Query psy4542
Match_columns 273
No_of_seqs 151 out of 738
Neff 7.9
Searched_HMMs 46136
Date Fri Aug 16 19:46:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4542.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4542hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2975|consensus 100.0 7E-78 1.5E-82 511.3 26.2 270 1-270 17-288 (288)
2 PLN03246 26S proteasome regula 100.0 1E-71 2.2E-76 499.8 32.3 269 3-271 4-279 (303)
3 cd08062 MPN_RPN7_8 Mpr1p, Pad1 100.0 3.3E-71 7.1E-76 493.1 33.9 266 6-271 2-273 (280)
4 cd08064 MPN_eIF3f Mpr1p, Pad1p 100.0 1.4E-70 3E-75 487.8 31.0 261 7-267 1-265 (265)
5 cd08063 MPN_CSN6 Mpr1p, Pad1p 100.0 1.4E-68 3E-73 480.0 28.2 266 5-271 1-277 (288)
6 KOG1556|consensus 100.0 1.1E-60 2.4E-65 402.2 21.6 265 5-269 9-279 (309)
7 KOG3050|consensus 100.0 1.8E-60 4E-65 400.3 20.8 269 2-271 6-282 (299)
8 cd08057 MPN_euk_non_mb Mpr1p, 100.0 3E-40 6.5E-45 272.0 16.9 150 7-163 1-157 (157)
9 cd08065 MPN_eIF3h Mpr1p, Pad1p 100.0 3.2E-34 7E-39 254.7 21.4 199 6-206 2-233 (266)
10 cd08069 MPN_RPN11_CSN5 Mov34/M 100.0 3.3E-29 7.3E-34 222.4 21.8 168 5-174 10-206 (268)
11 PF01398 JAB: JAB1/Mov34/MPN/P 99.9 6.4E-27 1.4E-31 182.6 10.0 108 2-111 1-114 (114)
12 KOG1560|consensus 99.9 1.2E-24 2.7E-29 187.1 14.2 203 5-207 13-255 (339)
13 smart00232 JAB_MPN JAB/MPN dom 99.9 1.9E-22 4.2E-27 161.0 15.6 128 6-135 1-134 (135)
14 PF13012 MitMem_reg: Maintenan 99.9 7.2E-24 1.6E-28 165.6 1.9 113 157-269 1-114 (115)
15 KOG1554|consensus 99.8 1.6E-18 3.4E-23 149.9 14.2 199 5-205 53-282 (347)
16 cd07767 MPN Mpr1p, Pad1p N-ter 99.7 4.7E-16 1E-20 121.0 12.3 111 15-131 2-116 (116)
17 cd08067 MPN_2A_DUB Mov34/MPN/P 99.6 9.7E-15 2.1E-19 123.1 14.8 145 4-157 4-164 (187)
18 cd08058 MPN_euk_mb Mpr1p, Pad1 99.6 1.3E-14 2.8E-19 114.0 11.4 109 13-134 2-119 (119)
19 cd08068 MPN_BRCC36 Mov34/MPN/P 99.4 2.6E-11 5.7E-16 105.7 15.8 148 5-157 2-170 (244)
20 KOG1555|consensus 99.1 4.4E-10 9.5E-15 100.3 8.2 131 3-135 29-173 (316)
21 cd08066 MPN_AMSH_like Mov34/MP 99.1 4.6E-09 1E-13 87.6 13.9 123 7-138 4-132 (173)
22 cd08060 MPN_UPF0172 Mov34/MPN/ 98.5 1.3E-06 2.8E-11 73.5 11.3 118 10-134 2-130 (182)
23 PF03665 UPF0172: Uncharacteri 98.5 9.5E-06 2.1E-10 69.1 16.1 124 5-133 2-135 (196)
24 cd08070 MPN_like Mpr1p, Pad1p 98.5 1.8E-06 3.8E-11 68.5 10.4 112 13-135 3-120 (128)
25 COG1310 Predicted metal-depend 98.1 2.2E-05 4.7E-10 62.8 9.4 101 7-119 2-106 (134)
26 KOG3289|consensus 97.7 0.00091 2E-08 55.1 12.1 122 6-132 3-134 (199)
27 cd08056 MPN_PRP8 Mpr1p, Pad1p 97.1 0.0025 5.5E-08 56.1 8.0 102 28-137 55-168 (252)
28 TIGR02256 ICE_VC0181 integrati 97.0 0.0089 1.9E-07 47.5 9.9 104 13-117 1-112 (131)
29 cd08072 MPN_archaeal Mov34/MPN 96.6 0.035 7.6E-07 43.3 10.4 99 13-134 5-108 (117)
30 PF14464 Prok-JAB: Prokaryotic 96.0 0.075 1.6E-06 39.9 8.9 66 13-92 4-69 (104)
31 cd08061 MPN_NPL4 Mov34/MPN/PAD 92.5 0.86 1.9E-05 40.9 8.7 108 28-137 33-161 (274)
32 cd08073 MPN_NLPC_P60 Mpr1p, Pa 92.0 1.5 3.3E-05 33.5 8.5 63 15-92 4-69 (108)
33 KOG2880|consensus 86.2 0.47 1E-05 43.6 2.0 96 28-134 275-377 (424)
34 PF05021 NPL4: NPL4 family; I 83.1 8.2 0.00018 35.2 8.7 103 32-136 2-143 (306)
35 cd08059 MPN_prok_mb Mpr1p, Pad 81.8 6.7 0.00014 29.2 6.5 70 16-100 5-78 (101)
36 PF06442 DHFR_2: R67 dihydrofo 73.4 1.6 3.4E-05 30.1 0.7 12 81-92 39-50 (78)
37 TIGR03735 PRTRC_A PRTRC system 67.6 20 0.00044 30.4 6.4 104 10-135 76-184 (192)
38 PF14778 ODR4-like: Olfactory 63.9 38 0.00083 31.6 8.2 61 33-93 1-74 (362)
39 KOG1795|consensus 58.3 18 0.00039 39.0 5.2 117 15-139 2101-2225(2321)
40 PF05184 SapB_1: Saposin-like 38.7 44 0.00096 19.8 2.9 30 199-229 10-39 (39)
41 PF11430 EGL-1: Programmed cel 30.6 91 0.002 16.5 2.8 11 215-225 1-11 (21)
42 KOG2834|consensus 30.5 53 0.0011 31.6 3.2 75 15-90 182-264 (510)
43 PF01381 HTH_3: Helix-turn-hel 29.9 1.1E+02 0.0024 19.3 4.0 38 189-226 12-49 (55)
44 PF13824 zf-Mss51: Zinc-finger 26.6 85 0.0019 21.0 2.8 26 57-82 27-52 (55)
45 KOG0130|consensus 23.3 1.1E+02 0.0024 24.6 3.4 53 78-134 64-119 (170)
46 PF12844 HTH_19: Helix-turn-he 23.2 1.5E+02 0.0032 19.5 3.7 39 188-226 14-52 (64)
47 COG4220 Phage DNA packaging pr 22.9 3.7E+02 0.008 22.3 6.4 42 216-258 113-154 (174)
48 PF09457 RBD-FIP: FIP domain ; 22.1 93 0.002 20.2 2.3 25 183-207 10-34 (48)
49 PF07002 Copine: Copine; Inte 22.0 95 0.0021 25.0 2.9 63 14-84 20-82 (146)
50 KOG0756|consensus 21.1 55 0.0012 29.7 1.5 49 28-90 12-72 (299)
No 1
>KOG2975|consensus
Probab=100.00 E-value=7e-78 Score=511.35 Aligned_cols=270 Identities=54% Similarity=0.928 Sum_probs=262.4
Q ss_pred CCCCceEEEehhhHhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhCC
Q psy4542 1 MSLNVSIKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVNP 80 (273)
Q Consensus 1 ~~~~~~V~lhPlvll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~p 80 (273)
|++..+|.+||+|+++|+|+|+||+.++.||||+|||+.++|.|||||||++||+|.+|++.+|++|++.|+++++++||
T Consensus 17 ~ss~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g~ieitNCFaVPhnEssdqvevdm~y~~~M~~l~~k~np 96 (288)
T KOG2975|consen 17 FSSNLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKGSVEVTNCFAVPHNESSDQVEVDMEYAKNMYELHKKVNP 96 (288)
T ss_pred CCCCceEEEcceEEeEeehhhhcCCccchhhhhheeecccCCeEEEEEeeeccCccccccceeeHHHHHHHHHHhcccCC
Confidence 56889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCeEEeecCCCCCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceeEEEeeecCCCCCcccceeeeeceEEecCchH
Q psy4542 81 SELIVGWWATGDEVTSQSSVIHDYYIRECKNPVHMTLDTNLKGPNMGIKGYVHVPIGVPGGKSGIMFTQIPAEVICYNSE 160 (273)
Q Consensus 81 ~~~iVGWY~~g~~~~~~~~~i~~~~~~~~~~pi~L~~D~~~~~~~l~ikay~~~~~~~~~~~~~~~f~~ip~~i~~~e~E 160 (273)
+|.+||||+||+++++++..||++|.+++++||||++|++.+++.+++|||.++++|++|++.+.+|.|+|+++.+.++|
T Consensus 97 nE~vvGWyaTg~dvt~~sslihdyYare~~~pvhLtVDT~~~n~rm~ikaYvss~~Gvpg~~~~~mF~plpvel~~~~~e 176 (288)
T KOG2975|consen 97 NELVVGWYATGHDVTEHSSLIHDYYAREAPNPVHLTVDTSLQNGRMSIKAYVSSLMGVPGRTMGVMFTPLPVELAYYDAE 176 (288)
T ss_pred CceeEEEEecCCCcccchhHHHHHhhccCCCCeEEEEeccccCCccceeEEEEeccCCCCcccceeeeeeeeEEeecchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhccCCC--CCccchHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHhhcCCCCCHHHHHH
Q psy4542 161 VTGLRLLHKSIKQGA--VQPLSELTLVSEAADKLTVLIDHVLRYVDEVLANRITPDNSIGRQLLDMVNSVPSMTQEQFET 238 (273)
Q Consensus 161 ~i~v~~l~~~~~~~~--~~~~~~l~~~~~a~~~L~~~l~~i~~Yl~~V~~g~~~~d~~ilr~l~~~~~~lp~~~~~~f~~ 238 (273)
|+|++.|.|.+.+.+ .++..+|+++..|..+|+.+|+++++|+++|.+|+.+||+.|||+|+++++++|++.+++|+.
T Consensus 177 rvgl~li~kt~~sp~r~~~l~~dLqQv~~at~~l~~~L~~Vl~YVedVl~gk~~pdn~VGR~Lmd~v~~vP~l~p~~Fe~ 256 (288)
T KOG2975|consen 177 RVGLDLIEKTSFSPSRVAGLSSDLQQVEGATARLQSLLERVLKYVEDVLAGKVKPDNAVGRFLMDLVTAVPKLVPDDFET 256 (288)
T ss_pred hhHHHHHHHhccChhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcchHHHHHHHHHHhcCCCCHHHHHH
Confidence 999999999986543 668999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhc
Q psy4542 239 MFNSNIKDLLMIMTLSQLTKTQLLLNEKLTLL 270 (273)
Q Consensus 239 ~~~~~~~D~lmv~yLs~ltk~~~~l~e~l~~~ 270 (273)
+|+++.+|.+|+.|||++||+|++|+|||+.+
T Consensus 257 mfn~nLrD~Lmv~yLa~ltqTQl~l~EKL~~l 288 (288)
T KOG2975|consen 257 MFNSNLRDLLMVIYLANLTQTQLALNEKLVNL 288 (288)
T ss_pred HHhhhHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 99999999999999999999999999999864
No 2
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=100.00 E-value=1e-71 Score=499.80 Aligned_cols=269 Identities=28% Similarity=0.449 Sum_probs=251.3
Q ss_pred CCceEEEehhhHhHHHHHHhhccCC-CceEEEEEeeeEeCCEEEEEEEEeeccccCchh---hHhhHHHHHHHHHHHhhh
Q psy4542 3 LNVSIKVHPVVLFQIVDAFERRNLD-SHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEM---VEAELNYAQDMFEMNQKV 78 (273)
Q Consensus 3 ~~~~V~lhPlvll~I~dh~~r~~~~-~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~---~~id~~~~~~m~~l~k~v 78 (273)
...+|.|||+|+|+|+|||+|+..+ +.||+|+|||.+.++.|||+|||++|++++++. |.+|.+|+++|+++||+|
T Consensus 4 ~~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~~~~~~ieItnsF~~p~~e~~~~~~~~~~D~~y~~~m~~~~k~V 83 (303)
T PLN03246 4 GIEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFRGRVDVTNSFAVPFEEDDKDPSIWFLDHNYLESMFGMFKRI 83 (303)
T ss_pred CCcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEeeecCCEEEEEeccccCcccCCCCccceeecHHHHHHHHHHHHHh
Confidence 4568999999999999999999765 689999999999999999999999999876543 789999999999999999
Q ss_pred CCCCCeEEeecCCCCCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceeEEEeeecCCCCCc--ccceeeeeceEEec
Q psy4542 79 NPSELIVGWWATGDEVTSQSSVIHDYYIRECKNPVHMTLDTNLKGPNMGIKGYVHVPIGVPGGK--SGIMFTQIPAEVIC 156 (273)
Q Consensus 79 ~p~~~iVGWY~~g~~~~~~~~~i~~~~~~~~~~pi~L~~D~~~~~~~l~ikay~~~~~~~~~~~--~~~~f~~ip~~i~~ 156 (273)
||++.+||||++|+.+++.|+.||++|++++++||||++|+...++++|++||++.+.+.+++. .+..|+++|++|++
T Consensus 84 ~~~~~vVGWY~tg~~i~~~d~~IH~~~~~~~~~Pv~L~vD~~~~~~~lpi~aY~s~~~~~~~~~~~~~~~F~~vp~~i~~ 163 (303)
T PLN03246 84 NAKEHVVGWYSTGPKLRENDLDIHELFNDYVPNPVLVIIDVQPKELGIPTKAYYAVEEVKENATQKSQKVFVHVPSEIGA 163 (303)
T ss_pred CCCCcEEeeecCCCCCCcchHHHHHHHHhhCCCCeEEEEecCCCCCCCceEEEEEEEeccCCCCcccccEEEECCeeeee
Confidence 9999999999999999999999999999999999999999998888899999999988876654 56789999999999
Q ss_pred CchHHHHHHHHHhhccCCC-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHhhcCCCCCHHH
Q psy4542 157 YNSEVTGLRLLHKSIKQGA-VQPLSELTLVSEAADKLTVLIDHVLRYVDEVLANRITPDNSIGRQLLDMVNSVPSMTQEQ 235 (273)
Q Consensus 157 ~e~E~i~v~~l~~~~~~~~-~~~~~~l~~~~~a~~~L~~~l~~i~~Yl~~V~~g~~~~d~~ilr~l~~~~~~lp~~~~~~ 235 (273)
+||||||++++.+...+.+ ..+..++..+.+|+++|..||+.|++||++|.+|+.++|++|||+|+++|+++|.+++++
T Consensus 164 ~EaE~Igve~l~r~~~~~~~s~l~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~g~~~~d~~IlR~l~~l~~~lP~l~~~~ 243 (303)
T PLN03246 164 HEAEEIGVEHLLRDVKDTTVSTLATEVTGKLTALKGLDARLREIRSYLDLVVEGKLPLNHEILYHLQDVFNLLPNLNVEE 243 (303)
T ss_pred cCHHHHHHHHHHhcccCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHhhCCCCCHHH
Confidence 9999999999999876544 347779999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhcc
Q psy4542 236 FETMFNSNIKDLLMIMTLSQLTKTQLLLNEKLTLLT 271 (273)
Q Consensus 236 f~~~~~~~~~D~lmv~yLs~ltk~~~~l~e~l~~~~ 271 (273)
|+++|+++.||++|++|||+|||+|++|++++++..
T Consensus 244 f~~~f~~~~nD~lmv~YLa~l~kt~~~l~e~l~~~~ 279 (303)
T PLN03246 244 LVKAFAVKTNDMMLVIYLSSLIRSVIALHNLINNKI 279 (303)
T ss_pred HHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 999999999999999999999999999999999864
No 3
>cd08062 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8. This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural.
Probab=100.00 E-value=3.3e-71 Score=493.11 Aligned_cols=266 Identities=27% Similarity=0.474 Sum_probs=250.5
Q ss_pred eEEEehhhHhHHHHHHhhccCC-CceEEEEEeeeEeCCEEEEEEEEeeccccCchh---hHhhHHHHHHHHHHHhhhCCC
Q psy4542 6 SIKVHPVVLFQIVDAFERRNLD-SHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEM---VEAELNYAQDMFEMNQKVNPS 81 (273)
Q Consensus 6 ~V~lhPlvll~I~dh~~r~~~~-~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~---~~id~~~~~~m~~l~k~v~p~ 81 (273)
+|.|||+|||+|+|||+|+..+ +.+|+|+|||.+.++.+||+|||++|++++++. +.+|.+|+++|+++||+|||+
T Consensus 2 ~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~~~~~~veItnsF~~p~~~~~~~~~~~~~d~~y~~~m~~~~kkv~~~ 81 (280)
T cd08062 2 KVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWKKGVLDVTNSFAVPFEEDEKDPSVWFLDHNYLENMYGMFKKVNAK 81 (280)
T ss_pred eEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEEEeCCEEEEEEeeecCccCCCCCcchhhhhHHHHHHHHHHHHHhCCC
Confidence 7999999999999999998755 689999999999999999999999999876553 689999999999999999999
Q ss_pred CCeEEeecCCCCCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceeEEEeeecCCCCCc-ccceeeeeceEEecCchH
Q psy4542 82 ELIVGWWATGDEVTSQSSVIHDYYIRECKNPVHMTLDTNLKGPNMGIKGYVHVPIGVPGGK-SGIMFTQIPAEVICYNSE 160 (273)
Q Consensus 82 ~~iVGWY~~g~~~~~~~~~i~~~~~~~~~~pi~L~~D~~~~~~~l~ikay~~~~~~~~~~~-~~~~f~~ip~~i~~~e~E 160 (273)
+.+||||++|+.+++.|+.||++|++++++||+|++||...++++|++||++.+.+.++++ .+..|+++|++|+++|||
T Consensus 82 e~vVGWY~tg~~~~~~d~~ih~~~~~~~~~pv~l~vd~~~~~~~lpi~aY~s~~~~~~~g~~~~~~F~~vp~~i~~~eaE 161 (280)
T cd08062 82 EKIVGWYSTGPKLRPNDLDINELFRRYCPNPVLVIIDVRPKDLGLPTEAYIAVEEVHDDGTPTSKTFVHVPSEIGAEEAE 161 (280)
T ss_pred CCeEEEecCCCCCCcchHHHHHHHHHhCCCCEEEEEecCCCCCCCceEEEEEeeeccCCCCcceeEEEEcceEeeccchH
Confidence 9999999999999999999999999999999999999999888999999999998887776 788999999999999999
Q ss_pred HHHHHHHHhhccCCC-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHhhcCCCCCHHHHHHH
Q psy4542 161 VTGLRLLHKSIKQGA-VQPLSELTLVSEAADKLTVLIDHVLRYVDEVLANRITPDNSIGRQLLDMVNSVPSMTQEQFETM 239 (273)
Q Consensus 161 ~i~v~~l~~~~~~~~-~~~~~~l~~~~~a~~~L~~~l~~i~~Yl~~V~~g~~~~d~~ilr~l~~~~~~lp~~~~~~f~~~ 239 (273)
|||++++.+...+.+ ..+..++..+.+|+++|+.||+.+++||++|.+|+.++|++|||+|+++|+++|.+++++|+++
T Consensus 162 ~igve~l~r~~~~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~IlR~l~~~~~~lP~l~~~~f~~~ 241 (280)
T cd08062 162 EVGVEHLLRDIKDVTVSTLSTRVTNKLNSLKGLQSKLKEIKDYLQLVVEGKLPINHQIIYNLQDIFNLLPNLNLPELVKA 241 (280)
T ss_pred HHHHHHHHhhccCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence 999999999766444 3367799999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhhhHHHHHHHHHHHHHHHHHHHHHHhcc
Q psy4542 240 FNSNIKDLLMIMTLSQLTKTQLLLNEKLTLLT 271 (273)
Q Consensus 240 ~~~~~~D~lmv~yLs~ltk~~~~l~e~l~~~~ 271 (273)
|+++.||++|++|||+|||+|++|+|++++..
T Consensus 242 ~~~~~nD~lmv~yLs~l~k~~~~l~~~~~~~~ 273 (280)
T cd08062 242 FAVKTNDQMLVIYLSSLIRSVIALHNLINNKI 273 (280)
T ss_pred HHhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999864
No 4
>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f. Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and ap
Probab=100.00 E-value=1.4e-70 Score=487.85 Aligned_cols=261 Identities=52% Similarity=0.904 Sum_probs=249.4
Q ss_pred EEEehhhHhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhCCCCCeEE
Q psy4542 7 IKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVNPSELIVG 86 (273)
Q Consensus 7 V~lhPlvll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~p~~~iVG 86 (273)
|+|||+|+|+|+|||+|++.++.+|+|+|||++.++.+||+|||++|++++++.+.+|.+|+++|+++||+|||++.+||
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~d~~y~~~m~~~~kkv~~~~~vVG 80 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNESEDQVAVDMEYHRTMYELHQKVNPKEVIVG 80 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCCEEEEEeCeecceeCCCCeEEEcHHHHHHHHHHHHHhCCCCcEEe
Confidence 68999999999999999987889999999999999999999999999998888889999999999999999999999999
Q ss_pred eecCCCCCCcccHHHHHHHHhhCC--CcEEEEEcCCCCCCCcceeEEEeeecCCCCCcccceeeeeceEEecCchHHHHH
Q psy4542 87 WWATGDEVTSQSSVIHDYYIRECK--NPVHMTLDTNLKGPNMGIKGYVHVPIGVPGGKSGIMFTQIPAEVICYNSEVTGL 164 (273)
Q Consensus 87 WY~~g~~~~~~~~~i~~~~~~~~~--~pi~L~~D~~~~~~~l~ikay~~~~~~~~~~~~~~~f~~ip~~i~~~e~E~i~v 164 (273)
||++|+++++.+..||++|++.++ +||+|++||..+++++|++||++.+.++.+++.+..|+++|++|.++++||||+
T Consensus 81 WY~tg~~~~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~~~~l~i~ay~~~~~~~~~~~~~~~F~~ip~~i~~~eaE~i~v 160 (265)
T cd08064 81 WYATGSEITEHSALIHDYYSRECTSYNPIHLTVDTSLDDGKMSIKAYVSSPLGVPGKTLGSMFVPIPLELLYSEAERVAL 160 (265)
T ss_pred eeeCCCCCCccHHHHHHHHHhhCCCCCCEEEEEeCCCCCCCcceEEEEEEecccCCCCcceEEEEcceeeecCcHHHHHH
Confidence 999999999999999999999988 999999999988779999999999988877778899999999999999999999
Q ss_pred HHHHhhccCCC--CCccchHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHhhcCCCCCHHHHHHHHHh
Q psy4542 165 RLLHKSIKQGA--VQPLSELTLVSEAADKLTVLIDHVLRYVDEVLANRITPDNSIGRQLLDMVNSVPSMTQEQFETMFNS 242 (273)
Q Consensus 165 ~~l~~~~~~~~--~~~~~~l~~~~~a~~~L~~~l~~i~~Yl~~V~~g~~~~d~~ilr~l~~~~~~lp~~~~~~f~~~~~~ 242 (273)
+++.+...+.+ ..+.++++++.+++++|..||+.+++||++|.+|+.++|++|||+|+++++++|.+++++|+++|++
T Consensus 161 ~~l~~~~~~~~~~~~~~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~i~r~l~~~~~~lp~~~~~~f~~~~~~ 240 (265)
T cd08064 161 DLLAKTLASPSRSAPLTSDLEQLEASLEKLQEMLDRVLRYVEDVLAGKVKADNAIGRYLMDALTSVPKLDPEEFEKMFNS 240 (265)
T ss_pred HHHHhhccCCcccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHh
Confidence 99999887654 2366899999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHH
Q psy4542 243 NIKDLLMIMTLSQLTKTQLLLNEKL 267 (273)
Q Consensus 243 ~~~D~lmv~yLs~ltk~~~~l~e~l 267 (273)
+.||++|++|||+|||+|++|+|||
T Consensus 241 ~~~D~lmv~YLs~l~k~~~~l~ekl 265 (265)
T cd08064 241 SLQDLLMVTYLSNLTKTQLALAEKL 265 (265)
T ss_pred hcchHHHHHHHHHHHHHHHHHhhhC
Confidence 9999999999999999999999996
No 5
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=100.00 E-value=1.4e-68 Score=480.04 Aligned_cols=266 Identities=24% Similarity=0.398 Sum_probs=248.4
Q ss_pred ceEEEehhhHhHHHHHHhhccCC----CceEEEEEeeeEeCCEEEEEEEEeeccccCc-hhhHhhHHHHHHHHHHHhhhC
Q psy4542 5 VSIKVHPVVLFQIVDAFERRNLD----SHRVIGTLLGTVDKGVVEVTNCFCVPHKEYD-EMVEAELNYAQDMFEMNQKVN 79 (273)
Q Consensus 5 ~~V~lhPlvll~I~dh~~r~~~~----~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~-~~~~id~~~~~~m~~l~k~v~ 79 (273)
.+|.|||+|||+|+|||+|+..+ +.+|+|+|||.+++++|||+|||++|+.+++ +.+.+|.+|+++|+++||+||
T Consensus 1 ~~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~id~~y~~~m~~~~kkV~ 80 (288)
T cd08063 1 LSVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGREIEIENSFELKYDTNEDGEIVLDKEFLETRLEQFKQVF 80 (288)
T ss_pred CeEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEcCCEEEEEEEEecccccCCCCceeeCHHHHHHHHHHHHHhc
Confidence 47999999999999999998653 5899999999999999999999999998876 678999999999999999999
Q ss_pred CCCCeEEeecCCCC-CCcccHHHHHHHHhhCCCcEEEEEcCCC--CCCCcceeEEEeeecCCCCCcccceeeeeceEEec
Q psy4542 80 PSELIVGWWATGDE-VTSQSSVIHDYYIRECKNPVHMTLDTNL--KGPNMGIKGYVHVPIGVPGGKSGIMFTQIPAEVIC 156 (273)
Q Consensus 80 p~~~iVGWY~~g~~-~~~~~~~i~~~~~~~~~~pi~L~~D~~~--~~~~l~ikay~~~~~~~~~~~~~~~f~~ip~~i~~ 156 (273)
|++.+||||++|+. ++..+..||++|++.+++||+|++||.. +++++|++||++...+.++ ..+..|+|+|++|++
T Consensus 81 ~~~~vVGWY~tg~~~~~~~~~~Ih~~~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~~~~~~-~~~~~F~~i~~~i~~ 159 (288)
T cd08063 81 KDLDFVGWYTTGPGGPTESDLPIHKQILEINESPVLLLLDPEANASGKDLPVTIYESVLELVDG-EATLRFRELPYTIET 159 (288)
T ss_pred cCCceEEEEecCCCCCCHHHHHHHHHHHhhCCCcEEEEEccccccCCCCCceeEEEEEEeccCC-ccccEEEeeeeEEEe
Confidence 99999999999998 9999999999999999999999999998 5789999999999877655 566889999999999
Q ss_pred CchHHHHHHHHHhhccCCC--C-CccchHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHhhcCCCCCH
Q psy4542 157 YNSEVTGLRLLHKSIKQGA--V-QPLSELTLVSEAADKLTVLIDHVLRYVDEVLANRITPDNSIGRQLLDMVNSVPSMTQ 233 (273)
Q Consensus 157 ~e~E~i~v~~l~~~~~~~~--~-~~~~~l~~~~~a~~~L~~~l~~i~~Yl~~V~~g~~~~d~~ilr~l~~~~~~lp~~~~ 233 (273)
+|+||||++++++.....+ . .+..+++.+.+|+++|+.||+.|++||++|.+|+.++|++|||+|+++|+++|.++.
T Consensus 160 ~eaErIgv~~l~~~~~~~~~~~~~~~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~g~~~~d~~ilR~l~~~~~~lP~~~~ 239 (288)
T cd08063 160 GEAERIGVDHVARGGASGSSEKSTVAAHLQAQHNAIKMLNSRVELILEYLKAVPVGEVPPDHSILRSISALCSRLPVLKS 239 (288)
T ss_pred ccCceeeHHHHHhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHhCccCCh
Confidence 9999999999998874322 2 367899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhcc
Q psy4542 234 EQFETMFNSNIKDLLMIMTLSQLTKTQLLLNEKLTLLT 271 (273)
Q Consensus 234 ~~f~~~~~~~~~D~lmv~yLs~ltk~~~~l~e~l~~~~ 271 (273)
++|+++|+++.||++|++|||++||++.+|+|+++++.
T Consensus 240 ~~~~~~~~~~~~D~lmv~yLs~lt~~~~~l~~~~~k~~ 277 (288)
T cd08063 240 EAFREELLAEYNDVLLVAYLATLTKGCNTLNELVDKFN 277 (288)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999875
No 6
>KOG1556|consensus
Probab=100.00 E-value=1.1e-60 Score=402.20 Aligned_cols=265 Identities=29% Similarity=0.477 Sum_probs=249.4
Q ss_pred ceEEEehhhHhHHHHHHhhccC-CCceEEEEEeeeEeCCEEEEEEEEeeccccCchh---hHhhHHHHHHHHHHHhhhCC
Q psy4542 5 VSIKVHPVVLFQIVDAFERRNL-DSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEM---VEAELNYAQDMFEMNQKVNP 80 (273)
Q Consensus 5 ~~V~lhPlvll~I~dh~~r~~~-~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~---~~id~~~~~~m~~l~k~v~p 80 (273)
.+|.+||||+|+++|||.|... +++||+|+|||..+++.+.|+|||++|++|++.. |++|.+|++.|+++|+++|.
T Consensus 9 ~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~~~~~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~mfkKvNa 88 (309)
T KOG1556|consen 9 EKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGSWNGDVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGMFKKVNA 88 (309)
T ss_pred ceeeeehhHHHHHHHHHhhhccCcCceEEEEEEecCCCCeEEeecceeccccccCCCCceEEeccHHHHHHHHHHHHhcc
Confidence 4799999999999999999854 3689999999999999999999999999997654 89999999999999999999
Q ss_pred CCCeEEeecCCCCCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceeEEEeeecCCCCC-cccceeeeeceEEecCch
Q psy4542 81 SELIVGWWATGDEVTSQSSVIHDYYIRECKNPVHMTLDTNLKGPNMGIKGYVHVPIGVPGG-KSGIMFTQIPAEVICYNS 159 (273)
Q Consensus 81 ~~~iVGWY~~g~~~~~~~~~i~~~~~~~~~~pi~L~~D~~~~~~~l~ikay~~~~~~~~~~-~~~~~f~~ip~~i~~~e~ 159 (273)
+|.+||||+|||.+.++|+.|++.+.+++++|+++++|..+.+-.||..||...+..-.++ ..+..|+.+|++|+++||
T Consensus 89 kekivGWYhTGPkl~~nDl~In~l~k~y~pnpvLvIIdvkpk~~gLPT~AY~aVeev~dDgt~t~ktF~Hvps~I~AeEA 168 (309)
T KOG1556|consen 89 KEKVVGWYHTGPKLRENDLDINELLKRYVPNPVLVIIDVKPKELGLPTEAYIAVEEVKDDGTPTSKTFVHVPSEIEAEEA 168 (309)
T ss_pred hhheeeeeccCCccccchhhHHHHHhhcCCCceEEEEecccccCCCCchheeeeeeeecCCCCccceeEecCcccchhHH
Confidence 9999999999999999999999999999999999999999988899999999987644444 456789999999999999
Q ss_pred HHHHHHHHHhhccCCCCC-ccchHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHhhcCCCCCHHHHHH
Q psy4542 160 EVTGLRLLHKSIKQGAVQ-PLSELTLVSEAADKLTVLIDHVLRYVDEVLANRITPDNSIGRQLLDMVNSVPSMTQEQFET 238 (273)
Q Consensus 160 E~i~v~~l~~~~~~~~~~-~~~~l~~~~~a~~~L~~~l~~i~~Yl~~V~~g~~~~d~~ilr~l~~~~~~lp~~~~~~f~~ 238 (273)
|.||++|+.|...+.+.+ +...+.++..+++.|+.++..|..||++|.+|+.|.|++|+.+++++++.+|.+...+|.+
T Consensus 169 EEvGVEHLlRDikd~t~gtla~rit~ql~sLkgl~~~L~eI~~YL~~Vi~g~lpiNh~Il~~lQdvfNllP~l~~~~~~~ 248 (309)
T KOG1556|consen 169 EEVGVEHLLRDIKDTTVGTLATRITNQLMSLKGLQSRLREIRSYLDKVIDGKLPINHEILYQLQDVFNLLPNLTRNELVK 248 (309)
T ss_pred HHhhHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHhhCccccchhhhh
Confidence 999999999999987755 8899999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHh
Q psy4542 239 MFNSNIKDLLMIMTLSQLTKTQLLLNEKLTL 269 (273)
Q Consensus 239 ~~~~~~~D~lmv~yLs~ltk~~~~l~e~l~~ 269 (273)
.|+-..||.||+.|+|+|+|+..+|++++++
T Consensus 249 a~~vktndql~~iY~sslvrsViAlhdLi~N 279 (309)
T KOG1556|consen 249 AFNVKTNDQLMVIYLSSLVRSVIALHDLINN 279 (309)
T ss_pred hhccccCceeeeeeHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999999999976
No 7
>KOG3050|consensus
Probab=100.00 E-value=1.8e-60 Score=400.31 Aligned_cols=269 Identities=22% Similarity=0.357 Sum_probs=248.7
Q ss_pred CCCceEEEehhhHhHHHHHHhhccCC--C--ceEEEEEeeeEeCCEEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhh
Q psy4542 2 SLNVSIKVHPVVLFQIVDAFERRNLD--S--HRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQK 77 (273)
Q Consensus 2 ~~~~~V~lhPlvll~I~dh~~r~~~~--~--~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~ 77 (273)
+++.+|.+|||||+||+|||+|.+.+ + ++|+|+|+|.+.|+.|||.|||++..+..++...+|.+|+.++.++||+
T Consensus 6 S~s~tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~~~~~~dke~l~kk~eqykq 85 (299)
T KOG3050|consen 6 SGSVTVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGKQRGRNVEIMNSFELKMDTEEDTETIDKEYLEKKEEQYKQ 85 (299)
T ss_pred CCceeEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheecccCceEEEeeeeEEEecchhhhhhccHHHHHHHHHHHHH
Confidence 36789999999999999999998653 2 3899999999999999999999999877666567999999999999999
Q ss_pred hCCCCCeEEeecCCCCCCcccHHHHHHHHhhCCCcEEEEEcCCCC-CCCcceeEEEeeecCCCCCcccceeeeeceEEec
Q psy4542 78 VNPSELIVGWWATGDEVTSQSSVIHDYYIRECKNPVHMTLDTNLK-GPNMGIKGYVHVPIGVPGGKSGIMFTQIPAEVIC 156 (273)
Q Consensus 78 v~p~~~iVGWY~~g~~~~~~~~~i~~~~~~~~~~pi~L~~D~~~~-~~~l~ikay~~~~~~~~~~~~~~~f~~ip~~i~~ 156 (273)
|||++.++|||++|.+.++.|+.||++.+..++.|++|.++|... ..+.|++.|++. ..+.+|.....|+|+.|.+.+
T Consensus 86 VFpdl~vlGwYttG~d~t~sd~~i~k~l~~i~esplflkLNp~t~~t~~~pv~lfese-~dvidg~~q~~f~~~tytl~t 164 (299)
T KOG3050|consen 86 VFPDLYVLGWYTTGSDPTPSDIHIHKQLMDINESPLFLKLNPATNHTDKDPVTLFESE-IDVIDGEAQMLFVPLTYTLAT 164 (299)
T ss_pred hcccceEEEEeecCCCCChhhhHHHHHHHhhhcCceEEEecchhccccCCCceeeeee-heeecCcceeeeeeeEEEEee
Confidence 999999999999999999999999999999999999999999876 455699999985 455677788999999999999
Q ss_pred CchHHHHHHHHHhhccCCC---CCccchHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHhhcCCCCCH
Q psy4542 157 YNSEVTGLRLLHKSIKQGA---VQPLSELTLVSEAADKLTVLIDHVLRYVDEVLANRITPDNSIGRQLLDMVNSVPSMTQ 233 (273)
Q Consensus 157 ~e~E~i~v~~l~~~~~~~~---~~~~~~l~~~~~a~~~L~~~l~~i~~Yl~~V~~g~~~~d~~ilr~l~~~~~~lp~~~~ 233 (273)
+||||||+||+++-...++ .++..++..+..|++||+.|++.|++|+++|.+|++++|.+|+|+...+|..||.++.
T Consensus 165 eEaERIgVdHVA~lt~~~gge~s~VaeHl~AQdsA~~ml~~Rvklil~Y~k~~e~G~l~~N~eILrea~~L~~~Lp~~~~ 244 (299)
T KOG3050|consen 165 EEAERIGVDHVARLTPSDGGEGSSVAEHLEAQDSAIKMLDNRVKLILAYLKKVEAGTLQPNFEILREAYALCHRLPVMES 244 (299)
T ss_pred hhhhhccchhheeeccCCCCCcchHHHHHhhHHHHHHHHhhHHHHHHHHHhhhhcCCcCccHHHHHHHHHHHhhccccch
Confidence 9999999999999876542 4578999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhcc
Q psy4542 234 EQFETMFNSNIKDLLMIMTLSQLTKTQLLLNEKLTLLT 271 (273)
Q Consensus 234 ~~f~~~~~~~~~D~lmv~yLs~ltk~~~~l~e~l~~~~ 271 (273)
++|.+.|..++||+.+++||+.+|+++..+++.+|+|.
T Consensus 245 ~~F~d~F~~e~nd~~l~syl~~iT~~~~nMn~~vnKfn 282 (299)
T KOG3050|consen 245 EKFQDNFYMECNDVGLISYLGTITKCCNNMNEVVNKFN 282 (299)
T ss_pred HHHhHHHHHhcchhhHHHHHHHHHHhhccHHHHHHHHH
Confidence 99999999999999999999999999999999999874
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=3e-40 Score=272.03 Aligned_cols=150 Identities=30% Similarity=0.539 Sum_probs=137.1
Q ss_pred EEEehhhHhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhCCCCCeEE
Q psy4542 7 IKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVNPSELIVG 86 (273)
Q Consensus 7 V~lhPlvll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~p~~~iVG 86 (273)
|+|||+|+|+|+|||+|+..++.+++|+|||.+.++.++|+|||++|++++++.+.+|.+|+++|++++|+|+|++.+||
T Consensus 1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~~~~~~veV~nsF~lp~~~~~~~~~~d~~y~~~m~~~~~~v~~~~~vVG 80 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGDKIEVTNSFELPFDEEEESIFIDTEYLEKRYNLHKKVYPQEKIVG 80 (157)
T ss_pred CEEccHHHhhHHHHHHhccCCCCeEEEEEEeEEeCCEEEEEEeEEccccCCCcchhhhHHHHHHHHHHHHHhCCCCCEEE
Confidence 68999999999999999876678999999999999999999999999988777788999999999999999999999999
Q ss_pred eecCCCC----CCcccHHHHHHHHhh-CCCcEEEEEcCCC--CCCCcceeEEEeeecCCCCCcccceeeeeceEEecCch
Q psy4542 87 WWATGDE----VTSQSSVIHDYYIRE-CKNPVHMTLDTNL--KGPNMGIKGYVHVPIGVPGGKSGIMFTQIPAEVICYNS 159 (273)
Q Consensus 87 WY~~g~~----~~~~~~~i~~~~~~~-~~~pi~L~~D~~~--~~~~l~ikay~~~~~~~~~~~~~~~f~~ip~~i~~~e~ 159 (273)
||++|+. ++..+..||++|+.. .++||+|++||.. .+++++++||++.+... .+.++|+++.++|+
T Consensus 81 WY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~~~-------~~~~~~~~i~~~e~ 153 (157)
T cd08057 81 WYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQREE-------NGAEITYEIGTEET 153 (157)
T ss_pred EEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEecCCC-------CCceeeeEEecccc
Confidence 9999987 889999999999987 7889999999987 37899999999986432 23399999999999
Q ss_pred HHHH
Q psy4542 160 EVTG 163 (273)
Q Consensus 160 E~i~ 163 (273)
||||
T Consensus 154 E~I~ 157 (157)
T cd08057 154 ERIA 157 (157)
T ss_pred cccC
Confidence 9985
No 9
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=100.00 E-value=3.2e-34 Score=254.71 Aligned_cols=199 Identities=22% Similarity=0.279 Sum_probs=155.8
Q ss_pred eEEEehhhHhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccCchh---hHhhHHHHHHHHHHHhhhCCCC
Q psy4542 6 SIKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEM---VEAELNYAQDMFEMNQKVNPSE 82 (273)
Q Consensus 6 ~V~lhPlvll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~---~~id~~~~~~m~~l~k~v~p~~ 82 (273)
+|.|||+|+++|+|||.|+ .+.+|+|+|||...++.+||+|||++|+.++++. ...|.+|+.+|+++++++++++
T Consensus 2 ~V~I~~~vllkIv~H~~~~--~p~~v~G~LLG~~~~~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~e 79 (266)
T cd08065 2 SVQIDGLVVLKIIKHCKEE--LPELVQGQLLGLDVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVDH 79 (266)
T ss_pred EEEEeHHHHHHHHHHHhcC--CCcEEEEEEeeeEcCCEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCCC
Confidence 6999999999999999997 4899999999999999999999999999887654 5667899999999999999999
Q ss_pred CeEEeecCCC-CCCcccHHHHHHHHh--hCCCcEEEEEcCCCC-CCCcceeEEEeeecCCC---------------CCcc
Q psy4542 83 LIVGWWATGD-EVTSQSSVIHDYYIR--ECKNPVHMTLDTNLK-GPNMGIKGYVHVPIGVP---------------GGKS 143 (273)
Q Consensus 83 ~iVGWY~~g~-~~~~~~~~i~~~~~~--~~~~pi~L~~D~~~~-~~~l~ikay~~~~~~~~---------------~~~~ 143 (273)
.+||||++++ ....+...++.+|.. ..+++|+|++||..+ +|.++++||++++.+++ +.+.
T Consensus 80 ~iVGWY~S~p~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s~~g~l~lkAyrl~~~~~~~~~~~~~~~~~l~~~~~~~ 159 (266)
T cd08065 80 NHVGWYQSTYLGSFFTRDLIETQYNYQEAIEESVVLVYDPSKTSQGSLSLKAYRLSEKFMELYKEGKFSTESLREANLTF 159 (266)
T ss_pred cEEEeEeecCCCCcCCHHHHHHHHHHhccCCCCEEEEECCCcccccceeeEEEEEcHHHHHHhhcCCcCHHHHHHhcCch
Confidence 9999999988 222224556666554 447899999999974 78899999999988765 3467
Q ss_pred cceeeeeceEEecCchHHHHHHHHHhhccCC--C--------C-CccchHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4542 144 GIMFTQIPAEVICYNSEVTGLRLLHKSIKQG--A--------V-QPLSELTLVSEAADKLTVLIDHVLRYVDEV 206 (273)
Q Consensus 144 ~~~f~~ip~~i~~~e~E~i~v~~l~~~~~~~--~--------~-~~~~~l~~~~~a~~~L~~~l~~i~~Yl~~V 206 (273)
+.+|.+||++|.++..+.+.+..+....... + . .+.+.++.+..+++.|......+..|-+.+
T Consensus 160 ~~if~eiPv~i~n~~l~~~~L~~l~~~~~~~~~~~~~l~l~~~~~le~~l~~l~~~id~l~~e~~~~~~y~r~~ 233 (266)
T cd08065 160 SNIFEEIPVVIRNSHLVNALLSELEEDSPSSQSDFDRLDLSTNSFLEKNLELLMESVDELSQEQGKFNYYQRNL 233 (266)
T ss_pred hcEEEEEEEEEEchHHHHHHHHhcccCCCcccCCcccccccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999999999886655432 1 0 133444444444445544444444444443
No 10
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i
Probab=99.97 E-value=3.3e-29 Score=222.38 Aligned_cols=168 Identities=16% Similarity=0.237 Sum_probs=151.2
Q ss_pred ceEEEehhhHhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccCchhhHhhHHHHHHHHH--HHhhhCCCC
Q psy4542 5 VSIKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEAELNYAQDMFE--MNQKVNPSE 82 (273)
Q Consensus 5 ~~V~lhPlvll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~--l~k~v~p~~ 82 (273)
.+|.|+|+|+++|++|+.|. .+..|+|+|+|..+++.++|++||++|+.++++.+..+.+|++.|.+ +++++++++
T Consensus 10 ~~V~Is~~allkil~Ha~~~--~p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~~~~~~~ 87 (268)
T cd08069 10 EKVYISSLALLKMLKHARAG--GPIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQTGRPE 87 (268)
T ss_pred cEEEECHHHHHHHHHHHhcc--CCceEEEEEEeeecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHHHhCCCc
Confidence 57999999999999999884 57899999999999999999999999988877777777799999999 999999999
Q ss_pred CeEEeecCCCC----CCcccHHHHHHHHhhCCCcEEEEEcCCCC--CCCcceeEEEeeecCCCC----C-----------
Q psy4542 83 LIVGWWATGDE----VTSQSSVIHDYYIRECKNPVHMTLDTNLK--GPNMGIKGYVHVPIGVPG----G----------- 141 (273)
Q Consensus 83 ~iVGWY~~g~~----~~~~~~~i~~~~~~~~~~pi~L~~D~~~~--~~~l~ikay~~~~~~~~~----~----------- 141 (273)
.+||||++++. ++..|+.+|..|++..+++|+|++||..+ +|++.++||++.+.+... .
T Consensus 88 ~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~~~~~~~~~~~~~s~~~~~~~~ 167 (268)
T cd08069 88 NVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIPPGYKPLEPRQTTSNIGHLPKP 167 (268)
T ss_pred eeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEECccccccCcccCccccCccCcH
Confidence 99999999764 89999999999999999999999999765 688999999999887542 2
Q ss_pred ------cccceeeeeceEEecCchHHHHHHHHHhhccCC
Q psy4542 142 ------KSGIMFTQIPAEVICYNSEVTGLRLLHKSIKQG 174 (273)
Q Consensus 142 ------~~~~~f~~ip~~i~~~e~E~i~v~~l~~~~~~~ 174 (273)
..+..|.+||+++..++.|+..+..+.+..+..
T Consensus 168 ~~~~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~~w~~ 206 (268)
T cd08069 168 KIEDFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNKYWVN 206 (268)
T ss_pred HHHHhCchhcEEEEeeeEEecCHHHHHHHHHHHHHhHHH
Confidence 257889999999999999999999999887754
No 11
>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain [] and PAD-1-like domain []. It has been shown that this domain occurs in prokaryotes []. Mov34 proteins act as the regulatory subunit of the 26 proteasome, which is involved in the ATP-dependent degradation of ubiquitinated proteins. The function of this domain is unclear, but it is found in the N terminus of the proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. A number of the proteins associated with this family belong to MEROPS peptidase family M67 (clan M-). This includes the Poh1 peptidase of Saccharomyces cerevisiae (Baker's yeast) which is a component of the 19S proteasome regulatory particle.; GO: 0005515 protein binding; PDB: 2ZNV_D 2ZNR_A 4E0Q_A 2P87_A 2P8R_A 2O96_B 2O95_A 3RZU_F 3RZV_A.
Probab=99.94 E-value=6.4e-27 Score=182.56 Aligned_cols=108 Identities=34% Similarity=0.587 Sum_probs=93.2
Q ss_pred CCCceEEEehhhHhHHHHHHhhccCCCceEEEEEeeeEeCC-EEEEEEEEeeccccCchhh-HhhHHHHHHHHHHHhhhC
Q psy4542 2 SLNVSIKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKG-VVEVTNCFCVPHKEYDEMV-EAELNYAQDMFEMNQKVN 79 (273)
Q Consensus 2 ~~~~~V~lhPlvll~I~dh~~r~~~~~~~v~G~LLG~~~~~-~veV~~sF~vp~~~~~~~~-~id~~~~~~m~~l~k~v~ 79 (273)
++..+|.|||+|+++|+||++|+.. .+|+|+|+|+++++ .++|++||++|+.++++.. ..+.++.++|++++++++
T Consensus 1 ~s~~~V~i~p~vll~i~~h~~r~~~--~~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (114)
T PF01398_consen 1 QSVQTVQIHPLVLLKIIDHATRSSP--NEVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVN 78 (114)
T ss_dssp -SCEEEEEEHHHHHHHHHHHHHHHC--TEEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCS
T ss_pred CCcEEEEECHHHHHHHHHHHhcCCC--CEEEEEEEEEecCceEEEEEEEEEeeEecCccccccchhhHHHHHHhhhcccc
Confidence 3678999999999999999999853 49999999999999 9999999999998765532 345666689999999999
Q ss_pred CCCCeEEeecCCCCC----CcccHHHHHHHHhhCCC
Q psy4542 80 PSELIVGWWATGDEV----TSQSSVIHDYYIRECKN 111 (273)
Q Consensus 80 p~~~iVGWY~~g~~~----~~~~~~i~~~~~~~~~~ 111 (273)
|++.+||||++++.. +..|+.+|.+|++.+++
T Consensus 79 ~~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 79 PNLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp TTSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred ccceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence 999999999997765 99999999999998764
No 12
>KOG1560|consensus
Probab=99.92 E-value=1.2e-24 Score=187.06 Aligned_cols=203 Identities=20% Similarity=0.303 Sum_probs=161.3
Q ss_pred ceEEEehhhHhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeecccc--Cchhh---HhhH---HHHHHHHHHHh
Q psy4542 5 VSIKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKE--YDEMV---EAEL---NYAQDMFEMNQ 76 (273)
Q Consensus 5 ~~V~lhPlvll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~--~~~~~---~id~---~~~~~m~~l~k 76 (273)
..|.+..||+++|++||.....+..-+.|+|+|.+-++.+|||||||.|... ++|.+ ..|. .|+..|+..++
T Consensus 13 k~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~Glvvd~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~mlrrlr 92 (339)
T KOG1560|consen 13 KRVELDSLVVMKIIKHCREEFPNGDGTQGVLLGLVVDGRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLAMLRRLR 92 (339)
T ss_pred ceeeehhHHHHHHHHHHHhhcCCcchhhheeeeeeecceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHHHHHHhh
Confidence 4788999999999999988754457899999999999999999999999743 22321 2343 68999999999
Q ss_pred hhCCCCCeEEeecC---CCCCCcccHHHHHHHHhhCCCcEEEEEcCCCC-CCCcceeEEEeeecCCC-------------
Q psy4542 77 KVNPSELIVGWWAT---GDEVTSQSSVIHDYYIRECKNPVHMTLDTNLK-GPNMGIKGYVHVPIGVP------------- 139 (273)
Q Consensus 77 ~v~p~~~iVGWY~~---g~~~~~~~~~i~~~~~~~~~~pi~L~~D~~~~-~~~l~ikay~~~~~~~~------------- 139 (273)
.+|.+...||||.+ |++++..-+..+..|+..+++.|.|+|||..+ +|.|++|||++.+..+.
T Consensus 93 ~vnid~~hVGwYqs~~vgs~lS~~lveSqy~YQ~a~pesVvliYD~~kssqG~L~lrAyrLTp~am~~~kekdwtpealk 172 (339)
T KOG1560|consen 93 YVNIDHLHVGWYQSAYVGSFLSPALVESQYAYQKAIPESVVLIYDPIKSSQGTLSLRAYRLTPEAMAAHKEKDWTPEALK 172 (339)
T ss_pred hcCccceeeeeeeeehhccccCHHHHHHHHHHHhcCCccEEEEeccccccCceEEeehhhcCHHHHHHHhcCCCCHHHHH
Confidence 99999999999988 78888766777888999999999999999987 79999999999885421
Q ss_pred --CCcccceeeeeceEEecCchHHHHHHHHH--hhccCCC-----------CCccchHHHHHHHHHHHHHHHHHHHHHHH
Q psy4542 140 --GGKSGIMFTQIPAEVICYNSEVTGLRLLH--KSIKQGA-----------VQPLSELTLVSEAADKLTVLIDHVLRYVD 204 (273)
Q Consensus 140 --~~~~~~~f~~ip~~i~~~e~E~i~v~~l~--~~~~~~~-----------~~~~~~l~~~~~a~~~L~~~l~~i~~Yl~ 204 (273)
+-+....|.++|+.|.++-.-.+-+..+. +.+.... ..+.+.++.+...+..|...+...-+|-+
T Consensus 173 ~~nltyenmfeElPIVIknS~L~nvlmseLs~~e~c~sdk~~~~~fdlgs~t~leknir~lme~vDEl~qe~~~l~kyqr 252 (339)
T KOG1560|consen 173 SANLTYENMFEELPIVIKNSHLANVLMSELSEPEDCESDKPLHSNFDLGSGTRLEKNIRLLMERVDELHQEIVNLNKYQR 252 (339)
T ss_pred hcCCCHHHHHhhcCeeeeccHHHHHHHHhccccccccccccccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 12467889999999999987777776665 3332211 12566677777777777777777777777
Q ss_pred HHh
Q psy4542 205 EVL 207 (273)
Q Consensus 205 ~V~ 207 (273)
.+.
T Consensus 253 ~~~ 255 (339)
T KOG1560|consen 253 QLA 255 (339)
T ss_pred HHH
Confidence 654
No 13
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=99.90 E-value=1.9e-22 Score=161.01 Aligned_cols=128 Identities=28% Similarity=0.426 Sum_probs=114.7
Q ss_pred eEEEehhhHhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccCchhh-HhhHHHHHHHHHHHhhhCCCCCe
Q psy4542 6 SIKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMV-EAELNYAQDMFEMNQKVNPSELI 84 (273)
Q Consensus 6 ~V~lhPlvll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~~-~id~~~~~~m~~l~k~v~p~~~i 84 (273)
.|.+||.++++|++|+.|. .+..++|+|+|...++.++|+++|++|...+++.+ ..+.+|.+.|.++++++++++.+
T Consensus 1 ~v~i~~~v~~~i~~h~~~~--~p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (135)
T smart00232 1 EVKVHPLVPLNILKHAIRD--GPEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQEYDEDYSHLMDEELKKVNKDLEI 78 (135)
T ss_pred CEEEcHHHHHHHHHHHhcC--CCcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchhhhhhhHHHHHHHHHHhhCCCceE
Confidence 4789999999999999885 57899999999998889999999999987655443 67899999999999999999999
Q ss_pred EEeecCCC----CCCcccHHHHHHHHhhCCCcEEEEEcCCCC-CCCcceeEEEeee
Q psy4542 85 VGWWATGD----EVTSQSSVIHDYYIRECKNPVHMTLDTNLK-GPNMGIKGYVHVP 135 (273)
Q Consensus 85 VGWY~~g~----~~~~~~~~i~~~~~~~~~~pi~L~~D~~~~-~~~l~ikay~~~~ 135 (273)
||||++++ .++..|+.+|..++.....++++.+|+..+ .++++++||++++
T Consensus 79 vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~~g~~~~~af~~~~ 134 (135)
T smart00232 79 VGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLTP 134 (135)
T ss_pred EEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccccCcEEEEEEEecC
Confidence 99999966 677889999999998888899999999987 4889999999864
No 14
>PF13012 MitMem_reg: Maintenance of mitochondrial structure and function; PDB: 2O96_B 2O95_A.
Probab=99.88 E-value=7.2e-24 Score=165.64 Aligned_cols=113 Identities=35% Similarity=0.479 Sum_probs=13.5
Q ss_pred CchHHHHHHHHHhhccCCC-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHhhcCCCCCHHH
Q psy4542 157 YNSEVTGLRLLHKSIKQGA-VQPLSELTLVSEAADKLTVLIDHVLRYVDEVLANRITPDNSIGRQLLDMVNSVPSMTQEQ 235 (273)
Q Consensus 157 ~e~E~i~v~~l~~~~~~~~-~~~~~~l~~~~~a~~~L~~~l~~i~~Yl~~V~~g~~~~d~~ilr~l~~~~~~lp~~~~~~ 235 (273)
+||||||++++.+...+.. .++.++++.+..++.+|.++++.+..|+++|.+|+.++|++++|+|+++|+++|.+++++
T Consensus 1 eEaErigv~~l~~~~~~~~~s~~~~~l~~~~~al~~L~~~l~~i~~Yl~~v~~g~~~~d~~i~r~l~~l~~~lp~~~~~~ 80 (115)
T PF13012_consen 1 EEAERIGVDHLARGLGDHYYSSLSSQLENEQNALKMLHKRLWQILDYLEDVISGEIPPDHEILRQLQDLLSSLPKYDPEE 80 (115)
T ss_dssp SHHHHHHHHHHHHH--S---------------------------------------------------------------
T ss_pred CchHHHHHHHHHccCCCccccHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcCCCchhHHHHHHHHHHhcccccHHH
Confidence 4899999999999766543 357799999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHh
Q psy4542 236 FETMFNSNIKDLLMIMTLSQLTKTQLLLNEKLTL 269 (273)
Q Consensus 236 f~~~~~~~~~D~lmv~yLs~ltk~~~~l~e~l~~ 269 (273)
|+++|.++.+|.+|+.|||++||++.++++++++
T Consensus 81 ~~~~~~~~~~D~l~v~yL~~l~k~~~~l~e~l~~ 114 (115)
T PF13012_consen 81 FEEEFNSEINDVLMVSYLAKLTKKQHALNELLNN 114 (115)
T ss_dssp ----------------------------------
T ss_pred HHHHHHhhchHHHHHHHHHHHhHHHHHHHHHHhc
Confidence 9999999999999999999999999999999975
No 15
>KOG1554|consensus
Probab=99.79 E-value=1.6e-18 Score=149.94 Aligned_cols=199 Identities=16% Similarity=0.237 Sum_probs=155.3
Q ss_pred ceEEEehhhHhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccCchhh---HhhHHHHHHHHHHHhhhCCC
Q psy4542 5 VSIKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMV---EAELNYAQDMFEMNQKVNPS 81 (273)
Q Consensus 5 ~~V~lhPlvll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~~---~id~~~~~~m~~l~k~v~p~ 81 (273)
..|+|..+++|+|.-|..|. ++-.++|.+.|+.+++.+.|.+||++|...++..+ .-..+|+-...+..+.+...
T Consensus 53 k~vkISalAllKm~~hA~~G--gnlEiMGlm~Gkv~g~t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k~~gr~ 130 (347)
T KOG1554|consen 53 KHVKISALALLKMVMHARSG--GNLEIMGLMQGKVDGDTIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEAKNVGRL 130 (347)
T ss_pred hhhhhHHHHHHHHHHHHhcC--CCeEEEeeecccccCCeEEEEeccccccccccceechHHHHHHHHHHHHHHHHHhhhh
Confidence 36889999999999887663 67899999999999999999999999998876533 23578999999999999999
Q ss_pred CCeEEeecC----CCCCCcccHHHHHHHHhhCCCcEEEEEcCCCC--CCCcceeEEEeeecCCCC---------------
Q psy4542 82 ELIVGWWAT----GDEVTSQSSVIHDYYIRECKNPVHMTLDTNLK--GPNMGIKGYVHVPIGVPG--------------- 140 (273)
Q Consensus 82 ~~iVGWY~~----g~~~~~~~~~i~~~~~~~~~~pi~L~~D~~~~--~~~l~ikay~~~~~~~~~--------------- 140 (273)
+.+||||++ |++++.-|+..|..-+++.++-+++++||..+ .|++.+-|||.-|.|...
T Consensus 131 envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRTyp~gyk~~d~~~seyqtipl~k 210 (347)
T KOG1554|consen 131 ENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTYPKGYKPPDEPPSEYQTIPLNK 210 (347)
T ss_pred hceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCccccccCceeeceeecccCCCCCCCCCchhhhccchhh
Confidence 999999999 56899999999988888878889999999987 799999999998876431
Q ss_pred ----CcccceeeeeceEEecCchHHHHHHHHHhhccCCC---CCccchHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4542 141 ----GKSGIMFTQIPAEVICYNSEVTGLRLLHKSIKQGA---VQPLSELTLVSEAADKLTVLIDHVLRYVDE 205 (273)
Q Consensus 141 ----~~~~~~f~~ip~~i~~~e~E~i~v~~l~~~~~~~~---~~~~~~l~~~~~a~~~L~~~l~~i~~Yl~~ 205 (273)
+..+..+..+++.+--+..++--++.+-...+-.+ .++.+..+.+...+..|.+++...-+.+..
T Consensus 211 ied~gvHck~yysl~isyfks~ld~kll~~Lwnkywv~Tlsss~ll~N~dy~~~qi~d~~ekl~q~~~~l~~ 282 (347)
T KOG1554|consen 211 IEDFGVHCKQYYSLEISYFKSSLDMKLLELLWNKYWVRTLSSSPLLKNIDYLNGQIRDLSEKLEQREDSLET 282 (347)
T ss_pred hhhcccceEEeeccchhhhhhhhhHHHHHHHHhhhhhcccccccccccchhhcchhhhHHHHHHhhhhhccc
Confidence 11233344444444444455555555554444333 347777888888888888888887777744
No 16
>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=99.69 E-value=4.7e-16 Score=120.96 Aligned_cols=111 Identities=26% Similarity=0.372 Sum_probs=88.8
Q ss_pred hHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhCCCCCeEEeecCCC--
Q psy4542 15 FQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVNPSELIVGWWATGD-- 92 (273)
Q Consensus 15 l~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~p~~~iVGWY~~g~-- 92 (273)
.+|++|+.+. .+..++|+|+|...++.++|+++|++|...++.. .+..+ -|....+.+.+++.+||||+|++
T Consensus 2 k~il~~a~~~--~~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~--~~~~~--~~~~~~~~~~~~~~iVGwyhshp~~ 75 (116)
T cd07767 2 KMFLDAAKSI--NGKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKD--DNVWF--LMYLDFKKLNAGLRIVGWYHTHPKP 75 (116)
T ss_pred HhHHHHHhcC--CCcEEEEEeEEEEcCCEEEEEEEEecccCCCCCc--cHHHH--HHHHHHHHhcCCCeEEEEEEcCCCC
Confidence 3577777663 4689999999999888999999999998664332 12111 25666677889999999999965
Q ss_pred --CCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceeEE
Q psy4542 93 --EVTSQSSVIHDYYIRECKNPVHMTLDTNLKGPNMGIKGY 131 (273)
Q Consensus 93 --~~~~~~~~i~~~~~~~~~~pi~L~~D~~~~~~~l~ikay 131 (273)
.++..|+..|..|++..+++++|++|+...+.+++++||
T Consensus 76 ~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~~~~~~~~~~~ 116 (116)
T cd07767 76 SCFLSPNDLATHELFQRYFPEKVMIIVDVKPKDLGNSWKCY 116 (116)
T ss_pred CCccCHHHHHHHHHHHHhCCCCEEEEEECCCccCCCCcccC
Confidence 378889999999998888899999999987667888887
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=99.63 E-value=9.7e-15 Score=123.09 Aligned_cols=145 Identities=15% Similarity=0.091 Sum_probs=113.5
Q ss_pred CceEEEehhhHhHHHHHHhhccCCCceEEEEEeeeEe--CCEEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhCCC
Q psy4542 4 NVSIKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVD--KGVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVNPS 81 (273)
Q Consensus 4 ~~~V~lhPlvll~I~dh~~r~~~~~~~v~G~LLG~~~--~~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~p~ 81 (273)
..+|.|++.|+|+|..|+... ...++|.|+|..+ ++.++|+++|++|...+.+.+.+|.+++.+|++..++.+
T Consensus 4 pf~V~Is~~all~m~~Ha~~~---~~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e~dp~~q~e~~~~l~~~g-- 78 (187)
T cd08067 4 PFKVTVSSNALLLMDFHCHLT---TSEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEMDPVSETEIRESLESRG-- 78 (187)
T ss_pred CEEEEECHHHHHHHHHHhcCC---CcEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccccCHHHHHHHHHHHHHcC--
Confidence 468999999999999999764 2789999999964 578999999999986655667789999999999988766
Q ss_pred CCeEEeecCCC----CCCcccHHHHHHHHhhCC-------CcEEEEEcCCCC---CCCcceeEEEeeecCCCCCccccee
Q psy4542 82 ELIVGWWATGD----EVTSQSSVIHDYYIRECK-------NPVHMTLDTNLK---GPNMGIKGYVHVPIGVPGGKSGIMF 147 (273)
Q Consensus 82 ~~iVGWY~~g~----~~~~~~~~i~~~~~~~~~-------~pi~L~~D~~~~---~~~l~ikay~~~~~~~~~~~~~~~f 147 (273)
+.+||||++.+ .++..|+..|..||...+ +.|.++++|..+ +.+-.|+||...+..-. ...-
T Consensus 79 l~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~~~~----~~~~ 154 (187)
T cd08067 79 LSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPPPEN----RPNE 154 (187)
T ss_pred CEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECCCCC----CCcc
Confidence 69999999965 567788888999987643 468999999764 34568999999864321 0123
Q ss_pred eeeceEEecC
Q psy4542 148 TQIPAEVICY 157 (273)
Q Consensus 148 ~~ip~~i~~~ 157 (273)
..+|+.+.+.
T Consensus 155 ~~~p~~~~~~ 164 (187)
T cd08067 155 YGVPMLMSYT 164 (187)
T ss_pred CCcCeEEEec
Confidence 3466666654
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=99.59 E-value=1.3e-14 Score=114.02 Aligned_cols=109 Identities=16% Similarity=0.183 Sum_probs=88.1
Q ss_pred hHhHHHHHHhhccCCCceEEEEEeeeEe-----CCEEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhCCCCCeEEe
Q psy4542 13 VLFQIVDAFERRNLDSHRVIGTLLGTVD-----KGVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVNPSELIVGW 87 (273)
Q Consensus 13 vll~I~dh~~r~~~~~~~v~G~LLG~~~-----~~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~p~~~iVGW 87 (273)
|+++|++|+.+. .+..++|.|+|... .+.++|+++|+.|...+. .+.|..+.+....++.+|||
T Consensus 2 ~~~~i~~ha~~~--~p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~~~---------~~~~~~~~~~~~~g~~~vG~ 70 (119)
T cd08058 2 ALLKMLQHAESN--TGIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCTG---------ENVEELFNVQTGRPLLVVGW 70 (119)
T ss_pred HHHHHHHHhcCC--CCeEEEEEeeeEEecCccceeEEEEeecCCCCCCchh---------HHHHHHHHHHhCCCCeEEEE
Confidence 789999999884 47899999999865 456899999999875422 11444555678899999999
Q ss_pred ecCCC----CCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceeEEEee
Q psy4542 88 WATGD----EVTSQSSVIHDYYIRECKNPVHMTLDTNLKGPNMGIKGYVHV 134 (273)
Q Consensus 88 Y~~g~----~~~~~~~~i~~~~~~~~~~pi~L~~D~~~~~~~l~ikay~~~ 134 (273)
|++.+ .++..|+..|..|+...++.++|++||..+ .+++++|+++
T Consensus 71 YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~--~~~~~a~rl~ 119 (119)
T cd08058 71 YHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHR--NKDTGIFRLT 119 (119)
T ss_pred EecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCC--CcccceEEeC
Confidence 99965 678888888888888878889999999763 8899999874
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=99.37 E-value=2.6e-11 Score=105.70 Aligned_cols=148 Identities=11% Similarity=0.179 Sum_probs=107.5
Q ss_pred ceEEEehhhHhHHHHHHhhccCCCceEEEEEeeeEe-------CCEEEEEEEEeecccc-CchhhHhhHH----HHHHHH
Q psy4542 5 VSIKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVD-------KGVVEVTNCFCVPHKE-YDEMVEAELN----YAQDMF 72 (273)
Q Consensus 5 ~~V~lhPlvll~I~dh~~r~~~~~~~v~G~LLG~~~-------~~~veV~~sF~vp~~~-~~~~~~id~~----~~~~m~ 72 (273)
.+|.|.+.++..|+.|..+. .+..+||.|+|..+ +..+.|..-++.+..+ ..+.+.+|.+ ..+.+.
T Consensus 2 ~~V~Is~~~l~~il~HA~~~--~P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea~ 79 (244)
T cd08068 2 SKVHLSADVYLVCLTHALST--EKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEAE 79 (244)
T ss_pred cEEEECHHHHHHHHHHHHhC--CCcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHHH
Confidence 47899999999999999874 68899999999874 3455554444443322 2345666654 334566
Q ss_pred HHHhhhCCCCCeEEeecCCC----CCCcccHHHHHHHHhhCCCcEEEEEcCCCC-----CCCcceeEEEeeecCCCCCcc
Q psy4542 73 EMNQKVNPSELIVGWWATGD----EVTSQSSVIHDYYIRECKNPVHMTLDTNLK-----GPNMGIKGYVHVPIGVPGGKS 143 (273)
Q Consensus 73 ~l~k~v~p~~~iVGWY~~g~----~~~~~~~~i~~~~~~~~~~pi~L~~D~~~~-----~~~l~ikay~~~~~~~~~~~~ 143 (273)
++.+.+..++.+||||++.+ .++..|+..|..|+...+..+++++++... .++..++||+..+.. + ..
T Consensus 80 ~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~g~-~--~~ 156 (244)
T cd08068 80 RLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQGN-K--AG 156 (244)
T ss_pred HHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecCCC-C--CC
Confidence 66778899999999999965 577888888888887667778999876432 367899999997521 1 12
Q ss_pred cceeeeeceEEecC
Q psy4542 144 GIMFTQIPAEVICY 157 (273)
Q Consensus 144 ~~~f~~ip~~i~~~ 157 (273)
.....++|+.|...
T Consensus 157 ~~~~~e~pl~i~~~ 170 (244)
T cd08068 157 QYERIEVPLEIVPT 170 (244)
T ss_pred cceEEEeeeEEecC
Confidence 35678899888763
No 20
>KOG1555|consensus
Probab=99.07 E-value=4.4e-10 Score=100.28 Aligned_cols=131 Identities=15% Similarity=0.265 Sum_probs=108.0
Q ss_pred CCceEEEehhhHhHHHHHHhhccCCCc-eEEEEE-ee---e-EeCCEEEEEEEEeeccccCchh---hHhhHHHHHHHHH
Q psy4542 3 LNVSIKVHPVVLFQIVDAFERRNLDSH-RVIGTL-LG---T-VDKGVVEVTNCFCVPHKEYDEM---VEAELNYAQDMFE 73 (273)
Q Consensus 3 ~~~~V~lhPlvll~I~dh~~r~~~~~~-~v~G~L-LG---~-~~~~~veV~~sF~vp~~~~~~~---~~id~~~~~~m~~ 73 (273)
.+.+|.++.++++.+++|-.-. .+. .++|.+ +| . .+..++.|.+.|+.|....+-. -++|.-|+.+|.+
T Consensus 29 ~~e~v~i~slall~m~rh~r~~--~p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg~~is~~~e~~d~V~q~q~~~ 106 (316)
T KOG1555|consen 29 EKETVYISSLALLKMLRHDRAG--SPEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAVDPVFQTQMMD 106 (316)
T ss_pred CcceeeeehhhhhhcccccccC--CchhhccceeecccccceeeecceeeeeeeccccccceecccchhccHHHHHHHHH
Confidence 4678999999999999876322 233 489999 99 3 4778899999999998875332 2589999999999
Q ss_pred HHhhhCCCCCeEEeecCC----CCCCcccHHHHHHHHhhCCCcEEEEEcCCCC-CCCcceeEEEeee
Q psy4542 74 MNQKVNPSELIVGWWATG----DEVTSQSSVIHDYYIRECKNPVHMTLDTNLK-GPNMGIKGYVHVP 135 (273)
Q Consensus 74 l~k~v~p~~~iVGWY~~g----~~~~~~~~~i~~~~~~~~~~pi~L~~D~~~~-~~~l~ikay~~~~ 135 (273)
+.++....+.+||||++. .+++..|+..|..|+...+..+..++||..+ .|+.-+.||+..+
T Consensus 107 ~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~g~vv~d~f~~In 173 (316)
T KOG1555|consen 107 LLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPYGKVVPDAFSSIN 173 (316)
T ss_pred HHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCCCCccCChhhhcC
Confidence 999999889999999994 4778899999999999988999999999877 5666666888764
No 21
>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al
Probab=99.06 E-value=4.6e-09 Score=87.64 Aligned_cols=123 Identities=12% Similarity=0.176 Sum_probs=90.2
Q ss_pred EEEehhhHhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccCchhhH-hhHHHHHHHHHHHhhhCCCCCeE
Q psy4542 7 IKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVE-AELNYAQDMFEMNQKVNPSELIV 85 (273)
Q Consensus 7 V~lhPlvll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~~~-id~~~~~~m~~l~k~v~p~~~iV 85 (273)
+.|-.-.+-+|+.|..++-..+..++|.|+|...++..+|++.|-.|...+...+. .|.. ++++. .-..++.+|
T Consensus 4 l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~~~~~~~~I~~i~~~~q~~~~~~~~~~~~~---e~~~~--~~~~gle~v 78 (173)
T cd08066 4 VVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSNNAFFITHLIIPKQSGTSDSCQTTNEE---ELFDF--QDQHDLITL 78 (173)
T ss_pred EEECHHHHHHHHHHHHhCCCCCCeEEEEEEeEcCCCeEEEEEEEeccccCCCceecCCCHH---HHHHH--HHhCCCeeE
Confidence 45666677888888877522357899999999877888999887777665544322 2321 12211 124589999
Q ss_pred EeecCCC----CCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceeEEEee-ecCC
Q psy4542 86 GWWATGD----EVTSQSSVIHDYYIRECKNPVHMTLDTNLKGPNMGIKGYVHV-PIGV 138 (273)
Q Consensus 86 GWY~~g~----~~~~~~~~i~~~~~~~~~~pi~L~~D~~~~~~~l~ikay~~~-~~~~ 138 (273)
|||+|.+ .++..|+..|..|+...+..++|+++|. ...++||++. +.|+
T Consensus 79 GwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~----~~~l~afrl~~~~g~ 132 (173)
T cd08066 79 GWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK----YNEFGIFRLTDPPGL 132 (173)
T ss_pred EEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC----CcEEeEEEeecCCcc
Confidence 9999954 6789999999999888788899999973 6789999998 6554
No 22
>cd08060 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p). This family includes Noc4p (neighbor of COX4; neighbor of Cytochrome c Oxidase 4; nucleolar complex associated 4 homolog) which belongs to the family of unknown function, UPF0172, with MPN/JAMM-like domains. Proteins in this family are homologs of the NOC4 gene which is conserved in eukaryotic members including human, dog, mouse, rat, chicken, zebrafish, fruit fly, mosquito, S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa, A.thaliana, and rice. NOC4 highly expressed in the pancreas and moderately in liver, heart, lung, kidney, brain, skeletal muscle, and placenta. This nucleolar protein forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=98.52 E-value=1.3e-06 Score=73.50 Aligned_cols=118 Identities=17% Similarity=0.213 Sum_probs=80.2
Q ss_pred ehhhHhHHHHHHhhccCCCceEEEEEeeeEe-CCEEEEEEEEeeccccCchhhHhhHHH--HHHHHHHHhhhCCCCCeEE
Q psy4542 10 HPVVLFQIVDAFERRNLDSHRVIGTLLGTVD-KGVVEVTNCFCVPHKEYDEMVEAELNY--AQDMFEMNQKVNPSELIVG 86 (273)
Q Consensus 10 hPlvll~I~dh~~r~~~~~~~v~G~LLG~~~-~~~veV~~sF~vp~~~~~~~~~id~~~--~~~m~~l~k~v~p~~~iVG 86 (273)
.+.+..+|..|..+. .+..|+|+|+|... ++.+.|++++|+.+.. +.++... ...+.+.+-+. .++.|||
T Consensus 2 s~~ay~ki~~HA~k~--p~~evcGlLlG~~~~~~~~~V~d~vPl~h~~----~~l~P~~Eval~~ve~~~~~-~gl~IvG 74 (182)
T cd08060 2 STLAYVKMLLHAAKY--PHCAVNGLLLGKKSSGGSVEITDAVPLFHSC----LALAPMLEVALALVDAYCKS-SGLVIVG 74 (182)
T ss_pred CHHHHHHHHHHHHHc--CCchheEEEEeeecCCCCEEEEEEEEcCCCc----cccCHHHHHHHHHHHHHHHH-CCCEEEE
Confidence 456788999999884 35699999999987 7789999999999852 3344332 22233333333 3799999
Q ss_pred eecCCCCCCc-----ccHHHHHHHHhhCCCcEEEEEcCCCCC---CCcceeEEEee
Q psy4542 87 WWATGDEVTS-----QSSVIHDYYIRECKNPVHMTLDTNLKG---PNMGIKGYVHV 134 (273)
Q Consensus 87 WY~~g~~~~~-----~~~~i~~~~~~~~~~pi~L~~D~~~~~---~~l~ikay~~~ 134 (273)
+|++.+.+.+ ....|=+.+.+.+++++++++|-..-. ..-.+.+|...
T Consensus 75 ~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~l~~~~~~~~~~~~~~~ 130 (182)
T cd08060 75 YYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEKLTLDCKGNALVVYKDK 130 (182)
T ss_pred EEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCccccccccCCceEEEEec
Confidence 9999875543 334455667777788999999876532 22245555554
No 23
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=98.50 E-value=9.5e-06 Score=69.05 Aligned_cols=124 Identities=17% Similarity=0.228 Sum_probs=87.1
Q ss_pred ceEEEehhhHhHHHHHHhhccCCCceEEEEEeeeEeCC--EEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhCCCC
Q psy4542 5 VSIKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKG--VVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVNPSE 82 (273)
Q Consensus 5 ~~V~lhPlvll~I~dh~~r~~~~~~~v~G~LLG~~~~~--~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~p~~ 82 (273)
.+|.+.+.+..+|+=|..+.+ ...|.|+|||...++ .|+|++|.|+=|.... ...-.+-.-.+.+.|-+. .++
T Consensus 2 ~~v~is~~AY~K~~LHaaKyP--~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~~--L~PmlEvAL~qvd~~~~~-~gl 76 (196)
T PF03665_consen 2 SSVEISSRAYAKMILHAAKYP--HCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWLS--LSPMLEVALAQVDAYAKS-NGL 76 (196)
T ss_pred ceEEEcHHHHHHHHHHhccCC--CCceeeEEEeccCCCCceEEEeeceeccccccC--cchHHHHHHHHHHHHHhh-CCC
Confidence 368999999999999998863 468999999998543 4999999999985432 222233344445555543 579
Q ss_pred CeEEeecCCCCC-----CcccHHHHHHHHhhCCCcEEEEEcCCCC---CCCcceeEEEe
Q psy4542 83 LIVGWWATGDEV-----TSQSSVIHDYYIRECKNPVHMTLDTNLK---GPNMGIKGYVH 133 (273)
Q Consensus 83 ~iVGWY~~g~~~-----~~~~~~i~~~~~~~~~~pi~L~~D~~~~---~~~l~ikay~~ 133 (273)
.|||+|+....+ ++....|=+.+.+.++.++++++|-..- .+..++.+|..
T Consensus 77 ~IvGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~kl~~~~~~~~~~~~~~ 135 (196)
T PF03665_consen 77 VIVGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKKLSSDCKAPAISVYQR 135 (196)
T ss_pred EEEEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcccccccCCCcceeeee
Confidence 999999996543 3333445566777778899999997643 23445567773
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=98.47 E-value=1.8e-06 Score=68.54 Aligned_cols=112 Identities=12% Similarity=0.055 Sum_probs=78.8
Q ss_pred hHhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccCc--hhhHhhHHHHHHHHHHHhhhCCCCCeEEeecC
Q psy4542 13 VLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYD--EMVEAELNYAQDMFEMNQKVNPSELIVGWWAT 90 (273)
Q Consensus 13 vll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~--~~~~id~~~~~~m~~l~k~v~p~~~iVGWY~~ 90 (273)
++-+|++|..+. .+..++|.|+|..++....|+..|++|....+ ..+.+|.+.+.+..+..++. ++.+||||+|
T Consensus 3 ~~~~il~ha~~~--~P~E~cGlL~G~~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~~~~~~~--g~~~vG~~HS 78 (128)
T cd08070 3 LLEAILAHAEAE--YPEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEIDPAEQLAAQREARER--GLEVVGIYHS 78 (128)
T ss_pred HHHHHHHHHHhC--CCCceEEEEEeecCCCCceEEEEEEccCCCCCCCceEEECHHHHHHHHHHHHHC--CCeEEEEEeC
Confidence 456788888774 57899999999987666677899999875543 35567877777766666544 6999999999
Q ss_pred CCC----CCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceeEEEeee
Q psy4542 91 GDE----VTSQSSVIHDYYIRECKNPVHMTLDTNLKGPNMGIKGYVHVP 135 (273)
Q Consensus 91 g~~----~~~~~~~i~~~~~~~~~~pi~L~~D~~~~~~~l~ikay~~~~ 135 (273)
.+. ++..|.... . ....+++++..... ...+++|....
T Consensus 79 HP~~~~~PS~~D~~~~--~---~~~~~~lIv~~~~~--~~~~~~~~~~~ 120 (128)
T cd08070 79 HPDGPARPSETDLRLA--W---PPGVSYLIVSLAGG--APELRAWRLEG 120 (128)
T ss_pred CCCCCCCCCHHHHHhc--c---CCCCeEEEEECCCC--CcEEEEEEEcC
Confidence 764 344443321 1 12467888876543 56789999863
No 25
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=98.12 E-value=2.2e-05 Score=62.75 Aligned_cols=101 Identities=18% Similarity=0.255 Sum_probs=64.5
Q ss_pred EEEehhhHhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccC--chhhHhhHHHHHHHHHHHhhhCCCCCe
Q psy4542 7 IKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEY--DEMVEAELNYAQDMFEMNQKVNPSELI 84 (273)
Q Consensus 7 V~lhPlvll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~--~~~~~id~~~~~~m~~l~k~v~p~~~i 84 (273)
+.+-..++-.|+.|..|. .+..++|.|.|...+ ...|+++.... .+...++.++.. +....+.. ++.+
T Consensus 2 ~~i~~~~l~~il~~a~~~--~p~E~~g~l~~~~~~-----~~~~~~~n~~~~~~~~~~~~~~~~~-~~~~~~~~--g~~v 71 (134)
T COG1310 2 LVIPKEVLGAILEHARRE--HPREVCGLLAGTREG-----ERYFPLKNVSVEPVEYFEIDPEYSL-FYLAAEDA--GEVV 71 (134)
T ss_pred ceecHHHHHHHHHHHHhc--CChheEEEEEeeccc-----ceeeccccccCCcceeEeeCHHHHH-HHHHHhhC--CCEE
Confidence 346677888999999885 468999999999876 44555554332 112234455444 33333333 3999
Q ss_pred EEeecCCCC--CCcccHHHHHHHHhhCCCcEEEEEcC
Q psy4542 85 VGWWATGDE--VTSQSSVIHDYYIRECKNPVHMTLDT 119 (273)
Q Consensus 85 VGWY~~g~~--~~~~~~~i~~~~~~~~~~pi~L~~D~ 119 (273)
||||+|++. ...++..++ +++..+.|.+++..+
T Consensus 72 vg~yHSHP~~~~~pS~~D~~--~~~~~~~~~~iv~~~ 106 (134)
T COG1310 72 VGWYHSHPGGPPYPSEADRR--LSKLGPLPWLIVSVP 106 (134)
T ss_pred EEEEcCCCCCCCCcCHHHHh--hccccCCCEEEEEcC
Confidence 999999773 334444444 677767777776654
No 26
>KOG3289|consensus
Probab=97.71 E-value=0.00091 Score=55.13 Aligned_cols=122 Identities=16% Similarity=0.224 Sum_probs=86.8
Q ss_pred eEEEehhhHhHHHHHHhhccCCCceEEEEEeee--EeCCEEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhCCCCC
Q psy4542 6 SIKVHPVVLFQIVDAFERRNLDSHRVIGTLLGT--VDKGVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVNPSEL 83 (273)
Q Consensus 6 ~V~lhPlvll~I~dh~~r~~~~~~~v~G~LLG~--~~~~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~p~~~ 83 (273)
.|++..++..+|+=|+.|.+ ...|-|.|+|. ..|+.++|++|.|+=|+.. .+..-.|-...|++-+- +--.+.
T Consensus 3 ~veis~~aY~kmiLH~akyp--h~aVnGLLla~~~~kg~~v~itdcVPLfH~~l--aLaPmlEvAl~lId~~~-~~~Glv 77 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYP--HAAVNGLLLAPATGKGECVEITDCVPLFHSHL--ALAPMLEVALNLIDVWG-AQAGLV 77 (199)
T ss_pred ceeehhhHHHHHHHHhccCc--ccceeeEEEeccCCCCCeEEEEecchhhcccc--ccccHHHHHHHHHHHHH-HhcCeE
Confidence 57889999999999999963 46899999994 5678999999999977642 12223344444555443 345899
Q ss_pred eEEeecCCCCCCcc-----cHHHHHHHHhhCCCcEEEEEcCCC-C-C-CCcceeEEE
Q psy4542 84 IVGWWATGDEVTSQ-----SSVIHDYYIRECKNPVHMTLDTNL-K-G-PNMGIKGYV 132 (273)
Q Consensus 84 iVGWY~~g~~~~~~-----~~~i~~~~~~~~~~pi~L~~D~~~-~-~-~~l~ikay~ 132 (273)
|+|.|++...+++. -..|-+.++++.+++.++++|-.. . + ..-|+-+|+
T Consensus 78 iaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~~l~~~~e~~~v~v~e 134 (199)
T KOG3289|consen 78 IAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNKKLVPQCERPPVIVLE 134 (199)
T ss_pred EEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEeccccccccCCCCEEEee
Confidence 99999997655432 244667788888877767766543 2 2 446888888
No 27
>cd08056 MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8. Members of this family are found in pre-mRNA-processing factor 8 (Prp8) which is a critical splicing factor, interacting with several other spliceosomal proteins, snRNAs, and the pre-mRNA, thus organizing and stabilizing the spliceosome catalytic core. Prp8 is one of the largest and most highly conserved of nuclear proteins, occupying a central position in the catalytic core of the spliceosome. Its C-terminal domain exhibits a JAB1/MPN-like core similar to deubiquitinating enzymes, but does not show catalytic isopeptidase activity, possibly because the putative isopeptidase center is covered by insertions and terminal appendices that are grafted onto this core, thus impairing the metal binding site. It is proposed that this domain is a protein interaction domain instead of a Zn(2+)-dependent metalloenzyme as proposed for some MPN proteins. The DEAD-box protein Brr2 and t
Probab=97.07 E-value=0.0025 Score=56.05 Aligned_cols=102 Identities=18% Similarity=0.248 Sum_probs=70.8
Q ss_pred CceEEEEEeeeEe---CCEEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhCCCCCeEEeecCCC----CCCcccHH
Q psy4542 28 SHRVIGTLLGTVD---KGVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVNPSELIVGWWATGD----EVTSQSSV 100 (273)
Q Consensus 28 ~~~v~G~LLG~~~---~~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~p~~~iVGWY~~g~----~~~~~~~~ 100 (273)
+..++|.|.|... .+.-||+.....|...+.+.+.+..+- -.+ +---++..|||=+|.+ .+++.|+.
T Consensus 55 rtQ~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~~-----~~~-~~l~~Le~LGWIHTqp~e~~~Lss~Dv~ 128 (252)
T cd08056 55 RTQIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQL-----PQH-EYLEDLEPLGWIHTQPNELPQLSPQDVT 128 (252)
T ss_pred cceEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCccC-----ccc-hhhCCCEeeEEEEcCCCCccccCHHHHH
Confidence 3589999999953 356688877777877655544321110 111 1134688999999953 67889999
Q ss_pred HHHHHHhhCC-----CcEEEEEcCCCCCCCcceeEEEeeecC
Q psy4542 101 IHDYYIRECK-----NPVHMTLDTNLKGPNMGIKGYVHVPIG 137 (273)
Q Consensus 101 i~~~~~~~~~-----~pi~L~~D~~~~~~~l~ikay~~~~~~ 137 (273)
.|..|+...+ +.|.+++- ++.|...+.||.+++.|
T Consensus 129 tha~~~~~~~~w~~~~~V~it~S--ftpGs~sl~ay~LT~~G 168 (252)
T cd08056 129 THAKILADNPSWDGEKTVILTCS--FTPGSCSLTAYKLTPEG 168 (252)
T ss_pred HHHHHHHhccccCCCcEEEEEEc--CCCCceEEEEEecCHHH
Confidence 9999988775 45555554 34678999999998765
No 28
>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=97.01 E-value=0.0089 Score=47.53 Aligned_cols=104 Identities=13% Similarity=0.114 Sum_probs=65.2
Q ss_pred hHhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccC-c--hhhHhhHHHHHHHHH-HHhhhCCCCCeEEee
Q psy4542 13 VLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEY-D--EMVEAELNYAQDMFE-MNQKVNPSELIVGWW 88 (273)
Q Consensus 13 vll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~-~--~~~~id~~~~~~m~~-l~k~v~p~~~iVGWY 88 (273)
+++++...|......+....|+|+|...+..+.|+.+- .|...+ . ..+..+.+.+++.++ .+++.+-....||=+
T Consensus 1 ~v~~~~~~~~Q~~~~~~EtGGiLiG~~~~~~~ii~~~t-~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylGeW 79 (131)
T TIGR02256 1 VVVAMLKSYRQWHDLSTETGGVLIGERRGAHAVITKIS-EPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGEW 79 (131)
T ss_pred CHHHHHHHHHhCcCCCCccceEEEEEEcCCcEEEEEEE-cCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEEec
Confidence 46777888877666678999999999987777787744 443332 1 133446666666554 455566669999999
Q ss_pred cCCCC----CCcccHHHHHHHHhhCCCcEEEEE
Q psy4542 89 ATGDE----VTSQSSVIHDYYIRECKNPVHMTL 117 (273)
Q Consensus 89 ~~g~~----~~~~~~~i~~~~~~~~~~pi~L~~ 117 (273)
+|.+. ++..|...-....+..+..+++++
T Consensus 80 HtHP~~~p~PS~~D~~~~~~~~~~~~~~l~iIv 112 (131)
T TIGR02256 80 HTHPEDQPEPSWTDRRSWRTIIRSPEAMLLLIV 112 (131)
T ss_pred CcCCCCCCCCCHHHHHHHHHHHhCCCeeEEEEE
Confidence 99764 334444333333333334445554
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=96.61 E-value=0.035 Score=43.26 Aligned_cols=99 Identities=17% Similarity=0.183 Sum_probs=62.1
Q ss_pred hHhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccCchhhH-hhHHHHHHHHHHHhhhCCCCCeEEeecCC
Q psy4542 13 VLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVE-AELNYAQDMFEMNQKVNPSELIVGWWATG 91 (273)
Q Consensus 13 vll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~~~-id~~~~~~m~~l~k~v~p~~~iVGWY~~g 91 (273)
.+-.|.+|..+. .+..++|.|+|... .|++.+++|....++... .+.+ |. -.+..++|-|++.
T Consensus 5 ~~~~i~~ha~~~--~P~E~CGlL~G~~~----~v~~~~~~~n~~~~~~~~~f~~~----~~------~~g~~ivgi~HSH 68 (117)
T cd08072 5 LLDSILEAAKSS--HPNEFAALLRGKDG----VITELLILPGTESGEVSAVFPLL----ML------PLDMSIVGSVHSH 68 (117)
T ss_pred HHHHHHHHHhhc--CCceEEEEEEeecc----EEEEEEECCCCCCCCcceeechH----Hh------cCCCeEEEEEEcC
Confidence 345678888764 58899999999764 588999999654432111 1221 11 2489999999997
Q ss_pred CC----CCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceeEEEee
Q psy4542 92 DE----VTSQSSVIHDYYIRECKNPVHMTLDTNLKGPNMGIKGYVHV 134 (273)
Q Consensus 92 ~~----~~~~~~~i~~~~~~~~~~pi~L~~D~~~~~~~l~ikay~~~ 134 (273)
+. ++..|.. ++.. +..+++++.... +.-.++||...
T Consensus 69 P~~~~~PS~~D~~----~~~~-~~~~~lIvs~~~--~~~~~~a~~~~ 108 (117)
T cd08072 69 PSGSPRPSDADLS----FFSK-TGLVHIIVGYPY--DEDDWRAYDSD 108 (117)
T ss_pred CCCCCCCCHHHHH----hhhc-CCCEEEEEECcC--CCCCEEEEecC
Confidence 63 4445432 2222 345677776432 22468899875
No 30
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=95.96 E-value=0.075 Score=39.89 Aligned_cols=66 Identities=23% Similarity=0.211 Sum_probs=41.9
Q ss_pred hHhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhCCCCCeEEeecCCC
Q psy4542 13 VLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVNPSELIVGWWATGD 92 (273)
Q Consensus 13 vll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~p~~~iVGWY~~g~ 92 (273)
++-.|.+|..+. .+...+|.|+|...+..+.++......-. +.+..... +....+..+||+|+|.+
T Consensus 4 ~~~~i~~~~~~~--~p~E~~G~L~g~~~~~~~~~~~~~~~~p~---~~~~~~~~---------~~~~~~~~~vg~~HSHP 69 (104)
T PF14464_consen 4 VLEQIIAHARAA--YPNEACGLLLGRRDDQRFIVVPNVNPDPR---DSFRRERF---------EARERGLEIVGIWHSHP 69 (104)
T ss_dssp HHHHHHHHHHHH--TTS-EEEEEEEEEECCEEEEEEEEE--HH---CHHHHHH----------HHHHHT-EEEEEEEEES
T ss_pred HHHHHHHHHhhC--CCCeEEEEEEEEecCCEEEEEeCCCCCcH---HHHHHHhh---------hhhcccceeeEEEEcCC
Confidence 455677777665 57899999999997777777776652111 11111111 45567899999999955
No 31
>cd08061 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain. Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=92.48 E-value=0.86 Score=40.88 Aligned_cols=108 Identities=14% Similarity=0.135 Sum_probs=69.8
Q ss_pred CceEEEEEeeeEeC-------CEEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhCCCCCeEEeecCCC--------
Q psy4542 28 SHRVIGTLLGTVDK-------GVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVNPSELIVGWWATGD-------- 92 (273)
Q Consensus 28 ~~~v~G~LLG~~~~-------~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~p~~~iVGWY~~g~-------- 92 (273)
...-+|.|.|+.+. .++.|.--|+=|...+.+.+.+..+-..+..+... ..-.+..|||=-|..
T Consensus 33 ~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~iA-~~lGL~~VG~IfT~l~~~~~d~~ 111 (274)
T cd08061 33 GQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAIA-AALGLERVGWIFTDLPREDKDGY 111 (274)
T ss_pred cceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhHHHHHH-HHcCCeEEEEEEecCCCCCCCce
Confidence 35678999999743 48899999998887665544433222222233322 345799999987743
Q ss_pred CCCcccHHHHHHHHh-----hCC-CcEEEEEcCCCCCCCcceeEEEeeecC
Q psy4542 93 EVTSQSSVIHDYYIR-----ECK-NPVHMTLDTNLKGPNMGIKGYVHVPIG 137 (273)
Q Consensus 93 ~~~~~~~~i~~~~~~-----~~~-~pi~L~~D~~~~~~~l~ikay~~~~~~ 137 (273)
.++..++.....+|. ... +-+-+++.+.. ++.+.+.||..++..
T Consensus 112 ~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~-~g~i~~~ayQvSdq~ 161 (274)
T cd08061 112 FLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDK-DGQIHFEAYQVSDQA 161 (274)
T ss_pred eECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCC-CCceeeeeeeecHHH
Confidence 345555555566663 223 33557777765 478999999998753
No 32
>cd08073 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains. This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=91.97 E-value=1.5 Score=33.48 Aligned_cols=63 Identities=13% Similarity=0.031 Sum_probs=39.0
Q ss_pred hHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccC--chhhHhhHH-HHHHHHHHHhhhCCCCCeEEeecCC
Q psy4542 15 FQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEY--DEMVEAELN-YAQDMFEMNQKVNPSELIVGWWATG 91 (273)
Q Consensus 15 l~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~--~~~~~id~~-~~~~m~~l~k~v~p~~~iVGWY~~g 91 (273)
-.|.+|..+. .+...+|.|+|.. .++..|+++.... ...+.+|.+ +.+-+ + ...+||.|++.
T Consensus 4 ~~i~~ha~~~--~P~E~CGll~g~~-----~~~~~~p~~N~~~~p~~~F~idp~e~~~a~----~----~~~ivgi~HSH 68 (108)
T cd08073 4 DAILAHAKAE--YPREACGLVVRKG-----RKLRYIPCRNIAADPEEHFEISPEDYAAAE----D----EGEIVAVVHSH 68 (108)
T ss_pred HHHHHHHhHC--CCCcceEEEEecC-----CceEEEECccCCCCccceEEeCHHHHHHHh----c----CCCEEEEEEcC
Confidence 3677777664 5789999999966 2344566653221 134566653 33222 1 33899999997
Q ss_pred C
Q psy4542 92 D 92 (273)
Q Consensus 92 ~ 92 (273)
+
T Consensus 69 P 69 (108)
T cd08073 69 P 69 (108)
T ss_pred C
Confidence 5
No 33
>KOG2880|consensus
Probab=86.17 E-value=0.47 Score=43.58 Aligned_cols=96 Identities=16% Similarity=0.204 Sum_probs=66.1
Q ss_pred CceEEEEEeeeEeCCEEEEEEEEeecccc-Cchhh-HhhHHHHHHHHHHHh-hhCCCCCeEEeecCCC----CCCcccHH
Q psy4542 28 SHRVIGTLLGTVDKGVVEVTNCFCVPHKE-YDEMV-EAELNYAQDMFEMNQ-KVNPSELIVGWWATGD----EVTSQSSV 100 (273)
Q Consensus 28 ~~~v~G~LLG~~~~~~veV~~sF~vp~~~-~~~~~-~id~~~~~~m~~l~k-~v~p~~~iVGWY~~g~----~~~~~~~~ 100 (273)
+-..||+|-|.-..|..-||+-. +|..+ +.|.+ ..+.+ ++|. +---++-.+||-+|.+ ++++.|+.
T Consensus 275 nlETCGiL~g~L~~n~f~IThli-iPkQeatsd~C~t~nee------elF~vQdq~~L~tlGWIHTHPTQt~FmSSVDlH 347 (424)
T KOG2880|consen 275 NLETCGILAGKLERNEFYITHLI-IPKQEATSDSCNTMNEE------ELFEVQDQHELLTLGWIHTHPTQTCFMSSVDLH 347 (424)
T ss_pred cchHHHHhhhHhhcCcEEEEEEE-eecccCCCccccccCHH------HHheecccccceeeeeeecCCccchhheecccc
Confidence 35789999999888899998765 45444 33311 11111 1221 2224677899999965 67888899
Q ss_pred HHHHHHhhCCCcEEEEEcCCCCCCCcceeEEEee
Q psy4542 101 IHDYYIRECKNPVHMTLDTNLKGPNMGIKGYVHV 134 (273)
Q Consensus 101 i~~~~~~~~~~pi~L~~D~~~~~~~l~ikay~~~ 134 (273)
.|-.||-..+.+|+++.-|...+ --.|++.
T Consensus 348 THcSYQiMlPEAiAIV~aPk~~~----tGiFrLt 377 (424)
T KOG2880|consen 348 THCSYQIMLPEAIAIVCAPKSKT----TGIFRLT 377 (424)
T ss_pred ccceeeeecchheeEEeccccCC----cceEEec
Confidence 99999988888999999887542 2367776
No 34
>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=83.13 E-value=8.2 Score=35.20 Aligned_cols=103 Identities=12% Similarity=0.091 Sum_probs=60.7
Q ss_pred EEEEeeeEeC-------CEEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhCCCCCeEEeecCCCC-----------
Q psy4542 32 IGTLLGTVDK-------GVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVNPSELIVGWWATGDE----------- 93 (273)
Q Consensus 32 ~G~LLG~~~~-------~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~p~~~iVGWY~~g~~----------- 93 (273)
+|.|.|+.+. -++.|.--|+=|...+.+.+.+..+-.++..+... ..-++..|||=-|...
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA-~~lGL~rVG~IfTdl~~~~~~~g~v~~ 80 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIA-SALGLERVGWIFTDLTDDGSGDGTVKC 80 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHH-HHCCCEEEEEEEecCcccccCCCceee
Confidence 7999999742 27899999999987665544432222222222222 1228999999877422
Q ss_pred --------CCcccHHHHHHHHhhCC------------C-cEEEEEcCCCCCCCcceeEEEeeec
Q psy4542 94 --------VTSQSSVIHDYYIRECK------------N-PVHMTLDTNLKGPNMGIKGYVHVPI 136 (273)
Q Consensus 94 --------~~~~~~~i~~~~~~~~~------------~-pi~L~~D~~~~~~~l~ikay~~~~~ 136 (273)
++...+..=..+|...+ + -|-+++.+. .++.+.+.||..++.
T Consensus 81 ~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~-~~g~i~~~ayQvS~q 143 (306)
T PF05021_consen 81 KRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGD-EEGEIHFEAYQVSNQ 143 (306)
T ss_pred ccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCC-CCCceeeEEeeehHH
Confidence 33333333333443221 2 245666653 468899999999874
No 35
>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic. This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=81.82 E-value=6.7 Score=29.16 Aligned_cols=70 Identities=11% Similarity=0.069 Sum_probs=42.5
Q ss_pred HHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhCCCCCeEEeecCCC---
Q psy4542 16 QIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVNPSELIVGWWATGD--- 92 (273)
Q Consensus 16 ~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~p~~~iVGWY~~g~--- 92 (273)
.|.+|+.+. .+...+|+|+|...+ .+.+..++|.... ..+..+ ......-+..+||-|++.+
T Consensus 5 ~i~~~~~~~--~p~E~~gll~~~~~~---~~~~~~~~~~~~~----~~~~~~------~~~a~~~~~~~v~i~HsHP~g~ 69 (101)
T cd08059 5 TILVHAKDA--HPDEFCGFLSGSKDN---VMDELIFLPFVSG----SVSAVI------DLAALEIGMKVVGLVHSHPSGS 69 (101)
T ss_pred HHHHHHHhc--CChhhheeeecCCCC---eEEEEEeCCCcCC----ccChHH------HHHHhhCCCcEEEEEecCcCCC
Confidence 345555443 367899999997643 5777788875431 122222 2233445778999999955
Q ss_pred -CCCcccHH
Q psy4542 93 -EVTSQSSV 100 (273)
Q Consensus 93 -~~~~~~~~ 100 (273)
.++..|..
T Consensus 70 ~~PS~~D~~ 78 (101)
T cd08059 70 CRPSEADLS 78 (101)
T ss_pred CCCCHHHHH
Confidence 45555544
No 36
>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=73.42 E-value=1.6 Score=30.10 Aligned_cols=12 Identities=33% Similarity=0.753 Sum_probs=7.5
Q ss_pred CCCeEEeecCCC
Q psy4542 81 SELIVGWWATGD 92 (273)
Q Consensus 81 ~~~iVGWY~~g~ 92 (273)
+-.+||||+|.-
T Consensus 39 qg~vvgwy~t~l 50 (78)
T PF06442_consen 39 QGQVVGWYCTKL 50 (78)
T ss_dssp EEEEEEEE--SS
T ss_pred cceEeEEEeccc
Confidence 357999999853
No 37
>TIGR03735 PRTRC_A PRTRC system protein A. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.
Probab=67.56 E-value=20 Score=30.36 Aligned_cols=104 Identities=8% Similarity=-0.022 Sum_probs=59.9
Q ss_pred ehhhHhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccC-chhhHhhHHHHHHHHHHHhhhCCCCCeEEee
Q psy4542 10 HPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEY-DEMVEAELNYAQDMFEMNQKVNPSELIVGWW 88 (273)
Q Consensus 10 hPlvll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~-~~~~~id~~~~~~m~~l~k~v~p~~~iVGWY 88 (273)
-.-.+=.|+.|+.+. .+..++|.+.|..+++.. ..+++...+. .+.+..|.. | -..++.+|+-|
T Consensus 76 p~~l~~~ii~hAr~~--~P~EacG~Iag~~~~~~~---r~~p~~N~~~Sp~~~~~d~~----~------~~~ge~lV~iy 140 (192)
T TIGR03735 76 PASLLEEFAEAARAA--LPNEVAAWIVWNSETGSL---RLAALESIEASPGHIDYRRP----R------LDDGEHLVVDL 140 (192)
T ss_pred CHHHHHHHHHHHHhc--CCcceEEEEEEcCCCCEE---EEEeccccccCCceEEEcch----H------HhCCCeEEEEE
Confidence 344566788888774 578999999997544443 4477765432 233344443 1 26789999999
Q ss_pred cCCC----CCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceeEEEeee
Q psy4542 89 ATGD----EVTSQSSVIHDYYIRECKNPVHMTLDTNLKGPNMGIKGYVHVP 135 (273)
Q Consensus 89 ~~g~----~~~~~~~~i~~~~~~~~~~pi~L~~D~~~~~~~l~ikay~~~~ 135 (273)
++.+ .++..|.. ....+-.++.++-.- +.+-|--+||+.-
T Consensus 141 HSH~~spA~PS~tD~~-----Dd~~~~k~~~ViG~~--~~~~p~~~~Rl~~ 184 (192)
T TIGR03735 141 HSHGTGSAFFSETDDA-----DDKGEVKISGVLGCL--DQGTPQAVFRLCL 184 (192)
T ss_pred cCCCCCCCCCCcccch-----hhcCceEEEEEEEec--CCCCceEEEEEEe
Confidence 9965 34444432 111123566666332 2223445566543
No 38
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=63.89 E-value=38 Score=31.56 Aligned_cols=61 Identities=13% Similarity=0.244 Sum_probs=44.9
Q ss_pred EEEeeeE-eCCEEEEEEEEeeccccCchh-----------hHhhHHHHHHHHHHHhhhCC-CCCeEEeecCCCC
Q psy4542 33 GTLLGTV-DKGVVEVTNCFCVPHKEYDEM-----------VEAELNYAQDMFEMNQKVNP-SELIVGWWATGDE 93 (273)
Q Consensus 33 G~LLG~~-~~~~veV~~sF~vp~~~~~~~-----------~~id~~~~~~m~~l~k~v~p-~~~iVGWY~~g~~ 93 (273)
|.|+|.. .++.--|.+..+.|..+++++ -.+|.++..+--.+-.+--| ...|||.|..++.
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 666677888889998765433 14788888776655555555 5789999998753
No 39
>KOG1795|consensus
Probab=58.29 E-value=18 Score=38.99 Aligned_cols=117 Identities=17% Similarity=0.249 Sum_probs=71.3
Q ss_pred hHHHHHHhhccCCCceEEEEEeeeE--eCCEEEEEEEEee-ccccCchhhHhhHHHHHHHHHHHhhhCCCCCeEEeecCC
Q psy4542 15 FQIVDAFERRNLDSHRVIGTLLGTV--DKGVVEVTNCFCV-PHKEYDEMVEAELNYAQDMFEMNQKVNPSELIVGWWATG 91 (273)
Q Consensus 15 l~I~dh~~r~~~~~~~v~G~LLG~~--~~~~veV~~sF~v-p~~~~~~~~~id~~~~~~m~~l~k~v~p~~~iVGWY~~g 91 (273)
.||++-+-+...-...+.|.+.|.. +..+|.=..||.+ |.-.+-..+.+- .+.- -..+--+.+.+||-+|.
T Consensus 2101 kNllkkFi~isD~r~qiag~~yG~s~~d~pqvkeIr~ivmvPQ~gs~~~v~lp-~~lP-----~~~~l~d~e~Lgw~hTq 2174 (2321)
T KOG1795|consen 2101 KNLLKKFITISDLRTQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGSHQGVHLP-SFLP-----IHGVLEDLEPLGWIHTQ 2174 (2321)
T ss_pred HHHHhhheeecchhhhhheeeeccCCCCCCccceEEEEEeccccccccccccC-ccCC-----cchhccCCcccchhhcC
Confidence 3555556554322457899999984 4455633355554 543321111110 0000 12345678899999996
Q ss_pred C----CCCcccHHHHHHHHhhCC-CcEEEEEcCCCCCCCcceeEEEeeecCCC
Q psy4542 92 D----EVTSQSSVIHDYYIRECK-NPVHMTLDTNLKGPNMGIKGYVHVPIGVP 139 (273)
Q Consensus 92 ~----~~~~~~~~i~~~~~~~~~-~pi~L~~D~~~~~~~l~ikay~~~~~~~~ 139 (273)
+ .+++.++.+|..+..... ..|.+.+ +.+-|..++.||.+++.|..
T Consensus 2175 ~~el~~lsp~dV~th~ki~~~~k~k~i~~t~--~~tpgs~sl~ay~lt~~G~e 2225 (2321)
T KOG1795|consen 2175 PNELPQLSPQDVTTHAKILVDNKEKCIIITC--SFTPGSCSLTAYKLTPSGYE 2225 (2321)
T ss_pred ccccccCCHHHhhhhhhhhhcCccceEEEEe--eccCCcceeeeeccCccccc
Confidence 4 578889999987765443 4565554 34458899999999987754
No 40
>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=38.68 E-value=44 Score=19.84 Aligned_cols=30 Identities=20% Similarity=0.432 Sum_probs=19.0
Q ss_pred HHHHHHHHhcCCCCCChHHHHHHHHHhhcCC
Q psy4542 199 VLRYVDEVLANRITPDNSIGRQLLDMVNSVP 229 (273)
Q Consensus 199 i~~Yl~~V~~g~~~~d~~ilr~l~~~~~~lp 229 (273)
++.++++... +-....+|...+.+.|+.+|
T Consensus 10 ~v~~i~~~l~-~~~t~~~I~~~l~~~C~~lP 39 (39)
T PF05184_consen 10 VVKEIEKLLK-NNKTEEEIKKALEKACNKLP 39 (39)
T ss_dssp HHHHHHHHHH-STCHHHHHHHHHHHHHTTSC
T ss_pred HHHHHHHHHH-cCccHHHHHHHHHHHHhhCc
Confidence 4444554443 22335688888888888887
No 41
>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=30.56 E-value=91 Score=16.48 Aligned_cols=11 Identities=36% Similarity=0.610 Sum_probs=8.5
Q ss_pred hHHHHHHHHHh
Q psy4542 215 NSIGRQLLDMV 225 (273)
Q Consensus 215 ~~ilr~l~~~~ 225 (273)
++||+++...|
T Consensus 1 ~~IG~kla~MC 11 (21)
T PF11430_consen 1 HEIGTKLAAMC 11 (21)
T ss_dssp HHHHHHHHHHH
T ss_pred CcHHHHHHHHH
Confidence 46888888776
No 42
>KOG2834|consensus
Probab=30.48 E-value=53 Score=31.57 Aligned_cols=75 Identities=19% Similarity=0.208 Sum_probs=46.1
Q ss_pred hHHHHHHhhccC-CCceEEEEEeeeE-eCCEE------EEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhCCCCCeEE
Q psy4542 15 FQIVDAFERRNL-DSHRVIGTLLGTV-DKGVV------EVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVNPSELIVG 86 (273)
Q Consensus 15 l~I~dh~~r~~~-~~~~v~G~LLG~~-~~~~v------eV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~p~~~iVG 86 (273)
-++.+||.+.+. ....-+|-|.|.. +.+.| +|.--|+=|.....|.+.+.++=-....+.- ...-.+..||
T Consensus 182 ~~~v~~Fl~~wr~sg~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~~~~dgl~l~~~~e~~~vD~~-a~~lGLrRVG 260 (510)
T KOG2834|consen 182 AELVNHFLNEWRASGVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQHGEEDGLELLEDDEAKRVDAI-AEGLGLRRVG 260 (510)
T ss_pred hHHHHHHHHHHHHhhhhhcceEEEeecccccccccceeeEEEEecCCccCCcCCeEEeccchhhhHHHH-HHhcCceeeE
Confidence 356778877642 2346689999997 45566 8988899887665555444311111112221 1345788999
Q ss_pred eecC
Q psy4542 87 WWAT 90 (273)
Q Consensus 87 WY~~ 90 (273)
|--|
T Consensus 261 ~IFT 264 (510)
T KOG2834|consen 261 WIFT 264 (510)
T ss_pred EEEe
Confidence 9866
No 43
>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=29.85 E-value=1.1e+02 Score=19.33 Aligned_cols=38 Identities=5% Similarity=0.100 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHhh
Q psy4542 189 ADKLTVLIDHVLRYVDEVLANRITPDNSIGRQLLDMVN 226 (273)
Q Consensus 189 ~~~L~~~l~~i~~Yl~~V~~g~~~~d~~ilr~l~~~~~ 226 (273)
.+.|-+++..=..++.+..+|+..++.+.+..|...+.
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~ 49 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKRNPSLDTLKKIAKALG 49 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHT
T ss_pred HHHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHC
Confidence 35666777777788888999999999999999998876
No 44
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=26.55 E-value=85 Score=21.00 Aligned_cols=26 Identities=23% Similarity=0.271 Sum_probs=21.5
Q ss_pred CchhhHhhHHHHHHHHHHHhhhCCCC
Q psy4542 57 YDEMVEAELNYAQDMFEMNQKVNPSE 82 (273)
Q Consensus 57 ~~~~~~id~~~~~~m~~l~k~v~p~~ 82 (273)
+.+.|.-|.+++.+....+|+||-++
T Consensus 27 S~ehw~~D~e~H~~~c~~LRqvNede 52 (55)
T PF13824_consen 27 SEEHWEDDYEEHRQLCERLRQVNEDE 52 (55)
T ss_pred CHHHHHHhHHHHHHHHHHHHHhcccc
Confidence 34577888899999999999999765
No 45
>KOG0130|consensus
Probab=23.29 E-value=1.1e+02 Score=24.60 Aligned_cols=53 Identities=26% Similarity=0.443 Sum_probs=35.2
Q ss_pred hCCCCCeEEeecC--CCCCCcccHHHHHHHHhhCC-CcEEEEEcCCCCCCCcceeEEEee
Q psy4542 78 VNPSELIVGWWAT--GDEVTSQSSVIHDYYIRECK-NPVHMTLDTNLKGPNMGIKGYVHV 134 (273)
Q Consensus 78 v~p~~~iVGWY~~--g~~~~~~~~~i~~~~~~~~~-~pi~L~~D~~~~~~~l~ikay~~~ 134 (273)
-.|+-.+=||-.. |-..-...-.||+.|+.+.+ ..|||-+|-.. --+|.|.+.
T Consensus 64 pgPqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRt----Gy~KGYaLv 119 (170)
T KOG0130|consen 64 PGPQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRT----GYVKGYALV 119 (170)
T ss_pred CCCccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeecccccc----ccccceeee
Confidence 3589999999754 43322334578999998876 45899988642 134555554
No 46
>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=23.20 E-value=1.5e+02 Score=19.45 Aligned_cols=39 Identities=8% Similarity=0.140 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHhh
Q psy4542 188 AADKLTVLIDHVLRYVDEVLANRITPDNSIGRQLLDMVN 226 (273)
Q Consensus 188 a~~~L~~~l~~i~~Yl~~V~~g~~~~d~~ilr~l~~~~~ 226 (273)
+...+-+++..=..|+.++.+|+..+....+++|...+.
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~~ 52 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEALG 52 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHhC
Confidence 344555566556888999999999999888888877764
No 47
>COG4220 Phage DNA packaging protein, Nu1 subunit of terminase [DNA replication, recombination, and repair]
Probab=22.95 E-value=3.7e+02 Score=22.35 Aligned_cols=42 Identities=24% Similarity=0.449 Sum_probs=28.3
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHhhhhhHHHHHHHHHHHH
Q psy4542 216 SIGRQLLDMVNSVPSMTQEQFETMFNSNIKDLLMIMTLSQLTK 258 (273)
Q Consensus 216 ~ilr~l~~~~~~lp~~~~~~f~~~~~~~~~D~lmv~yLs~ltk 258 (273)
.|+|.|.+++.++|....-.|-...+.|+ |.+.-...+.+.+
T Consensus 113 ~ia~~ia~~l~~ipls~qr~~p~l~~~hv-D~~~~~Ia~a~~~ 154 (174)
T COG4220 113 RIAREIASILDSIPLSVQRRFPELTNRHV-DFLKEDIAKAMNK 154 (174)
T ss_pred HHHHHHHHHHccccHHHHHhcchhhHHHH-HHHHHHHHHHHhh
Confidence 78999999999999766555655555554 6555544444443
No 48
>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=22.08 E-value=93 Score=20.19 Aligned_cols=25 Identities=16% Similarity=0.286 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q psy4542 183 TLVSEAADKLTVLIDHVLRYVDEVL 207 (273)
Q Consensus 183 ~~~~~a~~~L~~~l~~i~~Yl~~V~ 207 (273)
.....-..+-..++..+.+|+++..
T Consensus 10 ~~~e~~~~~k~~~v~eLe~YiD~LL 34 (48)
T PF09457_consen 10 KKQEEENARKDSRVRELEDYIDNLL 34 (48)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444455555556666999999865
No 49
>PF07002 Copine: Copine; InterPro: IPR010734 This represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca2+-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth [].
Probab=21.98 E-value=95 Score=24.99 Aligned_cols=63 Identities=14% Similarity=0.230 Sum_probs=37.3
Q ss_pred HhHHHHHHhhccCCCceEEEEEeeeEeCCEEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhCCCCCe
Q psy4542 14 LFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVNPSELI 84 (273)
Q Consensus 14 ll~I~dh~~r~~~~~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~p~~~i 84 (273)
+-+|+.+|.+.+ .-++.| +|-.....-.+.+||++-.+.++..+. =.+..++.|++..|+..+
T Consensus 20 vg~il~~Yd~dk--~~p~~G--FGa~~~~~~~vsh~F~ln~~~~~p~~~----Gi~gvl~~Y~~~~~~v~l 82 (146)
T PF07002_consen 20 VGEILQDYDSDK--MIPAYG--FGAKIPPDYSVSHCFPLNGNPQNPECQ----GIDGVLEAYRKALPKVQL 82 (146)
T ss_pred HHHHHHhhccCC--ccceec--cCCcCCCCcccccceeeecCCCCCccc----CHHHHHHHHHHHhhheEE
Confidence 456666675532 235555 344433345689999997654322221 135678888888887666
No 50
>KOG0756|consensus
Probab=21.06 E-value=55 Score=29.65 Aligned_cols=49 Identities=10% Similarity=0.243 Sum_probs=30.2
Q ss_pred CceEEEEEeeeEeCCEEEEEEEEeeccccCchhhHhhHHHHHHHHHHHhhhC------------CCCCeEEeecC
Q psy4542 28 SHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQKVN------------PSELIVGWWAT 90 (273)
Q Consensus 28 ~~~v~G~LLG~~~~~~veV~~sF~vp~~~~~~~~~id~~~~~~m~~l~k~v~------------p~~~iVGWY~~ 90 (273)
...+.|.++|-..+ -+|++-+||. ||.+.++++.+++. ..+-++|||.-
T Consensus 12 ~~s~~~~~~Gg~~G-~~E~c~~~P~-------------E~vKT~LQldrr~a~~~~~~~~~~tv~~~G~lglYrG 72 (299)
T KOG0756|consen 12 GGSASGIVAGGIAG-GIEICITQPT-------------EYVKTQLQLDRRSATTKARGPPDCTVNGHGFLGLYRG 72 (299)
T ss_pred CCchhhcccccccc-ceeeeecCch-------------hhhhheeehhhccccccccCCCceeeecCceeeEeec
Confidence 45666777777655 6777776554 35555555555432 22449999965
Done!