Query psy6336
Match_columns 73
No_of_seqs 108 out of 300
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 23:46:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6336.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6336hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1654|consensus 100.0 6.1E-35 1.3E-39 187.0 6.7 71 2-72 28-98 (116)
2 PF02991 Atg8: Autophagy prote 100.0 3.3E-34 7.1E-39 181.8 7.8 71 2-72 16-86 (104)
3 cd01611 GABARAP Ubiquitin doma 100.0 1.9E-33 4.1E-38 180.1 8.5 72 2-73 24-95 (112)
4 PTZ00380 microtubule-associate 100.0 3.7E-29 7.9E-34 162.4 7.1 67 2-73 27-94 (121)
5 cd01612 APG12_C Ubiquitin-like 99.9 1.2E-24 2.7E-29 134.0 7.6 62 11-72 8-70 (87)
6 KOG3439|consensus 99.8 6.1E-19 1.3E-23 113.2 5.8 61 13-73 39-100 (116)
7 PF04110 APG12: Ubiquitin-like 99.7 5.7E-18 1.2E-22 104.7 4.9 60 14-73 11-71 (87)
8 PF11976 Rad60-SLD: Ubiquitin- 92.8 0.36 7.9E-06 27.2 4.6 50 19-68 11-60 (72)
9 PF11816 DUF3337: Domain of un 92.4 0.84 1.8E-05 33.6 7.1 70 2-71 214-314 (331)
10 smart00213 UBQ Ubiquitin homol 90.3 1.2 2.6E-05 23.8 4.8 47 20-67 11-57 (64)
11 cd00196 UBQ Ubiquitin-like pro 89.7 1.4 3.1E-05 21.7 4.5 39 17-56 6-44 (69)
12 cd06406 PB1_P67 A PB1 domain i 87.9 0.53 1.2E-05 28.7 2.4 44 25-69 17-65 (80)
13 PF00240 ubiquitin: Ubiquitin 87.7 0.63 1.4E-05 25.9 2.5 46 21-67 8-53 (69)
14 cd01813 UBP_N UBP ubiquitin pr 87.4 1.1 2.4E-05 26.1 3.5 45 24-68 15-61 (74)
15 KOG2660|consensus 83.9 1.1 2.4E-05 33.7 2.8 55 14-69 159-215 (331)
16 cd01806 Nedd8 Nebb8-like ubiq 83.7 4.8 0.0001 22.5 4.9 44 23-67 15-58 (76)
17 cd01769 UBL Ubiquitin-like dom 83.4 4.2 9.1E-05 21.9 4.4 45 22-67 11-55 (69)
18 cd01798 parkin_N amino-termina 80.5 2.9 6.3E-05 23.5 3.2 44 23-67 13-56 (70)
19 cd01796 DDI1_N DNA damage indu 79.9 3.2 6.9E-05 23.7 3.2 44 23-66 14-57 (71)
20 cd01809 Scythe_N Ubiquitin-lik 77.6 8.4 0.00018 21.2 4.5 46 21-67 13-58 (72)
21 cd01803 Ubiquitin Ubiquitin. U 77.4 7.4 0.00016 21.6 4.2 45 22-67 14-58 (76)
22 cd01805 RAD23_N Ubiquitin-like 77.1 11 0.00023 21.2 4.9 45 22-67 14-60 (77)
23 cd01807 GDX_N ubiquitin-like d 76.9 5.5 0.00012 22.6 3.6 44 23-67 15-58 (74)
24 cd01763 Sumo Small ubiquitin-r 76.2 11 0.00024 22.3 4.9 48 19-67 22-69 (87)
25 PF12436 USP7_ICP0_bdg: ICP0-b 73.6 5.4 0.00012 28.2 3.6 34 22-55 88-121 (249)
26 cd01791 Ubl5 UBL5 ubiquitin-li 71.3 11 0.00024 21.9 4.0 43 24-67 17-59 (73)
27 cd06407 PB1_NLP A PB1 domain i 71.2 11 0.00023 22.6 4.0 38 19-56 10-48 (82)
28 PF05717 TnpB_IS66: IS66 Orf2 70.9 8.3 0.00018 24.2 3.6 27 30-56 16-43 (107)
29 cd01794 DC_UbP_C dendritic cel 70.4 13 0.00029 21.2 4.2 46 21-67 11-56 (70)
30 cd01804 midnolin_N Ubiquitin-l 70.1 9.5 0.00021 22.1 3.6 44 22-67 15-58 (78)
31 PTZ00044 ubiquitin; Provisiona 69.8 7.7 0.00017 21.9 3.1 45 22-67 14-58 (76)
32 cd01795 USP48_C USP ubiquitin- 69.7 11 0.00024 24.1 4.0 45 23-67 19-63 (107)
33 PF13019 Telomere_Sde2: Telome 68.7 13 0.00029 25.3 4.5 49 21-69 17-68 (162)
34 cd01808 hPLIC_N Ubiquitin-like 67.5 18 0.00039 20.3 4.3 45 22-67 13-57 (71)
35 PF14533 USP7_C2: Ubiquitin-sp 67.3 5.4 0.00012 27.5 2.4 50 19-68 34-90 (213)
36 cd01799 Hoil1_N Ubiquitin-like 67.0 11 0.00025 21.9 3.5 44 22-67 16-60 (75)
37 cd01792 ISG15_repeat1 ISG15 ub 66.7 10 0.00022 21.9 3.2 44 24-67 18-62 (80)
38 cd01776 Rin1_RA Ubiquitin doma 66.1 15 0.00032 22.8 3.9 36 21-56 16-53 (87)
39 PF14560 Ubiquitin_2: Ubiquiti 64.2 12 0.00026 21.9 3.2 31 23-53 18-49 (87)
40 PF10302 DUF2407: DUF2407 ubiq 64.0 21 0.00045 22.1 4.4 51 14-65 10-61 (97)
41 cd06398 PB1_Joka2 The PB1 doma 63.2 19 0.0004 22.1 4.0 36 20-55 11-52 (91)
42 cd03483 MutL_Trans_MLH1 MutL_T 60.6 7 0.00015 24.8 1.8 26 47-72 47-75 (127)
43 cd01789 Alp11_N Ubiquitin-like 59.4 19 0.00041 21.2 3.5 32 25-56 19-51 (84)
44 cd01812 BAG1_N Ubiquitin-like 59.1 21 0.00046 19.5 3.5 44 23-67 14-57 (71)
45 cd01810 ISG15_repeat2 ISG15 ub 57.2 26 0.00056 19.8 3.7 44 23-67 13-56 (74)
46 smart00666 PB1 PB1 domain. Pho 57.1 34 0.00074 19.3 5.5 52 19-70 11-66 (81)
47 cd01800 SF3a120_C Ubiquitin-li 57.0 24 0.00053 20.1 3.6 44 23-67 12-55 (76)
48 PF09358 UBA_e1_C: Ubiquitin-a 56.9 9.2 0.0002 24.6 1.9 50 22-71 36-93 (125)
49 cd06411 PB1_p51 The PB1 domain 54.9 12 0.00026 22.7 2.1 46 25-70 13-64 (78)
50 cd01815 BMSC_UbP_N Ubiquitin-l 54.5 32 0.0007 20.5 3.9 42 25-67 17-61 (75)
51 cd05992 PB1 The PB1 domain is 54.3 38 0.00081 19.0 4.8 52 19-70 10-66 (81)
52 cd01790 Herp_N Homocysteine-re 51.8 50 0.0011 19.7 5.1 49 20-69 13-65 (79)
53 PRK06437 hypothetical protein; 50.7 27 0.00059 19.8 3.1 39 22-65 14-52 (67)
54 PRK13669 hypothetical protein; 49.9 13 0.00029 22.5 1.7 24 48-71 45-71 (78)
55 PF11543 UN_NPL4: Nuclear pore 49.9 11 0.00024 22.4 1.4 33 22-55 17-49 (80)
56 TIGR01682 moaD molybdopterin c 49.4 22 0.00047 20.4 2.6 43 22-64 19-64 (80)
57 PF15130 DUF4566: Domain of un 49.2 17 0.00036 26.1 2.4 47 22-68 155-209 (241)
58 cd01793 Fubi Fubi ubiquitin-li 48.1 50 0.0011 18.6 4.2 48 19-67 9-56 (74)
59 PRK08364 sulfur carrier protei 46.6 36 0.00078 19.3 3.2 40 21-65 16-55 (70)
60 cd03482 MutL_Trans_MutL MutL_T 45.7 16 0.00035 22.9 1.7 26 47-72 43-71 (123)
61 PF08825 E2_bind: E2 binding d 43.6 27 0.00058 21.1 2.4 28 25-52 3-38 (84)
62 PF07293 DUF1450: Protein of u 43.1 19 0.00041 21.7 1.6 24 48-71 45-71 (78)
63 cd01797 NIRF_N amino-terminal 42.9 38 0.00083 19.6 3.0 42 25-67 19-60 (78)
64 PF09379 FERM_N: FERM N-termin 42.5 61 0.0013 18.1 3.7 35 20-54 8-42 (80)
65 COG2002 AbrB Regulators of sta 41.9 33 0.00071 20.5 2.6 21 36-56 20-40 (89)
66 PF00564 PB1: PB1 domain; Int 40.7 68 0.0015 18.0 4.5 48 23-70 16-67 (84)
67 PF12436 USP7_ICP0_bdg: ICP0-b 39.9 1.3E+02 0.0029 21.1 6.0 37 20-56 191-227 (249)
68 cd03485 MutL_Trans_hPMS_1_like 39.9 34 0.00074 21.6 2.6 27 46-72 47-77 (132)
69 COG2239 MgtE Mg/Co/Ni transpor 39.8 48 0.001 25.9 3.8 39 15-54 134-173 (451)
70 KOG0765|consensus 39.7 12 0.00025 28.3 0.4 36 16-51 29-70 (333)
71 cd00782 MutL_Trans MutL_Trans: 39.2 22 0.00048 21.7 1.6 27 46-72 42-71 (122)
72 PF07929 PRiA4_ORF3: Plasmid p 39.0 68 0.0015 21.1 4.0 35 21-55 20-54 (179)
73 cd06408 PB1_NoxR The PB1 domai 38.4 42 0.0009 20.6 2.7 28 23-52 16-43 (86)
74 PF04106 APG5: Autophagy prote 38.3 57 0.0012 22.3 3.7 27 46-72 157-183 (197)
75 cd01802 AN1_N ubiquitin-like d 37.7 59 0.0013 20.0 3.4 44 23-67 42-85 (103)
76 cd01768 RA RA (Ras-associating 37.4 81 0.0018 18.0 4.3 28 18-45 12-39 (87)
77 PRK04115 hypothetical protein; 36.9 93 0.002 20.7 4.3 43 2-53 67-113 (137)
78 cd06396 PB1_NBR1 The PB1 domai 35.7 63 0.0014 19.5 3.2 49 19-70 10-65 (81)
79 PF04014 Antitoxin-MazE: Antid 35.5 58 0.0013 16.9 2.7 21 36-56 13-33 (47)
80 cd01775 CYR1_RA Ubiquitin doma 35.0 92 0.002 19.6 3.9 35 22-56 16-52 (97)
81 PRK08577 hypothetical protein; 34.5 46 0.00099 21.1 2.6 21 36-56 19-39 (136)
82 KOG1209|consensus 34.1 95 0.0021 22.9 4.3 50 19-72 55-109 (289)
83 PF02597 ThiS: ThiS family; I 33.5 23 0.0005 19.7 0.9 39 20-58 13-52 (77)
84 PF01650 Peptidase_C13: Peptid 33.2 59 0.0013 23.2 3.2 31 26-56 77-115 (256)
85 PF04663 Phenol_monoox: Phenol 32.5 38 0.00082 20.0 1.7 18 21-38 28-45 (67)
86 PF12949 HeH: HeH/LEM domain; 31.4 43 0.00094 17.2 1.7 16 26-41 1-16 (35)
87 KOG4147|consensus 30.9 33 0.00071 22.4 1.4 21 27-47 32-52 (127)
88 PF08154 NLE: NLE (NUC135) dom 30.3 1.1E+02 0.0023 17.2 6.1 41 17-57 14-55 (65)
89 KOG0010|consensus 29.6 82 0.0018 25.1 3.6 47 19-66 25-71 (493)
90 cd00754 MoaD Ubiquitin domain 29.1 87 0.0019 17.4 2.9 44 21-64 18-64 (80)
91 PF10209 DUF2340: Uncharacteri 28.5 55 0.0012 21.4 2.1 21 27-47 25-45 (122)
92 PRK11130 moaD molybdopterin sy 27.9 75 0.0016 18.3 2.5 40 24-64 20-65 (81)
93 PF14732 UAE_UbL: Ubiquitin/SU 27.5 21 0.00045 21.5 0.0 21 26-46 6-27 (87)
94 PF03147 FDX-ACB: Ferredoxin-f 27.2 62 0.0014 19.2 2.1 22 22-43 11-32 (94)
95 COG3171 Uncharacterized protei 27.2 20 0.00044 23.3 -0.0 39 35-73 14-54 (119)
96 PF10367 Vps39_2: Vacuolar sor 26.7 47 0.001 19.4 1.5 20 24-43 19-38 (109)
97 PF01119 DNA_mis_repair: DNA m 26.1 57 0.0012 20.1 1.9 27 45-71 37-66 (119)
98 PF03459 TOBE: TOBE domain; I 26.0 65 0.0014 17.2 1.9 18 39-56 42-59 (64)
99 smart00148 PLCXc Phospholipase 25.5 72 0.0016 20.3 2.3 33 26-58 66-98 (135)
100 TIGR01683 thiS thiamine biosyn 25.3 1.3E+02 0.0028 16.5 3.5 36 19-59 4-40 (64)
101 PF02938 GAD: GAD domain; Int 24.9 1.1E+02 0.0024 18.2 3.0 25 32-56 63-87 (95)
102 TIGR02851 spore_V_T stage V sp 24.9 80 0.0017 21.4 2.5 20 36-55 19-38 (180)
103 PF00789 UBX: UBX domain; Int 24.7 1.1E+02 0.0023 17.3 2.8 53 15-67 13-69 (82)
104 PF01886 DUF61: Protein of unk 24.6 1.3E+02 0.0027 19.7 3.3 43 2-53 65-111 (132)
105 PF04320 DUF469: Protein with 24.6 58 0.0012 20.6 1.7 36 38-73 3-40 (101)
106 PF11470 TUG-UBL1: GLUT4 regul 23.2 1.6E+02 0.0035 16.8 3.7 40 17-57 5-44 (65)
107 PRK12577 succinate dehydrogena 23.1 1.5E+02 0.0032 21.8 3.8 42 1-42 1-42 (329)
108 PF00388 PI-PLC-X: Phosphatidy 22.8 43 0.00094 21.2 0.9 32 27-58 65-96 (146)
109 smart00295 B41 Band 4.1 homolo 22.1 2.3E+02 0.0049 18.2 4.8 50 19-68 14-69 (207)
110 COG3592 Uncharacterized conser 22.0 82 0.0018 18.9 1.9 36 6-41 24-64 (74)
111 PF08817 YukD: WXG100 protein 21.8 80 0.0017 18.1 1.8 44 23-66 17-66 (79)
112 PLN02768 AMP deaminase 21.8 1.4E+02 0.003 25.5 3.7 46 22-72 387-432 (835)
113 cd00329 TopoII_MutL_Trans MutL 21.6 1E+02 0.0023 17.5 2.3 11 47-57 43-53 (107)
114 PF13764 E3_UbLigase_R4: E3 ub 21.5 1.2E+02 0.0026 25.5 3.4 42 31-72 17-62 (802)
115 TIGR02609 doc_partner putative 21.4 1.2E+02 0.0026 17.4 2.6 21 36-56 16-36 (74)
116 TIGR01408 Ube1 ubiquitin-activ 21.2 1.4E+02 0.0031 25.6 3.8 48 23-71 916-971 (1008)
117 PLN02799 Molybdopterin synthas 21.2 83 0.0018 17.9 1.8 47 19-65 19-67 (82)
118 KOG4250|consensus 21.2 1.5E+02 0.0032 24.9 3.7 38 19-56 325-362 (732)
119 COG0278 Glutaredoxin-related p 20.9 60 0.0013 20.8 1.2 20 52-71 75-94 (105)
120 TIGR01439 lp_hng_hel_AbrB loop 20.4 1.1E+02 0.0023 15.0 2.0 19 36-54 13-31 (43)
No 1
>KOG1654|consensus
Probab=100.00 E-value=6.1e-35 Score=186.96 Aligned_cols=71 Identities=68% Similarity=0.983 Sum_probs=69.5
Q ss_pred eeEEEEEeCCCCCCCCCcceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHHHHhhh
Q psy6336 2 MWRVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGSLYQEI 72 (73)
Q Consensus 2 ~iPvIvEr~~~~~lP~Ldk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~lY~~f 72 (73)
|||||||+++++++|+|||+|||||.|+|||||+++|||||+|+|++|+|+||||.+|+++++|++||+++
T Consensus 28 riPVIvEk~~~~~lp~lDK~KyLVP~dltvgqfi~iIRkRiqL~~~kA~flfVn~~~p~ts~~ms~~Ye~~ 98 (116)
T KOG1654|consen 28 RIPVIVEKAGKSQLPDLDKKKYLVPDDLTVGQFIKIIRKRIQLSPEKAFFLFVNNTSPPTSATMSALYEEE 98 (116)
T ss_pred CCcEEEEecccccCcccccceeeccccccHHHHHHHHHHHhccChhHeEEEEEcCcCCcchhhHHHHHHhh
Confidence 89999999999999999999999999999999999999999999999999999999999999999999985
No 2
>PF02991 Atg8: Autophagy protein Atg8 ubiquitin like; InterPro: IPR004241 Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N terminus and the C terminus of Atg19. Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [] Related proteins that belong to this group include the human ganglioside expression factor and a symbiosis-related fungal protein.; PDB: 3ECI_A 3D32_B 1GNU_A 1KM7_A 1KLV_A 1KOT_A 3DOW_A 1KJT_A 1V49_A 2ZJD_C ....
Probab=100.00 E-value=3.3e-34 Score=181.76 Aligned_cols=71 Identities=63% Similarity=1.042 Sum_probs=63.1
Q ss_pred eeEEEEEeCCCCCCCCCcceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHHHHhhh
Q psy6336 2 MWRVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGSLYQEI 72 (73)
Q Consensus 2 ~iPvIvEr~~~~~lP~Ldk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~lY~~f 72 (73)
||||||||+++|++|+|||+|||||.++||+||+++||+||+|++++||||||||++|+++++||+||++|
T Consensus 16 ~IPVIvEr~~~s~lp~ldk~KfLvp~~~tv~qf~~~ir~rl~l~~~~alfl~Vn~~lp~~s~tm~elY~~~ 86 (104)
T PF02991_consen 16 KIPVIVERYPKSKLPDLDKKKFLVPKDLTVGQFVYIIRKRLQLSPEQALFLFVNNTLPSTSSTMGELYEKY 86 (104)
T ss_dssp EEEEEEEE-TTSSS---SSSEEEEETTSBHHHHHHHHHHHTT--TTS-EEEEBTTBESSTTSBHHHHHHHH
T ss_pred ccEEEEEEccCCChhhcCccEEEEcCCCchhhHHHHhhhhhcCCCCceEEEEEcCcccchhhHHHHHHHHh
Confidence 89999999999999999999999999999999999999999999999999999999999999999999987
No 3
>cd01611 GABARAP Ubiquitin domain of GABA-receptor-associated protein. GABARAP (GABA-receptor-associated protein) belongs ot a large family of proteins that mediate intracellular membrane trafficking and/or fusion. GABARAP binds not only to GABA, type A but also to tubulin, gephrin, and ULK1. Orthologues of GABARAP include Gate-16 (golgi-associated ATPase enhancer), LC3 (microtubule-associated protein light chain 3), and ATG8 (autophagy protein 8). ATG8 is a ubiquitin-like protein that is conjugated to the membrane phospholipid, phosphatidylethanolamine as part of a ubiquitin-like conjugation system essential for autophagosome-formation.
Probab=100.00 E-value=1.9e-33 Score=180.07 Aligned_cols=72 Identities=69% Similarity=1.061 Sum_probs=70.6
Q ss_pred eeEEEEEeCCCCCCCCCcceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHHHHhhhC
Q psy6336 2 MWRVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGSLYQEII 73 (73)
Q Consensus 2 ~iPvIvEr~~~~~lP~Ldk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~lY~~f~ 73 (73)
||||||||++++++|+|||+|||||+++||+||..+||+||+|++++||||||||++|++|++|++||++|.
T Consensus 24 ~iPVIvE~~~~~~~p~l~k~KflVp~~~tv~~f~~~irk~l~l~~~~slfl~Vn~~~p~~~~~~~~lY~~~k 95 (112)
T cd01611 24 RIPVIVERYPKSDLPDLDKKKYLVPSDLTVGQFVYIIRKRIQLRPEKALFLFVNNSLPPTSATMSQLYEEHK 95 (112)
T ss_pred ceEEEEEEcCCCCcccccCceEEecCCCCHHHHHHHHHHHhCCCccceEEEEECCccCCchhHHHHHHHHhC
Confidence 799999999999999999999999999999999999999999999999999999999999999999999983
No 4
>PTZ00380 microtubule-associated protein (MAP); Provisional
Probab=99.96 E-value=3.7e-29 Score=162.40 Aligned_cols=67 Identities=24% Similarity=0.358 Sum_probs=64.3
Q ss_pred eeEEEEEeCCCCCCCCCcceee-eecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHHHHhhhC
Q psy6336 2 MWRVIVEKAPKARIGDLDKKKY-LVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGSLYQEII 73 (73)
Q Consensus 2 ~iPvIvEr~~~~~lP~Ldk~Kf-LVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~lY~~f~ 73 (73)
||||||||+++++ ||+|| |||+|+|||||.++||+||+|++++ +||||||.+|+++++||+||++|.
T Consensus 27 rIPVIvEk~~~s~----dK~KfllVP~d~tV~qF~~iIRkrl~l~~~k-~flfVnn~lp~~s~~mg~lYe~~K 94 (121)
T PTZ00380 27 HVAVVVEAAEKAG----SKVHFLALPRDATVAELEAAVRQALGTSAKK-VTLAIEGSTPAVTATVGDIADACK 94 (121)
T ss_pred ccEEEEeecCCCC----CceEEEEcCCCCcHHHHHHHHHHHcCCChhH-EEEEECCccCCccchHHHHHHHhc
Confidence 7999999999998 89999 6999999999999999999999999 999999999999999999999873
No 5
>cd01612 APG12_C Ubiquitin-like domain of APG12. APG12_C The carboxy-terminal ubiquitin-like domain of APG12. Autophagy is a process in which cytoplasmic components are delivered to the lysosome/vacuole for degradation. Autophagy requires a ubiquitin-like protein conjugation system, in which APG12 is covalently bound to APG5.
Probab=99.91 E-value=1.2e-24 Score=134.05 Aligned_cols=62 Identities=26% Similarity=0.537 Sum_probs=59.3
Q ss_pred CCCCCCCCcceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcC-cCCCCcchHHHHHhhh
Q psy6336 11 PKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNN-VIPPTSATMGSLYQEI 72 (73)
Q Consensus 11 ~~~~lP~Ldk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~-~lp~~~~~m~~lY~~f 72 (73)
+-+++|+|+|+||+||+++|++||+.+||+||++++++|+|+|||| ++|++|++||+||++|
T Consensus 8 ~~g~~p~l~k~kflv~~~~tv~~~~~~lrk~L~l~~~~slflyvnn~f~p~~d~~~g~LY~~~ 70 (87)
T cd01612 8 PIGSAPILKQKVFKISATQSFQAVIDFLRKRLKLKASDSLFLYINNSFAPSPDENVGNLYRCF 70 (87)
T ss_pred ECCCCccccccEEEeCCCCCHHHHHHHHHHHhCCCccCeEEEEECCccCCCchhHHHHHHHhc
Confidence 4578999999999999999999999999999999999999999999 5899999999999998
No 6
>KOG3439|consensus
Probab=99.77 E-value=6.1e-19 Score=113.24 Aligned_cols=61 Identities=26% Similarity=0.492 Sum_probs=58.7
Q ss_pred CCCCCCcceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcC-cCCCCcchHHHHHhhhC
Q psy6336 13 ARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNN-VIPPTSATMGSLYQEII 73 (73)
Q Consensus 13 ~~lP~Ldk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~-~lp~~~~~m~~lY~~f~ 73 (73)
.++|.|+++||-|+++.|++.++.+|||+|+|+++++||+|||| ++||+|+.+++||+||-
T Consensus 39 G~~PilK~~k~~i~~t~tfa~vi~Flkk~Lkl~as~slflYVN~sFAPsPDq~v~~Ly~cf~ 100 (116)
T KOG3439|consen 39 GDAPILKKSKFKINPTQTFAKVILFLKKFLKLQASDSLFLYVNNSFAPSPDQIVGNLYECFG 100 (116)
T ss_pred CCCcceecceEEeCcchhhHHHHHHHHHHhCCcccCeEEEEEcCccCCCchhHHHHHHHhcC
Confidence 36999999999999999999999999999999999999999998 89999999999999983
No 7
>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=99.72 E-value=5.7e-18 Score=104.71 Aligned_cols=60 Identities=30% Similarity=0.592 Sum_probs=44.1
Q ss_pred CCCCCcceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcC-cCCCCcchHHHHHhhhC
Q psy6336 14 RIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNN-VIPPTSATMGSLYQEII 73 (73)
Q Consensus 14 ~lP~Ldk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~-~lp~~~~~m~~lY~~f~ 73 (73)
++|.|+++||-|.++.|++.++.+|||+|++.+++++|+|||+ +.|++|+++++||+||.
T Consensus 11 ~aPilk~~k~kI~~~~~f~~vi~fLrk~Lk~~~~~slFlYin~sFaPspDe~vg~L~~~f~ 71 (87)
T PF04110_consen 11 SAPILKQKKFKISASQTFATVIAFLRKKLKLKPSDSLFLYINNSFAPSPDETVGDLYRCFG 71 (87)
T ss_dssp T----S--EEEEETTSBTHHHHHHHHHHCT----SS-EEEEEEEE---TTSBHHHHHHHH-
T ss_pred CCccccCcEEEECCCCchHHHHHHHHHHhCCccCCeEEEEEcCccCCCchhHHHHHHHHhC
Confidence 6999999999999999999999999999999999999999998 89999999999999983
No 8
>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=92.84 E-value=0.36 Score=27.24 Aligned_cols=50 Identities=16% Similarity=0.193 Sum_probs=37.4
Q ss_pred cceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHHH
Q psy6336 19 DKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGSL 68 (73)
Q Consensus 19 dk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~l 68 (73)
+..+|-|.++.+++.+....+++.++++++++-|+-++.-...+.|.+++
T Consensus 11 ~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~~L~~~~T~~~~ 60 (72)
T PF11976_consen 11 KEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFDGKRLDPNDTPEDL 60 (72)
T ss_dssp EEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEETTEEE-TTSCHHHH
T ss_pred CEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEECCEEcCCCCCHHHC
Confidence 35678899999999999999999999996666666666444445566654
No 9
>PF11816 DUF3337: Domain of unknown function (DUF3337); InterPro: IPR021772 This family of proteins are functionally uncharacterised. This family is only found in eukaryotes. This presumed domain is typically between 285 to 342 amino acids in length.
Probab=92.39 E-value=0.84 Score=33.57 Aligned_cols=70 Identities=16% Similarity=0.253 Sum_probs=55.1
Q ss_pred eeEEEEEeCCCCCCCCCcce-----------------eeeecCCCChhhHHHHHHhhh--------------cCCCCCeE
Q psy6336 2 MWRVIVEKAPKARIGDLDKK-----------------KYLVPSDLTVGQFYFLIRKRV--------------QLRPEDAL 50 (73)
Q Consensus 2 ~iPvIvEr~~~~~lP~Ldk~-----------------KfLVp~~~tv~qf~~~iRk~L--------------~L~~~~al 50 (73)
+|+-+++.++.+..|.+..- |.-.|+-+.|.-+...|-.|+ .+.+++.|
T Consensus 214 Ki~F~L~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rL~A~~mLrvkKI~~yV~ek~~~~~~~~~~~~~~~~~~p~e~l 293 (331)
T PF11816_consen 214 KISFVLQPWDGSLPPNLKPDGKSQKKIKLPPLSEGNSRLNAPRMLRVKKILEYVAEKLEKTPESKTPEMKPKKLKPEEWL 293 (331)
T ss_pred eeEEEEeecCCCCccccCCCccccccccccccccccceecccchhhhHHHHHHHHHHhccCccccCccccccCCCCCceE
Confidence 45567777665554555444 888899999999999999999 46789999
Q ss_pred EEEEcCcCCCCcchHHHHHhh
Q psy6336 51 FFFVNNVIPPTSATMGSLYQE 71 (73)
Q Consensus 51 fl~Vn~~lp~~~~~m~~lY~~ 71 (73)
=|+||+.+.+.++||+.|=.-
T Consensus 294 El~C~gqvL~~~mtLaTVr~~ 314 (331)
T PF11816_consen 294 ELLCNGQVLPPDMTLATVRTF 314 (331)
T ss_pred EEEeCCeEcCCcCCHHHHHHh
Confidence 999999888889999988543
No 10
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=90.34 E-value=1.2 Score=23.85 Aligned_cols=47 Identities=13% Similarity=0.055 Sum_probs=34.1
Q ss_pred ceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 20 KKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 20 k~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
...+-|+.+.|++++...|.++.++++++- =|+.++.....+.++++
T Consensus 11 ~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~-~L~~~g~~L~d~~tL~~ 57 (64)
T smart00213 11 TITLEVKPSDTVSELKEKIAELTGIPVEQQ-RLIYKGKVLEDDRTLAD 57 (64)
T ss_pred eEEEEECCCCcHHHHHHHHHHHHCCCHHHE-EEEECCEECCCCCCHHH
Confidence 344669999999999999999999987643 33345554455667665
No 11
>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=89.70 E-value=1.4 Score=21.75 Aligned_cols=39 Identities=31% Similarity=0.402 Sum_probs=30.3
Q ss_pred CCcceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcC
Q psy6336 17 DLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNN 56 (73)
Q Consensus 17 ~Ldk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~ 56 (73)
.-...++.++.+.|++++...+.++.+. +.+...|+.|+
T Consensus 6 ~~~~~~~~~~~~~tv~~l~~~i~~~~~~-~~~~~~l~~~~ 44 (69)
T cd00196 6 DGKTVELLVPSGTTVADLKEKLAKKLGL-PPEQQRLLVNG 44 (69)
T ss_pred CCCEEEEEcCCCCcHHHHHHHHHHHHCc-ChHHeEEEECC
Confidence 4566778899999999999999999884 44455566665
No 12
>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=87.93 E-value=0.53 Score=28.70 Aligned_cols=44 Identities=14% Similarity=0.232 Sum_probs=31.2
Q ss_pred ecCCCChhhHHHHHHhhhcCCCCCeEEEEE-c---C-cCCCCcchHHHHH
Q psy6336 25 VPSDLTVGQFYFLIRKRVQLRPEDALFFFV-N---N-VIPPTSATMGSLY 69 (73)
Q Consensus 25 Vp~~~tv~qf~~~iRk~L~L~~~~alfl~V-n---~-~lp~~~~~m~~lY 69 (73)
||.+.+++|+..-|++||+++++ ++-|.- . + ..|-.+..|.+..
T Consensus 17 vp~~~~y~~L~~ki~~kLkl~~e-~i~LsYkde~s~~~v~l~d~dle~aw 65 (80)
T cd06406 17 VARGLSYATLLQKISSKLELPAE-HITLSYKSEASGEDVILSDTNMEDVW 65 (80)
T ss_pred cCCCCCHHHHHHHHHHHhCCCch-hcEEEeccCCCCCccCcChHHHHHHH
Confidence 89999999999999999999854 455533 2 1 2344566665543
No 13
>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=87.72 E-value=0.63 Score=25.89 Aligned_cols=46 Identities=20% Similarity=0.198 Sum_probs=34.8
Q ss_pred eeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 21 KKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 21 ~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
..+-|+.+.||+++...|.++.++++++--.+| ++.....+.++++
T Consensus 8 ~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~-~G~~L~d~~tL~~ 53 (69)
T PF00240_consen 8 FTLEVDPDDTVADLKQKIAEETGIPPEQQRLIY-NGKELDDDKTLSD 53 (69)
T ss_dssp EEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEE-TTEEESTTSBTGG
T ss_pred EEEEECCCCCHHHhhhhcccccccccccceeee-eeecccCcCcHHH
Confidence 345699999999999999999998887665554 5543366666654
No 14
>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=87.43 E-value=1.1 Score=26.08 Aligned_cols=45 Identities=18% Similarity=0.138 Sum_probs=36.4
Q ss_pred eecCCCChhhHHHHHHhhhcCCCCCeEEEE--EcCcCCCCcchHHHH
Q psy6336 24 LVPSDLTVGQFYFLIRKRVQLRPEDALFFF--VNNVIPPTSATMGSL 68 (73)
Q Consensus 24 LVp~~~tv~qf~~~iRk~L~L~~~~alfl~--Vn~~lp~~~~~m~~l 68 (73)
=|+.+.|+++|...|..+.+.++++-=.+| +.+.++..+.+++++
T Consensus 15 ~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~l~D~~~L~~~ 61 (74)
T cd01813 15 TTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKPAEDDVKISAL 61 (74)
T ss_pred EECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCcCCCCcCHHHc
Confidence 488899999999999999999998766666 345677778888764
No 15
>KOG2660|consensus
Probab=83.93 E-value=1.1 Score=33.71 Aligned_cols=55 Identities=16% Similarity=0.303 Sum_probs=44.7
Q ss_pred CCCCCcceeee-ecCCCChhhHHHHHHhhhc-CCCCCeEEEEEcCcCCCCcchHHHHH
Q psy6336 14 RIGDLDKKKYL-VPSDLTVGQFYFLIRKRVQ-LRPEDALFFFVNNVIPPTSATMGSLY 69 (73)
Q Consensus 14 ~lP~Ldk~KfL-Vp~~~tv~qf~~~iRk~L~-L~~~~alfl~Vn~~lp~~~~~m~~lY 69 (73)
.++.|. ++|+ ++...|++++..++|+++. ++.-..+=++.|+.+..-+.||.++.
T Consensus 159 ~~k~l~-~~fvrcsa~~Tv~hlkkfl~~k~~~~~~~~~idi~~~d~~l~~~~TLk~i~ 215 (331)
T KOG2660|consen 159 TLKDLV-RRFLRCSAAATVNHLKKFLRKKMDNLSNKSEIDILCEEELLGDYYTLKDIA 215 (331)
T ss_pred cccccc-cceEeccHHHHHHHHHHHHHHHhccccchhhheeecCCccccchhhhhhhh
Confidence 456666 6888 8888999999999999998 77777777788887888888887764
No 16
>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=83.70 E-value=4.8 Score=22.46 Aligned_cols=44 Identities=7% Similarity=0.085 Sum_probs=32.9
Q ss_pred eeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 23 YLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 23 fLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
+-++.+.|++++...|.++.++++++--++| ++.....+.++++
T Consensus 15 ~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~-~g~~L~d~~tl~~ 58 (76)
T cd01806 15 IDIEPTDKVERIKERVEEKEGIPPQQQRLIY-SGKQMNDDKTAAD 58 (76)
T ss_pred EEECCCCCHHHHHHHHhHhhCCChhhEEEEE-CCeEccCCCCHHH
Confidence 5589999999999999999999988644444 4444445666665
No 17
>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=83.37 E-value=4.2 Score=21.89 Aligned_cols=45 Identities=20% Similarity=0.255 Sum_probs=32.8
Q ss_pred eeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 22 KYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 22 KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
.+-++.+.|++++...|.++.+++++.--++| |+.....+.++++
T Consensus 11 ~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~-~g~~l~d~~~l~~ 55 (69)
T cd01769 11 ELEVSPDDTVAELKAKIAAKEGVPPEQQRLIY-AGKILKDDKTLSD 55 (69)
T ss_pred EEEECCCChHHHHHHHHHHHHCcChHHEEEEE-CCcCCCCcCCHHH
Confidence 46688999999999999999998876544443 5543355666654
No 18
>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=80.51 E-value=2.9 Score=23.50 Aligned_cols=44 Identities=16% Similarity=0.163 Sum_probs=32.9
Q ss_pred eeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 23 YLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 23 fLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
+=|.++.|++++...|-++.++++++- -|+.++.....+.++++
T Consensus 13 ~~v~~~~tV~~lK~~i~~~~gi~~~~q-~Li~~G~~L~d~~~l~~ 56 (70)
T cd01798 13 VEVDPDTDIKQLKEVVAKRQGVPPDQL-RVIFAGKELRNTTTIQE 56 (70)
T ss_pred EEECCCChHHHHHHHHHHHHCCCHHHe-EEEECCeECCCCCcHHH
Confidence 447899999999999999999987654 44455544466677776
No 19
>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=79.92 E-value=3.2 Score=23.70 Aligned_cols=44 Identities=11% Similarity=0.167 Sum_probs=30.5
Q ss_pred eeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHH
Q psy6336 23 YLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMG 66 (73)
Q Consensus 23 fLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~ 66 (73)
.-|.++.||+++...|..+-++++++---+|.+..+--.+.+++
T Consensus 14 l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~~Gk~L~D~~~~L~ 57 (71)
T cd01796 14 LDVDPDLELENFKALCEAESGIPASQQQLIYNGRELVDNKRLLA 57 (71)
T ss_pred EEECCcCCHHHHHHHHHHHhCCCHHHeEEEECCeEccCCcccHH
Confidence 45889999999999999999998875444444444532223444
No 20
>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=77.60 E-value=8.4 Score=21.18 Aligned_cols=46 Identities=15% Similarity=0.241 Sum_probs=32.8
Q ss_pred eeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 21 KKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 21 ~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
..+-++.+.|++++..-|.++.+.++++--.+| ++.....+.++++
T Consensus 13 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~-~g~~L~d~~~L~~ 58 (72)
T cd01809 13 HTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIY-SGRVLKDDETLSE 58 (72)
T ss_pred EEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEE-CCEECCCcCcHHH
Confidence 346688999999999999999998876433333 6555555666654
No 21
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=77.36 E-value=7.4 Score=21.64 Aligned_cols=45 Identities=11% Similarity=0.117 Sum_probs=32.7
Q ss_pred eeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 22 KYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 22 KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
.+-|+.+.|++++...|.++.++++++--.. .++.....+.++++
T Consensus 14 ~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~-~~g~~L~d~~~L~~ 58 (76)
T cd01803 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLSD 58 (76)
T ss_pred EEEECCcCcHHHHHHHHHHHhCCCHHHeEEE-ECCEECCCCCcHHH
Confidence 3669999999999999999999887543333 45544455666665
No 22
>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=77.09 E-value=11 Score=21.22 Aligned_cols=45 Identities=20% Similarity=0.156 Sum_probs=32.3
Q ss_pred eeeecCCCChhhHHHHHHhhhcC--CCCCeEEEEEcCcCCCCcchHHH
Q psy6336 22 KYLVPSDLTVGQFYFLIRKRVQL--RPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 22 KfLVp~~~tv~qf~~~iRk~L~L--~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
.+=|+.+.||+++...|..+.++ ++++--.+ .++.....+.++++
T Consensus 14 ~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~-~~G~~L~d~~~L~~ 60 (77)
T cd01805 14 PIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLI-YSGKILKDDTTLEE 60 (77)
T ss_pred EEEECCCCcHHHHHHHHHHhhCCCCChhHeEEE-ECCEEccCCCCHHH
Confidence 45588999999999999999988 66544433 45544456667765
No 23
>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=76.92 E-value=5.5 Score=22.62 Aligned_cols=44 Identities=9% Similarity=0.136 Sum_probs=31.9
Q ss_pred eeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 23 YLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 23 fLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
+=|..+.||+++...|..+-++++++ .-|+.++.....+.++++
T Consensus 15 l~v~~~~tV~~lK~~i~~~~gi~~~~-q~L~~~G~~L~d~~~L~~ 58 (74)
T cd01807 15 LQVSEKESVSTLKKLVSEHLNVPEEQ-QRLLFKGKALADDKRLSD 58 (74)
T ss_pred EEECCCCcHHHHHHHHHHHHCCCHHH-eEEEECCEECCCCCCHHH
Confidence 45889999999999999999998764 333355544455566654
No 24
>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=76.20 E-value=11 Score=22.28 Aligned_cols=48 Identities=13% Similarity=0.137 Sum_probs=37.5
Q ss_pred cceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 19 DKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 19 dk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
+...|-|..+.|+..+...+.++-++++++.=|+|-+..+-. +.|.++
T Consensus 22 ~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~G~~L~~-~~T~~~ 69 (87)
T cd01763 22 NEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFDGQRIRD-NQTPDD 69 (87)
T ss_pred CEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEECCeECCC-CCCHHH
Confidence 445688999999999999999999999988888876555443 445544
No 25
>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=73.55 E-value=5.4 Score=28.19 Aligned_cols=34 Identities=26% Similarity=0.497 Sum_probs=26.0
Q ss_pred eeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEc
Q psy6336 22 KYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVN 55 (73)
Q Consensus 22 KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn 55 (73)
...|+.+.+++++...|+++++++++..|-+|-.
T Consensus 88 h~~v~~~~~v~~l~~~i~~~~g~p~~t~l~lyEE 121 (249)
T PF12436_consen 88 HVYVPKNDKVSELVPLINERAGLPPDTPLLLYEE 121 (249)
T ss_dssp EEEEETT-BGGGTHHHHHHHHT--TT--EEEEEE
T ss_pred EEEECCCCCHHHHHHHHHHHcCCCCCCceEEEEE
Confidence 4579999999999999999999999999988865
No 26
>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=71.32 E-value=11 Score=21.88 Aligned_cols=43 Identities=23% Similarity=0.256 Sum_probs=32.0
Q ss_pred eecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 24 LVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 24 LVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
=|+++.||+++...|.++-++++++-=.+|.+ .+...+.++++
T Consensus 17 ~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~G-k~L~D~~tL~~ 59 (73)
T cd01791 17 KCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWY-TIFKDHISLGD 59 (73)
T ss_pred EeCCCCcHHHHHHHHHHHhCCChHHEEEEeCC-cCCCCCCCHHH
Confidence 48899999999999988889988766666653 44444556655
No 27
>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=71.18 E-value=11 Score=22.61 Aligned_cols=38 Identities=18% Similarity=0.358 Sum_probs=30.5
Q ss_pred cceeeeecCCCChhhHHHHHHhhhcCCCCCeEEE-EEcC
Q psy6336 19 DKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFF-FVNN 56 (73)
Q Consensus 19 dk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl-~Vn~ 56 (73)
|..-|-+|.+.++.++...|++|+++...+.+-| |.++
T Consensus 10 d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Dd 48 (82)
T cd06407 10 EKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDD 48 (82)
T ss_pred eEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECC
Confidence 4566889999999999999999999976455555 6653
No 28
>PF05717 TnpB_IS66: IS66 Orf2 like protein; InterPro: IPR008878 Thess proteins are found in insertion sequences related to IS66. The function of these proteins is uncertain, but they are probably essential for transposition []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=70.87 E-value=8.3 Score=24.24 Aligned_cols=27 Identities=30% Similarity=0.572 Sum_probs=23.2
Q ss_pred ChhhHHHHHHhhhcCCC-CCeEEEEEcC
Q psy6336 30 TVGQFYFLIRKRVQLRP-EDALFFFVNN 56 (73)
Q Consensus 30 tv~qf~~~iRk~L~L~~-~~alfl~Vn~ 56 (73)
.+.-+..+++..++++| +.++|+|.|.
T Consensus 16 g~dgL~~lV~~~~~~dp~~g~~fvF~nr 43 (107)
T PF05717_consen 16 GIDGLAALVREELGLDPFSGDLFVFCNR 43 (107)
T ss_pred ChhHHHHHHHHhhcCCCCcceEEEEEec
Confidence 57778899999999985 6899999995
No 29
>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=70.41 E-value=13 Score=21.18 Aligned_cols=46 Identities=22% Similarity=0.243 Sum_probs=33.6
Q ss_pred eeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 21 KKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 21 ~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
..+-|+++.||+++...|..+-++++++--.+| ++.....+.++++
T Consensus 11 ~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~-~G~~L~D~~~l~~ 56 (70)
T cd01794 11 VKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFF-SGKLLTDKTRLQE 56 (70)
T ss_pred EEEEECCcChHHHHHHHHHHHhCCCHHHeEEEE-CCeECCCCCCHHH
Confidence 345688999999999999999899886543344 4445556677766
No 30
>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=70.15 E-value=9.5 Score=22.12 Aligned_cols=44 Identities=18% Similarity=0.247 Sum_probs=31.7
Q ss_pred eeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 22 KYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 22 KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
..-|+.+.||+++...|.++.++++++--+.|-+..+.. + ++++
T Consensus 15 ~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~Gk~L~d-~-~L~~ 58 (78)
T cd01804 15 DLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSS-G-KLQD 58 (78)
T ss_pred EEEECCcCHHHHHHHHHHHHhCCChHHEEEEECCcCCCC-C-cHHH
Confidence 356899999999999999888988875555555444432 3 5554
No 31
>PTZ00044 ubiquitin; Provisional
Probab=69.75 E-value=7.7 Score=21.85 Aligned_cols=45 Identities=9% Similarity=0.208 Sum_probs=32.4
Q ss_pred eeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 22 KYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 22 KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
.+-|.++.|++++...|..+.++++++--.+|-+..+ ..+.++++
T Consensus 14 ~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L-~d~~~l~~ 58 (76)
T PTZ00044 14 SFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQM-SDDLKLSD 58 (76)
T ss_pred EEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEEc-cCCCcHHH
Confidence 4568899999999999999999988644444543344 45556654
No 32
>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=69.73 E-value=11 Score=24.14 Aligned_cols=45 Identities=20% Similarity=0.318 Sum_probs=33.0
Q ss_pred eeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 23 YLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 23 fLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
-.|.++.|++++...|..+++.+|.+.=-++.++.+--.+.++++
T Consensus 19 L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~dG~~L~DDsrTLss 63 (107)
T cd01795 19 LLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILSDDCATLGT 63 (107)
T ss_pred EEeCccccHHHHHHHHHHHhcCCcccceeeecCceeccCCccHHh
Confidence 459999999999999999999998743333335555555556654
No 33
>PF13019 Telomere_Sde2: Telomere stability and silencing
Probab=68.73 E-value=13 Score=25.32 Aligned_cols=49 Identities=22% Similarity=0.382 Sum_probs=38.3
Q ss_pred eeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEc-C-cC-CCCcchHHHHH
Q psy6336 21 KKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVN-N-VI-PPTSATMGSLY 69 (73)
Q Consensus 21 ~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn-~-~l-p~~~~~m~~lY 69 (73)
.-+-+|.+.|++.+...|..++.......++|+++ | .+ +..+..++.+.
T Consensus 17 l~~~lp~~ttv~dL~~~l~~~~~~~~~~~~~L~~~~n~~l~~~~~~~~s~l~ 68 (162)
T PF13019_consen 17 LSLSLPSTTTVSDLKDRLSERLPIPSSSQLYLTTNSNGQLSPSSDIPLSSLL 68 (162)
T ss_pred EEeeCCCCCcHHHHHHHHHhhcCCCccceeEEEEeCCCeeCCCccccHHhhc
Confidence 34669999999999999999999998887888886 4 44 45555566655
No 34
>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=67.53 E-value=18 Score=20.26 Aligned_cols=45 Identities=18% Similarity=0.289 Sum_probs=31.1
Q ss_pred eeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 22 KYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 22 KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
.+-+..+.||+++...|.++.+.++++-=.+| ++.....+.++++
T Consensus 13 ~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li~-~Gk~L~d~~tL~~ 57 (71)
T cd01808 13 EIEIAEDASVKDFKEAVSKKFKANQEQLVLIF-AGKILKDTDTLTQ 57 (71)
T ss_pred EEEECCCChHHHHHHHHHHHhCCCHHHEEEEE-CCeEcCCCCcHHH
Confidence 46688999999999999988887655433333 4444445566655
No 35
>PF14533 USP7_C2: Ubiquitin-specific protease C-terminal; PDB: 2YLM_A.
Probab=67.26 E-value=5.4 Score=27.54 Aligned_cols=50 Identities=28% Similarity=0.377 Sum_probs=28.2
Q ss_pred cceeeeecCCCChhhHHHHHHhhhcCCCC--CeEEEE-E-cC---cCCCCcchHHHH
Q psy6336 19 DKKKYLVPSDLTVGQFYFLIRKRVQLRPE--DALFFF-V-NN---VIPPTSATMGSL 68 (73)
Q Consensus 19 dk~KfLVp~~~tv~qf~~~iRk~L~L~~~--~alfl~-V-n~---~lp~~~~~m~~l 68 (73)
+.-.++||++-||+++..-++++++++++ +.|-++ | |+ ...+.+..+++|
T Consensus 34 ~~~~~~vpk~~tV~Dll~~l~~k~~~~~~~~~~lrl~ev~~~ki~~~~~~d~~i~~l 90 (213)
T PF14533_consen 34 QEYELLVPKTGTVSDLLEELQKKVGFSEEGTGKLRLWEVSNHKIYKILSEDEPISSL 90 (213)
T ss_dssp -EEEE--BTT-BHHHHHHHHHTT----TT----EEEEEEETTEEEEEE-TTSBGGGS
T ss_pred eEEEEEECCCCCHHHHHHHHHHHcCCCcCCcCcEEEEEeECCEEEeecCCCCchhhc
Confidence 55779999999999999999999999765 344443 3 22 245667666666
No 36
>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=66.97 E-value=11 Score=21.91 Aligned_cols=44 Identities=18% Similarity=0.153 Sum_probs=32.5
Q ss_pred eeeecCCCChhhHHHHHHhhhcCCCC-CeEEEEEcCcCCCCcchHHH
Q psy6336 22 KYLVPSDLTVGQFYFLIRKRVQLRPE-DALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 22 KfLVp~~~tv~qf~~~iRk~L~L~~~-~alfl~Vn~~lp~~~~~m~~ 67 (73)
.+-|+++.||+++...|-.+-+++++ +.| |-++.+-..+.++++
T Consensus 16 ~l~v~~~~TV~~lK~kI~~~~gip~~~QrL--~~G~~L~dD~~tL~~ 60 (75)
T cd01799 16 WLTVRPDMTVAQLKDKVFLDYGFPPAVQRW--VIGQRLARDQETLYS 60 (75)
T ss_pred EEEECCCCcHHHHHHHHHHHHCcCHHHEEE--EcCCeeCCCcCCHHH
Confidence 35689999999999999999999885 444 544455445566654
No 37
>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=66.66 E-value=10 Score=21.95 Aligned_cols=44 Identities=11% Similarity=0.127 Sum_probs=29.5
Q ss_pred eecCCCChhhHHHHHHhhhcCCCCC-eEEEEEcCcCCCCcchHHH
Q psy6336 24 LVPSDLTVGQFYFLIRKRVQLRPED-ALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 24 LVp~~~tv~qf~~~iRk~L~L~~~~-alfl~Vn~~lp~~~~~m~~ 67 (73)
=|+++.||+++..-|.++.++++++ .|.+.-++.....+.++++
T Consensus 18 ~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~~L~D~~tL~~ 62 (80)
T cd01792 18 SLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQDGVPLVS 62 (80)
T ss_pred EcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCCCCCCCCCHHH
Confidence 3688999999999999988887754 3322124444445556654
No 38
>cd01776 Rin1_RA Ubiquitin domain of RIN1 RAS effector. Rin1_RA RIN1 is a RAS effector that binds with specificity and high affinity to activated RAS via its carboxy-terminal RA (RAS-associated) domain. RIN1 competes directly with RAF1 for RAS binding and is thought to divert signaling away from RAF and the MAPK pathway while also shunting RAS signals through alternate pathways. In addition, Rin1 and Rin2 are Rab5-binding proteins, binding preferentially to the GTP-bound form, that enhance the GDP-GTP exchange reaction on Rab5 that regulate the docking and fusion processes of endocytic vesicles. In addition to the RA domain, RIN1 and RIN2 have an SH2 (Src homology 2) domain, a proline-rich SH3 domain, and a Vps9 domain.
Probab=66.08 E-value=15 Score=22.79 Aligned_cols=36 Identities=28% Similarity=0.425 Sum_probs=30.6
Q ss_pred eeeeecCCCChhhHHHHHHhhhcCC--CCCeEEEEEcC
Q psy6336 21 KKYLVPSDLTVGQFYFLIRKRVQLR--PEDALFFFVNN 56 (73)
Q Consensus 21 ~KfLVp~~~tv~qf~~~iRk~L~L~--~~~alfl~Vn~ 56 (73)
+.-.|+++.|..++-...-.+..+. .+=+||+|||+
T Consensus 16 KTL~V~P~~tt~~vc~lcA~Kf~V~qPe~y~LFl~vdg 53 (87)
T cd01776 16 KTLLVRPYITTEDVCQLCAEKFKVTQPEEYSLFLFVEE 53 (87)
T ss_pred eeeecCCCCcHHHHHHHHHHHhccCChhheeEEEEECC
Confidence 4467999999999999998888876 45789999997
No 39
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=64.23 E-value=12 Score=21.93 Aligned_cols=31 Identities=19% Similarity=0.210 Sum_probs=25.8
Q ss_pred eeecCCCChhhHHHHHHhhhcCCCC-CeEEEE
Q psy6336 23 YLVPSDLTVGQFYFLIRKRVQLRPE-DALFFF 53 (73)
Q Consensus 23 fLVp~~~tv~qf~~~iRk~L~L~~~-~alfl~ 53 (73)
--+|.++|++++..-|-+..+++++ +.|+++
T Consensus 18 kr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~ 49 (87)
T PF14560_consen 18 KRFPKSITVSELKQKLEKLTGIPPSDMRLQLK 49 (87)
T ss_dssp EEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE
T ss_pred EEcCCCCCHHHHHHHHHHHhCCCcccEEEEEE
Confidence 4589999999999999999999975 677775
No 40
>PF10302 DUF2407: DUF2407 ubiquitin-like domain; InterPro: IPR019413 This entry represents a family of proteins of unknown function found in fungi. They contain a characteristic GFDRL sequence motif.
Probab=64.03 E-value=21 Score=22.08 Aligned_cols=51 Identities=22% Similarity=0.216 Sum_probs=33.1
Q ss_pred CCCCCcceeeeecCCCChhhHHHHHHhhh-cCCCCCeEEEEEcCcCCCCcchH
Q psy6336 14 RIGDLDKKKYLVPSDLTVGQFYFLIRKRV-QLRPEDALFFFVNNVIPPTSATM 65 (73)
Q Consensus 14 ~lP~Ldk~KfLVp~~~tv~qf~~~iRk~L-~L~~~~alfl~Vn~~lp~~~~~m 65 (73)
.+|||.=. +--|...|+.++...||.++ .-.++..|=|.-++.+.+.++.+
T Consensus 10 sipDl~L~-I~~~~~~Tv~~LK~lIR~~~p~~~s~~rLRlI~~Gr~L~d~t~l 61 (97)
T PF10302_consen 10 SIPDLPLD-IPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRLLNDHTDL 61 (97)
T ss_pred CCCCceee-cCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCcccCccchh
Confidence 57774411 01458899999999999999 55556667665666544444444
No 41
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. 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 noncanonical PB1-interactions. The PB1 domain module
Probab=63.22 E-value=19 Score=22.06 Aligned_cols=36 Identities=17% Similarity=0.415 Sum_probs=27.8
Q ss_pred ceeeeecC-----CCChhhHHHHHHhhhcCCCCCeEEE-EEc
Q psy6336 20 KKKYLVPS-----DLTVGQFYFLIRKRVQLRPEDALFF-FVN 55 (73)
Q Consensus 20 k~KfLVp~-----~~tv~qf~~~iRk~L~L~~~~alfl-~Vn 55 (73)
...|-+|. +.++.++..-|+++++++++..+-| |-+
T Consensus 11 ~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~D 52 (91)
T cd06398 11 LRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTD 52 (91)
T ss_pred EEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEEC
Confidence 45677774 7999999999999999998544444 444
No 42
>cd03483 MutL_Trans_MLH1 MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH1 (MutL homologue 1). This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking hMLH1 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hMLH1 accounts for a large fraction of HNPCC families.
Probab=60.59 E-value=7 Score=24.78 Aligned_cols=26 Identities=15% Similarity=0.355 Sum_probs=19.2
Q ss_pred CCeEEEEEcCc---CCCCcchHHHHHhhh
Q psy6336 47 EDALFFFVNNV---IPPTSATMGSLYQEI 72 (73)
Q Consensus 47 ~~alfl~Vn~~---lp~~~~~m~~lY~~f 72 (73)
.+..|+|||+. .+.....+.+.|+.|
T Consensus 47 ~~~q~~fVNgR~V~~~~l~~aI~~~Y~~~ 75 (127)
T cd03483 47 KIIFILFINNRLVECSALRRAIENVYANY 75 (127)
T ss_pred CceEEEEEcCCEecCHHHHHHHHHHHHHh
Confidence 56789999984 445566777888776
No 43
>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=59.36 E-value=19 Score=21.24 Aligned_cols=32 Identities=16% Similarity=0.125 Sum_probs=26.7
Q ss_pred ecCCCChhhHHHHHHhhhcCCCC-CeEEEEEcC
Q psy6336 25 VPSDLTVGQFYFLIRKRVQLRPE-DALFFFVNN 56 (73)
Q Consensus 25 Vp~~~tv~qf~~~iRk~L~L~~~-~alfl~Vn~ 56 (73)
+|.++|++++..-|-+.-+++++ +.|.+|-++
T Consensus 19 ~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~ 51 (84)
T cd01789 19 YSRGLTIAELKKKLELVVGTPASSMRLQLFDGD 51 (84)
T ss_pred cCCCCcHHHHHHHHHHHHCCCccceEEEEEcCC
Confidence 79999999999999998899875 666666664
No 44
>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=59.10 E-value=21 Score=19.51 Aligned_cols=44 Identities=14% Similarity=0.209 Sum_probs=30.1
Q ss_pred eeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 23 YLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 23 fLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
.-|+.+.|++++..-|.++-++++++--.+ .++.....+.++++
T Consensus 14 i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~-~~g~~l~d~~~L~~ 57 (71)
T cd01812 14 LSISSQATFGDLKKMLAPVTGVEPRDQKLI-FKGKERDDAETLDM 57 (71)
T ss_pred EEECCCCcHHHHHHHHHHhhCCChHHeEEe-eCCcccCccCcHHH
Confidence 458899999999999999989987643333 34433334555544
No 45
>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=57.17 E-value=26 Score=19.79 Aligned_cols=44 Identities=14% Similarity=0.166 Sum_probs=32.3
Q ss_pred eeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 23 YLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 23 fLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
+-|.++.||+++...|..+-++++++--.+ -++.....+.++++
T Consensus 13 l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~-~~G~~L~D~~tL~~ 56 (74)
T cd01810 13 YEVQLTQTVATLKQQVSQRERVQADQFWLS-FEGRPMEDEHPLGE 56 (74)
T ss_pred EEECCcChHHHHHHHHHHHhCCCHHHeEEE-ECCEECCCCCCHHH
Confidence 568889999999999999988877644333 45544456677766
No 46
>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=57.10 E-value=34 Score=19.33 Aligned_cols=52 Identities=12% Similarity=0.255 Sum_probs=37.4
Q ss_pred cceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcC---c-CCCCcchHHHHHh
Q psy6336 19 DKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNN---V-IPPTSATMGSLYQ 70 (73)
Q Consensus 19 dk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~---~-lp~~~~~m~~lY~ 70 (73)
+...+.+|.+.|+.+|..-|.+++++..+.-..-|.++ . ..+.+..|....+
T Consensus 11 ~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~Dl~~a~~ 66 (81)
T smart00666 11 ETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDEDLEEAIE 66 (81)
T ss_pred EEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHHHHHHHHH
Confidence 35567899999999999999999999866555667763 1 3444555555443
No 47
>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=56.96 E-value=24 Score=20.09 Aligned_cols=44 Identities=7% Similarity=0.080 Sum_probs=31.4
Q ss_pred eeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 23 YLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 23 fLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
+-|+.+.||+++...|...-++++++--.+ .++..-..+.++++
T Consensus 12 l~v~~~~TV~~lK~~i~~~~gip~~~q~L~-~~G~~L~d~~tL~~ 55 (76)
T cd01800 12 FTLQLSDPVSVLKVKIHEETGMPAGKQKLQ-YEGIFIKDSNSLAY 55 (76)
T ss_pred EEECCCCcHHHHHHHHHHHHCCCHHHEEEE-ECCEEcCCCCcHHH
Confidence 458899999999999999999887643333 34544455566654
No 48
>PF09358 UBA_e1_C: Ubiquitin-activating enzyme e1 C-terminal domain; InterPro: IPR018965 This presumed domain found at the C terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterised. ; PDB: 3CMM_A.
Probab=56.89 E-value=9.2 Score=24.56 Aligned_cols=50 Identities=12% Similarity=0.185 Sum_probs=31.2
Q ss_pred eeeecCCCChhhHHHHHHhhhcCCCC----CeEEEEEcC----cCCCCcchHHHHHhh
Q psy6336 22 KYLVPSDLTVGQFYFLIRKRVQLRPE----DALFFFVNN----VIPPTSATMGSLYQE 71 (73)
Q Consensus 22 KfLVp~~~tv~qf~~~iRk~L~L~~~----~alfl~Vn~----~lp~~~~~m~~lY~~ 71 (73)
+|-|+.++|+++|+..++++-+|..+ ..-.||..- .-=-.+++|++|+++
T Consensus 36 r~~v~~~~Tl~~li~~~~~~~~lev~ml~~g~~~LY~~f~~~~~~~rl~~~i~elv~~ 93 (125)
T PF09358_consen 36 RIEVNGDMTLQELIDYFKEKYGLEVTMLSQGVSLLYSSFPPPKHKERLKMPISELVEE 93 (125)
T ss_dssp EEEEES--BHHHHHHHHHHTTS-EEEEEEETTEEEEETT-HHHHHHHTTSBHHHHHHH
T ss_pred EEEEcCCCCHHHHHHHHHHHhCceEEEEEeCCEEEEecCChhhhHHHhCCcHHHHHHH
Confidence 57888899999999999999887753 222334322 011146678888874
No 49
>cd06411 PB1_p51 The PB1 domain is present in the p51 protein, a homolog of the p67 protein. p51 plays an important role in NADPH oxidase activation during phagosytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction 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 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 mo
Probab=54.92 E-value=12 Score=22.67 Aligned_cols=46 Identities=11% Similarity=0.281 Sum_probs=34.3
Q ss_pred ecCCCChhhHHHHHHhhhcCCCCCeEEEEEc---C-c-CCCC-cchHHHHHh
Q psy6336 25 VPSDLTVGQFYFLIRKRVQLRPEDALFFFVN---N-V-IPPT-SATMGSLYQ 70 (73)
Q Consensus 25 Vp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn---~-~-lp~~-~~~m~~lY~ 70 (73)
+|...+++++...|+++|.+.++..-.=|-. + . +|-. +..|.++..
T Consensus 13 v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~~~~~~~~~v~l~~e~~me~aW~ 64 (78)
T cd06411 13 APRGADVSSLRALLSQALPQQAQRGQLSYRAPGEDGHWVPISGEESLQRAWQ 64 (78)
T ss_pred ccCCCCHHHHHHHHHHHhcCChhhcEEEecCCCCCccEeecCcchHHHHHHH
Confidence 7899999999999999999999876555553 1 2 3444 677776654
No 50
>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=54.48 E-value=32 Score=20.47 Aligned_cols=42 Identities=19% Similarity=0.206 Sum_probs=28.8
Q ss_pred ecCCCChhhHHHHHHhhhc--CC-CCCeEEEEEcCcCCCCcchHHH
Q psy6336 25 VPSDLTVGQFYFLIRKRVQ--LR-PEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 25 Vp~~~tv~qf~~~iRk~L~--L~-~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
-|.+.||+++...|..+.+ .. +++---+|.+.. ...+.++++
T Consensus 17 ~~~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKi-L~D~~TL~d 61 (75)
T cd01815 17 SPGGYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRK-LKDDQTLDF 61 (75)
T ss_pred CCccCcHHHHHHHHHHhhccCCCChHHeEEEeCCcC-CCCCCcHHH
Confidence 5899999999999999964 43 554444454443 456666664
No 51
>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=54.30 E-value=38 Score=18.99 Aligned_cols=52 Identities=6% Similarity=0.177 Sum_probs=36.6
Q ss_pred cceeeeec-CCCChhhHHHHHHhhhcCCCCCeEEEEEcC---c-CCCCcchHHHHHh
Q psy6336 19 DKKKYLVP-SDLTVGQFYFLIRKRVQLRPEDALFFFVNN---V-IPPTSATMGSLYQ 70 (73)
Q Consensus 19 dk~KfLVp-~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~---~-lp~~~~~m~~lY~ 70 (73)
+...|.+| .+.|+..|..-|++++++..+.-.+=|.++ . .-+.+..+.+..+
T Consensus 10 ~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~sd~Dl~~a~~ 66 (81)
T cd05992 10 EIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSDEDLEEAIE 66 (81)
T ss_pred CCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCCHHHHHHHHH
Confidence 34567888 999999999999999999865555556653 1 2344455555444
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=51.84 E-value=50 Score=19.71 Aligned_cols=49 Identities=12% Similarity=0.177 Sum_probs=34.3
Q ss_pred ceeeee--cCCCChhhHHHHHHhhhc--CCCCCeEEEEEcCcCCCCcchHHHHH
Q psy6336 20 KKKYLV--PSDLTVGQFYFLIRKRVQ--LRPEDALFFFVNNVIPPTSATMGSLY 69 (73)
Q Consensus 20 k~KfLV--p~~~tv~qf~~~iRk~L~--L~~~~alfl~Vn~~lp~~~~~m~~lY 69 (73)
+.-|-+ +.+.||+++...|..... -++++-=.+|-+. +...+.++++..
T Consensus 13 ~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GK-iLkD~~tL~~~~ 65 (79)
T cd01790 13 YEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGK-LLPDHLKLRDVL 65 (79)
T ss_pred eEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCe-eccchhhHHHHh
Confidence 334677 789999999999988774 3345444555544 557888888874
No 53
>PRK06437 hypothetical protein; Provisional
Probab=50.69 E-value=27 Score=19.81 Aligned_cols=39 Identities=15% Similarity=0.164 Sum_probs=26.1
Q ss_pred eeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchH
Q psy6336 22 KYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATM 65 (73)
Q Consensus 22 KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m 65 (73)
.+=++...|++++.. +|++++ +.+-+.+|+...+.+..+
T Consensus 14 ~~~i~~~~tv~dLL~----~Lgi~~-~~vaV~vNg~iv~~~~~L 52 (67)
T PRK06437 14 TIEIDHELTVNDIIK----DLGLDE-EEYVVIVNGSPVLEDHNV 52 (67)
T ss_pred EEEcCCCCcHHHHHH----HcCCCC-ccEEEEECCEECCCceEc
Confidence 344688899998774 568865 566777998544454443
No 54
>PRK13669 hypothetical protein; Provisional
Probab=49.92 E-value=13 Score=22.50 Aligned_cols=24 Identities=21% Similarity=0.365 Sum_probs=20.0
Q ss_pred CeEEEEEcC---cCCCCcchHHHHHhh
Q psy6336 48 DALFFFVNN---VIPPTSATMGSLYQE 71 (73)
Q Consensus 48 ~alfl~Vn~---~lp~~~~~m~~lY~~ 71 (73)
+..|-+||+ ..+..++.+..||+.
T Consensus 45 ~~~FAlVng~~V~a~t~eeL~~kI~~~ 71 (78)
T PRK13669 45 EGLFALVNGEVVEGETPEELVENIYAH 71 (78)
T ss_pred cCceEEECCeEeecCCHHHHHHHHHHH
Confidence 788999997 367888899999875
No 55
>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=49.91 E-value=11 Score=22.36 Aligned_cols=33 Identities=9% Similarity=0.079 Sum_probs=21.2
Q ss_pred eeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEc
Q psy6336 22 KYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVN 55 (73)
Q Consensus 22 KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn 55 (73)
..=++++-|++++..-|.+.++++.. ++.||.|
T Consensus 17 Rie~~~~~t~~~L~~kI~~~l~~~~~-~~~L~~~ 49 (80)
T PF11543_consen 17 RIEVSPSSTLSDLKEKISEQLSIPDS-SQSLSKD 49 (80)
T ss_dssp EEEE-TTSBHHHHHHHHHHHS---TT-T---BSS
T ss_pred EEEcCCcccHHHHHHHHHHHcCCCCc-ceEEEec
Confidence 34588899999999999999998865 4555555
No 56
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=49.37 E-value=22 Score=20.44 Aligned_cols=43 Identities=21% Similarity=0.234 Sum_probs=28.9
Q ss_pred eeeecCC-CChhhHHHHHHhhhc-C-CCCCeEEEEEcCcCCCCcch
Q psy6336 22 KYLVPSD-LTVGQFYFLIRKRVQ-L-RPEDALFFFVNNVIPPTSAT 64 (73)
Q Consensus 22 KfLVp~~-~tv~qf~~~iRk~L~-L-~~~~alfl~Vn~~lp~~~~~ 64 (73)
.+-+|.+ .|++++...|..+.. + .....+.++||+.....+..
T Consensus 19 ~~~~~~~~~tv~~L~~~L~~~~p~l~~~~~~~~v~vn~~~v~~~~~ 64 (80)
T TIGR01682 19 TLELPDESTTVGELKEHLAKEGPELAASRGQVMVAVNEEYVTDDAL 64 (80)
T ss_pred EEECCCCCcCHHHHHHHHHHhCchhhhhccceEEEECCEEcCCCcC
Confidence 4457777 899999999987753 2 22356788999754333443
No 57
>PF15130 DUF4566: Domain of unknown function (DUF4566)
Probab=49.22 E-value=17 Score=26.12 Aligned_cols=47 Identities=26% Similarity=0.434 Sum_probs=29.6
Q ss_pred eeeecCCCChhhHHHHHHhhhc-----CCCCCeEEEEEcC---cCCCCcchHHHH
Q psy6336 22 KYLVPSDLTVGQFYFLIRKRVQ-----LRPEDALFFFVNN---VIPPTSATMGSL 68 (73)
Q Consensus 22 KfLVp~~~tv~qf~~~iRk~L~-----L~~~~alfl~Vn~---~lp~~~~~m~~l 68 (73)
||=.-...--.||..++-++=+ =+|+|++|+|++. ..|.+-++|..|
T Consensus 155 kFeFhh~dyekQ~lh~lsrkdk~g~VlnNP~QsvFlfidrq~l~tpk~ka~~fkL 209 (241)
T PF15130_consen 155 KFEFHHGDYEKQFLHVLSRKDKPGAVLNNPEQSVFLFIDRQQLQTPKNKATMFKL 209 (241)
T ss_pred heeeccchHHHHHHHHHhcccCCCceecCCCceEEEEEeHhhhCCcchhhHHHHH
Confidence 3433333445677777765522 3589999999973 467776666543
No 58
>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=48.09 E-value=50 Score=18.57 Aligned_cols=48 Identities=19% Similarity=0.211 Sum_probs=35.0
Q ss_pred cceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 19 DKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 19 dk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
+...+=|.++.||+++...|..+-++++++---+| ++.....+.++++
T Consensus 9 ~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~-~Gk~L~D~~tL~~ 56 (74)
T cd01793 9 NTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLL-AGVPLEDDATLGQ 56 (74)
T ss_pred CEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEE-CCeECCCCCCHHH
Confidence 34556789999999999999999888876643333 4544456677766
No 59
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=46.59 E-value=36 Score=19.31 Aligned_cols=40 Identities=13% Similarity=0.169 Sum_probs=26.5
Q ss_pred eeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchH
Q psy6336 21 KKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATM 65 (73)
Q Consensus 21 ~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m 65 (73)
..+=++++.|++++. +.|++++ +..-+.+|+...+.+..+
T Consensus 16 ~~~~~~~~~tv~~ll----~~l~~~~-~~v~v~vNg~iv~~~~~l 55 (70)
T PRK08364 16 KEIEWRKGMKVADIL----RAVGFNT-ESAIAKVNGKVALEDDPV 55 (70)
T ss_pred eEEEcCCCCcHHHHH----HHcCCCC-ccEEEEECCEECCCCcCc
Confidence 344468888998876 4557765 668888998554444433
No 60
>cd03482 MutL_Trans_MutL MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from the ATP-binding site to the DNA breakage/reunion regions of the enzymes. It has been suggested that during initiation of DNA mismatch repair in E. coli, the mismatch recognition protein MutS recruits MutL in the presence of ATP. The MutS(ATP)-MutL ternary complex formed, then recruits the latent endonuclease MutH. Prokaryotic MutS and MutL are homodimers.
Probab=45.70 E-value=16 Score=22.94 Aligned_cols=26 Identities=23% Similarity=0.427 Sum_probs=17.7
Q ss_pred CCeEEEEEcCc---CCCCcchHHHHHhhh
Q psy6336 47 EDALFFFVNNV---IPPTSATMGSLYQEI 72 (73)
Q Consensus 47 ~~alfl~Vn~~---lp~~~~~m~~lY~~f 72 (73)
.+..|+|||+. -+.....+.+.|+.+
T Consensus 43 ~~~q~ifVN~R~V~~~~l~~ai~~~y~~~ 71 (123)
T cd03482 43 ADIQYFYVNGRMVRDKLISHAVRQAYSDV 71 (123)
T ss_pred CCcEEEEEcCcEECChHHHHHHHHHHHHh
Confidence 46789999984 234455677777764
No 61
>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=43.63 E-value=27 Score=21.08 Aligned_cols=28 Identities=18% Similarity=0.357 Sum_probs=21.2
Q ss_pred ecCCCChhhHHHHHHhh--hcCC------CCCeEEE
Q psy6336 25 VPSDLTVGQFYFLIRKR--VQLR------PEDALFF 52 (73)
Q Consensus 25 Vp~~~tv~qf~~~iRk~--L~L~------~~~alfl 52 (73)
|+++.|.++|+..|..+ +++. ++++||+
T Consensus 3 v~~~~TL~~lid~L~~~~~~qlk~PSlt~~~k~LYm 38 (84)
T PF08825_consen 3 VSPSWTLQDLIDSLCEKPEFQLKKPSLTTANKTLYM 38 (84)
T ss_dssp ESTTSBSHHHHHHHHHSTTT--SS-EEESSEEEEEE
T ss_pred cCccchHHHHHHHHHhChhhhcCCCcccCCCceEEE
Confidence 68899999999999988 6654 3577776
No 62
>PF07293 DUF1450: Protein of unknown function (DUF1450); InterPro: IPR009910 This entry consists of several hypothetical bacterial proteins of around 80 residues in length representing two families. Members contain four highly conserved cysteine residues and their function is unknown.
Probab=43.12 E-value=19 Score=21.68 Aligned_cols=24 Identities=13% Similarity=0.227 Sum_probs=19.5
Q ss_pred CeEEEEEcC---cCCCCcchHHHHHhh
Q psy6336 48 DALFFFVNN---VIPPTSATMGSLYQE 71 (73)
Q Consensus 48 ~alfl~Vn~---~lp~~~~~m~~lY~~ 71 (73)
+..|.+||+ ..++.+..+..||+.
T Consensus 45 ~~pFAlVnG~~V~A~t~eeL~~kI~~~ 71 (78)
T PF07293_consen 45 KKPFALVNGEIVAAETAEELLEKIKEK 71 (78)
T ss_pred CCccEEECCEEEecCCHHHHHHHHHHH
Confidence 788999998 367788888888875
No 63
>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=42.90 E-value=38 Score=19.64 Aligned_cols=42 Identities=14% Similarity=0.136 Sum_probs=29.9
Q ss_pred ecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 25 VPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 25 Vp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
+..+.||+++..-|..+-++++++-=.+| ++.....+.++++
T Consensus 19 v~~~~TV~~lK~~i~~~~gi~~~~QrLi~-~Gk~L~D~~tL~~ 60 (78)
T cd01797 19 LSRLTKVEELREKIQELFNVEPECQRLFY-RGKQMEDGHTLFD 60 (78)
T ss_pred cCCcCcHHHHHHHHHHHhCCCHHHeEEEe-CCEECCCCCCHHH
Confidence 67899999999999999888876433334 4444455666654
No 64
>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=42.46 E-value=61 Score=18.10 Aligned_cols=35 Identities=11% Similarity=0.112 Sum_probs=30.3
Q ss_pred ceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEE
Q psy6336 20 KKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFV 54 (73)
Q Consensus 20 k~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~V 54 (73)
...|-|.++.|+.++..-|-++|+|...+-+=|.+
T Consensus 8 ~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~ 42 (80)
T PF09379_consen 8 TKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQY 42 (80)
T ss_dssp EEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE
T ss_pred cEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEE
Confidence 45688999999999999999999999877666666
No 65
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=41.90 E-value=33 Score=20.49 Aligned_cols=21 Identities=24% Similarity=0.336 Sum_probs=18.8
Q ss_pred HHHHhhhcCCCCCeEEEEEcC
Q psy6336 36 FLIRKRVQLRPEDALFFFVNN 56 (73)
Q Consensus 36 ~~iRk~L~L~~~~alfl~Vn~ 56 (73)
.-+|++|++.+.+.+-++++.
T Consensus 20 keiR~~lgi~~Gd~lei~~~~ 40 (89)
T COG2002 20 KEIREALGIKEGDVLEIIVDG 40 (89)
T ss_pred HHHHHHhCCCCCCEEEEEEeC
Confidence 458999999999999999984
No 66
>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=40.74 E-value=68 Score=18.02 Aligned_cols=48 Identities=19% Similarity=0.279 Sum_probs=36.6
Q ss_pred eeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcC----cCCCCcchHHHHHh
Q psy6336 23 YLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNN----VIPPTSATMGSLYQ 70 (73)
Q Consensus 23 fLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~----~lp~~~~~m~~lY~ 70 (73)
+-++.+.++.+|...|+++.++.+++--+-|.+. ...+.+..+.+..+
T Consensus 16 ~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~ 67 (84)
T PF00564_consen 16 ISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKDEDGDLVTISSDEDLQEAIE 67 (84)
T ss_dssp EEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEETTSSEEEESSHHHHHHHHH
T ss_pred EEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeCCCCCEEEeCCHHHHHHHHH
Confidence 6799999999999999999999877777778873 23455555555443
No 67
>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=39.94 E-value=1.3e+02 Score=21.13 Aligned_cols=37 Identities=22% Similarity=0.321 Sum_probs=26.9
Q ss_pred ceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcC
Q psy6336 20 KKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNN 56 (73)
Q Consensus 20 k~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~ 56 (73)
....-++.++|..|+...|-++|+++|+.=-|.-+|+
T Consensus 191 ~F~l~ls~~~tY~~la~~Va~~l~~dP~~lr~~~~~~ 227 (249)
T PF12436_consen 191 EFTLWLSKKMTYDQLAEKVAEHLNVDPEHLRFFTVNP 227 (249)
T ss_dssp -EEEEEETT--HHHHHHHHHHHHTS-GGGEEEE---T
T ss_pred CEEEEECCCCCHHHHHHHHHHHHCCChHHEEEEEecc
Confidence 6667799999999999999999999999887777764
No 68
>cd03485 MutL_Trans_hPMS_1_like MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM1 (hPSM1) and yeast MLH2. hPSM1 and yMLH2 are members of the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. PMS1 forms a heterodimer with MLH1. The MLH1-PMS1 complex functions in meiosis. Loss of yMLH2 results in a small but significant decrease in spore viability and a significant increase in gene conversion frequencies. A role for hMLH1-hPMS1 in DNA mismatch repair has not been established. Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families, however there is no convincing evidence to support hPMS1 having a role in HNPCC predisposition.
Probab=39.90 E-value=34 Score=21.57 Aligned_cols=27 Identities=19% Similarity=0.209 Sum_probs=18.1
Q ss_pred CCCeEEEEEcCcCCCC----cchHHHHHhhh
Q psy6336 46 PEDALFFFVNNVIPPT----SATMGSLYQEI 72 (73)
Q Consensus 46 ~~~alfl~Vn~~lp~~----~~~m~~lY~~f 72 (73)
..+..|+|||+..... ...+.+.|..+
T Consensus 47 ~~~~q~~fVN~R~v~~~~~l~k~i~~~y~~~ 77 (132)
T cd03485 47 KSDGKFISVNSRPVSLGKDIGKLLRQYYSSA 77 (132)
T ss_pred cCCcEEEEECCeecccchHHHHHHHHHHHHH
Confidence 3577899999854433 55667777654
No 69
>COG2239 MgtE Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]
Probab=39.81 E-value=48 Score=25.85 Aligned_cols=39 Identities=26% Similarity=0.541 Sum_probs=29.1
Q ss_pred CCCCcceeee-ecCCCChhhHHHHHHhhhcCCCCCeEEEEE
Q psy6336 15 IGDLDKKKYL-VPSDLTVGQFYFLIRKRVQLRPEDALFFFV 54 (73)
Q Consensus 15 lP~Ldk~KfL-Vp~~~tv~qf~~~iRk~L~L~~~~alfl~V 54 (73)
+..+-...|+ ++.+.|++|-...||++=+ .++..-++||
T Consensus 134 aG~~Mt~e~v~l~~~~Tv~~al~~ir~~~~-~~e~~~~lyV 173 (451)
T COG2239 134 AGRIMTTEFVTLPEDVTVDEALDRIRERAE-DAETIYYLYV 173 (451)
T ss_pred hhccceeeeEEeccCcCHHHHHHHHHHhcc-cccccceEEE
Confidence 4444455555 9999999999999998877 5555556666
No 70
>KOG0765|consensus
Probab=39.66 E-value=12 Score=28.29 Aligned_cols=36 Identities=19% Similarity=0.378 Sum_probs=26.6
Q ss_pred CCCcceeeeecCCCChhhH------HHHHHhhhcCCCCCeEE
Q psy6336 16 GDLDKKKYLVPSDLTVGQF------YFLIRKRVQLRPEDALF 51 (73)
Q Consensus 16 P~Ldk~KfLVp~~~tv~qf------~~~iRk~L~L~~~~alf 51 (73)
.-|||+||.+-.-....-. ..+||.||++.+++.+|
T Consensus 29 e~lDK~kFy~~g~~l~~~Vr~aLYP~~vlkTrlQVq~~~~vy 70 (333)
T KOG0765|consen 29 EMLDKKKFYPLGAALFSGVRTALYPLTVLKTRLQVQKKNTVY 70 (333)
T ss_pred hhccccceeehhhHHhhcceeeeeehhhhhhHHhhccccchh
Confidence 4589999998765543332 56799999999887755
No 71
>cd00782 MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to human MLH1, hPMS2, hPMS1, hMLH3 and E. coli MutL, MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot synd
Probab=39.17 E-value=22 Score=21.68 Aligned_cols=27 Identities=26% Similarity=0.396 Sum_probs=17.7
Q ss_pred CCCeEEEEEcCcC---CCCcchHHHHHhhh
Q psy6336 46 PEDALFFFVNNVI---PPTSATMGSLYQEI 72 (73)
Q Consensus 46 ~~~alfl~Vn~~l---p~~~~~m~~lY~~f 72 (73)
..+..|+|||+.. +.....+.+.|+.+
T Consensus 42 ~~~~q~~fVN~R~v~~~~l~~ai~~~y~~~ 71 (122)
T cd00782 42 SKDRQFLFVNGRPVRDKLLSKAINEAYRSY 71 (122)
T ss_pred CCccEEEEECCeEecCHHHHHHHHHHHHHh
Confidence 4567899999843 34455566677664
No 72
>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=39.00 E-value=68 Score=21.13 Aligned_cols=35 Identities=20% Similarity=0.404 Sum_probs=23.3
Q ss_pred eeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEc
Q psy6336 21 KKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVN 55 (73)
Q Consensus 21 ~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn 55 (73)
..+.||.+.|+++|-.+|+.-++......--++++
T Consensus 20 Rri~Vp~~~tl~~Lh~~Iq~afgw~~~HL~~F~~~ 54 (179)
T PF07929_consen 20 RRIEVPADITLADLHEVIQAAFGWDDDHLYEFFIG 54 (179)
T ss_dssp EEEEEETT-BHHHHHHHHHHHTT----S-EEEEEE
T ss_pred EEEEECCCCCHHHHHHHHHHHhCcCCCEeEEEEEC
Confidence 45789999999999999999999886644444444
No 73
>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA. NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play 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
Probab=38.42 E-value=42 Score=20.57 Aligned_cols=28 Identities=18% Similarity=0.263 Sum_probs=23.9
Q ss_pred eeecCCCChhhHHHHHHhhhcCCCCCeEEE
Q psy6336 23 YLVPSDLTVGQFYFLIRKRVQLRPEDALFF 52 (73)
Q Consensus 23 fLVp~~~tv~qf~~~iRk~L~L~~~~alfl 52 (73)
..||++.++.+|..-||.+++++ +.+-+
T Consensus 16 i~v~~~i~f~dL~~kIrdkf~~~--~~~~i 43 (86)
T cd06408 16 IMIGPDTGFADFEDKIRDKFGFK--RRLKI 43 (86)
T ss_pred EEcCCCCCHHHHHHHHHHHhCCC--CceEE
Confidence 45999999999999999999996 45555
No 74
>PF04106 APG5: Autophagy protein Apg5 ; InterPro: IPR007239 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 autophagy protein 5 (Apg5).; GO: 0006914 autophagy, 0005737 cytoplasm; PDB: 2DYM_G 2DYO_A.
Probab=38.33 E-value=57 Score=22.30 Aligned_cols=27 Identities=11% Similarity=0.284 Sum_probs=19.1
Q ss_pred CCCeEEEEEcCcCCCCcchHHHHHhhh
Q psy6336 46 PEDALFFFVNNVIPPTSATMGSLYQEI 72 (73)
Q Consensus 46 ~~~alfl~Vn~~lp~~~~~m~~lY~~f 72 (73)
.......++++..++.++.+..+|++|
T Consensus 157 ~~~~~~~iihGI~ipldtpl~~l~~~l 183 (197)
T PF04106_consen 157 EPELARVIIHGIEIPLDTPLQWLYENL 183 (197)
T ss_dssp ----EEEEETTEEE-TTSBHHHHHHHH
T ss_pred CccccEEEEeCeeCCCCCcHHHHHHHc
Confidence 345667778887788899999999987
No 75
>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=37.74 E-value=59 Score=20.00 Aligned_cols=44 Identities=14% Similarity=0.028 Sum_probs=31.1
Q ss_pred eeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHH
Q psy6336 23 YLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGS 67 (73)
Q Consensus 23 fLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~ 67 (73)
+=|.++.||+++..-|..+-++++++--.+| ++.....+.++++
T Consensus 42 leV~~~~TV~~lK~kI~~~~gip~~~QrLi~-~Gk~L~D~~tL~d 85 (103)
T cd01802 42 LRVSPFETVISVKAKIQRLEGIPVAQQHLIW-NNMELEDEYCLND 85 (103)
T ss_pred EEeCCCCcHHHHHHHHHHHhCCChHHEEEEE-CCEECCCCCcHHH
Confidence 4589999999999999999998887543344 3433444455654
No 76
>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=37.44 E-value=81 Score=18.00 Aligned_cols=28 Identities=21% Similarity=0.108 Sum_probs=24.5
Q ss_pred CcceeeeecCCCChhhHHHHHHhhhcCC
Q psy6336 18 LDKKKYLVPSDLTVGQFYFLIRKRVQLR 45 (73)
Q Consensus 18 Ldk~KfLVp~~~tv~qf~~~iRk~L~L~ 45 (73)
-.-+-..|+++.|.++++..+-++.++.
T Consensus 12 ~~~kti~V~~~~t~~~Vi~~~l~k~~l~ 39 (87)
T cd01768 12 GTYKTLRVSKDTTAQDVIQQLLKKFGLD 39 (87)
T ss_pred ccEEEEEECCCCCHHHHHHHHHHHhCCc
Confidence 3446678999999999999999999999
No 77
>PRK04115 hypothetical protein; Provisional
Probab=36.91 E-value=93 Score=20.70 Aligned_cols=43 Identities=19% Similarity=0.244 Sum_probs=25.2
Q ss_pred eeEEEEEeCCCCCCCCCcceeeeecCCCChhhHHHHHHhhhcC----CCCCeEEEE
Q psy6336 2 MWRVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQL----RPEDALFFF 53 (73)
Q Consensus 2 ~iPvIvEr~~~~~lP~Ldk~KfLVp~~~tv~qf~~~iRk~L~L----~~~~alfl~ 53 (73)
|+|+|+|..+.. ..-.|.|-...- +.+|++=|+. ..+..+++|
T Consensus 67 rLPIile~~~~~-----~~g~~~VrG~~e----vk~IskiLg~~~~~~e~~~l~ly 113 (137)
T PRK04115 67 RLPIILEIDSSL-----GEGAIVVRGKEE----VKVISKILGKEDIFSEEDILYLY 113 (137)
T ss_pred eeeEEEEEecCC-----CceEEEEcCHHH----HHHHHHHhCccccccCCCEEEEe
Confidence 799999997632 223455555552 3445555553 356666665
No 78
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. 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. The NBR1 protein contains a type I PB1 domain.
Probab=35.68 E-value=63 Score=19.54 Aligned_cols=49 Identities=12% Similarity=0.257 Sum_probs=33.7
Q ss_pred cceeeeecC--CCChhhHHHHHHhhhcCCCCCeEEE-EEcC----cCCCCcchHHHHHh
Q psy6336 19 DKKKYLVPS--DLTVGQFYFLIRKRVQLRPEDALFF-FVNN----VIPPTSATMGSLYQ 70 (73)
Q Consensus 19 dk~KfLVp~--~~tv~qf~~~iRk~L~L~~~~alfl-~Vn~----~lp~~~~~m~~lY~ 70 (73)
+...|.+++ +.+..++..-+++|.+++ ++=+ |+++ .+.+.++.+.|-++
T Consensus 10 d~~rf~~~~~~~~~~~~L~~ev~~rf~l~---~f~lKYlDde~e~v~lssd~eLeE~~r 65 (81)
T cd06396 10 ESQSFLVSDSENTTWASVEAMVKVSFGLN---DIQIKYVDEENEEVSVNSQGEYEEALK 65 (81)
T ss_pred eEEEEEecCCCCCCHHHHHHHHHHHhCCC---cceeEEEcCCCCEEEEEchhhHHHHHH
Confidence 456788988 779999999999999999 3333 5553 24444555554433
No 79
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=35.49 E-value=58 Score=16.92 Aligned_cols=21 Identities=29% Similarity=0.401 Sum_probs=17.9
Q ss_pred HHHHhhhcCCCCCeEEEEEcC
Q psy6336 36 FLIRKRVQLRPEDALFFFVNN 56 (73)
Q Consensus 36 ~~iRk~L~L~~~~alfl~Vn~ 56 (73)
.-+|+.+++.+++.+.+.+++
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~ 33 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEG 33 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEET
T ss_pred HHHHHHcCCCCCCEEEEEEeC
Confidence 347899999999999998874
No 80
>cd01775 CYR1_RA Ubiquitin domain of CYR1 adenylate cyclase. CYR1 is a fungal adenylate cyclase with at least four domains, an N-terminal RA (Ras association) domain, a middle leucine-rich repeat domain, a catalytic domain. The N-terminal RA domain of CYR1 post-translationally modifies a small GTPase called Ras. The Ras-CYR1 pathway has been implicated in the transduction of a glucose-triggered signal to an intracellular environment where a protein phosphorylation cascade is initiated by cyclic AMP.
Probab=34.96 E-value=92 Score=19.59 Aligned_cols=35 Identities=17% Similarity=0.155 Sum_probs=28.8
Q ss_pred eeeecCCCChhhHHHHHHhhhcCCCC--CeEEEEEcC
Q psy6336 22 KYLVPSDLTVGQFYFLIRKRVQLRPE--DALFFFVNN 56 (73)
Q Consensus 22 KfLVp~~~tv~qf~~~iRk~L~L~~~--~alfl~Vn~ 56 (73)
.+..|-+-|++|++..+.++-.++++ -.|++.+++
T Consensus 16 Tls~~l~tTv~eli~~L~rK~~l~~~~ny~l~l~~~~ 52 (97)
T cd01775 16 TLSCPLNTTVSELIPQLAKKFYLPSGGNYQLSLKKHD 52 (97)
T ss_pred EEEcCCcCcHHHHHHHHHHhhcCCCCCCeEEEEEECC
Confidence 46789999999999999999998875 456666675
No 81
>PRK08577 hypothetical protein; Provisional
Probab=34.51 E-value=46 Score=21.08 Aligned_cols=21 Identities=14% Similarity=0.317 Sum_probs=18.4
Q ss_pred HHHHhhhcCCCCCeEEEEEcC
Q psy6336 36 FLIRKRVQLRPEDALFFFVNN 56 (73)
Q Consensus 36 ~~iRk~L~L~~~~alfl~Vn~ 56 (73)
.-+|++|++.+++.+-+++++
T Consensus 19 ~~~r~~l~~~~g~~~~~~~~~ 39 (136)
T PRK08577 19 LEIREALGIREGMYVLLIADT 39 (136)
T ss_pred HHHHHHcCcCCCCEEEEEEEC
Confidence 347999999999999999874
No 82
>KOG1209|consensus
Probab=34.07 E-value=95 Score=22.92 Aligned_cols=50 Identities=24% Similarity=0.216 Sum_probs=39.0
Q ss_pred cceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcC-----cCCCCcchHHHHHhhh
Q psy6336 19 DKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNN-----VIPPTSATMGSLYQEI 72 (73)
Q Consensus 19 dk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~-----~lp~~~~~m~~lY~~f 72 (73)
.-.|.=|.++..|.++...+|+. +.-.|=+++|| +.|..|.+++.+=+||
T Consensus 55 ~~~kLDV~~~~~V~~v~~evr~~----~~Gkld~L~NNAG~~C~~Pa~d~~i~ave~~f 109 (289)
T KOG1209|consen 55 KPYKLDVSKPEEVVTVSGEVRAN----PDGKLDLLYNNAGQSCTFPALDATIAAVEQCF 109 (289)
T ss_pred eeEEeccCChHHHHHHHHHHhhC----CCCceEEEEcCCCCCcccccccCCHHHHHhhh
Confidence 34555588888899999999875 56677788886 3688899999988877
No 83
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=33.50 E-value=23 Score=19.65 Aligned_cols=39 Identities=26% Similarity=0.270 Sum_probs=29.3
Q ss_pred ceeeeecCCCChhhHHHHHHhhhc-CCCCCeEEEEEcCcC
Q psy6336 20 KKKYLVPSDLTVGQFYFLIRKRVQ-LRPEDALFFFVNNVI 58 (73)
Q Consensus 20 k~KfLVp~~~tv~qf~~~iRk~L~-L~~~~alfl~Vn~~l 58 (73)
.....++...|++++...+..+.. +...+.+-++||+..
T Consensus 13 ~~~~~~~~~~tv~~ll~~l~~~~p~~~~~~~~~v~vN~~~ 52 (77)
T PF02597_consen 13 EEEIEVPEGSTVRDLLEALAERYPELALRDRVAVAVNGEI 52 (77)
T ss_dssp EEEEEESSTSBHHHHHHHHCHHTGGGHTTTTEEEEETTEE
T ss_pred CeEEecCCCCcHHHHHHHHHhhccccccCccEEEEECCEE
Confidence 456789999999999998886652 224477888899843
No 84
>PF01650 Peptidase_C13: Peptidase C13 family; InterPro: IPR001096 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C13 (legumain family, clan CD). A type example is legumain from Canavalia ensiformis (Jack bean, Horse bean). The blood fluke parasite Schistosoma mansoni has two cysteine proteases in its digestive tract, one a cathepsin B-like protease, the other termed hemoglobinase [, ]. The latter has been hard to purify, free of cathepsin B, and expressed forms in Escherichia coli prove to be inactive, suggesting that hemoglobinase may act in association with cathepsin B [, ]. Plant vacuolar processing enzyme and legumain from legumes [] have been shown to have sequence and functional similarity to hemoglobinase. The catalytic residues of the family are currently unknown, but sequence alignments reveal one totally conserved cysteine and two totally conserved histidines.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis
Probab=33.20 E-value=59 Score=23.17 Aligned_cols=31 Identities=19% Similarity=0.389 Sum_probs=25.6
Q ss_pred cCCCChhhHHHHHH--------hhhcCCCCCeEEEEEcC
Q psy6336 26 PSDLTVGQFYFLIR--------KRVQLRPEDALFFFVNN 56 (73)
Q Consensus 26 p~~~tv~qf~~~iR--------k~L~L~~~~alfl~Vn~ 56 (73)
-.+.|..+|..+|+ +.|+..+++-+|+|-.+
T Consensus 77 g~~v~~~~fl~vL~G~~~~~~~kvl~s~~~D~vfiy~~~ 115 (256)
T PF01650_consen 77 GEDVTPENFLNVLTGDKSVPSGKVLNSTENDNVFIYFTG 115 (256)
T ss_pred ccccCHHHHHHHhcCCCCCCccccccCCCCCeEEEEEec
Confidence 34788999999999 55678899999998863
No 85
>PF04663 Phenol_monoox: Phenol hydroxylase conserved region; InterPro: IPR006756 Under aerobic conditions, phenol is usually hydroxylated to catechol and degraded via the meta or ortho pathways. Two types of phenol hydroxylase are known: one is a multi-component enzyme the other is a single-component monooxygenase. This signature is found in both types of enzymes [, ].; PDB: 3U52_F 2INN_F 2INP_E.
Probab=32.53 E-value=38 Score=19.98 Aligned_cols=18 Identities=17% Similarity=0.399 Sum_probs=13.5
Q ss_pred eeeeecCCCChhhHHHHH
Q psy6336 21 KKYLVPSDLTVGQFYFLI 38 (73)
Q Consensus 21 ~KfLVp~~~tv~qf~~~i 38 (73)
.-|.||+++++|+++.-+
T Consensus 28 ~~~plpP~mpFg~l~~~v 45 (67)
T PF04663_consen 28 FAFPLPPDMPFGALVEQV 45 (67)
T ss_dssp EEEEE-TTSBHHHHHHHT
T ss_pred eeecCCCCCcHHHHHHHh
Confidence 457899999999997643
No 86
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=31.43 E-value=43 Score=17.17 Aligned_cols=16 Identities=31% Similarity=0.524 Sum_probs=10.5
Q ss_pred cCCCChhhHHHHHHhh
Q psy6336 26 PSDLTVGQFYFLIRKR 41 (73)
Q Consensus 26 p~~~tv~qf~~~iRk~ 41 (73)
|.++||+|+..++-.+
T Consensus 1 p~sltV~~Lk~iL~~~ 16 (35)
T PF12949_consen 1 PKSLTVAQLKRILDEH 16 (35)
T ss_dssp STT--SHHHHHHHHHH
T ss_pred CCcCcHHHHHHHHHHc
Confidence 6789999988877543
No 87
>KOG4147|consensus
Probab=30.89 E-value=33 Score=22.45 Aligned_cols=21 Identities=33% Similarity=0.645 Sum_probs=18.7
Q ss_pred CCCChhhHHHHHHhhhcCCCC
Q psy6336 27 SDLTVGQFYFLIRKRVQLRPE 47 (73)
Q Consensus 27 ~~~tv~qf~~~iRk~L~L~~~ 47 (73)
.+.|+.||..++.++++++++
T Consensus 32 ad~Tvk~f~~~~~~~Iq~~~s 52 (127)
T KOG4147|consen 32 ADQTVKEFIVFLKQDIQLRTS 52 (127)
T ss_pred hHhhHHHHHHHHHHhcccCCC
Confidence 467999999999999998876
No 88
>PF08154 NLE: NLE (NUC135) domain; InterPro: IPR012972 This domain is located N-terminal to WD40 repeats(IPR001680 from INTERPRO). It is found in the microtubule-associated protein Q12024 from SWISSPROT [].
Probab=30.26 E-value=1.1e+02 Score=17.21 Aligned_cols=41 Identities=17% Similarity=0.247 Sum_probs=33.8
Q ss_pred CCcceeeeecCCCChhhHHHHHHhhh-cCCCCCeEEEEEcCc
Q psy6336 17 DLDKKKYLVPSDLTVGQFYFLIRKRV-QLRPEDALFFFVNNV 57 (73)
Q Consensus 17 ~Ldk~KfLVp~~~tv~qf~~~iRk~L-~L~~~~alfl~Vn~~ 57 (73)
.....-+.||.+.|..++...+.+=| .......+=+++|+.
T Consensus 14 ~~~~~~~~VP~~~t~~~Ls~LvN~LL~~~~~~vpfdF~i~~~ 55 (65)
T PF08154_consen 14 EVPGTPISVPSNITRKELSELVNQLLDDEEEPVPFDFLINGE 55 (65)
T ss_pred cCCCCCEEEeCCCCHHHHHHHHHHHhccCCCCCcEEEEECCE
Confidence 55668899999999999999999988 666666666778874
No 89
>KOG0010|consensus
Probab=29.56 E-value=82 Score=25.14 Aligned_cols=47 Identities=26% Similarity=0.331 Sum_probs=36.3
Q ss_pred cceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHH
Q psy6336 19 DKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMG 66 (73)
Q Consensus 19 dk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~ 66 (73)
||.-|-|+.+.||.||+.-|-++-+.++++-.-+|.+.. .+.+.|+.
T Consensus 25 dk~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfaGrI-LKD~dTL~ 71 (493)
T KOG0010|consen 25 DKYEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYAGRI-LKDDDTLK 71 (493)
T ss_pred cceeEecccchHHHHHHHHHHHhcCCChhHeeeeecCcc-ccChhhHH
Confidence 377789999999999999999999888887776666543 33444443
No 90
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=29.14 E-value=87 Score=17.37 Aligned_cols=44 Identities=16% Similarity=0.110 Sum_probs=28.1
Q ss_pred eeeeecCCCChhhHHHHHHhhhcC---CCCCeEEEEEcCcCCCCcch
Q psy6336 21 KKYLVPSDLTVGQFYFLIRKRVQL---RPEDALFFFVNNVIPPTSAT 64 (73)
Q Consensus 21 ~KfLVp~~~tv~qf~~~iRk~L~L---~~~~alfl~Vn~~lp~~~~~ 64 (73)
..+-+|...|++++...+..+..- ...+.+-++||+...+.+..
T Consensus 18 ~~~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~~~~~ 64 (80)
T cd00754 18 EELELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVRLDTP 64 (80)
T ss_pred EEEECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcCCCcc
Confidence 345577889999998888766421 12356677889754334443
No 91
>PF10209 DUF2340: Uncharacterized conserved protein (DUF2340); InterPro: IPR018794 This entry consists of small proteins of approximately 150 amino acids whose function is unknown.
Probab=28.49 E-value=55 Score=21.42 Aligned_cols=21 Identities=24% Similarity=0.404 Sum_probs=17.8
Q ss_pred CCCChhhHHHHHHhhhcCCCC
Q psy6336 27 SDLTVGQFYFLIRKRVQLRPE 47 (73)
Q Consensus 27 ~~~tv~qf~~~iRk~L~L~~~ 47 (73)
.+.|++||...++++++.+++
T Consensus 25 ~~~Tv~~l~~~v~~~I~t~~~ 45 (122)
T PF10209_consen 25 KDTTVKDLKEQVKQDIKTRPG 45 (122)
T ss_pred ccCcHHHHHHHHHHHHhcCCC
Confidence 378999999999999986654
No 92
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=27.87 E-value=75 Score=18.31 Aligned_cols=40 Identities=15% Similarity=0.099 Sum_probs=25.3
Q ss_pred eec-CCCChhhHHHHHHhhh-----cCCCCCeEEEEEcCcCCCCcch
Q psy6336 24 LVP-SDLTVGQFYFLIRKRV-----QLRPEDALFFFVNNVIPPTSAT 64 (73)
Q Consensus 24 LVp-~~~tv~qf~~~iRk~L-----~L~~~~alfl~Vn~~lp~~~~~ 64 (73)
-++ ...|++++...|.++- .+. ...+-++||+...+.++.
T Consensus 20 ~v~~~~~tv~~l~~~L~~~~~~~~~~~~-~~~~~~aVN~~~~~~~~~ 65 (81)
T PRK11130 20 ELAADFPTVEALRQHLAQKGDRWALALE-DGKLLAAVNQTLVSFDHP 65 (81)
T ss_pred EecCCCCCHHHHHHHHHHhCccHHhhhc-CCCEEEEECCEEcCCCCC
Confidence 344 3579999999997663 122 334567899865444443
No 93
>PF14732 UAE_UbL: Ubiquitin/SUMO-activating enzyme ubiquitin-like domain; PDB: 1Y8Q_B 1Y8R_E 3KYD_B 3KYC_B.
Probab=27.55 E-value=21 Score=21.50 Aligned_cols=21 Identities=14% Similarity=0.460 Sum_probs=14.5
Q ss_pred cCCCChhhHHH-HHHhhhcCCC
Q psy6336 26 PSDLTVGQFYF-LIRKRVQLRP 46 (73)
Q Consensus 26 p~~~tv~qf~~-~iRk~L~L~~ 46 (73)
+..+|+++|+. +++++|++.+
T Consensus 6 ~~~~TL~~lv~~Vlk~~Lg~~~ 27 (87)
T PF14732_consen 6 TKKMTLGDLVEKVLKKKLGMNE 27 (87)
T ss_dssp TTT-BHHHHHHHCCCCCS--SS
T ss_pred chhCcHHHHHHHHHHhccCCCC
Confidence 46789999998 6677998875
No 94
>PF03147 FDX-ACB: Ferredoxin-fold anticodon binding domain; InterPro: IPR005121 Aminoacyl-tRNA synthetases (aaRSs) play a crucial role in the translation of the genetic code by means of covalent attachment of amino acids to their cognate tRNAs. Phenylalanine-tRNA synthetase (PheRS) is known to be among the most complex enzymes of the aaRS family. Bacterial and mitochondrial PheRSs share a ferredoxin-fold anticodon binding (FDX-ACB) domain, which represents a canonical double split alpha+beta motif having no insertions. The FDX-ACB domain displays a typical RNA recognition fold (RRM) (see PDOC00030 from PROSITEDOC) formed by the four-stranded antiparallel beta sheet, with two helices packed against it [, , , , ].; GO: 0000049 tRNA binding, 0000287 magnesium ion binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation, 0008033 tRNA processing; PDB: 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 3PCO_D 2RHS_D 2RHQ_B 2AKW_B 1B70_B ....
Probab=27.22 E-value=62 Score=19.15 Aligned_cols=22 Identities=23% Similarity=0.401 Sum_probs=18.4
Q ss_pred eeeecCCCChhhHHHHHHhhhc
Q psy6336 22 KYLVPSDLTVGQFYFLIRKRVQ 43 (73)
Q Consensus 22 KfLVp~~~tv~qf~~~iRk~L~ 43 (73)
-|.+|.+.+.+++...+|+--.
T Consensus 11 S~~v~~~~~~~~i~~~i~~~~~ 32 (94)
T PF03147_consen 11 SFVVPEDVPFADIEEVIRSAGG 32 (94)
T ss_dssp EEEEETTS-HHHHHHHHHHHHT
T ss_pred EEEECCCCCHHHHHHHHHHhCc
Confidence 4889999999999999997763
No 95
>COG3171 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.20 E-value=20 Score=23.34 Aligned_cols=39 Identities=18% Similarity=0.146 Sum_probs=27.3
Q ss_pred HHHHHhhhcCCCCCeEEEEEcCcCCCC--cchHHHHHhhhC
Q psy6336 35 YFLIRKRVQLRPEDALFFFVNNVIPPT--SATMGSLYQEII 73 (73)
Q Consensus 35 ~~~iRk~L~L~~~~alfl~Vn~~lp~~--~~~m~~lY~~f~ 73 (73)
..-+||+|+|..=|.|=+-||-+.+.. .....+..+.||
T Consensus 14 nRRlrKKlhl~EFQeLgF~v~~~~~eg~~ae~~dea~drFi 54 (119)
T COG3171 14 NRRLRKKLHLGEFQELGFSVQWSFHEGTSAEDVDEAVDRFI 54 (119)
T ss_pred hHHHHhhccHHHHHhhheeeEEEecCCccHHHHHHHHHHHH
Confidence 455789999999888888888766553 335566666654
No 96
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=26.66 E-value=47 Score=19.44 Aligned_cols=20 Identities=20% Similarity=0.428 Sum_probs=16.9
Q ss_pred eecCCCChhhHHHHHHhhhc
Q psy6336 24 LVPSDLTVGQFYFLIRKRVQ 43 (73)
Q Consensus 24 LVp~~~tv~qf~~~iRk~L~ 43 (73)
++|.+.+++++..+|.+-|.
T Consensus 19 ~LP~~~~l~~l~~fl~~~l~ 38 (109)
T PF10367_consen 19 LLPDDWPLSDLSDFLCKSLR 38 (109)
T ss_pred hCcCCCCHHHHHHHHHHHHH
Confidence 47999999999998887763
No 97
>PF01119 DNA_mis_repair: DNA mismatch repair protein, C-terminal domain; InterPro: IPR013507 This entry represents the C-terminal domain of DNA mismatch repair proteins, such as MutL. This domain functions in promoting dimerisation []. The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1B62_A 1NHJ_A 1BKN_B 1NHH_A 1B63_A 1NHI_A 3NA3_A 1EA6_A 1H7U_A 1H7S_B ....
Probab=26.10 E-value=57 Score=20.05 Aligned_cols=27 Identities=30% Similarity=0.454 Sum_probs=18.0
Q ss_pred CCCCeEEEEEcCcC---CCCcchHHHHHhh
Q psy6336 45 RPEDALFFFVNNVI---PPTSATMGSLYQE 71 (73)
Q Consensus 45 ~~~~alfl~Vn~~l---p~~~~~m~~lY~~ 71 (73)
...+..|+|||+.. +.....+.++|++
T Consensus 37 ~~~~~q~ifVN~R~V~~~~l~~~I~~~y~~ 66 (119)
T PF01119_consen 37 SSRDRQFIFVNGRPVENKALSKAINEAYRE 66 (119)
T ss_dssp SSCTCEEEEETTEEE--HHHHHHHHHHHHC
T ss_pred CCCCcEEEEeCCCeEeChHHHHHHHHHHhh
Confidence 34578999999843 4445556666663
No 98
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=25.98 E-value=65 Score=17.24 Aligned_cols=18 Identities=17% Similarity=0.471 Sum_probs=12.9
Q ss_pred HhhhcCCCCCeEEEEEcC
Q psy6336 39 RKRVQLRPEDALFFFVNN 56 (73)
Q Consensus 39 Rk~L~L~~~~alfl~Vn~ 56 (73)
..+|+|.+++.+|+.++-
T Consensus 42 ~~~L~L~~G~~V~~~ik~ 59 (64)
T PF03459_consen 42 AEELGLKPGDEVYASIKA 59 (64)
T ss_dssp HHHCT-STT-EEEEEE-G
T ss_pred HHHcCCCCCCEEEEEEeh
Confidence 578999999999999873
No 99
>smart00148 PLCXc Phospholipase C, catalytic domain (part); domain X. Phosphoinositide-specific phospholipases C. These enzymes contain 2 regions (X and Y) which together form a TIM barrel-like structure containing the active site residues. Phospholipase C enzymes (PI-PLC) act as signal transducers that generate two second messengers, inositol-1,4,5-trisphosphate and diacylglycerol. The bacterial enzyme [6] appears to be a homologue of the mammalian PLCs.
Probab=25.52 E-value=72 Score=20.33 Aligned_cols=33 Identities=6% Similarity=0.053 Sum_probs=28.4
Q ss_pred cCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcC
Q psy6336 26 PSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVI 58 (73)
Q Consensus 26 p~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~l 58 (73)
....++.+....|++.+.-.+++.+.+-+++..
T Consensus 66 ~~~~~~~dvL~~i~~fl~~~p~e~VIl~l~~~~ 98 (135)
T smart00148 66 TLPIKLSEVLEAIKDFAFVTSPYPVILSLENHC 98 (135)
T ss_pred cccEEHHHHHHHHHHHHHhCCCCcEEEeehhhC
Confidence 345688999999999999999999999998754
No 100
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=25.32 E-value=1.3e+02 Score=16.47 Aligned_cols=36 Identities=22% Similarity=0.304 Sum_probs=25.2
Q ss_pred cceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCc-CC
Q psy6336 19 DKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNV-IP 59 (73)
Q Consensus 19 dk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~-lp 59 (73)
..+++-+|.+.|+.++.. .+++++ +.+-+-+|+. +|
T Consensus 4 Ng~~~~~~~~~tv~~ll~----~l~~~~-~~v~v~vN~~iv~ 40 (64)
T TIGR01683 4 NGEPVEVEDGLTLAALLE----SLGLDP-RRVAVAVNGEIVP 40 (64)
T ss_pred CCeEEEcCCCCcHHHHHH----HcCCCC-CeEEEEECCEEcC
Confidence 456677888999888765 456665 6666788984 44
No 101
>PF02938 GAD: GAD domain; InterPro: IPR004115 This entry represetns an 2 layer alpha/beta insertion domain found in some glutamyl-tRNA amidotransferases and aspartyl tRNA synthetases [, ]. The function of this domain is not yet known.; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0005737 cytoplasm; PDB: 1ZQ1_D 1EQR_B 1IL2_B 1C0A_A 1L0W_A 1G51_B 1EFW_B 2D6F_D.
Probab=24.93 E-value=1.1e+02 Score=18.20 Aligned_cols=25 Identities=20% Similarity=0.345 Sum_probs=18.7
Q ss_pred hhHHHHHHhhhcCCCCCeEEEEEcC
Q psy6336 32 GQFYFLIRKRVQLRPEDALFFFVNN 56 (73)
Q Consensus 32 ~qf~~~iRk~L~L~~~~alfl~Vn~ 56 (73)
.+-..-|.+++++.+++.+|+..+.
T Consensus 63 e~~~~~l~~~~~a~~GD~ll~~Ag~ 87 (95)
T PF02938_consen 63 EEELKALIERLGAKPGDLLLFVAGK 87 (95)
T ss_dssp HHHHHHHHHHTT--TTEEEEEEEES
T ss_pred HHHHHHHHHHhCCCCCCEEEEECCC
Confidence 4456778899999999999998775
No 102
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=24.91 E-value=80 Score=21.42 Aligned_cols=20 Identities=30% Similarity=0.499 Sum_probs=17.9
Q ss_pred HHHHhhhcCCCCCeEEEEEc
Q psy6336 36 FLIRKRVQLRPEDALFFFVN 55 (73)
Q Consensus 36 ~~iRk~L~L~~~~alfl~Vn 55 (73)
.-||++|++.+.+.+=++++
T Consensus 19 ~~iR~~l~i~~gd~~~~~~~ 38 (180)
T TIGR02851 19 KEIRRTLRIREGDPLEIFTD 38 (180)
T ss_pred HHHHHHcCCCCCCeEEEEEe
Confidence 34899999999999999987
No 103
>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=24.70 E-value=1.1e+02 Score=17.30 Aligned_cols=53 Identities=11% Similarity=0.169 Sum_probs=34.6
Q ss_pred CCCCcceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEc--C-cCCCCc-chHHH
Q psy6336 15 IGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVN--N-VIPPTS-ATMGS 67 (73)
Q Consensus 15 lP~Ldk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn--~-~lp~~~-~~m~~ 67 (73)
+|+=.+-.--.+.+.|++.+..+|+..+.......+-|..+ . .+...+ +++++
T Consensus 13 lpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~~~Pr~~l~~~~~~tl~e 69 (82)
T PF00789_consen 13 LPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELITAFPRRELTDEDSKTLEE 69 (82)
T ss_dssp ETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEESSSTEECCSTTTSBTCC
T ss_pred CCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEeCCCCcCCCccccccHHH
Confidence 34433444456689999999999999988777655666554 1 344444 56554
No 104
>PF01886 DUF61: Protein of unknown function DUF61; InterPro: IPR002746 The proteins in this entry are functionally uncharacterised.
Probab=24.63 E-value=1.3e+02 Score=19.67 Aligned_cols=43 Identities=28% Similarity=0.389 Sum_probs=26.2
Q ss_pred eeEEEEEeCCCCCCCCCcceeeeecCCCChhhHHHHHHhhhcCCC----CCeEEEE
Q psy6336 2 MWRVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRP----EDALFFF 53 (73)
Q Consensus 2 ~iPvIvEr~~~~~lP~Ldk~KfLVp~~~tv~qf~~~iRk~L~L~~----~~alfl~ 53 (73)
++|+|+|..+ .++.-.|-|-+..-+ .+|++=|+.+- +.-++++
T Consensus 65 rLPIile~~~-----~~~~g~~~V~g~~e~----k~i~~ilg~~~~~~~~~~l~i~ 111 (132)
T PF01886_consen 65 RLPIILEIDP-----TLGEGSYRVRGKEEV----KAISKILGKEREFEEEDELYIY 111 (132)
T ss_pred eccEEEEEec-----cCCCceEEEeCHHHH----HHHHHHhCCCcccccCCeEEEc
Confidence 7899999965 244556667666532 33445555443 5666665
No 105
>PF04320 DUF469: Protein with unknown function (DUF469); InterPro: IPR007416 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.
Probab=24.58 E-value=58 Score=20.57 Aligned_cols=36 Identities=19% Similarity=0.318 Sum_probs=23.2
Q ss_pred HHhhhcCCCCCeEEEEEc-CcCC-CCcchHHHHHhhhC
Q psy6336 38 IRKRVQLRPEDALFFFVN-NVIP-PTSATMGSLYQEII 73 (73)
Q Consensus 38 iRk~L~L~~~~alfl~Vn-~~lp-~~~~~m~~lY~~f~ 73 (73)
+||+|.+..=+-|=+-|+ +.-. .........-++||
T Consensus 3 lRKKL~l~EFqelGF~v~~~~~~~~~~e~~D~~~D~fI 40 (101)
T PF04320_consen 3 LRKKLHLDEFQELGFEVSCRFAEGTSEEQIDAFVDAFI 40 (101)
T ss_pred hhhhhhhhhhheeEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 689999998888877777 3322 23345555555553
No 106
>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=23.23 E-value=1.6e+02 Score=16.84 Aligned_cols=40 Identities=23% Similarity=0.177 Sum_probs=25.5
Q ss_pred CCcceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCc
Q psy6336 17 DLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNV 57 (73)
Q Consensus 17 ~Ldk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~ 57 (73)
.-.+.+.-|.++.++.|+..---++.++++++ -.|.=|+.
T Consensus 5 ~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~-~~L~h~~k 44 (65)
T PF11470_consen 5 NFRRFKVKVTPNTTLNQVLEEACKKFGLDPSS-YDLKHNNK 44 (65)
T ss_dssp TS-EEEE---TTSBHHHHHHHHHHHTT--GGG--EEEETTE
T ss_pred CCcEEEEEECCCCCHHHHHHHHHHHcCCCccc-eEEEECCE
Confidence 45678889999999999999999999999983 33333443
No 107
>PRK12577 succinate dehydrogenase iron-sulfur subunit; Provisional
Probab=23.06 E-value=1.5e+02 Score=21.80 Aligned_cols=42 Identities=10% Similarity=-0.077 Sum_probs=34.9
Q ss_pred CeeEEEEEeCCCCCCCCCcceeeeecCCCChhhHHHHHHhhh
Q psy6336 1 MMWRVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRV 42 (73)
Q Consensus 1 ~~iPvIvEr~~~~~lP~Ldk~KfLVp~~~tv~qf~~~iRk~L 42 (73)
|.|-+.|-|......|..+...+-+++++||-+....|...+
T Consensus 1 ~~i~~~i~R~~~~~~p~~~~~~v~~~~~~tvL~~l~~i~~~~ 42 (329)
T PRK12577 1 MEVLFKILRQKQNSAPYVQTYTLEVEPGNTILDCLNRIKWEQ 42 (329)
T ss_pred CeEEEEEEeeCCCCCCeEEEEEEECCCCChHHHHHHHhCCcC
Confidence 667788888765568999999999999999999988887655
No 108
>PF00388 PI-PLC-X: Phosphatidylinositol-specific phospholipase C, X domain This entry is for the whole phospholipase C protein; InterPro: IPR000909 Phosphatidylinositol-specific phospholipase C (3.1.4.11 from EC), a eukaryotic intracellular enzyme, plays an important role in signal transduction processes []. It catalyzes the hydrolysis of 1-phosphatidyl-D-myo-inositol-3,4,5-triphosphate into the second messenger molecules diacylglycerol and inositol-1,4,5-triphosphate. This catalytic process is tightly regulated by reversible phosphorylation and binding of regulatory proteins [, , ]. In mammals, there are at least 6 different isoforms of PI-PLC, they differ in their domain structure, their regulation, and their tissue distribution. Lower eukaryotes also possess multiple isoforms of PI-PLC. All eukaryotic PI-PLCs contain two regions of homology, sometimes referred to as the 'X-box' and 'Y-box'. The order of these two regions is always the same (NH2-X-Y-COOH), but the spacing is variable. In most isoforms, the distance between these two regions is only 50-100 residues but in the gamma isoforms one PH domain, two SH2 domains, and one SH3 domain are inserted between the two PLC-specific domains. The two conserved regions have been shown to be important for the catalytic activity. By profile analysis, we could show that sequences with significant similarity to the X-box domain occur also in prokaryotic and trypanosome PI-specific phospholipases C. Apart from this region, the prokaryotic enzymes show no similarity to their eukaryotic counterparts.; GO: 0004629 phospholipase C activity, 0006629 lipid metabolic process, 0035556 intracellular signal transduction; PDB: 2FJU_B 2ZKM_X 3V18_A 3V1H_A 3V16_A 3QR1_D 3EA3_A 3EA1_A 2OR2_A 1T6M_B ....
Probab=22.84 E-value=43 Score=21.17 Aligned_cols=32 Identities=16% Similarity=0.187 Sum_probs=26.5
Q ss_pred CCCChhhHHHHHHhhhcCCCCCeEEEEEcCcC
Q psy6336 27 SDLTVGQFYFLIRKRVQLRPEDALFFFVNNVI 58 (73)
Q Consensus 27 ~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~l 58 (73)
...++.++...+++.|.-.|++.+.|-+++.-
T Consensus 65 ~~~~~~dvL~~i~~fl~~~p~E~VIl~~~~~~ 96 (146)
T PF00388_consen 65 SGITFEDVLNDIRDFLFEHPSEPVILSLKHEY 96 (146)
T ss_dssp -EEEHHHHHHHHHHHTTHSTTS-EEEEEEEES
T ss_pred eeEeHHHHHHHHHHHHhcCCCeEEEEEeeccc
Confidence 35689999999999999999999999998643
No 109
>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=22.09 E-value=2.3e+02 Score=18.16 Aligned_cols=50 Identities=10% Similarity=0.083 Sum_probs=34.1
Q ss_pred cceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEE--cC----cCCCCcchHHHH
Q psy6336 19 DKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFV--NN----VIPPTSATMGSL 68 (73)
Q Consensus 19 dk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~V--n~----~lp~~~~~m~~l 68 (73)
...++-+....|+.++...+.+++++...+-+=|+. ++ .....+.++.+.
T Consensus 14 ~~~~~~~~~~~t~~ev~~~v~~~~~l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~~ 69 (207)
T smart00295 14 TTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDPDEDLSHWLDPAKTLLDQ 69 (207)
T ss_pred CEEEEEECCCCCHHHHHHHHHHHhCCCccceeEEEEEcCCCCcCeeCCCccCHHHh
Confidence 345678899999999999999999997655444443 22 234455555543
No 110
>COG3592 Uncharacterized conserved protein [Function unknown]
Probab=21.97 E-value=82 Score=18.90 Aligned_cols=36 Identities=17% Similarity=0.372 Sum_probs=27.4
Q ss_pred EEEeCCCC-----CCCCCcceeeeecCCCChhhHHHHHHhh
Q psy6336 6 IVEKAPKA-----RIGDLDKKKYLVPSDLTVGQFYFLIRKR 41 (73)
Q Consensus 6 IvEr~~~~-----~lP~Ldk~KfLVp~~~tv~qf~~~iRk~ 41 (73)
||+-+.++ .+=.++++-|+.|....+.+.+.+|+..
T Consensus 24 iC~Hs~nCV~Gn~~vF~~~rkPWI~Pd~~~ve~i~~vi~sC 64 (74)
T COG3592 24 ICAHSGNCVRGNPKVFNLGRKPWIMPDAVDVEEIVKVIDTC 64 (74)
T ss_pred eeecccceecCCHhhcccCCCCccCCCCCCHHHHHHHHHhC
Confidence 56555544 1334788889999999999999999864
No 111
>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=21.81 E-value=80 Score=18.08 Aligned_cols=44 Identities=14% Similarity=0.221 Sum_probs=26.6
Q ss_pred eeecCCCChhhHHHHHHhhhcCCCCCe----EEEEE-cC-cCCCCcchHH
Q psy6336 23 YLVPSDLTVGQFYFLIRKRVQLRPEDA----LFFFV-NN-VIPPTSATMG 66 (73)
Q Consensus 23 fLVp~~~tv~qf~~~iRk~L~L~~~~a----lfl~V-n~-~lp~~~~~m~ 66 (73)
..+|.+.++++++.-|-..++++..++ -|-+. ++ ..-+.+.+++
T Consensus 17 l~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~~~~g~~L~~~~tL~ 66 (79)
T PF08817_consen 17 LALPADVPVAELIPELVELLGLPGDDPPGHGQWVLARAGGRPLDPDQTLA 66 (79)
T ss_dssp EEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG-GGTEEEETTSBCG
T ss_pred EEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEEecCCcccCCcCcHh
Confidence 469999999999999999999854432 35555 43 3334455443
No 112
>PLN02768 AMP deaminase
Probab=21.79 E-value=1.4e+02 Score=25.48 Aligned_cols=46 Identities=9% Similarity=0.321 Sum_probs=35.7
Q ss_pred eeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcCcCCCCcchHHHHHhhh
Q psy6336 22 KYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSATMGSLYQEI 72 (73)
Q Consensus 22 KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~~lp~~~~~m~~lY~~f 72 (73)
.....+-|+-.|+..+|+++++..|++-++. -++. ..|+.|+++.+
T Consensus 387 hvh~sacMnqk~LLrFIk~kl~~epd~vV~~-~dGk----~~TL~evFe~l 432 (835)
T PLN02768 387 HVHHSACMNQKHLLRFIKSKLRKEPDEVVIF-RDGT----YLTLKEVFESL 432 (835)
T ss_pred cchhhccCCHHHHHHHHHHHHhcCCCceeec-cCCc----cccHHHHHHHc
Confidence 3455567888999999999999999998873 2222 47999999864
No 113
>cd00329 TopoII_MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch
Probab=21.57 E-value=1e+02 Score=17.49 Aligned_cols=11 Identities=45% Similarity=0.622 Sum_probs=9.0
Q ss_pred CCeEEEEEcCc
Q psy6336 47 EDALFFFVNNV 57 (73)
Q Consensus 47 ~~alfl~Vn~~ 57 (73)
.+-.|+|||+.
T Consensus 43 ~~~~~~fvN~r 53 (107)
T cd00329 43 KDRQFSFVNGR 53 (107)
T ss_pred CCcEEEEEcCe
Confidence 56789999984
No 114
>PF13764 E3_UbLigase_R4: E3 ubiquitin-protein ligase UBR4
Probab=21.52 E-value=1.2e+02 Score=25.49 Aligned_cols=42 Identities=14% Similarity=0.286 Sum_probs=32.5
Q ss_pred hhhHHHHHHhhhcCC----CCCeEEEEEcCcCCCCcchHHHHHhhh
Q psy6336 31 VGQFYFLIRKRVQLR----PEDALFFFVNNVIPPTSATMGSLYQEI 72 (73)
Q Consensus 31 v~qf~~~iRk~L~L~----~~~alfl~Vn~~lp~~~~~m~~lY~~f 72 (73)
+..+...|.+-+.+. .+..+=|+|||.+.+.|-.+.++|++.
T Consensus 17 mrdvknkIc~d~~m~~lleDd~gmELlV~~~IisldL~v~~Vy~~v 62 (802)
T PF13764_consen 17 MRDVKNKICRDLEMIALLEDDNGMELLVNNKIISLDLPVRDVYEKV 62 (802)
T ss_pred HHHHHHHHhhhcccchhccCCcccceeecCeeecCCCcHHHHHHHH
Confidence 445555566666654 477788999999999999999999864
No 115
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=21.41 E-value=1.2e+02 Score=17.44 Aligned_cols=21 Identities=14% Similarity=0.191 Sum_probs=17.7
Q ss_pred HHHHhhhcCCCCCeEEEEEcC
Q psy6336 36 FLIRKRVQLRPEDALFFFVNN 56 (73)
Q Consensus 36 ~~iRk~L~L~~~~alfl~Vn~ 56 (73)
.-+++.|+|.+++.+++.+.+
T Consensus 16 k~i~~~lgl~~Gd~v~v~~~~ 36 (74)
T TIGR02609 16 KEVLESLGLKEGDTLYVDEEE 36 (74)
T ss_pred HHHHHHcCcCCCCEEEEEEEC
Confidence 347899999999999998764
No 116
>TIGR01408 Ube1 ubiquitin-activating enzyme E1. This model represents the full length, over a thousand amino acids, of a multicopy family of eukaryotic proteins, many of which are designated ubiquitin-activating enzyme E1. Members have two copies of the ThiF family domain (pfam00899), a repeat found in ubiquitin-activating proteins (pfam02134), and other regions.
Probab=21.18 E-value=1.4e+02 Score=25.61 Aligned_cols=48 Identities=19% Similarity=0.378 Sum_probs=31.2
Q ss_pred eeecCCCChhhHHHHHHhhhcCCCC----CeEEEEEcCcCCC----CcchHHHHHhh
Q psy6336 23 YLVPSDLTVGQFYFLIRKRVQLRPE----DALFFFVNNVIPP----TSATMGSLYQE 71 (73)
Q Consensus 23 fLVp~~~tv~qf~~~iRk~L~L~~~----~alfl~Vn~~lp~----~~~~m~~lY~~ 71 (73)
|-++.++|+.+|+..+.++-++... ..--|| +.+++. .+..|++|+++
T Consensus 916 ~~i~~~~Tl~~~i~~~~~~~~~~v~~is~g~~~lY-~~~~~~~~erl~~~l~el~~~ 971 (1008)
T TIGR01408 916 WTLHGDFTLLEFINAVKEKYGLEPTMVSQGVKLLY-VPVMPGHAERLKLKMHKLVKP 971 (1008)
T ss_pred EEecCCCcHHHHHHHHHHHhCCeeEEEEcCceEEE-eccchhhHHhcCCCHHHHHHH
Confidence 4588899999999999999876542 111122 222332 34578888875
No 117
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=21.18 E-value=83 Score=17.94 Aligned_cols=47 Identities=13% Similarity=0.161 Sum_probs=27.8
Q ss_pred cceeeeecCCCChhhHHHHHHhhh-cCCC-CCeEEEEEcCcCCCCcchH
Q psy6336 19 DKKKYLVPSDLTVGQFYFLIRKRV-QLRP-EDALFFFVNNVIPPTSATM 65 (73)
Q Consensus 19 dk~KfLVp~~~tv~qf~~~iRk~L-~L~~-~~alfl~Vn~~lp~~~~~m 65 (73)
+...+-+|...|++++...+..+- .+.. ..+.-+.||+...+.++.+
T Consensus 19 ~~~~~~~~~~~tv~~L~~~l~~~~p~l~~~~~~~~vavN~~~v~~~~~l 67 (82)
T PLN02799 19 SDMTLELPAGSTTADCLAELVAKFPSLEEVRSCCVLALNEEYTTESAAL 67 (82)
T ss_pred CeEEEECCCCCcHHHHHHHHHHHChhHHHHhhCcEEEECCEEcCCCcCc
Confidence 334556888999999988886543 1111 1234577887544444433
No 118
>KOG4250|consensus
Probab=21.18 E-value=1.5e+02 Score=24.92 Aligned_cols=38 Identities=18% Similarity=0.252 Sum_probs=34.8
Q ss_pred cceeeeecCCCChhhHHHHHHhhhcCCCCCeEEEEEcC
Q psy6336 19 DKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNN 56 (73)
Q Consensus 19 dk~KfLVp~~~tv~qf~~~iRk~L~L~~~~alfl~Vn~ 56 (73)
...+|.++.+.|..-|+.-|-+..+.+.+....||.|.
T Consensus 325 ~~~~~~~~~~ntl~~~~~~I~~~Tgipe~~qeLL~e~~ 362 (732)
T KOG4250|consen 325 TSHEYYVHADNTLHSLIERISKQTGIPEGKQELLFEGG 362 (732)
T ss_pred eEEEEecChhhhHHHHHHHHHHhhCCCCccceeeeecC
Confidence 45679999999999999999999999999999999986
No 119
>COG0278 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=20.86 E-value=60 Score=20.78 Aligned_cols=20 Identities=20% Similarity=0.381 Sum_probs=16.6
Q ss_pred EEEcCcCCCCcchHHHHHhh
Q psy6336 52 FFVNNVIPPTSATMGSLYQE 71 (73)
Q Consensus 52 l~Vn~~lp~~~~~m~~lY~~ 71 (73)
||||+.+.-.+..+.|+|+.
T Consensus 75 Lyi~GEfvGG~DIv~Em~q~ 94 (105)
T COG0278 75 LYVNGEFVGGCDIVREMYQS 94 (105)
T ss_pred eeECCEEeccHHHHHHHHHc
Confidence 67888888888888888874
No 120
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=20.44 E-value=1.1e+02 Score=15.02 Aligned_cols=19 Identities=26% Similarity=0.282 Sum_probs=15.8
Q ss_pred HHHHhhhcCCCCCeEEEEE
Q psy6336 36 FLIRKRVQLRPEDALFFFV 54 (73)
Q Consensus 36 ~~iRk~L~L~~~~alfl~V 54 (73)
.-+|+.|++.+++.+.+..
T Consensus 13 ~~~r~~l~~~~gd~~~i~~ 31 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIR 31 (43)
T ss_pred HHHHHHcCcCCCCEEEEEE
Confidence 3478999999999988874
Done!