Query psy13994
Match_columns 97
No_of_seqs 118 out of 2199
Neff 11.6
Searched_HMMs 46136
Date Fri Aug 16 16:48:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13994.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13994hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 2.6E-29 5.6E-34 139.6 4.4 97 1-97 135-239 (279)
2 KOG2462|consensus 99.9 1.6E-26 3.5E-31 128.6 4.5 93 1-95 166-265 (279)
3 KOG1074|consensus 99.9 1.5E-23 3.3E-28 130.3 1.1 48 1-48 358-405 (958)
4 KOG1074|consensus 99.9 3.4E-22 7.4E-27 124.4 3.5 48 50-97 884-931 (958)
5 KOG3576|consensus 99.7 5.1E-18 1.1E-22 91.7 3.0 75 21-95 114-195 (267)
6 KOG3623|consensus 99.7 1.1E-17 2.3E-22 103.9 2.2 94 2-95 216-331 (1007)
7 KOG3623|consensus 99.7 1.4E-17 3E-22 103.4 2.6 70 24-93 894-970 (1007)
8 KOG3608|consensus 99.6 8.9E-16 1.9E-20 89.0 6.6 96 2-97 185-316 (467)
9 KOG3576|consensus 99.6 4.8E-16 1E-20 84.2 2.0 96 1-96 122-235 (267)
10 KOG3608|consensus 99.5 8.6E-14 1.9E-18 80.9 6.1 95 1-95 268-374 (467)
11 KOG3993|consensus 99.4 1.9E-13 4.1E-18 80.9 1.8 96 1-96 272-379 (500)
12 PF13465 zf-H2C2_2: Zinc-finge 99.3 8.9E-13 1.9E-17 50.0 1.7 26 60-85 1-26 (26)
13 PHA00733 hypothetical protein 99.2 1.9E-11 4E-16 63.1 4.3 73 22-96 38-122 (128)
14 PF13465 zf-H2C2_2: Zinc-finge 99.2 7.6E-12 1.7E-16 47.4 2.1 26 11-36 1-26 (26)
15 PHA02768 hypothetical protein; 99.2 1.5E-11 3.3E-16 53.9 1.7 38 51-90 11-48 (55)
16 PLN03086 PRLI-interacting fact 99.0 8.4E-10 1.8E-14 68.6 5.9 86 2-94 459-561 (567)
17 PHA02768 hypothetical protein; 99.0 2E-10 4.4E-15 50.3 1.4 35 2-38 11-45 (55)
18 PHA00733 hypothetical protein 98.9 4.5E-09 9.6E-14 54.4 4.6 50 20-69 69-123 (128)
19 PLN03086 PRLI-interacting fact 98.8 1.2E-08 2.6E-13 63.7 5.4 71 22-95 451-536 (567)
20 PF00096 zf-C2H2: Zinc finger, 98.8 2.6E-09 5.6E-14 39.2 1.2 23 74-96 1-23 (23)
21 PHA00616 hypothetical protein 98.8 3.2E-09 6.9E-14 44.5 1.5 25 73-97 1-25 (44)
22 COG5189 SFP1 Putative transcri 98.7 1.4E-09 3.1E-14 63.0 -0.4 71 22-94 347-419 (423)
23 KOG3993|consensus 98.7 4.9E-09 1.1E-13 62.8 1.6 95 1-95 300-480 (500)
24 PHA00732 hypothetical protein 98.7 1.5E-08 3.2E-13 48.1 2.2 22 24-45 1-22 (79)
25 PF13912 zf-C2H2_6: C2H2-type 98.5 4.8E-08 1E-12 37.1 1.5 25 73-97 1-25 (27)
26 PF13894 zf-C2H2_4: C2H2-type 98.5 5.3E-08 1.2E-12 35.7 1.5 24 74-97 1-24 (24)
27 PF12756 zf-C2H2_2: C2H2 type 98.5 6.2E-08 1.3E-12 47.9 2.0 70 26-96 1-73 (100)
28 PF00096 zf-C2H2: Zinc finger, 98.4 2.3E-07 5E-12 33.8 1.9 22 25-46 1-22 (23)
29 smart00355 ZnF_C2H2 zinc finge 98.3 8.3E-07 1.8E-11 32.9 1.8 23 74-96 1-23 (26)
30 PHA00616 hypothetical protein 98.2 6.2E-07 1.3E-11 37.7 1.4 34 24-78 1-34 (44)
31 PF13894 zf-C2H2_4: C2H2-type 98.2 1.5E-06 3.2E-11 31.7 2.0 23 25-47 1-23 (24)
32 PF13912 zf-C2H2_6: C2H2-type 98.2 1E-06 2.2E-11 33.3 1.3 25 24-48 1-25 (27)
33 PHA00732 hypothetical protein 98.1 1.6E-06 3.5E-11 41.3 1.9 42 1-48 6-48 (79)
34 PF12874 zf-met: Zinc-finger o 97.9 5.4E-06 1.2E-10 30.7 1.1 23 74-96 1-23 (25)
35 smart00355 ZnF_C2H2 zinc finge 97.7 4.9E-05 1.1E-09 27.9 2.0 23 25-47 1-23 (26)
36 PF12874 zf-met: Zinc-finger o 97.6 3.1E-05 6.7E-10 28.6 1.2 22 25-46 1-22 (25)
37 PF09237 GAGA: GAGA factor; I 97.6 5.4E-05 1.2E-09 32.6 1.9 29 68-96 19-47 (54)
38 PF12171 zf-C2H2_jaz: Zinc-fin 97.6 1.6E-05 3.5E-10 30.0 0.1 22 74-95 2-23 (27)
39 PF13909 zf-H2C2_5: C2H2-type 97.5 5.1E-05 1.1E-09 27.7 1.3 22 74-96 1-22 (24)
40 PF05605 zf-Di19: Drought indu 97.5 0.00029 6.4E-09 31.1 3.8 50 24-96 2-52 (54)
41 PF12756 zf-C2H2_2: C2H2 type 97.5 0.0001 2.2E-09 36.3 2.5 20 1-20 4-23 (100)
42 PF05605 zf-Di19: Drought indu 97.4 0.00044 9.4E-09 30.5 3.6 44 1-47 7-52 (54)
43 PF09237 GAGA: GAGA factor; I 97.2 0.0004 8.7E-09 30.0 2.3 30 19-48 19-48 (54)
44 COG5189 SFP1 Putative transcri 97.1 0.00012 2.7E-09 43.2 0.1 44 2-45 357-419 (423)
45 PF12171 zf-C2H2_jaz: Zinc-fin 97.1 9.2E-05 2E-09 27.9 -0.3 22 25-46 2-23 (27)
46 PF13909 zf-H2C2_5: C2H2-type 97.0 0.00068 1.5E-08 24.6 1.6 22 25-47 1-22 (24)
47 smart00451 ZnF_U1 U1-like zinc 96.9 0.00078 1.7E-08 26.7 1.5 23 73-95 3-25 (35)
48 PF13913 zf-C2HC_2: zinc-finge 96.8 0.0011 2.5E-08 24.5 1.6 21 74-95 3-23 (25)
49 PRK04860 hypothetical protein; 96.7 0.0013 2.7E-08 35.6 1.7 30 57-86 127-156 (160)
50 smart00451 ZnF_U1 U1-like zinc 96.4 0.0027 5.8E-08 25.1 1.6 23 24-46 3-25 (35)
51 PRK04860 hypothetical protein; 96.4 0.0017 3.7E-08 35.1 1.2 30 8-37 127-156 (160)
52 COG5048 FOG: Zn-finger [Genera 96.3 0.00019 4.2E-09 43.6 -3.0 47 2-48 295-347 (467)
53 KOG1146|consensus 96.2 0.0012 2.6E-08 45.6 -0.2 75 19-95 460-540 (1406)
54 COG4049 Uncharacterized protei 95.0 0.015 3.2E-07 25.7 1.2 27 68-94 12-38 (65)
55 cd00350 rubredoxin_like Rubred 94.7 0.017 3.8E-07 22.7 0.9 10 72-81 16-25 (33)
56 KOG1146|consensus 94.7 0.0067 1.4E-07 42.3 -0.5 69 22-95 1282-1350(1406)
57 KOG4173|consensus 94.6 0.036 7.9E-07 31.2 2.2 71 24-94 79-167 (253)
58 PF02892 zf-BED: BED zinc fing 94.1 0.044 9.6E-07 22.9 1.6 25 70-94 13-41 (45)
59 KOG2231|consensus 93.5 0.15 3.2E-06 33.8 3.7 60 35-95 125-204 (669)
60 COG1592 Rubrerythrin [Energy p 93.4 0.049 1.1E-06 29.7 1.3 13 68-80 144-156 (166)
61 COG5048 FOG: Zn-finger [Genera 92.8 0.012 2.7E-07 35.9 -1.7 47 50-96 294-346 (467)
62 smart00614 ZnF_BED BED zinc fi 92.2 0.094 2E-06 22.6 1.2 23 74-96 19-47 (50)
63 TIGR00622 ssl1 transcription f 91.5 0.22 4.7E-06 25.5 2.1 73 22-96 13-104 (112)
64 smart00734 ZnF_Rad18 Rad18-lik 90.9 0.23 4.9E-06 18.4 1.4 19 75-94 3-21 (26)
65 PHA00626 hypothetical protein 90.3 0.12 2.6E-06 22.9 0.5 16 71-86 21-36 (59)
66 KOG2893|consensus 90.2 0.086 1.9E-06 30.5 -0.0 19 27-45 13-31 (341)
67 KOG4173|consensus 90.2 0.31 6.7E-06 27.7 2.1 60 4-66 89-167 (253)
68 KOG2785|consensus 90.1 0.39 8.5E-06 29.7 2.7 71 25-95 4-90 (390)
69 KOG2893|consensus 90.0 0.07 1.5E-06 30.8 -0.5 39 1-43 15-53 (341)
70 KOG0717|consensus 87.9 0.31 6.7E-06 31.0 1.2 22 74-95 293-314 (508)
71 KOG3408|consensus 87.9 0.47 1E-05 24.6 1.7 26 70-95 54-79 (129)
72 PF04959 ARS2: Arsenite-resist 87.3 0.52 1.1E-05 27.0 1.8 27 22-48 75-101 (214)
73 PF07754 DUF1610: Domain of un 87.2 0.21 4.5E-06 18.2 0.2 10 72-81 15-24 (24)
74 PF10571 UPF0547: Uncharacteri 86.1 0.3 6.5E-06 18.1 0.3 10 75-84 16-25 (26)
75 KOG4167|consensus 85.8 0.22 4.7E-06 33.4 -0.2 25 73-97 792-816 (907)
76 smart00834 CxxC_CXXC_SSSS Puta 85.4 0.27 5.9E-06 19.9 0.1 11 74-84 6-16 (41)
77 COG5152 Uncharacterized conser 85.0 0.73 1.6E-05 26.1 1.6 56 22-92 194-253 (259)
78 PF05290 Baculo_IE-1: Baculovi 84.9 0.54 1.2E-05 24.8 1.0 61 19-88 75-136 (140)
79 KOG2482|consensus 84.3 0.64 1.4E-05 28.5 1.3 35 59-95 183-217 (423)
80 KOG4167|consensus 84.2 0.25 5.3E-06 33.2 -0.5 25 24-48 792-816 (907)
81 KOG2231|consensus 84.1 2.1 4.7E-05 28.8 3.6 65 26-94 184-260 (669)
82 PF08790 zf-LYAR: LYAR-type C2 83.8 0.1 2.2E-06 19.8 -1.4 11 74-84 1-11 (28)
83 PF09723 Zn-ribbon_8: Zinc rib 83.3 0.36 7.8E-06 20.0 -0.0 12 74-85 6-17 (42)
84 PF09538 FYDLN_acid: Protein o 83.2 0.76 1.7E-05 23.4 1.1 14 72-85 25-38 (108)
85 PF15269 zf-C2H2_7: Zinc-finge 83.2 0.84 1.8E-05 19.3 1.1 21 74-94 21-41 (54)
86 COG5188 PRP9 Splicing factor 3 83.1 2.9 6.3E-05 26.0 3.6 27 66-92 367-394 (470)
87 PF12013 DUF3505: Protein of u 82.8 1 2.2E-05 22.8 1.5 23 74-96 81-107 (109)
88 PF05443 ROS_MUCR: ROS/MUCR tr 82.7 0.74 1.6E-05 24.3 1.0 23 71-96 70-92 (132)
89 PF13451 zf-trcl: Probable zin 82.6 0.4 8.7E-06 20.8 0.0 16 71-86 2-17 (49)
90 KOG0978|consensus 82.5 0.62 1.3E-05 31.3 0.8 53 24-90 643-695 (698)
91 KOG4124|consensus 81.8 0.097 2.1E-06 31.9 -2.7 68 22-91 347-416 (442)
92 PF04959 ARS2: Arsenite-resist 80.8 0.96 2.1E-05 26.0 1.1 26 70-95 74-99 (214)
93 KOG2785|consensus 79.9 7.1 0.00015 24.5 4.5 72 22-94 164-241 (390)
94 KOG2482|consensus 79.8 3.6 7.7E-05 25.5 3.2 25 24-48 195-219 (423)
95 TIGR02605 CxxC_CxxC_SSSS putat 79.7 0.59 1.3E-05 20.1 0.0 12 74-85 6-17 (52)
96 KOG2186|consensus 79.0 1.4 3.1E-05 25.9 1.4 28 63-92 20-47 (276)
97 COG3677 Transposase and inacti 78.4 0.99 2.1E-05 23.7 0.6 16 70-85 50-65 (129)
98 PF13878 zf-C2H2_3: zinc-finge 77.2 2.3 4.9E-05 17.6 1.4 24 73-96 13-38 (41)
99 COG1773 Rubredoxin [Energy pro 76.9 0.84 1.8E-05 20.3 0.1 12 73-84 3-14 (55)
100 PF01927 Mut7-C: Mut7-C RNAse 76.4 1.5 3.2E-05 23.5 1.0 21 73-93 124-144 (147)
101 smart00154 ZnF_AN1 AN1-like Zi 75.6 1.1 2.5E-05 18.3 0.3 13 73-85 12-24 (39)
102 PF01428 zf-AN1: AN1-like Zinc 74.8 0.75 1.6E-05 19.1 -0.3 14 72-85 12-25 (43)
103 KOG2636|consensus 74.4 2.7 5.8E-05 26.9 1.8 28 66-93 394-422 (497)
104 COG2888 Predicted Zn-ribbon RN 73.9 1.4 3.1E-05 19.8 0.4 11 71-81 48-58 (61)
105 cd00924 Cyt_c_Oxidase_Vb Cytoc 73.0 1.8 4E-05 21.6 0.7 19 18-37 74-92 (97)
106 PLN02294 cytochrome c oxidase 72.6 1.9 4.2E-05 23.8 0.8 16 22-37 139-154 (174)
107 PF07975 C1_4: TFIIH C1-like d 72.3 0.74 1.6E-05 20.1 -0.6 26 71-96 19-44 (51)
108 KOG2071|consensus 70.9 3 6.5E-05 27.6 1.5 26 71-96 416-441 (579)
109 cd00729 rubredoxin_SM Rubredox 70.8 1.5 3.2E-05 17.3 0.1 12 73-84 2-13 (34)
110 PF09986 DUF2225: Uncharacteri 70.6 1.9 4.1E-05 24.7 0.6 20 22-41 3-22 (214)
111 PF04780 DUF629: Protein of un 70.4 3.4 7.3E-05 26.7 1.6 22 74-95 58-79 (466)
112 PF02891 zf-MIZ: MIZ/SP-RING z 69.3 1.9 4.2E-05 18.6 0.3 9 73-81 41-49 (50)
113 PF13717 zinc_ribbon_4: zinc-r 68.5 3.4 7.4E-05 16.5 0.9 12 72-83 24-35 (36)
114 PF04423 Rad50_zn_hook: Rad50 68.5 4.5 9.8E-05 17.6 1.4 14 26-39 22-35 (54)
115 KOG2636|consensus 68.3 4.7 0.0001 25.9 1.9 30 17-46 394-424 (497)
116 PRK14890 putative Zn-ribbon RN 68.2 2.3 5.1E-05 19.2 0.5 11 71-81 46-56 (59)
117 KOG0717|consensus 68.1 3.6 7.7E-05 26.6 1.3 23 25-47 293-315 (508)
118 KOG1813|consensus 67.8 4.4 9.5E-05 24.6 1.6 59 21-94 238-300 (313)
119 TIGR02300 FYDLN_acid conserved 67.7 3.9 8.3E-05 21.6 1.2 10 25-34 10-19 (129)
120 KOG2593|consensus 67.3 5.3 0.00011 25.5 1.9 21 69-89 124-144 (436)
121 PTZ00448 hypothetical protein; 66.3 4.9 0.00011 25.1 1.7 23 73-95 314-336 (373)
122 COG4957 Predicted transcriptio 66.2 3.3 7.1E-05 22.0 0.8 20 74-96 77-96 (148)
123 cd00730 rubredoxin Rubredoxin; 65.9 2.2 4.8E-05 18.5 0.2 11 74-84 2-12 (50)
124 KOG1842|consensus 65.0 4.3 9.4E-05 26.1 1.3 23 73-95 15-37 (505)
125 PF01286 XPA_N: XPA protein N- 64.4 2.4 5.1E-05 16.9 0.1 13 75-87 5-17 (34)
126 PF10013 DUF2256: Uncharacteri 64.1 2.6 5.6E-05 17.6 0.2 12 75-86 10-21 (42)
127 PRK00398 rpoP DNA-directed RNA 63.7 2.5 5.5E-05 17.7 0.1 12 73-84 3-14 (46)
128 PF00301 Rubredoxin: Rubredoxi 63.7 2.1 4.5E-05 18.3 -0.1 11 74-84 2-12 (47)
129 PF04780 DUF629: Protein of un 63.5 6.9 0.00015 25.4 2.0 25 24-48 57-81 (466)
130 PRK00464 nrdR transcriptional 63.4 2.2 4.9E-05 23.2 -0.1 14 73-86 28-41 (154)
131 PF12907 zf-met2: Zinc-binding 63.1 6.8 0.00015 16.2 1.3 21 74-94 2-25 (40)
132 PLN03238 probable histone acet 60.6 7.7 0.00017 23.5 1.7 25 71-95 46-70 (290)
133 PF09845 DUF2072: Zn-ribbon co 60.4 3.9 8.5E-05 21.6 0.5 27 24-53 1-27 (131)
134 PF08792 A2L_zn_ribbon: A2L zi 59.2 3.6 7.8E-05 16.1 0.2 12 73-84 21-32 (33)
135 COG3357 Predicted transcriptio 59.2 4 8.6E-05 20.2 0.4 14 72-85 57-70 (97)
136 PF08209 Sgf11: Sgf11 (transcr 59.1 10 0.00022 14.9 1.5 21 24-45 4-24 (33)
137 PF06220 zf-U1: U1 zinc finger 58.0 12 0.00025 15.2 1.6 22 73-94 3-26 (38)
138 PTZ00043 cytochrome c oxidase 58.0 5.4 0.00012 23.2 0.8 18 21-38 178-195 (268)
139 COG5112 UFD2 U1-like Zn-finger 57.9 7.6 0.00017 19.8 1.2 24 72-95 54-77 (126)
140 KOG2807|consensus 57.6 15 0.00032 22.8 2.6 72 23-96 289-368 (378)
141 smart00531 TFIIE Transcription 56.0 15 0.00032 19.7 2.2 19 20-38 95-113 (147)
142 PF02176 zf-TRAF: TRAF-type zi 55.8 3.8 8.3E-05 18.0 0.0 27 59-85 24-54 (60)
143 COG5236 Uncharacterized conser 55.4 37 0.0008 21.5 4.0 22 27-48 223-244 (493)
144 PF10276 zf-CHCC: Zinc-finger 55.2 3.5 7.7E-05 17.0 -0.1 12 72-83 28-39 (40)
145 PLN00104 MYST -like histone ac 54.9 9.4 0.0002 24.7 1.5 25 71-95 196-220 (450)
146 PF14353 CpXC: CpXC protein 54.8 4.5 9.8E-05 21.0 0.2 16 71-86 36-51 (128)
147 COG3364 Zn-ribbon containing p 54.7 6.3 0.00014 19.9 0.7 27 23-52 1-27 (112)
148 PF15227 zf-C3HC4_4: zinc fing 54.6 3 6.5E-05 17.2 -0.4 28 50-79 15-42 (42)
149 PF01780 Ribosomal_L37ae: Ribo 54.2 4.7 0.0001 19.9 0.2 11 72-82 34-44 (90)
150 PF01215 COX5B: Cytochrome c o 54.0 4.7 0.0001 21.5 0.1 19 18-37 107-125 (136)
151 COG1656 Uncharacterized conser 54.0 11 0.00023 20.9 1.5 21 72-92 129-149 (165)
152 TIGR00373 conserved hypothetic 53.8 18 0.00038 19.8 2.3 23 18-40 103-125 (158)
153 KOG2747|consensus 53.8 8.8 0.00019 24.3 1.3 26 71-96 156-181 (396)
154 TIGR02098 MJ0042_CXXC MJ0042 f 53.5 4.8 0.0001 15.9 0.1 14 74-87 3-16 (38)
155 PF13824 zf-Mss51: Zinc-finger 53.1 7.6 0.00017 17.3 0.7 16 69-84 10-25 (55)
156 COG1198 PriA Primosomal protei 52.7 1.7 3.6E-05 29.6 -1.9 46 25-82 436-484 (730)
157 PF06397 Desulfoferrod_N: Desu 52.6 5.2 0.00011 16.1 0.2 12 72-83 5-16 (36)
158 PTZ00064 histone acetyltransfe 52.6 11 0.00025 24.8 1.6 26 70-95 277-302 (552)
159 PLN03239 histone acetyltransfe 51.9 11 0.00024 23.5 1.5 24 71-94 104-127 (351)
160 smart00659 RPOLCX RNA polymera 51.1 5.5 0.00012 16.8 0.1 13 73-85 2-14 (44)
161 PTZ00255 60S ribosomal protein 50.9 6.6 0.00014 19.4 0.4 11 72-82 35-45 (90)
162 PF05191 ADK_lid: Adenylate ki 49.8 4.9 0.00011 16.1 -0.1 11 74-84 2-12 (36)
163 PLN02748 tRNA dimethylallyltra 49.4 13 0.00029 24.2 1.6 24 23-46 417-441 (468)
164 COG0068 HypF Hydrogenase matur 49.4 1.1 2.4E-05 30.2 -3.1 50 26-81 125-181 (750)
165 TIGR00280 L37a ribosomal prote 48.7 7.8 0.00017 19.2 0.4 10 73-82 35-44 (91)
166 PF04438 zf-HIT: HIT zinc fing 48.6 6.8 0.00015 15.0 0.2 13 72-84 12-24 (30)
167 PHA02926 zinc finger-like prot 48.5 17 0.00036 21.4 1.8 73 13-85 159-231 (242)
168 PF04641 Rtf2: Rtf2 RING-finge 48.1 6.5 0.00014 23.3 0.1 52 22-85 111-162 (260)
169 PF13719 zinc_ribbon_5: zinc-r 47.8 9.2 0.0002 15.3 0.5 14 71-84 23-36 (37)
170 COG4530 Uncharacterized protei 47.6 9.6 0.00021 19.6 0.7 14 71-84 24-37 (129)
171 PF02748 PyrI_C: Aspartate car 47.6 7.1 0.00015 17.1 0.2 18 69-86 31-48 (52)
172 COG4391 Uncharacterized protei 47.1 6.7 0.00015 17.9 0.1 13 73-85 48-60 (62)
173 KOG0402|consensus 46.2 6.4 0.00014 19.1 -0.1 10 73-82 36-45 (92)
174 PLN03208 E3 ubiquitin-protein 46.1 18 0.00038 20.7 1.6 54 23-85 17-80 (193)
175 PRK06266 transcription initiat 45.9 23 0.0005 19.8 2.0 20 20-39 113-132 (178)
176 TIGR03831 YgiT_finger YgiT-typ 45.9 7.9 0.00017 15.8 0.2 13 73-85 32-44 (46)
177 PF11931 DUF3449: Domain of un 45.8 6.8 0.00015 22.3 0.0 25 68-92 96-121 (196)
178 PRK08222 hydrogenase 4 subunit 45.7 16 0.00034 20.5 1.4 20 71-90 112-131 (181)
179 PRK01343 zinc-binding protein; 44.3 13 0.00028 16.7 0.7 12 73-84 9-20 (57)
180 PRK03976 rpl37ae 50S ribosomal 44.2 9.6 0.00021 18.8 0.4 11 72-82 35-45 (90)
181 PF05129 Elf1: Transcription e 44.1 9.8 0.00021 18.3 0.4 10 71-80 20-29 (81)
182 TIGR00244 transcriptional regu 43.5 8.8 0.00019 20.8 0.2 15 73-87 28-42 (147)
183 PF08271 TF_Zn_Ribbon: TFIIB z 43.1 10 0.00022 15.6 0.3 9 74-82 1-9 (43)
184 KOG0320|consensus 43.0 7 0.00015 21.9 -0.2 48 24-84 131-178 (187)
185 COG2331 Uncharacterized protei 43.0 8.5 0.00018 18.4 0.1 12 73-84 12-23 (82)
186 PF03604 DNA_RNApol_7kD: DNA d 42.9 8.8 0.00019 15.0 0.1 11 74-84 1-11 (32)
187 KOG1729|consensus 42.9 15 0.00031 22.4 1.0 57 23-83 167-224 (288)
188 TIGR03829 YokU_near_AblA uncha 42.6 24 0.00051 17.5 1.6 21 23-43 34-54 (89)
189 TIGR01206 lysW lysine biosynth 41.7 12 0.00026 16.6 0.4 13 25-37 3-15 (54)
190 PRK12387 formate hydrogenlyase 41.1 19 0.00041 20.0 1.3 19 71-89 112-130 (180)
191 PF01096 TFIIS_C: Transcriptio 40.9 7.6 0.00016 15.7 -0.2 10 74-83 29-38 (39)
192 smart00504 Ubox Modified RING 40.5 36 0.00078 14.8 2.4 46 25-85 2-47 (63)
193 PF10083 DUF2321: Uncharacteri 40.1 11 0.00025 20.6 0.3 18 22-39 66-83 (158)
194 PF14354 Lar_restr_allev: Rest 40.1 15 0.00032 16.2 0.6 8 74-81 4-11 (61)
195 KOG4727|consensus 39.5 17 0.00036 20.4 0.9 21 73-93 75-95 (193)
196 COG1327 Predicted transcriptio 39.4 12 0.00025 20.5 0.3 15 73-87 28-42 (156)
197 COG5432 RAD18 RING-finger-cont 39.4 19 0.00042 22.0 1.2 44 25-83 26-69 (391)
198 PF00097 zf-C3HC4: Zinc finger 39.3 30 0.00066 13.6 1.8 9 71-79 33-41 (41)
199 PF14787 zf-CCHC_5: GAG-polypr 39.1 9.3 0.0002 15.4 -0.1 15 75-89 4-18 (36)
200 PRK09678 DNA-binding transcrip 38.9 5.6 0.00012 18.7 -0.8 15 71-85 25-41 (72)
201 smart00440 ZnF_C2C2 C2C2 Zinc 38.5 12 0.00026 15.3 0.2 11 74-84 29-39 (40)
202 TIGR00319 desulf_FeS4 desulfof 38.4 12 0.00026 14.4 0.2 12 72-83 6-17 (34)
203 COG1997 RPL43A Ribosomal prote 38.4 12 0.00025 18.4 0.1 14 72-85 52-65 (89)
204 PF14446 Prok-RING_1: Prokaryo 38.4 11 0.00024 16.7 0.1 11 74-84 6-16 (54)
205 cd00974 DSRD Desulforedoxin (D 38.2 12 0.00027 14.4 0.2 12 72-83 3-14 (34)
206 PF14369 zf-RING_3: zinc-finge 37.8 13 0.00027 14.8 0.2 10 75-84 23-32 (35)
207 COG4338 Uncharacterized protei 37.4 8.8 0.00019 16.5 -0.3 12 75-86 14-25 (54)
208 PF12230 PRP21_like_P: Pre-mRN 37.3 11 0.00024 21.8 0.0 25 71-96 166-190 (229)
209 PF14690 zf-ISL3: zinc-finger 37.2 17 0.00036 15.0 0.5 9 73-81 2-10 (47)
210 PF05766 NinG: Bacteriophage L 37.0 11 0.00023 21.4 -0.1 16 22-37 4-19 (189)
211 KOG1994|consensus 36.9 19 0.00042 21.1 0.9 22 71-92 237-258 (268)
212 COG1996 RPC10 DNA-directed RNA 36.6 9.8 0.00021 16.5 -0.2 13 72-84 5-17 (49)
213 COG5027 SAS2 Histone acetyltra 36.1 24 0.00053 22.2 1.3 26 71-96 156-181 (395)
214 PF03107 C1_2: C1 domain; Int 36.0 20 0.00044 13.4 0.6 8 73-80 15-22 (30)
215 KOG3214|consensus 35.9 14 0.00031 18.6 0.2 15 25-39 48-62 (109)
216 PF08274 PhnA_Zn_Ribbon: PhnA 35.8 10 0.00023 14.5 -0.2 11 75-85 4-14 (30)
217 PF03884 DUF329: Domain of unk 35.6 13 0.00028 16.7 0.1 12 74-85 3-14 (57)
218 COG1655 Uncharacterized protei 35.0 15 0.00032 21.7 0.3 16 71-86 17-32 (267)
219 PF06170 DUF983: Protein of un 34.9 16 0.00036 17.8 0.4 12 75-86 10-21 (86)
220 PF05741 zf-nanos: Nanos RNA b 34.7 13 0.00028 16.6 -0.0 11 72-82 32-42 (55)
221 PF13453 zf-TFIIB: Transcripti 34.2 36 0.00079 13.7 1.3 21 73-93 19-39 (41)
222 PF13240 zinc_ribbon_2: zinc-r 34.1 12 0.00026 13.2 -0.1 6 76-81 16-21 (23)
223 PF09855 DUF2082: Nucleic-acid 34.0 17 0.00038 16.7 0.3 7 74-80 1-7 (64)
224 PF14447 Prok-RING_4: Prokaryo 33.8 17 0.00036 16.2 0.3 16 71-86 37-52 (55)
225 PF06689 zf-C4_ClpX: ClpX C4-t 33.4 18 0.00038 14.8 0.3 11 75-85 3-13 (41)
226 KOG2164|consensus 33.3 53 0.0012 21.8 2.4 52 24-85 186-237 (513)
227 PF13821 DUF4187: Domain of un 32.3 24 0.00051 15.6 0.6 20 72-91 26-45 (55)
228 PF14255 Cys_rich_CPXG: Cystei 32.0 18 0.0004 15.8 0.3 10 75-84 2-11 (52)
229 KOG1088|consensus 31.7 20 0.00044 18.7 0.4 21 66-86 91-111 (124)
230 PF04810 zf-Sec23_Sec24: Sec23 31.5 19 0.00042 14.6 0.3 16 68-83 19-34 (40)
231 COG4888 Uncharacterized Zn rib 31.4 20 0.00044 18.1 0.4 13 71-83 20-32 (104)
232 TIGR03830 CxxCG_CxxCG_HTH puta 30.5 54 0.0012 16.7 1.9 23 23-45 30-52 (127)
233 COG5151 SSL1 RNA polymerase II 30.5 39 0.00084 21.0 1.4 26 71-96 386-411 (421)
234 COG4306 Uncharacterized protei 30.1 24 0.00051 18.7 0.5 17 22-38 66-82 (160)
235 KOG3362|consensus 30.0 15 0.00032 19.9 -0.3 23 73-95 129-151 (156)
236 PF14375 Cys_rich_CWC: Cystein 29.8 21 0.00045 15.3 0.2 8 76-83 1-8 (50)
237 smart00132 LIM Zinc-binding do 29.5 23 0.00051 13.4 0.4 11 73-83 27-37 (39)
238 PF07503 zf-HYPF: HypF finger; 29.3 32 0.0007 13.7 0.7 13 23-35 20-32 (35)
239 COG4640 Predicted membrane pro 29.0 36 0.00077 21.9 1.2 20 70-89 12-31 (465)
240 smart00661 RPOL9 RNA polymeras 28.9 21 0.00044 15.1 0.1 14 72-85 19-32 (52)
241 PF03811 Zn_Tnp_IS1: InsA N-te 28.9 5.4 0.00012 16.0 -1.6 17 63-79 19-35 (36)
242 TIGR00570 cdk7 CDK-activating 28.5 38 0.00082 21.0 1.2 53 25-86 4-56 (309)
243 PF04988 AKAP95: A-kinase anch 27.9 45 0.00097 18.6 1.3 23 25-47 1-23 (165)
244 COG3478 Predicted nucleic-acid 27.9 31 0.00067 16.0 0.6 9 73-81 4-12 (68)
245 PF07649 C1_3: C1-like domain; 27.8 23 0.00049 13.2 0.2 11 72-82 14-24 (30)
246 PF10164 DUF2367: Uncharacteri 27.6 28 0.00062 17.5 0.5 13 71-83 86-98 (98)
247 PF02148 zf-UBP: Zn-finger in 27.5 10 0.00022 17.0 -1.0 16 71-86 9-24 (63)
248 KOG4118|consensus 27.4 41 0.00088 15.6 0.9 22 74-95 39-60 (74)
249 PRK03824 hypA hydrogenase nick 27.2 21 0.00046 18.9 0.1 15 72-86 69-83 (135)
250 COG1885 Uncharacterized protei 27.2 29 0.00063 17.7 0.5 13 24-36 49-61 (115)
251 KOG1280|consensus 27.1 70 0.0015 20.3 2.1 27 22-48 77-103 (381)
252 COG3024 Uncharacterized protei 26.6 26 0.00056 16.2 0.2 11 74-84 8-18 (65)
253 PF03966 Trm112p: Trm112p-like 26.3 23 0.0005 16.2 0.1 17 68-84 48-64 (68)
254 KOG3352|consensus 26.1 33 0.00071 18.8 0.6 16 22-37 131-146 (153)
255 PF01194 RNA_pol_N: RNA polyme 25.4 48 0.001 15.1 1.0 17 23-39 3-19 (60)
256 cd00122 MBD MeCP2, MBD1, MBD2, 25.4 64 0.0014 14.4 1.4 19 77-95 31-49 (62)
257 COG1631 RPL42A Ribosomal prote 25.3 22 0.00048 17.7 -0.1 12 74-85 69-80 (94)
258 COG2879 Uncharacterized small 25.2 86 0.0019 14.5 1.9 17 8-24 24-40 (65)
259 TIGR00240 ATCase_reg aspartate 24.9 21 0.00046 19.5 -0.2 13 73-85 132-144 (150)
260 PRK00418 DNA gyrase inhibitor; 24.7 33 0.00071 15.7 0.4 11 73-83 6-16 (62)
261 KOG0562|consensus 24.3 56 0.0012 18.4 1.3 26 71-96 151-176 (184)
262 KOG4602|consensus 24.2 27 0.00058 21.0 0.1 11 72-82 267-277 (318)
263 PF13248 zf-ribbon_3: zinc-rib 24.2 27 0.00059 12.6 0.1 9 25-33 17-25 (26)
264 PF14634 zf-RING_5: zinc-RING 24.1 40 0.00088 13.7 0.6 11 71-81 34-44 (44)
265 PF10058 DUF2296: Predicted in 24.1 30 0.00065 15.3 0.2 11 71-81 42-52 (54)
266 PTZ00303 phosphatidylinositol 23.7 8.9 0.00019 26.9 -2.0 34 25-58 461-494 (1374)
267 PF01363 FYVE: FYVE zinc finge 23.0 37 0.00079 15.3 0.4 12 74-85 10-21 (69)
268 COG4847 Uncharacterized protei 23.0 34 0.00073 17.2 0.3 14 21-34 3-16 (103)
269 PF14952 zf-tcix: Putative tre 22.9 35 0.00075 14.4 0.3 9 74-82 12-20 (44)
270 PF03119 DNA_ligase_ZBD: NAD-d 22.9 35 0.00077 12.7 0.3 7 76-82 2-8 (28)
271 PF13696 zf-CCHC_2: Zinc knuck 22.9 33 0.00072 13.4 0.2 10 24-33 8-17 (32)
272 PF07282 OrfB_Zn_ribbon: Putat 22.0 35 0.00075 15.4 0.2 15 70-84 43-57 (69)
273 PF01844 HNH: HNH endonuclease 21.9 35 0.00075 13.8 0.2 11 76-86 1-11 (47)
274 PF06676 DUF1178: Protein of u 21.9 42 0.00092 18.3 0.5 24 22-45 30-53 (148)
275 PF14311 DUF4379: Domain of un 21.7 44 0.00094 14.5 0.5 16 73-88 28-43 (55)
276 COG1571 Predicted DNA-binding 21.6 52 0.0011 21.3 1.0 18 69-86 363-380 (421)
277 PRK00893 aspartate carbamoyltr 21.4 36 0.00077 18.7 0.2 16 70-85 131-146 (152)
278 COG1545 Predicted nucleic-acid 21.3 32 0.00069 18.4 0.0 13 74-86 30-42 (140)
279 PF09963 DUF2197: Uncharacteri 21.2 67 0.0015 14.4 1.0 12 23-34 30-41 (56)
280 PF02591 DUF164: Putative zinc 21.2 94 0.002 13.5 1.5 12 70-81 43-54 (56)
281 PF14149 YhfH: YhfH-like prote 21.0 31 0.00066 14.0 -0.1 11 74-84 14-24 (37)
282 PHA02998 RNA polymerase subuni 20.9 41 0.00089 19.1 0.4 13 74-86 172-184 (195)
283 smart00391 MBD Methyl-CpG bind 20.9 80 0.0017 15.0 1.3 19 77-95 34-52 (77)
284 KOG2907|consensus 20.9 30 0.00066 17.9 -0.1 12 74-85 103-114 (116)
285 COG1781 PyrI Aspartate carbamo 20.8 29 0.00062 19.0 -0.2 14 73-86 135-148 (153)
286 PRK00432 30S ribosomal protein 20.8 48 0.0011 14.3 0.5 12 72-83 36-47 (50)
287 PF12760 Zn_Tnp_IS1595: Transp 20.7 88 0.0019 12.9 2.4 9 25-33 19-27 (46)
288 COG5539 Predicted cysteine pro 20.7 78 0.0017 19.5 1.5 26 20-45 271-296 (306)
289 COG1594 RPB9 DNA-directed RNA 20.6 33 0.00071 17.7 -0.0 11 74-84 101-111 (113)
290 cd01396 MeCP2_MBD MeCP2, MBD1, 20.5 80 0.0017 15.0 1.3 20 77-96 32-51 (77)
291 PF03470 zf-XS: XS zinc finger 20.5 84 0.0018 13.3 1.2 11 82-93 11-21 (43)
292 PF14445 Prok-RING_2: Prokaryo 20.4 32 0.00068 15.1 -0.1 11 74-84 8-18 (57)
293 KOG0801|consensus 20.3 41 0.00088 18.8 0.3 12 74-85 139-150 (205)
294 smart00586 ZnF_DBF Zinc finger 20.3 71 0.0015 13.9 1.0 22 21-45 2-23 (49)
295 PF10367 Vps39_2: Vacuolar sor 20.1 45 0.00097 16.3 0.4 12 74-85 79-90 (109)
296 KOG2857|consensus 20.1 57 0.0012 17.8 0.8 22 24-45 17-38 (157)
297 smart00647 IBR In Between Ring 20.1 47 0.001 14.4 0.5 14 71-84 38-51 (64)
No 1
>KOG2462|consensus
Probab=99.96 E-value=2.6e-29 Score=139.64 Aligned_cols=97 Identities=32% Similarity=0.692 Sum_probs=87.3
Q ss_pred CcchhccCchHHHHHHhhccC---CCccccccccccccChHHHHHHHHHcc-----cccCccccChHHHHHHHHhccCCC
Q psy13994 1 VCNKQYHRKSVLIAHLQSHEG---VKKFGCEYCSARFSQKISCRVHMLRHR-----DVCNKPYHRKSVLIAHLQSHEGVK 72 (97)
Q Consensus 1 ~C~~~f~~~~~l~~h~~~h~~---~~~~~C~~C~~~f~~~~~l~~h~~~~~-----~~c~~~~~~~~~~~~h~~~h~~~~ 72 (97)
+||+.|...++|.+|...|.. .+.+.|..||+.+.+...|..|+++|+ +.|||.|.++=.|+.|+++|+|||
T Consensus 135 eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEK 214 (279)
T KOG2462|consen 135 ECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEK 214 (279)
T ss_pred ccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCC
Confidence 488999999999999998853 566889999999999999999999998 689999998888899999999999
Q ss_pred CcccccchhhccChHHHHHHhhhcC
Q psy13994 73 KFGCEYCSARFSQKISCRVHMLRHR 97 (97)
Q Consensus 73 ~~~C~~C~~~f~~~~~l~~H~~~h~ 97 (97)
||.|+.|+|+|.+.++|+.|+++|+
T Consensus 215 PF~C~hC~kAFADRSNLRAHmQTHS 239 (279)
T KOG2462|consen 215 PFSCPHCGKAFADRSNLRAHMQTHS 239 (279)
T ss_pred CccCCcccchhcchHHHHHHHHhhc
Confidence 9999999999999999999999984
No 2
>KOG2462|consensus
Probab=99.93 E-value=1.6e-26 Score=128.59 Aligned_cols=93 Identities=30% Similarity=0.517 Sum_probs=88.8
Q ss_pred CcchhccCchHHHHHHhhccCCCccccccccccccChHHHHHHHHHcc-------cccCccccChHHHHHHHHhccCCCC
Q psy13994 1 VCNKQYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCRVHMLRHR-------DVCNKPYHRKSVLIAHLQSHEGVKK 73 (97)
Q Consensus 1 ~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~-------~~c~~~~~~~~~~~~h~~~h~~~~~ 73 (97)
.||++|.+...|+.|+++|+ -+.+|.+||+.|.....|+.|+|+|+ +.|+++|...++|+.|+++|.+.|+
T Consensus 166 ~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~ 243 (279)
T KOG2462|consen 166 YCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKK 243 (279)
T ss_pred CCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCcc
Confidence 59999999999999999997 68999999999999999999999999 5799999999999999999999999
Q ss_pred cccccchhhccChHHHHHHhhh
Q psy13994 74 FGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 74 ~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
|+|..|+|+|+..+.|..|.+.
T Consensus 244 ~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 244 HQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred ccCcchhhHHHHHHHHHHhhhh
Confidence 9999999999999999999864
No 3
>KOG1074|consensus
Probab=99.87 E-value=1.5e-23 Score=130.33 Aligned_cols=48 Identities=44% Similarity=0.801 Sum_probs=45.5
Q ss_pred CcchhccCchHHHHHHhhccCCCccccccccccccChHHHHHHHHHcc
Q psy13994 1 VCNKQYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCRVHMLRHR 48 (97)
Q Consensus 1 ~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~ 48 (97)
.|.+.|.+.+.|..|++.|+|++||.|.+||.+|+++.+|+-|...|+
T Consensus 358 ~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~ 405 (958)
T KOG1074|consen 358 FCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHR 405 (958)
T ss_pred hhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeecc
Confidence 489999999999999999999999999999999999999999988776
No 4
>KOG1074|consensus
Probab=99.85 E-value=3.4e-22 Score=124.42 Aligned_cols=48 Identities=33% Similarity=0.708 Sum_probs=46.4
Q ss_pred ccCccccChHHHHHHHHhccCCCCcccccchhhccChHHHHHHhhhcC
Q psy13994 50 VCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCRVHMLRHR 97 (97)
Q Consensus 50 ~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 97 (97)
+|++.|...++|..|+++|+++|||.|.+|+++|....+|+.|+.+|.
T Consensus 884 vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~ 931 (958)
T KOG1074|consen 884 VCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHM 931 (958)
T ss_pred cchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhcccc
Confidence 699999999999999999999999999999999999999999999884
No 5
>KOG3576|consensus
Probab=99.71 E-value=5.1e-18 Score=91.70 Aligned_cols=75 Identities=25% Similarity=0.580 Sum_probs=68.8
Q ss_pred CCCccccccccccccChHHHHHHHHHcc-------cccCccccChHHHHHHHHhccCCCCcccccchhhccChHHHHHHh
Q psy13994 21 GVKKFGCEYCSARFSQKISCRVHMLRHR-------DVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCRVHM 93 (97)
Q Consensus 21 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~-------~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 93 (97)
+...+.|.+|++.|.....|..|+.-|. ..||+.|...-.|++|+++|+|.+||+|..|+|+|.+.-.|..|+
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 3456899999999999999999999887 369999999999999999999999999999999999999999997
Q ss_pred hh
Q psy13994 94 LR 95 (97)
Q Consensus 94 ~~ 95 (97)
+.
T Consensus 194 ~k 195 (267)
T KOG3576|consen 194 KK 195 (267)
T ss_pred HH
Confidence 64
No 6
>KOG3623|consensus
Probab=99.68 E-value=1.1e-17 Score=103.93 Aligned_cols=94 Identities=33% Similarity=0.618 Sum_probs=82.7
Q ss_pred cchhccCchHHHHHHhhcc--CCCccccccccccccChHHHHHHHHHcc--------------------cccCccccChH
Q psy13994 2 CNKQYHRKSVLIAHLQSHE--GVKKFGCEYCSARFSQKISCRVHMLRHR--------------------DVCNKPYHRKS 59 (97)
Q Consensus 2 C~~~f~~~~~l~~h~~~h~--~~~~~~C~~C~~~f~~~~~l~~h~~~~~--------------------~~c~~~~~~~~ 59 (97)
|.+.+.....|+.|+...+ .+..|.|..|..+|.+...|.+|+..|. ..|+|+|...-
T Consensus 216 cdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKH 295 (1007)
T KOG3623|consen 216 CDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKH 295 (1007)
T ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHH
Confidence 6667777788899987543 3445999999999999999999999886 36999999999
Q ss_pred HHHHHHHhccCCCCcccccchhhccChHHHHHHhhh
Q psy13994 60 VLIAHLQSHEGVKKFGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 60 ~~~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
.|+.|+++|.|||||.|+.|+|.|+....+..|+..
T Consensus 296 HLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 296 HLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred HHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 999999999999999999999999999999888753
No 7
>KOG3623|consensus
Probab=99.68 E-value=1.4e-17 Score=103.41 Aligned_cols=70 Identities=33% Similarity=0.646 Sum_probs=50.9
Q ss_pred ccccccccccccChHHHHHHHHHcc-------cccCccccChHHHHHHHHhccCCCCcccccchhhccChHHHHHHh
Q psy13994 24 KFGCEYCSARFSQKISCRVHMLRHR-------DVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCRVHM 93 (97)
Q Consensus 24 ~~~C~~C~~~f~~~~~l~~h~~~~~-------~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 93 (97)
+|.|+.|+++|...+.|.+|-.-|+ ..|.|+|...-.|..|++.|.|||||+|..|+|.|+....+.+|+
T Consensus 894 myaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 894 MYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred cchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 4555555555555555555544444 235556666667788999999999999999999999999999997
No 8
>KOG3608|consensus
Probab=99.64 E-value=8.9e-16 Score=88.98 Aligned_cols=96 Identities=26% Similarity=0.481 Sum_probs=79.6
Q ss_pred cchhccCchHHHHHHhhccCCCccccccccccccChHHHHHHHHHcc---------------------------------
Q psy13994 2 CNKQYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCRVHMLRHR--------------------------------- 48 (97)
Q Consensus 2 C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~--------------------------------- 48 (97)
|-+.+.+.+.|..|++.|++++-..|+.||.-|..+..|.-|++..+
T Consensus 185 Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~y 264 (467)
T KOG3608|consen 185 CTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCY 264 (467)
T ss_pred hhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcc
Confidence 56778888889999999988877777777777777777766666554
Q ss_pred --cccCccccChHHHHHHHHh-ccCCCCcccccchhhccChHHHHHHhhhcC
Q psy13994 49 --DVCNKPYHRKSVLIAHLQS-HEGVKKFGCEYCSARFSQKISCRVHMLRHR 97 (97)
Q Consensus 49 --~~c~~~~~~~~~~~~h~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 97 (97)
+.|.-+....+.|..|++. |..++||+|..|++.|.+.+.|..|...|+
T Consensus 265 kCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 265 KCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred cccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 5688888889999999885 778999999999999999999999998874
No 9
>KOG3576|consensus
Probab=99.59 E-value=4.8e-16 Score=84.18 Aligned_cols=96 Identities=27% Similarity=0.584 Sum_probs=75.6
Q ss_pred CcchhccCchHHHHHHhhccCCCccccccccccccChHHHHHHHHHcc-------cccCccccChHHHHHHHHh-c----
Q psy13994 1 VCNKQYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCRVHMLRHR-------DVCNKPYHRKSVLIAHLQS-H---- 68 (97)
Q Consensus 1 ~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~-------~~c~~~~~~~~~~~~h~~~-h---- 68 (97)
+|++.|.-.-.|.+|+.-|.+.+.+.|..||+.|...-+|+.|+++|+ ..|+++|.....|..|.+. |
T Consensus 122 vCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~ 201 (267)
T KOG3576|consen 122 VCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQH 201 (267)
T ss_pred hhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchH
Confidence 577888777778888888887778888888888888888888888887 3577888888777777642 2
Q ss_pred ------cCCCCcccccchhhccChHHHHHHhhhc
Q psy13994 69 ------EGVKKFGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 69 ------~~~~~~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
..++.|.|+.||.+-.....+..|++.|
T Consensus 202 ~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~ 235 (267)
T KOG3576|consen 202 QYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLH 235 (267)
T ss_pred HHHHHHhhhheeeecccCCCCCChhHHHHHHHhc
Confidence 2467899999999988888888888765
No 10
>KOG3608|consensus
Probab=99.50 E-value=8.6e-14 Score=80.94 Aligned_cols=95 Identities=23% Similarity=0.495 Sum_probs=81.8
Q ss_pred CcchhccCchHHHHHHhh-ccCCCccccccccccccChHHHHHHHHHcc--------cccCccccChHHHHHHHHh-ccC
Q psy13994 1 VCNKQYHRKSVLIAHLQS-HEGVKKFGCEYCSARFSQKISCRVHMLRHR--------DVCNKPYHRKSVLIAHLQS-HEG 70 (97)
Q Consensus 1 ~C~~~f~~~~~l~~h~~~-h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~--------~~c~~~~~~~~~~~~h~~~-h~~ 70 (97)
+|+..-...+.|..|++. |..++||+|+.|+..+...++|.+|...|. +.|...+.....+..|.+. |.|
T Consensus 268 lCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg 347 (467)
T KOG3608|consen 268 LCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHEG 347 (467)
T ss_pred ccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHHHhccC
Confidence 467777788899999885 778999999999999999999999999887 4588888888999999875 445
Q ss_pred CC--CcccccchhhccChHHHHHHhhh
Q psy13994 71 VK--KFGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 71 ~~--~~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
.+ +|.|..|++.|+...+|..|++.
T Consensus 348 ~np~~Y~CH~Cdr~ft~G~~L~~HL~k 374 (467)
T KOG3608|consen 348 NNPILYACHCCDRFFTSGKSLSAHLMK 374 (467)
T ss_pred CCCCceeeecchhhhccchhHHHHHHH
Confidence 44 69999999999999999999875
No 11
>KOG3993|consensus
Probab=99.37 E-value=1.9e-13 Score=80.90 Aligned_cols=96 Identities=20% Similarity=0.366 Sum_probs=71.4
Q ss_pred CcchhccCchHHHHHHhhccCCCccccccccccccChHHHHHHHHHcccc--cCcc--------ccChHHHHHHHH--hc
Q psy13994 1 VCNKQYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCRVHMLRHRDV--CNKP--------YHRKSVLIAHLQ--SH 68 (97)
Q Consensus 1 ~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~--c~~~--------~~~~~~~~~h~~--~h 68 (97)
+|...|.+...|.+|....+....|+|++|++.|+...+|..|+|+|.+. -.++ .......+.-.+ ..
T Consensus 272 LCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~d 351 (500)
T KOG3993|consen 272 LCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDD 351 (500)
T ss_pred HHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCc
Confidence 47788999999999999988888999999999999999999999999832 1110 011111100000 01
Q ss_pred cCCCCcccccchhhccChHHHHHHhhhc
Q psy13994 69 EGVKKFGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 69 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
..+..|.|..|+|.|.....|+.|+.+|
T Consensus 352 ss~gi~~C~~C~KkFrRqAYLrKHqlth 379 (500)
T KOG3993|consen 352 SSSGIFSCHTCGKKFRRQAYLRKHQLTH 379 (500)
T ss_pred ccCceeecHHhhhhhHHHHHHHHhHHhh
Confidence 2234799999999999999999998876
No 12
>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=99.32 E-value=8.9e-13 Score=49.96 Aligned_cols=26 Identities=38% Similarity=0.869 Sum_probs=23.9
Q ss_pred HHHHHHHhccCCCCcccccchhhccC
Q psy13994 60 VLIAHLQSHEGVKKFGCEYCSARFSQ 85 (97)
Q Consensus 60 ~~~~h~~~h~~~~~~~C~~C~~~f~~ 85 (97)
+|..|++.|.+++||.|+.|+++|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47899999999999999999999974
No 13
>PHA00733 hypothetical protein
Probab=99.23 E-value=1.9e-11 Score=63.14 Aligned_cols=73 Identities=14% Similarity=0.194 Sum_probs=55.6
Q ss_pred CCccccccccccccChHHHHHH--HHHcc----------cccCccccChHHHHHHHHhccCCCCcccccchhhccChHHH
Q psy13994 22 VKKFGCEYCSARFSQKISCRVH--MLRHR----------DVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISC 89 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~~~l~~h--~~~~~----------~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~~~~l 89 (97)
.+++.|.+|+..|.....|..+ +..+. +.|++.|.....|..|++.+ +.+|.|..|++.|.....|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHH
Confidence 4567888888777777666655 11111 46888888888888888866 3579999999999999999
Q ss_pred HHHhhhc
Q psy13994 90 RVHMLRH 96 (97)
Q Consensus 90 ~~H~~~h 96 (97)
..|+...
T Consensus 116 ~~H~~~~ 122 (128)
T PHA00733 116 LDHVCKK 122 (128)
T ss_pred HHHHHHh
Confidence 9998763
No 14
>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=99.23 E-value=7.6e-12 Score=47.37 Aligned_cols=26 Identities=38% Similarity=0.869 Sum_probs=23.8
Q ss_pred HHHHHHhhccCCCccccccccccccC
Q psy13994 11 VLIAHLQSHEGVKKFGCEYCSARFSQ 36 (97)
Q Consensus 11 ~l~~h~~~h~~~~~~~C~~C~~~f~~ 36 (97)
+|..|+++|++++||.|+.|+++|..
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 58899999999999999999999863
No 15
>PHA02768 hypothetical protein; Provisional
Probab=99.16 E-value=1.5e-11 Score=53.85 Aligned_cols=38 Identities=18% Similarity=0.385 Sum_probs=28.4
Q ss_pred cCccccChHHHHHHHHhccCCCCcccccchhhccChHHHH
Q psy13994 51 CNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCR 90 (97)
Q Consensus 51 c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~~~~l~ 90 (97)
||+.|...++|..|++.|. ++|+|..|++.|.+.+.|.
T Consensus 11 CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 11 CGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred hCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 4455555666677777777 6899999999999877663
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.04 E-value=8.4e-10 Score=68.64 Aligned_cols=86 Identities=15% Similarity=0.372 Sum_probs=57.2
Q ss_pred cchhccCchHHHHHHhhccCCCccccccccccccChHHHHHHHHHcc-------cccCccccC----------hHHHHHH
Q psy13994 2 CNKQYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCRVHMLRHR-------DVCNKPYHR----------KSVLIAH 64 (97)
Q Consensus 2 C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~-------~~c~~~~~~----------~~~~~~h 64 (97)
|++.|. ...|..|+..++ +|+.|+ ||..+ ....|..|+..+. +.|++.+.. ...|..|
T Consensus 459 Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~H 533 (567)
T PLN03086 459 CGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEH 533 (567)
T ss_pred CCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHH
Confidence 666664 466778887764 677887 87644 5577777776655 356666642 2357777
Q ss_pred HHhccCCCCcccccchhhccChHHHHHHhh
Q psy13994 65 LQSHEGVKKFGCEYCSARFSQKISCRVHML 94 (97)
Q Consensus 65 ~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 94 (97)
.... |.+++.|..||+.+... .|..|+.
T Consensus 534 E~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~ 561 (567)
T PLN03086 534 ESIC-GSRTAPCDSCGRSVMLK-EMDIHQI 561 (567)
T ss_pred HHhc-CCcceEccccCCeeeeh-hHHHHHH
Confidence 7764 67788888888777655 5566654
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.99 E-value=2e-10 Score=50.34 Aligned_cols=35 Identities=20% Similarity=0.450 Sum_probs=18.9
Q ss_pred cchhccCchHHHHHHhhccCCCccccccccccccChH
Q psy13994 2 CNKQYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKI 38 (97)
Q Consensus 2 C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~ 38 (97)
||+.|...++|..|+++|+ +|+.|..|++.|...+
T Consensus 11 CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s 45 (55)
T PHA02768 11 CGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTG 45 (55)
T ss_pred hCCeeccHHHHHHHHHhcC--CcccCCcccceecccc
Confidence 5555555555555555554 4555555555554433
No 18
>PHA00733 hypothetical protein
Probab=98.89 E-value=4.5e-09 Score=54.38 Aligned_cols=50 Identities=22% Similarity=0.500 Sum_probs=43.8
Q ss_pred cCCCccccccccccccChHHHHHHHHHcc-----cccCccccChHHHHHHHHhcc
Q psy13994 20 EGVKKFGCEYCSARFSQKISCRVHMLRHR-----DVCNKPYHRKSVLIAHLQSHE 69 (97)
Q Consensus 20 ~~~~~~~C~~C~~~f~~~~~l~~h~~~~~-----~~c~~~~~~~~~~~~h~~~h~ 69 (97)
.+++||.|+.||+.|.....|..|++.+. +.|++.|.....|..|+....
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 45889999999999999999999998542 689999999999999987654
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.82 E-value=1.2e-08 Score=63.69 Aligned_cols=71 Identities=18% Similarity=0.331 Sum_probs=58.6
Q ss_pred CCccccccccccccChHHHHHHHHHcc-----cccCccccChHHHHHHHHhccCCCCcccccchhhccC----------h
Q psy13994 22 VKKFGCEYCSARFSQKISCRVHMLRHR-----DVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQ----------K 86 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~~~l~~h~~~~~-----~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~----------~ 86 (97)
++++.|+.|++.|. ...|..|+..++ + |++.+ ....|..|+..|..++++.|..|++.|.. .
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~ 527 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFHEPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRL 527 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcCCCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhh
Confidence 45678999999996 678999999865 4 88655 56899999999999999999999999852 4
Q ss_pred HHHHHHhhh
Q psy13994 87 ISCRVHMLR 95 (97)
Q Consensus 87 ~~l~~H~~~ 95 (97)
+.|..|...
T Consensus 528 s~Lt~HE~~ 536 (567)
T PLN03086 528 RGMSEHESI 536 (567)
T ss_pred hhHHHHHHh
Confidence 578888765
No 20
>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=98.79 E-value=2.6e-09 Score=39.17 Aligned_cols=23 Identities=39% Similarity=0.801 Sum_probs=21.3
Q ss_pred cccccchhhccChHHHHHHhhhc
Q psy13994 74 FGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 74 ~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
|.|+.|++.|.....|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 68999999999999999999875
No 21
>PHA00616 hypothetical protein
Probab=98.79 E-value=3.2e-09 Score=44.50 Aligned_cols=25 Identities=24% Similarity=0.482 Sum_probs=23.4
Q ss_pred CcccccchhhccChHHHHHHhhhcC
Q psy13994 73 KFGCEYCSARFSQKISCRVHMLRHR 97 (97)
Q Consensus 73 ~~~C~~C~~~f~~~~~l~~H~~~h~ 97 (97)
||+|+.||+.|.+.++|..|+++|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~h 25 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVH 25 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhc
Confidence 6899999999999999999999874
No 22
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.73 E-value=1.4e-09 Score=62.98 Aligned_cols=71 Identities=20% Similarity=0.368 Sum_probs=50.9
Q ss_pred CCcccccc--ccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCcccccchhhccChHHHHHHhh
Q psy13994 22 VKKFGCEY--CSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCRVHML 94 (97)
Q Consensus 22 ~~~~~C~~--C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 94 (97)
++||.|++ |.+++.....|+-|+...+ |.........-..+...-..+|||+|++|+|.|.....|+-|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH--~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGH--QNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccc--cCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 59999976 9999999999999987544 22211111122233334566899999999999999999877754
No 23
>KOG3993|consensus
Probab=98.73 E-value=4.9e-09 Score=62.76 Aligned_cols=95 Identities=22% Similarity=0.379 Sum_probs=68.5
Q ss_pred CcchhccCchHHHHHHhhccC--------C-------------------------CccccccccccccChHHHHHHHHHc
Q psy13994 1 VCNKQYHRKSVLIAHLQSHEG--------V-------------------------KKFGCEYCSARFSQKISCRVHMLRH 47 (97)
Q Consensus 1 ~C~~~f~~~~~l~~h~~~h~~--------~-------------------------~~~~C~~C~~~f~~~~~l~~h~~~~ 47 (97)
+|+++|.-..+|..|.+.|.- . -.|.|.+|++.|.....|..|+.+|
T Consensus 300 EC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlth 379 (500)
T KOG3993|consen 300 ECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTH 379 (500)
T ss_pred cccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhh
Confidence 699999999999999999831 1 1378999999999999999999888
Q ss_pred c-----------------------------------------------------cccCccccChHHHHHHHHhccCCCCc
Q psy13994 48 R-----------------------------------------------------DVCNKPYHRKSVLIAHLQSHEGVKKF 74 (97)
Q Consensus 48 ~-----------------------------------------------------~~c~~~~~~~~~~~~h~~~h~~~~~~ 74 (97)
+ +.++..+.++..--.+.+.-..+.-|
T Consensus 380 q~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f 459 (500)
T KOG3993|consen 380 QRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGF 459 (500)
T ss_pred hccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCCCCCCCCcccCCCCCccccccchhhcc
Confidence 7 12332222222222222222234568
Q ss_pred ccccchhhccChHHHHHHhhh
Q psy13994 75 GCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 75 ~C~~C~~~f~~~~~l~~H~~~ 95 (97)
.|..|--+|.....|.+|+.+
T Consensus 460 ~~ky~~atfyss~~ltrhin~ 480 (500)
T KOG3993|consen 460 TCKYCPATFYSSPGLTRHINK 480 (500)
T ss_pred ccccchHhhhcCcchHhHhhh
Confidence 899999999999999998765
No 24
>PHA00732 hypothetical protein
Probab=98.68 E-value=1.5e-08 Score=48.15 Aligned_cols=22 Identities=18% Similarity=0.362 Sum_probs=15.9
Q ss_pred ccccccccccccChHHHHHHHH
Q psy13994 24 KFGCEYCSARFSQKISCRVHML 45 (97)
Q Consensus 24 ~~~C~~C~~~f~~~~~l~~h~~ 45 (97)
||.|..||+.|.....|..|++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r 22 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHAR 22 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhh
Confidence 5678888777777777776665
No 25
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.54 E-value=4.8e-08 Score=37.11 Aligned_cols=25 Identities=32% Similarity=0.564 Sum_probs=23.0
Q ss_pred CcccccchhhccChHHHHHHhhhcC
Q psy13994 73 KFGCEYCSARFSQKISCRVHMLRHR 97 (97)
Q Consensus 73 ~~~C~~C~~~f~~~~~l~~H~~~h~ 97 (97)
||.|..|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 6899999999999999999998873
No 26
>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=98.53 E-value=5.3e-08 Score=35.75 Aligned_cols=24 Identities=38% Similarity=0.728 Sum_probs=20.0
Q ss_pred cccccchhhccChHHHHHHhhhcC
Q psy13994 74 FGCEYCSARFSQKISCRVHMLRHR 97 (97)
Q Consensus 74 ~~C~~C~~~f~~~~~l~~H~~~h~ 97 (97)
|.|++|++.|.+...|..|+++|.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 689999999999999999999863
No 27
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.52 E-value=6.2e-08 Score=47.87 Aligned_cols=70 Identities=23% Similarity=0.426 Sum_probs=21.2
Q ss_pred ccccccccccChHHHHHHHHHccccc---CccccChHHHHHHHHhccCCCCcccccchhhccChHHHHHHhhhc
Q psy13994 26 GCEYCSARFSQKISCRVHMLRHRDVC---NKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 26 ~C~~C~~~f~~~~~l~~h~~~~~~~c---~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
.|..|+..|.....+..|+...+... ...+.....+..+.+... ...+.|..|++.|.....|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Ccccccccccccccccccccccccccccccccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 47889999999999999987666321 111222233333333222 23689999999999999999999864
No 28
>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=98.41 E-value=2.3e-07 Score=33.80 Aligned_cols=22 Identities=36% Similarity=0.747 Sum_probs=19.6
Q ss_pred cccccccccccChHHHHHHHHH
Q psy13994 25 FGCEYCSARFSQKISCRVHMLR 46 (97)
Q Consensus 25 ~~C~~C~~~f~~~~~l~~h~~~ 46 (97)
|.|+.|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 5799999999999999999876
No 29
>smart00355 ZnF_C2H2 zinc finger.
Probab=98.25 E-value=8.3e-07 Score=32.94 Aligned_cols=23 Identities=30% Similarity=0.651 Sum_probs=21.1
Q ss_pred cccccchhhccChHHHHHHhhhc
Q psy13994 74 FGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 74 ~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
|.|+.|+++|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 57999999999999999999876
No 30
>PHA00616 hypothetical protein
Probab=98.24 E-value=6.2e-07 Score=37.66 Aligned_cols=34 Identities=32% Similarity=0.552 Sum_probs=20.9
Q ss_pred ccccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCccccc
Q psy13994 24 KFGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKFGCEY 78 (97)
Q Consensus 24 ~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~ 78 (97)
||.|..||+.|..... +..|++.|++++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~---------------------l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKE---------------------VIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHH---------------------HHHHHHHhcCCCccceeE
Confidence 5677777666655554 555555666666666543
No 31
>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=98.21 E-value=1.5e-06 Score=31.71 Aligned_cols=23 Identities=39% Similarity=0.751 Sum_probs=18.5
Q ss_pred cccccccccccChHHHHHHHHHc
Q psy13994 25 FGCEYCSARFSQKISCRVHMLRH 47 (97)
Q Consensus 25 ~~C~~C~~~f~~~~~l~~h~~~~ 47 (97)
|.|++|++.|.....|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 57999999999999999998875
No 32
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.17 E-value=1e-06 Score=33.31 Aligned_cols=25 Identities=32% Similarity=0.564 Sum_probs=21.6
Q ss_pred ccccccccccccChHHHHHHHHHcc
Q psy13994 24 KFGCEYCSARFSQKISCRVHMLRHR 48 (97)
Q Consensus 24 ~~~C~~C~~~f~~~~~l~~h~~~~~ 48 (97)
||.|..|++.|.....|..|++.+.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 6889999999999999999987653
No 33
>PHA00732 hypothetical protein
Probab=98.15 E-value=1.6e-06 Score=41.26 Aligned_cols=42 Identities=17% Similarity=0.331 Sum_probs=33.7
Q ss_pred CcchhccCchHHHHHHhh-ccCCCccccccccccccChHHHHHHHHHcc
Q psy13994 1 VCNKQYHRKSVLIAHLQS-HEGVKKFGCEYCSARFSQKISCRVHMLRHR 48 (97)
Q Consensus 1 ~C~~~f~~~~~l~~h~~~-h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~ 48 (97)
+|++.|.....|..|++. |. ++.|+.||+.|. .+..|..+..
T Consensus 6 ~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 6 ICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccC
Confidence 589999999999999984 54 358999999997 4666765544
No 34
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.92 E-value=5.4e-06 Score=30.69 Aligned_cols=23 Identities=35% Similarity=0.681 Sum_probs=20.7
Q ss_pred cccccchhhccChHHHHHHhhhc
Q psy13994 74 FGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 74 ~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
|.|.+|++.|.....++.|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 57999999999999999999864
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.67 E-value=4.9e-05 Score=27.88 Aligned_cols=23 Identities=30% Similarity=0.651 Sum_probs=18.4
Q ss_pred cccccccccccChHHHHHHHHHc
Q psy13994 25 FGCEYCSARFSQKISCRVHMLRH 47 (97)
Q Consensus 25 ~~C~~C~~~f~~~~~l~~h~~~~ 47 (97)
+.|..|++.|.....+..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 46888988888888888887743
No 36
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.64 E-value=3.1e-05 Score=28.57 Aligned_cols=22 Identities=36% Similarity=0.703 Sum_probs=19.2
Q ss_pred cccccccccccChHHHHHHHHH
Q psy13994 25 FGCEYCSARFSQKISCRVHMLR 46 (97)
Q Consensus 25 ~~C~~C~~~f~~~~~l~~h~~~ 46 (97)
|.|.+|+..|.+...+..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 5799999999999999999864
No 37
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.61 E-value=5.4e-05 Score=32.64 Aligned_cols=29 Identities=21% Similarity=0.319 Sum_probs=20.2
Q ss_pred ccCCCCcccccchhhccChHHHHHHhhhc
Q psy13994 68 HEGVKKFGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 68 h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
...+.|-.|++|+..+.+..+|++|+++.
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~ 47 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIR 47 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHH
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHH
Confidence 34567889999999999999999999763
No 38
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.58 E-value=1.6e-05 Score=30.01 Aligned_cols=22 Identities=32% Similarity=0.614 Sum_probs=20.1
Q ss_pred cccccchhhccChHHHHHHhhh
Q psy13994 74 FGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 74 ~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
|.|..|++.|.+...+..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6799999999999999999875
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.55 E-value=5.1e-05 Score=27.72 Aligned_cols=22 Identities=36% Similarity=0.652 Sum_probs=17.7
Q ss_pred cccccchhhccChHHHHHHhhhc
Q psy13994 74 FGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 74 ~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
|+|+.|+.... ...|.+|+++|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 68999999888 88999999874
No 40
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.54 E-value=0.00029 Score=31.06 Aligned_cols=50 Identities=26% Similarity=0.414 Sum_probs=31.1
Q ss_pred ccccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCC-CCcccccchhhccChHHHHHHhhhc
Q psy13994 24 KFGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGV-KKFGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 24 ~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~-~~~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
.|.|+.|++ ......|..|... .|..+ +.+.|++|...+. .+|..|+..+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~--------------------~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCED--------------------EHRSESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHh--------------------HCcCCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 367777777 3334445444332 24333 4688999998655 4888998764
No 41
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.51 E-value=0.0001 Score=36.27 Aligned_cols=20 Identities=15% Similarity=0.564 Sum_probs=0.0
Q ss_pred CcchhccCchHHHHHHhhcc
Q psy13994 1 VCNKQYHRKSVLIAHLQSHE 20 (97)
Q Consensus 1 ~C~~~f~~~~~l~~h~~~h~ 20 (97)
.|+..|.+...|..|+...+
T Consensus 4 ~C~~~f~~~~~l~~H~~~~H 23 (100)
T PF12756_consen 4 FCDESFSSVDDLLQHMKKKH 23 (100)
T ss_dssp --------------------
T ss_pred cccccccccccccccccccc
Confidence 47888888888888886543
No 42
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.41 E-value=0.00044 Score=30.51 Aligned_cols=44 Identities=27% Similarity=0.470 Sum_probs=31.6
Q ss_pred CcchhccCchHHHHHHhh-ccC-CCccccccccccccChHHHHHHHHHc
Q psy13994 1 VCNKQYHRKSVLIAHLQS-HEG-VKKFGCEYCSARFSQKISCRVHMLRH 47 (97)
Q Consensus 1 ~C~~~f~~~~~l~~h~~~-h~~-~~~~~C~~C~~~f~~~~~l~~h~~~~ 47 (97)
.|++ ..+...|..|... |.. .+.+.|++|...+. .+|..|+...
T Consensus 7 ~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 7 YCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred CCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 4788 4567889999765 444 35699999997644 4777777654
No 43
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.25 E-value=0.0004 Score=30.02 Aligned_cols=30 Identities=20% Similarity=0.315 Sum_probs=20.1
Q ss_pred ccCCCccccccccccccChHHHHHHHHHcc
Q psy13994 19 HEGVKKFGCEYCSARFSQKISCRVHMLRHR 48 (97)
Q Consensus 19 h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~ 48 (97)
+..+.|..|++|+..+....+|..|+...+
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H 48 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRH 48 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHT
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHh
Confidence 345788999999999999999999986543
No 44
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.11 E-value=0.00012 Score=43.18 Aligned_cols=44 Identities=27% Similarity=0.532 Sum_probs=36.5
Q ss_pred cchhccCchHHHHHHhhcc-------------------CCCccccccccccccChHHHHHHHH
Q psy13994 2 CNKQYHRKSVLIAHLQSHE-------------------GVKKFGCEYCSARFSQKISCRVHML 45 (97)
Q Consensus 2 C~~~f~~~~~l~~h~~~h~-------------------~~~~~~C~~C~~~f~~~~~l~~h~~ 45 (97)
|++.|.....|+.|+..-+ .++||+|.+|++.+...+.|+-|+.
T Consensus 357 C~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 357 CNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred chhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 8899999999999986422 1489999999999999999888754
No 45
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.10 E-value=9.2e-05 Score=27.88 Aligned_cols=22 Identities=32% Similarity=0.614 Sum_probs=18.8
Q ss_pred cccccccccccChHHHHHHHHH
Q psy13994 25 FGCEYCSARFSQKISCRVHMLR 46 (97)
Q Consensus 25 ~~C~~C~~~f~~~~~l~~h~~~ 46 (97)
|.|..|++.|.....+..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6799999999999999888753
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.99 E-value=0.00068 Score=24.63 Aligned_cols=22 Identities=36% Similarity=0.652 Sum_probs=16.3
Q ss_pred cccccccccccChHHHHHHHHHc
Q psy13994 25 FGCEYCSARFSQKISCRVHMLRH 47 (97)
Q Consensus 25 ~~C~~C~~~f~~~~~l~~h~~~~ 47 (97)
|.|+.|+.... ...|..|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 57899998887 88888888764
No 47
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=96.88 E-value=0.00078 Score=26.75 Aligned_cols=23 Identities=30% Similarity=0.723 Sum_probs=20.4
Q ss_pred CcccccchhhccChHHHHHHhhh
Q psy13994 73 KFGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 73 ~~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
+|.|..|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999999764
No 48
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.80 E-value=0.0011 Score=24.47 Aligned_cols=21 Identities=19% Similarity=0.360 Sum_probs=16.8
Q ss_pred cccccchhhccChHHHHHHhhh
Q psy13994 74 FGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 74 ~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
..|+.||+.| ....|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4699999999 56678888765
No 49
>PRK04860 hypothetical protein; Provisional
Probab=96.67 E-value=0.0013 Score=35.60 Aligned_cols=30 Identities=17% Similarity=0.344 Sum_probs=26.1
Q ss_pred ChHHHHHHHHhccCCCCcccccchhhccCh
Q psy13994 57 RKSVLIAHLQSHEGVKKFGCEYCSARFSQK 86 (97)
Q Consensus 57 ~~~~~~~h~~~h~~~~~~~C~~C~~~f~~~ 86 (97)
....+..|.+++.++++|.|..|+..|...
T Consensus 127 ~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 127 HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 566788999999999999999999988754
No 50
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=96.43 E-value=0.0027 Score=25.13 Aligned_cols=23 Identities=30% Similarity=0.723 Sum_probs=19.7
Q ss_pred ccccccccccccChHHHHHHHHH
Q psy13994 24 KFGCEYCSARFSQKISCRVHMLR 46 (97)
Q Consensus 24 ~~~C~~C~~~f~~~~~l~~h~~~ 46 (97)
+|.|.+|+..|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999988888888764
No 51
>PRK04860 hypothetical protein; Provisional
Probab=96.40 E-value=0.0017 Score=35.09 Aligned_cols=30 Identities=17% Similarity=0.344 Sum_probs=23.0
Q ss_pred CchHHHHHHhhccCCCccccccccccccCh
Q psy13994 8 RKSVLIAHLQSHEGVKKFGCEYCSARFSQK 37 (97)
Q Consensus 8 ~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~ 37 (97)
....+..|.+++.++++|.|..|+..|...
T Consensus 127 ~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 127 HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 456677888888888888888888877644
No 52
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.32 E-value=0.00019 Score=43.63 Aligned_cols=47 Identities=38% Similarity=0.738 Sum_probs=41.6
Q ss_pred cchhccCchHHHHHHh--hccCC--Cccccc--cccccccChHHHHHHHHHcc
Q psy13994 2 CNKQYHRKSVLIAHLQ--SHEGV--KKFGCE--YCSARFSQKISCRVHMLRHR 48 (97)
Q Consensus 2 C~~~f~~~~~l~~h~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~h~~~~~ 48 (97)
|...|.....+..|.+ .|.++ +|+.|+ .|++.|.....+..|...+.
T Consensus 295 ~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~ 347 (467)
T COG5048 295 CNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHT 347 (467)
T ss_pred ccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCccccc
Confidence 5677888888999999 79999 999999 79999999999999988776
No 53
>KOG1146|consensus
Probab=96.17 E-value=0.0012 Score=45.61 Aligned_cols=75 Identities=17% Similarity=0.275 Sum_probs=53.3
Q ss_pred ccCCCccccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHh------ccCCCCcccccchhhccChHHHHHH
Q psy13994 19 HEGVKKFGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQS------HEGVKKFGCEYCSARFSQKISCRVH 92 (97)
Q Consensus 19 h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~------h~~~~~~~C~~C~~~f~~~~~l~~H 92 (97)
+...+.+.|+.|+..+.....|..|++..++.-+..+. .+.+.|.+. -.+-++|.|..|..+++...+|.+|
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c--~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsih 537 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYC--KAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIH 537 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccccccccchhHh--HhccccccccccccccCCCCcccceeeeeeeecchHHHHH
Confidence 45567899999999999999999999986633221111 111122211 2334789999999999999999999
Q ss_pred hhh
Q psy13994 93 MLR 95 (97)
Q Consensus 93 ~~~ 95 (97)
+..
T Consensus 538 lqS 540 (1406)
T KOG1146|consen 538 LQS 540 (1406)
T ss_pred HHH
Confidence 864
No 54
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=95.04 E-value=0.015 Score=25.66 Aligned_cols=27 Identities=19% Similarity=0.426 Sum_probs=22.7
Q ss_pred ccCCCCcccccchhhccChHHHHHHhh
Q psy13994 68 HEGVKKFGCEYCSARFSQKISCRVHML 94 (97)
Q Consensus 68 h~~~~~~~C~~C~~~f~~~~~l~~H~~ 94 (97)
..||--++|+-|+..|.....+.+|.-
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhh
Confidence 456777899999999999999888853
No 55
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=94.73 E-value=0.017 Score=22.70 Aligned_cols=10 Identities=30% Similarity=0.783 Sum_probs=7.9
Q ss_pred CCcccccchh
Q psy13994 72 KKFGCEYCSA 81 (97)
Q Consensus 72 ~~~~C~~C~~ 81 (97)
.++.|++|+.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 5788999874
No 56
>KOG1146|consensus
Probab=94.70 E-value=0.0067 Score=42.25 Aligned_cols=69 Identities=13% Similarity=0.199 Sum_probs=45.4
Q ss_pred CCccccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCcccccchhhccChHHHHHHhhh
Q psy13994 22 VKKFGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
..+|.|..|...|...+.+..|++ .|.+.+....-..-+...+.....| |..|...|+....|+.|+++
T Consensus 1282 ~~~~~~~~~~~~~~~~~~l~~~~~----k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~ 1350 (1406)
T KOG1146|consen 1282 THRYLCRQCKMAFDGEAPLTAHQR----KFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRS 1350 (1406)
T ss_pred chhHHHHHHHhhhcchhHHHHHHH----HHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHH
Confidence 346778888888888887777763 2333333222222233333434556 99999999999999999985
No 57
>KOG4173|consensus
Probab=94.55 E-value=0.036 Score=31.19 Aligned_cols=71 Identities=23% Similarity=0.525 Sum_probs=51.9
Q ss_pred cccccc--ccccccChHHHHHHHHHcc----cccCccccChHHHHHHHH----------hccCCCCccc--ccchhhccC
Q psy13994 24 KFGCEY--CSARFSQKISCRVHMLRHR----DVCNKPYHRKSVLIAHLQ----------SHEGVKKFGC--EYCSARFSQ 85 (97)
Q Consensus 24 ~~~C~~--C~~~f~~~~~l~~h~~~~~----~~c~~~~~~~~~~~~h~~----------~h~~~~~~~C--~~C~~~f~~ 85 (97)
.+.|++ |-+.|........|..+-+ ..|.+.|.+.-.|..|+. ...|..-|+| +.|+..|.+
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT 158 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHGNSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKT 158 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcccchhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhh
Confidence 366765 7788888888888776544 467788888777777763 2345556888 559999999
Q ss_pred hHHHHHHhh
Q psy13994 86 KISCRVHML 94 (97)
Q Consensus 86 ~~~l~~H~~ 94 (97)
......|+-
T Consensus 159 ~r~RkdH~I 167 (253)
T KOG4173|consen 159 SRDRKDHMI 167 (253)
T ss_pred hhhhhhHHH
Confidence 988888853
No 58
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=94.11 E-value=0.044 Score=22.93 Aligned_cols=25 Identities=24% Similarity=0.480 Sum_probs=16.3
Q ss_pred CCCCcccccchhhccCh----HHHHHHhh
Q psy13994 70 GVKKFGCEYCSARFSQK----ISCRVHML 94 (97)
Q Consensus 70 ~~~~~~C~~C~~~f~~~----~~l~~H~~ 94 (97)
++....|..|++.+... +.|..|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 44567899999988874 88999984
No 59
>KOG2231|consensus
Probab=93.49 E-value=0.15 Score=33.78 Aligned_cols=60 Identities=18% Similarity=0.183 Sum_probs=36.5
Q ss_pred cChHHHHHHHHHccc---------------ccCccccChHHHHHHHHhccC-CC----CcccccchhhccChHHHHHHhh
Q psy13994 35 SQKISCRVHMLRHRD---------------VCNKPYHRKSVLIAHLQSHEG-VK----KFGCEYCSARFSQKISCRVHML 94 (97)
Q Consensus 35 ~~~~~l~~h~~~~~~---------------~c~~~~~~~~~~~~h~~~h~~-~~----~~~C~~C~~~f~~~~~l~~H~~ 94 (97)
.+...|..|+...+. .+.+. -....|+.|++.-.- +. .-.|+.|...|.....|..|++
T Consensus 125 ~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~-Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~ 203 (669)
T KOG2231|consen 125 KSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKL-YTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLR 203 (669)
T ss_pred hHHHHHHHHHHHhhhhhccccccccceeeeeeeeh-ehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhc
Confidence 366778888866552 12222 235566667654221 22 1347888888888888888877
Q ss_pred h
Q psy13994 95 R 95 (97)
Q Consensus 95 ~ 95 (97)
.
T Consensus 204 ~ 204 (669)
T KOG2231|consen 204 F 204 (669)
T ss_pred c
Confidence 5
No 60
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=93.38 E-value=0.049 Score=29.72 Aligned_cols=13 Identities=38% Similarity=0.726 Sum_probs=10.2
Q ss_pred ccCCCCcccccch
Q psy13994 68 HEGVKKFGCEYCS 80 (97)
Q Consensus 68 h~~~~~~~C~~C~ 80 (97)
+.++.|-+||+||
T Consensus 144 ~~ge~P~~CPiCg 156 (166)
T COG1592 144 HEGEAPEVCPICG 156 (166)
T ss_pred ccCCCCCcCCCCC
Confidence 3457788999998
No 61
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.82 E-value=0.012 Score=35.89 Aligned_cols=47 Identities=38% Similarity=0.730 Sum_probs=38.8
Q ss_pred ccCccccChHHHHHHHH--hccCC--CCcccc--cchhhccChHHHHHHhhhc
Q psy13994 50 VCNKPYHRKSVLIAHLQ--SHEGV--KKFGCE--YCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 50 ~c~~~~~~~~~~~~h~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h 96 (97)
.|...|.....+..|.+ .|.++ +++.|+ .|++.|.....+..|..+|
T Consensus 294 ~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~ 346 (467)
T COG5048 294 QCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLH 346 (467)
T ss_pred cccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccc
Confidence 46667777778888888 78888 899998 7999999998888887765
No 62
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=92.24 E-value=0.094 Score=22.61 Aligned_cols=23 Identities=30% Similarity=0.764 Sum_probs=18.3
Q ss_pred cccccchhhccCh-----HHHHHHhh-hc
Q psy13994 74 FGCEYCSARFSQK-----ISCRVHML-RH 96 (97)
Q Consensus 74 ~~C~~C~~~f~~~-----~~l~~H~~-~h 96 (97)
-.|..|++.++.. +.|.+|++ +|
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 4599999988766 68999988 44
No 63
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.53 E-value=0.22 Score=25.47 Aligned_cols=73 Identities=15% Similarity=0.239 Sum_probs=42.4
Q ss_pred CCccccccccccccChHHHHHHHHHcc-------------------cccCccccChHHHHHHHHhccCCCCcccccchhh
Q psy13994 22 VKKFGCEYCSARFSQKISCRVHMLRHR-------------------DVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSAR 82 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~~~l~~h~~~~~-------------------~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~ 82 (97)
+-|..|++||-+......|.+....-- -.|...|........ ..-.....|+|+.|...
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~ 90 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNV 90 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCCc
Confidence 457888899888877777764321100 124444443211000 00112346999999999
Q ss_pred ccChHHHHHHhhhc
Q psy13994 83 FSQKISCRVHMLRH 96 (97)
Q Consensus 83 f~~~~~l~~H~~~h 96 (97)
|-..-+.-.|...|
T Consensus 91 FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 91 FCVDCDVFVHESLH 104 (112)
T ss_pred cccccchhhhhhcc
Confidence 98877777777665
No 64
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=90.91 E-value=0.23 Score=18.40 Aligned_cols=19 Identities=16% Similarity=0.293 Sum_probs=14.8
Q ss_pred ccccchhhccChHHHHHHhh
Q psy13994 75 GCEYCSARFSQKISCRVHML 94 (97)
Q Consensus 75 ~C~~C~~~f~~~~~l~~H~~ 94 (97)
.||+|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 599999988 5567778875
No 65
>PHA00626 hypothetical protein
Probab=90.31 E-value=0.12 Score=22.89 Aligned_cols=16 Identities=19% Similarity=0.360 Sum_probs=13.2
Q ss_pred CCCcccccchhhccCh
Q psy13994 71 VKKFGCEYCSARFSQK 86 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~ 86 (97)
...|.|+.||..|+..
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 4689999999988753
No 66
>KOG2893|consensus
Probab=90.17 E-value=0.086 Score=30.49 Aligned_cols=19 Identities=26% Similarity=0.534 Sum_probs=9.3
Q ss_pred cccccccccChHHHHHHHH
Q psy13994 27 CEYCSARFSQKISCRVHML 45 (97)
Q Consensus 27 C~~C~~~f~~~~~l~~h~~ 45 (97)
|..|.+.|.....|.+|+.
T Consensus 13 cwycnrefddekiliqhqk 31 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK 31 (341)
T ss_pred eeecccccchhhhhhhhhh
Confidence 5555555554444444443
No 67
>KOG4173|consensus
Probab=90.17 E-value=0.31 Score=27.65 Aligned_cols=60 Identities=15% Similarity=0.362 Sum_probs=41.3
Q ss_pred hhccCchHHHHHHhhccCCCccccccccccccChHHHHHHHHHcc-------------------cccCccccChHHHHHH
Q psy13994 4 KQYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCRVHMLRHR-------------------DVCNKPYHRKSVLIAH 64 (97)
Q Consensus 4 ~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~-------------------~~c~~~~~~~~~~~~h 64 (97)
..|.....+..|...-++ -.|..|.+.|.+...|..|+.-.+ ..|+..|...-.-..|
T Consensus 89 ~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH 165 (253)
T KOG4173|consen 89 QVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDH 165 (253)
T ss_pred HHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhH
Confidence 344444444455443333 379999999999999999987665 3588888887777777
Q ss_pred HH
Q psy13994 65 LQ 66 (97)
Q Consensus 65 ~~ 66 (97)
+.
T Consensus 166 ~I 167 (253)
T KOG4173|consen 166 MI 167 (253)
T ss_pred HH
Confidence 64
No 68
>KOG2785|consensus
Probab=90.15 E-value=0.39 Score=29.69 Aligned_cols=71 Identities=18% Similarity=0.343 Sum_probs=45.3
Q ss_pred cccccccccccChHHHHHHHHHcc-------------cccCccccChHH-HHH--HHHhccCCCCcccccchhhccChHH
Q psy13994 25 FGCEYCSARFSQKISCRVHMLRHR-------------DVCNKPYHRKSV-LIA--HLQSHEGVKKFGCEYCSARFSQKIS 88 (97)
Q Consensus 25 ~~C~~C~~~f~~~~~l~~h~~~~~-------------~~c~~~~~~~~~-~~~--h~~~h~~~~~~~C~~C~~~f~~~~~ 88 (97)
|.|..|...|........|+.+.. +.-...|..... ... -.....++-++.|..|.+.|.....
T Consensus 4 ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~a 83 (390)
T KOG2785|consen 4 FTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPKA 83 (390)
T ss_pred ceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChhh
Confidence 678999999988888888876532 111112221111 000 1112344567889999999999999
Q ss_pred HHHHhhh
Q psy13994 89 CRVHMLR 95 (97)
Q Consensus 89 l~~H~~~ 95 (97)
...|+..
T Consensus 84 ~~~hl~S 90 (390)
T KOG2785|consen 84 HENHLKS 90 (390)
T ss_pred HHHHHHH
Confidence 9999764
No 69
>KOG2893|consensus
Probab=89.97 E-value=0.07 Score=30.84 Aligned_cols=39 Identities=26% Similarity=0.684 Sum_probs=29.3
Q ss_pred CcchhccCchHHHHHHhhccCCCccccccccccccChHHHHHH
Q psy13994 1 VCNKQYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCRVH 43 (97)
Q Consensus 1 ~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~h 43 (97)
.|.+.|.+...|.+|++ .+-|+|.+|.+...+-..|..|
T Consensus 15 ycnrefddekiliqhqk----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 15 YCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred ecccccchhhhhhhhhh----hccceeeeehhhhccCCCceee
Confidence 48889999999988885 4569999998776555444444
No 70
>KOG0717|consensus
Probab=87.94 E-value=0.31 Score=30.98 Aligned_cols=22 Identities=18% Similarity=0.375 Sum_probs=19.4
Q ss_pred cccccchhhccChHHHHHHhhh
Q psy13994 74 FGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 74 ~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
+-|.+|+|+|.+..+|.+|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 5599999999999999999653
No 71
>KOG3408|consensus
Probab=87.88 E-value=0.47 Score=24.57 Aligned_cols=26 Identities=23% Similarity=0.439 Sum_probs=22.5
Q ss_pred CCCCcccccchhhccChHHHHHHhhh
Q psy13994 70 GVKKFGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 70 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
|-..|-|..|.+-|.+...|+.|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 44568899999999999999999875
No 72
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=87.29 E-value=0.52 Score=26.99 Aligned_cols=27 Identities=22% Similarity=0.491 Sum_probs=21.4
Q ss_pred CCccccccccccccChHHHHHHHHHcc
Q psy13994 22 VKKFGCEYCSARFSQKISCRVHMLRHR 48 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~~~l~~h~~~~~ 48 (97)
+.-|.|.+|++.|....-+.+|+...+
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcC
Confidence 445999999999999999999998866
No 73
>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=87.22 E-value=0.21 Score=18.22 Aligned_cols=10 Identities=30% Similarity=0.743 Sum_probs=8.1
Q ss_pred CCcccccchh
Q psy13994 72 KKFGCEYCSA 81 (97)
Q Consensus 72 ~~~~C~~C~~ 81 (97)
.+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4799999984
No 74
>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=86.12 E-value=0.3 Score=18.12 Aligned_cols=10 Identities=30% Similarity=0.673 Sum_probs=7.2
Q ss_pred ccccchhhcc
Q psy13994 75 GCEYCSARFS 84 (97)
Q Consensus 75 ~C~~C~~~f~ 84 (97)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4778887774
No 75
>KOG4167|consensus
Probab=85.82 E-value=0.22 Score=33.40 Aligned_cols=25 Identities=36% Similarity=0.568 Sum_probs=22.6
Q ss_pred CcccccchhhccChHHHHHHhhhcC
Q psy13994 73 KFGCEYCSARFSQKISCRVHMLRHR 97 (97)
Q Consensus 73 ~~~C~~C~~~f~~~~~l~~H~~~h~ 97 (97)
-|.|.+|+|.|--...+..|+++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4889999999999999999999883
No 76
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=85.43 E-value=0.27 Score=19.94 Aligned_cols=11 Identities=36% Similarity=1.044 Sum_probs=9.1
Q ss_pred cccccchhhcc
Q psy13994 74 FGCEYCSARFS 84 (97)
Q Consensus 74 ~~C~~C~~~f~ 84 (97)
|+|+.||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 78999998775
No 77
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=84.99 E-value=0.73 Score=26.07 Aligned_cols=56 Identities=14% Similarity=0.290 Sum_probs=37.4
Q ss_pred CCccccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCcccccchhh----ccChHHHHHH
Q psy13994 22 VKKFGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSAR----FSQKISCRVH 92 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~----f~~~~~l~~H 92 (97)
..||.|.+|.+.|.++.. ..||-.|.....+...+ +--.|-+||+. |.-.+.|+.-
T Consensus 194 ~IPF~C~iCKkdy~spvv---------t~CGH~FC~~Cai~~y~------kg~~C~~Cgk~t~G~f~V~~d~~km 253 (259)
T COG5152 194 KIPFLCGICKKDYESPVV---------TECGHSFCSLCAIRKYQ------KGDECGVCGKATYGRFWVVSDLQKM 253 (259)
T ss_pred CCceeehhchhhccchhh---------hhcchhHHHHHHHHHhc------cCCcceecchhhccceeHHhhHHHH
Confidence 468999999998876543 26888888776665543 23458888874 4445555443
No 78
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=84.90 E-value=0.54 Score=24.82 Aligned_cols=61 Identities=13% Similarity=0.273 Sum_probs=35.6
Q ss_pred ccCCCccccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCc-ccccchhhccChHH
Q psy13994 19 HEGVKKFGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKF-GCEYCSARFSQKIS 88 (97)
Q Consensus 19 h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~-~C~~C~~~f~~~~~ 88 (97)
-.+.+-|+|.+|..+.....-|+ ...-||......-..+-..-. ..| .||.|..+|...+.
T Consensus 75 F~d~~lYeCnIC~etS~ee~FLK-----PneCCgY~iCn~Cya~LWK~~----~~ypvCPvCkTSFKss~~ 136 (140)
T PF05290_consen 75 FLDPKLYECNICKETSAEERFLK-----PNECCGYSICNACYANLWKFC----NLYPVCPVCKTSFKSSSS 136 (140)
T ss_pred ecCCCceeccCcccccchhhcCC-----cccccchHHHHHHHHHHHHHc----ccCCCCCccccccccccc
Confidence 45567799999998865444332 234566654433222222111 123 49999999987653
No 79
>KOG2482|consensus
Probab=84.29 E-value=0.64 Score=28.53 Aligned_cols=35 Identities=29% Similarity=0.622 Sum_probs=26.2
Q ss_pred HHHHHHHHhccCCCCcccccchhhccChHHHHHHhhh
Q psy13994 59 SVLIAHLQSHEGVKKFGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 59 ~~~~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
..+..|..... ..+.|-.|.|.|.....|..||+.
T Consensus 183 nelLehLkekL--~r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 183 NELLEHLKEKL--ERLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred HHHHHHHHHHH--hhheeeeeccccCCcHHHHHHHHh
Confidence 34444544332 257899999999999999999986
No 80
>KOG4167|consensus
Probab=84.17 E-value=0.25 Score=33.18 Aligned_cols=25 Identities=36% Similarity=0.568 Sum_probs=23.1
Q ss_pred ccccccccccccChHHHHHHHHHcc
Q psy13994 24 KFGCEYCSARFSQKISCRVHMLRHR 48 (97)
Q Consensus 24 ~~~C~~C~~~f~~~~~l~~h~~~~~ 48 (97)
.|.|.+|++.|..-..+..||.+|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4899999999999999999999887
No 81
>KOG2231|consensus
Probab=84.14 E-value=2.1 Score=28.76 Aligned_cols=65 Identities=23% Similarity=0.534 Sum_probs=34.3
Q ss_pred ccccccccccChHHHHHHHHHccc---cc------CccccChHHHHHHHHhccCCCCcccc--cch-hhccChHHHHHHh
Q psy13994 26 GCEYCSARFSQKISCRVHMLRHRD---VC------NKPYHRKSVLIAHLQSHEGVKKFGCE--YCS-ARFSQKISCRVHM 93 (97)
Q Consensus 26 ~C~~C~~~f~~~~~l~~h~~~~~~---~c------~~~~~~~~~~~~h~~~h~~~~~~~C~--~C~-~~f~~~~~l~~H~ 93 (97)
.|..|...|.....|..|++..+. .| +..|..-..|..|-+ +.-|.|+ .|. +.|.....+..++
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h~~chfC~~~~~~neyy~~~~dLe~HfR----~~HflCE~~~C~~~~f~~~~~~ei~l 259 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDHEFCHFCDYKTGQNEYYNDYDDLEEHFR----KGHFLCEEEFCRTKKFYVAFELEIEL 259 (669)
T ss_pred cchhhhhhhccHHHHHHhhccceeheeecCcccccchhcccchHHHHHhh----hcCccccccccccceeeehhHHHHHH
Confidence 466677777777777777776652 22 223444445555544 3345565 452 3444443444444
Q ss_pred h
Q psy13994 94 L 94 (97)
Q Consensus 94 ~ 94 (97)
+
T Consensus 260 k 260 (669)
T KOG2231|consen 260 K 260 (669)
T ss_pred H
Confidence 4
No 82
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=83.85 E-value=0.1 Score=19.78 Aligned_cols=11 Identities=45% Similarity=1.026 Sum_probs=8.6
Q ss_pred cccccchhhcc
Q psy13994 74 FGCEYCSARFS 84 (97)
Q Consensus 74 ~~C~~C~~~f~ 84 (97)
|.|..|++.|.
T Consensus 1 ~sCiDC~~~F~ 11 (28)
T PF08790_consen 1 FSCIDCSKDFD 11 (28)
T ss_dssp EEETTTTEEEE
T ss_pred CeeecCCCCcC
Confidence 46888999884
No 83
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=83.30 E-value=0.36 Score=20.03 Aligned_cols=12 Identities=33% Similarity=0.935 Sum_probs=9.3
Q ss_pred cccccchhhccC
Q psy13994 74 FGCEYCSARFSQ 85 (97)
Q Consensus 74 ~~C~~C~~~f~~ 85 (97)
|+|..||..|-.
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 789999977753
No 84
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=83.21 E-value=0.76 Score=23.39 Aligned_cols=14 Identities=21% Similarity=0.634 Sum_probs=7.9
Q ss_pred CCcccccchhhccC
Q psy13994 72 KKFGCEYCSARFSQ 85 (97)
Q Consensus 72 ~~~~C~~C~~~f~~ 85 (97)
.|..|+.||..|.-
T Consensus 25 ~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 25 DPIVCPKCGTEFPP 38 (108)
T ss_pred CCccCCCCCCccCc
Confidence 45556666665543
No 85
>PF15269 zf-C2H2_7: Zinc-finger
Probab=83.19 E-value=0.84 Score=19.27 Aligned_cols=21 Identities=24% Similarity=0.376 Sum_probs=17.5
Q ss_pred cccccchhhccChHHHHHHhh
Q psy13994 74 FGCEYCSARFSQKISCRVHML 94 (97)
Q Consensus 74 ~~C~~C~~~f~~~~~l~~H~~ 94 (97)
|+|-+|..+....+.|.+|++
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 678888888888888988876
No 86
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=83.11 E-value=2.9 Score=25.99 Aligned_cols=27 Identities=22% Similarity=0.353 Sum_probs=18.9
Q ss_pred HhccCCCCcccccch-hhccChHHHHHH
Q psy13994 66 QSHEGVKKFGCEYCS-ARFSQKISCRVH 92 (97)
Q Consensus 66 ~~h~~~~~~~C~~C~-~~f~~~~~l~~H 92 (97)
+.|.-++-|.|.+|| +++.-...+.+|
T Consensus 367 klhgLd~ef~CEICgNyvy~GR~~FdrH 394 (470)
T COG5188 367 KLHGLDIEFECEICGNYVYYGRDRFDRH 394 (470)
T ss_pred HhcCCCcceeeeecccccccchHHHHhh
Confidence 446667789999998 666555555555
No 87
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=82.82 E-value=1 Score=22.76 Aligned_cols=23 Identities=22% Similarity=0.415 Sum_probs=21.1
Q ss_pred ccc----ccchhhccChHHHHHHhhhc
Q psy13994 74 FGC----EYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 74 ~~C----~~C~~~f~~~~~l~~H~~~h 96 (97)
|.| ..|+....+...++.|.+.+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~ 107 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKE 107 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHh
Confidence 889 99999999999999998874
No 88
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=82.67 E-value=0.74 Score=24.32 Aligned_cols=23 Identities=22% Similarity=0.456 Sum_probs=14.6
Q ss_pred CCCcccccchhhccChHHHHHHhhhc
Q psy13994 71 VKKFGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
+.-..|-+||+.|... .+|++.|
T Consensus 70 ~d~i~clecGk~~k~L---krHL~~~ 92 (132)
T PF05443_consen 70 PDYIICLECGKKFKTL---KRHLRTH 92 (132)
T ss_dssp SS-EE-TBT--EESBH---HHHHHHT
T ss_pred cCeeEEccCCcccchH---HHHHHHc
Confidence 3446799999998875 7888876
No 89
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=82.57 E-value=0.4 Score=20.75 Aligned_cols=16 Identities=31% Similarity=0.613 Sum_probs=12.8
Q ss_pred CCCcccccchhhccCh
Q psy13994 71 VKKFGCEYCSARFSQK 86 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~ 86 (97)
++++.|..||..|.-.
T Consensus 2 Dk~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFT 17 (49)
T ss_pred CeeEEcccCCCeEEEe
Confidence 5778999999988743
No 90
>KOG0978|consensus
Probab=82.47 E-value=0.62 Score=31.25 Aligned_cols=53 Identities=19% Similarity=0.464 Sum_probs=31.7
Q ss_pred ccccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCcccccchhhccChHHHH
Q psy13994 24 KFGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCR 90 (97)
Q Consensus 24 ~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~~~~l~ 90 (97)
...|+.|...+.... ...|+-.|.....-... +-+.-+||.|+.+|...--+.
T Consensus 643 ~LkCs~Cn~R~Kd~v---------I~kC~H~FC~~Cvq~r~-----etRqRKCP~Cn~aFganDv~~ 695 (698)
T KOG0978|consen 643 LLKCSVCNTRWKDAV---------ITKCGHVFCEECVQTRY-----ETRQRKCPKCNAAFGANDVHR 695 (698)
T ss_pred ceeCCCccCchhhHH---------HHhcchHHHHHHHHHHH-----HHhcCCCCCCCCCCCcccccc
Confidence 357899975543222 13688887754332221 123456999999998765443
No 91
>KOG4124|consensus
Probab=81.77 E-value=0.097 Score=31.92 Aligned_cols=68 Identities=21% Similarity=0.391 Sum_probs=41.1
Q ss_pred CCcccccc--ccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCcccccchhhccChHHHHH
Q psy13994 22 VKKFGCEY--CSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQKISCRV 91 (97)
Q Consensus 22 ~~~~~C~~--C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~ 91 (97)
.+|+.|++ |++.......|..|-.. ..|...-.....-.-|...-...|+|+|++|.+.+.....|.-
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~--~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~ 416 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLH--GHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKY 416 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeecccc--CcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCc
Confidence 47788854 88888887777655433 2233221111122234444455789999999998886655543
No 92
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=80.82 E-value=0.96 Score=25.95 Aligned_cols=26 Identities=23% Similarity=0.496 Sum_probs=20.1
Q ss_pred CCCCcccccchhhccChHHHHHHhhh
Q psy13994 70 GVKKFGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 70 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
.+..|.|+.|+|-|.-..=...|+..
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhh
Confidence 45579999999999998888888765
No 93
>KOG2785|consensus
Probab=79.94 E-value=7.1 Score=24.55 Aligned_cols=72 Identities=21% Similarity=0.383 Sum_probs=45.3
Q ss_pred CCccccccccccccChHHHHHHHHHcccc--cCcc-ccChHHHHHHHHhccCCCCcccccch---hhccChHHHHHHhh
Q psy13994 22 VKKFGCEYCSARFSQKISCRVHMLRHRDV--CNKP-YHRKSVLIAHLQSHEGVKKFGCEYCS---ARFSQKISCRVHML 94 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~--c~~~-~~~~~~~~~h~~~h~~~~~~~C~~C~---~~f~~~~~l~~H~~ 94 (97)
..|-.|-.|+..+........||..+++. -... .....-|...+..-.+ .-+.|..|+ +.|......+.|+.
T Consensus 164 ~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~-~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 164 LIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVG-IGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred cCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhc-cCceEEEeccccCcccccHHHHHHHh
Confidence 45678999999999999999999887721 1110 1112223333333332 345677776 77777777777765
No 94
>KOG2482|consensus
Probab=79.82 E-value=3.6 Score=25.52 Aligned_cols=25 Identities=32% Similarity=0.721 Sum_probs=22.1
Q ss_pred ccccccccccccChHHHHHHHHHcc
Q psy13994 24 KFGCEYCSARFSQKISCRVHMLRHR 48 (97)
Q Consensus 24 ~~~C~~C~~~f~~~~~l~~h~~~~~ 48 (97)
.+.|-.|.+.|..+..|.-||+...
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~ 219 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKR 219 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhcc
Confidence 4689999999999999999998754
No 95
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=79.75 E-value=0.59 Score=20.14 Aligned_cols=12 Identities=33% Similarity=0.966 Sum_probs=8.9
Q ss_pred cccccchhhccC
Q psy13994 74 FGCEYCSARFSQ 85 (97)
Q Consensus 74 ~~C~~C~~~f~~ 85 (97)
|+|..||..|-.
T Consensus 6 y~C~~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCTACGHRFEV 17 (52)
T ss_pred EEeCCCCCEeEE
Confidence 678888886653
No 96
>KOG2186|consensus
Probab=78.98 E-value=1.4 Score=25.88 Aligned_cols=28 Identities=25% Similarity=0.597 Sum_probs=13.8
Q ss_pred HHHHhccCCCCcccccchhhccChHHHHHH
Q psy13994 63 AHLQSHEGVKKFGCEYCSARFSQKISCRVH 92 (97)
Q Consensus 63 ~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H 92 (97)
.|+..-++ .-|.|..|+++|-. -.+..|
T Consensus 20 kH~srCrn-~~fSCIDC~k~F~~-~sYknH 47 (276)
T KOG2186|consen 20 KHMSRCRN-AYFSCIDCGKTFER-VSYKNH 47 (276)
T ss_pred HHHHhccC-CeeEEeeccccccc-chhhhh
Confidence 34433333 34566666666665 233444
No 97
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=78.37 E-value=0.99 Score=23.73 Aligned_cols=16 Identities=25% Similarity=0.904 Sum_probs=13.4
Q ss_pred CCCCcccccchhhccC
Q psy13994 70 GVKKFGCEYCSARFSQ 85 (97)
Q Consensus 70 ~~~~~~C~~C~~~f~~ 85 (97)
+...|+|+.|+++|..
T Consensus 50 ~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 50 GHQRYKCKSCGSTFTV 65 (129)
T ss_pred cccccccCCcCcceee
Confidence 3568999999999975
No 98
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=77.15 E-value=2.3 Score=17.57 Aligned_cols=24 Identities=21% Similarity=0.380 Sum_probs=16.7
Q ss_pred Ccccccchhhcc--ChHHHHHHhhhc
Q psy13994 73 KFGCEYCSARFS--QKISCRVHMLRH 96 (97)
Q Consensus 73 ~~~C~~C~~~f~--~~~~l~~H~~~h 96 (97)
...|+.||-.|. ....-..|.+-|
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHHHH
Confidence 357999998777 455666676655
No 99
>COG1773 Rubredoxin [Energy production and conversion]
Probab=76.91 E-value=0.84 Score=20.27 Aligned_cols=12 Identities=17% Similarity=0.811 Sum_probs=8.3
Q ss_pred Ccccccchhhcc
Q psy13994 73 KFGCEYCSARFS 84 (97)
Q Consensus 73 ~~~C~~C~~~f~ 84 (97)
.|+|..||..|-
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 577777777664
No 100
>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=76.41 E-value=1.5 Score=23.50 Aligned_cols=21 Identities=14% Similarity=0.227 Sum_probs=16.7
Q ss_pred CcccccchhhccChHHHHHHh
Q psy13994 73 KFGCEYCSARFSQKISCRVHM 93 (97)
Q Consensus 73 ~~~C~~C~~~f~~~~~l~~H~ 93 (97)
=+.|+.|++.|...+...+-.
T Consensus 124 f~~C~~C~kiyW~GsH~~~~~ 144 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGSHWRRME 144 (147)
T ss_pred EEECCCCCCEecccccHHHHH
Confidence 578999999999887765544
No 101
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=75.58 E-value=1.1 Score=18.25 Aligned_cols=13 Identities=31% Similarity=0.769 Sum_probs=10.8
Q ss_pred CcccccchhhccC
Q psy13994 73 KFGCEYCSARFSQ 85 (97)
Q Consensus 73 ~~~C~~C~~~f~~ 85 (97)
|+.|..|++.|-.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 7899999988854
No 102
>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=74.82 E-value=0.75 Score=19.13 Aligned_cols=14 Identities=29% Similarity=0.726 Sum_probs=9.0
Q ss_pred CCcccccchhhccC
Q psy13994 72 KKFGCEYCSARFSQ 85 (97)
Q Consensus 72 ~~~~C~~C~~~f~~ 85 (97)
.|+.|+.|++.|-.
T Consensus 12 ~~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 12 LPFKCKHCGKSFCL 25 (43)
T ss_dssp SHEE-TTTS-EE-T
T ss_pred CCeECCCCCcccCc
Confidence 47899999998864
No 103
>KOG2636|consensus
Probab=74.42 E-value=2.7 Score=26.93 Aligned_cols=28 Identities=18% Similarity=0.411 Sum_probs=22.5
Q ss_pred HhccCCCCcccccch-hhccChHHHHHHh
Q psy13994 66 QSHEGVKKFGCEYCS-ARFSQKISCRVHM 93 (97)
Q Consensus 66 ~~h~~~~~~~C~~C~-~~f~~~~~l~~H~ 93 (97)
+.|.-...|.|.+|| +++.-...+.+|.
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHh
Confidence 457777889999999 7888777887774
No 104
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=73.90 E-value=1.4 Score=19.83 Aligned_cols=11 Identities=18% Similarity=0.591 Sum_probs=9.0
Q ss_pred CCCcccccchh
Q psy13994 71 VKKFGCEYCSA 81 (97)
Q Consensus 71 ~~~~~C~~C~~ 81 (97)
.++|.|+.||-
T Consensus 48 g~~Y~Cp~CGF 58 (61)
T COG2888 48 GNPYRCPKCGF 58 (61)
T ss_pred CCceECCCcCc
Confidence 47999999984
No 105
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=73.03 E-value=1.8 Score=21.61 Aligned_cols=19 Identities=26% Similarity=0.450 Sum_probs=14.5
Q ss_pred hccCCCccccccccccccCh
Q psy13994 18 SHEGVKKFGCEYCSARFSQK 37 (97)
Q Consensus 18 ~h~~~~~~~C~~C~~~f~~~ 37 (97)
.+.+ +|.+|.+||..|...
T Consensus 74 l~~g-~~~rC~eCG~~fkL~ 92 (97)
T cd00924 74 LEKG-KPKRCPECGHVFKLV 92 (97)
T ss_pred EeCC-CceeCCCCCcEEEEE
Confidence 3444 799999999988643
No 106
>PLN02294 cytochrome c oxidase subunit Vb
Probab=72.56 E-value=1.9 Score=23.80 Aligned_cols=16 Identities=31% Similarity=0.706 Sum_probs=13.2
Q ss_pred CCccccccccccccCh
Q psy13994 22 VKKFGCEYCSARFSQK 37 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~ 37 (97)
.+|.+|++||..|..+
T Consensus 139 Gkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 139 GKSFECPVCTQYFELE 154 (174)
T ss_pred CCceeCCCCCCEEEEE
Confidence 4689999999998654
No 107
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=72.25 E-value=0.74 Score=20.10 Aligned_cols=26 Identities=19% Similarity=0.491 Sum_probs=13.1
Q ss_pred CCCcccccchhhccChHHHHHHhhhc
Q psy13994 71 VKKFGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
...|+|+.|+..|--.-..-.|...|
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CCeEECCCCCCccccCcChhhhcccc
Confidence 35789999998887666655555544
No 108
>KOG2071|consensus
Probab=70.86 E-value=3 Score=27.57 Aligned_cols=26 Identities=27% Similarity=0.392 Sum_probs=22.9
Q ss_pred CCCcccccchhhccChHHHHHHhhhc
Q psy13994 71 VKKFGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
+.|-+|..||..|........|+..|
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhh
Confidence 45788999999999999999988877
No 109
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=70.83 E-value=1.5 Score=17.30 Aligned_cols=12 Identities=17% Similarity=0.443 Sum_probs=8.7
Q ss_pred Ccccccchhhcc
Q psy13994 73 KFGCEYCSARFS 84 (97)
Q Consensus 73 ~~~C~~C~~~f~ 84 (97)
.|.|..||..+.
T Consensus 2 ~~~C~~CG~i~~ 13 (34)
T cd00729 2 VWVCPVCGYIHE 13 (34)
T ss_pred eEECCCCCCEeE
Confidence 478888887654
No 110
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=70.56 E-value=1.9 Score=24.68 Aligned_cols=20 Identities=30% Similarity=0.501 Sum_probs=15.6
Q ss_pred CCccccccccccccChHHHH
Q psy13994 22 VKKFGCEYCSARFSQKISCR 41 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~~~l~ 41 (97)
++...|++|+..|..+.-..
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs 22 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRS 22 (214)
T ss_pred CCceECCCCCCeeeeeEEEc
Confidence 45678999999998876543
No 111
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=70.37 E-value=3.4 Score=26.68 Aligned_cols=22 Identities=41% Similarity=0.770 Sum_probs=19.7
Q ss_pred cccccchhhccChHHHHHHhhh
Q psy13994 74 FGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 74 ~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
+.|+.|.+.|.....+..|+..
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~ 79 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQ 79 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHH
Confidence 5799999999999999999863
No 112
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=69.32 E-value=1.9 Score=18.59 Aligned_cols=9 Identities=33% Similarity=1.036 Sum_probs=3.8
Q ss_pred Ccccccchh
Q psy13994 73 KFGCEYCSA 81 (97)
Q Consensus 73 ~~~C~~C~~ 81 (97)
.|+|++|++
T Consensus 41 ~W~CPiC~~ 49 (50)
T PF02891_consen 41 KWKCPICNK 49 (50)
T ss_dssp --B-TTT--
T ss_pred CeECcCCcC
Confidence 499999985
No 113
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=68.47 E-value=3.4 Score=16.48 Aligned_cols=12 Identities=33% Similarity=0.852 Sum_probs=8.3
Q ss_pred CCcccccchhhc
Q psy13994 72 KKFGCEYCSARF 83 (97)
Q Consensus 72 ~~~~C~~C~~~f 83 (97)
...+|+.|+..|
T Consensus 24 ~~v~C~~C~~~f 35 (36)
T PF13717_consen 24 RKVRCSKCGHVF 35 (36)
T ss_pred cEEECCCCCCEe
Confidence 456788887765
No 114
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=68.45 E-value=4.5 Score=17.59 Aligned_cols=14 Identities=14% Similarity=0.534 Sum_probs=7.8
Q ss_pred ccccccccccChHH
Q psy13994 26 GCEYCSARFSQKIS 39 (97)
Q Consensus 26 ~C~~C~~~f~~~~~ 39 (97)
.|++|+..|.....
T Consensus 22 ~CPlC~r~l~~e~~ 35 (54)
T PF04423_consen 22 CCPLCGRPLDEEHR 35 (54)
T ss_dssp E-TTT--EE-HHHH
T ss_pred cCCCCCCCCCHHHH
Confidence 89999999976643
No 115
>KOG2636|consensus
Probab=68.34 E-value=4.7 Score=25.89 Aligned_cols=30 Identities=17% Similarity=0.355 Sum_probs=24.4
Q ss_pred hhccCCCcccccccc-ccccChHHHHHHHHH
Q psy13994 17 QSHEGVKKFGCEYCS-ARFSQKISCRVHMLR 46 (97)
Q Consensus 17 ~~h~~~~~~~C~~C~-~~f~~~~~l~~h~~~ 46 (97)
+.|.-...|.|.+|| .++.....+..|..-
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~E 424 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFNE 424 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhHH
Confidence 446567789999999 888999999988754
No 116
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=68.22 E-value=2.3 Score=19.16 Aligned_cols=11 Identities=18% Similarity=0.658 Sum_probs=9.0
Q ss_pred CCCcccccchh
Q psy13994 71 VKKFGCEYCSA 81 (97)
Q Consensus 71 ~~~~~C~~C~~ 81 (97)
.++|.|+.||.
T Consensus 46 ~~~Y~CP~CGF 56 (59)
T PRK14890 46 SNPYTCPKCGF 56 (59)
T ss_pred CCceECCCCCC
Confidence 36899999984
No 117
>KOG0717|consensus
Probab=68.06 E-value=3.6 Score=26.56 Aligned_cols=23 Identities=17% Similarity=0.368 Sum_probs=20.7
Q ss_pred cccccccccccChHHHHHHHHHc
Q psy13994 25 FGCEYCSARFSQKISCRVHMLRH 47 (97)
Q Consensus 25 ~~C~~C~~~f~~~~~l~~h~~~~ 47 (97)
+.|.+|.++|.+...+..|..+-
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSK 315 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSK 315 (508)
T ss_pred eEEeeccccccchHHHHhhHHHH
Confidence 88999999999999999998754
No 118
>KOG1813|consensus
Probab=67.75 E-value=4.4 Score=24.56 Aligned_cols=59 Identities=19% Similarity=0.328 Sum_probs=37.0
Q ss_pred CCCccccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCcccccchh----hccChHHHHHHhh
Q psy13994 21 GVKKFGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSA----RFSQKISCRVHML 94 (97)
Q Consensus 21 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~----~f~~~~~l~~H~~ 94 (97)
+..||.|.+|.+.|..+.. ..|+-.|....++..+++ .-.|.+|++ .|.....|..-+.
T Consensus 238 ~~~Pf~c~icr~~f~~pVv---------t~c~h~fc~~ca~~~~qk------~~~c~vC~~~t~g~~~~akeL~~~L~ 300 (313)
T KOG1813|consen 238 ELLPFKCFICRKYFYRPVV---------TKCGHYFCEVCALKPYQK------GEKCYVCSQQTHGSFNVAKELLVSLK 300 (313)
T ss_pred ccCCccccccccccccchh---------hcCCceeehhhhcccccc------CCcceecccccccccchHHHHHHHHH
Confidence 4578999999999866542 267777777666654422 223666654 4555666655544
No 119
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=67.68 E-value=3.9 Score=21.55 Aligned_cols=10 Identities=20% Similarity=0.421 Sum_probs=6.5
Q ss_pred cccccccccc
Q psy13994 25 FGCEYCSARF 34 (97)
Q Consensus 25 ~~C~~C~~~f 34 (97)
..|+.||..|
T Consensus 10 r~Cp~cg~kF 19 (129)
T TIGR02300 10 RICPNTGSKF 19 (129)
T ss_pred ccCCCcCccc
Confidence 4567776666
No 120
>KOG2593|consensus
Probab=67.29 E-value=5.3 Score=25.51 Aligned_cols=21 Identities=14% Similarity=0.464 Sum_probs=14.8
Q ss_pred cCCCCcccccchhhccChHHH
Q psy13994 69 EGVKKFGCEYCSARFSQKISC 89 (97)
Q Consensus 69 ~~~~~~~C~~C~~~f~~~~~l 89 (97)
....-|.|+.|.+.|...-.+
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~ 144 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEAL 144 (436)
T ss_pred cccccccCCccccchhhhHHH
Confidence 344568888888888766554
No 121
>PTZ00448 hypothetical protein; Provisional
Probab=66.34 E-value=4.9 Score=25.15 Aligned_cols=23 Identities=13% Similarity=0.339 Sum_probs=20.4
Q ss_pred CcccccchhhccChHHHHHHhhh
Q psy13994 73 KFGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 73 ~~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
.|.|..|+..|......+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 68899999999988888999875
No 122
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=66.18 E-value=3.3 Score=22.03 Aligned_cols=20 Identities=25% Similarity=0.398 Sum_probs=15.8
Q ss_pred cccccchhhccChHHHHHHhhhc
Q psy13994 74 FGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 74 ~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
..|-++||.|. .|++|+.+|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~ 96 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTH 96 (148)
T ss_pred EEEeccCcchH---HHHHHHhcc
Confidence 46888998885 578888876
No 123
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=65.86 E-value=2.2 Score=18.52 Aligned_cols=11 Identities=18% Similarity=0.860 Sum_probs=7.8
Q ss_pred cccccchhhcc
Q psy13994 74 FGCEYCSARFS 84 (97)
Q Consensus 74 ~~C~~C~~~f~ 84 (97)
|+|..||..|.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 67777777665
No 124
>KOG1842|consensus
Probab=65.05 E-value=4.3 Score=26.06 Aligned_cols=23 Identities=17% Similarity=0.273 Sum_probs=20.6
Q ss_pred CcccccchhhccChHHHHHHhhh
Q psy13994 73 KFGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 73 ~~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
-|.||+|.+.|.....|..|...
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~ 37 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDV 37 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhh
Confidence 58899999999999999999754
No 125
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=64.38 E-value=2.4 Score=16.87 Aligned_cols=13 Identities=23% Similarity=0.690 Sum_probs=6.9
Q ss_pred ccccchhhccChH
Q psy13994 75 GCEYCSARFSQKI 87 (97)
Q Consensus 75 ~C~~C~~~f~~~~ 87 (97)
.|..|++.|..+.
T Consensus 5 ~C~eC~~~f~dSy 17 (34)
T PF01286_consen 5 KCDECGKPFMDSY 17 (34)
T ss_dssp E-TTT--EES-SS
T ss_pred hHhHhCCHHHHHH
Confidence 5889999988653
No 126
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=64.09 E-value=2.6 Score=17.61 Aligned_cols=12 Identities=25% Similarity=0.675 Sum_probs=9.7
Q ss_pred ccccchhhccCh
Q psy13994 75 GCEYCSARFSQK 86 (97)
Q Consensus 75 ~C~~C~~~f~~~ 86 (97)
.|+.|++.|+..
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 399999999754
No 127
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=63.68 E-value=2.5 Score=17.72 Aligned_cols=12 Identities=17% Similarity=0.747 Sum_probs=6.9
Q ss_pred Ccccccchhhcc
Q psy13994 73 KFGCEYCSARFS 84 (97)
Q Consensus 73 ~~~C~~C~~~f~ 84 (97)
.|.|+.||..|.
T Consensus 3 ~y~C~~CG~~~~ 14 (46)
T PRK00398 3 EYKCARCGREVE 14 (46)
T ss_pred EEECCCCCCEEE
Confidence 456666665543
No 128
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=63.66 E-value=2.1 Score=18.34 Aligned_cols=11 Identities=18% Similarity=0.827 Sum_probs=7.5
Q ss_pred cccccchhhcc
Q psy13994 74 FGCEYCSARFS 84 (97)
Q Consensus 74 ~~C~~C~~~f~ 84 (97)
|+|..|+..|-
T Consensus 2 y~C~~CgyvYd 12 (47)
T PF00301_consen 2 YQCPVCGYVYD 12 (47)
T ss_dssp EEETTTSBEEE
T ss_pred cCCCCCCEEEc
Confidence 66777776654
No 129
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=63.46 E-value=6.9 Score=25.38 Aligned_cols=25 Identities=36% Similarity=0.647 Sum_probs=22.1
Q ss_pred ccccccccccccChHHHHHHHHHcc
Q psy13994 24 KFGCEYCSARFSQKISCRVHMLRHR 48 (97)
Q Consensus 24 ~~~C~~C~~~f~~~~~l~~h~~~~~ 48 (97)
-+.|+.|++.|.....+..|+...+
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH 81 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEH 81 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhh
Confidence 4789999999999999999998665
No 130
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=63.44 E-value=2.2 Score=23.18 Aligned_cols=14 Identities=29% Similarity=0.634 Sum_probs=11.8
Q ss_pred CcccccchhhccCh
Q psy13994 73 KFGCEYCSARFSQK 86 (97)
Q Consensus 73 ~~~C~~C~~~f~~~ 86 (97)
.++|+.||++|...
T Consensus 28 ~~~c~~c~~~f~~~ 41 (154)
T PRK00464 28 RRECLACGKRFTTF 41 (154)
T ss_pred eeeccccCCcceEe
Confidence 48899999999864
No 131
>PF12907 zf-met2: Zinc-binding
Probab=63.08 E-value=6.8 Score=16.19 Aligned_cols=21 Identities=19% Similarity=0.418 Sum_probs=15.9
Q ss_pred cccccchhhcc---ChHHHHHHhh
Q psy13994 74 FGCEYCSARFS---QKISCRVHML 94 (97)
Q Consensus 74 ~~C~~C~~~f~---~~~~l~~H~~ 94 (97)
+.|.+|.-+|. ....|.+|-.
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~e 25 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAE 25 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHH
Confidence 57999997666 4567888865
No 132
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=60.60 E-value=7.7 Score=23.48 Aligned_cols=25 Identities=32% Similarity=0.568 Sum_probs=22.2
Q ss_pred CCCcccccchhhccChHHHHHHhhh
Q psy13994 71 VKKFGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
+..|.|+.|-+-|.....|.+|+..
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHh
Confidence 5679999999999999999999864
No 133
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=60.41 E-value=3.9 Score=21.63 Aligned_cols=27 Identities=19% Similarity=0.415 Sum_probs=18.1
Q ss_pred ccccccccccccChHHHHHHHHHcccccCc
Q psy13994 24 KFGCEYCSARFSQKISCRVHMLRHRDVCNK 53 (97)
Q Consensus 24 ~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~ 53 (97)
|+.|..||+.|..-+. .+...-+.||-
T Consensus 1 PH~Ct~Cg~~f~dgs~---eil~GCP~CGg 27 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSK---EILSGCPECGG 27 (131)
T ss_pred CcccCcCCCCcCCCcH---HHHccCcccCC
Confidence 6789999999976552 14445566663
No 134
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=59.23 E-value=3.6 Score=16.14 Aligned_cols=12 Identities=25% Similarity=0.689 Sum_probs=8.5
Q ss_pred Ccccccchhhcc
Q psy13994 73 KFGCEYCSARFS 84 (97)
Q Consensus 73 ~~~C~~C~~~f~ 84 (97)
-+.|..|+.+|.
T Consensus 21 ~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 21 YEVCIFCGSSFP 32 (33)
T ss_pred eEEcccCCcEee
Confidence 356888887764
No 135
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=59.20 E-value=4 Score=20.16 Aligned_cols=14 Identities=21% Similarity=0.645 Sum_probs=11.7
Q ss_pred CCcccccchhhccC
Q psy13994 72 KKFGCEYCSARFSQ 85 (97)
Q Consensus 72 ~~~~C~~C~~~f~~ 85 (97)
+|-+|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 57789999998876
No 136
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=59.06 E-value=10 Score=14.91 Aligned_cols=21 Identities=14% Similarity=0.298 Sum_probs=12.4
Q ss_pred ccccccccccccChHHHHHHHH
Q psy13994 24 KFGCEYCSARFSQKISCRVHML 45 (97)
Q Consensus 24 ~~~C~~C~~~f~~~~~l~~h~~ 45 (97)
.+.|+.|++...... +..|+.
T Consensus 4 ~~~C~nC~R~v~a~R-fA~HLe 24 (33)
T PF08209_consen 4 YVECPNCGRPVAASR-FAPHLE 24 (33)
T ss_dssp EEE-TTTSSEEEGGG-HHHHHH
T ss_pred eEECCCCcCCcchhh-hHHHHH
Confidence 467888888765543 455543
No 137
>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=58.04 E-value=12 Score=15.18 Aligned_cols=22 Identities=18% Similarity=0.564 Sum_probs=9.4
Q ss_pred CcccccchhhccC-h-HHHHHHhh
Q psy13994 73 KFGCEYCSARFSQ-K-ISCRVHML 94 (97)
Q Consensus 73 ~~~C~~C~~~f~~-~-~~l~~H~~ 94 (97)
.|=|..|+.-|.. . +....|..
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~ 26 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHER 26 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT-
T ss_pred CeecccccceecCCChHHHHHhhc
Confidence 4679999998843 3 44466643
No 138
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=58.03 E-value=5.4 Score=23.25 Aligned_cols=18 Identities=17% Similarity=0.222 Sum_probs=14.4
Q ss_pred CCCccccccccccccChH
Q psy13994 21 GVKKFGCEYCSARFSQKI 38 (97)
Q Consensus 21 ~~~~~~C~~C~~~f~~~~ 38 (97)
..++.+|.+||..|....
T Consensus 178 EGkpqRCpECGqVFKLVr 195 (268)
T PTZ00043 178 EGFLYRCGECDQIFMLVR 195 (268)
T ss_pred CCCCccCCCCCcEEEEEE
Confidence 456899999999997644
No 139
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=57.91 E-value=7.6 Score=19.78 Aligned_cols=24 Identities=17% Similarity=0.202 Sum_probs=19.9
Q ss_pred CCcccccchhhccChHHHHHHhhh
Q psy13994 72 KKFGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 72 ~~~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
..+-|..|.+-|.+...|..|.+-
T Consensus 54 GqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 54 GQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred ceeeeehhHHHHHHHHHHHHHhcc
Confidence 346688999999999999999763
No 140
>KOG2807|consensus
Probab=57.61 E-value=15 Score=22.84 Aligned_cols=72 Identities=17% Similarity=0.224 Sum_probs=38.4
Q ss_pred CccccccccccccChHHHHHHHHHcccccCccccChHHHH--------HHHHhccCCCCcccccchhhccChHHHHHHhh
Q psy13994 23 KKFGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLI--------AHLQSHEGVKKFGCEYCSARFSQKISCRVHML 94 (97)
Q Consensus 23 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~--------~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 94 (97)
-|.+|++|+-+......|.+-.+.--+. +.|....... .-...-.+...|+|..|...|--.-+...|..
T Consensus 289 LP~eCpiC~ltLVss~hLARSyhhL~PL--~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLARSYHHLFPL--KPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred CCccCCccceeEecchHHHHHHHhhcCC--cchhhccccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHHhh
Confidence 4678888888887777776543321111 1111110000 00011123346899999888887666666655
Q ss_pred hc
Q psy13994 95 RH 96 (97)
Q Consensus 95 ~h 96 (97)
.|
T Consensus 367 Lh 368 (378)
T KOG2807|consen 367 LH 368 (378)
T ss_pred hh
Confidence 44
No 141
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=55.98 E-value=15 Score=19.75 Aligned_cols=19 Identities=11% Similarity=0.420 Sum_probs=13.3
Q ss_pred cCCCccccccccccccChH
Q psy13994 20 EGVKKFGCEYCSARFSQKI 38 (97)
Q Consensus 20 ~~~~~~~C~~C~~~f~~~~ 38 (97)
.+...|.|+.|+..|....
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~e 113 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLE 113 (147)
T ss_pred cCCcEEECcCCCCEeeHHH
Confidence 3455689999988876433
No 142
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=55.82 E-value=3.8 Score=17.98 Aligned_cols=27 Identities=26% Similarity=0.525 Sum_probs=13.9
Q ss_pred HHHHHHHHhccCCCCccccc----chhhccC
Q psy13994 59 SVLIAHLQSHEGVKKFGCEY----CSARFSQ 85 (97)
Q Consensus 59 ~~~~~h~~~h~~~~~~~C~~----C~~~f~~ 85 (97)
..|..|....-..++..|+. |+..+..
T Consensus 24 ~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 24 KELDDHLENECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp CCHHHHHHTTSTTSEEE-SS----S--EEEH
T ss_pred HHHHHHHHccCCCCcEECCCCCCCCCCccch
Confidence 35566666544455667777 7665543
No 143
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=55.39 E-value=37 Score=21.47 Aligned_cols=22 Identities=23% Similarity=0.439 Sum_probs=12.6
Q ss_pred cccccccccChHHHHHHHHHcc
Q psy13994 27 CEYCSARFSQKISCRVHMLRHR 48 (97)
Q Consensus 27 C~~C~~~f~~~~~l~~h~~~~~ 48 (97)
|..|...|-....|..|++..+
T Consensus 223 C~FC~~~FYdDDEL~~HcR~~H 244 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCRLRH 244 (493)
T ss_pred hhhccceecChHHHHHHHHhhh
Confidence 5555555555556666655544
No 144
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=55.17 E-value=3.5 Score=17.00 Aligned_cols=12 Identities=33% Similarity=1.005 Sum_probs=9.5
Q ss_pred CCcccccchhhc
Q psy13994 72 KKFGCEYCSARF 83 (97)
Q Consensus 72 ~~~~C~~C~~~f 83 (97)
++-.|+.|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 456799999877
No 145
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=54.88 E-value=9.4 Score=24.68 Aligned_cols=25 Identities=28% Similarity=0.518 Sum_probs=22.4
Q ss_pred CCCcccccchhhccChHHHHHHhhh
Q psy13994 71 VKKFGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
+..|.|+.|-+-|.....|..|+..
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~~ 220 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMKK 220 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHhc
Confidence 4679999999999999999999864
No 146
>PF14353 CpXC: CpXC protein
Probab=54.77 E-value=4.5 Score=21.00 Aligned_cols=16 Identities=25% Similarity=0.704 Sum_probs=12.1
Q ss_pred CCCcccccchhhccCh
Q psy13994 71 VKKFGCEYCSARFSQK 86 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~ 86 (97)
-..+.|+.||..|.-.
T Consensus 36 l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 36 LFSFTCPSCGHKFRLE 51 (128)
T ss_pred cCEEECCCCCCceecC
Confidence 3468899999987643
No 147
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=54.73 E-value=6.3 Score=19.93 Aligned_cols=27 Identities=19% Similarity=0.388 Sum_probs=17.4
Q ss_pred CccccccccccccChHHHHHHHHHcccccC
Q psy13994 23 KKFGCEYCSARFSQKISCRVHMLRHRDVCN 52 (97)
Q Consensus 23 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~c~ 52 (97)
.|+.|..||..|..-+.. +...-+.||
T Consensus 1 MpH~CtrCG~vf~~g~~~---il~GCp~CG 27 (112)
T COG3364 1 MPHQCTRCGEVFDDGSEE---ILSGCPKCG 27 (112)
T ss_pred CCceecccccccccccHH---HHccCcccc
Confidence 378899999999875332 233445555
No 148
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=54.58 E-value=3 Score=17.20 Aligned_cols=28 Identities=21% Similarity=0.496 Sum_probs=10.5
Q ss_pred ccCccccChHHHHHHHHhccCCCCcccccc
Q psy13994 50 VCNKPYHRKSVLIAHLQSHEGVKKFGCEYC 79 (97)
Q Consensus 50 ~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C 79 (97)
.||-.|-..- +........ ...+.|++|
T Consensus 15 ~CGH~FC~~C-l~~~~~~~~-~~~~~CP~C 42 (42)
T PF15227_consen 15 PCGHSFCRSC-LERLWKEPS-GSGFSCPEC 42 (42)
T ss_dssp SSSSEEEHHH-HHHHHCCSS-SST---SSS
T ss_pred CCcCHHHHHH-HHHHHHccC-CcCCCCcCC
Confidence 4666665433 222222222 223677765
No 149
>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=54.17 E-value=4.7 Score=19.88 Aligned_cols=11 Identities=27% Similarity=1.035 Sum_probs=7.3
Q ss_pred CCcccccchhh
Q psy13994 72 KKFGCEYCSAR 82 (97)
Q Consensus 72 ~~~~C~~C~~~ 82 (97)
..|.|++|++.
T Consensus 34 ~ky~Cp~Cgk~ 44 (90)
T PF01780_consen 34 AKYTCPFCGKT 44 (90)
T ss_dssp S-BEESSSSSS
T ss_pred CCCcCCCCCCc
Confidence 36888888764
No 150
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=54.04 E-value=4.7 Score=21.54 Aligned_cols=19 Identities=37% Similarity=0.656 Sum_probs=14.3
Q ss_pred hccCCCccccccccccccCh
Q psy13994 18 SHEGVKKFGCEYCSARFSQK 37 (97)
Q Consensus 18 ~h~~~~~~~C~~C~~~f~~~ 37 (97)
.+.+ +|.+|+.||..|...
T Consensus 107 l~~g-~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 107 LHKG-KPQRCPECGQVFKLK 125 (136)
T ss_dssp EETT-SEEEETTTEEEEEEE
T ss_pred EeCC-CccCCCCCCeEEEEE
Confidence 3444 589999999998654
No 151
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=53.98 E-value=11 Score=20.91 Aligned_cols=21 Identities=14% Similarity=0.328 Sum_probs=16.0
Q ss_pred CCcccccchhhccChHHHHHH
Q psy13994 72 KKFGCEYCSARFSQKISCRVH 92 (97)
Q Consensus 72 ~~~~C~~C~~~f~~~~~l~~H 92 (97)
.-|.|+.||+.|...+....-
T Consensus 129 ~f~~C~~CgkiYW~GsHw~~m 149 (165)
T COG1656 129 EFYRCPKCGKIYWKGSHWRRM 149 (165)
T ss_pred ceeECCCCcccccCchHHHHH
Confidence 346799999999987776443
No 152
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=53.82 E-value=18 Score=19.80 Aligned_cols=23 Identities=17% Similarity=0.166 Sum_probs=15.8
Q ss_pred hccCCCccccccccccccChHHH
Q psy13994 18 SHEGVKKFGCEYCSARFSQKISC 40 (97)
Q Consensus 18 ~h~~~~~~~C~~C~~~f~~~~~l 40 (97)
...+..-|.|+.|+..|+....+
T Consensus 103 ~e~~~~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 103 FETNNMFFICPNMCVRFTFNEAM 125 (158)
T ss_pred hccCCCeEECCCCCcEeeHHHHH
Confidence 34455678899898887666554
No 153
>KOG2747|consensus
Probab=53.81 E-value=8.8 Score=24.35 Aligned_cols=26 Identities=23% Similarity=0.494 Sum_probs=23.0
Q ss_pred CCCcccccchhhccChHHHHHHhhhc
Q psy13994 71 VKKFGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
...|.|++|-+-+.....|++|+...
T Consensus 156 ~~lYiCEfCLkY~~s~~~l~rH~~kC 181 (396)
T KOG2747|consen 156 DKLYICEFCLKYMKSRTSLQRHLKKC 181 (396)
T ss_pred CeEEEehHHHhHhchHHHHHHHHHhc
Confidence 56799999999999999999998753
No 154
>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=53.54 E-value=4.8 Score=15.95 Aligned_cols=14 Identities=21% Similarity=0.510 Sum_probs=9.6
Q ss_pred cccccchhhccChH
Q psy13994 74 FGCEYCSARFSQKI 87 (97)
Q Consensus 74 ~~C~~C~~~f~~~~ 87 (97)
+.|+.|+..|.-..
T Consensus 3 ~~CP~C~~~~~v~~ 16 (38)
T TIGR02098 3 IQCPNCKTSFRVVD 16 (38)
T ss_pred EECCCCCCEEEeCH
Confidence 56888888776443
No 155
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=53.09 E-value=7.6 Score=17.28 Aligned_cols=16 Identities=19% Similarity=0.403 Sum_probs=12.0
Q ss_pred cCCCCcccccchhhcc
Q psy13994 69 EGVKKFGCEYCSARFS 84 (97)
Q Consensus 69 ~~~~~~~C~~C~~~f~ 84 (97)
.+...|.|+.||..+-
T Consensus 10 ~~~v~~~Cp~cGipth 25 (55)
T PF13824_consen 10 PAHVNFECPDCGIPTH 25 (55)
T ss_pred ccccCCcCCCCCCcCc
Confidence 4456899999997554
No 156
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=52.69 E-value=1.7 Score=29.61 Aligned_cols=46 Identities=15% Similarity=0.217 Sum_probs=24.6
Q ss_pred cccccccccccChH---HHHHHHHHcccccCccccChHHHHHHHHhccCCCCcccccchhh
Q psy13994 25 FGCEYCSARFSQKI---SCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSAR 82 (97)
Q Consensus 25 ~~C~~C~~~f~~~~---~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~ 82 (97)
..|..||..+..+. .|.-|+..+. |.-|.--+....|..|+.||..
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~------------L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLTLHKATGQ------------LRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred eecccCCCcccCCCCCcceEEecCCCe------------eEeCCCCCCCCCCCCCCCCCCC
Confidence 45888887775553 2222222211 1222222344578889999865
No 157
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=52.63 E-value=5.2 Score=16.11 Aligned_cols=12 Identities=25% Similarity=0.670 Sum_probs=6.5
Q ss_pred CCcccccchhhc
Q psy13994 72 KKFGCEYCSARF 83 (97)
Q Consensus 72 ~~~~C~~C~~~f 83 (97)
.-|+|..||...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 358999998653
No 158
>PTZ00064 histone acetyltransferase; Provisional
Probab=52.61 E-value=11 Score=24.77 Aligned_cols=26 Identities=27% Similarity=0.295 Sum_probs=22.7
Q ss_pred CCCCcccccchhhccChHHHHHHhhh
Q psy13994 70 GVKKFGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 70 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
-+..|.|+.|-+-|.....|.+|+..
T Consensus 277 ~d~LYICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 277 VDTLHFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred CCeEEEccchhhhhCCHHHHHHHHhc
Confidence 35679999999999999999999864
No 159
>PLN03239 histone acetyltransferase; Provisional
Probab=51.92 E-value=11 Score=23.52 Aligned_cols=24 Identities=17% Similarity=0.184 Sum_probs=21.4
Q ss_pred CCCcccccchhhccChHHHHHHhh
Q psy13994 71 VKKFGCEYCSARFSQKISCRVHML 94 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~~~l~~H~~ 94 (97)
+..|.|+.|-+-|.....|.+|+.
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHH
Confidence 468999999999999999999975
No 160
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=51.11 E-value=5.5 Score=16.75 Aligned_cols=13 Identities=15% Similarity=0.345 Sum_probs=8.9
Q ss_pred CcccccchhhccC
Q psy13994 73 KFGCEYCSARFSQ 85 (97)
Q Consensus 73 ~~~C~~C~~~f~~ 85 (97)
.|.|..||..|.-
T Consensus 2 ~Y~C~~Cg~~~~~ 14 (44)
T smart00659 2 IYICGECGRENEI 14 (44)
T ss_pred EEECCCCCCEeec
Confidence 3778888876653
No 161
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=50.93 E-value=6.6 Score=19.40 Aligned_cols=11 Identities=27% Similarity=0.936 Sum_probs=8.1
Q ss_pred CCcccccchhh
Q psy13994 72 KKFGCEYCSAR 82 (97)
Q Consensus 72 ~~~~C~~C~~~ 82 (97)
..|.|++|++.
T Consensus 35 a~y~CpfCgk~ 45 (90)
T PTZ00255 35 AKYFCPFCGKH 45 (90)
T ss_pred CCccCCCCCCC
Confidence 36889998753
No 162
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=49.80 E-value=4.9 Score=16.10 Aligned_cols=11 Identities=18% Similarity=0.455 Sum_probs=7.2
Q ss_pred cccccchhhcc
Q psy13994 74 FGCEYCSARFS 84 (97)
Q Consensus 74 ~~C~~C~~~f~ 84 (97)
+.|+.||..|-
T Consensus 2 r~C~~Cg~~Yh 12 (36)
T PF05191_consen 2 RICPKCGRIYH 12 (36)
T ss_dssp EEETTTTEEEE
T ss_pred cCcCCCCCccc
Confidence 34777777664
No 163
>PLN02748 tRNA dimethylallyltransferase
Probab=49.44 E-value=13 Score=24.18 Aligned_cols=24 Identities=17% Similarity=0.337 Sum_probs=19.4
Q ss_pred Cccccccccc-cccChHHHHHHHHH
Q psy13994 23 KKFGCEYCSA-RFSQKISCRVHMLR 46 (97)
Q Consensus 23 ~~~~C~~C~~-~f~~~~~l~~h~~~ 46 (97)
+.|.|.+|+. ++.....+..|+..
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 4578999997 78888888888763
No 164
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=49.40 E-value=1.1 Score=30.24 Aligned_cols=50 Identities=20% Similarity=0.450 Sum_probs=25.6
Q ss_pred ccccccccccChHHHHHHHHHcc-------cccCccccChHHHHHHHHhccCCCCcccccchh
Q psy13994 26 GCEYCSARFSQKISCRVHMLRHR-------DVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSA 81 (97)
Q Consensus 26 ~C~~C~~~f~~~~~l~~h~~~~~-------~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~ 81 (97)
.|..||.+|+--..|.--+...+ +.|.+.+..+.+ ++.|. .|..|+.||-
T Consensus 125 ~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~n----RRfHA--Qp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLN----RRFHA--QPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccc----ccccc--ccccCcccCC
Confidence 47788888876655433222111 234444433322 22333 4677888875
No 165
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=48.65 E-value=7.8 Score=19.19 Aligned_cols=10 Identities=30% Similarity=1.175 Sum_probs=7.1
Q ss_pred Ccccccchhh
Q psy13994 73 KFGCEYCSAR 82 (97)
Q Consensus 73 ~~~C~~C~~~ 82 (97)
.|.|++|++.
T Consensus 35 ~y~CpfCgk~ 44 (91)
T TIGR00280 35 KYVCPFCGKK 44 (91)
T ss_pred CccCCCCCCC
Confidence 6778888653
No 166
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=48.60 E-value=6.8 Score=14.96 Aligned_cols=13 Identities=38% Similarity=1.032 Sum_probs=6.4
Q ss_pred CCcccccchhhcc
Q psy13994 72 KKFGCEYCSARFS 84 (97)
Q Consensus 72 ~~~~C~~C~~~f~ 84 (97)
..|.|+.|+..+-
T Consensus 12 ~kY~Cp~C~~~~C 24 (30)
T PF04438_consen 12 AKYRCPRCGARYC 24 (30)
T ss_dssp ESEE-TTT--EES
T ss_pred CEEECCCcCCcee
Confidence 3577888776553
No 167
>PHA02926 zinc finger-like protein; Provisional
Probab=48.53 E-value=17 Score=21.36 Aligned_cols=73 Identities=19% Similarity=0.202 Sum_probs=35.8
Q ss_pred HHHHhhccCCCccccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCcccccchhhccC
Q psy13994 13 IAHLQSHEGVKKFGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQ 85 (97)
Q Consensus 13 ~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~ 85 (97)
..........+.-.|.+|-.....+..-........+.|+-.|.....-............-.||.|...|..
T Consensus 159 ~~ye~~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 159 DKYEDVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN 231 (242)
T ss_pred HHHHHHHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence 3333334444557799986554322110000111225788888755443333221222234569999877653
No 168
>PF04641 Rtf2: Rtf2 RING-finger
Probab=48.08 E-value=6.5 Score=23.26 Aligned_cols=52 Identities=19% Similarity=0.351 Sum_probs=31.7
Q ss_pred CCccccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCcccccchhhccC
Q psy13994 22 VKKFGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQ 85 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~ 85 (97)
..+|.|++.+..|.....+ .....||-.|.....-.. . +...|++|++.|..
T Consensus 111 ~~~~~CPvt~~~~~~~~~f-----v~l~~cG~V~s~~alke~--k-----~~~~Cp~c~~~f~~ 162 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKF-----VYLRPCGCVFSEKALKEL--K-----KSKKCPVCGKPFTE 162 (260)
T ss_pred CceeECCCCCcccCCceeE-----EEEcCCCCEeeHHHHHhh--c-----ccccccccCCcccc
Confidence 4568999988887433211 112468888775433221 1 23459999999874
No 169
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=47.82 E-value=9.2 Score=15.26 Aligned_cols=14 Identities=29% Similarity=0.631 Sum_probs=9.9
Q ss_pred CCCcccccchhhcc
Q psy13994 71 VKKFGCEYCSARFS 84 (97)
Q Consensus 71 ~~~~~C~~C~~~f~ 84 (97)
....+|+.|+-.|.
T Consensus 23 ~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 23 GRKVRCPKCGHVFR 36 (37)
T ss_pred CcEEECCCCCcEee
Confidence 34677888887764
No 170
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.59 E-value=9.6 Score=19.58 Aligned_cols=14 Identities=7% Similarity=0.188 Sum_probs=11.5
Q ss_pred CCCcccccchhhcc
Q psy13994 71 VKKFGCEYCSARFS 84 (97)
Q Consensus 71 ~~~~~C~~C~~~f~ 84 (97)
..|..|+.||++|.
T Consensus 24 rdPiVsPytG~s~P 37 (129)
T COG4530 24 RDPIVSPYTGKSYP 37 (129)
T ss_pred CCccccCcccccch
Confidence 46888999999984
No 171
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=47.55 E-value=7.1 Score=17.09 Aligned_cols=18 Identities=22% Similarity=0.626 Sum_probs=11.6
Q ss_pred cCCCCcccccchhhccCh
Q psy13994 69 EGVKKFGCEYCSARFSQK 86 (97)
Q Consensus 69 ~~~~~~~C~~C~~~f~~~ 86 (97)
.....|+|..|++.+...
T Consensus 31 ~~~~~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 31 KEPIKLRCHYCERIITED 48 (52)
T ss_dssp TTTCEEEETTT--EEEHH
T ss_pred CCCCEEEeeCCCCEeccc
Confidence 345679999999887643
No 172
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.07 E-value=6.7 Score=17.85 Aligned_cols=13 Identities=38% Similarity=1.002 Sum_probs=9.7
Q ss_pred CcccccchhhccC
Q psy13994 73 KFGCEYCSARFSQ 85 (97)
Q Consensus 73 ~~~C~~C~~~f~~ 85 (97)
--.|+.|+..|..
T Consensus 48 ev~CPYC~t~y~l 60 (62)
T COG4391 48 EVVCPYCSTRYRL 60 (62)
T ss_pred cEecCccccEEEe
Confidence 3569999988763
No 173
>KOG0402|consensus
Probab=46.16 E-value=6.4 Score=19.11 Aligned_cols=10 Identities=30% Similarity=1.271 Sum_probs=8.5
Q ss_pred Ccccccchhh
Q psy13994 73 KFGCEYCSAR 82 (97)
Q Consensus 73 ~~~C~~C~~~ 82 (97)
.|.|++||+.
T Consensus 36 ky~CsfCGK~ 45 (92)
T KOG0402|consen 36 KYTCSFCGKK 45 (92)
T ss_pred hhhhhhcchh
Confidence 5899999974
No 174
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=46.12 E-value=18 Score=20.68 Aligned_cols=54 Identities=15% Similarity=0.345 Sum_probs=31.9
Q ss_pred CccccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHh----------ccCCCCcccccchhhccC
Q psy13994 23 KKFGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQS----------HEGVKKFGCEYCSARFSQ 85 (97)
Q Consensus 23 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~----------h~~~~~~~C~~C~~~f~~ 85 (97)
..+.|++|...+... ....||-.|...-....-... ....++..|+.|...+..
T Consensus 17 ~~~~CpICld~~~dP---------VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 17 GDFDCNICLDQVRDP---------VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CccCCccCCCcCCCc---------EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 468999998766432 123588877665443322110 112345789999877654
No 175
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=45.91 E-value=23 Score=19.82 Aligned_cols=20 Identities=30% Similarity=0.476 Sum_probs=14.3
Q ss_pred cCCCccccccccccccChHH
Q psy13994 20 EGVKKFGCEYCSARFSQKIS 39 (97)
Q Consensus 20 ~~~~~~~C~~C~~~f~~~~~ 39 (97)
....-|.|+.|+..|+....
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA 132 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEA 132 (178)
T ss_pred cCCCEEECCCCCcEEeHHHH
Confidence 34566889989888766654
No 176
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=45.86 E-value=7.9 Score=15.79 Aligned_cols=13 Identities=15% Similarity=0.611 Sum_probs=9.3
Q ss_pred CcccccchhhccC
Q psy13994 73 KFGCEYCSARFSQ 85 (97)
Q Consensus 73 ~~~C~~C~~~f~~ 85 (97)
-+.|+.||..+..
T Consensus 32 ~~~C~~CGE~~~~ 44 (46)
T TIGR03831 32 ALVCPQCGEEYLD 44 (46)
T ss_pred ccccccCCCEeeC
Confidence 4679999876654
No 177
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=45.85 E-value=6.8 Score=22.31 Aligned_cols=25 Identities=20% Similarity=0.489 Sum_probs=0.0
Q ss_pred ccCCCCcccccchh-hccChHHHHHH
Q psy13994 68 HEGVKKFGCEYCSA-RFSQKISCRVH 92 (97)
Q Consensus 68 h~~~~~~~C~~C~~-~f~~~~~l~~H 92 (97)
|.-.+.|.|.+||. +|.=...+.+|
T Consensus 96 hGL~~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 96 HGLGVEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp --------------------------
T ss_pred hCCCCeeeeEeCCCcceecHHHHHHh
Confidence 45557899999974 55555555555
No 178
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=45.71 E-value=16 Score=20.45 Aligned_cols=20 Identities=15% Similarity=0.390 Sum_probs=15.1
Q ss_pred CCCcccccchhhccChHHHH
Q psy13994 71 VKKFGCEYCSARFSQKISCR 90 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~~~l~ 90 (97)
.....|..||+.|.....+.
T Consensus 112 ~~~~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 112 FHLQRCSRCERPFAPQKTVA 131 (181)
T ss_pred cccCcCcccCCccCcHhHHH
Confidence 35778999999998665443
No 179
>PRK01343 zinc-binding protein; Provisional
Probab=44.31 E-value=13 Score=16.73 Aligned_cols=12 Identities=17% Similarity=0.360 Sum_probs=8.7
Q ss_pred Ccccccchhhcc
Q psy13994 73 KFGCEYCSARFS 84 (97)
Q Consensus 73 ~~~C~~C~~~f~ 84 (97)
...|+.|++.+.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 356888888765
No 180
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=44.23 E-value=9.6 Score=18.85 Aligned_cols=11 Identities=27% Similarity=0.597 Sum_probs=7.7
Q ss_pred CCcccccchhh
Q psy13994 72 KKFGCEYCSAR 82 (97)
Q Consensus 72 ~~~~C~~C~~~ 82 (97)
..|.|++|++.
T Consensus 35 a~y~CpfCgk~ 45 (90)
T PRK03976 35 AKHVCPVCGRP 45 (90)
T ss_pred cCccCCCCCCC
Confidence 36888888653
No 181
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=44.06 E-value=9.8 Score=18.33 Aligned_cols=10 Identities=40% Similarity=1.175 Sum_probs=3.9
Q ss_pred CCCcccccch
Q psy13994 71 VKKFGCEYCS 80 (97)
Q Consensus 71 ~~~~~C~~C~ 80 (97)
++.|.|+.|+
T Consensus 20 ~~~F~CPfC~ 29 (81)
T PF05129_consen 20 PKVFDCPFCN 29 (81)
T ss_dssp SS----TTT-
T ss_pred CceEcCCcCC
Confidence 4679999998
No 182
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=43.53 E-value=8.8 Score=20.80 Aligned_cols=15 Identities=27% Similarity=0.516 Sum_probs=11.9
Q ss_pred CcccccchhhccChH
Q psy13994 73 KFGCEYCSARFSQKI 87 (97)
Q Consensus 73 ~~~C~~C~~~f~~~~ 87 (97)
.-.|..|++.|++.-
T Consensus 28 RReC~~C~~RFTTyE 42 (147)
T TIGR00244 28 RRECLECHERFTTFE 42 (147)
T ss_pred cccCCccCCccceee
Confidence 456999999998753
No 183
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=43.14 E-value=10 Score=15.60 Aligned_cols=9 Identities=22% Similarity=0.955 Sum_probs=5.6
Q ss_pred cccccchhh
Q psy13994 74 FGCEYCSAR 82 (97)
Q Consensus 74 ~~C~~C~~~ 82 (97)
|.|+.|+..
T Consensus 1 m~Cp~Cg~~ 9 (43)
T PF08271_consen 1 MKCPNCGSK 9 (43)
T ss_dssp ESBTTTSSS
T ss_pred CCCcCCcCC
Confidence 457777654
No 184
>KOG0320|consensus
Probab=43.02 E-value=7 Score=21.92 Aligned_cols=48 Identities=17% Similarity=0.463 Sum_probs=29.1
Q ss_pred ccccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCcccccchhhcc
Q psy13994 24 KFGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFS 84 (97)
Q Consensus 24 ~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~ 84 (97)
-|.|++|-..+..+.. ....||-.|.....-. -. .+.-+|+.|+|...
T Consensus 131 ~~~CPiCl~~~sek~~-------vsTkCGHvFC~~Cik~-al-----k~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 131 TYKCPICLDSVSEKVP-------VSTKCGHVFCSQCIKD-AL-----KNTNKCPTCRKKIT 178 (187)
T ss_pred ccCCCceecchhhccc-------cccccchhHHHHHHHH-HH-----HhCCCCCCcccccc
Confidence 3899999777655443 2247888887543321 11 23456999997433
No 185
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.96 E-value=8.5 Score=18.37 Aligned_cols=12 Identities=33% Similarity=1.024 Sum_probs=9.2
Q ss_pred Ccccccchhhcc
Q psy13994 73 KFGCEYCSARFS 84 (97)
Q Consensus 73 ~~~C~~C~~~f~ 84 (97)
.|+|..|+..|.
T Consensus 12 ~Y~c~~cg~~~d 23 (82)
T COG2331 12 SYECTECGNRFD 23 (82)
T ss_pred EEeecccchHHH
Confidence 378999987664
No 186
>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=42.94 E-value=8.8 Score=14.96 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=5.1
Q ss_pred cccccchhhcc
Q psy13994 74 FGCEYCSARFS 84 (97)
Q Consensus 74 ~~C~~C~~~f~ 84 (97)
|.|..|+..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 44555555443
No 187
>KOG1729|consensus
Probab=42.88 E-value=15 Score=22.39 Aligned_cols=57 Identities=14% Similarity=0.187 Sum_probs=31.7
Q ss_pred CccccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCc-ccccchhhc
Q psy13994 23 KKFGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKF-GCEYCSARF 83 (97)
Q Consensus 23 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~-~C~~C~~~f 83 (97)
..-.|..|+.+..+...- +.|-..||..|.....-+.........++. .|..|-..+
T Consensus 167 ea~~C~~C~~~~Ftl~~R----RHHCR~CG~ivC~~Cs~n~~~l~~~~~k~~rvC~~CF~el 224 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSER----RHHCRNCGDIVCAPCSRNRFLLPNLSTKPIRVCDICFEEL 224 (288)
T ss_pred cceecccCCCccccHHHH----HHHHHhcchHhhhhhhcCcccccccCCCCceecHHHHHHH
Confidence 446899999964444332 223467888777643333222223334444 788886554
No 188
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=42.58 E-value=24 Score=17.47 Aligned_cols=21 Identities=10% Similarity=0.449 Sum_probs=16.1
Q ss_pred CccccccccccccChHHHHHH
Q psy13994 23 KKFGCEYCSARFSQKISCRVH 43 (97)
Q Consensus 23 ~~~~C~~C~~~f~~~~~l~~h 43 (97)
....|+.||..+.....+..=
T Consensus 34 Pa~~C~~CGe~y~~dev~~eI 54 (89)
T TIGR03829 34 PSISCSHCGMEYQDDTTVKEI 54 (89)
T ss_pred CcccccCCCcEeecHHHHHHH
Confidence 347899999999888766543
No 189
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=41.72 E-value=12 Score=16.58 Aligned_cols=13 Identities=31% Similarity=0.767 Sum_probs=8.6
Q ss_pred cccccccccccCh
Q psy13994 25 FGCEYCSARFSQK 37 (97)
Q Consensus 25 ~~C~~C~~~f~~~ 37 (97)
+.|+.||..+.-.
T Consensus 3 ~~CP~CG~~iev~ 15 (54)
T TIGR01206 3 FECPDCGAEIELE 15 (54)
T ss_pred cCCCCCCCEEecC
Confidence 5688887766443
No 190
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=41.06 E-value=19 Score=20.00 Aligned_cols=19 Identities=16% Similarity=0.413 Sum_probs=14.5
Q ss_pred CCCcccccchhhccChHHH
Q psy13994 71 VKKFGCEYCSARFSQKISC 89 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~~~l 89 (97)
..++.|..||+.|.....+
T Consensus 112 ~~~~~C~~CG~~f~~~~~i 130 (180)
T PRK12387 112 FALCNCRVCGRPFAVQKEI 130 (180)
T ss_pred eCcccchhhCCccccHHHH
Confidence 3577899999999866543
No 191
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=40.92 E-value=7.6 Score=15.74 Aligned_cols=10 Identities=30% Similarity=0.943 Sum_probs=7.0
Q ss_pred cccccchhhc
Q psy13994 74 FGCEYCSARF 83 (97)
Q Consensus 74 ~~C~~C~~~f 83 (97)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 6777777654
No 192
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=40.50 E-value=36 Score=14.81 Aligned_cols=46 Identities=13% Similarity=0.155 Sum_probs=25.4
Q ss_pred cccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCcccccchhhccC
Q psy13994 25 FGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQ 85 (97)
Q Consensus 25 ~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~ 85 (97)
+.|++|+..+.... ...||..|.... +..+... ...|+.|+..+..
T Consensus 2 ~~Cpi~~~~~~~Pv---------~~~~G~v~~~~~-i~~~~~~-----~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMKDPV---------ILPSGQTYERRA-IEKWLLS-----HGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCCCCE---------ECCCCCEEeHHH-HHHHHHH-----CCCCCCCcCCCCh
Confidence 45777777765431 124666666443 3334333 1358888876643
No 193
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=40.15 E-value=11 Score=20.61 Aligned_cols=18 Identities=11% Similarity=0.233 Sum_probs=14.9
Q ss_pred CCccccccccccccChHH
Q psy13994 22 VKKFGCEYCSARFSQKIS 39 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~~~ 39 (97)
+.|..|..||+.|+....
T Consensus 66 ~~PsYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPWTEN 83 (158)
T ss_pred CCChhHHhCCCCCchHHH
Confidence 578999999999987643
No 194
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=40.05 E-value=15 Score=16.22 Aligned_cols=8 Identities=25% Similarity=1.007 Sum_probs=4.9
Q ss_pred cccccchh
Q psy13994 74 FGCEYCSA 81 (97)
Q Consensus 74 ~~C~~C~~ 81 (97)
..||+||.
T Consensus 4 kPCPFCG~ 11 (61)
T PF14354_consen 4 KPCPFCGS 11 (61)
T ss_pred cCCCCCCC
Confidence 34777764
No 195
>KOG4727|consensus
Probab=39.50 E-value=17 Score=20.36 Aligned_cols=21 Identities=19% Similarity=0.513 Sum_probs=18.1
Q ss_pred CcccccchhhccChHHHHHHh
Q psy13994 73 KFGCEYCSARFSQKISCRVHM 93 (97)
Q Consensus 73 ~~~C~~C~~~f~~~~~l~~H~ 93 (97)
-|-|.+|+-+|....++..|+
T Consensus 75 GyyCdVCdcvvKDSinflDHi 95 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHI 95 (193)
T ss_pred ceeeeecceeehhhHHHHHHh
Confidence 477999999999988888875
No 196
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=39.45 E-value=12 Score=20.49 Aligned_cols=15 Identities=27% Similarity=0.530 Sum_probs=11.8
Q ss_pred CcccccchhhccChH
Q psy13994 73 KFGCEYCSARFSQKI 87 (97)
Q Consensus 73 ~~~C~~C~~~f~~~~ 87 (97)
.-.|+.|+..|++.-
T Consensus 28 RReC~~C~~RFTTfE 42 (156)
T COG1327 28 RRECLECGERFTTFE 42 (156)
T ss_pred hhcccccccccchhh
Confidence 456999999998753
No 197
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=39.42 E-value=19 Score=22.00 Aligned_cols=44 Identities=23% Similarity=0.613 Sum_probs=26.6
Q ss_pred cccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCcccccchhhc
Q psy13994 25 FGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARF 83 (97)
Q Consensus 25 ~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f 83 (97)
..|.+|...|...-. ..||-+|.+. -++.|.++.|+ |+.|...|
T Consensus 26 lrC~IC~~~i~ip~~---------TtCgHtFCsl-----CIR~hL~~qp~-CP~Cr~~~ 69 (391)
T COG5432 26 LRCRICDCRISIPCE---------TTCGHTFCSL-----CIRRHLGTQPF-CPVCREDP 69 (391)
T ss_pred HHhhhhhheeeccee---------cccccchhHH-----HHHHHhcCCCC-CccccccH
Confidence 467777655533221 3677777753 34557777777 88886544
No 198
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=39.25 E-value=30 Score=13.58 Aligned_cols=9 Identities=22% Similarity=0.722 Sum_probs=5.0
Q ss_pred CCCcccccc
Q psy13994 71 VKKFGCEYC 79 (97)
Q Consensus 71 ~~~~~C~~C 79 (97)
...+.|+.|
T Consensus 33 ~~~~~CP~C 41 (41)
T PF00097_consen 33 SGSVKCPLC 41 (41)
T ss_dssp TSSSBTTTT
T ss_pred cCCccCCcC
Confidence 345557665
No 199
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=39.07 E-value=9.3 Score=15.39 Aligned_cols=15 Identities=27% Similarity=0.642 Sum_probs=8.7
Q ss_pred ccccchhhccChHHH
Q psy13994 75 GCEYCSARFSQKISC 89 (97)
Q Consensus 75 ~C~~C~~~f~~~~~l 89 (97)
.|+.|++.|-..++.
T Consensus 4 ~CprC~kg~Hwa~~C 18 (36)
T PF14787_consen 4 LCPRCGKGFHWASEC 18 (36)
T ss_dssp C-TTTSSSCS-TTT-
T ss_pred cCcccCCCcchhhhh
Confidence 488888888766543
No 200
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=38.93 E-value=5.6 Score=18.74 Aligned_cols=15 Identities=33% Similarity=0.678 Sum_probs=10.0
Q ss_pred CCCcccc--cchhhccC
Q psy13994 71 VKKFGCE--YCSARFSQ 85 (97)
Q Consensus 71 ~~~~~C~--~C~~~f~~ 85 (97)
+.-++|. .||.+|..
T Consensus 25 ~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 25 ERYHQCQNVNCSATFIT 41 (72)
T ss_pred eeeeecCCCCCCCEEEE
Confidence 4556676 78877764
No 201
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=38.52 E-value=12 Score=15.25 Aligned_cols=11 Identities=27% Similarity=0.918 Sum_probs=7.9
Q ss_pred cccccchhhcc
Q psy13994 74 FGCEYCSARFS 84 (97)
Q Consensus 74 ~~C~~C~~~f~ 84 (97)
|.|..|+..+.
T Consensus 29 y~C~~C~~~w~ 39 (40)
T smart00440 29 YVCTKCGHRWR 39 (40)
T ss_pred EEeCCCCCEeC
Confidence 67888887654
No 202
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=38.44 E-value=12 Score=14.45 Aligned_cols=12 Identities=25% Similarity=0.753 Sum_probs=9.0
Q ss_pred CCcccccchhhc
Q psy13994 72 KKFGCEYCSARF 83 (97)
Q Consensus 72 ~~~~C~~C~~~f 83 (97)
+-|+|..||...
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 368999998654
No 203
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=38.42 E-value=12 Score=18.45 Aligned_cols=14 Identities=29% Similarity=0.790 Sum_probs=10.6
Q ss_pred CCcccccchhhccC
Q psy13994 72 KKFGCEYCSARFSQ 85 (97)
Q Consensus 72 ~~~~C~~C~~~f~~ 85 (97)
.-|.|..|+..|.-
T Consensus 52 GIW~C~kCg~~fAG 65 (89)
T COG1997 52 GIWKCRKCGAKFAG 65 (89)
T ss_pred CeEEcCCCCCeecc
Confidence 46888888888763
No 204
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=38.39 E-value=11 Score=16.71 Aligned_cols=11 Identities=27% Similarity=0.887 Sum_probs=8.7
Q ss_pred cccccchhhcc
Q psy13994 74 FGCEYCSARFS 84 (97)
Q Consensus 74 ~~C~~C~~~f~ 84 (97)
.+|+.|++.|.
T Consensus 6 ~~C~~Cg~~~~ 16 (54)
T PF14446_consen 6 CKCPVCGKKFK 16 (54)
T ss_pred ccChhhCCccc
Confidence 46889998885
No 205
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=38.22 E-value=12 Score=14.44 Aligned_cols=12 Identities=25% Similarity=0.755 Sum_probs=8.7
Q ss_pred CCcccccchhhc
Q psy13994 72 KKFGCEYCSARF 83 (97)
Q Consensus 72 ~~~~C~~C~~~f 83 (97)
+-|+|..||...
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 358899998654
No 206
>PF14369 zf-RING_3: zinc-finger
Probab=37.81 E-value=13 Score=14.76 Aligned_cols=10 Identities=30% Similarity=0.883 Sum_probs=8.0
Q ss_pred ccccchhhcc
Q psy13994 75 GCEYCSARFS 84 (97)
Q Consensus 75 ~C~~C~~~f~ 84 (97)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 5999988775
No 207
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.42 E-value=8.8 Score=16.54 Aligned_cols=12 Identities=33% Similarity=0.689 Sum_probs=9.2
Q ss_pred ccccchhhccCh
Q psy13994 75 GCEYCSARFSQK 86 (97)
Q Consensus 75 ~C~~C~~~f~~~ 86 (97)
.|+.|+..|+..
T Consensus 14 ICpvCqRPFsWR 25 (54)
T COG4338 14 ICPVCQRPFSWR 25 (54)
T ss_pred hhhhhcCchHHH
Confidence 489999888753
No 208
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=37.30 E-value=11 Score=21.78 Aligned_cols=25 Identities=16% Similarity=0.076 Sum_probs=0.0
Q ss_pred CCCcccccchhhccChHHHHHHhhhc
Q psy13994 71 VKKFGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
.+...|++||....- ..+..|+++.
T Consensus 166 ~~~~~cPitGe~IP~-~e~~eHmRi~ 190 (229)
T PF12230_consen 166 EKMIICPITGEMIPA-DEMDEHMRIE 190 (229)
T ss_dssp --------------------------
T ss_pred ccccccccccccccc-cccccccccc
Confidence 345789999987664 4788888763
No 209
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=37.19 E-value=17 Score=15.00 Aligned_cols=9 Identities=22% Similarity=0.608 Sum_probs=6.8
Q ss_pred Ccccccchh
Q psy13994 73 KFGCEYCSA 81 (97)
Q Consensus 73 ~~~C~~C~~ 81 (97)
|..|+.||.
T Consensus 2 ~~~Cp~Cg~ 10 (47)
T PF14690_consen 2 PPRCPHCGS 10 (47)
T ss_pred CccCCCcCC
Confidence 567888984
No 210
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=37.05 E-value=11 Score=21.44 Aligned_cols=16 Identities=25% Similarity=0.565 Sum_probs=10.5
Q ss_pred CCccccccccccccCh
Q psy13994 22 VKKFGCEYCSARFSQK 37 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~ 37 (97)
.++..|.+||..|...
T Consensus 4 ~k~rKCKvCg~~F~P~ 19 (189)
T PF05766_consen 4 PKRRKCKVCGEWFVPA 19 (189)
T ss_pred CCCCcCcccCCccccC
Confidence 3556777777777643
No 211
>KOG1994|consensus
Probab=36.91 E-value=19 Score=21.14 Aligned_cols=22 Identities=14% Similarity=0.520 Sum_probs=18.8
Q ss_pred CCCcccccchhhccChHHHHHH
Q psy13994 71 VKKFGCEYCSARFSQKISCRVH 92 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~~~l~~H 92 (97)
.-.|-|-+||.-|.+...|..|
T Consensus 237 ~eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred ccceEEEEeccccCCHHHHHHh
Confidence 3457899999999999999887
No 212
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=36.62 E-value=9.8 Score=16.51 Aligned_cols=13 Identities=15% Similarity=0.654 Sum_probs=10.1
Q ss_pred CCcccccchhhcc
Q psy13994 72 KKFGCEYCSARFS 84 (97)
Q Consensus 72 ~~~~C~~C~~~f~ 84 (97)
..|.|..||+.|.
T Consensus 5 ~~Y~C~~Cg~~~~ 17 (49)
T COG1996 5 MEYKCARCGREVE 17 (49)
T ss_pred EEEEhhhcCCeee
Confidence 4588988988874
No 213
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=36.14 E-value=24 Score=22.19 Aligned_cols=26 Identities=19% Similarity=0.363 Sum_probs=22.6
Q ss_pred CCCcccccchhhccChHHHHHHhhhc
Q psy13994 71 VKKFGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
+..|.|+.|-+-|.....|.+|.+..
T Consensus 156 d~vyICefClkY~~s~~~~~rH~~kC 181 (395)
T COG5027 156 DIVYICEFCLKYYGSQTSLVRHRKKC 181 (395)
T ss_pred ceEEEhhhhHHHhcchhHHHHHHhcC
Confidence 45699999999999999999998753
No 214
>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=35.99 E-value=20 Score=13.42 Aligned_cols=8 Identities=25% Similarity=0.874 Sum_probs=4.0
Q ss_pred Ccccccch
Q psy13994 73 KFGCEYCS 80 (97)
Q Consensus 73 ~~~C~~C~ 80 (97)
-|.|..|+
T Consensus 15 ~Y~C~~c~ 22 (30)
T PF03107_consen 15 FYHCSECC 22 (30)
T ss_pred eEEeCCCC
Confidence 35555554
No 215
>KOG3214|consensus
Probab=35.87 E-value=14 Score=18.63 Aligned_cols=15 Identities=27% Similarity=0.747 Sum_probs=12.4
Q ss_pred cccccccccccChHH
Q psy13994 25 FGCEYCSARFSQKIS 39 (97)
Q Consensus 25 ~~C~~C~~~f~~~~~ 39 (97)
..|.+|+.+|.....
T Consensus 48 ~sC~iC~esFqt~it 62 (109)
T KOG3214|consen 48 ASCRICEESFQTTIT 62 (109)
T ss_pred eeeeehhhhhccchH
Confidence 579999999987754
No 216
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=35.79 E-value=10 Score=14.52 Aligned_cols=11 Identities=18% Similarity=0.854 Sum_probs=2.8
Q ss_pred ccccchhhccC
Q psy13994 75 GCEYCSARFSQ 85 (97)
Q Consensus 75 ~C~~C~~~f~~ 85 (97)
+|+.|+..+.+
T Consensus 4 ~Cp~C~se~~y 14 (30)
T PF08274_consen 4 KCPLCGSEYTY 14 (30)
T ss_dssp --TTT-----E
T ss_pred CCCCCCCccee
Confidence 47788766543
No 217
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=35.60 E-value=13 Score=16.70 Aligned_cols=12 Identities=17% Similarity=0.487 Sum_probs=5.8
Q ss_pred cccccchhhccC
Q psy13994 74 FGCEYCSARFSQ 85 (97)
Q Consensus 74 ~~C~~C~~~f~~ 85 (97)
..|+.|++.+..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 469999987654
No 218
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.95 E-value=15 Score=21.66 Aligned_cols=16 Identities=25% Similarity=0.775 Sum_probs=12.6
Q ss_pred CCCcccccchhhccCh
Q psy13994 71 VKKFGCEYCSARFSQK 86 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~ 86 (97)
++.+.||+|+..|...
T Consensus 17 kk~ieCPvC~tkFkke 32 (267)
T COG1655 17 KKTIECPVCNTKFKKE 32 (267)
T ss_pred hceeccCcccchhhhh
Confidence 4678899999888643
No 219
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=34.87 E-value=16 Score=17.81 Aligned_cols=12 Identities=25% Similarity=0.730 Sum_probs=9.3
Q ss_pred ccccchhhccCh
Q psy13994 75 GCEYCSARFSQK 86 (97)
Q Consensus 75 ~C~~C~~~f~~~ 86 (97)
+|+.||..|...
T Consensus 10 ~C~~CG~d~~~~ 21 (86)
T PF06170_consen 10 RCPHCGLDYSHA 21 (86)
T ss_pred cccccCCccccC
Confidence 599999887753
No 220
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=34.73 E-value=13 Score=16.57 Aligned_cols=11 Identities=36% Similarity=0.972 Sum_probs=3.6
Q ss_pred CCcccccchhh
Q psy13994 72 KKFGCEYCSAR 82 (97)
Q Consensus 72 ~~~~C~~C~~~ 82 (97)
+.|.|+.||-+
T Consensus 32 r~y~Cp~CgAt 42 (55)
T PF05741_consen 32 RKYVCPICGAT 42 (55)
T ss_dssp GG---TTT---
T ss_pred hcCcCCCCcCc
Confidence 35889999854
No 221
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=34.22 E-value=36 Score=13.72 Aligned_cols=21 Identities=10% Similarity=0.070 Sum_probs=15.5
Q ss_pred CcccccchhhccChHHHHHHh
Q psy13994 73 KFGCEYCSARFSQKISCRVHM 93 (97)
Q Consensus 73 ~~~C~~C~~~f~~~~~l~~H~ 93 (97)
.+.|+.|+-.+.....|.+-+
T Consensus 19 id~C~~C~G~W~d~~el~~~~ 39 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELEKLL 39 (41)
T ss_pred EEECCCCCeEEccHHHHHHHH
Confidence 456889988888887776543
No 222
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=34.09 E-value=12 Score=13.24 Aligned_cols=6 Identities=33% Similarity=1.226 Sum_probs=3.1
Q ss_pred cccchh
Q psy13994 76 CEYCSA 81 (97)
Q Consensus 76 C~~C~~ 81 (97)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 555553
No 223
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=34.01 E-value=17 Score=16.69 Aligned_cols=7 Identities=29% Similarity=1.179 Sum_probs=3.9
Q ss_pred cccccch
Q psy13994 74 FGCEYCS 80 (97)
Q Consensus 74 ~~C~~C~ 80 (97)
|.|+.|+
T Consensus 1 y~C~KCg 7 (64)
T PF09855_consen 1 YKCPKCG 7 (64)
T ss_pred CCCCCCC
Confidence 4566665
No 224
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=33.76 E-value=17 Score=16.24 Aligned_cols=16 Identities=25% Similarity=0.729 Sum_probs=10.8
Q ss_pred CCCcccccchhhccCh
Q psy13994 71 VKKFGCEYCSARFSQK 86 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~ 86 (97)
++--.|++|++.|...
T Consensus 37 ~rYngCPfC~~~~~~~ 52 (55)
T PF14447_consen 37 ERYNGCPFCGTPFEFD 52 (55)
T ss_pred hhccCCCCCCCcccCC
Confidence 4434589999887643
No 225
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=33.36 E-value=18 Score=14.85 Aligned_cols=11 Identities=27% Similarity=0.794 Sum_probs=5.2
Q ss_pred ccccchhhccC
Q psy13994 75 GCEYCSARFSQ 85 (97)
Q Consensus 75 ~C~~C~~~f~~ 85 (97)
.|.+||+.-..
T Consensus 3 ~CSFCgr~~~~ 13 (41)
T PF06689_consen 3 RCSFCGRPESE 13 (41)
T ss_dssp B-TTT--BTTT
T ss_pred CccCCCCCHHH
Confidence 48888886543
No 226
>KOG2164|consensus
Probab=33.29 E-value=53 Score=21.84 Aligned_cols=52 Identities=15% Similarity=0.283 Sum_probs=33.7
Q ss_pred ccccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCcccccchhhccC
Q psy13994 24 KFGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQ 85 (97)
Q Consensus 24 ~~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~ 85 (97)
...|++|-........ ..||-.|..+..|+--... .-..+-.|+.|...+.-
T Consensus 186 ~~~CPICL~~~~~p~~---------t~CGHiFC~~CiLqy~~~s-~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVR---------TNCGHIFCGPCILQYWNYS-AIKGPCSCPICRSTITL 237 (513)
T ss_pred CCcCCcccCCCCcccc---------cccCceeeHHHHHHHHhhh-cccCCccCCchhhhccc
Confidence 6789999555433221 2599999887776544433 44456679999876654
No 227
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=32.26 E-value=24 Score=15.64 Aligned_cols=20 Identities=10% Similarity=0.401 Sum_probs=14.7
Q ss_pred CCcccccchhhccChHHHHH
Q psy13994 72 KKFGCEYCSARFSQKISCRV 91 (97)
Q Consensus 72 ~~~~C~~C~~~f~~~~~l~~ 91 (97)
.-+=|-.||..|.....|..
T Consensus 26 ~~~YC~~Cg~~Y~d~~dL~~ 45 (55)
T PF13821_consen 26 EHNYCFWCGTKYDDEEDLER 45 (55)
T ss_pred hCceeeeeCCccCCHHHHHh
Confidence 33458899998888877754
No 228
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=31.95 E-value=18 Score=15.84 Aligned_cols=10 Identities=30% Similarity=0.999 Sum_probs=6.5
Q ss_pred ccccchhhcc
Q psy13994 75 GCEYCSARFS 84 (97)
Q Consensus 75 ~C~~C~~~f~ 84 (97)
.|+.||..+.
T Consensus 2 ~CPyCge~~~ 11 (52)
T PF14255_consen 2 QCPYCGEPIE 11 (52)
T ss_pred CCCCCCCeeE
Confidence 5778876543
No 229
>KOG1088|consensus
Probab=31.71 E-value=20 Score=18.70 Aligned_cols=21 Identities=10% Similarity=0.034 Sum_probs=16.3
Q ss_pred HhccCCCCcccccchhhccCh
Q psy13994 66 QSHEGVKKFGCEYCSARFSQK 86 (97)
Q Consensus 66 ~~h~~~~~~~C~~C~~~f~~~ 86 (97)
.++..|....|+.||..|.-.
T Consensus 91 e~~v~EG~l~CpetG~vfpI~ 111 (124)
T KOG1088|consen 91 EIDVIEGELVCPETGRVFPIS 111 (124)
T ss_pred hhhhccceEecCCCCcEeecc
Confidence 346667789999999998743
No 230
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=31.49 E-value=19 Score=14.58 Aligned_cols=16 Identities=25% Similarity=0.800 Sum_probs=9.7
Q ss_pred ccCCCCcccccchhhc
Q psy13994 68 HEGVKKFGCEYCSARF 83 (97)
Q Consensus 68 h~~~~~~~C~~C~~~f 83 (97)
..+.+.|.|.+|+...
T Consensus 19 ~~~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 19 DDGGKTWICNFCGTKN 34 (40)
T ss_dssp ETTTTEEEETTT--EE
T ss_pred cCCCCEEECcCCCCcC
Confidence 3345679999998643
No 231
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=31.39 E-value=20 Score=18.14 Aligned_cols=13 Identities=31% Similarity=0.636 Sum_probs=9.7
Q ss_pred CCCcccccchhhc
Q psy13994 71 VKKFGCEYCSARF 83 (97)
Q Consensus 71 ~~~~~C~~C~~~f 83 (97)
++.|.|+.||..-
T Consensus 20 ~k~FtCp~Cghe~ 32 (104)
T COG4888 20 PKTFTCPRCGHEK 32 (104)
T ss_pred CceEecCccCCee
Confidence 5678999998643
No 232
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=30.47 E-value=54 Score=16.70 Aligned_cols=23 Identities=9% Similarity=0.235 Sum_probs=17.2
Q ss_pred CccccccccccccChHHHHHHHH
Q psy13994 23 KKFGCEYCSARFSQKISCRVHML 45 (97)
Q Consensus 23 ~~~~C~~C~~~f~~~~~l~~h~~ 45 (97)
.-+.|+.||..+........-.+
T Consensus 30 ~~~~C~~CGe~~~~~e~~~~~~~ 52 (127)
T TIGR03830 30 PGWYCPACGEELLDPEESKRNSA 52 (127)
T ss_pred eeeECCCCCCEEEcHHHHHHHHH
Confidence 45789999999988876655443
No 233
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=30.47 E-value=39 Score=21.04 Aligned_cols=26 Identities=23% Similarity=0.589 Sum_probs=20.5
Q ss_pred CCCcccccchhhccChHHHHHHhhhc
Q psy13994 71 VKKFGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
...|+|+.|...|-..-+.-.|...|
T Consensus 386 s~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 386 SGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ccceechhhhhhhhhhhHHHHHHHHh
Confidence 45799999999998877777776554
No 234
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.11 E-value=24 Score=18.69 Aligned_cols=17 Identities=24% Similarity=0.378 Sum_probs=13.8
Q ss_pred CCccccccccccccChH
Q psy13994 22 VKKFGCEYCSARFSQKI 38 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~~ 38 (97)
+.|.-|..||..|....
T Consensus 66 e~psfchncgs~fpwte 82 (160)
T COG4306 66 EPPSFCHNCGSRFPWTE 82 (160)
T ss_pred CCcchhhcCCCCCCcHH
Confidence 57788999999997653
No 235
>KOG3362|consensus
Probab=30.05 E-value=15 Score=19.94 Aligned_cols=23 Identities=17% Similarity=0.515 Sum_probs=14.2
Q ss_pred CcccccchhhccChHHHHHHhhh
Q psy13994 73 KFGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 73 ~~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
+|.|.-||-.+-...-+..|..+
T Consensus 129 ~ysC~~CG~kyCsv~C~~~HneT 151 (156)
T KOG3362|consen 129 KYSCVNCGTKYCSVRCLKTHNET 151 (156)
T ss_pred hhHHHhcCCceeechhhhhcccc
Confidence 46666666666666666666543
No 236
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=29.80 E-value=21 Score=15.32 Aligned_cols=8 Identities=50% Similarity=1.231 Sum_probs=4.2
Q ss_pred cccchhhc
Q psy13994 76 CEYCSARF 83 (97)
Q Consensus 76 C~~C~~~f 83 (97)
|+.||..|
T Consensus 1 CP~Cg~~f 8 (50)
T PF14375_consen 1 CPRCGAPF 8 (50)
T ss_pred CCCCCCcC
Confidence 45555554
No 237
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=29.50 E-value=23 Score=13.37 Aligned_cols=11 Identities=27% Similarity=0.767 Sum_probs=7.0
Q ss_pred Ccccccchhhc
Q psy13994 73 KFGCEYCSARF 83 (97)
Q Consensus 73 ~~~C~~C~~~f 83 (97)
=|.|..|++.+
T Consensus 27 Cf~C~~C~~~L 37 (39)
T smart00132 27 CFKCSKCGKPL 37 (39)
T ss_pred CCCCcccCCcC
Confidence 36677777654
No 238
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=29.25 E-value=32 Score=13.66 Aligned_cols=13 Identities=31% Similarity=0.866 Sum_probs=7.6
Q ss_pred Ccccccccccccc
Q psy13994 23 KKFGCEYCSARFS 35 (97)
Q Consensus 23 ~~~~C~~C~~~f~ 35 (97)
.+..|..||..++
T Consensus 20 ~~isC~~CGPr~~ 32 (35)
T PF07503_consen 20 QFISCTNCGPRYS 32 (35)
T ss_dssp TT--BTTCC-SCC
T ss_pred cCccCCCCCCCEE
Confidence 4567999998765
No 239
>COG4640 Predicted membrane protein [Function unknown]
Probab=28.95 E-value=36 Score=21.93 Aligned_cols=20 Identities=20% Similarity=0.526 Sum_probs=14.6
Q ss_pred CCCCcccccchhhccChHHH
Q psy13994 70 GVKKFGCEYCSARFSQKISC 89 (97)
Q Consensus 70 ~~~~~~C~~C~~~f~~~~~l 89 (97)
.|..++|++||..|...+..
T Consensus 12 ~Ed~~qC~qCG~~~t~~~sq 31 (465)
T COG4640 12 AEDDVQCTQCGHKFTSRQSQ 31 (465)
T ss_pred ccccccccccCCcCCchhhh
Confidence 34556699999988876554
No 240
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=28.95 E-value=21 Score=15.08 Aligned_cols=14 Identities=21% Similarity=0.562 Sum_probs=10.6
Q ss_pred CCcccccchhhccC
Q psy13994 72 KKFGCEYCSARFSQ 85 (97)
Q Consensus 72 ~~~~C~~C~~~f~~ 85 (97)
..+.|+.||..+.-
T Consensus 19 ~~~vC~~Cg~~~~~ 32 (52)
T smart00661 19 RRFVCRKCGYEEPI 32 (52)
T ss_pred CEEECCcCCCeEEC
Confidence 36889999976653
No 241
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=28.90 E-value=5.4 Score=16.02 Aligned_cols=17 Identities=24% Similarity=0.657 Sum_probs=9.7
Q ss_pred HHHHhccCCCCcccccc
Q psy13994 63 AHLQSHEGVKKFGCEYC 79 (97)
Q Consensus 63 ~h~~~h~~~~~~~C~~C 79 (97)
.|-....|...|.|..|
T Consensus 19 k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 19 KNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eCCCCCCCCEeEecCcC
Confidence 34444455566777766
No 242
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.53 E-value=38 Score=20.95 Aligned_cols=53 Identities=17% Similarity=0.293 Sum_probs=28.6
Q ss_pred cccccccccccChHHHHHHHHHcccccCccccChHHHHHHHHhccCCCCcccccchhhccCh
Q psy13994 25 FGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRKSVLIAHLQSHEGVKKFGCEYCSARFSQK 86 (97)
Q Consensus 25 ~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~~~~~~h~~~h~~~~~~~C~~C~~~f~~~ 86 (97)
+.|++|...-.....+ +.-...||-.|.....-.. . ...+..|+.|++.+...
T Consensus 4 ~~CP~Ck~~~y~np~~----kl~i~~CGH~~C~sCv~~l-~----~~~~~~CP~C~~~lrk~ 56 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSL----KLMVNVCGHTLCESCVDLL-F----VRGSGSCPECDTPLRKN 56 (309)
T ss_pred CCCCcCCCCCccCccc----ccccCCCCCcccHHHHHHH-h----cCCCCCCCCCCCccchh
Confidence 5799997642222221 1112268877775433222 1 22345799998866544
No 243
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=27.92 E-value=45 Score=18.57 Aligned_cols=23 Identities=22% Similarity=0.533 Sum_probs=19.1
Q ss_pred cccccccccccChHHHHHHHHHc
Q psy13994 25 FGCEYCSARFSQKISCRVHMLRH 47 (97)
Q Consensus 25 ~~C~~C~~~f~~~~~l~~h~~~~ 47 (97)
|.|..|.........+..|+...
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~ 23 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESK 23 (165)
T ss_pred CccceeeeecccHHHHHHHHccc
Confidence 56899998888889999988754
No 244
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=27.88 E-value=31 Score=15.97 Aligned_cols=9 Identities=33% Similarity=0.962 Sum_probs=5.2
Q ss_pred Ccccccchh
Q psy13994 73 KFGCEYCSA 81 (97)
Q Consensus 73 ~~~C~~C~~ 81 (97)
.++|+.||-
T Consensus 4 ~~kCpKCgn 12 (68)
T COG3478 4 AFKCPKCGN 12 (68)
T ss_pred cccCCCcCC
Confidence 345777763
No 245
>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=27.81 E-value=23 Score=13.18 Aligned_cols=11 Identities=18% Similarity=0.477 Sum_probs=4.7
Q ss_pred CCcccccchhh
Q psy13994 72 KKFGCEYCSAR 82 (97)
Q Consensus 72 ~~~~C~~C~~~ 82 (97)
..|.|.+|+..
T Consensus 14 ~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 14 WFYRCSECDFD 24 (30)
T ss_dssp -EEE-TTT---
T ss_pred ceEECccCCCc
Confidence 46788888643
No 246
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=27.56 E-value=28 Score=17.50 Aligned_cols=13 Identities=31% Similarity=0.838 Sum_probs=9.4
Q ss_pred CCCcccccchhhc
Q psy13994 71 VKKFGCEYCSARF 83 (97)
Q Consensus 71 ~~~~~C~~C~~~f 83 (97)
.+..+|..||..|
T Consensus 86 ~r~~rC~nCG~~f 98 (98)
T PF10164_consen 86 MRERRCSNCGATF 98 (98)
T ss_pred cCccccCCCCccC
Confidence 4567788888765
No 247
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=27.54 E-value=10 Score=17.03 Aligned_cols=16 Identities=13% Similarity=0.169 Sum_probs=11.0
Q ss_pred CCCcccccchhhccCh
Q psy13994 71 VKKFGCEYCSARFSQK 86 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~ 86 (97)
...|.|-.|+..+-..
T Consensus 9 ~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 9 SNLWLCLTCGYVGCGR 24 (63)
T ss_dssp SSEEEETTTS-EEETT
T ss_pred CceEEeCCCCcccccC
Confidence 4678898888877653
No 248
>KOG4118|consensus
Probab=27.38 E-value=41 Score=15.61 Aligned_cols=22 Identities=14% Similarity=0.425 Sum_probs=16.9
Q ss_pred cccccchhhccChHHHHHHhhh
Q psy13994 74 FGCEYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 74 ~~C~~C~~~f~~~~~l~~H~~~ 95 (97)
|.|.+|.........+.+|...
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~ 60 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFEN 60 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhh
Confidence 7799998877777777777654
No 249
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=27.22 E-value=21 Score=18.94 Aligned_cols=15 Identities=27% Similarity=0.638 Sum_probs=11.8
Q ss_pred CCcccccchhhccCh
Q psy13994 72 KKFGCEYCSARFSQK 86 (97)
Q Consensus 72 ~~~~C~~C~~~f~~~ 86 (97)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 458899999888653
No 250
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.19 E-value=29 Score=17.71 Aligned_cols=13 Identities=23% Similarity=0.657 Sum_probs=9.8
Q ss_pred ccccccccccccC
Q psy13994 24 KFGCEYCSARFSQ 36 (97)
Q Consensus 24 ~~~C~~C~~~f~~ 36 (97)
...|+.||..|..
T Consensus 49 ~t~CP~Cg~~~e~ 61 (115)
T COG1885 49 STSCPKCGEPFES 61 (115)
T ss_pred cccCCCCCCccce
Confidence 3689999987743
No 251
>KOG1280|consensus
Probab=27.08 E-value=70 Score=20.27 Aligned_cols=27 Identities=22% Similarity=0.449 Sum_probs=22.5
Q ss_pred CCccccccccccccChHHHHHHHHHcc
Q psy13994 22 VKKFGCEYCSARFSQKISCRVHMLRHR 48 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~~~l~~h~~~~~ 48 (97)
+..|.|+.|+........+..|....+
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~H 103 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQH 103 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcC
Confidence 456899999999999999988887665
No 252
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.63 E-value=26 Score=16.17 Aligned_cols=11 Identities=18% Similarity=0.525 Sum_probs=8.1
Q ss_pred cccccchhhcc
Q psy13994 74 FGCEYCSARFS 84 (97)
Q Consensus 74 ~~C~~C~~~f~ 84 (97)
-.|+.|||.-.
T Consensus 8 v~CP~Cgkpv~ 18 (65)
T COG3024 8 VPCPTCGKPVV 18 (65)
T ss_pred ccCCCCCCccc
Confidence 46999998544
No 253
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=26.27 E-value=23 Score=16.20 Aligned_cols=17 Identities=12% Similarity=0.307 Sum_probs=13.1
Q ss_pred ccCCCCcccccchhhcc
Q psy13994 68 HEGVKKFGCEYCSARFS 84 (97)
Q Consensus 68 h~~~~~~~C~~C~~~f~ 84 (97)
+..+....|+.|+..|.
T Consensus 48 ~i~eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 48 EIVEGELICPECGREYP 64 (68)
T ss_dssp ETTTTEEEETTTTEEEE
T ss_pred cccCCEEEcCCCCCEEe
Confidence 45566788999998875
No 254
>KOG3352|consensus
Probab=26.05 E-value=33 Score=18.80 Aligned_cols=16 Identities=19% Similarity=0.331 Sum_probs=11.9
Q ss_pred CCccccccccccccCh
Q psy13994 22 VKKFGCEYCSARFSQK 37 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~ 37 (97)
.+..+|.+||..|...
T Consensus 131 ge~~rc~eCG~~fkL~ 146 (153)
T KOG3352|consen 131 GETQRCPECGHYFKLV 146 (153)
T ss_pred CCcccCCcccceEEee
Confidence 3467899999888643
No 255
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=25.45 E-value=48 Score=15.10 Aligned_cols=17 Identities=18% Similarity=0.302 Sum_probs=11.1
Q ss_pred CccccccccccccChHH
Q psy13994 23 KKFGCEYCSARFSQKIS 39 (97)
Q Consensus 23 ~~~~C~~C~~~f~~~~~ 39 (97)
.|.+|-.||+....+..
T Consensus 3 iPVRCFTCGkvi~~~~e 19 (60)
T PF01194_consen 3 IPVRCFTCGKVIGNKWE 19 (60)
T ss_dssp -SSS-STTTSBTCGHHH
T ss_pred CceecCCCCCChhHhHH
Confidence 36789999988765543
No 256
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
Probab=25.44 E-value=64 Score=14.42 Aligned_cols=19 Identities=11% Similarity=0.212 Sum_probs=13.9
Q ss_pred ccchhhccChHHHHHHhhh
Q psy13994 77 EYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 77 ~~C~~~f~~~~~l~~H~~~ 95 (97)
.-||+.|.+..++...+..
T Consensus 31 sP~Gk~~Rs~~ev~~yL~~ 49 (62)
T cd00122 31 SPCGKKLRSKPEVARYLEK 49 (62)
T ss_pred CCCCceecCHHHHHHHHHh
Confidence 3478888888888777654
No 257
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=25.29 E-value=22 Score=17.66 Aligned_cols=12 Identities=17% Similarity=0.617 Sum_probs=9.3
Q ss_pred cccccchhhccC
Q psy13994 74 FGCEYCSARFSQ 85 (97)
Q Consensus 74 ~~C~~C~~~f~~ 85 (97)
|.|.+|+++-..
T Consensus 69 ~~Ct~Cgkah~~ 80 (94)
T COG1631 69 LRCTECGKAHQR 80 (94)
T ss_pred EEehhhcccccc
Confidence 889999986543
No 258
>COG2879 Uncharacterized small protein [Function unknown]
Probab=25.20 E-value=86 Score=14.46 Aligned_cols=17 Identities=12% Similarity=0.169 Sum_probs=11.0
Q ss_pred CchHHHHHHhhccCCCc
Q psy13994 8 RKSVLIAHLQSHEGVKK 24 (97)
Q Consensus 8 ~~~~l~~h~~~h~~~~~ 24 (97)
+..++..||+.++.++|
T Consensus 24 dYdnYVehmr~~hPd~p 40 (65)
T COG2879 24 DYDNYVEHMRKKHPDKP 40 (65)
T ss_pred cHHHHHHHHHHhCcCCC
Confidence 44566777877665555
No 259
>TIGR00240 ATCase_reg aspartate carbamoyltransferase, regulatory subunit. The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff.
Probab=24.91 E-value=21 Score=19.49 Aligned_cols=13 Identities=23% Similarity=0.802 Sum_probs=10.9
Q ss_pred CcccccchhhccC
Q psy13994 73 KFGCEYCSARFSQ 85 (97)
Q Consensus 73 ~~~C~~C~~~f~~ 85 (97)
.|+|..|++.|..
T Consensus 132 ~lrC~YCe~~~~~ 144 (150)
T TIGR00240 132 ALRCYYCEKEIEH 144 (150)
T ss_pred EEEEECCCCEEec
Confidence 5999999998863
No 260
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=24.72 E-value=33 Score=15.74 Aligned_cols=11 Identities=18% Similarity=0.619 Sum_probs=8.5
Q ss_pred Ccccccchhhc
Q psy13994 73 KFGCEYCSARF 83 (97)
Q Consensus 73 ~~~C~~C~~~f 83 (97)
...|+.|++..
T Consensus 6 ~v~CP~C~k~~ 16 (62)
T PRK00418 6 TVNCPTCGKPV 16 (62)
T ss_pred cccCCCCCCcc
Confidence 46799999864
No 261
>KOG0562|consensus
Probab=24.33 E-value=56 Score=18.36 Aligned_cols=26 Identities=12% Similarity=0.192 Sum_probs=19.3
Q ss_pred CCCcccccchhhccChHHHHHHhhhc
Q psy13994 71 VKKFGCEYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 71 ~~~~~C~~C~~~f~~~~~l~~H~~~h 96 (97)
+-+.+|-.|+..-.....|+.|++.+
T Consensus 151 k~dLrC~~Cq~~~~~~~kLK~Hl~~~ 176 (184)
T KOG0562|consen 151 KEDLRCWRCQTFGPHFPKLKAHLREE 176 (184)
T ss_pred ccceeehhhhhcccccHHHHHHHHHH
Confidence 34678999994444788899998763
No 262
>KOG4602|consensus
Probab=24.24 E-value=27 Score=21.00 Aligned_cols=11 Identities=27% Similarity=0.878 Sum_probs=8.6
Q ss_pred CCcccccchhh
Q psy13994 72 KKFGCEYCSAR 82 (97)
Q Consensus 72 ~~~~C~~C~~~ 82 (97)
+.|.|++||-+
T Consensus 267 R~YVCPiCGAT 277 (318)
T KOG4602|consen 267 RSYVCPICGAT 277 (318)
T ss_pred hhhcCcccccc
Confidence 45999999854
No 263
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=24.23 E-value=27 Score=12.56 Aligned_cols=9 Identities=33% Similarity=0.670 Sum_probs=5.0
Q ss_pred ccccccccc
Q psy13994 25 FGCEYCSAR 33 (97)
Q Consensus 25 ~~C~~C~~~ 33 (97)
--|+.||..
T Consensus 17 ~fC~~CG~~ 25 (26)
T PF13248_consen 17 KFCPNCGAK 25 (26)
T ss_pred ccChhhCCC
Confidence 346666643
No 264
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=24.11 E-value=40 Score=13.72 Aligned_cols=11 Identities=27% Similarity=0.612 Sum_probs=7.5
Q ss_pred CCCcccccchh
Q psy13994 71 VKKFGCEYCSA 81 (97)
Q Consensus 71 ~~~~~C~~C~~ 81 (97)
.+...|++|++
T Consensus 34 ~~~~~CP~C~k 44 (44)
T PF14634_consen 34 GKSVKCPICRK 44 (44)
T ss_pred CCCCCCcCCCC
Confidence 45667888864
No 265
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=24.06 E-value=30 Score=15.26 Aligned_cols=11 Identities=36% Similarity=1.050 Sum_probs=7.9
Q ss_pred CCCcccccchh
Q psy13994 71 VKKFGCEYCSA 81 (97)
Q Consensus 71 ~~~~~C~~C~~ 81 (97)
+-.|.|+.|+.
T Consensus 42 ~i~y~C~~Cg~ 52 (54)
T PF10058_consen 42 EIQYRCPYCGA 52 (54)
T ss_pred ceEEEcCCCCC
Confidence 34688988874
No 266
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=23.69 E-value=8.9 Score=26.87 Aligned_cols=34 Identities=15% Similarity=0.106 Sum_probs=20.0
Q ss_pred cccccccccccChHHHHHHHHHcccccCccccCh
Q psy13994 25 FGCEYCSARFSQKISCRVHMLRHRDVCNKPYHRK 58 (97)
Q Consensus 25 ~~C~~C~~~f~~~~~l~~h~~~~~~~c~~~~~~~ 58 (97)
-.|..|++.|.........++.|-..||..|...
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~ 494 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVF 494 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCcc
Confidence 5699999999765321111222446777766544
No 267
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=23.00 E-value=37 Score=15.33 Aligned_cols=12 Identities=33% Similarity=0.783 Sum_probs=5.5
Q ss_pred cccccchhhccC
Q psy13994 74 FGCEYCSARFSQ 85 (97)
Q Consensus 74 ~~C~~C~~~f~~ 85 (97)
-.|..|++.|..
T Consensus 10 ~~C~~C~~~F~~ 21 (69)
T PF01363_consen 10 SNCMICGKKFSL 21 (69)
T ss_dssp SB-TTT--B-BS
T ss_pred CcCcCcCCcCCC
Confidence 358889998853
No 268
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.99 E-value=34 Score=17.17 Aligned_cols=14 Identities=29% Similarity=0.862 Sum_probs=9.8
Q ss_pred CCCccccccccccc
Q psy13994 21 GVKKFGCEYCSARF 34 (97)
Q Consensus 21 ~~~~~~C~~C~~~f 34 (97)
+-+.|+|.+||.+.
T Consensus 3 ~lkewkC~VCg~~i 16 (103)
T COG4847 3 GLKEWKCYVCGGTI 16 (103)
T ss_pred ccceeeEeeeCCEe
Confidence 34568898887654
No 269
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=22.94 E-value=35 Score=14.44 Aligned_cols=9 Identities=22% Similarity=0.567 Sum_probs=6.1
Q ss_pred cccccchhh
Q psy13994 74 FGCEYCSAR 82 (97)
Q Consensus 74 ~~C~~C~~~ 82 (97)
-+|+.||..
T Consensus 12 rkCp~CGt~ 20 (44)
T PF14952_consen 12 RKCPKCGTY 20 (44)
T ss_pred ccCCcCcCc
Confidence 358888753
No 270
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=22.93 E-value=35 Score=12.67 Aligned_cols=7 Identities=29% Similarity=1.217 Sum_probs=2.7
Q ss_pred cccchhh
Q psy13994 76 CEYCSAR 82 (97)
Q Consensus 76 C~~C~~~ 82 (97)
|+.|+..
T Consensus 2 CP~C~s~ 8 (28)
T PF03119_consen 2 CPVCGSK 8 (28)
T ss_dssp -TTT--B
T ss_pred cCCCCCE
Confidence 7778753
No 271
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=22.85 E-value=33 Score=13.42 Aligned_cols=10 Identities=20% Similarity=0.840 Sum_probs=7.5
Q ss_pred cccccccccc
Q psy13994 24 KFGCEYCSAR 33 (97)
Q Consensus 24 ~~~C~~C~~~ 33 (97)
-|.|..|+..
T Consensus 8 ~Y~C~~C~~~ 17 (32)
T PF13696_consen 8 GYVCHRCGQK 17 (32)
T ss_pred CCEeecCCCC
Confidence 3888888765
No 272
>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=21.98 E-value=35 Score=15.43 Aligned_cols=15 Identities=20% Similarity=0.572 Sum_probs=10.9
Q ss_pred CCCCcccccchhhcc
Q psy13994 70 GVKKFGCEYCSARFS 84 (97)
Q Consensus 70 ~~~~~~C~~C~~~f~ 84 (97)
..+.|.|+.||..+-
T Consensus 43 ~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 43 SGRVFTCPNCGFEMD 57 (69)
T ss_pred ccceEEcCCCCCEEC
Confidence 346788999987654
No 273
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=21.94 E-value=35 Score=13.81 Aligned_cols=11 Identities=36% Similarity=0.918 Sum_probs=3.4
Q ss_pred cccchhhccCh
Q psy13994 76 CEYCSARFSQK 86 (97)
Q Consensus 76 C~~C~~~f~~~ 86 (97)
|..|++.+...
T Consensus 1 C~~C~~~~~~~ 11 (47)
T PF01844_consen 1 CQYCGKPGSDN 11 (47)
T ss_dssp -TTT--B--GG
T ss_pred CCCCCCcCccC
Confidence 56677665443
No 274
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=21.89 E-value=42 Score=18.32 Aligned_cols=24 Identities=13% Similarity=0.139 Sum_probs=15.2
Q ss_pred CCccccccccccccChHHHHHHHH
Q psy13994 22 VKKFGCEYCSARFSQKISCRVHML 45 (97)
Q Consensus 22 ~~~~~C~~C~~~f~~~~~l~~h~~ 45 (97)
.....|++||.+-..+..+..++.
T Consensus 30 ~glv~CP~Cgs~~V~K~lmAP~v~ 53 (148)
T PF06676_consen 30 RGLVSCPVCGSTEVSKALMAPAVA 53 (148)
T ss_pred cCCccCCCCCCCeEeeecCCCeec
Confidence 345789999877666655444433
No 275
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=21.74 E-value=44 Score=14.47 Aligned_cols=16 Identities=13% Similarity=0.563 Sum_probs=11.5
Q ss_pred CcccccchhhccChHH
Q psy13994 73 KFGCEYCSARFSQKIS 88 (97)
Q Consensus 73 ~~~C~~C~~~f~~~~~ 88 (97)
-++|+.||-.|...-.
T Consensus 28 ~W~C~~Cgh~w~~~v~ 43 (55)
T PF14311_consen 28 WWKCPKCGHEWKASVN 43 (55)
T ss_pred EEECCCCCCeeEccHh
Confidence 3789999887775443
No 276
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=21.60 E-value=52 Score=21.35 Aligned_cols=18 Identities=28% Similarity=0.693 Sum_probs=13.2
Q ss_pred cCCCCcccccchhhccCh
Q psy13994 69 EGVKKFGCEYCSARFSQK 86 (97)
Q Consensus 69 ~~~~~~~C~~C~~~f~~~ 86 (97)
.|.+-|+|+.||..+...
T Consensus 363 ~G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 363 AGRNGFRCKKCGTRARET 380 (421)
T ss_pred cCCCCcccccccccCCcc
Confidence 344479999999887654
No 277
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=21.44 E-value=36 Score=18.70 Aligned_cols=16 Identities=38% Similarity=0.887 Sum_probs=12.7
Q ss_pred CCCCcccccchhhccC
Q psy13994 70 GVKKFGCEYCSARFSQ 85 (97)
Q Consensus 70 ~~~~~~C~~C~~~f~~ 85 (97)
....|+|..|++.|..
T Consensus 131 ~~~~~rC~YCe~~~~~ 146 (152)
T PRK00893 131 EPIKLRCKYCEKEFSE 146 (152)
T ss_pred CCCEEEeeCCCCEech
Confidence 4457999999998874
No 278
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=21.25 E-value=32 Score=18.42 Aligned_cols=13 Identities=15% Similarity=0.465 Sum_probs=9.6
Q ss_pred cccccchhhccCh
Q psy13994 74 FGCEYCSARFSQK 86 (97)
Q Consensus 74 ~~C~~C~~~f~~~ 86 (97)
-+|+.||..|-..
T Consensus 30 ~kC~~CG~v~~PP 42 (140)
T COG1545 30 TKCKKCGRVYFPP 42 (140)
T ss_pred EEcCCCCeEEcCC
Confidence 3699999877544
No 279
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=21.22 E-value=67 Score=14.41 Aligned_cols=12 Identities=25% Similarity=0.863 Sum_probs=7.7
Q ss_pred Cccccccccccc
Q psy13994 23 KKFGCEYCSARF 34 (97)
Q Consensus 23 ~~~~C~~C~~~f 34 (97)
..|.|..|....
T Consensus 30 ~tYmC~eC~~RI 41 (56)
T PF09963_consen 30 HTYMCDECKERI 41 (56)
T ss_pred cceeChhHHHHH
Confidence 347788776543
No 280
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=21.16 E-value=94 Score=13.47 Aligned_cols=12 Identities=25% Similarity=0.517 Sum_probs=8.7
Q ss_pred CCCCcccccchh
Q psy13994 70 GVKKFGCEYCSA 81 (97)
Q Consensus 70 ~~~~~~C~~C~~ 81 (97)
++....|+.||.
T Consensus 43 ~~~i~~Cp~CgR 54 (56)
T PF02591_consen 43 GDEIVFCPNCGR 54 (56)
T ss_pred CCCeEECcCCCc
Confidence 356677999985
No 281
>PF14149 YhfH: YhfH-like protein
Probab=21.01 E-value=31 Score=14.03 Aligned_cols=11 Identities=18% Similarity=0.528 Sum_probs=7.7
Q ss_pred cccccchhhcc
Q psy13994 74 FGCEYCSARFS 84 (97)
Q Consensus 74 ~~C~~C~~~f~ 84 (97)
=.|..||+..-
T Consensus 14 K~C~~CG~~i~ 24 (37)
T PF14149_consen 14 KKCTECGKEIE 24 (37)
T ss_pred cccHHHHHHHH
Confidence 35899997643
No 282
>PHA02998 RNA polymerase subunit; Provisional
Probab=20.95 E-value=41 Score=19.07 Aligned_cols=13 Identities=23% Similarity=0.708 Sum_probs=10.2
Q ss_pred cccccchhhccCh
Q psy13994 74 FGCEYCSARFSQK 86 (97)
Q Consensus 74 ~~C~~C~~~f~~~ 86 (97)
|.|..||+.|..+
T Consensus 172 YkC~~CG~~wkpp 184 (195)
T PHA02998 172 HACRDCKKHFKPP 184 (195)
T ss_pred EEcCCCCCccCCc
Confidence 6899999887753
No 283
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=20.93 E-value=80 Score=15.01 Aligned_cols=19 Identities=11% Similarity=0.216 Sum_probs=14.0
Q ss_pred ccchhhccChHHHHHHhhh
Q psy13994 77 EYCSARFSQKISCRVHMLR 95 (97)
Q Consensus 77 ~~C~~~f~~~~~l~~H~~~ 95 (97)
.-||+.|.+..++...+..
T Consensus 34 sP~GkklRs~~ev~~YL~~ 52 (77)
T smart00391 34 SPCGKKLRSKSELARYLHK 52 (77)
T ss_pred CCCCCeeeCHHHHHHHHHh
Confidence 3488888888888777654
No 284
>KOG2907|consensus
Probab=20.91 E-value=30 Score=17.93 Aligned_cols=12 Identities=25% Similarity=0.977 Sum_probs=8.9
Q ss_pred cccccchhhccC
Q psy13994 74 FGCEYCSARFSQ 85 (97)
Q Consensus 74 ~~C~~C~~~f~~ 85 (97)
|.|+.|++.|+.
T Consensus 103 YTC~kC~~k~~e 114 (116)
T KOG2907|consen 103 YTCPKCKYKFTE 114 (116)
T ss_pred EEcCccceeeec
Confidence 678888877764
No 285
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=20.85 E-value=29 Score=19.03 Aligned_cols=14 Identities=36% Similarity=1.037 Sum_probs=11.5
Q ss_pred CcccccchhhccCh
Q psy13994 73 KFGCEYCSARFSQK 86 (97)
Q Consensus 73 ~~~C~~C~~~f~~~ 86 (97)
.++|..|++.|...
T Consensus 135 ~lrC~YCe~~~~~~ 148 (153)
T COG1781 135 ALRCKYCEKTFSED 148 (153)
T ss_pred EEEEEecCcEechh
Confidence 48999999988754
No 286
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.85 E-value=48 Score=14.30 Aligned_cols=12 Identities=17% Similarity=0.545 Sum_probs=8.4
Q ss_pred CCcccccchhhc
Q psy13994 72 KKFGCEYCSARF 83 (97)
Q Consensus 72 ~~~~C~~C~~~f 83 (97)
..+.|..||.++
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 467788887654
No 287
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=20.73 E-value=88 Score=12.95 Aligned_cols=9 Identities=33% Similarity=0.936 Sum_probs=6.1
Q ss_pred ccccccccc
Q psy13994 25 FGCEYCSAR 33 (97)
Q Consensus 25 ~~C~~C~~~ 33 (97)
+.|+.||..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 668888744
No 288
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=20.71 E-value=78 Score=19.52 Aligned_cols=26 Identities=19% Similarity=0.433 Sum_probs=20.2
Q ss_pred cCCCccccccccccccChHHHHHHHH
Q psy13994 20 EGVKKFGCEYCSARFSQKISCRVHML 45 (97)
Q Consensus 20 ~~~~~~~C~~C~~~f~~~~~l~~h~~ 45 (97)
++....+|.+||..|.......+|..
T Consensus 271 T~~~~ik~n~c~~~~~~e~~~~~Ha~ 296 (306)
T COG5539 271 TASPSIKCNICGTGFVGEKDYYAHAL 296 (306)
T ss_pred cCCceEEeeccccccchhhHHHHHHH
Confidence 34445789999999998888877754
No 289
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=20.63 E-value=33 Score=17.69 Aligned_cols=11 Identities=27% Similarity=0.951 Sum_probs=7.9
Q ss_pred cccccchhhcc
Q psy13994 74 FGCEYCSARFS 84 (97)
Q Consensus 74 ~~C~~C~~~f~ 84 (97)
|.|..||..+.
T Consensus 101 y~C~~Cg~~wr 111 (113)
T COG1594 101 YKCTRCGYRWR 111 (113)
T ss_pred EEecccCCEee
Confidence 67888877664
No 290
>cd01396 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
Probab=20.53 E-value=80 Score=15.03 Aligned_cols=20 Identities=10% Similarity=0.175 Sum_probs=15.4
Q ss_pred ccchhhccChHHHHHHhhhc
Q psy13994 77 EYCSARFSQKISCRVHMLRH 96 (97)
Q Consensus 77 ~~C~~~f~~~~~l~~H~~~h 96 (97)
.-+|+.|....++.+.+..+
T Consensus 32 sP~Gkk~RS~~ev~~yL~~~ 51 (77)
T cd01396 32 SPTGKKFRSKVELARYLEKN 51 (77)
T ss_pred CCCCCEEECHHHHHHHHHhC
Confidence 44788888888888887654
No 291
>PF03470 zf-XS: XS zinc finger domain; InterPro: IPR005381 This domain is a putative nucleic acid binding zinc finger and is found at the N terminus of proteins that also contain an adjacent XS domain IPR005380 from INTERPRO and in some proteins a C-terminal XH domain IPR005379 from INTERPRO.
Probab=20.47 E-value=84 Score=13.25 Aligned_cols=11 Identities=9% Similarity=0.024 Sum_probs=6.2
Q ss_pred hccChHHHHHHh
Q psy13994 82 RFSQKISCRVHM 93 (97)
Q Consensus 82 ~f~~~~~l~~H~ 93 (97)
.|. ...|.+|-
T Consensus 11 ~Y~-~~~LlqHA 21 (43)
T PF03470_consen 11 DYK-YRELLQHA 21 (43)
T ss_pred cee-hhHHHHHH
Confidence 355 55666664
No 292
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=20.41 E-value=32 Score=15.06 Aligned_cols=11 Identities=18% Similarity=1.008 Sum_probs=5.7
Q ss_pred cccccchhhcc
Q psy13994 74 FGCEYCSARFS 84 (97)
Q Consensus 74 ~~C~~C~~~f~ 84 (97)
|.|..|+.+|+
T Consensus 8 y~CDLCn~~~p 18 (57)
T PF14445_consen 8 YSCDLCNSSHP 18 (57)
T ss_pred HhHHhhcccCc
Confidence 45555555544
No 293
>KOG0801|consensus
Probab=20.34 E-value=41 Score=18.76 Aligned_cols=12 Identities=17% Similarity=0.556 Sum_probs=9.3
Q ss_pred cccccchhhccC
Q psy13994 74 FGCEYCSARFSQ 85 (97)
Q Consensus 74 ~~C~~C~~~f~~ 85 (97)
++|++|.|.-..
T Consensus 139 ~KCPvC~K~V~s 150 (205)
T KOG0801|consen 139 MKCPVCHKVVPS 150 (205)
T ss_pred ccCCccccccCC
Confidence 789999986543
No 294
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=20.29 E-value=71 Score=13.87 Aligned_cols=22 Identities=27% Similarity=0.552 Sum_probs=14.2
Q ss_pred CCCccccccccccccChHHHHHHHH
Q psy13994 21 GVKKFGCEYCSARFSQKISCRVHML 45 (97)
Q Consensus 21 ~~~~~~C~~C~~~f~~~~~l~~h~~ 45 (97)
..+|-.|..|...|. .|..|+.
T Consensus 2 ~~k~GYCE~Cr~kfd---~l~~Hi~ 23 (49)
T smart00586 2 EKKPGYCENCREKYD---DLETHLL 23 (49)
T ss_pred CCCCcccccHhHHHh---hHHHHhc
Confidence 346677888887775 4555543
No 295
>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=20.13 E-value=45 Score=16.35 Aligned_cols=12 Identities=17% Similarity=0.584 Sum_probs=9.3
Q ss_pred cccccchhhccC
Q psy13994 74 FGCEYCSARFSQ 85 (97)
Q Consensus 74 ~~C~~C~~~f~~ 85 (97)
-.|..|++.+..
T Consensus 79 ~~C~vC~k~l~~ 90 (109)
T PF10367_consen 79 TKCSVCGKPLGN 90 (109)
T ss_pred CCccCcCCcCCC
Confidence 359999987765
No 296
>KOG2857|consensus
Probab=20.11 E-value=57 Score=17.76 Aligned_cols=22 Identities=23% Similarity=0.566 Sum_probs=19.7
Q ss_pred ccccccccccccChHHHHHHHH
Q psy13994 24 KFGCEYCSARFSQKISCRVHML 45 (97)
Q Consensus 24 ~~~C~~C~~~f~~~~~l~~h~~ 45 (97)
-|+|+.|...+-+...++.|..
T Consensus 17 KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 17 KYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hccCCCCCCccccchhhhhccC
Confidence 5999999999999999998876
No 297
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=20.09 E-value=47 Score=14.41 Aligned_cols=14 Identities=21% Similarity=0.664 Sum_probs=8.8
Q ss_pred CCCcccccchhhcc
Q psy13994 71 VKKFGCEYCSARFS 84 (97)
Q Consensus 71 ~~~~~C~~C~~~f~ 84 (97)
.....|+.|+..|-
T Consensus 38 ~~~v~C~~C~~~fC 51 (64)
T smart00647 38 CNRVTCPKCGFSFC 51 (64)
T ss_pred CCeeECCCCCCeEC
Confidence 34566777776664
Done!