Query 023397
Match_columns 283
No_of_seqs 144 out of 705
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 03:44:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023397.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023397hhsearch_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 5E-66 1.1E-70 474.0 30.7 254 5-280 2-266 (303)
2 cd08062 MPN_RPN7_8 Mpr1p, Pad1 100.0 3.4E-65 7.3E-70 465.0 31.3 249 10-280 2-260 (280)
3 cd08063 MPN_CSN6 Mpr1p, Pad1p 100.0 1.7E-65 3.6E-70 470.0 29.1 257 9-280 1-264 (288)
4 KOG2975 Translation initiation 100.0 2.5E-65 5.3E-70 446.9 24.6 257 2-280 14-276 (288)
5 cd08064 MPN_eIF3f Mpr1p, Pad1p 100.0 1.5E-63 3.3E-68 452.2 29.8 248 11-280 1-256 (265)
6 KOG3050 COP9 signalosome, subu 100.0 1.2E-63 2.6E-68 431.6 23.7 265 1-281 1-270 (299)
7 KOG1556 26S proteasome regulat 100.0 3.7E-59 7.9E-64 404.3 21.2 257 2-280 2-268 (309)
8 cd08057 MPN_euk_non_mb Mpr1p, 100.0 1.4E-39 3E-44 273.8 17.0 150 11-184 1-157 (157)
9 cd08065 MPN_eIF3h Mpr1p, Pad1p 100.0 2.6E-30 5.7E-35 234.7 22.1 201 10-231 2-233 (266)
10 PF01398 JAB: JAB1/Mov34/MPN/P 99.9 1.6E-26 3.5E-31 184.0 11.7 105 7-131 2-114 (114)
11 cd08069 MPN_RPN11_CSN5 Mov34/M 99.9 7.9E-25 1.7E-29 198.8 21.6 166 6-191 7-202 (268)
12 KOG1560 Translation initiation 99.9 1.5E-20 3.3E-25 166.5 18.7 238 5-265 9-292 (339)
13 smart00232 JAB_MPN JAB/MPN dom 99.9 1.2E-20 2.6E-25 153.3 15.7 125 10-155 1-132 (135)
14 PF13012 MitMem_reg: Maintenan 99.8 2.2E-20 4.7E-25 149.1 1.4 100 178-280 1-103 (115)
15 cd07767 MPN Mpr1p, Pad1p N-ter 99.6 5.4E-15 1.2E-19 117.1 13.0 100 50-153 13-116 (116)
16 KOG1554 COP9 signalosome, subu 99.5 1.7E-13 3.8E-18 122.2 12.9 200 10-230 54-282 (347)
17 cd08067 MPN_2A_DUB Mov34/MPN/P 99.4 7.5E-12 1.6E-16 108.1 15.7 127 7-156 3-145 (187)
18 cd08058 MPN_euk_mb Mpr1p, Pad1 99.4 5.5E-12 1.2E-16 101.2 12.0 108 17-155 2-118 (119)
19 cd08068 MPN_BRCC36 Mov34/MPN/P 99.1 4.4E-09 9.6E-14 94.1 16.9 147 9-177 2-169 (244)
20 cd08066 MPN_AMSH_like Mov34/MP 98.6 9.6E-07 2.1E-11 75.5 13.3 116 11-156 4-127 (173)
21 KOG1555 26S proteasome regulat 98.6 2.1E-06 4.5E-11 79.0 15.5 131 5-155 27-171 (316)
22 PF03665 UPF0172: Uncharacteri 98.3 1.4E-05 2.9E-10 69.8 13.1 124 10-154 3-134 (196)
23 cd08060 MPN_UPF0172 Mov34/MPN/ 98.3 1.1E-05 2.4E-10 69.6 12.3 104 15-141 3-114 (182)
24 cd08070 MPN_like Mpr1p, Pad1p 98.0 9.2E-05 2E-09 59.9 11.7 108 17-155 3-118 (128)
25 COG1310 Predicted metal-depend 97.9 0.00014 3.1E-09 59.3 10.3 98 12-139 3-106 (134)
26 KOG3289 Uncharacterized conser 97.1 0.017 3.8E-07 49.1 12.6 124 10-154 3-134 (199)
27 TIGR02256 ICE_VC0181 integrati 96.7 0.036 7.7E-07 45.3 11.3 87 50-137 16-112 (131)
28 PF14464 Prok-JAB: Prokaryotic 95.1 0.32 7E-06 37.1 9.9 60 50-119 17-80 (104)
29 cd08072 MPN_archaeal Mov34/MPN 95.1 0.46 9.9E-06 37.9 10.9 83 50-155 18-107 (117)
30 cd08056 MPN_PRP8 Mpr1p, Pad1p 94.3 0.51 1.1E-05 42.7 10.4 98 51-156 56-165 (252)
31 cd08073 MPN_NLPC_P60 Mpr1p, Pa 86.1 2.8 6.1E-05 32.8 6.2 57 50-119 15-80 (108)
32 cd08059 MPN_prok_mb Mpr1p, Pad 78.3 13 0.00029 28.2 7.3 60 50-120 15-78 (101)
33 cd08061 MPN_NPL4 Mov34/MPN/PAD 71.5 61 0.0013 29.8 10.9 101 51-156 34-158 (274)
34 PF06442 DHFR_2: R67 dihydrofo 70.6 2.4 5.1E-05 30.2 1.2 12 102-113 40-51 (78)
35 PF14778 ODR4-like: Olfactory 64.9 36 0.00079 32.4 8.4 59 55-113 1-74 (362)
36 PF05021 NPL4: NPL4 family; I 63.1 1.3E+02 0.0028 28.1 11.4 97 54-155 2-140 (306)
37 KOG2880 SMAD6 interacting prot 51.7 7.1 0.00015 37.0 1.1 88 51-141 276-368 (424)
38 TIGR03735 PRTRC_A PRTRC system 46.9 84 0.0018 27.4 6.9 72 14-118 76-154 (192)
39 PF10073 DUF2312: Uncharacteri 45.5 1.2E+02 0.0026 22.3 8.8 62 205-278 11-72 (74)
40 PF09457 RBD-FIP: FIP domain ; 35.4 46 0.001 22.3 2.7 41 203-243 5-45 (48)
41 PF05184 SapB_1: Saposin-like 34.8 49 0.0011 20.2 2.7 17 238-254 23-39 (39)
42 PF05377 FlaC_arch: Flagella a 33.1 1.3E+02 0.0028 20.8 4.7 35 200-234 16-50 (55)
43 PF11430 EGL-1: Programmed cel 26.2 1.2E+02 0.0027 16.6 3.1 12 240-251 1-12 (21)
44 PF01381 HTH_3: Helix-turn-hel 25.9 1.4E+02 0.003 19.4 4.0 37 215-251 13-49 (55)
45 KOG3286 Selenoprotein T [Gener 23.2 1.5E+02 0.0033 26.1 4.5 40 59-106 65-104 (226)
46 PF05391 Lsm_interact: Lsm int 22.4 69 0.0015 17.7 1.5 13 254-266 8-20 (21)
47 PF12844 HTH_19: Helix-turn-he 20.3 1.8E+02 0.0039 19.5 3.7 38 215-252 16-53 (64)
48 KOG0756 Mitochondrial tricarbo 20.0 58 0.0013 30.2 1.4 49 51-111 13-73 (299)
No 1
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=100.00 E-value=5e-66 Score=473.96 Aligned_cols=254 Identities=27% Similarity=0.486 Sum_probs=229.4
Q ss_pred CCCCceEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCcc---
Q 023397 5 SSSGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPSTH--- 81 (283)
Q Consensus 5 ~~~~~~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~--- 81 (283)
..+..+|.|||+|||+|+|||+|+..+ .+.||+|+|||++.++.+||+|||++|++++++
T Consensus 2 ~~~~~~V~vhPlVll~I~dh~~R~~~~-----------------~~~rviG~LLG~~~~~~ieItnsF~~p~~e~~~~~~ 64 (303)
T PLN03246 2 PRGIEKVVVHPLVLLSIVDHYNRVAKD-----------------TRKRVVGVLLGSSFRGRVDVTNSFAVPFEEDDKDPS 64 (303)
T ss_pred CCCCcEEEECcHHHHHHHHHHHhccCC-----------------CCCeeEEEEEeeecCCEEEEEeccccCcccCCCCcc
Confidence 456678999999999999999998643 147999999999999999999999999987543
Q ss_pred --cccHHHHHHHHHHHHHhCCCcceEEEEecCCCCCcchHHHHHHHhhhCCCcEEEEEcCCCCCCCCCcceEEEEeeecc
Q 023397 82 --SLDRAFLEKKQELYKKVFPHFYILGWYSTGSDAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESELHV 159 (283)
Q Consensus 82 --~iD~~~~~~m~~l~k~V~p~~~iVGWY~tg~~~~~~d~~ih~~~~~~~~~pi~L~~D~~~~~~~~~lpi~~y~~~~~~ 159 (283)
++|++|+++|+++||+|||++.+||||++|++++++|+.||++|++++++||||++|+.+ ..++||+++|++....
T Consensus 65 ~~~~D~~y~~~m~~~~k~V~~~~~vVGWY~tg~~i~~~d~~IH~~~~~~~~~Pv~L~vD~~~--~~~~lpi~aY~s~~~~ 142 (303)
T PLN03246 65 IWFLDHNYLESMFGMFKRINAKEHVVGWYSTGPKLRENDLDIHELFNDYVPNPVLVIIDVQP--KELGIPTKAYYAVEEV 142 (303)
T ss_pred ceeecHHHHHHHHHHHHHhCCCCcEEeeecCCCCCCcchHHHHHHHHhhCCCCeEEEEecCC--CCCCCceEEEEEEEec
Confidence 399999999999999999999999999999999999999999999999999999999986 3578999999986544
Q ss_pred cc-CC--ceeeEEEeeeeeecchhhHHHHHHHhccCCCCCCChhhhhhhcHHHHHHHHHHHHHHHHHHHHHHHHhhcCCC
Q 023397 160 IE-GI--PQLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEI 236 (283)
Q Consensus 160 ~~-g~--~~~~f~~v~~~i~~~e~ErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~ 236 (283)
.+ |. .+..|+++|++|+++|||||||+|++|... +.+.+.+..++..+.+|+++|..||+.|++||++|.+|+.
T Consensus 143 ~~~~~~~~~~~F~~vp~~i~~~EaE~Igve~l~r~~~---~~~~s~l~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~g~~ 219 (303)
T PLN03246 143 KENATQKSQKVFVHVPSEIGAHEAEEIGVEHLLRDVK---DTTVSTLATEVTGKLTALKGLDARLREIRSYLDLVVEGKL 219 (303)
T ss_pred cCCCCcccccEEEECCeeeeecCHHHHHHHHHHhccc---CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 33 33 457899999999999999999999998643 2334567789999999999999999999999999999999
Q ss_pred CCChHHHHHHHHHHhcCCCCChHHHHHHHH---HHHHHHHHHHHhhc
Q 023397 237 PCENSLLRQVSSLLRRLPAIESEKFQDDFL---MVSLFSSFLNIFTI 280 (283)
Q Consensus 237 ~~d~~ilR~i~~l~~~lP~~~~~~f~~~~~---~~~lmv~yLs~lt~ 280 (283)
++|++|||+|+++|+++|.+++++|+++|+ +|+||++|||+||+
T Consensus 220 ~~d~~IlR~l~~l~~~lP~l~~~~f~~~f~~~~nD~lmv~YLa~l~k 266 (303)
T PLN03246 220 PLNHEILYHLQDVFNLLPNLNVEELVKAFAVKTNDMMLVIYLSSLIR 266 (303)
T ss_pred CCCHHHHHHHHHHHhhCCCCCHHHHHHHHHhhccHHHHHHHHHHHHH
Confidence 999999999999999999999999999995 68999999999997
No 2
>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=3.4e-65 Score=465.03 Aligned_cols=249 Identities=24% Similarity=0.462 Sum_probs=227.4
Q ss_pred eEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCcc-----ccc
Q 023397 10 TFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPSTH-----SLD 84 (283)
Q Consensus 10 ~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~-----~iD 84 (283)
+|.|||+|||+|+|||+|+..+ .+.+|+|+|||++.++.+||+|||++|++++++ ++|
T Consensus 2 ~V~ihplVLl~I~dh~~R~~~~-----------------~~~~ViG~LLG~~~~~~veItnsF~~p~~~~~~~~~~~~~d 64 (280)
T cd08062 2 KVVVHPLVLLSVVDHYNRVAKG-----------------TSKRVVGVLLGSWKKGVLDVTNSFAVPFEEDEKDPSVWFLD 64 (280)
T ss_pred eEEEehHHHHHHHHHHhhhcCC-----------------CCceEEEEEEEEEeCCEEEEEEeeecCccCCCCCcchhhhh
Confidence 6999999999999999998743 247999999999999999999999999987654 389
Q ss_pred HHHHHHHHHHHHHhCCCcceEEEEecCCCCCcchHHHHHHHhhhCCCcEEEEEcCCCCCCCCCcceEEEEeeeccc-cCC
Q 023397 85 RAFLEKKQELYKKVFPHFYILGWYSTGSDAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESELHVI-EGI 163 (283)
Q Consensus 85 ~~~~~~m~~l~k~V~p~~~iVGWY~tg~~~~~~d~~ih~~~~~~~~~pi~L~~D~~~~~~~~~lpi~~y~~~~~~~-~g~ 163 (283)
++|+++|+++||+|||++.+||||++|+.+++.|+.||++|++++++||+|++||... .++||+++|++..... +|.
T Consensus 65 ~~y~~~m~~~~kkv~~~e~vVGWY~tg~~~~~~d~~ih~~~~~~~~~pv~l~vd~~~~--~~~lpi~aY~s~~~~~~~g~ 142 (280)
T cd08062 65 HNYLENMYGMFKKVNAKEKIVGWYSTGPKLRPNDLDINELFRRYCPNPVLVIIDVRPK--DLGLPTEAYIAVEEVHDDGT 142 (280)
T ss_pred HHHHHHHHHHHHHhCCCCCeEEEecCCCCCCcchHHHHHHHHHhCCCCEEEEEecCCC--CCCCceEEEEEeeeccCCCC
Confidence 9999999999999999999999999999999999999999999999999999999863 5789999999865443 565
Q ss_pred -ceeeEEEeeeeeecchhhHHHHHHHhccCCCCCCChhhhhhhcHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHH
Q 023397 164 -PQLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSL 242 (283)
Q Consensus 164 -~~~~f~~v~~~i~~~e~ErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~i 242 (283)
.+..|+++|++|+++|||||||+|++|... +.+.+.+..++..+.+|+++|+.||+.|++||++|.+|+.|+|++|
T Consensus 143 ~~~~~F~~vp~~i~~~eaE~igve~l~r~~~---~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~I 219 (280)
T cd08062 143 PTSKTFVHVPSEIGAEEAEEVGVEHLLRDIK---DVTVSTLSTRVTNKLNSLKGLQSKLKEIKDYLQLVVEGKLPINHQI 219 (280)
T ss_pred cceeEEEEcceEeeccchHHHHHHHHHhhcc---CcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH
Confidence 678999999999999999999999998533 2234567779999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCChHHHHHHHH---HHHHHHHHHHHhhc
Q 023397 243 LRQVSSLLRRLPAIESEKFQDDFL---MVSLFSSFLNIFTI 280 (283)
Q Consensus 243 lR~i~~l~~~lP~~~~~~f~~~~~---~~~lmv~yLs~lt~ 280 (283)
||+|+++|+++|.+++++|+++|+ +|++|++|||+||+
T Consensus 220 lR~l~~~~~~lP~l~~~~f~~~~~~~~nD~lmv~yLs~l~k 260 (280)
T cd08062 220 IYNLQDIFNLLPNLNLPELVKAFAVKTNDQMLVIYLSSLIR 260 (280)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHhhccHHHHHHHHHHHHH
Confidence 999999999999999999999995 68999999999987
No 3
>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=1.7e-65 Score=470.05 Aligned_cols=257 Identities=49% Similarity=0.793 Sum_probs=233.4
Q ss_pred ceEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCc-c--cccH
Q 023397 9 LTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPST-H--SLDR 85 (283)
Q Consensus 9 ~~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~-~--~iD~ 85 (283)
++|.|||+|||+|+|||+|+..+.. ..+.+|+|+|||+++|++|||+|||++|+++++ + .+|+
T Consensus 1 ~~V~lHPlVll~I~dH~~R~~~~~~--------------~~~~~v~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~id~ 66 (288)
T cd08063 1 LSVKLHPLVILNISDHITRHRAQSQ--------------SEPPRVVGALLGQQDGREIEIENSFELKYDTNEDGEIVLDK 66 (288)
T ss_pred CeEEEecceeeeHHhhHhHHhccCC--------------CCCCcEEEEEEEEEcCCEEEEEEEEecccccCCCCceeeCH
Confidence 4799999999999999999986510 014799999999999999999999999998775 3 6999
Q ss_pred HHHHHHHHHHHHhCCCcceEEEEecCCC-CCcchHHHHHHHhhhCCCcEEEEEcCCCCCCCCCcceEEEEeeeccccCCc
Q 023397 86 AFLEKKQELYKKVFPHFYILGWYSTGSD-AQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESELHVIEGIP 164 (283)
Q Consensus 86 ~~~~~m~~l~k~V~p~~~iVGWY~tg~~-~~~~d~~ih~~~~~~~~~pi~L~~D~~~~~~~~~lpi~~y~~~~~~~~g~~ 164 (283)
+|+++|+++||+|||++.+||||++|+. ++..|+.||++|++++++||+|++||.....+++||++||++.....+|..
T Consensus 67 ~y~~~m~~~~kkV~~~~~vVGWY~tg~~~~~~~~~~Ih~~~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~~~~~~~~ 146 (288)
T cd08063 67 EFLETRLEQFKQVFKDLDFVGWYTTGPGGPTESDLPIHKQILEINESPVLLLLDPEANASGKDLPVTIYESVLELVDGEA 146 (288)
T ss_pred HHHHHHHHHHHHhccCCceEEEEecCCCCCCHHHHHHHHHHHhhCCCcEEEEEccccccCCCCCceeEEEEEEeccCCcc
Confidence 9999999999999999999999999998 999999999999999999999999998743578899999999766666667
Q ss_pred eeeEEEeeeeeecchhhHHHHHHHhccCCCCCCChhhhhhhcHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHH
Q 023397 165 QLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLR 244 (283)
Q Consensus 165 ~~~f~~v~~~i~~~e~ErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~ilR 244 (283)
...|+++||+|+++|+||||++|+++..+.. +.+.+.+..+++.+.+|+++|++||+.|++||++|.+|++++|++|||
T Consensus 147 ~~~F~~i~~~i~~~eaErIgv~~l~~~~~~~-~~~~~~~~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~g~~~~d~~ilR 225 (288)
T cd08063 147 TLRFRELPYTIETGEAERIGVDHVARGGASG-SSEKSTVAAHLQAQHNAIKMLNSRVELILEYLKAVPVGEVPPDHSILR 225 (288)
T ss_pred ccEEEeeeeEEEeccCceeeHHHHHhcCCCC-CCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHH
Confidence 7889999999999999999999999976432 344566788999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCCChHHHHHHHH---HHHHHHHHHHHhhc
Q 023397 245 QVSSLLRRLPAIESEKFQDDFL---MVSLFSSFLNIFTI 280 (283)
Q Consensus 245 ~i~~l~~~lP~~~~~~f~~~~~---~~~lmv~yLs~lt~ 280 (283)
+|+++|+++|.++.++|+++|+ +|++|++|||+||+
T Consensus 226 ~l~~~~~~lP~~~~~~~~~~~~~~~~D~lmv~yLs~lt~ 264 (288)
T cd08063 226 SISALCSRLPVLKSEAFREELLAEYNDVLLVAYLATLTK 264 (288)
T ss_pred HHHHHHHhCccCChHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 9999999999999999999995 67999999999997
No 4
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-65 Score=446.86 Aligned_cols=257 Identities=26% Similarity=0.402 Sum_probs=238.2
Q ss_pred CCCCCCCceEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCcc
Q 023397 2 ASSSSSGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPSTH 81 (283)
Q Consensus 2 ~~~~~~~~~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~ 81 (283)
+++.++.++|.|||+|+|||+|||.||..+ ..||||+|||+.++|.|||||||++||.|+++
T Consensus 14 ~~~~ss~ltv~ihP~Vlf~ivD~~~RR~~~------------------~~rviGTLLG~~~~g~ieitNCFaVPhnEssd 75 (288)
T KOG2975|consen 14 PSPFSSNLTVRLHPVVLFSIVDAYERRNKG------------------AERVIGTLLGTVDKGSVEVTNCFAVPHNESSD 75 (288)
T ss_pred CCCCCCCceEEEcceEEeEeehhhhcCCcc------------------chhhhhheeecccCCeEEEEEeeeccCccccc
Confidence 567888999999999999999999999865 47999999999999999999999999999877
Q ss_pred --cccHHHHHHHHHHHHHhCCCcceEEEEecCCCCCcchHHHHHHHhhhCCCcEEEEEcCCCCCCCCCcceEEEEee-ec
Q 023397 82 --SLDRAFLEKKQELYKKVFPHFYILGWYSTGSDAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESE-LH 158 (283)
Q Consensus 82 --~iD~~~~~~m~~l~k~V~p~~~iVGWY~tg~~~~~~d~~ih~~~~~~~~~pi~L~~D~~~~~~~~~lpi~~y~~~-~~ 158 (283)
-+|++|.+.|+++++|+||+|.+||||+||++++.++..||++|.+.+++||||++|++.. ++.+++++|.+. ++
T Consensus 76 qvevdm~y~~~M~~l~~k~npnE~vvGWyaTg~dvt~~sslihdyYare~~~pvhLtVDT~~~--n~rm~ikaYvss~~G 153 (288)
T KOG2975|consen 76 QVEVDMEYAKNMYELHKKVNPNELVVGWYATGHDVTEHSSLIHDYYAREAPNPVHLTVDTSLQ--NGRMSIKAYVSSLMG 153 (288)
T ss_pred cceeeHHHHHHHHHHhcccCCCceeEEEEecCCCcccchhHHHHHhhccCCCCeEEEEecccc--CCccceeEEEEeccC
Confidence 4999999999999999999999999999999999999999999999999999999999974 688999999874 55
Q ss_pred cccCCceeeEEEeeeeeecchhhHHHHHHHhccCCCCCCChhhhhhhcHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCC
Q 023397 159 VIEGIPQLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPC 238 (283)
Q Consensus 159 ~~~g~~~~~f~~v~~~i~~~e~ErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~ 238 (283)
..++....+|.|+|+++...|+||+|++.+.+.+.+ .+....+..+|+++..|...|+++|+++++|+++|.+|+.++
T Consensus 154 vpg~~~~~mF~plpvel~~~~~ervgl~li~kt~~s--p~r~~~l~~dLqQv~~at~~l~~~L~~Vl~YVedVl~gk~~p 231 (288)
T KOG2975|consen 154 VPGRTMGVMFTPLPVELAYYDAERVGLDLIEKTSFS--PSRVAGLSSDLQQVEGATARLQSLLERVLKYVEDVLAGKVKP 231 (288)
T ss_pred CCCcccceeeeeeeeEEeecchhhhHHHHHHHhccC--hhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCC
Confidence 555556779999999999999999999999998633 345667889999999999999999999999999999999999
Q ss_pred ChHHHHHHHHHHhcCCCCChHHHHHHHH---HHHHHHHHHHHhhc
Q 023397 239 ENSLLRQVSSLLRRLPAIESEKFQDDFL---MVSLFSSFLNIFTI 280 (283)
Q Consensus 239 d~~ilR~i~~l~~~lP~~~~~~f~~~~~---~~~lmv~yLs~lt~ 280 (283)
|..|||+|+++++++|++.+++|+.+|+ +|+||+.|||++|+
T Consensus 232 dn~VGR~Lmd~v~~vP~l~p~~Fe~mfn~nLrD~Lmv~yLa~ltq 276 (288)
T KOG2975|consen 232 DNAVGRFLMDLVTAVPKLVPDDFETMFNSNLRDLLMVIYLANLTQ 276 (288)
T ss_pred cchHHHHHHHHHHhcCCCCHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999996 68999999999986
No 5
>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=1.5e-63 Score=452.23 Aligned_cols=248 Identities=25% Similarity=0.419 Sum_probs=225.0
Q ss_pred EEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCcc--cccHHHH
Q 023397 11 FKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPSTH--SLDRAFL 88 (283)
Q Consensus 11 V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~--~iD~~~~ 88 (283)
|.|||+|||+|+|||+|+..+ +.+|+|+|||++.++.+||+|||++|++++++ .+|.+|+
T Consensus 1 v~ihPlVll~I~dH~~R~~~~------------------~~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~d~~y~ 62 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEG------------------QERVIGTLLGTRSEGEVEITNCFAVPHNESEDQVAVDMEYH 62 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCC------------------CcEEEEEEEEEEeCCEEEEEeCeecceeCCCCeEEEcHHHH
Confidence 689999999999999998744 47999999999999999999999999987665 5999999
Q ss_pred HHHHHHHHHhCCCcceEEEEecCCCCCcchHHHHHHHhhhCC--CcEEEEEcCCCCCCCCCcceEEEEeee-ccccCCce
Q 023397 89 EKKQELYKKVFPHFYILGWYSTGSDAQESDMHIHKALMDINE--SPVYVLLNPSINPAQKDLPVTIFESEL-HVIEGIPQ 165 (283)
Q Consensus 89 ~~m~~l~k~V~p~~~iVGWY~tg~~~~~~d~~ih~~~~~~~~--~pi~L~~D~~~~~~~~~lpi~~y~~~~-~~~~g~~~ 165 (283)
++|+++||+|||++.+||||++|+.++..+..||++|++.++ +||+|++||... .+++|++||++.. ...++..+
T Consensus 63 ~~m~~~~kkv~~~~~vVGWY~tg~~~~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~--~~~l~i~ay~~~~~~~~~~~~~ 140 (265)
T cd08064 63 RTMYELHQKVNPKEVIVGWYATGSEITEHSALIHDYYSRECTSYNPIHLTVDTSLD--DGKMSIKAYVSSPLGVPGKTLG 140 (265)
T ss_pred HHHHHHHHHhCCCCcEEeeeeCCCCCCccHHHHHHHHHhhCCCCCCEEEEEeCCCC--CCCcceEEEEEEecccCCCCcc
Confidence 999999999999999999999999999999999999999988 999999999864 3489999999753 33344567
Q ss_pred eeEEEeeeeeecchhhHHHHHHHhccCCCCCCChhhhhhhcHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHH
Q 023397 166 LIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQ 245 (283)
Q Consensus 166 ~~f~~v~~~i~~~e~ErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~ilR~ 245 (283)
.+|.++|++|.++|+||||++++++...... ....+.++++.+.+|+++|..||+.|++||++|.+|+.++|++|||+
T Consensus 141 ~~F~~ip~~i~~~eaE~i~v~~l~~~~~~~~--~~~~~~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~i~r~ 218 (265)
T cd08064 141 SMFVPIPLELLYSEAERVALDLLAKTLASPS--RSAPLTSDLEQLEASLEKLQEMLDRVLRYVEDVLAGKVKADNAIGRY 218 (265)
T ss_pred eEEEEcceeeecCcHHHHHHHHHHhhccCCc--ccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHH
Confidence 8999999999999999999999999755422 23345689999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCChHHHHHHHH---HHHHHHHHHHHhhc
Q 023397 246 VSSLLRRLPAIESEKFQDDFL---MVSLFSSFLNIFTI 280 (283)
Q Consensus 246 i~~l~~~lP~~~~~~f~~~~~---~~~lmv~yLs~lt~ 280 (283)
|+++++++|.+++++|+++|+ +|+||++|||+||+
T Consensus 219 l~~~~~~lp~~~~~~f~~~~~~~~~D~lmv~YLs~l~k 256 (265)
T cd08064 219 LMDALTSVPKLDPEEFEKMFNSSLQDLLMVTYLSNLTK 256 (265)
T ss_pred HHHHHhhCCCCCHHHHHHHHHhhcchHHHHHHHHHHHH
Confidence 999999999999999999996 57999999999997
No 6
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=1.2e-63 Score=431.59 Aligned_cols=265 Identities=54% Similarity=0.875 Sum_probs=243.5
Q ss_pred CCCCCCCCceEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCc
Q 023397 1 MASSSSSGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPST 80 (283)
Q Consensus 1 ~~~~~~~~~~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~ 80 (283)
|+.|++++.+|.+|||||+||+|||+|.+.+. +++.++|+|+|+|.|.|+.|||.|||++..+..+
T Consensus 1 ~Aps~S~s~tv~LHPLVImniSdH~tR~k~Q~--------------gpp~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~ 66 (299)
T KOG3050|consen 1 MAPSSSGSVTVKLHPLVIMNISDHYTRVKTQL--------------GPPVKQVYGALIGKQRGRNVEIMNSFELKMDTEE 66 (299)
T ss_pred CCCCCCCceeEEeccEEEEehhHHHHHHHhhc--------------CCcHHHhhhhheecccCceEEEeeeeEEEecchh
Confidence 57788889999999999999999999999762 1223589999999999999999999999998766
Q ss_pred c--cccHHHHHHHHHHHHHhCCCcceEEEEecCCCCCcchHHHHHHHhhhCCCcEEEEEcCCCCCCCCCcceEEEEeeec
Q 023397 81 H--SLDRAFLEKKQELYKKVFPHFYILGWYSTGSDAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESELH 158 (283)
Q Consensus 81 ~--~iD~~~~~~m~~l~k~V~p~~~iVGWY~tg~~~~~~d~~ih~~~~~~~~~pi~L~~D~~~~~~~~~lpi~~y~~~~~ 158 (283)
+ .+|.+|+.++.+|||+|||++.++|||++|+++++.|+.||++++..+++|++|.++|..+. ....|+.+|++..+
T Consensus 67 ~~~~~dke~l~kk~eqykqVFpdl~vlGwYttG~d~t~sd~~i~k~l~~i~esplflkLNp~t~~-t~~~pv~lfese~d 145 (299)
T KOG3050|consen 67 DTETIDKEYLEKKEEQYKQVFPDLYVLGWYTTGSDPTPSDIHIHKQLMDINESPLFLKLNPATNH-TDKDPVTLFESEID 145 (299)
T ss_pred hhhhccHHHHHHHHHHHHHhcccceEEEEeecCCCCChhhhHHHHHHHhhhcCceEEEecchhcc-ccCCCceeeeeehe
Confidence 5 69999999999999999999999999999999999999999999999999999999998653 34559999999988
Q ss_pred cccCCceeeEEEeeeeeecchhhHHHHHHHhccCCCCCCChhhhhhhcHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCC
Q 023397 159 VIEGIPQLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPC 238 (283)
Q Consensus 159 ~~~g~~~~~f~~v~~~i~~~e~ErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~ 238 (283)
+.||.+...|+|+.|+++++|||||||||+++-+++.++ ..+.+..++..+..|++||+.|++.|++||++|.+|++++
T Consensus 146 vidg~~q~~f~~~tytl~teEaERIgVdHVA~lt~~~gg-e~s~VaeHl~AQdsA~~ml~~Rvklil~Y~k~~e~G~l~~ 224 (299)
T KOG3050|consen 146 VIDGEAQMLFVPLTYTLATEEAERIGVDHVARLTPSDGG-EGSSVAEHLEAQDSAIKMLDNRVKLILAYLKKVEAGTLQP 224 (299)
T ss_pred eecCcceeeeeeeEEEEeehhhhhccchhheeeccCCCC-CcchHHHHHhhHHHHHHHHhhHHHHHHHHHhhhhcCCcCc
Confidence 999999999999999999999999999999999887653 3456789999999999999999999999999999999999
Q ss_pred ChHHHHHHHHHHhcCCCCChHHHHHHHHH---HHHHHHHHHHhhcc
Q 023397 239 ENSLLRQVSSLLRRLPAIESEKFQDDFLM---VSLFSSFLNIFTIF 281 (283)
Q Consensus 239 d~~ilR~i~~l~~~lP~~~~~~f~~~~~~---~~lmv~yLs~lt~~ 281 (283)
|.+|||+...+|++||.++.++|.+.|.. |+.+++||+.||..
T Consensus 225 N~eILrea~~L~~~Lp~~~~~~F~d~F~~e~nd~~l~syl~~iT~~ 270 (299)
T KOG3050|consen 225 NFEILREAYALCHRLPVMESEKFQDNFYMECNDVGLISYLGTITKC 270 (299)
T ss_pred cHHHHHHHHHHHhhccccchHHHhHHHHHhcchhhHHHHHHHHHHh
Confidence 99999999999999999999999999964 59999999999864
No 7
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.7e-59 Score=404.28 Aligned_cols=257 Identities=26% Similarity=0.457 Sum_probs=235.7
Q ss_pred CCCCCCCceEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCcc
Q 023397 2 ASSSSSGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPSTH 81 (283)
Q Consensus 2 ~~~~~~~~~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~ 81 (283)
..++-...+|.|||||||++.|||.|.... .++||+|+|||..+++.+.|+|||++||+|++.
T Consensus 2 ~~~~~~~~kViVhPLVLLS~VDhynR~~k~-----------------~~KRvvGvLLG~~~~~~i~vtnSfAvpFeEDdk 64 (309)
T KOG1556|consen 2 PISELTVEKVIVHPLVLLSAVDHYNRVGKD-----------------TNKRVVGVLLGSWNGDVIDVTNSFAVPFEEDDK 64 (309)
T ss_pred CccccccceeeeehhHHHHHHHHHhhhccC-----------------cCceEEEEEEecCCCCeEEeecceeccccccCC
Confidence 345566679999999999999999998753 248999999999999999999999999998765
Q ss_pred -----cccHHHHHHHHHHHHHhCCCcceEEEEecCCCCCcchHHHHHHHhhhCCCcEEEEEcCCCCCCCCCcceEEEEee
Q 023397 82 -----SLDRAFLEKKQELYKKVFPHFYILGWYSTGSDAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESE 156 (283)
Q Consensus 82 -----~iD~~~~~~m~~l~k~V~p~~~iVGWY~tg~~~~~~d~~ih~~~~~~~~~pi~L~~D~~~~~~~~~lpi~~y~~~ 156 (283)
|+|++|++.|+++|+|||.++.+||||+||+.+.++|+.|++.+.++|++|+.+++|..+ ..-+||..||.+.
T Consensus 65 ~~svWFlDh~Y~esM~~mfkKvNakekivGWYhTGPkl~~nDl~In~l~k~y~pnpvLvIIdvkp--k~~gLPT~AY~aV 142 (309)
T KOG1556|consen 65 DKSVWFLDHNYIESMFGMFKKVNAKEKVVGWYHTGPKLRENDLDINELLKRYVPNPVLVIIDVKP--KELGLPTEAYIAV 142 (309)
T ss_pred CCceEEeccHHHHHHHHHHHHhcchhheeeeeccCCccccchhhHHHHHhhcCCCceEEEEeccc--ccCCCCchheeee
Confidence 699999999999999999999999999999999999999999999999999999999986 4578999999886
Q ss_pred eccc-cCC-ceeeEEEeeeeeecchhhHHHHHHHhccCCCCCCChhhhhhhcHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q 023397 157 LHVI-EGI-PQLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKG 234 (283)
Q Consensus 157 ~~~~-~g~-~~~~f~~v~~~i~~~e~ErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G 234 (283)
.+.. ||. ++.+|.++|++|+++|||+|||+|+.|. .++.+.+++...+.++..+++.|+.++..|.+||++|.+|
T Consensus 143 eev~dDgt~t~ktF~Hvps~I~AeEAEEvGVEHLlRD---ikd~t~gtla~rit~ql~sLkgl~~~L~eI~~YL~~Vi~g 219 (309)
T KOG1556|consen 143 EEVKDDGTPTSKTFVHVPSEIEAEEAEEVGVEHLLRD---IKDTTVGTLATRITNQLMSLKGLQSRLREIRSYLDKVIDG 219 (309)
T ss_pred eeeecCCCCccceeEecCcccchhHHHHhhHHHHHHH---HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 5554 454 4678999999999999999999999997 4456778999999999999999999999999999999999
Q ss_pred CCCCChHHHHHHHHHHhcCCCCChHHHHHHHH---HHHHHHHHHHHhhc
Q 023397 235 EIPCENSLLRQVSSLLRRLPAIESEKFQDDFL---MVSLFSSFLNIFTI 280 (283)
Q Consensus 235 ~~~~d~~ilR~i~~l~~~lP~~~~~~f~~~~~---~~~lmv~yLs~lt~ 280 (283)
++|.|++|+.+++++++.||.+...+|.+.|+ +|.||+.|+|+|.|
T Consensus 220 ~lpiNh~Il~~lQdvfNllP~l~~~~~~~a~~vktndql~~iY~sslvr 268 (309)
T KOG1556|consen 220 KLPINHEILYQLQDVFNLLPNLTRNELVKAFNVKTNDQLMVIYLSSLVR 268 (309)
T ss_pred CCCCcHHHHHHHHHHHhhCccccchhhhhhhccccCceeeeeeHHHHHH
Confidence 99999999999999999999999999999995 57999999999987
No 8
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=100.00 E-value=1.4e-39 Score=273.85 Aligned_cols=150 Identities=41% Similarity=0.682 Sum_probs=134.0
Q ss_pred EEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCcc--cccHHHH
Q 023397 11 FKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPSTH--SLDRAFL 88 (283)
Q Consensus 11 V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~--~iD~~~~ 88 (283)
|.|||+|||+|+|||+|+..+ +.+|+|+|||++.++.++|+|||++|++++++ .+|.+|+
T Consensus 1 V~ihplvll~I~dh~~R~~~~------------------~~~v~G~LlG~~~~~~veV~nsF~lp~~~~~~~~~~d~~y~ 62 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYG------------------IKRVIGVLLGYVDGDKIEVTNSFELPFDEEEESIFIDTEYL 62 (157)
T ss_pred CEEccHHHhhHHHHHHhccCC------------------CCeEEEEEEeEEeCCEEEEEEeEEccccCCCcchhhhHHHH
Confidence 689999999999999998743 47999999999999999999999999987665 6999999
Q ss_pred HHHHHHHHHhCCCcceEEEEecCCC----CCcchHHHHHHHhhh-CCCcEEEEEcCCCCCCCCCcceEEEEeeeccccCC
Q 023397 89 EKKQELYKKVFPHFYILGWYSTGSD----AQESDMHIHKALMDI-NESPVYVLLNPSINPAQKDLPVTIFESELHVIEGI 163 (283)
Q Consensus 89 ~~m~~l~k~V~p~~~iVGWY~tg~~----~~~~d~~ih~~~~~~-~~~pi~L~~D~~~~~~~~~lpi~~y~~~~~~~~g~ 163 (283)
++|++++++|||++.+||||++++. +...+..||++|+.. +++||+|++||.....++++|++||++......
T Consensus 63 ~~m~~~~~~v~~~~~vVGWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~~~~-- 140 (157)
T cd08057 63 EKRYNLHKKVYPQEKIVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQREEN-- 140 (157)
T ss_pred HHHHHHHHHhCCCCCEEEEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEecCCCC--
Confidence 9999999999999999999999987 899999999999987 889999999998643568999999998643222
Q ss_pred ceeeEEEeeeeeecchhhHHH
Q 023397 164 PQLIFVRSSYTIETVEAERIS 184 (283)
Q Consensus 164 ~~~~f~~v~~~i~~~e~ErI~ 184 (283)
+.++|+++.++|+||||
T Consensus 141 ----~~~~~~~i~~~e~E~I~ 157 (157)
T cd08057 141 ----GAEITYEIGTEETERIA 157 (157)
T ss_pred ----CceeeeEEecccccccC
Confidence 33999999999999986
No 9
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=99.97 E-value=2.6e-30 Score=234.71 Aligned_cols=201 Identities=17% Similarity=0.221 Sum_probs=151.1
Q ss_pred eEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCcc-----ccc
Q 023397 10 TFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPSTH-----SLD 84 (283)
Q Consensus 10 ~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~-----~iD 84 (283)
+|.|||+|+++|+|||.|+. +.+|+|+|||...++.+||+|||++|+.++++ ..|
T Consensus 2 ~V~I~~~vllkIv~H~~~~~--------------------p~~v~G~LLG~~~~~~leVtn~Fp~P~~~~~~~~~~~~~~ 61 (266)
T cd08065 2 SVQIDGLVVLKIIKHCKEEL--------------------PELVQGQLLGLDVGGTLEVTNCFPFPKSEEDDSDRADEDI 61 (266)
T ss_pred EEEEeHHHHHHHHHHHhcCC--------------------CcEEEEEEeeeEcCCEEEEEeccCCCCCCCCCcchhhhhH
Confidence 69999999999999999875 47999999999999999999999999976543 366
Q ss_pred HHHHHHHHHHHHHhCCCcceEEEEecCC-CCCcchHHHHHHHhhh--CCCcEEEEEcCCCCCCCCCcceEEEEeeecccc
Q 023397 85 RAFLEKKQELYKKVFPHFYILGWYSTGS-DAQESDMHIHKALMDI--NESPVYVLLNPSINPAQKDLPVTIFESELHVIE 161 (283)
Q Consensus 85 ~~~~~~m~~l~k~V~p~~~iVGWY~tg~-~~~~~d~~ih~~~~~~--~~~pi~L~~D~~~~~~~~~lpi~~y~~~~~~~~ 161 (283)
.+|+.+|+++++++++++.+||||++++ ........|+.++... .+.+|+|++||... .++.++++||+.......
T Consensus 62 ~~yq~~m~~~~r~v~~~e~iVGWY~S~p~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s-~~g~l~lkAyrl~~~~~~ 140 (266)
T cd08065 62 ADYQLEMMRLLREVNVDHNHVGWYQSTYLGSFFTRDLIETQYNYQEAIEESVVLVYDPSKT-SQGSLSLKAYRLSEKFME 140 (266)
T ss_pred HHHHHHHHHHHHHhCCCCcEEEeEeecCCCCcCCHHHHHHHHHHhccCCCCEEEEECCCcc-cccceeeEEEEEcHHHHH
Confidence 7999999999999999999999999998 3232345667666554 47799999999863 467899999997532211
Q ss_pred ----------------CCceeeEEEeeeeeecchhhHHHHHHHhccCCCC-CC------ChhhhhhhcHHHHHHHHHHHH
Q 023397 162 ----------------GIPQLIFVRSSYTIETVEAERISVDHVAHLKPSD-GG------SAATQLAAHLTGIHSAIKMLN 218 (283)
Q Consensus 162 ----------------g~~~~~f~~v~~~i~~~e~ErI~v~~l~~~~~~~-~~------~~~~~~~~~l~~~~~ai~~L~ 218 (283)
...+.+|.+||++|..+..+.+.+..+....+.. .+ +....+..++..+..++..|.
T Consensus 141 ~~~~~~~~~~~l~~~~~~~~~if~eiPv~i~n~~l~~~~L~~l~~~~~~~~~~~~~l~l~~~~~le~~l~~l~~~id~l~ 220 (266)
T cd08065 141 LYKEGKFSTESLREANLTFSNIFEEIPVVIRNSHLVNALLSELEEDSPSSQSDFDRLDLSTNSFLEKNLELLMESVDELS 220 (266)
T ss_pred HhhcCCcCHHHHHHhcCchhcEEEEEEEEEEchHHHHHHHHhcccCCCcccCCcccccccCchhHHHHHHHHHHHHHHHH
Confidence 1347889999999999999999999996654331 10 112233444555555555555
Q ss_pred HHHHHHHHHHHHh
Q 023397 219 SRIRVLHHYLVAM 231 (283)
Q Consensus 219 ~~i~~i~~Yl~~V 231 (283)
.....+..|-+.+
T Consensus 221 ~e~~~~~~y~r~~ 233 (266)
T cd08065 221 QEQGKFNYYQRNL 233 (266)
T ss_pred HHHHHHHHHHHHH
Confidence 5555555555544
No 10
>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=99.94 E-value=1.6e-26 Score=183.99 Aligned_cols=105 Identities=38% Similarity=0.573 Sum_probs=93.3
Q ss_pred CCceEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCC-EEEEEEeEeeccCCCcc---c
Q 023397 7 SGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGR-TVEIFNSFELLYDPSTH---S 82 (283)
Q Consensus 7 ~~~~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~-~veI~nsF~vp~~~~~~---~ 82 (283)
+..+|.|||+|+++|+||++|+.. .+|+|+|+|+++++ .++|+|||++|+.++++ .
T Consensus 2 s~~~V~i~p~vll~i~~h~~r~~~--------------------~~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~ 61 (114)
T PF01398_consen 2 SVQTVQIHPLVLLKIIDHATRSSP--------------------NEVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDM 61 (114)
T ss_dssp SCEEEEEEHHHHHHHHHHHHHHHC--------------------TEEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEE
T ss_pred CcEEEEECHHHHHHHHHHHhcCCC--------------------CEEEEEEEEEecCceEEEEEEEEEeeEecCcccccc
Confidence 567999999999999999999872 48999999999999 99999999999976554 3
Q ss_pred ccHHHHHHHHHHHHHhCCCcceEEEEecCCCC----CcchHHHHHHHhhhCCC
Q 023397 83 LDRAFLEKKQELYKKVFPHFYILGWYSTGSDA----QESDMHIHKALMDINES 131 (283)
Q Consensus 83 iD~~~~~~m~~l~k~V~p~~~iVGWY~tg~~~----~~~d~~ih~~~~~~~~~ 131 (283)
.+.++..+|++++++++|++.+||||++++.. +..|+.+|++|++.+++
T Consensus 62 ~~~~~~~~~~~~~~~~~~~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 62 DDEDFQKKMIELLKKVNPNLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp ECCHHHHHHHHHHHHCSTTSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred chhhHHHHHHhhhccccccceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence 66777799999999999999999999998866 99999999999998653
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=99.94 E-value=7.9e-25 Score=198.83 Aligned_cols=166 Identities=13% Similarity=0.151 Sum_probs=142.3
Q ss_pred CCCceEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCcc--cc
Q 023397 6 SSGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPSTH--SL 83 (283)
Q Consensus 6 ~~~~~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~--~i 83 (283)
....+|.|+|+|+++|++|+.|.. +..|+|+|||..+++.++|++||++|..+.+. ..
T Consensus 7 ~~~~~V~Is~~allkil~Ha~~~~--------------------p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~ 66 (268)
T cd08069 7 DYFEKVYISSLALLKMLKHARAGG--------------------PIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNA 66 (268)
T ss_pred CcccEEEECHHHHHHHHHHHhccC--------------------CceEEEEEEeeecCCeEEEEEEEECCcCCCCCceec
Confidence 445689999999999999998843 46899999999999999999999999876555 25
Q ss_pred cHHHHHHHHH--HHHHhCCCcceEEEEecCCC----CCcchHHHHHHHhhhCCCcEEEEEcCCCCCCCCCcceEEEEeee
Q 023397 84 DRAFLEKKQE--LYKKVFPHFYILGWYSTGSD----AQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESEL 157 (283)
Q Consensus 84 D~~~~~~m~~--l~k~V~p~~~iVGWY~tg~~----~~~~d~~ih~~~~~~~~~pi~L~~D~~~~~~~~~lpi~~y~~~~ 157 (283)
+.+|++.|.+ +++++++++.+||||++++. ++..|+.+|..|++.++++|+|++||..+...+++.++||++..
T Consensus 67 ~~e~~~~m~~~~~~~~~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~ 146 (268)
T cd08069 67 QDEFQEYMVQYEMLKQTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIP 146 (268)
T ss_pred cHHHHHHHHHHHHHHHhCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEEC
Confidence 5699999999 99999999999999999986 89999999999999989999999999765357889999999742
Q ss_pred cc-c-----c----------------CCceeeEEEeeeeeecchhhHHHHHHHhcc
Q 023397 158 HV-I-----E----------------GIPQLIFVRSSYTIETVEAERISVDHVAHL 191 (283)
Q Consensus 158 ~~-~-----~----------------g~~~~~f~~v~~~i~~~e~ErI~v~~l~~~ 191 (283)
.. . + +.....|.++|+++..++.|+..++.+.+.
T Consensus 147 ~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~ 202 (268)
T cd08069 147 PGYKPLEPRQTTSNIGHLPKPKIEDFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNK 202 (268)
T ss_pred ccccccCcccCccccCccCcHHHHHhCchhcEEEEeeeEEecCHHHHHHHHHHHHH
Confidence 21 1 1 114578999999999999999999988874
No 12
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=99.86 E-value=1.5e-20 Score=166.48 Aligned_cols=238 Identities=16% Similarity=0.216 Sum_probs=175.4
Q ss_pred CCCCceEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCC--Ccc-
Q 023397 5 SSSGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDP--STH- 81 (283)
Q Consensus 5 ~~~~~~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~--~~~- 81 (283)
+.+-..|.+..||+++|++||.....+ ..-++|+|+|..-++.+|||||||.|-.. +++
T Consensus 9 ~p~vk~v~ldsLvVMkiiKHc~ee~~n------------------~d~~~GvL~Glvvd~~LeITncFp~p~~~~~edda 70 (339)
T KOG1560|consen 9 SPPVKRVELDSLVVMKIIKHCREEFPN------------------GDGTQGVLLGLVVDGRLEITNCFPFPSVLENEDDA 70 (339)
T ss_pred CCccceeeehhHHHHHHHHHHHhhcCC------------------cchhhheeeeeeecceeEeecccCCCccCCCccch
Confidence 344458999999999999999876533 36799999999999999999999999843 222
Q ss_pred ----cccH---HHHHHHHHHHHHhCCCcceEEEEec---CCCCCcchHHHHHHHhhhCCCcEEEEEcCCCCCCCCCcceE
Q 023397 82 ----SLDR---AFLEKKQELYKKVFPHFYILGWYST---GSDAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVT 151 (283)
Q Consensus 82 ----~iD~---~~~~~m~~l~k~V~p~~~iVGWY~t---g~~~~~~d~~ih~~~~~~~~~pi~L~~D~~~~~~~~~lpi~ 151 (283)
..|. .|+..|++.++.||-+..+||||.+ |+.++..-+.-+..|++-++..|.|++||..+ ++|.|.++
T Consensus 71 ~~~~~~de~rq~~~l~mlrrlr~vnid~~hVGwYqs~~vgs~lS~~lveSqy~YQ~a~pesVvliYD~~ks-sqG~L~lr 149 (339)
T KOG1560|consen 71 VNKSVSDEARQAYQLAMLRRLRYVNIDHLHVGWYQSAYVGSFLSPALVESQYAYQKAIPESVVLIYDPIKS-SQGTLSLR 149 (339)
T ss_pred hhhhhhHHHHHHHHHHHHHHhhhcCccceeeeeeeeehhccccCHHHHHHHHHHHhcCCccEEEEeccccc-cCceEEee
Confidence 2443 6999999999999999999999987 56787666666777888888899999999974 68999999
Q ss_pred EEEeeecc----ccC------------CceeeEEEeeeeeecchhhHHHHHHHh--ccCCCCCC-------Chhhhhhhc
Q 023397 152 IFESELHV----IEG------------IPQLIFVRSSYTIETVEAERISVDHVA--HLKPSDGG-------SAATQLAAH 206 (283)
Q Consensus 152 ~y~~~~~~----~~g------------~~~~~f~~v~~~i~~~e~ErI~v~~l~--~~~~~~~~-------~~~~~~~~~ 206 (283)
||+..... .++ .+..+|.++|+.|..+---.+-+..+. +..++... +....+.++
T Consensus 150 AyrLTp~am~~~kekdwtpealk~~nltyenmfeElPIVIknS~L~nvlmseLs~~e~c~sdk~~~~~fdlgs~t~lekn 229 (339)
T KOG1560|consen 150 AYRLTPEAMAAHKEKDWTPEALKSANLTYENMFEELPIVIKNSHLANVLMSELSEPEDCESDKPLHSNFDLGSGTRLEKN 229 (339)
T ss_pred hhhcCHHHHHHHhcCCCCHHHHHhcCCCHHHHHhhcCeeeeccHHHHHHHHhccccccccccccccccccccchhhHHHH
Confidence 99975322 222 146789999999999876666666665 32222111 123456667
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHH--------HHhcCCCCChHHHHHHH
Q 023397 207 LTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSS--------LLRRLPAIESEKFQDDF 265 (283)
Q Consensus 207 l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~ilR~i~~--------l~~~lP~~~~~~f~~~~ 265 (283)
+..+...+..|+..+..+-+|-+.+... |..+-+.++. .-.-.|.++.++..+.|
T Consensus 230 ir~lme~vDEl~qe~~~l~kyqr~~~rq----q~~~~q~~aKrqaENa~R~argep~lP~dd~kr~f 292 (339)
T KOG1560|consen 230 IRLLMERVDELHQEIVNLNKYQRQLARQ----QAKKHQWIAKRQAENANRAARGEPPLPEDDWKRIF 292 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHhhhhhhcCCCCCChHHHHHHh
Confidence 7777777888888888888888776532 3333333322 34457778888888777
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=99.86 E-value=1.2e-20 Score=153.26 Aligned_cols=125 Identities=26% Similarity=0.387 Sum_probs=110.5
Q ss_pred eEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCcc---cccHH
Q 023397 10 TFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPSTH---SLDRA 86 (283)
Q Consensus 10 ~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~---~iD~~ 86 (283)
.|.|||+|+++|++|+.|.. +..++|+|+|...++.++|+++|++|.....+ .++.+
T Consensus 1 ~v~i~~~v~~~i~~h~~~~~--------------------p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~~~~~~ 60 (135)
T smart00232 1 EVKVHPLVPLNILKHAIRDG--------------------PEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQEYDED 60 (135)
T ss_pred CEEEcHHHHHHHHHHHhcCC--------------------CcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchhhhhhh
Confidence 47899999999999998753 46899999999999999999999999875443 47889
Q ss_pred HHHHHHHHHHHhCCCcceEEEEecCC----CCCcchHHHHHHHhhhCCCcEEEEEcCCCCCCCCCcceEEEEe
Q 023397 87 FLEKKQELYKKVFPHFYILGWYSTGS----DAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFES 155 (283)
Q Consensus 87 ~~~~m~~l~k~V~p~~~iVGWY~tg~----~~~~~d~~ih~~~~~~~~~pi~L~~D~~~~~~~~~lpi~~y~~ 155 (283)
|.+.|.++++++++++.+||||++++ .++..|+.+|..++.....++++.+|+... ..+.++++||+.
T Consensus 61 ~~~~~~~~~~~~~~~~~~vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s-~~g~~~~~af~~ 132 (135)
T smart00232 61 YSHLMDEELKKVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKS-FQGRLSLRAFRL 132 (135)
T ss_pred HHHHHHHHHHhhCCCceEEEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCcc-ccCcEEEEEEEe
Confidence 99999999999999999999999986 577789999999998888899999999874 458899999986
No 14
>PF13012 MitMem_reg: Maintenance of mitochondrial structure and function; PDB: 2O96_B 2O95_A.
Probab=99.79 E-value=2.2e-20 Score=149.06 Aligned_cols=100 Identities=36% Similarity=0.543 Sum_probs=13.1
Q ss_pred chhhHHHHHHHhccCCCCCCChhhhhhhcHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhcCCCCC
Q 023397 178 VEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRLPAIE 257 (283)
Q Consensus 178 ~e~ErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~ilR~i~~l~~~lP~~~ 257 (283)
+|||||||+|+++.... ...+.+..+++.+.+|+.+|.+|++.+..||++|.+|+.++|++++|+|+++|+++|.++
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 EEAERIGVDHLARGLGD---HYYSSLSSQLENEQNALKMLHKRLWQILDYLEDVISGEIPPDHEILRQLQDLLSSLPKYD 77 (115)
T ss_dssp SHHHHHHHHHHHHH--S---------------------------------------------------------------
T ss_pred CchHHHHHHHHHccCCC---ccccHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcCCCchhHHHHHHHHHHhccccc
Confidence 58999999999995322 223477799999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHH---HHHHHHHHHHHhhc
Q 023397 258 SEKFQDDFL---MVSLFSSFLNIFTI 280 (283)
Q Consensus 258 ~~~f~~~~~---~~~lmv~yLs~lt~ 280 (283)
+++|+++|. +|.+|+.||++||+
T Consensus 78 ~~~~~~~~~~~~~D~l~v~yL~~l~k 103 (115)
T PF13012_consen 78 PEEFEEEFNSEINDVLMVSYLAKLTK 103 (115)
T ss_dssp --------------------------
T ss_pred HHHHHHHHHhhchHHHHHHHHHHHhH
Confidence 999999996 57999999999986
No 15
>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. J
Probab=99.63 E-value=5.4e-15 Score=117.10 Aligned_cols=100 Identities=15% Similarity=0.261 Sum_probs=80.7
Q ss_pred CCceEEEEeeEEeCCEEEEEEeEeeccCCCcccccHHHHHHHHHHHHHhCCCcceEEEEecCCC----CCcchHHHHHHH
Q 023397 50 QPRVYGCVIGIQRGRTVEIFNSFELLYDPSTHSLDRAFLEKKQELYKKVFPHFYILGWYSTGSD----AQESDMHIHKAL 125 (283)
Q Consensus 50 ~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~~iD~~~~~~m~~l~k~V~p~~~iVGWY~tg~~----~~~~d~~ih~~~ 125 (283)
+..++|+|+|...++.++|+++|++|........+..+ -|......+..++.+||||++++. ++..|+..|..|
T Consensus 13 ~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~iVGwyhshp~~~~~~s~~dv~~~~~~ 90 (116)
T cd07767 13 GKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWF--LMYLDFKKLNAGLRIVGWYHTHPKPSCFLSPNDLATHELF 90 (116)
T ss_pred CcEEEEEeEEEEcCCEEEEEEEEecccCCCCCccHHHH--HHHHHHHHhcCCCeEEEEEEcCCCCCCccCHHHHHHHHHH
Confidence 46899999999998899999999999865443233222 266667788899999999999764 788999999999
Q ss_pred hhhCCCcEEEEEcCCCCCCCCCcceEEE
Q 023397 126 MDINESPVYVLLNPSINPAQKDLPVTIF 153 (283)
Q Consensus 126 ~~~~~~pi~L~~D~~~~~~~~~lpi~~y 153 (283)
++..+++++|++|+... +.+++++||
T Consensus 91 q~~~~~~v~li~~~~~~--~~~~~~~~~ 116 (116)
T cd07767 91 QRYFPEKVMIIVDVKPK--DLGNSWKCY 116 (116)
T ss_pred HHhCCCCEEEEEECCCc--cCCCCcccC
Confidence 98888899999999862 346788876
No 16
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.52 E-value=1.7e-13 Score=122.18 Aligned_cols=200 Identities=14% Similarity=0.174 Sum_probs=139.3
Q ss_pred eEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCccc-----cc
Q 023397 10 TFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPSTHS-----LD 84 (283)
Q Consensus 10 ~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~~-----iD 84 (283)
.|.|..|++|+|.-|..|.. +-.|+|.++|+.+|+.+-|.+||++|.+..+.- --
T Consensus 54 ~vkISalAllKm~~hA~~Gg--------------------nlEiMGlm~Gkv~g~t~IvmD~FaLPVeGTETRVNAq~~A 113 (347)
T KOG1554|consen 54 HVKISALALLKMVMHARSGG--------------------NLEIMGLMQGKVDGDTIIVMDSFALPVEGTETRVNAQAEA 113 (347)
T ss_pred hhhhHHHHHHHHHHHHhcCC--------------------CeEEEeeecccccCCeEEEEeccccccccccceechHHHH
Confidence 68899999999988776532 468999999999999999999999999876541 44
Q ss_pred HHHHHHHHHHHHHhCCCcceEEEEecCCC----CCcchHHHHHHHhhhCCCcEEEEEcCCCCCCCCCcceEEEEeeecc-
Q 023397 85 RAFLEKKQELYKKVFPHFYILGWYSTGSD----AQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESELHV- 159 (283)
Q Consensus 85 ~~~~~~m~~l~k~V~p~~~iVGWY~tg~~----~~~~d~~ih~~~~~~~~~pi~L~~D~~~~~~~~~lpi~~y~~~~~~- 159 (283)
.+|+-...+..+.+...+.+||||++.+. ++..|+..+..-+++-++=+++++||..+.+.+++.+.||++-...
T Consensus 114 yEYmv~Y~e~~k~~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRTyp~gy 193 (347)
T KOG1554|consen 114 YEYMVQYIEEAKNVGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTYPKGY 193 (347)
T ss_pred HHHHHHHHHHHHHhhhhhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCccccccCceeeceeecccCCC
Confidence 78999999999999999999999999764 6777777777777777777899999998777899999999974211
Q ss_pred c--c-----------------CCceeeEEEeeeeeecchhhHHHHHHHhccCCCCCCChhhhhhhcHHHHHHHHHHHHHH
Q 023397 160 I--E-----------------GIPQLIFVRSSYTIETVEAERISVDHVAHLKPSDGGSAATQLAAHLTGIHSAIKMLNSR 220 (283)
Q Consensus 160 ~--~-----------------g~~~~~f~~v~~~i~~~e~ErI~v~~l~~~~~~~~~~~~~~~~~~l~~~~~ai~~L~~~ 220 (283)
+ + |..+..+..+++..--+-.++--++.+-. +.....-..+.+..+.+.+...+.-|..+
T Consensus 194 k~~d~~~seyqtipl~kied~gvHck~yysl~isyfks~ld~kll~~Lwn-kywv~Tlsss~ll~N~dy~~~qi~d~~ek 272 (347)
T KOG1554|consen 194 KPPDEPPSEYQTIPLNKIEDFGVHCKQYYSLEISYFKSSLDMKLLELLWN-KYWVRTLSSSPLLKNIDYLNGQIRDLSEK 272 (347)
T ss_pred CCCCCCchhhhccchhhhhhcccceEEeeccchhhhhhhhhHHHHHHHHh-hhhhcccccccccccchhhcchhhhHHHH
Confidence 1 0 01111122222222222233333333322 11111122345666677777777777777
Q ss_pred HHHHHHHHHH
Q 023397 221 IRVLHHYLVA 230 (283)
Q Consensus 221 i~~i~~Yl~~ 230 (283)
+...-+.+..
T Consensus 273 l~q~~~~l~~ 282 (347)
T KOG1554|consen 273 LEQREDSLET 282 (347)
T ss_pred HHhhhhhccc
Confidence 7777777643
No 17
>cd08067 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase. This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it p
Probab=99.42 E-value=7.5e-12 Score=108.13 Aligned_cols=127 Identities=13% Similarity=0.156 Sum_probs=100.2
Q ss_pred CCceEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEe--CCEEEEEEeEeeccCCCcc--c
Q 023397 7 SGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQR--GRTVEIFNSFELLYDPSTH--S 82 (283)
Q Consensus 7 ~~~~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~--~~~veI~nsF~vp~~~~~~--~ 82 (283)
.+.+|.|.++|+|.|..|+.... ..++|.|+|..+ ++.++|+++|++|...... -
T Consensus 3 ~pf~V~Is~~all~m~~Ha~~~~---------------------~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e 61 (187)
T cd08067 3 QPFKVTVSSNALLLMDFHCHLTT---------------------SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCE 61 (187)
T ss_pred CCEEEEECHHHHHHHHHHhcCCC---------------------cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccc
Confidence 57899999999999999997532 469999999975 5789999999999754323 3
Q ss_pred ccHHHHHHHHHHHHHhCCCcceEEEEecCC----CCCcchHHHHHHHhhhCC-------CcEEEEEcCCCCCC-CCCcce
Q 023397 83 LDRAFLEKKQELYKKVFPHFYILGWYSTGS----DAQESDMHIHKALMDINE-------SPVYVLLNPSINPA-QKDLPV 150 (283)
Q Consensus 83 iD~~~~~~m~~l~k~V~p~~~iVGWY~tg~----~~~~~d~~ih~~~~~~~~-------~pi~L~~D~~~~~~-~~~lpi 150 (283)
+|..++.+|.+..++.+ +.+||||++.+ .++..|+.-|..|+.... .-|.++++|..... ..+..+
T Consensus 62 ~dp~~q~e~~~~l~~~g--l~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i 139 (187)
T cd08067 62 MDPVSETEIRESLESRG--LSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQI 139 (187)
T ss_pred cCHHHHHHHHHHHHHcC--CEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcE
Confidence 78899999999998876 59999999975 467778888888887542 45999999975321 234578
Q ss_pred EEEEee
Q 023397 151 TIFESE 156 (283)
Q Consensus 151 ~~y~~~ 156 (283)
++|...
T Consensus 140 ~~f~~~ 145 (187)
T cd08067 140 TCFWVM 145 (187)
T ss_pred EEEEEE
Confidence 999864
No 18
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=99.39 E-value=5.5e-12 Score=101.22 Aligned_cols=108 Identities=12% Similarity=0.178 Sum_probs=84.7
Q ss_pred hhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEe-----CCEEEEEEeEeeccCCCcccccHHHHHHH
Q 023397 17 VIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQR-----GRTVEIFNSFELLYDPSTHSLDRAFLEKK 91 (283)
Q Consensus 17 Vll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~-----~~~veI~nsF~vp~~~~~~~iD~~~~~~m 91 (283)
|+++|++|+.+.. +..++|.|+|... ...++|+++|+.|...+. .+.|
T Consensus 2 ~~~~i~~ha~~~~--------------------p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~~~-------~~~~ 54 (119)
T cd08058 2 ALLKMLQHAESNT--------------------GIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCTG-------ENVE 54 (119)
T ss_pred HHHHHHHHhcCCC--------------------CeEEEEEeeeEEecCccceeEEEEeecCCCCCCchh-------HHHH
Confidence 7899999998743 4579999999875 456899999999874321 2245
Q ss_pred HHHHHHhCCCcceEEEEecCC----CCCcchHHHHHHHhhhCCCcEEEEEcCCCCCCCCCcceEEEEe
Q 023397 92 QELYKKVFPHFYILGWYSTGS----DAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFES 155 (283)
Q Consensus 92 ~~l~k~V~p~~~iVGWY~tg~----~~~~~d~~ih~~~~~~~~~pi~L~~D~~~~~~~~~lpi~~y~~ 155 (283)
..+.+...-++.+||||++.+ .++..|+..|.+|+...+..++|++||.. ..+.+++|+.
T Consensus 55 ~~~~~~~~~g~~~vG~YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~----~~~~~~a~rl 118 (119)
T cd08058 55 ELFNVQTGRPLLVVGWYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKH----RNKDTGIFRL 118 (119)
T ss_pred HHHHHHhCCCCeEEEEEecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCC----CCcccceEEe
Confidence 555667889999999999976 47888888888788777778999999973 3678899874
No 19
>cd08068 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex. BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-contai
Probab=99.11 E-value=4.4e-09 Score=94.10 Aligned_cols=147 Identities=15% Similarity=0.123 Sum_probs=101.0
Q ss_pred ceEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEe-------CCEEEEEEeEeeccCC-Cc
Q 023397 9 LTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQR-------GRTVEIFNSFELLYDP-ST 80 (283)
Q Consensus 9 ~~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~-------~~~veI~nsF~vp~~~-~~ 80 (283)
.+|.|.+.++..|..|..+.. +..+||.|+|..+ ++.+.|..-++.+..+ ..
T Consensus 2 ~~V~Is~~~l~~il~HA~~~~--------------------P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~ 61 (244)
T cd08068 2 SKVHLSADVYLVCLTHALSTE--------------------KEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRK 61 (244)
T ss_pred cEEEECHHHHHHHHHHHHhCC--------------------CcceeEEEEeecccccccccceeEEEeeeccccccCCCC
Confidence 368999999999999997653 4689999999875 3445555544443322 11
Q ss_pred c-c-ccHH----HHHHHHHHHHHhCCCcceEEEEecCC----CCCcchHHHHHHHhhhCCCcEEEEEcCCC---CCCCCC
Q 023397 81 H-S-LDRA----FLEKKQELYKKVFPHFYILGWYSTGS----DAQESDMHIHKALMDINESPVYVLLNPSI---NPAQKD 147 (283)
Q Consensus 81 ~-~-iD~~----~~~~m~~l~k~V~p~~~iVGWY~tg~----~~~~~d~~ih~~~~~~~~~pi~L~~D~~~---~~~~~~ 147 (283)
+ + +|.+ ..+.+.++.+.+..++.+||||++.+ .|+..|...+..|+...+.-+++++++.. +...++
T Consensus 62 ~r~eidPee~~~a~~ea~~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~ 141 (244)
T cd08068 62 DRVEISPEQLSAASTEAERLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGE 141 (244)
T ss_pred ceEEeCHHHHHHHHHHHHHHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCC
Confidence 2 3 6653 34566677778889999999999976 37777877767777666667899987542 222356
Q ss_pred cceEEEEeeeccccCCceeeEEEeeeeeec
Q 023397 148 LPVTIFESELHVIEGIPQLIFVRSSYTIET 177 (283)
Q Consensus 148 lpi~~y~~~~~~~~g~~~~~f~~v~~~i~~ 177 (283)
..+++|+...+.. .+.....++|+.|..
T Consensus 142 ~~i~aFr~~~g~~--~~~~~~~e~pl~i~~ 169 (244)
T cd08068 142 VQVTCFQSVQGNK--AGQYERIEVPLEIVP 169 (244)
T ss_pred EEEEEEEecCCCC--CCcceEEEeeeEEec
Confidence 7899999743211 124557788888854
No 20
>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al
Probab=98.62 E-value=9.6e-07 Score=75.51 Aligned_cols=116 Identities=14% Similarity=0.128 Sum_probs=82.6
Q ss_pred EEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCccc---ccHHH
Q 023397 11 FKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPSTHS---LDRAF 87 (283)
Q Consensus 11 V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~~---iD~~~ 87 (283)
+.|-.-.+-.|+.|..++... +..++|.|+|...++..+|++.|-.|....... .|..
T Consensus 4 l~Ipk~il~~~l~~A~~~~~~------------------p~E~cGlL~G~~~~~~~~I~~i~~~~q~~~~~~~~~~~~~- 64 (173)
T cd08066 4 VVVPADLMDKFLQLAEPNTSR------------------NLETCGILCGKLSNNAFFITHLIIPKQSGTSDSCQTTNEE- 64 (173)
T ss_pred EEECHHHHHHHHHHHHhCCCC------------------CCeEEEEEEeEcCCCeEEEEEEEeccccCCCceecCCCHH-
Confidence 445555677778877765311 357999999998888889998877666544432 3321
Q ss_pred HHHHHHHHHH-hCCCcceEEEEecCC----CCCcchHHHHHHHhhhCCCcEEEEEcCCCCCCCCCcceEEEEee
Q 023397 88 LEKKQELYKK-VFPHFYILGWYSTGS----DAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFESE 156 (283)
Q Consensus 88 ~~~m~~l~k~-V~p~~~iVGWY~tg~----~~~~~d~~ih~~~~~~~~~pi~L~~D~~~~~~~~~lpi~~y~~~ 156 (283)
+ .++. --.++.+||||+|.+ .++..|+..|..|+...+..++|+++|. ...+++|+..
T Consensus 65 --e---~~~~~~~~gle~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~------~~~l~afrl~ 127 (173)
T cd08066 65 --E---LFDFQDQHDLITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK------YNEFGIFRLT 127 (173)
T ss_pred --H---HHHHHHhCCCeeEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC------CcEEeEEEee
Confidence 1 2222 235789999999965 4788999999998887788899999974 3478999864
No 21
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=98.59 E-value=2.1e-06 Score=79.00 Aligned_cols=131 Identities=19% Similarity=0.309 Sum_probs=103.3
Q ss_pred CCCCceEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEE-ee---E-EeCCEEEEEEeEeeccCCC
Q 023397 5 SSSGLTFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCV-IG---I-QRGRTVEIFNSFELLYDPS 79 (283)
Q Consensus 5 ~~~~~~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~L-LG---~-~~~~~veI~nsF~vp~~~~ 79 (283)
+..+.+|.++-++++..++|-. .... ...++|.+ +| . .+...+.|..-|+.|....
T Consensus 27 ~~~~e~v~i~slall~m~rh~r-~~~p------------------~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg~ 87 (316)
T KOG1555|consen 27 SDEKETVYISSLALLKMLRHDR-AGSP------------------EETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGT 87 (316)
T ss_pred ccCcceeeeehhhhhhcccccc-cCCc------------------hhhccceeecccccceeeecceeeeeeeccccccc
Confidence 4567799999999999999753 2211 13489999 99 3 3677888899999998754
Q ss_pred cc-----cccHHHHHHHHHHHHHhCCCcceEEEEecCC----CCCcchHHHHHHHhhhCCCcEEEEEcCCCCCCCCCcce
Q 023397 80 TH-----SLDRAFLEKKQELYKKVFPHFYILGWYSTGS----DAQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPV 150 (283)
Q Consensus 80 ~~-----~iD~~~~~~m~~l~k~V~p~~~iVGWY~tg~----~~~~~d~~ih~~~~~~~~~pi~L~~D~~~~~~~~~lpi 150 (283)
+- ..|.-|..+|.++.++....+.+||||++.+ .++..|+..|+.|+..++..+..++||..+.. ++.-+
T Consensus 88 ~is~~~e~~d~V~q~q~~~~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~-g~vv~ 166 (316)
T KOG1555|consen 88 GISKFVEAVDPVFQTQMMDLLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPY-GKVVP 166 (316)
T ss_pred eecccchhccHHHHHHHHHHHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCC-CCccC
Confidence 32 4899999999999999888899999999975 46778999999999998999999999987544 34344
Q ss_pred EEEEe
Q 023397 151 TIFES 155 (283)
Q Consensus 151 ~~y~~ 155 (283)
.+|.+
T Consensus 167 d~f~~ 171 (316)
T KOG1555|consen 167 DAFSS 171 (316)
T ss_pred Chhhh
Confidence 47765
No 22
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=98.32 E-value=1.4e-05 Score=69.76 Aligned_cols=124 Identities=13% Similarity=0.207 Sum_probs=84.7
Q ss_pred eEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCE--EEEEEeEeeccCCCcccccHHH
Q 023397 10 TFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRT--VEIFNSFELLYDPSTHSLDRAF 87 (283)
Q Consensus 10 ~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~--veI~nsF~vp~~~~~~~iD~~~ 87 (283)
+|.+.+.+..+|.=|..+-. ...|.|+|||...++. |+|++|.|+=|..-.=.--.+-
T Consensus 3 ~v~is~~AY~K~~LHaaKyP--------------------~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~~L~PmlEv 62 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAKYP--------------------HCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWLSLSPMLEV 62 (196)
T ss_pred eEEEcHHHHHHHHHHhccCC--------------------CCceeeEEEeccCCCCceEEEeeceeccccccCcchHHHH
Confidence 68899999999999998765 2579999999986443 9999999998843211111122
Q ss_pred HHHHHHHHHHhCCCcceEEEEecCCC-----CCcchHHHHHHHhhhCCCcEEEEEcCCCCCC-CCCcceEEEE
Q 023397 88 LEKKQELYKKVFPHFYILGWYSTGSD-----AQESDMHIHKALMDINESPVYVLLNPSINPA-QKDLPVTIFE 154 (283)
Q Consensus 88 ~~~m~~l~k~V~p~~~iVGWY~tg~~-----~~~~d~~ih~~~~~~~~~pi~L~~D~~~~~~-~~~lpi~~y~ 154 (283)
--.+.+.|-+. .++.|||+|+.... +++.-..|=+.+.+.++.++++++|-..-.. .+..++.+|.
T Consensus 63 AL~qvd~~~~~-~gl~IvGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~kl~~~~~~~~~~~~~ 134 (196)
T PF03665_consen 63 ALAQVDAYAKS-NGLVIVGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKKLSSDCKAPAISVYQ 134 (196)
T ss_pred HHHHHHHHHhh-CCCEEEEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcccccccCCCcceeee
Confidence 23344445443 56999999999753 4444445556667778899999999654222 2333456776
No 23
>cd08060 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p). This family includes Noc4p (neighbor of COX4; neighbor of Cytochrome c Oxidase 4; nucleolar complex associated 4 homolog) which belongs to the family of unknown function, UPF0172, with MPN/JAMM-like domains. Proteins in this family are homologs of the NOC4 gene which is conserved in eukaryotic members including human, dog, mouse, rat, chicken, zebrafish, fruit fly, mosquito, S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa, A.thaliana, and rice. NOC4 highly expressed in the pancreas and moderately in liver, heart, lung, kidney, brain, skeletal muscle, and placenta. This nucleolar protein forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=98.32 E-value=1.1e-05 Score=69.55 Aligned_cols=104 Identities=17% Similarity=0.261 Sum_probs=73.2
Q ss_pred hhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEe-CCEEEEEEeEeeccCCCcccccHHH--HHHH
Q 023397 15 PLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQR-GRTVEIFNSFELLYDPSTHSLDRAF--LEKK 91 (283)
Q Consensus 15 PlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~-~~~veI~nsF~vp~~~~~~~iD~~~--~~~m 91 (283)
+.....|..|..+.. +..|+|+|+|... ++.+.|++++|+.+..- .++..- ...+
T Consensus 3 ~~ay~ki~~HA~k~p--------------------~~evcGlLlG~~~~~~~~~V~d~vPl~h~~~--~l~P~~Eval~~ 60 (182)
T cd08060 3 TLAYVKMLLHAAKYP--------------------HCAVNGLLLGKKSSGGSVEITDAVPLFHSCL--ALAPMLEVALAL 60 (182)
T ss_pred HHHHHHHHHHHHHcC--------------------CchheEEEEeeecCCCCEEEEEEEEcCCCcc--ccCHHHHHHHHH
Confidence 456778999998743 3589999999997 77899999999998521 244432 1222
Q ss_pred HHHHHHhCCCcceEEEEecCCC-----CCcchHHHHHHHhhhCCCcEEEEEcCCC
Q 023397 92 QELYKKVFPHFYILGWYSTGSD-----AQESDMHIHKALMDINESPVYVLLNPSI 141 (283)
Q Consensus 92 ~~l~k~V~p~~~iVGWY~tg~~-----~~~~d~~ih~~~~~~~~~pi~L~~D~~~ 141 (283)
.+.+-+- .++.|||+|++.+. +...-..|-+.+.+.++++++|++|-..
T Consensus 61 ve~~~~~-~gl~IvG~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~ 114 (182)
T cd08060 61 VDAYCKS-SGLVIVGYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEK 114 (182)
T ss_pred HHHHHHH-CCCEEEEEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCcc
Confidence 3333333 37899999999874 3334445666677778899999999664
No 24
>cd08070 MPN_like Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding). This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=98.04 E-value=9.2e-05 Score=59.92 Aligned_cols=108 Identities=14% Similarity=0.179 Sum_probs=73.7
Q ss_pred hhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCc--c--cccHHHHHHHH
Q 023397 17 VIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPST--H--SLDRAFLEKKQ 92 (283)
Q Consensus 17 Vll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~--~--~iD~~~~~~m~ 92 (283)
++-+|++|..+.. +..++|.|+|..++....|+..|++|....+ . .+|...+.+..
T Consensus 3 ~~~~il~ha~~~~--------------------P~E~cGlL~G~~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~ 62 (128)
T cd08070 3 LLEAILAHAEAEY--------------------PEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEIDPAEQLAAQ 62 (128)
T ss_pred HHHHHHHHHHhCC--------------------CCceEEEEEeecCCCCceEEEEEEccCCCCCCCceEEECHHHHHHHH
Confidence 4557778776643 4689999999998766677889999875432 2 37877666666
Q ss_pred HHHHHhCCCcceEEEEecCCC----CCcchHHHHHHHhhhCCCcEEEEEcCCCCCCCCCcceEEEEe
Q 023397 93 ELYKKVFPHFYILGWYSTGSD----AQESDMHIHKALMDINESPVYVLLNPSINPAQKDLPVTIFES 155 (283)
Q Consensus 93 ~l~k~V~p~~~iVGWY~tg~~----~~~~d~~ih~~~~~~~~~pi~L~~D~~~~~~~~~lpi~~y~~ 155 (283)
+..++. ++.+||||++.+. ++..|..... . ...+++++.... +...+++|..
T Consensus 63 ~~~~~~--g~~~vG~~HSHP~~~~~PS~~D~~~~~----~-~~~~~lIv~~~~----~~~~~~~~~~ 118 (128)
T cd08070 63 REARER--GLEVVGIYHSHPDGPARPSETDLRLAW----P-PGVSYLIVSLAG----GAPELRAWRL 118 (128)
T ss_pred HHHHHC--CCeEEEEEeCCCCCCCCCCHHHHHhcc----C-CCCeEEEEECCC----CCcEEEEEEE
Confidence 666555 5899999999764 4444542211 1 245788888652 2446888875
No 25
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=97.89 E-value=0.00014 Score=59.30 Aligned_cols=98 Identities=18% Similarity=0.256 Sum_probs=62.3
Q ss_pred EEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCc--c--cccHHH
Q 023397 12 KLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPST--H--SLDRAF 87 (283)
Q Consensus 12 ~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~--~--~iD~~~ 87 (283)
.+-..++-.|+.|..|.. +..++|.|+|+..+ ...|+++....+ . .++.++
T Consensus 3 ~i~~~~l~~il~~a~~~~--------------------p~E~~g~l~~~~~~-----~~~~~~~n~~~~~~~~~~~~~~~ 57 (134)
T COG1310 3 VIPKEVLGAILEHARREH--------------------PREVCGLLAGTREG-----ERYFPLKNVSVEPVEYFEIDPEY 57 (134)
T ss_pred eecHHHHHHHHHHHHhcC--------------------ChheEEEEEeeccc-----ceeeccccccCCcceeEeeCHHH
Confidence 455677888999988764 36899999999887 444555443222 1 255555
Q ss_pred HHHHHHHHHHhCCCcceEEEEecCCC--CCcchHHHHHHHhhhCCCcEEEEEcC
Q 023397 88 LEKKQELYKKVFPHFYILGWYSTGSD--AQESDMHIHKALMDINESPVYVLLNP 139 (283)
Q Consensus 88 ~~~m~~l~k~V~p~~~iVGWY~tg~~--~~~~d~~ih~~~~~~~~~pi~L~~D~ 139 (283)
.. +....+.. ++.+||||++++. +..++..+. +++..+.|.+++..+
T Consensus 58 ~~-~~~~~~~~--g~~vvg~yHSHP~~~~~pS~~D~~--~~~~~~~~~~iv~~~ 106 (134)
T COG1310 58 SL-FYLAAEDA--GEVVVGWYHSHPGGPPYPSEADRR--LSKLGPLPWLIVSVP 106 (134)
T ss_pred HH-HHHHHhhC--CCEEEEEEcCCCCCCCCcCHHHHh--hccccCCCEEEEEcC
Confidence 44 33333333 3999999999873 444454455 676656555665553
No 26
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=97.07 E-value=0.017 Score=49.08 Aligned_cols=124 Identities=15% Similarity=0.254 Sum_probs=81.9
Q ss_pred eEEEehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEee--EEeCCEEEEEEeEeeccCCCcccccHHH
Q 023397 10 TFKLHPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIG--IQRGRTVEIFNSFELLYDPSTHSLDRAF 87 (283)
Q Consensus 10 ~V~vHPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG--~~~~~~veI~nsF~vp~~~~~~~iD~~~ 87 (283)
.|.+..++..+|+=|+.|-+- .-|-|.|+| +..|+.|+|++|.|+=|+.-.=.--.+-
T Consensus 3 ~veis~~aY~kmiLH~akyph--------------------~aVnGLLla~~~~kg~~v~itdcVPLfH~~laLaPmlEv 62 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYPH--------------------AAVNGLLLAPATGKGECVEITDCVPLFHSHLALAPMLEV 62 (199)
T ss_pred ceeehhhHHHHHHHHhccCcc--------------------cceeeEEEeccCCCCCeEEEEecchhhccccccccHHHH
Confidence 467888899999999988752 479999999 4568999999999997753210111122
Q ss_pred HHHHHHHHHHhCCCcceEEEEecCCCCCc-----chHHHHHHHhhhCCCcEEEEEcCCCC-CCCCCcceEEEE
Q 023397 88 LEKKQELYKKVFPHFYILGWYSTGSDAQE-----SDMHIHKALMDINESPVYVLLNPSIN-PAQKDLPVTIFE 154 (283)
Q Consensus 88 ~~~m~~l~k~V~p~~~iVGWY~tg~~~~~-----~d~~ih~~~~~~~~~pi~L~~D~~~~-~~~~~lpi~~y~ 154 (283)
.-.|++-+- +--.+.|+|.|+....++. .-..|-.-+++++++..+|++|-..- ..-..-|+-+|+
T Consensus 63 Al~lId~~~-~~~GlviaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~~l~~~~e~~~v~v~e 134 (199)
T KOG3289|consen 63 ALNLIDVWG-AQAGLVIAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNKKLVPQCERPPVIVLE 134 (199)
T ss_pred HHHHHHHHH-HhcCeEEEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEeccccccccCCCCEEEee
Confidence 223333322 2347899999999864333 23456667778888777777775432 222335788887
No 27
>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family. This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize.
Probab=96.69 E-value=0.036 Score=45.29 Aligned_cols=87 Identities=14% Similarity=0.107 Sum_probs=53.7
Q ss_pred CCceEEEEeeEEeCCEEEEEEeEeeccCCCcc----c-ccHHHHHHHHH-HHHHhCCCcceEEEEecCCC----CCcchH
Q 023397 50 QPRVYGCVIGIQRGRTVEIFNSFELLYDPSTH----S-LDRAFLEKKQE-LYKKVFPHFYILGWYSTGSD----AQESDM 119 (283)
Q Consensus 50 ~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~----~-iD~~~~~~m~~-l~k~V~p~~~iVGWY~tg~~----~~~~d~ 119 (283)
+....|+|+|.+.+..+.|+..- .|...+-. | -+.+.+++.++ .+++.+-....||=++|.+. ++..|.
T Consensus 16 ~~EtGGiLiG~~~~~~~ii~~~t-~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylGeWHtHP~~~p~PS~~D~ 94 (131)
T TIGR02256 16 STETGGVLIGERRGAHAVITKIS-EPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGEWHTHPEDQPEPSWTDR 94 (131)
T ss_pred CCccceEEEEEEcCCcEEEEEEE-cCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEEecCcCCCCCCCCCHHHH
Confidence 46789999999987777777744 44333221 2 45666665555 45555566999999999763 444454
Q ss_pred HHHHHHhhhCCCcEEEEE
Q 023397 120 HIHKALMDINESPVYVLL 137 (283)
Q Consensus 120 ~ih~~~~~~~~~pi~L~~ 137 (283)
.--+.+.+..+..+++++
T Consensus 95 ~~~~~~~~~~~~~l~iIv 112 (131)
T TIGR02256 95 RSWRTIIRSPEAMLLLIV 112 (131)
T ss_pred HHHHHHHhCCCeeEEEEE
Confidence 433444444444444544
No 28
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=95.10 E-value=0.32 Score=37.15 Aligned_cols=60 Identities=8% Similarity=0.188 Sum_probs=35.0
Q ss_pred CCceEEEEeeEEeCCEEEEEEeEeeccCCCcccccHHHHHHHHHHHHHhCCCcceEEEEecCCC----CCcchH
Q 023397 50 QPRVYGCVIGIQRGRTVEIFNSFELLYDPSTHSLDRAFLEKKQELYKKVFPHFYILGWYSTGSD----AQESDM 119 (283)
Q Consensus 50 ~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~~iD~~~~~~m~~l~k~V~p~~~iVGWY~tg~~----~~~~d~ 119 (283)
+...+|.|+|...+..+.++......-.+ ++.... ++....+..+||+|+|.+. ++..|.
T Consensus 17 p~E~~G~L~g~~~~~~~~~~~~~~~~p~~--------~~~~~~--~~~~~~~~~~vg~~HSHP~~~a~pS~~D~ 80 (104)
T PF14464_consen 17 PNEACGLLLGRRDDQRFIVVPNVNPDPRD--------SFRRER--FEARERGLEIVGIWHSHPSGPAFPSSTDI 80 (104)
T ss_dssp TS-EEEEEEEEEECCEEEEEEEEE--HHC--------HHHHHH---HHHHHT-EEEEEEEEESSSSSS--HHHH
T ss_pred CCeEEEEEEEEecCCEEEEEeCCCCCcHH--------HHHHHh--hhhhcccceeeEEEEcCCCCCCCCCHHHH
Confidence 46899999999987787777766511110 111111 0455668899999999653 444553
No 29
>cd08072 MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme. This family contains only archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=95.08 E-value=0.46 Score=37.85 Aligned_cols=83 Identities=11% Similarity=0.066 Sum_probs=52.2
Q ss_pred CCceEEEEeeEEeCCEEEEEEeEeeccCCCcc---cccHHHHHHHHHHHHHhCCCcceEEEEecCCC----CCcchHHHH
Q 023397 50 QPRVYGCVIGIQRGRTVEIFNSFELLYDPSTH---SLDRAFLEKKQELYKKVFPHFYILGWYSTGSD----AQESDMHIH 122 (283)
Q Consensus 50 ~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~---~iD~~~~~~m~~l~k~V~p~~~iVGWY~tg~~----~~~~d~~ih 122 (283)
+..+||.|+|+.. .|++.+++|.....+ ..+.+ |. -.++.+||-|++.++ ++..|..
T Consensus 18 P~E~CGlL~G~~~----~v~~~~~~~n~~~~~~~~~f~~~----~~------~~g~~ivgi~HSHP~~~~~PS~~D~~-- 81 (117)
T cd08072 18 PNEFAALLRGKDG----VITELLILPGTESGEVSAVFPLL----ML------PLDMSIVGSVHSHPSGSPRPSDADLS-- 81 (117)
T ss_pred CceEEEEEEeecc----EEEEEEECCCCCCCCcceeechH----Hh------cCCCeEEEEEEcCCCCCCCCCHHHHH--
Confidence 5689999999764 588889998654332 12332 11 247899999999763 5666642
Q ss_pred HHHhhhCCCcEEEEEcCCCCCCCCCcceEEEEe
Q 023397 123 KALMDINESPVYVLLNPSINPAQKDLPVTIFES 155 (283)
Q Consensus 123 ~~~~~~~~~pi~L~~D~~~~~~~~~lpi~~y~~ 155 (283)
++.. ....++++.... +.=.+++|..
T Consensus 82 --~~~~-~~~~~lIvs~~~----~~~~~~a~~~ 107 (117)
T cd08072 82 --FFSK-TGLVHIIVGYPY----DEDDWRAYDS 107 (117)
T ss_pred --hhhc-CCCEEEEEECcC----CCCCEEEEec
Confidence 2322 234677776431 1226889974
No 30
>cd08056 MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8. Members of this family are found in pre-mRNA-processing factor 8 (Prp8) which is a critical splicing factor, interacting with several other spliceosomal proteins, snRNAs, and the pre-mRNA, thus organizing and stabilizing the spliceosome catalytic core. Prp8 is one of the largest and most highly conserved of nuclear proteins, occupying a central position in the catalytic core of the spliceosome. Its C-terminal domain exhibits a JAB1/MPN-like core similar to deubiquitinating enzymes, but does not show catalytic isopeptidase activity, possibly because the putative isopeptidase center is covered by insertions and terminal appendices that are grafted onto this core, thus impairing the metal binding site. It is proposed that this domain is a protein interaction domain instead of a Zn(2+)-dependent metalloenzyme as proposed for some MPN proteins. The DEAD-box protein Brr2 and t
Probab=94.30 E-value=0.51 Score=42.73 Aligned_cols=98 Identities=13% Similarity=0.153 Sum_probs=64.6
Q ss_pred CceEEEEeeEEeC---CEEEEEEeEeeccCCCcccccHHHHHHHHHHHHHhCCCcceEEEEecCC----CCCcchHHHHH
Q 023397 51 PRVYGCVIGIQRG---RTVEIFNSFELLYDPSTHSLDRAFLEKKQELYKKVFPHFYILGWYSTGS----DAQESDMHIHK 123 (283)
Q Consensus 51 ~~v~G~LLG~~~~---~~veI~nsF~vp~~~~~~~iD~~~~~~m~~l~k~V~p~~~iVGWY~tg~----~~~~~d~~ih~ 123 (283)
..++|.|.|.... +.-||+.-..+|...+.+.++..- . .-.+ +---++..|||=+|.+ .+++.|+..|.
T Consensus 56 tQ~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~--~-~~~~-~~l~~Le~LGWIHTqp~e~~~Lss~Dv~tha 131 (252)
T cd08056 56 TQIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQ--Q-LPQH-EYLEDLEPLGWIHTQPNELPQLSPQDVTTHA 131 (252)
T ss_pred ceEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCc--c-Cccc-hhhCCCEeeEEEEcCCCCccccCHHHHHHHH
Confidence 4699999999743 667888777777765443111100 0 0111 1123689999999964 47889999999
Q ss_pred HHhhhCC-----CcEEEEEcCCCCCCCCCcceEEEEee
Q 023397 124 ALMDINE-----SPVYVLLNPSINPAQKDLPVTIFESE 156 (283)
Q Consensus 124 ~~~~~~~-----~pi~L~~D~~~~~~~~~lpi~~y~~~ 156 (283)
.++..++ +.|.+++-.. .|...+.||...
T Consensus 132 ~~~~~~~~w~~~~~V~it~Sft----pGs~sl~ay~LT 165 (252)
T cd08056 132 KILADNPSWDGEKTVILTCSFT----PGSCSLTAYKLT 165 (252)
T ss_pred HHHHhccccCCCcEEEEEEcCC----CCceEEEEEecC
Confidence 9988765 4555555443 366789999864
No 31
>cd08073 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains. This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=86.09 E-value=2.8 Score=32.84 Aligned_cols=57 Identities=11% Similarity=0.054 Sum_probs=33.0
Q ss_pred CCceEEEEeeEEeCCEEEEEEeEeeccCC-Cc-c-c-ccH-HHHHHHHHHHHHhCCCcceEEEEecCC----CCCcchH
Q 023397 50 QPRVYGCVIGIQRGRTVEIFNSFELLYDP-ST-H-S-LDR-AFLEKKQELYKKVFPHFYILGWYSTGS----DAQESDM 119 (283)
Q Consensus 50 ~~~v~G~LLG~~~~~~veI~nsF~vp~~~-~~-~-~-iD~-~~~~~m~~l~k~V~p~~~iVGWY~tg~----~~~~~d~ 119 (283)
+...||.|+|... ++..|++.... +. . | +|. ++++.+ ....+||.|++.+ .++..|.
T Consensus 15 P~E~CGll~g~~~-----~~~~~p~~N~~~~p~~~F~idp~e~~~a~--------~~~~ivgi~HSHP~~~a~PS~~D~ 80 (108)
T cd08073 15 PREACGLVVRKGR-----KLRYIPCRNIAADPEEHFEISPEDYAAAE--------DEGEIVAVVHSHPDGSPAPSEADR 80 (108)
T ss_pred CCcceEEEEecCC-----ceEEEECccCCCCccceEEeCHHHHHHHh--------cCCCEEEEEEcCCCCCCCCCHHHH
Confidence 5689999999661 23345555322 11 1 3 664 444322 1338999999975 3555554
No 32
>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic. This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=78.26 E-value=13 Score=28.16 Aligned_cols=60 Identities=12% Similarity=0.134 Sum_probs=37.9
Q ss_pred CCceEEEEeeEEeCCEEEEEEeEeeccCCCcccccHHHHHHHHHHHHHhCCCcceEEEEecCC----CCCcchHH
Q 023397 50 QPRVYGCVIGIQRGRTVEIFNSFELLYDPSTHSLDRAFLEKKQELYKKVFPHFYILGWYSTGS----DAQESDMH 120 (283)
Q Consensus 50 ~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~~iD~~~~~~m~~l~k~V~p~~~iVGWY~tg~----~~~~~d~~ 120 (283)
+...+|+|+|...+ .+.+..++|.... ..+..+ .....--+..+||-|++.+ .|+..|..
T Consensus 15 p~E~~gll~~~~~~---~~~~~~~~~~~~~--~~~~~~------~~~a~~~~~~~v~i~HsHP~g~~~PS~~D~~ 78 (101)
T cd08059 15 PDEFCGFLSGSKDN---VMDELIFLPFVSG--SVSAVI------DLAALEIGMKVVGLVHSHPSGSCRPSEADLS 78 (101)
T ss_pred ChhhheeeecCCCC---eEEEEEeCCCcCC--ccChHH------HHHHhhCCCcEEEEEecCcCCCCCCCHHHHH
Confidence 35689999998654 5677777774321 123332 2233444678999999965 46666754
No 33
>cd08061 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain. Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=71.46 E-value=61 Score=29.79 Aligned_cols=101 Identities=10% Similarity=0.075 Sum_probs=65.7
Q ss_pred CceEEEEeeEEeC-------CEEEEEEeEeeccCCCcc---cccHHHHHHHHHHHHHhCCCcceEEEEecCC--------
Q 023397 51 PRVYGCVIGIQRG-------RTVEIFNSFELLYDPSTH---SLDRAFLEKKQELYKKVFPHFYILGWYSTGS-------- 112 (283)
Q Consensus 51 ~~v~G~LLG~~~~-------~~veI~nsF~vp~~~~~~---~iD~~~~~~m~~l~k~V~p~~~iVGWY~tg~-------- 112 (283)
..-+|.|.|+.+. .++.|..-||=|.....+ .+++....+ .+... ..-.+..|||=-|..
T Consensus 34 ~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~-vd~iA-~~lGL~~VG~IfT~l~~~~~d~~ 111 (274)
T cd08061 34 QQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADT-VDAIA-AALGLERVGWIFTDLPREDKDGY 111 (274)
T ss_pred ceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhH-HHHHH-HHcCCeEEEEEEecCCCCCCCce
Confidence 4579999999853 489999999988865444 244444433 33333 344799999988853
Q ss_pred CCCcchHHHHHHHhh-----hCCCc-EEEEEcCCCCCCCCCcceEEEEee
Q 023397 113 DAQESDMHIHKALMD-----INESP-VYVLLNPSINPAQKDLPVTIFESE 156 (283)
Q Consensus 113 ~~~~~d~~ih~~~~~-----~~~~p-i~L~~D~~~~~~~~~lpi~~y~~~ 156 (283)
.++..++.....++. ...+. +-+++.+.. ++...+.+|...
T Consensus 112 ~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~---~g~i~~~ayQvS 158 (274)
T cd08061 112 FLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDK---DGQIHFEAYQVS 158 (274)
T ss_pred eECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCC---CCceeeeeeeec
Confidence 255566666666763 23333 446677653 377889999853
No 34
>PF06442 DHFR_2: R67 dihydrofolate reductase; InterPro: IPR009159 Dihydrofolate reductase (DHFR) (1.5.1.3 from EC) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate, an essential step in de novo synthesis both of glycine and of purines and deoxythymidine phosphate (the precursors of DNA synthesis) [], and important also in the conversion of deoxyuridine monophosphate to deoxythymidine monophosphate. Although DHFR is found ubiquitously in prokaryotes and eukaryotes, and is found in all dividing cells, maintaining levels of fully reduced folate coenzymes, the catabolic steps are still not well understood []. Bacterial species possesses distinct DHFR enzymes (based on their pattern of binding diaminoheterocyclic molecules), but mammalian DHFRs are highly similar []. The active site is situated in the N-terminal half of the sequence, which includes a conserved Pro-Trp dipeptide; the tryptophan has been shown [] to be involved in the binding of substrate by the enzyme. Its central role in DNA precursor synthesis, coupled with its inhibition by antagonists such as trimethoprim and methotrexate, which are used as anti-bacterial or anti-cancer agents, has made DHFR a target of anticancer chemotherapy. However, resistance has developed against some drugs, as a result of changes in DHFR itself []. This entry represents a plasmid-encoded DHFR which shows a high level of resistance to the antibiotic trimethoprim. It is a homotetramer with an unusual pore, which contains the active site, passing through the middle of the molecule []. Its structure is unrelated to that of chromosomal DHFRs.; GO: 0004146 dihydrofolate reductase activity, 0042493 response to drug, 0055114 oxidation-reduction process; PDB: 1VIF_A 3SFM_A 2P4T_A 2GQV_A 2RK2_A 2RH2_A 2RK1_A 1VIE_A.
Probab=70.61 E-value=2.4 Score=30.23 Aligned_cols=12 Identities=33% Similarity=0.722 Sum_probs=7.2
Q ss_pred cceEEEEecCCC
Q 023397 102 FYILGWYSTGSD 113 (283)
Q Consensus 102 ~~iVGWY~tg~~ 113 (283)
-.|||||+|.-.
T Consensus 40 g~vvgwy~t~lt 51 (78)
T PF06442_consen 40 GQVVGWYCTKLT 51 (78)
T ss_dssp EEEEEEE--SS-
T ss_pred ceEeEEEecccc
Confidence 479999998643
No 35
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=64.90 E-value=36 Score=32.39 Aligned_cols=59 Identities=14% Similarity=0.318 Sum_probs=45.8
Q ss_pred EEEeeEE-eCCEEEEEEeEeeccCCCcc-------------cccHHHHHHHHHHHHHhCCC-cceEEEEecCCC
Q 023397 55 GCVIGIQ-RGRTVEIFNSFELLYDPSTH-------------SLDRAFLEKKQELYKKVFPH-FYILGWYSTGSD 113 (283)
Q Consensus 55 G~LLG~~-~~~~veI~nsF~vp~~~~~~-------------~iD~~~~~~m~~l~k~V~p~-~~iVGWY~tg~~ 113 (283)
|.|+|.. .+++--|..-.+.|.+++++ -+|.+++.+.-.+-.+--|. ..|||.|.++++
T Consensus 1 GLlIGq~~s~~kd~Vv~l~~tP~~d~~~~~~~~~~~~~~~~~id~~WVaeHA~qVsRMLPGGi~VlGifvv~~~ 74 (362)
T PF14778_consen 1 GLLIGQSSSSQKDYVVHLARTPPEDTDDEESDVRTSDSSIKDIDEEWVAEHARQVSRMLPGGISVLGIFVVAPD 74 (362)
T ss_pred CeEeccccCCCcceEEEecCCCCccccccccccccccccccccCHHHHHHHHHHHHhhCCCCcEEEEEEEEcCH
Confidence 8899998 67767788888888764221 28899988888887777665 599999998863
No 36
>PF05021 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation following ubiquitination of target proteins but preceding their recognition by the 26S proteasome []. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing [].
Probab=63.05 E-value=1.3e+02 Score=28.13 Aligned_cols=97 Identities=12% Similarity=0.181 Sum_probs=57.7
Q ss_pred EEEEeeEEe-------CCEEEEEEeEeeccCCCcc---cccHHHHHHHHHHHHHhCCCcceEEEEecCCC----------
Q 023397 54 YGCVIGIQR-------GRTVEIFNSFELLYDPSTH---SLDRAFLEKKQELYKKVFPHFYILGWYSTGSD---------- 113 (283)
Q Consensus 54 ~G~LLG~~~-------~~~veI~nsF~vp~~~~~~---~iD~~~~~~m~~l~k~V~p~~~iVGWY~tg~~---------- 113 (283)
+|.|.|+.+ |-++.|..-||=|...+.+ ..+++..+.--+.-+. -.+..|||=-|...
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~--lGL~rVG~IfTdl~~~~~~~g~v~ 79 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASA--LGLERVGWIFTDLTDDGSGDGTVK 79 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHH--CCCEEEEEEEecCcccccCCCcee
Confidence 799999985 2379999999999875544 2444333332222222 28999999877522
Q ss_pred ---------CCcchHHHHHHHhhhCC------------Cc-EEEEEcCCCCCCCCCcceEEEEe
Q 023397 114 ---------AQESDMHIHKALMDINE------------SP-VYVLLNPSINPAQKDLPVTIFES 155 (283)
Q Consensus 114 ---------~~~~d~~ih~~~~~~~~------------~p-i~L~~D~~~~~~~~~lpi~~y~~ 155 (283)
++..++..-..+|...+ +. |-+++.+. ..+.+.+.+|..
T Consensus 80 ~~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~---~~g~i~~~ayQv 140 (306)
T PF05021_consen 80 CKRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGD---EEGEIHFEAYQV 140 (306)
T ss_pred eccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCC---CCCceeeEEeee
Confidence 34444433344443221 21 44555554 357888999985
No 37
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=51.66 E-value=7.1 Score=37.04 Aligned_cols=88 Identities=17% Similarity=0.183 Sum_probs=58.2
Q ss_pred CceEEEEeeEEeCCEEEEEEeEeeccCCCcc-cccHHHHHHHHHHHHHhCCCcceEEEEecCC----CCCcchHHHHHHH
Q 023397 51 PRVYGCVIGIQRGRTVEIFNSFELLYDPSTH-SLDRAFLEKKQELYKKVFPHFYILGWYSTGS----DAQESDMHIHKAL 125 (283)
Q Consensus 51 ~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~-~iD~~~~~~m~~l~k~V~p~~~iVGWY~tg~----~~~~~d~~ih~~~ 125 (283)
-..||+|-|.-..+...||.-. +|-.+.+. ..+..--++.++- +---++-.+||-+|.+ .++.-|+..|-.|
T Consensus 276 lETCGiL~g~L~~n~f~IThli-iPkQeatsd~C~t~neeelF~v--Qdq~~L~tlGWIHTHPTQt~FmSSVDlHTHcSY 352 (424)
T KOG2880|consen 276 LETCGILAGKLERNEFYITHLI-IPKQEATSDSCNTMNEEELFEV--QDQHELLTLGWIHTHPTQTCFMSSVDLHTHCSY 352 (424)
T ss_pred chHHHHhhhHhhcCcEEEEEEE-eecccCCCccccccCHHHHhee--cccccceeeeeeecCCccchhheecccccccee
Confidence 4689999999999999998754 55544321 1111111111111 1123678899999986 3677788888777
Q ss_pred hhhCCCcEEEEEcCCC
Q 023397 126 MDINESPVYVLLNPSI 141 (283)
Q Consensus 126 ~~~~~~pi~L~~D~~~ 141 (283)
+--.+.+|++++-|..
T Consensus 353 QiMlPEAiAIV~aPk~ 368 (424)
T KOG2880|consen 353 QIMLPEAIAIVCAPKS 368 (424)
T ss_pred eeecchheeEEecccc
Confidence 7767778988888874
No 38
>TIGR03735 PRTRC_A PRTRC system protein A. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.
Probab=46.86 E-value=84 Score=27.37 Aligned_cols=72 Identities=7% Similarity=-0.044 Sum_probs=45.1
Q ss_pred ehhhhhhHHHHHHhhhccccCCCCCcccCCCCCCCCCCceEEEEeeEEeCCEEEEEEeEeeccCCCc-cc--ccHHHHHH
Q 023397 14 HPLVIVNISDHYTRVKSQMNHSSSATTTNDDNNNGAQPRVYGCVIGIQRGRTVEIFNSFELLYDPST-HS--LDRAFLEK 90 (283)
Q Consensus 14 HPlVll~I~dh~~R~~~~~~~~~~~~~~~~~~~~~~~~~v~G~LLG~~~~~~veI~nsF~vp~~~~~-~~--iD~~~~~~ 90 (283)
-.-.+=.|++|+.+.. +..++|.|.|..+++.. ..+++...+.. .. .|..
T Consensus 76 p~~l~~~ii~hAr~~~--------------------P~EacG~Iag~~~~~~~---r~~p~~N~~~Sp~~~~~d~~---- 128 (192)
T TIGR03735 76 PASLLEEFAEAARAAL--------------------PNEVAAWIVWNSETGSL---RLAALESIEASPGHIDYRRP---- 128 (192)
T ss_pred CHHHHHHHHHHHHhcC--------------------CcceEEEEEEcCCCCEE---EEEeccccccCCceEEEcch----
Confidence 3345567788887654 46899999998555554 33666543321 12 3333
Q ss_pred HHHHHHHhCCCcceEEEEecCCC----CCcch
Q 023397 91 KQELYKKVFPHFYILGWYSTGSD----AQESD 118 (283)
Q Consensus 91 m~~l~k~V~p~~~iVGWY~tg~~----~~~~d 118 (283)
|. ..++.+|+-|++.+. ++..|
T Consensus 129 ~~------~~ge~lV~iyHSH~~spA~PS~tD 154 (192)
T TIGR03735 129 RL------DDGEHLVVDLHSHGTGSAFFSETD 154 (192)
T ss_pred HH------hCCCeEEEEEcCCCCCCCCCCccc
Confidence 22 678999999999753 55555
No 39
>PF10073 DUF2312: Uncharacterized protein conserved in bacteria (DUF2312); InterPro: IPR018753 This entry is represented by Azospirillum phage Cd, Gp10. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family of hypothetical bacterial proteins have no known function.
Probab=45.52 E-value=1.2e+02 Score=22.26 Aligned_cols=62 Identities=11% Similarity=0.259 Sum_probs=37.8
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHh
Q 023397 205 AHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRRLPAIESEKFQDDFLMVSLFSSFLNIF 278 (283)
Q Consensus 205 ~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~ilR~i~~l~~~lP~~~~~~f~~~~~~~~lmv~yLs~l 278 (283)
..+.++..-.+.|...+..+..=.+. .| .|..++|+|-.+ .+.++++.++ ++.++-.|++.|
T Consensus 11 eRiErLEeEk~~i~~dikdVyaEAK~--~G---fD~K~lr~ii~l----Rk~d~~~r~E---~eail~~Y~~AL 72 (74)
T PF10073_consen 11 ERIERLEEEKKAISDDIKDVYAEAKG--NG---FDTKALRQIIRL----RKKDPDEREE---EEAILDLYMSAL 72 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh--CC---CCHHHHHHHHHH----HcCCHhHHHH---HHHHHHHHHHHh
Confidence 34444444445555555555444333 56 899999999876 4455555443 367788888766
No 40
>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=35.38 E-value=46 Score=22.28 Aligned_cols=41 Identities=22% Similarity=0.233 Sum_probs=26.6
Q ss_pred hhhcHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHH
Q 023397 203 LAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKGEIPCENSLL 243 (283)
Q Consensus 203 ~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G~~~~d~~il 243 (283)
+...+..+..-+..-..++..+.+|++++.-.-+...|+||
T Consensus 5 L~~~l~~~e~~~~~k~~~v~eLe~YiD~LL~rVmE~~P~IL 45 (48)
T PF09457_consen 5 LISLLKKQEEENARKDSRVRELEDYIDNLLVRVMEQTPSIL 45 (48)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-GGGG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcchh
Confidence 34445566666777777788899999987654444555554
No 41
>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=34.82 E-value=49 Score=20.21 Aligned_cols=17 Identities=18% Similarity=0.421 Sum_probs=14.5
Q ss_pred CChHHHHHHHHHHhcCC
Q 023397 238 CENSLLRQVSSLLRRLP 254 (283)
Q Consensus 238 ~d~~ilR~i~~l~~~lP 254 (283)
...+|...|.++|+.||
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 46789999999999888
No 42
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=33.10 E-value=1.3e+02 Score=20.78 Aligned_cols=35 Identities=6% Similarity=0.135 Sum_probs=25.4
Q ss_pred hhhhhhcHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q 023397 200 ATQLAAHLTGIHSAIKMLNSRIRVLHHYLVAMQKG 234 (283)
Q Consensus 200 ~~~~~~~l~~~~~ai~~L~~~i~~i~~Yl~~V~~G 234 (283)
..++..+.+.+..++.++.+.++.+++-=+-|..|
T Consensus 16 i~tvk~en~~i~~~ve~i~envk~ll~lYE~Vs~~ 50 (55)
T PF05377_consen 16 INTVKKENEEISESVEKIEENVKDLLSLYEVVSNQ 50 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 34566677777788888888888887777776665
No 43
>PF11430 EGL-1: Programmed cell death activator EGL-1; InterPro: IPR021543 Initiation of programmed cell death in C.elegans occurs by the binding of EGL-1 to CED-9 which disrupts a complex involving CED-4/CED-9 and allows CED-4 to activate CED-3, a caspase. It is the C-terminal domain of EGL-1 which is involved in the formation of the complex with CED-9. The formation of the complex induces structural rearrangements in CED-9 and EGL-1 adopts an extended alpha-helical conformation []. ; PDB: 1TY4_D.
Probab=26.20 E-value=1.2e+02 Score=16.61 Aligned_cols=12 Identities=0% Similarity=0.171 Sum_probs=9.5
Q ss_pred hHHHHHHHHHHh
Q 023397 240 NSLLRQVSSLLR 251 (283)
Q Consensus 240 ~~ilR~i~~l~~ 251 (283)
++||++++..|.
T Consensus 1 ~~IG~kla~MCD 12 (21)
T PF11430_consen 1 HEIGTKLAAMCD 12 (21)
T ss_dssp HHHHHHHHHHHH
T ss_pred CcHHHHHHHHHH
Confidence 478899988883
No 44
>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=25.89 E-value=1.4e+02 Score=19.37 Aligned_cols=37 Identities=14% Similarity=0.249 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHh
Q 023397 215 KMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLR 251 (283)
Q Consensus 215 ~~L~~~i~~i~~Yl~~V~~G~~~~d~~ilR~i~~l~~ 251 (283)
+.|-+++..=..++.+..+|+..++.+.+..|..++.
T Consensus 13 ~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~ 49 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENGKRNPSLDTLKKIAKALG 49 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHT
T ss_pred HHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHC
Confidence 4555566666677888888999999999999999887
No 45
>KOG3286 consensus Selenoprotein T [General function prediction only]
Probab=23.18 E-value=1.5e+02 Score=26.11 Aligned_cols=40 Identities=28% Similarity=0.374 Sum_probs=33.2
Q ss_pred eEEeCCEEEEEEeEeeccCCCcccccHHHHHHHHHHHHHhCCCcceEE
Q 023397 59 GIQRGRTVEIFNSFELLYDPSTHSLDRAFLEKKQELYKKVFPHFYILG 106 (283)
Q Consensus 59 G~~~~~~veI~nsF~vp~~~~~~~iD~~~~~~m~~l~k~V~p~~~iVG 106 (283)
|...+..++|.-|..+-+. ...++|.++.++.||+..|.|
T Consensus 65 ~~~~~ptl~i~fCvSCgYk--------~af~~~~~~l~ekyPgl~Ieg 104 (226)
T KOG3286|consen 65 HIKYGPTLEINFCVSCGYK--------QAFEQYKKFLKEKYPGLDIEG 104 (226)
T ss_pred ccccCCcEEEEEEEecCcH--------HHHHHHHHHHHhhCCCceeec
Confidence 4456788999999988776 356789999999999999986
No 46
>PF05391 Lsm_interact: Lsm interaction motif; InterPro: IPR008669 This short motif is found at the C terminus of Prp24 proteins and probably interacts with the Lsm proteins to promote U4/U6 formation [].
Probab=22.40 E-value=69 Score=17.68 Aligned_cols=13 Identities=23% Similarity=0.485 Sum_probs=10.4
Q ss_pred CCCChHHHHHHHH
Q 023397 254 PAIESEKFQDDFL 266 (283)
Q Consensus 254 P~~~~~~f~~~~~ 266 (283)
+.++.++|+++|+
T Consensus 8 ~p~SNddFrkmfl 20 (21)
T PF05391_consen 8 KPKSNDDFRKMFL 20 (21)
T ss_pred CccchHHHHHHHc
Confidence 4578899999885
No 47
>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=20.31 E-value=1.8e+02 Score=19.55 Aligned_cols=38 Identities=16% Similarity=0.243 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHhc
Q 023397 215 KMLNSRIRVLHHYLVAMQKGEIPCENSLLRQVSSLLRR 252 (283)
Q Consensus 215 ~~L~~~i~~i~~Yl~~V~~G~~~~d~~ilR~i~~l~~~ 252 (283)
..+-.++..=..|+..+.+|+..+....+++|...+..
T Consensus 16 ~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~~v 53 (64)
T PF12844_consen 16 KDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEALGV 53 (64)
T ss_dssp HHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHHTS
T ss_pred HHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHhCC
Confidence 33444455558888999999999999999999888764
No 48
>KOG0756 consensus Mitochondrial tricarboxylate/dicarboxylate carrier proteins [Energy production and conversion]
Probab=20.05 E-value=58 Score=30.25 Aligned_cols=49 Identities=20% Similarity=0.230 Sum_probs=32.6
Q ss_pred CceEEEEeeEEeCCEEEEEEeEeeccCCCcccccHHHHHHHHHHHHHhC------------CCcceEEEEecC
Q 023397 51 PRVYGCVIGIQRGRTVEIFNSFELLYDPSTHSLDRAFLEKKQELYKKVF------------PHFYILGWYSTG 111 (283)
Q Consensus 51 ~~v~G~LLG~~~~~~veI~nsF~vp~~~~~~~iD~~~~~~m~~l~k~V~------------p~~~iVGWY~tg 111 (283)
..+.|+++|-..| -+||+-+||. +|.+.++++.+++. ..+-++|||.--
T Consensus 13 ~s~~~~~~Gg~~G-~~E~c~~~P~-----------E~vKT~LQldrr~a~~~~~~~~~~tv~~~G~lglYrGl 73 (299)
T KOG0756|consen 13 GSASGIVAGGIAG-GIEICITQPT-----------EYVKTQLQLDRRSATTKARGPPDCTVNGHGFLGLYRGL 73 (299)
T ss_pred Cchhhcccccccc-ceeeeecCch-----------hhhhheeehhhccccccccCCCceeeecCceeeEeecc
Confidence 4667777776665 6788777654 46677777776532 224599999753
Done!