++.+++||+|++||.. +.+++|++||++...+.++ .....|+++|++|+
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 999999999999999 9999999999999999999999999998 5688999999999877765 56788999999999
Q ss_pred cCchHHHHHHHHHHHh
Q 026931 212 MIEAERVGCMYMLVIL 227 (230)
Q Consensus 212 ~~eaErI~v~~i~k~~ 227 (230)
++|+|||||+|+++..
T Consensus 159 ~~eaErIgv~~l~~~~ 174 (288)
T cd08063 159 TGEAERIGVDHVARGG 174 (288)
T ss_pred eccCceeeHHHHHhcC
Confidence 9999999999999754
No 6
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3e-43 Score=304.39 Aligned_cols=171 Identities=32% Similarity=0.478 Sum_probs=157.0
Q ss_pred CCCCcEEEEehhhHhhHhhhhhhccC-CCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcc---eeecHHHHHHHHHhh
Q 026931 56 ATSNVTAKVHPLVIFNICDCYVRRPD-QAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSH 131 (230)
Q Consensus 56 ~~~~~~V~IhPlVlL~I~DH~~R~~~-~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~---~~iD~~y~~~m~~l~ 131 (230)
.-...+|.+||||||+++|||.|... +++||+|.|||. ..++++.|+|||++|++|++.+ |++|.+|++.|+++|
T Consensus 5 ~~~~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~-~~~~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~mf 83 (309)
T KOG1556|consen 5 ELTVEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGS-WNGDVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGMF 83 (309)
T ss_pred ccccceeeeehhHHHHHHHHHhhhccCcCceEEEEEEec-CCCCeEEeecceeccccccCCCCceEEeccHHHHHHHHHH
Confidence 34467999999999999999999753 468999999996 7777899999999999998765 899999999999999
Q ss_pred cccCCCCcEEEEeecCCCCCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeEeeecC-CccccccEEEeceEE
Q 026931 132 LKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLG-DRQLAAQFQEIPLDL 210 (230)
Q Consensus 132 kkV~p~e~iVGWY~tg~~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~~~~~~-~~~~~~~F~~lp~~I 210 (230)
+|||.+|.+||||+|||.+.++|+.|++.+.++||+|+++++|..+++-+||..||...+..-. |.+....|+.+|++|
T Consensus 84 kKvNakekivGWYhTGPkl~~nDl~In~l~k~y~pnpvLvIIdvkpk~~gLPT~AY~aVeev~dDgt~t~ktF~Hvps~I 163 (309)
T KOG1556|consen 84 KKVNAKEKVVGWYHTGPKLRENDLDINELLKRYVPNPVLVIIDVKPKELGLPTEAYIAVEEVKDDGTPTSKTFVHVPSEI 163 (309)
T ss_pred HHhcchhheeeeeccCCccccchhhHHHHHhhcCCCceEEEEecccccCCCCchheeeeeeeecCCCCccceeEecCccc
Confidence 9999999999999999999999999999999999999999999999999999999999876554 455677999999999
Q ss_pred ecCchHHHHHHHHHHHh
Q 026931 211 RMIEAERVGCMYMLVIL 227 (230)
Q Consensus 211 ~~~eaErI~v~~i~k~~ 227 (230)
+++|||+|||+|+++.+
T Consensus 164 ~AeEAEEvGVEHLlRDi 180 (309)
T KOG1556|consen 164 EAEEAEEVGVEHLLRDI 180 (309)
T ss_pred chhHHHHhhHHHHHHHH
Confidence 99999999999999875
No 7
>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=1.9e-41 Score=279.15 Aligned_cols=150 Identities=31% Similarity=0.552 Sum_probs=135.8
Q ss_pred EEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEE
Q 026931 62 AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIV 141 (230)
Q Consensus 62 V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iV 141 (230)
|+|||+|||||+|||+|+..++.+|+|+|||+ +.|++++|+|||++|++++++.+.+|.+|+++|++++|+|+|++.+|
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 68999999999999999876688999999995 88999999999999998887778899999999999999999999999
Q ss_pred EEeecCCC----CCcChHHHHHHHhhh-CCCcEEEEEeccC--CCCceeEEEEEeEeeecCCccccccEEEeceEEecCc
Q 026931 142 GWFSTGLG----VTGGSALIHEFYCRE-VPNPVHLTVDTGF--RNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIE 214 (230)
Q Consensus 142 GWY~tg~~----~~~~~~~ih~~~~~~-~~~pI~L~vDp~~--~~~~l~ikAY~~~~~~~~~~~~~~~F~~lp~~I~~~e 214 (230)
|||++++. ++..+..+|++|++. +++||+|++||.. .+++++++||++.+... .+.++|++|.++|
T Consensus 80 GWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~~~-------~~~~~~~~i~~~e 152 (157)
T cd08057 80 GWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQREE-------NGAEITYEIGTEE 152 (157)
T ss_pred EEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEecCCC-------CCceeeeEEeccc
Confidence 99999998 788899999999987 8899999999987 46789999999984222 2339999999999
Q ss_pred hHHHH
Q 026931 215 AERVG 219 (230)
Q Consensus 215 aErI~ 219 (230)
+||||
T Consensus 153 ~E~I~ 157 (157)
T cd08057 153 TERIA 157 (157)
T ss_pred ccccC
Confidence 99986
No 8
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=1e-40 Score=288.24 Aligned_cols=172 Identities=27% Similarity=0.414 Sum_probs=154.4
Q ss_pred cCCCCCCCcEEEEehhhHhhHhhhhhhccCC---C-ceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHH
Q 026931 52 PSSAATSNVTAKVHPLVIFNICDCYVRRPDQ---A-ERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTM 127 (230)
Q Consensus 52 ~~~~~~~~~~V~IhPlVlL~I~DH~~R~~~~---~-~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m 127 (230)
++.+++++++|.+||||++||+|||+|.+.+ + ++|+|+|+| +|.|++|||.|||++..+..++...+|.+|++++
T Consensus 1 ~Aps~S~s~tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG-~Q~GR~vEi~NSFeL~~d~~~~~~~~dke~l~kk 79 (299)
T KOG3050|consen 1 MAPSSSGSVTVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIG-KQRGRNVEIMNSFELKMDTEEDTETIDKEYLEKK 79 (299)
T ss_pred CCCCCCCceeEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhhee-cccCceEEEeeeeEEEecchhhhhhccHHHHHHH
Confidence 3556788999999999999999999998643 2 489999999 6999999999999999887766668999999999
Q ss_pred HHhhcccCCCCcEEEEeecCCCCCcChHHHHHHHhhhCCCcEEEEEeccCCC-CceeEEEEEeEeeecCCccccccEEEe
Q 026931 128 LKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRN-GEGTVKAYVSVNLSLGDRQLAAQFQEI 206 (230)
Q Consensus 128 ~~l~kkV~p~e~iVGWY~tg~~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~-~~l~ikAY~~~~~~~~~~~~~~~F~~l 206 (230)
.++||+|||+..++|||+||.+.++.|+.+|.+++..++.|++|.++|.... .+.|++.|++. ..+.++.+..+|+|+
T Consensus 80 ~eqykqVFpdl~vlGwYttG~d~t~sd~~i~k~l~~i~esplflkLNp~t~~t~~~pv~lfese-~dvidg~~q~~f~~~ 158 (299)
T KOG3050|consen 80 EEQYKQVFPDLYVLGWYTTGSDPTPSDIHIHKQLMDINESPLFLKLNPATNHTDKDPVTLFESE-IDVIDGEAQMLFVPL 158 (299)
T ss_pred HHHHHHhcccceEEEEeecCCCCChhhhHHHHHHHhhhcCceEEEecchhccccCCCceeeeee-heeecCcceeeeeee
Confidence 9999999999999999999999999999999999999999999999998765 45599999986 344455778999999
Q ss_pred ceEEecCchHHHHHHHHHH
Q 026931 207 PLDLRMIEAERVGCMYMLV 225 (230)
Q Consensus 207 p~~I~~~eaErI~v~~i~k 225 (230)
.|+++++|||||||||+++
T Consensus 159 tytl~teEaERIgVdHVA~ 177 (299)
T KOG3050|consen 159 TYTLATEEAERIGVDHVAR 177 (299)
T ss_pred EEEEeehhhhhccchhhee
Confidence 9999999999999999986
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=1.1e-33 Score=251.44 Aligned_cols=160 Identities=24% Similarity=0.326 Sum_probs=135.6
Q ss_pred EEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcc---eeecHHHHHHHHHhhcccCCC
Q 026931 61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSHLKVNPQ 137 (230)
Q Consensus 61 ~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~---~~iD~~y~~~m~~l~kkV~p~ 137 (230)
+|+|||+|+++|+|||.|+ .+.+|+|+|||. ..|+++||||||++|+.+++++ ...|.+|+.+|++++++++++
T Consensus 2 ~V~I~~~vllkIv~H~~~~--~p~~v~G~LLG~-~~~~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~ 78 (266)
T cd08065 2 SVQIDGLVVLKIIKHCKEE--LPELVQGQLLGL-DVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVD 78 (266)
T ss_pred EEEEeHHHHHHHHHHHhcC--CCcEEEEEEeee-EcCCEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCC
Confidence 6999999999999999886 489999999995 7899999999999999887665 466789999999999999999
Q ss_pred CcEEEEeecCC-CCCcChHHHHHHHhhh--CCCcEEEEEeccCC-CCceeEEEEEeEeeecC---------------Ccc
Q 026931 138 EVIVGWFSTGL-GVTGGSALIHEFYCRE--VPNPVHLTVDTGFR-NGEGTVKAYVSVNLSLG---------------DRQ 198 (230)
Q Consensus 138 e~iVGWY~tg~-~~~~~~~~ih~~~~~~--~~~pI~L~vDp~~~-~~~l~ikAY~~~~~~~~---------------~~~ 198 (230)
+.+||||+|++ ....+...+|.+|... .+++|+|++||..+ +++++++||++++.++. +.+
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 99999999998 2222356667666554 47899999999874 67899999999998774 346
Q ss_pred ccccEEEeceEEecCchHHHHHHHH
Q 026931 199 LAAQFQEIPLDLRMIEAERVGCMYM 223 (230)
Q Consensus 199 ~~~~F~~lp~~I~~~eaErI~v~~i 223 (230)
.+.+|.|||++|.++..+.+.+..+
T Consensus 159 ~~~if~eiPv~i~n~~l~~~~L~~l 183 (266)
T cd08065 159 FSNIFEEIPVVIRNSHLVNALLSEL 183 (266)
T ss_pred hhcEEEEEEEEEEchHHHHHHHHhc
Confidence 7889999999999987777766655
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=9.2e-30 Score=226.73 Aligned_cols=168 Identities=15% Similarity=0.226 Sum_probs=150.4
Q ss_pred CCCCcEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHH--hhcc
Q 026931 56 ATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLK--SHLK 133 (230)
Q Consensus 56 ~~~~~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~--l~kk 133 (230)
.....+|.|+|+|+++|++|+.| ..+.+|+|.|+|. .++++++|+|||++|+.++++++..+.+|++.|++ ++++
T Consensus 6 ~~~~~~V~Is~~allkil~Ha~~--~~p~Ev~GlLlG~-~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~~ 82 (268)
T cd08069 6 PDYFEKVYISSLALLKMLKHARA--GGPIEVMGLMLGK-VDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQ 82 (268)
T ss_pred CCcccEEEECHHHHHHHHHHHhc--cCCceEEEEEEee-ecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHHH
Confidence 45567899999999999999977 3688999999995 88899999999999998888888888899999999 9999
Q ss_pred cCCCCcEEEEeecCCC----CCcChHHHHHHHhhhCCCcEEEEEeccCC--CCceeEEEEEeEeeecC----Cc------
Q 026931 134 VNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR--NGEGTVKAYVSVNLSLG----DR------ 197 (230)
Q Consensus 134 V~p~e~iVGWY~tg~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~--~~~l~ikAY~~~~~~~~----~~------ 197 (230)
+++++.+||||||++. ++..|+.+|..|++.++.+|+|++||..+ .|++.++||++.+.++. +.
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 9999999999999987 88899999999999988899999998765 57899999999998764 12
Q ss_pred -----------cccccEEEeceEEecCchHHHHHHHHHHH
Q 026931 198 -----------QLAAQFQEIPLDLRMIEAERVGCMYMLVI 226 (230)
Q Consensus 198 -----------~~~~~F~~lp~~I~~~eaErI~v~~i~k~ 226 (230)
..+..|.+||++|.+++.|+..++.+.+.
T Consensus 163 ~~~~~~~~~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~ 202 (268)
T cd08069 163 HLPKPKIEDFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNK 202 (268)
T ss_pred ccCcHHHHHhCchhcEEEEeeeEEecCHHHHHHHHHHHHH
Confidence 15678999999999999999999988765
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=99.95 E-value=1.4e-27 Score=185.88 Aligned_cols=107 Identities=36% Similarity=0.579 Sum_probs=94.1
Q ss_pred CCcEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCC-eEEEEEeeeecccCCCcce-eecHHHHHHHHHhhcccC
Q 026931 58 SNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDG-TVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKVN 135 (230)
Q Consensus 58 ~~~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~-~VeVtnsF~vp~~e~e~~~-~iD~~y~~~m~~l~kkV~ 135 (230)
+..+|.|||+|+++|+||++|+. +.+|+|+|+|+ .+++ .++|+|||++|+.+++++. ..+.++.++|++++++++
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 56799999999999999999974 34999999996 8888 9999999999999876653 456677799999999999
Q ss_pred CCCcEEEEeecCCCC----CcChHHHHHHHhhhCCC
Q 026931 136 PQEVIVGWFSTGLGV----TGGSALIHEFYCREVPN 167 (230)
Q Consensus 136 p~e~iVGWY~tg~~~----~~~~~~ih~~~~~~~~~ 167 (230)
|++.+||||+|++.. +..|+.+|++|++.+++
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 999999999999887 88999999999998764
No 12
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=6.6e-25 Score=193.22 Aligned_cols=166 Identities=22% Similarity=0.352 Sum_probs=134.9
Q ss_pred CCCCCcEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccC--CCcce---eec---HHHHHH
Q 026931 55 AATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNE--FSDQV---ALD---IEYHHT 126 (230)
Q Consensus 55 ~~~~~~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e--~e~~~---~iD---~~y~~~ 126 (230)
.+.+...|.++.||+++|++||.....+-.-+.|+|+| ...++.+|||||||.|... ++|.+ ..| ..|+..
T Consensus 8 ~~p~vk~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~G-lvvd~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~ 86 (339)
T KOG1560|consen 8 ESPPVKRVELDSLVVMKIIKHCREEFPNGDGTQGVLLG-LVVDGRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLA 86 (339)
T ss_pred CCCccceeeehhHHHHHHHHHHHhhcCCcchhhheeee-eeecceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHH
Confidence 46678899999999999999997664445689999999 6889999999999999843 22221 233 369999
Q ss_pred HHHhhcccCCCCcEEEEeec---CCCCCcChHHHHHHHhhhCCCcEEEEEeccCC-CCceeEEEEEeEeeecC-------
Q 026931 127 MLKSHLKVNPQEVIVGWFST---GLGVTGGSALIHEFYCREVPNPVHLTVDTGFR-NGEGTVKAYVSVNLSLG------- 195 (230)
Q Consensus 127 m~~l~kkV~p~e~iVGWY~t---g~~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~-~~~l~ikAY~~~~~~~~------- 195 (230)
|++.++.+|-+...||||++ |+.++..-+.-+-.|+.-+++.|+|++||..+ +|.|.++||++++..+.
T Consensus 87 mlrrlr~vnid~~hVGwYqs~~vgs~lS~~lveSqy~YQ~a~pesVvliYD~~kssqG~L~lrAyrLTp~am~~~kekdw 166 (339)
T KOG1560|consen 87 MLRRLRYVNIDHLHVGWYQSAYVGSFLSPALVESQYAYQKAIPESVVLIYDPIKSSQGTLSLRAYRLTPEAMAAHKEKDW 166 (339)
T ss_pred HHHHhhhcCccceeeeeeeeehhccccCHHHHHHHHHHHhcCCccEEEEeccccccCceEEeehhhcCHHHHHHHhcCCC
Confidence 99999999999999999997 56666444555666888899999999999987 58899999999987652
Q ss_pred --------CccccccEEEeceEEecCchHHHHHHHHHHHhcc
Q 026931 196 --------DRQLAAQFQEIPLDLRMIEAERVGCMYMLVILIH 229 (230)
Q Consensus 196 --------~~~~~~~F~~lp~~I~~~eaErI~v~~i~k~~~~ 229 (230)
+-+...+|.++|+.|++ +|+++.+|+
T Consensus 167 tpealk~~nltyenmfeElPIVIkn--------S~L~nvlms 200 (339)
T KOG1560|consen 167 TPEALKSANLTYENMFEELPIVIKN--------SHLANVLMS 200 (339)
T ss_pred CHHHHHhcCCCHHHHHhhcCeeeec--------cHHHHHHHH
Confidence 12567899999999999 777777765
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=99.90 E-value=3.9e-23 Score=163.31 Aligned_cols=128 Identities=31% Similarity=0.418 Sum_probs=113.1
Q ss_pred EEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcce-eecHHHHHHHHHhhcccCCCCc
Q 026931 61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKVNPQEV 139 (230)
Q Consensus 61 ~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~-~iD~~y~~~m~~l~kkV~p~e~ 139 (230)
+|.|||+|+++|++|+.|. .+.+++|.|+|. ..++.++|+++|++|...+.+.+ ..+.+|+++|.++++++++++.
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 4789999999999999875 678999999995 77889999999999987655544 6789999999999999999999
Q ss_pred EEEEeecCC----CCCcChHHHHHHHhhhCCCcEEEEEeccCCC-CceeEEEEEeEe
Q 026931 140 IVGWFSTGL----GVTGGSALIHEFYCREVPNPVHLTVDTGFRN-GEGTVKAYVSVN 191 (230)
Q Consensus 140 iVGWY~tg~----~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~-~~l~ikAY~~~~ 191 (230)
+||||+|++ .++..|+.+|..++...+.++++.+|+..+. ++++++||++++
T Consensus 78 ~vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~~g~~~~~af~~~~ 134 (135)
T smart00232 78 IVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLTP 134 (135)
T ss_pred EEEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccccCcEEEEEEEecC
Confidence 999999987 3667789999999988889999999998875 889999999863
No 14
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.72 E-value=2.4e-17 Score=146.03 Aligned_cols=134 Identities=17% Similarity=0.291 Sum_probs=111.1
Q ss_pred CCCcEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeec---HHHHHHHHHhhcc
Q 026931 57 TSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALD---IEYHHTMLKSHLK 133 (230)
Q Consensus 57 ~~~~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD---~~y~~~m~~l~kk 133 (230)
..-..|+|..|+||+|.-|..| +++-.|||.|+| +.+|+++.|.+||++|.+++|..+... .+|+....+.-|.
T Consensus 50 ~~fk~vkISalAllKm~~hA~~--GgnlEiMGlm~G-kv~g~t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k~ 126 (347)
T KOG1554|consen 50 HYFKHVKISALALLKMVMHARS--GGNLEIMGLMQG-KVDGDTIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEAKN 126 (347)
T ss_pred chhhhhhhHHHHHHHHHHHHhc--CCCeEEEeeecc-cccCCeEEEEeccccccccccceechHHHHHHHHHHHHHHHHH
Confidence 3456899999999999998854 478999999999 599999999999999999988765433 5777777888889
Q ss_pred cCCCCcEEEEeecCCC----CCcChHHHHHHHhhhCCCc-EEEEEeccCC--CCceeEEEEEeEeeec
Q 026931 134 VNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNP-VHLTVDTGFR--NGEGTVKAYVSVNLSL 194 (230)
Q Consensus 134 V~p~e~iVGWY~tg~~----~~~~~~~ih~~~~~~~~~p-I~L~vDp~~~--~~~l~ikAY~~~~~~~ 194 (230)
++..+++||||+++|. ++.-|+..|..-+++ ..| |++++||..+ .+++.|.|||..+.+.
T Consensus 127 ~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~f-QePfvAvViDP~Rtlsagkv~iGAFRTyp~gy 193 (347)
T KOG1554|consen 127 VGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRF-QEPFVAVVIDPTRTLSAGKVNIGAFRTYPKGY 193 (347)
T ss_pred hhhhhceeeeeecCCCCCccccCcchhHHHHhhhh-cCCeEEEEecCccccccCceeeceeecccCCC
Confidence 9999999999999887 566676665544443 556 9999999875 6899999999998776
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=99.72 E-value=8e-17 Score=124.34 Aligned_cols=111 Identities=25% Similarity=0.339 Sum_probs=88.8
Q ss_pred hhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEEEEeecCCC
Q 026931 70 FNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG 149 (230)
Q Consensus 70 L~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iVGWY~tg~~ 149 (230)
.+|++|+.+. .+.+|+|.|+|. ..++.++|+++|++|...++.. .+.. ..|....+.+..++.+||||+|++.
T Consensus 2 k~il~~a~~~--~~~ev~G~L~G~-~~~~~~~i~~~~~~~~~~~~~~--~~~~--~~~~~~~~~~~~~~~iVGwyhshp~ 74 (116)
T cd07767 2 KMFLDAAKSI--NGKEVIGLLYGS-KTKKVLDVDEVIAVPFDEGDKD--DNVW--FLMYLDFKKLNAGLRIVGWYHTHPK 74 (116)
T ss_pred HhHHHHHhcC--CCcEEEEEeEEE-EcCCEEEEEEEEecccCCCCCc--cHHH--HHHHHHHHHhcCCCeEEEEEEcCCC
Confidence 4688888653 478999999995 7788899999999998765432 2221 1266666778899999999999876
Q ss_pred ----CCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEE
Q 026931 150 ----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAY 187 (230)
Q Consensus 150 ----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY 187 (230)
++..|+..|..|++..+++++|++|+...+.+++++||
T Consensus 75 ~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~~~~~~~~~~~ 116 (116)
T cd07767 75 PSCFLSPNDLATHELFQRYFPEKVMIIVDVKPKDLGNSWKCY 116 (116)
T ss_pred CCCccCHHHHHHHHHHHHhCCCCEEEEEECCCccCCCCcccC
Confidence 67788899999998888999999999887667888887
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=99.65 E-value=4.2e-15 Score=126.38 Aligned_cols=129 Identities=14% Similarity=0.065 Sum_probs=104.5
Q ss_pred CcEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEee-CCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCC
Q 026931 59 NVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLP-DGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQ 137 (230)
Q Consensus 59 ~~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~-~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~ 137 (230)
+.+|+|+++|+|+|.+|+... ...|+|.|+|.+.. ++.++|+++|++|....+++..+|.+++.+|.+..++.+
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 679999999999999999643 28999999995333 468999999999987766667889999999999998877
Q ss_pred CcEEEEeecCCC----CCcChHHHHHHHhhhCC-------CcEEEEEeccCCC---CceeEEEEEeEee
Q 026931 138 EVIVGWFSTGLG----VTGGSALIHEFYCREVP-------NPVHLTVDTGFRN---GEGTVKAYVSVNL 192 (230)
Q Consensus 138 e~iVGWY~tg~~----~~~~~~~ih~~~~~~~~-------~pI~L~vDp~~~~---~~l~ikAY~~~~~ 192 (230)
+.+|||||+++. ++..|+..|..||...+ ..|.|++||-... ..-.+++|...+.
T Consensus 79 l~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~ 147 (187)
T cd08067 79 LSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPP 147 (187)
T ss_pred CEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECC
Confidence 599999999875 45567888888888654 2499999997642 3457899998754
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=99.63 E-value=2.1e-15 Score=118.69 Aligned_cols=110 Identities=13% Similarity=0.209 Sum_probs=86.4
Q ss_pred hHhhHhhhhhhccCCCceEEEEEeeeEee----CCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEEEE
Q 026931 68 VIFNICDCYVRRPDQAERVIGTLLGSVLP----DGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGW 143 (230)
Q Consensus 68 VlL~I~DH~~R~~~~~~~ViG~LLG~~~~----~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iVGW 143 (230)
|+++|++|+.+. .+..++|.|+|.... +..++|+++|+.|...+. .+.|..+.+....++++|||
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 789999999663 578999999995332 346899999999875422 22455556678889999999
Q ss_pred eecCCC----CCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeE
Q 026931 144 FSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV 190 (230)
Q Consensus 144 Y~tg~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~ 190 (230)
||+++. ++..|+..|.+|+...++.++|++||..+ ...++||+++
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 999883 66778887887888778889999999663 7899999873
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=99.37 E-value=4.1e-11 Score=105.65 Aligned_cols=148 Identities=17% Similarity=0.188 Sum_probs=105.1
Q ss_pred cEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEee-------CCeEEEEEeeeecccC-CCcceeecHHH----HHHH
Q 026931 60 VTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLP-------DGTVDIRNSYVVPHNE-FSDQVALDIEY----HHTM 127 (230)
Q Consensus 60 ~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~-------~~~VeVtnsF~vp~~e-~e~~~~iD~~y----~~~m 127 (230)
.+|.|.+.++.+|++|+.+. .+..++|.|+|. .+ ++.+.|..-++.+..+ ..+.+.+|.+- .+.+
T Consensus 2 ~~V~Is~~~l~~il~HA~~~--~P~EvCGLL~G~-~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea 78 (244)
T cd08068 2 SKVHLSADVYLVCLTHALST--EKEEVMGLLIGE-IEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEA 78 (244)
T ss_pred cEEEECHHHHHHHHHHHHhC--CCcceeEEEEee-cccccccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHH
Confidence 47999999999999999654 689999999995 43 3345555545543332 34567888652 3456
Q ss_pred HHhhcccCCCCcEEEEeecCCC----CCcChHHHHHHHhhhCCCcEEEEEeccCC-----CCceeEEEEEeEeeecCCcc
Q 026931 128 LKSHLKVNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR-----NGEGTVKAYVSVNLSLGDRQ 198 (230)
Q Consensus 128 ~~l~kkV~p~e~iVGWY~tg~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~-----~~~l~ikAY~~~~~~~~~~~ 198 (230)
-++.+....++.+||||||++. ++..|+..|..|+...+.-++|++++... .++..+++|+..+- .+.
T Consensus 79 ~~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~g---~~~ 155 (244)
T cd08068 79 ERLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQG---NKA 155 (244)
T ss_pred HHHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecCC---CCC
Confidence 6777788899999999999886 55667776677776667779999976432 25788999998631 112
Q ss_pred ccccEEEeceEEecC
Q 026931 199 LAAQFQEIPLDLRMI 213 (230)
Q Consensus 199 ~~~~F~~lp~~I~~~ 213 (230)
......++|++|...
T Consensus 156 ~~~~~~e~pl~i~~~ 170 (244)
T cd08068 156 GQYERIEVPLEIVPT 170 (244)
T ss_pred CcceEEEeeeEEecC
Confidence 235677888888743
No 19
>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=99.13 E-value=2e-09 Score=90.53 Aligned_cols=124 Identities=12% Similarity=0.134 Sum_probs=91.5
Q ss_pred EEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCccee-ecHHHHHHHHHhhcccCCCCc
Q 026931 61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVA-LDIEYHHTMLKSHLKVNPQEV 139 (230)
Q Consensus 61 ~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~-iD~~y~~~m~~l~kkV~p~e~ 139 (230)
.+.|-.-.+-+|+.|+.++...+..+.|.|+|. ..++..+|++.+-.|...++..+. .|. .++++.. --.++.
T Consensus 3 ~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~-~~~~~~~I~~i~~~~q~~~~~~~~~~~~---~e~~~~~--~~~gle 76 (173)
T cd08066 3 QVVVPADLMDKFLQLAEPNTSRNLETCGILCGK-LSNNAFFITHLIIPKQSGTSDSCQTTNE---EELFDFQ--DQHDLI 76 (173)
T ss_pred EEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeE-cCCCeEEEEEEEeccccCCCceecCCCH---HHHHHHH--HhCCCe
Confidence 456666778889999976532357999999995 777888999998878776655433 232 1122221 134789
Q ss_pred EEEEeecCCC----CCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeE-eeec
Q 026931 140 IVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV-NLSL 194 (230)
Q Consensus 140 iVGWY~tg~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~-~~~~ 194 (230)
+||||+|.+. ++..|+..|..|+...+..++|+++| +...++||+.. +.++
T Consensus 77 ~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp----~~~~l~afrl~~~~g~ 132 (173)
T cd08066 77 TLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAP----KYNEFGIFRLTDPPGL 132 (173)
T ss_pred eEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECC----CCcEEeEEEeecCCcc
Confidence 9999999774 67788999988888788899999997 36789999998 6655
No 20
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.10 E-value=2.3e-10 Score=103.58 Aligned_cols=135 Identities=21% Similarity=0.326 Sum_probs=110.8
Q ss_pred CCCCcEEEEehhhHhhHhhhhhhccCCCce-EEEEE-ee---eEeeCCeEEEEEeeeecccCCCcc--e-eecHHHHHHH
Q 026931 56 ATSNVTAKVHPLVIFNICDCYVRRPDQAER-VIGTL-LG---SVLPDGTVDIRNSYVVPHNEFSDQ--V-ALDIEYHHTM 127 (230)
Q Consensus 56 ~~~~~~V~IhPlVlL~I~DH~~R~~~~~~~-ViG~L-LG---~~~~~~~VeVtnsF~vp~~e~e~~--~-~iD~~y~~~m 127 (230)
.....+|.++.+++++.++|- |. ..+.. ++|.+ +| .+.+..++.|.+.|+.|....+-. + .+|..|+.+|
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-RA-GSPEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAVDPVFQTQM 104 (316)
T ss_pred ccCcceeeeehhhhhhccccc-cc-CCchhhccceeecccccceeeecceeeeeeeccccccceecccchhccHHHHHHH
Confidence 455779999999999999988 43 23444 89999 99 667888999999999998875432 1 5799999999
Q ss_pred HHhhcccCCCCcEEEEeecCCC----CCcChHHHHHHHhhhCCCcEEEEEeccCC-CCceeEEEEEeEee
Q 026931 128 LKSHLKVNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR-NGEGTVKAYVSVNL 192 (230)
Q Consensus 128 ~~l~kkV~p~e~iVGWY~tg~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~-~~~l~ikAY~~~~~ 192 (230)
.++.++....+.+|||||+++. ++..|+..|..|+...+..+..++||..+ .|+.-+.||+....
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 9999999888999999999886 45678999999999989999999999875 35555558877654
No 21
>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=98.48 E-value=5.7e-06 Score=65.70 Aligned_cols=113 Identities=15% Similarity=0.076 Sum_probs=78.6
Q ss_pred hHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCC--cceeecHHHHHHHHHhhcccCCCCcEEEEee
Q 026931 68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS--DQVALDIEYHHTMLKSHLKVNPQEVIVGWFS 145 (230)
Q Consensus 68 VlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e--~~~~iD~~y~~~m~~l~kkV~p~e~iVGWY~ 145 (230)
++-+|++|+.+. .+..+.|.|+|. .++....|+..+++|....+ ....+|.+.+.++.+..++. ++.+|||||
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 456888999763 588999999995 66666678899999986544 35678887777777666655 589999999
Q ss_pred cCCCCC--cChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeE
Q 026931 146 TGLGVT--GGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV 190 (230)
Q Consensus 146 tg~~~~--~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~ 190 (230)
|++... .+...+..+. ....++|++..... .-.+++|...
T Consensus 78 SHP~~~~~PS~~D~~~~~---~~~~~~lIv~~~~~--~~~~~~~~~~ 119 (128)
T cd08070 78 SHPDGPARPSETDLRLAW---PPGVSYLIVSLAGG--APELRAWRLE 119 (128)
T ss_pred CCCCCCCCCCHHHHHhcc---CCCCeEEEEECCCC--CcEEEEEEEc
Confidence 988622 2222222211 12458888875333 5678999875
No 22
>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=2e-06 Score=73.06 Aligned_cols=106 Identities=22% Similarity=0.234 Sum_probs=74.2
Q ss_pred ehhhHhhHhhhhhhccCCCceEEEEEeeeEee-CCeEEEEEeeeecccCCCcceeecHHH--HHHHHHhhcccCCCCcEE
Q 026931 65 HPLVIFNICDCYVRRPDQAERVIGTLLGSVLP-DGTVDIRNSYVVPHNEFSDQVALDIEY--HHTMLKSHLKVNPQEVIV 141 (230)
Q Consensus 65 hPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~-~~~VeVtnsF~vp~~e~e~~~~iD~~y--~~~m~~l~kkV~p~e~iV 141 (230)
.+.+..+|..|..+. .+..|.|.|+|. .. ++.+.|++++|+.+.. ..++... ...+.+.+-+- .+..||
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 STLAYVKMLLHAAKY--PHCAVNGLLLGK-KSSGGSVEITDAVPLFHSC----LALAPMLEVALALVDAYCKS-SGLVIV 73 (182)
T ss_pred CHHHHHHHHHHHHHc--CCchheEEEEee-ecCCCCEEEEEEEEcCCCc----cccCHHHHHHHHHHHHHHHH-CCCEEE
Confidence 356788999999874 466999999996 55 7789999999999853 3455442 22222333322 378999
Q ss_pred EEeecCCCCCcCh-----HHHHHHHhhhCCCcEEEEEeccCC
Q 026931 142 GWFSTGLGVTGGS-----ALIHEFYCREVPNPVHLTVDTGFR 178 (230)
Q Consensus 142 GWY~tg~~~~~~~-----~~ih~~~~~~~~~pI~L~vDp~~~ 178 (230)
|+|++.+...... ..|=+...++++++++|++|-..-
T Consensus 74 G~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~l 115 (182)
T cd08060 74 GYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEKL 115 (182)
T ss_pred EEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCccc
Confidence 9999988654322 234455677788999999997653
No 23
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=98.39 E-value=4.3e-06 Score=71.74 Aligned_cols=122 Identities=16% Similarity=0.191 Sum_probs=84.9
Q ss_pred EEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCe--EEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCC
Q 026931 61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT--VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQE 138 (230)
Q Consensus 61 ~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~--VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e 138 (230)
+|.+.+.+..+|+=|..+. ....|.|.|||. ..++. |+|+||.|+=|.... ..--.|-.-.+.+.|-+. .+.
T Consensus 3 ~v~is~~AY~K~~LHaaKy--P~~aVnGvLlg~-~~~~~~~v~i~DaVPLfH~~~~--L~PmlEvAL~qvd~~~~~-~gl 76 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAKY--PHCAVNGVLLGK-SSKSSSEVEIVDAVPLFHHWLS--LSPMLEVALAQVDAYAKS-NGL 76 (196)
T ss_pred eEEEcHHHHHHHHHHhccC--CCCceeeEEEec-cCCCCceEEEeeceeccccccC--cchHHHHHHHHHHHHHhh-CCC
Confidence 7899999999999999876 356899999997 54443 999999999995422 122234444556666543 469
Q ss_pred cEEEEeecCCCCCcC-----hHHHHHHHhhhCCCcEEEEEeccCCC---CceeEEEEE
Q 026931 139 VIVGWFSTGLGVTGG-----SALIHEFYCREVPNPVHLTVDTGFRN---GEGTVKAYV 188 (230)
Q Consensus 139 ~iVGWY~tg~~~~~~-----~~~ih~~~~~~~~~pI~L~vDp~~~~---~~l~ikAY~ 188 (230)
.|||+|+....+... -..|=+.+.+.++++++|++|-..-. +..++.+|.
T Consensus 77 ~IvGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~kl~~~~~~~~~~~~~ 134 (196)
T PF03665_consen 77 VIVGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKKLSSDCKAPAISVYQ 134 (196)
T ss_pred EEEEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcccccccCCCcceeee
Confidence 999999997644322 22334456667889999999976422 234456666
No 24
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=98.15 E-value=2.6e-05 Score=62.46 Aligned_cols=100 Identities=19% Similarity=0.249 Sum_probs=65.9
Q ss_pred EEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCC--cceeecHHHHHHHHHhhcccCCCCcE
Q 026931 63 KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS--DQVALDIEYHHTMLKSHLKVNPQEVI 140 (230)
Q Consensus 63 ~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e--~~~~iD~~y~~~m~~l~kkV~p~e~i 140 (230)
.+-..++-.|++|..|. .+.+++|.|+|+ ..+ ...|+++..+.+ ....++.++.. ++...++.+ +.+
T Consensus 3 ~i~~~~l~~il~~a~~~--~p~E~~g~l~~~-~~~-----~~~~~~~n~~~~~~~~~~~~~~~~~-~~~~~~~~g--~~v 71 (134)
T COG1310 3 VIPKEVLGAILEHARRE--HPREVCGLLAGT-REG-----ERYFPLKNVSVEPVEYFEIDPEYSL-FYLAAEDAG--EVV 71 (134)
T ss_pred eecHHHHHHHHHHHHhc--CChheEEEEEee-ccc-----ceeeccccccCCcceeEeeCHHHHH-HHHHHhhCC--CEE
Confidence 45677888999999775 468999999996 444 455555544332 23355666665 555444444 999
Q ss_pred EEEeecCCCC--CcChHHHHHHHhhhCCCcEEEEEec
Q 026931 141 VGWFSTGLGV--TGGSALIHEFYCREVPNPVHLTVDT 175 (230)
Q Consensus 141 VGWY~tg~~~--~~~~~~ih~~~~~~~~~pI~L~vDp 175 (230)
||||||+++. ..++..++ +++..+.|.+++..+
T Consensus 72 vg~yHSHP~~~~~pS~~D~~--~~~~~~~~~~iv~~~ 106 (134)
T COG1310 72 VGWYHSHPGGPPYPSEADRR--LSKLGPLPWLIVSVP 106 (134)
T ss_pred EEEEcCCCCCCCCcCHHHHh--hccccCCCEEEEEcC
Confidence 9999999863 34445554 666666666666653
No 25
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=97.69 E-value=0.0016 Score=55.08 Aligned_cols=123 Identities=16% Similarity=0.173 Sum_probs=86.0
Q ss_pred EEEEehhhHhhHhhhhhhccCCCceEEEEEee--eEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCC
Q 026931 61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLG--SVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQE 138 (230)
Q Consensus 61 ~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG--~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e 138 (230)
.|.+.-++..+|+=|+.|.. ..-|-|.|+| + ..|+.|||++|.|+=|+... +.--.|-...|.+-+-+- -..
T Consensus 3 ~veis~~aY~kmiLH~akyp--h~aVnGLLla~~~-~kg~~v~itdcVPLfH~~la--LaPmlEvAl~lId~~~~~-~Gl 76 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYP--HAAVNGLLLAPAT-GKGECVEITDCVPLFHSHLA--LAPMLEVALNLIDVWGAQ-AGL 76 (199)
T ss_pred ceeehhhHHHHHHHHhccCc--ccceeeEEEeccC-CCCCeEEEEecchhhccccc--cccHHHHHHHHHHHHHHh-cCe
Confidence 57888999999999998863 4679999999 5 56678999999999877531 122334455566655533 468
Q ss_pred cEEEEeecCCCCCcC-----hHHHHHHHhhhCCCcEEEEEeccC-CC--CceeEEEEEe
Q 026931 139 VIVGWFSTGLGVTGG-----SALIHEFYCREVPNPVHLTVDTGF-RN--GEGTVKAYVS 189 (230)
Q Consensus 139 ~iVGWY~tg~~~~~~-----~~~ih~~~~~~~~~pI~L~vDp~~-~~--~~l~ikAY~~ 189 (230)
.|+|.|++...++.. -..|-+.++++++++..|++|... .. ..-++-+|+-
T Consensus 77 viaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~~l~~~~e~~~v~v~e~ 135 (199)
T KOG3289|consen 77 VIAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNKKLVPQCERPPVIVLED 135 (199)
T ss_pred EEEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEeccccccccCCCCEEEeec
Confidence 999999997654321 133445677888887777777653 22 3457888884
No 26
>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=97.44 E-value=0.00084 Score=59.77 Aligned_cols=103 Identities=22% Similarity=0.298 Sum_probs=73.6
Q ss_pred CceEEEEEeeeEeeC---CeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEEEEeecCCC----CCcChH
Q 026931 83 AERVIGTLLGSVLPD---GTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG----VTGGSA 155 (230)
Q Consensus 83 ~~~ViG~LLG~~~~~---~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iVGWY~tg~~----~~~~~~ 155 (230)
..++.|.|.|. ... +.-||+-....|+.++.+.+.+-.+- -.+. ---++..|||=+|.+. +++.|+
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 35899999995 665 45688888888888766655442210 1111 1236889999999753 677889
Q ss_pred HHHHHHhhhCC-----CcEEEEEeccCCCCceeEEEEEeEeeec
Q 026931 156 LIHEFYCREVP-----NPVHLTVDTGFRNGEGTVKAYVSVNLSL 194 (230)
Q Consensus 156 ~ih~~~~~~~~-----~pI~L~vDp~~~~~~l~ikAY~~~~~~~ 194 (230)
..|..|+..++ +.|.+++- .+.|..++.||.+++.++
T Consensus 128 ~tha~~~~~~~~w~~~~~V~it~S--ftpGs~sl~ay~LT~~G~ 169 (252)
T cd08056 128 TTHAKILADNPSWDGEKTVILTCS--FTPGSCSLTAYKLTPEGY 169 (252)
T ss_pred HHHHHHHHhccccCCCcEEEEEEc--CCCCceEEEEEecCHHHH
Confidence 99998888776 46777664 457789999999997665
No 27
>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family. This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize.
Probab=96.53 E-value=0.054 Score=43.81 Aligned_cols=80 Identities=16% Similarity=0.158 Sum_probs=54.2
Q ss_pred hHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCC---cceeecHHHHHHHH-HhhcccCCCCcEEEE
Q 026931 68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS---DQVALDIEYHHTML-KSHLKVNPQEVIVGW 143 (230)
Q Consensus 68 VlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e---~~~~iD~~y~~~m~-~l~kkV~p~e~iVGW 143 (230)
++++++..|......+...-|.|+|. ..+..+.|+++- .|..++- ....-+.+.+++.+ +.+++.+-...-||=
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 46778888866655678999999996 667777777744 4443322 12334556655554 455555556899999
Q ss_pred eecCCC
Q 026931 144 FSTGLG 149 (230)
Q Consensus 144 Y~tg~~ 149 (230)
+||++.
T Consensus 79 WHtHP~ 84 (131)
T TIGR02256 79 WHTHPE 84 (131)
T ss_pred cCcCCC
Confidence 999886
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=96.49 E-value=0.069 Score=41.95 Aligned_cols=99 Identities=18% Similarity=0.206 Sum_probs=61.4
Q ss_pred hHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcce-eecHHHHHHHHHhhcccCCCCcEEEEeec
Q 026931 68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKVNPQEVIVGWFST 146 (230)
Q Consensus 68 VlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~-~iD~~y~~~m~~l~kkV~p~e~iVGWY~t 146 (230)
.+-.|++|+.+. -+..+.|.|+|. .. .|++.+++|.....+.. ..+.+ |. -.+..+||-|||
T Consensus 5 ~~~~i~~ha~~~--~P~E~CGlL~G~-~~----~v~~~~~~~n~~~~~~~~~f~~~----~~------~~g~~ivgi~HS 67 (117)
T cd08072 5 LLDSILEAAKSS--HPNEFAALLRGK-DG----VITELLILPGTESGEVSAVFPLL----ML------PLDMSIVGSVHS 67 (117)
T ss_pred HHHHHHHHHhhc--CCceEEEEEEee-cc----EEEEEEECCCCCCCCcceeechH----Hh------cCCCeEEEEEEc
Confidence 355788888654 688999999995 32 58899999966543221 12221 11 247899999999
Q ss_pred CCC----CCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeE
Q 026931 147 GLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV 190 (230)
Q Consensus 147 g~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~ 190 (230)
+++ ++..|+. ++.. +..++|++.... +.=.++||...
T Consensus 68 HP~~~~~PS~~D~~----~~~~-~~~~~lIvs~~~--~~~~~~a~~~~ 108 (117)
T cd08072 68 HPSGSPRPSDADLS----FFSK-TGLVHIIVGYPY--DEDDWRAYDSD 108 (117)
T ss_pred CCCCCCCCCHHHHH----hhhc-CCCEEEEEECcC--CCCCEEEEecC
Confidence 885 3333422 2222 345788886422 22457888764
No 29
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=96.00 E-value=0.056 Score=40.55 Aligned_cols=69 Identities=14% Similarity=0.013 Sum_probs=41.6
Q ss_pred hHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEEEEeecC
Q 026931 68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTG 147 (230)
Q Consensus 68 VlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iVGWY~tg 147 (230)
++-.|+.|+.+. .+....|.|+|. ..+..+.++......-.+ +...... +....+..+||+|||+
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 455677887664 578999999996 566777777666511010 1111110 3445678999999998
Q ss_pred CCCC
Q 026931 148 LGVT 151 (230)
Q Consensus 148 ~~~~ 151 (230)
+.-.
T Consensus 69 P~~~ 72 (104)
T PF14464_consen 69 PSGP 72 (104)
T ss_dssp SSSS
T ss_pred CCCC
Confidence 7643
No 30
>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=92.53 E-value=1.4 Score=39.93 Aligned_cols=109 Identities=17% Similarity=0.202 Sum_probs=71.0
Q ss_pred ceEEEEEeeeEeeC------CeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEEEEeecCCC--------
Q 026931 84 ERVIGTLLGSVLPD------GTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG-------- 149 (230)
Q Consensus 84 ~~ViG~LLG~~~~~------~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iVGWY~tg~~-------- 149 (230)
..-+|-|.|+.... .++.|.--++=|...+.+.+.+..+-.++..+... ..-.+..|||=-|...
T Consensus 34 ~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~iA-~~lGL~~VG~IfT~l~~~~~d~~~ 112 (274)
T cd08061 34 QQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAIA-AALGLERVGWIFTDLPREDKDGYF 112 (274)
T ss_pred ceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhHHHHHH-HHcCCeEEEEEEecCCCCCCCcee
Confidence 46699999975544 37889989999988777766654443333344443 2347999999988652
Q ss_pred CCcChHHHHHHHhh-----hC-CCcEEEEEeccCCCCceeEEEEEeEeeec
Q 026931 150 VTGGSALIHEFYCR-----EV-PNPVHLTVDTGFRNGEGTVKAYVSVNLSL 194 (230)
Q Consensus 150 ~~~~~~~ih~~~~~-----~~-~~pI~L~vDp~~~~~~l~ikAY~~~~~~~ 194 (230)
+++..+.....+|. .. .+=|-+++.+..+ +...+.||..+...+
T Consensus 113 LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~~-g~i~~~ayQvSdq~~ 162 (274)
T cd08061 113 LSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDKD-GQIHFEAYQVSDQAM 162 (274)
T ss_pred ECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCCC-CceeeeeeeecHHHH
Confidence 33334444455552 22 2336677876544 679999999987543
No 31
>PF05021 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation following ubiquitination of target proteins but preceding their recognition by the 26S proteasome []. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing [].
Probab=90.43 E-value=2.4 Score=38.92 Aligned_cols=106 Identities=20% Similarity=0.197 Sum_probs=65.1
Q ss_pred EEEEeeeEeeCC------eEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEEEEeecCCC-----------
Q 026931 87 IGTLLGSVLPDG------TVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG----------- 149 (230)
Q Consensus 87 iG~LLG~~~~~~------~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iVGWY~tg~~----------- 149 (230)
+|-|.|...... ++.|.--|+=|+..+.+.+.+..+-.++..+...+.- ++..|||=-|...
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~l-GL~rVG~IfTdl~~~~~~~g~v~~ 80 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASAL-GLERVGWIFTDLTDDGSGDGTVKC 80 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHHC-CCEEEEEEEecCcccccCCCceee
Confidence 799999655445 6899999999988777766663333333333333222 7899999877532
Q ss_pred --------CCcChHHHHHHHhhhCCC-------------cEEEEEeccCCCCceeEEEEEeEeeec
Q 026931 150 --------VTGGSALIHEFYCREVPN-------------PVHLTVDTGFRNGEGTVKAYVSVNLSL 194 (230)
Q Consensus 150 --------~~~~~~~ih~~~~~~~~~-------------pI~L~vDp~~~~~~l~ikAY~~~~~~~ 194 (230)
+++..+..=..+|...++ -|-+++.+. .++.+.+.||..+...+
T Consensus 81 ~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~-~~g~i~~~ayQvS~q~~ 145 (306)
T PF05021_consen 81 KRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGD-EEGEIHFEAYQVSNQCV 145 (306)
T ss_pred ccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCC-CCCceeeEEeeehHHHH
Confidence 222222222233332221 266677653 45789999999987543
No 32
>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=89.45 E-value=2.1 Score=33.08 Aligned_cols=65 Identities=8% Similarity=-0.059 Sum_probs=41.4
Q ss_pred HhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCC--cceeecH-HHHHHHHHhhcccCCCCcEEEEee
Q 026931 69 IFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS--DQVALDI-EYHHTMLKSHLKVNPQEVIVGWFS 145 (230)
Q Consensus 69 lL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e--~~~~iD~-~y~~~m~~l~kkV~p~e~iVGWY~ 145 (230)
+-.|++|..+. -+....|.|+|. . + ++..+++.....+ ....+|. ++.+.+ + ...+||-||
T Consensus 3 ~~~i~~ha~~~--~P~E~CGll~g~-~--~---~~~~~p~~N~~~~p~~~F~idp~e~~~a~----~----~~~ivgi~H 66 (108)
T cd08073 3 EDAILAHAKAE--YPREACGLVVRK-G--R---KLRYIPCRNIAADPEEHFEISPEDYAAAE----D----EGEIVAVVH 66 (108)
T ss_pred HHHHHHHHhHC--CCCcceEEEEec-C--C---ceEEEECccCCCCccceEEeCHHHHHHHh----c----CCCEEEEEE
Confidence 34678888654 578999999994 3 2 3445666643222 3466775 444332 2 228999999
Q ss_pred cCCC
Q 026931 146 TGLG 149 (230)
Q Consensus 146 tg~~ 149 (230)
|+++
T Consensus 67 SHP~ 70 (108)
T cd08073 67 SHPD 70 (108)
T ss_pred cCCC
Confidence 9875
No 33
>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=82.98 E-value=5.1 Score=29.92 Aligned_cols=63 Identities=13% Similarity=0.080 Sum_probs=39.0
Q ss_pred hHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEEEEeecCCC
Q 026931 71 NICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG 149 (230)
Q Consensus 71 ~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iVGWY~tg~~ 149 (230)
.|.+|+.+. -+....|.|+|. .. + .+.+..++|... ...+..+ ......-+..+||-|++++.
T Consensus 5 ~i~~~~~~~--~p~E~~gll~~~-~~-~--~~~~~~~~~~~~----~~~~~~~------~~~a~~~~~~~v~i~HsHP~ 67 (101)
T cd08059 5 TILVHAKDA--HPDEFCGFLSGS-KD-N--VMDELIFLPFVS----GSVSAVI------DLAALEIGMKVVGLVHSHPS 67 (101)
T ss_pred HHHHHHHhc--CChhhheeeecC-CC-C--eEEEEEeCCCcC----CccChHH------HHHHhhCCCcEEEEEecCcC
Confidence 455666432 367899999994 33 3 577888887543 1233333 22223346789999999875
No 34
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=81.84 E-value=2.4 Score=39.76 Aligned_cols=96 Identities=16% Similarity=0.221 Sum_probs=62.5
Q ss_pred CceEEEEEeeeEeeCCeEEEEEeeeecccC-CCcce-eecHHHHHHHHHhhc-ccCCCCcEEEEeecCCC----CCcChH
Q 026931 83 AERVIGTLLGSVLPDGTVDIRNSYVVPHNE-FSDQV-ALDIEYHHTMLKSHL-KVNPQEVIVGWFSTGLG----VTGGSA 155 (230)
Q Consensus 83 ~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e-~e~~~-~iD~~y~~~m~~l~k-kV~p~e~iVGWY~tg~~----~~~~~~ 155 (230)
+-.-.|.|-|. -..+.+-||.-. +|..+ +.|.. .-+. .++|. +---++--|||-+|++. +++-|+
T Consensus 275 nlETCGiL~g~-L~~n~f~IThli-iPkQeatsd~C~t~ne------eelF~vQdq~~L~tlGWIHTHPTQt~FmSSVDl 346 (424)
T KOG2880|consen 275 NLETCGILAGK-LERNEFYITHLI-IPKQEATSDSCNTMNE------EELFEVQDQHELLTLGWIHTHPTQTCFMSSVDL 346 (424)
T ss_pred cchHHHHhhhH-hhcCcEEEEEEE-eecccCCCccccccCH------HHHheecccccceeeeeeecCCccchhheeccc
Confidence 45679999995 788888888765 44443 33311 1111 11222 11235778999999875 445677
Q ss_pred HHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeE
Q 026931 156 LIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV 190 (230)
Q Consensus 156 ~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~ 190 (230)
..|-.||--.|.+|++++-|..++ -.+|+++
T Consensus 347 HTHcSYQiMlPEAiAIV~aPk~~~----tGiFrLt 377 (424)
T KOG2880|consen 347 HTHCSYQIMLPEAIAIVCAPKSKT----TGIFRLT 377 (424)
T ss_pred cccceeeeecchheeEEeccccCC----cceEEec
Confidence 777778877899999999987543 2367776
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=71.49 E-value=2.1 Score=30.64 Aligned_cols=10 Identities=40% Similarity=1.052 Sum_probs=6.8
Q ss_pred CcEEEEeecC
Q 026931 138 EVIVGWFSTG 147 (230)
Q Consensus 138 e~iVGWY~tg 147 (230)
-.|||||+|.
T Consensus 40 g~vvgwy~t~ 49 (78)
T PF06442_consen 40 GQVVGWYCTK 49 (78)
T ss_dssp EEEEEEE--S
T ss_pred ceEeEEEecc
Confidence 4799999985
No 36
>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=65.29 E-value=35 Score=29.34 Aligned_cols=71 Identities=10% Similarity=0.032 Sum_probs=47.3
Q ss_pred EEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCC-cceeecHHHHHHHHHhhcccCCCCcEE
Q 026931 63 KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS-DQVALDIEYHHTMLKSHLKVNPQEVIV 141 (230)
Q Consensus 63 ~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e-~~~~iD~~y~~~m~~l~kkV~p~e~iV 141 (230)
+|-.-.+=+|+.|+.+. -+..+.|.|.|. ..++.. ..+++...+.. +.+..|.. |. ..++.+|
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 44555677899999654 578999999994 444433 44777654432 33445544 22 6789999
Q ss_pred EEeecCCC
Q 026931 142 GWFSTGLG 149 (230)
Q Consensus 142 GWY~tg~~ 149 (230)
+-|||++.
T Consensus 138 ~iyHSH~~ 145 (192)
T TIGR03735 138 VDLHSHGT 145 (192)
T ss_pred EEEcCCCC
Confidence 99999875
No 37
>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=57.35 E-value=18 Score=39.55 Aligned_cols=117 Identities=21% Similarity=0.260 Sum_probs=72.9
Q ss_pred hhHhhhhhhccCCCceEEEEEeeeEeeCC--eE-EEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEEEEeec
Q 026931 70 FNICDCYVRRPDQAERVIGTLLGSVLPDG--TV-DIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFST 146 (230)
Q Consensus 70 L~I~DH~~R~~~~~~~ViG~LLG~~~~~~--~V-eVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iVGWY~t 146 (230)
.||++-+-+...-...+.|.+.| +...+ +| ||..---+|.-++-..+.+- .+.- -..+--+.+.+||-+|
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 KNLLKKFITISDLRTQIAGYLYG-VSPPDNPQVKEIRCIVMVPQWGSHQGVHLP-SFLP-----IHGVLEDLEPLGWIHT 2173 (2321)
T ss_pred HHHHhhheeecchhhhhheeeec-cCCCCCCccceEEEEEeccccccccccccC-ccCC-----cchhccCCcccchhhc
Confidence 46666676654334678999999 46443 44 55544456665432222110 0000 1123457889999999
Q ss_pred CCC----CCcChHHHHHHHhhhC-CCcEEEEEeccCCCCceeEEEEEeEeeecC
Q 026931 147 GLG----VTGGSALIHEFYCREV-PNPVHLTVDTGFRNGEGTVKAYVSVNLSLG 195 (230)
Q Consensus 147 g~~----~~~~~~~ih~~~~~~~-~~pI~L~vDp~~~~~~l~ikAY~~~~~~~~ 195 (230)
.++ +++.|+.+|..+.... +..|.+++ +.+-|..++.||.+++.+.+
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 764 6677899998665543 45666665 45667899999999877653
No 38
>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=44.67 E-value=29 Score=33.77 Aligned_cols=76 Identities=17% Similarity=0.177 Sum_probs=50.2
Q ss_pred HhhHhhhhhhccC-CCceEEEEEeeeEeeCCeE------EEEEeeeecccCCCcceeecHH-HHHHHHHhhcccCCCCcE
Q 026931 69 IFNICDCYVRRPD-QAERVIGTLLGSVLPDGTV------DIRNSYVVPHNEFSDQVALDIE-YHHTMLKSHLKVNPQEVI 140 (230)
Q Consensus 69 lL~I~DH~~R~~~-~~~~ViG~LLG~~~~~~~V------eVtnsF~vp~~e~e~~~~iD~~-y~~~m~~l~kkV~p~e~i 140 (230)
--+|++||.+... .-.+-+|-|.|...+.+.| +|---|+=|....+|.+.+..+ -++.+-+... .-....
T Consensus 181 ~~~~v~~Fl~~wr~sg~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~~~~dgl~l~~~~e~~~vD~~a~--~lGLrR 258 (510)
T KOG2834|consen 181 NAELVNHFLNEWRASGVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQHGEEDGLELLEDDEAKRVDAIAE--GLGLRR 258 (510)
T ss_pred chHHHHHHHHHHHHhhhhhcceEEEeecccccccccceeeEEEEecCCccCCcCCeEEeccchhhhHHHHHH--hcCcee
Confidence 3467777776532 1235589999987777788 9999999998887777665522 2222323332 236799
Q ss_pred EEEeec
Q 026931 141 VGWFST 146 (230)
Q Consensus 141 VGWY~t 146 (230)
|||--|
T Consensus 259 VG~IFT 264 (510)
T KOG2834|consen 259 VGWIFT 264 (510)
T ss_pred eEEEEe
Confidence 999865
No 39
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=42.32 E-value=1.8e+02 Score=27.07 Aligned_cols=61 Identities=15% Similarity=0.203 Sum_probs=44.2
Q ss_pred EEEeeeEe-eCCeEEEEEeeeecccCCCcc-----------eeecHHHHHHHHHhhccc-CCCCcEEEEeecCCC
Q 026931 88 GTLLGSVL-PDGTVDIRNSYVVPHNEFSDQ-----------VALDIEYHHTMLKSHLKV-NPQEVIVGWFSTGLG 149 (230)
Q Consensus 88 G~LLG~~~-~~~~VeVtnsF~vp~~e~e~~-----------~~iD~~y~~~m~~l~kkV-~p~e~iVGWY~tg~~ 149 (230)
|.|+|. . .+.+--|.+..+-|..+++++ -.+|.++..+...+-.+- .-...|||-|-.+++
T Consensus 1 GLlIGq-~~s~~kd~Vv~l~~tP~~d~~~~~~~~~~~~~~~~~id~~WVaeHA~qVsRMLPGGi~VlGifvv~~~ 74 (362)
T PF14778_consen 1 GLLIGQ-SSSSQKDYVVHLARTPPEDTDDEESDVRTSDSSIKDIDEEWVAEHARQVSRMLPGGISVLGIFVVAPD 74 (362)
T ss_pred CeEecc-ccCCCcceEEEecCCCCccccccccccccccccccccCHHHHHHHHHHHHhhCCCCcEEEEEEEEcCH
Confidence 789996 5 566667888889998765443 147888887766665544 446799999998764
No 40
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=34.49 E-value=96 Score=34.13 Aligned_cols=126 Identities=19% Similarity=0.209 Sum_probs=68.9
Q ss_pred EEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCC--eEEEEEeee-ecccCCCcceeecHHHHHHHHHhhcccCCC
Q 026931 61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDG--TVDIRNSYV-VPHNEFSDQVALDIEYHHTMLKSHLKVNPQ 137 (230)
Q Consensus 61 ~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~--~VeVtnsF~-vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~ 137 (230)
+++--+..-+|.++-+.|...-...|.|.+.|. ...+ +|.=.-||. ||.-+.-..+.+. .+.- -++ ----+
T Consensus 2131 ~~q~~y~lP~NLl~kF~~isD~~vqvag~vyG~-s~~d~p~ikeI~~~~lVPQlgs~~~vq~~-s~vP--~dl--p~~e~ 2204 (2365)
T COG5178 2131 SIQQMYRLPLNLLEKFMRISDPHVQVAGLVYGK-SGSDNPQIKEILSFGLVPQLGSLSGVQSS-SFVP--HDL--PGDED 2204 (2365)
T ss_pred hhhccccccHHHHHhhheecccceeeEEEEecc-CCccCcchhheeEEEeecccccccccccc-ccCC--CCC--CCccc
Confidence 344455566778888888754456899999993 5433 342233554 5654432211110 0000 000 00135
Q ss_pred CcEEEEeecCCC----CCcChHHHHHHH-hhhCCCcEEEEEeccCCCCceeEEEEEeEeeec
Q 026931 138 EVIVGWFSTGLG----VTGGSALIHEFY-CREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSL 194 (230)
Q Consensus 138 e~iVGWY~tg~~----~~~~~~~ih~~~-~~~~~~pI~L~vDp~~~~~~l~ikAY~~~~~~~ 194 (230)
..+|||-+|+.+ +...+...|... ...--.+|-|++- ..-+.+++.||.....+.
T Consensus 2205 le~lGwihtq~~el~~l~~~~v~th~k~~~d~~~d~v~ltv~--~~pgsiSl~ay~v~keG~ 2264 (2365)
T COG5178 2205 LEILGWIHTQDDELPYLEVAGVLTHRKKIVDPEWDAVTLTVS--YLPGSISLRAYVVKKEGC 2264 (2365)
T ss_pred ceeeEEEecCCcccchhhhhhhhhhhhcccCccccceeeeee--eccceeeeeeeeehhccc
Confidence 679999999976 555566666532 2111124555542 234678899999876655
Done!