Query 036425
Match_columns 252
No_of_seqs 120 out of 537
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 12:32:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036425.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036425hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03246 26S proteasome regula 100.0 7.4E-65 1.6E-69 455.7 27.9 247 2-248 51-297 (303)
2 KOG2975 Translation initiation 100.0 2.1E-63 4.5E-68 425.5 24.5 222 2-228 65-287 (288)
3 cd08062 MPN_RPN7_8 Mpr1p, Pad1 100.0 1.9E-62 4.2E-67 436.8 26.4 234 2-236 46-279 (280)
4 KOG1556 26S proteasome regulat 100.0 9.1E-59 2E-63 393.4 19.9 241 2-244 54-294 (309)
5 cd08063 MPN_CSN6 Mpr1p, Pad1p 100.0 1.8E-57 3.9E-62 407.4 25.2 225 2-231 49-278 (288)
6 cd08064 MPN_eIF3f Mpr1p, Pad1p 100.0 1.2E-56 2.6E-61 397.9 25.8 220 2-226 43-265 (265)
7 KOG3050 COP9 signalosome, subu 100.0 7.6E-48 1.6E-52 326.4 20.5 224 2-231 57-283 (299)
8 PF13012 MitMem_reg: Maintenan 99.9 1.6E-26 3.4E-31 180.5 1.5 114 115-228 1-114 (115)
9 cd08057 MPN_euk_non_mb Mpr1p, 99.9 6.2E-25 1.3E-29 180.6 10.6 108 2-121 43-157 (157)
10 cd08065 MPN_eIF3h Mpr1p, Pad1p 99.8 3.4E-19 7.4E-24 158.3 15.7 163 2-166 43-227 (266)
11 cd08069 MPN_RPN11_CSN5 Mov34/M 99.6 2.1E-14 4.6E-19 127.7 16.3 124 2-128 52-202 (268)
12 PF01398 JAB: JAB1/Mov34/MPN/P 99.3 2.1E-12 4.5E-17 100.3 3.4 64 2-67 47-114 (114)
13 smart00232 JAB_MPN JAB/MPN dom 99.3 1.8E-11 3.9E-16 97.0 8.5 87 2-90 42-133 (135)
14 cd07767 MPN Mpr1p, Pad1p N-ter 99.0 1.9E-09 4.2E-14 83.2 7.6 79 2-87 34-116 (116)
15 KOG1560 Translation initiation 98.4 9.6E-06 2.1E-10 71.4 12.8 163 2-166 57-255 (339)
16 KOG1554 COP9 signalosome, subu 97.6 0.00028 6.1E-09 62.5 8.6 92 2-93 95-192 (347)
17 cd08068 MPN_BRCC36 Mov34/MPN/P 97.4 0.0038 8.3E-08 54.9 12.1 94 16-114 63-169 (244)
18 cd08058 MPN_euk_mb Mpr1p, Pad1 97.3 0.00071 1.5E-08 52.8 6.6 62 26-89 53-118 (119)
19 cd08067 MPN_2A_DUB Mov34/MPN/P 97.2 0.0055 1.2E-07 51.9 11.2 87 2-93 48-148 (187)
20 KOG1555 26S proteasome regulat 97.2 0.00077 1.7E-08 60.9 6.0 89 3-91 80-173 (316)
21 cd08066 MPN_AMSH_like Mov34/MP 96.3 0.0086 1.9E-07 50.1 5.8 55 36-94 73-132 (173)
22 COG1310 Predicted metal-depend 94.8 0.13 2.9E-06 40.7 7.1 53 17-74 51-105 (134)
23 cd08070 MPN_like Mpr1p, Pad1p 89.0 7 0.00015 30.5 10.2 69 15-90 49-119 (128)
24 PF06442 DHFR_2: R67 dihydrofo 86.3 0.39 8.5E-06 33.4 1.2 12 38-49 40-51 (78)
25 cd08060 MPN_UPF0172 Mov34/MPN/ 82.3 2.1 4.5E-05 36.1 4.2 59 17-76 48-113 (182)
26 PF03665 UPF0172: Uncharacteri 78.9 6.8 0.00015 33.4 6.3 67 22-89 61-135 (196)
27 cd08056 MPN_PRP8 Mpr1p, Pad1p 65.7 15 0.00032 32.7 5.4 58 36-95 104-170 (252)
28 KOG0130 RNA-binding protein RB 52.9 19 0.00041 29.1 3.5 41 36-76 66-109 (170)
29 PF05184 SapB_1: Saposin-like 41.6 33 0.00072 20.5 2.7 30 158-188 10-39 (39)
30 KOG3289 Uncharacterized conser 39.0 1.1E+02 0.0023 25.9 6.0 65 24-89 63-135 (199)
31 PF11371 DUF3172: Protein of u 35.4 92 0.002 24.9 4.8 64 43-112 22-93 (140)
32 PF08255 Leader_Trp: Trp-opero 31.0 42 0.00092 16.2 1.4 9 39-47 6-14 (14)
33 cd07641 BAR_ASAP1 The Bin/Amph 28.9 3.8E+02 0.0082 23.2 7.9 25 142-166 5-29 (215)
34 PF12408 DUF3666: Ribose-5-pho 28.0 1.6E+02 0.0035 19.3 4.3 33 172-213 14-46 (48)
35 PF01381 HTH_3: Helix-turn-hel 27.0 1.4E+02 0.0029 18.9 4.0 38 148-185 12-49 (55)
36 KOG2213 Apoptosis inhibitor 5/ 25.2 95 0.0021 29.5 3.9 97 104-201 135-243 (460)
37 PF15039 DUF4530: Domain of un 24.6 1.4E+02 0.003 22.5 4.0 42 202-243 62-103 (111)
38 KOG0907 Thioredoxin [Posttrans 24.4 1.4E+02 0.0031 22.5 4.2 41 36-76 21-61 (106)
39 PF04740 LXG: LXG domain of WX 23.5 4.2E+02 0.0092 21.8 8.7 49 138-186 60-110 (204)
40 TIGR02543 List_Bact_rpt Lister 22.3 60 0.0013 20.6 1.5 11 36-46 4-14 (44)
41 PF10224 DUF2205: Predicted co 22.2 3.1E+02 0.0067 19.9 5.3 47 136-186 20-66 (80)
42 PF12844 HTH_19: Helix-turn-he 20.3 1.9E+02 0.0041 18.9 3.8 39 148-186 15-53 (64)
43 PF13821 DUF4187: Domain of un 20.2 96 0.0021 20.7 2.2 17 150-166 11-27 (55)
No 1
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=100.00 E-value=7.4e-65 Score=455.74 Aligned_cols=247 Identities=89% Similarity=1.327 Sum_probs=231.3
Q ss_pred eeeecccCCCCCCceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCCCCCCCcHHHHHHHhccCCCcEEEEEeCCCCCCC
Q 036425 2 VISVPFEEDDKDPGIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGPKLRENDLDIHQLFHNYVPNPVLVIIDVQPKELG 81 (252)
Q Consensus 2 sF~Vp~~e~~~~~~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~~~~~~~~~Ih~~~~~~~~~PI~L~vD~~~~~~~ 81 (252)
||++||++++++.++|++|++|+++|+++|++|||++.+||||+||++++++|+.||++|++++++||||+||+.+.+++
T Consensus 51 sF~~p~~e~~~~~~~~~~D~~y~~~m~~~~k~V~~~~~vVGWY~tg~~i~~~d~~IH~~~~~~~~~Pv~L~vD~~~~~~~ 130 (303)
T PLN03246 51 SFAVPFEEDDKDPSIWFLDHNYLESMFGMFKRINAKEHVVGWYSTGPKLRENDLDIHELFNDYVPNPVLVIIDVQPKELG 130 (303)
T ss_pred ccccCcccCCCCccceeecHHHHHHHHHHHHHhCCCCcEEeeecCCCCCCcchHHHHHHHHhhCCCCeEEEEecCCCCCC
Confidence 89999998877666799999999999999999999999999999999999999999999999999999999999998889
Q ss_pred CceEEEEeehhhhccccccccceeeeeeeeeeecchhHHHHHHHhhhcccCcccchhhhHHHHHHHHHHHHHHHHHHHHH
Q 036425 82 IPTKAYYDVEEVKENATQKSQKVFVHVPSEIAAHEVEEIGVEHLLRDVKDTTISTLANEVTGKLTALKGLDARLREIRGY 161 (252)
Q Consensus 82 lpi~~Y~~~~~~~~~~~~~~~~~F~~v~~~i~~~eaEri~vd~l~k~~~~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Y 161 (252)
||+++|++...+.+++.+..+..|+++||+|+++|||||||+|++|++.+.+.+++.+++.++.+|+++|.+||+.|++|
T Consensus 131 lpi~aY~s~~~~~~~~~~~~~~~F~~vp~~i~~~EaE~Igve~l~r~~~~~~~s~l~~~l~~~~~al~~L~~rl~~i~~Y 210 (303)
T PLN03246 131 IPTKAYYAVEEVKENATQKSQKVFVHVPSEIGAHEAEEIGVEHLLRDVKDTTVSTLATEVTGKLTALKGLDARLREIRSY 210 (303)
T ss_pred CceEEEEEEEeccCCCCcccccEEEECCeeeeecCHHHHHHHHHHhcccCCccchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999998887654335678999999999999999999999998877667788889999999999999999999999
Q ss_pred HHhhhCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHHHHHHHHhhhhchhhhhhccC
Q 036425 162 LDLVIDEKLPLNHEILYHLQDVFNLLPNLNVAELIKAFSVKTNDMMLVIYLSSLIRSVIALHNLINNKILNKEHEKTEDA 241 (252)
Q Consensus 162 l~~V~~G~~~~d~~ilR~l~~lv~~lP~~~~~~f~~~~~~~~~D~lmv~yLs~ltk~~~~l~e~l~~~~~~~~~~~~~~~ 241 (252)
|++|.+|+.++|++|||+|+++|+++|.+++++|+++|++++||++|++|||+|||+|++|+++++++.+|.++|+++..
T Consensus 211 l~~V~~g~~~~d~~IlR~l~~l~~~lP~l~~~~f~~~f~~~~nD~lmv~YLa~l~kt~~~l~e~l~~~~~~~~~~~~~~~ 290 (303)
T PLN03246 211 LDLVVEGKLPLNHEILYHLQDVFNLLPNLNVEELVKAFAVKTNDMMLVIYLSSLIRSVIALHNLINNKILNKEHEKAEDA 290 (303)
T ss_pred HHHHhcCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988877
Q ss_pred CCCCCCC
Q 036425 242 KPTAVPT 248 (252)
Q Consensus 242 ~~~~~~~ 248 (252)
++.+-+.
T Consensus 291 ~~~~~~~ 297 (303)
T PLN03246 291 KPAAKPA 297 (303)
T ss_pred ccccccc
Confidence 7665444
No 2
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.1e-63 Score=425.52 Aligned_cols=222 Identities=25% Similarity=0.441 Sum_probs=213.7
Q ss_pred eeeecccCCCCCCceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCCCCCCCcHHHHHHHhccCCCcEEEEEeCCCCCCC
Q 036425 2 VISVPFEEDDKDPGIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGPKLRENDLDIHQLFHNYVPNPVLVIIDVQPKELG 81 (252)
Q Consensus 2 sF~Vp~~e~~~~~~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~~~~~~~~~Ih~~~~~~~~~PI~L~vD~~~~~~~ 81 (252)
||+|||+|++|+ +.+|++|++.|+++|+||||+|.|||||+||+.++.++..||+||.+++++||||+|||+++++.
T Consensus 65 CFaVPhnEssdq---vevdm~y~~~M~~l~~k~npnE~vvGWyaTg~dvt~~sslihdyYare~~~pvhLtVDT~~~n~r 141 (288)
T KOG2975|consen 65 CFAVPHNESSDQ---VEVDMEYAKNMYELHKKVNPNELVVGWYATGHDVTEHSSLIHDYYAREAPNPVHLTVDTSLQNGR 141 (288)
T ss_pred eeeccCcccccc---ceeeHHHHHHHHHHhcccCCCceeEEEEecCCCcccchhHHHHHhhccCCCCeEEEEeccccCCc
Confidence 999999999988 78999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEeehhhhccccccccceeeeeeeeeeecchhHHHHHHHhhhcccC-cccchhhhHHHHHHHHHHHHHHHHHHHH
Q 036425 82 IPTKAYYDVEEVKENATQKSQKVFVHVPSEIAAHEVEEIGVEHLLRDVKDT-TISTLANEVTGKLTALKGLDARLREIRG 160 (252)
Q Consensus 82 lpi~~Y~~~~~~~~~~~~~~~~~F~~v~~~i~~~eaEri~vd~l~k~~~~~-~~~~l~~~l~~~~~al~~L~~~l~~i~~ 160 (252)
++|++|.+...|++|+. .+.+|.|+|+++.++|+||+|++.+.|...++ +..++.++|+++..|...|+++|+.+++
T Consensus 142 m~ikaYvss~~Gvpg~~--~~~mF~plpvel~~~~~ervgl~li~kt~~sp~r~~~l~~dLqQv~~at~~l~~~L~~Vl~ 219 (288)
T KOG2975|consen 142 MSIKAYVSSLMGVPGRT--MGVMFTPLPVELAYYDAERVGLDLIEKTSFSPSRVAGLSSDLQQVEGATARLQSLLERVLK 219 (288)
T ss_pred cceeEEEEeccCCCCcc--cceeeeeeeeEEeecchhhhHHHHHHHhccChhhhccccchHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999886 67799999999999999999999999987543 3457889999999999999999999999
Q ss_pred HHHhhhCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHHHHHHHHh
Q 036425 161 YLDLVIDEKLPLNHEILYHLQDVFNLLPNLNVAELIKAFSVKTNDMMLVIYLSSLIRSVIALHNLINN 228 (252)
Q Consensus 161 Yl~~V~~G~~~~d~~ilR~l~~lv~~lP~~~~~~f~~~~~~~~~D~lmv~yLs~ltk~~~~l~e~l~~ 228 (252)
|+++|.+|+.+||+.|||+|.++++++|.+.+++|+.+|+++++|.||+.|||+|||||++|+|+|++
T Consensus 220 YVedVl~gk~~pdn~VGR~Lmd~v~~vP~l~p~~Fe~mfn~nLrD~Lmv~yLa~ltqTQl~l~EKL~~ 287 (288)
T KOG2975|consen 220 YVEDVLAGKVKPDNAVGRFLMDLVTAVPKLVPDDFETMFNSNLRDLLMVIYLANLTQTQLALNEKLVN 287 (288)
T ss_pred HHHHHHcCCCCCcchHHHHHHHHHHhcCCCCHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999975
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=1.9e-62 Score=436.83 Aligned_cols=234 Identities=71% Similarity=1.173 Sum_probs=220.4
Q ss_pred eeeecccCCCCCCceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCCCCCCCcHHHHHHHhccCCCcEEEEEeCCCCCCC
Q 036425 2 VISVPFEEDDKDPGIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGPKLRENDLDIHQLFHNYVPNPVLVIIDVQPKELG 81 (252)
Q Consensus 2 sF~Vp~~e~~~~~~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~~~~~~~~~Ih~~~~~~~~~PI~L~vD~~~~~~~ 81 (252)
||++||++++++.++|++|++|+++|+++|++|||++.+||||+||+++++.|+.||++|++++++||||+|||..++++
T Consensus 46 sF~~p~~~~~~~~~~~~~d~~y~~~m~~~~kkv~~~e~vVGWY~tg~~~~~~d~~ih~~~~~~~~~pv~l~vd~~~~~~~ 125 (280)
T cd08062 46 SFAVPFEEDEKDPSVWFLDHNYLENMYGMFKKVNAKEKIVGWYSTGPKLRPNDLDINELFRRYCPNPVLVIIDVRPKDLG 125 (280)
T ss_pred eeecCccCCCCCcchhhhhHHHHHHHHHHHHHhCCCCCeEEEecCCCCCCcchHHHHHHHHHhCCCCEEEEEecCCCCCC
Confidence 89999999887767799999999999999999999999999999999999999999999999999999999999998889
Q ss_pred CceEEEEeehhhhccccccccceeeeeeeeeeecchhHHHHHHHhhhcccCcccchhhhHHHHHHHHHHHHHHHHHHHHH
Q 036425 82 IPTKAYYDVEEVKENATQKSQKVFVHVPSEIAAHEVEEIGVEHLLRDVKDTTISTLANEVTGKLTALKGLDARLREIRGY 161 (252)
Q Consensus 82 lpi~~Y~~~~~~~~~~~~~~~~~F~~v~~~i~~~eaEri~vd~l~k~~~~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Y 161 (252)
||+++|++...+.++|. ..+..|+|+||+|+++|||||||+|++|.+.+.+.+++..++..+.+|+++|.+||+.|++|
T Consensus 126 lpi~aY~s~~~~~~~g~-~~~~~F~~vp~~i~~~eaE~igve~l~r~~~~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Y 204 (280)
T cd08062 126 LPTEAYIAVEEVHDDGT-PTSKTFVHVPSEIGAEEAEEVGVEHLLRDIKDVTVSTLSTRVTNKLNSLKGLQSKLKEIKDY 204 (280)
T ss_pred CceEEEEEeeeccCCCC-cceeEEEEcceEeeccchHHHHHHHHHhhccCcccchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999998876552 25678999999999999999999999998776666778889999999999999999999999
Q ss_pred HHhhhCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHHHHHHHHhhhhchhhh
Q 036425 162 LDLVIDEKLPLNHEILYHLQDVFNLLPNLNVAELIKAFSVKTNDMMLVIYLSSLIRSVIALHNLINNKILNKEHE 236 (252)
Q Consensus 162 l~~V~~G~~~~d~~ilR~l~~lv~~lP~~~~~~f~~~~~~~~~D~lmv~yLs~ltk~~~~l~e~l~~~~~~~~~~ 236 (252)
|++|.+|+.++|++|||+|+++|+++|.+++++|+++|++++||++|++|||+|||+|.+|+++++++.+|++.+
T Consensus 205 l~~V~~g~~~~d~~IlR~l~~~~~~lP~l~~~~f~~~~~~~~nD~lmv~yLs~l~k~~~~l~~~~~~~~~~~~~~ 279 (280)
T cd08062 205 LQLVVEGKLPINHQIIYNLQDIFNLLPNLNLPELVKAFAVKTNDQMLVIYLSSLIRSVIALHNLINNKIANKEAE 279 (280)
T ss_pred HHHHHCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 999999999999999999999999999999999999999999999999999999999999999999998765544
No 4
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=9.1e-59 Score=393.45 Aligned_cols=241 Identities=72% Similarity=1.144 Sum_probs=231.3
Q ss_pred eeeecccCCCCCCceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCCCCCCCcHHHHHHHhccCCCcEEEEEeCCCCCCC
Q 036425 2 VISVPFEEDDKDPGIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGPKLRENDLDIHQLFHNYVPNPVLVIIDVQPKELG 81 (252)
Q Consensus 2 sF~Vp~~e~~~~~~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~~~~~~~~~Ih~~~~~~~~~PI~L~vD~~~~~~~ 81 (252)
||||||+|++++.++||+|++|+++|+++|+|||.+|.|||||+||+.+.++|+.|++.|.+++|||+.+++|..+.+-+
T Consensus 54 SfAvpFeEDdk~~svWFlDh~Y~esM~~mfkKvNakekivGWYhTGPkl~~nDl~In~l~k~y~pnpvLvIIdvkpk~~g 133 (309)
T KOG1556|consen 54 SFAVPFEEDDKDKSVWFLDHNYIESMFGMFKKVNAKEKVVGWYHTGPKLRENDLDINELLKRYVPNPVLVIIDVKPKELG 133 (309)
T ss_pred ceeccccccCCCCceEEeccHHHHHHHHHHHHhcchhheeeeeccCCccccchhhHHHHHhhcCCCceEEEEecccccCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceEEEEeehhhhccccccccceeeeeeeeeeecchhHHHHHHHhhhcccCcccchhhhHHHHHHHHHHHHHHHHHHHHH
Q 036425 82 IPTKAYYDVEEVKENATQKSQKVFVHVPSEIAAHEVEEIGVEHLLRDVKDTTISTLANEVTGKLTALKGLDARLREIRGY 161 (252)
Q Consensus 82 lpi~~Y~~~~~~~~~~~~~~~~~F~~v~~~i~~~eaEri~vd~l~k~~~~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Y 161 (252)
||..||.++....++|++ ....|+++|++|+++|||.|||+|+.|++++.+.++++..++++..+|+.|++++..|.+|
T Consensus 134 LPT~AY~aVeev~dDgt~-t~ktF~Hvps~I~AeEAEEvGVEHLlRDikd~t~gtla~rit~ql~sLkgl~~~L~eI~~Y 212 (309)
T KOG1556|consen 134 LPTEAYIAVEEVKDDGTP-TSKTFVHVPSEIEAEEAEEVGVEHLLRDIKDTTVGTLATRITNQLMSLKGLQSRLREIRSY 212 (309)
T ss_pred CCchheeeeeeeecCCCC-ccceeEecCcccchhHHHHhhHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999988777763 5678999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHHHHHHHHhhhhchhhhhhccC
Q 036425 162 LDLVIDEKLPLNHEILYHLQDVFNLLPNLNVAELIKAFSVKTNDMMLVIYLSSLIRSVIALHNLINNKILNKEHEKTEDA 241 (252)
Q Consensus 162 l~~V~~G~~~~d~~ilR~l~~lv~~lP~~~~~~f~~~~~~~~~D~lmv~yLs~ltk~~~~l~e~l~~~~~~~~~~~~~~~ 241 (252)
|++|.+|+.|.|++|+.++++++++||.+...+|.+.|+...||.||+.|||+|+|++.+|+++++|+++|...|+ ++.
T Consensus 213 L~~Vi~g~lpiNh~Il~~lQdvfNllP~l~~~~~~~a~~vktndql~~iY~sslvrsViAlhdLi~Nkl~nk~~e~-~d~ 291 (309)
T KOG1556|consen 213 LDKVIDGKLPINHEILYQLQDVFNLLPNLTRNELVKAFNVKTNDQLMVIYLSSLVRSVIALHDLINNKLANKKAEK-EDS 291 (309)
T ss_pred HHHHhcCCCCCcHHHHHHHHHHHhhCccccchhhhhhhccccCceeeeeeHHHHHHHHHHHHHHHHhHhhhhhhhh-hhc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999887 444
Q ss_pred CCC
Q 036425 242 KPT 244 (252)
Q Consensus 242 ~~~ 244 (252)
||.
T Consensus 292 K~k 294 (309)
T KOG1556|consen 292 KDK 294 (309)
T ss_pred ccc
Confidence 543
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=1.8e-57 Score=407.45 Aligned_cols=225 Identities=28% Similarity=0.484 Sum_probs=210.2
Q ss_pred eeeecccCCCCCCceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCCC-CCCCcHHHHHHHhccCCCcEEEEEeCCC--C
Q 036425 2 VISVPFEEDDKDPGIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGPK-LRENDLDIHQLFHNYVPNPVLVIIDVQP--K 78 (252)
Q Consensus 2 sF~Vp~~e~~~~~~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~~-~~~~~~~Ih~~~~~~~~~PI~L~vD~~~--~ 78 (252)
||++||+++++ +.|.+|++|+++|+++|++|||++.+||||+||+. ++++|+.||++|++++++||||++||.. +
T Consensus 49 sF~~p~~~~~~--~~~~id~~y~~~m~~~~kkV~~~~~vVGWY~tg~~~~~~~~~~Ih~~~~~~~~~pv~L~~D~~~~~~ 126 (288)
T cd08063 49 SFELKYDTNED--GEIVLDKEFLETRLEQFKQVFKDLDFVGWYTTGPGGPTESDLPIHKQILEINESPVLLLLDPEANAS 126 (288)
T ss_pred EEecccccCCC--CceeeCHHHHHHHHHHHHHhccCCceEEEEecCCCCCCHHHHHHHHHHHhhCCCcEEEEEccccccC
Confidence 89999999862 23899999999999999999999999999999999 9999999999999999999999999988 5
Q ss_pred CCCCceEEEEeehhhhccccccccceeeeeeeeeeecchhHHHHHHHhhhcc--cCcccchhhhHHHHHHHHHHHHHHHH
Q 036425 79 ELGIPTKAYYDVEEVKENATQKSQKVFVHVPSEIAAHEVEEIGVEHLLRDVK--DTTISTLANEVTGKLTALKGLDARLR 156 (252)
Q Consensus 79 ~~~lpi~~Y~~~~~~~~~~~~~~~~~F~~v~~~i~~~eaEri~vd~l~k~~~--~~~~~~l~~~l~~~~~al~~L~~~l~ 156 (252)
+++||+++|++...+.++ . ....|+|+||+|+++|||||||+|+++.+. +...+.+..++..+.+|+++|.+||+
T Consensus 127 ~~~lpi~ay~s~~~~~~~-~--~~~~F~~i~~~i~~~eaErIgv~~l~~~~~~~~~~~~~~~~~l~~~~~al~~L~~rl~ 203 (288)
T cd08063 127 GKDLPVTIYESVLELVDG-E--ATLRFRELPYTIETGEAERIGVDHVARGGASGSSEKSTVAAHLQAQHNAIKMLNSRVE 203 (288)
T ss_pred CCCCceeEEEEEEeccCC-c--cccEEEeeeeEEEeccCceeeHHHHHhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHH
Confidence 788999999999888765 2 567899999999999999999999999863 33455678899999999999999999
Q ss_pred HHHHHHHhhhCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 036425 157 EIRGYLDLVIDEKLPLNHEILYHLQDVFNLLPNLNVAELIKAFSVKTNDMMLVIYLSSLIRSVIALHNLINNKIL 231 (252)
Q Consensus 157 ~i~~Yl~~V~~G~~~~d~~ilR~l~~lv~~lP~~~~~~f~~~~~~~~~D~lmv~yLs~ltk~~~~l~e~l~~~~~ 231 (252)
.|++||++|.+|+.++|++|||+|+++|+++|.++.++|+++|..++||++|++|||+||||+.+|+++++||.-
T Consensus 204 ~i~~Yl~~V~~g~~~~d~~ilR~l~~~~~~lP~~~~~~~~~~~~~~~~D~lmv~yLs~lt~~~~~l~~~~~k~~~ 278 (288)
T cd08063 204 LILEYLKAVPVGEVPPDHSILRSISALCSRLPVLKSEAFREELLAEYNDVLLVAYLATLTKGCNTLNELVDKFNV 278 (288)
T ss_pred HHHHHHHHhcCCCCCCCHHHHHHHHHHHHhCccCChHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999965
No 6
>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f. Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and ap
Probab=100.00 E-value=1.2e-56 Score=397.87 Aligned_cols=220 Identities=26% Similarity=0.477 Sum_probs=206.7
Q ss_pred eeeecccCCCCCCceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCCCCCCCcHHHHHHHhccCC--CcEEEEEeCCCCC
Q 036425 2 VISVPFEEDDKDPGIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGPKLRENDLDIHQLFHNYVP--NPVLVIIDVQPKE 79 (252)
Q Consensus 2 sF~Vp~~e~~~~~~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~~~~~~~~~Ih~~~~~~~~--~PI~L~vD~~~~~ 79 (252)
||++||++++++ |.+|.+|+++|+++|++|||++.+||||+||+.+++++..||++|+++++ +||||++|+..++
T Consensus 43 sF~~p~~~~~~~---~~~d~~y~~~m~~~~kkv~~~~~vVGWY~tg~~~~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~~ 119 (265)
T cd08064 43 CFAVPHNESEDQ---VAVDMEYHRTMYELHQKVNPKEVIVGWYATGSEITEHSALIHDYYSRECTSYNPIHLTVDTSLDD 119 (265)
T ss_pred CeecceeCCCCe---EEEcHHHHHHHHHHHHHhCCCCcEEeeeeCCCCCCccHHHHHHHHHhhCCCCCCEEEEEeCCCCC
Confidence 899999998765 89999999999999999999999999999999999999999999999988 9999999999887
Q ss_pred CCCceEEEEeehhhhccccccccceeeeeeeeeeecchhHHHHHHHhhhcccCc-ccchhhhHHHHHHHHHHHHHHHHHH
Q 036425 80 LGIPTKAYYDVEEVKENATQKSQKVFVHVPSEIAAHEVEEIGVEHLLRDVKDTT-ISTLANEVTGKLTALKGLDARLREI 158 (252)
Q Consensus 80 ~~lpi~~Y~~~~~~~~~~~~~~~~~F~~v~~~i~~~eaEri~vd~l~k~~~~~~-~~~l~~~l~~~~~al~~L~~~l~~i 158 (252)
+++|++||++.+.+++++. ....|.++|++|.++|+|||||+|+++...+.+ ...+.+++..+.+|+++|.+||+.|
T Consensus 120 ~~l~i~ay~~~~~~~~~~~--~~~~F~~ip~~i~~~eaE~i~v~~l~~~~~~~~~~~~~~~~l~~~~~al~~L~~~l~~i 197 (265)
T cd08064 120 GKMSIKAYVSSPLGVPGKT--LGSMFVPIPLELLYSEAERVALDLLAKTLASPSRSAPLTSDLEQLEASLEKLQEMLDRV 197 (265)
T ss_pred CCcceEEEEEEecccCCCC--cceEEEEcceeeecCcHHHHHHHHHHhhccCCcccccchhhHHHHHHHHHHHHHHHHHH
Confidence 7999999999988776654 668899999999999999999999999876543 3346689999999999999999999
Q ss_pred HHHHHhhhCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHHHHHHH
Q 036425 159 RGYLDLVIDEKLPLNHEILYHLQDVFNLLPNLNVAELIKAFSVKTNDMMLVIYLSSLIRSVIALHNLI 226 (252)
Q Consensus 159 ~~Yl~~V~~G~~~~d~~ilR~l~~lv~~lP~~~~~~f~~~~~~~~~D~lmv~yLs~ltk~~~~l~e~l 226 (252)
++||++|.+|+.++|++|||+|+++|+++|.+++++|+++|++++||++|++|||+|||+|++|+|+|
T Consensus 198 ~~Yl~~V~~g~~~~d~~i~r~l~~~~~~lp~~~~~~f~~~~~~~~~D~lmv~YLs~l~k~~~~l~ekl 265 (265)
T cd08064 198 LRYVEDVLAGKVKADNAIGRYLMDALTSVPKLDPEEFEKMFNSSLQDLLMVTYLSNLTKTQLALAEKL 265 (265)
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHhhhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999985
No 7
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=7.6e-48 Score=326.38 Aligned_cols=224 Identities=23% Similarity=0.387 Sum_probs=205.8
Q ss_pred eeeecccCCCCCCceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCCCCCCCcHHHHHHHhccCCCcEEEEEeCCCCC-C
Q 036425 2 VISVPFEEDDKDPGIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGPKLRENDLDIHQLFHNYVPNPVLVIIDVQPKE-L 80 (252)
Q Consensus 2 sF~Vp~~e~~~~~~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~~~~~~~~~Ih~~~~~~~~~PI~L~vD~~~~~-~ 80 (252)
||++..+-.++. ..+|.+|+.++.+||++|||++.++|||+||+.+++.|+.||++++..+++|++|.++|...+ +
T Consensus 57 SFeL~~d~~~~~---~~~dke~l~kk~eqykqVFpdl~vlGwYttG~d~t~sd~~i~k~l~~i~esplflkLNp~t~~t~ 133 (299)
T KOG3050|consen 57 SFELKMDTEEDT---ETIDKEYLEKKEEQYKQVFPDLYVLGWYTTGSDPTPSDIHIHKQLMDINESPLFLKLNPATNHTD 133 (299)
T ss_pred eeEEEecchhhh---hhccHHHHHHHHHHHHHhcccceEEEEeecCCCCChhhhHHHHHHHhhhcCceEEEecchhcccc
Confidence 788887666544 469999999999999999999999999999999999999999999999999999999987763 5
Q ss_pred CCceEEEEeehhhhccccccccceeeeeeeeeeecchhHHHHHHHhhhcc--cCcccchhhhHHHHHHHHHHHHHHHHHH
Q 036425 81 GIPTKAYYDVEEVKENATQKSQKVFVHVPSEIAAHEVEEIGVEHLLRDVK--DTTISTLANEVTGKLTALKGLDARLREI 158 (252)
Q Consensus 81 ~lpi~~Y~~~~~~~~~~~~~~~~~F~~v~~~i~~~eaEri~vd~l~k~~~--~~~~~~l~~~l~~~~~al~~L~~~l~~i 158 (252)
+.|+.+|++....++|. .+..|+|+.|+++++|||||||||+++-.. ++..+++..++..+..|++||+.|++.|
T Consensus 134 ~~pv~lfese~dvidg~---~q~~f~~~tytl~teEaERIgVdHVA~lt~~~gge~s~VaeHl~AQdsA~~ml~~Rvkli 210 (299)
T KOG3050|consen 134 KDPVTLFESEIDVIDGE---AQMLFVPLTYTLATEEAERIGVDHVARLTPSDGGEGSSVAEHLEAQDSAIKMLDNRVKLI 210 (299)
T ss_pred CCCceeeeeeheeecCc---ceeeeeeeEEEEeehhhhhccchhheeeccCCCCCcchHHHHHhhHHHHHHHHhhHHHHH
Confidence 56999999998887654 678999999999999999999999999532 2334577899999999999999999999
Q ss_pred HHHHHhhhCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhchHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 036425 159 RGYLDLVIDEKLPLNHEILYHLQDVFNLLPNLNVAELIKAFSVKTNDMMLVIYLSSLIRSVIALHNLINNKIL 231 (252)
Q Consensus 159 ~~Yl~~V~~G~~~~d~~ilR~l~~lv~~lP~~~~~~f~~~~~~~~~D~lmv~yLs~ltk~~~~l~e~l~~~~~ 231 (252)
+.||++|.+|+.++|.+|+|+...+|..||.++.++|.+.|..++||+.+++||+.+|+|+..+++++|+|--
T Consensus 211 l~Y~k~~e~G~l~~N~eILrea~~L~~~Lp~~~~~~F~d~F~~e~nd~~l~syl~~iT~~~~nMn~~vnKfn~ 283 (299)
T KOG3050|consen 211 LAYLKKVEAGTLQPNFEILREAYALCHRLPVMESEKFQDNFYMECNDVGLISYLGTITKCCNNMNEVVNKFNT 283 (299)
T ss_pred HHHHhhhhcCCcCccHHHHHHHHHHHhhccccchHHHhHHHHHhcchhhHHHHHHHHHHhhccHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999954
No 8
>PF13012 MitMem_reg: Maintenance of mitochondrial structure and function; PDB: 2O96_B 2O95_A.
Probab=99.92 E-value=1.6e-26 Score=180.48 Aligned_cols=114 Identities=39% Similarity=0.631 Sum_probs=13.7
Q ss_pred cchhHHHHHHHhhhcccCcccchhhhHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCCHHHHHHHHHHHhhCCCCCHHH
Q 036425 115 HEVEEIGVEHLLRDVKDTTISTLANEVTGKLTALKGLDARLREIRGYLDLVIDEKLPLNHEILYHLQDVFNLLPNLNVAE 194 (252)
Q Consensus 115 ~eaEri~vd~l~k~~~~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~G~~~~d~~ilR~l~~lv~~lP~~~~~~ 194 (252)
+|||||||+|++|+..+...+++..++..+..|+.+|.++++.+..||++|.+|+.++|+++||+|+++|+++|.+++++
T Consensus 1 eEaErigv~~l~~~~~~~~~s~~~~~l~~~~~al~~L~~~l~~i~~Yl~~v~~g~~~~d~~i~r~l~~l~~~lp~~~~~~ 80 (115)
T PF13012_consen 1 EEAERIGVDHLARGLGDHYYSSLSSQLENEQNALKMLHKRLWQILDYLEDVISGEIPPDHEILRQLQDLLSSLPKYDPEE 80 (115)
T ss_dssp SHHHHHHHHHHHHH--S---------------------------------------------------------------
T ss_pred CchHHHHHHHHHccCCCccccHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcCCCchhHHHHHHHHHHhcccccHHH
Confidence 58999999999998766655588899999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhchHHHHHHHHHHHHHHHHHHHHHHh
Q 036425 195 LIKAFSVKTNDMMLVIYLSSLIRSVIALHNLINN 228 (252)
Q Consensus 195 f~~~~~~~~~D~lmv~yLs~ltk~~~~l~e~l~~ 228 (252)
|+++|..+++|.+|++|||.+||++.++++++++
T Consensus 81 ~~~~~~~~~~D~l~v~yL~~l~k~~~~l~e~l~~ 114 (115)
T PF13012_consen 81 FEEEFNSEINDVLMVSYLAKLTKKQHALNELLNN 114 (115)
T ss_dssp ----------------------------------
T ss_pred HHHHHHhhchHHHHHHHHHHHhHHHHHHHHHHhc
Confidence 9999999999999999999999999999999987
No 9
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=99.92 E-value=6.2e-25 Score=180.64 Aligned_cols=108 Identities=26% Similarity=0.560 Sum_probs=97.0
Q ss_pred eeeecccCCCCCCceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCCC----CCCCcHHHHHHHhcc-CCCcEEEEEeCC
Q 036425 2 VISVPFEEDDKDPGIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGPK----LRENDLDIHQLFHNY-VPNPVLVIIDVQ 76 (252)
Q Consensus 2 sF~Vp~~e~~~~~~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~~----~~~~~~~Ih~~~~~~-~~~PI~L~vD~~ 76 (252)
||++|++++++. +.+|.+|+++|+++|++|||++.+||||++|+. ++..+..||++|+.. .++||+|++||.
T Consensus 43 sF~lp~~~~~~~---~~~d~~y~~~m~~~~~~v~~~~~vVGWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~ 119 (157)
T cd08057 43 SFELPFDEEEES---IFIDTEYLEKRYNLHKKVYPQEKIVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPS 119 (157)
T ss_pred eEEccccCCCcc---hhhhHHHHHHHHHHHHHhCCCCCEEEEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCC
Confidence 899999888665 789999999999999999999999999999998 899999999999997 889999999998
Q ss_pred C--CCCCCceEEEEeehhhhccccccccceeeeeeeeeeecchhHHH
Q 036425 77 P--KELGIPTKAYYDVEEVKENATQKSQKVFVHVPSEIAAHEVEEIG 121 (252)
Q Consensus 77 ~--~~~~lpi~~Y~~~~~~~~~~~~~~~~~F~~v~~~i~~~eaEri~ 121 (252)
. .++++|+++|++.+... .+.++|+++.++|+||||
T Consensus 120 ~~~~~~~l~i~ay~~~~~~~---------~~~~~~~~i~~~e~E~I~ 157 (157)
T cd08057 120 LQSDSEKLEISTFTSAQREE---------NGAEITYEIGTEETERIA 157 (157)
T ss_pred cccCCCcccEEEEEEecCCC---------CCceeeeEEecccccccC
Confidence 6 46899999999985421 133999999999999996
No 10
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=99.82 E-value=3.4e-19 Score=158.28 Aligned_cols=163 Identities=17% Similarity=0.161 Sum_probs=123.3
Q ss_pred eeeecccCCCCCCceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCC-CCCCCcHHHHHHHhccC--CCcEEEEEeCCC-
Q 036425 2 VISVPFEEDDKDPGIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGP-KLRENDLDIHQLFHNYV--PNPVLVIIDVQP- 77 (252)
Q Consensus 2 sF~Vp~~e~~~~~~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~-~~~~~~~~Ih~~~~~~~--~~PI~L~vD~~~- 77 (252)
||++|+.+++++...+.+|.+|+.+|+++++++++++.+||||++++ ....+...||.+|.... +.||||++|+..
T Consensus 43 ~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~e~iVGWY~S~p~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s 122 (266)
T cd08065 43 CFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVDHNHVGWYQSTYLGSFFTRDLIETQYNYQEAIEESVVLVYDPSKT 122 (266)
T ss_pred ccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCCCcEEEeEeecCCCCcCCHHHHHHHHHHhccCCCCEEEEECCCcc
Confidence 89999998866533456788999999999999999999999999999 22334777888887653 779999999986
Q ss_pred CCCCCceEEEEeehhhhc---------------cccccccceeeeeeeeeeecchhHHHHHHHhhhcccC-c-cc-chhh
Q 036425 78 KELGIPTKAYYDVEEVKE---------------NATQKSQKVFVHVPSEIAAHEVEEIGVEHLLRDVKDT-T-IS-TLAN 139 (252)
Q Consensus 78 ~~~~lpi~~Y~~~~~~~~---------------~~~~~~~~~F~~v~~~i~~~eaEri~vd~l~k~~~~~-~-~~-~l~~ 139 (252)
.++.++++||...+.+++ +. ..+.+|.+||++|..+.-+.+.+..+....... . -. -..+
T Consensus 123 ~~g~l~lkAyrl~~~~~~~~~~~~~~~~~l~~~~~--~~~~if~eiPv~i~n~~l~~~~L~~l~~~~~~~~~~~~~l~l~ 200 (266)
T cd08065 123 SQGSLSLKAYRLSEKFMELYKEGKFSTESLREANL--TFSNIFEEIPVVIRNSHLVNALLSELEEDSPSSQSDFDRLDLS 200 (266)
T ss_pred cccceeeEEEEEcHHHHHHhhcCCcCHHHHHHhcC--chhcEEEEEEEEEEchHHHHHHHHhcccCCCcccCCccccccc
Confidence 467899999999988765 22 256899999999999999999999986643321 1 00 1112
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 036425 140 EVTGKLTALKGLDARLREIRGYLDLVI 166 (252)
Q Consensus 140 ~l~~~~~al~~L~~~l~~i~~Yl~~V~ 166 (252)
....+...+..|.+.||.+..+.++..
T Consensus 201 ~~~~le~~l~~l~~~id~l~~e~~~~~ 227 (266)
T cd08065 201 TNSFLEKNLELLMESVDELSQEQGKFN 227 (266)
T ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 244455666777777777776666543
No 11
>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=99.61 E-value=2.1e-14 Score=127.67 Aligned_cols=124 Identities=22% Similarity=0.319 Sum_probs=106.7
Q ss_pred eeeecccCCCCCCceeEeCHHHHHHHHH--HHhhcCCCCeeEEEEecCCC----CCCCcHHHHHHHhccCCCcEEEEEeC
Q 036425 2 VISVPFEEDDKDPGIWFLDHNYHESMYS--MFKRINAKEHVVGWYSTGPK----LRENDLDIHQLFHNYVPNPVLVIIDV 75 (252)
Q Consensus 2 sF~Vp~~e~~~~~~~~~iD~~~~~~m~~--l~kkV~p~e~iVGWYstg~~----~~~~~~~Ih~~~~~~~~~PI~L~vD~ 75 (252)
||++|+.+++.. +..+.+|...|.+ +++++++++.+||||++++. ++..|+.+|..|.+.++.+|+|++||
T Consensus 52 ~fp~p~~~t~~~---v~~~~e~~~~m~~~~~~~~~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP 128 (268)
T cd08069 52 VFALPVEGTETR---VNAQDEFQEYMVQYEMLKQTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDP 128 (268)
T ss_pred EEECCcCCCCCc---eeccHHHHHHHHHHHHHHHhCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeC
Confidence 899998887655 5677799999999 99999999999999999987 88999999999999988899999997
Q ss_pred CCC--CCCCceEEEEeehhhhcc----cc---------------ccccceeeeeeeeeeecchhHHHHHHHhhh
Q 036425 76 QPK--ELGIPTKAYYDVEEVKEN----AT---------------QKSQKVFVHVPSEIAAHEVEEIGVEHLLRD 128 (252)
Q Consensus 76 ~~~--~~~lpi~~Y~~~~~~~~~----~~---------------~~~~~~F~~v~~~i~~~eaEri~vd~l~k~ 128 (252)
..+ .+++.++||...+.+... +. ......|.+||+++..++.|+..++.+.+.
T Consensus 129 ~~t~~~g~~~i~Afr~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~ 202 (268)
T cd08069 129 IRSLVKGKVVIGAFRTIPPGYKPLEPRQTTSNIGHLPKPKIEDFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNK 202 (268)
T ss_pred CccccCCcceeeEEEEECccccccCcccCccccCccCcHHHHHhCchhcEEEEeeeEEecCHHHHHHHHHHHHH
Confidence 544 688999999999876541 10 014568999999999999999999999875
No 12
>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain [] and PAD-1-like domain []. It has been shown that this domain occurs in prokaryotes []. Mov34 proteins act as the regulatory subunit of the 26 proteasome, which is involved in the ATP-dependent degradation of ubiquitinated proteins. The function of this domain is unclear, but it is found in the N terminus of the proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. A number of the proteins associated with this family belong to MEROPS peptidase family M67 (clan M-). This includes the Poh1 peptidase of Saccharomyces cerevisiae (Baker's yeast) which is a component of the 19S proteasome regulatory particle.; GO: 0005515 protein binding; PDB: 2ZNV_D 2ZNR_A 4E0Q_A 2P87_A 2P8R_A 2O96_B 2O95_A 3RZU_F 3RZV_A.
Probab=99.28 E-value=2.1e-12 Score=100.32 Aligned_cols=64 Identities=25% Similarity=0.626 Sum_probs=55.5
Q ss_pred eeeecccCCCCCCceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCCCC----CCCcHHHHHHHhccCCC
Q 036425 2 VISVPFEEDDKDPGIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGPKL----RENDLDIHQLFHNYVPN 67 (252)
Q Consensus 2 sF~Vp~~e~~~~~~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~~~----~~~~~~Ih~~~~~~~~~ 67 (252)
||++|+.+++++. ...+.++.++|++++++++|++.+||||+|++.. +..|+.+|++|.+.+|+
T Consensus 47 ~f~~p~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 47 SFPVPHSESEDDC--DMDDEDFQKKMIELLKKVNPNLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp EEEESEEEESSEE--EEECCHHHHHHHHHHHHCSTTSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred EEEeeEecCcccc--ccchhhHHHHHHhhhccccccceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence 8999999886542 4577777899999999999999999999999987 89999999999988764
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=99.27 E-value=1.8e-11 Score=96.97 Aligned_cols=87 Identities=26% Similarity=0.428 Sum_probs=74.0
Q ss_pred eeeecccCCCCCCceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCC----CCCCCcHHHHHHHhccCCCcEEEEEeCCC
Q 036425 2 VISVPFEEDDKDPGIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGP----KLRENDLDIHQLFHNYVPNPVLVIIDVQP 77 (252)
Q Consensus 2 sF~Vp~~e~~~~~~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~----~~~~~~~~Ih~~~~~~~~~PI~L~vD~~~ 77 (252)
||++|.....+. ...++.+|.+.|.++++++++++.+||||++++ .++..|..+|..+....+.++++.+|+..
T Consensus 42 ~~~~p~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~ 119 (135)
T smart00232 42 VFAVPNEPQDDS--VQEYDEDYSHLMDEELKKVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIK 119 (135)
T ss_pred EEecCcCCCCcc--hhhhhhhHHHHHHHHHHhhCCCceEEEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCc
Confidence 688897665433 236899999999999999999999999999987 45677999999998888889999999887
Q ss_pred CC-CCCceEEEEee
Q 036425 78 KE-LGIPTKAYYDV 90 (252)
Q Consensus 78 ~~-~~lpi~~Y~~~ 90 (252)
+. +++++++|+..
T Consensus 120 s~~g~~~~~af~~~ 133 (135)
T smart00232 120 SFQGRLSLRAFRLT 133 (135)
T ss_pred cccCcEEEEEEEec
Confidence 64 88999999985
No 14
>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. J
Probab=98.97 E-value=1.9e-09 Score=83.22 Aligned_cols=79 Identities=52% Similarity=0.928 Sum_probs=61.9
Q ss_pred eeeecccCCCCCCceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCCC----CCCCcHHHHHHHhccCCCcEEEEEeCCC
Q 036425 2 VISVPFEEDDKDPGIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGPK----LRENDLDIHQLFHNYVPNPVLVIIDVQP 77 (252)
Q Consensus 2 sF~Vp~~e~~~~~~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~~----~~~~~~~Ih~~~~~~~~~PI~L~vD~~~ 77 (252)
||.+|+.++... .+..+ -|......+.+++.+||||+|++. ++..|...|..|.+..+++++|++|+..
T Consensus 34 ~~~~~~~~~~~~-----~~~~~--~~~~~~~~~~~~~~iVGwyhshp~~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~ 106 (116)
T cd07767 34 VIAVPFDEGDKD-----DNVWF--LMYLDFKKLNAGLRIVGWYHTHPKPSCFLSPNDLATHELFQRYFPEKVMIIVDVKP 106 (116)
T ss_pred EEecccCCCCCc-----cHHHH--HHHHHHHHhcCCCeEEEEEEcCCCCCCccCHHHHHHHHHHHHhCCCCEEEEEECCC
Confidence 688888766433 23222 266666778899999999999876 6788888898888877889999999998
Q ss_pred CCCCCceEEE
Q 036425 78 KELGIPTKAY 87 (252)
Q Consensus 78 ~~~~lpi~~Y 87 (252)
.+.++|+++|
T Consensus 107 ~~~~~~~~~~ 116 (116)
T cd07767 107 KDLGNSWKCY 116 (116)
T ss_pred ccCCCCcccC
Confidence 7667888887
No 15
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=98.35 E-value=9.6e-06 Score=71.39 Aligned_cols=163 Identities=17% Similarity=0.294 Sum_probs=104.4
Q ss_pred eeeecccC-CCCC-CceeEeCHH---HHHHHHHHHhhcCCCCeeEEEEec---CCCCCCCcHHHHHHH--hccCCCcEEE
Q 036425 2 VISVPFEE-DDKD-PGIWFLDHN---YHESMYSMFKRINAKEHVVGWYST---GPKLRENDLDIHQLF--HNYVPNPVLV 71 (252)
Q Consensus 2 sF~Vp~~e-~~~~-~~~~~iD~~---~~~~m~~l~kkV~p~e~iVGWYst---g~~~~~~~~~Ih~~~--~~~~~~PI~L 71 (252)
||.-|..+ .+|+ ++.-..|.. |...|+..++.||-+...||||-. |+-++ ...+--+| ..-+|.-|.|
T Consensus 57 cFp~p~~~~~edda~~~~~~de~rq~~~l~mlrrlr~vnid~~hVGwYqs~~vgs~lS--~~lveSqy~YQ~a~pesVvl 134 (339)
T KOG1560|consen 57 CFPFPSVLENEDDAVNKSVSDEARQAYQLAMLRRLRYVNIDHLHVGWYQSAYVGSFLS--PALVESQYAYQKAIPESVVL 134 (339)
T ss_pred ccCCCccCCCccchhhhhhhHHHHHHHHHHHHHHhhhcCccceeeeeeeeehhccccC--HHHHHHHHHHHhcCCccEEE
Confidence 89888533 3332 122234544 888999999999999999999975 44444 22223333 3346778999
Q ss_pred EEeCCCC-CCCCceEEEEeehhhhcc---cc------c----cccceeeeeeeeeeecchhHHHHHHHh--hhcccC---
Q 036425 72 IIDVQPK-ELGIPTKAYYDVEEVKEN---AT------Q----KSQKVFVHVPSEIAAHEVEEIGVEHLL--RDVKDT--- 132 (252)
Q Consensus 72 ~vD~~~~-~~~lpi~~Y~~~~~~~~~---~~------~----~~~~~F~~v~~~i~~~eaEri~vd~l~--k~~~~~--- 132 (252)
+.||.-+ .|.|.++||...+....- +. + ....+|..+|..|..+---.+-+.-+. +.+...
T Consensus 135 iYD~~kssqG~L~lrAyrLTp~am~~~kekdwtpealk~~nltyenmfeElPIVIknS~L~nvlmseLs~~e~c~sdk~~ 214 (339)
T KOG1560|consen 135 IYDPIKSSQGTLSLRAYRLTPEAMAAHKEKDWTPEALKSANLTYENMFEELPIVIKNSHLANVLMSELSEPEDCESDKPL 214 (339)
T ss_pred EeccccccCceEEeehhhcCHHHHHHHhcCCCCHHHHHhcCCCHHHHHhhcCeeeeccHHHHHHHHhccccccccccccc
Confidence 9999865 688999999998764310 00 0 134589999999998765555555554 222111
Q ss_pred -------cccchhhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 036425 133 -------TISTLANEVTGKLTALKGLDARLREIRGYLDLVI 166 (252)
Q Consensus 133 -------~~~~l~~~l~~~~~al~~L~~~l~~i~~Yl~~V~ 166 (252)
+...+..+++.++..+..|..-+...-+|-+.+.
T Consensus 215 ~~~fdlgs~t~leknir~lme~vDEl~qe~~~l~kyqr~~~ 255 (339)
T KOG1560|consen 215 HSNFDLGSGTRLEKNIRLLMERVDELHQEIVNLNKYQRQLA 255 (339)
T ss_pred cccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1224555666666666666666666677776664
No 16
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=97.63 E-value=0.00028 Score=62.47 Aligned_cols=92 Identities=21% Similarity=0.271 Sum_probs=66.9
Q ss_pred eeeecccCCCCCCceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCCC----CCCCcHHHHHHHhccCCCcEEEEEeCCC
Q 036425 2 VISVPFEEDDKDPGIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGPK----LRENDLDIHQLFHNYVPNPVLVIIDVQP 77 (252)
Q Consensus 2 sF~Vp~~e~~~~~~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~~----~~~~~~~Ih~~~~~~~~~PI~L~vD~~~ 77 (252)
||++|-..++--+++..--.+|+-.-.+.-+.|...|.+||||++.+. ++..|..-+..=.++-+.=+.++|||.-
T Consensus 95 ~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k~~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~R 174 (347)
T KOG1554|consen 95 SFALPVEGTETRVNAQAEAYEYMVQYIEEAKNVGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTR 174 (347)
T ss_pred ccccccccccceechHHHHHHHHHHHHHHHHHhhhhhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCcc
Confidence 899998777655555555678998888999999999999999999765 4555655443333332323788999864
Q ss_pred --CCCCCceEEEEeehhh
Q 036425 78 --KELGIPTKAYYDVEEV 93 (252)
Q Consensus 78 --~~~~lpi~~Y~~~~~~ 93 (252)
+.+++-+-||..-+.+
T Consensus 175 tlsagkv~iGAFRTyp~g 192 (347)
T KOG1554|consen 175 TLSAGKVNIGAFRTYPKG 192 (347)
T ss_pred ccccCceeeceeecccCC
Confidence 4678888888776654
No 17
>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=97.35 E-value=0.0038 Score=54.89 Aligned_cols=94 Identities=16% Similarity=0.203 Sum_probs=63.1
Q ss_pred eeEeCHHHH----HHHHHHHhhcCCCCeeEEEEecCCC----CCCCcHHHHHHHhccCCCcEEEEEeCCCC-----CCCC
Q 036425 16 IWFLDHNYH----ESMYSMFKRINAKEHVVGWYSTGPK----LRENDLDIHQLFHNYVPNPVLVIIDVQPK-----ELGI 82 (252)
Q Consensus 16 ~~~iD~~~~----~~m~~l~kkV~p~e~iVGWYstg~~----~~~~~~~Ih~~~~~~~~~PI~L~vD~~~~-----~~~l 82 (252)
-+.+|.+-+ +.+.++-+.+..++.+||||++-+. ++..|..-+..|....+.-++++|++... .++.
T Consensus 63 r~eidPee~~~a~~ea~~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~ 142 (244)
T cd08068 63 RVEISPEQLSAASTEAERLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEV 142 (244)
T ss_pred eEEeCHHHHHHHHHHHHHHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCE
Confidence 378898633 4555666777899999999999775 45566655444544456678999975432 2567
Q ss_pred ceEEEEeehhhhccccccccceeeeeeeeeee
Q 036425 83 PTKAYYDVEEVKENATQKSQKVFVHVPSEIAA 114 (252)
Q Consensus 83 pi~~Y~~~~~~~~~~~~~~~~~F~~v~~~i~~ 114 (252)
.+++|...+.. ++......++|+.|..
T Consensus 143 ~i~aFr~~~g~-----~~~~~~~~e~pl~i~~ 169 (244)
T cd08068 143 QVTCFQSVQGN-----KAGQYERIEVPLEIVP 169 (244)
T ss_pred EEEEEEecCCC-----CCCcceEEEeeeEEec
Confidence 78999986431 1234567788887765
No 18
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=97.33 E-value=0.00071 Score=52.81 Aligned_cols=62 Identities=16% Similarity=0.296 Sum_probs=44.5
Q ss_pred HHHHHHhhcCCCCeeEEEEecCCC----CCCCcHHHHHHHhccCCCcEEEEEeCCCCCCCCceEEEEe
Q 036425 26 SMYSMFKRINAKEHVVGWYSTGPK----LRENDLDIHQLFHNYVPNPVLVIIDVQPKELGIPTKAYYD 89 (252)
Q Consensus 26 ~m~~l~kkV~p~e~iVGWYstg~~----~~~~~~~Ih~~~~~~~~~PI~L~vD~~~~~~~lpi~~Y~~ 89 (252)
.|..+.....-++.+||||++.+. ++..|+..|..|....+..++|++|+.. ....+++|..
T Consensus 53 ~~~~~~~~~~~g~~~vG~YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~--~~~~~~a~rl 118 (119)
T cd08058 53 VEELFNVQTGRPLLVVGWYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKH--RNKDTGIFRL 118 (119)
T ss_pred HHHHHHHHhCCCCeEEEEEecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCC--CCcccceEEe
Confidence 344455567889999999999773 5566666566566666778999999865 2667777754
No 19
>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=97.21 E-value=0.0055 Score=51.88 Aligned_cols=87 Identities=14% Similarity=0.156 Sum_probs=59.0
Q ss_pred eeeecccCCCCCCceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCCC----CCCCcHHHHHHHhccCC-------CcEE
Q 036425 2 VISVPFEEDDKDPGIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGPK----LRENDLDIHQLFHNYVP-------NPVL 70 (252)
Q Consensus 2 sF~Vp~~e~~~~~~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~~----~~~~~~~Ih~~~~~~~~-------~PI~ 70 (252)
||.+|.....+. +.+|.++...|.+..++.+ +.+||||++.+. ++..|+.-|..|....+ .-|.
T Consensus 48 ~~p~~~~~~~~~---~e~dp~~q~e~~~~l~~~g--l~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~ 122 (187)
T cd08067 48 AFPCRSRLTGLD---CEMDPVSETEIRESLESRG--LSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVG 122 (187)
T ss_pred EEecCCCCCCcc---cccCHHHHHHHHHHHHHcC--CEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEE
Confidence 566665444333 6689999999998888754 799999999764 34445555555544332 2389
Q ss_pred EEEeCCCC---CCCCceEEEEeehhh
Q 036425 71 VIIDVQPK---ELGIPTKAYYDVEEV 93 (252)
Q Consensus 71 L~vD~~~~---~~~lpi~~Y~~~~~~ 93 (252)
++++|-.. +....|.+|-..+..
T Consensus 123 ~I~~P~~~~~~~~~s~i~~f~~~~~~ 148 (187)
T cd08067 123 LICSPYDRRNSTPESQITCFWVMPPP 148 (187)
T ss_pred EEEccccCCCCCCCCcEEEEEEECCC
Confidence 99998653 345678999887653
No 20
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=97.18 E-value=0.00077 Score=60.88 Aligned_cols=89 Identities=20% Similarity=0.344 Sum_probs=65.6
Q ss_pred eeecccCCCCCCceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCCC----CCCCcHHHHHHHhccCCCcEEEEEeCCCC
Q 036425 3 ISVPFEEDDKDPGIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGPK----LRENDLDIHQLFHNYVPNPVLVIIDVQPK 78 (252)
Q Consensus 3 F~Vp~~e~~~~~~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~~----~~~~~~~Ih~~~~~~~~~PI~L~vD~~~~ 78 (252)
|+.|+...+=..-+-++|.-|...|.++.++.-..+.|||||++-+. ++..|+.-++.|...++..+...||+..+
T Consensus 80 ~am~~sg~~is~~~e~~d~V~q~q~~~~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S 159 (316)
T KOG1555|consen 80 FAMPQSGTGISKFVEAVDPVFQTQMMDLLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQS 159 (316)
T ss_pred eccccccceecccchhccHHHHHHHHHHHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccC
Confidence 55665554321013469999999999999998877999999998654 56788888999988888888999998765
Q ss_pred -CCCCceEEEEeeh
Q 036425 79 -ELGIPTKAYYDVE 91 (252)
Q Consensus 79 -~~~lpi~~Y~~~~ 91 (252)
.++.-+.+|-.+.
T Consensus 160 ~~g~vv~d~f~~In 173 (316)
T KOG1555|consen 160 PYGKVVPDAFSSIN 173 (316)
T ss_pred CCCCccCChhhhcC
Confidence 3444444665543
No 21
>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al
Probab=96.34 E-value=0.0086 Score=50.06 Aligned_cols=55 Identities=16% Similarity=0.236 Sum_probs=43.3
Q ss_pred CCCeeEEEEecCCC----CCCCcHHHHHHHhccCCCcEEEEEeCCCCCCCCceEEEEee-hhhh
Q 036425 36 AKEHVVGWYSTGPK----LRENDLDIHQLFHNYVPNPVLVIIDVQPKELGIPTKAYYDV-EEVK 94 (252)
Q Consensus 36 p~e~iVGWYstg~~----~~~~~~~Ih~~~~~~~~~PI~L~vD~~~~~~~lpi~~Y~~~-~~~~ 94 (252)
.++.+||||+|-+. +++.|+..|..|....+..++|++++. ...+.+|... +.|.
T Consensus 73 ~gle~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~----~~~l~afrl~~~~g~ 132 (173)
T cd08066 73 HDLITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK----YNEFGIFRLTDPPGL 132 (173)
T ss_pred CCCeeEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC----CcEEeEEEeecCCcc
Confidence 68999999999653 677888888777666688899999863 5668899887 5544
No 22
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=94.79 E-value=0.13 Score=40.73 Aligned_cols=53 Identities=28% Similarity=0.484 Sum_probs=34.7
Q ss_pred eEeCHHHHHHHHHHHhhcCCCCeeEEEEecCCC--CCCCcHHHHHHHhccCCCcEEEEEe
Q 036425 17 WFLDHNYHESMYSMFKRINAKEHVVGWYSTGPK--LRENDLDIHQLFHNYVPNPVLVIID 74 (252)
Q Consensus 17 ~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~~--~~~~~~~Ih~~~~~~~~~PI~L~vD 74 (252)
..++.++.. ++..... ..+.|||||++.+. ..+++..++ +++..+.|-+++..
T Consensus 51 ~~~~~~~~~-~~~~~~~--~g~~vvg~yHSHP~~~~~pS~~D~~--~~~~~~~~~~iv~~ 105 (134)
T COG1310 51 FEIDPEYSL-FYLAAED--AGEVVVGWYHSHPGGPPYPSEADRR--LSKLGPLPWLIVSV 105 (134)
T ss_pred EeeCHHHHH-HHHHHhh--CCCEEEEEEcCCCCCCCCcCHHHHh--hccccCCCEEEEEc
Confidence 556666665 4444443 34999999999884 456666666 77776555566554
No 23
>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=89.04 E-value=7 Score=30.46 Aligned_cols=69 Identities=16% Similarity=0.200 Sum_probs=44.3
Q ss_pred ceeEeCHHHHHHHHHHHhhcCCCCeeEEEEecCCC--CCCCcHHHHHHHhccCCCcEEEEEeCCCCCCCCceEEEEee
Q 036425 15 GIWFLDHNYHESMYSMFKRINAKEHVVGWYSTGPK--LRENDLDIHQLFHNYVPNPVLVIIDVQPKELGIPTKAYYDV 90 (252)
Q Consensus 15 ~~~~iD~~~~~~m~~l~kkV~p~e~iVGWYstg~~--~~~~~~~Ih~~~~~~~~~PI~L~vD~~~~~~~lpi~~Y~~~ 90 (252)
..+.+|...+....+..++- ++.+||||+|-+. ..+....+..+.. ...+++++..... ...+++|...
T Consensus 49 ~~f~~d~~~~~~~~~~~~~~--g~~~vG~~HSHP~~~~~PS~~D~~~~~~---~~~~~lIv~~~~~--~~~~~~~~~~ 119 (128)
T cd08070 49 RRFEIDPAEQLAAQREARER--GLEVVGIYHSHPDGPARPSETDLRLAWP---PGVSYLIVSLAGG--APELRAWRLE 119 (128)
T ss_pred ceEEECHHHHHHHHHHHHHC--CCeEEEEEeCCCCCCCCCCHHHHHhccC---CCCeEEEEECCCC--CcEEEEEEEc
Confidence 34889998887777776653 6999999999775 2333333322211 2357888875432 4457888773
No 24
>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=86.27 E-value=0.39 Score=33.38 Aligned_cols=12 Identities=50% Similarity=0.974 Sum_probs=7.1
Q ss_pred CeeEEEEecCCC
Q 036425 38 EHVVGWYSTGPK 49 (252)
Q Consensus 38 e~iVGWYstg~~ 49 (252)
-.|||||+|.-.
T Consensus 40 g~vvgwy~t~lt 51 (78)
T PF06442_consen 40 GQVVGWYCTKLT 51 (78)
T ss_dssp EEEEEEE--SS-
T ss_pred ceEeEEEecccc
Confidence 479999998633
No 25
>cd08060 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p). This family includes Noc4p (neighbor of COX4; neighbor of Cytochrome c Oxidase 4; nucleolar complex associated 4 homolog) which belongs to the family of unknown function, UPF0172, with MPN/JAMM-like domains. Proteins in this family are homologs of the NOC4 gene which is conserved in eukaryotic members including human, dog, mouse, rat, chicken, zebrafish, fruit fly, mosquito, S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa, A.thaliana, and rice. NOC4 highly expressed in the pancreas and moderately in liver, heart, lung, kidney, brain, skeletal muscle, and placenta. This nucleolar protein forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=82.34 E-value=2.1 Score=36.06 Aligned_cols=59 Identities=15% Similarity=0.251 Sum_probs=38.6
Q ss_pred eEeCHHH--HHHHHHHHhhcCCCCeeEEEEecCCCCC-----CCcHHHHHHHhccCCCcEEEEEeCC
Q 036425 17 WFLDHNY--HESMYSMFKRINAKEHVVGWYSTGPKLR-----ENDLDIHQLFHNYVPNPVLVIIDVQ 76 (252)
Q Consensus 17 ~~iD~~~--~~~m~~l~kkV~p~e~iVGWYstg~~~~-----~~~~~Ih~~~~~~~~~PI~L~vD~~ 76 (252)
+.+|... ...+.+.+.+- .++.|||+|++.+... +....|=+.+.+.++++++|+||-.
T Consensus 48 ~~l~P~~Eval~~ve~~~~~-~gl~IvG~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~ 113 (182)
T cd08060 48 LALAPMLEVALALVDAYCKS-SGLVIVGYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNE 113 (182)
T ss_pred cccCHHHHHHHHHHHHHHHH-CCCEEEEEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCc
Confidence 3466553 23344444444 4799999999987543 3334455667777789999999844
No 26
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=78.88 E-value=6.8 Score=33.37 Aligned_cols=67 Identities=13% Similarity=0.202 Sum_probs=42.8
Q ss_pred HHHHHHHHHHhhcCCCCeeEEEEecCCCC-----CCCcHHHHHHHhccCCCcEEEEEeCCC-C--CCCCceEEEEe
Q 036425 22 NYHESMYSMFKRINAKEHVVGWYSTGPKL-----RENDLDIHQLFHNYVPNPVLVIIDVQP-K--ELGIPTKAYYD 89 (252)
Q Consensus 22 ~~~~~m~~l~kkV~p~e~iVGWYstg~~~-----~~~~~~Ih~~~~~~~~~PI~L~vD~~~-~--~~~lpi~~Y~~ 89 (252)
|-.-.+.+.|-+. .++.|||||.....+ ++.-.-|=+.+.+.++.++.++||-.. . .+..++.+|..
T Consensus 61 EvAL~qvd~~~~~-~gl~IvGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~kl~~~~~~~~~~~~~~ 135 (196)
T PF03665_consen 61 EVALAQVDAYAKS-NGLVIVGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKKLSSDCKAPAISVYQR 135 (196)
T ss_pred HHHHHHHHHHHhh-CCCEEEEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcccccccCCCcceeeee
Confidence 3344556666654 679999999987643 333344556677778889999999442 1 22334567763
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=65.70 E-value=15 Score=32.66 Aligned_cols=58 Identities=22% Similarity=0.265 Sum_probs=42.1
Q ss_pred CCCeeEEEEecCCC----CCCCcHHHHHHHhccCC-----CcEEEEEeCCCCCCCCceEEEEeehhhhc
Q 036425 36 AKEHVVGWYSTGPK----LRENDLDIHQLFHNYVP-----NPVLVIIDVQPKELGIPTKAYYDVEEVKE 95 (252)
Q Consensus 36 p~e~iVGWYstg~~----~~~~~~~Ih~~~~~~~~-----~PI~L~vD~~~~~~~lpi~~Y~~~~~~~~ 95 (252)
-++..|||=+|.+. +++.|+..|.-|...++ ..|.+++- +..|...+.+|.....|..
T Consensus 104 ~~Le~LGWIHTqp~e~~~Lss~Dv~tha~~~~~~~~w~~~~~V~it~S--ftpGs~sl~ay~LT~~G~~ 170 (252)
T cd08056 104 EDLEPLGWIHTQPNELPQLSPQDVTTHAKILADNPSWDGEKTVILTCS--FTPGSCSLTAYKLTPEGYE 170 (252)
T ss_pred CCCEeeEEEEcCCCCccccCHHHHHHHHHHHHhccccCCCcEEEEEEc--CCCCceEEEEEecCHHHHH
Confidence 56899999999753 57889999977766555 34555553 4456788999999877653
No 28
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=52.95 E-value=19 Score=29.13 Aligned_cols=41 Identities=27% Similarity=0.519 Sum_probs=30.3
Q ss_pred CCCeeEEE--EecCCCCCCCcHHHHHHHhccCCC-cEEEEEeCC
Q 036425 36 AKEHVVGW--YSTGPKLRENDLDIHQLFHNYVPN-PVLVIIDVQ 76 (252)
Q Consensus 36 p~e~iVGW--Ystg~~~~~~~~~Ih~~~~~~~~~-PI~L~vD~~ 76 (252)
|.-.|=|| |.||-......-.||+.|+.+-+- -|||-+|-.
T Consensus 66 PqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRR 109 (170)
T KOG0130|consen 66 PQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRR 109 (170)
T ss_pred CccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccc
Confidence 88999999 556654444566799999998542 389999843
No 29
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=41.64 E-value=33 Score=20.50 Aligned_cols=30 Identities=20% Similarity=0.273 Sum_probs=19.0
Q ss_pred HHHHHHhhhCCCCCCCHHHHHHHHHHHhhCC
Q 036425 158 IRGYLDLVIDEKLPLNHEILYHLQDVFNLLP 188 (252)
Q Consensus 158 i~~Yl~~V~~G~~~~d~~ilR~l~~lv~~lP 188 (252)
+++++++... +-.-..+|...|.+.|+.+|
T Consensus 10 ~v~~i~~~l~-~~~t~~~I~~~l~~~C~~lP 39 (39)
T PF05184_consen 10 VVKEIEKLLK-NNKTEEEIKKALEKACNKLP 39 (39)
T ss_dssp HHHHHHHHHH-STCHHHHHHHHHHHHHTTSC
T ss_pred HHHHHHHHHH-cCccHHHHHHHHHHHHhhCc
Confidence 3444444442 22345688889999999887
No 30
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=39.04 E-value=1.1e+02 Score=25.90 Aligned_cols=65 Identities=14% Similarity=0.308 Sum_probs=40.8
Q ss_pred HHHHHHHHhhcCCCCeeEEEEecCCCCCC-----CcHHHHHHHhccCCCcEEEEEeC-CCC--CCCCceEEEEe
Q 036425 24 HESMYSMFKRINAKEHVVGWYSTGPKLRE-----NDLDIHQLFHNYVPNPVLVIIDV-QPK--ELGIPTKAYYD 89 (252)
Q Consensus 24 ~~~m~~l~kkV~p~e~iVGWYstg~~~~~-----~~~~Ih~~~~~~~~~PI~L~vD~-~~~--~~~lpi~~Y~~ 89 (252)
.-.|.+-+-. --.+.|+|.|.....++. .-..|-+-++++.++..+|++|- .+. -..-||.+|+-
T Consensus 63 Al~lId~~~~-~~GlviaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~~l~~~~e~~~v~v~e~ 135 (199)
T KOG3289|consen 63 ALNLIDVWGA-QAGLVIAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNKKLVPQCERPPVIVLED 135 (199)
T ss_pred HHHHHHHHHH-hcCeEEEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEeccccccccCCCCEEEeec
Confidence 3444554442 367999999998765543 33445677788878765566553 332 24568999983
No 31
>PF11371 DUF3172: Protein of unknown function (DUF3172); InterPro: IPR021511 This family of proteins has no known function.
Probab=35.36 E-value=92 Score=24.94 Aligned_cols=64 Identities=16% Similarity=0.242 Sum_probs=38.8
Q ss_pred EEecCCCCCCCcHHHHHHHhccCCCc--------EEEEEeCCCCCCCCceEEEEeehhhhccccccccceeeeeeeee
Q 036425 43 WYSTGPKLRENDLDIHQLFHNYVPNP--------VLVIIDVQPKELGIPTKAYYDVEEVKENATQKSQKVFVHVPSEI 112 (252)
Q Consensus 43 WYstg~~~~~~~~~Ih~~~~~~~~~P--------I~L~vD~~~~~~~lpi~~Y~~~~~~~~~~~~~~~~~F~~v~~~i 112 (252)
|+++....++....=.+++.+-.|+| =.+++|...--.--|+..|++.+..- +++..+.-.+.|
T Consensus 22 ~~sS~~~~~p~NvAS~e~iD~~aPnpe~C~q~GASA~v~D~rvfvTlNPfnvyVsQP~~q------PGCVlRr~Nw~i 93 (140)
T PF11371_consen 22 AFSSTTNFNPSNVASREFIDRAAPNPEFCVQFGASAMVMDMRVFVTLNPFNVYVSQPEMQ------PGCVLRRNNWAI 93 (140)
T ss_pred EEecccccCcccchhHHHHhhcCCChHHHHhcCceeEEEeeEEEEEecCceeeeccCCCC------CceEEEeccHHH
Confidence 77777777777777777777766665 12333322111122788999988753 456777765543
No 32
>PF08255 Leader_Trp: Trp-operon Leader Peptide; InterPro: IPR013205 The tryptophan operon regulatory region of Citrobacter freundii (leader transcript) encodes a 14-residue peptide containing characteristic tandem tryptophan residues. It is about 10 nucleotides shorter than those of Escherichia coli and Salmonella typhimurium [].
Probab=31.02 E-value=42 Score=16.20 Aligned_cols=9 Identities=33% Similarity=1.007 Sum_probs=6.9
Q ss_pred eeEEEEecC
Q 036425 39 HVVGWYSTG 47 (252)
Q Consensus 39 ~iVGWYstg 47 (252)
.+.||+.|+
T Consensus 6 ~L~~WWrtS 14 (14)
T PF08255_consen 6 SLHGWWRTS 14 (14)
T ss_pred EEeeEEEcC
Confidence 578999874
No 33
>cd07641 BAR_ASAP1 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ASAP1 (ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 1) is also known as DDEF1 (Development and Differentiation Enhancing Factor 1), AMAP1, centaurin beta-4, or PAG2. ASAP1 is an Arf GTPase activating protein (GAP) with activity towards Arf1 and Arf5 but not Arf6 However, it has been shown to bind GTP-Arf6 stably without GAP activity. It has been implicated in cell growth, migration, and survival, as well as in tumor invasion and malignancy. It binds paxillin and cortactin, two components of invadopodia which are essential for tumor invasiveness. It also binds focal adhesion kinase (FAK) and the SH2/SH3 adaptor CrkL. ASAP1 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Ar
Probab=28.86 E-value=3.8e+02 Score=23.23 Aligned_cols=25 Identities=12% Similarity=0.093 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhh
Q 036425 142 TGKLTALKGLDARLREIRGYLDLVI 166 (252)
Q Consensus 142 ~~~~~al~~L~~~l~~i~~Yl~~V~ 166 (252)
..+..++..++.+|+.+.+.+..+.
T Consensus 5 ~~~ee~l~~~e~~L~Kl~K~~kam~ 29 (215)
T cd07641 5 NVLEEALDQDRTALQKVKKSVKAIY 29 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456677777777777777777664
No 34
>PF12408 DUF3666: Ribose-5-phosphate isomerase ; InterPro: IPR022133 This domain family is found in bacteria, and is approximately 50 amino acids in length. The family is found in association with PF02502 from PFAM. There are two completely conserved residues (D and F) that may be functionally important. ; PDB: 3ONO_A 3C5Y_N 2PPW_A.
Probab=28.00 E-value=1.6e+02 Score=19.26 Aligned_cols=33 Identities=9% Similarity=0.308 Sum_probs=22.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhchHHHHHHHH
Q 036425 172 LNHEILYHLQDVFNLLPNLNVAELIKAFSVKTNDMMLVIYLS 213 (252)
Q Consensus 172 ~d~~ilR~l~~lv~~lP~~~~~~f~~~~~~~~~D~lmv~yLs 213 (252)
.|+++++.. ++.+.|.+-|-.+.+|.-+..|+-
T Consensus 14 iDqdLvK~A---------isGe~Fqe~FF~ncqd~eI~~yvk 46 (48)
T PF12408_consen 14 IDQDLVKTA---------ISGERFQECFFANCQDEEIAAYVK 46 (48)
T ss_dssp S-HHHHHHH---------T-SHHHHHHHHHH---HHHHHHHH
T ss_pred hCHHHHHHH---------hccHHHHHHHHhcCCcHHHHHHHH
Confidence 566666554 566899999999999999999874
No 35
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=26.99 E-value=1.4e+02 Score=18.92 Aligned_cols=38 Identities=16% Similarity=0.167 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHHHhhhCCCCCCCHHHHHHHHHHHh
Q 036425 148 LKGLDARLREIRGYLDLVIDEKLPLNHEILYHLQDVFN 185 (252)
Q Consensus 148 l~~L~~~l~~i~~Yl~~V~~G~~~~d~~ilR~l~~lv~ 185 (252)
.+.|..++..=..++.+...|+..++.+.+..|.+.+.
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~ 49 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKRNPSLDTLKKIAKALG 49 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHT
T ss_pred HHHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHC
Confidence 35566666666677888888999999999999998887
No 36
>KOG2213 consensus Apoptosis inhibitor 5/fibroblast growth factor 2-interacting factor 2, and related proteins [Signal transduction mechanisms]
Probab=25.19 E-value=95 Score=29.53 Aligned_cols=97 Identities=18% Similarity=0.233 Sum_probs=63.1
Q ss_pred eeeeeeeeeeecchhHHHHHHHhhhcccCcccchhhhHHHHHHHHHHHH-----HHHHHHHHHHHhhhCCC---CCCCHH
Q 036425 104 VFVHVPSEIAAHEVEEIGVEHLLRDVKDTTISTLANEVTGKLTALKGLD-----ARLREIRGYLDLVIDEK---LPLNHE 175 (252)
Q Consensus 104 ~F~~v~~~i~~~eaEri~vd~l~k~~~~~~~~~l~~~l~~~~~al~~L~-----~~l~~i~~Yl~~V~~G~---~~~d~~ 175 (252)
...+++.++.+-|.|+-.++.+-+...+.+...+..=+ ....+++.++ .++..+.+|.+....=. ..-+.-
T Consensus 135 Kl~~l~~e~L~kevE~~iv~eikkal~dVtgeef~lfm-~~L~~lk~~~~k~~~a~lqeLa~~~e~~a~ldaf~~sD~d~ 213 (460)
T KOG2213|consen 135 KLITLKGEVLTKEVERHIVDEIKKALEDVTGEEFTLFM-DILASLKSLQTKAGEARLQELAEEQEGLADLDAFNVSDADY 213 (460)
T ss_pred HhhcccHHHhhhHHHHHHHHHHHHHHHhccHHHHHHHH-HHHHhhhcccCCCCHHHHHHHHHHHhhhhccCcccCCChHH
Confidence 45677888888999999999998887665543322211 2234455554 56777777777765432 333467
Q ss_pred HHHHHHHHHhhCCCCC----HHHHHHHHHh
Q 036425 176 ILYHLQDVFNLLPNLN----VAELIKAFSV 201 (252)
Q Consensus 176 ilR~l~~lv~~lP~~~----~~~f~~~~~~ 201 (252)
|=|.|+-+...+|-.. +..|-..++.
T Consensus 214 VdRfisCl~~AvPfFargapSskf~~y~n~ 243 (460)
T KOG2213|consen 214 VDRFISCLLMAVPFFARGAPSSKFVEYLNK 243 (460)
T ss_pred HHHHHHHHHHhhhhhhcCCchhHHHHHHHh
Confidence 8899999999999553 3445444443
No 37
>PF15039 DUF4530: Domain of unknown function (DUF4530)
Probab=24.65 E-value=1.4e+02 Score=22.52 Aligned_cols=42 Identities=24% Similarity=0.214 Sum_probs=33.2
Q ss_pred hhchHHHHHHHHHHHHHHHHHHHHHHhhhhchhhhhhccCCC
Q 036425 202 KTNDMMLVIYLSSLIRSVIALHNLINNKILNKEHEKTEDAKP 243 (252)
Q Consensus 202 ~~~D~lmv~yLs~ltk~~~~l~e~l~~~~~~~~~~~~~~~~~ 243 (252)
.--|+.+..-|++|.-...+|.+-+-.+++..+.+.++..++
T Consensus 62 rrvDvQlLgQLCsLgLEMgalreElvt~lEEEee~s~e~ee~ 103 (111)
T PF15039_consen 62 RRVDVQLLGQLCSLGLEMGALREELVTILEEEEEESEEEEED 103 (111)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHhHHhhccccchhhh
Confidence 446899999999999999999999999988655555554444
No 38
>KOG0907 consensus Thioredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=24.36 E-value=1.4e+02 Score=22.54 Aligned_cols=41 Identities=22% Similarity=0.197 Sum_probs=27.1
Q ss_pred CCCeeEEEEecCCCCCCCcHHHHHHHhccCCCcEEEEEeCC
Q 036425 36 AKEHVVGWYSTGPKLRENDLDIHQLFHNYVPNPVLVIIDVQ 76 (252)
Q Consensus 36 p~e~iVGWYstg~~~~~~~~~Ih~~~~~~~~~PI~L~vD~~ 76 (252)
-+..||=||++...+-..=..+-+.++...++.++|.||..
T Consensus 21 ~kliVvdF~a~wCgPCk~i~P~~~~La~~y~~v~Flkvdvd 61 (106)
T KOG0907|consen 21 DKLVVVDFYATWCGPCKAIAPKFEKLAEKYPDVVFLKVDVD 61 (106)
T ss_pred CCeEEEEEECCCCcchhhhhhHHHHHHHHCCCCEEEEEecc
Confidence 47889999999765432222233445555566889999987
No 39
>PF04740 LXG: LXG domain of WXG superfamily; InterPro: IPR006829 This group of putative transposases is found in Gram-positive bacteria, mostly Bacillus members and is thought to be a Cytosolic protein. However, we have also found a Bacillus subtilis bacteriophage SPbetac2 homologue (O64023 from SWISSPROT), possibly arising as a result of horizontal transfer. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=23.47 E-value=4.2e+02 Score=21.82 Aligned_cols=49 Identities=16% Similarity=0.234 Sum_probs=34.4
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHhhhC-CCCCCCHHHHH-HHHHHHhh
Q 036425 138 ANEVTGKLTALKGLDARLREIRGYLDLVID-EKLPLNHEILY-HLQDVFNL 186 (252)
Q Consensus 138 ~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~-G~~~~d~~ilR-~l~~lv~~ 186 (252)
.+-+.....++..+...+..+.+|...|.+ +..-.|.+.++ .|..-+..
T Consensus 60 ~pll~~~~~~~~~~~~~l~~~~~~~~~vd~~~~a~i~e~~L~~el~~~l~~ 110 (204)
T PF04740_consen 60 IPLLQGLILLLEEYQEALKFIKDFQSEVDSSSNAIIDEDFLESELKKKLNQ 110 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHcccccccccHHHHHHHHHHHHHH
Confidence 344567788888899999999999999964 44556777666 55444433
No 40
>TIGR02543 List_Bact_rpt Listeria/Bacterioides repeat. This model describes a conserved core region, about 43 residues in length, of at least two families of tandem repeats. These include 78-residue repeats from 2 to 15 in number, in some proteins of Bacteroides forsythus ATCC 43037, and 70-residue repeats in families of internalins of Listeria species. Single copies are found in proteins of Fibrobacter succinogenes, Geobacter sulfurreducens, and a few bacteria.
Probab=22.34 E-value=60 Score=20.61 Aligned_cols=11 Identities=27% Similarity=0.628 Sum_probs=8.9
Q ss_pred CCCeeEEEEec
Q 036425 36 AKEHVVGWYST 46 (252)
Q Consensus 36 p~e~iVGWYst 46 (252)
+.+.+.|||.-
T Consensus 4 ~GY~F~GWY~d 14 (44)
T TIGR02543 4 PGYVFDGWYGD 14 (44)
T ss_pred CCcEeeeeEEc
Confidence 67889999963
No 41
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=22.21 E-value=3.1e+02 Score=19.90 Aligned_cols=47 Identities=15% Similarity=0.200 Sum_probs=28.9
Q ss_pred chhhhHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCCCCHHHHHHHHHHHhh
Q 036425 136 TLANEVTGKLTALKGLDARLREIRGYLDLVIDEKLPLNHEILYHLQDVFNL 186 (252)
Q Consensus 136 ~l~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~G~~~~d~~ilR~l~~lv~~ 186 (252)
.+..++..+..+|..|..|++.+..=-++..+ -|.-+.-+|.++.+.
T Consensus 20 ~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~----EN~~Lq~YI~nLm~~ 66 (80)
T PF10224_consen 20 ELIQEILELQDSLEALSDRVEEVKEENEKLES----ENEYLQQYIGNLMSS 66 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHh
Confidence 34455666777788888887777665554443 345555566666544
No 42
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=20.32 E-value=1.9e+02 Score=18.95 Aligned_cols=39 Identities=15% Similarity=0.186 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHHhhhCCCCCCCHHHHHHHHHHHhh
Q 036425 148 LKGLDARLREIRGYLDLVIDEKLPLNHEILYHLQDVFNL 186 (252)
Q Consensus 148 l~~L~~~l~~i~~Yl~~V~~G~~~~d~~ilR~l~~lv~~ 186 (252)
...+..++..=..|+..+.+|+..+....++.|.+.+..
T Consensus 15 ~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~~v 53 (64)
T PF12844_consen 15 QKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEALGV 53 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHHTS
T ss_pred HHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHhCC
Confidence 344444554447889999999999998888888777754
No 43
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=20.19 E-value=96 Score=20.75 Aligned_cols=17 Identities=24% Similarity=0.315 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHhhh
Q 036425 150 GLDARLREIRGYLDLVI 166 (252)
Q Consensus 150 ~L~~~l~~i~~Yl~~V~ 166 (252)
.+..+|+.++.||+.+-
T Consensus 11 ~~~e~L~~l~~YLR~~~ 27 (55)
T PF13821_consen 11 SPEERLDKLLSYLREEH 27 (55)
T ss_pred CHHHHHHHHHHHHHhhC
Confidence 35788999999999874
Done!