Query 034926
Match_columns 78
No_of_seqs 107 out of 304
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 07:44:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034926.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034926hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1769 Ubiquitin-like protein 99.9 3.2E-27 6.9E-32 151.5 8.8 56 19-74 18-73 (99)
2 COG5227 SMT3 Ubiquitin-like pr 99.9 1.8E-24 3.8E-29 137.9 8.2 61 12-74 17-77 (103)
3 cd01763 Sumo Small ubiquitin-r 99.7 1E-16 2.2E-21 99.3 8.1 57 18-74 8-64 (87)
4 PF11976 Rad60-SLD: Ubiquitin- 99.6 3.5E-15 7.6E-20 88.2 6.5 54 22-75 1-55 (72)
5 cd01806 Nedd8 Nebb8-like ubiq 98.4 2.1E-06 4.4E-11 50.4 6.5 53 22-74 1-53 (76)
6 cd01809 Scythe_N Ubiquitin-lik 98.0 2.7E-05 5.9E-10 45.1 6.3 53 22-74 1-53 (72)
7 smart00213 UBQ Ubiquitin homol 97.8 0.0001 2.3E-09 41.2 6.0 52 22-74 1-52 (64)
8 cd01812 BAG1_N Ubiquitin-like 97.6 0.00022 4.8E-09 41.3 5.2 51 22-73 1-51 (71)
9 cd01807 GDX_N ubiquitin-like d 97.6 0.00042 9.1E-09 41.0 6.1 51 23-73 2-52 (74)
10 cd01803 Ubiquitin Ubiquitin. U 97.5 0.00047 1E-08 40.2 6.1 52 23-74 2-53 (76)
11 PTZ00044 ubiquitin; Provisiona 97.5 0.00055 1.2E-08 40.3 6.2 52 23-74 2-53 (76)
12 cd01769 UBL Ubiquitin-like dom 97.5 0.00046 1E-08 39.0 5.4 48 26-73 2-49 (69)
13 PF11470 TUG-UBL1: GLUT4 regul 97.4 0.00057 1.2E-08 40.8 5.6 50 26-75 1-50 (65)
14 cd01798 parkin_N amino-termina 97.4 0.00067 1.4E-08 39.7 5.6 49 25-73 2-50 (70)
15 PF00240 ubiquitin: Ubiquitin 97.3 0.0013 2.8E-08 37.9 5.9 46 29-74 3-48 (69)
16 cd01805 RAD23_N Ubiquitin-like 97.2 0.0028 6.1E-08 37.2 6.5 51 23-73 2-54 (77)
17 cd01791 Ubl5 UBL5 ubiquitin-li 97.1 0.0027 5.8E-08 38.2 6.3 51 22-72 2-52 (73)
18 cd01804 midnolin_N Ubiquitin-l 97.0 0.0042 9.2E-08 37.4 6.4 52 22-73 2-53 (78)
19 cd00196 UBQ Ubiquitin-like pro 97.0 0.0036 7.8E-08 32.4 5.1 46 29-74 5-50 (69)
20 cd01792 ISG15_repeat1 ISG15 ub 96.8 0.0045 9.8E-08 37.2 5.2 51 22-72 3-55 (80)
21 cd01810 ISG15_repeat2 ISG15 ub 96.8 0.007 1.5E-07 35.7 5.7 50 24-73 1-50 (74)
22 cd01808 hPLIC_N Ubiquitin-like 96.6 0.014 2.9E-07 34.2 6.1 51 22-73 1-51 (71)
23 cd01802 AN1_N ubiquitin-like d 96.5 0.019 4.1E-07 36.6 7.0 55 20-74 26-80 (103)
24 cd01794 DC_UbP_C dendritic cel 96.2 0.022 4.8E-07 33.7 5.5 51 24-74 1-51 (70)
25 cd01796 DDI1_N DNA damage indu 96.1 0.026 5.6E-07 33.3 5.4 49 25-73 2-51 (71)
26 cd06409 PB1_MUG70 The MUG70 pr 96.1 0.033 7.2E-07 34.9 6.1 52 24-75 3-60 (86)
27 cd01793 Fubi Fubi ubiquitin-li 96.1 0.039 8.5E-07 32.5 6.1 50 23-74 2-51 (74)
28 cd01797 NIRF_N amino-terminal 95.5 0.073 1.6E-06 32.1 5.8 52 23-74 2-55 (78)
29 cd01799 Hoil1_N Ubiquitin-like 95.1 0.1 2.2E-06 31.4 5.5 42 30-72 11-52 (75)
30 smart00455 RBD Raf-like Ras-bi 94.3 0.23 4.9E-06 29.6 5.6 50 24-73 2-51 (70)
31 TIGR00601 rad23 UV excision re 94.1 0.22 4.8E-06 38.4 6.5 52 23-74 2-56 (378)
32 smart00666 PB1 PB1 domain. Pho 94.0 0.42 9.1E-06 28.1 6.3 53 22-75 2-57 (81)
33 cd01790 Herp_N Homocysteine-re 93.7 0.6 1.3E-05 28.7 6.8 54 21-74 1-58 (79)
34 PF11543 UN_NPL4: Nuclear pore 93.5 0.12 2.6E-06 31.6 3.4 46 20-66 3-48 (80)
35 cd06407 PB1_NLP A PB1 domain i 92.5 0.95 2.1E-05 27.8 6.4 53 22-75 1-57 (82)
36 PF02196 RBD: Raf-like Ras-bin 92.2 0.83 1.8E-05 27.2 5.7 52 24-75 3-54 (71)
37 cd01800 SF3a120_C Ubiquitin-li 92.0 0.58 1.3E-05 27.6 4.9 43 30-72 6-48 (76)
38 KOG0005 Ubiquitin-like protein 92.0 0.28 6E-06 29.5 3.4 49 23-71 2-50 (70)
39 cd01777 SNX27_RA Ubiquitin dom 91.9 0.35 7.6E-06 30.5 4.0 42 22-63 2-43 (87)
40 PF00564 PB1: PB1 domain; Int 91.9 1.4 2.9E-05 25.8 6.4 54 22-75 2-58 (84)
41 KOG0010 Ubiquitin-like protein 91.9 0.74 1.6E-05 36.9 6.6 52 20-72 14-65 (493)
42 KOG0006 E3 ubiquitin-protein l 91.8 0.57 1.2E-05 36.4 5.7 45 33-77 15-59 (446)
43 cd01760 RBD Ubiquitin-like dom 90.9 1.1 2.3E-05 27.0 5.3 45 24-68 2-46 (72)
44 cd06396 PB1_NBR1 The PB1 domai 90.9 1.7 3.6E-05 27.0 6.2 51 22-75 1-56 (81)
45 cd06408 PB1_NoxR The PB1 domai 90.2 2.4 5.2E-05 26.6 6.6 53 21-75 2-56 (86)
46 cd05992 PB1 The PB1 domain is 89.9 2.5 5.3E-05 24.5 6.2 53 22-75 1-57 (81)
47 cd01813 UBP_N UBP ubiquitin pr 89.7 1.4 3.1E-05 26.1 5.1 48 23-71 2-52 (74)
48 smart00295 B41 Band 4.1 homolo 89.6 1.4 3.1E-05 29.3 5.6 39 20-58 2-40 (207)
49 PF00789 UBX: UBX domain; Int 89.5 2.9 6.2E-05 24.6 6.4 47 19-65 4-51 (82)
50 smart00166 UBX Domain present 88.7 3.5 7.5E-05 24.4 6.8 45 21-65 4-48 (80)
51 cd01814 NTGP5 Ubiquitin-like N 88.3 1.1 2.4E-05 29.5 4.2 54 20-73 3-64 (113)
52 cd06406 PB1_P67 A PB1 domain i 85.3 3.9 8.4E-05 25.4 5.3 44 22-67 3-46 (80)
53 PF09379 FERM_N: FERM N-termin 85.3 1.8 3.8E-05 25.2 3.6 41 26-66 1-42 (80)
54 PF00788 RA: Ras association ( 84.8 5.9 0.00013 23.2 6.1 43 22-64 3-51 (93)
55 cd01789 Alp11_N Ubiquitin-like 84.7 5.7 0.00012 24.0 5.8 48 23-70 3-52 (84)
56 cd01818 TIAM1_RBD Ubiquitin do 83.8 3.5 7.5E-05 25.6 4.5 37 25-61 3-39 (77)
57 PHA01623 hypothetical protein 83.7 0.82 1.8E-05 26.3 1.6 28 33-60 13-40 (56)
58 PLN02560 enoyl-CoA reductase 81.7 5.3 0.00012 30.0 5.7 45 23-67 2-50 (308)
59 PF14560 Ubiquitin_2: Ubiquiti 77.1 13 0.00028 22.2 6.7 46 22-67 2-49 (87)
60 cd01811 OASL_repeat1 2'-5' oli 74.6 17 0.00037 22.6 5.5 44 22-66 1-44 (80)
61 cd01817 RGS12_RBD Ubiquitin do 72.2 20 0.00042 21.9 5.4 51 25-75 3-53 (73)
62 cd01771 Faf1_UBX Faf1 UBX doma 70.8 21 0.00045 21.6 6.7 43 21-64 4-46 (80)
63 cd01774 Faf1_like2_UBX Faf1 ik 69.8 22 0.00049 21.6 6.9 46 20-66 3-48 (85)
64 PF10623 PilI: Plasmid conjuga 68.6 13 0.00029 23.2 4.1 35 19-53 6-40 (83)
65 PF05486 SRP9-21: Signal recog 67.4 23 0.0005 21.5 5.0 33 18-50 37-70 (79)
66 cd01773 Faf1_like1_UBX Faf1 ik 66.7 27 0.0006 21.5 6.9 44 21-65 5-48 (82)
67 PF10302 DUF2407: DUF2407 ubiq 63.5 29 0.00064 21.8 5.1 55 21-76 2-60 (97)
68 PLN02593 adrenodoxin-like ferr 61.9 25 0.00055 22.6 4.7 34 22-59 1-34 (117)
69 cd06398 PB1_Joka2 The PB1 doma 61.1 37 0.00081 21.1 6.3 51 23-74 2-61 (91)
70 PF13860 FlgD_ig: FlgD Ig-like 58.6 34 0.00073 20.2 4.5 38 19-71 24-61 (81)
71 PF13019 Telomere_Sde2: Telome 58.1 44 0.00095 23.2 5.5 45 22-66 1-50 (162)
72 PRK11675 LexA regulated protei 56.4 9.4 0.0002 24.2 1.8 34 27-60 44-77 (90)
73 COG4806 RhaA L-rhamnose isomer 56.3 8.2 0.00018 29.9 1.8 21 40-60 380-400 (419)
74 cd01768 RA RA (Ras-associating 55.8 40 0.00086 19.7 5.7 35 24-58 2-39 (87)
75 cd01795 USP48_C USP ubiquitin- 55.1 29 0.00064 22.7 4.0 40 33-72 16-55 (107)
76 PF13670 PepSY_2: Peptidase pr 55.1 32 0.00069 20.3 4.0 24 19-42 53-76 (83)
77 PF08817 YukD: WXG100 protein 54.8 41 0.00089 19.7 4.5 54 21-74 2-62 (79)
78 PRK08364 sulfur carrier protei 54.6 41 0.00088 19.5 6.0 49 22-75 5-53 (70)
79 cd01767 UBX UBX (ubiquitin reg 54.0 42 0.00091 19.4 6.3 44 21-65 2-45 (77)
80 KOG1363 Predicted regulator of 53.2 42 0.00091 26.8 5.4 38 16-53 378-415 (460)
81 cd01770 p47_UBX p47-like ubiqu 52.5 46 0.00099 19.9 4.4 44 21-64 4-48 (79)
82 PF06134 RhaA: L-rhamnose isom 52.4 14 0.00029 29.4 2.5 21 40-60 379-399 (417)
83 PF01402 RHH_1: Ribbon-helix-h 51.1 7.5 0.00016 19.7 0.7 25 36-60 2-26 (39)
84 KOG0011 Nucleotide excision re 51.1 41 0.00088 26.1 4.9 53 23-75 2-56 (340)
85 PRK08452 flagellar protein Fla 50.4 58 0.0013 21.6 5.0 38 19-57 81-118 (124)
86 KOG3439 Protein conjugation fa 49.3 76 0.0016 21.0 6.4 54 20-73 29-86 (116)
87 PF08722 Tn7_Tnp_TnsA_N: TnsA 49.1 32 0.00069 20.5 3.3 37 23-59 36-83 (88)
88 PF09631 Sen15: Sen15 protein; 47.6 29 0.00064 21.6 3.1 22 19-40 72-93 (101)
89 smart00314 RA Ras association 47.0 59 0.0013 19.1 5.4 37 23-59 4-43 (90)
90 cd06404 PB1_aPKC PB1 domain is 47.0 70 0.0015 20.0 6.1 53 22-75 1-57 (83)
91 cd00754 MoaD Ubiquitin domain 46.7 54 0.0012 18.6 4.6 43 33-75 17-63 (80)
92 PF08825 E2_bind: E2 binding d 45.5 32 0.00069 21.1 3.0 39 36-74 1-39 (84)
93 PF11548 Receptor_IA-2: Protei 44.9 28 0.00061 22.1 2.7 22 19-43 35-56 (91)
94 PF05932 CesT: Tir chaperone p 44.7 50 0.0011 19.6 3.8 29 46-74 1-35 (119)
95 PLN03060 inositol phosphatase- 43.2 7.5 0.00016 28.0 -0.1 23 40-62 67-89 (206)
96 PF12436 USP7_ICP0_bdg: ICP0-b 42.8 1.2E+02 0.0026 21.7 6.1 45 21-65 176-223 (249)
97 PF07377 DUF1493: Protein of u 42.4 15 0.00033 23.2 1.2 23 44-66 44-68 (111)
98 PF12167 DUF3596: Domain of un 41.9 26 0.00057 20.3 2.1 16 61-76 12-27 (64)
99 cd01772 SAKS1_UBX SAKS1-like U 41.2 76 0.0016 18.7 6.7 35 21-55 4-38 (79)
100 PHA01748 hypothetical protein 41.1 41 0.00089 19.3 2.8 26 35-60 4-29 (60)
101 PF04881 Adeno_GP19K: Adenovir 40.6 35 0.00077 23.2 2.8 32 20-53 48-79 (139)
102 PF10114 PocR: Sensory domain 40.2 45 0.00098 21.8 3.3 28 43-72 9-36 (173)
103 TIGR03060 PS_II_psb29 photosys 39.7 9.3 0.0002 27.7 -0.1 23 40-62 69-91 (214)
104 KOG3309 Ferredoxin [Energy pro 39.5 89 0.0019 21.8 4.7 29 19-47 41-69 (159)
105 cd02986 DLP Dim1 family, Dim1- 39.2 46 0.001 21.7 3.1 24 50-73 59-83 (114)
106 COG2080 CoxS Aerobic-type carb 39.1 1.3E+02 0.0028 20.8 6.2 49 21-72 3-58 (156)
107 PRK13266 Thf1-like protein; Re 38.5 9.9 0.00022 27.7 -0.1 23 40-62 69-91 (225)
108 PF04110 APG12: Ubiquitin-like 37.4 1E+02 0.0022 19.2 4.4 39 34-72 18-56 (87)
109 PF11264 ThylakoidFormat: Thyl 37.3 11 0.00024 27.2 -0.0 23 40-62 64-86 (216)
110 PTZ00490 Ferredoxin superfamil 37.2 74 0.0016 21.4 4.0 29 19-47 33-61 (143)
111 COG5077 Ubiquitin carboxyl-ter 36.6 80 0.0017 27.7 4.8 34 33-66 585-619 (1089)
112 KOG0003 Ubiquitin/60s ribosoma 35.7 19 0.0004 24.0 0.9 46 28-73 7-52 (128)
113 PF03857 Colicin_im: Colicin i 35.5 25 0.00055 23.9 1.5 14 41-54 23-36 (138)
114 KOG2378 cAMP-regulated guanine 35.3 1.9E+02 0.0042 23.8 6.6 57 17-73 231-289 (573)
115 TIGR02777 LigD_PE_dom DNA liga 35.2 38 0.00082 23.5 2.4 24 55-78 114-137 (156)
116 PRK01076 L-rhamnose isomerase; 34.9 31 0.00067 27.4 2.1 21 40-60 380-400 (419)
117 TIGR01748 rhaA L-rhamnose isom 34.5 31 0.00067 27.4 2.0 21 40-60 376-396 (414)
118 PF10646 Germane: Sporulation 34.4 42 0.00091 20.4 2.3 18 58-75 100-117 (117)
119 cd03489 Topoisomer_IB_N_Ldtopo 33.7 26 0.00055 25.5 1.4 17 59-75 18-34 (212)
120 KOG1529 Mercaptopyruvate sulfu 33.1 57 0.0012 24.7 3.2 26 43-68 69-94 (286)
121 cd01801 Tsc13_N Ubiquitin-like 32.9 1E+02 0.0022 17.8 4.5 34 39-72 20-56 (77)
122 cd00660 Topoisomer_IB_N Topois 32.8 25 0.00054 25.6 1.2 17 59-75 20-36 (215)
123 PF03607 DCX: Doublecortin; I 32.6 47 0.001 18.7 2.2 33 40-73 7-41 (60)
124 KOG2523 Predicted RNA-binding 32.6 87 0.0019 22.2 3.8 51 20-72 57-112 (181)
125 PF02919 Topoisom_I_N: Eukaryo 32.4 22 0.00047 25.9 0.8 17 59-75 21-37 (215)
126 KOG4248 Ubiquitin-like protein 32.0 1.1E+02 0.0024 27.3 5.0 52 22-73 3-54 (1143)
127 PF01361 Tautomerase: Tautomer 32.0 63 0.0014 17.6 2.6 26 43-68 19-44 (60)
128 PRK02853 hypothetical protein; 31.9 1.4E+02 0.0031 20.8 4.7 31 21-51 65-95 (161)
129 cd03488 Topoisomer_IB_N_htopoI 31.9 26 0.00057 25.5 1.2 17 59-75 20-36 (215)
130 cd06397 PB1_UP1 Uncharacterize 31.8 1.3E+02 0.0029 18.7 5.4 52 23-75 2-56 (82)
131 cd03490 Topoisomer_IB_N_1 Topo 31.4 29 0.00063 25.3 1.4 17 59-75 18-34 (217)
132 cd06411 PB1_p51 The PB1 domain 31.2 1.3E+02 0.0028 18.5 4.0 34 33-66 8-41 (78)
133 PF03479 DUF296: Domain of unk 30.4 1.2E+02 0.0027 19.1 4.1 31 32-62 2-32 (120)
134 PF03791 KNOX2: KNOX2 domain ; 30.1 44 0.00095 19.1 1.7 17 38-54 5-21 (52)
135 PLN00047 photosystem II biogen 29.8 17 0.00036 27.5 -0.1 23 40-62 120-142 (283)
136 PRK07738 flagellar protein Fla 29.3 1.7E+02 0.0037 19.2 5.0 38 19-57 74-111 (117)
137 PF05688 DUF824: Salmonella re 28.9 56 0.0012 18.2 2.0 24 21-44 16-42 (47)
138 KOG0001 Ubiquitin and ubiquiti 28.9 95 0.0021 16.2 7.1 48 25-72 3-50 (75)
139 PRK12633 flgD flagellar basal 28.8 1.7E+02 0.0037 21.0 4.9 21 18-38 127-148 (230)
140 PF13881 Rad60-SLD_2: Ubiquiti 28.3 1.7E+02 0.0036 18.8 7.7 53 21-73 2-62 (111)
141 cd07079 ALDH_F18-19_ProA-GPR G 27.7 1.3E+02 0.0028 23.0 4.4 38 30-67 134-176 (406)
142 PF02599 CsrA: Global regulato 27.3 1.1E+02 0.0024 17.3 3.1 22 19-40 15-36 (54)
143 PRK06655 flgD flagellar basal 27.1 2E+02 0.0043 20.6 5.0 20 19-38 125-145 (225)
144 PF12347 HJURP_C: Holliday jun 26.9 21 0.00046 20.9 0.0 21 41-61 28-48 (64)
145 PRK06437 hypothetical protein; 26.9 1.3E+02 0.0029 17.2 5.7 41 31-75 10-50 (67)
146 PF03790 KNOX1: KNOX1 domain ; 26.4 45 0.00097 18.5 1.3 18 43-60 12-31 (45)
147 cd01815 BMSC_UbP_N Ubiquitin-l 25.7 94 0.002 18.8 2.7 33 41-73 20-55 (75)
148 PF09358 UBA_e1_C: Ubiquitin-a 25.4 1.1E+02 0.0024 19.8 3.3 29 35-63 36-64 (125)
149 KOG3784 Sorting nexin protein 25.2 1.6E+02 0.0034 23.4 4.5 42 20-61 106-147 (407)
150 COG3906 Uncharacterized protei 25.2 47 0.001 21.7 1.4 17 22-38 14-30 (105)
151 COG5435 Uncharacterized conser 24.8 1.1E+02 0.0023 21.1 3.1 37 18-54 18-56 (147)
152 cd00103 IRF Interferon Regulat 24.8 53 0.0011 21.0 1.6 17 42-58 44-60 (107)
153 PF10787 YfmQ: Uncharacterised 24.7 84 0.0018 21.7 2.6 36 40-75 23-58 (149)
154 PF03462 PCRF: PCRF domain; I 24.5 91 0.002 19.8 2.6 25 43-67 67-91 (115)
155 KOG2689 Predicted ubiquitin re 24.3 3.2E+02 0.007 20.8 7.3 46 20-65 209-254 (290)
156 PF14977 FAM194: FAM194 protei 23.7 84 0.0018 22.5 2.6 20 18-37 119-138 (208)
157 PRK09619 flgD flagellar basal 23.6 2.5E+02 0.0053 20.0 5.0 20 19-38 122-141 (218)
158 KOG3112 Uncharacterized conser 23.2 40 0.00087 25.0 0.9 44 31-74 173-216 (262)
159 PF09079 Cdc6_C: CDC6, C termi 23.1 77 0.0017 18.6 2.0 20 41-60 15-37 (85)
160 PRK12634 flgD flagellar basal 23.1 2.5E+02 0.0055 20.0 5.0 35 19-69 121-156 (221)
161 PF03999 MAP65_ASE1: Microtubu 22.9 90 0.002 25.3 2.9 26 42-72 398-423 (619)
162 COG2029 Uncharacterized conser 22.8 16 0.00035 25.9 -1.2 15 63-77 12-26 (189)
163 PF09627 PrgU: PrgU-like prote 22.6 1.6E+02 0.0035 19.3 3.5 54 21-74 10-64 (122)
164 PRK02289 4-oxalocrotonate taut 22.6 1.5E+02 0.0032 16.3 3.0 26 44-69 21-46 (60)
165 PF11834 DUF3354: Domain of un 22.4 1.5E+02 0.0033 17.6 3.2 32 41-73 25-56 (69)
166 PF02566 OsmC: OsmC-like prote 22.3 72 0.0016 18.7 1.8 24 46-69 22-45 (100)
167 PF06793 UPF0262: Uncharacteri 22.3 2.4E+02 0.0052 19.6 4.5 32 20-51 61-92 (158)
168 smart00501 BRIGHT BRIGHT, ARID 22.1 1.2E+02 0.0025 18.2 2.7 30 43-73 5-34 (93)
169 PRK12813 flgD flagellar basal 22.1 1.9E+02 0.004 20.9 4.1 17 19-35 123-139 (223)
170 PF04221 RelB: RelB antitoxin; 21.9 66 0.0014 19.2 1.5 26 36-61 4-29 (83)
171 PF09274 ParG: ParG; InterPro 21.2 1.4E+02 0.0029 18.4 2.8 31 30-60 31-61 (76)
172 PF09264 Sial-lect-inser: Vibr 21.2 1E+02 0.0022 22.2 2.6 16 60-76 106-121 (198)
173 KOG1407 WD40 repeat protein [F 21.2 1.2E+02 0.0025 23.3 3.0 54 18-74 189-249 (313)
174 KOG0981 DNA topoisomerase I [R 21.1 55 0.0012 27.6 1.3 17 59-75 230-246 (759)
175 PF00722 Glyco_hydro_16: Glyco 21.0 1.1E+02 0.0024 19.9 2.6 18 58-75 128-145 (185)
176 PF08512 Rtt106: Histone chape 21.0 1.9E+02 0.0042 17.6 3.6 39 20-59 52-92 (95)
177 PRK12426 elongation factor P; 21.0 2E+02 0.0044 20.2 4.0 50 13-70 28-79 (185)
178 PF04800 ETC_C1_NDUFA4: ETC co 20.9 42 0.00091 21.5 0.5 12 48-59 61-72 (101)
179 COG4306 Uncharacterized protei 20.9 62 0.0014 22.2 1.4 13 45-57 24-36 (160)
180 TIGR02384 RelB_DinJ addiction 20.5 92 0.002 18.9 2.0 26 36-61 5-30 (83)
181 PF05534 HicB: HicB family; I 20.3 63 0.0014 17.9 1.1 27 35-61 19-45 (51)
182 PRK10738 hypothetical protein; 20.3 1.2E+02 0.0025 19.8 2.6 31 41-71 34-75 (134)
183 PF03633 Glyco_hydro_65C: Glyc 20.2 1.2E+02 0.0027 16.3 2.3 16 58-73 8-23 (54)
No 1
>KOG1769 consensus Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=3.2e-27 Score=151.49 Aligned_cols=56 Identities=57% Similarity=0.861 Sum_probs=54.2
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 19 SAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
..||+|||++|+|++++|+||++|||+|||+|||+|+|+++++|||+|||+||...
T Consensus 18 ~~hi~LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~Gl~~~s~RFlFdG~rI~~~ 73 (99)
T KOG1769|consen 18 SEHINLKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQGLSMNSLRFLFDGQRIRET 73 (99)
T ss_pred cceEEEEEecCCCCEEEEEeecCChHHHHHHHHHHHcCCccceEEEEECCcCcCCC
Confidence 68999999999999999999999999999999999999999999999999999865
No 2
>COG5227 SMT3 Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones]
Probab=99.91 E-value=1.8e-24 Score=137.91 Aligned_cols=61 Identities=46% Similarity=0.693 Sum_probs=56.3
Q ss_pred CCCCCCCCCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 12 DKKPNDQSAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 12 ~~kp~~~~~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
++|| ...||+|||.||||++++|+||++|+|+|||+|||.++|.+++++||||||.||.+-
T Consensus 17 ~vkp--~t~hinLkvv~qd~telfFkiKktT~f~klm~af~~rqGK~m~slRfL~dG~rI~~d 77 (103)
T COG5227 17 LVKP--ITKHINLKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQGKNMSSLRFLFDGKRIDLD 77 (103)
T ss_pred cccc--cccccceEEecCCCCEEEEEEeccchHHHHHHHHHHHhCcCcceeEEEEcceecCCC
Confidence 4445 357999999999999999999999999999999999999999999999999999863
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=99.70 E-value=1e-16 Score=99.34 Aligned_cols=57 Identities=63% Similarity=0.918 Sum_probs=54.3
Q ss_pred CCCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 18 QSAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 18 ~~~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
++.+|+|+|++++|..+.|+|+++++|++||++||++.|++++.+||+|||.+|...
T Consensus 8 ~~~~i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~G~~L~~~ 64 (87)
T cd01763 8 ISEHINLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFDGQRIRDN 64 (87)
T ss_pred CCCeEEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEECCeECCCC
Confidence 467999999999999999999999999999999999999999999999999999764
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=99.60 E-value=3.5e-15 Score=88.25 Aligned_cols=54 Identities=30% Similarity=0.554 Sum_probs=50.8
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCC-CeEEEEECCEeeccee
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL-NSIAFLYVHISAFLAW 75 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~-~s~rFlfdG~rI~~~~ 75 (78)
|+|+|++++|..+.|+|++++++++||++||++.|++. ++++|.|||.+|.+..
T Consensus 1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~~L~~~~ 55 (72)
T PF11976_consen 1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFDGKRLDPND 55 (72)
T ss_dssp EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEETTEEE-TTS
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEECCEEcCCCC
Confidence 78999999999999999999999999999999999999 9999999999998754
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=98.38 E-value=2.1e-06 Score=50.39 Aligned_cols=53 Identities=13% Similarity=0.236 Sum_probs=48.8
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
+.|.|+..+|..+.+.|.++.....|...++++.|++++..|+.|+|..+...
T Consensus 1 m~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~g~~L~d~ 53 (76)
T cd01806 1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDD 53 (76)
T ss_pred CEEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEECCeEccCC
Confidence 36788888999999999999999999999999999999999999999988654
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=98.04 E-value=2.7e-05 Score=45.09 Aligned_cols=53 Identities=15% Similarity=0.212 Sum_probs=48.8
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
|+|.|+..+|..+.+.+.++.+...|.+..+++.|++++..++.|+|..+...
T Consensus 1 i~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~ 53 (72)
T cd01809 1 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDD 53 (72)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCEECCCc
Confidence 57888889999999999999999999999999999999999999999987643
No 7
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=97.83 E-value=0.0001 Score=41.22 Aligned_cols=52 Identities=17% Similarity=0.231 Sum_probs=45.1
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
+.|.|+..+ ....+.|..++....|....+++.|++.+..+++|+|..+...
T Consensus 1 ~~i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~g~~L~d~ 52 (64)
T smart00213 1 IELTVKTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYKGKVLEDD 52 (64)
T ss_pred CEEEEEECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEECCCC
Confidence 356677766 5778999999999999999999999999999999999987643
No 8
>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=97.60 E-value=0.00022 Score=41.27 Aligned_cols=51 Identities=16% Similarity=0.146 Sum_probs=45.6
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecc
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFL 73 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~ 73 (78)
|+|+|+.. |....+.+.++.....|.+..+++.|++++..|++|+|..+..
T Consensus 1 i~i~vk~~-g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~l~d 51 (71)
T cd01812 1 IRVRVKHG-GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKERDD 51 (71)
T ss_pred CEEEEEEC-CEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeCCcccCc
Confidence 67788874 7777899999999999999999999999999999999988753
No 9
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=97.56 E-value=0.00042 Score=41.00 Aligned_cols=51 Identities=16% Similarity=0.143 Sum_probs=46.4
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecc
Q 034926 23 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFL 73 (78)
Q Consensus 23 ~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~ 73 (78)
.|.|+..+|..+.+.|.+++....|....|++.|++.+..|++|+|+.+.-
T Consensus 2 ~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~G~~L~d 52 (74)
T cd01807 2 FLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALAD 52 (74)
T ss_pred EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCC
Confidence 466677789999999999999999999999999999999999999999854
No 10
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=97.55 E-value=0.00047 Score=40.19 Aligned_cols=52 Identities=10% Similarity=0.191 Sum_probs=47.3
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 23 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 23 ~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
.|.|+..+|..+.+.+.++.....|.+..+++.|++.+..|+.|+|..+..+
T Consensus 2 ~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~g~~L~d~ 53 (76)
T cd01803 2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG 53 (76)
T ss_pred EEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEECCEECCCC
Confidence 5677888899999999999999999999999999999999999999887654
No 11
>PTZ00044 ubiquitin; Provisional
Probab=97.52 E-value=0.00055 Score=40.30 Aligned_cols=52 Identities=12% Similarity=0.270 Sum_probs=47.5
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 23 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 23 ~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
.|.|+..+|....+.+.++.....|....+++.|++.+..|+.|+|..+...
T Consensus 2 ~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~ 53 (76)
T PTZ00044 2 QILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDD 53 (76)
T ss_pred EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEEccCC
Confidence 5677788999999999999999999999999999999999999999988643
No 12
>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=97.48 E-value=0.00046 Score=38.98 Aligned_cols=48 Identities=13% Similarity=0.137 Sum_probs=43.1
Q ss_pred EEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecc
Q 034926 26 VKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFL 73 (78)
Q Consensus 26 V~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~ 73 (78)
|...+|....+.+..++++..|.+.++++.|++.+.+++.|+|+.+..
T Consensus 2 v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~g~~l~d 49 (69)
T cd01769 2 VKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKD 49 (69)
T ss_pred eEccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCcCCCC
Confidence 455578899999999999999999999999999999999999987753
No 13
>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=97.44 E-value=0.00057 Score=40.82 Aligned_cols=50 Identities=12% Similarity=0.140 Sum_probs=38.3
Q ss_pred EEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeeccee
Q 034926 26 VKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLAW 75 (78)
Q Consensus 26 V~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~~ 75 (78)
|...+++...++|.+++.|..+.+.-|++.|++.+...+.++++.|.+|-
T Consensus 1 vi~~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~~k~ldlsl 50 (65)
T PF11470_consen 1 VICYNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHNNKPLDLSL 50 (65)
T ss_dssp EE-TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEETTEEESSS-
T ss_pred CCccCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEECCEEecccc
Confidence 45678899999999999999999999999999999999999999998874
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=97.41 E-value=0.00067 Score=39.66 Aligned_cols=49 Identities=16% Similarity=0.247 Sum_probs=45.0
Q ss_pred EEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecc
Q 034926 25 KVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFL 73 (78)
Q Consensus 25 kV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~ 73 (78)
.|+..+|..+.+.+.++.....|.+..+++.|++.+..|+.|.|+.+.-
T Consensus 2 ~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~G~~L~d 50 (70)
T cd01798 2 YVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRN 50 (70)
T ss_pred EEEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEECCeECCC
Confidence 4667789999999999999999999999999999999999999999854
No 15
>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=97.31 E-value=0.0013 Score=37.89 Aligned_cols=46 Identities=7% Similarity=0.102 Sum_probs=42.3
Q ss_pred cCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 29 QDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 29 qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
.+|..+.+.|..++....|.+..+++.|++++..++.|+|+.+...
T Consensus 3 ~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~G~~L~d~ 48 (69)
T PF00240_consen 3 LSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYNGKELDDD 48 (69)
T ss_dssp TTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEETTEEESTT
T ss_pred CCCcEEEEEECCCCCHHHhhhhcccccccccccceeeeeeecccCc
Confidence 4678899999999999999999999999999999999999998543
No 16
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=97.18 E-value=0.0028 Score=37.24 Aligned_cols=51 Identities=6% Similarity=0.042 Sum_probs=45.6
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCC--CCCeEEEEECCEeecc
Q 034926 23 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSV--ELNSIAFLYVHISAFL 73 (78)
Q Consensus 23 ~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl--~~~s~rFlfdG~rI~~ 73 (78)
.|.|...+|....+.+..++....|....+++.|+ +++..++.|+|..+..
T Consensus 2 ~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~G~~L~d 54 (77)
T cd01805 2 KITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKD 54 (77)
T ss_pred EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEECCEEccC
Confidence 45666678899999999999999999999999999 9999999999998863
No 17
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=97.15 E-value=0.0027 Score=38.19 Aligned_cols=51 Identities=10% Similarity=0.057 Sum_probs=47.2
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeec
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAF 72 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~ 72 (78)
+.|.|.+..|..+.+.+.+++....|.+..+++.|++++..|+.|.|..+.
T Consensus 2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~Gk~L~ 52 (73)
T cd01791 2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFK 52 (73)
T ss_pred EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeCCcCCC
Confidence 678899888999889999999999999999999999999999999998765
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=97.03 E-value=0.0042 Score=37.35 Aligned_cols=52 Identities=15% Similarity=0.209 Sum_probs=47.2
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecc
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFL 73 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~ 73 (78)
++|.|+...|....+.+.+++....|.+..+++.|++....|+.|.|..+.-
T Consensus 2 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~Gk~L~d 53 (78)
T cd01804 2 MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSS 53 (78)
T ss_pred eEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEECCcCCCC
Confidence 5778888889998999999999999999999999999999999999987653
No 19
>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=96.97 E-value=0.0036 Score=32.43 Aligned_cols=46 Identities=13% Similarity=0.088 Sum_probs=41.7
Q ss_pred cCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 29 QDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 29 qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
.+|....+.+..++++..|.+..+++.|.+.+.+++.++|..+...
T Consensus 5 ~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~~~~~~~ 50 (69)
T cd00196 5 NDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDS 50 (69)
T ss_pred cCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECCeECCCC
Confidence 3788889999999999999999999999999999999999887654
No 20
>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=96.80 E-value=0.0045 Score=37.22 Aligned_cols=51 Identities=22% Similarity=0.209 Sum_probs=46.4
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEE--EECCEeec
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAF--LYVHISAF 72 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rF--lfdG~rI~ 72 (78)
+.|.|+...|..+.+.+.++.....|.+..+++.|++.+..|+ .|+|..+.
T Consensus 3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~~L~ 55 (80)
T cd01792 3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQ 55 (80)
T ss_pred eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCCCCC
Confidence 7788888889998889999999999999999999999999999 88898765
No 21
>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=96.77 E-value=0.007 Score=35.74 Aligned_cols=50 Identities=10% Similarity=0.206 Sum_probs=45.5
Q ss_pred EEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecc
Q 034926 24 LKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFL 73 (78)
Q Consensus 24 lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~ 73 (78)
|.|+...|..+.+.|.++.....|....+++.|++....++.|+|+.+.-
T Consensus 1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~G~~L~D 50 (74)
T cd01810 1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGRPMED 50 (74)
T ss_pred CEEECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCEECCC
Confidence 35677789999999999999999999999999999999999999998864
No 22
>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2. hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.
Probab=96.59 E-value=0.014 Score=34.16 Aligned_cols=51 Identities=14% Similarity=0.188 Sum_probs=44.0
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecc
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFL 73 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~ 73 (78)
|+|.|+...|.. .+.|.++.....|.+..+++.|++...+|+.|+|+-+.-
T Consensus 1 ~~i~vk~~~g~~-~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li~~Gk~L~d 51 (71)
T cd01808 1 IKVTVKTPKDKE-EIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKILKD 51 (71)
T ss_pred CEEEEEcCCCCE-EEEECCCChHHHHHHHHHHHhCCCHHHEEEEECCeEcCC
Confidence 356666777764 799999999999999999999999999999999997753
No 23
>cd01802 AN1_N ubiquitin-like domain of AN1. AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.
Probab=96.55 E-value=0.019 Score=36.58 Aligned_cols=55 Identities=5% Similarity=0.067 Sum_probs=50.6
Q ss_pred CcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 20 AHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 20 ~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
+.+.|.|+...|..+.+.|.+++....|...-+++.|++.+..|+.|.|+.+.-.
T Consensus 26 ~~M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~Gk~L~D~ 80 (103)
T cd01802 26 DTMELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNMELEDE 80 (103)
T ss_pred CCEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEECCEECCCC
Confidence 4688999999999999999999999999999999999999999999999988543
No 24
>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein. DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.
Probab=96.22 E-value=0.022 Score=33.74 Aligned_cols=51 Identities=14% Similarity=0.161 Sum_probs=45.7
Q ss_pred EEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 24 LKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 24 lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
|||+...|+.+.+.+.+++....|...-+++.|++....|++|.|+.+.-.
T Consensus 1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~G~~L~D~ 51 (70)
T cd01794 1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGKLLTDK 51 (70)
T ss_pred CeEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCC
Confidence 467777899999999999999999999999999999999999999987643
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=96.11 E-value=0.026 Score=33.25 Aligned_cols=49 Identities=6% Similarity=0.051 Sum_probs=42.9
Q ss_pred EEEcc-CCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecc
Q 034926 25 KVKGQ-DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFL 73 (78)
Q Consensus 25 kV~~q-dg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~ 73 (78)
.|+-. .|..+.+.|.++.....|...-+++.|++.+..|++|+|+.+.-
T Consensus 2 ~v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~~Gk~L~D 51 (71)
T cd01796 2 TVYTARSETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYNGRELVD 51 (71)
T ss_pred EEEECCCCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEECCeEccC
Confidence 34445 67788899999999999999999999999999999999999854
No 26
>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=96.10 E-value=0.033 Score=34.95 Aligned_cols=52 Identities=21% Similarity=0.237 Sum_probs=46.1
Q ss_pred EEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCC---CeEEEEE---CCEeeccee
Q 034926 24 LKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL---NSIAFLY---VHISAFLAW 75 (78)
Q Consensus 24 lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~---~s~rFlf---dG~rI~~~~ 75 (78)
+|.+++.|..++|++.++..+..|+.+-++|.|.+. +.+.+.| ||..+.+++
T Consensus 3 FK~~~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~YlDDEgD~VllT~ 60 (86)
T cd06409 3 FKFKDPKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSYVDDEGDIVLITS 60 (86)
T ss_pred EEeeCCCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEEEcCCCCEEEEec
Confidence 678899999999999999999999999999999986 6888888 677776664
No 27
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=96.06 E-value=0.039 Score=32.46 Aligned_cols=50 Identities=8% Similarity=0.131 Sum_probs=43.1
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 23 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 23 ~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
.|.|++ ++...+.|.++.....|...-+++.|++.+..|+.|.|+.+.-.
T Consensus 2 qi~vk~--~~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~Gk~L~D~ 51 (74)
T cd01793 2 QLFVRA--QNTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLEDD 51 (74)
T ss_pred EEEEEC--CCEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEECCeECCCC
Confidence 456665 35678999999999999999999999999999999999988543
No 28
>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=95.51 E-value=0.073 Score=32.10 Aligned_cols=52 Identities=19% Similarity=0.193 Sum_probs=44.3
Q ss_pred EEEEEccCCCE-EEEE-EeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 23 NLKVKGQDGNE-VFFR-IKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 23 ~lkV~~qdg~~-v~Fk-IK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
.|.|+...|.. ..+. +.++.....|...-+++.|++.+..|++|.|+.+...
T Consensus 2 ~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~Gk~L~D~ 55 (78)
T cd01797 2 WIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQMEDG 55 (78)
T ss_pred EEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeCCEECCCC
Confidence 46667778887 4674 7899999999999999999999999999999988654
No 29
>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=95.09 E-value=0.1 Score=31.36 Aligned_cols=42 Identities=2% Similarity=0.020 Sum_probs=38.3
Q ss_pred CCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeec
Q 034926 30 DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAF 72 (78)
Q Consensus 30 dg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~ 72 (78)
.|..+.+.|.++.....|...-+++.|++++..|+ |+|.++.
T Consensus 11 ~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~G~~L~ 52 (75)
T cd01799 11 HTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VIGQRLA 52 (75)
T ss_pred CCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-EcCCeeC
Confidence 36778899999999999999999999999999999 9999874
No 30
>smart00455 RBD Raf-like Ras-binding domain.
Probab=94.31 E-value=0.23 Score=29.65 Aligned_cols=50 Identities=8% Similarity=0.102 Sum_probs=42.5
Q ss_pred EEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecc
Q 034926 24 LKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFL 73 (78)
Q Consensus 24 lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~ 73 (78)
.+|.=+||..+..++|++.++.-+...-|++.|+++.......-|..-.+
T Consensus 2 ~~v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~g~~k~l 51 (70)
T smart00455 2 CKVHLPDNQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRGEKKPL 51 (70)
T ss_pred eEEECCCCCEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCcce
Confidence 46777899999999999999999999999999999998888775643333
No 31
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.08 E-value=0.22 Score=38.41 Aligned_cols=52 Identities=12% Similarity=0.081 Sum_probs=46.0
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcC---CCCCeEEEEECCEeecce
Q 034926 23 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQS---VELNSIAFLYVHISAFLA 74 (78)
Q Consensus 23 ~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~g---l~~~s~rFlfdG~rI~~~ 74 (78)
+|.|+.-+|..+.+.|..+.....|.+..++..| ++....|++|.|+.|.-.
T Consensus 2 kItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~GkiL~Dd 56 (378)
T TIGR00601 2 TLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDD 56 (378)
T ss_pred EEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEECCEECCCC
Confidence 5677777888888999999999999999999998 899999999999988643
No 32
>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=93.96 E-value=0.42 Score=28.09 Aligned_cols=53 Identities=15% Similarity=0.211 Sum_probs=42.3
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEE---CCEeeccee
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLY---VHISAFLAW 75 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlf---dG~rI~~~~ 75 (78)
+++||.- .|....|.+.++..+..|...=+++.++....+++.| ||.-|.+++
T Consensus 2 ~~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~s 57 (81)
T smart00666 2 VDVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTS 57 (81)
T ss_pred ccEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecC
Confidence 5677765 5556689999999999999999999999877888888 566665543
No 33
>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=93.74 E-value=0.6 Score=28.71 Aligned_cols=54 Identities=7% Similarity=-0.095 Sum_probs=44.8
Q ss_pred cEEEEEEccCCCEEEEEE--eCCchHHHHHHHHHhhcC--CCCCeEEEEECCEeecce
Q 034926 21 HINLKVKGQDGNEVFFRI--KRSTQLKKLMNAYCDRQS--VELNSIAFLYVHISAFLA 74 (78)
Q Consensus 21 ~I~lkV~~qdg~~v~FkI--K~~t~l~KLm~aYc~r~g--l~~~s~rFlfdG~rI~~~ 74 (78)
.|+|.|+..++....|.| ..+.....|.+.-++..+ -++...|+.|-|+-+.-.
T Consensus 1 ~i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKiLkD~ 58 (79)
T cd01790 1 PVTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDH 58 (79)
T ss_pred CeEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCeeccch
Confidence 388999999999877777 789999999998888775 457999999999977543
No 34
>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=93.49 E-value=0.12 Score=31.57 Aligned_cols=46 Identities=20% Similarity=0.294 Sum_probs=31.6
Q ss_pred CcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEE
Q 034926 20 AHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLY 66 (78)
Q Consensus 20 ~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlf 66 (78)
+.+-|||+++||.. ++.+.++..+..|++..++..+++..++.+..
T Consensus 3 ~~milRvrS~dG~~-Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L~~ 48 (80)
T PF11543_consen 3 SSMILRVRSKDGMK-RIEVSPSSTLSDLKEKISEQLSIPDSSQSLSK 48 (80)
T ss_dssp ---EEEEE-SSEEE-EEEE-TTSBHHHHHHHHHHHS---TTT---BS
T ss_pred ccEEEEEECCCCCE-EEEcCCcccHHHHHHHHHHHcCCCCcceEEEe
Confidence 46889999999976 88999999999999999999999988766543
No 35
>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=92.53 E-value=0.95 Score=27.79 Aligned_cols=53 Identities=15% Similarity=0.214 Sum_probs=41.7
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCC-CeEEEEE---CCEeeccee
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL-NSIAFLY---VHISAFLAW 75 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~-~s~rFlf---dG~rI~~~~ 75 (78)
++||+.- .|..+.|++.++..+..|.+.-+++.+++. ..+.+.| +|..+.+++
T Consensus 1 ~~vK~~~-~~d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~lts 57 (82)
T cd06407 1 VRVKATY-GEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTC 57 (82)
T ss_pred CEEEEEe-CCeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeec
Confidence 3566654 566789999999999999999999999875 7888887 565555543
No 36
>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=92.19 E-value=0.83 Score=27.15 Aligned_cols=52 Identities=12% Similarity=0.325 Sum_probs=40.9
Q ss_pred EEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeeccee
Q 034926 24 LKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLAW 75 (78)
Q Consensus 24 lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~~ 75 (78)
++|.=++|+.....++++..++-....-|++.|+++.......-|..-.+.|
T Consensus 3 ~~v~LP~~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V~~~~~~k~l~~ 54 (71)
T PF02196_consen 3 CRVHLPNGQRTVVQVRPGMTIRDALSKACKKRGLNPECCDVRLVGEKKPLDW 54 (71)
T ss_dssp EEEEETTTEEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEEEEEEEEEEE-T
T ss_pred EEEECCCCCEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCccccC
Confidence 5677789999999999999999999999999999999887777665555544
No 37
>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=92.02 E-value=0.58 Score=27.61 Aligned_cols=43 Identities=14% Similarity=0.149 Sum_probs=38.6
Q ss_pred CCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeec
Q 034926 30 DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAF 72 (78)
Q Consensus 30 dg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~ 72 (78)
+|..+.+.+.++.....|...-....|++.+..++.|.|..+.
T Consensus 6 ~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~G~~L~ 48 (76)
T cd01800 6 NGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEGIFIK 48 (76)
T ss_pred CCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEEcC
Confidence 5677789999999999999999999999999999999998764
No 38
>KOG0005 consensus Ubiquitin-like protein [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=91.97 E-value=0.28 Score=29.52 Aligned_cols=49 Identities=14% Similarity=0.296 Sum_probs=45.5
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEee
Q 034926 23 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISA 71 (78)
Q Consensus 23 ~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI 71 (78)
.|||+.-.|.++.+.|-++.+..++.+--.++-|+++..-|+.|.|+..
T Consensus 2 ~iKvktLt~KeIeidIep~DkverIKErvEEkeGIPp~qqrli~~gkqm 50 (70)
T KOG0005|consen 2 LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYAGKQM 50 (70)
T ss_pred eeeEeeeccceEEEeeCcchHHHHHHHHhhhhcCCCchhhhhhhccccc
Confidence 4677778899999999999999999999999999999999999999876
No 39
>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=91.92 E-value=0.35 Score=30.53 Aligned_cols=42 Identities=12% Similarity=0.288 Sum_probs=38.0
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEE
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIA 63 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~r 63 (78)
+.|+|.=+||..+..+|+++..-..++++-|.+.|++....+
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 678888899999999999999999999999999999976644
No 40
>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=91.89 E-value=1.4 Score=25.84 Aligned_cols=54 Identities=7% Similarity=0.058 Sum_probs=42.2
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEE---CCEeeccee
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLY---VHISAFLAW 75 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlf---dG~rI~~~~ 75 (78)
+.||+.-.++....|.+..+..+..|...=+++.+.....+++.| ||..|.+++
T Consensus 2 ~~vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~V~i~s 58 (84)
T PF00564_consen 2 VRVKVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKDEDGDLVTISS 58 (84)
T ss_dssp EEEEEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEETTSSEEEESS
T ss_pred EEEEEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeCCCCCEEEeCC
Confidence 667777644333238999999999999999999999888888888 676766653
No 41
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=91.85 E-value=0.74 Score=36.94 Aligned_cols=52 Identities=12% Similarity=0.159 Sum_probs=47.6
Q ss_pred CcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeec
Q 034926 20 AHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAF 72 (78)
Q Consensus 20 ~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~ 72 (78)
..|.|+|+..+. ...|.|-.+...+-|.+.-+.+.+.+.+.++++|.|+-++
T Consensus 14 ~~irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfaGrILK 65 (493)
T KOG0010|consen 14 SLIRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYAGRILK 65 (493)
T ss_pred ceeEEEEecCCc-ceeEecccchHHHHHHHHHHHhcCCChhHeeeeecCcccc
Confidence 468899988777 6699999999999999999999999999999999999876
No 42
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=91.77 E-value=0.57 Score=36.45 Aligned_cols=45 Identities=13% Similarity=0.157 Sum_probs=41.0
Q ss_pred EEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecceeec
Q 034926 33 EVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLAWAV 77 (78)
Q Consensus 33 ~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~~~~ 77 (78)
.+.+.|+-+|.+..|.+.-+.++|++.+.||..|-|+.++-+|.+
T Consensus 15 ~l~v~v~~~t~I~~lke~Vak~~gvp~D~L~viFaGKeLs~~ttv 59 (446)
T KOG0006|consen 15 GLPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELSNDTTV 59 (446)
T ss_pred ceeEEEecCCCHHHHHHHHHHhhCCChhheEEEEeccccccCcee
Confidence 356778999999999999999999999999999999999988764
No 43
>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=90.93 E-value=1.1 Score=27.04 Aligned_cols=45 Identities=7% Similarity=0.282 Sum_probs=38.2
Q ss_pred EEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECC
Q 034926 24 LKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVH 68 (78)
Q Consensus 24 lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG 68 (78)
++|.=+||......|+++..++-+...-|++.|+++...-..+-|
T Consensus 2 ~~V~LPng~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~~~ 46 (72)
T cd01760 2 CRVYLPNGQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLLG 46 (72)
T ss_pred EEEECcCCCeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEec
Confidence 467778999999999999999999999999999987765555443
No 44
>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=90.90 E-value=1.7 Score=27.03 Aligned_cols=51 Identities=18% Similarity=0.165 Sum_probs=40.4
Q ss_pred EEEEEEccCCCEEEEEEeC--CchHHHHHHHHHhhcCCCCCeEEEEE---CCEeeccee
Q 034926 22 INLKVKGQDGNEVFFRIKR--STQLKKLMNAYCDRQSVELNSIAFLY---VHISAFLAW 75 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~--~t~l~KLm~aYc~r~gl~~~s~rFlf---dG~rI~~~~ 75 (78)
|+||+.- .|..+.|++.+ ++.+..|..--+++.+++ .+..-| ||..+.+++
T Consensus 1 V~vKaty-~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~--~f~lKYlDde~e~v~lss 56 (81)
T cd06396 1 VNLKVTY-NGESQSFLVSDSENTTWASVEAMVKVSFGLN--DIQIKYVDEENEEVSVNS 56 (81)
T ss_pred CEEEEEE-CCeEEEEEecCCCCCCHHHHHHHHHHHhCCC--cceeEEEcCCCCEEEEEc
Confidence 5677764 77888999999 889999999999999999 666666 666666654
No 45
>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=90.22 E-value=2.4 Score=26.60 Aligned_cols=53 Identities=11% Similarity=0.117 Sum_probs=41.2
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEE--CCEeeccee
Q 034926 21 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLY--VHISAFLAW 75 (78)
Q Consensus 21 ~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlf--dG~rI~~~~ 75 (78)
.|+|||.- .|..+.+.|.++..|+.|.+.-.++.++. ..++..| +|..+..++
T Consensus 2 ~ikVKv~~-~~Dv~~i~v~~~i~f~dL~~kIrdkf~~~-~~~~iKykDEGD~iti~s 56 (86)
T cd06408 2 KIRVKVHA-QDDTRYIMIGPDTGFADFEDKIRDKFGFK-RRLKIKMKDDGDMITMGD 56 (86)
T ss_pred cEEEEEEe-cCcEEEEEcCCCCCHHHHHHHHHHHhCCC-CceEEEEEcCCCCccccC
Confidence 57888874 66788999999999999999999999985 4555555 565555543
No 46
>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=89.86 E-value=2.5 Score=24.53 Aligned_cols=53 Identities=19% Similarity=0.202 Sum_probs=40.7
Q ss_pred EEEEEEccCCCEEEEEEe-CCchHHHHHHHHHhhcCCCCCeEEEEE---CCEeeccee
Q 034926 22 INLKVKGQDGNEVFFRIK-RSTQLKKLMNAYCDRQSVELNSIAFLY---VHISAFLAW 75 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK-~~t~l~KLm~aYc~r~gl~~~s~rFlf---dG~rI~~~~ 75 (78)
|++|+.-. |....|.+. .++.+..|...=+++.+.....+++.| +|..|.+++
T Consensus 1 ~~vK~~~~-~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~s 57 (81)
T cd05992 1 VRVKVKYG-GEIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISS 57 (81)
T ss_pred CcEEEEec-CCCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCC
Confidence 35666653 556689999 999999999999999998767777777 566666554
No 47
>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=89.71 E-value=1.4 Score=26.12 Aligned_cols=48 Identities=17% Similarity=-0.012 Sum_probs=39.4
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEE---CCEee
Q 034926 23 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLY---VHISA 71 (78)
Q Consensus 23 ~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlf---dG~rI 71 (78)
+|.|+- .|....+.+..++....|.+.-+++.|++++.-+++| -|.-+
T Consensus 2 ~i~vk~-~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~l 52 (74)
T cd01813 2 PVIVKW-GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKPA 52 (74)
T ss_pred EEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCcC
Confidence 444444 5566778999999999999999999999999999996 66544
No 48
>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=89.58 E-value=1.4 Score=29.26 Aligned_cols=39 Identities=26% Similarity=0.395 Sum_probs=36.1
Q ss_pred CcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCC
Q 034926 20 AHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVE 58 (78)
Q Consensus 20 ~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~ 58 (78)
..+.++|.-.||..+.+.|..+|.-+.|++.=|++.|+.
T Consensus 2 ~~~~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~l~ 40 (207)
T smart00295 2 KPRVLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIR 40 (207)
T ss_pred CcEEEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhCCC
Confidence 358899999999999999999999999999999999984
No 49
>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=89.54 E-value=2.9 Score=24.59 Aligned_cols=47 Identities=19% Similarity=0.253 Sum_probs=35.0
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCe-EEEE
Q 034926 19 SAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNS-IAFL 65 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s-~rFl 65 (78)
...++|+|+-+||..+.-+...+.+++.|++--......+... +++.
T Consensus 4 ~~~~~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~ 51 (82)
T PF00789_consen 4 SDVVRIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELI 51 (82)
T ss_dssp SSEEEEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEE
T ss_pred CCEEEEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEE
Confidence 3478899999999999999999999999996554444344333 5553
No 50
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=88.68 E-value=3.5 Score=24.43 Aligned_cols=45 Identities=13% Similarity=0.202 Sum_probs=35.1
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEE
Q 034926 21 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFL 65 (78)
Q Consensus 21 ~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFl 65 (78)
..+|.|+-+||..+.-+...+.+++.|++.-....+.+...++|.
T Consensus 4 ~~~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~~~~~~f~L~ 48 (80)
T smart00166 4 QCRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALTDGNDPFTLN 48 (80)
T ss_pred eEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcccCCCCCEEEE
Confidence 567778889999999999999999999998855555554555553
No 51
>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=88.26 E-value=1.1 Score=29.53 Aligned_cols=54 Identities=15% Similarity=0.143 Sum_probs=45.6
Q ss_pred CcEEEEEEccCCCEE-EEEEeCCchHHHHHHHHHhhcC-------CCCCeEEEEECCEeecc
Q 034926 20 AHINLKVKGQDGNEV-FFRIKRSTQLKKLMNAYCDRQS-------VELNSIAFLYVHISAFL 73 (78)
Q Consensus 20 ~~I~lkV~~qdg~~v-~FkIK~~t~l~KLm~aYc~r~g-------l~~~s~rFlfdG~rI~~ 73 (78)
+.|.||.+-.||+.+ -|++.+++.-..|.+.-.+..+ .+.+.+++.|.|+.+.-
T Consensus 3 ~~~e~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGKiLeD 64 (113)
T cd01814 3 EQIEIKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGKILEN 64 (113)
T ss_pred ccEEEEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCeecCC
Confidence 368888888999888 8999999999999999985553 44899999999998753
No 52
>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=85.34 E-value=3.9 Score=25.38 Aligned_cols=44 Identities=16% Similarity=0.223 Sum_probs=38.8
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEEC
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYV 67 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfd 67 (78)
-.|||.-+. .|-++|.+..++.-|.+.-++|.+++.+.+.+.|-
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 88999999999999999999999999888888883
No 53
>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=85.30 E-value=1.8 Score=25.15 Aligned_cols=41 Identities=22% Similarity=0.423 Sum_probs=33.8
Q ss_pred EEccCCCEEEEEEeCCchHHHHHHHHHhhcCCC-CCeEEEEE
Q 034926 26 VKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVE-LNSIAFLY 66 (78)
Q Consensus 26 V~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~-~~s~rFlf 66 (78)
|.-.||+.+.|.|.+++.-+.|++.-|++.|+. ..-+-+.|
T Consensus 1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~ 42 (80)
T PF09379_consen 1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQY 42 (80)
T ss_dssp EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE
T ss_pred CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEE
Confidence 344688999999999999999999999999964 45566666
No 54
>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=84.76 E-value=5.9 Score=23.16 Aligned_cols=43 Identities=14% Similarity=0.230 Sum_probs=37.1
Q ss_pred EEEEEEccCCC----EEEEEEeCCchHHHHHHHHHhhcCC--CCCeEEE
Q 034926 22 INLKVKGQDGN----EVFFRIKRSTQLKKLMNAYCDRQSV--ELNSIAF 64 (78)
Q Consensus 22 I~lkV~~qdg~----~v~FkIK~~t~l~KLm~aYc~r~gl--~~~s~rF 64 (78)
-.|||-..++. ...++|..+|.-+.|..+-+++.++ ++..+.+
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~~~~~y~L 51 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCL 51 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEE
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEE
Confidence 46889888988 8999999999999999999999998 4555555
No 55
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=84.68 E-value=5.7 Score=23.98 Aligned_cols=48 Identities=10% Similarity=0.080 Sum_probs=37.8
Q ss_pred EEEEEcc-CCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEE-EECCEe
Q 034926 23 NLKVKGQ-DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAF-LYVHIS 70 (78)
Q Consensus 23 ~lkV~~q-dg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rF-lfdG~r 70 (78)
+|.|... .......|+.++.....|.+.=....|+++...|+ +|+|..
T Consensus 3 ~v~i~~~~~~~~~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~~ 52 (84)
T cd01789 3 TVNITSSADSFSFEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGDD 52 (84)
T ss_pred EEEEEeCCCceeeeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCCC
Confidence 4444432 24445778999999999999999999999999999 589884
No 56
>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=83.79 E-value=3.5 Score=25.55 Aligned_cols=37 Identities=14% Similarity=0.276 Sum_probs=33.5
Q ss_pred EEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCe
Q 034926 25 KVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNS 61 (78)
Q Consensus 25 kV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s 61 (78)
.|.-+||..+...|+++..+.-+.++-|.+.++++..
T Consensus 3 ~V~lPn~~~~~v~vrp~~tv~dvLe~aCk~~~ldp~e 39 (77)
T cd01818 3 WVCLPDNQPVLTYLRPGMSVEDFLESACKRKQLDPME 39 (77)
T ss_pred EEECCCCceEEEEECCCCCHHHHHHHHHHhcCCChhH
Confidence 4667899999999999999999999999999998764
No 57
>PHA01623 hypothetical protein
Probab=83.74 E-value=0.82 Score=26.29 Aligned_cols=28 Identities=25% Similarity=0.586 Sum_probs=24.7
Q ss_pred EEEEEEeCCchHHHHHHHHHhhcCCCCC
Q 034926 33 EVFFRIKRSTQLKKLMNAYCDRQSVELN 60 (78)
Q Consensus 33 ~v~FkIK~~t~l~KLm~aYc~r~gl~~~ 60 (78)
.++|.|+-+..|.+-++.||...|++..
T Consensus 13 ~~r~sVrldeel~~~Ld~y~~~~g~~rS 40 (56)
T PHA01623 13 KAVFGIYMDKDLKTRLKVYCAKNNLQLT 40 (56)
T ss_pred ceeEEEEeCHHHHHHHHHHHHHcCCCHH
Confidence 4689999999999999999999998743
No 58
>PLN02560 enoyl-CoA reductase
Probab=81.67 E-value=5.3 Score=29.97 Aligned_cols=45 Identities=16% Similarity=0.191 Sum_probs=37.4
Q ss_pred EEEEEccCCCEE---EEEEeCCchHHHHHHHHHhhcCC-CCCeEEEEEC
Q 034926 23 NLKVKGQDGNEV---FFRIKRSTQLKKLMNAYCDRQSV-ELNSIAFLYV 67 (78)
Q Consensus 23 ~lkV~~qdg~~v---~FkIK~~t~l~KLm~aYc~r~gl-~~~s~rFlfd 67 (78)
+|.|+...|..+ .+.+.+++....|.++++++.+. +++..|+.++
T Consensus 2 ~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~ 50 (308)
T PLN02560 2 KVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLP 50 (308)
T ss_pred EEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEe
Confidence 455666677776 68899999999999999999885 8899999983
No 59
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=77.08 E-value=13 Score=22.18 Aligned_cols=46 Identities=11% Similarity=0.155 Sum_probs=38.4
Q ss_pred EEEEEEccCC--CEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEEC
Q 034926 22 INLKVKGQDG--NEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYV 67 (78)
Q Consensus 22 I~lkV~~qdg--~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfd 67 (78)
|+|.|..... ..+..|+-++.++..|...-....|++++..|+.+-
T Consensus 2 v~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~ 49 (87)
T PF14560_consen 2 VKLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLK 49 (87)
T ss_dssp EEEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE
T ss_pred EEEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEE
Confidence 6677777554 378899999999999999999999999999998773
No 60
>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=74.59 E-value=17 Score=22.61 Aligned_cols=44 Identities=9% Similarity=0.178 Sum_probs=33.4
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEE
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLY 66 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlf 66 (78)
|.+.|.--.+....|+|++.+|.+||...--...|.+- .-|+.|
T Consensus 1 iqVtV~q~g~~dl~l~vnPy~pI~k~K~kI~~~~~~~g-~qrLsf 44 (80)
T cd01811 1 IQVTVEQTGYSDWILRVNPYSPIRKIKEKIRRSRNCSG-LQRLSF 44 (80)
T ss_pred CEEEeeecCCCceEEEeCCcchHHHHHHHHHHhhCccc-ceEEEe
Confidence 45667665677789999999999999998887777653 444444
No 61
>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=72.15 E-value=20 Score=21.90 Aligned_cols=51 Identities=14% Similarity=0.356 Sum_probs=40.3
Q ss_pred EEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeeccee
Q 034926 25 KVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLAW 75 (78)
Q Consensus 25 kV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~~ 75 (78)
+|.=+||+.-...+++...++-+..--|++.|+.+...-.+.-|.+--+.|
T Consensus 3 rV~LPdg~~T~V~vrpG~ti~d~L~kllekRgl~~~~~~vf~~g~~k~l~~ 53 (73)
T cd01817 3 RVILPDGSTTVVPTRPGESIRDLLSGLCEKRGINYAAVDLFLVGGDKPLVL 53 (73)
T ss_pred EEECCCCCeEEEEecCCCCHHHHHHHHHHHcCCChhHEEEEEecCCccccc
Confidence 455678888889999999999999999999999988766555565433333
No 62
>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=70.77 E-value=21 Score=21.57 Aligned_cols=43 Identities=19% Similarity=0.251 Sum_probs=34.2
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEE
Q 034926 21 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAF 64 (78)
Q Consensus 21 ~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rF 64 (78)
.++|.++=++|+.+.-+...+.+|+-|++.... .|-+...+++
T Consensus 4 ~~~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~-~~~~~~~f~L 46 (80)
T cd01771 4 ISKLRVRTPSGDFLERRFLGDTPLQVLLNFVAS-KGYPIDEYKL 46 (80)
T ss_pred eEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cCCCCCCEEE
Confidence 577888889999999999999999999988743 3555555555
No 63
>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=69.82 E-value=22 Score=21.64 Aligned_cols=46 Identities=11% Similarity=0.105 Sum_probs=34.7
Q ss_pred CcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEE
Q 034926 20 AHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLY 66 (78)
Q Consensus 20 ~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlf 66 (78)
+.++|.++=.+|+.+.-+...+.+++-|++.... .+.....+++..
T Consensus 3 ~~~~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~-~~~~~~~f~L~t 48 (85)
T cd01774 3 DTVKIVFKLPNGTRVERRFLFTQSLRVIHDFLFS-LKETPEKFQIVT 48 (85)
T ss_pred ceEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-CCCCCCcEEEec
Confidence 3578888889999999999999999999998743 333445555543
No 64
>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=68.59 E-value=13 Score=23.19 Aligned_cols=35 Identities=14% Similarity=0.359 Sum_probs=32.2
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHh
Q 034926 19 SAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCD 53 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~ 53 (78)
.+.+.|-|.+.++.+-.|.++.++-+.++...||-
T Consensus 6 ~grl~VLVv~n~c~~kL~~~~~~~D~~~i~r~f~T 40 (83)
T PF10623_consen 6 PGRLQVLVVSNHCERKLFDTKPDNDPDKIARRFCT 40 (83)
T ss_pred CCeEEEEEEeCCcceeEeecCCCCCHHHHHhhccC
Confidence 35799999999999999999999999999999985
No 65
>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=67.43 E-value=23 Score=21.52 Aligned_cols=33 Identities=12% Similarity=0.286 Sum_probs=25.1
Q ss_pred CCCcEEEEEEccC-CCEEEEEEeCCchHHHHHHH
Q 034926 18 QSAHINLKVKGQD-GNEVFFRIKRSTQLKKLMNA 50 (78)
Q Consensus 18 ~~~~I~lkV~~qd-g~~v~FkIK~~t~l~KLm~a 50 (78)
+...|.||+.|.. |..+.|+..+..-+++|..+
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 4678999999955 66889999999999999864
No 66
>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=66.73 E-value=27 Score=21.47 Aligned_cols=44 Identities=14% Similarity=0.190 Sum_probs=33.8
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEE
Q 034926 21 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFL 65 (78)
Q Consensus 21 ~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFl 65 (78)
.-.|.|+-++|+.+.-+...+++|+.|++.-.. .|.+...+.++
T Consensus 5 ~t~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~-~g~~~~~f~L~ 48 (82)
T cd01773 5 KARLMLRYPDGKREQIALPEQAKLLALVRHVQS-KGYPNERFELL 48 (82)
T ss_pred eeEEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cCCCCCCEEEe
Confidence 456667778999999999999999999985433 56676666654
No 67
>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=63.53 E-value=29 Score=21.81 Aligned_cols=55 Identities=9% Similarity=0.048 Sum_probs=37.9
Q ss_pred cEEEEEEccCCCEEEEEEe--CCchHHHHHHHHHhhc--CCCCCeEEEEECCEeecceee
Q 034926 21 HINLKVKGQDGNEVFFRIK--RSTQLKKLMNAYCDRQ--SVELNSIAFLYVHISAFLAWA 76 (78)
Q Consensus 21 ~I~lkV~~qdg~~v~FkIK--~~t~l~KLm~aYc~r~--gl~~~s~rFlfdG~rI~~~~~ 76 (78)
+|+|+..+ .--.+.+.|. .++.-..|...--++. ..+...+||.|+|+-|..++.
T Consensus 2 ~l~IRFs~-sipDl~L~I~~~~~~Tv~~LK~lIR~~~p~~~s~~rLRlI~~Gr~L~d~t~ 60 (97)
T PF10302_consen 2 YLTIRFSD-SIPDLPLDIPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRLLNDHTD 60 (97)
T ss_pred eEEEEECC-CCCCceeecCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCcccCccch
Confidence 46666665 2223566666 7777777777665555 477889999999998876543
No 68
>PLN02593 adrenodoxin-like ferredoxin protein
Probab=61.87 E-value=25 Score=22.56 Aligned_cols=34 Identities=24% Similarity=0.403 Sum_probs=25.3
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCC
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL 59 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~ 59 (78)
|+|++.+.+|.+..+.+.... .||+| +.+.|++.
T Consensus 1 ~~V~fi~~~G~~~~v~~~~G~---tLl~a-~~~~gi~i 34 (117)
T PLN02593 1 ISVTFVDKDGEERTVKAPVGM---SLLEA-AHENDIEL 34 (117)
T ss_pred CEEEEEcCCCCEEEEEECCCC---cHHHH-HHHcCCCC
Confidence 678888899998888887765 55665 66677764
No 69
>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=61.15 E-value=37 Score=21.08 Aligned_cols=51 Identities=18% Similarity=0.106 Sum_probs=39.1
Q ss_pred EEEEEccCCCEEEEEEeC-----CchHHHHHHHHHhhcCCCC-CeEEEEE---CCEeecce
Q 034926 23 NLKVKGQDGNEVFFRIKR-----STQLKKLMNAYCDRQSVEL-NSIAFLY---VHISAFLA 74 (78)
Q Consensus 23 ~lkV~~qdg~~v~FkIK~-----~t~l~KLm~aYc~r~gl~~-~s~rFlf---dG~rI~~~ 74 (78)
.|||.- +|....|++.. +..+..|.+.-+++.+++. ..+.+.| ||.-+.++
T Consensus 2 ~vKv~y-~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~ 61 (91)
T cd06398 2 VVKVKY-GGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLV 61 (91)
T ss_pred EEEEEe-CCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEc
Confidence 566665 56667999984 7999999999999999886 7788877 56555544
No 70
>PF13860 FlgD_ig: FlgD Ig-like domain; PDB: 3C12_A 3OSV_A.
Probab=58.56 E-value=34 Score=20.21 Aligned_cols=38 Identities=13% Similarity=0.178 Sum_probs=24.6
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEee
Q 034926 19 SAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISA 71 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI 71 (78)
...++|.|.|..|+.|+ ++.. -.++.....|.+||+.-
T Consensus 24 a~~v~v~I~d~~G~~V~-t~~~--------------~~~~~G~~~~~WdG~d~ 61 (81)
T PF13860_consen 24 ADNVTVTIYDSNGQVVR-TISL--------------GSQSAGEHSFTWDGKDD 61 (81)
T ss_dssp CEEEEEEEEETTS-EEE-EEEE--------------EECSSEEEEEEE-SB-T
T ss_pred ccEEEEEEEcCCCCEEE-EEEc--------------CCcCCceEEEEECCCCC
Confidence 34689999999998873 3331 12466789999998754
No 71
>PF13019 Telomere_Sde2: Telomere stability and silencing
Probab=58.11 E-value=44 Score=23.25 Aligned_cols=45 Identities=20% Similarity=0.311 Sum_probs=38.4
Q ss_pred EEEEEEccCC----CEEEEEEeCCchHHHHHHHHHhhcCCCCCe-EEEEE
Q 034926 22 INLKVKGQDG----NEVFFRIKRSTQLKKLMNAYCDRQSVELNS-IAFLY 66 (78)
Q Consensus 22 I~lkV~~qdg----~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s-~rFlf 66 (78)
|+|-|..-+| ..+.|.+..++++..|++...++.+.+... +.|.+
T Consensus 1 i~Vlvss~~g~~lp~tl~~~lp~~ttv~dL~~~l~~~~~~~~~~~~~L~~ 50 (162)
T PF13019_consen 1 INVLVSSFDGLTLPPTLSLSLPSTTTVSDLKDRLSERLPIPSSSQLYLTT 50 (162)
T ss_pred CeEEEecCCCCCCCCeEEeeCCCCCcHHHHHHHHHhhcCCCccceeEEEE
Confidence 6788888889 688999999999999999999999988776 44444
No 72
>PRK11675 LexA regulated protein; Provisional
Probab=56.37 E-value=9.4 Score=24.20 Aligned_cols=34 Identities=9% Similarity=0.149 Sum_probs=28.0
Q ss_pred EccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCC
Q 034926 27 KGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELN 60 (78)
Q Consensus 27 ~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~ 60 (78)
.|....-..+.||-+..+-.-++.||+..|++..
T Consensus 44 rdk~~glKRveVKldedl~ekL~eyAe~~nitRS 77 (90)
T PRK11675 44 RDKVRGLKRVELKLNADLVDALNELAEARNISRS 77 (90)
T ss_pred HHHHcCceeEEEEECHHHHHHHHHHHHHcCCCHH
Confidence 3445455689999999999999999999998754
No 73
>COG4806 RhaA L-rhamnose isomerase [Carbohydrate transport and metabolism]
Probab=56.25 E-value=8.2 Score=29.92 Aligned_cols=21 Identities=24% Similarity=0.580 Sum_probs=18.6
Q ss_pred CCchHHHHHHHHHhhcCCCCC
Q 034926 40 RSTQLKKLMNAYCDRQSVELN 60 (78)
Q Consensus 40 ~~t~l~KLm~aYc~r~gl~~~ 60 (78)
++-|++-+.+.||+++|++++
T Consensus 380 K~~P~~aiW~~yCe~~~VPv~ 400 (419)
T COG4806 380 KSLPWQAVWEMYCQRHDVPVG 400 (419)
T ss_pred hcCCHHHHHHHHHHhcCCCch
Confidence 477999999999999999865
No 74
>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=55.81 E-value=40 Score=19.72 Aligned_cols=35 Identities=17% Similarity=0.368 Sum_probs=31.4
Q ss_pred EEEEccC---CCEEEEEEeCCchHHHHHHHHHhhcCCC
Q 034926 24 LKVKGQD---GNEVFFRIKRSTQLKKLMNAYCDRQSVE 58 (78)
Q Consensus 24 lkV~~qd---g~~v~FkIK~~t~l~KLm~aYc~r~gl~ 58 (78)
|||...+ +....+.|.+++.-..+...-.++.+++
T Consensus 2 ikV~~~~~~~~~~kti~V~~~~t~~~Vi~~~l~k~~l~ 39 (87)
T cd01768 2 LRVYPEDPSGGTYKTLRVSKDTTAQDVIQQLLKKFGLD 39 (87)
T ss_pred EEEeCCcCCCccEEEEEECCCCCHHHHHHHHHHHhCCc
Confidence 6777777 8888999999999999999999999987
No 75
>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=55.13 E-value=29 Score=22.67 Aligned_cols=40 Identities=15% Similarity=-0.064 Sum_probs=35.5
Q ss_pred EEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeec
Q 034926 33 EVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAF 72 (78)
Q Consensus 33 ~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~ 72 (78)
++...|..++.+..|...--++.++++..=+++|||+-+.
T Consensus 16 ~~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~dG~~L~ 55 (107)
T cd01795 16 EKALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILS 55 (107)
T ss_pred CceEEeCccccHHHHHHHHHHHhcCCcccceeeecCceec
Confidence 5678899999999999999999999999999999999543
No 76
>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=55.09 E-value=32 Score=20.31 Aligned_cols=24 Identities=17% Similarity=0.344 Sum_probs=19.6
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCc
Q 034926 19 SAHINLKVKGQDGNEVFFRIKRST 42 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~FkIK~~t 42 (78)
+..+.+.+.+.+|..+.++|-+.|
T Consensus 53 ~g~yev~~~~~dG~~~ev~vD~~t 76 (83)
T PF13670_consen 53 DGCYEVEARDKDGKKVEVYVDPAT 76 (83)
T ss_pred CCEEEEEEEECCCCEEEEEEcCCC
Confidence 446889999999999988887654
No 77
>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=54.82 E-value=41 Score=19.72 Aligned_cols=54 Identities=7% Similarity=0.010 Sum_probs=36.8
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCC---C---eEEEE-ECCEeecce
Q 034926 21 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL---N---SIAFL-YVHISAFLA 74 (78)
Q Consensus 21 ~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~---~---s~rFl-fdG~rI~~~ 74 (78)
+++|.|...+|..+-+.+-.+.|+..|+..-.+..+.+. . ..++. -+|.+|.++
T Consensus 2 ~~rVtv~~~~~~~~Dl~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~~~~g~~L~~~ 62 (79)
T PF08817_consen 2 LCRVTVDAGNGRQVDLALPADVPVAELIPELVELLGLPGDDPPGHGQWVLARAGGRPLDPD 62 (79)
T ss_dssp EEEEEEE-TT--EEEEEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG-GGTEEEETT
T ss_pred EEEEEEEcCCCcEEEEEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEEecCCcccCCc
Confidence 678888886678999999999999999999999877632 2 34555 566666554
No 78
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=54.57 E-value=41 Score=19.45 Aligned_cols=49 Identities=16% Similarity=0.104 Sum_probs=36.7
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeeccee
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLAW 75 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~~ 75 (78)
|+|++-+.. .+..+.+...+.+..|.+.. +++...+....||.-+...+
T Consensus 5 m~v~vng~~-~~~~~~~~~~~tv~~ll~~l----~~~~~~v~v~vNg~iv~~~~ 53 (70)
T PRK08364 5 IRVKVIGRG-IEKEIEWRKGMKVADILRAV----GFNTESAIAKVNGKVALEDD 53 (70)
T ss_pred EEEEEeccc-cceEEEcCCCCcHHHHHHHc----CCCCccEEEEECCEECCCCc
Confidence 677775543 34567778888898888654 78888999999999886543
No 79
>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=53.98 E-value=42 Score=19.44 Aligned_cols=44 Identities=9% Similarity=0.215 Sum_probs=31.3
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEE
Q 034926 21 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFL 65 (78)
Q Consensus 21 ~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFl 65 (78)
..+|+|+-.||..+.-+...+.+++.|++.--.. +.+...+++.
T Consensus 2 ~t~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~-~~~~~~f~L~ 45 (77)
T cd01767 2 TTKIQIRLPDGKRLEQRFNSTHKLSDVRDFVESN-GPPAEPFTLM 45 (77)
T ss_pred cEEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHc-CCCCCCEEEE
Confidence 3567788889999999999999999998765332 2224444443
No 80
>KOG1363 consensus Predicted regulator of the ubiquitin pathway (contains UAS and UBX domains) [Signal transduction mechanisms]
Probab=53.16 E-value=42 Score=26.81 Aligned_cols=38 Identities=16% Similarity=0.217 Sum_probs=32.4
Q ss_pred CCCCCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHh
Q 034926 16 NDQSAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCD 53 (78)
Q Consensus 16 ~~~~~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~ 53 (78)
+...+.|+|.+..++|....-+.+++++++.||+-+..
T Consensus 378 a~~~~~~~l~iR~P~G~r~~RrF~~s~~~q~l~~~v~~ 415 (460)
T KOG1363|consen 378 ASEEEAITVAIRLPSGTRLERRFLKSDKLQILYDYVDS 415 (460)
T ss_pred cCcccceeeEEECCCCCeeeeeeecccchhHHHHHHHh
Confidence 33456899999999999999999999999999887743
No 81
>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=52.55 E-value=46 Score=19.88 Aligned_cols=44 Identities=7% Similarity=0.255 Sum_probs=31.1
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcC-CCCCeEEE
Q 034926 21 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQS-VELNSIAF 64 (78)
Q Consensus 21 ~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~g-l~~~s~rF 64 (78)
..+|.|+-.||+.+.-+...+.+++.|++.-....+ -+...+.+
T Consensus 4 ~t~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~~~~~~f~L 48 (79)
T cd01770 4 TTSIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPEFAARPFTL 48 (79)
T ss_pred eeEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCCCCCCCEEE
Confidence 466777788999998899999999988876544332 22344444
No 82
>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=52.37 E-value=14 Score=29.35 Aligned_cols=21 Identities=24% Similarity=0.597 Sum_probs=18.0
Q ss_pred CCchHHHHHHHHHhhcCCCCC
Q 034926 40 RSTQLKKLMNAYCDRQSVELN 60 (78)
Q Consensus 40 ~~t~l~KLm~aYc~r~gl~~~ 60 (78)
++.|+.-+.+.||.+.|++.+
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 578999999999999999865
No 83
>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=51.10 E-value=7.5 Score=19.71 Aligned_cols=25 Identities=8% Similarity=0.141 Sum_probs=20.3
Q ss_pred EEEeCCchHHHHHHHHHhhcCCCCC
Q 034926 36 FRIKRSTQLKKLMNAYCDRQSVELN 60 (78)
Q Consensus 36 FkIK~~t~l~KLm~aYc~r~gl~~~ 60 (78)
+.|.-+..+...++.+|++.|.+.+
T Consensus 2 iti~l~~~~~~~l~~~a~~~g~s~s 26 (39)
T PF01402_consen 2 ITIRLPDELYERLDELAKELGRSRS 26 (39)
T ss_dssp EEEEEEHHHHHHHHHHHHHHTSSHH
T ss_pred eEEEeCHHHHHHHHHHHHHHCcCHH
Confidence 4566677889999999999998754
No 84
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=51.06 E-value=41 Score=26.08 Aligned_cols=53 Identities=9% Similarity=0.033 Sum_probs=43.7
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcC--CCCCeEEEEECCEeeccee
Q 034926 23 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQS--VELNSIAFLYVHISAFLAW 75 (78)
Q Consensus 23 ~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~g--l~~~s~rFlfdG~rI~~~~ 75 (78)
+|.|+.-.+......++++..+.-+++.-..-+| .+...-.++|+|+-+.-..
T Consensus 2 ~lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLIy~GkiL~D~~ 56 (340)
T KOG0011|consen 2 KLTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLIYSGKILKDET 56 (340)
T ss_pred eeEeeeccCceeEeecCcchhHHHHHHHHHhccCCCCchhhheeeecceeccCCc
Confidence 3455555677778899999999999999999999 7788899999999887554
No 85
>PRK08452 flagellar protein FlaG; Provisional
Probab=50.42 E-value=58 Score=21.55 Aligned_cols=38 Identities=24% Similarity=0.257 Sum_probs=30.0
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCC
Q 034926 19 SAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSV 57 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl 57 (78)
.+.+.|+|.|.+..+|. |=-|.-.+-+|+...++..|+
T Consensus 81 ~~~~vVkVvD~~T~eVI-RqIP~Ee~L~l~~~m~e~~Gl 118 (124)
T PRK08452 81 IKGLVVSVKEANGGKVI-REIPSKEAIELMEYMRDVIGI 118 (124)
T ss_pred CCcEEEEEEECCCCcee-eeCCCHHHHHHHHHHHHhhhh
Confidence 45688999999888854 444678888899999998886
No 86
>KOG3439 consensus Protein conjugation factor involved in autophagy [Posttranslational modification, protein turnover, chaperones]
Probab=49.26 E-value=76 Score=21.03 Aligned_cols=54 Identities=15% Similarity=0.224 Sum_probs=42.0
Q ss_pred CcEEEEEEccCCCE----EEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecc
Q 034926 20 AHINLKVKGQDGNE----VFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFL 73 (78)
Q Consensus 20 ~~I~lkV~~qdg~~----v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~ 73 (78)
.+|+|+.+--.+.- -.|+|.++..+.++..---+..+++.+.=-|+|=.+.-.+
T Consensus 29 ~kV~i~l~aiG~~PilK~~k~~i~~t~tfa~vi~Flkk~Lkl~as~slflYVN~sFAP 86 (116)
T KOG3439|consen 29 RKVQIRLRAIGDAPILKKSKFKINPTQTFAKVILFLKKFLKLQASDSLFLYVNNSFAP 86 (116)
T ss_pred ceEEEEEeccCCCcceecceEEeCcchhhHHHHHHHHHHhCCcccCeEEEEEcCccCC
Confidence 57777776544322 3799999999999999999999999988888885554444
No 87
>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=49.06 E-value=32 Score=20.46 Aligned_cols=37 Identities=27% Similarity=0.497 Sum_probs=24.6
Q ss_pred EEEEEccCC---CEEEEEEeCCchHHH--------HHHHHHhhcCCCC
Q 034926 23 NLKVKGQDG---NEVFFRIKRSTQLKK--------LMNAYCDRQSVEL 59 (78)
Q Consensus 23 ~lkV~~qdg---~~v~FkIK~~t~l~K--------Lm~aYc~r~gl~~ 59 (78)
.+-|.-.+| ..+.+.||....|.+ +-..||+++|++.
T Consensus 36 DFlv~~~~g~~~~~~~ieVK~~~~l~~~~~~~k~~~~~~y~~~~g~~f 83 (88)
T PF08722_consen 36 DFLVTYRDGNGKKPVAIEVKPSSELEKPRTKEKLEIEREYWEEQGIPF 83 (88)
T ss_dssp EEEEEESSS--SSEEEEEE--GGGGGSHHHHHHHHHHHHHHHHCT--E
T ss_pred cEEEEEccCCcceEEEEEEccHHHhcChhHHHHHHHHHHHHHHcCCeE
Confidence 344555566 888999999988876 6678899988764
No 88
>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=47.58 E-value=29 Score=21.55 Aligned_cols=22 Identities=23% Similarity=0.472 Sum_probs=16.0
Q ss_pred CCcEEEEEEccCCCEEEEEEeC
Q 034926 19 SAHINLKVKGQDGNEVFFRIKR 40 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~FkIK~ 40 (78)
...|.|-+.+.||+.|+++|-.
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 5689999999999999999864
No 89
>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=47.04 E-value=59 Score=19.14 Aligned_cols=37 Identities=16% Similarity=0.238 Sum_probs=32.0
Q ss_pred EEEEEccC---CCEEEEEEeCCchHHHHHHHHHhhcCCCC
Q 034926 23 NLKVKGQD---GNEVFFRIKRSTQLKKLMNAYCDRQSVEL 59 (78)
Q Consensus 23 ~lkV~~qd---g~~v~FkIK~~t~l~KLm~aYc~r~gl~~ 59 (78)
.|||-..+ +....+.|.++|.-..|..+-.++.+++.
T Consensus 4 ~lrV~~~~~~~~~~kti~v~~~tTa~~Vi~~~l~k~~l~~ 43 (90)
T smart00314 4 VLRVYVDDLPGGTYKTLRVSSRTTARDVIQQLLEKFHLTD 43 (90)
T ss_pred EEEEecccCCCCcEEEEEECCCCCHHHHHHHHHHHhCCCC
Confidence 45666666 88889999999999999999999999875
No 90
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles 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,
Probab=47.03 E-value=70 Score=19.96 Aligned_cols=53 Identities=15% Similarity=0.172 Sum_probs=39.4
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCC-CeEEEEE---CCEeeccee
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL-NSIAFLY---VHISAFLAW 75 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~-~s~rFlf---dG~rI~~~~ 75 (78)
|++|+. ..|.-+.+.+..++.+..|.+.-.+...+.. ..+...| +|..+..|+
T Consensus 1 i~~K~~-y~gdi~it~~d~~~s~e~L~~~v~~~c~~~~~q~ft~kw~DEEGDp~tiSS 57 (83)
T cd06404 1 VRVKAA-YNGDIMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKWIDEEGDPCTISS 57 (83)
T ss_pred CeEEEE-ecCcEEEEEcCCCcCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCceeecC
Confidence 456665 3778888899999999999888888877655 3666666 577777665
No 91
>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=46.67 E-value=54 Score=18.60 Aligned_cols=43 Identities=14% Similarity=0.050 Sum_probs=33.4
Q ss_pred EEEEEEeCCchHHHHHHHHHhhcC----CCCCeEEEEECCEeeccee
Q 034926 33 EVFFRIKRSTQLKKLMNAYCDRQS----VELNSIAFLYVHISAFLAW 75 (78)
Q Consensus 33 ~v~FkIK~~t~l~KLm~aYc~r~g----l~~~s~rFlfdG~rI~~~~ 75 (78)
+..+.+...+.+..|.+..+.+.+ .....+++..||..+....
T Consensus 17 ~~~~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~~~~ 63 (80)
T cd00754 17 EEELELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVRLDT 63 (80)
T ss_pred eEEEECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcCCCc
Confidence 356667678899999999988764 3567899999999987443
No 92
>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=45.49 E-value=32 Score=21.15 Aligned_cols=39 Identities=13% Similarity=0.397 Sum_probs=26.8
Q ss_pred EEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 36 FRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 36 FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
..+.+++.|+.|++..|++.......=....+|..++..
T Consensus 1 i~v~~~~TL~~lid~L~~~~~~qlk~PSlt~~~k~LYm~ 39 (84)
T PF08825_consen 1 IEVSPSWTLQDLIDSLCEKPEFQLKKPSLTTANKTLYMQ 39 (84)
T ss_dssp EEESTTSBSHHHHHHHHHSTTT--SS-EEESSEEEEEES
T ss_pred CCcCccchHHHHHHHHHhChhhhcCCCcccCCCceEEEe
Confidence 367889999999999999965444444444777777653
No 93
>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=44.94 E-value=28 Score=22.06 Aligned_cols=22 Identities=36% Similarity=0.637 Sum_probs=14.8
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCch
Q 034926 19 SAHINLKVKGQDGNEVFFRIKRSTQ 43 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~FkIK~~t~ 43 (78)
+.-++|+|. |.+|.|||.++.+
T Consensus 35 ~~F~~i~V~---g~avTFrv~~N~~ 56 (91)
T PF11548_consen 35 SSFINISVV---GPAVTFRVRPNNK 56 (91)
T ss_dssp GGEEEEEEE---TTEEEEEE---TT
T ss_pred ccceeeeec---CceEEEEeccCcC
Confidence 345888885 5899999999874
No 94
>PF05932 CesT: Tir chaperone protein (CesT) family; InterPro: IPR010261 This family consists of a number of bacterial sequences, which are highly similar to the Tir chaperone protein in Escherichia coli. In many Gram-negative bacteria, a key indicator of pathogenic potential is the possession of a specialised type III secretion system, which is utilised to deliver virulence effector proteins directly into the host cell cytosol. Many of the proteins secreted from such systems require small cytosolic chaperones to maintain the secreted substrates in a secretion-competent state. CesT serves a chaperone function for the enteropathogenic E. coli (EPEC) translocated intimin receptor (Tir) protein, which confers upon EPEC the ability to alter host cell morphology following intimate bacterial attachment [].; GO: 0009405 pathogenesis, 0050708 regulation of protein secretion, 0005737 cytoplasm; PDB: 1K3E_A 3KXY_E 1S28_C 1JYA_B 1K6Z_B 2BSH_A 2BSJ_B 2BHO_A 2BSI_B 3EPU_A ....
Probab=44.66 E-value=50 Score=19.58 Aligned_cols=29 Identities=14% Similarity=0.090 Sum_probs=21.6
Q ss_pred HHHHHHHhhcCC------CCCeEEEEECCEeecce
Q 034926 46 KLMNAYCDRQSV------ELNSIAFLYVHISAFLA 74 (78)
Q Consensus 46 KLm~aYc~r~gl------~~~s~rFlfdG~rI~~~ 74 (78)
+|++.+|++.|+ .-+...|.+||..+...
T Consensus 1 ~ll~~l~~~lgl~~l~~d~~g~~~l~~~~~~~~~~ 35 (119)
T PF05932_consen 1 QLLAELGERLGLPPLEFDEDGACSLTVDGDFLILE 35 (119)
T ss_dssp HHHHHHHHHHTCSCEESSTTSEEEEEETTTEEEEE
T ss_pred CHHHHHHHHhCCCCCCCCCCCEEEEEECCeEEEEE
Confidence 588999999998 35567778877666544
No 95
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=43.16 E-value=7.5 Score=27.98 Aligned_cols=23 Identities=13% Similarity=0.264 Sum_probs=18.6
Q ss_pred CCchHHHHHHHHHhhcCCCCCeE
Q 034926 40 RSTQLKKLMNAYCDRQSVELNSI 62 (78)
Q Consensus 40 ~~t~l~KLm~aYc~r~gl~~~s~ 62 (78)
+......||+|||+-.|.++..+
T Consensus 67 Pee~~~~IF~Alc~a~~~dp~~~ 89 (206)
T PLN03060 67 NATDRDAIFKAYIEALGEDPDQY 89 (206)
T ss_pred ChHHHHHHHHHHHHHcCCCHHHH
Confidence 55677899999999999887644
No 96
>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=42.76 E-value=1.2e+02 Score=21.70 Aligned_cols=45 Identities=13% Similarity=0.336 Sum_probs=32.7
Q ss_pred cEEEEEEccC---CCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEE
Q 034926 21 HINLKVKGQD---GNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFL 65 (78)
Q Consensus 21 ~I~lkV~~qd---g~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFl 65 (78)
.|.|++.... +....+.+-+.....-|-++-+++.|+++..+||.
T Consensus 176 rv~V~f~~~~~~~~~~F~l~ls~~~tY~~la~~Va~~l~~dP~~lr~~ 223 (249)
T PF12436_consen 176 RVEVEFKPKDNPNDPEFTLWLSKKMTYDQLAEKVAEHLNVDPEHLRFF 223 (249)
T ss_dssp EEEEEEEETTSTT---EEEEEETT--HHHHHHHHHHHHTS-GGGEEEE
T ss_pred eEEEEEEECCCCCCCCEEEEECCCCCHHHHHHHHHHHHCCChHHEEEE
Confidence 4666665522 34678889999999999999999999999999997
No 97
>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=42.43 E-value=15 Score=23.24 Aligned_cols=23 Identities=26% Similarity=0.644 Sum_probs=19.7
Q ss_pred HHHHHHHHHhhcCCCCCeEEE--EE
Q 034926 44 LKKLMNAYCDRQSVELNSIAF--LY 66 (78)
Q Consensus 44 l~KLm~aYc~r~gl~~~s~rF--lf 66 (78)
...||++|+++.+++.+.+.| .|
T Consensus 44 a~elm~~f~~~F~Vd~~~f~~~~YF 68 (111)
T PF07377_consen 44 AEELMEDFFERFNVDLSDFDFDRYF 68 (111)
T ss_pred HHHHHHHHHHHhCCCcCccCHHHcc
Confidence 456999999999999999887 55
No 98
>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=41.92 E-value=26 Score=20.27 Aligned_cols=16 Identities=19% Similarity=0.152 Sum_probs=12.6
Q ss_pred eEEEEECCEeecceee
Q 034926 61 SIAFLYVHISAFLAWA 76 (78)
Q Consensus 61 s~rFlfdG~rI~~~~~ 76 (78)
-++|.|.|.|..++..
T Consensus 12 ~i~F~y~G~R~re~l~ 27 (64)
T PF12167_consen 12 RIDFTYQGKRCRESLG 27 (64)
T ss_pred EEEEEECCEEEEEeCC
Confidence 4789999999877653
No 99
>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=41.24 E-value=76 Score=18.72 Aligned_cols=35 Identities=14% Similarity=0.077 Sum_probs=29.1
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhc
Q 034926 21 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQ 55 (78)
Q Consensus 21 ~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~ 55 (78)
...|.|+-.||..+.-+...+++|..|++.-....
T Consensus 4 ~~~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~ 38 (79)
T cd01772 4 ETRIQIRLLDGTTLKQTFKAREQLAAVRLFVELNT 38 (79)
T ss_pred EEEEEEECCCCCEEEEEeCCCChHHHHHHHHHHcC
Confidence 46777888899999989999999999998876543
No 100
>PHA01748 hypothetical protein
Probab=41.14 E-value=41 Score=19.26 Aligned_cols=26 Identities=15% Similarity=0.327 Sum_probs=22.2
Q ss_pred EEEEeCCchHHHHHHHHHhhcCCCCC
Q 034926 35 FFRIKRSTQLKKLMNAYCDRQSVELN 60 (78)
Q Consensus 35 ~FkIK~~t~l~KLm~aYc~r~gl~~~ 60 (78)
.+.|+-+..+..-++.||++.|.+.+
T Consensus 4 ~iSvrLp~el~~eld~~a~~~g~~RS 29 (60)
T PHA01748 4 VITFKIEEDLLELLDRYAIKHGLNRS 29 (60)
T ss_pred EEEEECCHHHHHHHHHHHHHhCCCHH
Confidence 57788889999999999999998643
No 101
>PF04881 Adeno_GP19K: Adenovirus GP19K; InterPro: IPR006965 This 19 kDa glycoprotein binds the major histocompatibility (MHC) class I antigens in the endoplasmic reticulum (ER). The ER retention signal at the C terminus of Gp19K causes retention of the complex in the ER, preventing lysis of the cell by cytotoxic T-lymphocytes [].; GO: 0005537 mannose binding, 0050690 regulation of defense response to virus by virus
Probab=40.57 E-value=35 Score=23.21 Aligned_cols=32 Identities=22% Similarity=0.394 Sum_probs=25.3
Q ss_pred CcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHh
Q 034926 20 AHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCD 53 (78)
Q Consensus 20 ~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~ 53 (78)
+--++.|++.||+- |+...+--+.=+|..+|+
T Consensus 48 ~~ytVtV~G~dGs~--~~~n~tf~~~FiF~~mCD 79 (139)
T PF04881_consen 48 EWYTVTVQGPDGSI--RKSNNTFMYKFIFYEMCD 79 (139)
T ss_pred cceEEEEECCCCcc--eeccccchheeeHHHHHH
Confidence 46789999999975 667766677778888886
No 102
>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=40.20 E-value=45 Score=21.77 Aligned_cols=28 Identities=4% Similarity=0.055 Sum_probs=23.1
Q ss_pred hHHHHHHHHHhhcCCCCCeEEEEECCEeec
Q 034926 43 QLKKLMNAYCDRQSVELNSIAFLYVHISAF 72 (78)
Q Consensus 43 ~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~ 72 (78)
.|++++++|++-.|++ ..-+-.+|..|+
T Consensus 9 ~lq~i~~~fs~~tgl~--~~i~d~~G~~l~ 36 (173)
T PF10114_consen 9 ELQEIQDSFSKATGLS--IVIVDPDGNPLT 36 (173)
T ss_pred HHHHHHHHHHHHHCCc--EEEEeCCCCEEe
Confidence 6889999999999988 555668999883
No 103
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=39.69 E-value=9.3 Score=27.66 Aligned_cols=23 Identities=17% Similarity=0.489 Sum_probs=18.5
Q ss_pred CCchHHHHHHHHHhhcCCCCCeE
Q 034926 40 RSTQLKKLMNAYCDRQSVELNSI 62 (78)
Q Consensus 40 ~~t~l~KLm~aYc~r~gl~~~s~ 62 (78)
+......||+|||+-.|.++..+
T Consensus 69 Pee~~~~IF~Alc~a~~~dp~~~ 91 (214)
T TIGR03060 69 PEEHLDALFDALCNSNGFDPEQL 91 (214)
T ss_pred ChHHHHHHHHHHHHhcCCCHHHH
Confidence 55677899999999999887543
No 104
>KOG3309 consensus Ferredoxin [Energy production and conversion]
Probab=39.49 E-value=89 Score=21.78 Aligned_cols=29 Identities=21% Similarity=0.266 Sum_probs=23.7
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHH
Q 034926 19 SAHINLKVKGQDGNEVFFRIKRSTQLKKL 47 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~FkIK~~t~l~KL 47 (78)
.+.|+|...+.||.++..+.+-...+-.+
T Consensus 41 ~e~i~Itfv~~dG~~~~i~g~vGdtlLd~ 69 (159)
T KOG3309|consen 41 VEDIKITFVDPDGEEIKIKGKVGDTLLDA 69 (159)
T ss_pred CceEEEEEECCCCCEEEeeeecchHHHHH
Confidence 34599999999999999998887766544
No 105
>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=39.18 E-value=46 Score=21.69 Aligned_cols=24 Identities=13% Similarity=0.232 Sum_probs=18.3
Q ss_pred HHHhhcCCC-CCeEEEEECCEeecc
Q 034926 50 AYCDRQSVE-LNSIAFLYVHISAFL 73 (78)
Q Consensus 50 aYc~r~gl~-~~s~rFlfdG~rI~~ 73 (78)
.++++.++. .-++.|++||+.|..
T Consensus 59 dva~~y~I~amPtfvffkngkh~~~ 83 (114)
T cd02986 59 VYTQYFDISYIPSTIFFFNGQHMKV 83 (114)
T ss_pred HHHHhcCceeCcEEEEEECCcEEEE
Confidence 467777865 667779999998853
No 106
>COG2080 CoxS Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]
Probab=39.08 E-value=1.3e+02 Score=20.80 Aligned_cols=49 Identities=16% Similarity=0.182 Sum_probs=37.1
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHh----hcCCC---CCeEEEEECCEeec
Q 034926 21 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCD----RQSVE---LNSIAFLYVHISAF 72 (78)
Q Consensus 21 ~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~----r~gl~---~~s~rFlfdG~rI~ 72 (78)
.|+++| +|..+...+-+.++|..+..-+-. +.|-. =+.-..++||+++.
T Consensus 3 ~i~ltv---NG~~~~~~~~p~~~Ll~~LRd~l~ltgtk~GC~~g~CGACtVlvDG~~v~ 58 (156)
T COG2080 3 PITLTV---NGEPVELDVDPRTPLLDVLRDELGLTGTKKGCGHGQCGACTVLVDGEAVN 58 (156)
T ss_pred cEEEEE---CCeEEEEEeCCCChHHHHHHHhcCCCCcCCCCCCccCCceEEEECCeEeh
Confidence 467776 788899999999999999887644 33322 34578899999875
No 107
>PRK13266 Thf1-like protein; Reviewed
Probab=38.54 E-value=9.9 Score=27.68 Aligned_cols=23 Identities=13% Similarity=0.358 Sum_probs=18.5
Q ss_pred CCchHHHHHHHHHhhcCCCCCeE
Q 034926 40 RSTQLKKLMNAYCDRQSVELNSI 62 (78)
Q Consensus 40 ~~t~l~KLm~aYc~r~gl~~~s~ 62 (78)
+......||+|||+-.|.++..+
T Consensus 69 Pee~~~~IF~Alc~a~~~dp~~~ 91 (225)
T PRK13266 69 PEEHKDSIFNALCQAVGFDPEQL 91 (225)
T ss_pred ChHHHHHHHHHHHHHcCCCHHHH
Confidence 55677899999999999887543
No 108
>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=37.42 E-value=1e+02 Score=19.18 Aligned_cols=39 Identities=18% Similarity=0.260 Sum_probs=26.3
Q ss_pred EEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeec
Q 034926 34 VFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAF 72 (78)
Q Consensus 34 v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~ 72 (78)
-.|+|..+.++..|..--+++.++..+.--|+|=.....
T Consensus 18 ~k~kI~~~~~f~~vi~fLrk~Lk~~~~~slFlYin~sFa 56 (87)
T PF04110_consen 18 KKFKISASQTFATVIAFLRKKLKLKPSDSLFLYINNSFA 56 (87)
T ss_dssp -EEEEETTSBTHHHHHHHHHHCT----SS-EEEEEEEE-
T ss_pred cEEEECCCCchHHHHHHHHHHhCCccCCeEEEEEcCccC
Confidence 379999999999999999999988666666666444433
No 109
>PF11264 ThylakoidFormat: Thylakoid formation protein; InterPro: IPR017499 Psp29, originally designated sll1414 (P73956 from SWISSPROT) in Synechocystis sp. (strain PCC 6803), is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.; GO: 0010027 thylakoid membrane organization, 0015979 photosynthesis, 0009523 photosystem II
Probab=37.29 E-value=11 Score=27.24 Aligned_cols=23 Identities=13% Similarity=0.302 Sum_probs=18.4
Q ss_pred CCchHHHHHHHHHhhcCCCCCeE
Q 034926 40 RSTQLKKLMNAYCDRQSVELNSI 62 (78)
Q Consensus 40 ~~t~l~KLm~aYc~r~gl~~~s~ 62 (78)
+......||+|||+-.|.++..+
T Consensus 64 p~~~~~~If~Alc~a~~~dp~~~ 86 (216)
T PF11264_consen 64 PEEDKDSIFNALCQALGFDPEQY 86 (216)
T ss_pred ChhHHHHHHHHHHHHcCCCHHHH
Confidence 55667889999999999887654
No 110
>PTZ00490 Ferredoxin superfamily; Provisional
Probab=37.22 E-value=74 Score=21.43 Aligned_cols=29 Identities=17% Similarity=0.256 Sum_probs=23.0
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHH
Q 034926 19 SAHINLKVKGQDGNEVFFRIKRSTQLKKL 47 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~FkIK~~t~l~KL 47 (78)
...++|.+.++||.+..+.+...+.|-..
T Consensus 33 ~g~v~I~~~~~dG~~~~v~~~~G~sLLea 61 (143)
T PTZ00490 33 PGKVKVCVKKRDGTHCDVEVPVGMSLMHA 61 (143)
T ss_pred CCcEEEEEEcCCCCEEEEEECCCccHHHH
Confidence 45899999999998888888877665443
No 111
>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=36.60 E-value=80 Score=27.66 Aligned_cols=34 Identities=18% Similarity=0.179 Sum_probs=30.7
Q ss_pred EEEEEEeCCchHHHHHHHHHhhcCCCCCe-EEEEE
Q 034926 33 EVFFRIKRSTQLKKLMNAYCDRQSVELNS-IAFLY 66 (78)
Q Consensus 33 ~v~FkIK~~t~l~KLm~aYc~r~gl~~~s-~rFlf 66 (78)
-.+|+||+++++.-|++.-++..+.+... +|+++
T Consensus 585 l~qf~iKr~akisdl~~~iae~ln~pqs~~~r~w~ 619 (1089)
T COG5077 585 LAQFVIKRGAKISDLRNNIAEHLNTPQSLYLREWT 619 (1089)
T ss_pred ceeEEeecCCCHHHHHHHHHHHcCCCceeeeEEEE
Confidence 35899999999999999999999999888 88876
No 112
>KOG0003 consensus Ubiquitin/60s ribosomal protein L40 fusion [Translation, ribosomal structure and biogenesis]
Probab=35.71 E-value=19 Score=24.01 Aligned_cols=46 Identities=7% Similarity=0.158 Sum_probs=39.3
Q ss_pred ccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecc
Q 034926 28 GQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFL 73 (78)
Q Consensus 28 ~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~ 73 (78)
.-.|..++..+-++.....|.-.--++.|++++..|+.|+|+.+.-
T Consensus 7 ~~~GKT~~le~EpS~ti~~vKA~i~~~~Gi~~~~~~L~~~~k~LED 52 (128)
T KOG0003|consen 7 TLTGKTITLEVEPSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLED 52 (128)
T ss_pred EeeCceEEEEecccchHHHHHHHhccccCCCHHHHHHHhccccccc
Confidence 3457888899999999998888888899999999999999987653
No 113
>PF03857 Colicin_im: Colicin immunity protein; InterPro: IPR005557 Colicin immunity proteins are plasmid encoded proteins necessary for protecting the cell against colicins. Colicins are toxins released by bacteria during times of stress [].; GO: 0015643 toxin binding, 0030153 bacteriocin immunity
Probab=35.47 E-value=25 Score=23.93 Aligned_cols=14 Identities=36% Similarity=0.852 Sum_probs=11.9
Q ss_pred CchHHHHHHHHHhh
Q 034926 41 STQLKKLMNAYCDR 54 (78)
Q Consensus 41 ~t~l~KLm~aYc~r 54 (78)
+-.|.++|+.||+-
T Consensus 23 nP~mS~lm~~YcKt 36 (138)
T PF03857_consen 23 NPPMSKLMDLYCKT 36 (138)
T ss_pred CchHHHHHHHHHhh
Confidence 56799999999974
No 114
>KOG2378 consensus cAMP-regulated guanine nucleotide exchange factor [Signal transduction mechanisms]
Probab=35.28 E-value=1.9e+02 Score=23.80 Aligned_cols=57 Identities=16% Similarity=0.110 Sum_probs=47.4
Q ss_pred CCCCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCC--CeEEEEECCEeecc
Q 034926 17 DQSAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVEL--NSIAFLYVHISAFL 73 (78)
Q Consensus 17 ~~~~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~--~s~rFlfdG~rI~~ 73 (78)
-+++.|.-+|--.|-+.+..+++-++.-+.++.+-+++.|.+. .-+...+.|..+-+
T Consensus 231 ~~sDev~~~vy~~Dhsy~tl~~~vs~svqEI~~~va~k~~~seel~LV~v~s~GEkv~l 289 (573)
T KOG2378|consen 231 RGSDEVFCIVYLPDHSYVTLRIRVSASVQEILEAVAEKLGYSEELILVKVSSSGEKVIL 289 (573)
T ss_pred cCCCeeeEEEEecCceEEEEEeechhHHHHHHHHHHHHhccccceeEEEEccCCceeee
Confidence 3456789999999999999999999999999999999988654 45666778877654
No 115
>TIGR02777 LigD_PE_dom DNA ligase D, 3'-phosphoesterase domain. Most sequences in this family are the 3'-phosphoesterase domain of a multidomain, multifunctional DNA ligase, LigD, involved, along with bacterial Ku protein, in non-homologous end joining, the less common of two general mechanisms of repairing double-stranded breaks in DNA sequences. LigD is variable in architecture, as it lacks this domain in Bacillus subtilis, is permuted in Mycobacterium tuberculosis, and occasionally is encoded by tandem ORFs rather than as a multifuntional protein. In a few species (Dehalococcoides ethenogenes and the archaeal genus Methanosarcina), sequences corresponding to the ligase and polymerase domains of LigD are not found, and the role of this protein is unclear.
Probab=35.15 E-value=38 Score=23.51 Aligned_cols=24 Identities=13% Similarity=0.243 Sum_probs=20.7
Q ss_pred cCCCCCeEEEEECCEeecceeecC
Q 034926 55 QSVELNSIAFLYVHISAFLAWAVI 78 (78)
Q Consensus 55 ~gl~~~s~rFlfdG~rI~~~~~~~ 78 (78)
.++..+.+.|.+.|+++...|+.+
T Consensus 114 ~~l~~G~l~f~L~G~kl~G~~~Lv 137 (156)
T TIGR02777 114 KALKKGHLKFELHGEKLKGGWALV 137 (156)
T ss_pred hcccCCeEEEEEeceEEeeEEEEE
Confidence 467788999999999999999853
No 116
>PRK01076 L-rhamnose isomerase; Provisional
Probab=34.91 E-value=31 Score=27.43 Aligned_cols=21 Identities=24% Similarity=0.559 Sum_probs=18.5
Q ss_pred CCchHHHHHHHHHhhcCCCCC
Q 034926 40 RSTQLKKLMNAYCDRQSVELN 60 (78)
Q Consensus 40 ~~t~l~KLm~aYc~r~gl~~~ 60 (78)
++-|+.-+.+-||.+.|++.+
T Consensus 380 k~~p~g~vwd~~c~~~~vp~~ 400 (419)
T PRK01076 380 KSLPWGAVWDMYCQRHDVPVG 400 (419)
T ss_pred hcCChHHHHHHHHHhcCCCCc
Confidence 467999999999999999865
No 117
>TIGR01748 rhaA L-rhamnose isomerase. This enzyme interconverts L-rhamnose and L-rhamnulose. In some species, including E. 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. Characterization of this family is based on members in E. coli and Salmonella.
Probab=34.51 E-value=31 Score=27.38 Aligned_cols=21 Identities=24% Similarity=0.608 Sum_probs=18.5
Q ss_pred CCchHHHHHHHHHhhcCCCCC
Q 034926 40 RSTQLKKLMNAYCDRQSVELN 60 (78)
Q Consensus 40 ~~t~l~KLm~aYc~r~gl~~~ 60 (78)
++-|+.-+.+.||.+.|++.+
T Consensus 376 k~~p~gavw~~~c~~~~vp~~ 396 (414)
T TIGR01748 376 KSLPFGAVWEMYCERHGVPVG 396 (414)
T ss_pred hcCChHHHHHHHHHHcCCCCc
Confidence 477999999999999999865
No 118
>PF10646 Germane: Sporulation and spore germination; InterPro: IPR019606 The GerMN domain is a region of approximately 100 residues that is found, duplicated, in the Bacillus GerM protein and is implicated in both sporulation and spore germination. It is also found in lipoprotein LpqB. The domain is present in a number of different bacterial species both alone and in association with other domains such as Gmad1 and Gmad2. It is predicted to have a novel alpha-beta fold.
Probab=34.38 E-value=42 Score=20.45 Aligned_cols=18 Identities=11% Similarity=0.159 Sum_probs=15.3
Q ss_pred CCCeEEEEECCEeeccee
Q 034926 58 ELNSIAFLYVHISAFLAW 75 (78)
Q Consensus 58 ~~~s~rFlfdG~rI~~~~ 75 (78)
..+.++|+.||+.+..=|
T Consensus 100 ~v~~V~i~vdG~~~~~l~ 117 (117)
T PF10646_consen 100 GVKKVQILVDGKPLESLW 117 (117)
T ss_pred CccEEEEEECCEEcCccC
Confidence 388999999999987655
No 119
>cd03489 Topoisomer_IB_N_LdtopoI_like Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I differ from human
Probab=33.68 E-value=26 Score=25.49 Aligned_cols=17 Identities=18% Similarity=0.059 Sum_probs=15.1
Q ss_pred CCeEEEEECCEeeccee
Q 034926 59 LNSIAFLYVHISAFLAW 75 (78)
Q Consensus 59 ~~s~rFlfdG~rI~~~~ 75 (78)
+..+.|+|||+.|.++.
T Consensus 18 P~~Vk~~YdG~pv~L~p 34 (212)
T cd03489 18 PHGIPILYNGQPFDMTP 34 (212)
T ss_pred CCCccEeECCeECcCCH
Confidence 68899999999999874
No 120
>KOG1529 consensus Mercaptopyruvate sulfurtransferase/thiosulfate sulfurtransferase [Defense mechanisms]
Probab=33.14 E-value=57 Score=24.69 Aligned_cols=26 Identities=15% Similarity=0.275 Sum_probs=23.3
Q ss_pred hHHHHHHHHHhhcCCCCCeEEEEECC
Q 034926 43 QLKKLMNAYCDRQSVELNSIAFLYVH 68 (78)
Q Consensus 43 ~l~KLm~aYc~r~gl~~~s~rFlfdG 68 (78)
+-...|..||++.|++.++-...||+
T Consensus 69 p~~e~Fa~y~~~lGi~n~d~vViYd~ 94 (286)
T KOG1529|consen 69 PTAEHFAEYASRLGVDNGDHVVIYDR 94 (286)
T ss_pred ccHHHHHHHHHhcCCCCCCeEEEEcC
Confidence 34489999999999999999999987
No 121
>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=32.87 E-value=1e+02 Score=17.81 Aligned_cols=34 Identities=9% Similarity=0.017 Sum_probs=25.7
Q ss_pred eCCchHHHHHHHHHhhcC-CCCCeEEEE--ECCEeec
Q 034926 39 KRSTQLKKLMNAYCDRQS-VELNSIAFL--YVHISAF 72 (78)
Q Consensus 39 K~~t~l~KLm~aYc~r~g-l~~~s~rFl--fdG~rI~ 72 (78)
-.++....|.++++++.+ .+.+..|+. +.|..|.
T Consensus 20 ~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~~~~g~~L~ 56 (77)
T cd01801 20 SGDATIADLKKLIAKSSPQLTVNRQSLRLEPKGKSLK 56 (77)
T ss_pred CCCccHHHHHHHHHHHcCCCCcceeEEEeCCCCcccC
Confidence 366789999999999875 567887775 6676554
No 122
>cd00660 Topoisomer_IB_N Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I diffe
Probab=32.80 E-value=25 Score=25.60 Aligned_cols=17 Identities=18% Similarity=0.139 Sum_probs=14.3
Q ss_pred CCeEEEEECCEeeccee
Q 034926 59 LNSIAFLYVHISAFLAW 75 (78)
Q Consensus 59 ~~s~rFlfdG~rI~~~~ 75 (78)
+..+.|+|||+.|.++-
T Consensus 20 P~~Vk~~YdG~pv~L~p 36 (215)
T cd00660 20 PKNVKFYYDGKPVKLPP 36 (215)
T ss_pred cCCCCEEECCEECcCCH
Confidence 45899999999999863
No 123
>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=32.62 E-value=47 Score=18.73 Aligned_cols=33 Identities=12% Similarity=0.176 Sum_probs=25.3
Q ss_pred CCchHHHHHHHHHhhcCCCCCeEEEEE--CCEeecc
Q 034926 40 RSTQLKKLMNAYCDRQSVELNSIAFLY--VHISAFL 73 (78)
Q Consensus 40 ~~t~l~KLm~aYc~r~gl~~~s~rFlf--dG~rI~~ 73 (78)
....|..|++.-.++.+++.+ +|=+| ||++|.-
T Consensus 7 ~~~s~e~lL~~it~~v~l~~g-Vr~lyt~~G~~V~~ 41 (60)
T PF03607_consen 7 RFRSFEQLLDEITEKVQLPSG-VRKLYTLDGKRVKS 41 (60)
T ss_dssp THSSHHHHHHHHHHSSSSTTS--SEEEETTSSEESS
T ss_pred hhcCHHHHHHHHHhhcCCCcc-cceEECCCCCEeCC
Confidence 345788999999999999877 77666 8988853
No 124
>KOG2523 consensus Predicted RNA-binding protein with PUA domain [Translation, ribosomal structure and biogenesis]
Probab=32.56 E-value=87 Score=22.22 Aligned_cols=51 Identities=22% Similarity=0.377 Sum_probs=36.9
Q ss_pred CcEEEEEEccCCCEEEEEEeCC--chHHHHHHHHH---hhcCCCCCeEEEEECCEeec
Q 034926 20 AHINLKVKGQDGNEVFFRIKRS--TQLKKLMNAYC---DRQSVELNSIAFLYVHISAF 72 (78)
Q Consensus 20 ~~I~lkV~~qdg~~v~FkIK~~--t~l~KLm~aYc---~r~gl~~~s~rFlfdG~rI~ 72 (78)
+||.|-.. +|..++|..... -|=-+|...|- -++.+|.+.++|+..|..|.
T Consensus 57 d~i~L~s~--~G~~~fF~~~dg~~~PTLRllhk~p~~~~~~qvD~GAIkfvlsGAnIM 112 (181)
T KOG2523|consen 57 DHIELLSV--NGEVLFFCHRDGPYIPTLRLLHKYPFIFPHVQVDRGAIKFVLSGANIM 112 (181)
T ss_pred CeeEEEEe--CCEEEEEEecCCCccchhHHHhhCCCccceEEecCcceeeeecCCceE
Confidence 45666555 488889988763 44556666664 36779999999999998774
No 125
>PF02919 Topoisom_I_N: Eukaryotic DNA topoisomerase I, DNA binding fragment; InterPro: IPR008336 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the N-terminal DNA-binding domain found in eukaryotic topoisomerase I, which is a type IB enzymes. To cleave the DNA backbone, these enzymes must make a transient phosphotyrosine bond. The N-terminal domain of human topoisomerase I is thought to coordinate the restriction of free strand rotation during the topoisomerisation step of catalysis. A conserved tryptophan residue may be important for the DNA-interaction ability of the N-terminal domain []. Human topoisomerase I has been shown to be inhibited by camptothecin (CPT), a plant alkaloid with antitumour activity. A binding mode for the anticancer drug camptothecin has been proposed on the basis of chemical and biochemical information combined with the three-dimensional structures of topoisomerase I-DNA complexes []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003917 DNA topoisomerase type I activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1TL8_A 1K4T_A 1A36_A 1RR8_C 1T8I_A 1SC7_A 1EJ9_A 1LPQ_A 1RRJ_A 1A31_A ....
Probab=32.36 E-value=22 Score=25.87 Aligned_cols=17 Identities=18% Similarity=0.153 Sum_probs=10.6
Q ss_pred CCeEEEEECCEeeccee
Q 034926 59 LNSIAFLYVHISAFLAW 75 (78)
Q Consensus 59 ~~s~rFlfdG~rI~~~~ 75 (78)
+..+.|+|||+.|.++-
T Consensus 21 P~~V~~~YdGkpv~L~p 37 (215)
T PF02919_consen 21 PHGVKFYYDGKPVKLSP 37 (215)
T ss_dssp -TTS-EEETTEEE---H
T ss_pred CCCccEEECCEEeecCH
Confidence 56789999999999874
No 126
>KOG4248 consensus Ubiquitin-like protein, regulator of apoptosis [Posttranslational modification, protein turnover, chaperones]
Probab=32.01 E-value=1.1e+02 Score=27.35 Aligned_cols=52 Identities=15% Similarity=0.099 Sum_probs=46.0
Q ss_pred EEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecc
Q 034926 22 INLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFL 73 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~ 73 (78)
++++|+.-|..+-.|.|.--...+.+.+.-....++....=|+.|.|+-|--
T Consensus 3 ~~v~vktld~r~~t~~ig~q~ti~~~~d~~r~~~ni~s~~qr~i~~grvl~~ 54 (1143)
T KOG4248|consen 3 PNVLVKTLDSRTRTFIIGAQMTIKEFKDHIRASVNIPSEKQRLIYQGRVLQD 54 (1143)
T ss_pred cceeeeecccceeEEEechHHHHHHHHHHHHHhcccccccceeeecceeecc
Confidence 4577777788888999999999999999999999999999999999987643
No 127
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=31.98 E-value=63 Score=17.59 Aligned_cols=26 Identities=8% Similarity=0.118 Sum_probs=20.3
Q ss_pred hHHHHHHHHHhhcCCCCCeEEEEECC
Q 034926 43 QLKKLMNAYCDRQSVELNSIAFLYVH 68 (78)
Q Consensus 43 ~l~KLm~aYc~r~gl~~~s~rFlfdG 68 (78)
=.++|-++.++..|.+.+.++.+|+.
T Consensus 19 l~~~it~~~~~~lg~~~~~i~V~i~E 44 (60)
T PF01361_consen 19 LAEAITDAVVEVLGIPPERISVVIEE 44 (60)
T ss_dssp HHHHHHHHHHHHHTS-GGGEEEEEEE
T ss_pred HHHHHHHHHHHHhCcCCCeEEEEEEE
Confidence 35667788889999999999988764
No 128
>PRK02853 hypothetical protein; Provisional
Probab=31.95 E-value=1.4e+02 Score=20.83 Aligned_cols=31 Identities=19% Similarity=0.457 Sum_probs=19.2
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHH
Q 034926 21 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAY 51 (78)
Q Consensus 21 ~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aY 51 (78)
.+.+-|.+.+|..+.--+=.-+||+++.+-|
T Consensus 65 rLvfdI~~e~~~~~~~~~LsL~PfRrvvKDY 95 (161)
T PRK02853 65 RLVFDIRREDGEPVATHILSLTPFRRVVKDY 95 (161)
T ss_pred eeEEEecCCCCCeeeEEEeccccHHHHHHHH
Confidence 3444455555555433333468999999998
No 129
>cd03488 Topoisomer_IB_N_htopoI_like Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain.
Probab=31.87 E-value=26 Score=25.47 Aligned_cols=17 Identities=18% Similarity=0.155 Sum_probs=14.4
Q ss_pred CCeEEEEECCEeeccee
Q 034926 59 LNSIAFLYVHISAFLAW 75 (78)
Q Consensus 59 ~~s~rFlfdG~rI~~~~ 75 (78)
+..+.|+|||+.|.++-
T Consensus 20 P~~Vk~~YdG~pv~L~p 36 (215)
T cd03488 20 PKNVKFYYDGKPVKLSP 36 (215)
T ss_pred CCCCCEEECCEECcCCH
Confidence 45799999999999863
No 130
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=31.83 E-value=1.3e+02 Score=18.75 Aligned_cols=52 Identities=10% Similarity=-0.005 Sum_probs=32.0
Q ss_pred EEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEE---CCEeeccee
Q 034926 23 NLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLY---VHISAFLAW 75 (78)
Q Consensus 23 ~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlf---dG~rI~~~~ 75 (78)
+.||. .+|..-+|..-..-.+..|.+.-+.-..++..++-..| ||.-|++++
T Consensus 2 ~fKv~-~~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~~~~vtYiDeD~D~ITlss 56 (82)
T cd06397 2 QFKSS-FLGDTRRIVFPDIPTWEALASKLENLYNLPEIKVGVTYIDNDNDEITLSS 56 (82)
T ss_pred eEEEE-eCCceEEEecCCCccHHHHHHHHHHHhCCChhHeEEEEEcCCCCEEEecc
Confidence 44553 34445566666666677777777776777766666666 556666554
No 131
>cd03490 Topoisomer_IB_N_1 Topoisomer_IB_N_1: A subgroup of the N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB. Topo IB proteins include the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanoso
Probab=31.42 E-value=29 Score=25.28 Aligned_cols=17 Identities=12% Similarity=0.176 Sum_probs=15.2
Q ss_pred CCeEEEEECCEeeccee
Q 034926 59 LNSIAFLYVHISAFLAW 75 (78)
Q Consensus 59 ~~s~rFlfdG~rI~~~~ 75 (78)
+..+.|+|||+.|.++.
T Consensus 18 P~~Vk~~YdG~pv~L~p 34 (217)
T cd03490 18 PHNVPIMYKGETIHLPP 34 (217)
T ss_pred CCCccEeECCeECcCCH
Confidence 68899999999999874
No 132
>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=31.22 E-value=1.3e+02 Score=18.52 Aligned_cols=34 Identities=15% Similarity=0.173 Sum_probs=31.3
Q ss_pred EEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEE
Q 034926 33 EVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLY 66 (78)
Q Consensus 33 ~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlf 66 (78)
.|-.++.+..++..|-..-+++..++.....+.|
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 4667899999999999999999999999999988
No 133
>PF03479 DUF296: Domain of unknown function (DUF296); InterPro: IPR005175 This putative conserved domain is found in proteins that contain AT-hook motifs IPR000637 from INTERPRO, suggesting a DNA-binding function for the proteins as a whole, however, the function of this domain is unknown. Overexpression of a protein containing this domain, Q9S7C9 from SWISSPROT, in Arabidopsis thaliana causes late flowering and modified leaf development []. ; PDB: 2DT4_A 2P6Y_A 3HWU_A 3HTN_A 2NMU_A 2H6L_A 2HX0_A.
Probab=30.41 E-value=1.2e+02 Score=19.12 Aligned_cols=31 Identities=13% Similarity=0.293 Sum_probs=25.7
Q ss_pred CEEEEEEeCCchHHHHHHHHHhhcCCCCCeE
Q 034926 32 NEVFFRIKRSTQLKKLMNAYCDRQSVELNSI 62 (78)
Q Consensus 32 ~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~ 62 (78)
+.+.+++.+...+-.=+.++|+..++....+
T Consensus 2 r~~~~rl~~Gedl~~~l~~~~~~~~i~~~~i 32 (120)
T PF03479_consen 2 RVFVIRLDPGEDLLESLEAFAREHGIRSGVI 32 (120)
T ss_dssp EEEEEEEETTSBHHHHHHHHHHHHT-SSEEE
T ss_pred cEEEEEECCCCHHHHHHHHHHHHCCCcEEEE
Confidence 4568899999999999999999999876554
No 134
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=30.07 E-value=44 Score=19.08 Aligned_cols=17 Identities=41% Similarity=0.833 Sum_probs=13.2
Q ss_pred EeCCchHHHHHHHHHhh
Q 034926 38 IKRSTQLKKLMNAYCDR 54 (78)
Q Consensus 38 IK~~t~l~KLm~aYc~r 54 (78)
+..+-.|...|.+||..
T Consensus 5 ~~~dpELDqFMeaYc~~ 21 (52)
T PF03791_consen 5 IGADPELDQFMEAYCDM 21 (52)
T ss_pred CCCCccHHHHHHHHHHH
Confidence 34566788999999974
No 135
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=29.78 E-value=17 Score=27.49 Aligned_cols=23 Identities=9% Similarity=0.160 Sum_probs=18.3
Q ss_pred CCchHHHHHHHHHhhcCCCCCeE
Q 034926 40 RSTQLKKLMNAYCDRQSVELNSI 62 (78)
Q Consensus 40 ~~t~l~KLm~aYc~r~gl~~~s~ 62 (78)
+......||+|||+-.|.++..+
T Consensus 120 Pee~~~~IF~Alc~a~g~Dp~qy 142 (283)
T PLN00047 120 SDEDRDAIFKAYIKALGEDPEQY 142 (283)
T ss_pred ChHHHHHHHHHHHHHcCCCHHHH
Confidence 45677889999999999887543
No 136
>PRK07738 flagellar protein FlaG; Provisional
Probab=29.31 E-value=1.7e+02 Score=19.18 Aligned_cols=38 Identities=18% Similarity=0.180 Sum_probs=29.4
Q ss_pred CCcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCC
Q 034926 19 SAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSV 57 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl 57 (78)
.+.+-++|.|.+..+|- |=-+...+-+|+..-++..|+
T Consensus 74 t~~~vVkVvD~~T~EVI-RQIPpEe~L~l~~~m~e~~Gl 111 (117)
T PRK07738 74 LNEYYVQVVDERTNEVI-REIPPKKLLDMYAAMMEFVGL 111 (117)
T ss_pred CCcEEEEEEECCCCeee-eeCCCHHHHHHHHHHHHHhcc
Confidence 46788999998888754 444678888888888888775
No 137
>PF05688 DUF824: Salmonella repeat of unknown function (DUF824); InterPro: IPR008542 This family consists of a series of repeated sequences (of around 180 residues) which are found in Salmonella typhimurium, Salmonella typhi and Escherichia coli. These repeats are almost always found with this entry. The repeats are associated with RatA and RatB, the coding sequences of which are found in the pathogeneicity island of Salmonella. The sequences may be determinants of pathogenicity [, ].
Probab=28.94 E-value=56 Score=18.19 Aligned_cols=24 Identities=29% Similarity=0.484 Sum_probs=15.7
Q ss_pred cEEEEEEccCCCEE---EEEEeCCchH
Q 034926 21 HINLKVKGQDGNEV---FFRIKRSTQL 44 (78)
Q Consensus 21 ~I~lkV~~qdg~~v---~FkIK~~t~l 44 (78)
.++|.+.|.+|+-+ .|.|++....
T Consensus 16 ~ltVt~kda~G~pv~n~~f~l~r~~~~ 42 (47)
T PF05688_consen 16 PLTVTVKDANGNPVPNAPFTLTRGDAK 42 (47)
T ss_pred EEEEEEECCCCCCcCCceEEEEecCcc
Confidence 45555667667654 8888876543
No 138
>KOG0001 consensus Ubiquitin and ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=28.87 E-value=95 Score=16.16 Aligned_cols=48 Identities=13% Similarity=0.222 Sum_probs=40.4
Q ss_pred EEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeec
Q 034926 25 KVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAF 72 (78)
Q Consensus 25 kV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~ 72 (78)
.|....|....+.+.....+.-+-...+...|.+...-++.+-|..+.
T Consensus 3 ~~~~~~gk~~~~~~~~~~~i~~~k~~i~~~~~~~~~~q~~~~~~~~l~ 50 (75)
T KOG0001|consen 3 FVKTLDGKTITLEVSPSDTIEVVKAKIRDKEGIPVDQQRLIFGGKPLE 50 (75)
T ss_pred EEEecCCCEEEEEecCCCHHHHHHHHHHhhcCCCCeeEEEEECCEECc
Confidence 445567888899999999999997788888999999999888887765
No 139
>PRK12633 flgD flagellar basal body rod modification protein; Provisional
Probab=28.78 E-value=1.7e+02 Score=21.00 Aligned_cols=21 Identities=19% Similarity=0.365 Sum_probs=16.1
Q ss_pred CCCcEEEEEEccCCCEEE-EEE
Q 034926 18 QSAHINLKVKGQDGNEVF-FRI 38 (78)
Q Consensus 18 ~~~~I~lkV~~qdg~~v~-FkI 38 (78)
+...++|.|.|.+|+.|+ +.+
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 345799999999999874 444
No 140
>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A.
Probab=28.31 E-value=1.7e+02 Score=18.76 Aligned_cols=53 Identities=21% Similarity=0.184 Sum_probs=39.6
Q ss_pred cEEEEEEccCCC-EEEEEEeCCchHHHHHHHHHhhc-------CCCCCeEEEEECCEeecc
Q 034926 21 HINLKVKGQDGN-EVFFRIKRSTQLKKLMNAYCDRQ-------SVELNSIAFLYVHISAFL 73 (78)
Q Consensus 21 ~I~lkV~~qdg~-~v~FkIK~~t~l~KLm~aYc~r~-------gl~~~s~rFlfdG~rI~~ 73 (78)
.|+||.+-.+|. ...|..-.++.-..|.+.--..- -.+.+.+|++|.|+-|.-
T Consensus 2 ~i~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d 62 (111)
T PF13881_consen 2 KIELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILED 62 (111)
T ss_dssp SEEEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-S
T ss_pred eEEEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCC
Confidence 588999888999 67999999999999988875321 235778999999996653
No 141
>cd07079 ALDH_F18-19_ProA-GPR Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19. Gamma-glutamyl phosphate reductase (GPR), a L-proline biosynthetic pathway (PBP) enzyme that catalyzes the NADPH dependent reduction of L-gamma-glutamyl 5-phosphate into L-glutamate 5-semialdehyde and phosphate. The glutamate route of the PBP involves two enzymatic steps catalyzed by gamma-glutamyl kinase (GK, EC 2.7.2.11) and GPR (EC 1.2.1.41). These enzymes are fused into the bifunctional enzyme, ProA or delta(1)-pyrroline-5-carboxylate synthetase (P5CS) in plants and animals, whereas they are separate enzymes in bacteria and yeast. In humans, the P5CS (ALDH18A1), an inner mitochondrial membrane enzyme, is essential to the de novo synthesis of the amino acids proline and arginine. Tomato (Lycopersicon esculentum) has both the prokaryotic-like polycistronic operons encoding GK and GPR (PRO1, ALDH19) and the full-length, bifunctional P5CS (PRO2, ALDH18B1).
Probab=27.66 E-value=1.3e+02 Score=22.97 Aligned_cols=38 Identities=13% Similarity=0.247 Sum_probs=33.0
Q ss_pred CCCEEEEEEeCCch-----HHHHHHHHHhhcCCCCCeEEEEEC
Q 034926 30 DGNEVFFRIKRSTQ-----LKKLMNAYCDRQSVELNSIAFLYV 67 (78)
Q Consensus 30 dg~~v~FkIK~~t~-----l~KLm~aYc~r~gl~~~s~rFlfd 67 (78)
-|+.|.+|--..|+ |.+++..|+...|++.+.+.++..
T Consensus 134 aGN~vVlKps~~tp~~~~~l~~~~~~~l~~aG~P~gvv~~v~g 176 (406)
T cd07079 134 SGNAVILRGGSEALHSNRALVEIIQEALEEAGLPEDAVQLIPD 176 (406)
T ss_pred hCCEEEEeCCchhhhHHHHHHHHHHHHHHHcCCCcccEEEecC
Confidence 58898888777776 688899999999999999999984
No 142
>PF02599 CsrA: Global regulator protein family; InterPro: IPR003751 The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay []. CsrA is entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single RNA, CsrB. CsrA binds to the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [].; GO: 0003723 RNA binding, 0006109 regulation of carbohydrate metabolic process, 0006402 mRNA catabolic process; PDB: 1Y00_B 2JPP_A 1T3O_A 1VPZ_A.
Probab=27.26 E-value=1.1e+02 Score=17.34 Aligned_cols=22 Identities=23% Similarity=0.321 Sum_probs=17.6
Q ss_pred CCcEEEEEEccCCCEEEEEEeC
Q 034926 19 SAHINLKVKGQDGNEVFFRIKR 40 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~FkIK~ 40 (78)
++.|.|+|.+-+|+.|.+-|..
T Consensus 15 g~~I~I~Vl~i~~~~VklgI~A 36 (54)
T PF02599_consen 15 GDDIEITVLEISGGQVKLGIDA 36 (54)
T ss_dssp TTTEEEEEEEEETTEEEEEEEE
T ss_pred CCCEEEEEEEEcCCEEEEEEEC
Confidence 4589999999889988777653
No 143
>PRK06655 flgD flagellar basal body rod modification protein; Reviewed
Probab=27.07 E-value=2e+02 Score=20.61 Aligned_cols=20 Identities=10% Similarity=0.331 Sum_probs=15.2
Q ss_pred CCcEEEEEEccCCCEEE-EEE
Q 034926 19 SAHINLKVKGQDGNEVF-FRI 38 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~-FkI 38 (78)
...++|.|.|.+|+.|+ +.+
T Consensus 125 a~~vti~I~D~~G~~Vrt~~l 145 (225)
T PRK06655 125 ADNVTVTITDSAGQVVRTIDL 145 (225)
T ss_pred CcEEEEEEEcCCCCEEEEEec
Confidence 34699999999998874 443
No 144
>PF12347 HJURP_C: Holliday junction regulator protein family C-terminal repeat; InterPro: IPR022102 Although this family is conserved in the Holliday junction regulator, HJURP, proteins in higher eukaryotes, alongside an Scm3, PF10384 from PFAM, family, its exact function is not known. The C-terminal region of Scm3 proteins has been evolving rapidly, and this short repeat at the C-terminal end can be present in up to two copies in the higher eukaryotes. ; PDB: 3P57_A 3KOV_A.
Probab=26.93 E-value=21 Score=20.92 Aligned_cols=21 Identities=19% Similarity=0.373 Sum_probs=0.0
Q ss_pred CchHHHHHHHHHhhcCCCCCe
Q 034926 41 STQLKKLMNAYCDRQSVELNS 61 (78)
Q Consensus 41 ~t~l~KLm~aYc~r~gl~~~s 61 (78)
+..|.+||..||-..+++...
T Consensus 28 ~eeFD~l~q~y~~~~~~~p~~ 48 (64)
T PF12347_consen 28 NEEFDKLHQRYCLSPGKPPQN 48 (64)
T ss_dssp ---------------------
T ss_pred HHHHHHHHHHhCCCCCCCCCc
Confidence 578999999999887776443
No 145
>PRK06437 hypothetical protein; Provisional
Probab=26.90 E-value=1.3e+02 Score=17.20 Aligned_cols=41 Identities=2% Similarity=0.028 Sum_probs=32.4
Q ss_pred CCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeeccee
Q 034926 31 GNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLAW 75 (78)
Q Consensus 31 g~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~~ 75 (78)
+.+..+.+...+.+..|.+. .|++...+....||..|....
T Consensus 10 ~~~~~~~i~~~~tv~dLL~~----Lgi~~~~vaV~vNg~iv~~~~ 50 (67)
T PRK06437 10 HINKTIEIDHELTVNDIIKD----LGLDEEEYVVIVNGSPVLEDH 50 (67)
T ss_pred CcceEEEcCCCCcHHHHHHH----cCCCCccEEEEECCEECCCce
Confidence 44556778888888888865 588889999999999987554
No 146
>PF03790 KNOX1: KNOX1 domain ; InterPro: IPR005540 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=26.40 E-value=45 Score=18.55 Aligned_cols=18 Identities=22% Similarity=0.545 Sum_probs=14.0
Q ss_pred hHHHHHHHH--HhhcCCCCC
Q 034926 43 QLKKLMNAY--CDRQSVELN 60 (78)
Q Consensus 43 ~l~KLm~aY--c~r~gl~~~ 60 (78)
...+|..|| |.|.|-+++
T Consensus 12 ~Y~~Ll~Ayi~C~KVGAP~e 31 (45)
T PF03790_consen 12 LYPRLLAAYIDCQKVGAPPE 31 (45)
T ss_pred CcHHHHHHHHHHHhcCCCHH
Confidence 346789999 889987754
No 147
>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=25.66 E-value=94 Score=18.79 Aligned_cols=33 Identities=9% Similarity=0.004 Sum_probs=25.6
Q ss_pred CchHHHHHHHHHhhcC--C-CCCeEEEEECCEeecc
Q 034926 41 STQLKKLMNAYCDRQS--V-ELNSIAFLYVHISAFL 73 (78)
Q Consensus 41 ~t~l~KLm~aYc~r~g--l-~~~s~rFlfdG~rI~~ 73 (78)
++.-..|....+++.+ . +.+..|+.|.|+.+.-
T Consensus 20 ~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~D 55 (75)
T cd01815 20 GYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLKD 55 (75)
T ss_pred cCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCCC
Confidence 4556777888888864 5 4889999999998754
No 148
>PF09358 UBA_e1_C: Ubiquitin-activating enzyme e1 C-terminal domain; InterPro: IPR018965 This presumed domain found at the C terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterised. ; PDB: 3CMM_A.
Probab=25.42 E-value=1.1e+02 Score=19.83 Aligned_cols=29 Identities=10% Similarity=0.355 Sum_probs=22.1
Q ss_pred EEEEeCCchHHHHHHHHHhhcCCCCCeEE
Q 034926 35 FFRIKRSTQLKKLMNAYCDRQSVELNSIA 63 (78)
Q Consensus 35 ~FkIK~~t~l~KLm~aYc~r~gl~~~s~r 63 (78)
.|.|....+|+.|++.+-++.|++...+.
T Consensus 36 r~~v~~~~Tl~~li~~~~~~~~lev~ml~ 64 (125)
T PF09358_consen 36 RIEVNGDMTLQELIDYFKEKYGLEVTMLS 64 (125)
T ss_dssp EEEEES--BHHHHHHHHHHTTS-EEEEEE
T ss_pred EEEEcCCCCHHHHHHHHHHHhCceEEEEE
Confidence 67777789999999999999999876653
No 149
>KOG3784 consensus Sorting nexin protein SNX27 [General function prediction only; Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=25.19 E-value=1.6e+02 Score=23.45 Aligned_cols=42 Identities=12% Similarity=0.204 Sum_probs=36.3
Q ss_pred CcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCe
Q 034926 20 AHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNS 61 (78)
Q Consensus 20 ~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s 61 (78)
..+.+.|.-++|..+..++..+..=..+|++-|.+.|++...
T Consensus 106 ~~v~l~v~lpng~~i~i~~~~s~tt~~vl~~v~~kl~l~~e~ 147 (407)
T KOG3784|consen 106 EEVELDVFLPNGEKITINCLVSDTASLVLKSVCRKLGLPDEL 147 (407)
T ss_pred ceeEEEEEccCCceEEEEEEecccHHHHHHHHHhhcCCchHh
Confidence 356777777999999999999999999999999999988544
No 150
>COG3906 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.18 E-value=47 Score=21.65 Aligned_cols=17 Identities=41% Similarity=0.686 Sum_probs=13.1
Q ss_pred EEEEEEccCCCEEEEEE
Q 034926 22 INLKVKGQDGNEVFFRI 38 (78)
Q Consensus 22 I~lkV~~qdg~~v~FkI 38 (78)
=.|.+.|++|+++.|.+
T Consensus 14 e~itL~DE~GnE~lf~~ 30 (105)
T COG3906 14 EVITLIDEDGNEVLFEI 30 (105)
T ss_pred eEEEEECCCCceehhhe
Confidence 35677899999987764
No 151
>COG5435 Uncharacterized conserved protein [Function unknown]
Probab=24.83 E-value=1.1e+02 Score=21.11 Aligned_cols=37 Identities=27% Similarity=0.460 Sum_probs=28.6
Q ss_pred CCCcEEEEEEccCC-CEEEEEEeCCc-hHHHHHHHHHhh
Q 034926 18 QSAHINLKVKGQDG-NEVFFRIKRST-QLKKLMNAYCDR 54 (78)
Q Consensus 18 ~~~~I~lkV~~qdg-~~v~FkIK~~t-~l~KLm~aYc~r 54 (78)
.+..+||-+...+| ..+.|-|.|++ +=...+..||+|
T Consensus 18 ~DrSvNvf~~~~~gt~~~sfvIsRd~~~~g~~~~~y~~r 56 (147)
T COG5435 18 QDRSVNVFVSGDNGTSGFSFVISRDPLEPGDTFPEYVQR 56 (147)
T ss_pred ccceEEEEEecCCCcceeEEEEecCCCCCCCcHHHHHHH
Confidence 35689999988777 77899999865 456677888875
No 152
>cd00103 IRF Interferon Regulatory Factor (IRF); also known as tryptophan pentad repeat. The family of IRF transcription factors is important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. The IRF family is characterized by a unique 'tryptophan cluster' DNA-binding region. Viral IRFs bind to cellular IRFs; block type I and II interferons and host IRF-mediated transcriptional activation.
Probab=24.76 E-value=53 Score=21.02 Aligned_cols=17 Identities=12% Similarity=0.208 Sum_probs=13.9
Q ss_pred chHHHHHHHHHhhcCCC
Q 034926 42 TQLKKLMNAYCDRQSVE 58 (78)
Q Consensus 42 t~l~KLm~aYc~r~gl~ 58 (78)
..-.+||+|||...|.-
T Consensus 44 e~d~~iFkawa~~~Gk~ 60 (107)
T cd00103 44 EADAKIFKAWAVERGIY 60 (107)
T ss_pred hhhhHHHHHHHHHhCCC
Confidence 35689999999998854
No 153
>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=24.70 E-value=84 Score=21.67 Aligned_cols=36 Identities=3% Similarity=-0.127 Sum_probs=30.7
Q ss_pred CCchHHHHHHHHHhhcCCCCCeEEEEECCEeeccee
Q 034926 40 RSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLAW 75 (78)
Q Consensus 40 ~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~~ 75 (78)
++.-...|+..|+-+..++.......+||.+|....
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 455678899999999999999999999999997543
No 154
>PF03462 PCRF: PCRF domain; InterPro: IPR005139 This domain is found in peptide chain release factors. Peptide chain release factors are important for protein synthesis since they direct the termination of translation in response to the peptide chain termination codons UAG and UAA. These are structurally distinct but both contain the PCRF domain [].; GO: 0016149 translation release factor activity, codon specific, 0006415 translational termination, 0005737 cytoplasm; PDB: 3D5A_X 3D5C_X 3MR8_V 3MS0_V 3F1G_X 3F1E_X 1ZBT_A 2IHR_1 2X9R_Y 2X9T_Y ....
Probab=24.51 E-value=91 Score=19.79 Aligned_cols=25 Identities=12% Similarity=0.332 Sum_probs=17.9
Q ss_pred hHHHHHHHHHhhcCCCCCeEEEEEC
Q 034926 43 QLKKLMNAYCDRQSVELNSIAFLYV 67 (78)
Q Consensus 43 ~l~KLm~aYc~r~gl~~~s~rFlfd 67 (78)
-|-+++..||+++|....-+.+.-.
T Consensus 67 ~L~~MY~~~a~~~gw~~~~l~~~~~ 91 (115)
T PF03462_consen 67 ELFRMYQRYAERRGWKVEVLDYSPG 91 (115)
T ss_dssp HHHHHHHHHHHHTT-EEEEEEEEE-
T ss_pred HHHHHHHHHHHHcCCEEEEEecCCC
Confidence 4678888889999988777765553
No 155
>KOG2689 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]
Probab=24.33 E-value=3.2e+02 Score=20.79 Aligned_cols=46 Identities=13% Similarity=0.124 Sum_probs=33.6
Q ss_pred CcEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEE
Q 034926 20 AHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFL 65 (78)
Q Consensus 20 ~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFl 65 (78)
.+-+|.|+-+||..+.-.+...++|..+=.--.-+.|.+..-+.|+
T Consensus 209 s~crlQiRl~DG~Tl~~tF~a~E~L~~VR~wVd~n~~~~~~P~~f~ 254 (290)
T KOG2689|consen 209 SQCRLQIRLPDGQTLTQTFNARETLAAVRLWVDLNRGDGLDPYSFH 254 (290)
T ss_pred cceEEEEEcCCCCeeeeecCchhhHHHHHHHHHHhccCCCCCeeee
Confidence 4567777788999998888888999887665555666555455554
No 156
>PF14977 FAM194: FAM194 protein
Probab=23.66 E-value=84 Score=22.54 Aligned_cols=20 Identities=20% Similarity=0.378 Sum_probs=16.1
Q ss_pred CCCcEEEEEEccCCCEEEEE
Q 034926 18 QSAHINLKVKGQDGNEVFFR 37 (78)
Q Consensus 18 ~~~~I~lkV~~qdg~~v~Fk 37 (78)
-+++|+|+|.+||.-.+.|.
T Consensus 119 lN~~i~vri~~qd~I~itF~ 138 (208)
T PF14977_consen 119 LNEQIKVRILSQDKISITFT 138 (208)
T ss_pred ecCcEEEEEeccceEEEEEe
Confidence 36799999999998777664
No 157
>PRK09619 flgD flagellar basal body rod modification protein; Reviewed
Probab=23.61 E-value=2.5e+02 Score=20.04 Aligned_cols=20 Identities=15% Similarity=0.265 Sum_probs=14.5
Q ss_pred CCcEEEEEEccCCCEEEEEE
Q 034926 19 SAHINLKVKGQDGNEVFFRI 38 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~FkI 38 (78)
...++|.|.|.+|+...+..
T Consensus 122 a~~v~v~I~D~~G~v~t~~l 141 (218)
T PRK09619 122 APTLTLHITDILGQEKKIDL 141 (218)
T ss_pred CcEEEEEEEeCCCCEEEEec
Confidence 45699999999998534433
No 158
>KOG3112 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.16 E-value=40 Score=24.98 Aligned_cols=44 Identities=14% Similarity=0.015 Sum_probs=33.7
Q ss_pred CCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCEeecce
Q 034926 31 GNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 31 g~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~~ 74 (78)
|++-..+|--.-+...||+|+|++.=.=.--+||+-.|..|...
T Consensus 173 ~Svee~aipggg~~~~Lf~af~~~~v~m~~Ll~y~sEGDNipdA 216 (262)
T KOG3112|consen 173 GSVEEDAIPGGGNALQLFKAFDEQKVPMMLLLRYLSEGDNIPDA 216 (262)
T ss_pred CcceeeecCCCccHHHHHHHHHhcCCchhhHHHHhhcCCCCchH
Confidence 56667888889999999999998754334567888888877543
No 159
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=23.14 E-value=77 Score=18.56 Aligned_cols=20 Identities=15% Similarity=0.385 Sum_probs=12.7
Q ss_pred CchHHHHHHHH---HhhcCCCCC
Q 034926 41 STQLKKLMNAY---CDRQSVELN 60 (78)
Q Consensus 41 ~t~l~KLm~aY---c~r~gl~~~ 60 (78)
..+...+++.| |+..|.++-
T Consensus 15 ~~~~~~vy~~Y~~lc~~~~~~pl 37 (85)
T PF09079_consen 15 EVTTGEVYEVYEELCESLGVDPL 37 (85)
T ss_dssp SEEHHHHHHHHHHHHHHTTS---
T ss_pred ceeHHHHHHHHHHHHHHcCCCCC
Confidence 45677888888 778777643
No 160
>PRK12634 flgD flagellar basal body rod modification protein; Reviewed
Probab=23.06 E-value=2.5e+02 Score=20.02 Aligned_cols=35 Identities=11% Similarity=0.301 Sum_probs=23.9
Q ss_pred CCcEEEEEEccCCCEEE-EEEeCCchHHHHHHHHHhhcCCCCCeEEEEECCE
Q 034926 19 SAHINLKVKGQDGNEVF-FRIKRSTQLKKLMNAYCDRQSVELNSIAFLYVHI 69 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~-FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlfdG~ 69 (78)
...++|.|.|.+|+.|+ +.+. ..+.+...|.+||.
T Consensus 121 a~~v~i~I~d~~G~~V~t~~lg----------------~~~aG~~~f~WDG~ 156 (221)
T PRK12634 121 AGFVNFEITDANGAFVKQISVP----------------ASAAGEVSFAWDGT 156 (221)
T ss_pred CCeEEEEEEcCCCCEEEEEecC----------------CcCCCceeEEECCC
Confidence 45799999999998863 3332 23455677777775
No 161
>PF03999 MAP65_ASE1: Microtubule associated protein (MAP65/ASE1 family); InterPro: IPR007145 This is a family of microtubule associated proteins. One of its members is the yeast anaphase spindle elongation protein.; PDB: 3NRX_A 3NRY_A.
Probab=22.91 E-value=90 Score=25.34 Aligned_cols=26 Identities=19% Similarity=0.254 Sum_probs=19.5
Q ss_pred chHHHHHHHHHhhcCCCCCeEEEEECCEeec
Q 034926 42 TQLKKLMNAYCDRQSVELNSIAFLYVHISAF 72 (78)
Q Consensus 42 t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~ 72 (78)
..|.+...+|-+..|.+ |+|||.++-
T Consensus 398 ~~L~~~l~~wE~e~g~p-----Flv~G~~~l 423 (619)
T PF03999_consen 398 EELKKKLEEWEEEHGKP-----FLVDGERYL 423 (619)
T ss_dssp HHHHHHHHHHHHHHTS-------EETTEEHH
T ss_pred HHHHHHHHHHHHHcCCe-----EEEcCccHH
Confidence 35777888999888876 999999863
No 162
>COG2029 Uncharacterized conserved protein [Function unknown]
Probab=22.84 E-value=16 Score=25.95 Aligned_cols=15 Identities=27% Similarity=0.248 Sum_probs=13.2
Q ss_pred EEEECCEeecceeec
Q 034926 63 AFLYVHISAFLAWAV 77 (78)
Q Consensus 63 rFlfdG~rI~~~~~~ 77 (78)
||.|||..|.+.||.
T Consensus 12 ~ldYdGSqI~~~wA~ 26 (189)
T COG2029 12 RLDYDGSQIRSAWAY 26 (189)
T ss_pred cccCchhhhhhhHhH
Confidence 589999999999984
No 163
>PF09627 PrgU: PrgU-like protein; InterPro: IPR018589 This hypothetical protein of 125 residues is expressed in bacteria but is thought to be plasmid in origin. It forms a six beta-strand barrel with three accompanying alpha helices and is probably a homo-dimer in the cell. It may be involved in pheromone-inducible conjugation []. ; PDB: 2GMQ_B.
Probab=22.64 E-value=1.6e+02 Score=19.28 Aligned_cols=54 Identities=20% Similarity=0.292 Sum_probs=37.7
Q ss_pred cEEEEEEccCCCEEEEEEeCCchHHHHHHHHHhhcC-CCCCeEEEEECCEeecce
Q 034926 21 HINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQS-VELNSIAFLYVHISAFLA 74 (78)
Q Consensus 21 ~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aYc~r~g-l~~~s~rFlfdG~rI~~~ 74 (78)
.++++-++-.|.-+.+++|.+..|.-+.+.-----+ .....+..+=||+.+.+.
T Consensus 10 ~~~~~W~G~~GrL~~ir~K~~r~~Em~~N~QiT~ENI~EI~~i~iiKNGKsL~L~ 64 (122)
T PF09627_consen 10 DVNTQWQGFRGRLVMIRVKNTRTMEMWYNNQITPENIQEIDTIHIIKNGKSLTLK 64 (122)
T ss_dssp GEEEEEGGGTSBEEEEEE-HHHHHHHHHHTSS-TTTGGG--EEEEEETTEEEEEE
T ss_pred eeeeEEecCcceEEEEEeeCCeeeeehhhCCCChHHceeeeeeeeecCCcEEEEE
Confidence 588999999999999999988777766654322122 346788999999988753
No 164
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=22.62 E-value=1.5e+02 Score=16.33 Aligned_cols=26 Identities=4% Similarity=0.078 Sum_probs=20.9
Q ss_pred HHHHHHHHHhhcCCCCCeEEEEECCE
Q 034926 44 LKKLMNAYCDRQSVELNSIAFLYVHI 69 (78)
Q Consensus 44 l~KLm~aYc~r~gl~~~s~rFlfdG~ 69 (78)
...|.++.++..|.+..+++..|+..
T Consensus 21 ~~~it~a~~~~~~~p~~~v~V~i~ev 46 (60)
T PRK02289 21 AREVTEVVSRIAKAPKEAIHVFINDM 46 (60)
T ss_pred HHHHHHHHHHHhCcCcceEEEEEEEe
Confidence 45677788899999999999888643
No 165
>PF11834 DUF3354: Domain of unknown function (DUF3354); InterPro: IPR021789 Potassium channels take part in important processes of higher plants, including opening and closing of stomatal pores and leaf movement. Inward rectifying potassium (K(+)in) channels play an important role in turgor regulation and ion uptake in higher plants. All of them comprise, from their N-terminal to their C-terminal ends: a short hydrophilic region, a hydrophobic region structurally analogous and partially homologous to the transmembrane domain of voltage-gated animal channels from the Shaker superfamily, a putative cyclic nucleotide-binding domain, and a conserved C-terminal KHA domain. Between these last two regions, some of them (AKT1, AKT2 and SKT1) contain an ankyrin-repeat domain with six repeats homologous to those of human erythrocyte ankyrin. This entry represents the KHA domain which is unique to plant K(+)in channels. The KHA domain contains two high-homology blocks enriched for hydrophobic and acidic residues, respectively. The KHA domain is essential for interaction of plant K(+)in channels. The KHA domain mediates tetramerization and/or stabilisation of the heteromers [, , ].
Probab=22.43 E-value=1.5e+02 Score=17.56 Aligned_cols=32 Identities=6% Similarity=-0.034 Sum_probs=25.7
Q ss_pred CchHHHHHHHHHhhcCCCCCeEEEEECCEeecc
Q 034926 41 STQLKKLMNAYCDRQSVELNSIAFLYVHISAFL 73 (78)
Q Consensus 41 ~t~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~ 73 (78)
-..|..|++.-+++.|.. .+-.|.=||-.|..
T Consensus 25 P~SleeLl~ia~~kfg~~-~~~v~~~dgaeIdD 56 (69)
T PF11834_consen 25 PDSLEELLKIASEKFGFS-ATKVLNEDGAEIDD 56 (69)
T ss_pred CccHHHHHHHHHHHhCCC-ceEEEcCCCCEEeE
Confidence 368999999999999997 66667778877653
No 166
>PF02566 OsmC: OsmC-like protein; InterPro: IPR003718 Osmotically inducible protein C (OsmC) is a stress-induced protein found in Escherichia coli. The transcription of the osmC gene of E. coli is regulated as a function of the phase of growth and is induced during the late exponential phase when the growth rate slows before entry into stationary phase. The transcription is initiated by two overlapping promoters, osmCp1 and osmCp2 []. An organic hydroperoxide detoxification protein (OHR) from Xanthomonas campestris pv. phaseoli is highly induced by organic hydroperoxides, weakly induced by H2O2, and not induced at all by a superoxide generator. Ohr may be a new type of organic hydroperoxide detoxification protein [, ].; GO: 0006950 response to stress; PDB: 2D7V_A 2BJO_A 1USP_A 2PN2_A 2QL8_A 1N2F_A 1UKK_A 1VLA_D 3CJE_A 2ONF_B ....
Probab=22.30 E-value=72 Score=18.69 Aligned_cols=24 Identities=4% Similarity=0.149 Sum_probs=17.9
Q ss_pred HHHHHHHhhcCCCCCeEEEEECCE
Q 034926 46 KLMNAYCDRQSVELNSIAFLYVHI 69 (78)
Q Consensus 46 KLm~aYc~r~gl~~~s~rFlfdG~ 69 (78)
.-+..|++++|++...++....|.
T Consensus 22 ~~~~~~a~~~gi~~~~~~v~v~~~ 45 (100)
T PF02566_consen 22 MTLRMVAEKRGIDLEDLEVEVEGE 45 (100)
T ss_dssp HHHHHHHHHTT-EEEEEEEEEEEE
T ss_pred HHHHHHHHHcCCCcceEEEEEEEE
Confidence 346778899999999988877664
No 167
>PF06793 UPF0262: Uncharacterised protein family (UPF0262); InterPro: IPR008321 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=22.26 E-value=2.4e+02 Score=19.63 Aligned_cols=32 Identities=13% Similarity=0.379 Sum_probs=21.5
Q ss_pred CcEEEEEEccCCCEEEEEEeCCchHHHHHHHH
Q 034926 20 AHINLKVKGQDGNEVFFRIKRSTQLKKLMNAY 51 (78)
Q Consensus 20 ~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~aY 51 (78)
+.+.+-|.+.+|..+.=-+=.=+||+++++-|
T Consensus 61 ~RLvfdI~~e~~~~~~~~~LsL~PfRrvikDY 92 (158)
T PF06793_consen 61 NRLVFDIRDEDGEPLATHHLSLTPFRRVIKDY 92 (158)
T ss_pred CEEEEEecCCCCCEeeEEEeccccHHHHHHHH
Confidence 34555566666666533344568999999999
No 168
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=22.13 E-value=1.2e+02 Score=18.23 Aligned_cols=30 Identities=10% Similarity=0.067 Sum_probs=20.5
Q ss_pred hHHHHHHHHHhhcCCCCCeEEEEECCEeecc
Q 034926 43 QLKKLMNAYCDRQSVELNSIAFLYVHISAFL 73 (78)
Q Consensus 43 ~l~KLm~aYc~r~gl~~~s~rFlfdG~rI~~ 73 (78)
.|-.-..+|+++.|.+....-. ++|+.|.+
T Consensus 5 ~F~~~L~~F~~~~g~~~~~~P~-i~g~~vdL 34 (93)
T smart00501 5 LFLDRLYKFMEERGSPLKKIPV-IGGKPLDL 34 (93)
T ss_pred HHHHHHHHHHHHcCCcCCcCCe-ECCEeCcH
Confidence 3455667788888987655543 48988865
No 169
>PRK12813 flgD flagellar basal body rod modification protein; Reviewed
Probab=22.08 E-value=1.9e+02 Score=20.86 Aligned_cols=17 Identities=29% Similarity=0.403 Sum_probs=14.1
Q ss_pred CCcEEEEEEccCCCEEE
Q 034926 19 SAHINLKVKGQDGNEVF 35 (78)
Q Consensus 19 ~~~I~lkV~~qdg~~v~ 35 (78)
...++|.|.|.+|+.|+
T Consensus 123 a~~v~v~I~D~~G~vV~ 139 (223)
T PRK12813 123 ADKAELVVRDAAGAEVA 139 (223)
T ss_pred CceEEEEEEcCCCCEEE
Confidence 45799999999999873
No 170
>PF04221 RelB: RelB antitoxin; InterPro: IPR007337 Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. Several toxin/antitoxin pairs may occur in a single species. RelE and RelB form a toxin-antitoxin system; RelE represses translation, probably through binding ribosomes [, ]. RelB stably binds RelE, presumably deactivating it.; PDB: 2KC8_B 2K29_A.
Probab=21.90 E-value=66 Score=19.20 Aligned_cols=26 Identities=15% Similarity=0.281 Sum_probs=17.8
Q ss_pred EEEeCCchHHHHHHHHHhhcCCCCCe
Q 034926 36 FRIKRSTQLKKLMNAYCDRQSVELNS 61 (78)
Q Consensus 36 FkIK~~t~l~KLm~aYc~r~gl~~~s 61 (78)
+.++-+..+++-..+-|+.+|+++++
T Consensus 4 i~~Rid~~lK~~a~~il~~~Glt~s~ 29 (83)
T PF04221_consen 4 INVRIDEELKEEAEAILEELGLTLSD 29 (83)
T ss_dssp EEEEE-HHHHHHHHHHHHHTT--HHH
T ss_pred EEEEcCHHHHHHHHHHHHHcCCCHHH
Confidence 45566788888889999999988654
No 171
>PF09274 ParG: ParG; InterPro: IPR015354 This entry represents plasmid partition proteins; it adopts a ribbon-helix-helix fold, with a core of four alpha-helices. The proteins are an essential component of the DNA partition complex of the multi drug resistance plasmid TP228 []. ; PDB: 1P94_B.
Probab=21.23 E-value=1.4e+02 Score=18.36 Aligned_cols=31 Identities=13% Similarity=0.298 Sum_probs=22.1
Q ss_pred CCCEEEEEEeCCchHHHHHHHHHhhcCCCCC
Q 034926 30 DGNEVFFRIKRSTQLKKLMNAYCDRQSVELN 60 (78)
Q Consensus 30 dg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~ 60 (78)
.+......|.-+..+-+-|+++|-+.|.+..
T Consensus 31 s~k~Krvtv~i~EelH~r~K~~ca~~G~sis 61 (76)
T PF09274_consen 31 SEKTKRVTVNIDEELHRRFKAACAKQGTSIS 61 (76)
T ss_dssp TTTEEEE-EEEEHHHHHHHHHHHHHHT--HH
T ss_pred ccceEEEEEecCHHHHHHHHHHHHHcCCcHH
Confidence 3556666666688999999999999997753
No 172
>PF09264 Sial-lect-inser: Vibrio cholerae sialidase, lectin insertion; InterPro: IPR015344 This domain is predominantly found in Vibrio cholerae sialidase, and adopt a beta sandwich structure consisting of 12-14 strands arranged in two beta-sheets. It binds to lectins with high affinity helping to target the protein to sialic acid-rich environments, thereby enhancing the catalytic efficiency of the enzyme []. ; PDB: 1W0P_A 1W0O_A 1KIT_A 2W68_B.
Probab=21.16 E-value=1e+02 Score=22.21 Aligned_cols=16 Identities=19% Similarity=0.490 Sum_probs=13.4
Q ss_pred CeEEEEECCEeecceee
Q 034926 60 NSIAFLYVHISAFLAWA 76 (78)
Q Consensus 60 ~s~rFlfdG~rI~~~~~ 76 (78)
.+-.|.|||.-|. +|+
T Consensus 106 ~tASfy~DG~lI~-tw~ 121 (198)
T PF09264_consen 106 NTASFYFDGTLIA-TWS 121 (198)
T ss_dssp TEEEEEETTEEEE-EE-
T ss_pred CceEEEECCEEEe-ecc
Confidence 6899999999998 575
No 173
>KOG1407 consensus WD40 repeat protein [Function unknown]
Probab=21.16 E-value=1.2e+02 Score=23.28 Aligned_cols=54 Identities=20% Similarity=0.306 Sum_probs=41.7
Q ss_pred CCCcEEEEEEccCCCEEEEEEeCCchHHHHHHH---HHh----hcCCCCCeEEEEECCEeecce
Q 034926 18 QSAHINLKVKGQDGNEVFFRIKRSTQLKKLMNA---YCD----RQSVELNSIAFLYVHISAFLA 74 (78)
Q Consensus 18 ~~~~I~lkV~~qdg~~v~FkIK~~t~l~KLm~a---Yc~----r~gl~~~s~rFlfdG~rI~~~ 74 (78)
+.+.|.|++ +++|. +|.+.-...+-.|.+. -|. |...+..++.|.+||+-|...
T Consensus 189 ~snCicI~f-~p~Gr--yfA~GsADAlvSLWD~~ELiC~R~isRldwpVRTlSFS~dg~~lASa 249 (313)
T KOG1407|consen 189 PSNCICIEF-DPDGR--YFATGSADALVSLWDVDELICERCISRLDWPVRTLSFSHDGRMLASA 249 (313)
T ss_pred CcceEEEEE-CCCCc--eEeeccccceeeccChhHhhhheeeccccCceEEEEeccCcceeecc
Confidence 356888887 67886 4999888777777654 476 567889999999999987543
No 174
>KOG0981 consensus DNA topoisomerase I [Replication, recombination and repair]
Probab=21.07 E-value=55 Score=27.61 Aligned_cols=17 Identities=18% Similarity=0.114 Sum_probs=14.7
Q ss_pred CCeEEEEECCEeeccee
Q 034926 59 LNSIAFLYVHISAFLAW 75 (78)
Q Consensus 59 ~~s~rFlfdG~rI~~~~ 75 (78)
+..++|+|||..+.++-
T Consensus 230 P~~Vk~~YdGkpv~L~~ 246 (759)
T KOG0981|consen 230 PSGVKFYYDGKPVDLTP 246 (759)
T ss_pred CCCceEEeCCccccCCH
Confidence 67899999999998864
No 175
>PF00722 Glyco_hydro_16: Glycosyl hydrolases family 16; InterPro: IPR000757 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 16 GH16 from CAZY comprises enzymes with a number of known activities; lichenase (3.2.1.73 from EC); xyloglucan xyloglucosyltransferase (2.4.1.207 from EC); agarase (3.2.1.81 from EC); kappa-carrageenase (3.2.1.83 from EC); endo-beta-1,3-glucanase (3.2.1.39 from EC); endo-beta-1,3-1,4-glucanase (3.2.1.6 from EC); endo-beta-galactosidase (3.2.1.103 from EC).; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3DGT_A 2CL2_A 2WLQ_A 2WNE_A 2W39_A 2W52_A 3ILN_A 4DFS_A 1UMZ_A 1UN1_B ....
Probab=21.03 E-value=1.1e+02 Score=19.93 Aligned_cols=18 Identities=11% Similarity=-0.127 Sum_probs=14.5
Q ss_pred CCCeEEEEECCEeeccee
Q 034926 58 ELNSIAFLYVHISAFLAW 75 (78)
Q Consensus 58 ~~~s~rFlfdG~rI~~~~ 75 (78)
.++.++|.+||+.+....
T Consensus 128 ~~~~i~fyiDg~~~~~~~ 145 (185)
T PF00722_consen 128 TPDRIRFYIDGKLVRTVT 145 (185)
T ss_dssp ETTEEEEEETTEEEEEEE
T ss_pred ecCeEEEEECCEEEEEEe
Confidence 578999999999886543
No 176
>PF08512 Rtt106: Histone chaperone Rttp106-like; InterPro: IPR013719 This is a domain of unknown function that is associated with a number of different protein families. It is found in Rtt106p, which is a histone chaperone involved in heterochromatin-mediated silencing []. It is also found in genes annotated as transcription factors/regulators. This domain is the C-terminal domain of yeast Spt16p P32558 from SWISSPROT, which is a subunit of the heterodimeric yeast FACT complex (Spt16p-Pob3p, IPR000969 from INTERPRO) []. In addition Spt16p and its relatives, in this entry, are described as non-peptidase homologues belonging to the MEROPS peptidase family M24. The FACT complex facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilising and then reassembling nucleosome structure [, ]. ; PDB: 3TW1_A 3GYO_A 3TO1_A 3FSS_A 3TVV_B 3GYP_A 2GCJ_D 2GCL_A.
Probab=21.03 E-value=1.9e+02 Score=17.59 Aligned_cols=39 Identities=15% Similarity=0.264 Sum_probs=27.4
Q ss_pred CcEEEEEEccC--CCEEEEEEeCCchHHHHHHHHHhhcCCCC
Q 034926 20 AHINLKVKGQD--GNEVFFRIKRSTQLKKLMNAYCDRQSVEL 59 (78)
Q Consensus 20 ~~I~lkV~~qd--g~~v~FkIK~~t~l~KLm~aYc~r~gl~~ 59 (78)
..-.+.|.-.| +..+.|..=....+..|.+ |.+.+|+..
T Consensus 52 ktFDl~v~~k~~~~~~~~fs~I~~~e~~~l~~-~l~~~~i~~ 92 (95)
T PF08512_consen 52 KTFDLVVILKDYEGPPHEFSSIDREEYDNLKD-FLKSKNIKI 92 (95)
T ss_dssp SEEEEEEEETT-TS-EEEEEEEEGGGHHHHHH-HHHHCCHHC
T ss_pred eEEEEEEEEecCCCCcEEEeeECHHHHHHHHH-HHHHCCCEe
Confidence 34445555555 8889999888889999887 888777543
No 177
>PRK12426 elongation factor P; Provisional
Probab=20.98 E-value=2e+02 Score=20.20 Aligned_cols=50 Identities=14% Similarity=0.175 Sum_probs=35.3
Q ss_pred CCCCCCCCcEEEEEEcc-CCCEEEEEEeCCchHHHHHHHHHhhcCCCCCeEEEEE-CCEe
Q 034926 13 KKPNDQSAHINLKVKGQ-DGNEVFFRIKRSTQLKKLMNAYCDRQSVELNSIAFLY-VHIS 70 (78)
Q Consensus 13 ~kp~~~~~~I~lkV~~q-dg~~v~FkIK~~t~l~KLm~aYc~r~gl~~~s~rFlf-dG~r 70 (78)
.||-..+..+.+|+++- +|+.+.-+.+.+.++. ...++...+.|+| ||.-
T Consensus 28 ~kPGkg~A~vr~klknl~tG~~~e~tf~s~ek~e--------~a~ve~~~~qylY~dg~~ 79 (185)
T PRK12426 28 VTGPKGETFIKVSLQAADSDVVVERNFKAGQEVK--------EAQFEPRNLEYLYLEGDE 79 (185)
T ss_pred ecCCCCceEEEEEEEEcCCCCeEEEEECCCCeEE--------EeEEEeeEeEEEEECCCe
Confidence 45655566788888774 4777777777777763 4567888889998 5643
No 178
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=20.92 E-value=42 Score=21.47 Aligned_cols=12 Identities=25% Similarity=0.440 Sum_probs=8.8
Q ss_pred HHHHHhhcCCCC
Q 034926 48 MNAYCDRQSVEL 59 (78)
Q Consensus 48 m~aYc~r~gl~~ 59 (78)
--+||+++|+++
T Consensus 61 Ai~yaer~G~~Y 72 (101)
T PF04800_consen 61 AIAYAERNGWDY 72 (101)
T ss_dssp HHHHHHHCT-EE
T ss_pred HHHHHHHcCCeE
Confidence 348999999874
No 179
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.88 E-value=62 Score=22.17 Aligned_cols=13 Identities=31% Similarity=0.721 Sum_probs=11.0
Q ss_pred HHHHHHHHhhcCC
Q 034926 45 KKLMNAYCDRQSV 57 (78)
Q Consensus 45 ~KLm~aYc~r~gl 57 (78)
-.||++||.+.|-
T Consensus 24 pel~eafcskcge 36 (160)
T COG4306 24 PELMEAFCSKCGE 36 (160)
T ss_pred HHHHHHHHhhhch
Confidence 4799999999884
No 180
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=20.46 E-value=92 Score=18.86 Aligned_cols=26 Identities=19% Similarity=0.218 Sum_probs=20.1
Q ss_pred EEEeCCchHHHHHHHHHhhcCCCCCe
Q 034926 36 FRIKRSTQLKKLMNAYCDRQSVELNS 61 (78)
Q Consensus 36 FkIK~~t~l~KLm~aYc~r~gl~~~s 61 (78)
+.++-+..+++-+++-|+..|+++.+
T Consensus 5 i~~Rvd~~lK~~a~~i~~~lGl~~s~ 30 (83)
T TIGR02384 5 ISIRIDEELKKEAYAVFEELGLTPST 30 (83)
T ss_pred eEEeeCHHHHHHHHHHHHHhCCCHHH
Confidence 56666788888888888888887653
No 181
>PF05534 HicB: HicB family; InterPro: IPR008651 This family consists of several bacterial HicB related proteins. The function of HicB is unknown although it is thought to be involved in pilus formation. It has been speculated that HicB performs a function antagonistic to that of pili and yet is necessary for invasion of certain niches [].
Probab=20.29 E-value=63 Score=17.89 Aligned_cols=27 Identities=19% Similarity=0.359 Sum_probs=21.7
Q ss_pred EEEEeCCchHHHHHHHHHhhcCCCCCe
Q 034926 35 FFRIKRSTQLKKLMNAYCDRQSVELNS 61 (78)
Q Consensus 35 ~FkIK~~t~l~KLm~aYc~r~gl~~~s 61 (78)
.|.|+-+..|-+-....|.+.|++.+.
T Consensus 19 ~~~lRi~~~Lh~~l~~~A~~~gvSlN~ 45 (51)
T PF05534_consen 19 KFNLRIPPELHRALAEAAAAEGVSLNQ 45 (51)
T ss_pred ceeeeCCHHHHHHHHHHHHHhCCCHHH
Confidence 366777778888899999999988764
No 182
>PRK10738 hypothetical protein; Provisional
Probab=20.28 E-value=1.2e+02 Score=19.80 Aligned_cols=31 Identities=0% Similarity=0.029 Sum_probs=24.3
Q ss_pred CchHHHHHH-----------HHHhhcCCCCCeEEEEECCEee
Q 034926 41 STQLKKLMN-----------AYCDRQSVELNSIAFLYVHISA 71 (78)
Q Consensus 41 ~t~l~KLm~-----------aYc~r~gl~~~s~rFlfdG~rI 71 (78)
-+|+.-|.- .|+++++++...+....+|.|-
T Consensus 34 ~~P~EllL~aLg~Ct~i~v~~~l~k~~~~~~~~~v~v~~~r~ 75 (134)
T PRK10738 34 PSPMEMVLMAAGGCSAIDVVSILQKGRQDVVDCEVKLTSERR 75 (134)
T ss_pred CCHHHHHHHHHcCchHHHHHHHHHHCCCCcccEEEEEEEEEc
Confidence 567776654 5778999999999999988863
No 183
>PF03633 Glyco_hydro_65C: Glycosyl hydrolase family 65, C-terminal domain ; InterPro: IPR005194 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This family of glycosyl hydrolases (GH65 from CAZY) contains this domain and includes vacuolar acid trehalase and maltose phosphorylases. Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The C-terminal domain forms a two layered jelly roll motif. This domain is situated at the base of the catalytic domain, however its function remains unknown [].; PDB: 1H54_A.
Probab=20.15 E-value=1.2e+02 Score=16.30 Aligned_cols=16 Identities=13% Similarity=-0.141 Sum_probs=11.2
Q ss_pred CCCeEEEEECCEeecc
Q 034926 58 ELNSIAFLYVHISAFL 73 (78)
Q Consensus 58 ~~~s~rFlfdG~rI~~ 73 (78)
+.=+|+|.|-|.+|..
T Consensus 8 ~~l~F~~~~rg~~l~v 23 (54)
T PF03633_consen 8 SSLSFRLRYRGHWLEV 23 (54)
T ss_dssp SEEEEEEEETTEEEEE
T ss_pred CEeEEEEEECCEEEEE
Confidence 3346788888888764
Done!