Query psy8916
Match_columns 520
No_of_seqs 256 out of 381
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 22:45:03 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8916.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8916hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5100 NPL4 Nuclear pore prot 100.0 2E-111 4E-116 864.3 19.1 329 174-520 1-339 (571)
2 KOG2834|consensus 100.0 2.7E-96 6E-101 761.4 22.0 275 218-520 4-280 (510)
3 PF05020 zf-NPL4: NPL4 family, 100.0 2.3E-72 4.9E-77 514.3 11.8 141 297-437 1-147 (147)
4 PF05021 NPL4: NPL4 family; I 100.0 3.9E-49 8.5E-54 399.8 12.7 141 5-182 47-187 (306)
5 KOG2834|consensus 100.0 2.3E-47 4.9E-52 397.0 7.8 142 7-186 247-388 (510)
6 COG5100 NPL4 Nuclear pore prot 100.0 2.6E-45 5.5E-50 377.3 7.3 162 7-208 306-467 (571)
7 cd08061 MPN_NPL4 Mov34/MPN/PAD 100.0 8.6E-43 1.9E-47 349.0 13.8 106 405-510 1-107 (274)
8 cd08061 MPN_NPL4 Mov34/MPN/PAD 100.0 1.6E-37 3.4E-42 311.2 10.2 119 7-180 84-202 (274)
9 PF05021 NPL4: NPL4 family; I 100.0 1.9E-34 4E-39 292.9 11.0 82 439-520 1-82 (306)
10 PF11543 UN_NPL4: Nuclear pore 99.8 4E-20 8.8E-25 155.2 6.4 75 173-248 4-78 (80)
11 cd08056 MPN_PRP8 Mpr1p, Pad1p 99.1 1.5E-10 3.1E-15 116.1 9.4 83 417-509 37-119 (252)
12 cd08056 MPN_PRP8 Mpr1p, Pad1p 99.1 1.3E-10 2.9E-15 116.3 9.0 81 6-146 96-176 (252)
13 cd01806 Nedd8 Nebb8-like ubiq 97.6 0.0002 4.4E-09 57.5 7.0 72 174-250 1-72 (76)
14 cd01791 Ubl5 UBL5 ubiquitin-li 97.6 0.00026 5.7E-09 58.7 7.5 72 174-250 2-73 (73)
15 cd01809 Scythe_N Ubiquitin-lik 97.5 0.00032 7E-09 55.8 6.4 70 174-248 1-70 (72)
16 cd01807 GDX_N ubiquitin-like d 97.4 0.00055 1.2E-08 55.8 6.5 70 174-248 1-70 (74)
17 cd01763 Sumo Small ubiquitin-r 97.3 0.00094 2E-08 56.6 7.8 73 172-249 10-82 (87)
18 cd01799 Hoil1_N Ubiquitin-like 97.3 0.00053 1.1E-08 57.1 5.5 64 179-248 9-73 (75)
19 cd01803 Ubiquitin Ubiquitin. U 97.3 0.00087 1.9E-08 53.8 6.6 71 174-249 1-71 (76)
20 cd01805 RAD23_N Ubiquitin-like 97.3 0.00096 2.1E-08 54.2 6.8 70 174-248 1-72 (77)
21 cd07767 MPN Mpr1p, Pad1p N-ter 97.2 0.00085 1.8E-08 57.6 6.3 71 428-508 4-75 (116)
22 cd01810 ISG15_repeat2 ISG15 ub 97.1 0.0014 3E-08 53.5 6.3 68 177-249 2-69 (74)
23 PF11976 Rad60-SLD: Ubiquitin- 97.1 0.0012 2.5E-08 53.1 5.8 69 174-247 1-70 (72)
24 cd08066 MPN_AMSH_like Mov34/MP 97.0 0.0039 8.4E-08 59.7 9.3 77 421-507 7-86 (173)
25 cd01804 midnolin_N Ubiquitin-l 96.9 0.0032 7E-08 52.3 6.9 70 174-249 2-71 (78)
26 cd01796 DDI1_N DNA damage indu 96.9 0.0023 5E-08 52.2 5.9 68 177-248 2-70 (71)
27 smart00213 UBQ Ubiquitin homol 96.9 0.0021 4.6E-08 49.3 5.4 64 174-243 1-64 (64)
28 PF00240 ubiquitin: Ubiquitin 96.8 0.0036 7.8E-08 49.7 6.4 64 180-248 2-65 (69)
29 PTZ00044 ubiquitin; Provisiona 96.8 0.0043 9.3E-08 50.4 6.5 71 174-249 1-71 (76)
30 cd01798 parkin_N amino-termina 96.7 0.0042 9.2E-08 50.0 6.2 67 177-248 2-68 (70)
31 cd01812 BAG1_N Ubiquitin-like 96.7 0.0047 1E-07 49.2 6.4 68 175-248 2-69 (71)
32 cd01794 DC_UbP_C dendritic cel 96.7 0.0038 8.3E-08 51.2 5.9 68 176-248 1-68 (70)
33 cd01792 ISG15_repeat1 ISG15 ub 96.7 0.006 1.3E-07 50.7 7.0 74 174-250 3-76 (80)
34 cd01797 NIRF_N amino-terminal 96.6 0.0057 1.2E-07 51.2 6.2 71 174-249 1-73 (78)
35 cd01808 hPLIC_N Ubiquitin-like 96.3 0.012 2.7E-07 47.5 6.4 68 175-248 2-69 (71)
36 cd01795 USP48_C USP ubiquitin- 96.3 0.0084 1.8E-07 53.6 5.8 62 183-249 15-76 (107)
37 cd01802 AN1_N ubiquitin-like d 96.3 0.014 2.9E-07 51.6 7.1 71 174-249 28-98 (103)
38 PF00789 UBX: UBX domain; Int 96.1 0.029 6.3E-07 46.3 7.5 75 173-248 6-81 (82)
39 cd01793 Fubi Fubi ubiquitin-li 96.0 0.021 4.5E-07 46.7 6.5 69 174-249 1-69 (74)
40 smart00232 JAB_MPN JAB/MPN dom 96.0 0.028 6.2E-07 49.2 7.8 78 423-507 7-87 (135)
41 cd01769 UBL Ubiquitin-like dom 95.8 0.037 8E-07 42.9 6.8 66 178-248 2-67 (69)
42 cd01800 SF3a120_C Ubiquitin-li 95.4 0.036 7.9E-07 45.6 5.6 63 183-250 7-69 (76)
43 PF01398 JAB: JAB1/Mov34/MPN/P 95.1 0.054 1.2E-06 47.1 6.2 80 423-508 11-93 (114)
44 TIGR00601 rad23 UV excision re 95.0 0.083 1.8E-06 56.5 8.1 72 174-250 1-75 (378)
45 smart00166 UBX Domain present 94.0 0.32 7E-06 40.4 7.9 74 174-248 5-79 (80)
46 cd01813 UBP_N UBP ubiquitin pr 93.9 0.19 4.1E-06 41.7 6.4 62 185-248 11-72 (74)
47 cd00196 UBQ Ubiquitin-like pro 93.2 0.31 6.8E-06 34.4 5.8 65 179-248 3-67 (69)
48 cd06409 PB1_MUG70 The MUG70 pr 92.9 0.24 5.1E-06 43.1 5.5 41 176-216 3-46 (86)
49 PLN02560 enoyl-CoA reductase 92.7 0.28 6E-06 51.2 6.9 76 174-249 1-82 (308)
50 PF14560 Ubiquitin_2: Ubiquiti 92.6 0.75 1.6E-05 38.7 8.1 64 185-248 15-81 (87)
51 KOG0010|consensus 91.9 0.72 1.6E-05 51.0 8.9 74 172-251 14-87 (493)
52 cd01790 Herp_N Homocysteine-re 91.6 0.59 1.3E-05 39.9 6.3 71 174-249 2-78 (79)
53 cd07767 MPN Mpr1p, Pad1p N-ter 91.5 0.26 5.7E-06 42.2 4.2 43 8-65 55-97 (116)
54 cd01767 UBX UBX (ubiquitin reg 91.5 1.2 2.5E-05 36.7 7.9 71 175-248 4-75 (77)
55 cd01789 Alp11_N Ubiquitin-like 91.3 1.1 2.4E-05 37.9 7.7 72 176-248 4-79 (84)
56 cd08067 MPN_2A_DUB Mov34/MPN/P 91.1 1.1 2.4E-05 43.6 8.5 84 417-507 7-90 (187)
57 cd01772 SAKS1_UBX SAKS1-like U 90.6 1.3 2.8E-05 37.1 7.4 73 174-248 5-78 (79)
58 cd08066 MPN_AMSH_like Mov34/MP 90.5 0.65 1.4E-05 44.6 6.3 65 11-142 70-135 (173)
59 PF11470 TUG-UBL1: GLUT4 regul 90.3 0.63 1.4E-05 38.4 5.1 63 180-247 3-65 (65)
60 cd01773 Faf1_like1_UBX Faf1 ik 89.5 2 4.4E-05 37.0 7.8 70 175-248 7-79 (82)
61 cd01771 Faf1_UBX Faf1 UBX doma 89.4 2.2 4.8E-05 36.2 7.9 69 175-248 6-78 (80)
62 cd01770 p47_UBX p47-like ubiqu 88.8 1.8 3.9E-05 36.6 6.9 67 175-244 6-74 (79)
63 cd08069 MPN_RPN11_CSN5 Mov34/M 88.0 2.7 5.8E-05 43.1 8.9 89 410-506 5-97 (268)
64 PF08817 YukD: WXG100 protein 87.5 2.2 4.8E-05 35.5 6.6 68 176-247 5-78 (79)
65 cd08070 MPN_like Mpr1p, Pad1p 82.6 4.2 9E-05 36.5 6.5 76 424-507 3-81 (128)
66 cd01801 Tsc13_N Ubiquitin-like 81.7 5.3 0.00012 33.0 6.4 60 186-248 14-75 (77)
67 smart00232 JAB_MPN JAB/MPN dom 81.3 3.5 7.5E-05 36.1 5.5 39 11-64 71-109 (135)
68 cd01774 Faf1_like2_UBX Faf1 ik 79.5 10 0.00023 32.5 7.6 70 174-248 5-83 (85)
69 PF14836 Ubiquitin_3: Ubiquiti 76.1 11 0.00023 33.2 6.7 69 185-254 15-84 (88)
70 PF08825 E2_bind: E2 binding d 64.7 4.7 0.0001 34.8 2.1 60 188-248 1-69 (84)
71 KOG0005|consensus 62.8 14 0.0003 30.8 4.3 69 174-247 1-69 (70)
72 cd01788 ElonginB Ubiquitin-lik 62.6 14 0.0003 34.2 4.7 61 170-239 2-62 (119)
73 PF12436 USP7_ICP0_bdg: ICP0-b 62.6 11 0.00024 38.1 4.6 62 185-248 86-150 (249)
74 PF09379 FERM_N: FERM N-termin 60.0 44 0.00096 27.0 6.9 41 178-218 1-42 (80)
75 cd06406 PB1_P67 A PB1 domain i 59.7 19 0.00041 31.2 4.8 52 167-227 3-54 (80)
76 PF10790 DUF2604: Protein of U 58.3 24 0.00053 29.8 5.0 63 186-252 8-73 (76)
77 TIGR02256 ICE_VC0181 integrati 57.8 66 0.0014 30.1 8.4 78 425-509 3-86 (131)
78 PF14732 UAE_UbL: Ubiquitin/SU 56.8 24 0.00051 30.4 5.0 56 192-248 7-67 (87)
79 cd08065 MPN_eIF3h Mpr1p, Pad1p 55.9 37 0.0008 34.6 7.1 82 417-506 3-89 (266)
80 cd08058 MPN_euk_mb Mpr1p, Pad1 55.5 37 0.0008 30.0 6.2 39 10-63 59-97 (119)
81 cd01815 BMSC_UbP_N Ubiquitin-l 55.2 19 0.00042 30.7 4.1 51 192-248 19-73 (75)
82 cd01814 NTGP5 Ubiquitin-like N 53.4 14 0.00031 33.9 3.2 65 174-244 5-78 (113)
83 KOG2880|consensus 53.2 10 0.00023 40.9 2.7 76 422-507 258-336 (424)
84 cd08060 MPN_UPF0172 Mov34/MPN/ 51.2 23 0.00049 34.5 4.4 65 439-513 21-87 (182)
85 cd05992 PB1 The PB1 domain is 50.9 42 0.00092 27.1 5.4 40 176-216 3-43 (81)
86 cd08067 MPN_2A_DUB Mov34/MPN/P 49.2 60 0.0013 31.8 7.0 69 11-136 74-146 (187)
87 cd08068 MPN_BRCC36 Mov34/MPN/P 46.4 61 0.0013 33.3 6.9 82 423-507 9-100 (244)
88 PF00788 RA: Ras association ( 46.1 61 0.0013 26.5 5.7 42 175-216 4-51 (93)
89 cd08068 MPN_BRCC36 Mov34/MPN/P 45.7 58 0.0013 33.4 6.6 35 14-63 87-121 (244)
90 PF01398 JAB: JAB1/Mov34/MPN/P 44.5 36 0.00078 29.5 4.3 35 15-64 80-114 (114)
91 cd08057 MPN_euk_non_mb Mpr1p, 44.4 77 0.0017 29.5 6.7 70 431-507 15-87 (157)
92 cd08065 MPN_eIF3h Mpr1p, Pad1p 44.3 71 0.0015 32.6 7.0 35 115-149 113-149 (266)
93 PF11039 DUF2824: Protein of u 43.3 51 0.0011 31.4 5.3 47 459-506 63-127 (151)
94 smart00666 PB1 PB1 domain. Pho 43.0 70 0.0015 26.0 5.6 35 183-217 10-44 (81)
95 PF07929 PRiA4_ORF3: Plasmid p 39.9 64 0.0014 30.6 5.6 68 185-252 19-100 (179)
96 COG5178 PRP8 U5 snRNP spliceos 37.5 31 0.00068 42.5 3.6 62 436-506 2153-2215(2365)
97 KOG1364|consensus 36.8 30 0.00065 37.3 3.0 69 176-244 280-349 (356)
98 cd01768 RA RA (Ras-associating 36.5 1.6E+02 0.0034 24.3 6.8 46 176-221 2-52 (87)
99 smart00295 B41 Band 4.1 homolo 35.9 93 0.002 28.9 5.9 47 174-220 4-51 (207)
100 cd01787 GRB7_RA RA (RAS-associ 35.9 1E+02 0.0022 27.1 5.6 46 174-219 3-49 (85)
101 COG5178 PRP8 U5 snRNP spliceos 34.9 46 0.00099 41.3 4.3 65 13-141 2202-2266(2365)
102 cd06407 PB1_NLP A PB1 domain i 33.7 1.1E+02 0.0024 26.1 5.5 34 185-218 11-45 (82)
103 KOG0001|consensus 33.4 2E+02 0.0043 21.3 7.0 65 179-248 5-69 (75)
104 PF14583 Pectate_lyase22: Olig 32.6 30 0.00065 37.7 2.3 40 89-135 344-383 (386)
105 PF13881 Rad60-SLD_2: Ubiquiti 31.7 1.3E+02 0.0029 27.1 6.0 65 175-244 4-76 (111)
106 KOG4133|consensus 31.6 14 0.0003 38.4 -0.4 10 71-80 213-222 (290)
107 cd02176 GH16_XET Xyloglucan en 31.0 47 0.001 34.3 3.3 41 439-480 43-88 (263)
108 COG0380 OtsA Trehalose-6-phosp 30.8 32 0.00069 38.6 2.2 47 388-435 179-225 (486)
109 PHA00771 head assembly protein 30.5 93 0.002 29.6 4.8 62 438-506 48-127 (151)
110 cd08069 MPN_RPN11_CSN5 Mov34/M 30.0 98 0.0021 31.8 5.4 67 11-141 82-151 (268)
111 PF04110 APG12: Ubiquitin-like 29.4 80 0.0017 27.7 4.0 64 185-252 17-83 (87)
112 PF00564 PB1: PB1 domain; Int 28.2 1.7E+02 0.0038 23.7 5.7 41 176-217 4-45 (84)
113 KOG0011|consensus 27.9 1.2E+02 0.0026 32.8 5.6 72 174-250 1-74 (340)
114 TIGR02958 sec_mycoba_snm4 secr 27.6 2.2E+02 0.0047 31.6 7.9 67 178-249 7-79 (452)
115 smart00455 RBD Raf-like Ras-bi 27.0 1.1E+02 0.0025 25.2 4.3 43 176-218 2-44 (70)
116 PF06442 DHFR_2: R67 dihydrofo 26.6 38 0.00083 28.6 1.4 21 497-517 41-67 (78)
117 cd08058 MPN_euk_mb Mpr1p, Pad1 26.3 2.2E+02 0.0047 25.2 6.3 70 426-506 4-75 (119)
118 KOG0275|consensus 26.2 35 0.00075 36.9 1.4 31 95-132 212-242 (508)
119 PF03931 Skp1_POZ: Skp1 family 25.3 71 0.0015 25.4 2.7 36 174-210 1-36 (62)
120 smart00314 RA Ras association 25.2 2E+02 0.0044 23.9 5.6 38 183-220 15-54 (90)
121 PF08662 eIF2A: Eukaryotic tra 24.8 86 0.0019 30.1 3.7 61 64-135 63-133 (194)
122 KOG1795|consensus 24.7 40 0.00086 42.0 1.7 72 423-505 2102-2174(2321)
123 cd01777 SNX27_RA Ubiquitin dom 24.6 1.2E+02 0.0025 26.9 4.1 45 175-219 3-50 (87)
124 PF06877 RraB: Regulator of ri 24.6 62 0.0013 27.8 2.5 80 410-501 22-102 (104)
125 KOG1560|consensus 23.6 1.7E+02 0.0036 31.2 5.7 28 122-149 141-168 (339)
126 cd04509 PBP1_ABC_transporter_G 23.4 3E+02 0.0065 25.9 7.0 99 410-509 109-230 (299)
127 cd06397 PB1_UP1 Uncharacterize 23.3 1.3E+02 0.0027 26.5 4.0 41 185-225 11-51 (82)
128 KOG4495|consensus 22.2 1.3E+02 0.0028 27.4 3.9 63 170-239 2-64 (110)
129 PF02196 RBD: Raf-like Ras-bin 21.8 2.4E+02 0.0052 23.3 5.3 44 175-218 2-45 (71)
130 KOG0640|consensus 21.5 76 0.0016 34.4 2.8 55 47-130 82-139 (430)
131 COG1609 PurR Transcriptional r 21.3 1.7E+02 0.0037 30.4 5.4 45 403-447 140-185 (333)
132 cd01391 Periplasmic_Binding_Pr 21.2 4.1E+02 0.0089 24.0 7.3 99 411-510 98-222 (269)
133 cd06268 PBP1_ABC_transporter_L 20.1 4.5E+02 0.0097 24.7 7.5 96 413-509 110-227 (298)
134 KOG0006|consensus 20.1 1.9E+02 0.0041 31.4 5.3 41 174-216 3-46 (446)
No 1
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=100.00 E-value=1.7e-111 Score=864.32 Aligned_cols=329 Identities=37% Similarity=0.693 Sum_probs=296.0
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCC--CCcceeeecCCcccccc-ccccccccccCCCCcCeEEEeec
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELN--TYNFALFKQRNKTDEIF-SSRDQTIASVGLSNGDFVYMMNL 250 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls--~dsftL~~nr~~~~~l~-s~~~~tv~~lgLkHGDmlyl~~~ 250 (520)
||+|||||+| |.|++++++|.++.|.+||+..|..+ .+.++++.++++.+++. .++++++.+|||+|||||||.|+
T Consensus 1 Mi~rfRsk~G-~~Rve~qe~d~lg~l~~kll~~~~~n~~~e~~svc~~p~~qG~~~s~l~dqt~~dlGL~hGqmLyl~ys 79 (571)
T COG5100 1 MIFRFRSKEG-QRRVEVQESDVLGMLSPKLLAFFEVNYSPEQISVCSAPDGQGEIFSLLKDQTPDDLGLRHGQMLYLEYS 79 (571)
T ss_pred CeEEEecCCC-ceeeeccccchhhhhhHHHHhhhccCCCccceEEEeCCCCCceeeecccccChhhhccccCcEEEEEec
Confidence 8999999999 99999999999999999999998655 45889999998888754 57899999999999999999997
Q ss_pred CCCCCCCCCCCCCcccccc-ccccCCCCCCCCccccccccccCCCCCcccchhhhhhhhhccCcccccCCCcccccCCCc
Q psy8916 251 SSPNDEKPSTSSNHLNIYE-TKKKASTTPSTPTEFKSKLSNAFSSSNNIVEDEVDKELWKTDGQVKRKRDDKFCRHGANA 329 (520)
Q Consensus 251 ~~~~~~~~~~s~~~~~~~~-~~~~~~~~~~~p~~~~~~~~~~~~~~~~v~e~~vD~~L~K~dG~I~R~rd~klCrHG~~G 329 (520)
+-+++..+.-. ++ .++. +..+. -.-..+..+|+||+||+.|+|+||+|+|+. ++||+||+||
T Consensus 80 d~~snne~~~~------V~~~pkq----~~skg------i~~~k~sm~v~q~~iddslekedgli~rs~-t~lC~Hg~~g 142 (571)
T COG5100 80 DIASNNEKKRD------VPGKPKQ----DCSKG------IKREKDSMPVIQDPIDDSLEKEDGLIRRSM-TMLCQHGSNG 142 (571)
T ss_pred ccccccccccc------CCCCCcc----cCCcc------hhhcCCCCccccccchhhhhhccccchhhh-hHHhhcCCCc
Confidence 65543221100 11 1111 11111 122345689999999999999999999988 6799999999
Q ss_pred ccCccCCCCCCCHHHHhhcCcccchHHHHHHHHhcCCCC----CCc-cccccccccccCCCC-CCCCCCccccccccCCc
Q psy8916 330 LCIHCSPLEPYDEEYLREQNVKHMSFHAYLRKQCAGVDR----GKF-VVLEDLSCRIKEGCR-EHPPWPRGICSKCQPNA 403 (520)
Q Consensus 330 mC~~C~PLeP~D~~Yl~E~~IKHlSFhaYLrkl~~~~~k----~~~-~~l~~~~~ki~~~C~-~H~PwP~GiCskCqP~a 403 (520)
||+||+||||||++|+++++||||||||||+|||+.+|| .+| +||++|+|+|+..|+ ||+|||+|||+||||++
T Consensus 143 MC~yCsPL~PwDe~Y~~~NkIKhlSFhsYl~k~nsn~nk~~s~~Syi~pleep~f~vke~C~~gH~pwP~giC~kCQps~ 222 (571)
T COG5100 143 MCSYCSPLDPWDEKYYKDNKIKHLSFHSYLEKMNSNKNKLGSVESYIVPLEEPSFTVKETCEDGHGPWPHGICNKCQPSN 222 (571)
T ss_pred ccccCCCCCccchhhhhhcceeEeeHHHHHHHHhhhhhhccccccccCCcCCCcchhhccCCCCCCCCcccccccCCcce
Confidence 999999999999999999999999999999999999887 356 589999999999999 79999999999999999
Q ss_pred eeecCCCCCCcCeeeecCHHHHHHHHHHHHhcCceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEEcCCCC
Q psy8916 404 ITLNRQVYRHVDNVEFENRTLVERFLEYWRVTGHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDPK 483 (520)
Q Consensus 404 ItL~~Q~~R~VDhvef~~~~~v~~Fi~~wr~~g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~ll~d~~ 483 (520)
|+|++|+|||||||||+.+.+|++||+.||.+|.||||||||+|..|+++||||||||||||||||++++|||+|.+|.+
T Consensus 223 i~L~~Q~FRmvDHvEF~~~~iv~~Fi~~WR~sG~QRfGy~yG~y~~y~n~PLGiKaVveaIyEPpQ~de~DG~t~ee~~d 302 (571)
T COG5100 223 IILAPQVFRMVDHVEFDGKHIVENFIRNWRESGRQRFGYLYGRYMDYENIPLGIKAVVEAIYEPPQEDEPDGFTIEEWAD 302 (571)
T ss_pred eeecccceeeeeeeeecCchHHHHHHHHHHHhhhhhheeeeeehhhccCCcchhHHHhhhhcCCccccCCCceEeeeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHhcCCeEEEEEEecCccCCCCCceEEecC
Q psy8916 484 AEVVEEIASSLGLTQVGWIFTDLVAEDLQLGTYFQSR 520 (520)
Q Consensus 484 e~~Vd~iA~~LGL~rVG~IFTdl~~~~~~~GtV~ckR 520 (520)
|..+|+.|..+||+|||+|||||+++|.++|+|.|||
T Consensus 303 e~l~d~~a~~~GL~riG~IfTDl~d~gs~~GsV~ckr 339 (571)
T COG5100 303 EGLMDAPASGTGLERIGMIFTDLLDEGSNRGSVTCKR 339 (571)
T ss_pred cccccccccccCceeeeeeeeehhhccCCCCceeeec
Confidence 9999999999999999999999999999999999998
No 2
>KOG2834|consensus
Probab=100.00 E-value=2.7e-96 Score=761.39 Aligned_cols=275 Identities=48% Similarity=0.868 Sum_probs=247.9
Q ss_pred ecCCccccccccccccccccCCCCcCeEEEeecCCCCCCCCCCCCCccccccccccCCCCCCCCccccccccccCCCCCc
Q psy8916 218 KQRNKTDEIFSSRDQTIASVGLSNGDFVYMMNLSSPNDEKPSTSSNHLNIYETKKKASTTPSTPTEFKSKLSNAFSSSNN 297 (520)
Q Consensus 218 ~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~ 297 (520)
..++..+.++++.++++..+||||||||||. .+++.... .+. +|. +.-.+ ...
T Consensus 4 ~~~~~~g~~s~~~~~~~~~~~~~hG~ml~l~---~~~~~e~~----------~sv-------~~~------~~~~~-~~~ 56 (510)
T KOG2834|consen 4 IVRGKEGVDSSLVDGTLLLAGLKHGQMLVLS---APGNGELD----------KSV-------APG------AKGLR-GQR 56 (510)
T ss_pred eecCCcccchhcccchhHhhccccccEEEEe---cCCCCCcC----------ccc-------CCC------ccccC-CCc
Confidence 3455666778888999999999999999997 11111111 111 111 00011 237
Q ss_pred ccchhhhhhhhhccCcccccCCCcccccCCCcccCccCCCCCCCHHHHhhcCcccchHHHHHHHHhcCCCCCC--ccccc
Q psy8916 298 IVEDEVDKELWKTDGQVKRKRDDKFCRHGANALCIHCSPLEPYDEEYLREQNVKHMSFHAYLRKQCAGVDRGK--FVVLE 375 (520)
Q Consensus 298 v~e~~vD~~L~K~dG~I~R~rd~klCrHG~~GmC~~C~PLeP~D~~Yl~E~~IKHlSFhaYLrkl~~~~~k~~--~~~l~ 375 (520)
|++++||++|+|+||+|+|++++ +||||++|||+||+||+|||++||++++|||||||||+|||+++.||+. +.||+
T Consensus 57 vr~~dvde~ls~edg~I~rsk~~-lcrh~~~~mc~~c~pL~p~de~yl~~n~ikh~Sfhay~rkl~s~~nk~~~~~~~l~ 135 (510)
T KOG2834|consen 57 VRSRDVDERLSKEDGLITRSKDK-LCRHDPLQMCTHCSPLDPFDEEYLKKNKIKHLSFHAYLRKLLSSLNKGHGYIAPLE 135 (510)
T ss_pred eecccccchhhhcCCceeeccCc-ccccCccccCCcCCCCCcchHHHhhcCcceeeechhhHhhhhccccccCccccccc
Confidence 99999999999999999999986 9999999999999999999999999999999999999999999999975 57999
Q ss_pred cccccccCCCCCCCCCCccccccccCCceeecCCCCCCcCeeeecCHHHHHHHHHHHHhcCceeeEEEEEEEeeCCCCCc
Q psy8916 376 DLSCRIKEGCREHPPWPRGICSKCQPNAITLNRQVYRHVDNVEFENRTLVERFLEYWRVTGHQRLGLLYGKYQLHPDVPL 455 (520)
Q Consensus 376 ~~~~ki~~~C~~H~PwP~GiCskCqP~aItL~~Q~~R~VDhvef~~~~~v~~Fi~~wr~~g~QR~G~LYG~Y~~~~~vPl 455 (520)
+++|+++++|++|+|||+|||+||||++|||+||+|||||||||++++++|+||++||.+|+||||||||+|.+|++|||
T Consensus 136 e~s~~~~~~c~~h~p~p~gictkcqp~~i~L~rQ~frhvD~VeFd~~~~v~~Fl~~wr~sg~QR~GflyG~y~e~~~vPL 215 (510)
T KOG2834|consen 136 EPSCRGKPNCEAHSPGPKGICTKCQPSQITLNRQEFRHVDHVEFDNAELVNHFLNEWRASGVQRFGFLYGRYTEHGNVPL 215 (510)
T ss_pred CcccccCCCCcCCCCCCCceecccchhheEeccccceecceEeecchHHHHHHHHHHHHhhhhhcceEEEeecccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceEEEEEEecCCCCCCCCceEEcCCCChHHHHHHHHhcCCeEEEEEEecCccCCCCCceEEecC
Q psy8916 456 GIKAVVAAIYEPPQESSRDKIKLLPDPKAEVVEEIASSLGLTQVGWIFTDLVAEDLQLGTYFQSR 520 (520)
Q Consensus 456 GikAvVeAIYEPPQ~~~~dg~~ll~d~~e~~Vd~iA~~LGL~rVG~IFTdl~~~~~~~GtV~ckR 520 (520)
||||+|+|||||||++++|||+|++++++..||++|+.|||+||||||||++++|.++|||.|+|
T Consensus 216 Gika~V~aIYEPPQ~~~~dgl~l~~~~e~~~vD~~a~~lGLrRVG~IFTDl~~~~s~egtV~~~r 280 (510)
T KOG2834|consen 216 GIKAVVAAIYEPPQHGEEDGLELLEDDEAKRVDAIAEGLGLRRVGWIFTDLVTADSAEGTVHYKR 280 (510)
T ss_pred cceeeEEEEecCCccCCcCCeEEeccchhhhHHHHHHhcCceeeEEEEeeeecccCccceEEeee
Confidence 99999999999999999999999977778889999999999999999999999999999999998
No 3
>PF05020 zf-NPL4: NPL4 family, putative zinc binding region; InterPro: IPR007716 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 after ubiquitination of target proteins but before their recognition by the 26S proteasome []. This region of the protein contains possibly two zinc binding motifs. 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=100.00 E-value=2.3e-72 Score=514.32 Aligned_cols=141 Identities=62% Similarity=1.207 Sum_probs=136.1
Q ss_pred cccchhhhhhhhhccCcccccCCCcccccCCCcccCccCCCCCCCHHHHhhcCcccchHHHHHHHHhcCCCC---CC-c-
Q psy8916 297 NIVEDEVDKELWKTDGQVKRKRDDKFCRHGANALCIHCSPLEPYDEEYLREQNVKHMSFHAYLRKQCAGVDR---GK-F- 371 (520)
Q Consensus 297 ~v~e~~vD~~L~K~dG~I~R~rd~klCrHG~~GmC~~C~PLeP~D~~Yl~E~~IKHlSFhaYLrkl~~~~~k---~~-~- 371 (520)
+|+|++||++|+|+||+|+|+||++|||||++|||+||+||||||++||+|++||||||||||||||+++|+ |+ |
T Consensus 1 ~v~e~~vD~~l~k~dG~I~R~rd~~lC~Hg~kgmC~~C~pLeP~D~~Y~~e~~IKhlSFHaYlrkl~~~~nk~~~g~~~~ 80 (147)
T PF05020_consen 1 KVKEDPVDDELEKQDGKIPRKRDSKLCRHGPKGMCDYCSPLEPWDEKYLKENNIKHLSFHAYLRKLNSGTNKPESGKSYI 80 (147)
T ss_pred CccchHHHHHHHHccCccccccchhhhcCCCCCccCCCCCCCccCHHHHhhcccceeeHHHHHHHHhccCCCCCCccccc
Confidence 489999999999999999999999999999999999999999999999999999999999999999999988 54 3
Q ss_pred cccccccccccCCCCC-CCCCCccccccccCCceeecCCCCCCcCeeeecCHHHHHHHHHHHHhcCc
Q psy8916 372 VVLEDLSCRIKEGCRE-HPPWPRGICSKCQPNAITLNRQVYRHVDNVEFENRTLVERFLEYWRVTGH 437 (520)
Q Consensus 372 ~~l~~~~~ki~~~C~~-H~PwP~GiCskCqP~aItL~~Q~~R~VDhvef~~~~~v~~Fi~~wr~~g~ 437 (520)
+||++++|+|+++|++ |+|||+||||||||+|||||||+|||||||||+|+++||+||+|||+||+
T Consensus 81 ~pL~~~~y~vk~~C~~gH~pwP~gICskCqPsaITL~~Q~fR~VDhVeF~n~~iv~~Fl~~WR~tG~ 147 (147)
T PF05020_consen 81 PPLEEPSYKVKKGCPSGHPPWPKGICSKCQPSAITLQRQPFRHVDHVEFENPEIVNRFLDYWRKTGH 147 (147)
T ss_pred CCCCCcceeecCCCCCCCCCCCcccccCCCCCeeeecCcccccccceeecCHHHHHHHHHHHHhcCC
Confidence 5899999999999995 99999999999999999999999999999999999999999999999985
No 4
>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=100.00 E-value=3.9e-49 Score=399.79 Aligned_cols=141 Identities=51% Similarity=0.899 Sum_probs=131.0
Q ss_pred cccccccccCCCeEEEEEeeccccccCCCceeeeeecCCceeechHHHHHHHhhhhhCCCCCCCCCCCCCCcceeeeeec
Q psy8916 5 QKETLQQPNLGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVT 84 (520)
Q Consensus 5 ~~~~~~~~~lgl~~vG~Iftdl~~~~~~~g~v~~~r~~~s~fls~~E~~~aa~~Q~~~p~~~~~~~~~~~~~~~~~~~~~ 84 (520)
++-|.||+.|||+|||||||||++++.++|||+||||+|+|||||+||||||++|++|||+|||
T Consensus 47 ~~vd~iA~~lGL~rVG~IfTdl~~~~~~~g~v~~~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~---------------- 110 (306)
T PF05021_consen 47 ERVDAIASALGLERVGWIFTDLTDDGSGDGTVKCKRHKDSYFLSSLEIIFAAKLQNKHPNPCKY---------------- 110 (306)
T ss_pred HHHHHHHHHCCCEEEEEEEecCcccccCCCceeeccccccccccHHHHHHHHHHHHhcCccccc----------------
Confidence 3457899999999999999999999999999999999999999999999999999998877655
Q ss_pred chhhhhccccccCCCCCCccCCCCcCCCceEEEEEECCCCCceeeeeEechHHHHHHhhcCccccCCCCCcceEeccCCC
Q psy8916 85 VNECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTGDKDNQVHMEGYQVSNQCMALVRDGCLIPTKDAPELGYIKESSD 164 (520)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~g~~~s~fvT~~vsg~~~~~i~~~~yqvS~q~~alv~~~~~~~~~~~p~~~~~~~~~~ 164 (520)
|.+|+|||||||||||||++|+|+++|||||||||||||+|||.|+.+ |++++|+++++
T Consensus 111 --------------------s~~g~fgSkFVT~vvsg~~~g~i~~~ayQvS~q~~~Lv~~~~l~~s~~-p~~~~v~~~~~ 169 (306)
T PF05021_consen 111 --------------------SETGYFGSKFVTCVVSGDEEGEIHFEAYQVSNQCVALVRAGILEPSQD-PSLMYVRESTE 169 (306)
T ss_pred --------------------cCCCccCCeEEEEEEeCCCCCceeeEEeeehHHHHHHHHCCccccCCC-CceEEEecCCC
Confidence 667889999999999999999999999999999999999999999988 99999999999
Q ss_pred cccccccceeeeeeeCCC
Q psy8916 165 KQYVPDVFYKILRIQSPV 182 (520)
Q Consensus 165 ~~yvp~vfYMiIRfRSkd 182 (520)
+||||||||+.++-.+++
T Consensus 170 ~~yvpdV~y~~~neyG~~ 187 (306)
T PF05021_consen 170 ERYVPDVFYREKNEYGKE 187 (306)
T ss_pred cccccceEEEEccccchh
Confidence 999999999988755444
No 5
>KOG2834|consensus
Probab=100.00 E-value=2.3e-47 Score=397.02 Aligned_cols=142 Identities=53% Similarity=0.854 Sum_probs=132.8
Q ss_pred cccccccCCCeEEEEEeeccccccCCCceeeeeecCCceeechHHHHHHHhhhhhCCCCCCCCCCCCCCcceeeeeecch
Q psy8916 7 ETLQQPNLGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTVN 86 (520)
Q Consensus 7 ~~~~~~~lgl~~vG~Iftdl~~~~~~~g~v~~~r~~~s~fls~~E~~~aa~~Q~~~p~~~~~~~~~~~~~~~~~~~~~~~ 86 (520)
-|++|..|||+|||||||||++++.+.|||.|+||+|+|||||+|||+||+||++|||+|+|
T Consensus 247 vD~~a~~lGLrRVG~IFTDl~~~~s~egtV~~~rhkdsyFLSseE~~~aa~~Q~~hpn~~~~------------------ 308 (510)
T KOG2834|consen 247 VDAIAEGLGLRRVGWIFTDLVTADSAEGTVHYKRHKDSYFLSSEECITAAMFQNKHPNICEW------------------ 308 (510)
T ss_pred HHHHHHhcCceeeEEEEeeeecccCccceEEeeeccchhcccHHHHHHHhhhhhcCCchhee------------------
Confidence 47899999999999999999999999999999999999999999999999999998877766
Q ss_pred hhhhccccccCCCCCCccCCCCcCCCceEEEEEECCCCCceeeeeEechHHHHHHhhcCccccCCCCCcceEeccCCCcc
Q psy8916 87 ECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTGDKDNQVHMEGYQVSNQCMALVRDGCLIPTKDAPELGYIKESSDKQ 166 (520)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~g~~~s~fvT~~vsg~~~~~i~~~~yqvS~q~~alv~~~~~~~~~~~p~~~~~~~~~~~~ 166 (520)
+.+|+|||||||+|||||.+|+|||++|||||||||||+||+|.|+.+ |+++||+++.+.|
T Consensus 309 ------------------s~~~~fgSkfVT~visg~~~~~V~f~~YQVSnqc~alv~adl~~p~~~-pk~~yv~~t~~~r 369 (510)
T KOG2834|consen 309 ------------------SRDGHFGSKFVTLVISGDLDGEVHFEGYQVSNQCMALVEADLLCPSLD-PKLGYVKETPDPR 369 (510)
T ss_pred ------------------eccccccceeEEEEEecCCCcceeeeeeehhHHHHHHhhhhhccCCcC-cccceeccCCChh
Confidence 556778888889999999999999999999999999999999999988 9999999999999
Q ss_pred cccccceeeeeeeCCCccee
Q psy8916 167 YVPDVFYKILRIQSPVGIVK 186 (520)
Q Consensus 167 yvp~vfYMiIRfRSkdG~m~ 186 (520)
|||||||+..|-...++ |+
T Consensus 370 ~v~dv~~~~~~kyg~ev-~k 388 (510)
T KOG2834|consen 370 YVPDVQYSKKNKYGAEV-MK 388 (510)
T ss_pred cccchHHHhhhHHHHHH-Hh
Confidence 99999999999777776 54
No 6
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=100.00 E-value=2.6e-45 Score=377.30 Aligned_cols=162 Identities=35% Similarity=0.576 Sum_probs=143.1
Q ss_pred cccccccCCCeEEEEEeeccccccCCCceeeeeecCCceeechHHHHHHHhhhhhCCCCCCCCCCCCCCcceeeeeecch
Q psy8916 7 ETLQQPNLGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTVN 86 (520)
Q Consensus 7 ~~~~~~~lgl~~vG~Iftdl~~~~~~~g~v~~~r~~~s~fls~~E~~~aa~~Q~~~p~~~~~~~~~~~~~~~~~~~~~~~ 86 (520)
-|++|..+||+|||+|||||++++.++|+|.||||+||||||++||+|+|++|.+|||+||||
T Consensus 306 ~d~~a~~~GL~riG~IfTDl~d~gs~~GsV~ckrh~dsyFLSSLEv~~~A~~Qt~hpn~~k~s----------------- 368 (571)
T COG5100 306 MDAPASGTGLERIGMIFTDLLDEGSNRGSVTCKRHADSYFLSSLEVEFIAKMQTMHPNTVKDS----------------- 368 (571)
T ss_pred ccccccccCceeeeeeeeehhhccCCCCceeeeccccceehhhhhhHHHhhhhhcCCCccccc-----------------
Confidence 478899999999999999999999999999999999999999999999999999988877765
Q ss_pred hhhhccccccCCCCCCccCCCCcCCCceEEEEEECCCCCceeeeeEechHHHHHHhhcCccccCCCCCcceEeccCCCcc
Q psy8916 87 ECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTGDKDNQVHMEGYQVSNQCMALVRDGCLIPTKDAPELGYIKESSDKQ 166 (520)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~g~~~s~fvT~~vsg~~~~~i~~~~yqvS~q~~alv~~~~~~~~~~~p~~~~~~~~~~~~ 166 (520)
..|+|||||||||||||.+|+|++.+|||||||||||+||+|.|+.+ |.+++++.++++|
T Consensus 369 -------------------r~g~FgSkfvT~Visgnl~GeI~~~sYQVSn~~~ALv~ad~I~ps~d-P~r~l~~~~~q~R 428 (571)
T COG5100 369 -------------------REGEFGSKFVTIVISGNLDGEIGLQSYQVSNQCMALVKADYILPSED-PRRFLATKEDQTR 428 (571)
T ss_pred -------------------ccccccceeEEEEEecccCceeeeeEEeehhhhhHHhhcCcccCCcC-hhhhhhccccccc
Confidence 45778888888999999999999999999999999999999888865 9999999999999
Q ss_pred cccccceeeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcC
Q psy8916 167 YVPDVFYKILRIQSPVGIVKRININRSDTCKDLFEKINKEFE 208 (520)
Q Consensus 167 yvp~vfYMiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ 208 (520)
||||||||.-.-...+- -.+..|..++..|+.+|...|+
T Consensus 429 yvpdifYr~td~yg~~v---~enAkPafPv~flLVtLThGfp 467 (571)
T COG5100 429 YVPDIFYRYTDTYGEEV---MENAKPAFPVEFLLVTLTHGFP 467 (571)
T ss_pred cccceeeeecchhhhhH---HhcCCCCCceeEEEEEeccCCC
Confidence 99999999886444333 3456677777777777776665
No 7
>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=100.00 E-value=8.6e-43 Score=349.04 Aligned_cols=106 Identities=64% Similarity=1.108 Sum_probs=104.6
Q ss_pred eecCCCCCCcCeeeecCHHHHHHHHH-HHHhcCceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEEcCCCC
Q psy8916 405 TLNRQVYRHVDNVEFENRTLVERFLE-YWRVTGHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDPK 483 (520)
Q Consensus 405 tL~~Q~~R~VDhvef~~~~~v~~Fi~-~wr~~g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~ll~d~~ 483 (520)
||+||+|||||||||++..++++|++ +||+++.||||||||+|+++++|||||||+|||||||||+++.||+++++|++
T Consensus 1 tL~~Q~~r~Vd~vef~~~~~~~~f~~~~w~~~~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~ 80 (274)
T cd08061 1 TLKRQKYRHVDHVEFDNPSIVEFFLYVFWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPN 80 (274)
T ss_pred CCccccCCCcCEEEEecHHHHHHHHHHHHHhhcceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchh
Confidence 79999999999999999999999999 99999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHhcCCeEEEEEEecCccCC
Q psy8916 484 AEVVEEIASSLGLTQVGWIFTDLVAED 510 (520)
Q Consensus 484 e~~Vd~iA~~LGL~rVG~IFTdl~~~~ 510 (520)
++.||+||+.|||+|||||||||+++|
T Consensus 81 ~~~vd~iA~~lGL~~VG~IfT~l~~~~ 107 (274)
T cd08061 81 ADTVDAIAAALGLERVGWIFTDLPRED 107 (274)
T ss_pred hhHHHHHHHHcCCeEEEEEEecCCCCC
Confidence 999999999999999999999999987
No 8
>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=100.00 E-value=1.6e-37 Score=311.18 Aligned_cols=119 Identities=56% Similarity=0.871 Sum_probs=110.5
Q ss_pred cccccccCCCeEEEEEeeccccccCCCceeeeeecCCceeechHHHHHHHhhhhhCCCCCCCCCCCCCCcceeeeeecch
Q psy8916 7 ETLQQPNLGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTVN 86 (520)
Q Consensus 7 ~~~~~~~lgl~~vG~Iftdl~~~~~~~g~v~~~r~~~s~fls~~E~~~aa~~Q~~~p~~~~~~~~~~~~~~~~~~~~~~~ 86 (520)
-|.||+.|||+|||||||||++++ +|+|||||+|||+||++|++|
T Consensus 84 vd~iA~~lGL~~VG~IfT~l~~~~-----------~d~~~LSs~Evi~aA~~Q~~~------------------------ 128 (274)
T cd08061 84 VDAIAAALGLERVGWIFTDLPRED-----------KDGYFLSAEEVILAAKFQLKH------------------------ 128 (274)
T ss_pred HHHHHHHcCCeEEEEEEecCCCCC-----------CCceeECHHHHHHHHHHhhhc------------------------
Confidence 368999999999999999999877 899999999999999999987
Q ss_pred hhhhccccccCCCCCCccCCCCcCCCceEEEEEECCCCCceeeeeEechHHHHHHhhcCccccCCCCCcceEeccCCCcc
Q psy8916 87 ECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTGDKDNQVHMEGYQVSNQCMALVRDGCLIPTKDAPELGYIKESSDKQ 166 (520)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~g~~~s~fvT~~vsg~~~~~i~~~~yqvS~q~~alv~~~~~~~~~~~p~~~~~~~~~~~~ 166 (520)
++|+||||||||||||+++|+|+++|||||+|||+|||||||.++.+ |+++++++++..|
T Consensus 129 -------------------~~g~~gskFvT~vvs~~~~g~i~~~ayQvSdq~~~lv~~~~i~~s~~-~~~~~~~~~~~~~ 188 (274)
T cd08061 129 -------------------PTGKFGSKFVTVVVTGDKDGQIHFEAYQVSDQAMALVRDGLLLPTKD-ADELYVREPTLER 188 (274)
T ss_pred -------------------ccCCcCCeEEEEEEecCCCCceeeeeeeecHHHHHHHHcCccccCCC-cccccccCCchhe
Confidence 25889999999999999999999999999999999999999999986 6677999999999
Q ss_pred cccccceeeeeeeC
Q psy8916 167 YVPDVFYKILRIQS 180 (520)
Q Consensus 167 yvp~vfYMiIRfRS 180 (520)
|+|||||+.++..+
T Consensus 189 ~vpdVf~~~k~~yg 202 (274)
T cd08061 189 YVPDVFYSGKDKYG 202 (274)
T ss_pred eccceeeeehhhhc
Confidence 99999999987544
No 9
>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=100.00 E-value=1.9e-34 Score=292.91 Aligned_cols=82 Identities=59% Similarity=0.932 Sum_probs=81.5
Q ss_pred eeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEEcCCCChHHHHHHHHhcCCeEEEEEEecCccCCCCCceEEe
Q psy8916 439 RLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDPKAEVVEEIASSLGLTQVGWIFTDLVAEDLQLGTYFQ 518 (520)
Q Consensus 439 R~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~ll~d~~e~~Vd~iA~~LGL~rVG~IFTdl~~~~~~~GtV~c 518 (520)
|||||||||++|++|||||||+|||||||||+++.|||+|++|++++.||+||++|||+|||||||||+++|.++|||+|
T Consensus 1 R~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~lGL~rVG~IfTdl~~~~~~~g~v~~ 80 (306)
T PF05021_consen 1 RFGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASALGLERVGWIFTDLTDDGSGDGTVKC 80 (306)
T ss_pred CeEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHHCCCEEEEEEEecCcccccCCCceee
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cC
Q psy8916 519 SR 520 (520)
Q Consensus 519 kR 520 (520)
||
T Consensus 81 ~r 82 (306)
T PF05021_consen 81 KR 82 (306)
T ss_pred cc
Confidence 98
No 10
>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.
Probab=99.80 E-value=4e-20 Score=155.16 Aligned_cols=75 Identities=39% Similarity=0.600 Sum_probs=55.1
Q ss_pred eeeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 173 YKILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 173 YMiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
-|+|||||||| |+||++++++++++|+++|.+.|+++.++++|+.+++...++.+..+++|+++||+|||||||.
T Consensus 4 ~milRvrS~dG-~~Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L~~~~~~~~~l~s~~~~tl~~lglkHGdmlyL~ 78 (80)
T PF11543_consen 4 SMILRVRSKDG-MKRIEVSPSSTLSDLKEKISEQLSIPDSSQSLSKDRNNKEELKSSDSKTLSSLGLKHGDMLYLK 78 (80)
T ss_dssp --EEEEE-SSE-EEEEEE-TTSBHHHHHHHHHHHS---TTT---BSSGGGGGCSSS-TT-CCCCT---TT-EEE--
T ss_pred cEEEEEECCCC-CEEEEcCCcccHHHHHHHHHHHcCCCCcceEEEecCCCCcccccCCcCCHHHcCCCCccEEEEe
Confidence 48999999999 9999999999999999999999999999999999999888998778999999999999999996
No 11
>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=99.14 E-value=1.5e-10 Score=116.07 Aligned_cols=83 Identities=22% Similarity=0.272 Sum_probs=70.0
Q ss_pred eeecCHHHHHHHHHHHHhcCceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEEcCCCChHHHHHHHHhcCC
Q psy8916 417 VEFENRTLVERFLEYWRVTGHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDPKAEVVEEIASSLGL 496 (520)
Q Consensus 417 vef~~~~~v~~Fi~~wr~~g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~ll~d~~e~~Vd~iA~~LGL 496 (520)
.-+...+++..||.-- ....|++|||||.+.++.. +|| .|.+|++|||.|+.+++++..+. .+.+...||
T Consensus 37 t~vlPknllkkFi~ia-D~rtQ~~GyLyG~~~~d~~---~vk-eI~cIvipPQ~gt~~sv~l~~~~-----~~~~~l~~L 106 (252)
T cd08056 37 TYILPKNLLKKFISIS-DLRTQIAGYLYGKSPPDNP---QVK-EIRCIVLVPQLGTHQTVTLPQQL-----PQHEYLEDL 106 (252)
T ss_pred EEEeCHHHHHHHHHHh-hhcceEEEEEeccCCCCCC---CeE-EEEEEEECCEeCCcCcEECCccC-----ccchhhCCC
Confidence 3455678999999854 5567999999999998865 788 99999999999999999998663 566678999
Q ss_pred eEEEEEEecCccC
Q psy8916 497 TQVGWIFTDLVAE 509 (520)
Q Consensus 497 ~rVG~IFTdl~~~ 509 (520)
+.+|||+|+....
T Consensus 107 e~LGWIHTqp~e~ 119 (252)
T cd08056 107 EPLGWIHTQPNEL 119 (252)
T ss_pred EeeEEEEcCCCCc
Confidence 9999999998654
No 12
>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=99.13 E-value=1.3e-10 Score=116.33 Aligned_cols=81 Identities=15% Similarity=0.235 Sum_probs=71.4
Q ss_pred ccccccccCCCeEEEEEeeccccccCCCceeeeeecCCceeechHHHHHHHhhhhhCCCCCCCCCCCCCCcceeeeeecc
Q psy8916 6 KETLQQPNLGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTV 85 (520)
Q Consensus 6 ~~~~~~~~lgl~~vG~Iftdl~~~~~~~g~v~~~r~~~s~fls~~E~~~aa~~Q~~~p~~~~~~~~~~~~~~~~~~~~~~ 85 (520)
.....+...||+.+|||+|+. .+++|||+.|+.+.|++|+.||+ |+
T Consensus 96 ~~~~~~~l~~Le~LGWIHTqp---------------~e~~~Lss~Dv~tha~~~~~~~~---w~---------------- 141 (252)
T cd08056 96 QLPQHEYLEDLEPLGWIHTQP---------------NELPQLSPQDVTTHAKILADNPS---WD---------------- 141 (252)
T ss_pred cCccchhhCCCEeeEEEEcCC---------------CCccccCHHHHHHHHHHHHhccc---cC----------------
Confidence 345567788999999999998 45579999999999999999986 52
Q ss_pred hhhhhccccccCCCCCCccCCCCcCCCceEEEEEECCCCCceeeeeEechHHHHHHhhcCc
Q psy8916 86 NECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTGDKDNQVHMEGYQVSNQCMALVRDGC 146 (520)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~g~~~s~fvT~~vsg~~~~~i~~~~yqvS~q~~alv~~~~ 146 (520)
|++||+|++|++ .|.+++.||+++++|+++++.+.
T Consensus 142 -------------------------~~~~V~it~Sft-pGs~sl~ay~LT~~G~~wg~~n~ 176 (252)
T cd08056 142 -------------------------GEKTVILTCSFT-PGSCSLTAYKLTPEGYEWGKQNK 176 (252)
T ss_pred -------------------------CCcEEEEEEcCC-CCceEEEEEecCHHHHHHHHhCc
Confidence 578999999999 79999999999999999999984
No 13
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=97.62 E-value=0.0002 Score=57.54 Aligned_cols=72 Identities=15% Similarity=0.269 Sum_probs=60.4
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEeec
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMNL 250 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~~ 250 (520)
|.|.|++.+|++..+++++++++++|.++|....+++.+.+.|..+ ...+. .+.+++++|+++|+.|++...
T Consensus 1 m~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~---g~~L~--d~~tl~~~~i~~g~~i~l~~~ 72 (76)
T cd01806 1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYS---GKQMN--DDKTAADYKLEGGSVLHLVLA 72 (76)
T ss_pred CEEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEEC---CeEcc--CCCCHHHcCCCCCCEEEEEEE
Confidence 6788999999888999999999999999999999999887777643 22343 467999999999999999753
No 14
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=97.60 E-value=0.00026 Score=58.67 Aligned_cols=72 Identities=15% Similarity=0.084 Sum_probs=59.7
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEeec
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMNL 250 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~~ 250 (520)
|.|-|++..|..+.++++|++++++|.++|.+.++++.+.+.|... ...+. ++.+|++.||+.|+.|++-|+
T Consensus 2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~---Gk~L~--D~~tL~~ygi~~~stv~l~~~ 73 (73)
T cd01791 2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKW---YTIFK--DHISLGDYEIHDGMNLELYYQ 73 (73)
T ss_pred EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeC---CcCCC--CCCCHHHcCCCCCCEEEEEeC
Confidence 6788999988778889999999999999999999999887776543 12233 456899999999999999774
No 15
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=97.48 E-value=0.00032 Score=55.79 Aligned_cols=70 Identities=16% Similarity=0.211 Sum_probs=58.3
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
|.|.|++.+|++..+++++++++++|.++|....+++.+...|..+ ...+. .+.+|++.|+++|+.|++.
T Consensus 1 i~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~---g~~L~--d~~~L~~~~i~~~~~l~l~ 70 (72)
T cd01809 1 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYS---GRVLK--DDETLSEYKVEDGHTIHLV 70 (72)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEEC---CEECC--CcCcHHHCCCCCCCEEEEE
Confidence 5688999999888999999999999999999999998776666543 22343 4679999999999999875
No 16
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=97.36 E-value=0.00055 Score=55.81 Aligned_cols=70 Identities=7% Similarity=0.169 Sum_probs=59.5
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
|.|.||+.+|++..+++++++++.+|.++|.+..+++.+.+.|..+ ...+. ++.+|++.|+++|+.|.+.
T Consensus 1 m~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~---G~~L~--d~~~L~~~~i~~~~~l~l~ 70 (74)
T cd01807 1 MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFK---GKALA--DDKRLSDYSIGPNAKLNLV 70 (74)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEEC---CEECC--CCCCHHHCCCCCCCEEEEE
Confidence 6688999999788899999999999999999999999887777643 22344 5689999999999999886
No 17
>cd01763 Sumo Small ubiquitin-related modifier (SUMO). Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
Probab=97.33 E-value=0.00094 Score=56.61 Aligned_cols=73 Identities=22% Similarity=0.230 Sum_probs=62.3
Q ss_pred ceeeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEee
Q psy8916 172 FYKILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMN 249 (520)
Q Consensus 172 fYMiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~ 249 (520)
-.+.|++++.+|...+++|.+++++..|++++.+..+++.+.+.+..+ ..+|. .+.|+.++|+.+||+|.+..
T Consensus 10 ~~i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~---G~~L~--~~~T~~~l~m~d~d~I~v~l 82 (87)
T cd01763 10 EHINLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFD---GQRIR--DNQTPDDLGMEDGDEIEVML 82 (87)
T ss_pred CeEEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEEC---CeECC--CCCCHHHcCCCCCCEEEEEE
Confidence 478899999999888999999999999999999999999887776554 23444 46799999999999998863
No 18
>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.
Probab=97.27 E-value=0.00053 Score=57.14 Aligned_cols=64 Identities=17% Similarity=0.234 Sum_probs=51.8
Q ss_pred eCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCC-CcCeEEEe
Q psy8916 179 QSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLS-NGDFVYMM 248 (520)
Q Consensus 179 RSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLk-HGDmlyl~ 248 (520)
.|-+| +..+++++++++.+|.++|....+++.+...|+ +. +.+ .-.+.+|++.|++ |||||||-
T Consensus 9 ~~~~~-t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL~-~G---~~L-~dD~~tL~~ygi~~~g~~~~l~ 73 (75)
T cd01799 9 QSHTV-TIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRWV-IG---QRL-ARDQETLYSHGIRTNGDSAFLY 73 (75)
T ss_pred ccCCC-eEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEE-cC---Cee-CCCcCCHHHcCCCCCCCEEEEE
Confidence 45667 999999999999999999999999998877773 21 123 2245799999999 99999984
No 19
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=97.27 E-value=0.00087 Score=53.84 Aligned_cols=71 Identities=11% Similarity=0.153 Sum_probs=59.0
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEee
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMN 249 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~ 249 (520)
|.|-||+.+|+.+.+++++++++.+|.++|....+++.+...|..+ ...+. ++.+|+++|+++|+.|.+..
T Consensus 1 m~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~---g~~L~--d~~~L~~~~i~~~~~i~l~~ 71 (76)
T cd01803 1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA---GKQLE--DGRTLSDYNIQKESTLHLVL 71 (76)
T ss_pred CEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEEC---CEECC--CCCcHHHcCCCCCCEEEEEE
Confidence 5678999999888899999999999999999999998776766543 22344 46789999999999999874
No 20
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=97.25 E-value=0.00096 Score=54.20 Aligned_cols=70 Identities=21% Similarity=0.226 Sum_probs=57.2
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCC--CCCcceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFEL--NTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~l--s~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
|-|.|++..|..+-+++++++++.+|.++|....++ +.+.+.|..+ ...|. ++.+|+++|+++||.|++.
T Consensus 1 m~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~---G~~L~--d~~~L~~~~i~~~~~i~~~ 72 (77)
T cd01805 1 MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYS---GKILK--DDTTLEEYKIDEKDFVVVM 72 (77)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEEC---CEEcc--CCCCHHHcCCCCCCEEEEE
Confidence 568899999977889999999999999999999987 6666666543 22344 4679999999999999985
No 21
>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=97.20 E-value=0.00085 Score=57.61 Aligned_cols=71 Identities=23% Similarity=0.272 Sum_probs=50.2
Q ss_pred HHHHHHh-cCceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEEcCCCChHHHHHHHHhcCCeEEEEEEecC
Q psy8916 428 FLEYWRV-TGHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDPKAEVVEEIASSLGLTQVGWIFTDL 506 (520)
Q Consensus 428 Fi~~wr~-~g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~ll~d~~e~~Vd~iA~~LGL~rVG~IFTdl 506 (520)
|+..-+. ...+.+|+|+|++... ..+|..++..||....+.. .++ ....++..+...||+.|||+.||.
T Consensus 4 il~~a~~~~~~ev~G~L~G~~~~~-------~~~i~~~~~~~~~~~~~~~--~~~-~~~~~~~~~~~~~~~iVGwyhshp 73 (116)
T cd07767 4 FLDAAKSINGKEVIGLLYGSKTKK-------VLDVDEVIAVPFDEGDKDD--NVW-FLMYLDFKKLNAGLRIVGWYHTHP 73 (116)
T ss_pred HHHHHhcCCCcEEEEEeEEEEcCC-------EEEEEEEEecccCCCCCcc--HHH-HHHHHHHHHhcCCCeEEEEEEcCC
Confidence 4444444 3789999999997744 2488899999987654321 111 113577788889999999999998
Q ss_pred cc
Q psy8916 507 VA 508 (520)
Q Consensus 507 ~~ 508 (520)
..
T Consensus 74 ~~ 75 (116)
T cd07767 74 KP 75 (116)
T ss_pred CC
Confidence 64
No 22
>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=97.10 E-value=0.0014 Score=53.54 Aligned_cols=68 Identities=15% Similarity=0.197 Sum_probs=57.0
Q ss_pred eeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEee
Q psy8916 177 RIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMN 249 (520)
Q Consensus 177 RfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~ 249 (520)
-||+..|.++-+++++++++.+|.++|.+..+++.+.+.|..+ .+.|. ++.+|++.|+++|+.|++..
T Consensus 2 ~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~---G~~L~--D~~tL~~~~i~~~~tl~l~~ 69 (74)
T cd01810 2 LVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFE---GRPME--DEHPLGEYGLKPGCTVFMNL 69 (74)
T ss_pred EEECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEEC---CEECC--CCCCHHHcCCCCCCEEEEEE
Confidence 4789999778899999999999999999999999887777532 23344 56899999999999999874
No 23
>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins. SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....
Probab=97.10 E-value=0.0012 Score=53.13 Aligned_cols=69 Identities=16% Similarity=0.268 Sum_probs=56.6
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCC-CcceeeecCCccccccccccccccccCCCCcCeEEE
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNT-YNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYM 247 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~-dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl 247 (520)
|-|.+++++|...++.+.++++++.|+++..+..+++. ..+.+.-+ ..+|. .+.|++++||+.||+|=+
T Consensus 1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fd---G~~L~--~~~T~~~~~ied~d~Idv 70 (72)
T PF11976_consen 1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFD---GKRLD--PNDTPEDLGIEDGDTIDV 70 (72)
T ss_dssp EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEET---TEEE---TTSCHHHHT-STTEEEEE
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEEC---CEEcC--CCCCHHHCCCCCCCEEEE
Confidence 46889999998889999999999999999999999998 77777553 23454 467999999999999754
No 24
>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=97.00 E-value=0.0039 Score=59.70 Aligned_cols=77 Identities=21% Similarity=0.350 Sum_probs=59.5
Q ss_pred CHHHHHHHHHHHHhc---CceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEEcCCCChHHHHHHHHhcCCe
Q psy8916 421 NRTLVERFLEYWRVT---GHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDPKAEVVEEIASSLGLT 497 (520)
Q Consensus 421 ~~~~v~~Fi~~wr~~---g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~ll~d~~e~~Vd~iA~~LGL~ 497 (520)
..++++.|+.-=+.. ..+-+|||||+... +++ .|..|+-|||.++.+.+.+.+ +..+.+.|+.-||+
T Consensus 7 pk~il~~~l~~A~~~~~~p~E~cGlL~G~~~~------~~~-~I~~i~~~~q~~~~~~~~~~~---~~e~~~~~~~~gle 76 (173)
T cd08066 7 PADLMDKFLQLAEPNTSRNLETCGILCGKLSN------NAF-FITHLIIPKQSGTSDSCQTTN---EEELFDFQDQHDLI 76 (173)
T ss_pred CHHHHHHHHHHHHhCCCCCCeEEEEEEeEcCC------CeE-EEEEEEeccccCCCceecCCC---HHHHHHHHHhCCCe
Confidence 457999999988875 37999999998432 333 567788889999998877643 23366678889999
Q ss_pred EEEEEEecCc
Q psy8916 498 QVGWIFTDLV 507 (520)
Q Consensus 498 rVG~IFTdl~ 507 (520)
.|||+-||-.
T Consensus 77 ~vGwyHSHP~ 86 (173)
T cd08066 77 TLGWIHTHPT 86 (173)
T ss_pred eEEEEeccCC
Confidence 9999999874
No 25
>cd01804 midnolin_N Ubiquitin-like domain of midnolin. midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.
Probab=96.91 E-value=0.0032 Score=52.35 Aligned_cols=70 Identities=17% Similarity=0.341 Sum_probs=57.1
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEee
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMN 249 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~ 249 (520)
|.|-|++..|+.+-|++++++++++|.++|.+.++++.+.+.|... .+.+. ++ +|++.|++.|+-|++..
T Consensus 2 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~---Gk~L~--d~-~L~~~gi~~~~~i~l~~ 71 (78)
T cd01804 2 MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHR---ETRLS--SG-KLQDLGLGDGSKLTLVP 71 (78)
T ss_pred eEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEEC---CcCCC--CC-cHHHcCCCCCCEEEEEe
Confidence 6788999999777799999999999999999999988877766533 22333 24 79999999999999963
No 26
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=96.90 E-value=0.0023 Score=52.21 Aligned_cols=68 Identities=12% Similarity=0.193 Sum_probs=54.1
Q ss_pred eeeCC-CcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 177 RIQSP-VGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 177 RfRSk-dG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
.|+.. .|.++-|++++++++++|..+|.+..+++.+.+.|..+ .+.+. -...++++.|+++||+|+|.
T Consensus 2 ~v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~~---Gk~L~-D~~~~L~~~gi~~~~~l~l~ 70 (71)
T cd01796 2 TVYTARSETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYN---GRELV-DNKRLLALYGVKDGDLVVLR 70 (71)
T ss_pred EEEECCCCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEEC---CeEcc-CCcccHHHcCCCCCCEEEEe
Confidence 45666 77678899999999999999999999999887777543 22333 22468999999999999984
No 27
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=96.89 E-value=0.0021 Score=49.34 Aligned_cols=64 Identities=22% Similarity=0.278 Sum_probs=52.4
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcC
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGD 243 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGD 243 (520)
|-|+||+.++ ...+++++++++.+|.++|...++++.+.+.|..+. ..+. .+.+|+++|+++|+
T Consensus 1 ~~i~vk~~~~-~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~g---~~L~--d~~tL~~~~i~~~~ 64 (64)
T smart00213 1 IELTVKTLDG-TITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYKG---KVLE--DDRTLADYNIQDGS 64 (64)
T ss_pred CEEEEEECCc-eEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECC---EECC--CCCCHHHcCCcCCC
Confidence 4678888887 899999999999999999999999988766665432 2344 35799999999986
No 28
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=96.84 E-value=0.0036 Score=49.68 Aligned_cols=64 Identities=22% Similarity=0.370 Sum_probs=53.9
Q ss_pred CCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 180 SPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 180 SkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
+.+|..+.+++++++++.+|.++|....+++.+.+.|..+ ...+ ..+.+|+++|+++|+.|++.
T Consensus 2 ~~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~---G~~L--~d~~tL~~~~i~~~~~I~l~ 65 (69)
T PF00240_consen 2 TLSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYN---GKEL--DDDKTLSDYGIKDGSTIHLV 65 (69)
T ss_dssp ETTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEET---TEEE--STTSBTGGGTTSTTEEEEEE
T ss_pred CCCCcEEEEEECCCCCHHHhhhhcccccccccccceeeee---eecc--cCcCcHHHcCCCCCCEEEEE
Confidence 4567689999999999999999999999999888777653 2334 36789999999999999885
No 29
>PTZ00044 ubiquitin; Provisional
Probab=96.77 E-value=0.0043 Score=50.36 Aligned_cols=71 Identities=11% Similarity=0.182 Sum_probs=59.2
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEee
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMN 249 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~ 249 (520)
|.|-||+.+|.++-+++++++++.+|.++|....+++.+...|..+ ...+. ++.+|++.|+++|+.|.+..
T Consensus 1 m~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~---g~~L~--d~~~l~~~~i~~~~~i~l~~ 71 (76)
T PTZ00044 1 MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYS---GKQMS--DDLKLSDYKVVPGSTIHMVL 71 (76)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEEC---CEEcc--CCCcHHHcCCCCCCEEEEEE
Confidence 5678899999888999999999999999999999999887777642 22343 56789999999999998863
No 30
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=96.74 E-value=0.0042 Score=50.02 Aligned_cols=67 Identities=13% Similarity=0.183 Sum_probs=55.7
Q ss_pred eeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 177 RIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 177 RfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
-|+...|+++-+++++++++++|.++|.+..+++.+.+.|..+ ...|. ++.+|++.|+++|+.|++.
T Consensus 2 ~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~---G~~L~--d~~~l~~~~i~~~stl~l~ 68 (70)
T cd01798 2 YVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFA---GKELR--NTTTIQECDLGQQSILHAV 68 (70)
T ss_pred EEEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEEC---CeECC--CCCcHHHcCCCCCCEEEEE
Confidence 3677888888899999999999999999999999887777543 22343 5689999999999999985
No 31
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=96.74 E-value=0.0047 Score=49.20 Aligned_cols=68 Identities=18% Similarity=0.236 Sum_probs=55.0
Q ss_pred eeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 175 ILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 175 iIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
.|+|+.. |+.+-+++++++++.+|.++|....+++.+.+.|..+ ...+. .+.+|+++|+++|+.|++.
T Consensus 2 ~i~vk~~-g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~---g~~l~--d~~~L~~~~i~~g~~l~v~ 69 (71)
T cd01812 2 RVRVKHG-GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFK---GKERD--DAETLDMSGVKDGSKVMLL 69 (71)
T ss_pred EEEEEEC-CEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeC---CcccC--ccCcHHHcCCCCCCEEEEe
Confidence 4677777 6477789999999999999999999999887777643 12333 4679999999999999984
No 32
>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein. DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.
Probab=96.73 E-value=0.0038 Score=51.18 Aligned_cols=68 Identities=10% Similarity=0.180 Sum_probs=56.6
Q ss_pred eeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 176 LRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 176 IRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
++||...|+++-+++++++++.+|..+|.+..+++.+.+.|+.. ...+. ++.+|++.|++.|..|+|.
T Consensus 1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~---G~~L~--D~~~l~~~~i~~~~tv~~~ 68 (70)
T cd01794 1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFS---GKLLT--DKTRLQETKIQKDYVVQVI 68 (70)
T ss_pred CeEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEEC---CeECC--CCCCHHHcCCCCCCEEEEE
Confidence 46889999889999999999999999999999998877777532 22344 5689999999999999985
No 33
>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=96.69 E-value=0.006 Score=50.71 Aligned_cols=74 Identities=16% Similarity=0.189 Sum_probs=57.8
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEeec
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMNL 250 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~~ 250 (520)
|-|.|++..|+++-+++++++++++|.++|.+.++++.+.+.|..-- ....+. ++.+|+++|+++|+.|++.-.
T Consensus 3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~-~G~~L~--D~~tL~~~gi~~gs~l~l~~~ 76 (80)
T cd01792 3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLD-SREVLQ--DGVPLVSQGLGPGSTVLLVVQ 76 (80)
T ss_pred eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEecc-CCCCCC--CCCCHHHcCCCCCCEEEEEEE
Confidence 66788999997777788999999999999999999888776663211 122343 466899999999999998643
No 34
>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF. NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.
Probab=96.59 E-value=0.0057 Score=51.18 Aligned_cols=71 Identities=15% Similarity=0.285 Sum_probs=56.6
Q ss_pred eeeeeeCCCcce-eeEE-ecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEee
Q psy8916 174 KILRIQSPVGIV-KRIN-INRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMN 249 (520)
Q Consensus 174 MiIRfRSkdG~m-~RVe-v~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~ 249 (520)
|.|-|++..|++ +-++ +++++++++|.++|.+..+++.+.+.|... .+.+. .+.+|++.|+++|+.|.+.-
T Consensus 1 M~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~---Gk~L~--D~~tL~~y~i~~~~~i~l~~ 73 (78)
T cd01797 1 MWIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYR---GKQME--DGHTLFDYNVGLNDIIQLLV 73 (78)
T ss_pred CEEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeC---CEECC--CCCCHHHcCCCCCCEEEEEE
Confidence 678899999943 3574 789999999999999999998877776542 23344 56799999999999999863
No 35
>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2. hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.
Probab=96.32 E-value=0.012 Score=47.53 Aligned_cols=68 Identities=19% Similarity=0.321 Sum_probs=55.1
Q ss_pred eeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 175 ILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 175 iIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
.|-|++..| ..-|++++++++++|.++|.+..+++.+.+.|... ...|. ++.+|+++|++.|+.|++.
T Consensus 2 ~i~vk~~~g-~~~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li~~---Gk~L~--d~~tL~~~~i~~~stl~l~ 69 (71)
T cd01808 2 KVTVKTPKD-KEEIEIAEDASVKDFKEAVSKKFKANQEQLVLIFA---GKILK--DTDTLTQHNIKDGLTVHLV 69 (71)
T ss_pred EEEEEcCCC-CEEEEECCCChHHHHHHHHHHHhCCCHHHEEEEEC---CeEcC--CCCcHHHcCCCCCCEEEEE
Confidence 467889999 57899999999999999999999988777766431 22343 4678999999999999885
No 36
>cd01795 USP48_C USP ubiquitin-specific protease. The USP (ubiquitin-specific protease) family is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin and ubiquitin-like adducts. While the USP's have a conserved catalytic core domain, they differ in their domain architectures. This subfamily, which includes USP31, and USP48, has a carboxy-terminal ubiquitin-like domain in addition to a DUSP (domain of ubiquitin-specific proteases) domain,
Probab=96.32 E-value=0.0084 Score=53.57 Aligned_cols=62 Identities=18% Similarity=0.275 Sum_probs=52.8
Q ss_pred cceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEee
Q psy8916 183 GIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMN 249 (520)
Q Consensus 183 G~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~ 249 (520)
| -++++|++++++..|..+|...|+++.+..-|+.+ +. +|. -.++||+++||-.|..|+|.-
T Consensus 15 ~-~~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~d-G~--~L~-DDsrTLssyGv~sgSvl~Lli 76 (107)
T cd01795 15 G-EKALLVSANQTLKELKIQIMHAFSVAPFDQNLSID-GK--ILS-DDCATLGTLGVIPESVILLKA 76 (107)
T ss_pred C-CceEEeCccccHHHHHHHHHHHhcCCcccceeeec-Cc--eec-cCCccHHhcCCCCCCEEEEEe
Confidence 6 78999999999999999999999999887777766 22 333 357899999999999999974
No 37
>cd01802 AN1_N ubiquitin-like domain of AN1. AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.
Probab=96.30 E-value=0.014 Score=51.59 Aligned_cols=71 Identities=14% Similarity=0.111 Sum_probs=59.6
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEee
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMN 249 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~ 249 (520)
|.|-|++..|++.-+++++++++++|.++|....+++.+.+.|... ...|. ++.+|++.||+.|+.|++..
T Consensus 28 M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~---Gk~L~--D~~tL~dy~I~~~stL~l~~ 98 (103)
T cd01802 28 MELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWN---NMELE--DEYCLNDYNISEGCTLKLVL 98 (103)
T ss_pred EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEEC---CEECC--CCCcHHHcCCCCCCEEEEEE
Confidence 7888999999788899999999999999999999999877777532 22344 46799999999999999864
No 38
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=96.06 E-value=0.029 Score=46.33 Aligned_cols=75 Identities=17% Similarity=0.253 Sum_probs=58.2
Q ss_pred eeeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCc-ceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 173 YKILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYN-FALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 173 YMiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~ds-ftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
.-.|+||-|||....-...+++++.+|++-|...+..+..+ |.|...-. ...+....++||+++||..+..|+|.
T Consensus 6 ~~~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~~~P-r~~l~~~~~~tl~e~~l~p~~~l~v~ 81 (82)
T PF00789_consen 6 VVRIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELITAFP-RRELTDEDSKTLEEAGLLPSATLIVE 81 (82)
T ss_dssp EEEEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEESSS-TEECCSTTTSBTCCCTTSSCEEEEEE
T ss_pred EEEEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEeCCC-CcCCCccccccHHHhcCCCCeEEEEE
Confidence 35789999999556667779999999999998887666554 88865433 44455444789999999999999985
No 39
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=96.04 E-value=0.021 Score=46.67 Aligned_cols=69 Identities=10% Similarity=0.123 Sum_probs=54.6
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEee
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMN 249 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~ 249 (520)
|-|-||+. . ++-++++|++++.+|.++|.+..+++.+.+.|... .+.+. ++.+|++.|+++|+.|++..
T Consensus 1 mqi~vk~~-~-~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~---Gk~L~--D~~tL~~~~i~~~~tl~l~~ 69 (74)
T cd01793 1 MQLFVRAQ-N-THTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLA---GVPLE--DDATLGQCGVEELCTLEVAG 69 (74)
T ss_pred CEEEEECC-C-EEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEEC---CeECC--CCCCHHHcCCCCCCEEEEEE
Confidence 34556664 3 68899999999999999999999998877776542 22344 56899999999999999863
No 40
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=96.04 E-value=0.028 Score=49.22 Aligned_cols=78 Identities=21% Similarity=0.250 Sum_probs=54.4
Q ss_pred HHHHHHHHHHHh-cCceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCce-EEcCCCChHHHHHHH-HhcCCeEE
Q psy8916 423 TLVERFLEYWRV-TGHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKI-KLLPDPKAEVVEEIA-SSLGLTQV 499 (520)
Q Consensus 423 ~~v~~Fi~~wr~-~g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~-~ll~d~~e~~Vd~iA-~~LGL~rV 499 (520)
..+.+.++..+. ...+-+|+|+|.+..+ . .+|.-+|..|+....+.+ ....++.++..+..+ ...||+.|
T Consensus 7 ~v~~~i~~h~~~~~p~e~~G~L~G~~~~~-~------~~i~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v 79 (135)
T smart00232 7 LVPLNILKHAIRDGPEEVCGVLLGKSNKD-R------PEVKEVFAVPNEPQDDSVQEYDEDYSHLMDEELKKVNKDLEIV 79 (135)
T ss_pred HHHHHHHHHHhcCCCcEEEEEEEEEEcCC-E------EEEEEEEecCcCCCCcchhhhhhhHHHHHHHHHHhhCCCceEE
Confidence 466666666655 3568999999998643 3 377888998887766554 333455555555443 45899999
Q ss_pred EEEEecCc
Q psy8916 500 GWIFTDLV 507 (520)
Q Consensus 500 G~IFTdl~ 507 (520)
||+-|+..
T Consensus 80 Gwyhshp~ 87 (135)
T smart00232 80 GWYHSHPD 87 (135)
T ss_pred EEEEcCCC
Confidence 99999874
No 41
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=95.82 E-value=0.037 Score=42.92 Aligned_cols=66 Identities=17% Similarity=0.270 Sum_probs=52.7
Q ss_pred eeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 178 IQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 178 fRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
+++.+|+...++++++.++.+|.++|...++++.+.+.|..+. ..+. .+.+++++|+++|+.|++.
T Consensus 2 v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~g---~~l~--d~~~l~~~~v~~~~~i~v~ 67 (69)
T cd01769 2 VKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAG---KILK--DDKTLSDYGIQDGSTLHLV 67 (69)
T ss_pred eEccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECC---cCCC--CcCCHHHCCCCCCCEEEEE
Confidence 5566676788999999999999999999999888777664322 2343 4668999999999999986
No 42
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
Probab=95.41 E-value=0.036 Score=45.64 Aligned_cols=63 Identities=21% Similarity=0.155 Sum_probs=51.1
Q ss_pred cceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEeec
Q psy8916 183 GIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMNL 250 (520)
Q Consensus 183 G~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~~ 250 (520)
|.++-+++++++++.+|.++|....+++.+...|..+. ..+. .+++|+++|+++|+.|.+...
T Consensus 7 g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~G---~~L~--d~~tL~~~~i~~g~~l~v~~~ 69 (76)
T cd01800 7 GQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEG---IFIK--DSNSLAYYNLANGTIIHLQLK 69 (76)
T ss_pred CeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECC---EEcC--CCCcHHHcCCCCCCEEEEEEe
Confidence 55788999999999999999999999998877765432 2233 467999999999999998643
No 43
>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=95.15 E-value=0.054 Score=47.13 Aligned_cols=80 Identities=15% Similarity=0.244 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHhcCce-eeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEEcCCCChHHHHHHHHh--cCCeEE
Q psy8916 423 TLVERFLEYWRVTGHQ-RLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDPKAEVVEEIASS--LGLTQV 499 (520)
Q Consensus 423 ~~v~~Fi~~wr~~g~Q-R~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~ll~d~~e~~Vd~iA~~--LGL~rV 499 (520)
..+-++++..+..... -+|+|+|++.+... ..|...|+-|+..+.+.....+-.......+..++ -.+..|
T Consensus 11 ~vll~i~~h~~r~~~~~v~G~LlG~~~~~~~------v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iV 84 (114)
T PF01398_consen 11 LVLLKIIDHATRSSPNEVIGLLLGTQDGDNT------VEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVNPNLEIV 84 (114)
T ss_dssp HHHHHHHHHHHHHHCTEEEEEEEEEEETT-E------EEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCSTTSEEE
T ss_pred HHHHHHHHHHhcCCCCEEEEEEEEEecCceE------EEEEEEEEeeEecCccccccchhhHHHHHHhhhccccccceEE
Confidence 3667777777664444 49999999988763 48999999999999888776543333333344443 359999
Q ss_pred EEEEecCcc
Q psy8916 500 GWIFTDLVA 508 (520)
Q Consensus 500 G~IFTdl~~ 508 (520)
||.-|+..-
T Consensus 85 GWY~s~p~~ 93 (114)
T PF01398_consen 85 GWYHSHPNI 93 (114)
T ss_dssp EEEEEESSS
T ss_pred EEEEccCCc
Confidence 999998743
No 44
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.96 E-value=0.083 Score=56.54 Aligned_cols=72 Identities=22% Similarity=0.237 Sum_probs=58.1
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcC---CCCCcceeeecCCccccccccccccccccCCCCcCeEEEeec
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFE---LNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMNL 250 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~---ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~~ 250 (520)
|.|.|++-.|.++-|+|++++++.+|+++|....+ ++.+.+.|..+ .+.|. ++++|+++||++||.|.+...
T Consensus 1 MkItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~---GkiL~--Dd~tL~dy~I~e~~~Ivvmv~ 75 (378)
T TIGR00601 1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYS---GKILS--DDKTVREYKIKEKDFVVVMVS 75 (378)
T ss_pred CEEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEEC---CEECC--CCCcHHHcCCCCCCEEEEEec
Confidence 67889999998888999999999999999999887 77666666542 22343 467999999999999887654
No 45
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=93.97 E-value=0.32 Score=40.39 Aligned_cols=74 Identities=16% Similarity=0.155 Sum_probs=54.0
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccc-cccccccCCCCcCeEEEe
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSR-DQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~-~~tv~~lgLkHGDmlyl~ 248 (520)
-.|+||-|+|........+++++.+|++-|....+....+|.|...-. +..+.... ++||.++||-....|+|.
T Consensus 5 ~~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~~~~~~f~L~t~~P-rk~l~~~d~~~tL~e~gL~p~~~l~v~ 79 (80)
T smart00166 5 CRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALTDGNDPFTLNSPFP-RRTFTKDDYSKTLLELALLPSSTLVLE 79 (80)
T ss_pred EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcccCCCCCEEEEeCCC-CcCCccccccCCHHHCCCCCceEEEEe
Confidence 468999999932344667999999999999665665556788876532 23444332 679999999988888874
No 46
>cd01813 UBP_N UBP ubiquitin processing protease. The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.
Probab=93.94 E-value=0.19 Score=41.68 Aligned_cols=62 Identities=18% Similarity=0.100 Sum_probs=48.5
Q ss_pred eeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 185 VKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 185 m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
.+-|++++++++++|.++|.+..+++.+..-|... ..++.+.. ++.+|+++|++.|+-|.+-
T Consensus 11 ~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~-~~~Gk~l~-D~~~L~~~~i~~g~~i~lm 72 (74)
T cd01813 11 EYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGL-KVKGKPAE-DDVKISALKLKPNTKIMMM 72 (74)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEee-cccCCcCC-CCcCHHHcCCCCCCEEEEE
Confidence 67899999999999999999999999887766431 12233322 5789999999999988763
No 47
>cd00196 UBQ Ubiquitin-like proteins. Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate.
Probab=93.21 E-value=0.31 Score=34.41 Aligned_cols=65 Identities=22% Similarity=0.278 Sum_probs=46.8
Q ss_pred eCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 179 QSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 179 RSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
+.++|....+.+.+..++.+|++++...++.+.+.+.|+.+...... ...+...++++|+.+.+.
T Consensus 3 ~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~~~~~~-----~~~~~~~~~~~~~~i~~~ 67 (69)
T cd00196 3 KLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPD-----SLTLEDYGLQDGDELVLV 67 (69)
T ss_pred EecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECCeECCC-----CCcHHHcCCCCCCEEEEE
Confidence 34455567888888999999999999999988777888765322111 112256688999998875
No 48
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=92.88 E-value=0.24 Score=43.07 Aligned_cols=41 Identities=22% Similarity=0.466 Sum_probs=36.1
Q ss_pred eeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCC---ccee
Q psy8916 176 LRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTY---NFAL 216 (520)
Q Consensus 176 IRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~d---sftL 216 (520)
..|++|.||++|+.+.|++.+.+|.+.|...|+.... .+.|
T Consensus 3 FK~~~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L 46 (86)
T cd06409 3 FKFKDPKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYAL 46 (86)
T ss_pred EEeeCCCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccE
Confidence 4688999999999999999999999999999988863 4544
No 49
>PLN02560 enoyl-CoA reductase
Probab=92.74 E-value=0.28 Score=51.20 Aligned_cols=76 Identities=20% Similarity=0.189 Sum_probs=51.3
Q ss_pred eeeeeeCCCccee---eEEecCCcchHHHHHHHHhhcCC-CCCcceeeec--CCccccccccccccccccCCCCcCeEEE
Q psy8916 174 KILRIQSPVGIVK---RININRSDTCKDLFEKINKEFEL-NTYNFALFKQ--RNKTDEIFSSRDQTIASVGLSNGDFVYM 247 (520)
Q Consensus 174 MiIRfRSkdG~m~---RVev~ptDtfs~LleKLl~~f~l-s~dsftL~~n--r~~~~~l~s~~~~tv~~lgLkHGDmlyl 247 (520)
|-|-|.++.|+.. -|++++++++++|.+++.+..+. +.+.+.|..+ .+..+...-.++++|+++|++.|+.||+
T Consensus 1 M~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstLy~ 80 (308)
T PLN02560 1 MKVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTVVF 80 (308)
T ss_pred CEEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceEEE
Confidence 3455667777322 37999999999999999998765 4444444322 2211112112567899999999999999
Q ss_pred ee
Q psy8916 248 MN 249 (520)
Q Consensus 248 ~~ 249 (520)
+-
T Consensus 81 kD 82 (308)
T PLN02560 81 KD 82 (308)
T ss_pred Ee
Confidence 83
No 50
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=92.57 E-value=0.75 Score=38.73 Aligned_cols=64 Identities=19% Similarity=0.232 Sum_probs=48.1
Q ss_pred eeeEEecCCcchHHHHHHHHhhcCCCCCcceeeec-CCcccccc--ccccccccccCCCCcCeEEEe
Q psy8916 185 VKRININRSDTCKDLFEKINKEFELNTYNFALFKQ-RNKTDEIF--SSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 185 m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~n-r~~~~~l~--s~~~~tv~~lgLkHGDmlyl~ 248 (520)
.....++++.++++|..+|...++++.....|.-. ......+. ....++|+.+|+++|+.|++.
T Consensus 15 ~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~V~ 81 (87)
T PF14560_consen 15 SVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIHVV 81 (87)
T ss_dssp EEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEEEE
T ss_pred eEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEEEE
Confidence 56677889999999999999999999987766433 12222222 446889999999999999997
No 51
>KOG0010|consensus
Probab=91.88 E-value=0.72 Score=50.99 Aligned_cols=74 Identities=19% Similarity=0.293 Sum_probs=62.3
Q ss_pred ceeeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEeecC
Q psy8916 172 FYKILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMNLS 251 (520)
Q Consensus 172 fYMiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~~~ 251 (520)
--..++|++++. -+-|+|..+.++.+|+|+|+..|..+.+.+.|. +.++|.+ +..||.+.|++.|--|+|.-..
T Consensus 14 ~~irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLI----faGrILK-D~dTL~~~gI~Dg~TvHLVik~ 87 (493)
T KOG0010|consen 14 SLIRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFGAPPDQLVLI----YAGRILK-DDDTLKQYGIQDGHTVHLVIKS 87 (493)
T ss_pred ceeEEEEecCCc-ceeEecccchHHHHHHHHHHHhcCCChhHeeee----ecCcccc-ChhhHHHcCCCCCcEEEEEecc
Confidence 346678999999 899999999999999999999999998877654 3455554 6789999999999999997543
No 52
>cd01790 Herp_N Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein. Herp (Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein) , is an integral membrane protein that is induced by the endoplasmic reticulum (ER) stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. Herp has an N-terminal ubiquitin-like domain that is involved in Herp degradation, but is not necessary for its enhancement of amyloid beta-protein generation.
Probab=91.60 E-value=0.59 Score=39.92 Aligned_cols=71 Identities=13% Similarity=0.106 Sum_probs=49.6
Q ss_pred eeeeeeCCCcce--eeEEecCCcchHHHHHHHHhhcC--CCCCcceeeecCCccccccccccccccccC--CCCcCeEEE
Q psy8916 174 KILRIQSPVGIV--KRININRSDTCKDLFEKINKEFE--LNTYNFALFKQRNKTDEIFSSRDQTIASVG--LSNGDFVYM 247 (520)
Q Consensus 174 MiIRfRSkdG~m--~RVev~ptDtfs~LleKLl~~f~--ls~dsftL~~nr~~~~~l~s~~~~tv~~lg--LkHGDmlyl 247 (520)
+-|.|+|++|.. +-|++++++++.+|.++|.+.++ .+.+...|. ++|++.. ++.+|++.+ ++.|..+.|
T Consensus 2 i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLI----y~GKiLk-D~~tL~~~~~~~~~~~tiHL 76 (79)
T cd01790 2 VTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLI----YSGKLLP-DHLKLRDVLRKQDEYHMVHL 76 (79)
T ss_pred eEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEE----EcCeecc-chhhHHHHhhcccCCceEEE
Confidence 357899999954 33455899999999999999884 333444443 2344432 567888885 888888888
Q ss_pred ee
Q psy8916 248 MN 249 (520)
Q Consensus 248 ~~ 249 (520)
.+
T Consensus 77 V~ 78 (79)
T cd01790 77 VC 78 (79)
T ss_pred Ee
Confidence 64
No 53
>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=91.55 E-value=0.26 Score=42.22 Aligned_cols=43 Identities=28% Similarity=0.459 Sum_probs=35.2
Q ss_pred ccccccCCCeEEEEEeeccccccCCCceeeeeecCCceeechHHHHHHHhhhhhCCCC
Q psy8916 8 TLQQPNLGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPNP 65 (520)
Q Consensus 8 ~~~~~~lgl~~vG~Iftdl~~~~~~~g~v~~~r~~~s~fls~~E~~~aa~~Q~~~p~~ 65 (520)
...+...|++.|||+.|+.... .|+|+.++.+.+++|...|++
T Consensus 55 ~~~~~~~~~~iVGwyhshp~~~---------------~~~s~~dv~~~~~~q~~~~~~ 97 (116)
T cd07767 55 DFKKLNAGLRIVGWYHTHPKPS---------------CFLSPNDLATHELFQRYFPEK 97 (116)
T ss_pred HHHHhcCCCeEEEEEEcCCCCC---------------CccCHHHHHHHHHHHHhCCCC
Confidence 3456679999999999987543 389999999999999977754
No 54
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=91.48 E-value=1.2 Score=36.73 Aligned_cols=71 Identities=15% Similarity=0.205 Sum_probs=49.4
Q ss_pred eeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccc-cccccccccCCCCcCeEEEe
Q psy8916 175 ILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFS-SRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 175 iIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s-~~~~tv~~lgLkHGDmlyl~ 248 (520)
.|+||-|+|........+++++.+|++=|...... ..+|.|...-. ...+.. ..++||.++||. ...+.+.
T Consensus 4 ~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~~-~~~f~L~t~~P-r~~~~~~~~~~TL~e~gL~-~s~~~~~ 75 (77)
T cd01767 4 KIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGPP-AEPFTLMTSFP-RRVLTDLDYELTLQEAGLV-NEVVFQR 75 (77)
T ss_pred EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCCC-CCCEEEEeCCC-CccCCCCCccCcHHHcCCc-cceEEEE
Confidence 58999999933345677999999999998766533 45677765522 223433 368899999999 5555553
No 55
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=91.28 E-value=1.1 Score=37.95 Aligned_cols=72 Identities=14% Similarity=0.128 Sum_probs=52.4
Q ss_pred eeeeCCCcceeeEE--ecCCcchHHHHHHHHhhcCCCCCcceee-ecCCccc-cccccccccccccCCCCcCeEEEe
Q psy8916 176 LRIQSPVGIVKRIN--INRSDTCKDLFEKINKEFELNTYNFALF-KQRNKTD-EIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 176 IRfRSkdG~m~RVe--v~ptDtfs~LleKLl~~f~ls~dsftL~-~nr~~~~-~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
+.|.|... .+.+| ++++.++.+|.+++...++++.....|. .+..... .......++|+.+|+++|.-|.+.
T Consensus 4 v~i~~~~~-~~~~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~~~~~~~l~~d~~~L~~y~~~dg~~IhVv 79 (84)
T cd01789 4 VNITSSAD-SFSFEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGDDKLVSKLDDDDALLGSYPVDDGCRIHVI 79 (84)
T ss_pred EEEEeCCC-ceeeeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCCCCeEeecCCCccEeeeccCCCCCEEEEE
Confidence 44555544 46666 8899999999999999999998777663 3322211 112346779999999999999986
No 56
>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=91.14 E-value=1.1 Score=43.64 Aligned_cols=84 Identities=17% Similarity=0.229 Sum_probs=55.8
Q ss_pred eeecCHHHHHHHHHHHHhcCceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEEcCCCChHHHHHHHHhcCC
Q psy8916 417 VEFENRTLVERFLEYWRVTGHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDPKAEVVEEIASSLGL 496 (520)
Q Consensus 417 vef~~~~~v~~Fi~~wr~~g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~ll~d~~e~~Vd~iA~~LGL 496 (520)
|..+...++.-....+. +..--+|+|-|+++..+.+ ..|..++..|+..+.+.+.+-+ ..+..+.+.++..||
T Consensus 7 V~Is~~all~m~~Ha~~-~~~EvcGlL~G~~d~~~~~-----l~Vt~~~p~~~~~~~~~~e~dp-~~q~e~~~~l~~~gl 79 (187)
T cd08067 7 VTVSSNALLLMDFHCHL-TTSEVIGYLGGTWDPNTQN-----LTILQAFPCRSRLTGLDCEMDP-VSETEIRESLESRGL 79 (187)
T ss_pred EEECHHHHHHHHHHhcC-CCcEEEEEEEeEEcCCCCe-----EEEEEEEecCCCCCCcccccCH-HHHHHHHHHHHHcCC
Confidence 33444434433333443 3366889999998764332 3788889889988766666522 123456677889999
Q ss_pred eEEEEEEecCc
Q psy8916 497 TQVGWIFTDLV 507 (520)
Q Consensus 497 ~rVG~IFTdl~ 507 (520)
..|||.=||-.
T Consensus 80 ~vVGwYHSHP~ 90 (187)
T cd08067 80 SVVGWYHSHPT 90 (187)
T ss_pred EEEEEEecCCC
Confidence 99999988864
No 57
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=90.56 E-value=1.3 Score=37.10 Aligned_cols=73 Identities=8% Similarity=0.094 Sum_probs=51.3
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCcccccc-ccccccccccCCCCcCeEEEe
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIF-SSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~-s~~~~tv~~lgLkHGDmlyl~ 248 (520)
-.|+||-|+|.........++++.+|++-|.....-. .+|.|...-.. +.+. +-.++||.++||-.-.+|+|.
T Consensus 5 ~~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~~~-~~f~L~t~fPr-k~~~~~d~~~TL~elgL~Psa~L~v~ 78 (79)
T cd01772 5 TRIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTGNG-GPFTLMTPFPR-KVFTEDDMEKPLQELGLVPSAVLIVT 78 (79)
T ss_pred EEEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCCCC-CCEEEEeCCCC-eECCcccccCCHHHCCCCCceEEEEe
Confidence 4689999999334446778999999999987655322 56777654222 2232 234679999999999999873
No 58
>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=90.54 E-value=0.65 Score=44.63 Aligned_cols=65 Identities=18% Similarity=0.281 Sum_probs=50.5
Q ss_pred cccCCCeEEEEEeeccccccCCCceeeeeecCCceeechHHHHHHHhhhhhCCCCCCCCCCCCCCcceeeeeecchhhhh
Q psy8916 11 QPNLGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTVNECIM 90 (520)
Q Consensus 11 ~~~lgl~~vG~Iftdl~~~~~~~g~v~~~r~~~s~fls~~E~~~aa~~Q~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (520)
+..-||+.||||-|+-... -|+|+.++..-+++|+..|
T Consensus 70 ~~~~gle~vGwyHSHP~~~---------------~~pS~~Dv~t~~~~~~~~p--------------------------- 107 (173)
T cd08066 70 QDQHDLITLGWIHTHPTQT---------------CFLSSVDLHTHCSYQLMLP--------------------------- 107 (173)
T ss_pred HHhCCCeeEEEEeccCCCC---------------CccCHHHHHHHHHHHhcCC---------------------------
Confidence 3467999999999987543 3899999999999998754
Q ss_pred ccccccCCCCCCccCCCCcCCCceEEEEEECCCCCceeeeeEech-HHHHHHh
Q psy8916 91 AGHLQNLHPNPCRFAPSGYFGSKFVTICVTGDKDNQVHMEGYQVS-NQCMALV 142 (520)
Q Consensus 91 ~~~~~~~~~~~~~~~~~g~~~s~fvT~~vsg~~~~~i~~~~yqvS-~q~~alv 142 (520)
.++-+|||. +.+.+.||.+. ..+++..
T Consensus 108 ----------------------~~~~lIvSp---~~~~l~afrl~~~~g~~~~ 135 (173)
T cd08066 108 ----------------------EAIAIVCAP---KYNEFGIFRLTDPPGLDEI 135 (173)
T ss_pred ----------------------CeEEEEECC---CCcEEeEEEeecCCcceec
Confidence 245566774 46889999998 6676654
No 59
>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.
Probab=90.31 E-value=0.63 Score=38.40 Aligned_cols=63 Identities=13% Similarity=0.126 Sum_probs=38.6
Q ss_pred CCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEE
Q psy8916 180 SPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYM 247 (520)
Q Consensus 180 SkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl 247 (520)
+++||.++|.+.|+.++.+++++...+|+++.+.+.|..++ +.+. .+..+...||.+|..|-|
T Consensus 3 ~~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~~---k~ld--lslp~R~snL~n~akLeL 65 (65)
T PF11470_consen 3 CYNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHNN---KPLD--LSLPFRLSNLPNNAKLEL 65 (65)
T ss_dssp -TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEETT---EEES--SS-BHHHH---SS-EEEE
T ss_pred ccCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEECC---EEec--cccceeecCCCCCCEEeC
Confidence 45677899999999999999999999999999888776443 2333 244677789999987743
No 60
>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=89.54 E-value=2 Score=36.99 Aligned_cols=70 Identities=19% Similarity=0.266 Sum_probs=49.7
Q ss_pred eeeeeCCCcceeeE--EecCCcchHHHHHHHHhhcCCCCCcceeeecCCcccccc-ccccccccccCCCCcCeEEEe
Q psy8916 175 ILRIQSPVGIVKRI--NINRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIF-SSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 175 iIRfRSkdG~m~RV--ev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~-s~~~~tv~~lgLkHGDmlyl~ 248 (520)
.|+||=|+| .|+ ....++++..|+.=+.. .+.+.+.|.|..+=..+ .+. .-.+.||.++||.+-+.|||.
T Consensus 7 ~i~vRlP~G--~r~~rrF~~~~~L~~v~~fv~~-~g~~~~~f~L~t~FPRr-~~~~~d~~~TL~e~GL~P~~~LfVq 79 (82)
T cd01773 7 RLMLRYPDG--KREQIALPEQAKLLALVRHVQS-KGYPNERFELLTNFPRR-KLSHLDYDITLQEAGLCPQETVFVQ 79 (82)
T ss_pred EEEEECCCC--CEEEEEeCCCCcHHHHHHHHHh-cCCCCCCEEEecCCCCc-ccCCcccCCCHHHcCCCCCcEEEEe
Confidence 588999999 444 45678999988887766 45566778776551111 122 223579999999999999985
No 61
>cd01771 Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=89.36 E-value=2.2 Score=36.19 Aligned_cols=69 Identities=12% Similarity=0.208 Sum_probs=51.0
Q ss_pred eeeeeCCCcceeeE--EecCCcchHHHHHHHHhhcCCCCCcceeeec-CCcccccc-ccccccccccCCCCcCeEEEe
Q psy8916 175 ILRIQSPVGIVKRI--NINRSDTCKDLFEKINKEFELNTYNFALFKQ-RNKTDEIF-SSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 175 iIRfRSkdG~m~RV--ev~ptDtfs~LleKLl~~f~ls~dsftL~~n-r~~~~~l~-s~~~~tv~~lgLkHGDmlyl~ 248 (520)
.|+||=|+| .|+ ....++++.+|+.=|... +.+..+|.|..+ |. ..+. ...+.||.++||.....|||.
T Consensus 6 ~i~iRlP~G--~r~~rrF~~t~~L~~l~~fv~~~-~~~~~~f~L~t~fPR--k~~~~~d~~~TL~e~gL~p~~~L~Ve 78 (80)
T cd01771 6 KLRVRTPSG--DFLERRFLGDTPLQVLLNFVASK-GYPIDEYKLLSSWPR--RDLTQLDPNFTLLELKLYPQETLILE 78 (80)
T ss_pred EEEEECCCC--CEEEEEeCCCCcHHHHHHHHHhc-CCCCCCEEEecCCCC--CCCcCCCCCCcHHHcCCCCCcEEEEE
Confidence 588999999 555 577999999999888764 555567877654 32 2232 224679999999999999984
No 62
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=88.78 E-value=1.8 Score=36.56 Aligned_cols=67 Identities=18% Similarity=0.126 Sum_probs=48.1
Q ss_pred eeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCC-CCcceeeec-CCccccccccccccccccCCCCcCe
Q psy8916 175 ILRIQSPVGIVKRININRSDTCKDLFEKINKEFELN-TYNFALFKQ-RNKTDEIFSSRDQTIASVGLSNGDF 244 (520)
Q Consensus 175 iIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls-~dsftL~~n-r~~~~~l~s~~~~tv~~lgLkHGDm 244 (520)
.|.||-|||.........++++.+|++=|....+-+ ..+|.|... |. .++... +.||.++||.+.-+
T Consensus 6 ~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~~~~~~f~L~t~fP~--k~l~~~-~~Tl~eagL~~s~v 74 (79)
T cd01770 6 SIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPEFAARPFTLMTAFPV--KELSDE-SLTLKEANLLNAVI 74 (79)
T ss_pred EEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCCCCCCCEEEecCCCC--cccCCC-CCcHHHCCCcCcEE
Confidence 588999999323336779999999999998766432 356777654 32 345544 88999999997544
No 63
>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=88.03 E-value=2.7 Score=43.05 Aligned_cols=89 Identities=16% Similarity=0.243 Sum_probs=61.4
Q ss_pred CCCCcCeeeecCHHHHHHHHHHHHh-cCceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEEcCCCChHHHH
Q psy8916 410 VYRHVDNVEFENRTLVERFLEYWRV-TGHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDPKAEVVE 488 (520)
Q Consensus 410 ~~R~VDhvef~~~~~v~~Fi~~wr~-~g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~ll~d~~e~~Vd 488 (520)
....+..|..... .+..++.-.+. ...--+|.|.|+.+. +. .+|..+|..|++++.+-+...++..+.+++
T Consensus 5 ~~~~~~~V~Is~~-allkil~Ha~~~~p~Ev~GlLlG~~~~-~~------v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~ 76 (268)
T cd08069 5 DPDYFEKVYISSL-ALLKMLKHARAGGPIEVMGLMLGKVDD-YT------IIVVDVFALPVEGTETRVNAQDEFQEYMVQ 76 (268)
T ss_pred CCCcccEEEECHH-HHHHHHHHHhccCCceEEEEEEeeecC-Ce------EEEEEEEECCcCCCCCceeccHHHHHHHHH
Confidence 3455666777665 66666665555 346789999999542 22 488899999999988777765544444444
Q ss_pred --HH-HHhcCCeEEEEEEecC
Q psy8916 489 --EI-ASSLGLTQVGWIFTDL 506 (520)
Q Consensus 489 --~i-A~~LGL~rVG~IFTdl 506 (520)
.. +..-|+..|||.=||-
T Consensus 77 ~~~~~~~~~~~~vVGWYHSHP 97 (268)
T cd08069 77 YEMLKQTGRPENVVGWYHSHP 97 (268)
T ss_pred HHHHHHhCCCceeEeeeccCC
Confidence 22 2337899999999886
No 64
>PF08817 YukD: WXG100 protein secretion system (Wss), protein YukD; InterPro: IPR014921 YukD is a bacterial protein that adopts a ubiquitin-like fold []. Ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that YukD lacks the capacity for covalent bond formation with other proteins []. ; PDB: 2BPS_B.
Probab=87.49 E-value=2.2 Score=35.48 Aligned_cols=68 Identities=18% Similarity=0.288 Sum_probs=42.8
Q ss_pred eeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCC------cceeeecCCccccccccccccccccCCCCcCeEEE
Q psy8916 176 LRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTY------NFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYM 247 (520)
Q Consensus 176 IRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~d------sftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl 247 (520)
+-|..++|+..-+.+...-+++.|++.|...++.+.. .|.+. +.....+. .+.||++.|+.+||.|+|
T Consensus 5 Vtv~~~~~~~~Dl~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~--~~~g~~L~--~~~tL~~~gV~dGd~L~L 78 (79)
T PF08817_consen 5 VTVDAGNGRQVDLALPADVPVAELIPELVELLGLPGDDPPGHGQWVLA--RAGGRPLD--PDQTLADAGVRDGDVLVL 78 (79)
T ss_dssp EEEE-TT--EEEEEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG---GGTEEEE--TTSBCGGGT--TT-EEEE
T ss_pred EEEEcCCCcEEEEEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEE--ecCCcccC--CcCcHhHcCCCCCCEEEe
Confidence 3466666547778888999999999999999977542 24554 22222444 578999999999999987
No 65
>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=82.62 E-value=4.2 Score=36.45 Aligned_cols=76 Identities=21% Similarity=0.241 Sum_probs=51.2
Q ss_pred HHHHHHHHHHhc-CceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCC--CceEEcCCCChHHHHHHHHhcCCeEEE
Q psy8916 424 LVERFLEYWRVT-GHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSR--DKIKLLPDPKAEVVEEIASSLGLTQVG 500 (520)
Q Consensus 424 ~v~~Fi~~wr~~-g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~--dg~~ll~d~~e~~Vd~iA~~LGL~rVG 500 (520)
+.++++..-+.. -.=-+|+|.|++..... +|..++..|..... +.|.+-+. ....+.+.++..||+.||
T Consensus 3 ~~~~il~ha~~~~P~E~cGlL~G~~~~~~~-------~i~~~~p~~n~~~~~~~~f~~d~~-~~~~~~~~~~~~g~~~vG 74 (128)
T cd08070 3 LLEAILAHAEAEYPEECCGLLLGKGGGVTA-------IVTEVYPVRNVAESPRRRFEIDPA-EQLAAQREARERGLEVVG 74 (128)
T ss_pred HHHHHHHHHHhCCCCceEEEEEeecCCCCc-------eEEEEEEccCCCCCCCceEEECHH-HHHHHHHHHHHCCCeEEE
Confidence 556666666653 24578999999886654 34666766654333 45664432 224566677888999999
Q ss_pred EEEecCc
Q psy8916 501 WIFTDLV 507 (520)
Q Consensus 501 ~IFTdl~ 507 (520)
|.=||..
T Consensus 75 ~~HSHP~ 81 (128)
T cd08070 75 IYHSHPD 81 (128)
T ss_pred EEeCCCC
Confidence 9999975
No 66
>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-terminal domain of Tsc13. Tsc13 is an enoyl reductase involved in elongation of long chain fatty acids that localizes to the endoplasmic reticulum and is highly enriched in a novel structure marking nuclear-vacuolar junctions.
Probab=81.75 E-value=5.3 Score=32.95 Aligned_cols=60 Identities=20% Similarity=0.284 Sum_probs=40.7
Q ss_pred eeEEec-CCcchHHHHHHHHhhcCC-CCCcceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 186 KRININ-RSDTCKDLFEKINKEFEL-NTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 186 ~RVev~-ptDtfs~LleKLl~~f~l-s~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
.+++++ ++.++.+|.+.+....+. +...+.+.... ....|. .+.+|+++|++.|+.||+.
T Consensus 14 ~~~~~~~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~~~-~g~~L~--d~~tL~~~gv~~g~~lyvK 75 (77)
T cd01801 14 GKLKVSSGDATIADLKKLIAKSSPQLTVNRQSLRLEP-KGKSLK--DDDTLVDLGVGAGATLYVR 75 (77)
T ss_pred eecccCCCCccHHHHHHHHHHHcCCCCcceeEEEeCC-CCcccC--CcccHhhcCCCCCCEEEEe
Confidence 335555 788999999999988753 34444443222 222333 4568999999999999985
No 67
>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=81.32 E-value=3.5 Score=36.06 Aligned_cols=39 Identities=23% Similarity=0.272 Sum_probs=32.0
Q ss_pred cccCCCeEEEEEeeccccccCCCceeeeeecCCceeechHHHHHHHhhhhhCCC
Q psy8916 11 QPNLGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPN 64 (520)
Q Consensus 11 ~~~lgl~~vG~Iftdl~~~~~~~g~v~~~r~~~s~fls~~E~~~aa~~Q~~~p~ 64 (520)
+...|++.|||+-|+..... ++|...+.+++.+|...++
T Consensus 71 ~~~~~~~~vGwyhshp~~~~---------------~pS~~D~~~~~~~~~~~~~ 109 (135)
T smart00232 71 KVNKDLEIVGWYHSHPDESP---------------FPSEVDVATHESYQAPWPI 109 (135)
T ss_pred hhCCCceEEEEEEcCCCCCC---------------CcCHHHHHHHHHHHhcCCc
Confidence 45789999999999875433 7999999999999987664
No 68
>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=79.45 E-value=10 Score=32.47 Aligned_cols=70 Identities=13% Similarity=0.254 Sum_probs=49.1
Q ss_pred eeeeeeCCCcceeeE--EecCCcchHHHHHHHHhhcCCCCCcceeeec-CCcccccc------ccccccccccCCCCcCe
Q psy8916 174 KILRIQSPVGIVKRI--NINRSDTCKDLFEKINKEFELNTYNFALFKQ-RNKTDEIF------SSRDQTIASVGLSNGDF 244 (520)
Q Consensus 174 MiIRfRSkdG~m~RV--ev~ptDtfs~LleKLl~~f~ls~dsftL~~n-r~~~~~l~------s~~~~tv~~lgLkHGDm 244 (520)
-.|.||=|+| .|+ ....++++..|+.=|.. .+.....|.|..+ |. ..+. ...+.||+++||.+..+
T Consensus 5 ~~I~iRlp~G--~Rl~rrF~~~~tl~~l~~fv~~-~~~~~~~f~L~t~FPr--r~~~~~~~~~~~~~~TL~eaGL~~s~~ 79 (85)
T cd01774 5 VKIVFKLPNG--TRVERRFLFTQSLRVIHDFLFS-LKETPEKFQIVTNFPR--RVLPCLPSEGDPPPPTLLEAGLSNSEV 79 (85)
T ss_pred EEEEEECCCC--CEEEEEeCCCCcHHHHHHHHHh-CCCCCCcEEEecCCCC--ccccccccccCcCCCCHHHcCCCCccE
Confidence 3578999999 455 45688999999998854 3334456776543 21 1222 22477999999999999
Q ss_pred EEEe
Q psy8916 245 VYMM 248 (520)
Q Consensus 245 lyl~ 248 (520)
|||.
T Consensus 80 L~V~ 83 (85)
T cd01774 80 LFVQ 83 (85)
T ss_pred EEEe
Confidence 9985
No 69
>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A.
Probab=76.06 E-value=11 Score=33.18 Aligned_cols=69 Identities=17% Similarity=0.320 Sum_probs=42.7
Q ss_pred eeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCC-ccccccccccccccccCCCCcCeEEEeecCCCC
Q psy8916 185 VKRININRSDTCKDLFEKINKEFELNTYNFALFKQRN-KTDEIFSSRDQTIASVGLSNGDFVYMMNLSSPN 254 (520)
Q Consensus 185 m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~-~~~~l~s~~~~tv~~lgLkHGDmlyl~~~~~~~ 254 (520)
......+.+|+++.+.+.+.+.|.+.. ...|-.... .+-++......||.+.||.+|.+|-+.-.+..+
T Consensus 15 ~~t~~FSk~DTI~~v~~~~rklf~i~~-E~RLW~~~~~~~~e~L~~~~~Tv~da~L~~gQ~vliE~rn~DG 84 (88)
T PF14836_consen 15 VLTKQFSKTDTIGFVEKEMRKLFNIQE-ETRLWNKYSENSYELLNNPEITVEDAGLYDGQVVLIEERNEDG 84 (88)
T ss_dssp EEEEEE-TTSBHHHHHHHHHHHCT-TS--EEEEEECTTTCEEEE--TTSBTTTTT--TTEEEEEEE--TTS
T ss_pred HhHhhccccChHHHHHHHHHHHhCCCc-cceehhccCCcchhhhCCCCccHHHccCcCCCEEEEEeeccCC
Confidence 345677899999999999999999943 344532211 222333445779999999999999987555433
No 70
>PF08825 E2_bind: E2 binding domain; InterPro: IPR014929 E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades. This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The protein resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains []. ; GO: 0005524 ATP binding, 0016881 acid-amino acid ligase activity, 0045116 protein neddylation; PDB: 3GZN_D 3DBL_F 1R4N_H 1R4M_D 2NVU_B 1TT5_D 3DBR_D 3DBH_H 1YOV_B 3FN1_A ....
Probab=64.74 E-value=4.7 Score=34.79 Aligned_cols=60 Identities=22% Similarity=0.384 Sum_probs=40.1
Q ss_pred EEecCCcchHHHHHHHHhh--cCCCCCcc-----eeeec-CCcccc-ccccccccccccCCCCcCeEEEe
Q psy8916 188 ININRSDTCKDLFEKINKE--FELNTYNF-----ALFKQ-RNKTDE-IFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 188 Vev~ptDtfs~LleKLl~~--f~ls~dsf-----tL~~n-r~~~~~-l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
|+++++.++.+|++.+.+. |.+..-++ +||-. +..-.+ -....++++.+| +..|+.|+|+
T Consensus 1 i~v~~~~TL~~lid~L~~~~~~qlk~PSlt~~~k~LYm~~pp~Lee~Tr~NL~k~l~eL-~~~g~ei~Vt 69 (84)
T PF08825_consen 1 IEVSPSWTLQDLIDSLCEKPEFQLKKPSLTTANKTLYMQSPPSLEEATRPNLSKKLKEL-LSDGEEITVT 69 (84)
T ss_dssp EEESTTSBSHHHHHHHHHSTTT--SS-EEESSEEEEEESSSHHHHHHTGGGGSSBTTTT-HHSSEEEEEE
T ss_pred CCcCccchHHHHHHHHHhChhhhcCCCcccCCCceEEEeCCHHHHHHhhhhhhhhHHHH-hcCCCEEEEE
Confidence 6899999999999999998 54443222 23321 111112 224568899999 9999999996
No 71
>KOG0005|consensus
Probab=62.82 E-value=14 Score=30.84 Aligned_cols=69 Identities=16% Similarity=0.285 Sum_probs=47.6
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEE
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYM 247 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl 247 (520)
|+|.+.+-.|...-|+++|+|.+..+.+.+.+.-+++.....|.... +. ..++.+-.+.+|--|..|-+
T Consensus 1 m~iKvktLt~KeIeidIep~DkverIKErvEEkeGIPp~qqrli~~g---kq--m~DD~tA~~Y~~~~GSVlHl 69 (70)
T KOG0005|consen 1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYAG---KQ--MNDDKTAAHYNLLGGSVLHL 69 (70)
T ss_pred CeeeEeeeccceEEEeeCcchHHHHHHHHhhhhcCCCchhhhhhhcc---cc--ccccccHHHhhhccceeEee
Confidence 56777777785567888999999999999999999986533332111 11 22455666777777776654
No 72
>cd01788 ElonginB Ubiquitin-like domain of Elongin B. Elongin B is part of an E3 ubiquitin ligase complex called VEC that activates ubiquitylation by the E2 ubiquitin-conjugating enzyme Ubc5. VEC is composed of von Hippel-Lindau tumor suppressor protein (pVHL), elongin C, cullin 2, NEDD8, and Rbx1. ElonginB binds elonginC to form the elonginBC complex which is a positive regulator of RNA polymerase II elongation factor Elongin A. The BC complex then binds VHL (von Hippel-Lindau) tumour suppressor protein to form a VCB ternary complex. Elongin B has a ubiquitin-llike domain.
Probab=62.63 E-value=14 Score=34.20 Aligned_cols=61 Identities=20% Similarity=0.212 Sum_probs=45.9
Q ss_pred ccceeeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCC
Q psy8916 170 DVFYKILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGL 239 (520)
Q Consensus 170 ~vfYMiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgL 239 (520)
|||.|+.|- .- +.=+.+.++.++-+|..+|...+..+.....|+.+. ..+. .++||++.|+
T Consensus 2 dvFlmIrR~---KT-TiF~dakes~tVlelK~~iegI~k~pp~dQrL~kd~---qvLe--D~kTL~d~g~ 62 (119)
T cd01788 2 DVFLMIRRH---KT-TIFTDAKESTTVYELKRIVEGILKRPPEDQRLYKDD---QLLD--DGKTLGDCGF 62 (119)
T ss_pred ceEEEEEec---ce-EEEeecCCcccHHHHHHHHHHHhcCChhHheeecCc---eeec--ccccHHHcCc
Confidence 677777663 33 677999999999999999999998888777777321 2233 5778888887
No 73
>PF12436 USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-specific protease 7; InterPro: IPR024729 This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found in proteins of the peptidase C19 family, which contains contains ubiquitinyl hydrolases like ubiquitin-specific protease 7 (USP7). USP7 regulates the turnover of p53 [].; PDB: 2KVR_A 2YLM_A.
Probab=62.56 E-value=11 Score=38.06 Aligned_cols=62 Identities=21% Similarity=0.400 Sum_probs=43.1
Q ss_pred eeeEEecCCcchHHHHHHHHhhcCCCCC-cceeeec--CCccccccccccccccccCCCCcCeEEEe
Q psy8916 185 VKRININRSDTCKDLFEKINKEFELNTY-NFALFKQ--RNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 185 m~RVev~ptDtfs~LleKLl~~f~ls~d-sftL~~n--r~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
.-.+-|+.++.+++|...|.+.++++.+ .+.+|++ ++....+ -...++.+..|.|||+|-.-
T Consensus 86 iGh~~v~~~~~v~~l~~~i~~~~g~p~~t~l~lyEEi~~~~ie~i--~~~~t~~~~el~~GdIi~fQ 150 (249)
T PF12436_consen 86 IGHVYVPKNDKVSELVPLINERAGLPPDTPLLLYEEIKPNMIEPI--DPNQTFEKAELQDGDIICFQ 150 (249)
T ss_dssp EEEEEEETT-BGGGTHHHHHHHHT--TT--EEEEEEEETTEEEE----SSSBHHHTT--TTEEEEEE
T ss_pred EeEEEECCCCCHHHHHHHHHHHcCCCCCCceEEEEEeccceeeEc--CCCCchhhcccCCCCEEEEE
Confidence 5588999999999999999999999876 6777765 3333334 25678888999999998874
No 74
>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain. The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 1EF1_B 1SGH_A 1E5W_A 2KC2_A 2KMA_A 3IVF_A 1H4R_B 3U8Z_A 1ISN_A 3BIN_A ....
Probab=59.97 E-value=44 Score=26.99 Aligned_cols=41 Identities=22% Similarity=0.349 Sum_probs=33.4
Q ss_pred eeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCC-cceeee
Q psy8916 178 IQSPVGIVKRININRSDTCKDLFEKINKEFELNTY-NFALFK 218 (520)
Q Consensus 178 fRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~d-sftL~~ 218 (520)
|+-+||.+..++++++.+..+|+++|...+++... -|.|..
T Consensus 1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~ 42 (80)
T PF09379_consen 1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQY 42 (80)
T ss_dssp EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE
T ss_pred CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEE
Confidence 34578856899999999999999999999999864 455654
No 75
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=59.75 E-value=19 Score=31.20 Aligned_cols=52 Identities=25% Similarity=0.364 Sum_probs=38.0
Q ss_pred cccccceeeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCcccccc
Q psy8916 167 YVPDVFYKILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIF 227 (520)
Q Consensus 167 yvp~vfYMiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~ 227 (520)
||=.|||.. +.=|.+.+.-++.+|.++|.+.|.++.+...|+.....++++.
T Consensus 3 ~vvKV~f~~---------tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkde~s~~~v 54 (80)
T cd06406 3 YVVKVHFKY---------TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKSEASGEDV 54 (80)
T ss_pred eEEEEEEEE---------EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEeccCCCCCcc
Confidence 555566653 3556667777999999999999999877888876655555443
No 76
>PF10790 DUF2604: Protein of Unknown function (DUF2604); InterPro: IPR019726 This entry represents bacterial proteins with undetermined function.
Probab=58.32 E-value=24 Score=29.82 Aligned_cols=63 Identities=11% Similarity=0.256 Sum_probs=42.1
Q ss_pred eeEEecCCcchHHHHHHHHhhcC---CCCCcceeeecCCccccccccccccccccCCCCcCeEEEeecCC
Q psy8916 186 KRININRSDTCKDLFEKINKEFE---LNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMNLSS 252 (520)
Q Consensus 186 ~RVev~ptDtfs~LleKLl~~f~---ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~~~~ 252 (520)
-.||..++..+-.+.++.++.-+ .+...|.+ ++..+.+... ++.|+++|+.+|-.|||+..++
T Consensus 8 v~VEANvnaPLh~v~akALe~sgNvgQP~ENWEl---kDe~G~vlD~-~kKveD~GftngvkLFLsLKAG 73 (76)
T PF10790_consen 8 VQVEANVNAPLHPVRAKALEQSGNVGQPPENWEL---KDESGQVLDV-NKKVEDFGFTNGVKLFLSLKAG 73 (76)
T ss_pred eeeecCCCCcchHHHHHHHhhccccCCCccccee---eccCCcEeec-cchhhhccccccceEEEEeecc
Confidence 45677788888878777776542 22233433 2233444433 6789999999999999986654
No 77
>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=57.80 E-value=66 Score=30.09 Aligned_cols=78 Identities=23% Similarity=0.230 Sum_probs=52.4
Q ss_pred HHHHHHHHHhcCc--eeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEEcCCC--ChHHHHHHHHhc-C-CeE
Q psy8916 425 VERFLEYWRVTGH--QRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDP--KAEVVEEIASSL-G-LTQ 498 (520)
Q Consensus 425 v~~Fi~~wr~~g~--QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~ll~d~--~e~~Vd~iA~~L-G-L~r 498 (520)
++.|.+|=+.... =-.|+|.|++.. . .++|..+++|+-.+...-..+..+. .++.+++..+.- | +.-
T Consensus 3 ~~~~~~~~Q~~~~~~EtGGiLiG~~~~-~------~~ii~~~t~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~y 75 (131)
T TIGR02256 3 VAMLKSYRQWHDLSTETGGVLIGERRG-A------HAVITKISEPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTY 75 (131)
T ss_pred HHHHHHHHhCcCCCCccceEEEEEEcC-C------cEEEEEEEcCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEE
Confidence 4555555444333 478999999872 2 3588999998876655555555544 356788887664 3 888
Q ss_pred EEEEEecCccC
Q psy8916 499 VGWIFTDLVAE 509 (520)
Q Consensus 499 VG~IFTdl~~~ 509 (520)
||-==||....
T Consensus 76 lGeWHtHP~~~ 86 (131)
T TIGR02256 76 LGEWHTHPEDQ 86 (131)
T ss_pred EEecCcCCCCC
Confidence 99877777644
No 78
>PF14732 UAE_UbL: Ubiquitin/SUMO-activating enzyme ubiquitin-like domain; PDB: 1Y8Q_B 1Y8R_E 3KYD_B 3KYC_B.
Probab=56.77 E-value=24 Score=30.45 Aligned_cols=56 Identities=20% Similarity=0.355 Sum_probs=33.3
Q ss_pred CCcchHHHHHHHHh-hcCCCCCccee----eecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 192 RSDTCKDLFEKINK-EFELNTYNFAL----FKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 192 ptDtfs~LleKLl~-~f~ls~dsftL----~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
...++++|.++++. .|+...-.+.+ ..+++. +.-..+..++|+++|++||.+|-+.
T Consensus 7 ~~~TL~~lv~~Vlk~~Lg~~~P~v~~~~~ilyd~de-~~~~~~l~k~L~elgi~~gs~L~v~ 67 (87)
T PF14732_consen 7 KKMTLGDLVEKVLKKKLGMNEPDVSVGGTILYDSDE-EEYDDNLPKKLSELGIVNGSILTVD 67 (87)
T ss_dssp TT-BHHHHHHHCCCCCS--SSEEEEES-EEEE-SSS-SSSTTCTTSBGGGGT--TT-EEEEE
T ss_pred hhCcHHHHHHHHHHhccCCCCCEEEeCCCEEEcCCc-chhhhcccCChhHcCCCCCCEEEEE
Confidence 35688899999876 67766532322 222222 3345667889999999999999986
No 79
>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=55.86 E-value=37 Score=34.64 Aligned_cols=82 Identities=13% Similarity=0.127 Sum_probs=54.3
Q ss_pred eeecCHHHHHHHHH-HHHhcCceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCce--EEcCCCChHHHHHHHHh
Q psy8916 417 VEFENRTLVERFLE-YWRVTGHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKI--KLLPDPKAEVVEEIASS 493 (520)
Q Consensus 417 vef~~~~~v~~Fi~-~wr~~g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~--~ll~d~~e~~Vd~iA~~ 493 (520)
|..+.. .+.+.+. +.|....-=+|.|.|.... +. ..|.-.|.-|...+.+.- ...+......+.++++.
T Consensus 3 V~I~~~-vllkIv~H~~~~~p~~v~G~LLG~~~~-~~------leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~ 74 (266)
T cd08065 3 VQIDGL-VVLKIIKHCKEELPELVQGQLLGLDVG-GT------LEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLRE 74 (266)
T ss_pred EEEeHH-HHHHHHHHHhcCCCcEEEEEEeeeEcC-CE------EEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHH
Confidence 444444 4444444 4444555678999999863 32 377777998887775542 22233445667788899
Q ss_pred cCC--eEEEEEEecC
Q psy8916 494 LGL--TQVGWIFTDL 506 (520)
Q Consensus 494 LGL--~rVG~IFTdl 506 (520)
.|+ ..|||==|+-
T Consensus 75 v~~~e~iVGWY~S~p 89 (266)
T cd08065 75 VNVDHNHVGWYQSTY 89 (266)
T ss_pred hCCCCcEEEeEeecC
Confidence 999 9999988876
No 80
>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=55.46 E-value=37 Score=30.05 Aligned_cols=39 Identities=23% Similarity=0.304 Sum_probs=28.7
Q ss_pred ccccCCCeEEEEEeeccccccCCCceeeeeecCCceeechHHHHHHHhhhhhCC
Q psy8916 10 QQPNLGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHP 63 (520)
Q Consensus 10 ~~~~lgl~~vG~Iftdl~~~~~~~g~v~~~r~~~s~fls~~E~~~aa~~Q~~~p 63 (520)
.+...|+..|||.=++..... |+|...+..-+.+|+..|
T Consensus 59 ~~~~~g~~~vG~YHSHP~~~~---------------~pS~~Di~~~~~~q~~~p 97 (119)
T cd08058 59 VQTGRPLLVVGWYHSHPTFTA---------------WLSSVDIHTQASYQLMLP 97 (119)
T ss_pred HHhCCCCeEEEEEecCCCCCC---------------ccCHHHHHHHHHHhccCC
Confidence 356788999999988874333 789988877777777544
No 81
>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain.
Probab=55.19 E-value=19 Score=30.65 Aligned_cols=51 Identities=18% Similarity=0.241 Sum_probs=37.8
Q ss_pred CCcchHHHHHHHHhhcC--CC-CCcceeeecCCcccc-ccccccccccccCCCCcCeEEEe
Q psy8916 192 RSDTCKDLFEKINKEFE--LN-TYNFALFKQRNKTDE-IFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 192 ptDtfs~LleKLl~~f~--ls-~dsftL~~nr~~~~~-l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
.++++.+|.++|.+.++ +. .+.+.|.. .++ |. ++++|++.|++.|+.|++.
T Consensus 19 ~~~TV~~LK~kI~~~~~egi~~~dqQrLIy----~GKiL~--D~~TL~dygI~~gstlhLv 73 (75)
T cd01815 19 GGYQVSTLKQLIAAQLPDSLPDPELIDLIH----CGRKLK--DDQTLDFYGIQSGSTIHIL 73 (75)
T ss_pred ccCcHHHHHHHHHHhhccCCCChHHeEEEe----CCcCCC--CCCcHHHcCCCCCCEEEEE
Confidence 46899999999999974 43 44455432 222 33 5689999999999999874
No 82
>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and ATGP4 are plant-specific isoprenylated GTP-binding proteins with a single fold that resembles ubiquitin. The function of these proteins is unknown.
Probab=53.36 E-value=14 Score=33.85 Aligned_cols=65 Identities=14% Similarity=0.184 Sum_probs=43.1
Q ss_pred eeeeeeCCCccee--eEEecCCcchHHHHHHHHhhcCC-------CCCcceeeecCCccccccccccccccccCCCCcCe
Q psy8916 174 KILRIQSPVGIVK--RININRSDTCKDLFEKINKEFEL-------NTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDF 244 (520)
Q Consensus 174 MiIRfRSkdG~m~--RVev~ptDtfs~LleKLl~~f~l-------s~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDm 244 (520)
.-||||=.|| += ...+++++++..|.++|.+..+- +.+.+.|.. .+.+.. +++||++.++--||+
T Consensus 5 ~e~kfrl~dg-~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIy----sGKiLe-D~~TL~d~~~p~g~~ 78 (113)
T cd01814 5 IEIKFRLYDG-SDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLIS----AGKILE-NSKTVGECRSPVGDI 78 (113)
T ss_pred EEEEEEccCC-CccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEe----CCeecC-CCCcHHHhCCccccc
Confidence 4589999997 21 34456999999999999987742 233333322 233322 568999999666665
No 83
>KOG2880|consensus
Probab=53.22 E-value=10 Score=40.93 Aligned_cols=76 Identities=25% Similarity=0.378 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHHh---cCceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEEcCCCChHHHHHHHHhcCCeE
Q psy8916 422 RTLVERFLEYWRV---TGHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDPKAEVVEEIASSLGLTQ 498 (520)
Q Consensus 422 ~~~v~~Fi~~wr~---~g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~ll~d~~e~~Vd~iA~~LGL~r 498 (520)
..+++.|++--+. .+.--+|+|-|.-+.-.- .|..+--|-|+++.|.-.. .+|+.+=++-..-+|-.
T Consensus 258 ~~l~~~Fl~la~~NT~knlETCGiL~g~L~~n~f-------~IThliiPkQeatsd~C~t---~neeelF~vQdq~~L~t 327 (424)
T KOG2880|consen 258 ERLMEVFLQLAKSNTKKNLETCGILAGKLERNEF-------YITHLIIPKQEATSDSCNT---MNEEELFEVQDQHELLT 327 (424)
T ss_pred HHHHHHHHHHHhhcccccchHHHHhhhHhhcCcE-------EEEEEEeecccCCCccccc---cCHHHHheeccccccee
Confidence 3589999997765 367789999999765553 6889999999999997543 34556667778899999
Q ss_pred EEEEEecCc
Q psy8916 499 VGWIFTDLV 507 (520)
Q Consensus 499 VG~IFTdl~ 507 (520)
+|||-||-+
T Consensus 328 lGWIHTHPT 336 (424)
T KOG2880|consen 328 LGWIHTHPT 336 (424)
T ss_pred eeeeecCCc
Confidence 999999976
No 84
>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=51.16 E-value=23 Score=34.55 Aligned_cols=65 Identities=23% Similarity=0.205 Sum_probs=43.3
Q ss_pred eeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEEcCCC--ChHHHHHHHHhcCCeEEEEEEecCccCCCCC
Q psy8916 439 RLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDP--KAEVVEEIASSLGLTQVGWIFTDLVAEDLQL 513 (520)
Q Consensus 439 R~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~ll~d~--~e~~Vd~iA~~LGL~rVG~IFTdl~~~~~~~ 513 (520)
=+|+|.|+....+. +-|+++|.-.- ..+.|.|.. ...+|++-|+.-||+.||+-.+|-...+.+-
T Consensus 21 vcGlLlG~~~~~~~-----~~V~d~vPl~h-----~~~~l~P~~Eval~~ve~~~~~~gl~IvG~Yhsh~~~~d~~~ 87 (182)
T cd08060 21 VNGLLLGKKSSGGS-----VEITDAVPLFH-----SCLALAPMLEVALALVDAYCKSSGLVIVGYYQANERLDDSSP 87 (182)
T ss_pred heEEEEeeecCCCC-----EEEEEEEEcCC-----CccccCHHHHHHHHHHHHHHHHCCCEEEEEEecCCcccCCCC
Confidence 36999999653222 34667655443 225544432 2467999999999999999998877665443
No 85
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=50.92 E-value=42 Score=27.10 Aligned_cols=40 Identities=28% Similarity=0.460 Sum_probs=33.1
Q ss_pred eeeeCCCcceeeEEec-CCcchHHHHHHHHhhcCCCCCccee
Q psy8916 176 LRIQSPVGIVKRININ-RSDTCKDLFEKINKEFELNTYNFAL 216 (520)
Q Consensus 176 IRfRSkdG~m~RVev~-ptDtfs~LleKLl~~f~ls~dsftL 216 (520)
++++-.++ .+|+.+. ...++.+|..+|...|++....+.+
T Consensus 3 vK~~~~~~-~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l 43 (81)
T cd05992 3 VKVKYGGE-IRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKL 43 (81)
T ss_pred EEEEecCC-CEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEE
Confidence 45666677 8999999 9999999999999999987544555
No 86
>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=49.23 E-value=60 Score=31.78 Aligned_cols=69 Identities=13% Similarity=0.065 Sum_probs=50.1
Q ss_pred cccCCCeEEEEEeeccccccCCCceeeeeecCCceeechHHHHHHHhhhhhCCCCCCCCCCCCCCcceeeeeecchhhhh
Q psy8916 11 QPNLGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTVNECIM 90 (520)
Q Consensus 11 ~~~lgl~~vG~Iftdl~~~~~~~g~v~~~r~~~s~fls~~E~~~aa~~Q~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (520)
+...||..|||.=|+-... .++|...+-.-+.+|..-+. +
T Consensus 74 l~~~gl~vVGwYHSHP~~~---------------~~pS~~Di~tQ~~yQ~~~~~----~--------------------- 113 (187)
T cd08067 74 LESRGLSVVGWYHSHPTFP---------------PNPSLRDIDTQLDYQIMFKG----S--------------------- 113 (187)
T ss_pred HHHcCCEEEEEEecCCCCC---------------cCCCHHHHHHHHHHHhhccc----c---------------------
Confidence 4578999999999987433 58999999998999987552 0
Q ss_pred ccccccCCCCCCccCCCCcCCCceEEEEEECC----CCCceeeeeEechH
Q psy8916 91 AGHLQNLHPNPCRFAPSGYFGSKFVTICVTGD----KDNQVHMEGYQVSN 136 (520)
Q Consensus 91 ~~~~~~~~~~~~~~~~~g~~~s~fvT~~vsg~----~~~~i~~~~yqvS~ 136 (520)
..-+..||-+|++.- ...+..|.+|+|+.
T Consensus 114 -----------------~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~ 146 (187)
T cd08067 114 -----------------DSGYEPCVGLICSPYDRRNSTPESQITCFWVMP 146 (187)
T ss_pred -----------------ccCCCCeEEEEEccccCCCCCCCCcEEEEEEEC
Confidence 112367888888772 23567788888765
No 87
>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=46.38 E-value=61 Score=33.26 Aligned_cols=82 Identities=18% Similarity=0.256 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHhc-CceeeEEEEEEEeeCCCCCccceEEEE--EEecCCC-CCCCCceEEcCCCChHHHHHHHHh-----
Q psy8916 423 TLVERFLEYWRVT-GHQRLGLLYGKYQLHPDVPLGIKAVVA--AIYEPPQ-ESSRDKIKLLPDPKAEVVEEIASS----- 493 (520)
Q Consensus 423 ~~v~~Fi~~wr~~-g~QR~G~LYG~Y~~~~~vPlGikAvVe--AIYEPPQ-~~~~dg~~ll~d~~e~~Vd~iA~~----- 493 (520)
++++..+.-=+.+ -.==+|+|.|+.....+ .+..++|. .++.++. +...+.+++-+.+.. .+.+=|+.
T Consensus 9 ~~l~~il~HA~~~~P~EvCGLL~G~~~~~~~--~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~-~a~~ea~~~~~~~ 85 (244)
T cd08068 9 DVYLVCLTHALSTEKEEVMGLLIGEIEVSKK--GEEVAIVHISAVIILRRSDKRKDRVEISPEQLS-AASTEAERLTEET 85 (244)
T ss_pred HHHHHHHHHHHhCCCcceeEEEEeecccccc--cccceeEEEeeeccccccCCCCceEEeCHHHHH-HHHHHHHHHHhhc
Confidence 4555555555544 24568999999763111 11122343 4444433 446666777553221 22333444
Q ss_pred -cCCeEEEEEEecCc
Q psy8916 494 -LGLTQVGWIFTDLV 507 (520)
Q Consensus 494 -LGL~rVG~IFTdl~ 507 (520)
-||+.|||.=||-.
T Consensus 86 ~rgl~vVGwYHSHP~ 100 (244)
T cd08068 86 GRPMRVVGWYHSHPH 100 (244)
T ss_pred cCCceEEEEEecCCC
Confidence 88999999988863
No 88
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=46.08 E-value=61 Score=26.50 Aligned_cols=42 Identities=26% Similarity=0.464 Sum_probs=34.7
Q ss_pred eeeeeCCCcc----eeeEEecCCcchHHHHHHHHhhcCCCC--Cccee
Q psy8916 175 ILRIQSPVGI----VKRININRSDTCKDLFEKINKEFELNT--YNFAL 216 (520)
Q Consensus 175 iIRfRSkdG~----m~RVev~ptDtfs~LleKLl~~f~ls~--dsftL 216 (520)
+|||...+|. .+-|.|.++++..++++.++..|++.. ..|.|
T Consensus 4 ~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~~~~~y~L 51 (93)
T PF00788_consen 4 VLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCL 51 (93)
T ss_dssp EEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEE
T ss_pred EEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEE
Confidence 5778878874 577899999999999999999999833 36777
No 89
>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=45.69 E-value=58 Score=33.42 Aligned_cols=35 Identities=14% Similarity=0.173 Sum_probs=28.5
Q ss_pred CCCeEEEEEeeccccccCCCceeeeeecCCceeechHHHHHHHhhhhhCC
Q psy8916 14 LGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHP 63 (520)
Q Consensus 14 lgl~~vG~Iftdl~~~~~~~g~v~~~r~~~s~fls~~E~~~aa~~Q~~~p 63 (520)
-|+..|||.=|+..... ++|...+.....+|+..|
T Consensus 87 rgl~vVGwYHSHP~~~a---------------~PS~~Dv~tq~~~q~~~p 121 (244)
T cd08068 87 RPMRVVGWYHSHPHITV---------------WPSHVDVRTQAMYQMMDS 121 (244)
T ss_pred CCceEEEEEecCCCCCC---------------CCCHhHHHHHHHHHhhCC
Confidence 89999999999875443 799999988788887544
No 90
>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=44.53 E-value=36 Score=29.50 Aligned_cols=35 Identities=26% Similarity=0.428 Sum_probs=27.9
Q ss_pred CCeEEEEEeeccccccCCCceeeeeecCCceeechHHHHHHHhhhhhCCC
Q psy8916 15 GLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPN 64 (520)
Q Consensus 15 gl~~vG~Iftdl~~~~~~~g~v~~~r~~~s~fls~~E~~~aa~~Q~~~p~ 64 (520)
.+..|||.-|....+ .|+|...+..-..+|...||
T Consensus 80 ~~~iVGWY~s~p~~~---------------~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 80 NLEIVGWYHSHPNIS---------------CFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp TSEEEEEEEEESSS----------------SS--HHHHHHHHHHHHHTTT
T ss_pred cceEEEEEEccCCcc---------------ccCCHHHHHHHHHHHHhCCC
Confidence 489999999987443 48999999999999999886
No 91
>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=44.43 E-value=77 Score=29.46 Aligned_cols=70 Identities=17% Similarity=0.170 Sum_probs=44.4
Q ss_pred HHHhc--CceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEEcCCCChHHHHHHHHh-cCCeEEEEEEecCc
Q psy8916 431 YWRVT--GHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDPKAEVVEEIASS-LGLTQVGWIFTDLV 507 (520)
Q Consensus 431 ~wr~~--g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~ll~d~~e~~Vd~iA~~-LGL~rVG~IFTdl~ 507 (520)
+.|.. ...=+|.|.|+.. .+. ..|.--|+=|++.+.+.+.+..+-.+++++...+- -.+..|||--|.-.
T Consensus 15 ~~R~~~~~~~v~G~LlG~~~-~~~------veV~nsF~lp~~~~~~~~~~d~~y~~~m~~~~~~v~~~~~vVGWY~~~~~ 87 (157)
T cd08057 15 YTRRKYGIKRVIGVLLGYVD-GDK------IEVTNSFELPFDEEEESIFIDTEYLEKRYNLHKKVYPQEKIVGWYSIGSN 87 (157)
T ss_pred HHhccCCCCeEEEEEEeEEe-CCE------EEEEEeEEccccCCCcchhhhHHHHHHHHHHHHHhCCCCCEEEEEeecCC
Confidence 45555 4678999999876 333 48888888888777666433222223444433322 35799999888754
No 92
>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=44.30 E-value=71 Score=32.61 Aligned_cols=35 Identities=17% Similarity=0.413 Sum_probs=27.5
Q ss_pred EEEEEECC--CCCceeeeeEechHHHHHHhhcCcccc
Q psy8916 115 VTICVTGD--KDNQVHMEGYQVSNQCMALVRDGCLIP 149 (520)
Q Consensus 115 vT~~vsg~--~~~~i~~~~yqvS~q~~alv~~~~~~~ 149 (520)
|-+|+... ..|.+.+.||..+.++|.+.++|-+.+
T Consensus 113 v~Li~D~~~s~~g~l~lkAyrl~~~~~~~~~~~~~~~ 149 (266)
T cd08065 113 VVLVYDPSKTSQGSLSLKAYRLSEKFMELYKEGKFST 149 (266)
T ss_pred EEEEECCCcccccceeeEEEEEcHHHHHHhhcCCcCH
Confidence 55666665 568899999999999999988875443
No 93
>PF11039 DUF2824: Protein of unknown function (DUF2824); InterPro: IPR022568 This family of proteins has no known function. Members of the family are found in P22-like viruses and bacteria. Some of the phage members have been annotated as head assembly proteins, but this has not been confirmed.
Probab=43.28 E-value=51 Score=31.44 Aligned_cols=47 Identities=26% Similarity=0.349 Sum_probs=31.7
Q ss_pred EEEEEEecCCCCCCC------------------CceEEcCCCChHHHHHHHHhcCCeEEEEEEecC
Q psy8916 459 AVVAAIYEPPQESSR------------------DKIKLLPDPKAEVVEEIASSLGLTQVGWIFTDL 506 (520)
Q Consensus 459 AvVeAIYEPPQ~~~~------------------dg~~ll~d~~e~~Vd~iA~~LGL~rVG~IFTdl 506 (520)
..|+|||-|-=.|.. ..+++.++... -=.-+.++|||+|||.|=--+
T Consensus 63 vecHa~y~P~fRG~a~~~~~~F~kwlL~Ns~f~~vit~vp~kt~-~Grvic~llg~~RVG~id~~~ 127 (151)
T PF11039_consen 63 VECHAMYDPGFRGYALEIGRLFCKWLLENSPFQNVITFVPDKTR-YGRVICRLLGARRVGHIDDYF 127 (151)
T ss_pred EEEEeeeccccchhHHHHHHHHHHHHhcCCceeEEEEecccccc-cchhHhhhhCCceeeeHHHHh
Confidence 478999999866632 33555555432 234578899999999984433
No 94
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=43.01 E-value=70 Score=26.01 Aligned_cols=35 Identities=31% Similarity=0.536 Sum_probs=29.9
Q ss_pred cceeeEEecCCcchHHHHHHHHhhcCCCCCcceee
Q psy8916 183 GIVKRININRSDTCKDLFEKINKEFELNTYNFALF 217 (520)
Q Consensus 183 G~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~ 217 (520)
|.++|+.+++..++.+|..+|...|++....+.|.
T Consensus 10 ~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~ 44 (81)
T smart00666 10 GETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLK 44 (81)
T ss_pred CEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEE
Confidence 34789999999999999999999999876666663
No 95
>PF07929 PRiA4_ORF3: Plasmid pRiA4b ORF-3-like protein; InterPro: IPR012912 Members of this family are similar to the protein product of ORF-3 (Q44206 from SWISSPROT) found on plasmid pRiA4 in the bacterium Agrobacterium rhizogenes. This plasmid is responsible for tumourigenesis at wound sites of plants infected by this bacterium, but the ORF-3 product does not seem to be involved in the pathogenetic process []. Other proteins found in this family are annotated as being putative TnpR resolvases (Q9LCU7 from SWISSPROT, Q50439 from SWISSPROT), but no further evidence was found to back this. Moreover, another member of this family is described as a probable lexA repressor (Q7UEI4 from SWISSPROT) and in fact carries a LexA DNA binding domain (IPR006199 from INTERPRO), but no references were found to expand on this. ; PDB: 2I1S_A.
Probab=39.92 E-value=64 Score=30.58 Aligned_cols=68 Identities=22% Similarity=0.226 Sum_probs=41.7
Q ss_pred eeeEEecCCcchHHHHHHHHhhcCCCCC---cceeeecCCccc-----------cccccccccccccCCCCcCeEEEeec
Q psy8916 185 VKRININRSDTCKDLFEKINKEFELNTY---NFALFKQRNKTD-----------EIFSSRDQTIASVGLSNGDFVYMMNL 250 (520)
Q Consensus 185 m~RVev~ptDtfs~LleKLl~~f~ls~d---sftL~~nr~~~~-----------~l~s~~~~tv~~lgLkHGDmlyl~~~ 250 (520)
-.||.|..+.+|.+|-.-|+..|+...+ .|.+..+.-... ........+|+++.++.|+.+...|+
T Consensus 19 wRri~Vp~~~tl~~Lh~~Iq~afgw~~~HL~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~Y~YD 98 (179)
T PF07929_consen 19 WRRIEVPADITLADLHEVIQAAFGWDDDHLYEFFIGGERYGIPDEDGMDFSEGDEIKDASEVKLGELLLEEGDKFTYVYD 98 (179)
T ss_dssp EEEEEEETT-BHHHHHHHHHHHTT----S-EEEEEE-TTTSSESSS---------EEETTT-BHHHC-BTTC-EEEEEE-
T ss_pred EEEEEECCCCCHHHHHHHHHHHhCcCCCEeEEEEECCCccccccccccccccCCCcceeeeEEhhhhccCcCCEEEEEEc
Confidence 6799999999999999999999988765 444442221111 12233467888888899999888886
Q ss_pred CC
Q psy8916 251 SS 252 (520)
Q Consensus 251 ~~ 252 (520)
=+
T Consensus 99 fG 100 (179)
T PF07929_consen 99 FG 100 (179)
T ss_dssp TT
T ss_pred CC
Confidence 43
No 96
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=37.53 E-value=31 Score=42.55 Aligned_cols=62 Identities=26% Similarity=0.266 Sum_probs=39.8
Q ss_pred CceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEE-cCCCChHHHHHHHHhcCCeEEEEEEecC
Q psy8916 436 GHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKL-LPDPKAEVVEEIASSLGLTQVGWIFTDL 506 (520)
Q Consensus 436 g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~l-l~d~~e~~Vd~iA~~LGL~rVG~IFTdl 506 (520)
..|-+||+||.-..+.---..|+.++ --||-|...|+++ ..-|. .+-.-=||+.+|||-|.-
T Consensus 2153 ~vqvag~vyG~s~~d~p~ikeI~~~~----lVPQlgs~~~vq~~s~vP~-----dlp~~e~le~lGwihtq~ 2215 (2365)
T COG5178 2153 HVQVAGLVYGKSGSDNPQIKEILSFG----LVPQLGSLSGVQSSSFVPH-----DLPGDEDLEILGWIHTQD 2215 (2365)
T ss_pred ceeeEEEEeccCCccCcchhheeEEE----eeccccccccccccccCCC-----CCCCcccceeeEEEecCC
Confidence 57999999997543332113344443 3599999999998 21111 011124899999999964
No 97
>KOG1364|consensus
Probab=36.80 E-value=30 Score=37.32 Aligned_cols=69 Identities=17% Similarity=0.251 Sum_probs=49.7
Q ss_pred eeeeCCCcceeeEEecCCcchHHHHHHHHhhc-CCCCCcceeeecCCccccccccccccccccCCCCcCe
Q psy8916 176 LRIQSPVGIVKRININRSDTCKDLFEKINKEF-ELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDF 244 (520)
Q Consensus 176 IRfRSkdG~m~RVev~ptDtfs~LleKLl~~f-~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDm 244 (520)
|-+|-||||.+-+..-+++++..|+.-...+. +..++.|.|......++.+....+.|+.++||.|--.
T Consensus 280 i~vR~pdG~R~qrkf~~sepv~ll~~~~~s~~dg~~k~~FkLv~a~P~~k~l~~~~daT~~eaGL~nS~~ 349 (356)
T KOG1364|consen 280 IQVRFPDGRRKQRKFLKSEPVQLLWSFCYSHMDGSDKKRFKLVQAIPASKTLDYGADATFKEAGLANSET 349 (356)
T ss_pred EEEecCCccHHHHhhccccHHHHHHHHHHHhhcccccccceeeecccchhhhhccccchHHHhccCcccc
Confidence 66788999545455567999888887766665 5556788887665445556655678999999988654
No 98
>cd01768 RA RA (Ras-associating) ubiquitin domain. The RA (Ras-associating) domain is structurally similar to ubiquitin and is present in one or two copies in a number of signalling molecules that bind and regulate a small GTPase called Ras or the Ras-related GTPases, Ral and Rap. RA-containing proteins include RalGDS, AF6, RIN1, RASSF1, SNX27, CYR1, STE50, and phospholipase C epsilon.
Probab=36.46 E-value=1.6e+02 Score=24.33 Aligned_cols=46 Identities=24% Similarity=0.480 Sum_probs=34.8
Q ss_pred eeeeCCC---cceeeEEecCCcchHHHHHHHHhhcCCCC--CcceeeecCC
Q psy8916 176 LRIQSPV---GIVKRININRSDTCKDLFEKINKEFELNT--YNFALFKQRN 221 (520)
Q Consensus 176 IRfRSkd---G~m~RVev~ptDtfs~LleKLl~~f~ls~--dsftL~~nr~ 221 (520)
|||...+ |-.+-|.|.++++..++++.++.+|+++. +.|.|++--.
T Consensus 2 ikV~~~~~~~~~~kti~V~~~~t~~~Vi~~~l~k~~l~~~~~~y~L~ev~~ 52 (87)
T cd01768 2 LRVYPEDPSGGTYKTLRVSKDTTAQDVIQQLLKKFGLDDDPEDYALVEVLG 52 (87)
T ss_pred EEEeCCcCCCccEEEEEECCCCCHHHHHHHHHHHhCCcCCcccEEEEEEEC
Confidence 4444444 53578999999999999999999998883 4677776433
No 99
>smart00295 B41 Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
Probab=35.88 E-value=93 Score=28.92 Aligned_cols=47 Identities=17% Similarity=0.349 Sum_probs=39.2
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCC-CcceeeecC
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNT-YNFALFKQR 220 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~-dsftL~~nr 220 (520)
+.+||.-+||....|+++++.+..++++.+...+++.. ..|.|+...
T Consensus 4 ~~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~l~~~~~F~L~~~~ 51 (207)
T smart00295 4 RVLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFED 51 (207)
T ss_pred EEEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhCCCccceeEEEEEc
Confidence 56889999996669999999999999999999999965 366676443
No 100
>cd01787 GRB7_RA RA (RAS-associated like) domain of Grb7. Grb7_RA The RA (RAS-associated like) domain of Grb7. Grb7 is an adaptor molecule that mediates signal transduction from multiple cell surface receptors to various downstream signaling pathways. Grb7 and its related family members Grb10 and Grb14 share a conserved domain architecture that includes an amino-terminal proline-rich region, a central segment termed the GM region (for Grb and Mig) which includes the RA, PIR, and PH domains, and a carboxyl-terminal SH2 domain. Grb7/10/14 family proteins are phosphorylated on serine/threonine as well as tyrosine residues and are mainly localized to the cytoplasm.
Probab=35.86 E-value=1e+02 Score=27.09 Aligned_cols=46 Identities=13% Similarity=0.312 Sum_probs=38.8
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCC-Ccceeeec
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNT-YNFALFKQ 219 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~-dsftL~~n 219 (520)
.+++|.+.||..+-|.|+++-+.+++.+.+..+-.... .+++|++.
T Consensus 3 ~vvkv~~~Dg~sK~l~V~~~~Ta~dV~~~L~~K~h~~~~~~W~LvE~ 49 (85)
T cd01787 3 QVVKVYSEDGASKSLEVDERMTARDVCQLLVDKNHCQDDSSWTLVEH 49 (85)
T ss_pred eEEEEEecCCCeeEEEEcCCCcHHHHHHHHHHHhCCCCCCCeEEEEe
Confidence 47899999997788999999999999999998876554 47888764
No 101
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=34.86 E-value=46 Score=41.27 Aligned_cols=65 Identities=17% Similarity=0.205 Sum_probs=44.5
Q ss_pred cCCCeEEEEEeeccccccCCCceeeeeecCCceeechHHHHHHHhhhhhCCCCCCCCCCCCCCcceeeeeecchhhhhcc
Q psy8916 13 NLGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTVNECIMAG 92 (520)
Q Consensus 13 ~lgl~~vG~Iftdl~~~~~~~g~v~~~r~~~s~fls~~E~~~aa~~Q~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 (520)
.-||+.+|||-|.-..- -||++.++..-++.=.-| +|.
T Consensus 2202 ~e~le~lGwihtq~~el---------------~~l~~~~v~th~k~~~d~----~~d----------------------- 2239 (2365)
T COG5178 2202 DEDLEILGWIHTQDDEL---------------PYLEVAGVLTHRKKIVDP----EWD----------------------- 2239 (2365)
T ss_pred cccceeeEEEecCCccc---------------chhhhhhhhhhhhcccCc----ccc-----------------------
Confidence 35899999999975332 279998887766654433 221
Q ss_pred ccccCCCCCCccCCCCcCCCceEEEEEECCCCCceeeeeEechHHHHHH
Q psy8916 93 HLQNLHPNPCRFAPSGYFGSKFVTICVTGDKDNQVHMEGYQVSNQCMAL 141 (520)
Q Consensus 93 ~~~~~~~~~~~~~~~g~~~s~fvT~~vsg~~~~~i~~~~yqvS~q~~al 141 (520)
-||..|+--. |.|+..||-|+..+..-
T Consensus 2240 ---------------------~v~ltv~~~p-gsiSl~ay~v~keG~~W 2266 (2365)
T COG5178 2240 ---------------------AVTLTVSYLP-GSISLRAYVVKKEGCNW 2266 (2365)
T ss_pred ---------------------ceeeeeeecc-ceeeeeeeeehhccccc
Confidence 2556665544 89999999999876543
No 102
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=33.71 E-value=1.1e+02 Score=26.14 Aligned_cols=34 Identities=26% Similarity=0.291 Sum_probs=29.8
Q ss_pred eeeEEecCCcchHHHHHHHHhhcCCCC-Ccceeee
Q psy8916 185 VKRININRSDTCKDLFEKINKEFELNT-YNFALFK 218 (520)
Q Consensus 185 m~RVev~ptDtfs~LleKLl~~f~ls~-dsftL~~ 218 (520)
+.|+.+.++..+.+|.++|.+.|++.. .+|+|..
T Consensus 11 ~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY 45 (82)
T cd06407 11 KIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKY 45 (82)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEE
Confidence 689999999999999999999999875 5777743
No 103
>KOG0001|consensus
Probab=33.44 E-value=2e+02 Score=21.30 Aligned_cols=65 Identities=15% Similarity=0.172 Sum_probs=46.0
Q ss_pred eCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCCCCcCeEEEe
Q psy8916 179 QSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMM 248 (520)
Q Consensus 179 RSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~ 248 (520)
..-.|.+..+++.+++++..+..++....+++.+...+.. . ...+. .+.++.+.++.++..+.+.
T Consensus 5 ~~~~gk~~~~~~~~~~~i~~~k~~i~~~~~~~~~~q~~~~-~--~~~l~--d~~~l~~~~i~~~~~~~l~ 69 (75)
T KOG0001|consen 5 KTLDGKTITLEVSPSDTIEVVKAKIRDKEGIPVDQQRLIF-G--GKPLE--DGRTLADYNIQEGSTLHLV 69 (75)
T ss_pred EecCCCEEEEEecCCCHHHHHHHHHHhhcCCCCeeEEEEE-C--CEECc--CCCcHHHhCCCCCCEEEEE
Confidence 3345547789999999999998889988877765444322 1 12233 3378888899999988875
No 104
>PF14583 Pectate_lyase22: Oligogalacturonate lyase; PDB: 3C5M_C 3PE7_A.
Probab=32.58 E-value=30 Score=37.74 Aligned_cols=40 Identities=23% Similarity=0.502 Sum_probs=24.7
Q ss_pred hhccccccCCCCCCccCCCCcCCCceEEEEEECCCCCceeeeeEech
Q psy8916 89 IMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTGDKDNQVHMEGYQVS 135 (520)
Q Consensus 89 ~~~~~~~~~~~~~~~~~~~g~~~s~fvT~~vsg~~~~~i~~~~yqvS 135 (520)
++.|+-|.+|||| +|+|+|+. ++-+-|.+|...+-+=.|.
T Consensus 344 v~~~~~q~~hPhp-~FSPDgk~------VlF~Sd~~G~~~vY~v~i~ 383 (386)
T PF14583_consen 344 VLDGDRQVTHPHP-SFSPDGKW------VLFRSDMEGPPAVYLVEIP 383 (386)
T ss_dssp -BTTBSSTT-----EE-TTSSE------EEEEE-TTSS-EEEEEE--
T ss_pred eecCCCccCCCCC-ccCCCCCE------EEEECCCCCCccEEEEeCc
Confidence 5789999999999 69999995 7888888998877655443
No 105
>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A.
Probab=31.74 E-value=1.3e+02 Score=27.13 Aligned_cols=65 Identities=22% Similarity=0.321 Sum_probs=40.9
Q ss_pred eeeeeCCCcc-eeeEEecCCcchHHHHHHHHhhcCCCCC-------cceeeecCCccccccccccccccccCCCCcCe
Q psy8916 175 ILRIQSPVGI-VKRININRSDTCKDLFEKINKEFELNTY-------NFALFKQRNKTDEIFSSRDQTIASVGLSNGDF 244 (520)
Q Consensus 175 iIRfRSkdG~-m~RVev~ptDtfs~LleKLl~~f~ls~d-------sftL~~nr~~~~~l~s~~~~tv~~lgLkHGDm 244 (520)
-||||=.+|. ..-+.+++++++.+|.+.|...-+-.-. .+.|. ..+++.. ++.+|+++++..|+.
T Consensus 4 ~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI----~~GriL~-d~~tL~~~~~~~~~~ 76 (111)
T PF13881_consen 4 ELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLI----YAGRILE-DNKTLSDCRLPSGET 76 (111)
T ss_dssp EEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEE----ETTEEE--SSSBTGGGT--TTSE
T ss_pred EEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEE----eCCeecC-CcCcHHHhCCCCCCC
Confidence 4677777883 3667788999999999999987633211 22222 1233333 678999999999986
No 106
>KOG4133|consensus
Probab=31.59 E-value=14 Score=38.42 Aligned_cols=10 Identities=40% Similarity=0.949 Sum_probs=8.4
Q ss_pred CCCCCcceee
Q psy8916 71 SGYFGSKFVT 80 (520)
Q Consensus 71 ~~~~~~~~~~ 80 (520)
.|.||.+|+.
T Consensus 213 ggrFGgdFlv 222 (290)
T KOG4133|consen 213 GGRFGGDFLV 222 (290)
T ss_pred ccccCceeEe
Confidence 5889999986
No 107
>cd02176 GH16_XET Xyloglucan endotransglycosylase, member of glycosyl hydrolase family 16. Xyloglucan endotransglycosylases (XETs) cleave and religate xyloglucan polymers in plant cell walls via a transglycosylation mechanism. Xyloglucan is a soluble hemicellulose with a backbone of beta-1,4-linked glucose units, partially substituted with alpha-1,6-linked xylopyranose branches. It binds noncovalently to cellulose, cross-linking the adjacent cellulose microfibrils, giving it a key structural role as a matrix polymer. Therefore, XET plays an important role in all plant processes that require cell wall remodeling.
Probab=31.05 E-value=47 Score=34.33 Aligned_cols=41 Identities=22% Similarity=0.427 Sum_probs=32.2
Q ss_pred eeEEEEEEEeeCCCCCcc-ceEEEEEEecC----CCCCCCCceEEcC
Q psy8916 439 RLGLLYGKYQLHPDVPLG-IKAVVAAIYEP----PQESSRDKIKLLP 480 (520)
Q Consensus 439 R~G~LYG~Y~~~~~vPlG-ikAvVeAIYEP----PQ~~~~dg~~ll~ 480 (520)
+.-|+||+++---++|-| ..-+|-|+|-= |..+|.| ++.+.
T Consensus 43 k~~f~YG~~E~riKlp~g~s~G~~pAFwl~~~~wp~~~EID-~E~lG 88 (263)
T cd02176 43 KNKYLFGFFSMRIKLPPGDSAGTVTAFYLSSQGPDNHDEID-FEFLG 88 (263)
T ss_pred ccEEEEEEEEEEEEeCCCCCCCeEEEEEECCCCCCCCCeEE-EEEec
Confidence 356899999998889888 57899999954 5567777 77664
No 108
>COG0380 OtsA Trehalose-6-phosphate synthase [Carbohydrate transport and metabolism]
Probab=30.78 E-value=32 Score=38.59 Aligned_cols=47 Identities=19% Similarity=0.346 Sum_probs=33.1
Q ss_pred CCCCCccccccccCCceeecCCCCCCcCeeeecCHHHHHHHHHHHHhc
Q psy8916 388 HPPWPRGICSKCQPNAITLNRQVYRHVDNVEFENRTLVERFLEYWRVT 435 (520)
Q Consensus 388 H~PwP~GiCskCqP~aItL~~Q~~R~VDhvef~~~~~v~~Fi~~wr~~ 435 (520)
|-|||--=-=+|.|--=.|=+ ---..|-|.|+..+-..+|++.+++.
T Consensus 179 HiPfPssEvfr~lP~r~eIl~-gll~~dligFqt~~y~~nF~~~~~r~ 225 (486)
T COG0380 179 HIPFPSSEVFRCLPWREEILE-GLLGADLIGFQTESYARNFLDLCSRL 225 (486)
T ss_pred eCCCCCHHHHhhCchHHHHHH-HhhcCCeeEecCHHHHHHHHHHHHHh
Confidence 999997666677771110000 01145789999999999999999984
No 109
>PHA00771 head assembly protein
Probab=30.54 E-value=93 Score=29.62 Aligned_cols=62 Identities=23% Similarity=0.254 Sum_probs=39.5
Q ss_pred eeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCC------------------ceEEcCCCChHHHHHHHHhcCCeEE
Q psy8916 438 QRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRD------------------KIKLLPDPKAEVVEEIASSLGLTQV 499 (520)
Q Consensus 438 QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~d------------------g~~ll~d~~e~~Vd~iA~~LGL~rV 499 (520)
|--|++| |.+-. |+ -.-|+|+|-|-=.|..- .+++.++.. +-=..+.++|||+||
T Consensus 48 ~yeGivl--~~eV~--p~--~~ecHa~y~P~fRG~ya~~~r~F~kwlL~Nt~f~~vit~vp~kt-~~G~vic~lig~rRV 120 (151)
T PHA00771 48 QFGGIVY--YNEIQ--PL--TFDCHAMYLPEIRGFSKEIGLAFWRYILTNTTVQCVTSFAARKF-RHGQMYCAMIGLKRV 120 (151)
T ss_pred eeeeEEE--EEEee--eE--EEEEEeeeCccccchhHHHHHHHHHHHhcCCceeEEEEeccccc-ccchhhhhhhCCcee
Confidence 6668888 55443 33 46789999998666432 233444432 123457889999999
Q ss_pred EEEEecC
Q psy8916 500 GWIFTDL 506 (520)
Q Consensus 500 G~IFTdl 506 (520)
|.|=--+
T Consensus 121 G~id~a~ 127 (151)
T PHA00771 121 GTIKKYF 127 (151)
T ss_pred eeHHHHh
Confidence 9884333
No 110
>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=30.03 E-value=98 Score=31.81 Aligned_cols=67 Identities=18% Similarity=0.195 Sum_probs=49.4
Q ss_pred cccCCCeEEEEEeeccccccCCCceeeeeecCCceeechHHHHHHHhhhhhCCCCCCCCCCCCCCcceeeeeecchhhhh
Q psy8916 11 QPNLGLTQVGWIFTDLVAEDLQLGTVRHTRNIDSHFLSAHECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTVNECIM 90 (520)
Q Consensus 11 ~~~lgl~~vG~Iftdl~~~~~~~g~v~~~r~~~s~fls~~E~~~aa~~Q~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (520)
+..-|+..|||.=|+---. -|+|...+..-..+|...++
T Consensus 82 ~~~~~~~vVGWYHSHP~~g---------------~~~S~~Dv~tq~~yq~~~~~-------------------------- 120 (268)
T cd08069 82 QTGRPENVVGWYHSHPGYG---------------CWLSGIDVNTQQLNQQLQDP-------------------------- 120 (268)
T ss_pred HhCCCceeEeeeccCCCcC---------------CcCCHHHHHHHHHHHhcCCC--------------------------
Confidence 4567899999999985322 38999998888888876432
Q ss_pred ccccccCCCCCCccCCCCcCCCceEEEEEEC--C-CCCceeeeeEechHHHHHH
Q psy8916 91 AGHLQNLHPNPCRFAPSGYFGSKFVTICVTG--D-KDNQVHMEGYQVSNQCMAL 141 (520)
Q Consensus 91 ~~~~~~~~~~~~~~~~~g~~~s~fvT~~vsg--~-~~~~i~~~~yqvS~q~~al 141 (520)
||-+||-. + ..|.+.+.||..+...+.+
T Consensus 121 -----------------------~V~lViDP~~t~~~g~~~i~Afr~~~~~~~~ 151 (268)
T cd08069 121 -----------------------FVAVVVDPIRSLVKGKVVIGAFRTIPPGYKP 151 (268)
T ss_pred -----------------------cEEEEEeCCccccCCcceeeEEEEECccccc
Confidence 24455543 3 5688999999999987765
No 111
>PF04110 APG12: Ubiquitin-like autophagy protein Apg12 ; InterPro: IPR007242 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents Apg12, which is covalently bound to Apg5 [].; GO: 0000045 autophagic vacuole assembly, 0005737 cytoplasm; PDB: 1WZ3_B.
Probab=29.39 E-value=80 Score=27.70 Aligned_cols=64 Identities=16% Similarity=0.263 Sum_probs=41.3
Q ss_pred eeeEEecCCcchHHHHHHHHhhcCCC-CCcceeeecCCcccccccccccccccc--CCCCcCeEEEeecCC
Q psy8916 185 VKRININRSDTCKDLFEKINKEFELN-TYNFALFKQRNKTDEIFSSRDQTIASV--GLSNGDFVYMMNLSS 252 (520)
Q Consensus 185 m~RVev~ptDtfs~LleKLl~~f~ls-~dsftL~~nr~~~~~l~s~~~~tv~~l--gLkHGDmlyl~~~~~ 252 (520)
...+.++++++|+.+..-|...|.+. .+++.+|-|.. .+-..+.+|++| ..+.++.|=|.|..+
T Consensus 17 ~~k~kI~~~~~f~~vi~fLrk~Lk~~~~~slFlYin~s----FaPspDe~vg~L~~~f~~~~~Liv~Ys~t 83 (87)
T PF04110_consen 17 QKKFKISASQTFATVIAFLRKKLKLKPSDSLFLYINNS----FAPSPDETVGDLYRCFGTNGELIVSYSKT 83 (87)
T ss_dssp --EEEEETTSBTHHHHHHHHHHCT----SS-EEEEEEE----E---TTSBHHHHHHHH-BTTBEEEEEESS
T ss_pred CcEEEECCCCchHHHHHHHHHHhCCccCCeEEEEEcCc----cCCCchhHHHHHHHHhCCCCEEEEEEecc
Confidence 45788999999999999999999873 45777775432 233456677766 355677777998754
No 112
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=28.22 E-value=1.7e+02 Score=23.66 Aligned_cols=41 Identities=24% Similarity=0.392 Sum_probs=32.0
Q ss_pred eeeeCCCcceee-EEecCCcchHHHHHHHHhhcCCCCCcceee
Q psy8916 176 LRIQSPVGIVKR-ININRSDTCKDLFEKINKEFELNTYNFALF 217 (520)
Q Consensus 176 IRfRSkdG~m~R-Vev~ptDtfs~LleKLl~~f~ls~dsftL~ 217 (520)
++++=.++ ..| +.+....++..|..+|...|+.....+.|.
T Consensus 4 vK~~~~~~-~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~ 45 (84)
T PF00564_consen 4 VKVRYGGD-IRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLK 45 (84)
T ss_dssp EEEEETTE-EEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEE
T ss_pred EEEEECCe-eEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEE
Confidence 34444556 677 999999999999999999999975566663
No 113
>KOG0011|consensus
Probab=27.87 E-value=1.2e+02 Score=32.78 Aligned_cols=72 Identities=15% Similarity=0.140 Sum_probs=51.6
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCC--CCCcceeeecCCccccccccccccccccCCCCcCeEEEeec
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFEL--NTYNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMNL 250 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~l--s~dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~~ 250 (520)
|.|-|++=.|.+|-|++.|.+++..++++|...-+. +....-|..+ .+.|. +.++|...+++-++.|-|...
T Consensus 1 m~lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLIy~---GkiL~--D~~tv~Eykv~E~~fiVvMls 74 (340)
T KOG0011|consen 1 MKLTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLIYS---GKILK--DETTVGEYKVKEKKFIVVMLS 74 (340)
T ss_pred CeeEeeeccCceeEeecCcchhHHHHHHHHHhccCCCCchhhheeeec---ceecc--CCcchhhhccccCceEEEEEe
Confidence 567788888889999999999999999999887663 3222222211 12233 577999999999998766543
No 114
>TIGR02958 sec_mycoba_snm4 secretion protein snm4. Members of this family are the 12-transmembrane domain protein snm4, where snm stands for secretion in mycocbacteria. This system acts on Mycobacterium tuberculosis related pair of virulence factors ESAT-6 and CFP-10 and on other homologs. The system is conserved in many Actinobacteria, including the non-pathogenic Mycobacterium smegmatis.
Probab=27.62 E-value=2.2e+02 Score=31.57 Aligned_cols=67 Identities=12% Similarity=0.237 Sum_probs=47.0
Q ss_pred eeCCCcceeeEEecCCcchHHHHHHHHhhcCCCC------CcceeeecCCccccccccccccccccCCCCcCeEEEee
Q psy8916 178 IQSPVGIVKRININRSDTCKDLFEKINKEFELNT------YNFALFKQRNKTDEIFSSRDQTIASVGLSNGDFVYMMN 249 (520)
Q Consensus 178 fRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~------dsftL~~nr~~~~~l~s~~~~tv~~lgLkHGDmlyl~~ 249 (520)
|.+++. +.-+-+...-++.+|+..++..++-.. ..+.+. +-+...+. .++|+.+.|+..||+|||..
T Consensus 7 V~~~~~-~~DlaLPa~~PvaellP~ll~~~~~~~~~~~~~~~w~L~--r~gG~pL~--~~~sL~~~gV~DG~~L~L~p 79 (452)
T TIGR02958 7 VLAGRR-AVDVALPADVPVAELIPDLVDLLDDRGAAELGAVRWALA--RAGGSPLD--PDASLAEAGVRDGELLVLVP 79 (452)
T ss_pred EeeCCe-eeeeecCCCCcHHHHHHHHHHHhCcccccCCCCcceEEe--cCCCCCCC--CCCCHHHcCCCCCCeEEEee
Confidence 556666 566666788889999999999885432 234442 21223344 57899999999999999974
No 115
>smart00455 RBD Raf-like Ras-binding domain.
Probab=27.00 E-value=1.1e+02 Score=25.25 Aligned_cols=43 Identities=16% Similarity=0.155 Sum_probs=36.0
Q ss_pred eeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeee
Q psy8916 176 LRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFK 218 (520)
Q Consensus 176 IRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~ 218 (520)
.|+-=|+|+.-.|.+.|+.++.++++++.+..+++.+...++.
T Consensus 2 ~~v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~ 44 (70)
T smart00455 2 CKVHLPDNQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRL 44 (70)
T ss_pred eEEECCCCCEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence 4566789978889999999999999999999999876555553
No 116
>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=26.64 E-value=38 Score=28.65 Aligned_cols=21 Identities=33% Similarity=0.531 Sum_probs=13.0
Q ss_pred eEEEEEEecCccCC------CCCceEE
Q psy8916 497 TQVGWIFTDLVAED------LQLGTYF 517 (520)
Q Consensus 497 ~rVG~IFTdl~~~~------~~~GtV~ 517 (520)
+.|||-.|+|+++| ..-|+|.
T Consensus 41 ~vvgwy~t~ltpegyavese~hpgsvq 67 (78)
T PF06442_consen 41 QVVGWYCTKLTPEGYAVESESHPGSVQ 67 (78)
T ss_dssp EEEEEE--SS-SSEEEEEESSSTT-EE
T ss_pred eEeEEEeccccccceeeecccCCCcEE
Confidence 68999999999887 3456664
No 117
>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=26.25 E-value=2.2e+02 Score=25.18 Aligned_cols=70 Identities=20% Similarity=0.250 Sum_probs=37.4
Q ss_pred HHHHHHHHhc-CceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEEcCCCC-hHHHHHHHHhcCCeEEEEEE
Q psy8916 426 ERFLEYWRVT-GHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDPK-AEVVEEIASSLGLTQVGWIF 503 (520)
Q Consensus 426 ~~Fi~~wr~~-g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~ll~d~~-e~~Vd~iA~~LGL~rVG~IF 503 (520)
..++..-+.. -.--+|+|.|++.+.... ..+ ..|..+...|. ..+ +. +-.+..-+...|+..|||.=
T Consensus 4 ~~i~~ha~~~~p~E~cGlL~G~~~~~~~~-~~~-~~v~~~~p~~~--~~~-------~~~~~~~~~~~~~~g~~~vG~YH 72 (119)
T cd08058 4 LKMLQHAESNTGIEVMGLLCGELTHNEFT-DKH-VIVPKQSAGPD--SCT-------GENVEELFNVQTGRPLLVVGWYH 72 (119)
T ss_pred HHHHHHhcCCCCeEEEEEeeeEEecCccc-eeE-EEEeecCCCCC--Cch-------hHHHHHHHHHHhCCCCeEEEEEe
Confidence 3344433333 455789999998754311 011 12222333332 111 21 22344556779999999998
Q ss_pred ecC
Q psy8916 504 TDL 506 (520)
Q Consensus 504 Tdl 506 (520)
||-
T Consensus 73 SHP 75 (119)
T cd08058 73 SHP 75 (119)
T ss_pred cCC
Confidence 886
No 118
>KOG0275|consensus
Probab=26.16 E-value=35 Score=36.93 Aligned_cols=31 Identities=32% Similarity=0.593 Sum_probs=25.7
Q ss_pred ccCCCCCCccCCCCcCCCceEEEEEECCCCCceeeeeE
Q psy8916 95 QNLHPNPCRFAPSGYFGSKFVTICVTGDKDNQVHMEGY 132 (520)
Q Consensus 95 ~~~~~~~~~~~~~g~~~s~fvT~~vsg~~~~~i~~~~y 132 (520)
|.-||.--||||+|.| .|||..||-|++--|
T Consensus 212 ~KSh~EcA~FSPDgqy-------LvsgSvDGFiEVWny 242 (508)
T KOG0275|consen 212 QKSHVECARFSPDGQY-------LVSGSVDGFIEVWNY 242 (508)
T ss_pred cccchhheeeCCCCce-------Eeeccccceeeeehh
Confidence 4567777799999998 789999999887654
No 119
>PF03931 Skp1_POZ: Skp1 family, tetramerisation domain; InterPro: IPR016073 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a POZ domain with a core structure consisting of beta(2)/alpha(2)/beta(2)/alpha(2) in two layers, alpha/beta. This domain is found at the N-terminal of SKP1 proteins [] as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1LM8_C 2XAI_E 1VCB_E 3ZRC_K 3ZRF_E 3DCG_B 2C9W_C 1LQB_B 2IZV_C 1HV2_A ....
Probab=25.34 E-value=71 Score=25.42 Aligned_cols=36 Identities=6% Similarity=0.078 Sum_probs=20.0
Q ss_pred eeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCC
Q psy8916 174 KILRIQSPVGIVKRININRSDTCKDLFEKINKEFELN 210 (520)
Q Consensus 174 MiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls 210 (520)
|.++++|.||..|+|+.+... .+.++..+++.++..
T Consensus 1 ~~v~L~SsDg~~f~V~~~~a~-~S~~i~~ml~~~~~~ 36 (62)
T PF03931_consen 1 MYVKLVSSDGQEFEVSREAAK-QSKTIKNMLEDLGDE 36 (62)
T ss_dssp -EEEEEETTSEEEEEEHHHHT-TSHHHHHHHHCTCCC
T ss_pred CEEEEEcCCCCEEEeeHHHHH-HhHHHHHHHhhhccc
Confidence 678999999954555433322 334445555544443
No 120
>smart00314 RA Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.)
Probab=25.24 E-value=2e+02 Score=23.90 Aligned_cols=38 Identities=18% Similarity=0.440 Sum_probs=31.3
Q ss_pred cceeeEEecCCcchHHHHHHHHhhcCCCC--CcceeeecC
Q psy8916 183 GIVKRININRSDTCKDLFEKINKEFELNT--YNFALFKQR 220 (520)
Q Consensus 183 G~m~RVev~ptDtfs~LleKLl~~f~ls~--dsftL~~nr 220 (520)
+-.+-|.|.+.++..+++..++++|+++. ..|.|++.-
T Consensus 15 ~~~kti~v~~~tTa~~Vi~~~l~k~~l~~~~~~y~L~e~~ 54 (90)
T smart00314 15 GTYKTLRVSSRTTARDVIQQLLEKFHLTDDPEEYVLVEVL 54 (90)
T ss_pred CcEEEEEECCCCCHHHHHHHHHHHhCCCCCcccEEEEEEe
Confidence 53577899999999999999999999976 367777653
No 121
>PF08662 eIF2A: Eukaryotic translation initiation factor eIF2A; InterPro: IPR013979 This entry contains beta propellor domains found in eukaryotic translation initiation factors and TolB domain-containing proteins.
Probab=24.79 E-value=86 Score=30.11 Aligned_cols=61 Identities=16% Similarity=0.370 Sum_probs=40.0
Q ss_pred CCCCCCCCCCCCcceeeeeec--------chhhhhccccccCCCCCCccCCCCcCCCceEEEEEEC--CCCCceeeeeEe
Q psy8916 64 NPCRFAPSGYFGSKFVTICVT--------VNECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTG--DKDNQVHMEGYQ 133 (520)
Q Consensus 64 ~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~g~~~s~fvT~~vsg--~~~~~i~~~~yq 133 (520)
....|++.| .+|+.|.-. --+|..--.|.+.+.|..+|||.|.| +++.| +.+|+|.| |.
T Consensus 63 ~~~~WsP~g---~~favi~g~~~~~v~lyd~~~~~i~~~~~~~~n~i~wsP~G~~------l~~~g~~n~~G~l~~--wd 131 (194)
T PF08662_consen 63 HDVAWSPNG---NEFAVIYGSMPAKVTLYDVKGKKIFSFGTQPRNTISWSPDGRF------LVLAGFGNLNGDLEF--WD 131 (194)
T ss_pred EEEEECcCC---CEEEEEEccCCcccEEEcCcccEeEeecCCCceEEEECCCCCE------EEEEEccCCCcEEEE--EE
Confidence 456788874 566554211 11355556778888899999999986 44443 66788777 66
Q ss_pred ch
Q psy8916 134 VS 135 (520)
Q Consensus 134 vS 135 (520)
+.
T Consensus 132 ~~ 133 (194)
T PF08662_consen 132 VR 133 (194)
T ss_pred CC
Confidence 55
No 122
>KOG1795|consensus
Probab=24.67 E-value=40 Score=42.03 Aligned_cols=72 Identities=26% Similarity=0.335 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHhcCceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEE-cCCCChHHHHHHHHhcCCeEEEE
Q psy8916 423 TLVERFLEYWRVTGHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKL-LPDPKAEVVEEIASSLGLTQVGW 501 (520)
Q Consensus 423 ~~v~~Fi~~wr~~g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~l-l~d~~e~~Vd~iA~~LGL~rVG~ 501 (520)
+++..|+. -..-..|-+|||||---++.---..|+++|- +||-|...||.+ ..-| ..--.-+|+..||
T Consensus 2102 NllkkFi~-isD~r~qiag~~yG~s~~d~pqvkeIr~ivm----vPQ~gs~~~v~lp~~lP------~~~~l~d~e~Lgw 2170 (2321)
T KOG1795|consen 2102 NLLKKFIT-ISDLRTQIAGYLYGVSPPDNPQVKEIRCIVM----VPQWGSHQGVHLPSFLP------IHGVLEDLEPLGW 2170 (2321)
T ss_pred HHHhhhee-ecchhhhhheeeeccCCCCCCccceEEEEEe----ccccccccccccCccCC------cchhccCCcccch
Q ss_pred EEec
Q psy8916 502 IFTD 505 (520)
Q Consensus 502 IFTd 505 (520)
|=|.
T Consensus 2171 ~hTq 2174 (2321)
T KOG1795|consen 2171 IHTQ 2174 (2321)
T ss_pred hhcC
No 123
>cd01777 SNX27_RA Ubiquitin domain of SNX27 (sorting nexin protein 27). SNX27_RA SNX27 (sorting nexin protein 27) belongs to a large family of endosome-localized proteins related to sorting nexin1 which is implicated in regulating membrane traffic. The domain architecture of SNX27 includes an amino-terminal PDZ domain, a PX (PhoX homologous) domain, and a carboxy-terminal RA (RAS-associated) domain.
Probab=24.61 E-value=1.2e+02 Score=26.89 Aligned_cols=45 Identities=22% Similarity=0.457 Sum_probs=37.6
Q ss_pred eeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCC---cceeeec
Q psy8916 175 ILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTY---NFALFKQ 219 (520)
Q Consensus 175 iIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~d---sftL~~n 219 (520)
-||+.=|||....|+|..+++...+++.+...++++.+ -|.|+.-
T Consensus 3 ~L~V~Lpdg~~i~V~v~~s~~a~~Vleav~~kl~L~~e~~~YFaLFev 50 (87)
T cd01777 3 ELRIALPDKATVTVRVRKNATTDQVYQALVAKAGMDSYTQNYFALFEV 50 (87)
T ss_pred EEEEEccCCCEEEEEEEEcccHHHHHHHHHHHhCCCHHHHhheeeeEE
Confidence 47788888977788999999999999999999999975 4556654
No 124
>PF06877 RraB: Regulator of ribonuclease activity B; InterPro: IPR009671 This entry occurs in several hypothetical bacterial proteins of around 120 residues in length. The function of these proteins is unknown. The protein structure has been determined for one member of this group, the hypothetical protein VCO424 from Vibrio cholerae; it has an alpha+beta sandwich fold.; PDB: 1NXI_A.
Probab=24.59 E-value=62 Score=27.82 Aligned_cols=80 Identities=19% Similarity=0.282 Sum_probs=44.0
Q ss_pred CCCCcCe-eeecCHHHHHHHHHHHHhcCceeeEEEEEEEeeCCCCCccceEEEEEEecCCCCCCCCceEEcCCCChHHHH
Q psy8916 410 VYRHVDN-VEFENRTLVERFLEYWRVTGHQRLGLLYGKYQLHPDVPLGIKAVVAAIYEPPQESSRDKIKLLPDPKAEVVE 488 (520)
Q Consensus 410 ~~R~VDh-vef~~~~~v~~Fi~~wr~~g~QR~G~LYG~Y~~~~~vPlGikAvVeAIYEPPQ~~~~dg~~ll~d~~e~~Vd 488 (520)
.-|.|+| +.|.+.+-++.|+..-...|.+ +-..+-. .++++.+..+.+..+-. |.. +.| +.......
T Consensus 22 ~~r~ieh~~~f~~~~~~~~f~~~~~~~g~~-v~~~~~~-~~d~~~~~~~~~~~~~~---~~~---~~I----~~~~~~l~ 89 (104)
T PF06877_consen 22 KPRPIEHWFYFEDEEDAEKFAEELEKLGYE-VESAEED-EEDGDGPYCLDISREMV---LDY---EDI----NAITQELE 89 (104)
T ss_dssp S-EEEEEEEEES-HHHHHHHHHHHHHHS----B----B--SS-SSBEEEEEEEEE----S-H---HHH----HHHHHHHH
T ss_pred CCeEEEEEEEeCCHHHHHHHHHHHHHCCCE-EEEeecc-cCCCCceEEEEEEEecC---CCH---HHH----HHHHHHHH
Confidence 4577888 9999999999999988877544 2211111 34445555555554422 000 000 11234577
Q ss_pred HHHHhcCCeEEEE
Q psy8916 489 EIASSLGLTQVGW 501 (520)
Q Consensus 489 ~iA~~LGL~rVG~ 501 (520)
+||+.+|-+-=||
T Consensus 90 ~lA~~~~g~YDGW 102 (104)
T PF06877_consen 90 DLAKEFGGEYDGW 102 (104)
T ss_dssp HHHHHHT-EEEEE
T ss_pred HHHHHhCcEecCc
Confidence 8999999999998
No 125
>KOG1560|consensus
Probab=23.63 E-value=1.7e+02 Score=31.23 Aligned_cols=28 Identities=14% Similarity=0.382 Sum_probs=24.5
Q ss_pred CCCCceeeeeEechHHHHHHhhcCcccc
Q psy8916 122 DKDNQVHMEGYQVSNQCMALVRDGCLIP 149 (520)
Q Consensus 122 ~~~~~i~~~~yqvS~q~~alv~~~~~~~ 149 (520)
...|...+.||+++-++|++.+++-..|
T Consensus 141 ssqG~L~lrAyrLTp~am~~~kekdwtp 168 (339)
T KOG1560|consen 141 SSQGTLSLRAYRLTPEAMAAHKEKDWTP 168 (339)
T ss_pred ccCceEEeehhhcCHHHHHHHhcCCCCH
Confidence 4569999999999999999999986655
No 126
>cd04509 PBP1_ABC_transporter_GCPR_C_like Family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems. This CD includes members of the family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems. The family C GPCR includes glutamate/glycine-gated ion channels such as the NMDA receptor, G-protein-coupled receptors, metabotropic glutamate, GABA-B, calcium sensing, phermone receptors, and atrial natriuretic peptide-guanylate cyclase receptors. The glutamate receptors that form cation-selective ion channels, iGluR, can be classified into three different subgroups according to their binding-affinity for the agonists NMDA (N-methyl-D-asparate), AMPA (alpha-amino-3-dihydro-5-methyl-3-oxo-4-isoxazolepropionic acid), and kainate. L-glutamate is a major neurotransmitter in the brain of vertebrates and acts th
Probab=23.42 E-value=3e+02 Score=25.90 Aligned_cols=99 Identities=18% Similarity=0.150 Sum_probs=60.2
Q ss_pred CCCCcCeeeecCHHHHHHHHHHHHhcCceeeEEEEEEEeeCCC---------CCccceEEEEEEecCCCC----------
Q psy8916 410 VYRHVDNVEFENRTLVERFLEYWRVTGHQRLGLLYGKYQLHPD---------VPLGIKAVVAAIYEPPQE---------- 470 (520)
Q Consensus 410 ~~R~VDhvef~~~~~v~~Fi~~wr~~g~QR~G~LYG~Y~~~~~---------vPlGikAvVeAIYEPPQ~---------- 470 (520)
.+..+.++...+........+++...|..+++++|........ --.|++.+.. ++-++..
T Consensus 109 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~v~iv~~~~~~~~~~~~~~~~~~~~~g~~i~~~-~~~~~~~~~~~~~~~~l 187 (299)
T cd04509 109 GYPYLFRTGPSDEQQAEALADYIKEYNWKKVAILYDDDSYGRGLLEAFKAAFKKKGGTVVGE-EYYPLGTTDFTSLLQKL 187 (299)
T ss_pred CCCCEEEecCCcHHHHHHHHHHHHHcCCcEEEEEecCchHHHHHHHHHHHHHHHcCCEEEEE-ecCCCCCccHHHHHHHH
Confidence 4455566666777788888999999999999999887542111 1123444332 3333321
Q ss_pred --CCCCceEEcCC-CChHHHHHHHHhcCCe-EEEEEEecCccC
Q psy8916 471 --SSRDKIKLLPD-PKAEVVEEIASSLGLT-QVGWIFTDLVAE 509 (520)
Q Consensus 471 --~~~dg~~ll~d-~~e~~Vd~iA~~LGL~-rVG~IFTdl~~~ 509 (520)
..++.|-+..+ +....+-+-++.+|+. .+-||.+++...
T Consensus 188 ~~~~~~~v~~~~~~~~~~~~~~~~~~~g~~~~~~~i~~~~~~~ 230 (299)
T cd04509 188 KAAKPDVIVLCGSGEDAATILKQAAEAGLTGGYPILGITLGLS 230 (299)
T ss_pred HhcCCCEEEEcccchHHHHHHHHHHHcCCCCCCcEEecccccC
Confidence 12455655555 3445555667788984 566888776543
No 127
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=23.29 E-value=1.3e+02 Score=26.49 Aligned_cols=41 Identities=22% Similarity=0.276 Sum_probs=32.6
Q ss_pred eeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCcccc
Q psy8916 185 VKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDE 225 (520)
Q Consensus 185 m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~ 225 (520)
+.|+..+-.-++..|.+||...|+++.+.+.|..--++..+
T Consensus 11 ~RRf~~~~~pt~~~L~~kl~~Lf~lp~~~~~vtYiDeD~D~ 51 (82)
T cd06397 11 TRRIVFPDIPTWEALASKLENLYNLPEIKVGVTYIDNDNDE 51 (82)
T ss_pred eEEEecCCCccHHHHHHHHHHHhCCChhHeEEEEEcCCCCE
Confidence 78999999999999999999999999877776433333333
No 128
>KOG4495|consensus
Probab=22.18 E-value=1.3e+02 Score=27.43 Aligned_cols=63 Identities=19% Similarity=0.265 Sum_probs=40.5
Q ss_pred ccceeeeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeeecCCccccccccccccccccCC
Q psy8916 170 DVFYKILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFKQRNKTDEIFSSRDQTIASVGL 239 (520)
Q Consensus 170 ~vfYMiIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~nr~~~~~l~s~~~~tv~~lgL 239 (520)
|||+|+-|-+| +.-+.++++.++-+|..++...+.-+.+...|++=. ....|. +++||++-|+
T Consensus 2 ~~f~~VrR~kt----tif~da~es~tV~elK~~l~gi~~~Pvn~qrL~kmd-~eqlL~--D~ktL~d~gf 64 (110)
T KOG4495|consen 2 DVFLRVRRHKT----TIFTDAKESSTVFELKRKLEGILKRPVNEQRLYKMD-TEQLLD--DGKTLGDCGF 64 (110)
T ss_pred ceeeeeeecce----eEEeecCccccHHHHHHHHHHHHhCCCcchheeecC-HHHHhh--ccchhhhccc
Confidence 56666665443 567899999999999999888775555544454311 111222 4677777664
No 129
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=21.77 E-value=2.4e+02 Score=23.34 Aligned_cols=44 Identities=20% Similarity=0.186 Sum_probs=34.9
Q ss_pred eeeeeCCCcceeeEEecCCcchHHHHHHHHhhcCCCCCcceeee
Q psy8916 175 ILRIQSPVGIVKRININRSDTCKDLFEKINKEFELNTYNFALFK 218 (520)
Q Consensus 175 iIRfRSkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL~~ 218 (520)
.+|+-=|+|..-.|++-|..++.+++.++.+.-+++.....++.
T Consensus 2 ~~~v~LP~~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V~~ 45 (71)
T PF02196_consen 2 TCRVHLPNGQRTVVQVRPGMTIRDALSKACKKRGLNPECCDVRL 45 (71)
T ss_dssp EEEEEETTTEEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEEEE
T ss_pred eEEEECCCCCEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence 56777789966789999999999999999999999987776664
No 130
>KOG0640|consensus
Probab=21.49 E-value=76 Score=34.35 Aligned_cols=55 Identities=27% Similarity=0.616 Sum_probs=42.4
Q ss_pred echHHHHHHHhhhhhCCCCCCCCCCCCCCcceeeeeecchhhhhccccccCCCCCCc---cCCCCcCCCceEEEEEECCC
Q psy8916 47 LSAHECIMAGHLQNLHPNPCRFAPSGYFGSKFVTICVTVNECIMAGHLQNLHPNPCR---FAPSGYFGSKFVTICVTGDK 123 (520)
Q Consensus 47 ls~~E~~~aa~~Q~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~g~~~s~fvT~~vsg~~ 123 (520)
++.+..-+-|..|...|.|.+| -+++|| .|-.||| ||++|.+ |.||..
T Consensus 82 ~~giDle~dadaq~~s~e~~~y------Et~ylt----------------~HK~~cR~aafs~DG~l-------vATGsa 132 (430)
T KOG0640|consen 82 TAGIDLEFDADAQGSSPEPSEY------ETKYLT----------------SHKSPCRAAAFSPDGSL-------VATGSA 132 (430)
T ss_pred cCceeeeeccccccCCCCCccc------ceEEEe----------------ecccceeeeeeCCCCcE-------EEccCC
Confidence 4555666778889999988754 577888 6889997 6788875 789999
Q ss_pred CCceeee
Q psy8916 124 DNQVHME 130 (520)
Q Consensus 124 ~~~i~~~ 130 (520)
|-.|.+.
T Consensus 133 D~SIKil 139 (430)
T KOG0640|consen 133 DASIKIL 139 (430)
T ss_pred cceEEEe
Confidence 8887764
No 131
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=21.31 E-value=1.7e+02 Score=30.40 Aligned_cols=45 Identities=20% Similarity=0.194 Sum_probs=38.9
Q ss_pred ceeecCCC-CCCcCeeeecCHHHHHHHHHHHHhcCceeeEEEEEEE
Q psy8916 403 AITLNRQV-YRHVDNVEFENRTLVERFLEYWRVTGHQRLGLLYGKY 447 (520)
Q Consensus 403 aItL~~Q~-~R~VDhvef~~~~~v~~Fi~~wr~~g~QR~G~LYG~Y 447 (520)
-|.+.+.. ...++.|-++|......-.++.-+.|++|+||+.|.-
T Consensus 140 ~V~i~~~~~~~~~~~V~~Dn~~~~~~a~~~L~~~G~~~i~~i~~~~ 185 (333)
T COG1609 140 VVVIDRSPPGLGVPSVGIDNFAGAYLATEHLIELGHRRIAFIGGPL 185 (333)
T ss_pred EEEEeCCCccCCCCEEEEChHHHHHHHHHHHHHCCCceEEEEeCCC
Confidence 46666643 4778999999999999999999999999999999985
No 132
>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins con
Probab=21.22 E-value=4.1e+02 Score=24.00 Aligned_cols=99 Identities=26% Similarity=0.223 Sum_probs=60.3
Q ss_pred CCCcCeeeecCHHHHHHHHHHHHhcCceeeEEEEEEEeeCCC----------CCccceEEEEEEecCCCC----------
Q psy8916 411 YRHVDNVEFENRTLVERFLEYWRVTGHQRLGLLYGKYQLHPD----------VPLGIKAVVAAIYEPPQE---------- 470 (520)
Q Consensus 411 ~R~VDhvef~~~~~v~~Fi~~wr~~g~QR~G~LYG~Y~~~~~----------vPlGikAvVeAIYEPPQ~---------- 470 (520)
+.++..+.+.+........+++.+.+..|+|++++....... --.|++.+ ...+.+...
T Consensus 98 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 176 (269)
T cd01391 98 YPYVFRVGPDNEQAGEAAAEYLAEKGWKRVALIYGDDGAYGRERLEGFKAALKKAGIEVV-AIEYGDLDTEKGFQALLQL 176 (269)
T ss_pred CceEEEEcCCcHHHHHHHHHHHHHhCCceEEEEecCCcchhhHHHHHHHHHHHhcCcEEE-eccccCCCccccHHHHHHH
Confidence 445566777788888888998888899999999987631110 00112211 111112111
Q ss_pred ---C-CCCceEEcCCCChHHHHHHHHhcCC--eEEEEEEecCccCC
Q psy8916 471 ---S-SRDKIKLLPDPKAEVVEEIASSLGL--TQVGWIFTDLVAED 510 (520)
Q Consensus 471 ---~-~~dg~~ll~d~~e~~Vd~iA~~LGL--~rVG~IFTdl~~~~ 510 (520)
. ..++|-+..+.....+-+.+..+|+ +.+.||..|.....
T Consensus 177 l~~~~~~~~i~~~~~~~a~~~~~~~~~~g~~~~~~~ii~~~~~~~~ 222 (269)
T cd01391 177 LKAAPKPDAIFACNDEMAAGALKAAREAGLTPGDISIIGFDGSPAA 222 (269)
T ss_pred HhcCCCCCEEEEcCchHHHHHHHHHHHcCCCCCCCEEEeccccccc
Confidence 1 3455555555555566666778899 58889888876554
No 133
>cd06268 PBP1_ABC_transporter_LIVBP_like Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. They are mostly present in archaea and eubacteria, and are primarily involved in scavenging solutes from the environment. ABC-type transporters couple ATP hydrolysis with the uptake and efflux of a wide range of substrates across bacterial membranes, including amino acids, peptides, lipids and sterols, and various drugs. These systems are comprised of transmembrane domains, nucleotide binding domains, and in most bacterial uptake systems, periplasmic binding proteins (PBPs) which transfer the ligand to the extracellular gate of the transmembrane domains. These PBPs bind their substrates selectively and with high affinity. Members of this group include ABC
Probab=20.07 E-value=4.5e+02 Score=24.68 Aligned_cols=96 Identities=20% Similarity=0.239 Sum_probs=56.4
Q ss_pred CcCeeeecCHHHHHHHHHHHHhcC-ceeeEEEEEEEeeCCC---------CCccceEEEEEEecCCCC-----------C
Q psy8916 413 HVDNVEFENRTLVERFLEYWRVTG-HQRLGLLYGKYQLHPD---------VPLGIKAVVAAIYEPPQE-----------S 471 (520)
Q Consensus 413 ~VDhvef~~~~~v~~Fi~~wr~~g-~QR~G~LYG~Y~~~~~---------vPlGikAvVeAIYEPPQ~-----------~ 471 (520)
.+-++...+.+......++....+ ..|++++|+.+..... --.|++.+.+..|.+-.. .
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~~~~~~~~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~~l~~~ 189 (298)
T cd06268 110 YVFRTAPSDAQQAAALADYLAEKGKVKKVAIIYDDYAYGRGLAAAFREALKKLGGEVVAEETYPPGATDFSPLIAKLKAA 189 (298)
T ss_pred eEEEcccCcHHHHHHHHHHHHHhcCCCEEEEEEcCCchhHHHHHHHHHHHHHcCCEEEEEeccCCCCccHHHHHHHHHhc
Confidence 344444566678888888888777 8999999987651111 123455444444443211 2
Q ss_pred CCCceEEcCC-CChHHHHHHHHhcCCeEEEEEEecCccC
Q psy8916 472 SRDKIKLLPD-PKAEVVEEIASSLGLTQVGWIFTDLVAE 509 (520)
Q Consensus 472 ~~dg~~ll~d-~~e~~Vd~iA~~LGL~rVG~IFTdl~~~ 509 (520)
.+|.|.+..+ +....+-+-+++.|+ .+-||.+|....
T Consensus 190 ~~~~vi~~~~~~~~~~~~~~~~~~g~-~~~~~~~~~~~~ 227 (298)
T cd06268 190 GPDAVFLAGYGGDAALFLKQAREAGL-KVPIVGGDGAAA 227 (298)
T ss_pred CCCEEEEccccchHHHHHHHHHHcCC-CCcEEecCccCC
Confidence 2456665555 333445555667887 666777766544
No 134
>KOG0006|consensus
Probab=20.06 E-value=1.9e+02 Score=31.42 Aligned_cols=41 Identities=12% Similarity=0.214 Sum_probs=35.3
Q ss_pred eeeeee---CCCcceeeEEecCCcchHHHHHHHHhhcCCCCCccee
Q psy8916 174 KILRIQ---SPVGIVKRININRSDTCKDLFEKINKEFELNTYNFAL 216 (520)
Q Consensus 174 MiIRfR---SkdG~m~RVev~ptDtfs~LleKLl~~f~ls~dsftL 216 (520)
.+++|+ +..| +.|+|+.+.++.+|.+.+.+..+++.|.+.+
T Consensus 3 ~lvqf~~~~~~h~--l~v~v~~~t~I~~lke~Vak~~gvp~D~L~v 46 (446)
T KOG0006|consen 3 VLVQFNKTGSSHG--LPVEVDSDTSIFQLKEVVAKRQGVPADQLRV 46 (446)
T ss_pred EEEEeCCccccCc--eeEEEecCCCHHHHHHHHHHhhCCChhheEE
Confidence 467777 6677 8999999999999999999999999887654
Done!