Query 026489
Match_columns 238
No_of_seqs 111 out of 456
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 08:40:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026489.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026489hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd08063 MPN_CSN6 Mpr1p, Pad1p 100.0 1.6E-47 3.4E-52 343.8 21.9 201 26-227 77-282 (288)
2 PLN03246 26S proteasome regula 100.0 1E-46 2.2E-51 340.0 22.1 192 26-222 81-279 (303)
3 cd08062 MPN_RPN7_8 Mpr1p, Pad1 100.0 3E-46 6.4E-51 334.1 22.2 192 26-222 76-273 (280)
4 KOG3050 COP9 signalosome, subu 100.0 3E-46 6.4E-51 320.5 18.1 212 25-238 83-299 (299)
5 KOG2975 Translation initiation 100.0 3.8E-45 8.3E-50 316.6 19.9 197 19-223 90-287 (288)
6 cd08064 MPN_eIF3f Mpr1p, Pad1p 100.0 3.3E-42 7E-47 306.1 21.4 187 26-216 70-263 (265)
7 KOG1556 26S proteasome regulat 100.0 1.6E-40 3.5E-45 285.6 14.8 194 25-223 83-282 (309)
8 PF13012 MitMem_reg: Maintenan 99.9 7.1E-27 1.5E-31 182.8 1.7 114 104-220 1-114 (115)
9 cd08057 MPN_euk_non_mb Mpr1p, 99.3 3E-12 6.5E-17 105.4 5.8 80 25-110 69-157 (157)
10 cd08065 MPN_eIF3h Mpr1p, Pad1p 98.8 1.6E-08 3.4E-13 90.3 9.7 132 26-158 73-227 (266)
11 cd08069 MPN_RPN11_CSN5 Mov34/M 98.2 3.5E-06 7.5E-11 75.4 8.0 91 27-117 82-202 (268)
12 smart00232 JAB_MPN JAB/MPN dom 96.7 0.0019 4.1E-08 50.6 3.6 56 27-83 71-134 (135)
13 cd07767 MPN Mpr1p, Pad1p N-ter 96.6 0.0016 3.5E-08 49.8 3.0 52 26-79 57-116 (116)
14 KOG1560 Translation initiation 91.9 0.78 1.7E-05 41.5 7.7 139 19-159 90-256 (339)
15 PF01398 JAB: JAB1/Mov34/MPN/P 90.2 0.083 1.8E-06 40.5 -0.1 32 26-57 75-114 (114)
16 cd08058 MPN_euk_mb Mpr1p, Pad1 88.2 0.63 1.4E-05 36.2 3.6 50 27-80 60-117 (119)
17 cd08068 MPN_BRCC36 Mov34/MPN/P 80.2 5.4 0.00012 35.4 6.3 73 30-104 87-170 (244)
18 cd08066 MPN_AMSH_like Mov34/MP 79.8 2.6 5.7E-05 35.3 4.0 51 30-86 73-132 (173)
19 PF04740 LXG: LXG domain of WX 55.5 94 0.002 25.9 8.5 48 130-177 60-109 (204)
20 PF09457 RBD-FIP: FIP domain ; 50.7 21 0.00045 23.7 2.9 42 128-169 4-45 (48)
21 PF01381 HTH_3: Helix-turn-hel 46.0 40 0.00087 21.7 3.9 38 140-177 12-49 (55)
22 PF02841 GBP_C: Guanylate-bind 42.3 2.1E+02 0.0046 25.6 9.2 37 186-222 100-136 (297)
23 PF12844 HTH_19: Helix-turn-he 37.4 57 0.0012 21.7 3.6 41 139-179 14-54 (64)
24 cd08067 MPN_2A_DUB Mov34/MPN/P 36.4 74 0.0016 26.9 4.9 55 30-84 77-147 (187)
25 KOG2213 Apoptosis inhibitor 5/ 35.4 74 0.0016 30.5 5.0 88 92-183 134-229 (460)
26 PF03127 GAT: GAT domain; Int 33.4 2E+02 0.0044 21.3 9.0 87 134-228 7-94 (100)
27 PF05184 SapB_1: Saposin-like 32.8 53 0.0011 19.8 2.6 17 164-180 23-39 (39)
28 PF07097 DUF1359: Protein of u 32.3 1.7E+02 0.0037 22.0 5.6 53 145-197 30-85 (102)
29 cd08060 MPN_UPF0172 Mov34/MPN/ 29.1 46 0.001 28.1 2.4 36 31-66 69-113 (182)
30 PRK08359 transcription factor; 28.2 63 0.0014 27.3 3.1 40 140-179 101-140 (176)
31 PHA01976 helix-turn-helix prot 27.8 82 0.0018 21.1 3.2 38 140-177 18-55 (67)
32 PF10224 DUF2205: Predicted co 27.5 2.5E+02 0.0053 20.6 5.7 47 128-178 20-66 (80)
33 KOG3650 Predicted coiled-coil 27.3 1.6E+02 0.0035 22.7 4.8 43 139-181 64-109 (120)
34 PF10776 DUF2600: Protein of u 26.8 98 0.0021 28.8 4.3 72 143-221 57-130 (330)
35 KOG1554 COP9 signalosome, subu 26.2 69 0.0015 29.3 3.1 129 27-156 126-282 (347)
36 KOG3046 Transcription factor, 25.5 3.8E+02 0.0082 22.0 7.9 59 143-222 10-68 (147)
37 COG1813 Predicted transcriptio 25.2 88 0.0019 26.2 3.4 40 140-179 95-134 (165)
38 PF04157 EAP30: EAP30/Vps36 fa 24.6 4.3E+02 0.0093 22.6 7.8 89 132-223 24-125 (223)
39 KOG3227 Calcium-responsive tra 24.1 1.7E+02 0.0037 25.6 5.0 20 148-175 23-42 (231)
40 PF08020 DUF1706: Protein of u 24.0 3E+02 0.0065 22.9 6.4 80 135-223 45-124 (166)
41 cd08064 MPN_eIF3f Mpr1p, Pad1p 23.5 29 0.00062 30.9 0.2 20 17-36 66-85 (265)
42 COG4220 Phage DNA packaging pr 22.4 3.8E+02 0.0082 22.6 6.5 29 167-195 113-141 (174)
43 PRK06424 transcription factor; 21.7 1.1E+02 0.0023 25.0 3.2 37 142-178 102-138 (144)
44 PF13560 HTH_31: Helix-turn-he 20.8 1.6E+02 0.0034 19.7 3.5 40 139-178 16-56 (64)
45 TIGR03070 couple_hipB transcri 20.7 1.3E+02 0.0027 19.0 2.9 37 141-177 19-55 (58)
46 KOG1555 26S proteasome regulat 20.5 1.1E+02 0.0024 28.3 3.3 49 32-81 115-171 (316)
47 TIGR00270 conserved hypothetic 20.4 1.1E+02 0.0024 25.1 3.1 39 140-178 85-123 (154)
No 1
>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=1.6e-47 Score=343.80 Aligned_cols=201 Identities=48% Similarity=0.727 Sum_probs=183.2
Q ss_pred ceeecCCeeeccccC-----CCCcHHHHHHHhccCCCceEEEEcCCCCCCCCCCCeeEEEEeeeeeCCccceeeEeecee
Q 026489 26 TSIYLDGTPQGVMLK-----NPICTSIKLYLMDINESPVYVLLNPSINPAQKDLPVTIFESELHVIEGIPQLIFVRSSYT 100 (238)
Q Consensus 26 ~~~~~~~~~~g~~~~-----~~~~~~IH~~~~~~~~~PI~L~vD~~~~~~~~~LPi~aYes~~~~~~g~~~~~F~~ip~~ 100 (238)
++|+++..++|||++ ++++..||++|++++++||||++||....++++||+++|+++.++.+|.....|+++||+
T Consensus 77 kkV~~~~~vVGWY~tg~~~~~~~~~~Ih~~~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~~~~~~~~~~~F~~i~~~ 156 (288)
T cd08063 77 KQVFKDLDFVGWYTTGPGGPTESDLPIHKQILEINESPVLLLLDPEANASGKDLPVTIYESVLELVDGEATLRFRELPYT 156 (288)
T ss_pred HHhccCCceEEEEecCCCCCCHHHHHHHHHHHhhCCCcEEEEEccccccCCCCCceeEEEEEEeccCCccccEEEeeeeE
Confidence 566677777777763 446999999999999999999999987423678999999999999888778999999999
Q ss_pred eeccchhHHHHHHHhhhCCCCCCChhhhhHhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhcCC
Q 026489 101 IETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRLP 180 (238)
Q Consensus 101 I~t~EaErIgVd~l~~~~~~~~~~~~~~l~~~l~~~~~al~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~lP 180 (238)
|+++|||||||||+++..... +.+.+.+.++++++.+|++||++||+.|++||++|.+|++++|++|||+|+++|+++|
T Consensus 157 i~~~eaErIgv~~l~~~~~~~-~~~~~~~~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~g~~~~d~~ilR~l~~~~~~lP 235 (288)
T cd08063 157 IETGEAERIGVDHVARGGASG-SSEKSTVAAHLQAQHNAIKMLNSRVELILEYLKAVPVGEVPPDHSILRSISALCSRLP 235 (288)
T ss_pred EEeccCceeeHHHHHhcCCCC-CCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHhCc
Confidence 999999999999999976433 2345677899999999999999999999999999999999999999999999999999
Q ss_pred CCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Q 026489 181 AIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDKFNTAYDR 227 (238)
Q Consensus 181 ~~~~~~f~~~~~~~~~D~lmvsyLs~Ltk~~~al~el~~Kl~~~~~~ 227 (238)
.++.++|+++|++++||++|++|||+|||++.+|+++++||+.++++
T Consensus 236 ~~~~~~~~~~~~~~~~D~lmv~yLs~lt~~~~~l~~~~~k~~~~~~~ 282 (288)
T cd08063 236 VLKSEAFREELLAEYNDVLLVAYLATLTKGCNTLNELVDKFNVVYDR 282 (288)
T ss_pred cCChHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 99999999999999999999999999999999999999999999997
No 2
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=100.00 E-value=1e-46 Score=339.97 Aligned_cols=192 Identities=23% Similarity=0.366 Sum_probs=173.6
Q ss_pred ceeecCCeeecccc----CCCCcHHHHHHHhccCCCceEEEEcCCCCCCCCCCCeeEEEEeeeeeCC-c--cceeeEeec
Q 026489 26 TSIYLDGTPQGVML----KNPICTSIKLYLMDINESPVYVLLNPSINPAQKDLPVTIFESELHVIEG-I--PQLIFVRSS 98 (238)
Q Consensus 26 ~~~~~~~~~~g~~~----~~~~~~~IH~~~~~~~~~PI~L~vD~~~~~~~~~LPi~aYes~~~~~~g-~--~~~~F~~ip 98 (238)
++|+++...+|||. .+++|.+||++|++++++||||+||+.+. +++||+++|+++.++.+| . ....|+++|
T Consensus 81 k~V~~~~~vVGWY~tg~~i~~~d~~IH~~~~~~~~~Pv~L~vD~~~~--~~~lpi~aY~s~~~~~~~~~~~~~~~F~~vp 158 (303)
T PLN03246 81 KRINAKEHVVGWYSTGPKLRENDLDIHELFNDYVPNPVLVIIDVQPK--ELGIPTKAYYAVEEVKENATQKSQKVFVHVP 158 (303)
T ss_pred HHhCCCCcEEeeecCCCCCCcchHHHHHHHHhhCCCCeEEEEecCCC--CCCCceEEEEEEEeccCCCCcccccEEEECC
Confidence 55666666677776 37799999999999999999999999875 578999999999988764 2 358899999
Q ss_pred eeeeccchhHHHHHHHhhhCCCCCCChhhhhHhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhc
Q 026489 99 YTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRR 178 (238)
Q Consensus 99 ~~I~t~EaErIgVd~l~~~~~~~~~~~~~~l~~~l~~~~~al~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~ 178 (238)
|+|+++|||||||||++|...+ .+.+.+.++++++.+|++||.+||+.|++||++|.+|++++|++|||+|+++|++
T Consensus 159 ~~i~~~EaE~Igve~l~r~~~~---~~~s~l~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~g~~~~d~~IlR~l~~l~~~ 235 (303)
T PLN03246 159 SEIGAHEAEEIGVEHLLRDVKD---TTVSTLATEVTGKLTALKGLDARLREIRSYLDLVVEGKLPLNHEILYHLQDVFNL 235 (303)
T ss_pred eeeeecCHHHHHHHHHHhcccC---CccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhh
Confidence 9999999999999999997653 2345678899999999999999999999999999999999999999999999999
Q ss_pred CCCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026489 179 LPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDKFN 222 (238)
Q Consensus 179 lP~~~~~~f~~~~~~~~~D~lmvsyLs~Ltk~~~al~el~~Kl~ 222 (238)
+|.+++++|+++|++++||++|++|||+|||+|++||++.++..
T Consensus 236 lP~l~~~~f~~~f~~~~nD~lmv~YLa~l~kt~~~l~e~l~~~~ 279 (303)
T PLN03246 236 LPNLNVEELVKAFAVKTNDMMLVIYLSSLIRSVIALHNLINNKI 279 (303)
T ss_pred CCCCCHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 99999999999999999999999999999999999999988875
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=3e-46 Score=334.12 Aligned_cols=192 Identities=19% Similarity=0.334 Sum_probs=174.1
Q ss_pred ceeecCCeeecccc----CCCCcHHHHHHHhccCCCceEEEEcCCCCCCCCCCCeeEEEEeeeeeC-Cc-cceeeEeece
Q 026489 26 TSIYLDGTPQGVML----KNPICTSIKLYLMDINESPVYVLLNPSINPAQKDLPVTIFESELHVIE-GI-PQLIFVRSSY 99 (238)
Q Consensus 26 ~~~~~~~~~~g~~~----~~~~~~~IH~~~~~~~~~PI~L~vD~~~~~~~~~LPi~aYes~~~~~~-g~-~~~~F~~ip~ 99 (238)
++|++++..+|||+ .+++|..||++|+++|++||||+|||... +++||+++|+++.++.+ |. ....|+|+||
T Consensus 76 kkv~~~e~vVGWY~tg~~~~~~d~~ih~~~~~~~~~pv~l~vd~~~~--~~~lpi~aY~s~~~~~~~g~~~~~~F~~vp~ 153 (280)
T cd08062 76 KKVNAKEKIVGWYSTGPKLRPNDLDINELFRRYCPNPVLVIIDVRPK--DLGLPTEAYIAVEEVHDDGTPTSKTFVHVPS 153 (280)
T ss_pred HHhCCCCCeEEEecCCCCCCcchHHHHHHHHHhCCCCEEEEEecCCC--CCCCceEEEEEeeeccCCCCcceeEEEEcce
Confidence 66777777788887 36699999999999999999999999875 67899999999998874 55 4799999999
Q ss_pred eeeccchhHHHHHHHhhhCCCCCCChhhhhHhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhcC
Q 026489 100 TIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRL 179 (238)
Q Consensus 100 ~I~t~EaErIgVd~l~~~~~~~~~~~~~~l~~~l~~~~~al~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~l 179 (238)
+|+++|||||||||++|...+ .+.+.+.+++.++.+|+++|+.||+.|++||++|.+|+.++|++|||+|+++|+++
T Consensus 154 ~i~~~eaE~igve~l~r~~~~---~~~~~l~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~IlR~l~~~~~~l 230 (280)
T cd08062 154 EIGAEEAEEVGVEHLLRDIKD---VTVSTLSTRVTNKLNSLKGLQSKLKEIKDYLQLVVEGKLPINHQIIYNLQDIFNLL 230 (280)
T ss_pred EeeccchHHHHHHHHHhhccC---cccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHhC
Confidence 999999999999999996543 23456778999999999999999999999999999999999999999999999999
Q ss_pred CCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026489 180 PAIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDKFN 222 (238)
Q Consensus 180 P~~~~~~f~~~~~~~~~D~lmvsyLs~Ltk~~~al~el~~Kl~ 222 (238)
|.+++++|+++|++++||++|++|||+|||+|++|+++.+...
T Consensus 231 P~l~~~~f~~~~~~~~nD~lmv~yLs~l~k~~~~l~~~~~~~~ 273 (280)
T cd08062 231 PNLNLPELVKAFAVKTNDQMLVIYLSSLIRSVIALHNLINNKI 273 (280)
T ss_pred CCCCHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999998888877664
No 4
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=3e-46 Score=320.51 Aligned_cols=212 Identities=47% Similarity=0.740 Sum_probs=198.6
Q ss_pred cceeecCCeeecccc----CCCCcHHHHHHHhccCCCceEEEEcCCCCCCCCCCCeeEEEEeeeeeCCccceeeEeecee
Q 026489 25 HTSIYLDGTPQGVML----KNPICTSIKLYLMDINESPVYVLLNPSINPAQKDLPVTIFESELHVIEGIPQLIFVRSSYT 100 (238)
Q Consensus 25 ~~~~~~~~~~~g~~~----~~~~~~~IH~~~~~~~~~PI~L~vD~~~~~~~~~LPi~aYes~~~~~~g~~~~~F~~ip~~ 100 (238)
+++||++-+..|||+ ++|.|..||++++..+++|+||.++|.... .++.|+.+|++....+||.++..|+|+.|+
T Consensus 83 ykqVFpdl~vlGwYttG~d~t~sd~~i~k~l~~i~esplflkLNp~t~~-t~~~pv~lfese~dvidg~~q~~f~~~tyt 161 (299)
T KOG3050|consen 83 YKQVFPDLYVLGWYTTGSDPTPSDIHIHKQLMDINESPLFLKLNPATNH-TDKDPVTLFESEIDVIDGEAQMLFVPLTYT 161 (299)
T ss_pred HHHhcccceEEEEeecCCCCChhhhHHHHHHHhhhcCceEEEecchhcc-ccCCCceeeeeeheeecCcceeeeeeeEEE
Confidence 588999999999999 677999999999999999999999997653 344599999999999999999999999999
Q ss_pred eeccchhHHHHHHHhhhCCCCCCChhhhhHhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhcCC
Q 026489 101 IETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRLP 180 (238)
Q Consensus 101 I~t~EaErIgVd~l~~~~~~~~~~~~~~l~~~l~~~~~al~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~lP 180 (238)
++++|||||||||+++..+++|+. .+.+..|+.++.+|++||+.|++.|++||++|.+|++++|++|||+...+|..||
T Consensus 162 l~teEaERIgVdHVA~lt~~~gge-~s~VaeHl~AQdsA~~ml~~Rvklil~Y~k~~e~G~l~~N~eILrea~~L~~~Lp 240 (299)
T KOG3050|consen 162 LATEEAERIGVDHVARLTPSDGGE-GSSVAEHLEAQDSAIKMLDNRVKLILAYLKKVEAGTLQPNFEILREAYALCHRLP 240 (299)
T ss_pred EeehhhhhccchhheeeccCCCCC-cchHHHHHhhHHHHHHHHhhHHHHHHHHHhhhhcCCcCccHHHHHHHHHHHhhcc
Confidence 999999999999999988877654 3456899999999999999999999999999999999999999999999999999
Q ss_pred CCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcC-CCCCCCccCC
Q 026489 181 AIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDKFNTAYDRH-SRRGGRTAFI 238 (238)
Q Consensus 181 ~~~~~~f~~~~~~~~~D~lmvsyLs~Ltk~~~al~el~~Kl~~~~~~~-~~~~~~~~~~ 238 (238)
.++.++|.+.|..++||+.+++||+.+|+++..||++++||+..++++ ++||||..|.
T Consensus 241 ~~~~~~F~d~F~~e~nd~~l~syl~~iT~~~~nMn~~vnKfn~~ydr~gt~R~~r~~~f 299 (299)
T KOG3050|consen 241 VMESEKFQDNFYMECNDVGLISYLGTITKCCNNMNEVVNKFNTLYDRQGTRRRMRGLFF 299 (299)
T ss_pred ccchHHHhHHHHHhcchhhHHHHHHHHHHhhccHHHHHHHHHHHHHhhhhhccccccCC
Confidence 999999999999999999999999999999999999999999999999 5999998874
No 5
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.8e-45 Score=316.61 Aligned_cols=197 Identities=19% Similarity=0.296 Sum_probs=184.7
Q ss_pred cccccccceeecCCeeeccccCCCCcHHHHHHHhccCCCceEEEEcCCCCCCCCCCCeeEEEEeeeeeCCcc-ceeeEee
Q 026489 19 SIRRCSHTSIYLDGTPQGVMLKNPICTSIKLYLMDINESPVYVLLNPSINPAQKDLPVTIFESELHVIEGIP-QLIFVRS 97 (238)
Q Consensus 19 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~IH~~~~~~~~~PI~L~vD~~~~~~~~~LPi~aYes~~~~~~g~~-~~~F~~i 97 (238)
.-+|+|+++...||+.||.++ +.++.+||+||.+++++||||+||++.+ ++.+++++|++...|++|.. ..+|.|+
T Consensus 90 l~~k~npnE~vvGWyaTg~dv-t~~sslihdyYare~~~pvhLtVDT~~~--n~rm~ikaYvss~~Gvpg~~~~~mF~pl 166 (288)
T KOG2975|consen 90 LHKKVNPNELVVGWYATGHDV-TEHSSLIHDYYAREAPNPVHLTVDTSLQ--NGRMSIKAYVSSLMGVPGRTMGVMFTPL 166 (288)
T ss_pred HhcccCCCceeEEEEecCCCc-ccchhHHHHHhhccCCCCeEEEEecccc--CCccceeEEEEeccCCCCcccceeeeee
Confidence 457899999999999999999 9999999999999999999999999998 78999999999999999865 6899999
Q ss_pred ceeeeccchhHHHHHHHhhhCCCCCCChhhhhHhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHh
Q 026489 98 SYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLR 177 (238)
Q Consensus 98 p~~I~t~EaErIgVd~l~~~~~~~~~~~~~~l~~~l~~~~~al~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~ 177 (238)
|+++.++|+||+|++.+.+...+ .++...+.++|+++..|...|+++|+.+++|+++|++|+.+||+.|||+|+++++
T Consensus 167 pvel~~~~~ervgl~li~kt~~s--p~r~~~l~~dLqQv~~at~~l~~~L~~Vl~YVedVl~gk~~pdn~VGR~Lmd~v~ 244 (288)
T KOG2975|consen 167 PVELAYYDAERVGLDLIEKTSFS--PSRVAGLSSDLQQVEGATARLQSLLERVLKYVEDVLAGKVKPDNAVGRFLMDLVT 244 (288)
T ss_pred eeEEeecchhhhHHHHHHHhccC--hhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcchHHHHHHHHHH
Confidence 99999999999999999998733 2355678899999999999999999999999999999999999999999999999
Q ss_pred cCCCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026489 178 RLPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDKFNT 223 (238)
Q Consensus 178 ~lP~~~~~~f~~~~~~~~~D~lmvsyLs~Ltk~~~al~el~~Kl~~ 223 (238)
++|.+.+++|+.+|+++++|++|++|||++||+|+ +|++||..
T Consensus 245 ~vP~l~p~~Fe~mfn~nLrD~Lmv~yLa~ltqTQl---~l~EKL~~ 287 (288)
T KOG2975|consen 245 AVPKLVPDDFETMFNSNLRDLLMVIYLANLTQTQL---ALNEKLVN 287 (288)
T ss_pred hcCCCCHHHHHHHHhhhHHHHHHHHHHHHHHHHHH---HHHHHhhc
Confidence 99999999999999999999999999999999999 88889875
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=3.3e-42 Score=306.08 Aligned_cols=187 Identities=18% Similarity=0.310 Sum_probs=165.0
Q ss_pred ceeecCCeeeccccC----CCCcHHHHHHHhccCC--CceEEEEcCCCCCCCCCCCeeEEEEeeeeeCCc-cceeeEeec
Q 026489 26 TSIYLDGTPQGVMLK----NPICTSIKLYLMDINE--SPVYVLLNPSINPAQKDLPVTIFESELHVIEGI-PQLIFVRSS 98 (238)
Q Consensus 26 ~~~~~~~~~~g~~~~----~~~~~~IH~~~~~~~~--~PI~L~vD~~~~~~~~~LPi~aYes~~~~~~g~-~~~~F~~ip 98 (238)
++|+.+...+|||++ ++++..||++|+++++ +||||++|+... +++||++||++.+.+..+. ....|++||
T Consensus 70 kkv~~~~~vVGWY~tg~~~~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~--~~~l~i~ay~~~~~~~~~~~~~~~F~~ip 147 (265)
T cd08064 70 QKVNPKEVIVGWYATGSEITEHSALIHDYYSRECTSYNPIHLTVDTSLD--DGKMSIKAYVSSPLGVPGKTLGSMFVPIP 147 (265)
T ss_pred HHhCCCCcEEeeeeCCCCCCccHHHHHHHHHhhCCCCCCEEEEEeCCCC--CCCcceEEEEEEecccCCCCcceEEEEcc
Confidence 455555666666652 5579999999999998 999999999876 4589999999998877654 469999999
Q ss_pred eeeeccchhHHHHHHHhhhCCCCCCChhhhhHhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhc
Q 026489 99 YTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRR 178 (238)
Q Consensus 99 ~~I~t~EaErIgVd~l~~~~~~~~~~~~~~l~~~l~~~~~al~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~ 178 (238)
++|.++|||||||||+++.....+ ..+.+.++++++.+|+++|.+||+.|.+||++|.+|+.++|++|||+|++++++
T Consensus 148 ~~i~~~eaE~i~v~~l~~~~~~~~--~~~~~~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~i~r~l~~~~~~ 225 (265)
T cd08064 148 LELLYSEAERVALDLLAKTLASPS--RSAPLTSDLEQLEASLEKLQEMLDRVLRYVEDVLAGKVKADNAIGRYLMDALTS 225 (265)
T ss_pred eeeecCcHHHHHHHHHHhhccCCc--ccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhh
Confidence 999999999999999999876532 233466999999999999999999999999999999999999999999999999
Q ss_pred CCCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHH
Q 026489 179 LPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNE 216 (238)
Q Consensus 179 lP~~~~~~f~~~~~~~~~D~lmvsyLs~Ltk~~~al~e 216 (238)
+|.+++++|+++|++++||++|++|||+|||+|++|+|
T Consensus 226 lp~~~~~~f~~~~~~~~~D~lmv~YLs~l~k~~~~l~e 263 (265)
T cd08064 226 VPKLDPEEFEKMFNSSLQDLLMVTYLSNLTKTQLALAE 263 (265)
T ss_pred CCCCCHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999999999999994443
No 7
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.6e-40 Score=285.64 Aligned_cols=194 Identities=23% Similarity=0.374 Sum_probs=181.5
Q ss_pred cceeecCCeeeccccCCC----CcHHHHHHHhccCCCceEEEEcCCCCCCCCCCCeeEEEEeeeeeC-Ccc-ceeeEeec
Q 026489 25 HTSIYLDGTPQGVMLKNP----ICTSIKLYLMDINESPVYVLLNPSINPAQKDLPVTIFESELHVIE-GIP-QLIFVRSS 98 (238)
Q Consensus 25 ~~~~~~~~~~~g~~~~~~----~~~~IH~~~~~~~~~PI~L~vD~~~~~~~~~LPi~aYes~~~~~~-g~~-~~~F~~ip 98 (238)
|++|.+.+..+||||++| +|+.||+.+.+||++|+++++|..+. +-+||..||.++.+..+ |++ +..|.|+|
T Consensus 83 fkKvNakekivGWYhTGPkl~~nDl~In~l~k~y~pnpvLvIIdvkpk--~~gLPT~AY~aVeev~dDgt~t~ktF~Hvp 160 (309)
T KOG1556|consen 83 FKKVNAKEKVVGWYHTGPKLRENDLDINELLKRYVPNPVLVIIDVKPK--ELGLPTEAYIAVEEVKDDGTPTSKTFVHVP 160 (309)
T ss_pred HHHhcchhheeeeeccCCccccchhhHHHHHhhcCCCceEEEEecccc--cCCCCchheeeeeeeecCCCCccceeEecC
Confidence 378888999999999777 99999999999999999999999886 67899999999998876 554 68999999
Q ss_pred eeeeccchhHHHHHHHhhhCCCCCCChhhhhHhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhc
Q 026489 99 YTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRR 178 (238)
Q Consensus 99 ~~I~t~EaErIgVd~l~~~~~~~~~~~~~~l~~~l~~~~~al~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~ 178 (238)
++|+++|||+|||||+.|.+.+ .+.+++...+.++..+++.|+.+|..|.+||++|.+|++|.||+|+.++|++++.
T Consensus 161 s~I~AeEAEEvGVEHLlRDikd---~t~gtla~rit~ql~sLkgl~~~L~eI~~YL~~Vi~g~lpiNh~Il~~lQdvfNl 237 (309)
T KOG1556|consen 161 SEIEAEEAEEVGVEHLLRDIKD---TTVGTLATRITNQLMSLKGLQSRLREIRSYLDKVIDGKLPINHEILYQLQDVFNL 237 (309)
T ss_pred cccchhHHHHhhHHHHHHHHHh---hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHhh
Confidence 9999999999999999998875 4567899999999999999999999999999999999999999999999999999
Q ss_pred CCCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026489 179 LPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDKFNT 223 (238)
Q Consensus 179 lP~~~~~~f~~~~~~~~~D~lmvsyLs~Ltk~~~al~el~~Kl~~ 223 (238)
+|.+...+|.+.|+...||.||+.|||+|+|++.|||+|.++...
T Consensus 238 lP~l~~~~~~~a~~vktndql~~iY~sslvrsViAlhdLi~Nkl~ 282 (309)
T KOG1556|consen 238 LPNLTRNELVKAFNVKTNDQLMVIYLSSLVRSVIALHDLINNKLA 282 (309)
T ss_pred CccccchhhhhhhccccCceeeeeeHHHHHHHHHHHHHHHHhHhh
Confidence 999999999999999999999999999999999999999987653
No 8
>PF13012 MitMem_reg: Maintenance of mitochondrial structure and function; PDB: 2O96_B 2O95_A.
Probab=99.92 E-value=7.1e-27 Score=182.80 Aligned_cols=114 Identities=38% Similarity=0.612 Sum_probs=13.5
Q ss_pred cchhHHHHHHHhhhCCCCCCChhhhhHhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhcCCCCC
Q 026489 104 VEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRLPAIE 183 (238)
Q Consensus 104 ~EaErIgVd~l~~~~~~~~~~~~~~l~~~l~~~~~al~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~lP~~~ 183 (238)
+|||||||+|+++....+ ..+.+.++++++.+|+.+|+.|++.+..||++|.+|+.++|+++||+|+++|+++|.++
T Consensus 1 eEaErigv~~l~~~~~~~---~~s~~~~~l~~~~~al~~L~~~l~~i~~Yl~~v~~g~~~~d~~i~r~l~~l~~~lp~~~ 77 (115)
T PF13012_consen 1 EEAERIGVDHLARGLGDH---YYSSLSSQLENEQNALKMLHKRLWQILDYLEDVISGEIPPDHEILRQLQDLLSSLPKYD 77 (115)
T ss_dssp SHHHHHHHHHHHHH--S---------------------------------------------------------------
T ss_pred CchHHHHHHHHHccCCCc---cccHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcCCCchhHHHHHHHHHHhccccc
Confidence 589999999999965442 23477899999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHH
Q 026489 184 SEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDK 220 (238)
Q Consensus 184 ~~~f~~~~~~~~~D~lmvsyLs~Ltk~~~al~el~~K 220 (238)
+++|+++|.++++|.+||.||+++||++.+++++.+|
T Consensus 78 ~~~~~~~~~~~~~D~l~v~yL~~l~k~~~~l~e~l~~ 114 (115)
T PF13012_consen 78 PEEFEEEFNSEINDVLMVSYLAKLTKKQHALNELLNN 114 (115)
T ss_dssp -------------------------------------
T ss_pred HHHHHHHHHhhchHHHHHHHHHHHhHHHHHHHHHHhc
Confidence 9999999999999999999999999999988888765
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=99.30 E-value=3e-12 Score=105.44 Aligned_cols=80 Identities=25% Similarity=0.340 Sum_probs=65.4
Q ss_pred cceeecCCeeeccccC--------CCCcHHHHHHHhcc-CCCceEEEEcCCCCCCCCCCCeeEEEEeeeeeCCccceeeE
Q 026489 25 HTSIYLDGTPQGVMLK--------NPICTSIKLYLMDI-NESPVYVLLNPSINPAQKDLPVTIFESELHVIEGIPQLIFV 95 (238)
Q Consensus 25 ~~~~~~~~~~~g~~~~--------~~~~~~IH~~~~~~-~~~PI~L~vD~~~~~~~~~LPi~aYes~~~~~~g~~~~~F~ 95 (238)
+++|+++..++|||+. ...+..||++|+.+ +++||+|++||.....+++||+++|++..... .+.
T Consensus 69 ~~~v~~~~~vVGWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~~~------~~~ 142 (157)
T cd08057 69 HKKVYPQEKIVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQREE------NGA 142 (157)
T ss_pred HHHhCCCCCEEEEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEecCCC------CCc
Confidence 3677888889999983 34589999999998 89999999999763336789999999985322 244
Q ss_pred eeceeeeccchhHHH
Q 026489 96 RSSYTIETVEAERIS 110 (238)
Q Consensus 96 ~ip~~I~t~EaErIg 110 (238)
++||+++++|+||||
T Consensus 143 ~~~~~i~~~e~E~I~ 157 (157)
T cd08057 143 EITYEIGTEETERIA 157 (157)
T ss_pred eeeeEEecccccccC
Confidence 999999999999996
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=98.85 E-value=1.6e-08 Score=90.32 Aligned_cols=132 Identities=13% Similarity=0.104 Sum_probs=93.1
Q ss_pred ceeecCCeeeccccCCC---C--cHHHHHHHhccC--CCceEEEEcCCCCCCCCCCCeeEEEEeeeeeC-----------
Q 026489 26 TSIYLDGTPQGVMLKNP---I--CTSIKLYLMDIN--ESPVYVLLNPSINPAQKDLPVTIFESELHVIE----------- 87 (238)
Q Consensus 26 ~~~~~~~~~~g~~~~~~---~--~~~IH~~~~~~~--~~PI~L~vD~~~~~~~~~LPi~aYes~~~~~~----------- 87 (238)
.++..+...+|||++.| + ...||.+|.... +.||+|++|+... .++.++++||...+.+.+
T Consensus 73 r~v~~~e~iVGWY~S~p~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s-~~g~l~lkAyrl~~~~~~~~~~~~~~~~~ 151 (266)
T cd08065 73 REVNVDHNHVGWYQSTYLGSFFTRDLIETQYNYQEAIEESVVLVYDPSKT-SQGSLSLKAYRLSEKFMELYKEGKFSTES 151 (266)
T ss_pred HHhCCCCcEEEeEeecCCCCcCCHHHHHHHHHHhccCCCCEEEEECCCcc-cccceeeEEEEEcHHHHHHhhcCCcCHHH
Confidence 45666778888888444 2 678899888764 7799999999753 257899999999887654
Q ss_pred ----C-ccceeeEeeceeeeccchhHHHHHHHhhhCCCCCCChhhhhHhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026489 88 ----G-IPQLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQ 158 (238)
Q Consensus 88 ----g-~~~~~F~~ip~~I~t~EaErIgVd~l~~~~~~~~~~~~~~l~~~l~~~~~al~~L~~rL~~i~~YL~~V~ 158 (238)
+ .....|.+||++|...+-+.+.+..+....+....+...-..+....+...+..|.+.+|.+..+.++..
T Consensus 152 l~~~~~~~~~if~eiPv~i~n~~l~~~~L~~l~~~~~~~~~~~~~l~l~~~~~le~~l~~l~~~id~l~~e~~~~~ 227 (266)
T cd08065 152 LREANLTFSNIFEEIPVVIRNSHLVNALLSELEEDSPSSQSDFDRLDLSTNSFLEKNLELLMESVDELSQEQGKFN 227 (266)
T ss_pred HHHhcCchhcEEEEEEEEEEchHHHHHHHHhcccCCCcccCCcccccccCchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2 2369999999999999999999999976543310111111123445566667777777777776666653
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=98.25 E-value=3.5e-06 Score=75.43 Aligned_cols=91 Identities=8% Similarity=-0.032 Sum_probs=74.8
Q ss_pred eeecCCeeecccc--------CCCCcHHHHHHHhccCCCceEEEEcCCCCCCCCCCCeeEEEEeeeeeC----Cc-----
Q 026489 27 SIYLDGTPQGVML--------KNPICTSIKLYLMDINESPVYVLLNPSINPAQKDLPVTIFESELHVIE----GI----- 89 (238)
Q Consensus 27 ~~~~~~~~~g~~~--------~~~~~~~IH~~~~~~~~~PI~L~vD~~~~~~~~~LPi~aYes~~~~~~----g~----- 89 (238)
.+..+...+|||| ++..|..+|.+|.+.++.+|+|++||..+...+++.++||...+.+.. ++
T Consensus 82 ~~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~~~~~~~~~~~~~s~~ 161 (268)
T cd08069 82 QTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIPPGYKPLEPRQTTSNI 161 (268)
T ss_pred HhCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEECccccccCcccCcccc
Confidence 3556788999998 345788999999999888999999986542367899999999987643 11
Q ss_pred -------------cceeeEeeceeeeccchhHHHHHHHhhh
Q 026489 90 -------------PQLIFVRSSYTIETVEAERISVDHVAHL 117 (238)
Q Consensus 90 -------------~~~~F~~ip~~I~t~EaErIgVd~l~~~ 117 (238)
....|.+||+++...+.|+..++.+.+-
T Consensus 162 ~~~~~~~~~~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~ 202 (268)
T cd08069 162 GHLPKPKIEDFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNK 202 (268)
T ss_pred CccCcHHHHHhCchhcEEEEeeeEEecCHHHHHHHHHHHHH
Confidence 3589999999999999999999999984
No 12
>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=96.66 E-value=0.0019 Score=50.57 Aligned_cols=56 Identities=13% Similarity=0.039 Sum_probs=44.8
Q ss_pred eeecCCeeeccccC--------CCCcHHHHHHHhccCCCceEEEEcCCCCCCCCCCCeeEEEEee
Q 026489 27 SIYLDGTPQGVMLK--------NPICTSIKLYLMDINESPVYVLLNPSINPAQKDLPVTIFESEL 83 (238)
Q Consensus 27 ~~~~~~~~~g~~~~--------~~~~~~IH~~~~~~~~~PI~L~vD~~~~~~~~~LPi~aYes~~ 83 (238)
....+..++||||+ +..|..+|..+......++++.+|+.... .+.+++++|+...
T Consensus 71 ~~~~~~~~vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~-~g~~~~~af~~~~ 134 (135)
T smart00232 71 KVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSF-QGRLSLRAFRLTP 134 (135)
T ss_pred hhCCCceEEEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccc-cCcEEEEEEEecC
Confidence 35688899999982 23488889988888888999999988753 3779999999853
No 13
>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=96.63 E-value=0.0016 Score=49.78 Aligned_cols=52 Identities=6% Similarity=-0.019 Sum_probs=40.0
Q ss_pred ceeecCCeeeccccC--------CCCcHHHHHHHhccCCCceEEEEcCCCCCCCCCCCeeEE
Q 026489 26 TSIYLDGTPQGVMLK--------NPICTSIKLYLMDINESPVYVLLNPSINPAQKDLPVTIF 79 (238)
Q Consensus 26 ~~~~~~~~~~g~~~~--------~~~~~~IH~~~~~~~~~PI~L~vD~~~~~~~~~LPi~aY 79 (238)
.....|.+++||||+ ++.+...|..|.+..+++++|++|+... +.++|++||
T Consensus 57 ~~~~~~~~iVGwyhshp~~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~~--~~~~~~~~~ 116 (116)
T cd07767 57 KKLNAGLRIVGWYHTHPKPSCFLSPNDLATHELFQRYFPEKVMIIVDVKPK--DLGNSWKCY 116 (116)
T ss_pred HHhcCCCeEEEEEEcCCCCCCccCHHHHHHHHHHHHhCCCCEEEEEECCCc--cCCCCcccC
Confidence 445578899999983 3355677888887777899999998874 456888887
No 14
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=91.93 E-value=0.78 Score=41.46 Aligned_cols=139 Identities=11% Similarity=0.122 Sum_probs=80.0
Q ss_pred cccccccceeecCCeeeccccCCC-CcHHHHHHHh--ccCCCceEEEEcCCCCCCCCCCCeeEEEEeeeeeC----C---
Q 026489 19 SIRRCSHTSIYLDGTPQGVMLKNP-ICTSIKLYLM--DINESPVYVLLNPSINPAQKDLPVTIFESELHVIE----G--- 88 (238)
Q Consensus 19 ~~~~~~~~~~~~~~~~~g~~~~~~-~~~~IH~~~~--~~~~~PI~L~vD~~~~~~~~~LPi~aYes~~~~~~----g--- 88 (238)
..|.+|....|.||+...++- +- ...++-.+|. .-++.-|.|+.||.-+ .++.|-.+||--.++..+ +
T Consensus 90 rlr~vnid~~hVGwYqs~~vg-s~lS~~lveSqy~YQ~a~pesVvliYD~~ks-sqG~L~lrAyrLTp~am~~~kekdwt 167 (339)
T KOG1560|consen 90 RLRYVNIDHLHVGWYQSAYVG-SFLSPALVESQYAYQKAIPESVVLIYDPIKS-SQGTLSLRAYRLTPEAMAAHKEKDWT 167 (339)
T ss_pred HhhhcCccceeeeeeeeehhc-cccCHHHHHHHHHHHhcCCccEEEEeccccc-cCceEEeehhhcCHHHHHHHhcCCCC
Confidence 356667666665555433222 22 2334444444 2356679999998754 368899999998875421 1
Q ss_pred ---------ccceeeEeeceeeeccchhHHHHHHHh--hhCCCCCC-------ChhhhhHhhHHHHHHHHHHHHHHHHHH
Q 026489 89 ---------IPQLIFVRSSYTIETVEAERISVDHVA--HLKPSDGG-------SAATQLAAHLTGIHSAIKMLNSRIRVL 150 (238)
Q Consensus 89 ---------~~~~~F~~ip~~I~t~EaErIgVd~l~--~~~~~~~~-------~~~~~l~~~l~~~~~al~~L~~rL~~i 150 (238)
.....|.++|.-|..+----|-+..+. +....+.. ++...+..++..+...+..|+.-+..+
T Consensus 168 pealk~~nltyenmfeElPIVIknS~L~nvlmseLs~~e~c~sdk~~~~~fdlgs~t~leknir~lme~vDEl~qe~~~l 247 (339)
T KOG1560|consen 168 PEALKSANLTYENMFEELPIVIKNSHLANVLMSELSEPEDCESDKPLHSNFDLGSGTRLEKNIRLLMERVDELHQEIVNL 247 (339)
T ss_pred HHHHHhcCCCHHHHHhhcCeeeeccHHHHHHHHhccccccccccccccccccccchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 136899999999988765455554444 22111100 112334455555555555555555556
Q ss_pred HHHHHHhhc
Q 026489 151 HHYLVAMQK 159 (238)
Q Consensus 151 ~~YL~~V~~ 159 (238)
-+|-+.+..
T Consensus 248 ~kyqr~~~r 256 (339)
T KOG1560|consen 248 NKYQRQLAR 256 (339)
T ss_pred HHHHHHHHH
Confidence 667666543
No 15
>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=90.16 E-value=0.083 Score=40.54 Aligned_cols=32 Identities=9% Similarity=0.016 Sum_probs=24.8
Q ss_pred ceeecCCeeecccc--------CCCCcHHHHHHHhccCCC
Q 026489 26 TSIYLDGTPQGVML--------KNPICTSIKLYLMDINES 57 (238)
Q Consensus 26 ~~~~~~~~~~g~~~--------~~~~~~~IH~~~~~~~~~ 57 (238)
+.++.+..++|||+ +++.|..+|++|.+.+++
T Consensus 75 ~~~~~~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 75 KKVNPNLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp HHCSTTSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred ccccccceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence 45667889999998 356889999999988764
No 16
>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=88.23 E-value=0.63 Score=36.16 Aligned_cols=50 Identities=8% Similarity=0.020 Sum_probs=33.0
Q ss_pred eeecCCeeecccc--------CCCCcHHHHHHHhccCCCceEEEEcCCCCCCCCCCCeeEEE
Q 026489 27 SIYLDGTPQGVML--------KNPICTSIKLYLMDINESPVYVLLNPSINPAQKDLPVTIFE 80 (238)
Q Consensus 27 ~~~~~~~~~g~~~--------~~~~~~~IH~~~~~~~~~PI~L~vD~~~~~~~~~LPi~aYe 80 (238)
..-.|...+|||| |+..|..-|.+|....+.-++|++|+.. ..+.+++|.
T Consensus 60 ~~~~g~~~vG~YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~----~~~~~~a~r 117 (119)
T cd08058 60 QTGRPLLVVGWYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKH----RNKDTGIFR 117 (119)
T ss_pred HhCCCCeEEEEEecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCC----CCcccceEE
Confidence 3556789999998 2334444444455555677999999853 256677764
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=80.22 E-value=5.4 Score=35.40 Aligned_cols=73 Identities=11% Similarity=-0.021 Sum_probs=44.6
Q ss_pred cCCeeecccc--------CCCCcHHHHHHHhccCCCceEEEEcCCCC---CCCCCCCeeEEEEeeeeeCCccceeeEeec
Q 026489 30 LDGTPQGVML--------KNPICTSIKLYLMDINESPVYVLLNPSIN---PAQKDLPVTIFESELHVIEGIPQLIFVRSS 98 (238)
Q Consensus 30 ~~~~~~g~~~--------~~~~~~~IH~~~~~~~~~PI~L~vD~~~~---~~~~~LPi~aYes~~~~~~g~~~~~F~~ip 98 (238)
.++.++|||| |+..|..-+.-|-...+.-++|++++... ...++.-+++|....-.. .+.....++|
T Consensus 87 rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~g~~--~~~~~~~e~p 164 (244)
T cd08068 87 RPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQGNK--AGQYERIEVP 164 (244)
T ss_pred CCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecCCCC--CCcceEEEee
Confidence 6789999998 33344443333333445669999986532 112456688888853211 1246678888
Q ss_pred eeeecc
Q 026489 99 YTIETV 104 (238)
Q Consensus 99 ~~I~t~ 104 (238)
++|...
T Consensus 165 l~i~~~ 170 (244)
T cd08068 165 LEIVPT 170 (244)
T ss_pred eEEecC
Confidence 887753
No 18
>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=79.78 E-value=2.6 Score=35.30 Aligned_cols=51 Identities=10% Similarity=-0.002 Sum_probs=38.1
Q ss_pred cCCeeecccc--------CCCCcHHHHHHHhccCCCceEEEEcCCCCCCCCCCCeeEEEEe-eeee
Q 026489 30 LDGTPQGVML--------KNPICTSIKLYLMDINESPVYVLLNPSINPAQKDLPVTIFESE-LHVI 86 (238)
Q Consensus 30 ~~~~~~g~~~--------~~~~~~~IH~~~~~~~~~PI~L~vD~~~~~~~~~LPi~aYes~-~~~~ 86 (238)
.+.++.|||| +++.|..-|..|....+..++|++++. ...+++|.-. ++|.
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 5899999999 355777777777766677899999962 3567788877 5443
No 19
>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=55.47 E-value=94 Score=25.90 Aligned_cols=48 Identities=8% Similarity=0.248 Sum_probs=36.0
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHhhc-CCCCCChHHHH-HHHHHHh
Q 026489 130 AAHLTGIHSAIKMLNSRIRVLHHYLVAMQK-GEIPCENSLLR-QVSSLLR 177 (238)
Q Consensus 130 ~~~l~~~~~al~~L~~rL~~i~~YL~~V~~-G~~~~d~~IlR-~l~~l~~ 177 (238)
.+-+.+...++..+...++.+.+|...|.. +..-.|.+.+. .|..-+.
T Consensus 60 ~pll~~~~~~~~~~~~~l~~~~~~~~~vd~~~~a~i~e~~L~~el~~~l~ 109 (204)
T PF04740_consen 60 IPLLQGLILLLEEYQEALKFIKDFQSEVDSSSNAIIDEDFLESELKKKLN 109 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHcccccccccHHHHHHHHHHHHH
Confidence 344678899999999999999999999964 44566777776 5544433
No 20
>PF09457 RBD-FIP: FIP domain ; InterPro: IPR019018 The Rab11 GTPase regulates recycling of internalized plasma membrane receptors and is essential for completion of cytokinesis. A family of Rab11 interacting proteins (FIPs) that conserve a C-terminal Rab-binding domain (RBD) selectively recognise the active form of Rab11. FIPs are diverse in sequence length and composition toward their N-termini, presumably a feature that underpins their specific roles in Rab11-mediated vesicle trafficking. They have been divided into three subfamilies (classe I, II, and III)on the basis of domain architecture. Class I FIPs comprises a subfamily of three proteins (Rip11/pp75/FIP5, Rab-coupling protein (RCP), and FIP2) that possess an N- terminal C2 domain, localize to recycling endosomes, and regulate plasma membrane recycling. The class II subfamily consists of two proteins (FIP3/eferin/arfophilin and FIP4) with tandem EF hands and a proline-rich region. Class II FIPs localize to recycling endosomes, the trans-Golgi network, and have been implicated in the regulation of membrane trafficking during cytokinesis. The class III subfamily consists of a single protein, FIP1, which does not contain obvious homology domains or motifs other than the FIP-RBD [, , , ]. The FIP-RBD domain is also found in Rab6-interacting protein Erc1/Elks. Erc1 is the regulatory subunit of the IKK complex and probably recruits IkappaBalpha/NFKBIA to the complex []. It may be involved in the organisation of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. It may also be involved in vesicle trafficking at the CAZ, as well as in Rab-6 regulated endosomes to Golgi transport []. The FIB-RBD domain consists of an N-terminal long alpha-helix, followed by a 90 degrees bend at a conserved proline residue, a 3(10) helix and a C-terminal short beta-strand, adopting an "L" shape. The long alpha-helix forms a parallel coiled-coil homodimer that symmetrically interacts with two Rab11 molecules on both sides, forming a quaternary Rab11-(FIP)2-Rab11 complex. The Rab11-interacting region of FIP-RBD is confined to the C-terminal 24 amino acids, which cover the C-terminal half of the long alpha-helix and the short beta-strand [, , , ]. This entry represents the FIP-RBD domain.; PDB: 2HV8_E 2D7C_D 2K6S_B 2GZD_D 2GZH_B.
Probab=50.68 E-value=21 Score=23.74 Aligned_cols=42 Identities=21% Similarity=0.241 Sum_probs=29.6
Q ss_pred hhHhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHH
Q 026489 128 QLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLL 169 (238)
Q Consensus 128 ~l~~~l~~~~~al~~L~~rL~~i~~YL~~V~~G~~~~d~~Il 169 (238)
.+...+..++.-+..-..++..+.+|++++.--=+.-+|+||
T Consensus 4 eL~~~l~~~e~~~~~k~~~v~eLe~YiD~LL~rVmE~~P~IL 45 (48)
T PF09457_consen 4 ELISLLKKQEEENARKDSRVRELEDYIDNLLVRVMEQTPSIL 45 (48)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-GGGG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcchh
Confidence 566677778888888888889999999997643333444443
No 21
>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=46.04 E-value=40 Score=21.67 Aligned_cols=38 Identities=13% Similarity=0.225 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHh
Q 026489 140 IKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLR 177 (238)
Q Consensus 140 l~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~ 177 (238)
.+.|..++..=..+|.+...|+..++.+.+..|.+++.
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 36677777788889999999999999999999999887
No 22
>PF02841 GBP_C: Guanylate-binding protein, C-terminal domain; InterPro: IPR003191 Guanylate-binding protein is a GTPase that is induced by interferon (IFN)-gamma. GTPases induced by IFN-gamma are key to the protective immunity against microbial and viral pathogens. These GTPases are classified into three groups: the small 47-kd GTPases, the Mx proteins, and the large 65- to 67-kd GTPases. Guanylate-binding proteins (GBP) fall into the last class. In humans, there are seven GBPs (hGBP1-7) []. Structurally, hGBP1 consists of two domains: a compact globular N-terminal domain harbouring the GTPase function (IPR015894 from INTERPRO), and an alpha-helical finger-like C-terminal domain. Human GBP1 is secreted from cells without the need of a leader peptide, and has been shown to exhibit antiviral activity against Vesicular stomatitis virus and Encephalomyocarditis virus, as well as being able to regulate the inhibition of proliferation and invasion of endothelial cells in response to IFN-gamma [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 1DG3_A 2D4H_A 2B8W_B 2B92_A 2BC9_A 1F5N_A.
Probab=42.26 E-value=2.1e+02 Score=25.61 Aligned_cols=37 Identities=14% Similarity=0.222 Sum_probs=27.0
Q ss_pred HHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026489 186 KFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDKFN 222 (238)
Q Consensus 186 ~f~~~~~~~~~D~lmvsyLs~Ltk~~~al~el~~Kl~ 222 (238)
.+...+.....+..--..-++..+|+..|+.+...+.
T Consensus 100 ~L~~~i~~~~~~~~~~N~~~s~~~C~~~l~~l~~~le 136 (297)
T PF02841_consen 100 KLMEQIEKKFEEFCKQNEEASEKKCQALLQELFQPLE 136 (297)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3555556667777777788888888888888776664
No 23
>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=37.43 E-value=57 Score=21.72 Aligned_cols=41 Identities=15% Similarity=0.198 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhcC
Q 026489 139 AIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRL 179 (238)
Q Consensus 139 al~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~l 179 (238)
+...+..++..=..|+..+.+|+..+....+..|.+.+.--
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~~v~ 54 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEALGVS 54 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHHTS-
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHhCCC
Confidence 34455556666689999999999999999999888887543
No 24
>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=36.45 E-value=74 Score=26.93 Aligned_cols=55 Identities=16% Similarity=0.023 Sum_probs=32.9
Q ss_pred cCCeeeccccC------CC--CcHHHHHHHhccC-------CCceEEEEcCCCCC-CCCCCCeeEEEEeee
Q 026489 30 LDGTPQGVMLK------NP--ICTSIKLYLMDIN-------ESPVYVLLNPSINP-AQKDLPVTIFESELH 84 (238)
Q Consensus 30 ~~~~~~g~~~~------~~--~~~~IH~~~~~~~-------~~PI~L~vD~~~~~-~~~~LPi~aYes~~~ 84 (238)
.+...+||||. .| .|..-|..|.... +.-|-+++||-... ...+-.+++|-..+.
T Consensus 77 ~gl~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~ 147 (187)
T cd08067 77 RGLSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPP 147 (187)
T ss_pred cCCEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECC
Confidence 45689999982 23 3333333333322 23499999987532 234567899988754
No 25
>KOG2213 consensus Apoptosis inhibitor 5/fibroblast growth factor 2-interacting factor 2, and related proteins [Signal transduction mechanisms]
Probab=35.39 E-value=74 Score=30.50 Aligned_cols=88 Identities=18% Similarity=0.208 Sum_probs=61.0
Q ss_pred eeeEeeceeeeccchhHHHHHHHhhhCCCCCCChhhhhHhhHHHHHHHHHHHH-----HHHHHHHHHHHHhhcC---CCC
Q 026489 92 LIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLN-----SRIRVLHHYLVAMQKG---EIP 163 (238)
Q Consensus 92 ~~F~~ip~~I~t~EaErIgVd~l~~~~~~~~~~~~~~l~~~l~~~~~al~~L~-----~rL~~i~~YL~~V~~G---~~~ 163 (238)
.+..+++-++.+.|.|+-.|+.+-+...+ -..+++.-- -....+++.|+ .+++.+.+|.+...+- ...
T Consensus 134 tKl~~l~~e~L~kevE~~iv~eikkal~d---Vtgeef~lf-m~~L~~lk~~~~k~~~a~lqeLa~~~e~~a~ldaf~~s 209 (460)
T KOG2213|consen 134 TKLITLKGEVLTKEVERHIVDEIKKALED---VTGEEFTLF-MDILASLKSLQTKAGEARLQELAEEQEGLADLDAFNVS 209 (460)
T ss_pred HHhhcccHHHhhhHHHHHHHHHHHHHHHh---ccHHHHHHH-HHHHHhhhcccCCCCHHHHHHHHHHHhhhhccCcccCC
Confidence 45577888888899999999999886543 122233222 23445555555 7888888888876543 234
Q ss_pred CChHHHHHHHHHHhcCCCCC
Q 026489 164 CENSLLRQVSSLLRRLPAIE 183 (238)
Q Consensus 164 ~d~~IlR~l~~l~~~lP~~~ 183 (238)
.++-|=|.|+-+...+|.+.
T Consensus 210 D~d~VdRfisCl~~AvPfFa 229 (460)
T KOG2213|consen 210 DADYVDRFISCLLMAVPFFA 229 (460)
T ss_pred ChHHHHHHHHHHHHhhhhhh
Confidence 55788999999999999664
No 26
>PF03127 GAT: GAT domain; InterPro: IPR004152 The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 [] and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins [].; GO: 0006886 intracellular protein transport, 0005622 intracellular; PDB: 1YD8_H 1WR6_C 1WRD_A 1O3X_A 1J2J_B 1NWM_X 1X79_A 1OXZ_A 1NAF_A.
Probab=33.42 E-value=2e+02 Score=21.35 Aligned_cols=87 Identities=11% Similarity=0.242 Sum_probs=55.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCC-hHHHHHHHHHHhcCCCCChHHHHHHHHHhhchHHHHHHHHHHHHHHH
Q 026489 134 TGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCE-NSLLRQVSSLLRRLPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCAS 212 (238)
Q Consensus 134 ~~~~~al~~L~~rL~~i~~YL~~V~~G~~~~d-~~IlR~l~~l~~~lP~~~~~~f~~~~~~~~~D~lmvsyLs~Ltk~~~ 212 (238)
....+.+......+..+.+-|.....|+...+ .+++..+.+.|..+- +.+.+......+|= +|+.+...-.
T Consensus 7 ~k~~~~l~~v~~~~~lL~emL~~~~~~~~~~~~~el~~eL~~~ck~~r----~~i~~li~~~~dee----~l~~lL~~ND 78 (100)
T PF03127_consen 7 SKRRSELEKVKNNAKLLNEMLDNYDPGEESSSDNELIQELYESCKSMR----PRIQRLIEEVEDEE----LLGELLQAND 78 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTTTTTSTHHHHHHHHHHHHHHHHHH----HHHHHHHHTSTTCH----HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHH----HHHHHHHhhcCcHH----HHHHHHHHHH
Confidence 34455566666666666666777777775544 488888888887663 34444443333332 6666767777
Q ss_pred HHHHHHHHHhhhhhcC
Q 026489 213 TMNELVDKFNTAYDRH 228 (238)
Q Consensus 213 al~el~~Kl~~~~~~~ 228 (238)
.|+....||..+..++
T Consensus 79 ~L~~~l~~Y~~l~~~~ 94 (100)
T PF03127_consen 79 ELNQALERYDRLVKGQ 94 (100)
T ss_dssp HHHHHHHHHHHHHCCC
T ss_pred HHHHHHHHHHHHHcCc
Confidence 7778888887766544
No 27
>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=32.84 E-value=53 Score=19.78 Aligned_cols=17 Identities=18% Similarity=0.421 Sum_probs=13.5
Q ss_pred CChHHHHHHHHHHhcCC
Q 026489 164 CENSLLRQVSSLLRRLP 180 (238)
Q Consensus 164 ~d~~IlR~l~~l~~~lP 180 (238)
-..+|...|.++|+.+|
T Consensus 23 t~~~I~~~l~~~C~~lP 39 (39)
T PF05184_consen 23 TEEEIKKALEKACNKLP 39 (39)
T ss_dssp HHHHHHHHHHHHHTTSC
T ss_pred cHHHHHHHHHHHHhhCc
Confidence 34688888888888887
No 28
>PF07097 DUF1359: Protein of unknown function (DUF1359); InterPro: IPR010772 This family consists of several hypothetical bacterial and phage proteins of around 100 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this species. The function of this family is unknown.
Probab=32.33 E-value=1.7e+02 Score=22.02 Aligned_cols=53 Identities=9% Similarity=0.099 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhcCC---CCChHHHHHHHHHhhch
Q 026489 145 SRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRLP---AIESEKFQDDFLMEYND 197 (238)
Q Consensus 145 ~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~lP---~~~~~~f~~~~~~~~~D 197 (238)
..-+.+.=-+++..+|+++.|...+-.|-+-++-+- .+....+-..+..+..|
T Consensus 30 ~Q~~~~~i~~D~~k~~~i~~~~Kf~~~L~~~~~~~~~~~~I~VGTLI~LL~~NIE~ 85 (102)
T PF07097_consen 30 RQTELVKIVLDDLKNNHIKKDTKFELNLGDRFGVLKCSVKINVGTLIPLLEQNIED 85 (102)
T ss_pred hhhhHHHHHHHHHhcCCCCCcchhceecccccceEEEeeecchhhhhHHHHhcccc
Confidence 333333444678889999999988877764443332 23334444555555555
No 29
>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=29.06 E-value=46 Score=28.07 Aligned_cols=36 Identities=11% Similarity=0.148 Sum_probs=26.5
Q ss_pred CCeeeccccCC---------CCcHHHHHHHhccCCCceEEEEcCC
Q 026489 31 DGTPQGVMLKN---------PICTSIKLYLMDINESPVYVLLNPS 66 (238)
Q Consensus 31 ~~~~~g~~~~~---------~~~~~IH~~~~~~~~~PI~L~vD~~ 66 (238)
+..+.|+||.+ +...-|=+.+.+.++++++|+||-.
T Consensus 69 gl~IvG~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~ 113 (182)
T cd08060 69 GLVIVGYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNE 113 (182)
T ss_pred CCEEEEEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCc
Confidence 67899999832 3344556677777789999999954
No 30
>PRK08359 transcription factor; Validated
Probab=28.15 E-value=63 Score=27.27 Aligned_cols=40 Identities=10% Similarity=0.097 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhcC
Q 026489 140 IKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRL 179 (238)
Q Consensus 140 l~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~l 179 (238)
-+.|-.++..=..|+..+..|+..|+.++++.|.+.+.--
T Consensus 101 QeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l~Vs 140 (176)
T PRK08359 101 YEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYFKIK 140 (176)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHhCCc
Confidence 4556677778889999999999999999999999998755
No 31
>PHA01976 helix-turn-helix protein
Probab=27.84 E-value=82 Score=21.12 Aligned_cols=38 Identities=16% Similarity=0.127 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHh
Q 026489 140 IKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLR 177 (238)
Q Consensus 140 l~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~ 177 (238)
...|-.++..-..+|.+..+|+..|+.+.+..|.+++.
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~~p~~~~l~~ia~~l~ 55 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALG 55 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHC
Confidence 44566667777788889999999899998888888875
No 32
>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=27.46 E-value=2.5e+02 Score=20.65 Aligned_cols=47 Identities=11% Similarity=0.255 Sum_probs=30.5
Q ss_pred hhHhhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhc
Q 026489 128 QLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRR 178 (238)
Q Consensus 128 ~l~~~l~~~~~al~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~ 178 (238)
.+..++..+.+++..|..|++.+..=-++..+ -|.-+.-+|.++++.
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 56777778888888888888877766555543 244444555555443
No 33
>KOG3650 consensus Predicted coiled-coil protein [General function prediction only]
Probab=27.26 E-value=1.6e+02 Score=22.68 Aligned_cols=43 Identities=9% Similarity=0.118 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCC---CCCChHHHHHHHHHHhcCCC
Q 026489 139 AIKMLNSRIRVLHHYLVAMQKGE---IPCENSLLRQVSSLLRRLPA 181 (238)
Q Consensus 139 al~~L~~rL~~i~~YL~~V~~G~---~~~d~~IlR~l~~l~~~lP~ 181 (238)
-+-.|+.-|+.+..-|++|.... ..-|.-+|.+|..+++.-..
T Consensus 64 QVLELQnTLdDLSqRVdsVKEEnLKLrSENQVLGQYIeNLMSaSSV 109 (120)
T KOG3650|consen 64 QVLELQNTLDDLSQRVDSVKEENLKLRSENQVLGQYIENLMSASSV 109 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhhhh
Confidence 33344444444555555555443 24678899999999876553
No 34
>PF10776 DUF2600: Protein of unknown function (DUF2600); InterPro: IPR019712 This is a bacterial family of proteins. Some members in the family are annotated as YtpB, however no function is currently known.
Probab=26.80 E-value=98 Score=28.77 Aligned_cols=72 Identities=11% Similarity=0.165 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhcC--CCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHH
Q 026489 143 LNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRL--PAIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDK 220 (238)
Q Consensus 143 L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~l--P~~~~~~f~~~~~~~~~D~lmvsyLs~Ltk~~~al~el~~K 220 (238)
+.--.++|.+||++..+-....|+.-.|+|...+.-. |..... .+.....+--=-.||..|++++. +...+
T Consensus 57 fIVAyQTIsDYLDNLcDrs~~~d~~~Fr~LH~am~dAl~p~a~~~----dYY~~~~~~dDGGYL~~LV~tCq---~~l~~ 129 (330)
T PF10776_consen 57 FIVAYQTISDYLDNLCDRSTSLDPKDFRQLHQAMLDALDPGAPLS----DYYRYRPEQDDGGYLRALVRTCQ---QVLAQ 129 (330)
T ss_pred HHHHHHHHHHHHHhhhhccCCCChHHHHHHHHHHHHHcCCCCCcc----hHHHcCCccccChHHHHHHHHHH---HHHHh
Confidence 4444789999999999988888999889887755332 222211 12222111112489999999887 54444
Q ss_pred H
Q 026489 221 F 221 (238)
Q Consensus 221 l 221 (238)
+
T Consensus 130 l 130 (330)
T PF10776_consen 130 L 130 (330)
T ss_pred C
Confidence 4
No 35
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=26.25 E-value=69 Score=29.34 Aligned_cols=129 Identities=12% Similarity=0.061 Sum_probs=66.4
Q ss_pred eeecCCeeecccc--CCC------CcHHHHHHHhccCCCceEEEEcCCCCCCCCCCCeeEEEEeeeeeCC--ccceeeEe
Q 026489 27 SIYLDGTPQGVML--KNP------ICTSIKLYLMDINESPVYVLLNPSINPAQKDLPVTIFESELHVIEG--IPQLIFVR 96 (238)
Q Consensus 27 ~~~~~~~~~g~~~--~~~------~~~~IH~~~~~~~~~PI~L~vD~~~~~~~~~LPi~aYes~~~~~~g--~~~~~F~~ 96 (238)
.+..-+-.+|||| |+- .|..-+..=.++-+.-+.+++||.-+-+.+++-+-||-.-+.+-.. .+...|..
T Consensus 126 ~~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRTyp~gyk~~d~~~seyqt 205 (347)
T KOG1554|consen 126 NVGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTYPKGYKPPDEPPSEYQT 205 (347)
T ss_pred HhhhhhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCccccccCceeeceeecccCCCCCCCCCchhhhc
Confidence 3344566789997 333 3333333223344555899999975544677888888777655311 11111222
Q ss_pred ec--------eeeeccchhHHH----------HHHHhhhCCCCCCChhhhhHhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 026489 97 SS--------YTIETVEAERIS----------VDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVA 156 (238)
Q Consensus 97 ip--------~~I~t~EaErIg----------Vd~l~~~~~~~~~~~~~~l~~~l~~~~~al~~L~~rL~~i~~YL~~ 156 (238)
+| +....+.++.|. ++.+-.- .....-+.+.+..+.+-+...+..|.+++.+.-+.+..
T Consensus 206 ipl~kied~gvHck~yysl~isyfks~ld~kll~~Lwnk-ywv~Tlsss~ll~N~dy~~~qi~d~~ekl~q~~~~l~~ 282 (347)
T KOG1554|consen 206 IPLNKIEDFGVHCKQYYSLEISYFKSSLDMKLLELLWNK-YWVRTLSSSPLLKNIDYLNGQIRDLSEKLEQREDSLET 282 (347)
T ss_pred cchhhhhhcccceEEeeccchhhhhhhhhHHHHHHHHhh-hhhcccccccccccchhhcchhhhHHHHHHhhhhhccc
Confidence 11 111111234443 2332221 11111123456677777777778887777776666643
No 36
>KOG3046 consensus Transcription factor, subunit of SRB subcomplex of RNA polymerase II [Transcription]
Probab=25.54 E-value=3.8e+02 Score=21.97 Aligned_cols=59 Identities=12% Similarity=0.272 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhcCCCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026489 143 LNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRLPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTMNELVDKFN 222 (238)
Q Consensus 143 L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~lP~~~~~~f~~~~~~~~~D~lmvsyLs~Ltk~~~al~el~~Kl~ 222 (238)
+.+.+..+.+-|++.. +..|+|.-+++..|......+.+.++ .|++....|+.+..|++
T Consensus 10 ~~ekl~~l~~~le~~~--------e~~~~Lgl~vs~F~~tsq~~L~qrl~-------------tLv~~L~~l~~~s~k~n 68 (147)
T KOG3046|consen 10 MQEKLAQLENSLEKFL--------ENFRQLGLIVSNFQPTSQDALNQRLN-------------TLVRGLQDLDKLSSKLN 68 (147)
T ss_pred HHHHHHHHHHHHHHHH--------HHHHHHhHhhhcCCCCcHHHHHHHHH-------------HHHHHhhhhHHHHHhhc
Confidence 3344444445555543 45788889999988766544433333 45555555556666665
No 37
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=25.19 E-value=88 Score=26.20 Aligned_cols=40 Identities=13% Similarity=0.194 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhcC
Q 026489 140 IKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRL 179 (238)
Q Consensus 140 l~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~l 179 (238)
-+.|-.+|..=..-|+++.+|++.||..+.+.|-.++.-.
T Consensus 95 qedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIk 134 (165)
T COG1813 95 QEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIK 134 (165)
T ss_pred HHHHHHHhcccHHHHHHHHhcccCccHHHHHHHHHHhCce
Confidence 3445566666666777899999999999999999887643
No 38
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=24.60 E-value=4.3e+02 Score=22.57 Aligned_cols=89 Identities=12% Similarity=0.207 Sum_probs=52.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhcCCCC-------------ChHHHHHHHHHhhchH
Q 026489 132 HLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRLPAI-------------ESEKFQDDFLMEYNDT 198 (238)
Q Consensus 132 ~l~~~~~al~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~lP~~-------------~~~~f~~~~~~~~~D~ 198 (238)
..+++..-+.++......+.+|-++.. .++..|++.=.++++.|.++-.. ....|-.++-.++-|+
T Consensus 24 a~~dl~~L~~qa~~~~~~l~~fa~k~~-~~i~~~~~~r~~f~~~~~~lGvdp~~s~~~~s~~l~~~~~f~~ELa~qi~e~ 102 (223)
T PF04157_consen 24 AFQDLEALMSQAKDFVELLENFARKHK-SEIKSDPEFRSQFQSMCASLGVDPLASSKFWSESLKGSGDFYYELAVQIAEV 102 (223)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCSHHHHHHHHHHHHHHT--CHCCTTCCCCCCSCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh-ccccCCchHHHHHHHHHHHcCCCcccchhhhhhccccchhHHHHHHHHHHHH
Confidence 345666666677777777777777764 46677887766777777766421 3345666677666665
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q 026489 199 LLIAYLAMFTNCASTMNELVDKFNT 223 (238)
Q Consensus 199 lmvsyLs~Ltk~~~al~el~~Kl~~ 223 (238)
++-.. . -..+..+|.|+...++.
T Consensus 103 c~~~~-~-~~GGii~L~dl~~~~nr 125 (223)
T PF04157_consen 103 CLATR-S-KNGGIISLSDLYCRYNR 125 (223)
T ss_dssp HHHHC-C-TTTSEEEHHHHHHHHHH
T ss_pred HHHHH-h-cCCCEEEHHHHHHHHHH
Confidence 55111 1 11224556666666554
No 39
>KOG3227 consensus Calcium-responsive transcription coactivator [Transcription]
Probab=24.09 E-value=1.7e+02 Score=25.56 Aligned_cols=20 Identities=10% Similarity=0.202 Sum_probs=10.6
Q ss_pred HHHHHHHHHhhcCCCCCChHHHHHHHHH
Q 026489 148 RVLHHYLVAMQKGEIPCENSLLRQVSSL 175 (238)
Q Consensus 148 ~~i~~YL~~V~~G~~~~d~~IlR~l~~l 175 (238)
+.|.+||+. |..++++|.+-
T Consensus 23 ~~IQk~LdE--------N~~LI~~I~e~ 42 (231)
T KOG3227|consen 23 EQIQKMLDE--------NKHLIQCIVES 42 (231)
T ss_pred HHHHHHHHh--------hhHHHHHHHHh
Confidence 345555555 55555555443
No 40
>PF08020 DUF1706: Protein of unknown function (DUF1706) ; InterPro: IPR012550 This family contains many hypothetical proteins from bacteria and yeast.
Probab=23.98 E-value=3e+02 Score=22.86 Aligned_cols=80 Identities=16% Similarity=0.176 Sum_probs=60.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhcCCCCChHHHHHHHHHhhchHHHHHHHHHHHHHHHHH
Q 026489 135 GIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRLPAIESEKFQDDFLMEYNDTLLIAYLAMFTNCASTM 214 (238)
Q Consensus 135 ~~~~al~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~lP~~~~~~f~~~~~~~~~D~lmvsyLs~Ltk~~~al 214 (238)
...+-|.-|....+.+++++++=.+|+.+.=++=|..= + .-..+.+.|...++|.-+-..++.|..++..+
T Consensus 45 ~~~DvLayl~gW~~LlL~W~~~~~~G~~~~fp~~gykW----n-----~lg~Ln~~f~~~y~~~sl~e~~~~l~~s~~~v 115 (166)
T PF08020_consen 45 NPRDVLAYLYGWHELLLKWEEDEQAGEEVDFPAPGYKW----N-----QLGELNQSFYEKYQDTSLEELKALLKESHQKV 115 (166)
T ss_pred CHHHHHHHHHHHHHHHHHHHhhccCCCCCCCCCCCCCh----h-----hhhHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 46677788888999999999998888744322211111 0 12568889999999999999999999999998
Q ss_pred HHHHHHHhh
Q 026489 215 NELVDKFNT 223 (238)
Q Consensus 215 ~el~~Kl~~ 223 (238)
-++++.|+.
T Consensus 116 ~~lI~~~sd 124 (166)
T PF08020_consen 116 IALIESFSD 124 (166)
T ss_pred HHHHHhCcc
Confidence 899988863
No 41
>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=23.48 E-value=29 Score=30.86 Aligned_cols=20 Identities=5% Similarity=0.071 Sum_probs=16.2
Q ss_pred cccccccccceeecCCeeec
Q 026489 17 KNSIRRCSHTSIYLDGTPQG 36 (238)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~g 36 (238)
.+.-|++++++.+.||+-+|
T Consensus 66 ~~~~kkv~~~~~vVGWY~tg 85 (265)
T cd08064 66 YELHQKVNPKEVIVGWYATG 85 (265)
T ss_pred HHHHHHhCCCCcEEeeeeCC
Confidence 34568889999999998887
No 42
>COG4220 Phage DNA packaging protein, Nu1 subunit of terminase [DNA replication, recombination, and repair]
Probab=22.42 E-value=3.8e+02 Score=22.62 Aligned_cols=29 Identities=17% Similarity=0.314 Sum_probs=23.2
Q ss_pred HHHHHHHHHHhcCCCCChHHHHHHHHHhh
Q 026489 167 SLLRQVSSLLRRLPAIESEKFQDDFLMEY 195 (238)
Q Consensus 167 ~IlR~l~~l~~~lP~~~~~~f~~~~~~~~ 195 (238)
.|+|.|..++.++|....-.|....+.|+
T Consensus 113 ~ia~~ia~~l~~ipls~qr~~p~l~~~hv 141 (174)
T COG4220 113 RIAREIASILDSIPLSVQRRFPELTNRHV 141 (174)
T ss_pred HHHHHHHHHHccccHHHHHhcchhhHHHH
Confidence 78999999999999766666766666665
No 43
>PRK06424 transcription factor; Provisional
Probab=21.70 E-value=1.1e+02 Score=24.96 Aligned_cols=37 Identities=14% Similarity=0.260 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhc
Q 026489 142 MLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRR 178 (238)
Q Consensus 142 ~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~ 178 (238)
.|-.++..=..+|..+.+|+..|+.+.+..|.+.+.-
T Consensus 102 eLA~~iGvs~stIskiE~G~~~Ps~~~l~kLa~~Lgv 138 (144)
T PRK06424 102 DLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGI 138 (144)
T ss_pred HHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCC
Confidence 4445555556899999999999999999999998864
No 44
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=20.84 E-value=1.6e+02 Score=19.68 Aligned_cols=40 Identities=18% Similarity=0.277 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCC-CChHHHHHHHHHHhc
Q 026489 139 AIKMLNSRIRVLHHYLVAMQKGEIP-CENSLLRQVSSLLRR 178 (238)
Q Consensus 139 al~~L~~rL~~i~~YL~~V~~G~~~-~d~~IlR~l~~l~~~ 178 (238)
+...+-.++..=..||..+..|..+ |+...+..|.+++..
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~~~p~~~~l~~l~~~l~~ 56 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRRPRPSPDTLQRLARALGV 56 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSSS-BHHHHHHHHHHTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCCCCCCHHHHHHHHHHHCc
Confidence 4456666777788899999999994 999999888888764
No 45
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=20.65 E-value=1.3e+02 Score=19.04 Aligned_cols=37 Identities=14% Similarity=0.092 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHh
Q 026489 141 KMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLR 177 (238)
Q Consensus 141 ~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~ 177 (238)
..|-.++..-..++.++.+|+..++.+-+..+.+.+.
T Consensus 19 ~~lA~~~gvs~~~vs~~e~g~~~~~~~~~~~i~~~lg 55 (58)
T TIGR03070 19 ADLADLAGVGLRFIRDVENGKPTVRLDKVLRVLDALG 55 (58)
T ss_pred HHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHcC
Confidence 4455666677888999999998888877777766653
No 46
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=20.49 E-value=1.1e+02 Score=28.31 Aligned_cols=49 Identities=18% Similarity=0.202 Sum_probs=33.7
Q ss_pred Ceeecccc--------CCCCcHHHHHHHhccCCCceEEEEcCCCCCCCCCCCeeEEEE
Q 026489 32 GTPQGVML--------KNPICTSIKLYLMDINESPVYVLLNPSINPAQKDLPVTIFES 81 (238)
Q Consensus 32 ~~~~g~~~--------~~~~~~~IH~~~~~~~~~PI~L~vD~~~~~~~~~LPi~aYes 81 (238)
.-.+|||| ++.-|..-|+-|...++..+-..||+-.++.++..|- +|-.
T Consensus 115 ~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~g~vv~d-~f~~ 171 (316)
T KOG1555|consen 115 ELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPYGKVVPD-AFSS 171 (316)
T ss_pred ceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCCCCccCC-hhhh
Confidence 45699998 3446666677788888888889999876654444443 4444
No 47
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=20.41 E-value=1.1e+02 Score=25.05 Aligned_cols=39 Identities=18% Similarity=0.304 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhc
Q 026489 140 IKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRR 178 (238)
Q Consensus 140 l~~L~~rL~~i~~YL~~V~~G~~~~d~~IlR~l~~l~~~ 178 (238)
.+.|-.++..=..|+..+.+|+..|+.+.+..|.+++.-
T Consensus 85 qeeLA~~lgvs~s~IsriE~G~~~Ps~~~l~kLa~~Lgv 123 (154)
T TIGR00270 85 QEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLLKI 123 (154)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCC
Confidence 455666777778999999999999999999999998753
Done!