Query 033214
Match_columns 125
No_of_seqs 105 out of 362
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 11:12:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033214.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033214hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1654 Microtubule-associated 100.0 4.9E-53 1.1E-57 297.0 12.1 116 3-118 1-116 (116)
2 cd01611 GABARAP Ubiquitin doma 100.0 1.8E-51 3.8E-56 292.0 13.5 112 7-118 1-112 (112)
3 PTZ00380 microtubule-associate 100.0 3.2E-50 6.9E-55 288.3 12.2 113 5-122 2-115 (121)
4 PF02991 Atg8: Autophagy prote 100.0 1.5E-48 3.2E-53 273.9 11.3 104 15-118 1-104 (104)
5 cd01612 APG12_C Ubiquitin-like 100.0 2.9E-33 6.3E-38 190.8 10.0 85 33-118 2-87 (87)
6 PF04110 APG12: Ubiquitin-like 99.9 1E-24 2.2E-29 148.7 6.5 83 35-118 4-87 (87)
7 KOG3439 Protein conjugation fa 99.9 2.8E-23 6.1E-28 146.4 9.4 85 33-118 31-116 (116)
8 PF04106 APG5: Autophagy prote 96.5 0.0092 2E-07 45.9 6.2 99 12-112 89-195 (197)
9 PF11816 DUF3337: Domain of un 95.5 0.12 2.6E-06 42.5 9.1 86 28-113 212-328 (331)
10 PF11976 Rad60-SLD: Ubiquitin- 92.8 0.29 6.3E-06 30.8 4.6 49 48-96 12-60 (72)
11 KOG2660 Locus-specific chromos 90.9 0.41 9E-06 39.9 4.5 73 42-115 159-235 (331)
12 cd06406 PB1_P67 A PB1 domain i 90.7 1.1 2.5E-05 30.1 5.8 55 52-109 16-75 (80)
13 PF13019 Telomere_Sde2: Telome 87.4 4.9 0.00011 30.4 7.8 79 31-112 1-82 (162)
14 smart00213 UBQ Ubiquitin homol 85.4 2.6 5.6E-05 25.1 4.6 46 49-95 12-57 (64)
15 KOG2976 Protein involved in au 84.0 15 0.00031 30.0 9.3 91 13-111 162-273 (278)
16 PF00240 ubiquitin: Ubiquitin 82.9 1.5 3.3E-05 27.1 2.8 46 50-96 9-54 (69)
17 cd05992 PB1 The PB1 domain is 82.0 10 0.00022 23.9 6.8 63 48-110 11-79 (81)
18 PF03671 Ufm1: Ubiquitin fold 80.3 7 0.00015 26.0 5.3 59 44-102 13-71 (76)
19 smart00666 PB1 PB1 domain. Pho 79.0 14 0.0003 23.5 6.5 62 48-109 12-78 (81)
20 cd06398 PB1_Joka2 The PB1 doma 78.8 5.3 0.00011 27.2 4.5 52 48-99 11-72 (91)
21 cd00196 UBQ Ubiquitin-like pro 78.4 8.9 0.00019 20.9 5.3 39 46-85 7-45 (69)
22 cd01763 Sumo Small ubiquitin-r 78.2 11 0.00025 24.7 6.0 48 48-96 23-70 (87)
23 cd06396 PB1_NBR1 The PB1 domai 78.1 11 0.00023 25.4 5.8 62 47-111 10-78 (81)
24 cd06407 PB1_NLP A PB1 domain i 77.6 16 0.00034 24.3 6.5 54 47-100 10-68 (82)
25 cd01813 UBP_N UBP ubiquitin pr 75.0 4.6 9.9E-05 26.1 3.3 45 52-96 15-61 (74)
26 cd01806 Nedd8 Nebb8-like ubiq 72.3 12 0.00026 23.1 4.7 57 51-112 15-72 (76)
27 cd01807 GDX_N ubiquitin-like d 70.1 7.9 0.00017 24.5 3.5 44 51-95 15-58 (74)
28 cd01769 UBL Ubiquitin-like dom 69.2 17 0.00036 21.7 4.8 57 50-111 11-68 (69)
29 PF10302 DUF2407: DUF2407 ubiq 69.1 26 0.00057 24.0 6.2 71 42-113 10-94 (97)
30 cd01798 parkin_N amino-termina 68.2 9.5 0.00021 23.7 3.6 55 51-109 13-67 (70)
31 cd01810 ISG15_repeat2 ISG15 ub 68.0 17 0.00036 23.0 4.7 58 51-112 13-70 (74)
32 PF00837 T4_deiodinase: Iodoth 67.0 9.4 0.0002 30.5 4.0 34 5-39 158-191 (237)
33 PF00788 RA: Ras association ( 66.8 30 0.00066 22.0 7.2 66 45-110 15-89 (93)
34 cd01790 Herp_N Homocysteine-re 65.9 36 0.00079 22.5 7.0 62 50-112 15-79 (79)
35 PF08154 NLE: NLE (NUC135) dom 64.7 32 0.0007 21.6 6.0 41 45-85 14-55 (65)
36 cd01805 RAD23_N Ubiquitin-like 63.5 16 0.00036 22.8 4.0 57 50-111 14-73 (77)
37 cd01803 Ubiquitin Ubiquitin. U 62.6 19 0.00041 22.3 4.2 59 50-112 14-72 (76)
38 PF00564 PB1: PB1 domain; Int 62.5 22 0.00047 22.5 4.5 52 51-102 16-71 (84)
39 PF14836 Ubiquitin_3: Ubiquiti 62.4 8.3 0.00018 26.3 2.6 47 52-98 19-71 (88)
40 PF12752 SUZ: SUZ domain; Int 61.8 9 0.0002 23.8 2.5 20 7-26 34-53 (59)
41 cd01776 Rin1_RA Ubiquitin doma 60.9 19 0.00042 24.6 4.1 42 50-91 17-62 (87)
42 cd01809 Scythe_N Ubiquitin-lik 60.2 25 0.00054 21.4 4.4 45 50-95 14-58 (72)
43 cd01799 Hoil1_N Ubiquitin-like 59.6 26 0.00057 22.6 4.5 57 50-109 16-72 (75)
44 PF14533 USP7_C2: Ubiquitin-sp 58.0 8 0.00017 29.8 2.1 51 46-96 33-90 (213)
45 cd01796 DDI1_N DNA damage indu 56.9 17 0.00036 23.0 3.2 56 51-110 14-70 (71)
46 cd01812 BAG1_N Ubiquitin-like 56.9 21 0.00045 21.8 3.6 44 51-95 14-57 (71)
47 PF12436 USP7_ICP0_bdg: ICP0-b 56.4 15 0.00032 29.0 3.4 61 50-113 88-153 (249)
48 cd01793 Fubi Fubi ubiquitin-li 55.6 33 0.00072 21.5 4.4 59 48-110 10-68 (74)
49 cd01808 hPLIC_N Ubiquitin-like 54.8 49 0.0011 20.5 5.6 58 50-111 13-70 (71)
50 cd01794 DC_UbP_C dendritic cel 52.6 33 0.00072 21.7 4.1 45 50-95 12-56 (70)
51 cd01791 Ubl5 UBL5 ubiquitin-li 51.2 32 0.00068 22.1 3.8 56 52-111 17-72 (73)
52 PTZ00044 ubiquitin; Provisiona 49.6 41 0.00089 20.9 4.1 57 50-111 14-71 (76)
53 cd01800 SF3a120_C Ubiquitin-li 45.2 41 0.00088 21.3 3.6 58 51-112 12-69 (76)
54 cd01804 midnolin_N Ubiquitin-l 44.1 82 0.0018 20.1 5.0 58 51-113 16-73 (78)
55 COG3343 RpoE DNA-directed RNA 42.8 30 0.00065 26.5 3.1 48 56-119 30-78 (175)
56 cd01792 ISG15_repeat1 ISG15 ub 42.5 36 0.00077 21.8 3.1 58 52-112 18-76 (80)
57 cd01795 USP48_C USP ubiquitin- 38.4 61 0.0013 22.9 3.8 24 52-75 20-43 (107)
58 TIGR00601 rad23 UV excision re 37.7 1.3E+02 0.0028 25.5 6.4 64 47-114 9-77 (378)
59 PF12436 USP7_ICP0_bdg: ICP0-b 36.9 63 0.0014 25.4 4.2 53 29-84 175-227 (249)
60 PF11767 SET_assoc: Histone ly 36.6 94 0.002 19.9 4.3 55 50-112 5-62 (66)
61 KOG1209 1-Acyl dihydroxyaceton 36.4 71 0.0015 26.0 4.4 52 46-101 54-110 (289)
62 PF09358 UBA_e1_C: Ubiquitin-a 34.7 40 0.00086 24.0 2.5 52 48-100 34-94 (125)
63 cd01815 BMSC_UbP_N Ubiquitin-l 34.7 83 0.0018 20.7 3.9 52 53-109 17-72 (75)
64 PRK13669 hypothetical protein; 33.9 36 0.00079 22.7 2.1 27 76-102 45-74 (78)
65 cd01768 RA RA (Ras-associating 33.9 97 0.0021 19.7 4.2 55 47-101 13-74 (87)
66 cd06408 PB1_NoxR The PB1 domai 33.0 63 0.0014 21.9 3.1 49 51-101 16-68 (86)
67 PF11543 UN_NPL4: Nuclear pore 32.8 44 0.00095 22.0 2.3 56 50-109 17-77 (80)
68 PF09379 FERM_N: FERM N-termin 31.8 88 0.0019 19.5 3.6 35 48-82 8-42 (80)
69 COG0669 CoaD Phosphopantethein 31.7 84 0.0018 23.8 3.9 95 8-107 43-146 (159)
70 PRK06437 hypothetical protein; 31.2 74 0.0016 20.0 3.1 38 51-93 15-52 (67)
71 cd01802 AN1_N ubiquitin-like d 31.0 93 0.002 21.3 3.8 58 51-112 42-99 (103)
72 cd01766 Ufm1 Urm1-like ubiquit 30.1 76 0.0016 21.3 3.1 58 44-102 13-71 (82)
73 PF14560 Ubiquitin_2: Ubiquiti 29.7 62 0.0013 21.0 2.7 33 49-81 16-49 (87)
74 cd00952 CHBPH_aldolase Trans-o 29.4 68 0.0015 25.9 3.4 29 11-39 58-86 (309)
75 PRK10953 cysJ sulfite reductas 29.0 3.8E+02 0.0082 24.0 8.2 88 27-115 432-523 (600)
76 PF06970 RepA_N: Replication i 28.8 25 0.00054 23.0 0.6 17 100-116 42-58 (76)
77 PF05717 TnpB_IS66: IS66 Orf2 28.8 78 0.0017 22.0 3.1 27 58-84 16-43 (107)
78 cd01775 CYR1_RA Ubiquitin doma 28.8 1.2E+02 0.0025 21.2 4.0 35 50-84 16-52 (97)
79 TIGR01682 moaD molybdopterin c 28.6 65 0.0014 20.5 2.6 38 50-87 19-59 (80)
80 TIGR02609 doc_partner putative 28.5 67 0.0015 20.6 2.6 21 64-84 16-36 (74)
81 PF01886 DUF61: Protein of unk 27.8 1.6E+02 0.0035 21.3 4.8 56 17-81 46-111 (132)
82 PF00255 GSHPx: Glutathione pe 27.4 76 0.0017 22.1 2.9 28 90-119 39-66 (108)
83 cd06411 PB1_p51 The PB1 domain 26.5 2E+02 0.0044 19.1 5.7 52 52-103 12-69 (78)
84 cd03483 MutL_Trans_MLH1 MutL_T 26.4 1.1E+02 0.0023 21.5 3.6 26 75-100 47-75 (127)
85 PF05768 DUF836: Glutaredoxin- 26.2 61 0.0013 20.7 2.1 18 21-38 40-57 (81)
86 PRK02363 DNA-directed RNA poly 25.4 69 0.0015 23.2 2.4 51 54-119 17-67 (129)
87 PF11470 TUG-UBL1: GLUT4 regul 25.4 1.4E+02 0.003 19.0 3.6 40 45-85 5-44 (65)
88 cd01797 NIRF_N amino-terminal 25.3 1.2E+02 0.0026 19.5 3.4 57 53-113 19-75 (78)
89 PRK00805 putative deoxyhypusin 25.2 1.3E+02 0.0029 25.1 4.4 101 13-119 156-270 (329)
90 cd00951 KDGDH 5-dehydro-4-deox 25.2 89 0.0019 24.9 3.3 99 10-114 49-161 (289)
91 cd00408 DHDPS-like Dihydrodipi 25.0 92 0.002 24.3 3.3 99 10-113 46-160 (281)
92 PF10336 DUF2420: Protein of u 24.6 2.2E+02 0.0048 19.8 4.9 63 56-118 10-98 (113)
93 smart00148 PLCXc Phospholipase 24.4 83 0.0018 22.4 2.7 43 55-97 67-110 (135)
94 TIGR00683 nanA N-acetylneurami 23.6 99 0.0022 24.7 3.3 30 10-39 50-79 (290)
95 TIGR02728 spore_gerQ spore coa 23.4 87 0.0019 21.1 2.4 33 87-119 2-34 (82)
96 PRK04115 hypothetical protein; 23.4 3.1E+02 0.0067 20.2 5.9 55 18-81 50-113 (137)
97 PF10137 TIR-like: Predicted n 23.2 1.4E+02 0.003 21.3 3.7 16 102-117 110-125 (125)
98 PRK13125 trpA tryptophan synth 23.1 79 0.0017 24.6 2.6 17 101-119 150-166 (244)
99 smart00314 RA Ras association 23.0 2.1E+02 0.0046 18.2 5.6 39 44-82 13-54 (90)
100 KOG3483 Uncharacterized conser 22.9 1.3E+02 0.0027 20.4 3.1 59 43-102 23-82 (94)
101 PRK08364 sulfur carrier protei 22.9 1E+02 0.0022 19.4 2.6 37 50-91 17-53 (70)
102 PF01704 UDPGP: UTP--glucose-1 22.7 1.9E+02 0.004 24.9 4.9 56 13-87 88-143 (420)
103 cd00137 PI-PLCc Catalytic doma 22.6 93 0.002 24.8 3.0 52 56-109 73-127 (274)
104 cd00754 MoaD Ubiquitin domain 22.3 81 0.0018 19.6 2.1 41 50-90 19-62 (80)
105 PRK03170 dihydrodipicolinate s 22.3 1.1E+02 0.0023 24.2 3.3 30 10-39 50-79 (292)
106 PF08825 E2_bind: E2 binding d 22.1 89 0.0019 20.8 2.3 44 53-96 3-59 (84)
107 PRK04147 N-acetylneuraminate l 21.8 1.1E+02 0.0024 24.3 3.2 30 10-39 53-82 (293)
108 KOG0010 Ubiquitin-like protein 21.8 1.3E+02 0.0029 26.6 3.9 53 48-105 26-78 (493)
109 cd06401 PB1_TFG The PB1 domain 21.8 2.1E+02 0.0045 19.3 4.0 22 50-71 13-35 (81)
110 PRK03620 5-dehydro-4-deoxygluc 21.6 1.2E+02 0.0025 24.5 3.3 29 10-38 56-84 (303)
111 PHA01078 putative upper collar 21.6 1.3E+02 0.0028 24.1 3.5 38 61-101 20-58 (249)
112 PF00701 DHDPS: Dihydrodipicol 21.5 95 0.0021 24.5 2.8 100 10-114 50-165 (289)
113 smart00295 B41 Band 4.1 homolo 21.4 2.2E+02 0.0048 20.4 4.6 50 48-97 15-70 (207)
114 COG2002 AbrB Regulators of sta 20.9 1.1E+02 0.0023 20.3 2.5 21 64-84 20-40 (89)
115 cd01789 Alp11_N Ubiquitin-like 20.8 2.1E+02 0.0046 18.5 3.9 33 52-84 18-51 (84)
116 PF14060 DUF4252: Domain of un 20.5 1.2E+02 0.0027 21.4 3.0 25 89-113 20-44 (155)
117 PF08216 CTNNBL: Catenin-beta- 20.0 99 0.0021 21.9 2.3 20 11-30 33-52 (108)
118 PF08469 NPHI_C: Nucleoside tr 20.0 72 0.0016 23.8 1.7 21 88-108 102-122 (148)
No 1
>KOG1654 consensus Microtubule-associated anchor protein involved in autophagy and membrane trafficking [Cytoskeleton]
Probab=100.00 E-value=4.9e-53 Score=297.01 Aligned_cols=116 Identities=55% Similarity=0.968 Sum_probs=113.9
Q ss_pred CCCCCcccCCHHHHHHHHHHHHhhCCCcccEEEEccCCCCCCCCccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEE
Q 033214 3 KMQSFKDEFTFEQRLEESREIIAKYPDRVPVIAERYSKADLPDMEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFV 82 (125)
Q Consensus 3 ~~~~fk~~~s~e~R~~e~~~~r~kyp~~ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~V 82 (125)
++++||++|||++|++|+.+||+|||+|||||||+.+++++|.|||+|||||.++|||||+.+|||||+|++++++||||
T Consensus 1 ~~~~FK~~~~fe~R~~E~~~Ir~kyP~riPVIvEk~~~~~lp~lDK~KyLVP~dltvgqfi~iIRkRiqL~~~kA~flfV 80 (116)
T KOG1654|consen 1 MKSSFKERHPFEKRKAEVRRIREKYPDRIPVIVEKAGKSQLPDLDKKKYLVPDDLTVGQFIKIIRKRIQLSPEKAFFLFV 80 (116)
T ss_pred CcchhhccCCHHHHHHHHHHHHHHCCCCCcEEEEecccccCcccccceeeccccccHHHHHHHHHHHhccChhHeEEEEE
Confidence 46799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCccCCccchHHHHHhHcCCCCceEEEEeccccccC
Q 033214 83 KDTLPQTATLMDSVYESFKDEDGFLYMCYSSEKTFG 118 (125)
Q Consensus 83 nn~lp~~~~~m~~lY~~~kd~DGfLyi~Ys~~~~fG 118 (125)
||.+|+++++|++||+++||+||||||+||+|+|||
T Consensus 81 n~~~p~ts~~ms~~Ye~~kdeDgFLYm~Ys~e~tfG 116 (116)
T KOG1654|consen 81 NNTSPPTSATMSALYEEEKDEDGFLYMTYSGENTFG 116 (116)
T ss_pred cCcCCcchhhHHHHHHhhcccCcEEEEEeccccccC
Confidence 999999999999999999999999999999999999
No 2
>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=1.8e-51 Score=292.01 Aligned_cols=112 Identities=60% Similarity=1.065 Sum_probs=111.1
Q ss_pred CcccCCHHHHHHHHHHHHhhCCCcccEEEEccCCCCCCCCccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCcc
Q 033214 7 FKDEFTFEQRLEESREIIAKYPDRVPVIAERYSKADLPDMEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTL 86 (125)
Q Consensus 7 fk~~~s~e~R~~e~~~~r~kyp~~ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~l 86 (125)
||++||||+|++|++++|+|||+|||||||+++++++|.|+++||+||+++||+||+.+||++|+|++++||||||||.+
T Consensus 1 fk~~~s~e~R~~e~~~ir~kyp~~iPVIvE~~~~~~~p~l~k~KflVp~~~tv~~f~~~irk~l~l~~~~slfl~Vn~~~ 80 (112)
T cd01611 1 FKERHPFEKRKAEVERIRAKYPDRIPVIVERYPKSDLPDLDKKKYLVPSDLTVGQFVYIIRKRIQLRPEKALFLFVNNSL 80 (112)
T ss_pred CccccCHHHHHHHHHHHHHHCCCceEEEEEEcCCCCcccccCceEEecCCCCHHHHHHHHHHHhCCCccceEEEEECCcc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccchHHHHHhHcCCCCceEEEEeccccccC
Q 033214 87 PQTATLMDSVYESFKDEDGFLYMCYSSEKTFG 118 (125)
Q Consensus 87 p~~~~~m~~lY~~~kd~DGfLyi~Ys~~~~fG 118 (125)
|++|++||+||++|||+||||||+||+++|||
T Consensus 81 p~~~~~~~~lY~~~kd~DGfLyl~Ys~~~tfG 112 (112)
T cd01611 81 PPTSATMSQLYEEHKDEDGFLYMTYSSEETFG 112 (112)
T ss_pred CCchhHHHHHHHHhCCCCCEEEEEEeccccCC
Confidence 99999999999999999999999999999999
No 3
>PTZ00380 microtubule-associated protein (MAP); Provisional
Probab=100.00 E-value=3.2e-50 Score=288.32 Aligned_cols=113 Identities=26% Similarity=0.447 Sum_probs=108.7
Q ss_pred CCCcccCCHHHHHHHHHHHHhhCCCcccEEEEccCCCCCCCCccceE-eecCCCchHhHHHHHhhhhCCCCCCeEEEEEc
Q 033214 5 QSFKDEFTFEQRLEESREIIAKYPDRVPVIAERYSKADLPDMEKKKF-LVPRDMSVGQFIHILSSRLHLTPGKALFVFVK 83 (125)
Q Consensus 5 ~~fk~~~s~e~R~~e~~~~r~kyp~~ipVIvE~~~~~~~p~L~k~Kf-lvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vn 83 (125)
++||++||||+|++|+++||+|||++||||||++++++ +++|| |||.|+||+||+++||+||+|++++ +|||||
T Consensus 2 ~~fK~~~s~e~R~~e~~~Ir~kyPdrIPVIvEk~~~s~----dK~KfllVP~d~tV~qF~~iIRkrl~l~~~k-~flfVn 76 (121)
T PTZ00380 2 SAYHSSNPVEARRAECARLQAKYPGHVAVVVEAAEKAG----SKVHFLALPRDATVAELEAAVRQALGTSAKK-VTLAIE 76 (121)
T ss_pred cchhhcCCHHHHHHHHHHHHHHCCCccEEEEeecCCCC----CceEEEEcCCCCcHHHHHHHHHHHcCCChhH-EEEEEC
Confidence 68999999999999999999999999999999999887 79999 6999999999999999999999999 999999
Q ss_pred CccCCccchHHHHHhHcCCCCceEEEEeccccccCCccc
Q 033214 84 DTLPQTATLMDSVYESFKDEDGFLYMCYSSEKTFGYERI 122 (125)
Q Consensus 84 n~lp~~~~~m~~lY~~~kd~DGfLyi~Ys~~~~fG~~~~ 122 (125)
|.+|+++++||+||++|||+||||||+||+++|||+.+.
T Consensus 77 n~lp~~s~~mg~lYe~~KDeDGFLYi~Ys~e~tFG~~~~ 115 (121)
T PTZ00380 77 GSTPAVTATVGDIADACKRDDGFLYVSVRTEQAMGAFAS 115 (121)
T ss_pred CccCCccchHHHHHHHhcCCCCeEEEEEccccccccchh
Confidence 999999999999999999999999999999999998543
No 4
>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=1.5e-48 Score=273.88 Aligned_cols=104 Identities=62% Similarity=1.107 Sum_probs=95.2
Q ss_pred HHHHHHHHHHhhCCCcccEEEEccCCCCCCCCccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHH
Q 033214 15 QRLEESREIIAKYPDRVPVIAERYSKADLPDMEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMD 94 (125)
Q Consensus 15 ~R~~e~~~~r~kyp~~ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~ 94 (125)
+|++|+++||+|||+|||||||+++++++|+|+++|||||.++||+||+.+||+||+|+++++|||||||.+|+++++||
T Consensus 1 ~R~~e~~~ir~kyP~~IPVIvEr~~~s~lp~ldk~KfLvp~~~tv~qf~~~ir~rl~l~~~~alfl~Vn~~lp~~s~tm~ 80 (104)
T PF02991_consen 1 ERKEESERIREKYPDKIPVIVERYPKSKLPDLDKKKFLVPKDLTVGQFVYIIRKRLQLSPEQALFLFVNNTLPSTSSTMG 80 (104)
T ss_dssp HHHHHHHHHHHHSTTEEEEEEEE-TTSSS---SSSEEEEETTSBHHHHHHHHHHHTT--TTS-EEEEBTTBESSTTSBHH
T ss_pred CcHHHHHHHHHHCCCccEEEEEEccCCChhhcCccEEEEcCCCchhhHHHHhhhhhcCCCCceEEEEEcCcccchhhHHH
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhHcCCCCceEEEEeccccccC
Q 033214 95 SVYESFKDEDGFLYMCYSSEKTFG 118 (125)
Q Consensus 95 ~lY~~~kd~DGfLyi~Ys~~~~fG 118 (125)
+||++|||+||||||+||++++||
T Consensus 81 elY~~~kdeDGFLY~~Ys~e~tFG 104 (104)
T PF02991_consen 81 ELYEKYKDEDGFLYMTYSSEETFG 104 (104)
T ss_dssp HHHHHHB-TTSSEEEEEESSSSBC
T ss_pred HHHHHhCCCCCeEEEEeccccccC
Confidence 999999999999999999999999
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=100.00 E-value=2.9e-33 Score=190.79 Aligned_cols=85 Identities=24% Similarity=0.448 Sum_probs=79.8
Q ss_pred EEEEccCCCCCCCCccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcC-ccCCccchHHHHHhHcCCCCceEEEEe
Q 033214 33 VIAERYSKADLPDMEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKD-TLPQTATLMDSVYESFKDEDGFLYMCY 111 (125)
Q Consensus 33 VIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn-~lp~~~~~m~~lY~~~kd~DGfLyi~Y 111 (125)
|.|--.+.+++|.|+++||+||+++||++|+.+||+||++++++|+|||||| ++|++|++||+||++| ++||||||+|
T Consensus 2 v~i~~~~~g~~p~l~k~kflv~~~~tv~~~~~~lrk~L~l~~~~slflyvnn~f~p~~d~~~g~LY~~~-~~dGfLyi~Y 80 (87)
T cd01612 2 VTIRFKPIGSAPILKQKVFKISATQSFQAVIDFLRKRLKLKASDSLFLYINNSFAPSPDENVGNLYRCF-GTNGELIVSY 80 (87)
T ss_pred eEEEEEECCCCccccccEEEeCCCCCHHHHHHHHHHHhCCCccCeEEEEECCccCCCchhHHHHHHHhc-CCCCEEEEEE
Confidence 4454456689999999999999999999999999999999999999999999 6999999999999999 8999999999
Q ss_pred ccccccC
Q 033214 112 SSEKTFG 118 (125)
Q Consensus 112 s~~~~fG 118 (125)
|.++|||
T Consensus 81 s~~~afG 87 (87)
T cd01612 81 CKTVAFG 87 (87)
T ss_pred eCccccC
Confidence 9999999
No 6
>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=99.91 E-value=1e-24 Score=148.74 Aligned_cols=83 Identities=23% Similarity=0.496 Sum_probs=60.3
Q ss_pred EEccCCCCCCCCccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcC-ccCCccchHHHHHhHcCCCCceEEEEecc
Q 033214 35 AERYSKADLPDMEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKD-TLPQTATLMDSVYESFKDEDGFLYMCYSS 113 (125)
Q Consensus 35 vE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn-~lp~~~~~m~~lY~~~kd~DGfLyi~Ys~ 113 (125)
|--.+-+++|.|+++||.|.++.|++.++.+|||+|+++++++||+|||| |.|++|+++|+||++|+ .||.|.|+||.
T Consensus 4 v~fk~iG~aPilk~~k~kI~~~~~f~~vi~fLrk~Lk~~~~~slFlYin~sFaPspDe~vg~L~~~f~-~~~~Liv~Ys~ 82 (87)
T PF04110_consen 4 VRFKAIGSAPILKQKKFKISASQTFATVIAFLRKKLKLKPSDSLFLYINNSFAPSPDETVGDLYRCFG-TNGELIVSYSK 82 (87)
T ss_dssp EEEEEETT----S--EEEEETTSBTHHHHHHHHHHCT----SS-EEEEEEEE---TTSBHHHHHHHH--BTTBEEEEEES
T ss_pred EEEEecCCCccccCcEEEECCCCchHHHHHHHHHHhCCccCCeEEEEEcCccCCCchhHHHHHHHHhC-CCCEEEEEEec
Confidence 33334478999999999999999999999999999999999999999999 99999999999999998 89999999999
Q ss_pred ccccC
Q 033214 114 EKTFG 118 (125)
Q Consensus 114 ~~~fG 118 (125)
++|||
T Consensus 83 t~A~G 87 (87)
T PF04110_consen 83 TPAWG 87 (87)
T ss_dssp SS---
T ss_pred ccccC
Confidence 99999
No 7
>KOG3439 consensus Protein conjugation factor involved in autophagy [Posttranslational modification, protein turnover, chaperones]
Probab=99.90 E-value=2.8e-23 Score=146.42 Aligned_cols=85 Identities=26% Similarity=0.466 Sum_probs=79.0
Q ss_pred EEEEccCCCCCCCCccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcC-ccCCccchHHHHHhHcCCCCceEEEEe
Q 033214 33 VIAERYSKADLPDMEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKD-TLPQTATLMDSVYESFKDEDGFLYMCY 111 (125)
Q Consensus 33 VIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn-~lp~~~~~m~~lY~~~kd~DGfLyi~Y 111 (125)
|.|.-.+-+++|.|+++||.|+.+.||+.++.+|||+|+|++.++||||||| |+|++|+.+|+||+||+ .||.|.++|
T Consensus 31 V~i~l~aiG~~PilK~~k~~i~~t~tfa~vi~Flkk~Lkl~as~slflYVN~sFAPsPDq~v~~Ly~cf~-~d~~Lvl~Y 109 (116)
T KOG3439|consen 31 VQIRLRAIGDAPILKKSKFKINPTQTFAKVILFLKKFLKLQASDSLFLYVNNSFAPSPDQIVGNLYECFG-TDGKLVLNY 109 (116)
T ss_pred EEEEEeccCCCcceecceEEeCcchhhHHHHHHHHHHhCCcccCeEEEEEcCccCCCchhHHHHHHHhcC-CCCEEEEEE
Confidence 4443334578999999999999999999999999999999999999999999 99999999999999996 899999999
Q ss_pred ccccccC
Q 033214 112 SSEKTFG 118 (125)
Q Consensus 112 s~~~~fG 118 (125)
|...|||
T Consensus 110 c~s~A~G 116 (116)
T KOG3439|consen 110 CISVAWG 116 (116)
T ss_pred eeecccC
Confidence 9999999
No 8
>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=96.48 E-value=0.0092 Score=45.89 Aligned_cols=99 Identities=15% Similarity=0.191 Sum_probs=47.6
Q ss_pred CHHHHHHHHHHHH---hhCCCcccEEEEccCCCCCCCCccceEeec---CCCchHhHHHHHhhhh--CCCCCCeEEEEEc
Q 033214 12 TFEQRLEESREII---AKYPDRVPVIAERYSKADLPDMEKKKFLVP---RDMSVGQFIHILSSRL--HLTPGKALFVFVK 83 (125)
Q Consensus 12 s~e~R~~e~~~~r---~kyp~~ipVIvE~~~~~~~p~L~k~Kflvp---~~~tv~~~~~~lRk~L--~l~~~~slfl~Vn 83 (125)
.|++=..-..++. ..-..+|||.|-.... .|.++..--.+. ...|++++...+=--+ .-+......++++
T Consensus 89 ~~~~f~~i~~kl~~~~~~~~r~IPiRiy~~~~--~~~iQ~~i~~~~~~g~~~TL~d~L~~~lp~~f~s~~~~~~~~~iih 166 (197)
T PF04106_consen 89 DFDQFWSINSKLMPPDPSKFRHIPIRIYLPGS--VPVIQPPIPPIKEDGQPQTLGDALSELLPELFPSSDEPELARVIIH 166 (197)
T ss_dssp -HHHHHHHHHHHS----SS-SB--EEEEE-SS----EE----B----TT---BTGGGHHHHHTTT--T------EEEEET
T ss_pred CHHHHHHHHHHHHhhcCCCcceeEEEEEeCCC--cceEecccccccCCCCcCcHHHHHHHhChhhcccccCccccEEEEe
Confidence 3443334445555 5666899999977543 333333222221 2246666544332111 0123455677888
Q ss_pred CccCCccchHHHHHhHcCCCCceEEEEec
Q 033214 84 DTLPQTATLMDSVYESFKDEDGFLYMCYS 112 (125)
Q Consensus 84 n~lp~~~~~m~~lY~~~kd~DGfLyi~Ys 112 (125)
+..++.|+.|..||+.+.-.||||||.-.
T Consensus 167 GI~ipldtpl~~l~~~l~~~D~FLhivv~ 195 (197)
T PF04106_consen 167 GIEIPLDTPLQWLYENLSYPDGFLHIVVR 195 (197)
T ss_dssp TEEE-TTSBHHHHHHHH--TTS-EEEEEE
T ss_pred CeeCCCCCcHHHHHHHccCCCCeEEEEEE
Confidence 87778899999999999999999999753
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=95.54 E-value=0.12 Score=42.53 Aligned_cols=86 Identities=14% Similarity=0.327 Sum_probs=69.9
Q ss_pred CCcccEEEEccCCCCCCCCccc-----------------eEeecCCCchHhHHHHHhhhh--------------CCCCCC
Q 033214 28 PDRVPVIAERYSKADLPDMEKK-----------------KFLVPRDMSVGQFIHILSSRL--------------HLTPGK 76 (125)
Q Consensus 28 p~~ipVIvE~~~~~~~p~L~k~-----------------Kflvp~~~tv~~~~~~lRk~L--------------~l~~~~ 76 (125)
+.+|+-++.++..+..|.+..- |.--+.-+.|..+..+|-.|+ .+.+++
T Consensus 212 ~~Ki~F~L~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rL~A~~mLrvkKI~~yV~ek~~~~~~~~~~~~~~~~~~p~e 291 (331)
T PF11816_consen 212 PPKISFVLQPWDGSLPPNLKPDGKSQKKIKLPPLSEGNSRLNAPRMLRVKKILEYVAEKLEKTPESKTPEMKPKKLKPEE 291 (331)
T ss_pred CCeeEEEEeecCCCCccccCCCccccccccccccccccceecccchhhhHHHHHHHHHHhccCccccCccccccCCCCCc
Confidence 4677778888875545555544 777888889999999999999 457789
Q ss_pred eEEEEEcCccCCccchHHHHHhHcCCCCceEEEEecc
Q 033214 77 ALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMCYSS 113 (125)
Q Consensus 77 slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Ys~ 113 (125)
.|=|+||+.+.++++||+.|=.-+=-..|-|.+.|..
T Consensus 292 ~lEl~C~gqvL~~~mtLaTVr~~~WK~~~di~L~YR~ 328 (331)
T PF11816_consen 292 WLELLCNGQVLPPDMTLATVRTFIWKSSGDIVLHYRR 328 (331)
T ss_pred eEEEEeCCeEcCCcCCHHHHHHhhccCCCeEEEEEEe
Confidence 9999999999999999999988854468899999964
No 10
>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=92.83 E-value=0.29 Score=30.81 Aligned_cols=49 Identities=12% Similarity=0.218 Sum_probs=39.6
Q ss_pred cceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHH
Q 033214 48 KKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSV 96 (125)
Q Consensus 48 k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~l 96 (125)
...|.|..+.+++.++..++++.++++.+++-|+.++....++.|++++
T Consensus 12 ~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~~L~~~~T~~~~ 60 (72)
T PF11976_consen 12 EIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFDGKRLDPNDTPEDL 60 (72)
T ss_dssp EEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEETTEEE-TTSCHHHH
T ss_pred EEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEECCEEcCCCCCHHHC
Confidence 5578899999999999999999999986677777887656666777765
No 11
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=90.89 E-value=0.41 Score=39.88 Aligned_cols=73 Identities=15% Similarity=0.286 Sum_probs=60.1
Q ss_pred CCCCCccceEe-ecCCCchHhHHHHHhhhhC-CCCCCeEEEEEcCccCCccchHHHHHhHcCC--CCceEEEEecccc
Q 033214 42 DLPDMEKKKFL-VPRDMSVGQFIHILSSRLH-LTPGKALFVFVKDTLPQTATLMDSVYESFKD--EDGFLYMCYSSEK 115 (125)
Q Consensus 42 ~~p~L~k~Kfl-vp~~~tv~~~~~~lRk~L~-l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd--~DGfLyi~Ys~~~ 115 (125)
.++.|. ++|+ ++...|+.++..++++++. ++..-.+=+++|+.+..-+.||.++.-.+.. .||-|-+.|...+
T Consensus 159 ~~k~l~-~~fvrcsa~~Tv~hlkkfl~~k~~~~~~~~~idi~~~d~~l~~~~TLk~i~~~~~~~~r~~pL~l~y~v~p 235 (331)
T KOG2660|consen 159 TLKDLV-RRFLRCSAAATVNHLKKFLRKKMDNLSNKSEIDILCEEELLGDYYTLKDIAYAYRWRSRDPPLPLRYRVKP 235 (331)
T ss_pred cccccc-cceEeccHHHHHHHHHHHHHHHhccccchhhheeecCCccccchhhhhhhhhhhcccccCCcceeEecccc
Confidence 355555 6787 8999999999999999999 6666667788888888999999999887766 4999999998443
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=90.71 E-value=1.1 Score=30.09 Aligned_cols=55 Identities=27% Similarity=0.404 Sum_probs=42.4
Q ss_pred eecCCCchHhHHHHHhhhhCCCCCCeEEEEEcC-----ccCCccchHHHHHhHcCCCCceEEE
Q 033214 52 LVPRDMSVGQFIHILSSRLHLTPGKALFVFVKD-----TLPQTATLMDSVYESFKDEDGFLYM 109 (125)
Q Consensus 52 lvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn-----~lp~~~~~m~~lY~~~kd~DGfLyi 109 (125)
-||.+++++++...|++||++++ +.+.|.-.. ..|-.|+.|...+.+=+ ||-|-+
T Consensus 16 rvp~~~~y~~L~~ki~~kLkl~~-e~i~LsYkde~s~~~v~l~d~dle~aws~~~--~~~lTL 75 (80)
T cd06406 16 QVARGLSYATLLQKISSKLELPA-EHITLSYKSEASGEDVILSDTNMEDVWSQAK--DGCLTL 75 (80)
T ss_pred EcCCCCCHHHHHHHHHHHhCCCc-hhcEEEeccCCCCCccCcChHHHHHHHHhhc--CCeEEE
Confidence 48999999999999999999985 457775442 45567888998888876 665543
No 13
>PF13019 Telomere_Sde2: Telomere stability and silencing
Probab=87.37 E-value=4.9 Score=30.42 Aligned_cols=79 Identities=22% Similarity=0.411 Sum_probs=55.0
Q ss_pred ccEEEEccCCCCCCCCccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEc-C-cc-CCccchHHHHHhHcCCCCceE
Q 033214 31 VPVIAERYSKADLPDMEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVK-D-TL-PQTATLMDSVYESFKDEDGFL 107 (125)
Q Consensus 31 ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vn-n-~l-p~~~~~m~~lY~~~kd~DGfL 107 (125)
|-|+|...+.-.+| ....+-+|.+.|++++...|..++.......++|+++ | .+ +..+..++.+...-.+. +|+
T Consensus 1 i~Vlvss~~g~~lp--~tl~~~lp~~ttv~dL~~~l~~~~~~~~~~~~~L~~~~n~~l~~~~~~~~s~l~~~~~~~-~~~ 77 (162)
T PF13019_consen 1 INVLVSSFDGLTLP--PTLSLSLPSTTTVSDLKDRLSERLPIPSSSQLYLTTNSNGQLSPSSDIPLSSLLSSSQDS-DFI 77 (162)
T ss_pred CeEEEecCCCCCCC--CeEEeeCCCCCcHHHHHHHHHhhcCCCccceeEEEEeCCCeeCCCccccHHhhccCcCCC-Cce
Confidence 34666554332221 2335669999999999999999999988877888876 4 44 46677888888776543 676
Q ss_pred EEEec
Q 033214 108 YMCYS 112 (125)
Q Consensus 108 yi~Ys 112 (125)
.+...
T Consensus 78 ~l~l~ 82 (162)
T PF13019_consen 78 TLRLS 82 (162)
T ss_pred EEEEE
Confidence 66553
No 14
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=85.45 E-value=2.6 Score=25.10 Aligned_cols=46 Identities=7% Similarity=0.042 Sum_probs=34.7
Q ss_pred ceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHH
Q 033214 49 KKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDS 95 (125)
Q Consensus 49 ~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~ 95 (125)
..+-|+.+.|++++...|.++.++++.. +-|+.++.....+.+|++
T Consensus 12 ~~~~v~~~~tv~~lk~~i~~~~~~~~~~-~~L~~~g~~L~d~~tL~~ 57 (64)
T smart00213 12 ITLEVKPSDTVSELKEKIAELTGIPVEQ-QRLIYKGKVLEDDRTLAD 57 (64)
T ss_pred EEEEECCCCcHHHHHHHHHHHHCCCHHH-EEEEECCEECCCCCCHHH
Confidence 3466999999999999999999998753 555566655555666654
No 15
>KOG2976 consensus Protein involved in autophagy and nutrient starvation [Posttranslational modification, protein turnover, chaperones]
Probab=83.96 E-value=15 Score=30.03 Aligned_cols=91 Identities=20% Similarity=0.285 Sum_probs=55.1
Q ss_pred HHHHHHHHHHHHhh----CCCcccEEEEcc--C-------CCCCCCCccceEeecCCCchHhHHHHHhhhhC--CCC---
Q 033214 13 FEQRLEESREIIAK----YPDRVPVIAERY--S-------KADLPDMEKKKFLVPRDMSVGQFIHILSSRLH--LTP--- 74 (125)
Q Consensus 13 ~e~R~~e~~~~r~k----yp~~ipVIvE~~--~-------~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~L~--l~~--- 74 (125)
|++=..-+.++..- .+-+||+.+... + +...|. .-.+|-+.+.+-.+|.+++. +++
T Consensus 162 fd~F~~Is~Kl~~s~e~n~~r~IPL~iy~sq~~t~r~f~~~~~~P~------~~~~d~~~stlge~l~d~~~~s~~s~d~ 235 (278)
T KOG2976|consen 162 FDDFWEISNKLMESVEDNRSRHIPLRIYTSQVKTARDFRTSLTFPC------ISQPDGSLSTLGEFLKDRLPDSLDSKDD 235 (278)
T ss_pred HHHHHHHHHHHHhhccccccccceeEeeccccccccchhhccccce------eecCchhhhhhhHHHHhhcccccCcccc
Confidence 34333444444444 788999999743 1 122331 11234445555556677775 221
Q ss_pred ---CCeEEEEEcCccCCccchHHHHHhHcCCCCceEEEEe
Q 033214 75 ---GKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMCY 111 (125)
Q Consensus 75 ---~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Y 111 (125)
.+. +.+.+--++..+.+..||......||||||+.
T Consensus 236 ~~~~~~--viihGIei~l~tpL~~l~~~L~ypD~FLHI~l 273 (278)
T KOG2976|consen 236 INGNDP--VIIHGIEIPLHTPLYWLYSNLSYPDGFLHIVL 273 (278)
T ss_pred ccccCc--eEEecccccccchHHHHHhhccCCCcceEEEE
Confidence 222 44445456778899999999999999999975
No 16
>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=82.89 E-value=1.5 Score=27.06 Aligned_cols=46 Identities=9% Similarity=0.118 Sum_probs=37.2
Q ss_pred eEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHH
Q 033214 50 KFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSV 96 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~l 96 (125)
.+-|+.+.||+++...|-.+.++++++ +-|+.++.....+.+|+++
T Consensus 9 ~~~v~~~~tV~~lK~~i~~~~~~~~~~-~~L~~~G~~L~d~~tL~~~ 54 (69)
T PF00240_consen 9 TLEVDPDDTVADLKQKIAEETGIPPEQ-QRLIYNGKELDDDKTLSDY 54 (69)
T ss_dssp EEEEETTSBHHHHHHHHHHHHTSTGGG-EEEEETTEEESTTSBTGGG
T ss_pred EEEECCCCCHHHhhhhccccccccccc-ceeeeeeecccCcCcHHHc
Confidence 456999999999999999999998865 5666677655777888765
No 17
>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=82.00 E-value=10 Score=23.90 Aligned_cols=63 Identities=11% Similarity=0.174 Sum_probs=46.8
Q ss_pred cceEeec-CCCchHhHHHHHhhhhCCCCCCeEEEEEcC---c-cCCccchHHHHHhHcCC-CCceEEEE
Q 033214 48 KKKFLVP-RDMSVGQFIHILSSRLHLTPGKALFVFVKD---T-LPQTATLMDSVYESFKD-EDGFLYMC 110 (125)
Q Consensus 48 k~Kflvp-~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn---~-lp~~~~~m~~lY~~~kd-~DGfLyi~ 110 (125)
...|.++ .+.++.+|...|++++++....-.+-|.++ . ....|..|...++.++. .++.|.|.
T Consensus 11 ~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~sd~Dl~~a~~~~~~~~~~~l~l~ 79 (81)
T cd05992 11 IRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSDEDLEEAIEEARRSGSKKLRLF 79 (81)
T ss_pred CEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCCHHHHHHHHHHHhhcCCccEEEE
Confidence 4567788 999999999999999998764445556663 2 34677888888888864 46666554
No 18
>PF03671 Ufm1: Ubiquitin fold modifier 1 protein; InterPro: IPR005375 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-like molecules (UBLs) can be divided into two subclasses: type-1 UBLs, which ligate to target proteins in a manner similar, but not identical, to the ubiquitylation pathway, such as SUMO, NEDD8, and UCRP/ISG15, and type-2 UBLs (also called UDPs, ubiquitin-domain proteins), which contain ubiquitin-like structure embedded in a variety of different classes of large proteins with apparently distinct functions, such as Rad23, Elongin B, Scythe, Parkin, and HOIL-1. This entry represents Ufm1 (ubiquitin-fold modifier), which is a ubiquitin-like protein with structural similarities to ubiquitin [, ]. Ufm1 is one of a number of ubiquitin-like modifiers that conjugate to target proteins in cells through Uba5 (E1) and Ufc1 (E2). The Ufm1-system is conserved in metazoa and plants, suggesting it has a potential role in multicellular organisms []. Human Ufm1 is synthesized as a precursor consisting of 85 amino-acid residues. Prior to activation by Uba5, the extra amino acids at the C-terminal region of Ufm1 are removed to expose Gly, which is necessary for conjugation to target molecule(s). C-terminal processing of Ufm1 requires two specific cysteine peptidases (IPR012462 from INTERPRO): UfSP1 and UfSP2; both peptidases are also able to release Ufm1 from Ufm1-conjugated cellular proteins. UfSP2 is present in most, if not all, of multi-cellular organisms including plant, nematode, fly, and mammal, whereas UfSP1 is not present in plants and nematodes []. For further information on ubiquitin, please see Protein of the Month [].; PDB: 1J0G_A 1WXS_A 1L7Y_A.
Probab=80.29 E-value=7 Score=25.99 Aligned_cols=59 Identities=10% Similarity=0.210 Sum_probs=44.1
Q ss_pred CCCccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCC
Q 033214 44 PDMEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKD 102 (125)
Q Consensus 44 p~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd 102 (125)
|.+.-+.+-||++..+.-++.+--...++++.++.-+--+..-..+.++-|+++-+|..
T Consensus 13 p~~p~kv~sVPE~apftaVlkfaAeeF~vp~~tsaiItndG~GInP~QTag~vflKhGs 71 (76)
T PF03671_consen 13 PKLPYKVISVPEEAPFTAVLKFAAEEFKVPPATSAIITNDGVGINPQQTAGNVFLKHGS 71 (76)
T ss_dssp STS-EEEEEEETTSBHHHHHHHHHHHTTS-SSSEEEEESSS-EE-TTSBHHHHHHHT-S
T ss_pred CCCcceEEecCCCCchHHHHHHHHHHcCCCCceEEEEecCCcccccchhhhhhHhhcCc
Confidence 56677888899999999999999999999998884332223667888999999999964
No 19
>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=78.99 E-value=14 Score=23.47 Aligned_cols=62 Identities=15% Similarity=0.260 Sum_probs=45.6
Q ss_pred cceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcC----ccCCccchHHHHHhHcCCC-CceEEE
Q 033214 48 KKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKD----TLPQTATLMDSVYESFKDE-DGFLYM 109 (125)
Q Consensus 48 k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn----~lp~~~~~m~~lY~~~kd~-DGfLyi 109 (125)
...|.+|.+.|+.+|...|.+++++..+.-..-|.++ ...+.++.|....+.++.. .+.|-|
T Consensus 12 ~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~Dl~~a~~~~~~~~~~~l~l 78 (81)
T smart00666 12 TRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDEDLEEAIEEYDSLGSKKLRL 78 (81)
T ss_pred EEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHHHHHHHHHHHHHcCCceEEE
Confidence 4567899999999999999999998765555567764 2346777888888877643 344433
No 20
>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=78.80 E-value=5.3 Score=27.20 Aligned_cols=52 Identities=12% Similarity=0.264 Sum_probs=36.1
Q ss_pred cceEeecC-----CCchHhHHHHHhhhhCCCCCCeEEE-EEcC----ccCCccchHHHHHhH
Q 033214 48 KKKFLVPR-----DMSVGQFIHILSSRLHLTPGKALFV-FVKD----TLPQTATLMDSVYES 99 (125)
Q Consensus 48 k~Kflvp~-----~~tv~~~~~~lRk~L~l~~~~slfl-~Vnn----~lp~~~~~m~~lY~~ 99 (125)
..+|.+|. +.++.++...|++++++++...+-| |-+. .....|..+.+.-+.
T Consensus 11 ~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~ 72 (91)
T cd06398 11 LRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQY 72 (91)
T ss_pred EEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHH
Confidence 45778885 7999999999999999987444444 4442 233566666655555
No 21
>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=78.38 E-value=8.9 Score=20.93 Aligned_cols=39 Identities=23% Similarity=0.383 Sum_probs=30.4
Q ss_pred CccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCc
Q 033214 46 MEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDT 85 (125)
Q Consensus 46 L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~ 85 (125)
.....+.++.+.|++++...|..+.+..+ +...|+++..
T Consensus 7 ~~~~~~~~~~~~tv~~l~~~i~~~~~~~~-~~~~l~~~~~ 45 (69)
T cd00196 7 GKTVELLVPSGTTVADLKEKLAKKLGLPP-EQQRLLVNGK 45 (69)
T ss_pred CCEEEEEcCCCCcHHHHHHHHHHHHCcCh-HHeEEEECCe
Confidence 34566778899999999999999988554 4577777763
No 22
>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=78.18 E-value=11 Score=24.74 Aligned_cols=48 Identities=15% Similarity=0.241 Sum_probs=37.8
Q ss_pred cceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHH
Q 033214 48 KKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSV 96 (125)
Q Consensus 48 k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~l 96 (125)
...|.|..+.+++.++..+..+.++++++--|+| ++.....+.|+.++
T Consensus 23 ~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f-~G~~L~~~~T~~~l 70 (87)
T cd01763 23 EVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLF-DGQRIRDNQTPDDL 70 (87)
T ss_pred EEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEE-CCeECCCCCCHHHc
Confidence 4568899999999999999999999987655555 55545556777776
No 23
>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=78.05 E-value=11 Score=25.37 Aligned_cols=62 Identities=15% Similarity=0.241 Sum_probs=48.6
Q ss_pred ccceEeecC--CCchHhHHHHHhhhhCCCCCCeEEE-EEcC----ccCCccchHHHHHhHcCCCCceEEEEe
Q 033214 47 EKKKFLVPR--DMSVGQFIHILSSRLHLTPGKALFV-FVKD----TLPQTATLMDSVYESFKDEDGFLYMCY 111 (125)
Q Consensus 47 ~k~Kflvp~--~~tv~~~~~~lRk~L~l~~~~slfl-~Vnn----~lp~~~~~m~~lY~~~kd~DGfLyi~Y 111 (125)
+...|.+++ +.++.++...|+++.+++ ++=+ |+++ .+.+.++.+.+.++.+......|-|+-
T Consensus 10 d~~rf~~~~~~~~~~~~L~~ev~~rf~l~---~f~lKYlDde~e~v~lssd~eLeE~~rl~~~~~~~l~~~v 78 (81)
T cd06396 10 ESQSFLVSDSENTTWASVEAMVKVSFGLN---DIQIKYVDEENEEVSVNSQGEYEEALKSAVRQGNLLQMNV 78 (81)
T ss_pred eEEEEEecCCCCCCHHHHHHHHHHHhCCC---cceeEEEcCCCCEEEEEchhhHHHHHHHHHhCCCEEEEEE
Confidence 355789988 779999999999999999 3434 6663 577888899998888866666776654
No 24
>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=77.64 E-value=16 Score=24.32 Aligned_cols=54 Identities=17% Similarity=0.335 Sum_probs=39.7
Q ss_pred ccceEeecCCCchHhHHHHHhhhhCCCCCCeEEE-EEcC----ccCCccchHHHHHhHc
Q 033214 47 EKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFV-FVKD----TLPQTATLMDSVYESF 100 (125)
Q Consensus 47 ~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl-~Vnn----~lp~~~~~m~~lY~~~ 100 (125)
+...|-+|++.++.++...|++|+++.....+-| |.++ .+.+.|+-|.+..+-+
T Consensus 10 d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~eai~i~ 68 (82)
T cd06407 10 EKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEECIDVY 68 (82)
T ss_pred eEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHHHHHHH
Confidence 3457889999999999999999999976445555 6664 4557777776644444
No 25
>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=74.97 E-value=4.6 Score=26.06 Aligned_cols=45 Identities=9% Similarity=0.115 Sum_probs=36.7
Q ss_pred eecCCCchHhHHHHHhhhhCCCCCCeEEEE--EcCccCCccchHHHH
Q 033214 52 LVPRDMSVGQFIHILSSRLHLTPGKALFVF--VKDTLPQTATLMDSV 96 (125)
Q Consensus 52 lvp~~~tv~~~~~~lRk~L~l~~~~slfl~--Vnn~lp~~~~~m~~l 96 (125)
=|+.+.|+++|...|-.+.+++++.-=.+| +...++..+.+++++
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 388999999999999999999987666666 445677778888876
No 26
>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=72.26 E-value=12 Score=23.15 Aligned_cols=57 Identities=11% Similarity=0.115 Sum_probs=40.9
Q ss_pred EeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCc-eEEEEec
Q 033214 51 FLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDG-FLYMCYS 112 (125)
Q Consensus 51 flvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DG-fLyi~Ys 112 (125)
+-|+.+.||+++...|..+.+++++.--++ .++.....+.++++. .-.|| .|++...
T Consensus 15 ~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~-~~g~~L~d~~tl~~~----~i~~g~~i~l~~~ 72 (76)
T cd01806 15 IDIEPTDKVERIKERVEEKEGIPPQQQRLI-YSGKQMNDDKTAADY----KLEGGSVLHLVLA 72 (76)
T ss_pred EEECCCCCHHHHHHHHhHhhCCChhhEEEE-ECCeEccCCCCHHHc----CCCCCCEEEEEEE
Confidence 569999999999999999999988764444 566555666777663 33344 7777654
No 27
>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=70.06 E-value=7.9 Score=24.47 Aligned_cols=44 Identities=14% Similarity=0.189 Sum_probs=34.4
Q ss_pred EeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHH
Q 033214 51 FLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDS 95 (125)
Q Consensus 51 flvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~ 95 (125)
+-|+.+.||+++...|..+-++++++ .-|+.++.....+.++++
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 45889999999999999999998754 556677766666677754
No 28
>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=69.22 E-value=17 Score=21.70 Aligned_cols=57 Identities=9% Similarity=0.175 Sum_probs=39.0
Q ss_pred eEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCC-CCceEEEEe
Q 033214 50 KFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKD-EDGFLYMCY 111 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd-~DGfLyi~Y 111 (125)
.+-++.+.|++++...|.++.+++++. +=|..++.....+.++++ +.- ++..+|+..
T Consensus 11 ~~~~~~~~ti~~lK~~i~~~~~~~~~~-~~l~~~g~~l~d~~~l~~----~~v~~~~~i~v~~ 68 (69)
T cd01769 11 ELEVSPDDTVAELKAKIAAKEGVPPEQ-QRLIYAGKILKDDKTLSD----YGIQDGSTLHLVL 68 (69)
T ss_pred EEEECCCChHHHHHHHHHHHHCcChHH-EEEEECCcCCCCcCCHHH----CCCCCCCEEEEEE
Confidence 456888999999999999999988764 344556654456667755 222 344666653
No 29
>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=69.06 E-value=26 Score=24.00 Aligned_cols=71 Identities=18% Similarity=0.240 Sum_probs=44.1
Q ss_pred CCCCCccceEeecCCCchHhHHHHHhhhh-CCCCCCeEEEEEcCccCCccchHHHHHhHc---------CCCCc----eE
Q 033214 42 DLPDMEKKKFLVPRDMSVGQFIHILSSRL-HLTPGKALFVFVKDTLPQTATLMDSVYESF---------KDEDG----FL 107 (125)
Q Consensus 42 ~~p~L~k~Kflvp~~~tv~~~~~~lRk~L-~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~---------kd~DG----fL 107 (125)
.+|+|.=. +--|.+.|+.++...||.++ .-.+...|=|.-++.+.+.++.++..-... |..++ -.
T Consensus 10 sipDl~L~-I~~~~~~Tv~~LK~lIR~~~p~~~s~~rLRlI~~Gr~L~d~t~l~~~l~~~~~~~~~~~gk~~~~~~~~~~ 88 (97)
T PF10302_consen 10 SIPDLPLD-IPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRLLNDHTDLSSELKLPTARSSKGKGKAPERQEAPRI 88 (97)
T ss_pred CCCCceee-cCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCcccCccchhhhhhccccccCccccCcCccCCCCCeE
Confidence 67774311 01458899999999999999 444455565555666555555555544444 22333 77
Q ss_pred EEEecc
Q 033214 108 YMCYSS 113 (125)
Q Consensus 108 yi~Ys~ 113 (125)
||+.+.
T Consensus 89 yIhCsI 94 (97)
T PF10302_consen 89 YIHCSI 94 (97)
T ss_pred EEEEec
Confidence 777653
No 30
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=68.18 E-value=9.5 Score=23.74 Aligned_cols=55 Identities=16% Similarity=0.214 Sum_probs=39.7
Q ss_pred EeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCceEEE
Q 033214 51 FLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYM 109 (125)
Q Consensus 51 flvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi 109 (125)
+-|.++.||+++...|-.+.++++++ .-|+.++.....+.++++ |.-. ++-.|++
T Consensus 13 ~~v~~~~tV~~lK~~i~~~~gi~~~~-q~Li~~G~~L~d~~~l~~-~~i~--~~stl~l 67 (70)
T cd01798 13 VEVDPDTDIKQLKEVVAKRQGVPPDQ-LRVIFAGKELRNTTTIQE-CDLG--QQSILHA 67 (70)
T ss_pred EEECCCChHHHHHHHHHHHHCCCHHH-eEEEECCeECCCCCcHHH-cCCC--CCCEEEE
Confidence 44889999999999999999997754 566667655567788887 4332 2335554
No 31
>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=68.03 E-value=17 Score=22.97 Aligned_cols=58 Identities=10% Similarity=0.156 Sum_probs=42.1
Q ss_pred EeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCceEEEEec
Q 033214 51 FLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMCYS 112 (125)
Q Consensus 51 flvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Ys 112 (125)
+-|..+.||+++...|-.+-++++++ .-|+.++.....+.++++ |.-. ++-.|++.-.
T Consensus 13 l~v~~~~tV~~lK~~I~~~~gi~~~~-q~L~~~G~~L~D~~tL~~-~~i~--~~~tl~l~~~ 70 (74)
T cd01810 13 YEVQLTQTVATLKQQVSQRERVQADQ-FWLSFEGRPMEDEHPLGE-YGLK--PGCTVFMNLR 70 (74)
T ss_pred EEECCcChHHHHHHHHHHHhCCCHHH-eEEEECCEECCCCCCHHH-cCCC--CCCEEEEEEE
Confidence 55889999999999999998887653 555667766677788887 4332 3447777643
No 32
>PF00837 T4_deiodinase: Iodothyronine deiodinase; InterPro: IPR000643 Iodothyronine deiodinase (1.97.1.10 from EC) (DI) [] is the vertebrate enzyme responsible for the deiodination of the prohormone thyroxine (T4 or 3,5,3',5'-tetraiodothyronine) into the biologically active hormone T3 (3,5,3'-triiodothyronine) and of T3 into the inactive metabolite T2 (3,3'-diiodothyronine). All known DI are proteins of about 250 residues that contain a selenocysteine at their active site. Three types of DI are known, type II is essential for providing the brain with the appropriate levels of T3 during the critical period of development, and type III is essential for the regulation of thyroid hormone inactivation during embryological development.; GO: 0004800 thyroxine 5'-deiodinase activity, 0055114 oxidation-reduction process
Probab=66.97 E-value=9.4 Score=30.55 Aligned_cols=34 Identities=15% Similarity=0.470 Sum_probs=29.9
Q ss_pred CCCcccCCHHHHHHHHHHHHhhCCCcccEEEEccC
Q 033214 5 QSFKDEFTFEQRLEESREIIAKYPDRVPVIAERYS 39 (125)
Q Consensus 5 ~~fk~~~s~e~R~~e~~~~r~kyp~~ipVIvE~~~ 39 (125)
..+++..|+|+|..-++.+++++| .+||+|-.-.
T Consensus 158 ~~i~qh~sledR~~aA~~l~~~~~-~~pi~vD~md 191 (237)
T PF00837_consen 158 YEIPQHRSLEDRLRAAKLLKEEFP-QCPIVVDTMD 191 (237)
T ss_pred eeecCCCCHHHHHHHHHHHHhhCC-CCCEEEEccC
Confidence 578899999999999999999997 5899997654
No 33
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=66.79 E-value=30 Score=22.00 Aligned_cols=66 Identities=6% Similarity=0.055 Sum_probs=45.3
Q ss_pred CCccceEeecCCCchHhHHHHHhhhhCCCCC-CeEEE--EEcC----ccCCccchHHHHHhHcCCC--CceEEEE
Q 033214 45 DMEKKKFLVPRDMSVGQFIHILSSRLHLTPG-KALFV--FVKD----TLPQTATLMDSVYESFKDE--DGFLYMC 110 (125)
Q Consensus 45 ~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~-~slfl--~Vnn----~lp~~~~~m~~lY~~~kd~--DGfLyi~ 110 (125)
...-+.+.|+.+.|+.+++..+-+++++..+ ....| +... ....+++..-.+....... ++.+++.
T Consensus 15 ~~~~k~i~v~~~tTa~evi~~~l~k~~l~~~~~~y~L~~~~~~~~~er~L~~~E~pl~i~~~~~~~~~~~~f~lr 89 (93)
T PF00788_consen 15 GSTYKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCLVEVEESGGEERPLDDDECPLQIQLQWPKDSQNSRFVLR 89 (93)
T ss_dssp CCSEEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEEEEEECTTTEEEEETTTSBHHHHHHTTSSGTTTEEEEEE
T ss_pred CccEEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEEEEEEcCCCEEEEcCCCCchHHHHHhCccccCceEEEEE
Confidence 3346778899999999999999999999433 33444 2332 3456677777777777553 6666654
No 34
>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=65.86 E-value=36 Score=22.54 Aligned_cols=62 Identities=13% Similarity=0.046 Sum_probs=41.7
Q ss_pred eEee--cCCCchHhHHHHHhhhhC-CCCCCeEEEEEcCccCCccchHHHHHhHcCCCCceEEEEec
Q 033214 50 KFLV--PRDMSVGQFIHILSSRLH-LTPGKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMCYS 112 (125)
Q Consensus 50 Kflv--p~~~tv~~~~~~lRk~L~-l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Ys 112 (125)
-|-| +.+.||+++...|....+ ..+.+..=|.-.+.+...+.+|++..+.-+ .+--+++.|+
T Consensus 15 ~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKiLkD~~tL~~~~~~~~-~~~tiHLV~~ 79 (79)
T cd01790 15 DQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRDVLRKQD-EYHMVHLVCA 79 (79)
T ss_pred EEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCeeccchhhHHHHhhccc-CCceEEEEeC
Confidence 3666 789999999999988774 332233334444556688899999987753 3445666553
No 35
>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=64.74 E-value=32 Score=21.57 Aligned_cols=41 Identities=7% Similarity=0.183 Sum_probs=34.2
Q ss_pred CCccceEeecCCCchHhHHHHHhhhh-CCCCCCeEEEEEcCc
Q 033214 45 DMEKKKFLVPRDMSVGQFIHILSSRL-HLTPGKALFVFVKDT 85 (125)
Q Consensus 45 ~L~k~Kflvp~~~tv~~~~~~lRk~L-~l~~~~slfl~Vnn~ 85 (125)
.+...-+.||.++|..++...|.+-| ........=++||+.
T Consensus 14 ~~~~~~~~VP~~~t~~~Ls~LvN~LL~~~~~~vpfdF~i~~~ 55 (65)
T PF08154_consen 14 EVPGTPISVPSNITRKELSELVNQLLDDEEEPVPFDFLINGE 55 (65)
T ss_pred cCCCCCEEEeCCCCHHHHHHHHHHHhccCCCCCcEEEEECCE
Confidence 45667899999999999999999999 666666777788874
No 36
>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=63.46 E-value=16 Score=22.82 Aligned_cols=57 Identities=14% Similarity=0.218 Sum_probs=39.0
Q ss_pred eEeecCCCchHhHHHHHhhhhCC--CCCCeEEEEEcCccCCccchHHHHHhHcCCC-CceEEEEe
Q 033214 50 KFLVPRDMSVGQFIHILSSRLHL--TPGKALFVFVKDTLPQTATLMDSVYESFKDE-DGFLYMCY 111 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~l--~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~-DGfLyi~Y 111 (125)
.+=|+.+.||+++...|..+.++ ++++ .-|..++.....+.++++ | +-. +..|++.-
T Consensus 14 ~l~v~~~~TV~~lK~~i~~~~~i~~~~~~-q~L~~~G~~L~d~~~L~~-~---~i~~~~~i~~~~ 73 (77)
T cd01805 14 PIEVDPDDTVAELKEKIEEEKGCDYPPEQ-QKLIYSGKILKDDTTLEE-Y---KIDEKDFVVVMV 73 (77)
T ss_pred EEEECCCCcHHHHHHHHHHhhCCCCChhH-eEEEECCEEccCCCCHHH-c---CCCCCCEEEEEE
Confidence 34588999999999999999888 6554 445556655566677776 3 333 33666643
No 37
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=62.60 E-value=19 Score=22.25 Aligned_cols=59 Identities=7% Similarity=0.125 Sum_probs=40.8
Q ss_pred eEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCceEEEEec
Q 033214 50 KFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMCYS 112 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Ys 112 (125)
.+-|+.+.||+++...|.++.+++++. .=|+.++.....+.++++ |.-. ++..+++...
T Consensus 14 ~~~v~~~~tV~~lK~~i~~~~g~~~~~-q~L~~~g~~L~d~~~L~~-~~i~--~~~~i~l~~~ 72 (76)
T cd01803 14 TLEVEPSDTIENVKAKIQDKEGIPPDQ-QRLIFAGKQLEDGRTLSD-YNIQ--KESTLHLVLR 72 (76)
T ss_pred EEEECCcCcHHHHHHHHHHHhCCCHHH-eEEEECCEECCCCCcHHH-cCCC--CCCEEEEEEE
Confidence 356999999999999999999987654 444467665566677766 3221 3446666654
No 38
>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=62.45 E-value=22 Score=22.54 Aligned_cols=52 Identities=12% Similarity=0.194 Sum_probs=42.8
Q ss_pred EeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcC----ccCCccchHHHHHhHcCC
Q 033214 51 FLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKD----TLPQTATLMDSVYESFKD 102 (125)
Q Consensus 51 flvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn----~lp~~~~~m~~lY~~~kd 102 (125)
+-++.+.++.+|...|++++++.+..-..-|.+. ...+.|..+.+..+.++.
T Consensus 16 ~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~~ 71 (84)
T PF00564_consen 16 ISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKDEDGDLVTISSDEDLQEAIEQAKE 71 (84)
T ss_dssp EEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEETTSSEEEESSHHHHHHHHHHHHH
T ss_pred EEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeCCCCCEEEeCCHHHHHHHHHHHHh
Confidence 6799999999999999999999877777778874 345778888888888764
No 39
>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A.
Probab=62.45 E-value=8.3 Score=26.35 Aligned_cols=47 Identities=9% Similarity=0.203 Sum_probs=30.6
Q ss_pred eecCCCchHhHHHHHhhhhCCCCCCeEEEEEc-C---ccCCccchHHH--HHh
Q 033214 52 LVPRDMSVGQFIHILSSRLHLTPGKALFVFVK-D---TLPQTATLMDS--VYE 98 (125)
Q Consensus 52 lvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vn-n---~lp~~~~~m~~--lY~ 98 (125)
..++..||+.+...+|+.+.++.+-.|+-+-+ | -|-.++.|+.+ ||+
T Consensus 19 ~FSk~DTI~~v~~~~rklf~i~~E~RLW~~~~~~~~e~L~~~~~Tv~da~L~~ 71 (88)
T PF14836_consen 19 QFSKTDTIGFVEKEMRKLFNIQEETRLWNKYSENSYELLNNPEITVEDAGLYD 71 (88)
T ss_dssp EE-TTSBHHHHHHHHHHHCT-TS-EEEEEECTTTCEEEE--TTSBTTTTT--T
T ss_pred hccccChHHHHHHHHHHHhCCCccceehhccCCcchhhhCCCCccHHHccCcC
Confidence 47889999999999999999977777777655 3 24466666655 554
No 40
>PF12752 SUZ: SUZ domain; InterPro: IPR024771 The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterised in the Caenorhabditis elegans protein SZY-20 where it has been shown to bind RNA and allow their localization to the centrosome [].
Probab=61.82 E-value=9 Score=23.81 Aligned_cols=20 Identities=25% Similarity=0.217 Sum_probs=16.9
Q ss_pred CcccCCHHHHHHHHHHHHhh
Q 033214 7 FKDEFTFEQRLEESREIIAK 26 (125)
Q Consensus 7 fk~~~s~e~R~~e~~~~r~k 26 (125)
=....|||+|.++++..|.+
T Consensus 34 ~~~~kSlEERE~eY~~AR~R 53 (59)
T PF12752_consen 34 KRPSKSLEEREAEYAEARAR 53 (59)
T ss_pred ccccCCHHHHHHHHHHHHHH
Confidence 35678999999999999874
No 41
>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=60.86 E-value=19 Score=24.55 Aligned_cols=42 Identities=19% Similarity=0.354 Sum_probs=33.3
Q ss_pred eEeecCCCchHhHHHHHhhhhCCC--CCCeEEEEEcC--ccCCccc
Q 033214 50 KFLVPRDMSVGQFIHILSSRLHLT--PGKALFVFVKD--TLPQTAT 91 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~l~--~~~slfl~Vnn--~lp~~~~ 91 (125)
--.|+++.|..++-...-.+.++. ..-+||+||++ +..++|+
T Consensus 17 TL~V~P~~tt~~vc~lcA~Kf~V~qPe~y~LFl~vdg~~~qLadd~ 62 (87)
T cd01776 17 TLLVRPYITTEDVCQLCAEKFKVTQPEEYSLFLFVEETWQQLAPDT 62 (87)
T ss_pred eeecCCCCcHHHHHHHHHHHhccCChhheeEEEEECCcEEEcCccc
Confidence 457999999999999999998874 46789999997 4444443
No 42
>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=60.19 E-value=25 Score=21.42 Aligned_cols=45 Identities=7% Similarity=0.152 Sum_probs=33.8
Q ss_pred eEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHH
Q 033214 50 KFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDS 95 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~ 95 (125)
.+-|+.+.||+++...|.++.+++++. .=|+.++.....+.++++
T Consensus 14 ~~~v~~~~tv~~lK~~i~~~~gi~~~~-q~L~~~g~~L~d~~~L~~ 58 (72)
T cd01809 14 TFTVEEEITVLDLKEKIAEEVGIPVEQ-QRLIYSGRVLKDDETLSE 58 (72)
T ss_pred EEEECCCCcHHHHHHHHHHHHCcCHHH-eEEEECCEECCCcCcHHH
Confidence 466889999999999999999987654 334446666666667765
No 43
>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=59.58 E-value=26 Score=22.59 Aligned_cols=57 Identities=14% Similarity=0.099 Sum_probs=37.2
Q ss_pred eEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCceEEE
Q 033214 50 KFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYM 109 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi 109 (125)
.+-|+++.||+++...|-.+-+++++. .-||-+..+-..+.+|++ |.-. +++-.||+
T Consensus 16 ~l~v~~~~TV~~lK~kI~~~~gip~~~-QrL~~G~~L~dD~~tL~~-ygi~-~~g~~~~l 72 (75)
T cd01799 16 WLTVRPDMTVAQLKDKVFLDYGFPPAV-QRWVIGQRLARDQETLYS-HGIR-TNGDSAFL 72 (75)
T ss_pred EEEECCCCcHHHHHHHHHHHHCcCHHH-EEEEcCCeeCCCcCCHHH-cCCC-CCCCEEEE
Confidence 356899999999999999999998753 333444454445567765 3322 23345554
No 44
>PF14533 USP7_C2: Ubiquitin-specific protease C-terminal; PDB: 2YLM_A.
Probab=57.97 E-value=8 Score=29.82 Aligned_cols=51 Identities=16% Similarity=0.328 Sum_probs=30.3
Q ss_pred CccceEeecCCCchHhHHHHHhhhhCCCCC--CeEEEE-EcC----ccCCccchHHHH
Q 033214 46 MEKKKFLVPRDMSVGQFIHILSSRLHLTPG--KALFVF-VKD----TLPQTATLMDSV 96 (125)
Q Consensus 46 L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~--~slfl~-Vnn----~lp~~~~~m~~l 96 (125)
-+.-.++||++-||+++...++++++++++ ..|-|+ |.+ ...+.+..+++|
T Consensus 33 ~~~~~~~vpk~~tV~Dll~~l~~k~~~~~~~~~~lrl~ev~~~ki~~~~~~d~~i~~l 90 (213)
T PF14533_consen 33 EQEYELLVPKTGTVSDLLEELQKKVGFSEEGTGKLRLWEVSNHKIYKILSEDEPISSL 90 (213)
T ss_dssp E-EEEE--BTT-BHHHHHHHHHTT----TT----EEEEEEETTEEEEEE-TTSBGGGS
T ss_pred eeEEEEEECCCCCHHHHHHHHHHHcCCCcCCcCcEEEEEeECCEEEeecCCCCchhhc
Confidence 356679999999999999999999998764 344443 433 356788888887
No 45
>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=56.89 E-value=17 Score=22.97 Aligned_cols=56 Identities=11% Similarity=0.180 Sum_probs=35.9
Q ss_pred EeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCcc-chHHHHHhHcCCCCceEEEE
Q 033214 51 FLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTA-TLMDSVYESFKDEDGFLYMC 110 (125)
Q Consensus 51 flvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~-~~m~~lY~~~kd~DGfLyi~ 110 (125)
.-|+++.||+++...|-.+-++++++ .-|+.++.....+ .++++ |. -+ ++.+|++.
T Consensus 14 l~v~~~~TV~~lK~~I~~~~gip~~~-q~Li~~Gk~L~D~~~~L~~-~g-i~-~~~~l~l~ 70 (71)
T cd01796 14 LDVDPDLELENFKALCEAESGIPASQ-QQLIYNGRELVDNKRLLAL-YG-VK-DGDLVVLR 70 (71)
T ss_pred EEECCcCCHHHHHHHHHHHhCCCHHH-eEEEECCeEccCCcccHHH-cC-CC-CCCEEEEe
Confidence 45889999999999999999998764 4444455433444 33433 32 21 45566653
No 46
>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=56.86 E-value=21 Score=21.84 Aligned_cols=44 Identities=14% Similarity=0.235 Sum_probs=31.3
Q ss_pred EeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHH
Q 033214 51 FLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDS 95 (125)
Q Consensus 51 flvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~ 95 (125)
+-|+.+.|++++...|..+-+++++. .-|+.+......+.++++
T Consensus 14 i~v~~~~tv~~lK~~i~~~~gi~~~~-q~L~~~g~~l~d~~~L~~ 57 (71)
T cd01812 14 LSISSQATFGDLKKMLAPVTGVEPRD-QKLIFKGKERDDAETLDM 57 (71)
T ss_pred EEECCCCcHHHHHHHHHHhhCCChHH-eEEeeCCcccCccCcHHH
Confidence 45889999999999999999988754 344455543444556544
No 47
>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=56.35 E-value=15 Score=29.04 Aligned_cols=61 Identities=11% Similarity=0.360 Sum_probs=36.7
Q ss_pred eEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEc---Cc--cCCccchHHHHHhHcCCCCceEEEEecc
Q 033214 50 KFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVK---DT--LPQTATLMDSVYESFKDEDGFLYMCYSS 113 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vn---n~--lp~~~~~m~~lY~~~kd~DGfLyi~Ys~ 113 (125)
.+.|+.+.+++++...|+++++++++..|-||-. +. ...++.++.+ .+-. ....|+.+-..
T Consensus 88 h~~v~~~~~v~~l~~~i~~~~g~p~~t~l~lyEEi~~~~ie~i~~~~t~~~--~el~-~GdIi~fQ~~~ 153 (249)
T PF12436_consen 88 HVYVPKNDKVSELVPLINERAGLPPDTPLLLYEEIKPNMIEPIDPNQTFEK--AELQ-DGDIICFQRAP 153 (249)
T ss_dssp EEEEETT-BGGGTHHHHHHHHT--TT--EEEEEEEETTEEEE--SSSBHHH--TT---TTEEEEEEE--
T ss_pred EEEECCCCCHHHHHHHHHHHcCCCCCCceEEEEEeccceeeEcCCCCchhh--cccC-CCCEEEEEecc
Confidence 4679999999999999999999999999998854 21 2266667766 2221 23366666544
No 48
>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=55.64 E-value=33 Score=21.54 Aligned_cols=59 Identities=7% Similarity=-0.016 Sum_probs=41.9
Q ss_pred cceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCceEEEE
Q 033214 48 KKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMC 110 (125)
Q Consensus 48 k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~ 110 (125)
...+-|.++.||+++...|-.+-++++++ .-|+.++.....+.++++ |.-. ++--|++.
T Consensus 10 ~~~l~v~~~~tV~~lK~~i~~~~gip~~~-q~Li~~Gk~L~D~~tL~~-~~i~--~~~tl~l~ 68 (74)
T cd01793 10 THTLEVTGQETVSDIKAHVAGLEGIDVED-QVLLLAGVPLEDDATLGQ-CGVE--ELCTLEVA 68 (74)
T ss_pred EEEEEECCcCcHHHHHHHHHhhhCCCHHH-EEEEECCeECCCCCCHHH-cCCC--CCCEEEEE
Confidence 34566899999999999999998887754 455566666677788877 4432 23355554
No 49
>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=54.80 E-value=49 Score=20.50 Aligned_cols=58 Identities=10% Similarity=0.197 Sum_probs=39.3
Q ss_pred eEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCceEEEEe
Q 033214 50 KFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMCY 111 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Y 111 (125)
.+-|..+.||+++...|..+.++++. .+-|..+......+.++++. . - .++..|+|.-
T Consensus 13 ~l~v~~~~TV~~lK~~I~~~~~i~~~-~~~Li~~Gk~L~d~~tL~~~-~-i-~~~stl~l~~ 70 (71)
T cd01808 13 EIEIAEDASVKDFKEAVSKKFKANQE-QLVLIFAGKILKDTDTLTQH-N-I-KDGLTVHLVI 70 (71)
T ss_pred EEEECCCChHHHHHHHHHHHhCCCHH-HEEEEECCeEcCCCCcHHHc-C-C-CCCCEEEEEE
Confidence 45688999999999999988887654 44554466555566677553 1 2 1455787753
No 50
>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=52.59 E-value=33 Score=21.68 Aligned_cols=45 Identities=22% Similarity=0.217 Sum_probs=34.3
Q ss_pred eEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHH
Q 033214 50 KFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDS 95 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~ 95 (125)
.+-|+++.||+++...|..+-++++++- -|+.+......+.++++
T Consensus 12 ~l~v~~~~TV~~lK~~I~~~~gi~~~~q-~Li~~G~~L~D~~~l~~ 56 (70)
T cd01794 12 KLSVSSKDTVGQLKKQLQAAEGVDPCCQ-RWFFSGKLLTDKTRLQE 56 (70)
T ss_pred EEEECCcChHHHHHHHHHHHhCCCHHHe-EEEECCeECCCCCCHHH
Confidence 3558889999999999999988887643 34455666677788877
No 51
>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=51.19 E-value=32 Score=22.09 Aligned_cols=56 Identities=16% Similarity=0.249 Sum_probs=37.7
Q ss_pred eecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCceEEEEe
Q 033214 52 LVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMCY 111 (125)
Q Consensus 52 lvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Y 111 (125)
-|+++.||+++...|-.+-+++++.--.+|. +.+...+.+|++ |. -+ ++--++|-|
T Consensus 17 ~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~-Gk~L~D~~tL~~-yg-i~-~~stv~l~~ 72 (73)
T cd01791 17 KCNPDDTIGDLKKLIAAQTGTRPEKIVLKKW-YTIFKDHISLGD-YE-IH-DGMNLELYY 72 (73)
T ss_pred EeCCCCcHHHHHHHHHHHhCCChHHEEEEeC-CcCCCCCCCHHH-cC-CC-CCCEEEEEe
Confidence 4889999999999998888888876555554 444555667766 32 22 334555555
No 52
>PTZ00044 ubiquitin; Provisional
Probab=49.55 E-value=41 Score=20.92 Aligned_cols=57 Identities=12% Similarity=0.070 Sum_probs=37.8
Q ss_pred eEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCC-CCceEEEEe
Q 033214 50 KFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKD-EDGFLYMCY 111 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd-~DGfLyi~Y 111 (125)
.+-|+++.||+++...|..+.++++++--.+ .++.....+.++++. .- ++-.|++.-
T Consensus 14 ~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~-~~g~~L~d~~~l~~~----~i~~~~~i~l~~ 71 (76)
T PTZ00044 14 SFNFEPDNTVQQVKMALQEKEGIDVKQIRLI-YSGKQMSDDLKLSDY----KVVPGSTIHMVL 71 (76)
T ss_pred EEEECCCCcHHHHHHHHHHHHCCCHHHeEEE-ECCEEccCCCcHHHc----CCCCCCEEEEEE
Confidence 4568999999999999999999987643333 455444566666432 22 233555543
No 53
>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=45.22 E-value=41 Score=21.33 Aligned_cols=58 Identities=7% Similarity=0.076 Sum_probs=39.7
Q ss_pred EeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCceEEEEec
Q 033214 51 FLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMCYS 112 (125)
Q Consensus 51 flvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Ys 112 (125)
+-|+.+.||++|...|....+++++. .=|..+......+.++++. . -+ ++..|+|.-.
T Consensus 12 l~v~~~~TV~~lK~~i~~~~gip~~~-q~L~~~G~~L~d~~tL~~~-~-i~-~g~~l~v~~~ 69 (76)
T cd01800 12 FTLQLSDPVSVLKVKIHEETGMPAGK-QKLQYEGIFIKDSNSLAYY-N-LA-NGTIIHLQLK 69 (76)
T ss_pred EEECCCCcHHHHHHHHHHHHCCCHHH-EEEEECCEEcCCCCcHHHc-C-CC-CCCEEEEEEe
Confidence 44889999999999999999988754 4445566655666777643 2 21 3447776654
No 54
>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=44.05 E-value=82 Score=20.09 Aligned_cols=58 Identities=17% Similarity=0.275 Sum_probs=39.0
Q ss_pred EeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCceEEEEecc
Q 033214 51 FLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMCYSS 113 (125)
Q Consensus 51 flvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Ys~ 113 (125)
.-|+.+.||+++...|..+.+++++. .-|..++.....+ ++++ | .- .++..||+.-+-
T Consensus 16 l~v~~~~TV~~LK~~I~~~~~~~~~~-qrL~~~Gk~L~d~-~L~~-~-gi-~~~~~i~l~~~~ 73 (78)
T cd01804 16 LSVPPDETVEGLKKRISQRLKVPKER-LALLHRETRLSSG-KLQD-L-GL-GDGSKLTLVPTV 73 (78)
T ss_pred EEECCcCHHHHHHHHHHHHhCCChHH-EEEEECCcCCCCC-cHHH-c-CC-CCCCEEEEEeec
Confidence 45899999999999999888887754 4444445433334 5554 2 22 246688887655
No 55
>COG3343 RpoE DNA-directed RNA polymerase, delta subunit [Transcription]
Probab=42.76 E-value=30 Score=26.52 Aligned_cols=48 Identities=15% Similarity=0.419 Sum_probs=38.0
Q ss_pred CCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCc-eEEEEeccccccCC
Q 033214 56 DMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDG-FLYMCYSSEKTFGY 119 (125)
Q Consensus 56 ~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DG-fLyi~Ys~~~~fG~ 119 (125)
.++++.++.-|++.+++...+ .-..++++|... ..|| |++| +.+.||-
T Consensus 30 ~~~F~dii~EI~~~~~~s~~e------------i~~~i~~FYTdl-n~DgrFi~L---Gdn~WgL 78 (175)
T COG3343 30 PFNFSDIINEIQKLLGVSKEE------------IRSRIGQFYTDL-NIDGRFISL---GDNKWGL 78 (175)
T ss_pred CccHHHHHHHHHHHhCcCHHH------------HHHHHHHHHHHh-ccCCceeec---cccccch
Confidence 688999999999999887543 235799999999 5666 7765 7889983
No 56
>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=42.49 E-value=36 Score=21.83 Aligned_cols=58 Identities=7% Similarity=0.107 Sum_probs=37.4
Q ss_pred eecCCCchHhHHHHHhhhhCCCCCCeEEE-EEcCccCCccchHHHHHhHcCCCCceEEEEec
Q 033214 52 LVPRDMSVGQFIHILSSRLHLTPGKALFV-FVKDTLPQTATLMDSVYESFKDEDGFLYMCYS 112 (125)
Q Consensus 52 lvp~~~tv~~~~~~lRk~L~l~~~~slfl-~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Ys 112 (125)
-|+.+.||+++...|-++.+++++.--.- ..+......+.++++ |. - .++..|++.-+
T Consensus 18 ~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~~L~D~~tL~~-~g-i-~~gs~l~l~~~ 76 (80)
T cd01792 18 SLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQDGVPLVS-QG-L-GPGSTVLLVVQ 76 (80)
T ss_pred EcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCCCCCCCCCHHH-cC-C-CCCCEEEEEEE
Confidence 36889999999999999888876533221 224455555667765 22 2 14568887654
No 57
>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=38.38 E-value=61 Score=22.95 Aligned_cols=24 Identities=13% Similarity=0.214 Sum_probs=21.0
Q ss_pred eecCCCchHhHHHHHhhhhCCCCC
Q 033214 52 LVPRDMSVGQFIHILSSRLHLTPG 75 (125)
Q Consensus 52 lvp~~~tv~~~~~~lRk~L~l~~~ 75 (125)
.|+++.||+++...|-.++++++.
T Consensus 20 ~V~~~~TVg~LK~lImQ~f~V~P~ 43 (107)
T cd01795 20 LVSANQTLKELKIQIMHAFSVAPF 43 (107)
T ss_pred EeCccccHHHHHHHHHHHhcCCcc
Confidence 488999999999999999998765
No 58
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.69 E-value=1.3e+02 Score=25.55 Aligned_cols=64 Identities=14% Similarity=0.239 Sum_probs=44.4
Q ss_pred ccceEe--ecCCCchHhHHHHHhhhhC---CCCCCeEEEEEcCccCCccchHHHHHhHcCCCCceEEEEeccc
Q 033214 47 EKKKFL--VPRDMSVGQFIHILSSRLH---LTPGKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMCYSSE 114 (125)
Q Consensus 47 ~k~Kfl--vp~~~tv~~~~~~lRk~L~---l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Ys~~ 114 (125)
+.++|. |..+.||.++...|...-+ ++.++ +-|+.++.+...+.+|++ |. -+ ++.+|++.-+..
T Consensus 9 ~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~-QkLIy~GkiL~Dd~tL~d-y~-I~-e~~~Ivvmv~k~ 77 (378)
T TIGR00601 9 QQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQ-QKLIYSGKILSDDKTVRE-YK-IK-EKDFVVVMVSKP 77 (378)
T ss_pred CCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhH-eEEEECCEECCCCCcHHH-cC-CC-CCCEEEEEeccC
Confidence 334444 7899999999999988876 66543 455566767777788876 32 22 566888877653
No 59
>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=36.89 E-value=63 Score=25.44 Aligned_cols=53 Identities=19% Similarity=0.307 Sum_probs=34.6
Q ss_pred CcccEEEEccCCCCCCCCccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcC
Q 033214 29 DRVPVIAERYSKADLPDMEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKD 84 (125)
Q Consensus 29 ~~ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn 84 (125)
+||-|.+.+....+-| ....-++..+|..++...|-++|+++|..--|.-+++
T Consensus 175 nrv~V~f~~~~~~~~~---~F~l~ls~~~tY~~la~~Va~~l~~dP~~lr~~~~~~ 227 (249)
T PF12436_consen 175 NRVEVEFKPKDNPNDP---EFTLWLSKKMTYDQLAEKVAEHLNVDPEHLRFFTVNP 227 (249)
T ss_dssp HEEEEEEEETTSTT------EEEEEETT--HHHHHHHHHHHHTS-GGGEEEE---T
T ss_pred CeEEEEEEECCCCCCC---CEEEEECCCCCHHHHHHHHHHHHCCChHHEEEEEecc
Confidence 5777777664433332 5566799999999999999999999998766766764
No 60
>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes. This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].
Probab=36.56 E-value=94 Score=19.87 Aligned_cols=55 Identities=22% Similarity=0.413 Sum_probs=39.5
Q ss_pred eEeecCCCchHhHHHHHhhhhC---CCCCCeEEEEEcCccCCccchHHHHHhHcCCCCceEEEEec
Q 033214 50 KFLVPRDMSVGQFIHILSSRLH---LTPGKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMCYS 112 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~---l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Ys 112 (125)
+|.-....++.++...||+.-= +.....+|+..||.- +-=+||..+||-+..+|.
T Consensus 5 ~~vp~~~~~v~d~K~~Lr~y~~~~I~~d~tGfYIvF~~~~--------Ea~rC~~~~~~~~~f~y~ 62 (66)
T PF11767_consen 5 KFVPVHGVTVEDFKKRLRKYRWDRIRDDRTGFYIVFNDSK--------EAERCFRAEDGTLFFTYR 62 (66)
T ss_pred ccCCCCCccHHHHHHHHhcCCcceEEecCCEEEEEECChH--------HHHHHHHhcCCCEEEEEE
Confidence 4455566788887777765421 456778999888732 777888889999988885
No 61
>KOG1209 consensus 1-Acyl dihydroxyacetone phosphate reductase and related dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism]
Probab=36.42 E-value=71 Score=25.97 Aligned_cols=52 Identities=19% Similarity=0.263 Sum_probs=42.1
Q ss_pred CccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcC-----ccCCccchHHHHHhHcC
Q 033214 46 MEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKD-----TLPQTATLMDSVYESFK 101 (125)
Q Consensus 46 L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn-----~lp~~~~~m~~lY~~~k 101 (125)
|.-.|.=|.++..|.++...+|+. +.-+|-+.+|| ..|..|.+++++=++++
T Consensus 54 l~~~kLDV~~~~~V~~v~~evr~~----~~Gkld~L~NNAG~~C~~Pa~d~~i~ave~~f~ 110 (289)
T KOG1209|consen 54 LKPYKLDVSKPEEVVTVSGEVRAN----PDGKLDLLYNNAGQSCTFPALDATIAAVEQCFK 110 (289)
T ss_pred CeeEEeccCChHHHHHHHHHHhhC----CCCceEEEEcCCCCCcccccccCCHHHHHhhhc
Confidence 444555699999999999999986 44578888897 36889999999999995
No 62
>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=34.69 E-value=40 Score=24.02 Aligned_cols=52 Identities=13% Similarity=0.229 Sum_probs=33.1
Q ss_pred cceEeecCCCchHhHHHHHhhhhCCCCC----CeEEEEEcCc-cC----CccchHHHHHhHc
Q 033214 48 KKKFLVPRDMSVGQFIHILSSRLHLTPG----KALFVFVKDT-LP----QTATLMDSVYESF 100 (125)
Q Consensus 48 k~Kflvp~~~tv~~~~~~lRk~L~l~~~----~slfl~Vnn~-lp----~~~~~m~~lY~~~ 100 (125)
+-+|-|+.++|+++|+..++++-++... ..-.||.. + .+ ..+++|.+|++.-
T Consensus 34 WDr~~v~~~~Tl~~li~~~~~~~~lev~ml~~g~~~LY~~-f~~~~~~~rl~~~i~elv~~v 94 (125)
T PF09358_consen 34 WDRIEVNGDMTLQELIDYFKEKYGLEVTMLSQGVSLLYSS-FPPPKHKERLKMPISELVEEV 94 (125)
T ss_dssp T-EEEEES--BHHHHHHHHHHTTS-EEEEEEETTEEEEET-T-HHHHHHHTTSBHHHHHHHH
T ss_pred eeEEEEcCCCCHHHHHHHHHHHhCceEEEEEeCCEEEEec-CChhhhHHHhCCcHHHHHHHh
Confidence 4588999999999999999999987642 11222322 2 11 3467999999954
No 63
>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=34.69 E-value=83 Score=20.71 Aligned_cols=52 Identities=12% Similarity=0.153 Sum_probs=32.8
Q ss_pred ecCCCchHhHHHHHhhhhC--CC-CCCeEEEEEcCccCCccchHHHHHhHcCC-CCceEEE
Q 033214 53 VPRDMSVGQFIHILSSRLH--LT-PGKALFVFVKDTLPQTATLMDSVYESFKD-EDGFLYM 109 (125)
Q Consensus 53 vp~~~tv~~~~~~lRk~L~--l~-~~~slfl~Vnn~lp~~~~~m~~lY~~~kd-~DGfLyi 109 (125)
-|.+.||+++...|..+.+ .. +++ .=|..++.....+.+|++. += ++.+|+|
T Consensus 17 ~~~~~TV~~LK~kI~~~~~egi~~~dq-QrLIy~GKiL~D~~TL~dy----gI~~gstlhL 72 (75)
T cd01815 17 SPGGYQVSTLKQLIAAQLPDSLPDPEL-IDLIHCGRKLKDDQTLDFY----GIQSGSTIHI 72 (75)
T ss_pred CCccCcHHHHHHHHHHhhccCCCChHH-eEEEeCCcCCCCCCcHHHc----CCCCCCEEEE
Confidence 4789999999999999964 54 433 3333344455666777652 22 3446665
No 64
>PRK13669 hypothetical protein; Provisional
Probab=33.92 E-value=36 Score=22.74 Aligned_cols=27 Identities=19% Similarity=0.493 Sum_probs=22.5
Q ss_pred CeEEEEEcC---ccCCccchHHHHHhHcCC
Q 033214 76 KALFVFVKD---TLPQTATLMDSVYESFKD 102 (125)
Q Consensus 76 ~slfl~Vnn---~lp~~~~~m~~lY~~~kd 102 (125)
...|.+||+ ..+.+++.+..||+.-++
T Consensus 45 ~~~FAlVng~~V~a~t~eeL~~kI~~~i~e 74 (78)
T PRK13669 45 EGLFALVNGEVVEGETPEELVENIYAHLEE 74 (78)
T ss_pred cCceEEECCeEeecCCHHHHHHHHHHHHhh
Confidence 578999998 567889999999987653
No 65
>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=33.86 E-value=97 Score=19.73 Aligned_cols=55 Identities=18% Similarity=0.143 Sum_probs=35.8
Q ss_pred ccceEeecCCCchHhHHHHHhhhhCCC-CCC--eEEEEEcC----ccCCccchHHHHHhHcC
Q 033214 47 EKKKFLVPRDMSVGQFIHILSSRLHLT-PGK--ALFVFVKD----TLPQTATLMDSVYESFK 101 (125)
Q Consensus 47 ~k~Kflvp~~~tv~~~~~~lRk~L~l~-~~~--slfl~Vnn----~lp~~~~~m~~lY~~~k 101 (125)
.-+...|+++.|.++++..+-++.++. ..+ +||-.+++ ....+++..-++.....
T Consensus 13 ~~kti~V~~~~t~~~Vi~~~l~k~~l~~~~~~y~L~ev~~~~~~er~L~~~e~pl~~~~~~~ 74 (87)
T cd01768 13 TYKTLRVSKDTTAQDVIQQLLKKFGLDDDPEDYALVEVLGDGGLERLLLPDECPLQIQLNAP 74 (87)
T ss_pred cEEEEEECCCCCHHHHHHHHHHHhCCcCCcccEEEEEEECCceEEEEeCCCCChHHHHHhcC
Confidence 445678999999999999999999998 333 33333444 23445555545544443
No 66
>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=32.95 E-value=63 Score=21.89 Aligned_cols=49 Identities=10% Similarity=0.227 Sum_probs=32.5
Q ss_pred EeecCCCchHhHHHHHhhhhCCCCCCeEEE-EEcC---ccCCccchHHHHHhHcC
Q 033214 51 FLVPRDMSVGQFIHILSSRLHLTPGKALFV-FVKD---TLPQTATLMDSVYESFK 101 (125)
Q Consensus 51 flvp~~~tv~~~~~~lRk~L~l~~~~slfl-~Vnn---~lp~~~~~m~~lY~~~k 101 (125)
..||++.++.+|..-||.+++++ +.+-+ |.+. ...+.+..|....+..+
T Consensus 16 i~v~~~i~f~dL~~kIrdkf~~~--~~~~iKykDEGD~iti~sq~DLd~Ai~~a~ 68 (86)
T cd06408 16 IMIGPDTGFADFEDKIRDKFGFK--RRLKIKMKDDGDMITMGDQDDLDMAIDTAR 68 (86)
T ss_pred EEcCCCCCHHHHHHHHHHHhCCC--CceEEEEEcCCCCccccCHHHHHHHHHHHH
Confidence 45999999999999999999996 35555 3332 22344445544444433
No 67
>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=32.76 E-value=44 Score=21.96 Aligned_cols=56 Identities=14% Similarity=0.220 Sum_probs=29.6
Q ss_pred eEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcC----ccC-CccchHHHHHhHcCCCCceEEE
Q 033214 50 KFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKD----TLP-QTATLMDSVYESFKDEDGFLYM 109 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn----~lp-~~~~~m~~lY~~~kd~DGfLyi 109 (125)
+.-++++.|++++...|...++++.. ++.||.+. .+. +.+.+++++==+|+| .||+
T Consensus 17 Rie~~~~~t~~~L~~kI~~~l~~~~~-~~~L~~~~~~~~~l~s~~~~tl~~lglkHGd---mlyL 77 (80)
T PF11543_consen 17 RIEVSPSSTLSDLKEKISEQLSIPDS-SQSLSKDRNNKEELKSSDSKTLSSLGLKHGD---MLYL 77 (80)
T ss_dssp EEEE-TTSBHHHHHHHHHHHS---TT-T---BSSGGGGGCSSS-TT-CCCCT---TT----EEE-
T ss_pred EEEcCCcccHHHHHHHHHHHcCCCCc-ceEEEecCCCCcccccCCcCCHHHcCCCCcc---EEEE
Confidence 45689999999999999999999865 56666663 122 345566655545542 5555
No 68
>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=31.76 E-value=88 Score=19.46 Aligned_cols=35 Identities=14% Similarity=0.143 Sum_probs=29.7
Q ss_pred cceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEE
Q 033214 48 KKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFV 82 (125)
Q Consensus 48 k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~V 82 (125)
...|-|+++.|+.++...|-++|+|...+-.=|.+
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 44688999999999999999999999877665666
No 69
>COG0669 CoaD Phosphopantetheine adenylyltransferase [Coenzyme metabolism]
Probab=31.65 E-value=84 Score=23.75 Aligned_cols=95 Identities=22% Similarity=0.203 Sum_probs=63.2
Q ss_pred cccCCHHHHHHHHHHHHhhCCCcccEEEEccCCCCCCC---CccceEeecCCCchHhHHHHHh-----hhhCCCCCCeEE
Q 033214 8 KDEFTFEQRLEESREIIAKYPDRVPVIAERYSKADLPD---MEKKKFLVPRDMSVGQFIHILS-----SRLHLTPGKALF 79 (125)
Q Consensus 8 k~~~s~e~R~~e~~~~r~kyp~~ipVIvE~~~~~~~p~---L~k~Kflvp~~~tv~~~~~~lR-----k~L~l~~~~slf 79 (125)
+--.|+|+|.+-.++.....|+- -|....+ =+-+ -..-+++|..=-++++|-+.+. ++|.- .=+++|
T Consensus 43 ~plFsleER~~l~~~~~~~l~nV---~V~~f~~-Llvd~ak~~~a~~ivRGLR~~sDfeYE~qma~~N~~L~~-eveTvF 117 (159)
T COG0669 43 KPLFSLEERVELIREATKHLPNV---EVVGFSG-LLVDYAKKLGATVLVRGLRAVSDFEYELQMAHMNRKLAP-EVETVF 117 (159)
T ss_pred CCCcCHHHHHHHHHHHhcCCCce---EEEeccc-HHHHHHHHcCCCEEEEeccccchHHHHHHHHHHHHhhcc-cccEEE
Confidence 34579999999999998877763 3433321 1111 1244688988888888866654 44422 467999
Q ss_pred EEEcC-ccCCccchHHHHHhHcCCCCceE
Q 033214 80 VFVKD-TLPQTATLMDSVYESFKDEDGFL 107 (125)
Q Consensus 80 l~Vnn-~lp~~~~~m~~lY~~~kd~DGfL 107 (125)
|.-.. ...-.++.+.+|..--.|.++|+
T Consensus 118 l~~s~~~~~iSSs~Vreia~~ggdvs~~V 146 (159)
T COG0669 118 LMPSPEYSFISSSLVREIAAFGGDVSEFV 146 (159)
T ss_pred ecCCcceehhhHHHHHHHHHhCCCchhhC
Confidence 98775 55556677888887777666553
No 70
>PRK06437 hypothetical protein; Provisional
Probab=31.23 E-value=74 Score=19.98 Aligned_cols=38 Identities=16% Similarity=0.247 Sum_probs=25.9
Q ss_pred EeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchH
Q 033214 51 FLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLM 93 (125)
Q Consensus 51 flvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m 93 (125)
+-++...|++++.. .|++++ +.+.+.+|+...+.+..|
T Consensus 15 ~~i~~~~tv~dLL~----~Lgi~~-~~vaV~vNg~iv~~~~~L 52 (67)
T PRK06437 15 IEIDHELTVNDIIK----DLGLDE-EEYVVIVNGSPVLEDHNV 52 (67)
T ss_pred EEcCCCCcHHHHHH----HcCCCC-ccEEEEECCEECCCceEc
Confidence 44788889999774 457865 567888998544444433
No 71
>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=30.98 E-value=93 Score=21.26 Aligned_cols=58 Identities=9% Similarity=0.024 Sum_probs=39.4
Q ss_pred EeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCceEEEEec
Q 033214 51 FLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMCYS 112 (125)
Q Consensus 51 flvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Ys 112 (125)
+-|..+.||+++...|..+-++++++ .=|+.++.....+.++++ |.- .++.-|++.-.
T Consensus 42 leV~~~~TV~~lK~kI~~~~gip~~~-QrLi~~Gk~L~D~~tL~d-y~I--~~~stL~l~~~ 99 (103)
T cd01802 42 LRVSPFETVISVKAKIQRLEGIPVAQ-QHLIWNNMELEDEYCLND-YNI--SEGCTLKLVLA 99 (103)
T ss_pred EEeCCCCcHHHHHHHHHHHhCCChHH-EEEEECCEECCCCCcHHH-cCC--CCCCEEEEEEe
Confidence 45899999999999999999988764 333455555566677755 321 13456777643
No 72
>cd01766 Ufm1 Urm1-like ubiquitin domain. Ufm1 (ubiquitin-fold modifier 1) is a post-translational UBL (ubiquitin-like) modifier with a tertiary structure similar to that of ubiquitin. Ufm1 is initially expressed as a precursor which undergoes C-terminal cleavage to expose a conserved glycine residue that is required for the conjugation reactions involving Ufm1.
Probab=30.07 E-value=76 Score=21.28 Aligned_cols=58 Identities=12% Similarity=0.217 Sum_probs=45.4
Q ss_pred CCCccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcC-ccCCccchHHHHHhHcCC
Q 033214 44 PDMEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKD-TLPQTATLMDSVYESFKD 102 (125)
Q Consensus 44 p~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn-~lp~~~~~m~~lY~~~kd 102 (125)
|.+.-+..-||++.-+.-++.+--...++++..| -+.-|+ .=..+.++-|+++=+|..
T Consensus 13 p~lpfkvlsVpE~aPftAvlkfaAEeFkv~~~Ts-AiiTndGvGINP~qtAGnvflkhgs 71 (82)
T cd01766 13 PKLPFKVLSVPESTPFTAVLKFAAEEFKVPAATS-AIITNDGIGINPAQTAGNVFLKHGS 71 (82)
T ss_pred CCCcceEEeccccCchHHHHHHHHHhcCCCccce-eEEecCccccChhhcccceeeecCC
Confidence 4455666779999999999888889999998887 444554 556788888999988863
No 73
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=29.68 E-value=62 Score=20.98 Aligned_cols=33 Identities=15% Similarity=0.220 Sum_probs=25.9
Q ss_pred ceEeecCCCchHhHHHHHhhhhCCCCC-CeEEEE
Q 033214 49 KKFLVPRDMSVGQFIHILSSRLHLTPG-KALFVF 81 (125)
Q Consensus 49 ~Kflvp~~~tv~~~~~~lRk~L~l~~~-~slfl~ 81 (125)
..-.+|.++||+++...|-+..+++++ ..|+++
T Consensus 16 ~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~ 49 (87)
T PF14560_consen 16 VEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLK 49 (87)
T ss_dssp EEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE
T ss_pred EEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEE
Confidence 345699999999999999999999865 455554
No 74
>cd00952 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=29.36 E-value=68 Score=25.93 Aligned_cols=29 Identities=21% Similarity=0.379 Sum_probs=25.5
Q ss_pred CCHHHHHHHHHHHHhhCCCcccEEEEccC
Q 033214 11 FTFEQRLEESREIIAKYPDRVPVIAERYS 39 (125)
Q Consensus 11 ~s~e~R~~e~~~~r~kyp~~ipVIvE~~~ 39 (125)
-|.|||.+-.+...+.-.+++|||+--..
T Consensus 58 Lt~eEr~~v~~~~~~~~~grvpvi~Gv~~ 86 (309)
T cd00952 58 LTWEEKQAFVATVVETVAGRVPVFVGATT 86 (309)
T ss_pred CCHHHHHHHHHHHHHHhCCCCCEEEEecc
Confidence 46799999999999999999999997754
No 75
>PRK10953 cysJ sulfite reductase subunit alpha; Provisional
Probab=28.99 E-value=3.8e+02 Score=24.05 Aligned_cols=88 Identities=14% Similarity=0.248 Sum_probs=58.5
Q ss_pred CCCcccEEEEccCCCCCCC-CccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCc
Q 033214 27 YPDRVPVIAERYSKADLPD-MEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDG 105 (125)
Q Consensus 27 yp~~ipVIvE~~~~~~~p~-L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DG 105 (125)
-.+.|+|-+.+.+.=.+|. -+..-.+|-...=++-|..+|+.+........++||.++.-...|-.-.+=.+.+. .+|
T Consensus 432 ~Gd~v~v~~~~~~~F~lp~~~~~piImIg~GTGIAPfrsflq~r~~~~~~~~~~LffG~R~~~~D~lY~~El~~~~-~~g 510 (600)
T PRK10953 432 EEGEVRVFIEHNDNFRLPANPETPVIMIGPGTGIAPFRAFMQQRAADGAPGKNWLFFGNPHFTEDFLYQVEWQRYV-KEG 510 (600)
T ss_pred CCCEEEEEeccCCcccCCCCCCCCEEEEecCcCcHHHHHHHHHHHHcCCCCCeEEEeeccCCccchhHHHHHHHHH-HcC
Confidence 3577888775543335664 34556678888889999999999887655456778888766666655555555553 345
Q ss_pred e---EEEEecccc
Q 033214 106 F---LYMCYSSEK 115 (125)
Q Consensus 106 f---Lyi~Ys~~~ 115 (125)
. |.+.||.++
T Consensus 511 ~l~~l~~afSRd~ 523 (600)
T PRK10953 511 LLTRIDLAWSRDQ 523 (600)
T ss_pred CcceEEEEECCCC
Confidence 3 667777554
No 76
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=28.84 E-value=25 Score=23.03 Aligned_cols=17 Identities=35% Similarity=0.696 Sum_probs=14.6
Q ss_pred cCCCCceEEEEeccccc
Q 033214 100 FKDEDGFLYMCYSSEKT 116 (125)
Q Consensus 100 ~kd~DGfLyi~Ys~~~~ 116 (125)
+-|+||-+|+.|+.++.
T Consensus 42 wiDe~G~vYi~~s~eel 58 (76)
T PF06970_consen 42 WIDENGNVYIIFSIEEL 58 (76)
T ss_pred cCCCCCCEEEEeeHHHH
Confidence 56899999999998764
No 77
>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=28.77 E-value=78 Score=21.98 Aligned_cols=27 Identities=26% Similarity=0.533 Sum_probs=22.6
Q ss_pred chHhHHHHHhhhhCCCC-CCeEEEEEcC
Q 033214 58 SVGQFIHILSSRLHLTP-GKALFVFVKD 84 (125)
Q Consensus 58 tv~~~~~~lRk~L~l~~-~~slfl~Vnn 84 (125)
.+.-+...++..++++| +.++|+|+|.
T Consensus 16 g~dgL~~lV~~~~~~dp~~g~~fvF~nr 43 (107)
T PF05717_consen 16 GIDGLAALVREELGLDPFSGDLFVFCNR 43 (107)
T ss_pred ChhHHHHHHHHhhcCCCCcceEEEEEec
Confidence 46788899999999864 6789999995
No 78
>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=28.76 E-value=1.2e+02 Score=21.15 Aligned_cols=35 Identities=23% Similarity=0.352 Sum_probs=28.7
Q ss_pred eEeecCCCchHhHHHHHhhhhCCCCC--CeEEEEEcC
Q 033214 50 KFLVPRDMSVGQFIHILSSRLHLTPG--KALFVFVKD 84 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~l~~~--~slfl~Vnn 84 (125)
-+.+|-+.||++++..|.++..+++. -.|++.+++
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 46788999999999999999998864 456666776
No 79
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=28.65 E-value=65 Score=20.49 Aligned_cols=38 Identities=18% Similarity=0.301 Sum_probs=26.3
Q ss_pred eEeecCC-CchHhHHHHHhhhhC-C-CCCCeEEEEEcCccC
Q 033214 50 KFLVPRD-MSVGQFIHILSSRLH-L-TPGKALFVFVKDTLP 87 (125)
Q Consensus 50 Kflvp~~-~tv~~~~~~lRk~L~-l-~~~~slfl~Vnn~lp 87 (125)
.+-++.+ .|+.++...|..+.. + .....+.+.||+...
T Consensus 19 ~~~~~~~~~tv~~L~~~L~~~~p~l~~~~~~~~v~vn~~~v 59 (80)
T TIGR01682 19 TLELPDESTTVGELKEHLAKEGPELAASRGQVMVAVNEEYV 59 (80)
T ss_pred EEECCCCCcCHHHHHHHHHHhCchhhhhccceEEEECCEEc
Confidence 3446766 899999999988764 2 223567889998433
No 80
>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=28.53 E-value=67 Score=20.62 Aligned_cols=21 Identities=24% Similarity=0.343 Sum_probs=17.9
Q ss_pred HHHhhhhCCCCCCeEEEEEcC
Q 033214 64 HILSSRLHLTPGKALFVFVKD 84 (125)
Q Consensus 64 ~~lRk~L~l~~~~slfl~Vnn 84 (125)
.-++..|+|.+++.+++.+.+
T Consensus 16 k~i~~~lgl~~Gd~v~v~~~~ 36 (74)
T TIGR02609 16 KEVLESLGLKEGDTLYVDEEE 36 (74)
T ss_pred HHHHHHcCcCCCCEEEEEEEC
Confidence 457899999999999998775
No 81
>PF01886 DUF61: Protein of unknown function DUF61; InterPro: IPR002746 The proteins in this entry are functionally uncharacterised.
Probab=27.80 E-value=1.6e+02 Score=21.28 Aligned_cols=56 Identities=21% Similarity=0.362 Sum_probs=35.5
Q ss_pred HHHHHHHHhhCCC------cccEEEEccCCCCCCCCccceEeecCCCchHhHHHHHhhhhCCCC----CCeEEEE
Q 033214 17 LEESREIIAKYPD------RVPVIAERYSKADLPDMEKKKFLVPRDMSVGQFIHILSSRLHLTP----GKALFVF 81 (125)
Q Consensus 17 ~~e~~~~r~kyp~------~ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~----~~slfl~ 81 (125)
+.|.+.+.+.-|. ++|+|+|..+. +..-.|.|....-+ .+|++-|++.. ++.+++|
T Consensus 46 k~ELe~L~~~lp~~~~~~lrLPIile~~~~-----~~~g~~~V~g~~e~----k~i~~ilg~~~~~~~~~~l~i~ 111 (132)
T PF01886_consen 46 KEELERLAEILPEYEWSKLRLPIILEIDPT-----LGEGSYRVRGKEEV----KAISKILGKEREFEEEDELYIY 111 (132)
T ss_pred HHHHHHHHHhCCHHHHhceeccEEEEEecc-----CCCceEEEeCHHHH----HHHHHHhCCCcccccCCeEEEc
Confidence 4677788887774 58999998542 34456777777633 34455555443 4556654
No 82
>PF00255 GSHPx: Glutathione peroxidase; InterPro: IPR000889 Glutathione peroxidase (GSHPx) (1.11.1.9 from EC) is an enzyme that catalyses the reduction of hydroxyperoxides by glutathione [, ]. Its main function is to protect against the damaging effect of endogenously formed hydroxyperoxides. In higher vertebrates, several forms of GSHPx are known, including a ubiquitous cytosolic form (GSHPx-1), a gastrointestinal cytosolic form (GSHPx-GI), a plasma secreted form (GSHPx-P), and an epididymal secretory form (GSHPx-EP). In addition to these characterised forms, the sequence of a protein of unknown function [] has been shown to be evolutionary related to those of GSHPx's. In filarial nematode parasites, the major soluble cuticular protein (gp29) is a secreted GSHPx, which may provide a mechanism of resistance to the immune reaction of the mammalian host by neutralising the products of the oxidative burst of leukocytes []. The Escherichia coli protein btuE, a periplasmic protein involved in vitamin B12 transport, is evolutionarily related to GSHPxs, although the significance of this relationship is unclear. The structure of bovine seleno-glutathione peroxidase has been determined []. The protein belongs to the alpha-beta class, with a 3 layer(aba) sandwich architecture. The catalyic site of GSHPx contains a conserved residue which is either a cysteine or, in many eukaryotic GSHPx, a selenocysteine []. ; GO: 0004602 glutathione peroxidase activity, 0006979 response to oxidative stress, 0055114 oxidation-reduction process; PDB: 3E0U_A 2VUP_A 2RM5_A 2RM6_A 3DWV_B 2P31_B 2R37_B 1GP1_B 2F8A_B 3KIJ_C ....
Probab=27.42 E-value=76 Score=22.09 Aligned_cols=28 Identities=21% Similarity=0.654 Sum_probs=22.5
Q ss_pred cchHHHHHhHcCCCCceEEEEeccccccCC
Q 033214 90 ATLMDSVYESFKDEDGFLYMCYSSEKTFGY 119 (125)
Q Consensus 90 ~~~m~~lY~~~kd~DGfLyi~Ys~~~~fG~ 119 (125)
=..|.+||++|+ ++||..|.+-..+ ||.
T Consensus 39 y~~L~~L~~ky~-~~gl~ILaFPcnq-Fg~ 66 (108)
T PF00255_consen 39 YKQLNELYEKYK-DKGLEILAFPCNQ-FGN 66 (108)
T ss_dssp HHHHHHHHHHHG-GGTEEEEEEEBST-TTT
T ss_pred cHHHHHHHHHHh-cCCeEEEeeehHH-hcc
Confidence 358999999998 5789999998544 664
No 83
>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=26.51 E-value=2e+02 Score=19.15 Aligned_cols=52 Identities=15% Similarity=0.301 Sum_probs=39.2
Q ss_pred eecCCCchHhHHHHHhhhhCCCCCCeEEEEEcC----c-cCCc-cchHHHHHhHcCCC
Q 033214 52 LVPRDMSVGQFIHILSSRLHLTPGKALFVFVKD----T-LPQT-ATLMDSVYESFKDE 103 (125)
Q Consensus 52 lvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn----~-lp~~-~~~m~~lY~~~kd~ 103 (125)
.||...+++++...|+++|.+.++..-.=|-.. . +|-. ++.|.+.+..=++.
T Consensus 12 ~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~~~~~~~~~v~l~~e~~me~aW~~v~~~ 69 (78)
T cd06411 12 RAPRGADVSSLRALLSQALPQQAQRGQLSYRAPGEDGHWVPISGEESLQRAWQDVADG 69 (78)
T ss_pred EccCCCCHHHHHHHHHHHhcCChhhcEEEecCCCCCccEeecCcchHHHHHHHhccCC
Confidence 478889999999999999999987654445431 2 4544 88899998887643
No 84
>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=26.45 E-value=1.1e+02 Score=21.45 Aligned_cols=26 Identities=12% Similarity=0.416 Sum_probs=18.4
Q ss_pred CCeEEEEEcCc---cCCccchHHHHHhHc
Q 033214 75 GKALFVFVKDT---LPQTATLMDSVYESF 100 (125)
Q Consensus 75 ~~slfl~Vnn~---lp~~~~~m~~lY~~~ 100 (125)
.+..|+|||+. .+.....+.+.|..+
T Consensus 47 ~~~q~~fVNgR~V~~~~l~~aI~~~Y~~~ 75 (127)
T cd03483 47 KIIFILFINNRLVECSALRRAIENVYANY 75 (127)
T ss_pred CceEEEEEcCCEecCHHHHHHHHHHHHHh
Confidence 46799999994 344455677777776
No 85
>PF05768 DUF836: Glutaredoxin-like domain (DUF836); InterPro: IPR008554 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This family contains several viral glutaredoxins, and many related bacterial and eukaryotic proteins of unknown function. The best characterised member of this family is G4L (P68460 from SWISSPROT) from Vaccinia virus (strain Western Reserve/WR) (VACV), which is necessary for virion morphogenesis and virus replication []. This is a cytomplasmic protein which functions as a shuttle in a redox pathway between membrane-associated E10R and L1R or F9L []. ; PDB: 1TTZ_A 1XPV_A 2FGX_A 2G2Q_C 1WJK_A.
Probab=26.15 E-value=61 Score=20.70 Aligned_cols=18 Identities=33% Similarity=0.499 Sum_probs=14.5
Q ss_pred HHHHhhCCCcccEEEEcc
Q 033214 21 REIIAKYPDRVPVIAERY 38 (125)
Q Consensus 21 ~~~r~kyp~~ipVIvE~~ 38 (125)
..+..+|..+|||+.-..
T Consensus 40 ~~l~~~Y~~~IPVl~~~~ 57 (81)
T PF05768_consen 40 PELFEKYGYRIPVLHIDG 57 (81)
T ss_dssp HHHHHHSCTSTSEEEETT
T ss_pred HHHHHHhcCCCCEEEEcC
Confidence 347889999999988554
No 86
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=25.44 E-value=69 Score=23.17 Aligned_cols=51 Identities=14% Similarity=0.241 Sum_probs=37.3
Q ss_pred cCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCceEEEEeccccccCC
Q 033214 54 PRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMCYSSEKTFGY 119 (125)
Q Consensus 54 p~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Ys~~~~fG~ 119 (125)
...+++.+++..|.+.++++.++ ....++++|-.- ..||- ..+.+++.||-
T Consensus 17 ~~~m~f~dL~~ev~~~~~~s~e~------------~~~~iaq~YtdL-n~DGR--Fi~lG~n~WgL 67 (129)
T PRK02363 17 KEPMSFYDLVNEIQKYLGKSDEE------------IRERIAQFYTDL-NLDGR--FISLGDNKWGL 67 (129)
T ss_pred CCcccHHHHHHHHHHHhCCCHHH------------HHHHHHHHHHHH-hccCC--eeEcCCCceec
Confidence 35678888888888888765432 136889999988 57772 34678999994
No 87
>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=25.44 E-value=1.4e+02 Score=18.97 Aligned_cols=40 Identities=13% Similarity=0.223 Sum_probs=26.0
Q ss_pred CCccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCc
Q 033214 45 DMEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDT 85 (125)
Q Consensus 45 ~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~ 85 (125)
.-.+.++.|.++.++.++....-++.+++++ .-.|.-|+.
T Consensus 5 ~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~-~~~L~h~~k 44 (65)
T PF11470_consen 5 NFRRFKVKVTPNTTLNQVLEEACKKFGLDPS-SYDLKHNNK 44 (65)
T ss_dssp TS-EEEE---TTSBHHHHHHHHHHHTT--GG-G-EEEETTE
T ss_pred CCcEEEEEECCCCCHHHHHHHHHHHcCCCcc-ceEEEECCE
Confidence 3467788999999999999999999999987 344544553
No 88
>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=25.33 E-value=1.2e+02 Score=19.50 Aligned_cols=57 Identities=9% Similarity=0.127 Sum_probs=39.0
Q ss_pred ecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCceEEEEecc
Q 033214 53 VPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMCYSS 113 (125)
Q Consensus 53 vp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Ys~ 113 (125)
+..+.||+++...|-.+.++++.+- =|+.++.....+.++++ |.-. ++.++++.-..
T Consensus 19 v~~~~TV~~lK~~i~~~~gi~~~~Q-rLi~~Gk~L~D~~tL~~-y~i~--~~~~i~l~~~~ 75 (78)
T cd01797 19 LSRLTKVEELREKIQELFNVEPECQ-RLFYRGKQMEDGHTLFD-YNVG--LNDIIQLLVRQ 75 (78)
T ss_pred cCCcCcHHHHHHHHHHHhCCCHHHe-EEEeCCEECCCCCCHHH-cCCC--CCCEEEEEEec
Confidence 5788999999999999988887543 23346666667778866 3222 45577775443
No 89
>PRK00805 putative deoxyhypusine synthase; Provisional
Probab=25.22 E-value=1.3e+02 Score=25.15 Aligned_cols=101 Identities=11% Similarity=0.217 Sum_probs=57.2
Q ss_pred HHHHHHH---HHHHHhhCCCcccEEEEccCCCCCCC---C-cc--ceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEc
Q 033214 13 FEQRLEE---SREIIAKYPDRVPVIAERYSKADLPD---M-EK--KKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVK 83 (125)
Q Consensus 13 ~e~R~~e---~~~~r~kyp~~ipVIvE~~~~~~~p~---L-~k--~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vn 83 (125)
+.++..+ .+-++.-|-+.|||.|.-...+.+-. + .+ .++.|.. +.++... ..+...++++=.+.++
T Consensus 156 lGk~i~~~~~~Sil~~Ayk~~VPVf~Pa~~DssiG~~l~~~~~~~~~~~iD~---~~D~~~l--~~~~~~a~~~G~iilG 230 (329)
T PRK00805 156 LGKWLNEKDIDSIVAAAYRANVPIFVPALCDSSIGIGLVIARRRGHRVVIDQ---IKDVDEI--TEIVEKSKKTGVIYIG 230 (329)
T ss_pred HHHhhcccCcchHHHHHHHcCCCEEcCCcchhhhhHHHHHHhccCCceeeeH---HHHHHHH--HHHHhccCceeEEEEC
Confidence 4555554 67788889999999996665554432 1 11 1122211 2222111 1234556677888899
Q ss_pred CccCCccchHHHHH----hHcCC-CCceEEEEeccccccCC
Q 033214 84 DTLPQTATLMDSVY----ESFKD-EDGFLYMCYSSEKTFGY 119 (125)
Q Consensus 84 n~lp~~~~~m~~lY----~~~kd-~DGfLyi~Ys~~~~fG~ 119 (125)
.-+|.....-..++ ...+. -|.++||+=+. +.+|+
T Consensus 231 GGvpKh~~~~~~l~~~~~~~~~~G~dYaVqItta~-~~dGs 270 (329)
T PRK00805 231 GGVPKNFIQQTEVIASILGEDVEGHEYAIQYTTDA-PHWGG 270 (329)
T ss_pred CchhHhHHHHHHHHHHhhccCCCCCcEEEEEeCCC-CCccc
Confidence 88887665433344 33333 57788887544 44676
No 90
>cd00951 KDGDH 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH), which is member of dihydrodipicolinate synthase (DHDPS) family that comprises several pyruvate-dependent class I aldolases. The enzyme is involved in glucarate metabolism, and its mechanism presumbly involves a Schiff-base intermediate similar to members of DHDPS family. While in the case of Pseudomonas sp. 5-dehydro-4-deoxy-D-glucarate is degraded by KDGDH to 2,5-dioxopentanoate, in certain species of Enterobacteriaceae it is degraded instead to pyruvate and glycerate.
Probab=25.15 E-value=89 Score=24.88 Aligned_cols=99 Identities=14% Similarity=0.141 Sum_probs=53.3
Q ss_pred cCCHHHHHHHHHHHHhhCCCcccEEEEccCCCCCCC---Ccc-------c-eEeecCCC---chHhHHHHHhhhhCCCCC
Q 033214 10 EFTFEQRLEESREIIAKYPDRVPVIAERYSKADLPD---MEK-------K-KFLVPRDM---SVGQFIHILSSRLHLTPG 75 (125)
Q Consensus 10 ~~s~e~R~~e~~~~r~kyp~~ipVIvE~~~~~~~p~---L~k-------~-Kflvp~~~---tv~~~~~~lRk~L~l~~~ 75 (125)
.-|.|||..-.+...+.-.+++|||+--.. +..+ +.+ . -.++|+-. +-..+..+.+.=..-. .
T Consensus 49 ~Ls~eEr~~l~~~~~~~~~~~~pvi~gv~~--~t~~~i~~a~~a~~~Gad~v~~~pP~y~~~~~~~i~~~f~~v~~~~-~ 125 (289)
T cd00951 49 SLTPDEYAQVVRAAVEETAGRVPVLAGAGY--GTATAIAYAQAAEKAGADGILLLPPYLTEAPQEGLYAHVEAVCKST-D 125 (289)
T ss_pred cCCHHHHHHHHHHHHHHhCCCCCEEEecCC--CHHHHHHHHHHHHHhCCCEEEECCCCCCCCCHHHHHHHHHHHHhcC-C
Confidence 457899999999999988899999997643 1111 100 0 12222221 2233444443332221 3
Q ss_pred CeEEEEEcCccCCccchHHHHHhHcCCCCceEEEEeccc
Q 033214 76 KALFVFVKDTLPQTATLMDSVYESFKDEDGFLYMCYSSE 114 (125)
Q Consensus 76 ~slfl~Vnn~lp~~~~~m~~lY~~~kd~DGfLyi~Ys~~ 114 (125)
-.+++|=+....-+...+.+|-+++ +.+..|.+|+.
T Consensus 126 ~pi~lYn~~g~~l~~~~l~~L~~~~---pnivgiKds~~ 161 (289)
T cd00951 126 LGVIVYNRANAVLTADSLARLAERC---PNLVGFKDGVG 161 (289)
T ss_pred CCEEEEeCCCCCCCHHHHHHHHhcC---CCEEEEEeCCC
Confidence 4588884322222234666665434 45777777643
No 91
>cd00408 DHDPS-like Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family.
Probab=24.96 E-value=92 Score=24.29 Aligned_cols=99 Identities=16% Similarity=0.174 Sum_probs=53.6
Q ss_pred cCCHHHHHHHHHHHHhhCCCcccEEEEccCCCC--CCCC-------c-cceEeecCCC---chHhHHHHHhhhhCCCCCC
Q 033214 10 EFTFEQRLEESREIIAKYPDRVPVIAERYSKAD--LPDM-------E-KKKFLVPRDM---SVGQFIHILSSRLHLTPGK 76 (125)
Q Consensus 10 ~~s~e~R~~e~~~~r~kyp~~ipVIvE~~~~~~--~p~L-------~-k~Kflvp~~~---tv~~~~~~lRk~L~l~~~~ 76 (125)
.-|.+||++-.+..++.-.+++|||+--...+. +-.+ . .--.++|+.. +-.++..+.+.=..- ..-
T Consensus 46 ~ls~~Er~~l~~~~~~~~~~~~~vi~gv~~~~~~~~i~~a~~a~~~Gad~v~v~pP~y~~~~~~~~~~~~~~ia~~-~~~ 124 (281)
T cd00408 46 TLTDEERKEVIEAVVEAVAGRVPVIAGVGANSTREAIELARHAEEAGADGVLVVPPYYNKPSQEGIVAHFKAVADA-SDL 124 (281)
T ss_pred cCCHHHHHHHHHHHHHHhCCCCeEEEecCCccHHHHHHHHHHHHHcCCCEEEECCCcCCCCCHHHHHHHHHHHHhc-CCC
Confidence 457799999999999988899999997654321 0000 0 0012222211 223333333332221 234
Q ss_pred eEEEEEcCc---cCCccchHHHHHhHcCCCCceEEEEecc
Q 033214 77 ALFVFVKDT---LPQTATLMDSVYESFKDEDGFLYMCYSS 113 (125)
Q Consensus 77 slfl~Vnn~---lp~~~~~m~~lY~~~kd~DGfLyi~Ys~ 113 (125)
.+++|=+-. .+-+...+.+|-+ .+.+..+.++.
T Consensus 125 pi~iYn~P~~tg~~l~~~~~~~L~~----~~~v~giK~s~ 160 (281)
T cd00408 125 PVILYNIPGRTGVDLSPETIARLAE----HPNIVGIKDSS 160 (281)
T ss_pred CEEEEECccccCCCCCHHHHHHHhc----CCCEEEEEeCC
Confidence 688874422 2222345666653 35788888776
No 92
>PF10336 DUF2420: Protein of unknown function (DUF2420); InterPro: IPR018822 This entry represents a family of proteins conserved in fungi. Their function is not known.
Probab=24.64 E-value=2.2e+02 Score=19.83 Aligned_cols=63 Identities=11% Similarity=0.246 Sum_probs=42.0
Q ss_pred CCchHhHHHHHhhhhC------CCCCCeEEEEEcC--------ccCCccchHHHH---HhHcCCC---------CceEEE
Q 033214 56 DMSVGQFIHILSSRLH------LTPGKALFVFVKD--------TLPQTATLMDSV---YESFKDE---------DGFLYM 109 (125)
Q Consensus 56 ~~tv~~~~~~lRk~L~------l~~~~slfl~Vnn--------~lp~~~~~m~~l---Y~~~kd~---------DGfLyi 109 (125)
+.++++|...+|+.+. +..++-|.|-+.. .+-..+.++++| |...+.. =+-||+
T Consensus 10 ~~~l~~lf~~lR~~le~~~g~~~~~~~ELvl~i~~L~L~i~EDn~y~~~iTl~di~~lf~~L~~n~~~~~~~~~p~~L~i 89 (113)
T PF10336_consen 10 NEPLEELFAALRQFLENEEGELFSAEDELVLDIPELGLEISEDNVYCSDITLSDIVDLFDILCENDGKNEEPDLPEPLYI 89 (113)
T ss_pred hCCHHHHHHHHHHHHHhccccccCCCCEEEEEeccCCcEEeccccccccCcHHHHHHHHHHHHhccCccccCCCCCcEEE
Confidence 3568899999999984 4556667776654 233445566655 4444222 238999
Q ss_pred EeccccccC
Q 033214 110 CYSSEKTFG 118 (125)
Q Consensus 110 ~Ys~~~~fG 118 (125)
+-+..+.|-
T Consensus 90 ~LstrPRFi 98 (113)
T PF10336_consen 90 TLSTRPRFI 98 (113)
T ss_pred EEecCccHH
Confidence 999998885
No 93
>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=24.44 E-value=83 Score=22.37 Aligned_cols=43 Identities=7% Similarity=0.228 Sum_probs=32.1
Q ss_pred CCCchHhHHHHHhhhhCCCCCCeEEEEEcCcc-CCccchHHHHH
Q 033214 55 RDMSVGQFIHILSSRLHLTPGKALFVFVKDTL-PQTATLMDSVY 97 (125)
Q Consensus 55 ~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~l-p~~~~~m~~lY 97 (125)
...++.++...|++-|.-.+.+.|.+-+++.. +.....|.++.
T Consensus 67 ~~~~~~dvL~~i~~fl~~~p~e~VIl~l~~~~~~~~~~~l~~~l 110 (135)
T smart00148 67 LPIKLSEVLEAIKDFAFVTSPYPVILSLENHCSPDQQAKMAQMF 110 (135)
T ss_pred ccEEHHHHHHHHHHHHHhCCCCcEEEeehhhCCHHHHHHHHHHH
Confidence 45689999999999999999999999999843 33233444333
No 94
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=23.55 E-value=99 Score=24.70 Aligned_cols=30 Identities=23% Similarity=0.182 Sum_probs=25.5
Q ss_pred cCCHHHHHHHHHHHHhhCCCcccEEEEccC
Q 033214 10 EFTFEQRLEESREIIAKYPDRVPVIAERYS 39 (125)
Q Consensus 10 ~~s~e~R~~e~~~~r~kyp~~ipVIvE~~~ 39 (125)
.-|.|||++-.+...+.-.+++|||+--..
T Consensus 50 ~Lt~eEr~~~~~~~~~~~~~~~pvi~gv~~ 79 (290)
T TIGR00683 50 MLSTEEKKEIFRIAKDEAKDQIALIAQVGS 79 (290)
T ss_pred cCCHHHHHHHHHHHHHHhCCCCcEEEecCC
Confidence 347899999999999988999999997653
No 95
>TIGR02728 spore_gerQ spore coat protein GerQ. Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase.
Probab=23.45 E-value=87 Score=21.11 Aligned_cols=33 Identities=9% Similarity=0.362 Sum_probs=26.8
Q ss_pred CCccchHHHHHhHcCCCCceEEEEeccccccCC
Q 033214 87 PQTATLMDSVYESFKDEDGFLYMCYSSEKTFGY 119 (125)
Q Consensus 87 p~~~~~m~~lY~~~kd~DGfLyi~Ys~~~~fG~ 119 (125)
|-..+=+.+|-.-.+..=|-.|++|...+-|++
T Consensus 2 p~eqSyieNILRlN~GK~~T~y~Tfenn~ew~a 34 (82)
T TIGR02728 2 PVEQSYIENILRMNRGKTATVYMTFENSPEWAA 34 (82)
T ss_pred cchHHHHHHHHHhcCCceEEEEEEEcCChHhhh
Confidence 444566778888888888999999999999975
No 96
>PRK04115 hypothetical protein; Provisional
Probab=23.36 E-value=3.1e+02 Score=20.19 Aligned_cols=55 Identities=20% Similarity=0.274 Sum_probs=32.6
Q ss_pred HHHHHHHhhCCC-----cccEEEEccCCCCCCCCccceEeecCCCchHhHHHHHhhhhCCC----CCCeEEEE
Q 033214 18 EESREIIAKYPD-----RVPVIAERYSKADLPDMEKKKFLVPRDMSVGQFIHILSSRLHLT----PGKALFVF 81 (125)
Q Consensus 18 ~e~~~~r~kyp~-----~ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~L~l~----~~~slfl~ 81 (125)
.|.+.+.+--|. |+|+|+|..+.. ..-.|.|....-| .+|.+-|+.. .++.+++|
T Consensus 50 ~ELe~L~~~l~~~~~~lrLPIile~~~~~-----~~g~~~VrG~~ev----k~IskiLg~~~~~~e~~~l~ly 113 (137)
T PRK04115 50 RELEFLKELLDEDACRLRLPIILEIDSSL-----GEGAIVVRGKEEV----KVISKILGKEDIFSEEDILYLY 113 (137)
T ss_pred HHHHHHHHhccchhhheeeeEEEEEecCC-----CceEEEEcCHHHH----HHHHHHhCccccccCCCEEEEe
Confidence 455555555553 589999997532 2345677776633 4455555533 45566665
No 97
>PF10137 TIR-like: Predicted nucleotide-binding protein containing TIR-like domain; InterPro: IPR019302 This entry represents a TIR-like domain found in a family of prokaryotic predicted nucleotide-binding proteins. Their exact function has not, as yet, been defined.
Probab=23.20 E-value=1.4e+02 Score=21.34 Aligned_cols=16 Identities=19% Similarity=0.659 Sum_probs=14.3
Q ss_pred CCCceEEEEecccccc
Q 033214 102 DEDGFLYMCYSSEKTF 117 (125)
Q Consensus 102 d~DGfLyi~Ys~~~~f 117 (125)
|-+|..|+.|....+|
T Consensus 110 Dl~Gi~~~~~~~~~~w 125 (125)
T PF10137_consen 110 DLSGITYIRFDDNRSW 125 (125)
T ss_pred ccCCeEEEEcCCCCCC
Confidence 6799999999998887
No 98
>PRK13125 trpA tryptophan synthase subunit alpha; Provisional
Probab=23.14 E-value=79 Score=24.57 Aligned_cols=17 Identities=24% Similarity=0.270 Sum_probs=13.4
Q ss_pred CCCCceEEEEeccccccCC
Q 033214 101 KDEDGFLYMCYSSEKTFGY 119 (125)
Q Consensus 101 kd~DGfLyi~Ys~~~~fG~ 119 (125)
+..|||||| +.++.+|.
T Consensus 150 ~~~~~~l~m--sv~~~~g~ 166 (244)
T PRK13125 150 KLSPLFIYY--GLRPATGV 166 (244)
T ss_pred HhCCCEEEE--EeCCCCCC
Confidence 347999999 67888885
No 99
>smart00314 RA Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.)
Probab=23.04 E-value=2.1e+02 Score=18.24 Aligned_cols=39 Identities=23% Similarity=0.288 Sum_probs=30.2
Q ss_pred CCCccceEeecCCCchHhHHHHHhhhhCCCCC---CeEEEEE
Q 033214 44 PDMEKKKFLVPRDMSVGQFIHILSSRLHLTPG---KALFVFV 82 (125)
Q Consensus 44 p~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~---~slfl~V 82 (125)
|.-.-+-..|+.+.|+++++..+-++.+++.. =+||..+
T Consensus 13 ~~~~~kti~v~~~tTa~~Vi~~~l~k~~l~~~~~~y~L~e~~ 54 (90)
T smart00314 13 PGGTYKTLRVSSRTTARDVIQQLLEKFHLTDDPEEYVLVEVL 54 (90)
T ss_pred CCCcEEEEEECCCCCHHHHHHHHHHHhCCCCCcccEEEEEEe
Confidence 44455667899999999999999999999763 3455555
No 100
>KOG3483 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.90 E-value=1.3e+02 Score=20.40 Aligned_cols=59 Identities=12% Similarity=0.197 Sum_probs=44.4
Q ss_pred CCCCccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcC-ccCCccchHHHHHhHcCC
Q 033214 43 LPDMEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKD-TLPQTATLMDSVYESFKD 102 (125)
Q Consensus 43 ~p~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn-~lp~~~~~m~~lY~~~kd 102 (125)
-|.|..+.+-||+...+.-+..+--...+.++..|--+ -|+ .=..+.++-|++|=+|.+
T Consensus 23 dpklpfkv~svpestpftavlkfaaeefkvpaatsaii-tndgiginpaq~agnvflkhgs 82 (94)
T KOG3483|consen 23 DPKLPFKVLSVPESTPFTAVLKFAAEEFKVPAATSAII-TNDGIGINPAQTAGNVFLKHGS 82 (94)
T ss_pred CCCCccceecCCCCCchHHHHHHHHHHccCCccceeEE-ecCccccCccccccceeeccCC
Confidence 46777888889999999888888888888888766443 454 445667778888887764
No 101
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=22.85 E-value=1e+02 Score=19.38 Aligned_cols=37 Identities=8% Similarity=0.165 Sum_probs=24.8
Q ss_pred eEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccc
Q 033214 50 KFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTAT 91 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~ 91 (125)
.+-+++..|++++.. .|++++ +.+.+.+|+...+.+.
T Consensus 17 ~~~~~~~~tv~~ll~----~l~~~~-~~v~v~vNg~iv~~~~ 53 (70)
T PRK08364 17 EIEWRKGMKVADILR----AVGFNT-ESAIAKVNGKVALEDD 53 (70)
T ss_pred EEEcCCCCcHHHHHH----HcCCCC-ccEEEEECCEECCCCc
Confidence 344688889988764 446665 5688889985444443
No 102
>PF01704 UDPGP: UTP--glucose-1-phosphate uridylyltransferase; InterPro: IPR002618 This family consists of UTP--glucose-1-phosphate uridylyltransferases (2.7.7.9 from EC). Also known as UDP-glucose pyrophosphorylase (UDPGP) and Glucose-1-phosphate uridylyltransferase. UTP--glucose-1-phosphate uridylyltransferase catalyses the interconversion of MgUTP + glucose-1-phosphate and UDP-glucose + MgPPi []. UDP-glucose is an important intermediate in mammalian carbohydrate interconversion involved in various metabolic roles depending on tissue type []. In Dictyostelium discoideum (Slime mold), mutants in this enzyme abort the development cycle []. Also within this family is UDP-N-acetylglucosamine pyrophosphorylase (Q16222 from SWISSPROT) [] and two hypothetical proteins from Borrelia burgdorferi, the Lyme disease spirochaete (O51893 from SWISSPROT and O51036 from SWISSPROT).; GO: 0016779 nucleotidyltransferase activity, 0008152 metabolic process; PDB: 2OEG_A 2OEF_A 2YQS_A 2YQJ_A 2YQH_B 2YQC_A 3OH4_A 3OGZ_A 3OH3_A 3OH1_A ....
Probab=22.72 E-value=1.9e+02 Score=24.88 Aligned_cols=56 Identities=18% Similarity=0.263 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHhhCCCcccEEEEccCCCCCCCCccceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccC
Q 033214 13 FEQRLEESREIIAKYPDRVPVIAERYSKADLPDMEKKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLP 87 (125)
Q Consensus 13 ~e~R~~e~~~~r~kyp~~ipVIvE~~~~~~~p~L~k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp 87 (125)
|+-..++...++++|.-.||+++=- +..|-++...++++.-+++.+ +++|.-+.+|
T Consensus 88 ldl~~~qi~~l~~~~~~~iPl~iMt-----------------S~~T~~~T~~~l~kyfg~~~~--v~~F~Q~~~P 143 (420)
T PF01704_consen 88 LDLIVEQIEALNKKYGVDIPLYIMT-----------------SFNTHEDTRKFLEKYFGLDVD--VFFFKQSKLP 143 (420)
T ss_dssp HHHHHHHHHHHHHHHTTT-EEEEEE-----------------ETTTHHHHHHHHHHGCGSSCC--EEEEEE-EEE
T ss_pred HHHHHHHHHHHhccccccceEEEec-----------------CcccHHHHHHHHHHhcCCCcc--eEEEeecCcc
Confidence 4566677788888888888877633 345667788888887677655 7766655444
No 103
>cd00137 PI-PLCc Catalytic domain of prokaryotic and eukaryotic phosphoinositide-specific phospholipase C. This subfamily corresponds to the catalytic domain present in prokaryotic and eukaryotic phosphoinositide-specific phospholipase C (PI-PLC), which is a ubiquitous enzyme catalyzing the cleavage of the sn3-phosphodiester bond in the membrane phosphoinositides (phosphatidylinositol, PI; Phosphatidylinositol-4-phosphate, PIP; phosphatidylinositol 4,5-bisphosphate, PIP2) to yield inositol phosphates (inositol monosphosphate, InsP; inositol diphosphate, InsP2; inositol trisphosphate, InsP3) and diacylglycerol (DAG). The higher eukaryotic PI-PLCs (EC 3.1.4.11) have a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. They play a critical role in most signal transduction pathways, controlling numerous cellular events, such as cell growth, proliferation, excitation and secretion. These PI-PLCs strictly require Ca2+ for their catalytic a
Probab=22.63 E-value=93 Score=24.84 Aligned_cols=52 Identities=13% Similarity=0.208 Sum_probs=40.4
Q ss_pred CCchHhHHHHHhhhhCCCCCCeEEEEEcC-ccC--CccchHHHHHhHcCCCCceEEE
Q 033214 56 DMSVGQFIHILSSRLHLTPGKALFVFVKD-TLP--QTATLMDSVYESFKDEDGFLYM 109 (125)
Q Consensus 56 ~~tv~~~~~~lRk~L~l~~~~slfl~Vnn-~lp--~~~~~m~~lY~~~kd~DGfLyi 109 (125)
..++.+++..|++-|.-.+.+.|.|-+++ .-+ .....|.+.+.... +.+||.
T Consensus 73 ~~~f~dvl~~i~~fl~~~p~e~vIlsl~~~~~~~~~~q~~~~~~~~~~~--g~~l~~ 127 (274)
T cd00137 73 DIFLKEVIEAIAQFLKKNPPETIIMSLKNEVDSMDSFQAKMAEYCRTIF--GDMLLT 127 (274)
T ss_pred CcCHHHHHHHHHHHHHHCCCCeEEEEEEecCCCcHHHHHHHHHHHHHhh--hhhhcc
Confidence 67899999999999999999999999998 333 45567777777664 335544
No 104
>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=22.33 E-value=81 Score=19.57 Aligned_cols=41 Identities=15% Similarity=0.210 Sum_probs=26.9
Q ss_pred eEeecCCCchHhHHHHHhhhhCC---CCCCeEEEEEcCccCCcc
Q 033214 50 KFLVPRDMSVGQFIHILSSRLHL---TPGKALFVFVKDTLPQTA 90 (125)
Q Consensus 50 Kflvp~~~tv~~~~~~lRk~L~l---~~~~slfl~Vnn~lp~~~ 90 (125)
.+-++...|+++++..|..+..- .....+-++||+...+.+
T Consensus 19 ~~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~~~ 62 (80)
T cd00754 19 ELELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVRLD 62 (80)
T ss_pred EEECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcCCC
Confidence 44567789999999988776421 123467788998443333
No 105
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=22.28 E-value=1.1e+02 Score=24.23 Aligned_cols=30 Identities=37% Similarity=0.420 Sum_probs=26.0
Q ss_pred cCCHHHHHHHHHHHHhhCCCcccEEEEccC
Q 033214 10 EFTFEQRLEESREIIAKYPDRVPVIAERYS 39 (125)
Q Consensus 10 ~~s~e~R~~e~~~~r~kyp~~ipVIvE~~~ 39 (125)
.-|.+||++-.+..++.-++++|||+--..
T Consensus 50 ~ls~~Er~~~~~~~~~~~~~~~~vi~gv~~ 79 (292)
T PRK03170 50 TLTHEEHEELIRAVVEAVNGRVPVIAGTGS 79 (292)
T ss_pred cCCHHHHHHHHHHHHHHhCCCCcEEeecCC
Confidence 467899999999999999999999987654
No 106
>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=22.12 E-value=89 Score=20.84 Aligned_cols=44 Identities=18% Similarity=0.357 Sum_probs=29.3
Q ss_pred ecCCCchHhHHHHHhhh--hCCCC------CCeEEEE-E----cCccCCccchHHHH
Q 033214 53 VPRDMSVGQFIHILSSR--LHLTP------GKALFVF-V----KDTLPQTATLMDSV 96 (125)
Q Consensus 53 vp~~~tv~~~~~~lRk~--L~l~~------~~slfl~-V----nn~lp~~~~~m~~l 96 (125)
|+++.|+++|+..|..+ +++.. +++||+= + ...-|..+.+|.+|
T Consensus 3 v~~~~TL~~lid~L~~~~~~qlk~PSlt~~~k~LYm~~pp~Lee~Tr~NL~k~l~eL 59 (84)
T PF08825_consen 3 VSPSWTLQDLIDSLCEKPEFQLKKPSLTTANKTLYMQSPPSLEEATRPNLSKKLKEL 59 (84)
T ss_dssp ESTTSBSHHHHHHHHHSTTT--SS-EEESSEEEEEESSSHHHHHHTGGGGSSBTTTT
T ss_pred cCccchHHHHHHHHHhChhhhcCCCcccCCCceEEEeCCHHHHHHhhhhhhhhHHHH
Confidence 78999999999999988 65532 3555541 1 11346677788888
No 107
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=21.81 E-value=1.1e+02 Score=24.31 Aligned_cols=30 Identities=17% Similarity=0.138 Sum_probs=25.4
Q ss_pred cCCHHHHHHHHHHHHhhCCCcccEEEEccC
Q 033214 10 EFTFEQRLEESREIIAKYPDRVPVIAERYS 39 (125)
Q Consensus 10 ~~s~e~R~~e~~~~r~kyp~~ipVIvE~~~ 39 (125)
.-|.+||..-.+...+.-++++|||+--..
T Consensus 53 ~Ls~eEr~~~~~~~~~~~~~~~~viagvg~ 82 (293)
T PRK04147 53 LLSTEEKKQVLEIVAEEAKGKVKLIAQVGS 82 (293)
T ss_pred cCCHHHHHHHHHHHHHHhCCCCCEEecCCC
Confidence 346799999999999999999999997643
No 108
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=21.80 E-value=1.3e+02 Score=26.64 Aligned_cols=53 Identities=21% Similarity=0.335 Sum_probs=40.5
Q ss_pred cceEeecCCCchHhHHHHHhhhhCCCCCCeEEEEEcCccCCccchHHHHHhHcCCCCc
Q 033214 48 KKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVFVKDTLPQTATLMDSVYESFKDEDG 105 (125)
Q Consensus 48 k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~~~m~~lY~~~kd~DG 105 (125)
|.-|-|+.+.||.+|...|-++-+.+++. +-|....++.+.+.|+. .|+-.||
T Consensus 26 k~~~~V~~~ssV~qlKE~I~~~f~a~~dq-lvLIfaGrILKD~dTL~----~~gI~Dg 78 (493)
T KOG0010|consen 26 KYEVNVASDSSVLQLKELIAQRFGAPPDQ-LVLIYAGRILKDDDTLK----QYGIQDG 78 (493)
T ss_pred ceeEecccchHHHHHHHHHHHhcCCChhH-eeeeecCccccChhhHH----HcCCCCC
Confidence 66788999999999999999999888765 44545556666777765 3555677
No 109
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. 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. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=21.75 E-value=2.1e+02 Score=19.25 Aligned_cols=22 Identities=0% Similarity=0.303 Sum_probs=16.0
Q ss_pred eEeecCC-CchHhHHHHHhhhhC
Q 033214 50 KFLVPRD-MSVGQFIHILSSRLH 71 (125)
Q Consensus 50 Kflvp~~-~tv~~~~~~lRk~L~ 71 (125)
.+-+|.+ .|+.+++..+.+..+
T Consensus 13 ~~~~~~~~~t~~~L~~~v~~~F~ 35 (81)
T cd06401 13 RIPIHNEDITYDELLLMMQRVFR 35 (81)
T ss_pred EEeccCccccHHHHHHHHHHHhc
Confidence 3567764 699999999975544
No 110
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=21.59 E-value=1.2e+02 Score=24.45 Aligned_cols=29 Identities=28% Similarity=0.299 Sum_probs=24.8
Q ss_pred cCCHHHHHHHHHHHHhhCCCcccEEEEcc
Q 033214 10 EFTFEQRLEESREIIAKYPDRVPVIAERY 38 (125)
Q Consensus 10 ~~s~e~R~~e~~~~r~kyp~~ipVIvE~~ 38 (125)
.-|.|||++-.+...+.-.+++|||+--.
T Consensus 56 ~Lt~eEr~~~~~~~~~~~~~~~pvi~gv~ 84 (303)
T PRK03620 56 SLTPDEYSQVVRAAVETTAGRVPVIAGAG 84 (303)
T ss_pred cCCHHHHHHHHHHHHHHhCCCCcEEEecC
Confidence 35779999999999998899999998664
No 111
>PHA01078 putative upper collar protein
Probab=21.56 E-value=1.3e+02 Score=24.06 Aligned_cols=38 Identities=18% Similarity=0.352 Sum_probs=27.7
Q ss_pred hHHHHHhhhhCCCCCCeEEEEEcCccCCcc-chHHHHHhHcC
Q 033214 61 QFIHILSSRLHLTPGKALFVFVKDTLPQTA-TLMDSVYESFK 101 (125)
Q Consensus 61 ~~~~~lRk~L~l~~~~slfl~Vnn~lp~~~-~~m~~lY~~~k 101 (125)
.|..-++++|. ++-|++.+++.||+.+ ..+..+|+.+-
T Consensus 20 n~~~~~~~~l~---~~di~fi~~~~l~~~~~~~~~~~~d~~~ 58 (249)
T PHA01078 20 NFNFQFQKRLT---KEDIYFIVPDYLIPDDCLQIHKLYDNCM 58 (249)
T ss_pred ccchhhhcccc---CCceEEEecCccCCchHHHHHHHhcccc
Confidence 34455667763 4469999999999877 47788888775
No 112
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A ....
Probab=21.46 E-value=95 Score=24.45 Aligned_cols=100 Identities=16% Similarity=0.166 Sum_probs=54.8
Q ss_pred cCCHHHHHHHHHHHHhhCCCcccEEEEccCCCC--C-------CCCc-cceEeecCC---CchHhHHHHHhhhhCCCCCC
Q 033214 10 EFTFEQRLEESREIIAKYPDRVPVIAERYSKAD--L-------PDME-KKKFLVPRD---MSVGQFIHILSSRLHLTPGK 76 (125)
Q Consensus 10 ~~s~e~R~~e~~~~r~kyp~~ipVIvE~~~~~~--~-------p~L~-k~Kflvp~~---~tv~~~~~~lRk~L~l~~~~ 76 (125)
.-|.+||+.-.+...+.-+.++|||+--...+- + ..+. .--.++|+- .+-.++..+.+.=... .+-
T Consensus 50 ~Lt~~Er~~l~~~~~~~~~~~~~vi~gv~~~st~~~i~~a~~a~~~Gad~v~v~~P~~~~~s~~~l~~y~~~ia~~-~~~ 128 (289)
T PF00701_consen 50 SLTDEERKELLEIVVEAAAGRVPVIAGVGANSTEEAIELARHAQDAGADAVLVIPPYYFKPSQEELIDYFRAIADA-TDL 128 (289)
T ss_dssp GS-HHHHHHHHHHHHHHHTTSSEEEEEEESSSHHHHHHHHHHHHHTT-SEEEEEESTSSSCCHHHHHHHHHHHHHH-SSS
T ss_pred cCCHHHHHHHHHHHHHHccCceEEEecCcchhHHHHHHHHHHHhhcCceEEEEeccccccchhhHHHHHHHHHHhh-cCC
Confidence 457899999999999988999999997654220 0 0011 012233332 2334444444433321 345
Q ss_pred eEEEEEcC---ccCCccchHHHHHhHcCCCCceEEEEeccc
Q 033214 77 ALFVFVKD---TLPQTATLMDSVYESFKDEDGFLYMCYSSE 114 (125)
Q Consensus 77 slfl~Vnn---~lp~~~~~m~~lY~~~kd~DGfLyi~Ys~~ 114 (125)
.+++|-+. ...-...++.+|.+ + +.+-.+.++.-
T Consensus 129 pi~iYn~P~~tg~~ls~~~l~~L~~-~---~nv~giK~s~~ 165 (289)
T PF00701_consen 129 PIIIYNNPARTGNDLSPETLARLAK-I---PNVVGIKDSSG 165 (289)
T ss_dssp EEEEEEBHHHHSSTSHHHHHHHHHT-S---TTEEEEEESSS
T ss_pred CEEEEECCCccccCCCHHHHHHHhc-C---CcEEEEEcCch
Confidence 68888764 22223345666665 3 45666666554
No 113
>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=21.43 E-value=2.2e+02 Score=20.44 Aligned_cols=50 Identities=10% Similarity=0.086 Sum_probs=34.0
Q ss_pred cceEeecCCCchHhHHHHHhhhhCCCCCCeEEEE--EcC----ccCCccchHHHHH
Q 033214 48 KKKFLVPRDMSVGQFIHILSSRLHLTPGKALFVF--VKD----TLPQTATLMDSVY 97 (125)
Q Consensus 48 k~Kflvp~~~tv~~~~~~lRk~L~l~~~~slfl~--Vnn----~lp~~~~~m~~lY 97 (125)
...+.+.+..|+.++...|.+++++...+-.-|+ ..+ .-+.++.+|.+.-
T Consensus 15 ~~~~~~~~~~t~~ev~~~v~~~~~l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~~~ 70 (207)
T smart00295 15 TLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDPDEDLSHWLDPAKTLLDQD 70 (207)
T ss_pred EEEEEECCCCCHHHHHHHHHHHhCCCccceeEEEEEcCCCCcCeeCCCccCHHHhc
Confidence 4467899999999999999999999754433333 322 2244555655543
No 114
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=20.91 E-value=1.1e+02 Score=20.29 Aligned_cols=21 Identities=19% Similarity=0.327 Sum_probs=18.9
Q ss_pred HHHhhhhCCCCCCeEEEEEcC
Q 033214 64 HILSSRLHLTPGKALFVFVKD 84 (125)
Q Consensus 64 ~~lRk~L~l~~~~slfl~Vnn 84 (125)
.-+|++|++.+.+.+-+++..
T Consensus 20 keiR~~lgi~~Gd~lei~~~~ 40 (89)
T COG2002 20 KEIREALGIKEGDVLEIIVDG 40 (89)
T ss_pred HHHHHHhCCCCCCEEEEEEeC
Confidence 568999999999999999885
No 115
>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=20.76 E-value=2.1e+02 Score=18.53 Aligned_cols=33 Identities=15% Similarity=0.193 Sum_probs=26.0
Q ss_pred eecCCCchHhHHHHHhhhhCCCCC-CeEEEEEcC
Q 033214 52 LVPRDMSVGQFIHILSSRLHLTPG-KALFVFVKD 84 (125)
Q Consensus 52 lvp~~~tv~~~~~~lRk~L~l~~~-~slfl~Vnn 84 (125)
.+|.++||+++...|-...+++++ ..|.+|.+.
T Consensus 18 r~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~ 51 (84)
T cd01789 18 KYSRGLTIAELKKKLELVVGTPASSMRLQLFDGD 51 (84)
T ss_pred ecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCC
Confidence 489999999999999999999765 445455554
No 116
>PF14060 DUF4252: Domain of unknown function (DUF4252)
Probab=20.51 E-value=1.2e+02 Score=21.39 Aligned_cols=25 Identities=8% Similarity=0.311 Sum_probs=21.0
Q ss_pred ccchHHHHHhHcCCCCceEEEEecc
Q 033214 89 TATLMDSVYESFKDEDGFLYMCYSS 113 (125)
Q Consensus 89 ~~~~m~~lY~~~kd~DGfLyi~Ys~ 113 (125)
....+..+|++|++.+|+.+++-+.
T Consensus 20 ~~~~~~~~~~~~~~~~~~~~v~i~~ 44 (155)
T PF14060_consen 20 QGQSLQKYFDKYSENKGVTSVNISK 44 (155)
T ss_pred cchhHHHHHHHhCCCCCeEEEEECH
Confidence 3478889999999999999998753
No 117
>PF08216 CTNNBL: Catenin-beta-like, Arm-motif containing nuclear; InterPro: IPR013180 This domain is found in eukaryotic proteins. A human nuclear protein with this domain (Q8WYA6 from SWISSPROT) is thought to have a role in apoptosis [].
Probab=20.05 E-value=99 Score=21.85 Aligned_cols=20 Identities=40% Similarity=0.891 Sum_probs=17.5
Q ss_pred CCHHHHHHHHHHHHhhCCCc
Q 033214 11 FTFEQRLEESREIIAKYPDR 30 (125)
Q Consensus 11 ~s~e~R~~e~~~~r~kyp~~ 30 (125)
..||.|...-+..|-|||+-
T Consensus 33 l~fek~i~kN~e~R~K~~dd 52 (108)
T PF08216_consen 33 LSFEKRINKNQEMRIKYPDD 52 (108)
T ss_pred HHHHHHHHHhHHHHHhCCCC
Confidence 35899999999999999974
No 118
>PF08469 NPHI_C: Nucleoside triphosphatase I C-terminal; InterPro: IPR013676 This viral domain is found to the C terminus of Poxvirus nucleoside triphosphatase phosphohydrolase I (NPH I) [] together with the helicase conserved C-terminal domain (IPR001650 from INTERPRO). ; GO: 0005524 ATP binding, 0017111 nucleoside-triphosphatase activity, 0006351 transcription, DNA-dependent
Probab=20.02 E-value=72 Score=23.84 Aligned_cols=21 Identities=24% Similarity=0.515 Sum_probs=18.8
Q ss_pred CccchHHHHHhHcCCCCceEE
Q 033214 88 QTATLMDSVYESFKDEDGFLY 108 (125)
Q Consensus 88 ~~~~~m~~lY~~~kd~DGfLy 108 (125)
+.+..|..++..||..||.+|
T Consensus 102 s~s~~l~tI~kGfk~~dg~iy 122 (148)
T PF08469_consen 102 SFSSRLVTIHKGFKTKDGRIY 122 (148)
T ss_pred EccchhHHHHhcccCCCCcEe
Confidence 667889999999999999887
Done!