Query 034095
Match_columns 104
No_of_seqs 100 out of 386
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 09:43:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034095.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034095hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1769 Ubiquitin-like protein 100.0 9.6E-33 2.1E-37 187.4 10.6 74 22-95 18-91 (99)
2 COG5227 SMT3 Ubiquitin-like pr 100.0 4.8E-30 1E-34 172.7 8.0 82 11-94 13-94 (103)
3 cd01763 Sumo Small ubiquitin-r 99.9 4.8E-24 1E-28 140.5 10.7 76 21-96 8-83 (87)
4 PF11976 Rad60-SLD: Ubiquitin- 99.9 7.1E-24 1.5E-28 133.5 7.7 71 25-95 1-72 (72)
5 cd01806 Nedd8 Nebb8-like ubiq 99.2 1.5E-10 3.3E-15 72.5 8.4 71 25-95 1-71 (76)
6 cd01809 Scythe_N Ubiquitin-lik 98.9 1.2E-08 2.7E-13 63.1 8.1 70 25-94 1-70 (72)
7 cd01812 BAG1_N Ubiquitin-like 98.8 3.9E-08 8.5E-13 60.9 6.8 69 25-94 1-69 (71)
8 PF00240 ubiquitin: Ubiquitin 98.7 9.4E-08 2E-12 59.0 8.1 64 32-95 3-66 (69)
9 cd01803 Ubiquitin Ubiquitin. U 98.7 1E-07 2.2E-12 59.6 8.2 70 26-95 2-71 (76)
10 smart00213 UBQ Ubiquitin homol 98.7 9E-08 2E-12 57.4 7.0 63 26-89 2-64 (64)
11 cd01807 GDX_N ubiquitin-like d 98.7 1.7E-07 3.6E-12 59.3 8.2 70 26-95 2-71 (74)
12 PTZ00044 ubiquitin; Provisiona 98.7 1.8E-07 4E-12 58.9 8.3 71 26-96 2-72 (76)
13 cd01769 UBL Ubiquitin-like dom 98.7 1.8E-07 3.9E-12 56.7 7.5 67 29-95 2-68 (69)
14 cd01798 parkin_N amino-termina 98.6 2.8E-07 6.1E-12 57.6 7.6 67 28-94 2-68 (70)
15 cd01805 RAD23_N Ubiquitin-like 98.6 5.3E-07 1.1E-11 56.8 8.4 70 26-95 2-73 (77)
16 cd01791 Ubl5 UBL5 ubiquitin-li 98.6 6.6E-07 1.4E-11 57.4 8.2 71 25-95 2-72 (73)
17 cd01810 ISG15_repeat2 ISG15 ub 98.5 9E-07 1.9E-11 56.0 7.5 69 27-95 1-69 (74)
18 cd01804 midnolin_N Ubiquitin-l 98.5 1.9E-06 4.1E-11 55.4 8.4 71 25-96 2-72 (78)
19 cd01792 ISG15_repeat1 ISG15 ub 98.4 1.4E-06 3.1E-11 56.0 7.3 74 25-98 3-78 (80)
20 cd01802 AN1_N ubiquitin-like d 98.4 3.7E-06 8E-11 57.2 9.1 75 22-96 25-99 (103)
21 cd01808 hPLIC_N Ubiquitin-like 98.4 4.3E-06 9.3E-11 52.4 8.1 70 25-95 1-70 (71)
22 cd01794 DC_UbP_C dendritic cel 98.3 4.2E-06 9.1E-11 53.0 7.6 69 27-95 1-69 (70)
23 cd01793 Fubi Fubi ubiquitin-li 98.3 7.2E-06 1.6E-10 51.8 8.1 68 26-95 2-69 (74)
24 cd01797 NIRF_N amino-terminal 98.3 6.4E-06 1.4E-10 53.2 7.8 70 26-95 2-73 (78)
25 cd01796 DDI1_N DNA damage indu 98.1 1.7E-05 3.7E-10 50.0 6.7 65 29-93 3-69 (71)
26 cd00196 UBQ Ubiquitin-like pro 98.0 5.1E-05 1.1E-09 42.3 7.0 64 31-94 4-67 (69)
27 cd01800 SF3a120_C Ubiquitin-li 98.0 3.9E-05 8.6E-10 48.8 6.9 63 33-95 6-68 (76)
28 TIGR00601 rad23 UV excision re 98.0 4.7E-05 1E-09 62.2 8.3 73 26-98 2-77 (378)
29 KOG0005 Ubiquitin-like protein 97.6 0.0001 2.2E-09 46.8 4.0 67 26-92 2-68 (70)
30 cd01799 Hoil1_N Ubiquitin-like 97.6 0.00057 1.2E-08 43.9 7.3 62 33-95 11-74 (75)
31 PF11543 UN_NPL4: Nuclear pore 97.6 0.00012 2.7E-09 47.7 4.1 70 23-93 3-77 (80)
32 cd01813 UBP_N UBP ubiquitin pr 97.4 0.001 2.2E-08 42.4 7.0 67 27-94 3-72 (74)
33 KOG0010 Ubiquitin-like protein 97.0 0.0035 7.5E-08 53.0 8.1 76 22-98 13-88 (493)
34 PF11470 TUG-UBL1: GLUT4 regul 97.0 0.0024 5.1E-08 40.4 5.4 62 29-90 1-62 (65)
35 cd01790 Herp_N Homocysteine-re 96.9 0.0085 1.8E-07 39.2 7.6 69 25-93 2-76 (79)
36 PLN02560 enoyl-CoA reductase 96.5 0.014 3.1E-07 46.5 7.5 69 26-94 2-81 (308)
37 cd01815 BMSC_UbP_N Ubiquitin-l 96.5 0.008 1.7E-07 39.1 4.9 52 44-95 20-74 (75)
38 cd01789 Alp11_N Ubiquitin-like 96.4 0.046 9.9E-07 35.5 8.1 70 25-94 2-79 (84)
39 PF08817 YukD: WXG100 protein 96.3 0.018 3.9E-07 36.8 5.8 70 24-93 2-78 (79)
40 cd01814 NTGP5 Ubiquitin-like N 96.2 0.0099 2.2E-07 41.6 4.7 70 23-92 3-80 (113)
41 PF00789 UBX: UBX domain; Int 95.9 0.17 3.7E-06 31.9 8.9 72 22-93 4-80 (82)
42 cd01801 Tsc13_N Ubiquitin-like 95.8 0.051 1.1E-06 34.4 6.3 53 42-94 20-75 (77)
43 PF14560 Ubiquitin_2: Ubiquiti 95.3 0.14 3E-06 33.0 7.1 70 25-94 2-81 (87)
44 cd06409 PB1_MUG70 The MUG70 pr 94.9 0.12 2.5E-06 34.5 5.8 50 26-75 2-57 (86)
45 cd01774 Faf1_like2_UBX Faf1 ik 94.1 0.88 1.9E-05 29.7 8.6 71 22-93 2-82 (85)
46 KOG0011 Nucleotide excision re 94.1 0.19 4.2E-06 40.9 6.5 72 27-98 3-76 (340)
47 PRK08364 sulfur carrier protei 93.9 0.69 1.5E-05 28.9 7.5 60 25-94 5-64 (70)
48 PF12436 USP7_ICP0_bdg: ICP0-b 93.6 0.21 4.5E-06 38.4 5.6 71 24-94 70-150 (249)
49 COG5417 Uncharacterized small 93.1 1.1 2.3E-05 29.6 7.6 70 25-94 7-81 (81)
50 PF13881 Rad60-SLD_2: Ubiquiti 92.7 1.3 2.9E-05 30.4 8.0 68 23-90 1-76 (111)
51 PF03671 Ufm1: Ubiquitin fold 92.5 0.65 1.4E-05 30.3 5.8 65 24-88 2-70 (76)
52 smart00455 RBD Raf-like Ras-bi 92.1 1.4 3.1E-05 27.8 7.0 45 27-71 2-46 (70)
53 cd01795 USP48_C USP ubiquitin- 92.0 0.69 1.5E-05 32.0 5.8 60 36-95 16-76 (107)
54 cd01766 Ufm1 Urm1-like ubiquit 91.4 0.7 1.5E-05 30.4 5.1 68 24-91 2-73 (82)
55 cd00754 MoaD Ubiquitin domain 91.4 1.3 2.9E-05 27.3 6.3 54 36-94 17-74 (80)
56 KOG0006 E3 ubiquitin-protein l 90.3 1 2.2E-05 37.2 6.1 46 36-81 15-60 (446)
57 smart00166 UBX Domain present 90.0 3.4 7.3E-05 26.0 7.8 71 23-93 3-78 (80)
58 cd01767 UBX UBX (ubiquitin reg 89.6 3.5 7.6E-05 25.7 7.8 67 24-91 2-73 (77)
59 PRK06944 sulfur carrier protei 89.4 3 6.6E-05 25.0 6.6 55 33-95 6-60 (65)
60 PRK06437 hypothetical protein; 89.2 3.4 7.3E-05 25.6 6.8 52 34-94 10-61 (67)
61 smart00666 PB1 PB1 domain. Pho 89.2 2 4.4E-05 26.7 5.8 44 25-69 2-45 (81)
62 KOG4248 Ubiquitin-like protein 88.9 1.1 2.5E-05 41.4 6.0 68 26-94 4-71 (1143)
63 cd01770 p47_UBX p47-like ubiqu 88.6 4.7 0.0001 25.8 7.8 68 24-91 4-75 (79)
64 TIGR01687 moaD_arch MoaD famil 88.1 4.2 9E-05 25.8 6.9 56 35-94 16-82 (88)
65 PRK07440 hypothetical protein; 87.7 4.9 0.00011 25.2 6.8 61 24-94 4-64 (70)
66 cd01777 SNX27_RA Ubiquitin dom 87.7 1.3 2.7E-05 29.7 4.2 42 25-66 2-43 (87)
67 cd06407 PB1_NLP A PB1 domain i 87.4 2.9 6.4E-05 27.2 5.9 44 25-69 1-45 (82)
68 PRK05659 sulfur carrier protei 87.1 4.4 9.6E-05 24.4 6.3 55 33-94 6-60 (66)
69 cd01811 OASL_repeat1 2'-5' oli 86.9 6 0.00013 26.1 7.0 68 25-93 1-73 (80)
70 cd06396 PB1_NBR1 The PB1 domai 86.8 3.4 7.3E-05 27.2 5.9 48 25-75 1-53 (81)
71 KOG3439 Protein conjugation fa 86.6 6.6 0.00014 27.6 7.5 62 22-83 28-95 (116)
72 cd06406 PB1_P67 A PB1 domain i 86.5 2.7 5.8E-05 27.7 5.3 44 25-70 3-46 (80)
73 PF00564 PB1: PB1 domain; Int 86.0 5 0.00011 24.9 6.3 45 25-69 2-46 (84)
74 PRK06488 sulfur carrier protei 85.9 5 0.00011 24.3 6.1 54 33-94 6-59 (65)
75 cd06408 PB1_NoxR The PB1 domai 85.4 5.5 0.00012 26.5 6.4 44 24-69 2-45 (86)
76 PRK06083 sulfur carrier protei 85.2 5.3 0.00011 26.2 6.2 61 24-94 18-78 (84)
77 KOG0003 Ubiquitin/60s ribosoma 85.1 0.51 1.1E-05 33.2 1.4 64 29-92 5-68 (128)
78 PRK08053 sulfur carrier protei 84.2 7.4 0.00016 23.7 6.4 55 33-94 6-60 (66)
79 smart00295 B41 Band 4.1 homolo 83.5 4.2 9.2E-05 28.8 5.7 39 23-61 2-40 (207)
80 PRK05863 sulfur carrier protei 83.4 5 0.00011 24.5 5.3 54 33-94 6-59 (65)
81 cd01771 Faf1_UBX Faf1 UBX doma 83.0 9.3 0.0002 24.6 6.6 69 23-92 3-76 (80)
82 PF00788 RA: Ras association ( 82.8 9.1 0.0002 23.8 6.9 63 25-87 3-77 (93)
83 PLN02799 Molybdopterin synthas 82.6 5.8 0.00013 24.9 5.5 55 35-94 19-76 (82)
84 TIGR01682 moaD molybdopterin c 81.8 10 0.00022 23.7 6.9 54 36-94 17-74 (80)
85 cd01760 RBD Ubiquitin-like dom 81.5 7.2 0.00016 24.9 5.6 44 27-70 2-45 (72)
86 TIGR01683 thiS thiamine biosyn 80.0 8.8 0.00019 23.2 5.4 51 39-94 8-58 (64)
87 PF02196 RBD: Raf-like Ras-bin 79.4 4.8 0.0001 25.3 4.2 45 27-71 3-47 (71)
88 cd05992 PB1 The PB1 domain is 79.0 11 0.00023 23.1 5.7 43 26-69 2-45 (81)
89 COG2080 CoxS Aerobic-type carb 78.0 5.2 0.00011 29.4 4.6 63 24-91 3-72 (156)
90 PF09379 FERM_N: FERM N-termin 77.9 4.4 9.5E-05 24.9 3.7 40 30-69 2-42 (80)
91 KOG4225 Sorbin and SH3 domain- 76.9 1.3 2.8E-05 37.6 1.3 18 77-94 443-460 (489)
92 PF02597 ThiS: ThiS family; I 76.6 8.6 0.00019 23.3 4.7 57 36-94 13-71 (77)
93 PF13019 Telomere_Sde2: Telome 75.5 15 0.00033 27.1 6.4 58 25-82 1-65 (162)
94 cd00565 ThiS ThiaminS ubiquiti 74.3 9.8 0.00021 23.0 4.5 51 39-94 9-59 (65)
95 PF10302 DUF2407: DUF2407 ubiq 74.2 14 0.0003 24.8 5.5 52 24-76 2-57 (97)
96 PF14451 Ub-Mut7C: Mut7-C ubiq 73.9 17 0.00037 23.6 5.8 52 34-94 22-74 (81)
97 cd01818 TIAM1_RBD Ubiquitin do 72.8 19 0.00042 23.6 5.8 42 28-69 3-46 (77)
98 KOG3483 Uncharacterized conser 72.8 20 0.00044 23.8 5.9 55 38-92 30-85 (94)
99 cd01768 RA RA (Ras-associating 70.9 23 0.00049 22.2 5.8 57 27-83 2-69 (87)
100 cd01772 SAKS1_UBX SAKS1-like U 70.6 24 0.00052 22.3 8.9 70 23-93 3-77 (79)
101 PRK07696 sulfur carrier protei 69.7 23 0.0005 21.8 6.4 56 33-95 6-62 (67)
102 PHA01623 hypothetical protein 68.2 4.6 0.0001 24.5 2.0 27 37-63 14-40 (56)
103 cd06398 PB1_Joka2 The PB1 doma 67.9 32 0.00069 22.7 6.2 48 26-74 2-58 (91)
104 PF08825 E2_bind: E2 binding d 67.2 6.6 0.00014 25.8 2.7 52 39-93 1-68 (84)
105 PF04110 APG12: Ubiquitin-like 67.1 16 0.00035 24.2 4.6 59 25-83 2-66 (87)
106 KOG0001 Ubiquitin and ubiquiti 67.0 21 0.00045 20.2 8.7 65 28-92 3-67 (75)
107 PF03607 DCX: Doublecortin; I 66.3 9.7 0.00021 23.0 3.2 46 43-94 7-54 (60)
108 PF10623 PilI: Plasmid conjuga 61.9 19 0.00041 23.9 4.1 54 22-75 6-62 (83)
109 cd01773 Faf1_like1_UBX Faf1 ik 58.2 50 0.0011 21.6 8.4 69 24-93 5-78 (82)
110 PF13860 FlgD_ig: FlgD Ig-like 57.4 34 0.00073 21.5 4.7 43 22-80 24-67 (81)
111 COG2104 ThiS Sulfur transfer p 54.2 48 0.001 20.8 4.9 60 25-94 3-62 (68)
112 KOG1363 Predicted regulator of 53.6 36 0.00077 29.0 5.4 51 18-69 377-427 (460)
113 PRK11433 aldehyde oxidoreducta 53.2 56 0.0012 25.2 6.0 67 22-93 49-122 (217)
114 TIGR02958 sec_mycoba_snm4 secr 53.2 63 0.0014 27.1 6.8 68 25-93 3-77 (452)
115 PRK11840 bifunctional sulfur c 52.8 54 0.0012 26.8 6.1 55 33-94 6-60 (326)
116 KOG1407 WD40 repeat protein [F 52.1 31 0.00066 27.9 4.5 52 22-76 190-248 (313)
117 PF11620 GABP-alpha: GA-bindin 51.8 26 0.00056 23.5 3.5 51 37-87 5-55 (88)
118 COG5100 NPL4 Nuclear pore prot 48.9 80 0.0017 27.2 6.7 68 27-95 3-78 (571)
119 PF05486 SRP9-21: Signal recog 47.6 71 0.0015 20.5 5.0 33 21-53 37-70 (79)
120 PF08620 RPAP1_C: RPAP1-like, 44.1 13 0.00029 23.9 1.1 12 63-74 1-12 (73)
121 COG3435 Gentisate 1,2-dioxygen 42.6 16 0.00035 29.9 1.7 32 61-96 111-146 (351)
122 COG5077 Ubiquitin carboxyl-ter 42.1 48 0.001 30.7 4.6 35 36-70 585-620 (1089)
123 cd06395 PB1_Map2k5 PB1 domain 41.5 79 0.0017 21.2 4.5 54 26-94 2-57 (91)
124 cd02986 DLP Dim1 family, Dim1- 40.5 21 0.00046 24.7 1.8 23 53-75 59-82 (114)
125 PF01402 RHH_1: Ribbon-helix-h 40.5 17 0.00037 19.5 1.1 26 39-64 2-27 (39)
126 KOG2378 cAMP-regulated guanine 40.3 1.2E+02 0.0027 26.4 6.6 58 18-75 229-288 (573)
127 cd02791 MopB_CT_Nitrate-R-NapA 40.2 12 0.00026 24.6 0.5 25 72-97 37-61 (122)
128 cd01611 GABARAP Ubiquitin doma 40.2 1.2E+02 0.0026 20.7 5.7 61 23-83 23-90 (112)
129 cd01612 APG12_C Ubiquitin-like 40.2 1E+02 0.0023 20.0 6.1 34 38-71 19-53 (87)
130 PF12436 USP7_ICP0_bdg: ICP0-b 40.1 1.3E+02 0.0028 23.0 6.3 46 24-69 176-224 (249)
131 KOG3493 Ubiquitin-like protein 40.1 17 0.00037 23.4 1.2 69 25-93 2-70 (73)
132 PF01982 CTP-dep_RFKase: Domai 37.7 19 0.00041 25.4 1.2 15 81-95 107-121 (121)
133 PF09631 Sen15: Sen15 protein; 37.5 47 0.001 21.9 3.1 22 22-43 72-93 (101)
134 PF00018 SH3_1: SH3 domain; I 36.9 22 0.00048 19.9 1.2 18 78-95 9-26 (48)
135 cd02790 MopB_CT_Formate-Dh_H F 36.6 15 0.00032 23.8 0.5 24 72-96 37-60 (116)
136 PF09014 Sushi_2: Beta-2-glyco 36.1 18 0.00039 24.1 0.9 33 60-94 6-39 (85)
137 cd02792 MopB_CT_Formate-Dh-Na- 35.3 14 0.0003 24.3 0.2 19 77-95 41-59 (122)
138 PRK14132 riboflavin kinase; Pr 35.0 24 0.00053 25.0 1.4 15 81-95 112-126 (126)
139 PF06487 SAP18: Sin3 associate 34.7 32 0.00069 24.1 2.0 62 34-95 36-120 (120)
140 PF06134 RhaA: L-rhamnose isom 34.7 34 0.00075 28.8 2.5 21 43-63 379-399 (417)
141 smart00314 RA Ras association 33.9 1.2E+02 0.0026 18.9 7.7 63 26-88 4-76 (90)
142 PRK11130 moaD molybdopterin sy 33.4 1.2E+02 0.0027 18.9 5.5 45 45-94 26-75 (81)
143 COG4806 RhaA L-rhamnose isomer 33.2 30 0.00066 28.5 1.9 21 43-63 380-400 (419)
144 cd00508 MopB_CT_Fdh-Nap-like T 32.5 19 0.00042 23.3 0.6 24 72-96 37-60 (120)
145 PF01568 Molydop_binding: Moly 32.2 17 0.00036 23.4 0.2 18 77-94 36-53 (110)
146 PF12167 DUF3596: Domain of un 32.2 33 0.00071 21.1 1.6 19 64-82 12-34 (64)
147 TIGR02988 YaaA_near_RecF S4 do 32.2 9 0.0002 22.7 -1.0 45 44-93 5-58 (59)
148 PF14604 SH3_9: Variant SH3 do 31.9 29 0.00062 19.9 1.2 18 77-94 7-24 (49)
149 cd06411 PB1_p51 The PB1 domain 31.7 1.1E+02 0.0024 19.9 4.1 34 36-69 8-41 (78)
150 PF07653 SH3_2: Variant SH3 do 31.7 30 0.00066 19.9 1.3 18 77-94 10-27 (55)
151 PRK11675 LexA regulated protei 30.3 66 0.0014 21.6 2.8 33 31-63 45-77 (90)
152 PF08722 Tn7_Tnp_TnsA_N: TnsA 30.3 96 0.0021 19.5 3.6 36 27-62 37-83 (88)
153 cd02788 MopB_CT_NDH-1_NuoG2-N7 30.2 23 0.0005 22.8 0.6 20 77-96 35-54 (96)
154 PF06071 YchF-GTPase_C: Protei 30.0 35 0.00075 22.6 1.4 15 81-95 69-83 (84)
155 TIGR03193 4hydroxCoAred 4-hydr 29.9 1.3E+02 0.0028 21.8 4.5 55 25-82 2-63 (148)
156 PF10787 YfmQ: Uncharacterised 29.8 52 0.0011 24.1 2.4 36 43-78 23-58 (149)
157 PRK01777 hypothetical protein; 29.6 1.7E+02 0.0037 19.4 6.8 53 37-94 19-74 (95)
158 PF07377 DUF1493: Protein of u 28.4 34 0.00073 23.0 1.2 24 46-69 43-68 (111)
159 KOG3391 Transcriptional co-rep 28.4 40 0.00088 24.6 1.7 62 36-98 53-138 (151)
160 cd02787 MopB_CT_ydeP The MopB_ 28.2 21 0.00045 23.4 0.2 21 73-94 34-54 (112)
161 cd01817 RGS12_RBD Ubiquitin do 27.8 1.7E+02 0.0037 18.8 6.2 53 28-80 3-56 (73)
162 PF13670 PepSY_2: Peptidase pr 27.6 1.4E+02 0.0031 18.6 4.0 24 22-45 53-76 (83)
163 PF00498 FHA: FHA domain; Int 27.4 50 0.0011 19.3 1.8 23 68-93 45-67 (68)
164 cd02783 MopB_CT_2 The MopB_CT_ 26.7 24 0.00052 24.9 0.2 19 77-95 38-56 (156)
165 cd02786 MopB_CT_3 The MopB_CT_ 26.6 24 0.00052 23.0 0.2 18 77-94 37-54 (116)
166 PHA01748 hypothetical protein 26.4 96 0.0021 18.8 2.9 26 38-63 4-29 (60)
167 cd02785 MopB_CT_4 The MopB_CT_ 26.4 24 0.00052 23.5 0.2 19 77-95 38-56 (124)
168 cd02781 MopB_CT_Acetylene-hydr 26.4 25 0.00054 23.4 0.3 20 77-96 39-58 (130)
169 PF15044 CLU_N: Mitochondrial 26.3 1.7E+02 0.0036 18.5 4.2 52 43-94 3-56 (76)
170 TIGR03317 ygfZ_signature folat 26.1 42 0.00092 20.3 1.3 28 70-97 15-46 (67)
171 cd02779 MopB_CT_Arsenite-Ox Th 25.9 30 0.00064 22.8 0.6 23 73-96 36-58 (115)
172 PRK09908 xanthine dehydrogenas 25.8 1.4E+02 0.0031 21.9 4.2 55 24-82 8-69 (159)
173 PF11548 Receptor_IA-2: Protei 25.3 86 0.0019 21.1 2.7 22 22-46 35-56 (91)
174 TIGR03198 pucE xanthine dehydr 24.9 1.4E+02 0.003 21.6 3.9 55 24-81 3-64 (151)
175 COG1188 Ribosome-associated he 24.7 1.2E+02 0.0025 20.8 3.3 30 63-97 32-61 (100)
176 KOG0004 Ubiquitin/40S ribosoma 24.3 70 0.0015 23.6 2.3 64 28-91 4-67 (156)
177 cd02789 MopB_CT_FmdC-FwdD The 24.1 29 0.00064 22.9 0.3 18 77-94 37-54 (106)
178 PF02991 Atg8: Autophagy prote 23.6 2.4E+02 0.0052 19.0 5.5 60 23-82 15-81 (104)
179 cd02777 MopB_CT_DMSOR-like The 23.6 30 0.00064 23.2 0.2 22 73-95 37-58 (127)
180 cd02794 MopB_CT_DmsA-EC The Mo 23.4 31 0.00066 22.9 0.3 21 73-94 33-53 (121)
181 COG5435 Uncharacterized conser 23.3 1.2E+02 0.0025 22.2 3.2 36 22-57 19-56 (147)
182 cd02778 MopB_CT_Thiosulfate-R- 22.7 37 0.0008 22.3 0.6 19 77-95 36-54 (123)
183 PF10114 PocR: Sensory domain 22.2 1.3E+02 0.0029 20.8 3.4 29 45-75 8-36 (173)
184 PF12754 Blt1: Cell-cycle cont 22.2 30 0.00064 28.1 0.0 65 22-86 76-160 (309)
185 cd02782 MopB_CT_1 The MopB_CT_ 22.1 37 0.00081 22.6 0.5 20 77-96 39-58 (129)
186 KOG1639 Steroid reductase requ 22.0 2.1E+02 0.0047 23.0 4.8 54 41-94 19-77 (297)
187 KOG0013 Uncharacterized conser 22.0 1.7E+02 0.0037 22.9 4.1 66 24-89 145-211 (231)
188 PRK14165 winged helix-turn-hel 21.4 61 0.0013 24.7 1.6 15 81-95 201-215 (217)
189 PRK12426 elongation factor P; 21.2 1.7E+02 0.0036 21.9 3.9 73 15-95 27-115 (185)
190 PRK01076 L-rhamnose isomerase; 20.7 75 0.0016 26.9 2.1 21 43-63 380-400 (419)
191 PRK12633 flgD flagellar basal 20.7 3.2E+02 0.0069 20.8 5.4 21 21-41 127-148 (230)
192 cd02784 MopB_CT_PHLH The MopB_ 20.6 37 0.0008 23.9 0.2 19 77-95 44-62 (137)
193 COG4869 PduL Propanediol utili 20.4 1.5E+02 0.0032 22.6 3.4 72 26-97 78-165 (210)
194 smart00326 SH3 Src homology 3 20.4 96 0.0021 16.6 2.0 18 78-95 14-31 (58)
195 cd02780 MopB_CT_Tetrathionate_ 20.3 53 0.0012 22.5 1.0 20 77-96 36-55 (143)
196 PF14268 YoaP: YoaP-like 20.3 1.1E+02 0.0024 17.8 2.2 23 55-77 13-35 (44)
197 cd02793 MopB_CT_DMSOR-BSOR-TMA 20.2 39 0.00085 22.8 0.3 19 77-95 39-57 (129)
198 PF10957 DUF2758: Protein of u 20.2 71 0.0015 19.8 1.4 16 85-100 26-41 (60)
199 COG0160 GabT 4-aminobutyrate a 20.1 58 0.0013 27.6 1.3 59 41-104 12-74 (447)
No 1
>KOG1769 consensus Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=9.6e-33 Score=187.42 Aligned_cols=74 Identities=53% Similarity=0.816 Sum_probs=72.3
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 22 SAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 22 ~~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
..+|+|||++|++++++|+||++|||+|||++||+++|+++++|||+|||+||.+.+||++|+|||||.|+|.-
T Consensus 18 ~~hi~LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~Gl~~~s~RFlFdG~rI~~~~TP~~L~mEd~D~Iev~~ 91 (99)
T KOG1769|consen 18 SEHINLKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQGLSMNSLRFLFDGQRIRETHTPADLEMEDGDEIEVVQ 91 (99)
T ss_pred cceEEEEEecCCCCEEEEEeecCChHHHHHHHHHHHcCCccceEEEEECCcCcCCCCChhhhCCcCCcEEEEEe
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999964
No 2
>COG5227 SMT3 Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=4.8e-30 Score=172.70 Aligned_cols=82 Identities=41% Similarity=0.671 Sum_probs=77.4
Q ss_pred CCCCCCCCCCCCCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCce
Q 034095 11 GQEEDKKPVDQSAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAF 90 (104)
Q Consensus 11 ~~~~~~kp~~~~~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdi 90 (104)
+..+++||+ ..+|+|||.+|+|++++|+||.+|+|+|||+|||.++|.+.++|||+|||+||..++||.+|+|||||+
T Consensus 13 ~~~p~vkp~--t~hinLkvv~qd~telfFkiKktT~f~klm~af~~rqGK~m~slRfL~dG~rI~~dqTP~dldmEdnd~ 90 (103)
T COG5227 13 NENPLVKPI--TKHINLKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQGKNMSSLRFLFDGKRIDLDQTPGDLDMEDNDE 90 (103)
T ss_pred ccCcccccc--ccccceEEecCCCCEEEEEEeccchHHHHHHHHHHHhCcCcceeEEEEcceecCCCCChhhcCCccchH
Confidence 456778885 689999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeee
Q 034095 91 CSCK 94 (104)
Q Consensus 91 i~~~ 94 (104)
|.+.
T Consensus 91 iEav 94 (103)
T COG5227 91 IEAV 94 (103)
T ss_pred HHHH
Confidence 9765
No 3
>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=99.91 E-value=4.8e-24 Score=140.45 Aligned_cols=76 Identities=59% Similarity=0.892 Sum_probs=73.3
Q ss_pred CCCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeeec
Q 034095 21 QSAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKYG 96 (104)
Q Consensus 21 ~~~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~~ 96 (104)
++.+|+|+|++++|..+.|+|+++++|++||++||++.|++++.+||+|+|.+|.+++||++|+|+|||+|||.+.
T Consensus 8 ~~~~i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~G~~L~~~~T~~~l~m~d~d~I~v~l~ 83 (87)
T cd01763 8 ISEHINLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFDGQRIRDNQTPDDLGMEDGDEIEVMLE 83 (87)
T ss_pred CCCeEEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEECCeECCCCCCHHHcCCCCCCEEEEEEe
Confidence 4789999999999999999999999999999999999999999999999999999999999999999999999753
No 4
>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=99.90 E-value=7.1e-24 Score=133.47 Aligned_cols=71 Identities=32% Similarity=0.632 Sum_probs=66.9
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCcc-ceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL-NSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~-~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
|+|+|++++|..+.|+|+++++|++||++||++.+++. ++++|.|||++|.+++||++++|+|||+|+|.|
T Consensus 1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~~L~~~~T~~~~~ied~d~Idv~I 72 (72)
T PF11976_consen 1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFDGKRLDPNDTPEDLGIEDGDTIDVII 72 (72)
T ss_dssp EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEETTEEE-TTSCHHHHT-STTEEEEEE-
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEECCEEcCCCCCHHHCCCCCCCEEEEEC
Confidence 78999999999999999999999999999999999999 999999999999999999999999999999986
No 5
>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=99.20 E-value=1.5e-10 Score=72.47 Aligned_cols=71 Identities=13% Similarity=0.274 Sum_probs=67.6
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
+.|.|+..+|..+.+++.++...+.|.+.++++.|++++..|++|+|..+.++.|.++++++||+.|.+..
T Consensus 1 m~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~g~~L~d~~tl~~~~i~~g~~i~l~~ 71 (76)
T cd01806 1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHLVL 71 (76)
T ss_pred CEEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEECCeEccCCCCHHHcCCCCCCEEEEEE
Confidence 35788888999999999999999999999999999999999999999999999999999999999999986
No 6
>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=98.91 E-value=1.2e-08 Score=63.11 Aligned_cols=70 Identities=17% Similarity=0.252 Sum_probs=66.3
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
|+|.|+..+|..+.+.+.++.+...|.+..+++.|++++..+++|+|..+.++.|.+++++.+|..|.+.
T Consensus 1 i~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~l~l~ 70 (72)
T cd01809 1 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDETLSEYKVEDGHTIHLV 70 (72)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCEECCCcCcHHHCCCCCCCEEEEE
Confidence 5788888899999999999999999999999999999999999999999999999999999999999875
No 7
>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=98.77 E-value=3.9e-08 Score=60.92 Aligned_cols=69 Identities=17% Similarity=0.151 Sum_probs=63.5
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
|+|.|+.. |....+.+.++.....|++..++..|++++..+++|+|..+.++.|..++++.+|+.|.|.
T Consensus 1 i~i~vk~~-g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~l~d~~~L~~~~i~~g~~l~v~ 69 (71)
T cd01812 1 IRVRVKHG-GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKERDDAETLDMSGVKDGSKVMLL 69 (71)
T ss_pred CEEEEEEC-CEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeCCcccCccCcHHHcCCCCCCEEEEe
Confidence 56777775 7777899999999999999999999999999999999999999999999999999999775
No 8
>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=98.75 E-value=9.4e-08 Score=59.00 Aligned_cols=64 Identities=8% Similarity=0.170 Sum_probs=60.4
Q ss_pred cCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 32 QDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 32 ~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
.+|..+.+.|.+++....|.+..++..+++++..+++|+|+.+.++.|-.++++.+|++|.+.+
T Consensus 3 ~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l~~ 66 (69)
T PF00240_consen 3 LSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHLVI 66 (69)
T ss_dssp TTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEETTEEESTTSBTGGGTTSTTEEEEEEE
T ss_pred CCCcEEEEEECCCCCHHHhhhhcccccccccccceeeeeeecccCcCcHHHcCCCCCCEEEEEE
Confidence 4677889999999999999999999999999999999999999999999999999999988764
No 9
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=98.74 E-value=1e-07 Score=59.56 Aligned_cols=70 Identities=13% Similarity=0.227 Sum_probs=66.2
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 26 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 26 ~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
.|.|+..+|..+.+.+.++.....|.+..+++.|++++..+++|+|..+.++.|-+++++.+|+.|.+..
T Consensus 2 ~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i~l~~ 71 (76)
T cd01803 2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 71 (76)
T ss_pred EEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCcHHHcCCCCCCEEEEEE
Confidence 4677888899999999999999999999999999999999999999999999999999999999999876
No 10
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=98.71 E-value=9e-08 Score=57.35 Aligned_cols=63 Identities=16% Similarity=0.296 Sum_probs=57.4
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCc
Q 034095 26 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCA 89 (104)
Q Consensus 26 ~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgd 89 (104)
.|.|+..+ ....+.+.+++....|....+++.|++++..+++|+|..+.++.|..++++.+|+
T Consensus 2 ~i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~g~~L~d~~tL~~~~i~~~~ 64 (64)
T smart00213 2 ELTVKTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYKGKVLEDDRTLADYNIQDGS 64 (64)
T ss_pred EEEEEECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEECCCCCCHHHcCCcCCC
Confidence 56666666 5778999999999999999999999999999999999999999999999999985
No 11
>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=98.69 E-value=1.7e-07 Score=59.28 Aligned_cols=70 Identities=17% Similarity=0.177 Sum_probs=64.9
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 26 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 26 ~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
.|.|+..+|..+.+.|.+++..+.|.+..+++.|++.+..+++|+|+.+.+++|.+++++.+|+.|.+..
T Consensus 2 ~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~l~l~~ 71 (74)
T cd01807 2 FLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKRLSDYSIGPNAKLNLVV 71 (74)
T ss_pred EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCCHHHCCCCCCCEEEEEE
Confidence 4667777899999999999999999999999999999999999999999999999999999999997653
No 12
>PTZ00044 ubiquitin; Provisional
Probab=98.69 E-value=1.8e-07 Score=58.89 Aligned_cols=71 Identities=8% Similarity=0.265 Sum_probs=66.7
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeeec
Q 034095 26 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKYG 96 (104)
Q Consensus 26 ~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~~ 96 (104)
.|.|+..+|..+.+.+.+++....|....+++.|++++..|++|+|..+.++.|-+++++.+|+.|.+..-
T Consensus 2 ~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~ 72 (76)
T PTZ00044 2 QILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQ 72 (76)
T ss_pred EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEEccCCCcHHHcCCCCCCEEEEEEE
Confidence 46777889999999999999999999999999999999999999999999999999999999999998764
No 13
>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=98.67 E-value=1.8e-07 Score=56.69 Aligned_cols=67 Identities=12% Similarity=0.174 Sum_probs=62.0
Q ss_pred EEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 29 VKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 29 V~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
|+..+|..+.+.+.++++++.|.+.++++.|++.+..+++|+|+.+..+.|..++++.+|+.|.|+.
T Consensus 2 v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~g~~l~d~~~l~~~~v~~~~~i~v~~ 68 (69)
T cd01769 2 VKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHLVL 68 (69)
T ss_pred eEccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCcCCCCcCCHHHCCCCCCCEEEEEE
Confidence 4555788889999999999999999999999999999999999999999999999999999998864
No 14
>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=98.62 E-value=2.8e-07 Score=57.56 Aligned_cols=67 Identities=22% Similarity=0.307 Sum_probs=63.0
Q ss_pred EEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 28 KVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 28 kV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
.|+...|..+.+.+.++...+.|.+..+++.|++.+..+++|.|+.+..++|.+++++.+|..+.+.
T Consensus 2 ~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~G~~L~d~~~l~~~~i~~~stl~l~ 68 (70)
T cd01798 2 YVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRNTTTIQECDLGQQSILHAV 68 (70)
T ss_pred EEEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEE
Confidence 4667789999999999999999999999999999999999999999999999999999999999874
No 15
>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=98.60 E-value=5.3e-07 Score=56.80 Aligned_cols=70 Identities=10% Similarity=0.162 Sum_probs=64.5
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCC--ccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 26 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSV--ELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 26 ~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~--~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
.|.|...+|....+.+.+++....|.+..+++.|+ +++..+++|+|..+.++.|-+++++.+|+.|-|.+
T Consensus 2 ~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~i~~~~ 73 (77)
T cd01805 2 KITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEEYKIDEKDFVVVMV 73 (77)
T ss_pred EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEECCEEccCCCCHHHcCCCCCCEEEEEE
Confidence 46667778889899999999999999999999999 99999999999999999999999999999988764
No 16
>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=98.56 E-value=6.6e-07 Score=57.35 Aligned_cols=71 Identities=8% Similarity=0.017 Sum_probs=66.8
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
+.|.|.+..|..+.+.+.+++..+.|.+..+++.|++++..|+.|.|..+.++.|-+++++.+|..|...|
T Consensus 2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~Gk~L~D~~tL~~ygi~~~stv~l~~ 72 (73)
T cd01791 2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHISLGDYEIHDGMNLELYY 72 (73)
T ss_pred EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeCCcCCCCCCCHHHcCCCCCCEEEEEe
Confidence 57888898899988999999999999999999999999999999999999999999999999999998876
No 17
>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=98.50 E-value=9e-07 Score=56.00 Aligned_cols=69 Identities=16% Similarity=0.267 Sum_probs=64.3
Q ss_pred EEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 27 LKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 27 lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
|.|+...|..+.+.|.++.....|.+..+++.|++.+..+++|+|+.+.++.|..++++.+|+.+++..
T Consensus 1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~G~~L~D~~tL~~~~i~~~~tl~l~~ 69 (74)
T cd01810 1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGRPMEDEHPLGEYGLKPGCTVFMNL 69 (74)
T ss_pred CEEECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCCHHHcCCCCCCEEEEEE
Confidence 356778899999999999999999999999999999999999999999999999999999999998764
No 18
>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=98.46 E-value=1.9e-06 Score=55.42 Aligned_cols=71 Identities=15% Similarity=0.152 Sum_probs=65.7
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeeec
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKYG 96 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~~ 96 (104)
++|.|+...|....+.+.+++..+.|.+..+++.+++++..|+.|.|..+.++ |-++++++||+.|.+..+
T Consensus 2 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~Gk~L~d~-~L~~~gi~~~~~i~l~~~ 72 (78)
T cd01804 2 MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSSG-KLQDLGLGDGSKLTLVPT 72 (78)
T ss_pred eEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEECCcCCCCC-cHHHcCCCCCCEEEEEee
Confidence 56788888888889999999999999999999999999999999999999988 999999999999998764
No 19
>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=98.43 E-value=1.4e-06 Score=55.98 Aligned_cols=74 Identities=18% Similarity=0.058 Sum_probs=67.8
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEE--EECCEecCCCCCccccCCcCCceeeeeeccc
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAF--LFDGRRLRGEQTPDEVILLFCAFCSCKYGRL 98 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF--~fdG~rI~~~~TP~~L~Medgdii~~~~~~~ 98 (104)
+.|.|+...|..+.+.+.++.....|.+..+++.|++.+..|+ .|+|..+.++.|-+++++.+|+.|.+..-.+
T Consensus 3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~~L~D~~tL~~~gi~~gs~l~l~~~~~ 78 (80)
T cd01792 3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQDGVPLVSQGLGPGSTVLLVVQNC 78 (80)
T ss_pred eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCCCCCCCCCHHHcCCCCCCEEEEEEEcc
Confidence 6788888889999899999999999999999999999999999 8999999999999999999999998876543
No 20
>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=98.40 E-value=3.7e-06 Score=57.17 Aligned_cols=75 Identities=7% Similarity=0.049 Sum_probs=70.4
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeeec
Q 034095 22 SAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKYG 96 (104)
Q Consensus 22 ~~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~~ 96 (104)
.+.+.|.|+...|..+.+.|.+++....|.+.-+++.|++.+..+++|.|+.+.++.|-+++++.+|+.|++...
T Consensus 25 ~~~M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~Gk~L~D~~tL~dy~I~~~stL~l~~~ 99 (103)
T cd01802 25 YDTMELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNMELEDEYCLNDYNISEGCTLKLVLA 99 (103)
T ss_pred CCCEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEe
Confidence 456888899999999999999999999999999999999999999999999999999999999999999998764
No 21
>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=98.36 E-value=4.3e-06 Score=52.38 Aligned_cols=70 Identities=16% Similarity=0.202 Sum_probs=62.4
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
|+|.|+...|.. .+.+.++.....|.+..+++.|++...+++.|.|+.+.++.|-+++++++|..|.+..
T Consensus 1 ~~i~vk~~~g~~-~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li~~Gk~L~d~~tL~~~~i~~~stl~l~~ 70 (71)
T cd01808 1 IKVTVKTPKDKE-EIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKILKDTDTLTQHNIKDGLTVHLVI 70 (71)
T ss_pred CEEEEEcCCCCE-EEEECCCChHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEE
Confidence 346666767764 7999999999999999999999999999999999999999999999999999998753
No 22
>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=98.33 E-value=4.2e-06 Score=53.04 Aligned_cols=69 Identities=16% Similarity=0.209 Sum_probs=64.7
Q ss_pred EEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 27 LKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 27 lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
|||+...|..+.+.+.+++....|...-+++.|++....|++|.|+.+.++.|..+.++.+|..|.|.+
T Consensus 1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~G~~L~D~~~l~~~~i~~~~tv~~~~ 69 (70)
T cd01794 1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGKLLTDKTRLQETKIQKDYVVQVIV 69 (70)
T ss_pred CeEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCCCHHHcCCCCCCEEEEEe
Confidence 477788899999999999999999999999999999999999999999999999999999999998864
No 23
>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=98.30 E-value=7.2e-06 Score=51.81 Aligned_cols=68 Identities=10% Similarity=0.113 Sum_probs=61.3
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 26 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 26 ~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
.|.|+. +....+.|.+++....|...-+++.|++.+..+++|.|+.+.+++|.+++++.++..|++..
T Consensus 2 qi~vk~--~~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~Gk~L~D~~tL~~~~i~~~~tl~l~~ 69 (74)
T cd01793 2 QLFVRA--QNTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLEDDATLGQCGVEELCTLEVAG 69 (74)
T ss_pred EEEEEC--CCEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEECCeECCCCCCHHHcCCCCCCEEEEEE
Confidence 345555 35678999999999999999999999999999999999999999999999999999999864
No 24
>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=98.29 E-value=6.4e-06 Score=53.21 Aligned_cols=70 Identities=16% Similarity=0.201 Sum_probs=62.9
Q ss_pred EEEEEccCCCE-EEEE-EeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 26 NLKVKGQDGNE-VFFR-IKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 26 ~lkV~~~~g~~-v~Fk-IK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
.|.|+...|.. +.+. +.++...+.|.+.-+++.|++.+..|++|.|+.+.+++|-+++++.+|++|.+..
T Consensus 2 ~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~Gk~L~D~~tL~~y~i~~~~~i~l~~ 73 (78)
T cd01797 2 WIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQMEDGHTLFDYNVGLNDIIQLLV 73 (78)
T ss_pred EEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeCCEECCCCCCHHHcCCCCCCEEEEEE
Confidence 46677778887 4674 7899999999999999999999999999999999999999999999999999864
No 25
>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=98.10 E-value=1.7e-05 Score=50.03 Aligned_cols=65 Identities=8% Similarity=0.073 Sum_probs=57.3
Q ss_pred EEcc-CCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCC-CCccccCCcCCceeee
Q 034095 29 VKGQ-DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGE-QTPDEVILLFCAFCSC 93 (104)
Q Consensus 29 V~~~-~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~-~TP~~L~Medgdii~~ 93 (104)
|+.. .|..+.+.+.++...+.|...-+++.|++.+..+++|+|+.+..+ .|-+++++.+|++|-+
T Consensus 3 v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~~Gk~L~D~~~~L~~~gi~~~~~l~l 69 (71)
T cd01796 3 VYTARSETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYNGRELVDNKRLLALYGVKDGDLVVL 69 (71)
T ss_pred EEECCCCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEECCeEccCCcccHHHcCCCCCCEEEE
Confidence 4444 677789999999999999999999999999999999999999887 4678999999998753
No 26
>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=98.02 E-value=5.1e-05 Score=42.29 Aligned_cols=64 Identities=16% Similarity=0.111 Sum_probs=58.3
Q ss_pred ccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 31 GQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 31 ~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
..++....+.+..+++++.|.+..+++.|.+.+.+++.++|..+....+..+....+|+.|.+.
T Consensus 4 ~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~ 67 (69)
T cd00196 4 LNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVLV 67 (69)
T ss_pred ecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECCeECCCCCcHHHcCCCCCCEEEEE
Confidence 3378888899999999999999999999999999999999999999988888899999998875
No 27
>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=97.99 E-value=3.9e-05 Score=48.77 Aligned_cols=63 Identities=10% Similarity=0.123 Sum_probs=58.7
Q ss_pred CCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 33 DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 33 ~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
+|..+.+.+.+++....|.+.-.+..|++++..+++|.|..+..+.|-+++++.+|++|.|..
T Consensus 6 ~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~G~~L~d~~tL~~~~i~~g~~l~v~~ 68 (76)
T cd01800 6 NGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIHLQL 68 (76)
T ss_pred CCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEEcCCCCcHHHcCCCCCCEEEEEE
Confidence 567778999999999999999999999999999999999999999999999999999998765
No 28
>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=97.95 E-value=4.7e-05 Score=62.23 Aligned_cols=73 Identities=14% Similarity=0.178 Sum_probs=67.2
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcC---CccceEEEEECCEecCCCCCccccCCcCCceeeeeeccc
Q 034095 26 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQS---VELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKYGRL 98 (104)
Q Consensus 26 ~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g---~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~~~~ 98 (104)
+|.|+...|..+.+.|..+.....|.+..++..| ++.+..|++|.|+.|.++.|-+++++.+|++|-|+.++-
T Consensus 2 kItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~GkiL~Dd~tL~dy~I~e~~~Ivvmv~k~ 77 (378)
T TIGR00601 2 TLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVREYKIKEKDFVVVMVSKP 77 (378)
T ss_pred EEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEECCEECCCCCcHHHcCCCCCCEEEEEeccC
Confidence 5677777888889999999999999999999998 999999999999999999999999999999999988764
No 29
>KOG0005 consensus Ubiquitin-like protein [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=97.60 E-value=0.0001 Score=46.80 Aligned_cols=67 Identities=15% Similarity=0.308 Sum_probs=62.7
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceee
Q 034095 26 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCS 92 (104)
Q Consensus 26 ~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~ 92 (104)
.|||+.-.|.++.+.|-++++..++.+...++-|+|+..-|++|-|...+++.|++...++.|-++-
T Consensus 2 ~iKvktLt~KeIeidIep~DkverIKErvEEkeGIPp~qqrli~~gkqm~DD~tA~~Y~~~~GSVlH 68 (70)
T KOG0005|consen 2 LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYAGKQMNDDKTAAHYNLLGGSVLH 68 (70)
T ss_pred eeeEeeeccceEEEeeCcchHHHHHHHHhhhhcCCCchhhhhhhccccccccccHHHhhhccceeEe
Confidence 4688888899999999999999999999999999999999999999999999999999999997763
No 30
>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.
Probab=97.57 E-value=0.00057 Score=43.88 Aligned_cols=62 Identities=8% Similarity=0.003 Sum_probs=54.8
Q ss_pred CCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecC-CCCCccccCCc-CCceeeeee
Q 034095 33 DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLR-GEQTPDEVILL-FCAFCSCKY 95 (104)
Q Consensus 33 ~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~-~~~TP~~L~Me-dgdii~~~~ 95 (104)
.|..+.+.+.++...+.|...-+++.|++++..|+ |+|.++. ++.|-++++++ +||.+-+.|
T Consensus 11 ~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~G~~L~dD~~tL~~ygi~~~g~~~~l~~ 74 (75)
T cd01799 11 HTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VIGQRLARDQETLYSHGIRTNGDSAFLYI 74 (75)
T ss_pred CCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-EcCCeeCCCcCCHHHcCCCCCCCEEEEEe
Confidence 56777899999999999999999999999999999 9999996 66999999999 778775543
No 31
>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=97.56 E-value=0.00012 Score=47.75 Aligned_cols=70 Identities=19% Similarity=0.209 Sum_probs=44.7
Q ss_pred CcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEEC---CEec--CCCCCccccCCcCCceeee
Q 034095 23 AHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFD---GRRL--RGEQTPDEVILLFCAFCSC 93 (104)
Q Consensus 23 ~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fd---G~rI--~~~~TP~~L~Medgdii~~ 93 (104)
..+-|+|++.+|.. ++.+.++..+..|++...+..+++.+++.++.+ ...+ ..++|-++|++..||++-+
T Consensus 3 ~~milRvrS~dG~~-Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L~~~~~~~~~l~s~~~~tl~~lglkHGdmlyL 77 (80)
T PF11543_consen 3 SSMILRVRSKDGMK-RIEVSPSSTLSDLKEKISEQLSIPDSSQSLSKDRNNKEELKSSDSKTLSSLGLKHGDMLYL 77 (80)
T ss_dssp ---EEEEE-SSEEE-EEEE-TTSBHHHHHHHHHHHS---TTT---BSSGGGGGCSSS-TT-CCCCT---TT-EEE-
T ss_pred ccEEEEEECCCCCE-EEEcCCcccHHHHHHHHHHHcCCCCcceEEEecCCCCcccccCCcCCHHHcCCCCccEEEE
Confidence 46789999999966 778999999999999999999999888776554 3445 4689999999999999854
No 32
>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=97.42 E-value=0.001 Score=42.42 Aligned_cols=67 Identities=13% Similarity=-0.018 Sum_probs=58.3
Q ss_pred EEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE---CCEecCCCCCccccCCcCCceeeee
Q 034095 27 LKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF---DGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 27 lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f---dG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
|.|.- .|....+.+..++++..|.+.-++..|++++.-+++| .|..+.++.|-.++++.+|+.|-++
T Consensus 3 i~vk~-~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~l~D~~~L~~~~i~~g~~i~lm 72 (74)
T cd01813 3 VIVKW-GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKPAEDDVKISALKLKPNTKIMMM 72 (74)
T ss_pred EEEEE-CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCcCCCCcCHHHcCCCCCCEEEEE
Confidence 34433 5666678999999999999999999999999999996 8999999999999999999998653
No 33
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=97.04 E-value=0.0035 Score=53.05 Aligned_cols=76 Identities=12% Similarity=0.149 Sum_probs=70.0
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeeeccc
Q 034095 22 SAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKYGRL 98 (104)
Q Consensus 22 ~~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~~~~ 98 (104)
...|.|+|+..+. ...|.|-.+...+-|.+.-+.+.+.+.+.++++|.|+-+++++|-..+++.||=-|-+.|..-
T Consensus 13 ~~~irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfaGrILKD~dTL~~~gI~Dg~TvHLVik~~ 88 (493)
T KOG0010|consen 13 ASLIRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYAGRILKDDDTLKQYGIQDGHTVHLVIKSQ 88 (493)
T ss_pred cceeEEEEecCCc-ceeEecccchHHHHHHHHHHHhcCCChhHeeeeecCccccChhhHHHcCCCCCcEEEEEeccC
Confidence 3578888888777 668999999999999999999999999999999999999999999999999999999988764
No 34
>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=97.01 E-value=0.0024 Score=40.44 Aligned_cols=62 Identities=13% Similarity=0.080 Sum_probs=43.1
Q ss_pred EEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCce
Q 034095 29 VKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAF 90 (104)
Q Consensus 29 V~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdi 90 (104)
|...+++...+++.+++.|..+.+.-|++.+++.+...+.+++..|.-+.+-.-.++-+|+-
T Consensus 1 vi~~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~~k~ldlslp~R~snL~n~ak 62 (65)
T PF11470_consen 1 VICYNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHNNKPLDLSLPFRLSNLPNNAK 62 (65)
T ss_dssp EE-TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEETTEEESSS-BHHHH---SS-E
T ss_pred CCccCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEECCEEeccccceeecCCCCCCE
Confidence 45678899999999999999999999999999999999999999998777666666666653
No 35
>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=96.93 E-value=0.0085 Score=39.24 Aligned_cols=69 Identities=9% Similarity=0.022 Sum_probs=58.8
Q ss_pred EEEEEEccCCCEEEEEE--eCCchHHHHHHHHHHHcC--CccceEEEEECCEecCCCCCccccC--CcCCceeee
Q 034095 25 INLKVKGQDGNEVFFRI--KRSTQLKKLMNAYCDRQS--VELNSIAFLFDGRRLRGEQTPDEVI--LLFCAFCSC 93 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkI--K~tt~L~kLm~aY~~~~g--~~~~~lrF~fdG~rI~~~~TP~~L~--Medgdii~~ 93 (104)
|+|.|+..++....|.| .++...+.|.+.-++..+ .+++..|++|.|+-+.+++|-+++. +.+|-.|-.
T Consensus 2 i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKiLkD~~tL~~~~~~~~~~~tiHL 76 (79)
T cd01790 2 VTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRDVLRKQDEYHMVHL 76 (79)
T ss_pred eEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCeeccchhhHHHHhhcccCCceEEE
Confidence 78999998988877777 799999999999998875 4579999999999999999999985 777766643
No 36
>PLN02560 enoyl-CoA reductase
Probab=96.48 E-value=0.014 Score=46.49 Aligned_cols=69 Identities=16% Similarity=0.152 Sum_probs=57.5
Q ss_pred EEEEEccCCCEE---EEEEeCCchHHHHHHHHHHHcCC-ccceEEEEEC---CE----ecCCCCCccccCCcCCceeeee
Q 034095 26 NLKVKGQDGNEV---FFRIKRSTQLKKLMNAYCDRQSV-ELNSIAFLFD---GR----RLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 26 ~lkV~~~~g~~v---~FkIK~tt~L~kLm~aY~~~~g~-~~~~lrF~fd---G~----rI~~~~TP~~L~Medgdii~~~ 94 (104)
+|.|+..+|..+ .+.+.++++.+.|.++++++.+. +++..|+.++ |. .+..+.|-.++++.+|..|-|+
T Consensus 2 ~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstLy~k 81 (308)
T PLN02560 2 KVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTVVFK 81 (308)
T ss_pred EEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceEEEE
Confidence 455667677776 68899999999999999999885 8899999983 43 6788889999999999988776
No 37
>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=96.45 E-value=0.008 Score=39.11 Aligned_cols=52 Identities=19% Similarity=0.154 Sum_probs=45.3
Q ss_pred CchHHHHHHHHHHHc--CC-ccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 44 STQLKKLMNAYCDRQ--SV-ELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 44 tt~L~kLm~aY~~~~--g~-~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
++.-..|.+..+++. |+ +.+..|++|.|+.+.++.|-++.++.+|++|-++.
T Consensus 20 ~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~ 74 (75)
T cd01815 20 GYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR 74 (75)
T ss_pred cCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence 446778888888886 46 48999999999999999999999999999998875
No 38
>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=96.35 E-value=0.046 Score=35.48 Aligned_cols=70 Identities=13% Similarity=0.107 Sum_probs=55.4
Q ss_pred EEEEEEcc-CCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEE-EECCE-----ec-CCCCCccccCCcCCceeeee
Q 034095 25 INLKVKGQ-DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAF-LFDGR-----RL-RGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 25 I~lkV~~~-~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF-~fdG~-----rI-~~~~TP~~L~Medgdii~~~ 94 (104)
|+|.|.+. .......++.++.+...|.+.-....|++++..|+ +|+|. .+ .++.|-.+++++||..|-|.
T Consensus 2 v~v~i~~~~~~~~~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~~~~~~~l~~d~~~L~~y~~~dg~~IhVv 79 (84)
T cd01789 2 VTVNITSSADSFSFEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGDDKLVSKLDDDDALLGSYPVDDGCRIHVI 79 (84)
T ss_pred EEEEEEeCCCceeeeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCCCCeEeecCCCccEeeeccCCCCCEEEEE
Confidence 34555543 23344677999999999999999999999999999 57888 34 46788999999999998764
No 39
>PF08817 YukD: WXG100 protein secretion system (Wss), protein YukD; InterPro: IPR014921 YukD is a bacterial protein that adopts a ubiquitin-like fold []. Ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that YukD lacks the capacity for covalent bond formation with other proteins []. ; PDB: 2BPS_B.
Probab=96.29 E-value=0.018 Score=36.78 Aligned_cols=70 Identities=13% Similarity=0.103 Sum_probs=51.0
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCcc---c---eEEEE-ECCEecCCCCCccccCCcCCceeee
Q 034095 24 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL---N---SIAFL-FDGRRLRGEQTPDEVILLFCAFCSC 93 (104)
Q Consensus 24 ~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~---~---~lrF~-fdG~rI~~~~TP~~L~Medgdii~~ 93 (104)
.+.|.|...+|..+-+.+-.+.|++.|+..-.+..+.+. . .+++. -+|..+.+++|-++.+..|||++-+
T Consensus 2 ~~rVtv~~~~~~~~Dl~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~~~~g~~L~~~~tL~~~gV~dGd~L~L 78 (79)
T PF08817_consen 2 LCRVTVDAGNGRQVDLALPADVPVAELIPELVELLGLPGDDPPGHGQWVLARAGGRPLDPDQTLADAGVRDGDVLVL 78 (79)
T ss_dssp EEEEEEE-TT--EEEEEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG-GGTEEEETTSBCGGGT--TT-EEEE
T ss_pred EEEEEEEcCCCcEEEEEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEEecCCcccCCcCcHhHcCCCCCCEEEe
Confidence 467777775678899999999999999999999877522 2 46666 6899999999999999999998754
No 40
>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and ATGP4 are plant-specific isoprenylated GTP-binding proteins with a single fold that resembles ubiquitin. The function of these proteins is unknown.
Probab=96.25 E-value=0.0099 Score=41.55 Aligned_cols=70 Identities=17% Similarity=0.219 Sum_probs=61.1
Q ss_pred CcEEEEEEccCCCEE-EEEEeCCchHHHHHHHHHHHcC-------CccceEEEEECCEecCCCCCccccCCcCCceee
Q 034095 23 AHINLKVKGQDGNEV-FFRIKRSTQLKKLMNAYCDRQS-------VELNSIAFLFDGRRLRGEQTPDEVILLFCAFCS 92 (104)
Q Consensus 23 ~~I~lkV~~~~g~~v-~FkIK~tt~L~kLm~aY~~~~g-------~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~ 92 (104)
+.|.||.+-.||+.| -|++.+++.-..|.+.-.+..+ .+.+.++++|.|+.+..+.|-+++++-=||+++
T Consensus 3 ~~~e~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGKiLeD~~TL~d~~~p~g~~~~ 80 (113)
T cd01814 3 EQIEIKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGKILENSKTVGECRSPVGDIAG 80 (113)
T ss_pred ccEEEEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCeecCCCCcHHHhCCcccccCC
Confidence 467899999999999 9999999999999999885553 448999999999999999999999977777754
No 41
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=95.87 E-value=0.17 Score=31.93 Aligned_cols=72 Identities=25% Similarity=0.268 Sum_probs=56.3
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccce-EEEE--ECCEecCCCC--CccccCCcCCceeee
Q 034095 22 SAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNS-IAFL--FDGRRLRGEQ--TPDEVILLFCAFCSC 93 (104)
Q Consensus 22 ~~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~-lrF~--fdG~rI~~~~--TP~~L~Medgdii~~ 93 (104)
.+.++|+|+-.+|..+.-+..++.+++.|++.-......+... +++. |--..+..++ |-+++++--+..+-|
T Consensus 4 ~~~~~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~~~Pr~~l~~~~~~tl~e~~l~p~~~l~v 80 (82)
T PF00789_consen 4 SDVVRIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELITAFPRRELTDEDSKTLEEAGLLPSATLIV 80 (82)
T ss_dssp SSEEEEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEESSSTEECCSTTTSBTCCCTTSSCEEEEE
T ss_pred CCEEEEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEeCCCCcCCCccccccHHHhcCCCCeEEEE
Confidence 4678999999999999999999999999997766665555444 7775 5567777654 889998888777654
No 42
>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-terminal domain of Tsc13. Tsc13 is an enoyl reductase involved in elongation of long chain fatty acids that localizes to the endoplasmic reticulum and is highly enriched in a novel structure marking nuclear-vacuolar junctions.
Probab=95.83 E-value=0.051 Score=34.43 Aligned_cols=53 Identities=11% Similarity=0.117 Sum_probs=44.7
Q ss_pred eCCchHHHHHHHHHHHcC-CccceEEEE--ECCEecCCCCCccccCCcCCceeeee
Q 034095 42 KRSTQLKKLMNAYCDRQS-VELNSIAFL--FDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 42 K~tt~L~kLm~aY~~~~g-~~~~~lrF~--fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
.++.....|.+++++..+ ++.+..|+. +.|..|..+.|-.++++.+|..|-|+
T Consensus 20 ~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~~~~g~~L~d~~tL~~~gv~~g~~lyvK 75 (77)
T cd01801 20 SGDATIADLKKLIAKSSPQLTVNRQSLRLEPKGKSLKDDDTLVDLGVGAGATLYVR 75 (77)
T ss_pred CCCccHHHHHHHHHHHcCCCCcceeEEEeCCCCcccCCcccHhhcCCCCCCEEEEe
Confidence 466789999999999875 577887775 78999999999999999999877664
No 43
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=95.35 E-value=0.14 Score=32.98 Aligned_cols=70 Identities=9% Similarity=0.075 Sum_probs=55.4
Q ss_pred EEEEEEccCC--CEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEEC----CEec----CCCCCccccCCcCCceeeee
Q 034095 25 INLKVKGQDG--NEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFD----GRRL----RGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 25 I~lkV~~~~g--~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fd----G~rI----~~~~TP~~L~Medgdii~~~ 94 (104)
|+|.|.+..- ..+..++.++.++..|...-....|++++..++.+- +..+ .++.|-.++++.||+.|-|.
T Consensus 2 v~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~V~ 81 (87)
T PF14560_consen 2 VKLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIHVV 81 (87)
T ss_dssp EEEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEEEE
T ss_pred EEEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEEEE
Confidence 6677776554 377899999999999999999999999999998874 3333 35788889999999999774
No 44
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=94.90 E-value=0.12 Score=34.46 Aligned_cols=50 Identities=22% Similarity=0.312 Sum_probs=43.2
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCcc---ceEEEEE---CCEecC
Q 034095 26 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL---NSIAFLF---DGRRLR 75 (104)
Q Consensus 26 ~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~---~~lrF~f---dG~rI~ 75 (104)
..|++++.|..++|++.++..+..|+++-++|.|.+. +.+.+.| +|..|.
T Consensus 2 ~FK~~~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~YlDDEgD~Vl 57 (86)
T cd06409 2 AFKFKDPKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSYVDDEGDIVL 57 (86)
T ss_pred cEEeeCCCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEEEcCCCCEEE
Confidence 3688899999999999999999999999999999886 6888888 465553
No 45
>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=94.10 E-value=0.88 Score=29.74 Aligned_cols=71 Identities=14% Similarity=0.025 Sum_probs=55.6
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECC--EecC--------CCCCccccCCcCCcee
Q 034095 22 SAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDG--RRLR--------GEQTPDEVILLFCAFC 91 (104)
Q Consensus 22 ~~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG--~rI~--------~~~TP~~L~Medgdii 91 (104)
.+.++|.|+-.+|+.+.-+...+.+++.|++.... .+..+..+++..+= +.+. .+.|-+++||....++
T Consensus 2 ~~~~~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~-~~~~~~~f~L~t~FPrr~~~~~~~~~~~~~~TL~eaGL~~s~~L 80 (85)
T cd01774 2 PDTVKIVFKLPNGTRVERRFLFTQSLRVIHDFLFS-LKETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLLEAGLSNSEVL 80 (85)
T ss_pred CceEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-CCCCCCcEEEecCCCCccccccccccCcCCCCHHHcCCCCccEE
Confidence 35678888899999999999999999999998843 45556778877754 5554 3679999999888776
Q ss_pred ee
Q 034095 92 SC 93 (104)
Q Consensus 92 ~~ 93 (104)
-|
T Consensus 81 ~V 82 (85)
T cd01774 81 FV 82 (85)
T ss_pred EE
Confidence 55
No 46
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=94.09 E-value=0.19 Score=40.92 Aligned_cols=72 Identities=14% Similarity=0.158 Sum_probs=63.3
Q ss_pred EEEEccCCCEEEEEEeCCchHHHHHHHHHHHcC--CccceEEEEECCEecCCCCCccccCCcCCceeeeeeccc
Q 034095 27 LKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQS--VELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKYGRL 98 (104)
Q Consensus 27 lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g--~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~~~~ 98 (104)
|.|+.-.+......++++..+..++..-+...| .+...-+++|+|+-+.++.|-.+....+++||-|..-+-
T Consensus 3 lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLIy~GkiL~D~~tv~Eykv~E~~fiVvMlsK~ 76 (340)
T KOG0011|consen 3 LTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLIYSGKILKDETTVGEYKVKEKKFIVVMLSKD 76 (340)
T ss_pred eEeeeccCceeEeecCcchhHHHHHHHHHhccCCCCchhhheeeecceeccCCcchhhhccccCceEEEEEecC
Confidence 445555666778899999999999999999998 888999999999999999999999999999999976543
No 47
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=93.87 E-value=0.69 Score=28.88 Aligned_cols=60 Identities=13% Similarity=0.160 Sum_probs=45.6
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
|+|++-+.. .+..+.+...+.++.|.+. .+++...+....||+-+. .+--+.+||.|.++
T Consensus 5 m~v~vng~~-~~~~~~~~~~~tv~~ll~~----l~~~~~~v~v~vNg~iv~-----~~~~l~~gD~Veii 64 (70)
T PRK08364 5 IRVKVIGRG-IEKEIEWRKGMKVADILRA----VGFNTESAIAKVNGKVAL-----EDDPVKDGDYVEVI 64 (70)
T ss_pred EEEEEeccc-cceEEEcCCCCcHHHHHHH----cCCCCccEEEEECCEECC-----CCcCcCCCCEEEEE
Confidence 677774432 2446777888888888855 478888999999999994 45669999999886
No 48
>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=93.60 E-value=0.21 Score=38.42 Aligned_cols=71 Identities=11% Similarity=0.163 Sum_probs=50.0
Q ss_pred cEEEEEEccCCCEE----EEEEeCCchHHHHHHHHHHHcCCccceEEEEECC------EecCCCCCccccCCcCCceeee
Q 034095 24 HINLKVKGQDGNEV----FFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDG------RRLRGEQTPDEVILLFCAFCSC 93 (104)
Q Consensus 24 ~I~lkV~~~~g~~v----~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG------~rI~~~~TP~~L~Medgdii~~ 93 (104)
-|-||.=|.....+ ++-|.++.+++.|....+++.|++.++=-.+|+- +.|..+.|-+..++.|||||-+
T Consensus 70 LlFlK~fDp~~q~L~~iGh~~v~~~~~v~~l~~~i~~~~g~p~~t~l~lyEEi~~~~ie~i~~~~t~~~~el~~GdIi~f 149 (249)
T PF12436_consen 70 LLFLKYFDPETQTLRYIGHVYVPKNDKVSELVPLINERAGLPPDTPLLLYEEIKPNMIEPIDPNQTFEKAELQDGDIICF 149 (249)
T ss_dssp EEEEEEEETTTTEEEEEEEEEEETT-BGGGTHHHHHHHHT--TT--EEEEEEEETTEEEE--SSSBHHHTT--TTEEEEE
T ss_pred EEEEEeeCCCCCEEEEEeEEEECCCCCHHHHHHHHHHHcCCCCCCceEEEEEeccceeeEcCCCCchhhcccCCCCEEEE
Confidence 34555557766665 7889999999999999999999988765555643 5577899999999999999976
Q ss_pred e
Q 034095 94 K 94 (104)
Q Consensus 94 ~ 94 (104)
=
T Consensus 150 Q 150 (249)
T PF12436_consen 150 Q 150 (249)
T ss_dssp E
T ss_pred E
Confidence 3
No 49
>COG5417 Uncharacterized small protein [Function unknown]
Probab=93.14 E-value=1.1 Score=29.58 Aligned_cols=70 Identities=11% Similarity=0.188 Sum_probs=57.9
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCcc-----ceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL-----NSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~-----~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
||+-....+|.+.-.++.---|.++|..--.+...++. ..+|..=.++-+.+++--.+.+..||||.-.|
T Consensus 7 VTvD~t~y~g~~yDLrl~d~~pikklIdivwe~~kis~~~reg~~Ikv~nKa~llsgd~kL~d~~IadGD~LeiL 81 (81)
T COG5417 7 VTVDFTNYNGGTYDLRLPDYLPIKKLIDIVWESLKISIFDREGTQIKVMNKAQLLSGDDKLIDYQIADGDILEIL 81 (81)
T ss_pred EEEEeEecCCceEEEeccccchHHHHHHHHHHHhhccccccCCCEEEEeccceEecCCceEEeccccCCCEEEeC
Confidence 45556778899999999999999999999888765433 45667677899999999999999999997654
No 50
>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A.
Probab=92.66 E-value=1.3 Score=30.43 Aligned_cols=68 Identities=22% Similarity=0.255 Sum_probs=52.5
Q ss_pred CcEEEEEEccCCC-EEEEEEeCCchHHHHHHHHHHHc-------CCccceEEEEECCEecCCCCCccccCCcCCce
Q 034095 23 AHINLKVKGQDGN-EVFFRIKRSTQLKKLMNAYCDRQ-------SVELNSIAFLFDGRRLRGEQTPDEVILLFCAF 90 (104)
Q Consensus 23 ~~I~lkV~~~~g~-~v~FkIK~tt~L~kLm~aY~~~~-------g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdi 90 (104)
+.|+||.+-.+|. ...|..-+++.-..|.+.--..- -.+.+.+|++|.|+-|.++.|-.++.+--|+.
T Consensus 1 ~~i~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d~~tL~~~~~~~~~~ 76 (111)
T PF13881_consen 1 DKIELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILEDNKTLSDCRLPSGET 76 (111)
T ss_dssp TSEEEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-SSSBTGGGT--TTSE
T ss_pred CeEEEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCCcCcHHHhCCCCCCC
Confidence 3688999988999 66999999999999998776542 23568999999999999999999998887774
No 51
>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=92.48 E-value=0.65 Score=30.33 Aligned_cols=65 Identities=14% Similarity=0.172 Sum_probs=45.7
Q ss_pred cEEEEEEc---cCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE-CCEecCCCCCccccCCcCC
Q 034095 24 HINLKVKG---QDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF-DGRRLRGEQTPDEVILLFC 88 (104)
Q Consensus 24 ~I~lkV~~---~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f-dG~rI~~~~TP~~L~Medg 88 (104)
++++|+.- ..--...|.|-..+||..+.+.-|+...++..+--.+- ||.-|++.||.-+.-|..|
T Consensus 2 kvtfKI~ltsDp~~p~kv~sVPE~apftaVlkfaAeeF~vp~~tsaiItndG~GInP~QTag~vflKhG 70 (76)
T PF03671_consen 2 KVTFKITLTSDPKLPYKVISVPEEAPFTAVLKFAAEEFKVPPATSAIITNDGVGINPQQTAGNVFLKHG 70 (76)
T ss_dssp EEEEEEEESTSSTS-EEEEEEETTSBHHHHHHHHHHHTTS-SSSEEEEESSS-EE-TTSBHHHHHHHT-
T ss_pred cEEEEEEEccCCCCcceEEecCCCCchHHHHHHHHHHcCCCCceEEEEecCCcccccchhhhhhHhhcC
Confidence 45555542 22233478899999999999999999999886555544 8999999999987766555
No 52
>smart00455 RBD Raf-like Ras-binding domain.
Probab=92.06 E-value=1.4 Score=27.77 Aligned_cols=45 Identities=9% Similarity=0.220 Sum_probs=40.2
Q ss_pred EEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECC
Q 034095 27 LKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDG 71 (104)
Q Consensus 27 lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG 71 (104)
.+|.-++|......+|++.++..+...-|++.|+.+......+-|
T Consensus 2 ~~v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~g 46 (70)
T smart00455 2 CKVHLPDNQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRG 46 (70)
T ss_pred eEEECCCCCEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEcC
Confidence 466778999999999999999999999999999999888887754
No 53
>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=92.01 E-value=0.69 Score=32.03 Aligned_cols=60 Identities=18% Similarity=0.063 Sum_probs=54.5
Q ss_pred EEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCC-CCCccccCCcCCceeeeee
Q 034095 36 EVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRG-EQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 36 ~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~-~~TP~~L~Medgdii~~~~ 95 (104)
++...|.+++.+..|...--++.++++..=+++|||+-+.+ ..|-.++++--+.+|-+|+
T Consensus 16 ~~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~Lli 76 (107)
T cd01795 16 EKALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKA 76 (107)
T ss_pred CceEEeCccccHHHHHHHHHHHhcCCcccceeeecCceeccCCccHHhcCCCCCCEEEEEe
Confidence 56778999999999999999999999999999999998886 6688899999999999987
No 54
>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=91.43 E-value=0.7 Score=30.41 Aligned_cols=68 Identities=16% Similarity=0.221 Sum_probs=52.2
Q ss_pred cEEEEEEccCCCEE---EEEEeCCchHHHHHHHHHHHcCCccceEEEEE-CCEecCCCCCccccCCcCCcee
Q 034095 24 HINLKVKGQDGNEV---FFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF-DGRRLRGEQTPDEVILLFCAFC 91 (104)
Q Consensus 24 ~I~lkV~~~~g~~v---~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f-dG~rI~~~~TP~~L~Medgdii 91 (104)
+++.|+.-.....+ .++|-..+||..+.+.-|+...++..+--.+- ||.-|++.||+-..-|..|--+
T Consensus 2 KVtFkitltSdp~lpfkvlsVpE~aPftAvlkfaAEeFkv~~~TsAiiTndGvGINP~qtAGnvflkhgsel 73 (82)
T cd01766 2 KVTFKITLTSDPKLPFKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSEL 73 (82)
T ss_pred ceEEEEEecCCCCCcceEEeccccCchHHHHHHHHHhcCCCccceeEEecCccccChhhcccceeeecCCEe
Confidence 45556554333333 56788999999999999999999886655544 8999999999999988877544
No 55
>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=91.37 E-value=1.3 Score=27.31 Aligned_cols=54 Identities=15% Similarity=0.110 Sum_probs=42.9
Q ss_pred EEEEEEeCCchHHHHHHHHHHHcC----CccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 36 EVFFRIKRSTQLKKLMNAYCDRQS----VELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 36 ~v~FkIK~tt~L~kLm~aY~~~~g----~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
+..+.+...+.++.|.+...++.+ .....+.+..||+.+. .+.-+.+||.|.++
T Consensus 17 ~~~~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~-----~~~~l~~gD~v~i~ 74 (80)
T cd00754 17 EEELELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVR-----LDTPLKDGDEVAII 74 (80)
T ss_pred eEEEECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcC-----CCcccCCCCEEEEe
Confidence 456677678899999999988864 3567889999999998 33459999999875
No 56
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=90.28 E-value=1 Score=37.24 Aligned_cols=46 Identities=20% Similarity=0.369 Sum_probs=42.3
Q ss_pred EEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCcc
Q 034095 36 EVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPD 81 (104)
Q Consensus 36 ~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~ 81 (104)
.+.+.|+-+|....|.+..+++.|++.+.|+.+|-|+.++.+-|-.
T Consensus 15 ~l~v~v~~~t~I~~lke~Vak~~gvp~D~L~viFaGKeLs~~ttv~ 60 (446)
T KOG0006|consen 15 GLPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELSNDTTVQ 60 (446)
T ss_pred ceeEEEecCCCHHHHHHHHHHhhCCChhheEEEEeccccccCceee
Confidence 3577889999999999999999999999999999999999888777
No 57
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=89.97 E-value=3.4 Score=26.04 Aligned_cols=71 Identities=15% Similarity=0.139 Sum_probs=52.0
Q ss_pred CcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE--CCEecCC---CCCccccCCcCCceeee
Q 034095 23 AHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF--DGRRLRG---EQTPDEVILLFCAFCSC 93 (104)
Q Consensus 23 ~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f--dG~rI~~---~~TP~~L~Medgdii~~ 93 (104)
+..+|.|+-.+|..+.-+...+++++.|++......+.+...+.|.- --+.+.. +.|-.++++--+..+-|
T Consensus 3 ~~~~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~~~~~~f~L~t~~Prk~l~~~d~~~tL~e~gL~p~~~l~v 78 (80)
T smart00166 3 DQCRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALTDGNDPFTLNSPFPRRTFTKDDYSKTLLELALLPSSTLVL 78 (80)
T ss_pred CeEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcccCCCCCEEEEeCCCCcCCccccccCCHHHCCCCCceEEEE
Confidence 45678888899999999999999999999988555555555666654 3444443 35888888776666544
No 58
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=89.64 E-value=3.5 Score=25.73 Aligned_cols=67 Identities=15% Similarity=0.146 Sum_probs=49.0
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE--CCEecC---CCCCccccCCcCCcee
Q 034095 24 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF--DGRRLR---GEQTPDEVILLFCAFC 91 (104)
Q Consensus 24 ~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f--dG~rI~---~~~TP~~L~Medgdii 91 (104)
..+|+|+-.+|+.+.-+...+++++.|++.--.... +...+.++- -.+.+. .+.|-+++|+....++
T Consensus 2 ~t~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~-~~~~f~L~t~~Pr~~~~~~~~~~TL~e~gL~~s~~~ 73 (77)
T cd01767 2 TTKIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGP-PAEPFTLMTSFPRRVLTDLDYELTLQEAGLVNEVVF 73 (77)
T ss_pred cEEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCC-CCCCEEEEeCCCCccCCCCCccCcHHHcCCccceEE
Confidence 357888889999998899999999999987654432 255566654 345554 4889999999955443
No 59
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=89.41 E-value=3 Score=25.00 Aligned_cols=55 Identities=11% Similarity=0.097 Sum_probs=37.6
Q ss_pred CCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 33 DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 33 ~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
+|.. +.+...+.+..|.+.+ ++. ..+.+..||+.+...+ -.+.-+.+||.|.++-
T Consensus 6 Ng~~--~~~~~~~tl~~ll~~l----~~~-~~~~v~vN~~~v~~~~-~~~~~L~~gD~vei~~ 60 (65)
T PRK06944 6 NQQT--LSLPDGATVADALAAY----GAR-PPFAVAVNGDFVARTQ-HAARALAAGDRLDLVQ 60 (65)
T ss_pred CCEE--EECCCCCcHHHHHHhh----CCC-CCeEEEECCEEcCchh-cccccCCCCCEEEEEe
Confidence 4544 4556677788888765 333 4578899999986432 2233499999999873
No 60
>PRK06437 hypothetical protein; Provisional
Probab=89.23 E-value=3.4 Score=25.65 Aligned_cols=52 Identities=4% Similarity=0.017 Sum_probs=42.0
Q ss_pred CCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 34 GNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 34 g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
+.+..+.+...+.++.|.+. .+++...+-...||+.|. .+.-+.+||.|.++
T Consensus 10 ~~~~~~~i~~~~tv~dLL~~----Lgi~~~~vaV~vNg~iv~-----~~~~L~dgD~Veiv 61 (67)
T PRK06437 10 HINKTIEIDHELTVNDIIKD----LGLDEEEYVVIVNGSPVL-----EDHNVKKEDDVLIL 61 (67)
T ss_pred CcceEEEcCCCCcHHHHHHH----cCCCCccEEEEECCEECC-----CceEcCCCCEEEEE
Confidence 34456778888888888865 588999999999999996 56678899999886
No 61
>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=89.16 E-value=2 Score=26.70 Aligned_cols=44 Identities=14% Similarity=0.320 Sum_probs=37.1
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF 69 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f 69 (104)
++|||.- .+....|.+.+..+|..|...-+++.+.+...+++.|
T Consensus 2 ~~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y 45 (81)
T smart00666 2 VDVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKY 45 (81)
T ss_pred ccEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEE
Confidence 4667765 5556699999999999999999999998878888888
No 62
>KOG4248 consensus Ubiquitin-like protein, regulator of apoptosis [Posttranslational modification, protein turnover, chaperones]
Probab=88.91 E-value=1.1 Score=41.38 Aligned_cols=68 Identities=16% Similarity=0.191 Sum_probs=62.5
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 26 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 26 ~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
+|+|+.-|..+..|.|.--...+.+.+.-.++++++.+.=|++|.|+-|..++|-.+.+. ||-+|-+.
T Consensus 4 ~v~vktld~r~~t~~ig~q~ti~~~~d~~r~~~ni~s~~qr~i~~grvl~~~k~vq~~~v-dgk~~hlv 71 (1143)
T KOG4248|consen 4 NVLVKTLDSRTRTFIIGAQMTIKEFKDHIRASVNIPSEKQRLIYQGRVLQDDKKVQEYNV-DGKVIHLV 71 (1143)
T ss_pred ceeeeecccceeEEEechHHHHHHHHHHHHHhcccccccceeeecceeeccchhhhhccC-CCeEEEee
Confidence 477777788888999999999999999999999999999999999999999999999999 99888653
No 63
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=88.60 E-value=4.7 Score=25.83 Aligned_cols=68 Identities=13% Similarity=0.261 Sum_probs=50.7
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcC-CccceEEEE--ECCEecCC-CCCccccCCcCCcee
Q 034095 24 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQS-VELNSIAFL--FDGRRLRG-EQTPDEVILLFCAFC 91 (104)
Q Consensus 24 ~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g-~~~~~lrF~--fdG~rI~~-~~TP~~L~Medgdii 91 (104)
..+|.|+-.||+.+.-+...+.+++.|++.-....+ -....+.+. |=.+.+.. +.|-++++|.+.-++
T Consensus 4 ~t~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~~~~~~f~L~t~fP~k~l~~~~~Tl~eagL~~s~v~ 75 (79)
T cd01770 4 TTSIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPEFAARPFTLMTAFPVKELSDESLTLKEANLLNAVIV 75 (79)
T ss_pred eeEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCCCCCCCEEEecCCCCcccCCCCCcHHHCCCcCcEEE
Confidence 457888889999998899999999999987766543 223556664 55665554 789999999975554
No 64
>TIGR01687 moaD_arch MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.
Probab=88.14 E-value=4.2 Score=25.81 Aligned_cols=56 Identities=14% Similarity=0.109 Sum_probs=41.4
Q ss_pred CEEEEEEeCCchHHHHHHHHHHHcCC-----------ccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 35 NEVFFRIKRSTQLKKLMNAYCDRQSV-----------ELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 35 ~~v~FkIK~tt~L~kLm~aY~~~~g~-----------~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
.++.+.+. .+.++.|++..+++..- -...+.+..||+.+..++. ..++|||.|.++
T Consensus 16 ~~~~v~~~-~~tv~~l~~~l~~~~p~~~~~~l~~~~~~~~~~~v~vN~~~v~~~~~---~~l~dgdev~i~ 82 (88)
T TIGR01687 16 KSEEIEIE-GKTVGDLLNELMARYPKEFSELFKEGLGLVPNVIILVNGRNVDWGLG---TELKDGDVVAIF 82 (88)
T ss_pred ceEEEEeC-CCCHHHHHHHHHHHCcHHHHHhCccCCcccccEEEEECCEecCccCC---CCCCCCCEEEEe
Confidence 34555665 78899999999888641 1245899999999986542 569999999875
No 65
>PRK07440 hypothetical protein; Provisional
Probab=87.73 E-value=4.9 Score=25.16 Aligned_cols=61 Identities=16% Similarity=0.178 Sum_probs=46.1
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 24 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 24 ~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
.|+|+| +|.. +.+.....+..|.+ ..+++...+-.-.||+-|..++= ++..+.+||.|.++
T Consensus 4 ~m~i~v---NG~~--~~~~~~~tl~~lL~----~l~~~~~~vav~~N~~iv~r~~w-~~~~L~~gD~IEIv 64 (70)
T PRK07440 4 PITLQV---NGET--RTCSSGTSLPDLLQ----QLGFNPRLVAVEYNGEILHRQFW-EQTQVQPGDRLEIV 64 (70)
T ss_pred ceEEEE---CCEE--EEcCCCCCHHHHHH----HcCCCCCeEEEEECCEEeCHHHc-CceecCCCCEEEEE
Confidence 577777 5544 56667777887775 67889999999999999985433 34459999999886
No 66
>cd01777 SNX27_RA Ubiquitin domain of SNX27 (sorting nexin protein 27). SNX27_RA SNX27 (sorting nexin protein 27) belongs to a large family of endosome-localized proteins related to sorting nexin1 which is implicated in regulating membrane traffic. The domain architecture of SNX27 includes an amino-terminal PDZ domain, a PX (PhoX homologous) domain, and a carboxy-terminal RA (RAS-associated) domain.
Probab=87.68 E-value=1.3 Score=29.72 Aligned_cols=42 Identities=12% Similarity=0.288 Sum_probs=37.5
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEE
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIA 66 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lr 66 (104)
+.|+|.=+||..+..+|+++..-+.++++-|++.|+|....+
T Consensus 2 V~L~V~Lpdg~~i~V~v~~s~~a~~Vleav~~kl~L~~e~~~ 43 (87)
T cd01777 2 VELRIALPDKATVTVRVRKNATTDQVYQALVAKAGMDSYTQN 43 (87)
T ss_pred eEEEEEccCCCEEEEEEEEcccHHHHHHHHHHHhCCCHHHHh
Confidence 568888889999999999999999999999999999875543
No 67
>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=87.45 E-value=2.9 Score=27.18 Aligned_cols=44 Identities=14% Similarity=0.258 Sum_probs=36.4
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCcc-ceEEEEE
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL-NSIAFLF 69 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~-~~lrF~f 69 (104)
++||+.- +|..+.|++.++..+..|.+.-+++.+++. ..+.+.|
T Consensus 1 ~~vK~~~-~~d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY 45 (82)
T cd06407 1 VRVKATY-GEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKY 45 (82)
T ss_pred CEEEEEe-CCeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEE
Confidence 3566544 667789999999999999999999999865 7788887
No 68
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=87.13 E-value=4.4 Score=24.40 Aligned_cols=55 Identities=13% Similarity=0.154 Sum_probs=40.4
Q ss_pred CCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 33 DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 33 ~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
+|.. +.+...+.+..|.+ ..+++...+-..+||+-|...+- .+.-+.|||.|.++
T Consensus 6 NG~~--~~~~~~~tl~~lL~----~l~~~~~~vav~vNg~iv~r~~~-~~~~l~~gD~vei~ 60 (66)
T PRK05659 6 NGEP--RELPDGESVAALLA----REGLAGRRVAVEVNGEIVPRSQH-ASTALREGDVVEIV 60 (66)
T ss_pred CCeE--EEcCCCCCHHHHHH----hcCCCCCeEEEEECCeEeCHHHc-CcccCCCCCEEEEE
Confidence 5544 45666677777765 46888899999999988886543 34459999999886
No 69
>cd01811 OASL_repeat1 2'-5' oligoadenylate synthetase-like protein, repeat 1 of 2. OASL_repeat1 (2'-5' oligoadenylate synthetase-like protein) belongs to a family of interferon-induced 2'-5' oligoadenylate synthetases which are important for the antiviral activity of interferons. While each member of this famliy has a conserved N-terminal OAS catalytic domain, only OASL has two tandem ubiquitin-like repeats located at the C-terminus and this CD represents one of those repeats.
Probab=86.94 E-value=6 Score=26.09 Aligned_cols=68 Identities=12% Similarity=0.165 Sum_probs=50.5
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE---CCEe--cCCCCCccccCCcCCceeee
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF---DGRR--LRGEQTPDEVILLFCAFCSC 93 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f---dG~r--I~~~~TP~~L~Medgdii~~ 93 (104)
|.|.|.--......|+|++.+|.+||.+.--...+.+- .-|+.| .|+| ++..+|-++.|+--+=.|-+
T Consensus 1 iqVtV~q~g~~dl~l~vnPy~pI~k~K~kI~~~~~~~g-~qrLsfQepgg~rqlL~s~~sLA~yGiFs~~~i~l 73 (80)
T cd01811 1 IQVTVEQTGYSDWILRVNPYSPIRKIKEKIRRSRNCSG-LQRLSFQEPGGERQLLSSRKSLADYGIFSKTNICL 73 (80)
T ss_pred CEEEeeecCCCceEEEeCCcchHHHHHHHHHHhhCccc-ceEEEeecCCcccccccccccHhhhcceeccEEEE
Confidence 35666666677889999999999999999998888754 566666 3443 66788888888765544433
No 70
>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=86.84 E-value=3.4 Score=27.22 Aligned_cols=48 Identities=17% Similarity=0.264 Sum_probs=38.2
Q ss_pred EEEEEEccCCCEEEEEEeC--CchHHHHHHHHHHHcCCccceEEEEE---CCEecC
Q 034095 25 INLKVKGQDGNEVFFRIKR--STQLKKLMNAYCDRQSVELNSIAFLF---DGRRLR 75 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~--tt~L~kLm~aY~~~~g~~~~~lrF~f---dG~rI~ 75 (104)
|+||+. ..|..+.|++.+ +..+..|...-+++.+++ .+...| ||+.|.
T Consensus 1 V~vKat-y~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~--~f~lKYlDde~e~v~ 53 (81)
T cd06396 1 VNLKVT-YNGESQSFLVSDSENTTWASVEAMVKVSFGLN--DIQIKYVDEENEEVS 53 (81)
T ss_pred CEEEEE-ECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC--cceeEEEcCCCCEEE
Confidence 466764 478888999999 889999999999999998 666666 455544
No 71
>KOG3439 consensus Protein conjugation factor involved in autophagy [Posttranslational modification, protein turnover, chaperones]
Probab=86.57 E-value=6.6 Score=27.59 Aligned_cols=62 Identities=10% Similarity=0.226 Sum_probs=46.6
Q ss_pred CCcEEEEEEccCCCEE----EEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecC--CCCCcccc
Q 034095 22 SAHINLKVKGQDGNEV----FFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLR--GEQTPDEV 83 (104)
Q Consensus 22 ~~~I~lkV~~~~g~~v----~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~--~~~TP~~L 83 (104)
.++|+|+++...+.-+ .|+|.++.++.++...--+..+++.+.=-|+|=..... ++++-.+|
T Consensus 28 ~~kV~i~l~aiG~~PilK~~k~~i~~t~tfa~vi~Flkk~Lkl~as~slflYVN~sFAPsPDq~v~~L 95 (116)
T KOG3439|consen 28 IRKVQIRLRAIGDAPILKKSKFKINPTQTFAKVILFLKKFLKLQASDSLFLYVNNSFAPSPDQIVGNL 95 (116)
T ss_pred cceEEEEEeccCCCcceecceEEeCcchhhHHHHHHHHHHhCCcccCeEEEEEcCccCCCchhHHHHH
Confidence 4789999887554333 89999999999999999999999888888888444333 35554444
No 72
>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=86.50 E-value=2.7 Score=27.68 Aligned_cols=44 Identities=14% Similarity=0.219 Sum_probs=39.1
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEEC
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFD 70 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fd 70 (104)
..|||.-+. .|.++|.+.-+++.|.+.-++|.+++.+.+++.|-
T Consensus 3 ~vvKV~f~~--tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYk 46 (80)
T cd06406 3 YVVKVHFKY--TVAIQVARGLSYATLLQKISSKLELPAEHITLSYK 46 (80)
T ss_pred eEEEEEEEE--EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEec
Confidence 467887765 78999999999999999999999999999999984
No 73
>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=86.05 E-value=5 Score=24.87 Aligned_cols=45 Identities=7% Similarity=0.136 Sum_probs=35.9
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF 69 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f 69 (104)
+.||+.-.+.....+.+.....|..|.+.-+++.+.+...+++.|
T Consensus 2 ~~vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y 46 (84)
T PF00564_consen 2 VRVKVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLKY 46 (84)
T ss_dssp EEEEEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEEE
T ss_pred EEEEEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEEe
Confidence 556665533333338999999999999999999999888999988
No 74
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=85.89 E-value=5 Score=24.27 Aligned_cols=54 Identities=19% Similarity=0.148 Sum_probs=38.1
Q ss_pred CCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 33 DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 33 ~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
+|..+.+ ..+.+..|.+.. +++...+..-.||+-|..++ =.+.-+.|||.|.++
T Consensus 6 Ng~~~~~---~~~tl~~Ll~~l----~~~~~~vavavN~~iv~~~~-~~~~~L~dgD~Ieiv 59 (65)
T PRK06488 6 NGETLQT---EATTLALLLAEL----DYEGNWLATAVNGELVHKEA-RAQFVLHEGDRIEIL 59 (65)
T ss_pred CCeEEEc---CcCcHHHHHHHc----CCCCCeEEEEECCEEcCHHH-cCccccCCCCEEEEE
Confidence 5666554 345677777653 77778889999999998532 223558999999886
No 75
>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=85.39 E-value=5.5 Score=26.48 Aligned_cols=44 Identities=14% Similarity=0.262 Sum_probs=37.6
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE
Q 034095 24 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF 69 (104)
Q Consensus 24 ~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f 69 (104)
+|+|||.- .|..+.+.|.++..|+.|.+.-.++.++. ..|+..|
T Consensus 2 ~ikVKv~~-~~Dv~~i~v~~~i~f~dL~~kIrdkf~~~-~~~~iKy 45 (86)
T cd06408 2 KIRVKVHA-QDDTRYIMIGPDTGFADFEDKIRDKFGFK-RRLKIKM 45 (86)
T ss_pred cEEEEEEe-cCcEEEEEcCCCCCHHHHHHHHHHHhCCC-CceEEEE
Confidence 67888874 67788999999999999999999999985 5777766
No 76
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=85.20 E-value=5.3 Score=26.16 Aligned_cols=61 Identities=11% Similarity=0.132 Sum_probs=46.7
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 24 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 24 ~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
.++|.| +|.. +.+.....+..|.+. .+++...+-.-.||+-|..+ .=++.-+.+||.|.++
T Consensus 18 ~m~I~V---NG~~--~~~~~~~tl~~LL~~----l~~~~~~vAVevNg~iVpr~-~w~~t~L~egD~IEIv 78 (84)
T PRK06083 18 LITISI---NDQS--IQVDISSSLAQIIAQ----LSLPELGCVFAINNQVVPRS-EWQSTVLSSGDAISLF 78 (84)
T ss_pred eEEEEE---CCeE--EEcCCCCcHHHHHHH----cCCCCceEEEEECCEEeCHH-HcCcccCCCCCEEEEE
Confidence 566776 6655 556677778888775 58889999999999999753 3445569999999986
No 77
>KOG0003 consensus Ubiquitin/60s ribosomal protein L40 fusion [Translation, ribosomal structure and biogenesis]
Probab=85.15 E-value=0.51 Score=33.23 Aligned_cols=64 Identities=14% Similarity=0.256 Sum_probs=56.5
Q ss_pred EEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceee
Q 034095 29 VKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCS 92 (104)
Q Consensus 29 V~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~ 92 (104)
|..-.|..++..+-++.....|....-++-|++++-.++.|+|..+.+.-|-++.+|.--|-|-
T Consensus 5 ~~~~~GKT~~le~EpS~ti~~vKA~i~~~~Gi~~~~~~L~~~~k~LED~~Tla~Y~i~~~~Tl~ 68 (128)
T KOG0003|consen 5 VKTLTGKTITLEVEPSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLH 68 (128)
T ss_pred EEEeeCceEEEEecccchHHHHHHHhccccCCCHHHHHHHhcccccccCCcccccCccchhhhh
Confidence 4444678889999999999999999999999999999999999999999999999998776653
No 78
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=84.16 E-value=7.4 Score=23.75 Aligned_cols=55 Identities=7% Similarity=-0.014 Sum_probs=40.1
Q ss_pred CCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 33 DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 33 ~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
+|.. +.+...+.+..|.+. .+.+...+.+-.||+-|..+ ..++.-+.+||.|.++
T Consensus 6 Ng~~--~~~~~~~tl~~ll~~----l~~~~~~vaVavN~~iv~r~-~w~~~~L~~gD~Ieii 60 (66)
T PRK08053 6 NDQP--MQCAAGQTVHELLEQ----LNQLQPGAALAINQQIIPRE-QWAQHIVQDGDQILLF 60 (66)
T ss_pred CCeE--EEcCCCCCHHHHHHH----cCCCCCcEEEEECCEEeChH-HcCccccCCCCEEEEE
Confidence 5555 455666678877753 67777889999999999743 3344469999999876
No 79
>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=83.53 E-value=4.2 Score=28.76 Aligned_cols=39 Identities=26% Similarity=0.395 Sum_probs=35.7
Q ss_pred CcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCc
Q 034095 23 AHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVE 61 (104)
Q Consensus 23 ~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~ 61 (104)
..+.|+|.-.||+.+.+.+..++.-+.|++.-|++.|+.
T Consensus 2 ~~~~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~l~ 40 (207)
T smart00295 2 KPRVLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIR 40 (207)
T ss_pred CcEEEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhCCC
Confidence 357889999999999999999999999999999999984
No 80
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=83.42 E-value=5 Score=24.54 Aligned_cols=54 Identities=15% Similarity=0.081 Sum_probs=40.8
Q ss_pred CCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 33 DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 33 ~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
+|.. +.+...+.+..|.+. .+++...+-..+||.-|...+=.. . +.|||.|.++
T Consensus 6 NG~~--~~~~~~~tl~~ll~~----l~~~~~~vav~~N~~iv~r~~~~~-~-L~~gD~ieIv 59 (65)
T PRK05863 6 NEEQ--VEVDEQTTVAALLDS----LGFPEKGIAVAVDWSVLPRSDWAT-K-LRDGARLEVV 59 (65)
T ss_pred CCEE--EEcCCCCcHHHHHHH----cCCCCCcEEEEECCcCcChhHhhh-h-cCCCCEEEEE
Confidence 5544 455566777777764 688999999999999888654443 3 8999999986
No 81
>cd01771 Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=83.00 E-value=9.3 Score=24.57 Aligned_cols=69 Identities=20% Similarity=0.146 Sum_probs=49.4
Q ss_pred CcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEEC--CEec---CCCCCccccCCcCCceee
Q 034095 23 AHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFD--GRRL---RGEQTPDEVILLFCAFCS 92 (104)
Q Consensus 23 ~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fd--G~rI---~~~~TP~~L~Medgdii~ 92 (104)
+.++|.|+-.+|+.+.-+...+++|+.|++.... .|.+...+++.-. =+.+ ..+.|-.+++|--.+.+-
T Consensus 3 ~~~~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~-~~~~~~~f~L~t~fPRk~~~~~d~~~TL~e~gL~p~~~L~ 76 (80)
T cd01771 3 PISKLRVRTPSGDFLERRFLGDTPLQVLLNFVAS-KGYPIDEYKLLSSWPRRDLTQLDPNFTLLELKLYPQETLI 76 (80)
T ss_pred CeEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cCCCCCCEEEecCCCCCCCcCCCCCCcHHHcCCCCCcEEE
Confidence 4678889999999999999999999999998865 3666667776532 1222 235677777776555443
No 82
>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=82.82 E-value=9.1 Score=23.80 Aligned_cols=63 Identities=16% Similarity=0.291 Sum_probs=47.5
Q ss_pred EEEEEEccCCC----EEEEEEeCCchHHHHHHHHHHHcCC--ccceEEEE-E----C-CEecCCCCCccccCCcC
Q 034095 25 INLKVKGQDGN----EVFFRIKRSTQLKKLMNAYCDRQSV--ELNSIAFL-F----D-GRRLRGEQTPDEVILLF 87 (104)
Q Consensus 25 I~lkV~~~~g~----~v~FkIK~tt~L~kLm~aY~~~~g~--~~~~lrF~-f----d-G~rI~~~~TP~~L~Med 87 (104)
-.|+|-..+++ ...++|..+|+-+.|+.+-+++.++ ++..+.++ + + -+.|.++.-|..+-+.+
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~~~~~y~L~~~~~~~~~er~L~~~E~pl~i~~~~ 77 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCLVEVEESGGEERPLDDDECPLQIQLQW 77 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEEEEEECTTTEEEEETTTSBHHHHHHTT
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEEEEEEcCCCEEEEcCCCCchHHHHHhC
Confidence 46888888888 8899999999999999999999997 55667664 2 1 23455666666555444
No 83
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=82.55 E-value=5.8 Score=24.89 Aligned_cols=55 Identities=5% Similarity=0.029 Sum_probs=40.3
Q ss_pred CEEEEEEeCCchHHHHHHHHHHHc-CCcc--ceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 35 NEVFFRIKRSTQLKKLMNAYCDRQ-SVEL--NSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 35 ~~v~FkIK~tt~L~kLm~aY~~~~-g~~~--~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
++..+.+...+.+..|.+....+. ++.. ..+.+..||+.+. .+.-++|||-|.++
T Consensus 19 ~~~~~~~~~~~tv~~L~~~l~~~~p~l~~~~~~~~vavN~~~v~-----~~~~l~dgDeVai~ 76 (82)
T PLN02799 19 SDMTLELPAGSTTADCLAELVAKFPSLEEVRSCCVLALNEEYTT-----ESAALKDGDELAII 76 (82)
T ss_pred CeEEEECCCCCcHHHHHHHHHHHChhHHHHhhCcEEEECCEEcC-----CCcCcCCCCEEEEe
Confidence 456777778888999998887765 2222 4567888999874 34458999999876
No 84
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=81.83 E-value=10 Score=23.69 Aligned_cols=54 Identities=7% Similarity=0.065 Sum_probs=41.5
Q ss_pred EEEEEEeCC-chHHHHHHHHHHHcC-C--ccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 36 EVFFRIKRS-TQLKKLMNAYCDRQS-V--ELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 36 ~v~FkIK~t-t~L~kLm~aY~~~~g-~--~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
+..+.+... +.++.|.+..+++.. + ....+++..||+.+.. +.-++|||-|.++
T Consensus 17 ~~~~~~~~~~~tv~~L~~~L~~~~p~l~~~~~~~~v~vn~~~v~~-----~~~l~dgDevai~ 74 (80)
T TIGR01682 17 EETLELPDESTTVGELKEHLAKEGPELAASRGQVMVAVNEEYVTD-----DALLNEGDEVAFI 74 (80)
T ss_pred eEEEECCCCCcCHHHHHHHHHHhCchhhhhccceEEEECCEEcCC-----CcCcCCCCEEEEe
Confidence 346677666 789999999988874 1 2366889999999883 5679999999875
No 85
>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases. The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.
Probab=81.50 E-value=7.2 Score=24.85 Aligned_cols=44 Identities=7% Similarity=0.270 Sum_probs=37.5
Q ss_pred EEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEEC
Q 034095 27 LKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFD 70 (104)
Q Consensus 27 lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fd 70 (104)
++|.=+||+.....+++...++-+.+.-|++.|+.+...-.++-
T Consensus 2 ~~V~LPng~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~~ 45 (72)
T cd01760 2 CRVYLPNGQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLL 45 (72)
T ss_pred EEEECcCCCeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEe
Confidence 46777889999999999999999999999999998866655553
No 86
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=79.99 E-value=8.8 Score=23.15 Aligned_cols=51 Identities=14% Similarity=0.165 Sum_probs=38.0
Q ss_pred EEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 39 FRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 39 FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
+.+...+.+..|.+. .++++..+.+..||+-|..++ ..+..+.|||.|.++
T Consensus 8 ~~~~~~~tv~~ll~~----l~~~~~~v~v~vN~~iv~~~~-~~~~~L~~gD~veii 58 (64)
T TIGR01683 8 VEVEDGLTLAALLES----LGLDPRRVAVAVNGEIVPRSE-WDDTILKEGDRIEIV 58 (64)
T ss_pred EEcCCCCcHHHHHHH----cCCCCCeEEEEECCEEcCHHH-cCceecCCCCEEEEE
Confidence 455666677777764 567789999999999996433 334569999999886
No 87
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=79.43 E-value=4.8 Score=25.30 Aligned_cols=45 Identities=9% Similarity=0.320 Sum_probs=36.3
Q ss_pred EEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECC
Q 034095 27 LKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDG 71 (104)
Q Consensus 27 lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG 71 (104)
++|.=++|+.....+++..+++-....-|++.|+.+..+..+.-|
T Consensus 3 ~~v~LP~~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V~~~~ 47 (71)
T PF02196_consen 3 CRVHLPNGQRTVVQVRPGMTIRDALSKACKKRGLNPECCDVRLVG 47 (71)
T ss_dssp EEEEETTTEEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEEEEEE
T ss_pred EEEECCCCCEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEEEEcC
Confidence 577778999999999999999999999999999998877666543
No 88
>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=78.98 E-value=11 Score=23.14 Aligned_cols=43 Identities=21% Similarity=0.295 Sum_probs=35.2
Q ss_pred EEEEEccCCCEEEEEEe-CCchHHHHHHHHHHHcCCccceEEEEE
Q 034095 26 NLKVKGQDGNEVFFRIK-RSTQLKKLMNAYCDRQSVELNSIAFLF 69 (104)
Q Consensus 26 ~lkV~~~~g~~v~FkIK-~tt~L~kLm~aY~~~~g~~~~~lrF~f 69 (104)
+||+.-. |....|.+. ....+..|...-+++.+.+...+++.|
T Consensus 2 ~vK~~~~-~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y 45 (81)
T cd05992 2 RVKVKYG-GEIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKY 45 (81)
T ss_pred cEEEEec-CCCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEe
Confidence 5666553 556689999 999999999999999998767777777
No 89
>COG2080 CoxS Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]
Probab=77.99 E-value=5.2 Score=29.41 Aligned_cols=63 Identities=19% Similarity=0.149 Sum_probs=48.2
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCc-------cceEEEEECCEecCCCCCccccCCcCCcee
Q 034095 24 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVE-------LNSIAFLFDGRRLRGEQTPDEVILLFCAFC 91 (104)
Q Consensus 24 ~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~-------~~~lrF~fdG~rI~~~~TP~~L~Medgdii 91 (104)
.|++.| +|..+...+-+.++|..+...+-.-.|.. =.....++||++|+..-||+. +-+|.-|
T Consensus 3 ~i~ltv---NG~~~~~~~~p~~~Ll~~LRd~l~ltgtk~GC~~g~CGACtVlvDG~~v~SCl~~a~--~~~G~~I 72 (156)
T COG2080 3 PITLTV---NGEPVELDVDPRTPLLDVLRDELGLTGTKKGCGHGQCGACTVLVDGEAVNSCLTLAV--QAEGAEI 72 (156)
T ss_pred cEEEEE---CCeEEEEEeCCCChHHHHHHHhcCCCCcCCCCCCccCCceEEEECCeEehHHHHHHH--HhCCCeE
Confidence 467777 89999999999999999988766554432 278899999999999888874 3444443
No 90
>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=77.93 E-value=4.4 Score=24.94 Aligned_cols=40 Identities=18% Similarity=0.383 Sum_probs=33.0
Q ss_pred EccCCCEEEEEEeCCchHHHHHHHHHHHcCCc-cceEEEEE
Q 034095 30 KGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVE-LNSIAFLF 69 (104)
Q Consensus 30 ~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~-~~~lrF~f 69 (104)
.-.||+.+.|.|.+++.-+.|++.-|++.++. ..-+-+.|
T Consensus 2 ~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~ 42 (80)
T PF09379_consen 2 RLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQY 42 (80)
T ss_dssp EESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE
T ss_pred CCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEE
Confidence 44588899999999999999999999999863 35566666
No 91
>KOG4225 consensus Sorbin and SH3 domain-containing protein [Signal transduction mechanisms]
Probab=76.87 E-value=1.3 Score=37.62 Aligned_cols=18 Identities=22% Similarity=0.080 Sum_probs=15.9
Q ss_pred CCCccccCCcCCceeeee
Q 034095 77 EQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~ 94 (104)
-+.+++|+|.+||||||+
T Consensus 443 pqnedeLEl~egDii~Vm 460 (489)
T KOG4225|consen 443 PQNEDELELREGDIIDVM 460 (489)
T ss_pred CCCchhheeccCCEEeee
Confidence 456789999999999997
No 92
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=76.65 E-value=8.6 Score=23.29 Aligned_cols=57 Identities=12% Similarity=0.105 Sum_probs=46.6
Q ss_pred EEEEEEeCCchHHHHHHHHHHHcCC--ccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 36 EVFFRIKRSTQLKKLMNAYCDRQSV--ELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 36 ~v~FkIK~tt~L~kLm~aY~~~~g~--~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
+....+.....++.|.++.+.+... ....+.+..||+.+.. + -.+..+.+||.|.++
T Consensus 13 ~~~~~~~~~~tv~~ll~~l~~~~p~~~~~~~~~v~vN~~~v~~-~-~~~~~l~~gD~V~i~ 71 (77)
T PF02597_consen 13 EEEIEVPEGSTVRDLLEALAERYPELALRDRVAVAVNGEIVPD-D-GLDTPLKDGDEVAIL 71 (77)
T ss_dssp EEEEEESSTSBHHHHHHHHCHHTGGGHTTTTEEEEETTEEEGG-G-TTTSBEETTEEEEEE
T ss_pred CeEEecCCCCcHHHHHHHHHhhccccccCccEEEEECCEEcCC-c-cCCcCcCCCCEEEEE
Confidence 5577888899999999999888741 3478999999999998 3 566778999999875
No 93
>PF13019 Telomere_Sde2: Telomere stability and silencing
Probab=75.48 E-value=15 Score=27.12 Aligned_cols=58 Identities=19% Similarity=0.296 Sum_probs=44.2
Q ss_pred EEEEEEccCC----CEEEEEEeCCchHHHHHHHHHHHcCCccce-EEEEE--CCEecCCCCCccc
Q 034095 25 INLKVKGQDG----NEVFFRIKRSTQLKKLMNAYCDRQSVELNS-IAFLF--DGRRLRGEQTPDE 82 (104)
Q Consensus 25 I~lkV~~~~g----~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~-lrF~f--dG~rI~~~~TP~~ 82 (104)
|+|-|..-+| ..+.|.+..++++..|++...++.+++... +.|.+ +|.-...+++|-+
T Consensus 1 i~Vlvss~~g~~lp~tl~~~lp~~ttv~dL~~~l~~~~~~~~~~~~~L~~~~n~~l~~~~~~~~s 65 (162)
T PF13019_consen 1 INVLVSSFDGLTLPPTLSLSLPSTTTVSDLKDRLSERLPIPSSSQLYLTTNSNGQLSPSSDIPLS 65 (162)
T ss_pred CeEEEecCCCCCCCCeEEeeCCCCCcHHHHHHHHHhhcCCCccceeEEEEeCCCeeCCCccccHH
Confidence 5778888888 688999999999999999999999988766 44555 3444444555443
No 94
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=74.29 E-value=9.8 Score=22.96 Aligned_cols=51 Identities=10% Similarity=0.098 Sum_probs=37.0
Q ss_pred EEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 39 FRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 39 FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
+.+...+.+..|.+. .+++...+....||+-|..++= .+..+.+||.|.++
T Consensus 9 ~~~~~~~tv~~ll~~----l~~~~~~i~V~vNg~~v~~~~~-~~~~L~~gD~V~ii 59 (65)
T cd00565 9 REVEEGATLAELLEE----LGLDPRGVAVALNGEIVPRSEW-ASTPLQDGDRIEIV 59 (65)
T ss_pred EEcCCCCCHHHHHHH----cCCCCCcEEEEECCEEcCHHHc-CceecCCCCEEEEE
Confidence 455666677777755 4678889999999999876431 12349999999876
No 95
>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=74.23 E-value=14 Score=24.79 Aligned_cols=52 Identities=13% Similarity=0.238 Sum_probs=38.7
Q ss_pred cEEEEEEccCCCEEEEEEe--CCchHHHHHHHHHHHc--CCccceEEEEECCEecCC
Q 034095 24 HINLKVKGQDGNEVFFRIK--RSTQLKKLMNAYCDRQ--SVELNSIAFLFDGRRLRG 76 (104)
Q Consensus 24 ~I~lkV~~~~g~~v~FkIK--~tt~L~kLm~aY~~~~--g~~~~~lrF~fdG~rI~~ 76 (104)
.|+|+..+ .--.+.+.|. .++.-..|...--++. ..+...+||+|+|+-|.+
T Consensus 2 ~l~IRFs~-sipDl~L~I~~~~~~Tv~~LK~lIR~~~p~~~s~~rLRlI~~Gr~L~d 57 (97)
T PF10302_consen 2 YLTIRFSD-SIPDLPLDIPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRLLND 57 (97)
T ss_pred eEEEEECC-CCCCceeecCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCcccCc
Confidence 46677665 2222566676 7788888888777776 467799999999999985
No 96
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=73.88 E-value=17 Score=23.58 Aligned_cols=52 Identities=12% Similarity=0.172 Sum_probs=42.2
Q ss_pred CCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE-CCEecCCCCCccccCCcCCceeeee
Q 034095 34 GNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF-DGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 34 g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f-dG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
+..+.+.+...+.++.+.++ .|++...+-+++ ||+.+..+ .-+++||.|.|.
T Consensus 22 ~~~~~~~~~~~~tvkd~IEs----LGVP~tEV~~i~vNG~~v~~~-----~~~~~Gd~v~V~ 74 (81)
T PF14451_consen 22 GGPFTHPFDGGATVKDVIES----LGVPHTEVGLILVNGRPVDFD-----YRLKDGDRVAVY 74 (81)
T ss_pred CCceEEecCCCCcHHHHHHH----cCCChHHeEEEEECCEECCCc-----ccCCCCCEEEEE
Confidence 34567788899999998865 799999998888 89888776 455699999885
No 97
>cd01818 TIAM1_RBD Ubiquitin domain of Tiam1 guanine nucleotide exchange factor. Tiam1 (T lymphoma invasion and metastasis 1) a guanine nucleotide exchange factor that activates Rac, is an important regulator of Rho GTPase functions in tumor cells including regulation of cell shape and invasiveness in epithelial cells and fibroblasts. TIAM1 has an RBD (Ras-binding domain) similar to that of Raf kinase as well as PH (pleckstrin homology), PDZ, and RhoGEF domains.
Probab=72.81 E-value=19 Score=23.57 Aligned_cols=42 Identities=14% Similarity=0.299 Sum_probs=35.4
Q ss_pred EEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccc--eEEEEE
Q 034095 28 KVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELN--SIAFLF 69 (104)
Q Consensus 28 kV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~--~lrF~f 69 (104)
+|.-++|..+...|++...+..+.++-|++.+++++ -+|+.+
T Consensus 3 ~V~lPn~~~~~v~vrp~~tv~dvLe~aCk~~~ldp~eh~Lrlk~ 46 (77)
T cd01818 3 WVCLPDNQPVLTYLRPGMSVEDFLESACKRKQLDPMEHYLRLKF 46 (77)
T ss_pred EEECCCCceEEEEECCCCCHHHHHHHHHHhcCCChhHheeEEEE
Confidence 566789999999999999999999999999999874 444444
No 98
>KOG3483 consensus Uncharacterized conserved protein [Function unknown]
Probab=72.77 E-value=20 Score=23.81 Aligned_cols=55 Identities=18% Similarity=0.206 Sum_probs=46.1
Q ss_pred EEEEeCCchHHHHHHHHHHHcCCccceEEEEE-CCEecCCCCCccccCCcCCceee
Q 034095 38 FFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF-DGRRLRGEQTPDEVILLFCAFCS 92 (104)
Q Consensus 38 ~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f-dG~rI~~~~TP~~L~Medgdii~ 92 (104)
++.|-..+||-.+.+.-|+...++..+--.+- ||.-|++.||+-..-|..|--.-
T Consensus 30 v~svpestpftavlkfaaeefkvpaatsaiitndgiginpaq~agnvflkhgselr 85 (94)
T KOG3483|consen 30 VLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELR 85 (94)
T ss_pred eecCCCCCchHHHHHHHHHHccCCccceeEEecCccccCccccccceeeccCCEEE
Confidence 67788999999999999999998876555544 89999999999998888886543
No 99
>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=70.95 E-value=23 Score=22.16 Aligned_cols=57 Identities=19% Similarity=0.341 Sum_probs=42.3
Q ss_pred EEEEccC---CCEEEEEEeCCchHHHHHHHHHHHcCCc--cceEEEEE---C---CEecCCCCCcccc
Q 034095 27 LKVKGQD---GNEVFFRIKRSTQLKKLMNAYCDRQSVE--LNSIAFLF---D---GRRLRGEQTPDEV 83 (104)
Q Consensus 27 lkV~~~~---g~~v~FkIK~tt~L~kLm~aY~~~~g~~--~~~lrF~f---d---G~rI~~~~TP~~L 83 (104)
|||...+ +....+.|.++++.+.++..-.++.+++ ++.+.++- + .+.+.++.-|-.+
T Consensus 2 ikV~~~~~~~~~~kti~V~~~~t~~~Vi~~~l~k~~l~~~~~~y~L~ev~~~~~~er~L~~~e~pl~~ 69 (87)
T cd01768 2 LRVYPEDPSGGTYKTLRVSKDTTAQDVIQQLLKKFGLDDDPEDYALVEVLGDGGLERLLLPDECPLQI 69 (87)
T ss_pred EEEeCCcCCCccEEEEEECCCCCHHHHHHHHHHHhCCcCCcccEEEEEEECCceEEEEeCCCCChHHH
Confidence 5677666 8888999999999999999999999876 45555443 2 2345567767654
No 100
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=70.58 E-value=24 Score=22.27 Aligned_cols=70 Identities=13% Similarity=0.065 Sum_probs=51.0
Q ss_pred CcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE--CCEecCC---CCCccccCCcCCceeee
Q 034095 23 AHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF--DGRRLRG---EQTPDEVILLFCAFCSC 93 (104)
Q Consensus 23 ~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f--dG~rI~~---~~TP~~L~Medgdii~~ 93 (104)
....|.|+-.+|+.+.-+...+++|+.|++.-....+- ...+.|.- =-+.+.. +.|-.+++|-..+.+-|
T Consensus 3 ~~~~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~~-~~~f~L~t~fPrk~~~~~d~~~TL~elgL~Psa~L~v 77 (79)
T cd01772 3 TETRIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTGN-GGPFTLMTPFPRKVFTEDDMEKPLQELGLVPSAVLIV 77 (79)
T ss_pred cEEEEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCCC-CCCEEEEeCCCCeECCcccccCCHHHCCCCCceEEEE
Confidence 34678888899999988999999999999988765432 24455544 3444442 57899999888777644
No 101
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=69.71 E-value=23 Score=21.75 Aligned_cols=56 Identities=9% Similarity=0.143 Sum_probs=39.8
Q ss_pred CCCEEEEEEeCC-chHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeeee
Q 034095 33 DGNEVFFRIKRS-TQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 33 ~g~~v~FkIK~t-t~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~ 95 (104)
+|.. +.+... +.+..|.+ ..+++...+-.-+||+-|..++= ++.-+.+||.|.++.
T Consensus 6 NG~~--~~~~~~~~tv~~lL~----~l~~~~~~vav~vN~~iv~r~~w-~~~~L~~gD~iEIv~ 62 (67)
T PRK07696 6 NGNQ--IEVPESVKTVAELLT----HLELDNKIVVVERNKDILQKDDH-TDTSVFDGDQIEIVT 62 (67)
T ss_pred CCEE--EEcCCCcccHHHHHH----HcCCCCCeEEEEECCEEeCHHHc-CceecCCCCEEEEEE
Confidence 5544 455554 45666654 57889999999999999986433 334589999998863
No 102
>PHA01623 hypothetical protein
Probab=68.21 E-value=4.6 Score=24.54 Aligned_cols=27 Identities=26% Similarity=0.593 Sum_probs=24.0
Q ss_pred EEEEEeCCchHHHHHHHHHHHcCCccc
Q 034095 37 VFFRIKRSTQLKKLMNAYCDRQSVELN 63 (104)
Q Consensus 37 v~FkIK~tt~L~kLm~aY~~~~g~~~~ 63 (104)
+.|.|+-+..|..-++.||...|++.+
T Consensus 14 ~r~sVrldeel~~~Ld~y~~~~g~~rS 40 (56)
T PHA01623 14 AVFGIYMDKDLKTRLKVYCAKNNLQLT 40 (56)
T ss_pred eeEEEEeCHHHHHHHHHHHHHcCCCHH
Confidence 578999999999999999999998753
No 103
>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=67.90 E-value=32 Score=22.75 Aligned_cols=48 Identities=19% Similarity=0.218 Sum_probs=37.4
Q ss_pred EEEEEccCCCEEEEEEeC-----CchHHHHHHHHHHHcCCcc-ceEEEEE---CCEec
Q 034095 26 NLKVKGQDGNEVFFRIKR-----STQLKKLMNAYCDRQSVEL-NSIAFLF---DGRRL 74 (104)
Q Consensus 26 ~lkV~~~~g~~v~FkIK~-----tt~L~kLm~aY~~~~g~~~-~~lrF~f---dG~rI 74 (104)
.|||.- +|..+.|++.. +..|..|.+.-+++..++. ..+.+.| +|.-|
T Consensus 2 ~vKv~y-~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V 58 (91)
T cd06398 2 VVKVKY-GGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVV 58 (91)
T ss_pred EEEEEe-CCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEE
Confidence 466644 66677999984 7899999999999999877 7888877 35444
No 104
>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=67.21 E-value=6.6 Score=25.77 Aligned_cols=52 Identities=15% Similarity=0.234 Sum_probs=36.3
Q ss_pred EEEeCCchHHHHHHHHHHHc--CCccceEEEEECCEecC--------------CCCCccccCCcCCceeee
Q 034095 39 FRIKRSTQLKKLMNAYCDRQ--SVELNSIAFLFDGRRLR--------------GEQTPDEVILLFCAFCSC 93 (104)
Q Consensus 39 FkIK~tt~L~kLm~aY~~~~--g~~~~~lrF~fdG~rI~--------------~~~TP~~L~Medgdii~~ 93 (104)
..+.+++.|+.+++..|++. .+..-+++ ..|..+. =+.+-.+| +.+|+.|-|
T Consensus 1 i~v~~~~TL~~lid~L~~~~~~qlk~PSlt--~~~k~LYm~~pp~Lee~Tr~NL~k~l~eL-~~~g~ei~V 68 (84)
T PF08825_consen 1 IEVSPSWTLQDLIDSLCEKPEFQLKKPSLT--TANKTLYMQSPPSLEEATRPNLSKKLKEL-LSDGEEITV 68 (84)
T ss_dssp EEESTTSBSHHHHHHHHHSTTT--SS-EEE--SSEEEEEESSSHHHHHHTGGGGSSBTTTT-HHSSEEEEE
T ss_pred CCcCccchHHHHHHHHHhChhhhcCCCccc--CCCceEEEeCCHHHHHHhhhhhhhhHHHH-hcCCCEEEE
Confidence 36789999999999999995 44333443 5555544 25666788 899998876
No 105
>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=67.08 E-value=16 Score=24.23 Aligned_cols=59 Identities=12% Similarity=0.263 Sum_probs=34.3
Q ss_pred EEEEEEccCCC----EEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE-CCEec-CCCCCcccc
Q 034095 25 INLKVKGQDGN----EVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF-DGRRL-RGEQTPDEV 83 (104)
Q Consensus 25 I~lkV~~~~g~----~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f-dG~rI-~~~~TP~~L 83 (104)
|+|+.+...+. .-.|+|..+.+|+.+...-.++.++..+.--|+| |...- ++++|-.+|
T Consensus 2 V~v~fk~iG~aPilk~~k~kI~~~~~f~~vi~fLrk~Lk~~~~~slFlYin~sFaPspDe~vg~L 66 (87)
T PF04110_consen 2 VTVRFKAIGSAPILKQKKFKISASQTFATVIAFLRKKLKLKPSDSLFLYINNSFAPSPDETVGDL 66 (87)
T ss_dssp EEEEEEEETT----S--EEEEETTSBTHHHHHHHHHHCT----SS-EEEEEEEE---TTSBHHHH
T ss_pred EEEEEEecCCCccccCcEEEECCCCchHHHHHHHHHHhCCccCCeEEEEEcCccCCCchhHHHHH
Confidence 45555543332 2389999999999999999999997554444555 44332 346665544
No 106
>KOG0001 consensus Ubiquitin and ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=67.02 E-value=21 Score=20.17 Aligned_cols=65 Identities=15% Similarity=0.258 Sum_probs=53.8
Q ss_pred EEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceee
Q 034095 28 KVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCS 92 (104)
Q Consensus 28 kV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~ 92 (104)
.|....|..+.+.+.+...+..+-...+...+++...-++.+.|..+.++.|=.+.++..+..+.
T Consensus 3 ~~~~~~gk~~~~~~~~~~~i~~~k~~i~~~~~~~~~~q~~~~~~~~l~d~~~l~~~~i~~~~~~~ 67 (75)
T KOG0001|consen 3 FVKTLDGKTITLEVSPSDTIEVVKAKIRDKEGIPVDQQRLIFGGKPLEDGRTLADYNIQEGSTLH 67 (75)
T ss_pred EEEecCCCEEEEEecCCCHHHHHHHHHHhhcCCCCeeEEEEECCEECcCCCcHHHhCCCCCCEEE
Confidence 44556788889999999999999888888889999999999999999988777777766665554
No 107
>PF03607 DCX: Doublecortin; InterPro: IPR003533 X-linked lissencephaly is a severe brain malformation affecting males. Recently it has been demonstrated that the doublecortin gene is implicated in this disorder []. Doublecortin was found to bind to the microtubule cytoskeleton. In vivo and in vitro assays show that Doublecortin stabilises microtubules and causes bundling []. Doublecortin is a basic protein with an iso-electric point of 10, typical of microtubule-binding proteins. However, its sequence contains no known microtubule-binding domain(s). The detailed sequence analysis of Doublecortin and Doublecortin-like proteins allowed the identification of an evolutionarily conserved Doublecortin (DC) domain. This domain is found in the N terminus of proteins and consists of one or two tandemly repeated copies of an around 80 amino acids region. It has been suggested that the first DC domain of Doublecortin binds tubulin and enhances microtubule polymerisation []. Some proteins known to contain a DC domain are listed below: Doublecortin. It is required for neuronal migration []. A large number of point mutations in the human DCX gene leading to lissencephaly are located within the DC domains []. Human serine/threonine-protein kinase DCAMKL1. It is a probable kinase that may be involved in a calcium-signaling pathway controling neuronal migration in the developing brain []. Retinitis pigmentosa 1 protein. It could play a role in the differentiation of photoreceptor cells. Mutation in the human RP1 gene cause retinitis pigmentosa of type 1 []. ; GO: 0035556 intracellular signal transduction; PDB: 1UF0_A 1MG4_A 1MFW_A 2DNF_A 2XRP_I 2BQQ_A 1MJD_A.
Probab=66.26 E-value=9.7 Score=23.02 Aligned_cols=46 Identities=20% Similarity=0.353 Sum_probs=34.1
Q ss_pred CCchHHHHHHHHHHHcCCccceEEEEE--CCEecCCCCCccccCCcCCceeeee
Q 034095 43 RSTQLKKLMNAYCDRQSVELNSIAFLF--DGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 43 ~tt~L~kLm~aY~~~~g~~~~~lrF~f--dG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
....|..|++.-.++.+++.. +|=+| +|.+|. +.++ ++||++.-|-
T Consensus 7 ~~~s~e~lL~~it~~v~l~~g-Vr~lyt~~G~~V~---~l~~--l~dg~~yVa~ 54 (60)
T PF03607_consen 7 RFRSFEQLLDEITEKVQLPSG-VRKLYTLDGKRVK---SLDE--LEDGGSYVAS 54 (60)
T ss_dssp THSSHHHHHHHHHHSSSSTTS--SEEEETTSSEES---SGGG--S-TTEEEEEE
T ss_pred hhcCHHHHHHHHHhhcCCCcc-cceEECCCCCEeC---CHHH--HCCCCEEEEE
Confidence 345789999999999999877 88777 899994 5666 6788875543
No 108
>PF10623 PilI: Plasmid conjugative transfer protein PilI; InterPro: IPR018897 The thin pilus of plasmid R64 belongs to the type IV family and is required for liquid matings. PilI is one of 14 genes that have been identified as being involved in biogenesis of the R64 thin pilus [].
Probab=61.95 E-value=19 Score=23.89 Aligned_cols=54 Identities=19% Similarity=0.341 Sum_probs=39.8
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcC---CccceEEEEECCEecC
Q 034095 22 SAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQS---VELNSIAFLFDGRRLR 75 (104)
Q Consensus 22 ~~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g---~~~~~lrF~fdG~rI~ 75 (104)
+.++.|-|.+.++.+-.|.+++++-+.++...||---+ +-...-||+|.=+|+-
T Consensus 6 ~grl~VLVv~n~c~~kL~~~~~~~D~~~i~r~f~TpdN~lV~V~~~nr~l~r~eR~p 62 (83)
T PF10623_consen 6 PGRLQVLVVSNHCERKLFDTKPDNDPDKIARRFCTPDNCLVCVLQDNRFLFRWERAP 62 (83)
T ss_pred CCeEEEEEEeCCcceeEeecCCCCCHHHHHhhccCcCCeEEEEEeCCceEEEEeeCC
Confidence 46899999999999999999999999999999885432 2223344555444443
No 109
>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=58.22 E-value=50 Score=21.58 Aligned_cols=69 Identities=16% Similarity=0.115 Sum_probs=50.7
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEEC--CEec---CCCCCccccCCcCCceeee
Q 034095 24 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFD--GRRL---RGEQTPDEVILLFCAFCSC 93 (104)
Q Consensus 24 ~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fd--G~rI---~~~~TP~~L~Medgdii~~ 93 (104)
.-.|.|+-.+|+.+.-+...+++|+.|+..... .|.+...+.++-+ =+.+ ..+.|-+++||---+.+-|
T Consensus 5 ~t~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~-~g~~~~~f~L~t~FPRr~~~~~d~~~TL~e~GL~P~~~LfV 78 (82)
T cd01773 5 KARLMLRYPDGKREQIALPEQAKLLALVRHVQS-KGYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFV 78 (82)
T ss_pred eeEEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cCCCCCCEEEecCCCCcccCCcccCCCHHHcCCCCCcEEEE
Confidence 447788889999998899999999999985554 6777777887754 1222 2246888888877766544
No 110
>PF13860 FlgD_ig: FlgD Ig-like domain; PDB: 3C12_A 3OSV_A.
Probab=57.37 E-value=34 Score=21.50 Aligned_cols=43 Identities=19% Similarity=0.411 Sum_probs=27.5
Q ss_pred CCcEEEEEEccCCCEE-EEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCc
Q 034095 22 SAHINLKVKGQDGNEV-FFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTP 80 (104)
Q Consensus 22 ~~~I~lkV~~~~g~~v-~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP 80 (104)
...++|.|.+.+|..| .+.+. ..+.....|.+||..-.++.-|
T Consensus 24 a~~v~v~I~d~~G~~V~t~~~~----------------~~~~G~~~~~WdG~d~~G~~~~ 67 (81)
T PF13860_consen 24 ADNVTVTIYDSNGQVVRTISLG----------------SQSAGEHSFTWDGKDDDGNPVP 67 (81)
T ss_dssp CEEEEEEEEETTS-EEEEEEEE----------------ECSSEEEEEEE-SB-TTS-B--
T ss_pred ccEEEEEEEcCCCCEEEEEEcC----------------CcCCceEEEEECCCCCCcCCCC
Confidence 5578999999999886 33332 2356789999999988776544
No 111
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=54.25 E-value=48 Score=20.79 Aligned_cols=60 Identities=17% Similarity=0.255 Sum_probs=43.2
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
|+|.+ +|.. ..+...+++.-|.. ..+++...+-..+||+-|..++ -++..+++||.|.|+
T Consensus 3 m~i~~---ng~~--~e~~~~~tv~dLL~----~l~~~~~~vav~vNg~iVpr~~-~~~~~l~~gD~ievv 62 (68)
T COG2104 3 MTIQL---NGKE--VEIAEGTTVADLLA----QLGLNPEGVAVAVNGEIVPRSQ-WADTILKEGDRIEVV 62 (68)
T ss_pred EEEEE---CCEE--EEcCCCCcHHHHHH----HhCCCCceEEEEECCEEccchh-hhhccccCCCEEEEE
Confidence 44544 3444 55666677777665 4789999999999999986432 256778999999875
No 112
>KOG1363 consensus Predicted regulator of the ubiquitin pathway (contains UAS and UBX domains) [Signal transduction mechanisms]
Probab=53.64 E-value=36 Score=28.95 Aligned_cols=51 Identities=12% Similarity=0.140 Sum_probs=40.0
Q ss_pred CCCCCCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE
Q 034095 18 PVDQSAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF 69 (104)
Q Consensus 18 p~~~~~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f 69 (104)
++.+.+.|+|.|+..+|....=+.+++++++.||+.+...- .....+.|..
T Consensus 377 ~a~~~~~~~l~iR~P~G~r~~RrF~~s~~~q~l~~~v~~~~-~~~~e~~~~~ 427 (460)
T KOG1363|consen 377 SASEEEAITVAIRLPSGTRLERRFLKSDKLQILYDYVDSNG-FHPEEYSLNT 427 (460)
T ss_pred CcCcccceeeEEECCCCCeeeeeeecccchhHHHHHHHhcc-CCchhhcccc
Confidence 45667899999999999999889999999999998776554 4444444444
No 113
>PRK11433 aldehyde oxidoreductase 2Fe-2S subunit; Provisional
Probab=53.19 E-value=56 Score=25.15 Aligned_cols=67 Identities=19% Similarity=0.201 Sum_probs=46.4
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCcc-------ceEEEEECCEecCCCCCccccCCcCCceeee
Q 034095 22 SAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL-------NSIAFLFDGRRLRGEQTPDEVILLFCAFCSC 93 (104)
Q Consensus 22 ~~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~-------~~lrF~fdG~rI~~~~TP~~L~Medgdii~~ 93 (104)
...|+|.| +|..+.+.+.+.++|-........-.|... .....++||++++.-.||.- +.+|.-|-=
T Consensus 49 ~~~i~~~V---NG~~~~~~v~~~~tLLd~LR~~l~ltGtK~GC~~G~CGACTVlVdG~~v~SCl~la~--~~~G~~ItT 122 (217)
T PRK11433 49 ISPVTLKV---NGKTEQLEVDTRTTLLDALREHLHLTGTKKGCDHGQCGACTVLVNGRRLNACLTLAV--MHQGAEITT 122 (217)
T ss_pred CceEEEEE---CCEEEEEecCCCCcHHHHHHHhcCCCCCCCCCCCCCcCceEEEECCEEeeeeeeehh--hcCCCEEEE
Confidence 34577777 787877889999998887776544444333 56677999999998888752 345554443
No 114
>TIGR02958 sec_mycoba_snm4 secretion protein snm4. Members of this family are the 12-transmembrane domain protein snm4, where snm stands for secretion in mycocbacteria. This system acts on Mycobacterium tuberculosis related pair of virulence factors ESAT-6 and CFP-10 and on other homologs. The system is conserved in many Actinobacteria, including the non-pathogenic Mycobacterium smegmatis.
Probab=53.15 E-value=63 Score=27.11 Aligned_cols=68 Identities=12% Similarity=0.014 Sum_probs=51.2
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCc------cceEEEEE-CCEecCCCCCccccCCcCCceeee
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVE------LNSIAFLF-DGRRLRGEQTPDEVILLFCAFCSC 93 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~------~~~lrF~f-dG~rI~~~~TP~~L~Medgdii~~ 93 (104)
..|.|... .+.+-.-+--+.|+..|+..--+..+-. ....+|.= +|..+.+++|..+.+..|||..-.
T Consensus 3 ~RVtV~~~-~~~~DlaLPa~~PvaellP~ll~~~~~~~~~~~~~~~w~L~r~gG~pL~~~~sL~~~gV~DG~~L~L 77 (452)
T TIGR02958 3 CRVTVLAG-RRAVDVALPADVPVAELIPDLVDLLDDRGAAELGAVRWALARAGGSPLDPDASLAEAGVRDGELLVL 77 (452)
T ss_pred EEEEEeeC-CeeeeeecCCCCcHHHHHHHHHHHhCcccccCCCCcceEEecCCCCCCCCCCCHHHcCCCCCCeEEE
Confidence 34556553 3457888899999999999888877542 23344433 899999999999999999998643
No 115
>PRK11840 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional
Probab=52.80 E-value=54 Score=26.80 Aligned_cols=55 Identities=9% Similarity=0.013 Sum_probs=41.2
Q ss_pred CCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 33 DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 33 ~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
+|.. +.+...+.+..|.+. .+++...+-..+||+-|..++ =.+.-+.|||.|.++
T Consensus 6 NGk~--~el~e~~TL~dLL~~----L~i~~~~VAVeVNgeIVpr~~-w~~t~LkeGD~IEII 60 (326)
T PRK11840 6 NGEP--RQVPAGLTIAALLAE----LGLAPKKVAVERNLEIVPRSE-YGQVALEEGDELEIV 60 (326)
T ss_pred CCEE--EecCCCCcHHHHHHH----cCCCCCeEEEEECCEECCHHH-cCccccCCCCEEEEE
Confidence 5544 566777778777754 688999999999999997433 233459999999886
No 116
>KOG1407 consensus WD40 repeat protein [Function unknown]
Probab=52.12 E-value=31 Score=27.95 Aligned_cols=52 Identities=27% Similarity=0.503 Sum_probs=40.7
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHHH---HHHHHH----cCCccceEEEEECCEecCC
Q 034095 22 SAHINLKVKGQDGNEVFFRIKRSTQLKKLM---NAYCDR----QSVELNSIAFLFDGRRLRG 76 (104)
Q Consensus 22 ~~~I~lkV~~~~g~~v~FkIK~tt~L~kLm---~aY~~~----~g~~~~~lrF~fdG~rI~~ 76 (104)
...|.|++ +++|. +|.+.-...+--|. +.-|.| +..+.+++.|.+||+-|..
T Consensus 190 snCicI~f-~p~Gr--yfA~GsADAlvSLWD~~ELiC~R~isRldwpVRTlSFS~dg~~lAS 248 (313)
T KOG1407|consen 190 SNCICIEF-DPDGR--YFATGSADALVSLWDVDELICERCISRLDWPVRTLSFSHDGRMLAS 248 (313)
T ss_pred cceEEEEE-CCCCc--eEeeccccceeeccChhHhhhheeeccccCceEEEEeccCcceeec
Confidence 56888886 66774 58888777766665 556776 5789999999999999974
No 117
>PF11620 GABP-alpha: GA-binding protein alpha chain; InterPro: IPR024668 GA-binding protein alpha is a transcription factor capable of interacting with purine rich repeats (GA repeats). This N-terminal domain found in the transcription factor GABP alpha consists of a five-stranded beta-sheet crossed by a distorted helix and has been termed OST domain. The surface of the GABP alpha OST domain contains two clusters of negatively-charged residues suggesting there are positively-charged partner proteins. The OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300 [].; PDB: 2JUO_A.
Probab=51.83 E-value=26 Score=23.55 Aligned_cols=51 Identities=12% Similarity=0.145 Sum_probs=35.5
Q ss_pred EEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcC
Q 034095 37 VFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLF 87 (104)
Q Consensus 37 v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Med 87 (104)
+.-.|.-.+||+.|-+.-..|.+++.+...||.-...+.++.+--+-+.+.
T Consensus 5 I~q~mDI~epl~~Lk~lLe~Rl~~~L~~~~f~LQD~~L~~~k~L~dQcVqg 55 (88)
T PF11620_consen 5 IMQHMDIREPLSTLKKLLERRLGISLSDYEFWLQDIQLEPHKSLVDQCVQG 55 (88)
T ss_dssp EEEEEESSSBGGGHHHHSHHHH-S--SS-EEEETTEE--TTSBTTTSS---
T ss_pred EEEEEecCCcHHHHHHHHHHhhCCCcCCCeEEeccceecCCccHHHhhccc
Confidence 455677889999999999999999999999999887788888766655543
No 118
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=48.87 E-value=80 Score=27.18 Aligned_cols=68 Identities=19% Similarity=0.252 Sum_probs=48.9
Q ss_pred EEEEccCCCEEEEEEeCCchHHHHHHHHHHHc--CCccceEEEEE--C--CEec--CCCCCccccCCcCCceeeeee
Q 034095 27 LKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQ--SVELNSIAFLF--D--GRRL--RGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 27 lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~--g~~~~~lrF~f--d--G~rI--~~~~TP~~L~Medgdii~~~~ 95 (104)
+++++.+|.. +..+.++.-|..|...--... +.+++.+...= + |.-+ -.++||.+|||..|+..-+-|
T Consensus 3 ~rfRsk~G~~-Rve~qe~d~lg~l~~kll~~~~~n~~~e~~svc~~p~~qG~~~s~l~dqt~~dlGL~hGqmLyl~y 78 (571)
T COG5100 3 FRFRSKEGQR-RVEVQESDVLGMLSPKLLAFFEVNYSPEQISVCSAPDGQGEIFSLLKDQTPDDLGLRHGQMLYLEY 78 (571)
T ss_pred EEEecCCCce-eeeccccchhhhhhHHHHhhhccCCCccceEEEeCCCCCceeeecccccChhhhccccCcEEEEEe
Confidence 6788888865 668889998987665544442 45666766655 3 4422 259999999999999877766
No 119
>PF05486 SRP9-21: Signal recognition particle 9 kDa protein (SRP9); InterPro: IPR008832 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the 9 kDa SRP9 component. Both SRP9 and SRP14 have the same (beta)-alpha-beta(3)-alpha fold. The heterodimer has pseudo two-fold symmetry and is saddle-like, consisting of a curved six-stranded beta-sheet that has four helices packed on the convex side and an exposed concave surface lined with positively charged residues. The SRP9/SRP14 heterodimer is essential for SRP RNA binding, mediating the pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP [].; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0045900 negative regulation of translational elongation, 0048500 signal recognition particle; PDB: 1E8O_A 1RY1_C.
Probab=47.60 E-value=71 Score=20.54 Aligned_cols=33 Identities=12% Similarity=0.286 Sum_probs=24.9
Q ss_pred CCCcEEEEEEccC-CCEEEEEEeCCchHHHHHHH
Q 034095 21 QSAHINLKVKGQD-GNEVFFRIKRSTQLKKLMNA 53 (104)
Q Consensus 21 ~~~~I~lkV~~~~-g~~v~FkIK~tt~L~kLm~a 53 (104)
....|+||+.+.. |..+.|+..+..-+++|...
T Consensus 37 ~~~~l~lK~td~~~g~clKykT~k~~dv~Rl~~~ 70 (79)
T PF05486_consen 37 PTGKLVLKTTDPHSGVCLKYKTDKAKDVSRLESF 70 (79)
T ss_dssp TTTBEEEEEE-SS---EEEEEE-SGGGHHHHHHH
T ss_pred CCceEEEEEeCCCceeEEEEEeCHHHHHHHHHHH
Confidence 4679999999853 66899999999999999864
No 120
>PF08620 RPAP1_C: RPAP1-like, C-terminal; InterPro: IPR013929 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans.
Probab=44.14 E-value=13 Score=23.92 Aligned_cols=12 Identities=42% Similarity=0.742 Sum_probs=10.6
Q ss_pred ceEEEEECCEec
Q 034095 63 NSIAFLFDGRRL 74 (104)
Q Consensus 63 ~~lrF~fdG~rI 74 (104)
+.+||-|+|..|
T Consensus 1 ~~~RFdf~G~l~ 12 (73)
T PF08620_consen 1 SELRFDFDGNLL 12 (73)
T ss_pred CCccccCCCCEe
Confidence 368999999999
No 121
>COG3435 Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=42.64 E-value=16 Score=29.94 Aligned_cols=32 Identities=22% Similarity=0.403 Sum_probs=24.0
Q ss_pred ccceEEEEECCEe----cCCCCCccccCCcCCceeeeeec
Q 034095 61 ELNSIAFLFDGRR----LRGEQTPDEVILLFCAFCSCKYG 96 (104)
Q Consensus 61 ~~~~lrF~fdG~r----I~~~~TP~~L~Medgdii~~~~~ 96 (104)
+.+.+||++.|+= |.++.|| |+.||||-.=-+
T Consensus 111 sqsAlRFvveG~Ga~T~VdGer~~----M~~GDfilTP~w 146 (351)
T COG3435 111 NQSALRFVVEGKGAYTVVDGERTP----MEAGDFILTPAW 146 (351)
T ss_pred cccceEEEEeccceeEeecCceee----ccCCCEEEccCc
Confidence 4589999998876 5566665 899999865433
No 122
>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=42.08 E-value=48 Score=30.70 Aligned_cols=35 Identities=17% Similarity=0.143 Sum_probs=31.8
Q ss_pred EEEEEEeCCchHHHHHHHHHHHcCCccce-EEEEEC
Q 034095 36 EVFFRIKRSTQLKKLMNAYCDRQSVELNS-IAFLFD 70 (104)
Q Consensus 36 ~v~FkIK~tt~L~kLm~aY~~~~g~~~~~-lrF~fd 70 (104)
-.+|+||++++++-|+..-++.++.+.+. +|+|+-
T Consensus 585 l~qf~iKr~akisdl~~~iae~ln~pqs~~~r~w~m 620 (1089)
T COG5077 585 LAQFVIKRGAKISDLRNNIAEHLNTPQSLYLREWTM 620 (1089)
T ss_pred ceeEEeecCCCHHHHHHHHHHHcCCCceeeeEEEEE
Confidence 34899999999999999999999999988 898883
No 123
>cd06395 PB1_Map2k5 PB1 domain is essential part of the mitogen-activated protein kinase kinase 5 (Map2k5, alias MEK5) one of the key member of the signaling kinases cascade which involved in angiogenesis and early cardiovascular development. The PB1 domain of Map2k5 interacts with the PB1 domain of another members of kinase cascade MEKK2 (or MEKK3). A canonical PB1-PB1 interaction, involving 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 Map2k5 protein contains a type I PB1 domain.
Probab=41.45 E-value=79 Score=21.20 Aligned_cols=54 Identities=9% Similarity=0.048 Sum_probs=34.2
Q ss_pred EEEEEccCCCEEEEEEe--CCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 26 NLKVKGQDGNEVFFRIK--RSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 26 ~lkV~~~~g~~v~FkIK--~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
.|+++-++|..+--.|. ..-.|..|.++-.+-+.- ..-|+-+.+=|+||.|-|-
T Consensus 2 VIRIk~p~gg~vDw~V~~~~~L~F~DvL~~I~~vlp~---------------aT~tAFeYEDE~gDRITVR 57 (91)
T cd06395 2 VIRIKIPNGGAVDWTVQSGPQLLFRDVLDVIGQVLPE---------------ATTTAFEYEDEDGDRITVR 57 (91)
T ss_pred eEEEeCCCCCcccccccCcccccHHHHHHHHHHhccc---------------ccccceeeccccCCeeEec
Confidence 46677777777766666 344677777777665521 1344555666778888763
No 124
>cd02986 DLP Dim1 family, Dim1-like protein (DLP) subfamily; DLP is a novel protein which shares 38% sequence identity to Dim1. Like Dim1, it is also implicated in pre-mRNA splicing and cell cycle progression. DLP is located in the nucleus and has been shown to interact with the U5 small nuclear ribonucleoprotein particle (snRNP)-specific 102kD protein (or Prp6). Dim1 protein, also known as U5 snRNP-specific 15kD protein is a component of U5 snRNP, which pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5] tri-snRNP complex required for pre-mRNA splicing. Dim1 adopts a thioredoxin fold but does not contain the redox active CXXC motif.
Probab=40.51 E-value=21 Score=24.74 Aligned_cols=23 Identities=22% Similarity=0.621 Sum_probs=17.5
Q ss_pred HHHHHcCCc-cceEEEEECCEecC
Q 034095 53 AYCDRQSVE-LNSIAFLFDGRRLR 75 (104)
Q Consensus 53 aY~~~~g~~-~~~lrF~fdG~rI~ 75 (104)
.++++.++. .-++.|+++|+.+.
T Consensus 59 dva~~y~I~amPtfvffkngkh~~ 82 (114)
T cd02986 59 VYTQYFDISYIPSTIFFFNGQHMK 82 (114)
T ss_pred HHHHhcCceeCcEEEEEECCcEEE
Confidence 466677764 56777999999987
No 125
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=40.46 E-value=17 Score=19.49 Aligned_cols=26 Identities=8% Similarity=0.138 Sum_probs=20.4
Q ss_pred EEEeCCchHHHHHHHHHHHcCCccce
Q 034095 39 FRIKRSTQLKKLMNAYCDRQSVELNS 64 (104)
Q Consensus 39 FkIK~tt~L~kLm~aY~~~~g~~~~~ 64 (104)
+.|+-+..+...++.+|++.|.+.+.
T Consensus 2 iti~l~~~~~~~l~~~a~~~g~s~s~ 27 (39)
T PF01402_consen 2 ITIRLPDELYERLDELAKELGRSRSE 27 (39)
T ss_dssp EEEEEEHHHHHHHHHHHHHHTSSHHH
T ss_pred eEEEeCHHHHHHHHHHHHHHCcCHHH
Confidence 45566678889999999999987653
No 126
>KOG2378 consensus cAMP-regulated guanine nucleotide exchange factor [Signal transduction mechanisms]
Probab=40.32 E-value=1.2e+02 Score=26.37 Aligned_cols=58 Identities=19% Similarity=0.221 Sum_probs=48.3
Q ss_pred CCCCCCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCcc--ceEEEEECCEecC
Q 034095 18 PVDQSAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL--NSIAFLFDGRRLR 75 (104)
Q Consensus 18 p~~~~~~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~--~~lrF~fdG~rI~ 75 (104)
|.-+++.|.-+|--.|-+.++.+++-++.-+.++++-+++.|.+. .-+...+.|+.+-
T Consensus 229 ~v~~sDev~~~vy~~Dhsy~tl~~~vs~svqEI~~~va~k~~~seel~LV~v~s~GEkv~ 288 (573)
T KOG2378|consen 229 PVRGSDEVFCIVYLPDHSYVTLRIRVSASVQEILEAVAEKLGYSEELILVKVSSSGEKVI 288 (573)
T ss_pred CccCCCeeeEEEEecCceEEEEEeechhHHHHHHHHHHHHhccccceeEEEEccCCceee
Confidence 445577888999999999999999999999999999999998665 4556667888764
No 127
>cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs
Probab=40.23 E-value=12 Score=24.61 Aligned_cols=25 Identities=8% Similarity=0.004 Sum_probs=19.3
Q ss_pred EecCCCCCccccCCcCCceeeeeecc
Q 034095 72 RRLRGEQTPDEVILLFCAFCSCKYGR 97 (104)
Q Consensus 72 ~rI~~~~TP~~L~Medgdii~~~~~~ 97 (104)
..|+ .+++++|++++||.|.|.-++
T Consensus 37 v~in-~~dA~~lgi~~Gd~V~v~~~~ 61 (122)
T cd02791 37 VEIH-PEDAARLGLKEGDLVRVTSRR 61 (122)
T ss_pred EEEC-HHHHHHcCCCCCCEEEEEcCC
Confidence 3444 568999999999999887554
No 128
>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=40.22 E-value=1.2e+02 Score=20.73 Aligned_cols=61 Identities=11% Similarity=0.143 Sum_probs=41.4
Q ss_pred CcEEEEEEccCCC------EEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE-CCEecCCCCCcccc
Q 034095 23 AHINLKVKGQDGN------EVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF-DGRRLRGEQTPDEV 83 (104)
Q Consensus 23 ~~I~lkV~~~~g~------~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f-dG~rI~~~~TP~~L 83 (104)
++|-|.|.-..++ .-.|.|..+.++..++..--++..++++.--|+| ++.-...++|=.+|
T Consensus 23 ~~iPVIvE~~~~~~~p~l~k~KflVp~~~tv~~f~~~irk~l~l~~~~slfl~Vn~~~p~~~~~~~~l 90 (112)
T cd01611 23 DRIPVIVERYPKSDLPDLDKKKYLVPSDLTVGQFVYIIRKRIQLRPEKALFLFVNNSLPPTSATMSQL 90 (112)
T ss_pred CceEEEEEEcCCCCcccccCceEEecCCCCHHHHHHHHHHHhCCCccceEEEEECCccCCchhHHHHH
Confidence 4566666533321 2478999999999999999999998887766666 65433344444433
No 129
>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=40.21 E-value=1e+02 Score=20.04 Aligned_cols=34 Identities=15% Similarity=0.420 Sum_probs=28.8
Q ss_pred EEEEeCCchHHHHHHHHHHHcCCccceEEEEE-CC
Q 034095 38 FFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF-DG 71 (104)
Q Consensus 38 ~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f-dG 71 (104)
.|.|..+.++..++..=.++.+++.+.--|+| |.
T Consensus 19 kflv~~~~tv~~~~~~lrk~L~l~~~~slflyvnn 53 (87)
T cd01612 19 VFKISATQSFQAVIDFLRKRLKLKASDSLFLYINN 53 (87)
T ss_pred EEEeCCCCCHHHHHHHHHHHhCCCccCeEEEEECC
Confidence 79999999999999999999998776655666 54
No 130
>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=40.09 E-value=1.3e+02 Score=22.99 Aligned_cols=46 Identities=11% Similarity=0.295 Sum_probs=33.0
Q ss_pred cEEEEEEcc---CCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE
Q 034095 24 HINLKVKGQ---DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF 69 (104)
Q Consensus 24 ~I~lkV~~~---~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f 69 (104)
+|.|++... +.....+.+.......-|-++-|++.++++..+||+=
T Consensus 176 rv~V~f~~~~~~~~~~F~l~ls~~~tY~~la~~Va~~l~~dP~~lr~~~ 224 (249)
T PF12436_consen 176 RVEVEFKPKDNPNDPEFTLWLSKKMTYDQLAEKVAEHLNVDPEHLRFFT 224 (249)
T ss_dssp EEEEEEEETTSTT---EEEEEETT--HHHHHHHHHHHHTS-GGGEEEE-
T ss_pred eEEEEEEECCCCCCCCEEEEECCCCCHHHHHHHHHHHHCCChHHEEEEE
Confidence 466666542 2346788999999999999999999999999999984
No 131
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=40.08 E-value=17 Score=23.43 Aligned_cols=69 Identities=9% Similarity=0.009 Sum_probs=51.2
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCceeee
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSC 93 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~ 93 (104)
|.+.+.+.=|..++.+..++.....+.+.-|...|-.++.+++.=-+.-+.+.-|-++.+|-||--...
T Consensus 2 iev~~nDrLGKKVRvKCn~dDtiGD~KKliaaQtGT~~~kivl~k~~~i~kd~I~L~dyeihdg~~lel 70 (73)
T KOG3493|consen 2 IEVVLNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHITLSDYEIHDGMNLEL 70 (73)
T ss_pred ceehhhhhcCceEEEEeCCcccccCHHHHHHHhhCCChhHhHHHhhhhhhhcccceeeEEeccCccEEE
Confidence 345556667888889999999998888889999998787777664455556677778888877754433
No 132
>PF01982 CTP-dep_RFKase: Domain of unknown function DUF120; InterPro: IPR023602 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents a CTP-dependent riboflavin kinase domain, found primarily in archaea, that catalyses the phosphorylation of riboflavin to form flavin mononucleotide in riboflavin biosynthesis. Its structure resembles a RIFT barrel, structurally similar to but topologically distinct from bacterial and eukaryotic examples []. The N-terminal is a winged helix-turn-helix DNA-binding domain, and the C-terminal half is most similar in sequence to a group of cradle-loop barrels.; GO: 0016773 phosphotransferase activity, alcohol group as acceptor; PDB: 2VBV_A 2VBU_A 2VBS_A 2VBT_A 2P3M_A 2OYN_A 3CTA_A.
Probab=37.70 E-value=19 Score=25.37 Aligned_cols=15 Identities=13% Similarity=-0.144 Sum_probs=9.6
Q ss_pred cccCCcCCceeeeee
Q 034095 81 DEVILLFCAFCSCKY 95 (104)
Q Consensus 81 ~~L~Medgdii~~~~ 95 (104)
+.|+++|||.|.|.+
T Consensus 107 ~~L~L~DGD~V~v~V 121 (121)
T PF01982_consen 107 DTLGLKDGDEVEVEV 121 (121)
T ss_dssp HHTT--TT-EEEEEE
T ss_pred hhcCCCCCCEEEEEC
Confidence 469999999998864
No 133
>PF09631 Sen15: Sen15 protein; InterPro: IPR018593 The Sen15 subunit of the tRNA intron-splicing endonuclease is one of the two structural subunits of this heterotetrameric enzyme. Residues 36-157 of this subunit possess a novel homodimeric fold. Each monomer consists of three alpha-helices and a mixed antiparallel/parallel beta-sheet. Two monomers of Sen15 fold with two monomers of Sen34, one of the two catalytic subunits, to form an alpha2-beta2 tetramer as part of the functional endonuclease assembly []. ; PDB: 2GW6_B.
Probab=37.49 E-value=47 Score=21.91 Aligned_cols=22 Identities=23% Similarity=0.472 Sum_probs=16.0
Q ss_pred CCcEEEEEEccCCCEEEEEEeC
Q 034095 22 SAHINLKVKGQDGNEVFFRIKR 43 (104)
Q Consensus 22 ~~~I~lkV~~~~g~~v~FkIK~ 43 (104)
...|.|.+.+.|++.++|+|..
T Consensus 72 ~~ri~LAiv~~DsTiVYY~i~~ 93 (101)
T PF09631_consen 72 PKRILLAIVDDDSTIVYYKIHD 93 (101)
T ss_dssp --EEEEEEE-TTS-EEEEEEE-
T ss_pred CcEEEEEEEcCCCCEEEEEEeC
Confidence 5799999999999999999864
No 134
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=36.94 E-value=22 Score=19.92 Aligned_cols=18 Identities=17% Similarity=0.136 Sum_probs=14.4
Q ss_pred CCccccCCcCCceeeeee
Q 034095 78 QTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 78 ~TP~~L~Medgdii~~~~ 95 (104)
..+.+|.++-||+|.|+-
T Consensus 9 ~~~~eLs~~~Gd~i~v~~ 26 (48)
T PF00018_consen 9 EDPDELSFKKGDIIEVLE 26 (48)
T ss_dssp SSTTBSEB-TTEEEEEEE
T ss_pred CCCCEEeEECCCEEEEEE
Confidence 458999999999999863
No 135
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=36.63 E-value=15 Score=23.85 Aligned_cols=24 Identities=0% Similarity=-0.158 Sum_probs=18.9
Q ss_pred EecCCCCCccccCCcCCceeeeeec
Q 034095 72 RRLRGEQTPDEVILLFCAFCSCKYG 96 (104)
Q Consensus 72 ~rI~~~~TP~~L~Medgdii~~~~~ 96 (104)
..|+ .++++.|++++||.|.|.-+
T Consensus 37 v~in-~~dA~~lgi~~Gd~V~v~~~ 60 (116)
T cd02790 37 VEIN-PEDAKRLGIEDGEKVRVSSR 60 (116)
T ss_pred EEEC-HHHHHHcCCCCCCEEEEEcC
Confidence 3444 47999999999999988654
No 136
>PF09014 Sushi_2: Beta-2-glycoprotein-1 fifth domain; InterPro: IPR015104 The fifth domain of beta-2-glycoprotein-1 (b2GP-1) is composed of four well-defined anti-parallel beta-strands and two short alpha-helices, as well as a long highly flexible loop. It plays an important role in the binding of b2GP-1 to negatively charged compounds and subsequent capture for binding of anti-b2GP-1 antibodies []. ; PDB: 1C1Z_A 3OP8_B 2KRI_A 1QUB_A 1G4G_A 1G4F_A.
Probab=36.12 E-value=18 Score=24.13 Aligned_cols=33 Identities=12% Similarity=0.196 Sum_probs=22.7
Q ss_pred CccceEEEEECCEecCC-CCCccccCCcCCceeeee
Q 034095 60 VELNSIAFLFDGRRLRG-EQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 60 ~~~~~lrF~fdG~rI~~-~~TP~~L~Medgdii~~~ 94 (104)
++...-|.+|+|+++.. +.+|. +|-.||+|++.
T Consensus 6 i~vkra~Vly~g~k~~i~d~~~~--~v~Hge~Vsff 39 (85)
T PF09014_consen 6 IPVKRARVLYNGEKVWIQDLFKN--GVLHGEIVSFF 39 (85)
T ss_dssp -SSSS-EEEETTEEEEHHHHTTT---BETT-EEEEE
T ss_pred cceeEEEEEECCEEechhhcccC--ceeeCCEEEEE
Confidence 56778899999999996 44443 67889998864
No 137
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=35.32 E-value=14 Score=24.26 Aligned_cols=19 Identities=5% Similarity=-0.193 Sum_probs=16.2
Q ss_pred CCCccccCCcCCceeeeee
Q 034095 77 EQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~~ 95 (104)
.++++.|++++||.|-|.-
T Consensus 41 p~dA~~lgi~~Gd~V~v~s 59 (122)
T cd02792 41 PELAAERGIKNGDMVWVSS 59 (122)
T ss_pred HHHHHHcCCCCCCEEEEEc
Confidence 5689999999999997754
No 138
>PRK14132 riboflavin kinase; Provisional
Probab=35.03 E-value=24 Score=24.98 Aligned_cols=15 Identities=7% Similarity=-0.277 Sum_probs=12.6
Q ss_pred cccCCcCCceeeeee
Q 034095 81 DEVILLFCAFCSCKY 95 (104)
Q Consensus 81 ~~L~Medgdii~~~~ 95 (104)
+.|+|+|||.|.+.+
T Consensus 112 ~~L~LkDGD~V~I~i 126 (126)
T PRK14132 112 KFLNLKDGDVVKIVI 126 (126)
T ss_pred hhcCCCCCCEEEEEC
Confidence 469999999998864
No 139
>PF06487 SAP18: Sin3 associated polypeptide p18 (SAP18); InterPro: IPR010516 This family consists of several eukaryotic Sin3 associated polypeptide p18 (SAP18) sequences. SAP18 is known to be a component of the Sin3-containing complex, which is responsible for the repression of transcription via the modification of histone polypeptides []. SAP18 is also present in the ASAP complex which is thought to be involved in the regulation of splicing during the execution of programmed cell death [].; PDB: 2HDE_A 4A90_A 4A6Q_A 4A8X_C.
Probab=34.73 E-value=32 Score=24.05 Aligned_cols=62 Identities=16% Similarity=0.224 Sum_probs=36.4
Q ss_pred CCEEEEEEeCCchHHHHHHHHHHHc-----CCccceEEEEE-C---CE-------------e-cCCCCCccccCCcCCce
Q 034095 34 GNEVFFRIKRSTQLKKLMNAYCDRQ-----SVELNSIAFLF-D---GR-------------R-LRGEQTPDEVILLFCAF 90 (104)
Q Consensus 34 g~~v~FkIK~tt~L~kLm~aY~~~~-----g~~~~~lrF~f-d---G~-------------r-I~~~~TP~~L~Medgdi 90 (104)
.+++++-.=+++.|+.|-..-.+.. .-..=+|++.| | |. + -.++.|-+++...-||+
T Consensus 36 ~~elqIYtW~d~TLrEL~~Lik~~~~~~r~~~tr~~F~~VypD~~~~r~~~kdlGsv~~g~~~~d~~kTL~~~~F~iGDy 115 (120)
T PF06487_consen 36 RNELQIYTWMDATLRELADLIKDVNPPARRRGTRLSFRLVYPDTRSGRYVSKDLGSVVSGRKGPDDNKTLADLRFVIGDY 115 (120)
T ss_dssp TTEEEEEE-TT-BHHHHHHHHHHH-HHHHSTT-EEEEEEEEECTTTTCEEEEEEEEEETTB--TTTTSBCGGGT--TT-E
T ss_pred cCeeEEEEcccCCHHHHHHHHHHhCcccCCCCCEEEEEEEeecCCCCceeeecCCeEECCCCCCCcccCHhhCCcccCCE
Confidence 3677777788888888776555431 11223455555 3 11 1 23689999999999999
Q ss_pred eeeee
Q 034095 91 CSCKY 95 (104)
Q Consensus 91 i~~~~ 95 (104)
|||-|
T Consensus 116 idvaI 120 (120)
T PF06487_consen 116 IDVAI 120 (120)
T ss_dssp EEEEE
T ss_pred EEEeC
Confidence 99965
No 140
>PF06134 RhaA: L-rhamnose isomerase (RhaA); InterPro: IPR009308 This family consists of several bacterial L-rhamnose isomerase proteins (5.3.1.14 from EC). This enzyme interconverts L-rhamnose and L-rhamnulose. In some species, including Escherichia coli, this is the first step in rhamnose catabolism. Sequential steps are catalyzed by rhamnulose kinase (rhaB), then rhamnulose-1-phosphate aldolase (rhaD) to yield glycerone phosphate and (S)-lactaldehyde. ; GO: 0008740 L-rhamnose isomerase activity, 0030145 manganese ion binding, 0019299 rhamnose metabolic process; PDB: 1DE5_A 1D8W_D 1DE6_B 3P14_B 3UU0_B.
Probab=34.69 E-value=34 Score=28.82 Aligned_cols=21 Identities=24% Similarity=0.597 Sum_probs=17.8
Q ss_pred CCchHHHHHHHHHHHcCCccc
Q 034095 43 RSTQLKKLMNAYCDRQSVELN 63 (104)
Q Consensus 43 ~tt~L~kLm~aY~~~~g~~~~ 63 (104)
++.|++.+.+.||.+.|+|..
T Consensus 379 K~~P~gaVwd~yC~~~~vP~~ 399 (417)
T PF06134_consen 379 KSLPFGAVWDYYCERNGVPVG 399 (417)
T ss_dssp CCSSHHHHHHHHHHHTTS-ST
T ss_pred hcCCHHHHHHHHHHHcCCCCc
Confidence 578999999999999999864
No 141
>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=33.94 E-value=1.2e+02 Score=18.91 Aligned_cols=63 Identities=19% Similarity=0.331 Sum_probs=47.5
Q ss_pred EEEEEccC---CCEEEEEEeCCchHHHHHHHHHHHcCCcc--ceEEEE--E-CC--EecCCCCCccccCCcCC
Q 034095 26 NLKVKGQD---GNEVFFRIKRSTQLKKLMNAYCDRQSVEL--NSIAFL--F-DG--RRLRGEQTPDEVILLFC 88 (104)
Q Consensus 26 ~lkV~~~~---g~~v~FkIK~tt~L~kLm~aY~~~~g~~~--~~lrF~--f-dG--~rI~~~~TP~~L~Medg 88 (104)
.|||-..+ +....+.|.++++-+.+...-.++.+++. ..+.++ . +| +.|.++.-|-.+-+.++
T Consensus 4 ~lrV~~~~~~~~~~kti~v~~~tTa~~Vi~~~l~k~~l~~~~~~y~L~e~~~~~~er~L~~~e~Pl~~~~~~~ 76 (90)
T smart00314 4 VLRVYVDDLPGGTYKTLRVSSRTTARDVIQQLLEKFHLTDDPEEYVLVEVLPDGKERVLPDDENPLQLQKLWP 76 (90)
T ss_pred EEEEecccCCCCcEEEEEECCCCCHHHHHHHHHHHhCCCCCcccEEEEEEeCCcEEEEeCCCCcceEehhhCC
Confidence 35666655 88889999999999999999999999864 344433 2 44 56667788888777665
No 142
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=33.42 E-value=1.2e+02 Score=18.85 Aligned_cols=45 Identities=9% Similarity=0.024 Sum_probs=30.3
Q ss_pred chHHHHHHHHHHHcC-----CccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 45 TQLKKLMNAYCDRQS-----VELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 45 t~L~kLm~aY~~~~g-----~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
+..+.|.+.-+++.. +..+.+++..|++-+ +.+|| +.|||-|.++
T Consensus 26 ~tv~~l~~~L~~~~~~~~~~~~~~~~~~aVN~~~~-~~~~~----l~dgDeVai~ 75 (81)
T PRK11130 26 PTVEALRQHLAQKGDRWALALEDGKLLAAVNQTLV-SFDHP----LTDGDEVAFF 75 (81)
T ss_pred CCHHHHHHHHHHhCccHHhhhcCCCEEEEECCEEc-CCCCC----CCCCCEEEEe
Confidence 566666666666642 234667888888655 34554 9999999775
No 143
>COG4806 RhaA L-rhamnose isomerase [Carbohydrate transport and metabolism]
Probab=33.23 E-value=30 Score=28.47 Aligned_cols=21 Identities=24% Similarity=0.580 Sum_probs=18.3
Q ss_pred CCchHHHHHHHHHHHcCCccc
Q 034095 43 RSTQLKKLMNAYCDRQSVELN 63 (104)
Q Consensus 43 ~tt~L~kLm~aY~~~~g~~~~ 63 (104)
++-|++.+.+.||+++++|..
T Consensus 380 K~~P~~aiW~~yCe~~~VPv~ 400 (419)
T COG4806 380 KSLPWQAVWEMYCQRHDVPVG 400 (419)
T ss_pred hcCCHHHHHHHHHHhcCCCch
Confidence 467999999999999999864
No 144
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=32.54 E-value=19 Score=23.32 Aligned_cols=24 Identities=0% Similarity=-0.086 Sum_probs=18.7
Q ss_pred EecCCCCCccccCCcCCceeeeeec
Q 034095 72 RRLRGEQTPDEVILLFCAFCSCKYG 96 (104)
Q Consensus 72 ~rI~~~~TP~~L~Medgdii~~~~~ 96 (104)
..|+ .++++.|++++||.|-|.-+
T Consensus 37 v~in-p~dA~~lgi~~Gd~V~v~~~ 60 (120)
T cd00508 37 VEIH-PEDAARLGIKDGDLVRVSSR 60 (120)
T ss_pred EEEC-HHHHHHcCCCCCCEEEEEeC
Confidence 4454 46899999999999987643
No 145
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=32.24 E-value=17 Score=23.40 Aligned_cols=18 Identities=0% Similarity=-0.051 Sum_probs=13.5
Q ss_pred CCCccccCCcCCceeeee
Q 034095 77 EQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~ 94 (104)
..+++.|+++|||.|-|.
T Consensus 36 p~dA~~~Gi~~Gd~V~v~ 53 (110)
T PF01568_consen 36 PEDAAKLGIKDGDWVRVS 53 (110)
T ss_dssp HHHHHHCT--TTCEEEEE
T ss_pred HHHHHHhcCcCCCEEEEE
Confidence 457889999999999885
No 146
>PF12167 DUF3596: Domain of unknown function (DUF3596); InterPro: IPR022000 This N-terminal domain is found in Bacteriophage P27p02, it is functionally uncharacterised, though it is considered to be an integrase. Integrase is necessary for integration of the phage into the host genome by site-specific recombination. In conjunction with excisionase, integrase is also necessary for excision of the prophage from the host genome. This domain is found in related proteins in other bacteriophage, and prophage regions of bacterial genomes. The domain is approximately 90 amino acids in length and is found is associated with the C-terminal domain characterised by PF00589 from PFAM.
Probab=32.22 E-value=33 Score=21.10 Aligned_cols=19 Identities=37% Similarity=0.749 Sum_probs=13.4
Q ss_pred eEEEEECCEecCC----CCCccc
Q 034095 64 SIAFLFDGRRLRG----EQTPDE 82 (104)
Q Consensus 64 ~lrF~fdG~rI~~----~~TP~~ 82 (104)
-+.|.|.|.|... .+||+.
T Consensus 12 ~i~F~y~G~R~re~l~l~dT~~N 34 (64)
T PF12167_consen 12 RIDFTYQGKRCRESLGLPDTPAN 34 (64)
T ss_pred EEEEEECCEEEEEeCCCCCCHHH
Confidence 4678889999764 556553
No 147
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=32.19 E-value=9 Score=22.72 Aligned_cols=45 Identities=9% Similarity=-0.009 Sum_probs=25.4
Q ss_pred CchHHHHHHHHHHHcCC--ccceEEEEE-------CCEecCCCCCccccCCcCCceeee
Q 034095 44 STQLKKLMNAYCDRQSV--ELNSIAFLF-------DGRRLRGEQTPDEVILLFCAFCSC 93 (104)
Q Consensus 44 tt~L~kLm~aY~~~~g~--~~~~lrF~f-------dG~rI~~~~TP~~L~Medgdii~~ 93 (104)
.++..+|- .|-.+.++ |.+.++.++ ||..+. ..+.-+.-||.|.+
T Consensus 5 ~~~~~rLd-~~L~~~~~~~SR~~~k~li~~G~V~VNg~~~~----~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 5 FTEYITLG-QLLKELGIIDSGGQAKWFLQENEVLVNGELEN----RRGKKLYPGDVIEI 58 (59)
T ss_pred cchHHHHH-HHHHHcCCccCHHHHHHHHHcCCEEECCEEcc----CCCCCCCCCCEEEe
Confidence 34555553 44444465 665555554 444432 44668888998864
No 148
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=31.85 E-value=29 Score=19.90 Aligned_cols=18 Identities=22% Similarity=0.211 Sum_probs=13.8
Q ss_pred CCCccccCCcCCceeeee
Q 034095 77 EQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~ 94 (104)
.+.|.+|.+.-||+|-|+
T Consensus 7 ~~~~dELs~~~Gd~i~v~ 24 (49)
T PF14604_consen 7 AQDPDELSFKKGDVITVL 24 (49)
T ss_dssp SSSTTB-EB-TTEEEEEE
T ss_pred CCCcCEeeEcCCCEEEEE
Confidence 456789999999999998
No 149
>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=31.69 E-value=1.1e+02 Score=19.93 Aligned_cols=34 Identities=12% Similarity=0.146 Sum_probs=31.3
Q ss_pred EEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE
Q 034095 36 EVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF 69 (104)
Q Consensus 36 ~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f 69 (104)
.+..++.+..++..|-..-+++..++.+..++.|
T Consensus 8 TVai~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY 41 (78)
T cd06411 8 TVALRAPRGADVSSLRALLSQALPQQAQRGQLSY 41 (78)
T ss_pred EEEEEccCCCCHHHHHHHHHHHhcCChhhcEEEe
Confidence 3567889999999999999999999999999999
No 150
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=31.67 E-value=30 Score=19.91 Aligned_cols=18 Identities=17% Similarity=0.169 Sum_probs=14.2
Q ss_pred CCCccccCCcCCceeeee
Q 034095 77 EQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~ 94 (104)
..+|.+|.+.-||+|.|+
T Consensus 10 ~~~~~~Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 10 AEDPDELSFKKGDVIEVL 27 (55)
T ss_dssp SSSTTB-EB-TTEEEEEE
T ss_pred CCCCCceEEecCCEEEEE
Confidence 367899999999999998
No 151
>PRK11675 LexA regulated protein; Provisional
Probab=30.32 E-value=66 Score=21.59 Aligned_cols=33 Identities=9% Similarity=0.126 Sum_probs=26.9
Q ss_pred ccCCCEEEEEEeCCchHHHHHHHHHHHcCCccc
Q 034095 31 GQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELN 63 (104)
Q Consensus 31 ~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~ 63 (104)
|...-...+.||-+..+-.-++.||+..+++.+
T Consensus 45 dk~~glKRveVKldedl~ekL~eyAe~~nitRS 77 (90)
T PRK11675 45 DKVRGLKRVELKLNADLVDALNELAEARNISRS 77 (90)
T ss_pred HHHcCceeEEEEECHHHHHHHHHHHHHcCCCHH
Confidence 333344589999999999999999999998764
No 152
>PF08722 Tn7_Tnp_TnsA_N: TnsA endonuclease N terminal; InterPro: IPR014833 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The N-terminal domain of TnsA is catalytic. ; PDB: 1F1Z_B 1T0F_B.
Probab=30.27 E-value=96 Score=19.48 Aligned_cols=36 Identities=28% Similarity=0.491 Sum_probs=22.9
Q ss_pred EEEEccCC---CEEEEEEeCCchHHH--------HHHHHHHHcCCcc
Q 034095 27 LKVKGQDG---NEVFFRIKRSTQLKK--------LMNAYCDRQSVEL 62 (104)
Q Consensus 27 lkV~~~~g---~~v~FkIK~tt~L~k--------Lm~aY~~~~g~~~ 62 (104)
+-|.-.+| ..+.+.||+...|.+ +-..||+..|++.
T Consensus 37 Flv~~~~g~~~~~~~ieVK~~~~l~~~~~~~k~~~~~~y~~~~g~~f 83 (88)
T PF08722_consen 37 FLVTYRDGNGKKPVAIEVKPSSELEKPRTKEKLEIEREYWEEQGIPF 83 (88)
T ss_dssp EEEEESSS--SSEEEEEE--GGGGGSHHHHHHHHHHHHHHHHCT--E
T ss_pred EEEEEccCCcceEEEEEEccHHHhcChhHHHHHHHHHHHHHHcCCeE
Confidence 33444555 778999999988876 5567888888754
No 153
>cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups
Probab=30.20 E-value=23 Score=22.82 Aligned_cols=20 Identities=10% Similarity=0.021 Sum_probs=16.5
Q ss_pred CCCccccCCcCCceeeeeec
Q 034095 77 EQTPDEVILLFCAFCSCKYG 96 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~~~ 96 (104)
.++++.|++++||.|-|.-+
T Consensus 35 p~dA~~lGi~~Gd~V~v~s~ 54 (96)
T cd02788 35 PADAARLGLADGDLVEFSLG 54 (96)
T ss_pred HHHHHHcCCCCCCEEEEEEC
Confidence 56899999999999977544
No 154
>PF06071 YchF-GTPase_C: Protein of unknown function (DUF933); InterPro: IPR013029 This domain is found at the C terminus of family of conserved hypothetical proteins found in both prokaryotes and eukaryotes. While the function of these proteins is not known, the crystal structure of P44681 from SWISSPROT from Haemophilus influenzae has been determined []. This protein consists of three domains: an N-terminal domain which has a mononucleotide binding fold typical for the P-loop NTPases, a central domain which forms an alpha-helical coiled coil, and this C-terminal domain which is composed of a six-stranded half-barrel curved around an alpha helix. The central domain and this domain are topologically similar to RNA-binding proteins, while the N-terminal region contains the features typical of GTP-dependent molecular switches. The purified protein was capable of binding both double-stranded nucleic acid and GTP. It was suggested, therefore, that this protein might be part of a nucleoprotein complex and could function as a GTP-dependent translation factor.; PDB: 1NI3_A 1JAL_A 2DWQ_B 2DBY_A 2OHF_A.
Probab=30.01 E-value=35 Score=22.64 Aligned_cols=15 Identities=7% Similarity=0.140 Sum_probs=9.5
Q ss_pred cccCCcCCceeeeee
Q 034095 81 DEVILLFCAFCSCKY 95 (104)
Q Consensus 81 ~~L~Medgdii~~~~ 95 (104)
.+.-|+|||||-++.
T Consensus 69 K~YivqDGDIi~f~f 83 (84)
T PF06071_consen 69 KDYIVQDGDIIHFRF 83 (84)
T ss_dssp TT-B--TTEEEEEEE
T ss_pred CceeEeCCCEEEEEc
Confidence 467899999998764
No 155
>TIGR03193 4hydroxCoAred 4-hydroxybenzoyl-CoA reductase, gamma subunit. 4-hydroxybenzoyl-CoA reductase converts 4-hydroxybenzoyl-CoA to benzoyl-CoA, a common intermediate in the degradation of aromatic compounds. This protein family represents the gamma chain of this three-subunit enzyme.
Probab=29.87 E-value=1.3e+02 Score=21.76 Aligned_cols=55 Identities=16% Similarity=0.129 Sum_probs=38.9
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCcc-------ceEEEEECCEecCCCCCccc
Q 034095 25 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL-------NSIAFLFDGRRLRGEQTPDE 82 (104)
Q Consensus 25 I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~-------~~lrF~fdG~rI~~~~TP~~ 82 (104)
|++.| +|..+.+.+.+.++|-........-.|... .+...++||+.++.-.+|.-
T Consensus 2 i~~~v---NG~~~~~~~~~~~~Ll~~LR~~lgltg~K~gC~~G~CGACtVlvdg~~v~SCl~~~~ 63 (148)
T TIGR03193 2 LRLTV---NGRWREDAVADNMLLVDYLRDTVGLTGTKQGCDGGECGACTVLVDGRPRLACSTLAH 63 (148)
T ss_pred EEEEE---CCEEEEeecCCCCcHHHHHHHhcCCCCCCCCCCCCCCCCCEEEECCeEeeccHhhHh
Confidence 56666 777888888888888777665433333322 56778899999998777764
No 156
>PF10787 YfmQ: Uncharacterised protein from bacillus cereus group; InterPro: IPR019723 This entry represents proteins conserved in the Bacillus cereus group. Several members are called YfmQ but the function is not known.
Probab=29.83 E-value=52 Score=24.06 Aligned_cols=36 Identities=19% Similarity=0.401 Sum_probs=31.4
Q ss_pred CCchHHHHHHHHHHHcCCccceEEEEECCEecCCCC
Q 034095 43 RSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQ 78 (104)
Q Consensus 43 ~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~ 78 (104)
|+.-...|+..|+-+..++.......+||.+|.+.+
T Consensus 23 Pt~vVe~liskfe~H~kL~~~~~tVti~G~~Lege~ 58 (149)
T PF10787_consen 23 PTSVVEWLISKFELHPKLDEENTTVTIDGKRLEGED 58 (149)
T ss_pred cHHHHHHHHHHheecccccccceEEEECCeecCchH
Confidence 566778999999999999999999999999998654
No 157
>PRK01777 hypothetical protein; Validated
Probab=29.58 E-value=1.7e+02 Score=19.37 Aligned_cols=53 Identities=8% Similarity=-0.006 Sum_probs=37.5
Q ss_pred EEEEEeCCchHHHHHHHHH--HH-cCCccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 37 VFFRIKRSTQLKKLMNAYC--DR-QSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 37 v~FkIK~tt~L~kLm~aY~--~~-~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
..+.+...++...+.++.- +. -.+++....+..+|+.+.. +--+.+||.|.+.
T Consensus 19 ~~l~vp~GtTv~dal~~sgi~~~~pei~~~~~~vgI~Gk~v~~-----d~~L~dGDRVeIy 74 (95)
T PRK01777 19 QRLTLQEGATVEEAIRASGLLELRTDIDLAKNKVGIYSRPAKL-----TDVLRDGDRVEIY 74 (95)
T ss_pred EEEEcCCCCcHHHHHHHcCCCccCcccccccceEEEeCeECCC-----CCcCCCCCEEEEe
Confidence 4778888999888887652 11 1234445688889998865 3478999999874
No 158
>PF07377 DUF1493: Protein of unknown function (DUF1493); InterPro: IPR010862 This family consists of several bacterial proteins of around 115 residues in length. Members of this family are largely found in Salmonella and Yersinia species and several have been described as being putative cytoplasmic proteins. The function of this family is unknown.
Probab=28.41 E-value=34 Score=22.98 Aligned_cols=24 Identities=29% Similarity=0.656 Sum_probs=21.2
Q ss_pred hHHHHHHHHHHHcCCccceEEE--EE
Q 034095 46 QLKKLMNAYCDRQSVELNSIAF--LF 69 (104)
Q Consensus 46 ~L~kLm~aY~~~~g~~~~~lrF--~f 69 (104)
-...||++|+++.+++.+.+.| +|
T Consensus 43 da~elm~~f~~~F~Vd~~~f~~~~YF 68 (111)
T PF07377_consen 43 DAEELMEDFFERFNVDLSDFDFDRYF 68 (111)
T ss_pred HHHHHHHHHHHHhCCCcCccCHHHcc
Confidence 4567999999999999999998 77
No 159
>KOG3391 consensus Transcriptional co-repressor component [Transcription]
Probab=28.35 E-value=40 Score=24.60 Aligned_cols=62 Identities=11% Similarity=0.155 Sum_probs=39.2
Q ss_pred EEEEEEeCCchHHHHHHHHHH------HcCCccceEEEEE-C----CEe-------------cCCCCCccccCCcCCcee
Q 034095 36 EVFFRIKRSTQLKKLMNAYCD------RQSVELNSIAFLF-D----GRR-------------LRGEQTPDEVILLFCAFC 91 (104)
Q Consensus 36 ~v~FkIK~tt~L~kLm~aY~~------~~g~~~~~lrF~f-d----G~r-------------I~~~~TP~~L~Medgdii 91 (104)
++++--=++..|..|-..-++ +.|... .|++.| | |-+ +.++.|-.+...+=||++
T Consensus 53 elQiYtW~datL~ELtsLvkevnpeaR~kgt~f-~fa~Vf~d~~~~~y~~RevG~t~~g~Kg~ddnktL~~~kf~iGD~l 131 (151)
T KOG3391|consen 53 ELQIYTWMDATLRELTSLVKEVNPEARKKGTSF-DFAVVFPDKKSPRYIVREVGTTCLGRKGIDDNKTLQQTKFEIGDYL 131 (151)
T ss_pred heeEeehhhhhHHHHHHHHHHcCHHHhccCceE-EEEEEeccCCCCCceeeeecccccCcccCCccchhhhCCccccceE
Confidence 355555567777777655543 344433 233333 2 222 347999999999999999
Q ss_pred eeeeccc
Q 034095 92 SCKYGRL 98 (104)
Q Consensus 92 ~~~~~~~ 98 (104)
||-|---
T Consensus 132 DVaI~~p 138 (151)
T KOG3391|consen 132 DVAITPP 138 (151)
T ss_pred EEEecCc
Confidence 9988543
No 160
>cd02787 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=28.25 E-value=21 Score=23.36 Aligned_cols=21 Identities=5% Similarity=-0.165 Sum_probs=16.7
Q ss_pred ecCCCCCccccCCcCCceeeee
Q 034095 73 RLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 73 rI~~~~TP~~L~Medgdii~~~ 94 (104)
.|+ .++++.|++.|||.|-|.
T Consensus 34 ~i~-p~dA~~lgI~dGd~V~v~ 54 (112)
T cd02787 34 FMN-PDDIARLGLKAGDRVDLE 54 (112)
T ss_pred EEC-HHHHHHhCCCCCCEEEEE
Confidence 445 455999999999999775
No 161
>cd01817 RGS12_RBD Ubiquitin domain of RGS12 and RGS14. RGS12 (regulator of G signalling 12), and RGS14, are members of a family of GTPase-activating proteins (GAP's) specific for the G-alpha subunit, which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. Their domain architecture includes tandem RBD domains as well as PDZ , PTB, and RGS, and GoLoco domains.
Probab=27.82 E-value=1.7e+02 Score=18.82 Aligned_cols=53 Identities=11% Similarity=0.365 Sum_probs=39.5
Q ss_pred EEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE-CCEecCCCCCc
Q 034095 28 KVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF-DGRRLRGEQTP 80 (104)
Q Consensus 28 kV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f-dG~rI~~~~TP 80 (104)
+|.=+||+.-...+++...++.+...-|++.|+.+..+-.+. .|...-..+|+
T Consensus 3 rV~LPdg~~T~V~vrpG~ti~d~L~kllekRgl~~~~~~vf~~g~~k~l~~~qD 56 (73)
T cd01817 3 RVILPDGSTTVVPTRPGESIRDLLSGLCEKRGINYAAVDLFLVGGDKPLVLDQD 56 (73)
T ss_pred EEECCCCCeEEEEecCCCCHHHHHHHHHHHcCCChhHEEEEEecCCcccccCCc
Confidence 345578888889999999999999999999999887665554 44333334443
No 162
>PF13670 PepSY_2: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification.
Probab=27.59 E-value=1.4e+02 Score=18.56 Aligned_cols=24 Identities=17% Similarity=0.344 Sum_probs=19.3
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCc
Q 034095 22 SAHINLKVKGQDGNEVFFRIKRST 45 (104)
Q Consensus 22 ~~~I~lkV~~~~g~~v~FkIK~tt 45 (104)
...+.+.+.+.+|..+.++|.+.|
T Consensus 53 ~g~yev~~~~~dG~~~ev~vD~~t 76 (83)
T PF13670_consen 53 DGCYEVEARDKDGKKVEVYVDPAT 76 (83)
T ss_pred CCEEEEEEEECCCCEEEEEEcCCC
Confidence 446888888999999888887654
No 163
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=27.37 E-value=50 Score=19.31 Aligned_cols=23 Identities=22% Similarity=0.203 Sum_probs=15.5
Q ss_pred EECCEecCCCCCccccCCcCCceeee
Q 034095 68 LFDGRRLRGEQTPDEVILLFCAFCSC 93 (104)
Q Consensus 68 ~fdG~rI~~~~TP~~L~Medgdii~~ 93 (104)
++||++|.+ -....|.+||+|.+
T Consensus 45 ~vng~~l~~---~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 45 FVNGQRLGP---GEPVPLKDGDIIRF 67 (68)
T ss_dssp EETTEEESS---TSEEEE-TTEEEEE
T ss_pred EECCEEcCC---CCEEECCCCCEEEc
Confidence 459999987 23456788888853
No 164
>cd02783 MopB_CT_2 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=26.66 E-value=24 Score=24.94 Aligned_cols=19 Identities=11% Similarity=-0.020 Sum_probs=16.5
Q ss_pred CCCccccCCcCCceeeeee
Q 034095 77 EQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~~ 95 (104)
.+++++|+++|||.|-|.-
T Consensus 38 p~dA~~~GI~dGd~V~v~s 56 (156)
T cd02783 38 PKTAKELGIKDGDWVWVES 56 (156)
T ss_pred HHHHHHcCCCCCCEEEEEc
Confidence 6789999999999998753
No 165
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=26.64 E-value=24 Score=23.00 Aligned_cols=18 Identities=0% Similarity=-0.269 Sum_probs=15.2
Q ss_pred CCCccccCCcCCceeeee
Q 034095 77 EQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~ 94 (104)
.+++++|+++|||.|-|.
T Consensus 37 p~dA~~lgi~~Gd~V~v~ 54 (116)
T cd02786 37 PADAAARGIADGDLVVVF 54 (116)
T ss_pred HHHHHHcCCCCCCEEEEE
Confidence 567889999999998664
No 166
>PHA01748 hypothetical protein
Probab=26.43 E-value=96 Score=18.80 Aligned_cols=26 Identities=15% Similarity=0.327 Sum_probs=22.0
Q ss_pred EEEEeCCchHHHHHHHHHHHcCCccc
Q 034095 38 FFRIKRSTQLKKLMNAYCDRQSVELN 63 (104)
Q Consensus 38 ~FkIK~tt~L~kLm~aY~~~~g~~~~ 63 (104)
.+.|+-+..+..-++.||++.|++.+
T Consensus 4 ~iSvrLp~el~~eld~~a~~~g~~RS 29 (60)
T PHA01748 4 VITFKIEEDLLELLDRYAIKHGLNRS 29 (60)
T ss_pred EEEEECCHHHHHHHHHHHHHhCCCHH
Confidence 57788888999999999999998653
No 167
>cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=26.40 E-value=24 Score=23.49 Aligned_cols=19 Identities=0% Similarity=-0.190 Sum_probs=16.2
Q ss_pred CCCccccCCcCCceeeeee
Q 034095 77 EQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~~ 95 (104)
.++++.|+++|||.|-|.=
T Consensus 38 p~dA~~~gi~~Gd~V~v~s 56 (124)
T cd02785 38 PIDAAARGIAHGDLVEVYN 56 (124)
T ss_pred HHHHHHcCCCCCCEEEEEe
Confidence 6789999999999997653
No 168
>cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=26.39 E-value=25 Score=23.41 Aligned_cols=20 Identities=5% Similarity=-0.081 Sum_probs=16.6
Q ss_pred CCCccccCCcCCceeeeeec
Q 034095 77 EQTPDEVILLFCAFCSCKYG 96 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~~~ 96 (104)
.++++.|++++||.|-|.-+
T Consensus 39 p~dA~~~gi~~Gd~V~v~s~ 58 (130)
T cd02781 39 PETAAKLGIADGDWVWVETP 58 (130)
T ss_pred HHHHHHcCCCCCCEEEEECC
Confidence 56899999999999977543
No 169
>PF15044 CLU_N: Mitochondrial function, CLU-N-term
Probab=26.29 E-value=1.7e+02 Score=18.46 Aligned_cols=52 Identities=10% Similarity=0.118 Sum_probs=34.2
Q ss_pred CCchHHHHHHHHHHHcC-CccceEEEEECCEecCCCCCccccC-CcCCceeeee
Q 034095 43 RSTQLKKLMNAYCDRQS-VELNSIAFLFDGRRLRGEQTPDEVI-LLFCAFCSCK 94 (104)
Q Consensus 43 ~tt~L~kLm~aY~~~~g-~~~~~lrF~fdG~rI~~~~TP~~L~-Medgdii~~~ 94 (104)
++..+..|-+.=+.... .....+.|.++|.+|.+...-.++. +.+|..+.+.
T Consensus 3 ~~d~v~dvrq~L~~~~~t~~~Tn~~L~~~g~~L~~~~el~~i~~~~~~~~L~lv 56 (76)
T PF15044_consen 3 PTDTVQDVRQVLAESPETCYLTNFSLEHNGQRLDDFVELSEIEGIKDGCVLELV 56 (76)
T ss_pred hhhHHHHHHHHHHhCccccceeEEEEEECCCccCCchhhhhhhCCCCCcEEEEE
Confidence 44555555555555543 4567899999999998766655554 5666666554
No 170
>TIGR03317 ygfZ_signature folate-binding protein YgfZ. YgfZ is a protein from Escherichia coli, homologous to the glycine cleavage system T protein, or aminomethyltransferase, GcvT (TIGR00528). Homologs of YgfZ other than members of the GcvT family share a well-conserved signature region that includes the motif, KGCYxGQE. Elsewhere, sequence diverge and length variation are substantial. Members of this family are mostly bacterial, largely absent from the Firmicutes and otherwise usually present. A few eukaryotic examples are found among the Apicomplexa, and a few archaeal sequences are found. Two functions implicated for this folate-binding protein are RNA modification (a function likely to be conserved) and replication initiation (a function likely to be highly variable). Many members of this family are, at the time of construction of this model, misnamed as the glycine cleavage system T protein.
Probab=26.13 E-value=42 Score=20.34 Aligned_cols=28 Identities=32% Similarity=0.388 Sum_probs=20.6
Q ss_pred CCEecCCCCCccccCCcCCceee----eeecc
Q 034095 70 DGRRLRGEQTPDEVILLFCAFCS----CKYGR 97 (104)
Q Consensus 70 dG~rI~~~~TP~~L~Medgdii~----~~~~~ 97 (104)
-|..+.++.||.+++|..=..|| |.+|+
T Consensus 15 ~g~el~~~~~P~E~gl~~~~~v~~~Kg~yiGq 46 (67)
T TIGR03317 15 GGAETSGEFLPQELNLDALGGVSFKKGCYVGQ 46 (67)
T ss_pred cccccCCCCCHhHcCCCccCcEeCCCCCccCH
Confidence 45667889999999999844565 44554
No 171
>cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin.
Probab=25.94 E-value=30 Score=22.85 Aligned_cols=23 Identities=4% Similarity=-0.087 Sum_probs=17.9
Q ss_pred ecCCCCCccccCCcCCceeeeeec
Q 034095 73 RLRGEQTPDEVILLFCAFCSCKYG 96 (104)
Q Consensus 73 rI~~~~TP~~L~Medgdii~~~~~ 96 (104)
.|+ .++++.|++++||.|-|--.
T Consensus 36 ~in-~~dA~~lgi~~Gd~V~v~s~ 58 (115)
T cd02779 36 EVN-PEDAKREGLKNGDLVEVYND 58 (115)
T ss_pred EEC-HHHHHHcCCCCCCEEEEEeC
Confidence 344 45899999999999987543
No 172
>PRK09908 xanthine dehydrogenase subunit XdhC; Provisional
Probab=25.82 E-value=1.4e+02 Score=21.86 Aligned_cols=55 Identities=18% Similarity=0.213 Sum_probs=40.7
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCcc-------ceEEEEECCEecCCCCCccc
Q 034095 24 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL-------NSIAFLFDGRRLRGEQTPDE 82 (104)
Q Consensus 24 ~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~-------~~lrF~fdG~rI~~~~TP~~ 82 (104)
.|+++| +|..+.+.+.+.++|-.+.... .-.|... .....++||+.++.-.+|.-
T Consensus 8 ~i~~~v---NG~~~~~~~~~~~~Ll~~LR~~-gltgtK~GC~~G~CGACtVlvdg~~v~SCl~~a~ 69 (159)
T PRK09908 8 TIECTI---NGMPFQLHAAPGTPLSELLREQ-GLLSVKQGCCVGECGACTVLVDGTAIDSCLYLAA 69 (159)
T ss_pred eEEEEE---CCEEEEEecCCCCcHHHHHHHc-CCCCCCCCcCCCCCCCcEEEECCcEeehhHhhHH
Confidence 477777 8888888999999999888753 3334322 56778899999987776654
No 173
>PF11548 Receptor_IA-2: Protein-tyrosine phosphatase receptor IA-2; InterPro: IPR021613 IA-2 is a protein-tyrosine phosphatase receptor that upon exocytosis, the cytoplasmic domain is cleaved and moves to the nucleus where it enhances transcription of the insulin gene. The mature exodomain of IA-2 participates in adhesion to the extracellular matrix and is self-proteolyzed in vitro by reactive oxygen species which may be a new shedding mechanism. ; PDB: 2QT7_B 3N01_B 3N4W_B 3NG8_A.
Probab=25.26 E-value=86 Score=21.09 Aligned_cols=22 Identities=36% Similarity=0.619 Sum_probs=15.3
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCch
Q 034095 22 SAHINLKVKGQDGNEVFFRIKRSTQ 46 (104)
Q Consensus 22 ~~~I~lkV~~~~g~~v~FkIK~tt~ 46 (104)
+..++|+| .|..++|||.++.+
T Consensus 35 ~~F~~i~V---~g~avTFrv~~N~~ 56 (91)
T PF11548_consen 35 SSFINISV---VGPAVTFRVRPNNK 56 (91)
T ss_dssp GGEEEEEE---ETTEEEEEE---TT
T ss_pred ccceeeee---cCceEEEEeccCcC
Confidence 45788888 67899999998874
No 174
>TIGR03198 pucE xanthine dehydrogenase E subunit. This gene has been characterized in B. subtilis as the Iron-sulfur cluster binding-subunit of xanthine dehydrogenase (pucE), acting in conjunction with pucC, the FAD-binding subunit and pucD, the molybdopterin binding subunit. The more common XDH complex (GenProp0640) includes the xdhA gene as the Fe-S cluster binding component.
Probab=24.92 E-value=1.4e+02 Score=21.60 Aligned_cols=55 Identities=16% Similarity=0.214 Sum_probs=40.5
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCcc-------ceEEEEECCEecCCCCCcc
Q 034095 24 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL-------NSIAFLFDGRRLRGEQTPD 81 (104)
Q Consensus 24 ~I~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~-------~~lrF~fdG~rI~~~~TP~ 81 (104)
.|++.| ||..+...+.++++|..+......-.|... .....++||+.++.-.||.
T Consensus 3 ~i~f~v---NG~~~~~~~~~~~~Ll~~LR~~~~ltgtK~gC~~G~CGACtVlvdG~~v~SCl~~~ 64 (151)
T TIGR03198 3 QFRFTV---NGQAWEVAAVPTTRLSDLLRKELQLTGTKVSCGIGRCGACSVLIDGKLANACLTMA 64 (151)
T ss_pred cEEEEE---CCEEEEeecCCCcHHHHHHHhccCCCCCCCCCCCCcCCccEEEECCcEEechHHHH
Confidence 367777 888888888899998887776555444433 5677888999988776665
No 175
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=24.67 E-value=1.2e+02 Score=20.80 Aligned_cols=30 Identities=10% Similarity=0.227 Sum_probs=24.8
Q ss_pred ceEEEEECCEecCCCCCccccCCcCCceeeeeecc
Q 034095 63 NSIAFLFDGRRLRGEQTPDEVILLFCAFCSCKYGR 97 (104)
Q Consensus 63 ~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~~~~ 97 (104)
..-+..+||.++.++. +.+-||+|.+-+|+
T Consensus 32 ~~GrV~vNG~~aKpS~-----~VK~GD~l~i~~~~ 61 (100)
T COG1188 32 EGGRVKVNGQRAKPSK-----EVKVGDILTIRFGN 61 (100)
T ss_pred HCCeEEECCEEccccc-----ccCCCCEEEEEeCC
Confidence 5778899999997665 46789999999886
No 176
>KOG0004 consensus Ubiquitin/40S ribosomal protein S27a fusion [Translation, ribosomal structure and biogenesis]
Probab=24.28 E-value=70 Score=23.57 Aligned_cols=64 Identities=13% Similarity=0.239 Sum_probs=51.5
Q ss_pred EEEccCCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCcee
Q 034095 28 KVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCAFC 91 (104)
Q Consensus 28 kV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii 91 (104)
-|+.-.+..+++.+.++.....+...--+.-|++++.=|.+|.|.+|.+.-|-.+....--.-|
T Consensus 4 fVk~l~~kti~~eve~~~ti~~~Kakiq~~egIp~dqqrlifag~qLedgrtlSDY~Iqkestl 67 (156)
T KOG0004|consen 4 FVKTLTGKTITLEVEANDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTL 67 (156)
T ss_pred chhhccccceeeeecccccHHHHHHhhhcccCCCchhhhhhhhhcccccCCccccccccccceE
Confidence 3444456678889999999999887777889999999999999999999888887776554444
No 177
>cd02789 MopB_CT_FmdC-FwdD The MopB_FmdC-FwdD CD includes the C-terminus of subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC) and subunit D of tungsten formylmethanofuran dehydrogenase (FwdD), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding superfamily of proteins. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=24.08 E-value=29 Score=22.87 Aligned_cols=18 Identities=0% Similarity=-0.378 Sum_probs=15.3
Q ss_pred CCCccccCCcCCceeeee
Q 034095 77 EQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~ 94 (104)
.++++.|++++||.|.|.
T Consensus 37 p~dA~~lgi~~Gd~V~v~ 54 (106)
T cd02789 37 PEDYKLLGKPEGDKVKVT 54 (106)
T ss_pred HHHHHHcCCCCCCEEEEE
Confidence 456999999999999765
No 178
>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=23.61 E-value=2.4e+02 Score=19.02 Aligned_cols=60 Identities=15% Similarity=0.177 Sum_probs=38.7
Q ss_pred CcEEEEEEccCCCE------EEEEEeCCchHHHHHHHHHHHcCCccceEEEEE-CCEecCCCCCccc
Q 034095 23 AHINLKVKGQDGNE------VFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF-DGRRLRGEQTPDE 82 (104)
Q Consensus 23 ~~I~lkV~~~~g~~------v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f-dG~rI~~~~TP~~ 82 (104)
++|-|.|.-..++. -.|-|-.+..+.-++..--++..++.+.--|+| ++.-+..+.|=.+
T Consensus 15 ~~IPVIvEr~~~s~lp~ldk~KfLvp~~~tv~qf~~~ir~rl~l~~~~alfl~Vn~~lp~~s~tm~e 81 (104)
T PF02991_consen 15 DKIPVIVERYPKSKLPDLDKKKFLVPKDLTVGQFVYIIRKRLQLSPEQALFLFVNNTLPSTSSTMGE 81 (104)
T ss_dssp TEEEEEEEE-TTSSS---SSSEEEEETTSBHHHHHHHHHHHTT--TTS-EEEEBTTBESSTTSBHHH
T ss_pred CccEEEEEEccCCChhhcCccEEEEcCCCchhhHHHHhhhhhcCCCCceEEEEEcCcccchhhHHHH
Confidence 45666665433322 268899999999999999999999887666666 7755555555444
No 179
>cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom
Probab=23.58 E-value=30 Score=23.16 Aligned_cols=22 Identities=0% Similarity=-0.256 Sum_probs=17.5
Q ss_pred ecCCCCCccccCCcCCceeeeee
Q 034095 73 RLRGEQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 73 rI~~~~TP~~L~Medgdii~~~~ 95 (104)
.|+ .+++++|+++|||.|-|--
T Consensus 37 ~i~-p~dA~~lgi~~Gd~V~v~s 58 (127)
T cd02777 37 WIN-PLDAAARGIKDGDIVRVFN 58 (127)
T ss_pred EEC-HHHHHHcCCCCCCEEEEEc
Confidence 444 4789999999999997653
No 180
>cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=23.36 E-value=31 Score=22.88 Aligned_cols=21 Identities=0% Similarity=-0.342 Sum_probs=16.7
Q ss_pred ecCCCCCccccCCcCCceeeee
Q 034095 73 RLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 73 rI~~~~TP~~L~Medgdii~~~ 94 (104)
.|+ .++++.|+++|||.|-|.
T Consensus 33 ~i~-p~~A~~~gi~~Gd~V~v~ 53 (121)
T cd02794 33 WIN-PLDAAARGIKDGDRVLVF 53 (121)
T ss_pred EEC-HHHHHHcCCCCCCEEEEE
Confidence 455 456999999999999764
No 181
>COG5435 Uncharacterized conserved protein [Function unknown]
Probab=23.27 E-value=1.2e+02 Score=22.22 Aligned_cols=36 Identities=25% Similarity=0.448 Sum_probs=29.4
Q ss_pred CCcEEEEEEccCC-CEEEEEEeCCc-hHHHHHHHHHHH
Q 034095 22 SAHINLKVKGQDG-NEVFFRIKRST-QLKKLMNAYCDR 57 (104)
Q Consensus 22 ~~~I~lkV~~~~g-~~v~FkIK~tt-~L~kLm~aY~~~ 57 (104)
+..++|-+...+| +.+.|-|.|++ +=...|..||+|
T Consensus 19 DrSvNvf~~~~~gt~~~sfvIsRd~~~~g~~~~~y~~r 56 (147)
T COG5435 19 DRSVNVFVSGDNGTSGFSFVISRDPLEPGDTFPEYVQR 56 (147)
T ss_pred cceEEEEEecCCCcceeEEEEecCCCCCCCcHHHHHHH
Confidence 4678888888777 77899999987 667788888887
No 182
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=22.71 E-value=37 Score=22.27 Aligned_cols=19 Identities=5% Similarity=-0.164 Sum_probs=16.0
Q ss_pred CCCccccCCcCCceeeeee
Q 034095 77 EQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~~ 95 (104)
-++++.|++++||.|-|.-
T Consensus 36 p~dA~~~gi~~Gd~V~v~s 54 (123)
T cd02778 36 PETAARLGIKDGDRVEVSS 54 (123)
T ss_pred HHHHHHcCCCCCCEEEEEe
Confidence 5689999999999997754
No 183
>PF10114 PocR: Sensory domain found in PocR; InterPro: IPR018771 This entry is thought to act as a sensory domain in histidine kinases catalysing the reaction: ATP + protein L-histidine = ADP + protein N- phospho-L-histidine.
Probab=22.18 E-value=1.3e+02 Score=20.78 Aligned_cols=29 Identities=14% Similarity=0.326 Sum_probs=23.3
Q ss_pred chHHHHHHHHHHHcCCccceEEEEECCEecC
Q 034095 45 TQLKKLMNAYCDRQSVELNSIAFLFDGRRLR 75 (104)
Q Consensus 45 t~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~ 75 (104)
..|+.+++.|++-.|++ ..-+-.+|..|.
T Consensus 8 ~~lq~i~~~fs~~tgl~--~~i~d~~G~~l~ 36 (173)
T PF10114_consen 8 EELQEIQDSFSKATGLS--IVIVDPDGNPLT 36 (173)
T ss_pred HHHHHHHHHHHHHHCCc--EEEEeCCCCEEe
Confidence 46899999999999987 444558899984
No 184
>PF12754 Blt1: Cell-cycle control medial ring component; InterPro: IPR024737 During size-dependent cell cycle transitions controlled by the ubiquitous cyclin-dependent kinase Cdk1, Blt1 has been shown to co-localise with Cdr2 in the medial interphase nodes, as well as with Mid1 which was previously shown to localise to similar interphase structures. Physical interactions between Blt1-Mid1, Blt1-Cdr2 and Cdr2-Mid1 were detected, indicating that medial cortical nodes are formed by the ordered, Cdr2-dependent assembly of multiple interacting proteins during interphase[].; PDB: 2LO0_A.
Probab=22.17 E-value=30 Score=28.13 Aligned_cols=65 Identities=20% Similarity=0.286 Sum_probs=0.0
Q ss_pred CCcEEEEEEccCCCEEEEEE---eC--CchHHHHHHHHHH----------HcCCccceEE-----EEECCEecCCCCCcc
Q 034095 22 SAHINLKVKGQDGNEVFFRI---KR--STQLKKLMNAYCD----------RQSVELNSIA-----FLFDGRRLRGEQTPD 81 (104)
Q Consensus 22 ~~~I~lkV~~~~g~~v~FkI---K~--tt~L~kLm~aY~~----------~~g~~~~~lr-----F~fdG~rI~~~~TP~ 81 (104)
...|+|.+++.-+-.+.+++ .+ +|....|-+++|+ ..+++.+.++ .||+-.+|....|-+
T Consensus 76 ~~sItV~Lks~rnp~l~i~L~~~~plattSv~dlk~~v~~rv~~~~~~~~~~~vp~dKik~~~~~lL~~kkPv~~~ktl~ 155 (309)
T PF12754_consen 76 SKSITVHLKSLRNPPLDISLPNVPPLATTSVQDLKDAVQQRVHPSQATYDETRVPLDKIKNFRCRLLYKKKPVGDSKTLA 155 (309)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CceEEEEeecCCCCCceeEeCCCCcCCcCcHHHHHHHHHhhhcccccccccccCCHHHhhhhhhhheecCccCCCcCcHH
Confidence 45677887776554443433 23 6788999999999 7789999999 999999998888887
Q ss_pred ccCCc
Q 034095 82 EVILL 86 (104)
Q Consensus 82 ~L~Me 86 (104)
++.=+
T Consensus 156 e~l~~ 160 (309)
T PF12754_consen 156 EVLAD 160 (309)
T ss_dssp -----
T ss_pred HHHhc
Confidence 77544
No 185
>cd02782 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=22.12 E-value=37 Score=22.61 Aligned_cols=20 Identities=5% Similarity=-0.182 Sum_probs=16.4
Q ss_pred CCCccccCCcCCceeeeeec
Q 034095 77 EQTPDEVILLFCAFCSCKYG 96 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~~~ 96 (104)
.++++.|+++|||.|-|.-+
T Consensus 39 p~dA~~~gi~~Gd~V~v~s~ 58 (129)
T cd02782 39 PDDAAALGLADGDKVRVTSA 58 (129)
T ss_pred HHHHHHcCCCCCCEEEEEcC
Confidence 56899999999999977543
No 186
>KOG1639 consensus Steroid reductase required for elongation of the very long chain fatty acids [Lipid transport and metabolism]
Probab=22.04 E-value=2.1e+02 Score=23.00 Aligned_cols=54 Identities=15% Similarity=0.023 Sum_probs=42.3
Q ss_pred EeCCchHHHHHHHHHHHc-C----CccceEEEEECCEecCCCCCccccCCcCCceeeee
Q 034095 41 IKRSTQLKKLMNAYCDRQ-S----VELNSIAFLFDGRRLRGEQTPDEVILLFCAFCSCK 94 (104)
Q Consensus 41 IK~tt~L~kLm~aY~~~~-g----~~~~~lrF~fdG~rI~~~~TP~~L~Medgdii~~~ 94 (104)
++..++...+-++...+. . ..+.++|+--.|..+-+++|-++++...|+.|-|+
T Consensus 19 ~s~~~ti~d~~~~~~~~~~k~~~~~~r~tlr~e~kgkpl~~~s~l~e~~~~s~~~i~vK 77 (297)
T KOG1639|consen 19 LSGSETIDDLLKAISAKNLKITPYRIRLTLRVEPKGKPLIDNSKLQEYGDGSGATIYVK 77 (297)
T ss_pred CCCCCcHHHHHHHHHHhhhccCccchhheeeccCCCccccchhHHHHhccCCCCEEEEe
Confidence 345567777777776653 2 34578888889999999999999999999888776
No 187
>KOG0013 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.97 E-value=1.7e+02 Score=22.86 Aligned_cols=66 Identities=14% Similarity=0.138 Sum_probs=49.3
Q ss_pred cEEEEEEcc-CCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEECCEecCCCCCccccCCcCCc
Q 034095 24 HINLKVKGQ-DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLFDGRRLRGEQTPDEVILLFCA 89 (104)
Q Consensus 24 ~I~lkV~~~-~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~fdG~rI~~~~TP~~L~Medgd 89 (104)
..-++++.. .++.+..+..-...-..+..+-...-+++..+-|..|.|..|..+.--.+..+|.|.
T Consensus 145 e~~lk~rlTtT~~d~~lta~~~Dtv~eik~~L~Aaeg~D~~sQrif~Sg~~l~dkt~LeEc~iekg~ 211 (231)
T KOG0013|consen 145 EPILKLRLTTTREDFWLTAPHYDTVGEIKRALRAAEGVDPLSQRIFFSGGVLVDKTDLEECKIEKGQ 211 (231)
T ss_pred CcchHHHhhhhhhheeecccCcCcHHHHHHHHHHhhccchhhheeeccCCceeccccceeeeecCCC
Confidence 344666654 677777776555555556666555678888899999999999988888899999984
No 188
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=21.40 E-value=61 Score=24.73 Aligned_cols=15 Identities=13% Similarity=-0.175 Sum_probs=12.5
Q ss_pred cccCCcCCceeeeee
Q 034095 81 DEVILLFCAFCSCKY 95 (104)
Q Consensus 81 ~~L~Medgdii~~~~ 95 (104)
+.|+++|||.|.|.+
T Consensus 201 ~~l~l~dgd~v~i~i 215 (217)
T PRK14165 201 KELNLKDGDRVEVLV 215 (217)
T ss_pred HhcCCCCCCEEEEEE
Confidence 369999999998865
No 189
>PRK12426 elongation factor P; Provisional
Probab=21.16 E-value=1.7e+02 Score=21.90 Aligned_cols=73 Identities=14% Similarity=0.126 Sum_probs=48.7
Q ss_pred CCCCCCCCCcEEEEEEcc-CCCEEEEEEeCCchHHHHHHHHHHHcCCccceEEEEE-CCEecC--CCCCcc-------cc
Q 034095 15 DKKPVDQSAHINLKVKGQ-DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLF-DGRRLR--GEQTPD-------EV 83 (104)
Q Consensus 15 ~~kp~~~~~~I~lkV~~~-~g~~v~FkIK~tt~L~kLm~aY~~~~g~~~~~lrF~f-dG~rI~--~~~TP~-------~L 83 (104)
=+||-.+...+.+|+++- +|+.+.-+.+...++. ...++...++|+| ||.... ...|-+ .|
T Consensus 27 h~kPGkg~A~vr~klknl~tG~~~e~tf~s~ek~e--------~a~ve~~~~qylY~dg~~~~FMd~etyeQi~i~~~~l 98 (185)
T PRK12426 27 KVTGPKGETFIKVSLQAADSDVVVERNFKAGQEVK--------EAQFEPRNLEYLYLEGDEYLFLDLGNYDKIYIPKEIM 98 (185)
T ss_pred EecCCCCceEEEEEEEEcCCCCeEEEEECCCCeEE--------EeEEEeeEeEEEEECCCeEEEecCCCceEEEeCHHHh
Confidence 356766666888888874 6888877778777773 3567888999999 676542 223332 22
Q ss_pred C-----CcCCceeeeee
Q 034095 84 I-----LLFCAFCSCKY 95 (104)
Q Consensus 84 ~-----Medgdii~~~~ 95 (104)
+ |.+|..|+|++
T Consensus 99 gd~~~fL~e~~~v~v~~ 115 (185)
T PRK12426 99 KDNFLFLKAGVTVSALV 115 (185)
T ss_pred hhHHhhccCCCEEEEEE
Confidence 2 77777777754
No 190
>PRK01076 L-rhamnose isomerase; Provisional
Probab=20.72 E-value=75 Score=26.89 Aligned_cols=21 Identities=24% Similarity=0.559 Sum_probs=18.1
Q ss_pred CCchHHHHHHHHHHHcCCccc
Q 034095 43 RSTQLKKLMNAYCDRQSVELN 63 (104)
Q Consensus 43 ~tt~L~kLm~aY~~~~g~~~~ 63 (104)
++-||+.+.+.||.+.++|..
T Consensus 380 k~~p~g~vwd~~c~~~~vp~~ 400 (419)
T PRK01076 380 KSLPWGAVWDMYCQRHDVPVG 400 (419)
T ss_pred hcCChHHHHHHHHHhcCCCCc
Confidence 366999999999999999864
No 191
>PRK12633 flgD flagellar basal body rod modification protein; Provisional
Probab=20.66 E-value=3.2e+02 Score=20.83 Aligned_cols=21 Identities=19% Similarity=0.381 Sum_probs=16.2
Q ss_pred CCCcEEEEEEccCCCEE-EEEE
Q 034095 21 QSAHINLKVKGQDGNEV-FFRI 41 (104)
Q Consensus 21 ~~~~I~lkV~~~~g~~v-~FkI 41 (104)
+...++|.|.+.+|..| .+.+
T Consensus 127 ~a~~v~v~I~D~~G~vV~t~~l 148 (230)
T PRK12633 127 DATKVTVKVLDPSGAVVRTMEL 148 (230)
T ss_pred cCcEEEEEEEeCCCCEEEEEec
Confidence 45679999999999887 3544
No 192
>cd02784 MopB_CT_PHLH The MopB_CT_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding proteins. This CD is of the PHLH region homologous to the conserved molybdopterin-binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=20.59 E-value=37 Score=23.86 Aligned_cols=19 Identities=16% Similarity=0.118 Sum_probs=16.0
Q ss_pred CCCccccCCcCCceeeeee
Q 034095 77 EQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~~ 95 (104)
-.|++.|+++|||.|-|--
T Consensus 44 P~dA~~lGI~dGD~V~V~s 62 (137)
T cd02784 44 PRTAEALGLLQGDVVRIRR 62 (137)
T ss_pred HHHHHHcCCCCCCEEEEEe
Confidence 5688999999999997753
No 193
>COG4869 PduL Propanediol utilization protein [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.42 E-value=1.5e+02 Score=22.63 Aligned_cols=72 Identities=17% Similarity=0.087 Sum_probs=45.6
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHHHcC----------CccceEEEEECCEecCC---CCCc---cccCCcCCc
Q 034095 26 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQS----------VELNSIAFLFDGRRLRG---EQTP---DEVILLFCA 89 (104)
Q Consensus 26 ~lkV~~~~g~~v~FkIK~tt~L~kLm~aY~~~~g----------~~~~~lrF~fdG~rI~~---~~TP---~~L~Medgd 89 (104)
++++.++-...-+..|.+|+...-=+++=-...| +++..--|+=.|.-|.. ..|| +.++..+||
T Consensus 78 nVriLGPlRk~tQVEiSrTDa~~LGik~PvR~SGdieGTPGI~lvs~~~~l~l~kGvIvAkRHIHm~p~dA~~~~Vkq~d 157 (210)
T COG4869 78 NVRILGPLRKKTQVEISRTDARALGIKAPVRESGDIEGTPGILLVSPKNELQLPKGVIVAKRHIHMTPEDAAKYGVKQGD 157 (210)
T ss_pred eeEEeccccceeeEEEeecchhhhcccccccccCcccCCCCeEEEcCCCeEecccceEEEeeeccCCHHHHHHhCcccCc
Confidence 4566666555556777777755433433333322 34555666667777663 4455 468999999
Q ss_pred eeeeeecc
Q 034095 90 FCSCKYGR 97 (104)
Q Consensus 90 ii~~~~~~ 97 (104)
+++|+++.
T Consensus 158 iVsV~v~~ 165 (210)
T COG4869 158 IVSVKVES 165 (210)
T ss_pred EEEEEecC
Confidence 99999974
No 194
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=20.42 E-value=96 Score=16.60 Aligned_cols=18 Identities=22% Similarity=0.178 Sum_probs=15.4
Q ss_pred CCccccCCcCCceeeeee
Q 034095 78 QTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 78 ~TP~~L~Medgdii~~~~ 95 (104)
..|.+|.+.-||+|.|+-
T Consensus 14 ~~~~~l~~~~Gd~v~v~~ 31 (58)
T smart00326 14 QDPDELSFKKGDIITVLE 31 (58)
T ss_pred CCCCCCCCCCCCEEEEEE
Confidence 568889999999999874
No 195
>cd02780 MopB_CT_Tetrathionate_Arsenate-R This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins.
Probab=20.35 E-value=53 Score=22.46 Aligned_cols=20 Identities=0% Similarity=-0.208 Sum_probs=16.8
Q ss_pred CCCccccCCcCCceeeeeec
Q 034095 77 EQTPDEVILLFCAFCSCKYG 96 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~~~ 96 (104)
..+++.|+++|||.|-|.-+
T Consensus 36 p~dA~~lgI~~Gd~V~v~s~ 55 (143)
T cd02780 36 PEDAAKLGIKTGDRVRVVTP 55 (143)
T ss_pred HHHHHHcCCCCCCEEEEEeC
Confidence 55899999999999987653
No 196
>PF14268 YoaP: YoaP-like
Probab=20.32 E-value=1.1e+02 Score=17.80 Aligned_cols=23 Identities=13% Similarity=0.452 Sum_probs=17.8
Q ss_pred HHHcCCccceEEEEECCEecCCC
Q 034095 55 CDRQSVELNSIAFLFDGRRLRGE 77 (104)
Q Consensus 55 ~~~~g~~~~~lrF~fdG~rI~~~ 77 (104)
|+..-.+..++.+.|+|+-|..+
T Consensus 13 Aq~~P~pft~yalFYnGkfiT~e 35 (44)
T PF14268_consen 13 AQNAPCPFTTYALFYNGKFITNE 35 (44)
T ss_pred HhcCCCceeEEEEEECCEEEEee
Confidence 34455678999999999998754
No 197
>cd02793 MopB_CT_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO.This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=20.25 E-value=39 Score=22.77 Aligned_cols=19 Identities=0% Similarity=-0.282 Sum_probs=15.8
Q ss_pred CCCccccCCcCCceeeeee
Q 034095 77 EQTPDEVILLFCAFCSCKY 95 (104)
Q Consensus 77 ~~TP~~L~Medgdii~~~~ 95 (104)
.++++.|+++|||.|-|.=
T Consensus 39 p~dA~~~gi~~Gd~V~v~s 57 (129)
T cd02793 39 PADAAARGIADGDIVRVFN 57 (129)
T ss_pred HHHHHHcCCCCCCEEEEEc
Confidence 4569999999999997753
No 198
>PF10957 DUF2758: Protein of unknown function (DUF2758); InterPro: IPR020296 Cse60 is expressed during sporulation in Bacillus subtilis. Transcription commences around 2h after the start of sporulation and had an absolute requirement for the transcription factor sigmaE. Maximal expression of cse60 further depended on the DNA-binding protein SpoIIID. Cse60 is an acidic product of only 60 residues, whose function is not known [].
Probab=20.24 E-value=71 Score=19.79 Aligned_cols=16 Identities=19% Similarity=-0.029 Sum_probs=11.9
Q ss_pred CcCCceeeeeeccccc
Q 034095 85 LLFCAFCSCKYGRLNT 100 (104)
Q Consensus 85 Medgdii~~~~~~~~~ 100 (104)
+++..+||++|.--.+
T Consensus 26 ~~~~~viDIKy~va~~ 41 (60)
T PF10957_consen 26 LDDDQVIDIKYQVAAS 41 (60)
T ss_pred CCCCcEEEEEEEEEEe
Confidence 5677899999975443
No 199
>COG0160 GabT 4-aminobutyrate aminotransferase and related aminotransferases [Amino acid transport and metabolism]
Probab=20.08 E-value=58 Score=27.57 Aligned_cols=59 Identities=8% Similarity=-0.009 Sum_probs=34.5
Q ss_pred EeCCchHHHHHHHHHHHcCCccce--EEEEECCEecCCCCCccccCCcCCceeeeee--cccccCcCC
Q 034095 41 IKRSTQLKKLMNAYCDRQSVELNS--IAFLFDGRRLRGEQTPDEVILLFCAFCSCKY--GRLNTGHCR 104 (104)
Q Consensus 41 IK~tt~L~kLm~aY~~~~g~~~~~--lrF~fdG~rI~~~~TP~~L~Medgdii~~~~--~~~~~~~~~ 104 (104)
..+..+...+++...+...-+... +-+.+ ....-+.=.+.+.+..||++- +-+|+|||-
T Consensus 12 ~~~~~~~~~~~~r~~~~~~r~~~~~~~p~~~-----~ra~G~~l~DvdG~~ylDf~sgi~v~~~GH~h 74 (447)
T COG0160 12 EAPGPKALELIERREEALARSYGRFRFPLVI-----VRAEGAYLYDVDGNEYLDFLSGIAVLNLGHNH 74 (447)
T ss_pred cCCCcchHHHHHHHHHHhccccccccCcceE-----EecccCEEEeCCCCEEEEcccCcchhccCCCC
Confidence 345556666777666544333222 22222 112223334578899999998 899999983
Done!