Query psy7966
Match_columns 194
No_of_seqs 134 out of 312
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 23:24:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7966.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7966hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01816 Raf_RBD Ubiquitin doma 100.0 9.8E-36 2.1E-40 217.4 6.8 70 3-72 1-74 (74)
2 KOG0193|consensus 100.0 1.6E-32 3.5E-37 261.6 9.3 139 2-146 97-240 (678)
3 cd01817 RGS12_RBD Ubiquitin do 99.9 9.4E-26 2E-30 164.8 7.0 68 4-71 2-69 (73)
4 PF02196 RBD: Raf-like Ras-bin 99.9 1.1E-25 2.3E-30 162.4 5.6 69 3-71 2-70 (71)
5 cd01760 RBD Ubiquitin-like dom 99.9 5.4E-24 1.2E-28 154.8 6.3 69 3-71 1-71 (72)
6 smart00455 RBD Raf-like Ras-bi 99.9 3.1E-22 6.6E-27 144.3 7.2 69 3-71 1-69 (70)
7 KOG4236|consensus 99.4 2.6E-14 5.6E-19 137.2 2.5 57 74-133 140-200 (888)
8 PF00130 C1_1: Phorbol esters/ 99.4 1.7E-13 3.6E-18 91.9 2.5 48 83-130 1-52 (53)
9 KOG4236|consensus 99.3 3.5E-13 7.6E-18 129.6 -0.3 71 60-132 247-321 (888)
10 cd00029 C1 Protein kinase C co 99.2 5.4E-12 1.2E-16 82.5 1.4 46 83-128 1-50 (50)
11 KOG0696|consensus 99.2 3.2E-12 7E-17 120.4 0.1 52 79-130 107-162 (683)
12 smart00109 C1 Protein kinase C 99.1 1.2E-11 2.6E-16 80.0 1.2 46 83-128 1-49 (49)
13 KOG0696|consensus 98.9 4.4E-10 9.6E-15 106.2 0.5 51 82-132 45-99 (683)
14 KOG1011|consensus 98.7 1.2E-09 2.6E-14 107.0 -2.7 73 60-132 144-226 (1283)
15 KOG0694|consensus 98.4 5.7E-08 1.2E-12 95.0 1.2 56 79-134 227-286 (694)
16 cd01818 TIAM1_RBD Ubiquitin do 98.3 1E-06 2.2E-11 65.4 4.3 37 5-41 3-39 (77)
17 KOG0694|consensus 98.0 1.4E-06 3E-11 85.5 -0.5 51 82-132 158-212 (694)
18 KOG0695|consensus 97.7 1.8E-05 3.9E-10 74.1 1.7 51 81-131 129-183 (593)
19 KOG2996|consensus 97.7 9.9E-06 2.1E-10 79.1 -0.2 49 81-130 522-574 (865)
20 KOG4239|consensus 97.4 3.2E-05 6.9E-10 70.5 -0.2 54 82-135 51-108 (348)
21 KOG3564|consensus 96.8 0.00032 7E-09 67.3 0.5 51 81-131 285-338 (604)
22 cd00196 UBQ Ubiquitin-like pro 96.8 0.0038 8.3E-08 38.3 4.8 45 5-49 1-45 (69)
23 PF11470 TUG-UBL1: GLUT4 regul 95.3 0.042 9.1E-07 39.4 5.0 42 6-47 1-42 (65)
24 KOG1169|consensus 94.8 0.0094 2E-07 58.8 0.6 51 81-131 97-154 (634)
25 PF08746 zf-RING-like: RING-li 94.8 0.0085 1.8E-07 39.5 0.2 28 96-123 1-30 (43)
26 PF03107 C1_2: C1 domain; Int 94.6 0.02 4.4E-07 34.8 1.5 27 95-121 2-30 (30)
27 PF00788 RA: Ras association ( 94.2 0.12 2.6E-06 36.8 5.0 36 2-37 3-42 (93)
28 PF07649 C1_3: C1-like domain; 93.8 0.017 3.7E-07 34.9 -0.0 27 95-121 2-30 (30)
29 cd01777 SNX27_RA Ubiquitin dom 93.3 0.15 3.2E-06 38.9 4.2 40 2-41 2-41 (87)
30 cd01768 RA RA (Ras-associating 93.0 0.31 6.7E-06 35.0 5.5 45 3-47 1-50 (87)
31 KOG1453|consensus 91.1 0.084 1.8E-06 54.1 0.9 42 92-133 555-597 (918)
32 smart00314 RA Ras association 90.0 0.88 1.9E-05 32.9 5.3 44 2-45 3-51 (90)
33 smart00295 B41 Band 4.1 homolo 89.6 0.71 1.5E-05 37.0 4.9 37 2-38 4-40 (207)
34 PF14446 Prok-RING_1: Prokaryo 86.9 0.24 5.2E-06 34.7 0.5 32 94-125 6-40 (54)
35 PF02150 RNA_POL_M_15KD: RNA p 85.2 0.45 9.7E-06 30.1 1.0 23 94-116 2-30 (35)
36 PF09379 FERM_N: FERM N-termin 84.5 1.4 3E-05 30.9 3.5 33 6-38 1-33 (80)
37 smart00661 RPOL9 RNA polymeras 83.9 0.63 1.4E-05 30.5 1.4 24 94-117 1-31 (52)
38 PLN02593 adrenodoxin-like ferr 79.9 3.1 6.7E-05 32.5 4.1 44 3-46 2-51 (117)
39 KOG4718|consensus 77.8 0.53 1.1E-05 41.5 -0.8 31 92-122 180-210 (235)
40 cd01668 TGS_RelA_SpoT TGS_RelA 76.9 3.7 7.9E-05 26.8 3.3 47 4-56 1-47 (60)
41 PRK00432 30S ribosomal protein 73.7 2 4.4E-05 29.2 1.4 25 94-118 21-49 (50)
42 cd02340 ZZ_NBR1_like Zinc fing 73.4 1.8 3.9E-05 28.4 1.1 29 95-123 2-32 (43)
43 PF00628 PHD: PHD-finger; Int 72.4 2.4 5.1E-05 27.5 1.4 30 95-124 1-32 (51)
44 COG1571 Predicted DNA-binding 72.1 11 0.00024 36.1 6.3 48 8-56 207-257 (421)
45 cd01781 AF6_RA_repeat2 Ubiquit 70.5 14 0.00031 28.7 5.6 47 1-47 1-51 (100)
46 TIGR01384 TFS_arch transcripti 70.0 2.4 5.2E-05 31.8 1.2 26 94-119 1-29 (104)
47 PF13901 DUF4206: Domain of un 69.9 2.6 5.6E-05 35.8 1.5 35 94-130 153-194 (202)
48 cd01787 GRB7_RA RA (RAS-associ 69.8 13 0.00029 28.1 5.2 46 3-48 4-50 (85)
49 cd01763 Sumo Small ubiquitin-r 69.3 22 0.00049 25.8 6.2 50 2-53 12-61 (87)
50 smart00154 ZnF_AN1 AN1-like Zi 68.5 2.7 5.9E-05 27.1 1.0 21 96-116 1-22 (39)
51 PF13831 PHD_2: PHD-finger; PD 65.8 2.2 4.7E-05 27.1 0.2 16 107-122 5-20 (36)
52 PHA00626 hypothetical protein 65.8 3.6 7.8E-05 29.3 1.3 15 105-119 22-36 (59)
53 cd00207 fer2 2Fe-2S iron-sulfu 62.4 9.7 0.00021 26.4 3.0 22 9-30 5-26 (84)
54 PF14847 Ras_bdg_2: Ras-bindin 59.8 11 0.00024 29.3 3.2 46 3-48 2-49 (105)
55 PF11976 Rad60-SLD: Ubiquitin- 58.5 34 0.00074 23.3 5.2 45 2-46 1-46 (72)
56 PF14804 Jag_N: Jag N-terminus 57.7 9.8 0.00021 26.0 2.3 31 20-50 3-33 (52)
57 PF02824 TGS: TGS domain; Int 57.4 21 0.00046 24.4 4.0 24 4-29 1-24 (60)
58 KOG3532|consensus 57.1 2.2 4.8E-05 43.5 -1.4 47 78-124 68-116 (1051)
59 PF10531 SLBB: SLBB domain; I 56.5 7 0.00015 26.5 1.4 18 14-31 12-29 (59)
60 PF07282 OrfB_Zn_ribbon: Putat 56.0 9.7 0.00021 26.3 2.1 30 90-119 25-59 (69)
61 PF00789 UBX: UBX domain; Int 55.1 71 0.0015 22.4 8.0 56 2-57 7-63 (82)
62 KOG0612|consensus 55.0 2.9 6.2E-05 44.6 -1.0 67 81-148 1208-1277(1317)
63 cd01806 Nedd8 Nebb8-like ubiq 53.3 40 0.00087 22.9 4.9 44 2-45 1-44 (76)
64 PF08827 DUF1805: Domain of un 53.1 5.1 0.00011 28.6 0.3 14 17-30 45-58 (59)
65 cd02339 ZZ_Mind_bomb Zinc fing 52.3 7.3 0.00016 25.9 0.9 28 95-122 2-32 (45)
66 KOG3532|consensus 51.5 3.6 7.9E-05 42.1 -0.9 49 82-130 746-798 (1051)
67 PF06750 DiS_P_DiS: Bacterial 51.3 9.3 0.0002 28.8 1.5 26 91-116 31-68 (92)
68 KOG3784|consensus 51.2 28 0.00061 33.2 4.9 37 2-38 108-144 (407)
69 cd01807 GDX_N ubiquitin-like d 51.0 38 0.00081 23.5 4.5 40 2-41 1-40 (74)
70 smart00249 PHD PHD zinc finger 50.8 8.6 0.00019 23.3 1.0 29 95-123 1-31 (47)
71 TIGR01566 ZF_HD_prot_N ZF-HD h 50.5 7.2 0.00016 27.3 0.7 23 97-119 19-51 (53)
72 PF01428 zf-AN1: AN1-like Zinc 50.5 8.9 0.00019 24.8 1.1 21 96-116 1-23 (43)
73 COG3677 Transposase and inacti 50.2 9.2 0.0002 30.6 1.4 26 94-119 31-66 (129)
74 TIGR02008 fdx_plant ferredoxin 50.0 29 0.00063 25.7 4.0 28 4-31 5-32 (97)
75 PF00111 Fer2: 2Fe-2S iron-sul 49.5 17 0.00037 25.1 2.5 40 9-48 3-49 (78)
76 PF00794 PI3K_rbd: PI3-kinase 48.4 38 0.00083 25.3 4.5 33 2-34 17-50 (106)
77 PF10790 DUF2604: Protein of U 48.3 21 0.00045 26.4 2.8 30 9-38 3-32 (76)
78 COG2023 RPR2 RNase P subunit R 47.5 8.4 0.00018 30.4 0.7 17 94-110 57-73 (105)
79 PTZ00490 Ferredoxin superfamil 46.6 34 0.00074 28.0 4.2 46 3-48 37-89 (143)
80 PF04770 ZF-HD_dimer: ZF-HD pr 46.6 9 0.00019 27.5 0.7 23 97-119 23-55 (60)
81 PF10367 Vps39_2: Vacuolar sor 46.2 12 0.00026 27.1 1.4 31 93-123 78-109 (109)
82 smart00213 UBQ Ubiquitin homol 45.3 57 0.0012 21.0 4.4 39 2-41 1-39 (64)
83 PF13240 zinc_ribbon_2: zinc-r 44.8 11 0.00023 21.8 0.7 21 95-115 1-22 (23)
84 TIGR02007 fdx_isc ferredoxin, 44.0 23 0.0005 27.0 2.7 36 13-48 15-56 (110)
85 PF02641 DUF190: Uncharacteriz 41.9 35 0.00076 25.7 3.4 42 2-50 4-45 (101)
86 cd01796 DDI1_N DNA damage indu 41.3 48 0.001 23.1 3.8 42 4-45 1-44 (71)
87 PRK13552 frdB fumarate reducta 41.2 50 0.0011 28.7 4.6 65 12-77 24-99 (239)
88 COG1594 RPB9 DNA-directed RNA 40.8 15 0.00032 28.8 1.2 27 93-119 2-35 (113)
89 KOG2907|consensus 40.6 9.8 0.00021 30.5 0.2 28 91-118 5-37 (116)
90 KOG2906|consensus 40.6 16 0.00034 28.8 1.3 25 93-117 1-32 (105)
91 PHA02768 hypothetical protein; 39.6 12 0.00026 26.2 0.5 14 105-118 4-17 (55)
92 PF14803 Nudix_N_2: Nudix N-te 39.2 16 0.00035 23.0 1.0 22 95-116 2-32 (34)
93 cd01794 DC_UbP_C dendritic cel 38.7 55 0.0012 23.0 3.8 38 4-41 1-38 (70)
94 TIGR01053 LSD1 zinc finger dom 38.7 17 0.00036 22.6 0.9 20 95-114 3-27 (31)
95 PF07660 STN: Secretin and Ton 38.3 18 0.0004 23.3 1.2 27 11-38 13-39 (52)
96 PTZ00038 ferredoxin; Provision 38.1 43 0.00094 28.7 3.7 27 4-31 98-124 (191)
97 cd02335 ZZ_ADA2 Zinc finger, Z 37.5 17 0.00037 24.1 0.9 26 95-120 2-30 (49)
98 PF07754 DUF1610: Domain of un 36.6 20 0.00044 21.2 1.1 19 96-114 1-24 (24)
99 PF03658 Ub-RnfH: RnfH family 36.6 42 0.00091 25.3 3.0 24 8-31 9-33 (84)
100 PRK11433 aldehyde oxidoreducta 35.0 49 0.0011 29.0 3.6 62 4-68 52-121 (217)
101 PF11275 DUF3077: Protein of u 35.0 40 0.00087 25.1 2.7 25 10-34 12-36 (79)
102 cd02249 ZZ Zinc finger, ZZ typ 34.7 20 0.00042 23.3 0.9 30 95-124 2-33 (46)
103 KOG1829|consensus 34.4 9.2 0.0002 38.0 -1.1 24 107-130 532-555 (580)
104 TIGR00568 alkb DNA alkylation 33.7 80 0.0017 26.2 4.5 39 24-62 79-117 (169)
105 PRK11872 antC anthranilate dio 33.7 55 0.0012 29.3 3.9 28 4-31 5-32 (340)
106 COG2888 Predicted Zn-ribbon RN 33.6 22 0.00048 25.6 1.0 8 107-114 51-58 (61)
107 PF00096 zf-C2H2: Zinc finger, 33.5 19 0.00042 19.4 0.6 12 107-118 1-12 (23)
108 CHL00134 petF ferredoxin; Vali 33.4 47 0.001 24.9 2.8 28 4-31 4-34 (99)
109 PF10571 UPF0547: Uncharacteri 33.0 25 0.00054 20.9 1.0 21 96-116 3-24 (26)
110 PRK05950 sdhB succinate dehydr 32.9 69 0.0015 27.4 4.2 65 12-77 18-94 (232)
111 PF13510 Fer2_4: 2Fe-2S iron-s 32.6 35 0.00077 24.7 2.0 17 15-31 12-28 (82)
112 PRK05659 sulfur carrier protei 32.5 1.2E+02 0.0027 20.4 4.7 48 15-67 9-57 (66)
113 COG1198 PriA Primosomal protei 32.3 67 0.0014 32.9 4.5 80 24-115 405-484 (730)
114 PRK08640 sdhB succinate dehydr 32.1 86 0.0019 27.5 4.7 64 12-77 23-104 (249)
115 PF13894 zf-C2H2_4: C2H2-type 31.9 23 0.00049 18.6 0.7 12 107-118 1-12 (24)
116 PF13085 Fer2_3: 2Fe-2S iron-s 29.9 1.4E+02 0.0031 23.3 5.1 65 12-77 19-97 (110)
117 PTZ00044 ubiquitin; Provisiona 29.8 1.4E+02 0.003 20.5 4.6 41 3-43 2-42 (76)
118 COG0675 Transposase and inacti 29.7 38 0.00083 28.6 2.1 29 90-119 306-335 (364)
119 PF01780 Ribosomal_L37ae: Ribo 29.4 24 0.00051 27.1 0.7 25 93-117 35-64 (90)
120 cd01792 ISG15_repeat1 ISG15 ub 29.2 1.3E+02 0.0029 21.2 4.5 40 2-41 3-42 (80)
121 COG5349 Uncharacterized protei 28.9 22 0.00049 28.9 0.5 29 94-122 22-56 (126)
122 PF06220 zf-U1: U1 zinc finger 28.9 23 0.00049 22.7 0.4 11 94-104 4-14 (38)
123 PRK12386 fumarate reductase ir 28.7 1E+02 0.0022 27.2 4.6 64 12-77 20-96 (251)
124 PRK07570 succinate dehydrogena 28.6 1E+02 0.0022 27.2 4.5 66 12-77 20-109 (250)
125 PF09297 zf-NADH-PPase: NADH p 28.5 31 0.00067 20.8 0.9 22 94-115 4-30 (32)
126 PF04106 APG5: Autophagy prote 28.4 32 0.0007 29.1 1.4 32 3-34 112-150 (197)
127 cd01809 Scythe_N Ubiquitin-lik 28.1 1.6E+02 0.0035 19.5 4.7 40 2-41 1-40 (72)
128 PF13824 zf-Mss51: Zinc-finger 27.9 36 0.00077 23.9 1.3 23 95-117 1-25 (55)
129 KOG0612|consensus 27.9 6 0.00013 42.3 -3.7 45 83-133 894-942 (1317)
130 PF13465 zf-H2C2_2: Zinc-finge 27.5 29 0.00063 20.0 0.7 10 107-116 15-24 (26)
131 COG2818 Tag 3-methyladenine DN 27.1 43 0.00093 28.9 1.9 17 22-38 140-156 (188)
132 TIGR02098 MJ0042_CXXC MJ0042 f 26.8 42 0.00092 20.6 1.4 24 94-117 3-36 (38)
133 PF01783 Ribosomal_L32p: Ribos 26.4 34 0.00075 23.4 1.0 23 92-114 25-47 (56)
134 cd01802 AN1_N ubiquitin-like d 26.3 1.7E+02 0.0037 22.2 4.9 40 2-41 28-67 (103)
135 PRK08364 sulfur carrier protei 25.5 2.4E+02 0.0052 19.6 6.3 31 14-48 16-46 (70)
136 COG0479 FrdB Succinate dehydro 25.2 3.2E+02 0.0069 24.2 7.0 73 4-77 7-95 (234)
137 cd01783 DAGK_delta_RA Ubiquiti 25.0 81 0.0018 24.5 2.9 48 14-61 19-74 (97)
138 PF12773 DZR: Double zinc ribb 24.9 39 0.00084 21.8 1.0 24 93-116 12-39 (50)
139 PRK14890 putative Zn-ribbon RN 24.8 40 0.00086 24.1 1.1 8 107-114 49-56 (59)
140 COG1645 Uncharacterized Zn-fin 24.8 40 0.00086 27.5 1.2 23 94-116 29-54 (131)
141 smart00659 RPOLCX RNA polymera 24.7 45 0.00097 22.0 1.3 20 96-115 5-28 (44)
142 PF13248 zf-ribbon_3: zinc-rib 24.4 41 0.0009 19.5 0.9 21 94-114 3-24 (26)
143 COG1993 PII-like signaling pro 24.1 96 0.0021 24.7 3.2 65 2-73 7-75 (109)
144 PF01927 Mut7-C: Mut7-C RNAse 23.6 1.3E+02 0.0028 24.0 4.0 76 16-107 63-138 (147)
145 PRK12576 succinate dehydrogena 23.4 1.3E+02 0.0027 26.9 4.2 65 12-77 25-103 (279)
146 KOG1701|consensus 23.4 66 0.0014 31.3 2.6 74 21-114 341-435 (468)
147 COG4379 Mu-like prophage tail 23.2 62 0.0013 30.7 2.3 26 13-38 142-167 (386)
148 TIGR01031 rpmF_bact ribosomal 23.0 42 0.00092 23.1 0.9 26 89-114 22-47 (55)
149 PF14369 zf-RING_3: zinc-finge 23.0 48 0.001 20.8 1.1 23 94-116 3-31 (35)
150 PF03604 DNA_RNApol_7kD: DNA d 23.0 45 0.00098 20.8 1.0 20 96-115 3-26 (32)
151 TIGR00624 tag DNA-3-methyladen 22.9 74 0.0016 27.0 2.5 22 17-38 131-152 (179)
152 KOG3799|consensus 22.8 27 0.00058 29.2 -0.1 33 93-125 65-100 (169)
153 PRK12286 rpmF 50S ribosomal pr 22.3 48 0.001 23.1 1.1 25 90-114 24-48 (57)
154 COG1997 RPL43A Ribosomal prote 22.3 49 0.0011 25.5 1.2 29 92-120 34-67 (89)
155 PF04502 DUF572: Family of unk 22.2 43 0.00092 30.4 1.0 14 94-107 41-54 (324)
156 PF11781 RRN7: RNA polymerase 22.1 40 0.00087 21.4 0.6 19 96-114 11-33 (36)
157 PRK05978 hypothetical protein; 21.9 45 0.00097 27.6 1.0 26 94-119 34-65 (148)
158 PF09082 DUF1922: Domain of un 21.6 39 0.00085 24.7 0.6 21 96-118 6-31 (68)
159 KOG2462|consensus 21.1 47 0.001 30.3 1.0 12 106-117 187-198 (279)
160 PF13909 zf-H2C2_5: C2H2-type 21.1 47 0.001 18.2 0.7 10 107-116 1-10 (24)
161 PF02591 DUF164: Putative zinc 20.8 39 0.00085 22.7 0.4 13 91-103 44-56 (56)
162 PRK15401 alpha-ketoglutarate-d 20.7 1.9E+02 0.0041 25.1 4.7 26 36-61 112-137 (213)
163 cd02338 ZZ_PCMF_like Zinc fing 20.7 49 0.0011 22.0 0.8 19 95-113 2-22 (49)
164 cd02344 ZZ_HERC2 Zinc finger, 20.4 52 0.0011 21.9 0.9 26 95-120 2-30 (45)
165 PF06943 zf-LSD1: LSD1 zinc fi 20.4 57 0.0012 19.5 1.0 19 96-114 1-24 (25)
166 cd06406 PB1_P67 A PB1 domain i 20.4 2E+02 0.0044 21.5 4.2 44 2-47 3-47 (80)
167 PF08792 A2L_zn_ribbon: A2L zi 20.3 63 0.0014 20.2 1.2 23 94-116 4-31 (33)
No 1
>cd01816 Raf_RBD Ubiquitin domain of Raf serine/threonine kinases. The Raf serine/threonine kinases are composed of three conserved regions, CR1, CR2 and CR3. CR1 has two Ras binding domains (RBD and CRD), CR2 is a serine/threonine rich domain and CR3 is the catalytic kinase domain. The RBD of Raf is structurally similar to ubiquitin with little of no sequence similarity.The Raf signalling pathway plays an important role in the proliferation and survival of tumor cells.
Probab=100.00 E-value=9.8e-36 Score=217.39 Aligned_cols=70 Identities=47% Similarity=0.808 Sum_probs=66.4
Q ss_pred eEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccEEEecCCC----CcccCCCCCCCCCCcceeeeee
Q psy7966 3 LLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTG----VSLQWDTDSDHLPTTEIRVEVQ 72 (194)
Q Consensus 3 ~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~~~----~~i~w~tD~~~L~~eel~V~~~ 72 (194)
+|||||||||||+|+|||||||+|||+||||+|||+||||+||+.+++ ..|+||||+++|.|+||+||++
T Consensus 1 ~ir~~LPnqQrT~V~vrpG~tl~daL~KaLk~R~l~pe~C~V~~~~~~~~~~~~i~W~td~~~L~geEL~V~~l 74 (74)
T cd01816 1 LIRVFLPNKQRTVVNVRPGMTLRDALAKALKVRGLQPECCAVFRLGDGSSKKLRIDWDTDISSLIGEELQVEVL 74 (74)
T ss_pred CeeEECCCCCeEEEEecCCcCHHHHHHHHHHHcCCChhHeEEEEcCCCcccccccchhhhhhhccCceEEEEeC
Confidence 589999999999999999999999999999999999999999999866 4599999999999999999973
No 2
>KOG0193|consensus
Probab=99.97 E-value=1.6e-32 Score=261.65 Aligned_cols=139 Identities=42% Similarity=0.784 Sum_probs=125.7
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccEEEecC--CCCc--ccCCCCCCCCCCcceeeeeehhcCC
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSN--TGVS--LQWDTDSDHLPTTEIRVEVQERFPA 77 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~--~~~~--i~w~tD~~~L~~eel~V~~~~~~p~ 77 (194)
.+++|||||+|||+|+|+.|++++|+|+|||++|+++|++|+||+.. .+.. ++|+++++++.|+|+.||.++.+|+
T Consensus 97 ~~~~v~Lpn~q~t~v~~~~g~s~~d~~~k~l~~r~~tP~~c~v~~~~~~~~~r~~~~~~~~~~~l~geE~~ve~l~~vpl 176 (678)
T KOG0193|consen 97 PTKRVHLPNKQRTVVSVRSGVSVRDSLLKALKKRGLTPDCCVVFRSLLTKGRRTRLPWDTIASPLDGEELHVEPLENVPL 176 (678)
T ss_pred CceEEeccCcceeEEEeecCCccchHHHhhhhhccCCCccceeehhhhhhccccccCcccCCCCCCccceeeeeccCCCc
Confidence 36899999999999999999999999999999999999999999984 3333 8999999999999999999999999
Q ss_pred CCCccceeeccccCCccCCc-cccccccccccccccCceecccccccccccccccccchhhhhhhccCCC
Q psy7966 78 AINIEHNITRRTFFAIAFCD-ACHKLLFSGHLCRTCGFKFHRACNLAVPYLCQVERIQQTYYQMLLASNA 146 (194)
Q Consensus 78 ~~~~~H~F~~~Tf~~ptfCd-~C~klL~QG~kCk~Cg~~~HkrC~~~Vp~~C~~~~~~~~~~~~ll~~~p 146 (194)
.+ |+|++|||+.++||| .|.++|++||+|+.|+|+||++|+.+||..|+.. +..++.+.+..|
T Consensus 177 ~~---H~~~rktf~~~~fC~~~~~~~l~~gfrC~~C~~KfHq~Cs~~vp~~C~~~---~~~~~~~~~~~~ 240 (678)
T KOG0193|consen 177 TT---HNFVRKTFFPLAFCDSCCNKFLFTGFRCQTCGYKFHQSCSPRVPTSCVNP---DHLRQLLVFEFP 240 (678)
T ss_pred cc---eeeeeccccchhhhhhhcchhhhcccccCCCCCccccccCCCCCCCCCCc---chHhhhhhhccc
Confidence 76 999999999999999 7788899999999999999999999999999943 555566666565
No 3
>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=99.92 E-value=9.4e-26 Score=164.83 Aligned_cols=68 Identities=26% Similarity=0.333 Sum_probs=65.7
Q ss_pred EEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccEEEecCCCCcccCCCCCCCCCCcceeeee
Q psy7966 4 LRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTGVSLQWDTDSDHLPTTEIRVEV 71 (194)
Q Consensus 4 irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~~~~~i~w~tD~~~L~~eel~V~~ 71 (194)
-||||||+|+|+|+||||+||+|+|+|+|++|||.+++|+||..+...+|+||+|++.|.|+||.||-
T Consensus 2 crV~LPdg~~T~V~vrpG~ti~d~L~kllekRgl~~~~~~vf~~g~~k~l~~~qD~~~L~~~El~vE~ 69 (73)
T cd01817 2 CRVILPDGSTTVVPTRPGESIRDLLSGLCEKRGINYAAVDLFLVGGDKPLVLDQDSSVLAGQEVRLEK 69 (73)
T ss_pred cEEECCCCCeEEEEecCCCCHHHHHHHHHHHcCCChhHEEEEEecCCcccccCCccceeeccEEEEEE
Confidence 58999999999999999999999999999999999999999999888889999999999999999984
No 4
>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=99.92 E-value=1.1e-25 Score=162.39 Aligned_cols=69 Identities=48% Similarity=0.700 Sum_probs=62.8
Q ss_pred eEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccEEEecCCCCcccCCCCCCCCCCcceeeee
Q psy7966 3 LLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTGVSLQWDTDSDHLPTTEIRVEV 71 (194)
Q Consensus 3 ~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~~~~~i~w~tD~~~L~~eel~V~~ 71 (194)
++||||||+|+|+|+||||+|++|||+|+|++|||.+++|.||+.+....++||+|++.|.|+|++||.
T Consensus 2 ~~~v~LP~~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V~~~~~~k~l~~~~d~~~L~~~El~ve~ 70 (71)
T PF02196_consen 2 TCRVHLPNGQRTVVQVRPGMTIRDALSKACKKRGLNPECCDVRLVGEKKPLDWDQDSSSLPGEELRVEK 70 (71)
T ss_dssp EEEEEETTTEEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEEEEEEEEEEE-TTSBGGGGTTSEEEEEE
T ss_pred eEEEECCCCCEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCccccCCCceeeecCCEEEEEe
Confidence 689999999999999999999999999999999999999999999977889999999999999999985
No 5
>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=99.90 E-value=5.4e-24 Score=154.76 Aligned_cols=69 Identities=42% Similarity=0.586 Sum_probs=66.0
Q ss_pred eEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccEEEecCCC--CcccCCCCCCCCCCcceeeee
Q psy7966 3 LLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTG--VSLQWDTDSDHLPTTEIRVEV 71 (194)
Q Consensus 3 ~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~~~--~~i~w~tD~~~L~~eel~V~~ 71 (194)
++||||||+|+|+|+||||||++|+|+|||++|||.|++|.||..+.+ ..++|++|++.|.++||+|+.
T Consensus 1 ~~~V~LPng~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~~~~~~~~~~~~~~d~~~L~~~El~Ve~ 71 (72)
T cd01760 1 LCRVYLPNGQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLLGLDEKKPLDLDTDSSSLAGEELEVEP 71 (72)
T ss_pred CEEEECcCCCeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEecCCCcCCcCchhhhhhhcCCEEEEEe
Confidence 479999999999999999999999999999999999999999999877 679999999999999999985
No 6
>smart00455 RBD Raf-like Ras-binding domain.
Probab=99.87 E-value=3.1e-22 Score=144.28 Aligned_cols=69 Identities=35% Similarity=0.510 Sum_probs=66.2
Q ss_pred eEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccEEEecCCCCcccCCCCCCCCCCcceeeee
Q psy7966 3 LLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTGVSLQWDTDSDHLPTTEIRVEV 71 (194)
Q Consensus 3 ~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~~~~~i~w~tD~~~L~~eel~V~~ 71 (194)
.++|||||+|+|+|.||||+|++|+|+|+|++|||.|++|.||..+.+.+++|++|++.|.|+|+++|.
T Consensus 1 ~~~v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~g~~k~ldl~~~~~~l~~~el~ve~ 69 (70)
T smart00455 1 TCKVHLPDNQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRGEKKPLDLNQPISSLDGQELVVEE 69 (70)
T ss_pred CeEEECCCCCEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCcceecCCccccccCceEEEEe
Confidence 379999999999999999999999999999999999999999999888889999999999999999985
No 7
>KOG4236|consensus
Probab=99.45 E-value=2.6e-14 Score=137.24 Aligned_cols=57 Identities=32% Similarity=0.794 Sum_probs=51.6
Q ss_pred hcCCCCCccceeeccccCCccCCcccccccc----ccccccccCceeccccccccccccccccc
Q psy7966 74 RFPAAINIEHNITRRTFFAIAFCDACHKLLF----SGHLCRTCGFKFHRACNLAVPYLCQVERI 133 (194)
Q Consensus 74 ~~p~~~~~~H~F~~~Tf~~ptfCd~C~klL~----QG~kCk~Cg~~~HkrC~~~Vp~~C~~~~~ 133 (194)
+|.+. +|....|+|+.|||||+|+++|| ||+||+.||.|+||||+.++|++|.+.+.
T Consensus 140 d~~i~---PH~l~vhSY~~PtFCD~CGEmL~GLvrQGlKC~gCglNyHKRCa~kipNNCsG~r~ 200 (888)
T KOG4236|consen 140 DFQIR---PHTLFVHSYKAPTFCDFCGEMLFGLVRQGLKCEGCGLNYHKRCAFKIPNNCSGVRK 200 (888)
T ss_pred ceeee---cceeeeecccCchHHHHHHHHHHHHHHccccccCCCCcHhhhhhhcCCCCCCcccc
Confidence 35554 49999999999999999999999 99999999999999999999999977543
No 8
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=99.39 E-value=1.7e-13 Score=91.93 Aligned_cols=48 Identities=33% Similarity=0.784 Sum_probs=43.0
Q ss_pred ceeeccccCCccCCcccccccc----ccccccccCceecccccccccccccc
Q psy7966 83 HNITRRTFFAIAFCDACHKLLF----SGHLCRTCGFKFHRACNLAVPYLCQV 130 (194)
Q Consensus 83 H~F~~~Tf~~ptfCd~C~klL~----QG~kCk~Cg~~~HkrC~~~Vp~~C~~ 130 (194)
|+|+..+|..|++|++|+++|| |||+|+.|++.+|++|.+.++..|+.
T Consensus 1 H~f~~~~~~~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~~~~C~~ 52 (53)
T PF00130_consen 1 HHFVPTTFSKPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKVPPSCGC 52 (53)
T ss_dssp -EEEEEESSSTEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTSSSBSST
T ss_pred CeEEEccCCCCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhcCCCCCC
Confidence 8999999999999999999995 99999999999999999999999863
No 9
>KOG4236|consensus
Probab=99.29 E-value=3.5e-13 Score=129.56 Aligned_cols=71 Identities=25% Similarity=0.510 Sum_probs=59.3
Q ss_pred CCCCCcceeeeeehhcCCCCCccceeeccccCCccCCcccccccc----ccccccccCceecccccccccccccccc
Q psy7966 60 DHLPTTEIRVEVQERFPAAINIEHNITRRTFFAIAFCDACHKLLF----SGHLCRTCGFKFHRACNLAVPYLCQVER 132 (194)
Q Consensus 60 ~~L~~eel~V~~~~~~p~~~~~~H~F~~~Tf~~ptfCd~C~klL~----QG~kCk~Cg~~~HkrC~~~Vp~~C~~~~ 132 (194)
.+..|..+|.+... -.+...+|+|..|+|..||.|.+|+++|- ||++|++|+|||||||+.+||.+|.+..
T Consensus 247 ~S~sgrpi~~ek~~--~~rvkvPHTf~vHSY~rpTVCq~CkkLLkGL~rQGlqCkDCk~NcHkrCa~~v~~dClge~ 321 (888)
T KOG4236|consen 247 LSWSGRPIWMEKML--MSRVKVPHTFIVHSYTRPTVCQYCKKLLKGLFRQGLQCKDCKFNCHKRCAMKVPNDCLGEV 321 (888)
T ss_pred ccccCCCchhhhhh--hhcccCCeeEEEeeccCchHHHHHHHHHHHHHhcCcccccCCcchhhhhhhhcccccccce
Confidence 33567777766432 23455789999999999999999999874 9999999999999999999999998754
No 10
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=99.19 E-value=5.4e-12 Score=82.54 Aligned_cols=46 Identities=39% Similarity=0.916 Sum_probs=44.1
Q ss_pred ceeeccccCCccCCcccccccc----ccccccccCceecccccccccccc
Q psy7966 83 HNITRRTFFAIAFCDACHKLLF----SGHLCRTCGFKFHRACNLAVPYLC 128 (194)
Q Consensus 83 H~F~~~Tf~~ptfCd~C~klL~----QG~kCk~Cg~~~HkrC~~~Vp~~C 128 (194)
|.|...+|..+++|++|+++|| ||++|+.|++.+|++|..+|+..|
T Consensus 1 H~f~~~~~~~~~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~~v~~~C 50 (50)
T cd00029 1 HRFVRKSFFKPTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADKVPPSC 50 (50)
T ss_pred CccEEeeCCCCCChhhcchhhhccccceeEcCCCCCchhhhhhccCCCCC
Confidence 8899999999999999999999 999999999999999999999876
No 11
>KOG0696|consensus
Probab=99.18 E-value=3.2e-12 Score=120.45 Aligned_cols=52 Identities=35% Similarity=0.768 Sum_probs=49.3
Q ss_pred CCccceeeccccCCccCCcccccccc----ccccccccCceecccccccccccccc
Q psy7966 79 INIEHNITRRTFFAIAFCDACHKLLF----SGHLCRTCGFKFHRACNLAVPYLCQV 130 (194)
Q Consensus 79 ~~~~H~F~~~Tf~~ptfCd~C~klL~----QG~kCk~Cg~~~HkrC~~~Vp~~C~~ 130 (194)
++..|.|..+||.+|||||||+++|+ ||+||+.|..|+|++|...||+.|+-
T Consensus 107 pr~kHkf~~~tYssPTFCDhCGsLLyGl~HQGmKC~~C~mNVH~rCv~nVPslCG~ 162 (683)
T KOG0696|consen 107 PRSKHKFKIHTYSSPTFCDHCGSLLYGLIHQGMKCDTCDMNVHHRCVENVPSLCGT 162 (683)
T ss_pred cccccceeeeecCCCchhhhHHHHHHHHHhcccccccccchHHHHHhhcCCcccCC
Confidence 44679999999999999999999998 99999999999999999999999985
No 12
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=99.14 E-value=1.2e-11 Score=80.02 Aligned_cols=46 Identities=35% Similarity=0.725 Sum_probs=43.4
Q ss_pred ceeeccccCCccCCcccccccc---ccccccccCceecccccccccccc
Q psy7966 83 HNITRRTFFAIAFCDACHKLLF---SGHLCRTCGFKFHRACNLAVPYLC 128 (194)
Q Consensus 83 H~F~~~Tf~~ptfCd~C~klL~---QG~kCk~Cg~~~HkrC~~~Vp~~C 128 (194)
|.|...+|..+++|++|+++|| ||++|+.|++.+|++|..+|+..|
T Consensus 1 H~~~~~~~~~~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~~v~~~C 49 (49)
T smart00109 1 HHFVERTFKKPTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAEKVPQPC 49 (49)
T ss_pred CceEEeccCCCCCccccccccCcCCCCcCCCCCCchHHHHHHhhcCCCC
Confidence 7899999999999999999999 699999999999999999999876
No 13
>KOG0696|consensus
Probab=98.86 E-value=4.4e-10 Score=106.22 Aligned_cols=51 Identities=27% Similarity=0.738 Sum_probs=48.5
Q ss_pred cceeeccccCCccCCcccccccc----ccccccccCceecccccccccccccccc
Q psy7966 82 EHNITRRTFFAIAFCDACHKLLF----SGHLCRTCGFKFHRACNLAVPYLCQVER 132 (194)
Q Consensus 82 ~H~F~~~Tf~~ptfCd~C~klL~----QG~kCk~Cg~~~HkrC~~~Vp~~C~~~~ 132 (194)
.|.|..+.|++||||.||..||| |||+|+.|.|..|+||.+.|...|.+..
T Consensus 45 ~HkF~aRFFKqPTfCsHCkDFiwGfgKQGfQCqvC~fvvHkrChefVtF~CPGad 99 (683)
T KOG0696|consen 45 SHKFIARFFKQPTFCSHCKDFIWGFGKQGFQCQVCCFVVHKRCHEFVTFSCPGAD 99 (683)
T ss_pred cceeeehhccCCchhhhhhhheeccccCceeeeEEeehhhhhhcceEEEECCCCC
Confidence 49999999999999999999999 9999999999999999999999998753
No 14
>KOG1011|consensus
Probab=98.69 E-value=1.2e-09 Score=106.97 Aligned_cols=73 Identities=27% Similarity=0.599 Sum_probs=64.9
Q ss_pred CCCCCcceeeeeehh------cCCCCCccceeeccccCCccCCcccccccc----ccccccccCceeccccccccccccc
Q psy7966 60 DHLPTTEIRVEVQER------FPAAINIEHNITRRTFFAIAFCDACHKLLF----SGHLCRTCGFKFHRACNLAVPYLCQ 129 (194)
Q Consensus 60 ~~L~~eel~V~~~~~------~p~~~~~~H~F~~~Tf~~ptfCd~C~klL~----QG~kCk~Cg~~~HkrC~~~Vp~~C~ 129 (194)
.++..+||..|+.++ .|++.-.+|||...||..||||.-|..+|| ||++|..|++++|.+|.+.+.+.|.
T Consensus 144 tt~~d~elkthvykktlqaliypis~ttphnf~~~t~~tpt~cyecegllwglarqglrctqc~vk~hdkc~ell~adcl 223 (1283)
T KOG1011|consen 144 TTFSDTELKTHVYKKTLQALIYPISATTPHNFATTTFQTPTFCYECEGLLWGLARQGLRCTQCQVKVHDKCRELLSADCL 223 (1283)
T ss_pred cccchHHHHHHHHHHHHHHheeecccCCCCceeeeeccCCchhhhhhhHHHHHhhcccchhhccccHHHHHHHHhhhHHH
Confidence 346678888887765 788877899999999999999999999999 9999999999999999999999997
Q ss_pred ccc
Q psy7966 130 VER 132 (194)
Q Consensus 130 ~~~ 132 (194)
.+.
T Consensus 224 qra 226 (1283)
T KOG1011|consen 224 QRA 226 (1283)
T ss_pred HHH
Confidence 654
No 15
>KOG0694|consensus
Probab=98.44 E-value=5.7e-08 Score=95.04 Aligned_cols=56 Identities=27% Similarity=0.540 Sum_probs=51.5
Q ss_pred CCccceeeccccCCccCCcccccccc----ccccccccCceecccccccccccccccccc
Q psy7966 79 INIEHNITRRTFFAIAFCDACHKLLF----SGHLCRTCGFKFHRACNLAVPYLCQVERIQ 134 (194)
Q Consensus 79 ~~~~H~F~~~Tf~~ptfCd~C~klL~----QG~kCk~Cg~~~HkrC~~~Vp~~C~~~~~~ 134 (194)
.+++|.|.+++|..|+||+||+++|| ||++|..|+.++|.+|...++..|+..+..
T Consensus 227 ~~~Phrf~~~~~q~ptFc~hCGs~L~r~~qqGlkCs~Cg~n~H~~c~~~va~~CG~s~t~ 286 (694)
T KOG0694|consen 227 FRNPHRFVKLNRQRPTFCDHCGSVLYRLRQQGLKCSTCGRNVHNRCVENLAPNCGGSRTF 286 (694)
T ss_pred ccCCCcchhhhccCccHHHhcchhhhhhcccCeeehhhhccccHHHHHhcccCCCCchhh
Confidence 34569999999999999999999998 999999999999999999999999987643
No 16
>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=98.28 E-value=1e-06 Score=65.43 Aligned_cols=37 Identities=27% Similarity=0.360 Sum_probs=35.1
Q ss_pred EEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCc
Q psy7966 5 RAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEM 41 (194)
Q Consensus 5 rv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~ 41 (194)
.|+|||+|+..|.||||||+.|.|+-|+|+|+|.|.-
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 5899999999999999999999999999999998874
No 17
>KOG0694|consensus
Probab=97.96 E-value=1.4e-06 Score=85.52 Aligned_cols=51 Identities=25% Similarity=0.635 Sum_probs=48.5
Q ss_pred cceeeccccCCccCCcccccccc----ccccccccCceecccccccccccccccc
Q psy7966 82 EHNITRRTFFAIAFCDACHKLLF----SGHLCRTCGFKFHRACNLAVPYLCQVER 132 (194)
Q Consensus 82 ~H~F~~~Tf~~ptfCd~C~klL~----QG~kCk~Cg~~~HkrC~~~Vp~~C~~~~ 132 (194)
.|.|.-+.|.+|++|.+|.+|+| |||+|..|...+|++|..+|...|....
T Consensus 158 gH~F~aT~l~Qpt~Cs~C~kFi~gL~kqGyQCqvC~~vvHKkCh~kvv~~C~~~~ 212 (694)
T KOG0694|consen 158 GHKFGATSLRQPTFCSWCQKFIWGLRKQGYQCQVCWRVVHKKCHVKVVTLCDFLD 212 (694)
T ss_pred CcEEEEeeccCcchhhhhhhheeccCCCceEEeeeeehHhhhhHHHHHHhccCcC
Confidence 49999999999999999999999 8999999999999999999999998764
No 18
>KOG0695|consensus
Probab=97.66 E-value=1.8e-05 Score=74.11 Aligned_cols=51 Identities=25% Similarity=0.616 Sum_probs=48.5
Q ss_pred ccceeeccccCCccCCcccccccc----ccccccccCceeccccccccccccccc
Q psy7966 81 IEHNITRRTFFAIAFCDACHKLLF----SGHLCRTCGFKFHRACNLAVPYLCQVE 131 (194)
Q Consensus 81 ~~H~F~~~Tf~~ptfCd~C~klL~----QG~kCk~Cg~~~HkrC~~~Vp~~C~~~ 131 (194)
..|.|.-|.|-.-+.|..|...|| |||+|-.|..-+|++|...|+..|+.-
T Consensus 129 ngh~fqakr~nrr~~c~ic~d~iwglgrqgyrcinckl~vhkkch~~v~~~cg~~ 183 (593)
T KOG0695|consen 129 NGHLFQAKRFNRRAYCGICSDRIWGLGRQGYRCINCKLLVHKKCHGLVPLTCGKH 183 (593)
T ss_pred cCcchhhhhhccceeeeechhhhhhcccccceeecceeehhhhhcccccchhhhh
Confidence 359999999999999999999999 999999999999999999999999875
No 19
>KOG2996|consensus
Probab=97.65 E-value=9.9e-06 Score=79.10 Aligned_cols=49 Identities=33% Similarity=0.644 Sum_probs=44.6
Q ss_pred ccceeeccccCCccCCcccccccc----ccccccccCceecccccccccccccc
Q psy7966 81 IEHNITRRTFFAIAFCDACHKLLF----SGHLCRTCGFKFHRACNLAVPYLCQV 130 (194)
Q Consensus 81 ~~H~F~~~Tf~~ptfCd~C~klL~----QG~kCk~Cg~~~HkrC~~~Vp~~C~~ 130 (194)
..|.|..+||..+|.|+.|..+|- |||+|.-||...|+-|..+||+ |+.
T Consensus 522 n~H~fqmhtF~~~tsCkvC~mllrGtfYQGY~C~~c~~~ahkecl~~vp~-cgr 574 (865)
T KOG2996|consen 522 NNHDFQMHTFKNTTSCKVCQMLLRGTFYQGYKCEKCGADAHKECLGRVPP-CGR 574 (865)
T ss_pred cCcceEEEeccCCcchHHHHHHhhhhhhcceeeeeccccHHHHhccCCCC-ccc
Confidence 459999999999999999999873 9999999999999999999994 743
No 20
>KOG4239|consensus
Probab=97.41 E-value=3.2e-05 Score=70.51 Aligned_cols=54 Identities=26% Similarity=0.643 Sum_probs=49.2
Q ss_pred cceeeccccCCccCCcccccccc----ccccccccCceecccccccccccccccccch
Q psy7966 82 EHNITRRTFFAIAFCDACHKLLF----SGHLCRTCGFKFHRACNLAVPYLCQVERIQQ 135 (194)
Q Consensus 82 ~H~F~~~Tf~~ptfCd~C~klL~----QG~kCk~Cg~~~HkrC~~~Vp~~C~~~~~~~ 135 (194)
.|+|.-..-.-|+.||.|+.++| +|++|..|||.||-||...+-.+|.+....+
T Consensus 51 ~~~~~~~g~~~~~~~~~c~~~~~~vl~egL~c~~c~~tch~rcr~lv~ldc~~p~~sS 108 (348)
T KOG4239|consen 51 GHNFYTAGLLLPTWCDKCGDFIWGVLREGLLCIHCKFTCHIRCRMLVDLDCRSPPSSS 108 (348)
T ss_pred ccccccccccccccchhhhHHHHHHHHHHHhhhhcCCccCHHHHhhhhhhhcCCCCCc
Confidence 49999888888999999999999 9999999999999999999999998876333
No 21
>KOG3564|consensus
Probab=96.84 E-value=0.00032 Score=67.32 Aligned_cols=51 Identities=22% Similarity=0.377 Sum_probs=47.0
Q ss_pred ccceeeccccCCccCCcccccccc---ccccccccCceeccccccccccccccc
Q psy7966 81 IEHNITRRTFFAIAFCDACHKLLF---SGHLCRTCGFKFHRACNLAVPYLCQVE 131 (194)
Q Consensus 81 ~~H~F~~~Tf~~ptfCd~C~klL~---QG~kCk~Cg~~~HkrC~~~Vp~~C~~~ 131 (194)
-.|.|+.++|..+-+|++|++-|- -++||++|-..+|..|..+.+..|...
T Consensus 285 r~htfi~kt~~~~~~Cv~C~krIkfg~~sLkCRdC~v~~H~~Cr~~l~lpCIP~ 338 (604)
T KOG3564|consen 285 RLHTFISKTVIKPENCVPCGKRIKFGKLSLKCRDCPVVCHIECRDKLTLPCIPT 338 (604)
T ss_pred ccchhhHhhccCcccchhhhhhhhhhhcccccccCCeeechhHHhcCCCCCcCc
Confidence 459999999999999999999884 589999999999999999999999863
No 22
>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=96.76 E-value=0.0038 Score=38.34 Aligned_cols=45 Identities=18% Similarity=0.228 Sum_probs=40.8
Q ss_pred EEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccEEEecCC
Q psy7966 5 RAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNT 49 (194)
Q Consensus 5 rv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~~ 49 (194)
+|++++++..++.+.++.|+.+.+.+++++.|+.++...++..+.
T Consensus 1 ~v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~~ 45 (69)
T cd00196 1 KVKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGK 45 (69)
T ss_pred CeEecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECCe
Confidence 478899999999999999999999999999999999898887653
No 23
>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=95.35 E-value=0.042 Score=39.40 Aligned_cols=42 Identities=24% Similarity=0.196 Sum_probs=29.5
Q ss_pred EEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccEEEec
Q psy7966 6 AQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDS 47 (194)
Q Consensus 6 v~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~ 47 (194)
+..||.+|.+|.|-|+++|.|.|..|+++-||.++.......
T Consensus 1 vi~~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~ 42 (65)
T PF11470_consen 1 VICYNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHN 42 (65)
T ss_dssp EE-TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEET
T ss_pred CCccCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEEC
Confidence 346899999999999999999999999999999996665543
No 24
>KOG1169|consensus
Probab=94.83 E-value=0.0094 Score=58.80 Aligned_cols=51 Identities=25% Similarity=0.464 Sum_probs=45.5
Q ss_pred ccceeeccccCCccCCcccccccc-------ccccccccCceeccccccccccccccc
Q psy7966 81 IEHNITRRTFFAIAFCDACHKLLF-------SGHLCRTCGFKFHRACNLAVPYLCQVE 131 (194)
Q Consensus 81 ~~H~F~~~Tf~~ptfCd~C~klL~-------QG~kCk~Cg~~~HkrC~~~Vp~~C~~~ 131 (194)
..|.+..+.|.+|++|..|.++.. ||+.|.-|++..|.+|..++...|...
T Consensus 97 ~~~~~~~~~~~~~~~c~~c~~~c~~~~~~~~~g~~C~~C~~~vh~~C~~~~~~~~~~~ 154 (634)
T KOG1169|consen 97 GDHVWRPKHLWKPAYCFVCPKSCGSCGVGIKQGLCCDWCGRTVHERCVRRADPECQCK 154 (634)
T ss_pred CceeccCCCCCCCceEEeccccccchhhcccCceeeccccchHHHHHHhhcCcccccc
Confidence 458889999999999999999862 999999999999999999999986654
No 25
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=94.81 E-value=0.0085 Score=39.51 Aligned_cols=28 Identities=29% Similarity=0.921 Sum_probs=18.0
Q ss_pred Ccccccccccccccc--ccCceeccccccc
Q psy7966 96 CDACHKLLFSGHLCR--TCGFKFHRACNLA 123 (194)
Q Consensus 96 Cd~C~klL~QG~kCk--~Cg~~~HkrC~~~ 123 (194)
|..|.+++.||.+|. +|+..+|..|...
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~ 30 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKK 30 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHH
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHH
Confidence 788999999999999 7999999999653
No 26
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=94.63 E-value=0.02 Score=34.80 Aligned_cols=27 Identities=30% Similarity=0.780 Sum_probs=23.8
Q ss_pred CCcccccccc-c-cccccccCceeccccc
Q psy7966 95 FCDACHKLLF-S-GHLCRTCGFKFHRACN 121 (194)
Q Consensus 95 fCd~C~klL~-Q-G~kCk~Cg~~~HkrC~ 121 (194)
.|+.|++.+- . +|.|+.|++..|-+|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCCeEcCccC
Confidence 4999999875 5 9999999999999985
No 27
>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=94.16 E-value=0.12 Score=36.81 Aligned_cols=36 Identities=17% Similarity=0.159 Sum_probs=34.9
Q ss_pred ceEEEEcCCCC----eeeEEeecCCcHHHHHHHHHHhcCC
Q psy7966 2 ILLRAQLPNQQ----RTSVHIRKGQTLLEALSKAMKLRNL 37 (194)
Q Consensus 2 ~~irv~LPn~Q----rT~V~v~~G~tl~~aL~Kalk~R~L 37 (194)
++||||.++.+ .++|.|-+..|.+|.+..+|++-+|
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l 42 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGL 42 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTT
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCC
Confidence 68999999999 9999999999999999999999999
No 28
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=93.82 E-value=0.017 Score=34.92 Aligned_cols=27 Identities=37% Similarity=0.761 Sum_probs=12.7
Q ss_pred CCcccccccc--ccccccccCceeccccc
Q psy7966 95 FCDACHKLLF--SGHLCRTCGFKFHRACN 121 (194)
Q Consensus 95 fCd~C~klL~--QG~kCk~Cg~~~HkrC~ 121 (194)
.|+.|++.+. ..|.|..|+|..|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhcC
Confidence 4899999887 58999999999999984
No 29
>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=93.26 E-value=0.15 Score=38.91 Aligned_cols=40 Identities=20% Similarity=0.306 Sum_probs=37.5
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCc
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEM 41 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~ 41 (194)
..|||+|||+++-+|+|+--.+..+.|.++.++-||.-++
T Consensus 2 V~L~V~Lpdg~~i~V~v~~s~~a~~Vleav~~kl~L~~e~ 41 (87)
T cd01777 2 VELRIALPDKATVTVRVRKNATTDQVYQALVAKAGMDSYT 41 (87)
T ss_pred eEEEEEccCCCEEEEEEEEcccHHHHHHHHHHHhCCCHHH
Confidence 4699999999999999999999999999999999998776
No 30
>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=92.98 E-value=0.31 Score=35.03 Aligned_cols=45 Identities=18% Similarity=0.259 Sum_probs=38.5
Q ss_pred eEEEEcCC---CCeeeEEeecCCcHHHHHHHHHHhcCCC--CCccEEEec
Q psy7966 3 LLRAQLPN---QQRTSVHIRKGQTLLEALSKAMKLRNLK--PEMCTAYDS 47 (194)
Q Consensus 3 ~irv~LPn---~QrT~V~v~~G~tl~~aL~Kalk~R~L~--~~~C~Vy~~ 47 (194)
.||||..+ ++..+|.|.++.|..|.+..+|++-+|. ++..+.|-.
T Consensus 1 ~ikV~~~~~~~~~~kti~V~~~~t~~~Vi~~~l~k~~l~~~~~~y~L~ev 50 (87)
T cd01768 1 VLRVYPEDPSGGTYKTLRVSKDTTAQDVIQQLLKKFGLDDDPEDYALVEV 50 (87)
T ss_pred CEEEeCCcCCCccEEEEEECCCCCHHHHHHHHHHHhCCcCCcccEEEEEE
Confidence 48999999 9999999999999999999999999997 555554443
No 31
>KOG1453|consensus
Probab=91.11 E-value=0.084 Score=54.07 Aligned_cols=42 Identities=29% Similarity=0.587 Sum_probs=39.4
Q ss_pred CccCCcccccccc-ccccccccCceeccccccccccccccccc
Q psy7966 92 AIAFCDACHKLLF-SGHLCRTCGFKFHRACNLAVPYLCQVERI 133 (194)
Q Consensus 92 ~ptfCd~C~klL~-QG~kCk~Cg~~~HkrC~~~Vp~~C~~~~~ 133 (194)
+|+.|..|..+.| ++.-|..|...||++|...+...|+....
T Consensus 555 ~P~~c~~c~~~~~~~~~~c~~c~~~chkkc~~~~~~~~~~~~l 597 (918)
T KOG1453|consen 555 KPAPCRTCETYSWFMELECELCRLVCHKKCLEALKSLCGHERL 597 (918)
T ss_pred CCcccccccccchhhhcccceeeeeccccchhhccccCccccc
Confidence 5999999999999 88999999999999999999999998765
No 32
>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=90.04 E-value=0.88 Score=32.91 Aligned_cols=44 Identities=11% Similarity=0.181 Sum_probs=37.2
Q ss_pred ceEEEEcCC---CCeeeEEeecCCcHHHHHHHHHHhcCCCC--CccEEE
Q psy7966 2 ILLRAQLPN---QQRTSVHIRKGQTLLEALSKAMKLRNLKP--EMCTAY 45 (194)
Q Consensus 2 ~~irv~LPn---~QrT~V~v~~G~tl~~aL~Kalk~R~L~~--~~C~Vy 45 (194)
..||||.-+ ++..+|.|.+..|.+|.+..+|++-+|.. +.++.+
T Consensus 3 ~~lrV~~~~~~~~~~kti~v~~~tTa~~Vi~~~l~k~~l~~~~~~y~L~ 51 (90)
T smart00314 3 FVLRVYVDDLPGGTYKTLRVSSRTTARDVIQQLLEKFHLTDDPEEYVLV 51 (90)
T ss_pred eEEEEecccCCCCcEEEEEECCCCCHHHHHHHHHHHhCCCCCcccEEEE
Confidence 468999766 99999999999999999999999999975 344433
No 33
>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=89.60 E-value=0.71 Score=37.00 Aligned_cols=37 Identities=14% Similarity=0.169 Sum_probs=34.9
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCC
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLK 38 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~ 38 (194)
..|+|||||++.-.|.+.+-.|++|.+....++=||.
T Consensus 4 ~~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~l~ 40 (207)
T smart00295 4 RVLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIR 40 (207)
T ss_pred EEEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhCCC
Confidence 4799999999999999999999999999999999994
No 34
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=86.94 E-value=0.24 Score=34.68 Aligned_cols=32 Identities=28% Similarity=0.607 Sum_probs=28.0
Q ss_pred cCCcccccccc---ccccccccCceeccccccccc
Q psy7966 94 AFCDACHKLLF---SGHLCRTCGFKFHRACNLAVP 125 (194)
Q Consensus 94 tfCd~C~klL~---QG~kCk~Cg~~~HkrC~~~Vp 125 (194)
.-|+.|++-+. ..+.|.+||...|+.|.++.-
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g 40 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAG 40 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhCC
Confidence 67999999886 668999999999999987664
No 35
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=85.16 E-value=0.45 Score=30.11 Aligned_cols=23 Identities=43% Similarity=1.109 Sum_probs=16.6
Q ss_pred cCCcccccccc---cc---ccccccCcee
Q psy7966 94 AFCDACHKLLF---SG---HLCRTCGFKF 116 (194)
Q Consensus 94 tfCd~C~klL~---QG---~kCk~Cg~~~ 116 (194)
.||..|+.+|. .. ..|+.|+|..
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~ 30 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGYEE 30 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-EE
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCCcc
Confidence 69999999998 11 2599999864
No 36
>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=84.54 E-value=1.4 Score=30.87 Aligned_cols=33 Identities=15% Similarity=0.145 Sum_probs=31.6
Q ss_pred EEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCC
Q psy7966 6 AQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLK 38 (194)
Q Consensus 6 v~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~ 38 (194)
|+|||++.-+++|-+..|.+|.+.+.+++-||.
T Consensus 1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~ 33 (80)
T PF09379_consen 1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLK 33 (80)
T ss_dssp EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTS
T ss_pred CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCC
Confidence 789999999999999999999999999999994
No 37
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=83.95 E-value=0.63 Score=30.52 Aligned_cols=24 Identities=33% Similarity=1.003 Sum_probs=18.9
Q ss_pred cCCcccccccc-----c--cccccccCceec
Q psy7966 94 AFCDACHKLLF-----S--GHLCRTCGFKFH 117 (194)
Q Consensus 94 tfCd~C~klL~-----Q--G~kCk~Cg~~~H 117 (194)
.||..|+.+|+ + =+.|..||+.+.
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeEE
Confidence 38999999997 2 278999997544
No 38
>PLN02593 adrenodoxin-like ferredoxin protein
Probab=79.88 E-value=3.1 Score=32.48 Aligned_cols=44 Identities=18% Similarity=0.135 Sum_probs=31.6
Q ss_pred eEEEEcCCCCeeeEEeecCCcHHHHHHHHHHh-----cC-CCCCccEEEe
Q psy7966 3 LLRAQLPNQQRTSVHIRKGQTLLEALSKAMKL-----RN-LKPEMCTAYD 46 (194)
Q Consensus 3 ~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~-----R~-L~~~~C~Vy~ 46 (194)
.|.+.-|.+++.+|++.+|+||.+|+.++=-- +| -..-.|.|+.
T Consensus 2 ~V~fi~~~G~~~~v~~~~G~tLl~a~~~~gi~i~~~CgG~g~C~tC~V~V 51 (117)
T PLN02593 2 SVTFVDKDGEERTVKAPVGMSLLEAAHENDIELEGACEGSLACSTCHVIV 51 (117)
T ss_pred EEEEEcCCCCEEEEEECCCCcHHHHHHHcCCCCCccCCCcceeCCCEEEE
Confidence 45666799999999999999999998754100 22 2444688887
No 39
>KOG4718|consensus
Probab=77.82 E-value=0.53 Score=41.47 Aligned_cols=31 Identities=32% Similarity=0.915 Sum_probs=27.5
Q ss_pred CccCCccccccccccccccccCceecccccc
Q psy7966 92 AIAFCDACHKLLFSGHLCRTCGFKFHRACNL 122 (194)
Q Consensus 92 ~ptfCd~C~klL~QG~kCk~Cg~~~HkrC~~ 122 (194)
.+-.|.-|++++-||.+|..||...|..|..
T Consensus 180 nlk~Cn~Ch~LvIqg~rCg~c~i~~h~~c~q 210 (235)
T KOG4718|consen 180 NLKNCNLCHCLVIQGIRCGSCNIQYHRGCIQ 210 (235)
T ss_pred HHHHHhHhHHHhheeeccCcccchhhhHHHH
Confidence 3456999999999999999999999999964
No 40
>cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown.
Probab=76.88 E-value=3.7 Score=26.79 Aligned_cols=47 Identities=15% Similarity=0.200 Sum_probs=28.6
Q ss_pred EEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccEEEecCCCCcccCC
Q psy7966 4 LRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTGVSLQWD 56 (194)
Q Consensus 4 irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~~~~~i~w~ 56 (194)
|-||+||++ .+++..|+|+.+.+. .+.. ++..+..++.. .|..++++
T Consensus 1 ~~~~~~~g~--~~~~~~~~t~~~~~~-~~~~-~~~~~~va~~v--ng~~vdl~ 47 (60)
T cd01668 1 IYVFTPKGE--IIELPAGATVLDFAY-AIHT-EIGNRCVGAKV--NGKLVPLS 47 (60)
T ss_pred CEEECCCCC--EEEcCCCCCHHHHHH-HHCh-HhhhheEEEEE--CCEECCCC
Confidence 468999986 688999999999554 3321 22233344442 34445555
No 41
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=73.68 E-value=2 Score=29.17 Aligned_cols=25 Identities=24% Similarity=0.785 Sum_probs=20.7
Q ss_pred cCCccccc-ccc---ccccccccCceecc
Q psy7966 94 AFCDACHK-LLF---SGHLCRTCGFKFHR 118 (194)
Q Consensus 94 tfCd~C~k-lL~---QG~kCk~Cg~~~Hk 118 (194)
.||.-|+. +|. -.+.|..||+..-+
T Consensus 21 ~fCP~Cg~~~m~~~~~r~~C~~Cgyt~~~ 49 (50)
T PRK00432 21 KFCPRCGSGFMAEHLDRWHCGKCGYTEFK 49 (50)
T ss_pred CcCcCCCcchheccCCcEECCCcCCEEec
Confidence 48999999 777 46899999998754
No 42
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=73.42 E-value=1.8 Score=28.39 Aligned_cols=29 Identities=21% Similarity=0.725 Sum_probs=24.0
Q ss_pred CCcccccccc-cccccccc-Cceeccccccc
Q psy7966 95 FCDACHKLLF-SGHLCRTC-GFKFHRACNLA 123 (194)
Q Consensus 95 fCd~C~klL~-QG~kCk~C-g~~~HkrC~~~ 123 (194)
.||.|++.|. -.|+|..| +|.....|...
T Consensus 2 ~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~ 32 (43)
T cd02340 2 ICDGCQGPIVGVRYKCLVCPDYDLCESCEAK 32 (43)
T ss_pred CCCCCCCcCcCCeEECCCCCCccchHHhhCc
Confidence 6999999665 66899999 79999898654
No 43
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=72.39 E-value=2.4 Score=27.53 Aligned_cols=30 Identities=20% Similarity=0.491 Sum_probs=22.9
Q ss_pred CCcccccccc--ccccccccCceecccccccc
Q psy7966 95 FCDACHKLLF--SGHLCRTCGFKFHRACNLAV 124 (194)
Q Consensus 95 fCd~C~klL~--QG~kCk~Cg~~~HkrC~~~V 124 (194)
+|..|++.-. .=+.|+.|+..+|..|....
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~ 32 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPP 32 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSS
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCC
Confidence 5778887333 34799999999999997543
No 44
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=72.13 E-value=11 Score=36.06 Aligned_cols=48 Identities=23% Similarity=0.216 Sum_probs=36.3
Q ss_pred cCCCCeeeEEeecCCcHHHHHHHHHHh-cCCCCCccEEEecCC--CCcccCC
Q psy7966 8 LPNQQRTSVHIRKGQTLLEALSKAMKL-RNLKPEMCTAYDSNT--GVSLQWD 56 (194)
Q Consensus 8 LPn~QrT~V~v~~G~tl~~aL~Kalk~-R~L~~~~C~Vy~~~~--~~~i~w~ 56 (194)
-|+.|=-+.-..-|.. -++|.||++. +++.++.=+.|.++. +..+-|.
T Consensus 207 ~P~t~~PVl~GIRg~~-p~~l~~a~~~i~~e~~e~~~if~TNqatD~hl~~~ 257 (421)
T COG1571 207 PPHTPNPVLYGIRGAV-PEVLLKAMSLIKRELVERSAIFETNQATDDHLVDK 257 (421)
T ss_pred CCCCCCCEEEEEecCC-HHHHHHHHHHHhccCcceEEEEeccchhhhhcccc
Confidence 4666666777778888 8999999887 588899999998863 3335566
No 45
>cd01781 AF6_RA_repeat2 Ubiquitin domain of AT-6, second repeat. The AF-6 protein (also known as afadin and canoe) is a multidomain cell junction protein that contains two N-terminal Ras-associating (RA) domains in addition to FHA (forkhead-associated), DIL (class V myosin homology region), and PDZ domains and a proline-rich region. AF6 acts downstream of the Egfr (Epidermal Growth Factor-receptor)/Ras signalling pathway and provides a link from Egfr to cytoskeletal elements.
Probab=70.51 E-value=14 Score=28.75 Aligned_cols=47 Identities=15% Similarity=0.167 Sum_probs=39.2
Q ss_pred CceEEEE---c-CCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccEEEec
Q psy7966 1 GILLRAQ---L-PNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDS 47 (194)
Q Consensus 1 ~~~irv~---L-Pn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~ 47 (194)
|++|+|| | |+-=.-+|-|-.--+..+++.+||.+-||..+...-|.+
T Consensus 1 gG~LKIYg~~L~~~~~YKSIlvt~~~~a~~vV~eALeKygL~~e~p~~Y~L 51 (100)
T cd01781 1 GGTLKIYGGSLVPTRPYKTILLSINDNADRIVGEALEKYGLEKSDPDDYCL 51 (100)
T ss_pred CCeEEEcCCcccCCCCeEEEEecCCccHHHHHHHHHHHhCCCccCccceEE
Confidence 6778887 4 677778899999999999999999999998887555554
No 46
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=69.99 E-value=2.4 Score=31.79 Aligned_cols=26 Identities=27% Similarity=0.825 Sum_probs=21.5
Q ss_pred cCCcccccccc---ccccccccCceeccc
Q psy7966 94 AFCDACHKLLF---SGHLCRTCGFKFHRA 119 (194)
Q Consensus 94 tfCd~C~klL~---QG~kCk~Cg~~~Hkr 119 (194)
.||..|+.+|. .-++|..|++....+
T Consensus 1 ~fC~~Cg~~l~~~~~~~~C~~C~~~~~~~ 29 (104)
T TIGR01384 1 KFCPKCGSLMTPKNGVYVCPSCGYEKEKK 29 (104)
T ss_pred CCCcccCcccccCCCeEECcCCCCccccc
Confidence 38999999997 458999999987653
No 47
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=69.89 E-value=2.6 Score=35.80 Aligned_cols=35 Identities=26% Similarity=0.736 Sum_probs=26.6
Q ss_pred cCCccccc--ccc----cc-ccccccCceecccccccccccccc
Q psy7966 94 AFCDACHK--LLF----SG-HLCRTCGFKFHRACNLAVPYLCQV 130 (194)
Q Consensus 94 tfCd~C~k--lL~----QG-~kCk~Cg~~~HkrC~~~Vp~~C~~ 130 (194)
-.|+.|.+ .|| ++ .+|..|+.-||+.|... ..|..
T Consensus 153 fiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~--~~Cpk 194 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK--KSCPK 194 (202)
T ss_pred CCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC--CCCCC
Confidence 46888874 676 23 69999999999999886 45654
No 48
>cd01787 GRB7_RA RA (RAS-associated like) domain of Grb7. Grb7_RA The RA (RAS-associated like) domain of Grb7. Grb7 is an adaptor molecule that mediates signal transduction from multiple cell surface receptors to various downstream signaling pathways. Grb7 and its related family members Grb10 and Grb14 share a conserved domain architecture that includes an amino-terminal proline-rich region, a central segment termed the GM region (for Grb and Mig) which includes the RA, PIR, and PH domains, and a carboxyl-terminal SH2 domain. Grb7/10/14 family proteins are phosphorylated on serine/threonine as well as tyrosine residues and are mainly localized to the cytoplasm.
Probab=69.76 E-value=13 Score=28.12 Aligned_cols=46 Identities=7% Similarity=0.057 Sum_probs=38.2
Q ss_pred eEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCc-cEEEecC
Q psy7966 3 LLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEM-CTAYDSN 48 (194)
Q Consensus 3 ~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~-C~Vy~~~ 48 (194)
.|+||+++.---+|.|-++||++|++.....+-.+.++. .+.+-..
T Consensus 4 vvkv~~~Dg~sK~l~V~~~~Ta~dV~~~L~~K~h~~~~~~W~LvE~~ 50 (85)
T cd01787 4 VVKVYSEDGASKSLEVDERMTARDVCQLLVDKNHCQDDSSWTLVEHL 50 (85)
T ss_pred EEEEEecCCCeeEEEEcCCCcHHHHHHHHHHHhCCCCCCCeEEEEec
Confidence 589999999888999999999999999999998876655 4444433
No 49
>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=69.25 E-value=22 Score=25.83 Aligned_cols=50 Identities=12% Similarity=0.134 Sum_probs=42.4
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccEEEecCCCCcc
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTGVSL 53 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~~~~~i 53 (194)
++|.|.-+++..-.++|++-.+|.....+..++.|+.++....+-. |..|
T Consensus 12 i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~--G~~L 61 (87)
T cd01763 12 INLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFD--GQRI 61 (87)
T ss_pred EEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEEC--CeEC
Confidence 5789999999888999999999999999999999999887665553 4444
No 50
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=68.46 E-value=2.7 Score=27.08 Aligned_cols=21 Identities=43% Similarity=0.912 Sum_probs=17.3
Q ss_pred Cccccccccc-cccccccCcee
Q psy7966 96 CDACHKLLFS-GHLCRTCGFKF 116 (194)
Q Consensus 96 Cd~C~klL~Q-G~kCk~Cg~~~ 116 (194)
|+.|++..+- +|+|+.|+..|
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~F 22 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLF 22 (39)
T ss_pred CcccCCcccccCeECCccCCcc
Confidence 7789887764 99999999776
No 51
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=65.81 E-value=2.2 Score=27.12 Aligned_cols=16 Identities=25% Similarity=0.787 Sum_probs=11.3
Q ss_pred ccccccCceecccccc
Q psy7966 107 HLCRTCGFKFHRACNL 122 (194)
Q Consensus 107 ~kCk~Cg~~~HkrC~~ 122 (194)
++|+.|++.+|+.|-.
T Consensus 5 l~C~~C~v~VH~~CYG 20 (36)
T PF13831_consen 5 LFCDNCNVAVHQSCYG 20 (36)
T ss_dssp EE-SSS--EEEHHHHT
T ss_pred EEeCCCCCcCChhhCC
Confidence 5899999999999954
No 52
>PHA00626 hypothetical protein
Probab=65.80 E-value=3.6 Score=29.34 Aligned_cols=15 Identities=20% Similarity=0.693 Sum_probs=13.2
Q ss_pred ccccccccCceeccc
Q psy7966 105 SGHLCRTCGFKFHRA 119 (194)
Q Consensus 105 QG~kCk~Cg~~~Hkr 119 (194)
|-|+|.+|||.|-+.
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 789999999999764
No 53
>cd00207 fer2 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis and ferredoxins, which participate in redox chains (from bacteria to mammals). Fold is ismilar to thioredoxin.
Probab=62.44 E-value=9.7 Score=26.39 Aligned_cols=22 Identities=27% Similarity=0.404 Sum_probs=17.7
Q ss_pred CCCCeeeEEeecCCcHHHHHHH
Q psy7966 9 PNQQRTSVHIRKGQTLLEALSK 30 (194)
Q Consensus 9 Pn~QrT~V~v~~G~tl~~aL~K 30 (194)
.|++..+|++.+|.||.+||..
T Consensus 5 ~~~~~~~~~~~~g~~ll~al~~ 26 (84)
T cd00207 5 VPGSGVEVEVPEGETLLDAARE 26 (84)
T ss_pred cCCCCEEEEECCCCcHHHHHHH
Confidence 3455677999999999998775
No 54
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=59.82 E-value=11 Score=29.34 Aligned_cols=46 Identities=15% Similarity=0.133 Sum_probs=33.2
Q ss_pred eEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCC--CccEEEecC
Q psy7966 3 LLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKP--EMCTAYDSN 48 (194)
Q Consensus 3 ~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~--~~C~Vy~~~ 48 (194)
++++.+.++|--+|+|.-=-+..+.+.|+||+=|+.. ..-.+|...
T Consensus 2 vi~~I~~dG~tk~VNV~~c~~a~eI~~rvLKKfg~~~~~~~~~~~v~d 49 (105)
T PF14847_consen 2 VIRFILEDGSTKTVNVSGCFNAQEIKRRVLKKFGLPEHPRNYCFYVLD 49 (105)
T ss_dssp EEEEEETTTEEEEEE--S--HHHHHHHHHHHHHTSS--CCCEEEEEE-
T ss_pred EEEEECCCCcEEEEEECCCCCHHHHHHHHHHHcCCccccccceEEEec
Confidence 5889999999999999999999999999999999866 234445543
No 55
>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=58.50 E-value=34 Score=23.32 Aligned_cols=45 Identities=11% Similarity=0.200 Sum_probs=38.3
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCC-CccEEEe
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKP-EMCTAYD 46 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~-~~C~Vy~ 46 (194)
|+|.|--.+++...+.|++..++...+.+..++.|+.+ +....+-
T Consensus 1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~f 46 (72)
T PF11976_consen 1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIF 46 (72)
T ss_dssp EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEE
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEE
Confidence 46777788999999999999999999999999999998 5544443
No 56
>PF14804 Jag_N: Jag N-terminus; PDB: 3GKU_B.
Probab=57.69 E-value=9.8 Score=26.04 Aligned_cols=31 Identities=29% Similarity=0.269 Sum_probs=21.8
Q ss_pred cCCcHHHHHHHHHHhcCCCCCccEEEecCCC
Q psy7966 20 KGQTLLEALSKAMKLRNLKPEMCTAYDSNTG 50 (194)
Q Consensus 20 ~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~~~ 50 (194)
.|.|+.+||.+|++.-|+..+.-.+-....|
T Consensus 3 ~gkt~eeAi~~A~~~l~~~~~~~~~eVi~~g 33 (52)
T PF14804_consen 3 EGKTVEEAIEKALKELGVPREELEYEVIEEG 33 (52)
T ss_dssp EESSHHHHHHHHHHHTT--GGGEEEEEEE--
T ss_pred eECCHHHHHHHHHHHhCCChHHEEEEEEEcC
Confidence 4889999999999999998776655554433
No 57
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=57.43 E-value=21 Score=24.45 Aligned_cols=24 Identities=25% Similarity=0.487 Sum_probs=20.1
Q ss_pred EEEEcCCCCeeeEEeecCCcHHHHHH
Q psy7966 4 LRAQLPNQQRTSVHIRKGQTLLEALS 29 (194)
Q Consensus 4 irv~LPn~QrT~V~v~~G~tl~~aL~ 29 (194)
|+|+||++ ...++..|.|..|+-.
T Consensus 1 I~v~lpdG--~~~~~~~g~T~~d~A~ 24 (60)
T PF02824_consen 1 IRVYLPDG--SIKELPEGSTVLDVAY 24 (60)
T ss_dssp EEEEETTS--CEEEEETTBBHHHHHH
T ss_pred CEEECCCC--CeeeCCCCCCHHHHHH
Confidence 78999998 4677999999988754
No 58
>KOG3532|consensus
Probab=57.08 E-value=2.2 Score=43.54 Aligned_cols=47 Identities=6% Similarity=-0.096 Sum_probs=38.9
Q ss_pred CCCccceeeccccCCccCCcccccccc--ccccccccCceecccccccc
Q psy7966 78 AINIEHNITRRTFFAIAFCDACHKLLF--SGHLCRTCGFKFHRACNLAV 124 (194)
Q Consensus 78 ~~~~~H~F~~~Tf~~ptfCd~C~klL~--QG~kCk~Cg~~~HkrC~~~V 124 (194)
.+...|+|....|-.+|||++|.+-.| ---.|-.|+|.+|+.|.++-
T Consensus 68 ~~~N~~r~~~t~~~~~t~~~~~~~~~~~~~AS~c~s~~~V~h~lfqE~k 116 (1051)
T KOG3532|consen 68 PPINQFRPAQIPEELRTFLKSGEDGQGISKASSCNSISLVLHMLFQEHK 116 (1051)
T ss_pred CchhhcChhcCcccccccccccccchhhHHHHHHHHHHHHHHHHHHHhh
Confidence 345679999999999999999999988 45688888888888887653
No 59
>PF10531 SLBB: SLBB domain; InterPro: IPR019554 The soluble ligand-binding beta-grasp domain (SLBB) contains a beta-grasp fold. They are found in a diverse set of proteins that include the animal vitamin B12 uptake proteins; transcobalamin, intrinsic factor and the bacterial polysaccharide export proteins []. Some proteins may be part of a membrane complex involved in electron transport, others are probably involved in the export of the extracellular polysaccharide colanic acid from the cell to medium.; PDB: 3IAS_S 2FUG_A 3I9V_A 3M9S_1 3IAM_A 2YBB_1 2W8I_E 2W8H_E 2J58_D.
Probab=56.54 E-value=7 Score=26.47 Aligned_cols=18 Identities=28% Similarity=0.462 Sum_probs=14.6
Q ss_pred eeEEeecCCcHHHHHHHH
Q psy7966 14 TSVHIRKGQTLLEALSKA 31 (194)
Q Consensus 14 T~V~v~~G~tl~~aL~Ka 31 (194)
-++++.+|+||.|||++|
T Consensus 12 G~~~~~~g~tl~~~i~~A 29 (59)
T PF10531_consen 12 GTYELPPGTTLSDAIAQA 29 (59)
T ss_dssp EEEEEETT-BHHHHHHCT
T ss_pred EEEEECCCCcHHHHHHHh
Confidence 468999999999999864
No 60
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=56.03 E-value=9.7 Score=26.27 Aligned_cols=30 Identities=23% Similarity=0.562 Sum_probs=23.3
Q ss_pred cCCccCCcccccccc-----ccccccccCceeccc
Q psy7966 90 FFAIAFCDACHKLLF-----SGHLCRTCGFKFHRA 119 (194)
Q Consensus 90 f~~ptfCd~C~klL~-----QG~kCk~Cg~~~Hkr 119 (194)
+++...|..|+...- ..|.|..||+..|+-
T Consensus 25 ~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 25 AYTSQTCPRCGHRNKKRRSGRVFTCPNCGFEMDRD 59 (69)
T ss_pred CCCccCccCcccccccccccceEEcCCCCCEECcH
Confidence 335577999988764 569999999998864
No 61
>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=55.10 E-value=71 Score=22.39 Aligned_cols=56 Identities=14% Similarity=0.089 Sum_probs=38.7
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCc-cEEEecCCCCcccCCC
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEM-CTAYDSNTGVSLQWDT 57 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~-C~Vy~~~~~~~i~w~t 57 (194)
..|++-|||+++-+-...+--||.+...-.........+. -..+...+...+.++.
T Consensus 7 ~~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~~~Pr~~l~~~~ 63 (82)
T PF00789_consen 7 VRIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELITAFPRRELTDED 63 (82)
T ss_dssp EEEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEESSSTEECCSTT
T ss_pred EEEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEeCCCCcCCCccc
Confidence 4699999999999999999999988777666665555443 3333333444466555
No 62
>KOG0612|consensus
Probab=55.04 E-value=2.9 Score=44.64 Aligned_cols=67 Identities=24% Similarity=0.378 Sum_probs=51.7
Q ss_pred ccceeeccccCCccCCccccccccc---cccccccCceecccccccccccccccccchhhhhhhccCCCCc
Q psy7966 81 IEHNITRRTFFAIAFCDACHKLLFS---GHLCRTCGFKFHRACNLAVPYLCQVERIQQTYYQMLLASNAET 148 (194)
Q Consensus 81 ~~H~F~~~Tf~~ptfCd~C~klL~Q---G~kCk~Cg~~~HkrC~~~Vp~~C~~~~~~~~~~~~ll~~~p~~ 148 (194)
-.|.|..-.|..|++|+.|-+.||+ -|.|.-|..++|+.=..++-..|- ......-+-.|++.+++.
T Consensus 1208 ~~~~~~~~l~~~~~~~~~~~k~l~~~~~~ye~~~~~~~~~~d~~~k~m~p~k-y~~~~a~~l~l~a~~~~d 1277 (1317)
T KOG0612|consen 1208 KGHEFIPFLYHFPTNCEACIKPLWHMFKAYECRRCHIKCHKDHMDKIMAPCK-YDTSSARHLLLLAESTED 1277 (1317)
T ss_pred CCCcchHHHhhcchhHHHHhhhcccchhHHHHHHhhccccccccccccCccc-ccccCCccceeccCCchH
Confidence 4599999999999999999999996 789999999999999888766666 222222334566656543
No 63
>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=53.33 E-value=40 Score=22.87 Aligned_cols=44 Identities=7% Similarity=0.166 Sum_probs=36.7
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccEEE
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAY 45 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy 45 (194)
|.|.|-.++++...++|.+..|+.+--.+.-+.-|+.++.-...
T Consensus 1 m~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~ 44 (76)
T cd01806 1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLI 44 (76)
T ss_pred CEEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEE
Confidence 46788889999999999999999998888878888888764444
No 64
>PF08827 DUF1805: Domain of unknown function (DUF1805); InterPro: IPR014931 This protein is found in bacteria and archaea and has an N-terminal tetramerisation region that is composed of beta sheets. ; PDB: 1QW2_A.
Probab=53.13 E-value=5.1 Score=28.56 Aligned_cols=14 Identities=50% Similarity=0.468 Sum_probs=9.7
Q ss_pred EeecCCcHHHHHHH
Q psy7966 17 HIRKGQTLLEALSK 30 (194)
Q Consensus 17 ~v~~G~tl~~aL~K 30 (194)
.+++|||.+|||.|
T Consensus 45 GI~~Gm~g~eAL~~ 58 (59)
T PF08827_consen 45 GIKPGMTGREALEK 58 (59)
T ss_dssp T--TT-BHHHHGGG
T ss_pred CCCCCCCHHHHHHh
Confidence 36899999999976
No 65
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=52.28 E-value=7.3 Score=25.89 Aligned_cols=28 Identities=25% Similarity=0.714 Sum_probs=22.3
Q ss_pred CCcccccccc--cccccccc-Cceecccccc
Q psy7966 95 FCDACHKLLF--SGHLCRTC-GFKFHRACNL 122 (194)
Q Consensus 95 fCd~C~klL~--QG~kCk~C-g~~~HkrC~~ 122 (194)
.||.|++... -.|+|..| +|-....|..
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~ 32 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYH 32 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhC
Confidence 6999996444 55899999 7888888865
No 66
>KOG3532|consensus
Probab=51.52 E-value=3.6 Score=42.06 Aligned_cols=49 Identities=2% Similarity=-0.270 Sum_probs=40.3
Q ss_pred cceeeccccCCccCCcccccccc--ccccccccCceecccccc--cccccccc
Q psy7966 82 EHNITRRTFFAIAFCDACHKLLF--SGHLCRTCGFKFHRACNL--AVPYLCQV 130 (194)
Q Consensus 82 ~H~F~~~Tf~~ptfCd~C~klL~--QG~kCk~Cg~~~HkrC~~--~Vp~~C~~ 130 (194)
.|.|.+.-|..-+-|+.|++-|| --..|+.|..-+|++|.- .....|+.
T Consensus 746 ~~d~~~~h~~r~~~~~~~~~ki~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~ 798 (1051)
T KOG3532|consen 746 GGDDEEAHLDRKRSASTRKAKIQATFAAGKKKVLDLMPQKRKNTDASDLNGES 798 (1051)
T ss_pred CCchHHhhhhhhcccchhccceeehhhhcccHHHHhcchhhhcchhhhccCCc
Confidence 49999999999999999999999 667899999999999953 33334443
No 67
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=51.31 E-value=9.3 Score=28.78 Aligned_cols=26 Identities=31% Similarity=0.714 Sum_probs=20.1
Q ss_pred CCccCCccccccc-c-----------ccccccccCcee
Q psy7966 91 FAIAFCDACHKLL-F-----------SGHLCRTCGFKF 116 (194)
Q Consensus 91 ~~ptfCd~C~klL-~-----------QG~kCk~Cg~~~ 116 (194)
..+.+||+|++.| | +.-||+.|+.+.
T Consensus 31 ~~rS~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I 68 (92)
T PF06750_consen 31 FPRSHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPI 68 (92)
T ss_pred CCCCcCcCCCCcCcccccchHHHHHHhCCCCcccCCCC
Confidence 3468999999876 2 778999998543
No 68
>KOG3784|consensus
Probab=51.21 E-value=28 Score=33.24 Aligned_cols=37 Identities=19% Similarity=0.217 Sum_probs=32.6
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCC
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLK 38 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~ 38 (194)
..+.|+|||+|.++|+++--.|-...|.-++.+=||.
T Consensus 108 v~l~v~lpng~~i~i~~~~s~tt~~vl~~v~~kl~l~ 144 (407)
T KOG3784|consen 108 VELDVFLPNGEKITINCLVSDTASLVLKSVCRKLGLP 144 (407)
T ss_pred eEEEEEccCCceEEEEEEecccHHHHHHHHHhhcCCc
Confidence 4689999999999999999888888888888887775
No 69
>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=51.02 E-value=38 Score=23.54 Aligned_cols=40 Identities=13% Similarity=0.179 Sum_probs=34.5
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCc
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEM 41 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~ 41 (194)
+.|-|-.++++..+++|.+..|+.+--.+...+-|+.++.
T Consensus 1 m~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~ 40 (74)
T cd01807 1 MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQ 40 (74)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHH
Confidence 3566777899999999999999999999998888987775
No 70
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain. This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565.
Probab=50.52 E-value=7.2 Score=27.28 Aligned_cols=23 Identities=35% Similarity=0.860 Sum_probs=17.3
Q ss_pred cccccccc--------ccccccccC--ceeccc
Q psy7966 97 DACHKLLF--------SGHLCRTCG--FKFHRA 119 (194)
Q Consensus 97 d~C~klL~--------QG~kCk~Cg--~~~Hkr 119 (194)
|-|++|+- ..++|..|| .|||+|
T Consensus 19 DGCgEFmps~g~~~~~~al~CaACgCHRnFHRr 51 (53)
T TIGR01566 19 DGCGEFMPSSGEEGDPESLTCAACGCHRNFHRK 51 (53)
T ss_pred ccccccccCCCCCCCCcceeeeecCcccccccC
Confidence 77888886 248999876 678875
No 72
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=50.46 E-value=8.9 Score=24.80 Aligned_cols=21 Identities=38% Similarity=0.885 Sum_probs=13.3
Q ss_pred Ccc--ccccccccccccccCcee
Q psy7966 96 CDA--CHKLLFSGHLCRTCGFKF 116 (194)
Q Consensus 96 Cd~--C~klL~QG~kCk~Cg~~~ 116 (194)
|.+ |++.++-+++|+.|+..|
T Consensus 1 C~~~~C~~~~~~~~~C~~C~~~F 23 (43)
T PF01428_consen 1 CSFPGCKKKDFLPFKCKHCGKSF 23 (43)
T ss_dssp -SSTTT--BCTSHEE-TTTS-EE
T ss_pred CccCcCcCccCCCeECCCCCccc
Confidence 455 888888899999999877
No 73
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=50.20 E-value=9.2 Score=30.58 Aligned_cols=26 Identities=23% Similarity=0.576 Sum_probs=19.6
Q ss_pred cCCccccccc----------cccccccccCceeccc
Q psy7966 94 AFCDACHKLL----------FSGHLCRTCGFKFHRA 119 (194)
Q Consensus 94 tfCd~C~klL----------~QG~kCk~Cg~~~Hkr 119 (194)
..|-.|+..- .|.|+|+.|++.|-..
T Consensus 31 ~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 31 VNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred CcCCCCCccceeeECCccccccccccCCcCcceeee
Confidence 4577776654 3999999999988754
No 74
>TIGR02008 fdx_plant ferredoxin [2Fe-2S]. This model represents single domain 2Fe-2S (also called plant type) ferredoxins. In general, these occur as a single domain proteins or with a chloroplast transit peptide. Species tend to be photosynthetic, but several forms may occur in one species and individually may not be associated with photocynthesis. Halobacterial forms differ somewhat in architecture; they score between trusted and noise cutoffs. Sequences scoring below the noise cutoff tend to be ferredoxin-related domains of larger proteins.
Probab=50.04 E-value=29 Score=25.75 Aligned_cols=28 Identities=18% Similarity=0.274 Sum_probs=21.5
Q ss_pred EEEEcCCCCeeeEEeecCCcHHHHHHHH
Q psy7966 4 LRAQLPNQQRTSVHIRKGQTLLEALSKA 31 (194)
Q Consensus 4 irv~LPn~QrT~V~v~~G~tl~~aL~Ka 31 (194)
|+++-|+++--++.+.+|.||-||+.++
T Consensus 5 v~~~~~~~~~~~~~~~~g~tLLda~~~~ 32 (97)
T TIGR02008 5 VTLVNPDGGEETIECPDDQYILDAAEEA 32 (97)
T ss_pred EEEEECCCCEEEEEECCCCcHHHHHHHc
Confidence 3443388877789999999999997653
No 75
>PF00111 Fer2: 2Fe-2S iron-sulfur cluster binding domain; InterPro: IPR001041 The ferredoxin protein family are electron carrier proteins with an iron-sulphur cofactor that act in a wide variety of metabolic reactions. Ferredoxins can be divided into several subgroups depending upon the physiological nature of the iron-sulphur cluster(s) and according to sequence similarities. This entry represents members of the 2Fe-2S ferredoxin family that have a general core structure consisting of beta(2)-alpha-beta(2), which includes putidaredoxin and terpredoxin, and adrenodoxin [, , , ]. They are proteins of around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This conserved region is also found as a domain in various metabolic enzymes and in multidomain proteins, such as aldehyde oxidoreductase (N-terminal), xanthine oxidase (N-terminal), phthalate dioxygenase reductase (C-terminal), succinate dehydrogenase iron-sulphur protein (N-terminal), and methane monooxygenase reductase (N-terminal).; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3 1JQ4_A 1DOX_A 1DOY_A 2KAJ_A ....
Probab=49.46 E-value=17 Score=25.08 Aligned_cols=40 Identities=25% Similarity=0.284 Sum_probs=28.6
Q ss_pred CCCCeeeEEeecCCc-HHHHHHHH-H-Hh----cCCCCCccEEEecC
Q psy7966 9 PNQQRTSVHIRKGQT-LLEALSKA-M-KL----RNLKPEMCTAYDSN 48 (194)
Q Consensus 9 Pn~QrT~V~v~~G~t-l~~aL~Ka-l-k~----R~L~~~~C~Vy~~~ 48 (194)
.|.+..+|++.+|.| |.||+.++ - .. ++=..-.|.|....
T Consensus 3 i~g~~~~~~~~~~~~~ll~~~~~~~gi~i~~~C~~g~Cg~C~v~v~~ 49 (78)
T PF00111_consen 3 INGKGVTVEVPPGETLLLDALERAGGIGIPYSCGGGGCGTCRVRVLE 49 (78)
T ss_dssp TTTEEEEEEEETTSBBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEE
T ss_pred ECCeEEEEEeCCCccHHHHHHHHcCCCCcccCCCCCccCCcEEEEee
Confidence 367788999999999 99999864 1 11 22236778888754
No 76
>PF00794 PI3K_rbd: PI3-kinase family, ras-binding domain; InterPro: IPR000341 Phosphatidylinositol 3-kinase (PI3K) (2.7.1.137 from EC) is an enzyme that phosphorylates phosphoinositides on the 3-hydroxyl group of the inositol ring. A subset of PI3Ks has the capacity to bind and be activated by the GTP-bound small GTPase p21Ras (Ras). PI3Ks are recognised as one of the principal effectors of Ras signalling to the cell-cycle control machinery. In the structure of the Ras-PI3K gamma complex, contacts between the two molecules are made primarily via the so-called switch I region of Ras and the PI3K RBD. The RBD fold comprises a five-stranded mixed beta-sheet, flanked by two alpha-helices. Interaction between Ras and the PI3K RBD is primarily polar in character and, as characterised by kinetic measurements, is reversible and transient [].; GO: 0016303 1-phosphatidylinositol-3-kinase activity, 0005942 phosphatidylinositol 3-kinase complex; PDB: 2RD0_A 3HIZ_A 3HHM_A 1E8W_A 1E8X_A 1E7V_A 1E90_A 1E7U_A 2Y3A_A 3L54_A ....
Probab=48.44 E-value=38 Score=25.34 Aligned_cols=33 Identities=21% Similarity=0.277 Sum_probs=29.2
Q ss_pred ceEEEEcC-CCCeeeEEeecCCcHHHHHHHHHHh
Q psy7966 2 ILLRAQLP-NQQRTSVHIRKGQTLLEALSKAMKL 34 (194)
Q Consensus 2 ~~irv~LP-n~QrT~V~v~~G~tl~~aL~Kalk~ 34 (194)
..|.||++ +++..++.|-+..|..+.+..++++
T Consensus 17 i~v~v~~~~~~~~~t~~~~~~~t~~~li~~~l~k 50 (106)
T PF00794_consen 17 IKVSVHFENSQQSFTFQVDPNSTPEELIAQALKK 50 (106)
T ss_dssp EEEEEEETTCSEEEEEEEETTS-HHHHHHHHHHH
T ss_pred EEEEEEEcCCCcEEEEEECCCCCHHHHHHHHHHH
Confidence 46899999 7888899999999999999999998
No 77
>PF10790 DUF2604: Protein of Unknown function (DUF2604); InterPro: IPR019726 This entry represents bacterial proteins with undetermined function.
Probab=48.33 E-value=21 Score=26.40 Aligned_cols=30 Identities=20% Similarity=0.102 Sum_probs=27.0
Q ss_pred CCCCeeeEEeecCCcHHHHHHHHHHhcCCC
Q psy7966 9 PNQQRTSVHIRKGQTLLEALSKAMKLRNLK 38 (194)
Q Consensus 9 Pn~QrT~V~v~~G~tl~~aL~Kalk~R~L~ 38 (194)
=|.|-+.||.-+-..|.-+++|||..-|=.
T Consensus 3 VNGqPv~VEANvnaPLh~v~akALe~sgNv 32 (76)
T PF10790_consen 3 VNGQPVQVEANVNAPLHPVRAKALEQSGNV 32 (76)
T ss_pred eCCCceeeecCCCCcchHHHHHHHhhcccc
Confidence 389999999999999999999999987643
No 78
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=47.45 E-value=8.4 Score=30.36 Aligned_cols=17 Identities=29% Similarity=0.671 Sum_probs=13.8
Q ss_pred cCCcccccccccccccc
Q psy7966 94 AFCDACHKLLFSGHLCR 110 (194)
Q Consensus 94 tfCd~C~klL~QG~kCk 110 (194)
+||..|..+||-|..|+
T Consensus 57 ~~CkkC~t~Lvpg~n~r 73 (105)
T COG2023 57 TICKKCYTPLVPGKNAR 73 (105)
T ss_pred HhccccCcccccCcceE
Confidence 89999999999665443
No 79
>PTZ00490 Ferredoxin superfamily; Provisional
Probab=46.60 E-value=34 Score=27.97 Aligned_cols=46 Identities=17% Similarity=0.320 Sum_probs=34.3
Q ss_pred eEEEEcCCCCeeeEEeecCCcHHHHHHHH--HHh--c---CCCCCccEEEecC
Q psy7966 3 LLRAQLPNQQRTSVHIRKGQTLLEALSKA--MKL--R---NLKPEMCTAYDSN 48 (194)
Q Consensus 3 ~irv~LPn~QrT~V~v~~G~tl~~aL~Ka--lk~--R---~L~~~~C~Vy~~~ 48 (194)
.|.+.-+++.+.+|++.+|.||-+|+... .-. - +..+-.|.||...
T Consensus 37 ~I~~~~~dG~~~~v~~~~G~sLLeal~~~~~i~i~~~CGG~g~CgtC~V~V~~ 89 (143)
T PTZ00490 37 KVCVKKRDGTHCDVEVPVGMSLMHALRDVAKLDVEGTCNGCMQCATCHVYLSA 89 (143)
T ss_pred EEEEEcCCCCEEEEEECCCccHHHHHHHcCCCCccccCCCCCEeCCCEEEECC
Confidence 46777788888999999999999998863 111 1 2355679999955
No 80
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=46.56 E-value=9 Score=27.47 Aligned_cols=23 Identities=39% Similarity=0.876 Sum_probs=18.0
Q ss_pred ccccccccc--------cccccccC--ceeccc
Q psy7966 97 DACHKLLFS--------GHLCRTCG--FKFHRA 119 (194)
Q Consensus 97 d~C~klL~Q--------G~kCk~Cg--~~~Hkr 119 (194)
|-|++||-- -++|..|| .|||+|
T Consensus 23 DGCgEFm~~~g~eg~~~al~CaACgCHRnFHRr 55 (60)
T PF04770_consen 23 DGCGEFMPSPGEEGTPEALKCAACGCHRNFHRR 55 (60)
T ss_pred ccccccccCCCCCCCcccceecccCcchhcccC
Confidence 788888852 48999887 688876
No 81
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=46.18 E-value=12 Score=27.15 Aligned_cols=31 Identities=26% Similarity=0.485 Sum_probs=23.0
Q ss_pred ccCCcccccccccc-ccccccCceeccccccc
Q psy7966 93 IAFCDACHKLLFSG-HLCRTCGFKFHRACNLA 123 (194)
Q Consensus 93 ptfCd~C~klL~QG-~kCk~Cg~~~HkrC~~~ 123 (194)
-+.|..|++.|..+ |.---||..+|..|..+
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~r 109 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIKR 109 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEecccccC
Confidence 46799999999744 33335678999999753
No 82
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=45.27 E-value=57 Score=20.98 Aligned_cols=39 Identities=18% Similarity=0.227 Sum_probs=32.7
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCc
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEM 41 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~ 41 (194)
+.|+|-.++ ....++|.+..|+.+--.+..+.-++.++.
T Consensus 1 ~~i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~ 39 (64)
T smart00213 1 IELTVKTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQ 39 (64)
T ss_pred CEEEEEECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHH
Confidence 467888888 688899999999999888888888887764
No 83
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=44.81 E-value=11 Score=21.75 Aligned_cols=21 Identities=24% Similarity=0.815 Sum_probs=13.4
Q ss_pred CCcccccccc-ccccccccCce
Q psy7966 95 FCDACHKLLF-SGHLCRTCGFK 115 (194)
Q Consensus 95 fCd~C~klL~-QG~kCk~Cg~~ 115 (194)
||.+|+.-|- ..--|..||..
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCc
Confidence 5777777766 33457777754
No 84
>TIGR02007 fdx_isc ferredoxin, 2Fe-2S type, ISC system. This family consists of proteobacterial ferredoxins associated with and essential to the ISC system of 2Fe-2S cluster assembly. This family is closely related to (but excludes) eukaryotic (mitochondrial) adrenodoxins, which are ferredoxins involved in electron transfer to P450 cytochromes.
Probab=44.01 E-value=23 Score=26.98 Aligned_cols=36 Identities=14% Similarity=0.253 Sum_probs=22.5
Q ss_pred eeeEEeecCCcHHHHHHHH---HHh--cC-CCCCccEEEecC
Q psy7966 13 RTSVHIRKGQTLLEALSKA---MKL--RN-LKPEMCTAYDSN 48 (194)
Q Consensus 13 rT~V~v~~G~tl~~aL~Ka---lk~--R~-L~~~~C~Vy~~~ 48 (194)
..+|++.+|.||.||+..+ +-. +| -....|.|+...
T Consensus 15 ~~~~~~~~g~tLL~a~~~~gi~i~~~CgG~G~CgtC~v~V~~ 56 (110)
T TIGR02007 15 GAVVEAKPGETILDVALDNGIEIEHACEKSCACTTCHCIVRE 56 (110)
T ss_pred CeEEEECCCChHHHHHHHcCCCccccCCCCceeCCCEEEEee
Confidence 3469999999998887542 100 22 245567777644
No 85
>PF02641 DUF190: Uncharacterized ACR, COG1993; InterPro: IPR003793 This is an uncharacterised domain found in proteins of unknown function.; PDB: 2DCL_C 1O51_A.
Probab=41.91 E-value=35 Score=25.70 Aligned_cols=42 Identities=26% Similarity=0.343 Sum_probs=32.8
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccEEEecCCC
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTG 50 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~~~ 50 (194)
..||+|+=+++| ..|..|+++|...++..||.. +.|++...|
T Consensus 4 ~~Lriy~~e~~~-----~~g~~l~~~ll~~~~~~gi~G--aTV~rgi~G 45 (101)
T PF02641_consen 4 KLLRIYLSESDR-----WGGKPLYEWLLERAREAGIAG--ATVFRGIEG 45 (101)
T ss_dssp EEEEEEEETT-E-----ETTEEHHHHHHHHHHHTT-SE--EEEEE-SEE
T ss_pred EEEEEEEcCccc-----cCceEHHHHHHHHHHHCCCCe--EEEEcceee
Confidence 368999988866 589999999999999988875 899997543
No 86
>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=41.33 E-value=48 Score=23.09 Aligned_cols=42 Identities=7% Similarity=0.022 Sum_probs=33.0
Q ss_pred EEEEcC-CCCeeeEEeecCCcHHHHHHHHHHhcCCCCCc-cEEE
Q psy7966 4 LRAQLP-NQQRTSVHIRKGQTLLEALSKAMKLRNLKPEM-CTAY 45 (194)
Q Consensus 4 irv~LP-n~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~-C~Vy 45 (194)
|.|.++ +++.-+|+|.|.+|+.+.-.+.-..-|+.++. .-+|
T Consensus 1 l~v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~ 44 (71)
T cd01796 1 ITVYTARSETTFSLDVDPDLELENFKALCEAESGIPASQQQLIY 44 (71)
T ss_pred CEEEECCCCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEE
Confidence 356788 66667799999999999998888888987664 4444
No 87
>PRK13552 frdB fumarate reductase iron-sulfur subunit; Provisional
Probab=41.19 E-value=50 Score=28.75 Aligned_cols=65 Identities=18% Similarity=0.115 Sum_probs=43.9
Q ss_pred CeeeEEeecCCcHHHHHHHHHHh-----------cCCCCCccEEEecCCCCcccCCCCCCCCCCcceeeeeehhcCC
Q psy7966 12 QRTSVHIRKGQTLLEALSKAMKL-----------RNLKPEMCTAYDSNTGVSLQWDTDSDHLPTTEIRVEVQERFPA 77 (194)
Q Consensus 12 QrT~V~v~~G~tl~~aL~Kalk~-----------R~L~~~~C~Vy~~~~~~~i~w~tD~~~L~~eel~V~~~~~~p~ 77 (194)
|.=.|++.+|+|+-|||.++=.+ |.=..-.|++...+.+. +-..|.+..+..+++.|+=+..||+
T Consensus 24 ~~y~v~~~~~~tvLdaL~~Ik~~~D~sL~fr~sCr~giCGsCam~ING~~~-LAC~t~v~~~~~~~i~iePl~~fpV 99 (239)
T PRK13552 24 VTYQLEETPGMTLFIALNRIREEQDPSLQFDFVCRAGICGSCAMVINGRPT-LACRTLTSDYPDGVITLMPLPVFKL 99 (239)
T ss_pred EEEEecCCCCCCHHHHHHHHHhcCCCCeeEeccCCCCCCCCceeEECCeEh-hhhhccHhhcCCCcEEEEECCCCCc
Confidence 55689999999999999987654 33345568887766332 3455555555445777776666666
No 88
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=40.75 E-value=15 Score=28.76 Aligned_cols=27 Identities=37% Similarity=1.073 Sum_probs=21.8
Q ss_pred ccCCcccccccc-----cc--ccccccCceeccc
Q psy7966 93 IAFCDACHKLLF-----SG--HLCRTCGFKFHRA 119 (194)
Q Consensus 93 ptfCd~C~klL~-----QG--~kCk~Cg~~~Hkr 119 (194)
..||.-|+.+|. .| +.|+.||+...-.
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 469999999998 12 7999999887654
No 89
>KOG2907|consensus
Probab=40.59 E-value=9.8 Score=30.49 Aligned_cols=28 Identities=32% Similarity=0.674 Sum_probs=22.2
Q ss_pred CCccCCcccccccc-----ccccccccCceecc
Q psy7966 91 FAIAFCDACHKLLF-----SGHLCRTCGFKFHR 118 (194)
Q Consensus 91 ~~ptfCd~C~klL~-----QG~kCk~Cg~~~Hk 118 (194)
..+-||..||.+|. -++.|..|+..+-.
T Consensus 5 ~~~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v 37 (116)
T KOG2907|consen 5 GDLDFCSDCGSLLEEPSAQSTVLCIRCKIEYPV 37 (116)
T ss_pred cCcchhhhhhhhcccccccCceEeccccccCCH
Confidence 47899999999997 34669999876653
No 90
>KOG2906|consensus
Probab=40.58 E-value=16 Score=28.81 Aligned_cols=25 Identities=36% Similarity=0.986 Sum_probs=19.9
Q ss_pred ccCCcccccccc-------ccccccccCceec
Q psy7966 93 IAFCDACHKLLF-------SGHLCRTCGFKFH 117 (194)
Q Consensus 93 ptfCd~C~klL~-------QG~kCk~Cg~~~H 117 (194)
+.||--|+.+|- .-|-|+.|.|.+-
T Consensus 1 m~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 1 MLFCPTCGNMLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred CcccCCCCCEEEEecCCeEeeEEcCCCCceee
Confidence 379999999886 3488999998664
No 91
>PHA02768 hypothetical protein; Provisional
Probab=39.63 E-value=12 Score=26.21 Aligned_cols=14 Identities=29% Similarity=0.648 Sum_probs=11.3
Q ss_pred ccccccccCceecc
Q psy7966 105 SGHLCRTCGFKFHR 118 (194)
Q Consensus 105 QG~kCk~Cg~~~Hk 118 (194)
-||.|..||..|.+
T Consensus 4 ~~y~C~~CGK~Fs~ 17 (55)
T PHA02768 4 LGYECPICGEIYIK 17 (55)
T ss_pred cccCcchhCCeecc
Confidence 48999999987753
No 92
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=39.22 E-value=16 Score=23.04 Aligned_cols=22 Identities=36% Similarity=0.872 Sum_probs=13.0
Q ss_pred CCcccccccc---------ccccccccCcee
Q psy7966 95 FCDACHKLLF---------SGHLCRTCGFKF 116 (194)
Q Consensus 95 fCd~C~klL~---------QG~kCk~Cg~~~ 116 (194)
||..|+..|- .-+.|..||+..
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCEE
Confidence 8999988763 347899998753
No 93
>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=38.74 E-value=55 Score=23.00 Aligned_cols=38 Identities=11% Similarity=0.184 Sum_probs=32.9
Q ss_pred EEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCc
Q psy7966 4 LRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEM 41 (194)
Q Consensus 4 irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~ 41 (194)
+.|.++++....|+|.|-.|+.+.=.+.-...|+.++.
T Consensus 1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~ 38 (70)
T cd01794 1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCC 38 (70)
T ss_pred CeEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHH
Confidence 46788999999999999999999988888888887764
No 94
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=38.71 E-value=17 Score=22.58 Aligned_cols=20 Identities=35% Similarity=0.838 Sum_probs=16.8
Q ss_pred CCcccccccc-----ccccccccCc
Q psy7966 95 FCDACHKLLF-----SGHLCRTCGF 114 (194)
Q Consensus 95 fCd~C~klL~-----QG~kCk~Cg~ 114 (194)
.|..|+.+|+ ..++|..|..
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCCe
Confidence 5899999987 6689999975
No 95
>PF07660 STN: Secretin and TonB N terminus short domain; InterPro: IPR011662 This is a conserved region found at the N-terminal region of bacterial proteins involved in either protein secretion or the uptake of selective substrates, including: Bundle-forming pilus protein B, an outer-membrane protein absolutely required for pilus biogenesis, and for enteropathogenic Escherichia coli localized adherence and autoaggregation []. PilQ, which is required for type IV pilus biogenesis and competence and is thought to function both as a pore for exit of the pilus and as a channel for entry of haem and antimicrobial agents and uptake of transforming DNA []. PupB, a specific receptor for the siderophores ferric pseudobactin BN8 and ferric pseudobactin BN7, iron chelating molecules that allow the organism to extract iron from the environment, especially under iron-restricted conditions []. TonB, which couples the electrochemical potential of the cytoplasmic membrane to the active transport of iron-siderophores and vitamin B12 across the outer membrane []. ; GO: 0019867 outer membrane; PDB: 2D1U_A 1ZZV_A 2W75_B 2O5P_A 2W77_A 2W16_A 2W6U_B 2W6T_A 2W76_B 2W78_B ....
Probab=38.27 E-value=18 Score=23.34 Aligned_cols=27 Identities=26% Similarity=0.434 Sum_probs=17.9
Q ss_pred CCeeeEEeecCCcHHHHHHHHHHhcCCC
Q psy7966 11 QQRTSVHIRKGQTLLEALSKAMKLRNLK 38 (194)
Q Consensus 11 ~QrT~V~v~~G~tl~~aL~Kalk~R~L~ 38 (194)
.+..+|+++. +++.+||...|+--||+
T Consensus 13 ~~~vsl~~~~-~~~~~~L~~ll~~t~l~ 39 (52)
T PF07660_consen 13 KKKVSLDVKN-MSLEEALDQLLKGTGLT 39 (52)
T ss_dssp -BE--EE-EE-E-HHHHHHHHTTTSTEE
T ss_pred CcceeEEcCC-cCHHHHHHHHHccCCcE
Confidence 3455555554 99999999999998886
No 96
>PTZ00038 ferredoxin; Provisional
Probab=38.10 E-value=43 Score=28.75 Aligned_cols=27 Identities=15% Similarity=0.359 Sum_probs=20.9
Q ss_pred EEEEcCCCCeeeEEeecCCcHHHHHHHH
Q psy7966 4 LRAQLPNQQRTSVHIRKGQTLLEALSKA 31 (194)
Q Consensus 4 irv~LPn~QrT~V~v~~G~tl~~aL~Ka 31 (194)
|.+-+|++. -++++.+|.||-||+.++
T Consensus 98 Vt~~~~~g~-~~~~v~~geTILdAae~a 124 (191)
T PTZ00038 98 ITLQTPDGE-KVIECDEDEYILDAAERQ 124 (191)
T ss_pred EEEEeCCCc-EEEEeCCCCcHHHHHHHc
Confidence 455578775 459999999999997754
No 97
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=37.47 E-value=17 Score=24.09 Aligned_cols=26 Identities=31% Similarity=0.768 Sum_probs=19.0
Q ss_pred CCcccccccccc--cccccc-Cceecccc
Q psy7966 95 FCDACHKLLFSG--HLCRTC-GFKFHRAC 120 (194)
Q Consensus 95 fCd~C~klL~QG--~kCk~C-g~~~HkrC 120 (194)
.||.|.+.++.| ++|..| +|..=..|
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~C 30 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLEC 30 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHh
Confidence 399999988866 799999 44443444
No 98
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=36.59 E-value=20 Score=21.18 Aligned_cols=19 Identities=32% Similarity=1.018 Sum_probs=12.3
Q ss_pred Ccccccccc---cc--ccccccCc
Q psy7966 96 CDACHKLLF---SG--HLCRTCGF 114 (194)
Q Consensus 96 Cd~C~klL~---QG--~kCk~Cg~ 114 (194)
|..|+..|- +| |.|-.||+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 566766664 23 78888874
No 99
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=36.58 E-value=42 Score=25.30 Aligned_cols=24 Identities=25% Similarity=0.538 Sum_probs=19.1
Q ss_pred cCCCCee-eEEeecCCcHHHHHHHH
Q psy7966 8 LPNQQRT-SVHIRKGQTLLEALSKA 31 (194)
Q Consensus 8 LPn~QrT-~V~v~~G~tl~~aL~Ka 31 (194)
+|++|+- +++|-+|.|+.|||..+
T Consensus 9 ~p~~q~~~~l~vp~GtTv~~Ai~~S 33 (84)
T PF03658_consen 9 LPERQVILTLEVPEGTTVAQAIEAS 33 (84)
T ss_dssp ETTCEEEEEEEEETT-BHHHHHHHH
T ss_pred CCCeEEEEEEECCCcCcHHHHHHHc
Confidence 7888764 58999999999999754
No 100
>PRK11433 aldehyde oxidoreductase 2Fe-2S subunit; Provisional
Probab=35.01 E-value=49 Score=29.00 Aligned_cols=62 Identities=23% Similarity=0.271 Sum_probs=39.1
Q ss_pred EEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCC-------CCCccEEEecCCCCcc-cCCCCCCCCCCccee
Q psy7966 4 LRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNL-------KPEMCTAYDSNTGVSL-QWDTDSDHLPTTEIR 68 (194)
Q Consensus 4 irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L-------~~~~C~Vy~~~~~~~i-~w~tD~~~L~~eel~ 68 (194)
|++.+ |++.-.|++.|++||-|+|...+.+-|. ....|.|-. +|..+ +.-+.+....|.+|.
T Consensus 52 i~~~V-NG~~~~~~v~~~~tLLd~LR~~l~ltGtK~GC~~G~CGACTVlV--dG~~v~SCl~la~~~~G~~It 121 (217)
T PRK11433 52 VTLKV-NGKTEQLEVDTRTTLLDALREHLHLTGTKKGCDHGQCGACTVLV--NGRRLNACLTLAVMHQGAEIT 121 (217)
T ss_pred EEEEE-CCEEEEEecCCCCcHHHHHHHhcCCCCCCCCCCCCCcCceEEEE--CCEEeeeeeeehhhcCCCEEE
Confidence 44443 6767778999999999999987765332 233477744 34442 344555555666543
No 101
>PF11275 DUF3077: Protein of unknown function (DUF3077); InterPro: IPR021427 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=34.98 E-value=40 Score=25.11 Aligned_cols=25 Identities=24% Similarity=0.276 Sum_probs=20.3
Q ss_pred CCCeeeEEeecCCcHHHHHHHHHHh
Q psy7966 10 NQQRTSVHIRKGQTLLEALSKAMKL 34 (194)
Q Consensus 10 n~QrT~V~v~~G~tl~~aL~Kalk~ 34 (194)
|+...-..|+||+.+.|||+-|--+
T Consensus 12 ~~~~pLF~v~pgip~~dAl~~aS~L 36 (79)
T PF11275_consen 12 NPHHPLFRVNPGIPCEDALEHASVL 36 (79)
T ss_pred CCCCCeeeeCCCCCHHHHHHHHHHH
Confidence 4445778999999999999987654
No 102
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=34.73 E-value=20 Score=23.35 Aligned_cols=30 Identities=27% Similarity=0.617 Sum_probs=23.0
Q ss_pred CCcccccccc-ccccccccC-ceecccccccc
Q psy7966 95 FCDACHKLLF-SGHLCRTCG-FKFHRACNLAV 124 (194)
Q Consensus 95 fCd~C~klL~-QG~kCk~Cg-~~~HkrC~~~V 124 (194)
.||.|++.|+ .-|+|..|. |..-..|-...
T Consensus 2 ~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~ 33 (46)
T cd02249 2 SCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKG 33 (46)
T ss_pred CCcCCCCCCcCCEEECCCCCCCcCHHHHHCcC
Confidence 4999999776 557999997 77777776543
No 103
>KOG1829|consensus
Probab=34.41 E-value=9.2 Score=37.98 Aligned_cols=24 Identities=29% Similarity=0.552 Sum_probs=20.2
Q ss_pred ccccccCceecccccccccccccc
Q psy7966 107 HLCRTCGFKFHRACNLAVPYLCQV 130 (194)
Q Consensus 107 ~kCk~Cg~~~HkrC~~~Vp~~C~~ 130 (194)
.+|..|+..||++|.......|..
T Consensus 532 ~rC~~C~avfH~~C~~r~s~~CPr 555 (580)
T KOG1829|consen 532 RRCSTCLAVFHKKCLRRKSPCCPR 555 (580)
T ss_pred eeHHHHHHHHHHHHHhccCCCCCc
Confidence 699999999999998877766654
No 104
>TIGR00568 alkb DNA alkylation damage repair protein AlkB. Proteins in this family have an as of yet undetermined function in the repair of alkylation damage to DNA. Alignment and family designation based on phylogenomic analysis of Jonathan A. Eisen (PhD Thesis, Stanford University, 1999).
Probab=33.70 E-value=80 Score=26.20 Aligned_cols=39 Identities=23% Similarity=0.440 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhcCCCCCccEEEecCCCCcccCCCCCCCC
Q psy7966 24 LLEALSKAMKLRNLKPEMCTAYDSNTGVSLQWDTDSDHL 62 (194)
Q Consensus 24 l~~aL~Kalk~R~L~~~~C~Vy~~~~~~~i~w~tD~~~L 62 (194)
|++.+++++..-+..++.|.|..-.+|..|.|..|-..+
T Consensus 79 L~~~v~~~~g~~~~~~n~~LvN~Y~~Gd~mg~H~D~~e~ 117 (169)
T TIGR00568 79 LCERVATAAGFPDFQPDACLVNRYAPGATLSLHQDRDEP 117 (169)
T ss_pred HHHHHHHHhCCCCCCCCEEEEEeecCCCccccccccccc
Confidence 455555554434459999999998888889999995444
No 105
>PRK11872 antC anthranilate dioxygenase reductase; Provisional
Probab=33.69 E-value=55 Score=29.26 Aligned_cols=28 Identities=14% Similarity=0.215 Sum_probs=22.3
Q ss_pred EEEEcCCCCeeeEEeecCCcHHHHHHHH
Q psy7966 4 LRAQLPNQQRTSVHIRKGQTLLEALSKA 31 (194)
Q Consensus 4 irv~LPn~QrT~V~v~~G~tl~~aL~Ka 31 (194)
|++-++|++...++|.+|.||-||+.++
T Consensus 5 v~~~~~~~~~~~~~~~~g~tlL~a~~~~ 32 (340)
T PRK11872 5 VALSFADGKTLFFPVGKDELLLDAALRN 32 (340)
T ss_pred EEEEecCCcEEEEEeCCCCcHHHHHHHc
Confidence 4444589988889999999999987653
No 106
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=33.58 E-value=22 Score=25.57 Aligned_cols=8 Identities=50% Similarity=1.306 Sum_probs=4.6
Q ss_pred ccccccCc
Q psy7966 107 HLCRTCGF 114 (194)
Q Consensus 107 ~kCk~Cg~ 114 (194)
|+|..|||
T Consensus 51 Y~Cp~CGF 58 (61)
T COG2888 51 YRCPKCGF 58 (61)
T ss_pred eECCCcCc
Confidence 55666655
No 107
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=33.48 E-value=19 Score=19.43 Aligned_cols=12 Identities=33% Similarity=0.755 Sum_probs=8.7
Q ss_pred ccccccCceecc
Q psy7966 107 HLCRTCGFKFHR 118 (194)
Q Consensus 107 ~kCk~Cg~~~Hk 118 (194)
|+|..|+..|-.
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 578888877654
No 108
>CHL00134 petF ferredoxin; Validated
Probab=33.37 E-value=47 Score=24.89 Aligned_cols=28 Identities=11% Similarity=0.204 Sum_probs=20.3
Q ss_pred EEEEcCC--C-CeeeEEeecCCcHHHHHHHH
Q psy7966 4 LRAQLPN--Q-QRTSVHIRKGQTLLEALSKA 31 (194)
Q Consensus 4 irv~LPn--~-QrT~V~v~~G~tl~~aL~Ka 31 (194)
.+|++.+ + +--++++.+|.||-||+.++
T Consensus 4 ~~v~~~~~~~~~~~~~~~~~~~tLL~a~~~~ 34 (99)
T CHL00134 4 YKVTLLSEEEGIDVTIDCPDDVYILDAAEEQ 34 (99)
T ss_pred EEEEEEecCCCCeEEEEECCCCcHHHHHHHc
Confidence 3566654 3 33479999999999988754
No 109
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=32.98 E-value=25 Score=20.92 Aligned_cols=21 Identities=33% Similarity=0.983 Sum_probs=15.5
Q ss_pred Ccccccccc-ccccccccCcee
Q psy7966 96 CDACHKLLF-SGHLCRTCGFKF 116 (194)
Q Consensus 96 Cd~C~klL~-QG~kCk~Cg~~~ 116 (194)
|--|++.+. .=-.|..||+.|
T Consensus 3 CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 3 CPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred CCCCcCCchhhcCcCCCCCCCC
Confidence 677777776 445888888876
No 110
>PRK05950 sdhB succinate dehydrogenase iron-sulfur subunit; Reviewed
Probab=32.91 E-value=69 Score=27.36 Aligned_cols=65 Identities=20% Similarity=0.125 Sum_probs=43.1
Q ss_pred CeeeEEee-cCCcHHHHHHHHHH--------hcCC---CCCccEEEecCCCCcccCCCCCCCCCCcceeeeeehhcCC
Q psy7966 12 QRTSVHIR-KGQTLLEALSKAMK--------LRNL---KPEMCTAYDSNTGVSLQWDTDSDHLPTTEIRVEVQERFPA 77 (194)
Q Consensus 12 QrT~V~v~-~G~tl~~aL~Kalk--------~R~L---~~~~C~Vy~~~~~~~i~w~tD~~~L~~eel~V~~~~~~p~ 77 (194)
|-=.|+|. +|+||-|||.++-. +.+. ....|+|...+... +...+.+..+.++++.+|=+..||+
T Consensus 18 ~~~~v~~~~~~~tvl~~L~~~~~~~~~~l~~~~~c~~g~Cg~C~v~vnG~~~-laC~t~~~~~~~~~~tiepl~~~~v 94 (232)
T PRK05950 18 QTYEVDVDECGPMVLDALIKIKNEIDPTLTFRRSCREGVCGSDAMNINGKNG-LACITPISDLKKGKIVIRPLPGLPV 94 (232)
T ss_pred EEEEeCCCCCCCHHHHHHHHhCCccCCcceeeCCCCCCCCCCCEEEECCcCc-cchhChHhHcCCCeEEEEECCCCCe
Confidence 45568898 99999999998631 1233 22357888865332 3566666666567788886666666
No 111
>PF13510 Fer2_4: 2Fe-2S iron-sulfur cluster binding domain; PDB: 1Y56_A 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 2GAG_A 2GAH_A.
Probab=32.65 E-value=35 Score=24.72 Aligned_cols=17 Identities=47% Similarity=0.653 Sum_probs=13.5
Q ss_pred eEEeecCCcHHHHHHHH
Q psy7966 15 SVHIRKGQTLLEALSKA 31 (194)
Q Consensus 15 ~V~v~~G~tl~~aL~Ka 31 (194)
.|++.+|.||-+||.++
T Consensus 12 ~v~~~~G~til~al~~~ 28 (82)
T PF13510_consen 12 PVEVPPGETILEALLAA 28 (82)
T ss_dssp EEEEEET-BHHHHHHHT
T ss_pred EEEEcCCCHHHHHHHHC
Confidence 48899999999998764
No 112
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=32.50 E-value=1.2e+02 Score=20.37 Aligned_cols=48 Identities=8% Similarity=0.023 Sum_probs=29.4
Q ss_pred eEEeecCCcHHHHHHHHHHhcCCCCCccEEEecCCC-CcccCCCCCCCCCCcce
Q psy7966 15 SVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTG-VSLQWDTDSDHLPTTEI 67 (194)
Q Consensus 15 ~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~~~-~~i~w~tD~~~L~~eel 67 (194)
.+++..|.||.++|. .-++.++..+|-..+.- .+-.|++..-. .|+.+
T Consensus 9 ~~~~~~~~tl~~lL~----~l~~~~~~vav~vNg~iv~r~~~~~~~l~-~gD~v 57 (66)
T PRK05659 9 PRELPDGESVAALLA----REGLAGRRVAVEVNGEIVPRSQHASTALR-EGDVV 57 (66)
T ss_pred EEEcCCCCCHHHHHH----hcCCCCCeEEEEECCeEeCHHHcCcccCC-CCCEE
Confidence 457788999998875 34788888887643210 11357665533 34443
No 113
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=32.25 E-value=67 Score=32.85 Aligned_cols=80 Identities=18% Similarity=0.123 Sum_probs=38.5
Q ss_pred HHHHHHHHHHhcCCCCCccEEEecCCCCcccCCCCCCCCCCcceeeeeehhcCCCCCccceeeccccCCccCCccccccc
Q psy7966 24 LLEALSKAMKLRNLKPEMCTAYDSNTGVSLQWDTDSDHLPTTEIRVEVQERFPAAINIEHNITRRTFFAIAFCDACHKLL 103 (194)
Q Consensus 24 l~~aL~Kalk~R~L~~~~C~Vy~~~~~~~i~w~tD~~~L~~eel~V~~~~~~p~~~~~~H~F~~~Tf~~ptfCd~C~klL 103 (194)
+...|.++++.+--.-++-.+|-..-|.+ +-+++-.|..+. -=+.-...++-|.+..-..|+||+.--
T Consensus 405 lS~~Ll~~i~~~l~~geQ~llflnRRGys----~~l~C~~Cg~v~--------~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~ 472 (730)
T COG1198 405 LSPALLEAIRKTLERGEQVLLFLNRRGYA----PLLLCRDCGYIA--------ECPNCDSPLTLHKATGQLRCHYCGYQE 472 (730)
T ss_pred CCHHHHHHHHHHHhcCCeEEEEEccCCcc----ceeecccCCCcc--------cCCCCCcceEEecCCCeeEeCCCCCCC
Confidence 55666666665544445555554443331 122222333222 111122334444555667777776553
Q ss_pred cccccccccCce
Q psy7966 104 FSGHLCRTCGFK 115 (194)
Q Consensus 104 ~QG~kCk~Cg~~ 115 (194)
-.=..|..||..
T Consensus 473 ~~p~~Cp~Cgs~ 484 (730)
T COG1198 473 PIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCC
Confidence 233577777744
No 114
>PRK08640 sdhB succinate dehydrogenase iron-sulfur subunit; Reviewed
Probab=32.11 E-value=86 Score=27.50 Aligned_cols=64 Identities=17% Similarity=0.188 Sum_probs=41.3
Q ss_pred CeeeEEeecCCcHHHHHHHHHHh------------------cCCCCCccEEEecCCCCcccCCCCCCCCCCcceeeeeeh
Q psy7966 12 QRTSVHIRKGQTLLEALSKAMKL------------------RNLKPEMCTAYDSNTGVSLQWDTDSDHLPTTEIRVEVQE 73 (194)
Q Consensus 12 QrT~V~v~~G~tl~~aL~Kalk~------------------R~L~~~~C~Vy~~~~~~~i~w~tD~~~L~~eel~V~~~~ 73 (194)
|-=.|++.+|||+-|||.++=.. |.=..-.|++...+.+. +-..+.+..+ ++++.++=+.
T Consensus 23 q~y~v~~~~~~tvLdaL~~I~~~~~~~~g~~~~~l~fr~sCr~giCGsCam~ING~p~-LAC~t~v~~~-~~~i~iePl~ 100 (249)
T PRK08640 23 EEFEIPYRPNMNVISALMEIRRNPVNAKGEKTTPVVWDMNCLEEVCGACSMVINGKPR-QACTALIDQL-EQPIRLEPMS 100 (249)
T ss_pred EEEEecCCCCCcHHHHHHHHHhcccccccccCCCeeEecccCCCCCCcCeeEECCccc-hhhhChHHHc-CCcEEEEECC
Confidence 55678999999999999987543 22234457777765433 3444444333 4667777666
Q ss_pred hcCC
Q psy7966 74 RFPA 77 (194)
Q Consensus 74 ~~p~ 77 (194)
.||+
T Consensus 101 ~fpV 104 (249)
T PRK08640 101 TFPV 104 (249)
T ss_pred CCCc
Confidence 6666
No 115
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=31.90 E-value=23 Score=18.56 Aligned_cols=12 Identities=33% Similarity=0.849 Sum_probs=6.7
Q ss_pred ccccccCceecc
Q psy7966 107 HLCRTCGFKFHR 118 (194)
Q Consensus 107 ~kCk~Cg~~~Hk 118 (194)
|+|..|++.|-.
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 568888877643
No 116
>PF13085 Fer2_3: 2Fe-2S iron-sulfur cluster binding domain; PDB: 3P4Q_N 1KFY_N 3CIR_N 3P4R_B 2B76_N 1KF6_B 3P4P_N 3P4S_B 1L0V_B 1ZOY_B ....
Probab=29.87 E-value=1.4e+02 Score=23.27 Aligned_cols=65 Identities=25% Similarity=0.269 Sum_probs=41.1
Q ss_pred CeeeEEeecCCcHHHHHHHHHHhc-----------CCCCCccEEEecCCCCcccCCCCCCCCCCc---ceeeeeehhcCC
Q psy7966 12 QRTSVHIRKGQTLLEALSKAMKLR-----------NLKPEMCTAYDSNTGVSLQWDTDSDHLPTT---EIRVEVQERFPA 77 (194)
Q Consensus 12 QrT~V~v~~G~tl~~aL~Kalk~R-----------~L~~~~C~Vy~~~~~~~i~w~tD~~~L~~e---el~V~~~~~~p~ 77 (194)
|-=.|++.+|+|+-|||.++=+.. .=.+-.|+|...+.. .+-..+-+..+... ++.++=+..||+
T Consensus 19 ~~y~v~~~~~~tVLd~L~~Ik~~~D~sLafr~sCr~giCGsCam~ING~~-~LAC~t~v~~~~~~~~~~i~IePL~~fpV 97 (110)
T PF13085_consen 19 QEYEVPVEPGMTVLDALNYIKEEQDPSLAFRYSCRSGICGSCAMRINGRP-RLACKTQVDDLIEKFGNVITIEPLPNFPV 97 (110)
T ss_dssp EEEEEEGGSTSBHHHHHHHHHHHT-TT--B--SSSSSSSSTTEEEETTEE-EEGGGSBGGGCTTSETBEEEEEESTTSBE
T ss_pred EEEEecCCCCCcHHHHHHHHHhccCCCeEEEecCCCCCCCCCEEEECCce-ecceeeEchhccCCCcceEEEEECCCCCc
Confidence 445789999999999999886662 223456888776532 14555555555543 477664444443
No 117
>PTZ00044 ubiquitin; Provisional
Probab=29.82 E-value=1.4e+02 Score=20.45 Aligned_cols=41 Identities=5% Similarity=0.032 Sum_probs=33.4
Q ss_pred eEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccE
Q psy7966 3 LLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCT 43 (194)
Q Consensus 3 ~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~ 43 (194)
.|-|=.++++-.+++|.+..|+.+.=.+.-++-|+.++.-.
T Consensus 2 ~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~ 42 (76)
T PTZ00044 2 QILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIR 42 (76)
T ss_pred EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeE
Confidence 45556678888899999999999998888888898777533
No 118
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.71 E-value=38 Score=28.59 Aligned_cols=29 Identities=28% Similarity=0.705 Sum_probs=22.6
Q ss_pred cCCccCCcccccccc-ccccccccCceeccc
Q psy7966 90 FFAIAFCDACHKLLF-SGHLCRTCGFKFHRA 119 (194)
Q Consensus 90 f~~ptfCd~C~klL~-QG~kCk~Cg~~~Hkr 119 (194)
+.+-..|..|+. +- .-+.|..||+..|+-
T Consensus 306 ~~tS~~C~~cg~-~~~r~~~C~~cg~~~~rD 335 (364)
T COG0675 306 YYTSKTCPCCGH-LSGRLFKCPRCGFVHDRD 335 (364)
T ss_pred CCCcccccccCC-ccceeEECCCCCCeehhh
Confidence 555578999999 44 448999999988853
No 119
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=29.41 E-value=24 Score=27.10 Aligned_cols=25 Identities=36% Similarity=0.743 Sum_probs=18.2
Q ss_pred ccCCcccccccc----cc-ccccccCceec
Q psy7966 93 IAFCDACHKLLF----SG-HLCRTCGFKFH 117 (194)
Q Consensus 93 ptfCd~C~klL~----QG-~kCk~Cg~~~H 117 (194)
.-+|..|++.-. -| .+|+.|++.|=
T Consensus 35 ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp -BEESSSSSSEEEEEETTEEEETTTTEEEE
T ss_pred CCcCCCCCCceeEEeeeEEeecCCCCCEEe
Confidence 456899988654 44 59999998764
No 120
>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=29.23 E-value=1.3e+02 Score=21.20 Aligned_cols=40 Identities=13% Similarity=0.056 Sum_probs=31.8
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCc
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEM 41 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~ 41 (194)
+.|.|-.++++..+|+|.+..|+.+-=.+.-+.-++.++.
T Consensus 3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~ 42 (80)
T cd01792 3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQ 42 (80)
T ss_pred eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHH
Confidence 5677778888888899999999998777766776776654
No 121
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.93 E-value=22 Score=28.85 Aligned_cols=29 Identities=31% Similarity=0.703 Sum_probs=22.0
Q ss_pred cCCccccc-cccccc-----cccccCceecccccc
Q psy7966 94 AFCDACHK-LLFSGH-----LCRTCGFKFHRACNL 122 (194)
Q Consensus 94 tfCd~C~k-lL~QG~-----kCk~Cg~~~HkrC~~ 122 (194)
--|-+|++ -||+|| .|+.||.-.|..=.+
T Consensus 22 grCP~CGeGrLF~gFLK~~p~C~aCG~dyg~~~a~ 56 (126)
T COG5349 22 GRCPRCGEGRLFRGFLKVVPACEACGLDYGFADAD 56 (126)
T ss_pred CCCCCCCCchhhhhhcccCchhhhccccccCCccc
Confidence 45999988 688886 799999877754333
No 122
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=28.88 E-value=23 Score=22.70 Aligned_cols=11 Identities=45% Similarity=1.029 Sum_probs=4.8
Q ss_pred cCCcccccccc
Q psy7966 94 AFCDACHKLLF 104 (194)
Q Consensus 94 tfCd~C~klL~ 104 (194)
-|||+|...|-
T Consensus 4 yyCdyC~~~~~ 14 (38)
T PF06220_consen 4 YYCDYCKKYLT 14 (38)
T ss_dssp -B-TTT--B-S
T ss_pred eecccccceec
Confidence 48999988873
No 123
>PRK12386 fumarate reductase iron-sulfur subunit; Provisional
Probab=28.71 E-value=1e+02 Score=27.24 Aligned_cols=64 Identities=19% Similarity=0.285 Sum_probs=40.2
Q ss_pred CeeeEEeecCCcHHHHHHHHHHhc------------CCCCCccEEEecCCCCcccCCCCCCCCCC-cceeeeeehhcCC
Q psy7966 12 QRTSVHIRKGQTLLEALSKAMKLR------------NLKPEMCTAYDSNTGVSLQWDTDSDHLPT-TEIRVEVQERFPA 77 (194)
Q Consensus 12 QrT~V~v~~G~tl~~aL~Kalk~R------------~L~~~~C~Vy~~~~~~~i~w~tD~~~L~~-eel~V~~~~~~p~ 77 (194)
|-=.|++.+|+||-|||.. ++.. .=..-.|+|...+... ....+.+..+.+ +++.+|=+..||+
T Consensus 20 q~y~v~~~~~~tvLd~L~~-i~~~~d~~l~~r~~C~~g~CGsCa~~InG~p~-laC~t~~~~~~~~~~itiepl~~fpV 96 (251)
T PRK12386 20 QDYTVEVNEGEVVLDVIHR-LQATQAPDLAVRWNCKAGKCGSCSAEINGRPR-LMCMTRMSTFDEDETVTVTPMRTFPV 96 (251)
T ss_pred EEEEEeCCCCCCHHHHHHH-hccccCCCCcccCCCCCCcCCCCEEEECccEe-ccHHhHHHHhCCCCeEEEccCCCCCc
Confidence 5567899999999999998 6652 1134458888866332 344444444443 4566665555555
No 124
>PRK07570 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated
Probab=28.56 E-value=1e+02 Score=27.20 Aligned_cols=66 Identities=18% Similarity=0.177 Sum_probs=41.9
Q ss_pred CeeeEE-eecCCcHHHHHHHHHHh---------------cCCCCCccEEEecCCCC-----cccCCCCCCCCC-Ccceee
Q psy7966 12 QRTSVH-IRKGQTLLEALSKAMKL---------------RNLKPEMCTAYDSNTGV-----SLQWDTDSDHLP-TTEIRV 69 (194)
Q Consensus 12 QrT~V~-v~~G~tl~~aL~Kalk~---------------R~L~~~~C~Vy~~~~~~-----~i~w~tD~~~L~-~eel~V 69 (194)
|.=.|+ +.+|+|+-|||.++=.. |.=..-.|++...+.+. .+...|.+..+. +++|.+
T Consensus 20 q~y~v~~~~~~~tvLd~L~~Ik~~~~~~~~~~l~fr~sCr~~iCGsCam~ING~p~~~~~~~LAC~t~~~~~~~~~~i~i 99 (250)
T PRK07570 20 ETYEVDDISPDMSFLEMLDVLNEQLIEKGEEPVAFDHDCREGICGMCGLVINGRPHGPDRGTTTCQLHMRSFKDGDTITI 99 (250)
T ss_pred EEEEecCCCCCCcHHHHHHHHHHHhhccCCCCeeEeccccCCcCCcceeEECCccCCCCcccchhhhhhhhcCCCCeEEE
Confidence 556788 78999999999988221 12234457887776552 344555555443 467777
Q ss_pred eeeh--hcCC
Q psy7966 70 EVQE--RFPA 77 (194)
Q Consensus 70 ~~~~--~~p~ 77 (194)
+=+. .||+
T Consensus 100 ePl~~~~fpv 109 (250)
T PRK07570 100 EPWRAAAFPV 109 (250)
T ss_pred EECCCCCCCe
Confidence 7665 5665
No 125
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=28.51 E-value=31 Score=20.81 Aligned_cols=22 Identities=27% Similarity=0.714 Sum_probs=12.9
Q ss_pred cCCcccccccc-----ccccccccCce
Q psy7966 94 AFCDACHKLLF-----SGHLCRTCGFK 115 (194)
Q Consensus 94 tfCd~C~klL~-----QG~kCk~Cg~~ 115 (194)
.||..|+..+. -..+|..||..
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred cccCcCCccccCCCCcCEeECCCCcCE
Confidence 58999998764 33689998853
No 126
>PF04106 APG5: Autophagy protein Apg5 ; InterPro: IPR007239 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents autophagy protein 5 (Apg5).; GO: 0006914 autophagy, 0005737 cytoplasm; PDB: 2DYM_G 2DYO_A.
Probab=28.41 E-value=32 Score=29.07 Aligned_cols=32 Identities=31% Similarity=0.240 Sum_probs=18.9
Q ss_pred eEEEEcCCC-CeeeEEeecC------CcHHHHHHHHHHh
Q psy7966 3 LLRAQLPNQ-QRTSVHIRKG------QTLLEALSKAMKL 34 (194)
Q Consensus 3 ~irv~LPn~-QrT~V~v~~G------~tl~~aL~Kalk~ 34 (194)
=||+|+|++ ....-.|.|- .||.|||.+.|..
T Consensus 112 PiRiy~~~~~~~iQ~~i~~~~~~g~~~TL~d~L~~~lp~ 150 (197)
T PF04106_consen 112 PIRIYLPGSVPVIQPPIPPIKEDGQPQTLGDALSELLPE 150 (197)
T ss_dssp -EEEEE-SS--EE----B----TT---BTGGGHHHHHTT
T ss_pred EEEEEeCCCcceEecccccccCCCCcCcHHHHHHHhChh
Confidence 489999999 5544455553 6999999999854
No 127
>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=28.09 E-value=1.6e+02 Score=19.53 Aligned_cols=40 Identities=15% Similarity=0.185 Sum_probs=32.9
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCc
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEM 41 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~ 41 (194)
|.|.|--++++.-.++|.+..|+.+--.+..+.-|+.++.
T Consensus 1 i~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~ 40 (72)
T cd01809 1 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQ 40 (72)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHH
Confidence 4577778888888899999999999888887777886664
No 128
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=27.95 E-value=36 Score=23.94 Aligned_cols=23 Identities=35% Similarity=0.779 Sum_probs=17.0
Q ss_pred CCcccccccc--ccccccccCceec
Q psy7966 95 FCDACHKLLF--SGHLCRTCGFKFH 117 (194)
Q Consensus 95 fCd~C~klL~--QG~kCk~Cg~~~H 117 (194)
+|-+|.+-+- +-|-|..||+..|
T Consensus 1 ~Cpv~~~~~~~~v~~~Cp~cGipth 25 (55)
T PF13824_consen 1 LCPVCKKDLPAHVNFECPDCGIPTH 25 (55)
T ss_pred CCCCCccccccccCCcCCCCCCcCc
Confidence 4667766432 7899999998877
No 129
>KOG0612|consensus
Probab=27.89 E-value=6 Score=42.35 Aligned_cols=45 Identities=11% Similarity=0.249 Sum_probs=38.1
Q ss_pred ceeeccccCCccCCcccccccc----ccccccccCceeccccccccccccccccc
Q psy7966 83 HNITRRTFFAIAFCDACHKLLF----SGHLCRTCGFKFHRACNLAVPYLCQVERI 133 (194)
Q Consensus 83 H~F~~~Tf~~ptfCd~C~klL~----QG~kCk~Cg~~~HkrC~~~Vp~~C~~~~~ 133 (194)
|.|...+|.+| .+.+. ||+.|++|.+.||.-|...++..|.....
T Consensus 894 ~el~~e~~~~~------t~~~~g~hRqe~~~k~~t~ac~~e~~~~l~q~~~i~~~ 942 (1317)
T KOG0612|consen 894 EELEQEKISKK------TKDVLGLHRQELTCKDCTLACLEETNRTLTQKCKLLSE 942 (1317)
T ss_pred HHHHHHHhhhh------HHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhhcCCchh
Confidence 88998889888 22222 99999999999999999999999988743
No 130
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=27.46 E-value=29 Score=19.98 Aligned_cols=10 Identities=40% Similarity=0.876 Sum_probs=6.9
Q ss_pred ccccccCcee
Q psy7966 107 HLCRTCGFKF 116 (194)
Q Consensus 107 ~kCk~Cg~~~ 116 (194)
|+|..|+..|
T Consensus 15 ~~C~~C~k~F 24 (26)
T PF13465_consen 15 YKCPYCGKSF 24 (26)
T ss_dssp EEESSSSEEE
T ss_pred CCCCCCcCee
Confidence 6777777665
No 131
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=27.08 E-value=43 Score=28.93 Aligned_cols=17 Identities=47% Similarity=0.622 Sum_probs=14.4
Q ss_pred CcHHHHHHHHHHhcCCC
Q psy7966 22 QTLLEALSKAMKLRNLK 38 (194)
Q Consensus 22 ~tl~~aL~Kalk~R~L~ 38 (194)
..+.++++|+||+||.+
T Consensus 140 t~~S~~mskaLKkrGf~ 156 (188)
T COG2818 140 TELSDAMSKALKKRGFK 156 (188)
T ss_pred chhHHHHHHHHHHccCe
Confidence 45789999999999964
No 132
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=26.82 E-value=42 Score=20.57 Aligned_cols=24 Identities=25% Similarity=0.661 Sum_probs=16.1
Q ss_pred cCCcccccccc--------cc--ccccccCceec
Q psy7966 94 AFCDACHKLLF--------SG--HLCRTCGFKFH 117 (194)
Q Consensus 94 tfCd~C~klL~--------QG--~kCk~Cg~~~H 117 (194)
.-|.+|+.... .| ++|..|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 34788877543 33 78888887664
No 133
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=26.41 E-value=34 Score=23.42 Aligned_cols=23 Identities=22% Similarity=0.803 Sum_probs=19.9
Q ss_pred CccCCccccccccccccccccCc
Q psy7966 92 AIAFCDACHKLLFSGHLCRTCGF 114 (194)
Q Consensus 92 ~ptfCd~C~klL~QG~kCk~Cg~ 114 (194)
.++.|..|+++..-..-|..|||
T Consensus 25 ~l~~c~~cg~~~~~H~vc~~cG~ 47 (56)
T PF01783_consen 25 NLVKCPNCGEPKLPHRVCPSCGY 47 (56)
T ss_dssp SEEESSSSSSEESTTSBCTTTBB
T ss_pred ceeeeccCCCEecccEeeCCCCe
Confidence 67889999998888889999984
No 134
>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=26.30 E-value=1.7e+02 Score=22.21 Aligned_cols=40 Identities=10% Similarity=0.077 Sum_probs=34.5
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCc
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEM 41 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~ 41 (194)
+.|-|-..+++..+++|.+..|+.+.-.|.-++.|+.++.
T Consensus 28 M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~ 67 (103)
T cd01802 28 MELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQ 67 (103)
T ss_pred EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHH
Confidence 5677777888888899999999999999999999987764
No 135
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=25.46 E-value=2.4e+02 Score=19.64 Aligned_cols=31 Identities=19% Similarity=0.247 Sum_probs=22.9
Q ss_pred eeEEeecCCcHHHHHHHHHHhcCCCCCccEEEecC
Q psy7966 14 TSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSN 48 (194)
Q Consensus 14 T~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~ 48 (194)
-.+++.+|+|+.|-|. .-++.++..+|-+.+
T Consensus 16 ~~~~~~~~~tv~~ll~----~l~~~~~~v~v~vNg 46 (70)
T PRK08364 16 KEIEWRKGMKVADILR----AVGFNTESAIAKVNG 46 (70)
T ss_pred eEEEcCCCCcHHHHHH----HcCCCCccEEEEECC
Confidence 4678899999998764 337888877777644
No 136
>COG0479 FrdB Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit [Energy production and conversion]
Probab=25.21 E-value=3.2e+02 Score=24.18 Aligned_cols=73 Identities=23% Similarity=0.211 Sum_probs=47.6
Q ss_pred EEEEcCCC-----CeeeEEeecCCcHHHHHHHHHHh-----------cCCCCCccEEEecCCCCcccCCCCCCCCCCcce
Q psy7966 4 LRAQLPNQ-----QRTSVHIRKGQTLLEALSKAMKL-----------RNLKPEMCTAYDSNTGVSLQWDTDSDHLPTTEI 67 (194)
Q Consensus 4 irv~LPn~-----QrT~V~v~~G~tl~~aL~Kalk~-----------R~L~~~~C~Vy~~~~~~~i~w~tD~~~L~~eel 67 (194)
|.-|-|.. |.=.|++.+|+|+-|||.++=+. |.=..-.|++...+.+. +...+.+..+...++
T Consensus 7 i~R~~p~~~~p~~~~yev~~~~~~~vLdaL~~Ik~e~d~~Lsfr~sCR~gICGSCam~ING~pr-LAC~t~~~~~~~~~i 85 (234)
T COG0479 7 IYRYNPDDDKPYWQTYEVPYDEGMTVLDALLYIKEEQDPTLSFRRSCREGICGSCAMNINGKPR-LACKTLMKDLEEGVI 85 (234)
T ss_pred EEEECCCCCCcceEEEEecCCCCCcHHHHHHHHHHhcCCccchhhhccCCcCCcceeEECCccc-cchhchhhhccCCce
Confidence 34455544 66678889999999999986543 33345558888766433 566666666665566
Q ss_pred eeeeehhcCC
Q psy7966 68 RVEVQERFPA 77 (194)
Q Consensus 68 ~V~~~~~~p~ 77 (194)
.|+=+..||+
T Consensus 86 ~iePL~~fpV 95 (234)
T COG0479 86 TIEPLPNFPV 95 (234)
T ss_pred EEEECCCCCc
Confidence 6665555555
No 137
>cd01783 DAGK_delta_RA Ubiquitin-like domain of Diacylgylcerol kinase (DAGK). DAGK_delta_RA Diacylgylcerol kinase (DAGK) phosphorylates the second messenger diacylglycerol to phosphatidic acid as part of a protein kinase C pathway. Nine mammalian DAGK isotypes have been identified, which are classified into five subgroups according to their domain architecture and the DAGK-delta and -theta isozymes, which fall into one such group, contain an RA (Ras-associated) domain. DAGKs also contain a conserved catalytic domain (DAGKc), an assesory domain (DAGKa), and an array of conserved motifs that are likely to play a role in lipid-protein and protein-protein interactions in various DAG/PA-dependent signalling pathways.
Probab=25.01 E-value=81 Score=24.46 Aligned_cols=48 Identities=15% Similarity=0.209 Sum_probs=35.7
Q ss_pred eeEEeecCCcHHHHHHHHHHhcCCCCCccEEEecC-----CC---CcccCCCCCCC
Q psy7966 14 TSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSN-----TG---VSLQWDTDSDH 61 (194)
Q Consensus 14 T~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~-----~~---~~i~w~tD~~~ 61 (194)
-+|.|-.-.|..|++.-||++=||.-++..=|++. .+ ..++|++....
T Consensus 19 ~sv~V~~~tt~~dvv~eaL~kfGl~~~~~~~y~LvEV~ld~gv~ER~l~~~E~Pl~ 74 (97)
T cd01783 19 VSIRVNKDTTVQDVILEVLPLFGLQAECPESFRLIEVLLDRGVVERTVLPQEKPLQ 74 (97)
T ss_pred EEEEecccchHHHHHHHHHHHhCcccCCccccEEEEEEecCCeeeeeCCCccChHH
Confidence 38899999999999999999999987665555442 22 22677776654
No 138
>PF12773 DZR: Double zinc ribbon
Probab=24.88 E-value=39 Score=21.82 Aligned_cols=24 Identities=29% Similarity=0.718 Sum_probs=17.4
Q ss_pred ccCCcccccccc--c--cccccccCcee
Q psy7966 93 IAFCDACHKLLF--S--GHLCRTCGFKF 116 (194)
Q Consensus 93 ptfCd~C~klL~--Q--G~kCk~Cg~~~ 116 (194)
-.||.+|+..|. . ...|..||...
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAEN 39 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCC
Confidence 468888988876 2 36788888653
No 139
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=24.82 E-value=40 Score=24.09 Aligned_cols=8 Identities=50% Similarity=1.344 Sum_probs=3.8
Q ss_pred ccccccCc
Q psy7966 107 HLCRTCGF 114 (194)
Q Consensus 107 ~kCk~Cg~ 114 (194)
|+|..|||
T Consensus 49 Y~CP~CGF 56 (59)
T PRK14890 49 YTCPKCGF 56 (59)
T ss_pred eECCCCCC
Confidence 44544544
No 140
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=24.81 E-value=40 Score=27.55 Aligned_cols=23 Identities=35% Similarity=0.992 Sum_probs=18.7
Q ss_pred cCCcccccccc--cc-ccccccCcee
Q psy7966 94 AFCDACHKLLF--SG-HLCRTCGFKF 116 (194)
Q Consensus 94 tfCd~C~klL~--QG-~kCk~Cg~~~ 116 (194)
..|.-|+-.|| +| ..|-.|++.+
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~~~~ 54 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCGYRE 54 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCCceE
Confidence 45999999999 77 5899999744
No 141
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=24.68 E-value=45 Score=22.03 Aligned_cols=20 Identities=30% Similarity=0.828 Sum_probs=12.2
Q ss_pred Ccccccccc----ccccccccCce
Q psy7966 96 CDACHKLLF----SGHLCRTCGFK 115 (194)
Q Consensus 96 Cd~C~klL~----QG~kCk~Cg~~ 115 (194)
|..|+.-.- .+++|..||+.
T Consensus 5 C~~Cg~~~~~~~~~~irC~~CG~r 28 (44)
T smart00659 5 CGECGRENEIKSKDVVRCRECGYR 28 (44)
T ss_pred CCCCCCEeecCCCCceECCCCCce
Confidence 566665321 56778777754
No 142
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=24.41 E-value=41 Score=19.51 Aligned_cols=21 Identities=29% Similarity=0.825 Sum_probs=12.1
Q ss_pred cCCcccccccccc-ccccccCc
Q psy7966 94 AFCDACHKLLFSG-HLCRTCGF 114 (194)
Q Consensus 94 tfCd~C~klL~QG-~kCk~Cg~ 114 (194)
.+|..|+..+-.+ -.|..||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 4566776655433 35666664
No 143
>COG1993 PII-like signaling protein [Signal transduction mechanisms]
Probab=24.06 E-value=96 Score=24.67 Aligned_cols=65 Identities=22% Similarity=0.298 Sum_probs=41.2
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccEEEecCC--CCc-ccCCCCCCCCC-Ccceeeeeeh
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNT--GVS-LQWDTDSDHLP-TTEIRVEVQE 73 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~~--~~~-i~w~tD~~~L~-~eel~V~~~~ 73 (194)
.++|+||-.+-++ .|..+++||.+.|+..||.- ..|||.-. |.+ .-=.+++..|+ .=++.+++-|
T Consensus 7 ~lLrIy~~E~d~~-----eGkp~~~~iverlre~Gi~G--ATVlRGI~GfG~~~~~h~~~if~Ls~~LPVviEvVD 75 (109)
T COG1993 7 KLLRIYLGENDKH-----EGKPLYEAIVERLREEGIRG--ATVLRGIAGFGKDGKIHGSKIFRLSTDLPVVVEVVD 75 (109)
T ss_pred eeeEEEEcccccc-----CCeEHHHHHHHHHHHcCcCc--eeeeeeeeccCCCCcccccchhhccCCCCEEEEEeC
Confidence 3689999877544 39999999999999988865 46888642 221 11234444443 3345555543
No 144
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=23.58 E-value=1.3e+02 Score=23.95 Aligned_cols=76 Identities=16% Similarity=0.156 Sum_probs=38.8
Q ss_pred EEeecCCcHHHHHHHHHHhcCCCCCccEEEecCCCCcccCCCCCCCCCCcceeeeeehhcCCCCCccceeeccccCCccC
Q psy7966 16 VHIRKGQTLLEALSKAMKLRNLKPEMCTAYDSNTGVSLQWDTDSDHLPTTEIRVEVQERFPAAINIEHNITRRTFFAIAF 95 (194)
Q Consensus 16 V~v~~G~tl~~aL~Kalk~R~L~~~~C~Vy~~~~~~~i~w~tD~~~L~~eel~V~~~~~~p~~~~~~H~F~~~Tf~~ptf 95 (194)
|-+ ..-...+.|...+++=+|.++.- +.-.....|+...+.+.++ .+.-.+ ...+..+|..-..
T Consensus 63 ~li-~~~~~~~QL~ev~~~~~l~~~~~-------------~~~sRC~~CN~~L~~v~~~-~v~~~v-p~~v~~~~~~f~~ 126 (147)
T PF01927_consen 63 ILI-RSDDPEEQLREVLERFGLKLRLD-------------PIFSRCPKCNGPLRPVSKE-EVKDRV-PPYVYETYDEFWR 126 (147)
T ss_pred EEE-cCCCHHHHHHHHHHHcCCccccC-------------CCCCccCCCCcEeeechhh-cccccc-CccccccCCeEEE
Confidence 444 55667777777777777655310 0011223444433332211 110001 2223345555677
Q ss_pred Cccccccccccc
Q psy7966 96 CDACHKLLFSGH 107 (194)
Q Consensus 96 Cd~C~klL~QG~ 107 (194)
|..|++.-|.|-
T Consensus 127 C~~C~kiyW~Gs 138 (147)
T PF01927_consen 127 CPGCGKIYWEGS 138 (147)
T ss_pred CCCCCCEecccc
Confidence 999999999773
No 145
>PRK12576 succinate dehydrogenase iron-sulfur subunit; Provisional
Probab=23.42 E-value=1.3e+02 Score=26.87 Aligned_cols=65 Identities=17% Similarity=0.127 Sum_probs=41.8
Q ss_pred CeeeEEeecCCcHHHHHHHHHHh--------cCC---CCCccEEEecCCCCcccCCCCCCCCC---CcceeeeeehhcCC
Q psy7966 12 QRTSVHIRKGQTLLEALSKAMKL--------RNL---KPEMCTAYDSNTGVSLQWDTDSDHLP---TTEIRVEVQERFPA 77 (194)
Q Consensus 12 QrT~V~v~~G~tl~~aL~Kalk~--------R~L---~~~~C~Vy~~~~~~~i~w~tD~~~L~---~eel~V~~~~~~p~ 77 (194)
|.-.|++.+|+||-|||.++=.. .+. ....|+|...+.. .+...+.+..+. ++++.+|=+..||+
T Consensus 25 ~~~~v~~~~~~tvLd~L~~i~~~~d~tl~~~~~C~~G~CgsC~v~ING~~-~laC~t~v~~~~~~~~~~~tiePl~~~~v 103 (279)
T PRK12576 25 QEYKVKVDRFTQVTEALRRIKEEQDPTLSYRASCHMAVCGSCGMKINGEP-RLACKTLVLDVAKKYNSVITIEPMDYFKV 103 (279)
T ss_pred EEEEEecCCCCHHHHHHHHhCCccCCCceecCCCCCCCCCCCEEEECCcE-eccccCcHHHhhcCCCCcEEEEECCCCce
Confidence 55678999999999999985211 111 1224888775422 146677776652 56788886655665
No 146
>KOG1701|consensus
Probab=23.38 E-value=66 Score=31.25 Aligned_cols=74 Identities=16% Similarity=0.400 Sum_probs=0.0
Q ss_pred CCcHHHHHHHHHHh-cCCCCCccEEEecCCCCcccCCCCCCCCCCcceeeeeehhcCCCCCccceeeccccCCccCCccc
Q psy7966 21 GQTLLEALSKAMKL-RNLKPEMCTAYDSNTGVSLQWDTDSDHLPTTEIRVEVQERFPAAINIEHNITRRTFFAIAFCDAC 99 (194)
Q Consensus 21 G~tl~~aL~Kalk~-R~L~~~~C~Vy~~~~~~~i~w~tD~~~L~~eel~V~~~~~~p~~~~~~H~F~~~Tf~~ptfCd~C 99 (194)
|.-|.|-|..||=+ -.-..+.|.|.... |.|....|++..++--...+--.|. .-|..|
T Consensus 341 g~~I~d~iLrA~GkayHp~CF~Cv~C~r~-------------ldgipFtvd~~n~v~Cv~dfh~kfA-------PrCs~C 400 (468)
T KOG1701|consen 341 GEPIMDRILRALGKAYHPGCFTCVVCARC-------------LDGIPFTVDSQNNVYCVPDFHKKFA-------PRCSVC 400 (468)
T ss_pred hhHHHHHHHHhcccccCCCceEEEEeccc-------------cCCccccccCCCceeeehhhhhhcC-------cchhhc
Q ss_pred ccccc--cc------------------ccccccCc
Q psy7966 100 HKLLF--SG------------------HLCRTCGF 114 (194)
Q Consensus 100 ~klL~--QG------------------~kCk~Cg~ 114 (194)
++-|+ .| |+|++||.
T Consensus 401 ~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~ 435 (468)
T KOG1701|consen 401 GNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGL 435 (468)
T ss_pred cCCccCCCCCcceEEEEEccccccccceehhhcCc
No 147
>COG4379 Mu-like prophage tail protein gpP [General function prediction only]
Probab=23.15 E-value=62 Score=30.66 Aligned_cols=26 Identities=23% Similarity=0.275 Sum_probs=23.6
Q ss_pred eeeEEeecCCcHHHHHHHHHHhcCCC
Q psy7966 13 RTSVHIRKGQTLLEALSKAMKLRNLK 38 (194)
Q Consensus 13 rT~V~v~~G~tl~~aL~Kalk~R~L~ 38 (194)
..++.+.||.|+-|||.++-+++||.
T Consensus 142 ~~~~~iEpGETa~daL~~iAr~~gll 167 (386)
T COG4379 142 LPKFTIEPGETAWDALTHIARHVGLL 167 (386)
T ss_pred CceeEcCCcchHHHHHHHHHhhccee
Confidence 45789999999999999999999984
No 148
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=23.02 E-value=42 Score=23.14 Aligned_cols=26 Identities=23% Similarity=0.774 Sum_probs=21.6
Q ss_pred ccCCccCCccccccccccccccccCc
Q psy7966 89 TFFAIAFCDACHKLLFSGHLCRTCGF 114 (194)
Q Consensus 89 Tf~~ptfCd~C~klL~QG~kCk~Cg~ 114 (194)
+...++.|..|+++..--.-|..||+
T Consensus 22 ~~p~l~~C~~cG~~~~~H~vc~~cG~ 47 (55)
T TIGR01031 22 TAPTLVVCPNCGEFKLPHRVCPSCGY 47 (55)
T ss_pred cCCcceECCCCCCcccCeeECCccCe
Confidence 34567789999999888889999985
No 149
>PF14369 zf-RING_3: zinc-finger
Probab=23.01 E-value=48 Score=20.82 Aligned_cols=23 Identities=22% Similarity=0.774 Sum_probs=13.3
Q ss_pred cCCcccccccc-----cccc-ccccCcee
Q psy7966 94 AFCDACHKLLF-----SGHL-CRTCGFKF 116 (194)
Q Consensus 94 tfCd~C~klL~-----QG~k-Ck~Cg~~~ 116 (194)
-||+.|.+.+. .... |-.|+-.|
T Consensus 3 ywCh~C~~~V~~~~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 3 YWCHQCNRFVRIAPSPDSDVACPRCHGGF 31 (35)
T ss_pred EeCccCCCEeEeCcCCCCCcCCcCCCCcE
Confidence 36777776654 3344 66666444
No 150
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=22.99 E-value=45 Score=20.76 Aligned_cols=20 Identities=25% Similarity=0.702 Sum_probs=11.7
Q ss_pred Ccccccccc----ccccccccCce
Q psy7966 96 CDACHKLLF----SGHLCRTCGFK 115 (194)
Q Consensus 96 Cd~C~klL~----QG~kCk~Cg~~ 115 (194)
|..|+...- ...+|..||+.
T Consensus 3 C~~Cg~~~~~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 3 CGECGAEVELKPGDPIRCPECGHR 26 (32)
T ss_dssp ESSSSSSE-BSTSSTSSBSSSS-S
T ss_pred CCcCCCeeEcCCCCcEECCcCCCe
Confidence 556655432 55788888864
No 151
>TIGR00624 tag DNA-3-methyladenine glycosylase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.87 E-value=74 Score=27.00 Aligned_cols=22 Identities=27% Similarity=0.376 Sum_probs=16.7
Q ss_pred EeecCCcHHHHHHHHHHhcCCC
Q psy7966 17 HIRKGQTLLEALSKAMKLRNLK 38 (194)
Q Consensus 17 ~v~~G~tl~~aL~Kalk~R~L~ 38 (194)
+|-.-..+.++|+|.||+||..
T Consensus 131 ~~p~~t~~S~~lskdLKkrGfk 152 (179)
T TIGR00624 131 EIPSSTPESKAMSKELKKRGFR 152 (179)
T ss_pred cCCCCCHHHHHHHHHHHHcCCe
Confidence 3333344899999999999975
No 152
>KOG3799|consensus
Probab=22.80 E-value=27 Score=29.24 Aligned_cols=33 Identities=39% Similarity=0.776 Sum_probs=27.4
Q ss_pred ccCCcccccccc---ccccccccCceeccccccccc
Q psy7966 93 IAFCDACHKLLF---SGHLCRTCGFKFHRACNLAVP 125 (194)
Q Consensus 93 ptfCd~C~klL~---QG~kCk~Cg~~~HkrC~~~Vp 125 (194)
-+.|..|.+.-| -|-+|..|...|--||-.+|.
T Consensus 65 datC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~ 100 (169)
T KOG3799|consen 65 DATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVS 100 (169)
T ss_pred CcchhhhhhcccccccCcccchhhhhHHHhcCCeee
Confidence 366999988877 788999999999999976653
No 153
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=22.33 E-value=48 Score=23.11 Aligned_cols=25 Identities=20% Similarity=0.660 Sum_probs=20.3
Q ss_pred cCCccCCccccccccccccccccCc
Q psy7966 90 FFAIAFCDACHKLLFSGHLCRTCGF 114 (194)
Q Consensus 90 f~~ptfCd~C~klL~QG~kCk~Cg~ 114 (194)
--.+..|..|+++...-..|..||+
T Consensus 24 ~~~l~~C~~CG~~~~~H~vC~~CG~ 48 (57)
T PRK12286 24 APGLVECPNCGEPKLPHRVCPSCGY 48 (57)
T ss_pred CCcceECCCCCCccCCeEECCCCCc
Confidence 3445669999999988889999985
No 154
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=22.31 E-value=49 Score=25.47 Aligned_cols=29 Identities=34% Similarity=0.748 Sum_probs=20.5
Q ss_pred CccCCcccccccc----cc-ccccccCceecccc
Q psy7966 92 AIAFCDACHKLLF----SG-HLCRTCGFKFHRAC 120 (194)
Q Consensus 92 ~ptfCd~C~klL~----QG-~kCk~Cg~~~HkrC 120 (194)
.+--|..|++... .| .+|+-||+.|-.-.
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGga 67 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGGA 67 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCeecccc
Confidence 4456888988754 45 48999998886443
No 155
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=22.16 E-value=43 Score=30.44 Aligned_cols=14 Identities=21% Similarity=0.975 Sum_probs=12.2
Q ss_pred cCCccccccccccc
Q psy7966 94 AFCDACHKLLFSGH 107 (194)
Q Consensus 94 tfCd~C~klL~QG~ 107 (194)
.+|..|+.+|++|.
T Consensus 41 i~C~~C~~~I~kG~ 54 (324)
T PF04502_consen 41 IWCNTCGEYIYKGV 54 (324)
T ss_pred CcCCCCccccccce
Confidence 57999999999884
No 156
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=22.13 E-value=40 Score=21.37 Aligned_cols=19 Identities=37% Similarity=1.036 Sum_probs=14.7
Q ss_pred Ccccccccc---cc-ccccccCc
Q psy7966 96 CDACHKLLF---SG-HLCRTCGF 114 (194)
Q Consensus 96 Cd~C~klL~---QG-~kCk~Cg~ 114 (194)
|+.|++..| -| +.|..||.
T Consensus 11 C~~C~~~~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 11 CPVCGSRWFYSDDGFYYCDRCGH 33 (36)
T ss_pred CCCCCCeEeEccCCEEEhhhCce
Confidence 888998865 55 58988884
No 157
>PRK05978 hypothetical protein; Provisional
Probab=21.94 E-value=45 Score=27.58 Aligned_cols=26 Identities=35% Similarity=0.791 Sum_probs=19.5
Q ss_pred cCCccccc-cccccc-----cccccCceeccc
Q psy7966 94 AFCDACHK-LLFSGH-----LCRTCGFKFHRA 119 (194)
Q Consensus 94 tfCd~C~k-lL~QG~-----kCk~Cg~~~Hkr 119 (194)
--|-.|++ -||.|| +|..||..++..
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCccccC
Confidence 34888987 577664 799999888764
No 158
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=21.59 E-value=39 Score=24.73 Aligned_cols=21 Identities=38% Similarity=1.116 Sum_probs=13.8
Q ss_pred Ccccccccc--cc---ccccccCceecc
Q psy7966 96 CDACHKLLF--SG---HLCRTCGFKFHR 118 (194)
Q Consensus 96 Cd~C~klL~--QG---~kCk~Cg~~~Hk 118 (194)
|| |+..|+ .| -+| .||++.+=
T Consensus 6 C~-Cgr~lya~e~~kTkkC-~CG~~l~v 31 (68)
T PF09082_consen 6 CD-CGRYLYAKEGAKTKKC-VCGKTLKV 31 (68)
T ss_dssp ET-TS--EEEETT-SEEEE-TTTEEEE-
T ss_pred ec-CCCEEEecCCcceeEe-cCCCeeee
Confidence 74 999998 55 388 99988774
No 159
>KOG2462|consensus
Probab=21.14 E-value=47 Score=30.33 Aligned_cols=12 Identities=33% Similarity=0.706 Sum_probs=6.8
Q ss_pred cccccccCceec
Q psy7966 106 GHLCRTCGFKFH 117 (194)
Q Consensus 106 G~kCk~Cg~~~H 117 (194)
+.+|..||..|+
T Consensus 187 ~c~C~iCGKaFS 198 (279)
T KOG2462|consen 187 PCECGICGKAFS 198 (279)
T ss_pred Cccccccccccc
Confidence 455556665555
No 160
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=21.06 E-value=47 Score=18.22 Aligned_cols=10 Identities=20% Similarity=0.697 Sum_probs=6.4
Q ss_pred ccccccCcee
Q psy7966 107 HLCRTCGFKF 116 (194)
Q Consensus 107 ~kCk~Cg~~~ 116 (194)
|+|..|.|..
T Consensus 1 y~C~~C~y~t 10 (24)
T PF13909_consen 1 YKCPHCSYST 10 (24)
T ss_dssp EE-SSSS-EE
T ss_pred CCCCCCCCcC
Confidence 6889998876
No 161
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=20.79 E-value=39 Score=22.72 Aligned_cols=13 Identities=38% Similarity=0.940 Sum_probs=11.0
Q ss_pred CCccCCccccccc
Q psy7966 91 FAIAFCDACHKLL 103 (194)
Q Consensus 91 ~~ptfCd~C~klL 103 (194)
....+|++|+.+|
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 6689999999876
No 162
>PRK15401 alpha-ketoglutarate-dependent dioxygenase AlkB; Provisional
Probab=20.74 E-value=1.9e+02 Score=25.15 Aligned_cols=26 Identities=23% Similarity=0.510 Sum_probs=22.4
Q ss_pred CCCCCccEEEecCCCCcccCCCCCCC
Q psy7966 36 NLKPEMCTAYDSNTGVSLQWDTDSDH 61 (194)
Q Consensus 36 ~L~~~~C~Vy~~~~~~~i~w~tD~~~ 61 (194)
+..|+.|.|..-.+|..+.|..|-..
T Consensus 112 ~~~p~a~LvN~Y~~G~~mg~H~D~~E 137 (213)
T PRK15401 112 GFQPDACLINRYAPGAKLSLHQDKDE 137 (213)
T ss_pred CCCCCEEEEEeccCcCccccccCCCc
Confidence 34999999999988889999999753
No 163
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=20.65 E-value=49 Score=22.02 Aligned_cols=19 Identities=26% Similarity=0.555 Sum_probs=14.4
Q ss_pred CCcccc-cccc-ccccccccC
Q psy7966 95 FCDACH-KLLF-SGHLCRTCG 113 (194)
Q Consensus 95 fCd~C~-klL~-QG~kCk~Cg 113 (194)
.||.|+ +.|+ ..|+|..|.
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~ 22 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICY 22 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCC
Confidence 599999 5565 458999884
No 164
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=20.40 E-value=52 Score=21.95 Aligned_cols=26 Identities=35% Similarity=0.984 Sum_probs=16.8
Q ss_pred CCcccccccc--ccccccccC-ceecccc
Q psy7966 95 FCDACHKLLF--SGHLCRTCG-FKFHRAC 120 (194)
Q Consensus 95 fCd~C~klL~--QG~kCk~Cg-~~~HkrC 120 (194)
.||.|+..-. --|+|..|. |..=+.|
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~C 30 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENC 30 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHh
Confidence 4999986443 447999986 4333344
No 165
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=20.39 E-value=57 Score=19.46 Aligned_cols=19 Identities=32% Similarity=0.856 Sum_probs=14.0
Q ss_pred Ccccccccc-----ccccccccCc
Q psy7966 96 CDACHKLLF-----SGHLCRTCGF 114 (194)
Q Consensus 96 Cd~C~klL~-----QG~kCk~Cg~ 114 (194)
|..|+.+|. .-.+|..|..
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 677888775 4478888864
No 166
>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=20.37 E-value=2e+02 Score=21.51 Aligned_cols=44 Identities=18% Similarity=0.321 Sum_probs=32.2
Q ss_pred ceEEEEcCCCCeeeEEeecCCcHHHHHHHHHHhcCCCCCccE-EEec
Q psy7966 2 ILLRAQLPNQQRTSVHIRKGQTLLEALSKAMKLRNLKPEMCT-AYDS 47 (194)
Q Consensus 2 ~~irv~LPn~QrT~V~v~~G~tl~~aL~Kalk~R~L~~~~C~-Vy~~ 47 (194)
-+|+||.=. =-.|.|.+|.+..+-..|..++.+|.++.=. .|+.
T Consensus 3 ~vvKV~f~~--tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkd 47 (80)
T cd06406 3 YVVKVHFKY--TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKS 47 (80)
T ss_pred eEEEEEEEE--EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEecc
Confidence 367787754 3356889999999999999999999766533 3443
No 167
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=20.33 E-value=63 Score=20.16 Aligned_cols=23 Identities=26% Similarity=0.605 Sum_probs=15.7
Q ss_pred cCCccccccc-c---cc-ccccccCcee
Q psy7966 94 AFCDACHKLL-F---SG-HLCRTCGFKF 116 (194)
Q Consensus 94 tfCd~C~klL-~---QG-~kCk~Cg~~~ 116 (194)
--|..|+..+ + ++ +.|..||..+
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 4588887743 3 55 5899998754
Done!