Query psy13164
Match_columns 193
No_of_seqs 174 out of 2140
Neff 10.2
Searched_HMMs 46136
Date Fri Aug 16 21:50:11 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13164.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13164hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 1.2E-26 2.7E-31 168.7 5.5 129 53-183 126-265 (279)
2 KOG2462|consensus 99.9 3.2E-25 6.9E-30 161.4 5.6 108 84-192 128-246 (279)
3 KOG1074|consensus 99.6 2.2E-16 4.8E-21 130.0 2.3 38 56-94 352-389 (958)
4 KOG3608|consensus 99.6 3E-15 6.5E-20 112.8 5.7 130 56-188 236-379 (467)
5 KOG3576|consensus 99.6 7.6E-16 1.7E-20 107.8 2.1 111 55-187 115-238 (267)
6 KOG3576|consensus 99.5 1.6E-15 3.6E-20 106.1 1.1 82 105-186 115-198 (267)
7 KOG1074|consensus 99.5 3.3E-15 7.1E-20 123.2 2.4 54 136-189 881-935 (958)
8 KOG3623|consensus 99.5 4.5E-15 9.8E-20 120.8 1.4 106 58-183 211-331 (1007)
9 KOG3608|consensus 99.5 3.7E-14 8.1E-19 107.0 4.4 139 54-192 204-355 (467)
10 KOG3623|consensus 99.5 1.4E-14 3E-19 118.0 1.8 75 107-181 894-970 (1007)
11 PHA00733 hypothetical protein 99.1 8.2E-11 1.8E-15 79.1 3.4 80 106-186 39-124 (128)
12 PHA02768 hypothetical protein; 99.1 4.5E-11 9.7E-16 66.9 1.7 42 135-177 6-47 (55)
13 PLN03086 PRLI-interacting fact 99.1 2.9E-10 6.3E-15 92.8 6.4 126 56-192 406-544 (567)
14 PHA02768 hypothetical protein; 98.9 6.8E-10 1.5E-14 62.2 1.7 43 107-150 5-47 (55)
15 PLN03086 PRLI-interacting fact 98.9 5.2E-09 1.1E-13 85.6 6.3 109 59-183 435-562 (567)
16 PHA00733 hypothetical protein 98.8 4.7E-09 1E-13 70.6 3.9 56 103-159 69-124 (128)
17 KOG3993|consensus 98.7 1.4E-08 3.1E-13 78.9 3.1 22 162-183 459-480 (500)
18 PF13465 zf-H2C2_2: Zinc-finge 98.6 2.2E-08 4.7E-13 48.0 2.3 24 149-172 1-25 (26)
19 PHA00616 hypothetical protein 98.6 1.5E-08 3.3E-13 54.0 1.8 32 161-192 1-32 (44)
20 KOG3993|consensus 98.6 6.8E-09 1.5E-13 80.6 -0.2 79 108-186 268-381 (500)
21 PHA00732 hypothetical protein 98.4 2.1E-07 4.5E-12 57.0 2.2 48 107-159 1-49 (79)
22 PF13465 zf-H2C2_2: Zinc-finge 98.4 3.4E-07 7.4E-12 43.8 2.3 24 122-145 1-25 (26)
23 PHA00616 hypothetical protein 98.3 4E-07 8.6E-12 48.6 1.5 38 134-171 1-39 (44)
24 PHA00732 hypothetical protein 98.3 6E-07 1.3E-11 55.0 2.3 47 134-185 1-48 (79)
25 PF00096 zf-C2H2: Zinc finger, 98.2 1.5E-06 3.2E-11 40.3 1.9 23 162-184 1-23 (23)
26 PF05605 zf-Di19: Drought indu 98.1 6.1E-06 1.3E-10 46.9 4.0 48 135-185 3-53 (54)
27 PF00096 zf-C2H2: Zinc finger, 97.9 6.8E-06 1.5E-10 38.0 2.0 22 135-156 1-22 (23)
28 PF12756 zf-C2H2_2: C2H2 type 97.9 6.8E-06 1.5E-10 52.7 2.6 73 109-184 1-73 (100)
29 PF13894 zf-C2H2_4: C2H2-type 97.8 1.7E-05 3.6E-10 36.8 2.1 23 162-184 1-23 (24)
30 PF13912 zf-C2H2_6: C2H2-type 97.8 1.3E-05 2.7E-10 38.6 1.7 25 161-185 1-25 (27)
31 PF05605 zf-Di19: Drought indu 97.7 7E-05 1.5E-09 42.5 4.1 48 108-158 3-53 (54)
32 PF13894 zf-C2H2_4: C2H2-type 97.6 7.1E-05 1.5E-09 34.6 2.3 23 135-157 1-23 (24)
33 PF09237 GAGA: GAGA factor; I 97.5 6.4E-05 1.4E-09 41.1 1.9 29 161-189 24-52 (54)
34 PF12756 zf-C2H2_2: C2H2 type 97.5 0.0001 2.2E-09 47.2 2.6 24 59-82 1-24 (100)
35 smart00355 ZnF_C2H2 zinc finge 97.4 0.00014 3.1E-09 34.1 2.3 24 162-185 1-24 (26)
36 PF13912 zf-C2H2_6: C2H2-type 97.4 0.00012 2.6E-09 35.1 1.9 23 108-130 2-24 (27)
37 smart00355 ZnF_C2H2 zinc finge 97.0 0.00072 1.6E-08 31.6 2.1 24 135-158 1-24 (26)
38 COG5189 SFP1 Putative transcri 96.9 0.00024 5.3E-09 53.9 0.4 22 160-181 397-418 (423)
39 COG5189 SFP1 Putative transcri 96.8 0.00053 1.1E-08 52.2 0.9 51 104-154 346-418 (423)
40 PF12874 zf-met: Zinc-finger o 96.7 0.00089 1.9E-08 31.3 1.4 22 162-183 1-22 (25)
41 PF13909 zf-H2C2_5: C2H2-type 96.7 0.0011 2.4E-08 30.7 1.5 22 162-184 1-22 (24)
42 PF09237 GAGA: GAGA factor; I 96.6 0.0018 3.8E-08 35.5 2.0 26 134-159 24-49 (54)
43 PRK04860 hypothetical protein; 96.5 0.0019 4.2E-08 45.1 2.3 37 134-174 119-156 (160)
44 PF12874 zf-met: Zinc-finger o 96.5 0.0019 4E-08 30.2 1.5 22 135-156 1-22 (25)
45 PF13909 zf-H2C2_5: C2H2-type 96.2 0.0041 8.8E-08 28.7 1.7 21 135-156 1-21 (24)
46 PF13913 zf-C2HC_2: zinc-finge 95.8 0.0083 1.8E-07 28.1 1.9 20 163-183 4-23 (25)
47 PF12171 zf-C2H2_jaz: Zinc-fin 95.8 0.0023 5.1E-08 30.5 0.0 22 162-183 2-23 (27)
48 PRK04860 hypothetical protein; 95.6 0.009 1.9E-07 41.8 2.1 37 107-147 119-156 (160)
49 PF12171 zf-C2H2_jaz: Zinc-fin 95.0 0.0054 1.2E-07 29.2 -0.2 22 135-156 2-23 (27)
50 smart00451 ZnF_U1 U1-like zinc 94.1 0.037 8.1E-07 27.9 1.6 23 161-183 3-25 (35)
51 KOG1146|consensus 92.9 0.023 4.9E-07 51.3 -0.6 129 53-184 461-641 (1406)
52 smart00451 ZnF_U1 U1-like zinc 92.9 0.082 1.8E-06 26.6 1.7 23 134-156 3-25 (35)
53 PF12013 DUF3505: Protein of u 92.0 0.35 7.7E-06 31.5 4.3 25 162-186 81-109 (109)
54 KOG2186|consensus 90.9 0.19 4.2E-06 37.4 2.3 46 108-155 4-49 (276)
55 cd00350 rubredoxin_like Rubred 90.2 0.2 4.2E-06 25.1 1.3 10 108-117 2-11 (33)
56 COG5048 FOG: Zn-finger [Genera 90.0 0.051 1.1E-06 43.7 -1.4 54 107-160 289-349 (467)
57 COG5048 FOG: Zn-finger [Genera 89.8 0.063 1.4E-06 43.2 -1.1 59 134-192 289-354 (467)
58 PF06524 NOA36: NOA36 protein; 88.5 0.073 1.6E-06 39.7 -1.3 24 134-157 209-232 (314)
59 KOG1146|consensus 88.5 0.14 3.1E-06 46.5 0.2 116 57-183 1228-1350(1406)
60 KOG2231|consensus 87.9 0.8 1.7E-05 39.2 4.1 116 58-182 100-264 (669)
61 KOG2893|consensus 87.1 0.18 3.8E-06 37.3 -0.1 41 110-153 13-53 (341)
62 PF09538 FYDLN_acid: Protein o 86.2 0.44 9.6E-06 31.0 1.4 12 161-172 26-37 (108)
63 KOG2231|consensus 85.2 1.5 3.3E-05 37.6 4.4 47 135-184 183-235 (669)
64 KOG2186|consensus 84.8 0.7 1.5E-05 34.5 2.0 50 134-185 3-52 (276)
65 COG5236 Uncharacterized conser 83.5 0.82 1.8E-05 35.8 2.0 75 108-183 152-242 (493)
66 TIGR00622 ssl1 transcription f 83.4 1.2 2.5E-05 29.2 2.4 76 107-185 15-105 (112)
67 KOG4173|consensus 83.1 0.53 1.2E-05 34.0 0.8 73 108-182 80-167 (253)
68 KOG2482|consensus 82.9 4 8.6E-05 32.1 5.4 56 134-189 144-225 (423)
69 COG5236 Uncharacterized conser 82.7 1.8 3.9E-05 34.0 3.5 121 57-183 151-303 (493)
70 KOG2785|consensus 82.7 3.9 8.5E-05 32.6 5.4 74 107-183 166-242 (390)
71 COG4049 Uncharacterized protei 82.5 0.74 1.6E-05 25.8 1.0 25 105-129 15-39 (65)
72 PF12013 DUF3505: Protein of u 82.2 3.8 8.2E-05 26.6 4.5 26 134-159 80-109 (109)
73 PRK14890 putative Zn-ribbon RN 81.0 1.9 4.2E-05 24.6 2.4 9 134-142 48-56 (59)
74 PHA00626 hypothetical protein 79.8 1.4 2.9E-05 24.8 1.5 11 108-118 24-34 (59)
75 smart00659 RPOLCX RNA polymera 79.5 1.6 3.4E-05 23.4 1.7 9 108-116 3-11 (44)
76 KOG2785|consensus 79.2 2 4.3E-05 34.2 2.7 73 54-129 163-242 (390)
77 KOG2482|consensus 79.1 3.9 8.4E-05 32.2 4.2 22 162-183 280-301 (423)
78 smart00614 ZnF_BED BED zinc fi 78.0 2 4.3E-05 23.6 1.8 10 135-144 19-28 (50)
79 PF05443 ROS_MUCR: ROS/MUCR tr 77.6 1.7 3.6E-05 29.4 1.7 22 162-186 73-94 (132)
80 PF09986 DUF2225: Uncharacteri 77.0 0.42 9.1E-06 35.2 -1.4 41 107-147 5-61 (214)
81 PF09723 Zn-ribbon_8: Zinc rib 76.5 0.94 2E-05 24.0 0.3 9 108-116 6-14 (42)
82 PF12907 zf-met2: Zinc-binding 75.5 1.6 3.5E-05 22.9 0.9 32 162-193 2-37 (40)
83 PF02892 zf-BED: BED zinc fing 75.5 2.1 4.6E-05 22.7 1.5 20 162-181 17-40 (45)
84 cd00729 rubredoxin_SM Rubredox 75.4 1.9 4.1E-05 21.6 1.2 9 108-116 3-11 (34)
85 COG2888 Predicted Zn-ribbon RN 75.3 2.7 6E-05 24.0 1.9 11 132-142 48-58 (61)
86 smart00834 CxxC_CXXC_SSSS Puta 73.9 1.3 2.9E-05 22.9 0.4 10 108-117 6-15 (41)
87 TIGR02098 MJ0042_CXXC MJ0042 f 73.7 2.8 6E-05 21.4 1.6 10 135-144 26-35 (38)
88 COG1592 Rubrerythrin [Energy p 73.2 2.1 4.6E-05 30.1 1.4 22 107-141 134-156 (166)
89 PF13719 zinc_ribbon_5: zinc-r 72.7 3.3 7.1E-05 21.2 1.7 11 107-117 25-35 (37)
90 COG1997 RPL43A Ribosomal prote 72.2 2.3 5E-05 26.3 1.2 11 135-145 54-64 (89)
91 KOG2893|consensus 71.2 1.8 3.9E-05 32.2 0.7 43 34-76 11-53 (341)
92 PF14353 CpXC: CpXC protein 70.3 3.7 8.1E-05 27.4 2.1 49 108-156 2-60 (128)
93 smart00734 ZnF_Rad18 Rad18-lik 69.0 4.7 0.0001 18.8 1.6 19 163-182 3-21 (26)
94 TIGR02605 CxxC_CxxC_SSSS putat 67.8 2.1 4.5E-05 23.6 0.3 10 108-117 6-15 (52)
95 COG1198 PriA Primosomal protei 67.3 3.4 7.3E-05 36.2 1.6 9 161-169 475-483 (730)
96 smart00531 TFIIE Transcription 66.9 4.8 0.0001 27.7 2.1 12 135-146 100-111 (147)
97 TIGR00373 conserved hypothetic 66.7 6.5 0.00014 27.5 2.7 29 135-171 110-138 (158)
98 PF05443 ROS_MUCR: ROS/MUCR tr 66.5 4.5 9.8E-05 27.4 1.8 24 134-160 72-95 (132)
99 TIGR02300 FYDLN_acid conserved 66.4 4.1 8.8E-05 27.2 1.5 12 134-145 26-37 (129)
100 TIGR00373 conserved hypothetic 66.0 3.9 8.4E-05 28.6 1.5 32 105-144 107-138 (158)
101 PRK06266 transcription initiat 65.9 3.2 6.8E-05 29.7 1.0 29 135-171 118-146 (178)
102 PF06524 NOA36: NOA36 protein; 65.5 2 4.4E-05 32.3 0.0 81 103-185 138-233 (314)
103 KOG4167|consensus 64.8 2.3 4.9E-05 36.8 0.1 25 134-158 792-816 (907)
104 PF15269 zf-C2H2_7: Zinc-finge 64.7 6.2 0.00013 21.1 1.7 21 162-182 21-41 (54)
105 PRK00398 rpoP DNA-directed RNA 64.3 3.6 7.8E-05 22.1 0.9 8 108-115 22-29 (46)
106 PF13717 zinc_ribbon_4: zinc-r 64.3 5.5 0.00012 20.2 1.5 9 135-143 26-34 (36)
107 COG1996 RPC10 DNA-directed RNA 63.7 4.5 9.7E-05 22.2 1.1 10 108-117 7-16 (49)
108 PRK00464 nrdR transcriptional 63.3 2.9 6.4E-05 29.1 0.5 15 108-122 29-43 (154)
109 KOG4167|consensus 59.8 2.5 5.4E-05 36.6 -0.4 24 162-185 793-816 (907)
110 KOG3408|consensus 59.0 6.2 0.00013 26.1 1.4 23 161-183 57-79 (129)
111 PF09963 DUF2197: Uncharacteri 58.9 1.8 4E-05 24.4 -0.9 36 59-94 4-39 (56)
112 PRK04023 DNA polymerase II lar 58.8 10 0.00023 34.4 3.0 11 161-171 663-673 (1121)
113 PF03604 DNA_RNApol_7kD: DNA d 56.8 5.4 0.00012 19.8 0.6 8 108-115 18-25 (32)
114 TIGR00595 priA primosomal prot 56.1 6.2 0.00013 33.2 1.3 8 134-141 253-260 (505)
115 KOG4173|consensus 55.3 7.9 0.00017 28.2 1.5 46 135-182 80-127 (253)
116 PF13878 zf-C2H2_3: zinc-finge 54.4 14 0.0003 19.4 2.0 24 162-185 14-39 (41)
117 COG4957 Predicted transcriptio 52.2 7.5 0.00016 26.2 0.9 22 135-159 77-98 (148)
118 KOG3507|consensus 52.1 5.7 0.00012 22.6 0.3 28 87-118 21-48 (62)
119 PRK14873 primosome assembly pr 50.4 9 0.00019 33.4 1.4 8 88-95 385-392 (665)
120 PF08274 PhnA_Zn_Ribbon: PhnA 48.9 9.2 0.0002 18.6 0.7 8 134-141 19-26 (30)
121 PF01927 Mut7-C: Mut7-C RNAse 47.6 12 0.00026 25.7 1.5 18 134-151 124-141 (147)
122 PF04959 ARS2: Arsenite-resist 47.4 16 0.00034 27.0 2.1 23 134-156 77-99 (214)
123 KOG0696|consensus 46.4 8.3 0.00018 31.6 0.6 57 105-169 71-129 (683)
124 PF04959 ARS2: Arsenite-resist 46.0 9.8 0.00021 28.1 0.8 25 161-185 77-101 (214)
125 PF10571 UPF0547: Uncharacteri 44.3 11 0.00024 17.6 0.6 9 163-171 16-24 (26)
126 PF07754 DUF1610: Domain of un 41.6 12 0.00026 17.2 0.5 7 108-114 17-23 (24)
127 PF01363 FYVE: FYVE zinc finge 40.4 15 0.00033 21.4 0.9 9 109-117 11-19 (69)
128 PF13453 zf-TFIIB: Transcripti 40.1 21 0.00045 18.5 1.3 16 108-123 20-35 (41)
129 COG3364 Zn-ribbon containing p 40.1 18 0.00038 23.2 1.2 12 135-146 3-14 (112)
130 KOG2593|consensus 39.5 22 0.00048 29.0 2.0 35 105-142 126-161 (436)
131 PRK05580 primosome assembly pr 38.0 17 0.00037 31.8 1.3 9 134-142 421-429 (679)
132 TIGR01206 lysW lysine biosynth 38.0 24 0.00051 19.8 1.4 7 109-115 24-30 (54)
133 COG4896 Uncharacterized protei 37.2 7.2 0.00016 22.4 -0.8 11 83-93 28-38 (68)
134 KOG3408|consensus 36.9 23 0.00049 23.5 1.3 23 134-156 57-79 (129)
135 COG1656 Uncharacterized conser 36.2 36 0.00079 24.0 2.4 18 134-151 130-147 (165)
136 KOG2593|consensus 36.2 34 0.00074 28.0 2.5 35 134-171 128-163 (436)
137 PF10537 WAC_Acf1_DNA_bd: ATP- 36.0 56 0.0012 21.0 3.1 37 107-143 3-39 (102)
138 COG5151 SSL1 RNA polymerase II 35.2 20 0.00043 28.0 1.0 48 136-184 364-411 (421)
139 PF01780 Ribosomal_L37ae: Ribo 34.6 11 0.00024 23.6 -0.3 11 135-145 54-64 (90)
140 PF02176 zf-TRAF: TRAF-type zi 34.1 31 0.00067 19.3 1.6 8 148-155 24-31 (60)
141 PF13451 zf-trcl: Probable zin 33.9 33 0.00071 18.9 1.5 11 108-118 5-15 (49)
142 KOG2907|consensus 33.5 21 0.00046 23.3 0.8 10 60-69 10-19 (116)
143 KOG2807|consensus 33.4 61 0.0013 25.6 3.4 24 161-184 345-368 (378)
144 smart00154 ZnF_AN1 AN1-like Zi 33.3 19 0.00042 18.6 0.5 13 161-173 12-24 (39)
145 TIGR00100 hypA hydrogenase nic 32.2 23 0.0005 23.3 0.9 10 108-117 71-80 (115)
146 COG4530 Uncharacterized protei 30.9 27 0.00059 22.7 1.0 11 134-144 26-36 (129)
147 PRK12380 hydrogenase nickel in 30.8 26 0.00056 23.0 0.9 10 108-117 71-80 (113)
148 cd00924 Cyt_c_Oxidase_Vb Cytoc 30.8 21 0.00045 22.8 0.5 20 154-173 72-91 (97)
149 PLN02294 cytochrome c oxidase 30.7 15 0.00032 26.0 -0.3 23 151-173 131-153 (174)
150 PF08271 TF_Zn_Ribbon: TFIIB z 30.4 30 0.00066 18.1 1.0 8 108-115 20-27 (43)
151 KOG2071|consensus 30.1 31 0.00067 29.4 1.4 25 161-185 418-442 (579)
152 PF03811 Zn_Tnp_IS1: InsA N-te 29.5 33 0.00071 17.4 1.0 8 106-113 28-35 (36)
153 COG5112 UFD2 U1-like Zn-finger 29.4 26 0.00057 22.6 0.7 22 161-182 55-76 (126)
154 PF01428 zf-AN1: AN1-like Zinc 28.4 19 0.00042 18.9 0.0 13 161-173 13-25 (43)
155 COG3091 SprT Zn-dependent meta 28.3 27 0.00058 24.3 0.7 33 134-170 117-149 (156)
156 cd00065 FYVE FYVE domain; Zinc 28.2 37 0.00081 18.7 1.2 8 110-117 5-12 (57)
157 PF04810 zf-Sec23_Sec24: Sec23 28.0 35 0.00076 17.6 1.0 10 106-115 23-32 (40)
158 smart00661 RPOL9 RNA polymeras 27.6 46 0.00099 17.9 1.5 9 108-116 21-29 (52)
159 PF04423 Rad50_zn_hook: Rad50 27.0 24 0.00052 19.5 0.2 12 163-174 22-33 (54)
160 PF12760 Zn_Tnp_IS1595: Transp 26.9 46 0.00099 17.7 1.3 7 108-114 38-44 (46)
161 COG1998 RPS31 Ribosomal protei 26.9 39 0.00084 18.6 1.0 9 161-169 37-45 (51)
162 PF07282 OrfB_Zn_ribbon: Putat 26.5 95 0.0021 17.9 2.8 9 108-116 47-55 (69)
163 smart00731 SprT SprT homologue 26.3 36 0.00078 23.3 1.1 31 107-144 112-143 (146)
164 PF04780 DUF629: Protein of un 26.3 50 0.0011 27.5 2.0 26 134-159 57-83 (466)
165 PF07975 C1_4: TFIIH C1-like d 26.1 12 0.00026 20.8 -1.1 25 106-130 20-44 (51)
166 PF08790 zf-LYAR: LYAR-type C2 26.0 17 0.00038 17.4 -0.4 9 163-171 2-10 (28)
167 PRK00564 hypA hydrogenase nick 25.9 33 0.00071 22.7 0.8 10 108-117 72-81 (117)
168 PRK04351 hypothetical protein; 25.0 38 0.00083 23.4 1.0 31 108-145 113-143 (149)
169 PF03833 PolC_DP2: DNA polymer 24.8 24 0.00053 31.5 0.0 11 134-144 680-690 (900)
170 KOG2272|consensus 24.3 82 0.0018 24.0 2.6 20 54-73 96-115 (332)
171 PRK00432 30S ribosomal protein 24.2 61 0.0013 17.8 1.5 9 108-116 38-46 (50)
172 PF02150 RNA_POL_M_15KD: RNA p 23.3 25 0.00053 17.7 -0.2 8 109-116 22-29 (35)
173 PF06397 Desulfoferrod_N: Desu 23.0 40 0.00086 17.2 0.6 11 107-117 6-16 (36)
174 COG2331 Uncharacterized protei 22.9 31 0.00067 20.9 0.2 9 108-116 13-21 (82)
175 PF06220 zf-U1: U1 zinc finger 22.8 76 0.0017 16.2 1.6 11 161-171 3-13 (38)
176 PF14311 DUF4379: Domain of un 22.4 64 0.0014 17.8 1.4 8 135-142 29-36 (55)
177 smart00064 FYVE Protein presen 22.3 47 0.001 19.1 0.9 10 109-118 12-21 (68)
178 COG1773 Rubredoxin [Energy pro 22.3 44 0.00094 18.9 0.7 13 107-119 3-15 (55)
179 PRK03824 hypA hydrogenase nick 22.3 41 0.0009 22.8 0.7 12 108-119 71-82 (135)
180 PF10013 DUF2256: Uncharacteri 21.7 56 0.0012 17.3 1.0 12 163-174 10-21 (42)
181 PF14205 Cys_rich_KTR: Cystein 21.2 25 0.00054 19.7 -0.4 8 134-141 28-35 (55)
182 PF04438 zf-HIT: HIT zinc fing 21.1 65 0.0014 15.5 1.1 11 108-118 14-24 (30)
183 KOG0717|consensus 20.9 57 0.0012 27.1 1.3 22 162-183 293-314 (508)
184 COG3677 Transposase and inacti 20.9 41 0.0009 22.6 0.5 13 161-173 53-65 (129)
185 TIGR00280 L37a ribosomal prote 20.8 40 0.00087 21.2 0.4 13 134-146 53-65 (91)
186 PF14803 Nudix_N_2: Nudix N-te 20.4 56 0.0012 16.3 0.8 8 108-115 23-30 (34)
187 PTZ00448 hypothetical protein; 20.4 71 0.0015 25.7 1.7 23 161-183 314-336 (373)
188 KOG1842|consensus 20.1 66 0.0014 26.6 1.5 26 107-132 15-41 (505)
No 1
>KOG2462|consensus
Probab=99.93 E-value=1.2e-26 Score=168.75 Aligned_cols=129 Identities=19% Similarity=0.431 Sum_probs=115.0
Q ss_pred cCCCCcccchhHhhccCchhhccccccccc--CCCCccCCCCccc-------chhhhhhcCCCceecccccccccChhHH
Q psy13164 53 NNGNDAVTRDCLEFFKSHDSTLKNESDHER--RSINYNCQQSYKV-------GKLNKILHRGIRYKCDLCSKEYFHKGSL 123 (193)
Q Consensus 53 ~~~~~~~c~~c~~~f~~~~~~~~h~~~~~~--~~~~~~C~~c~~~-------~~~~~~~~~~~~~~C~~C~~~f~~~~~l 123 (193)
.....+.|..|++.+.+...|.+|.+.|.. ..+.+.|..|+++ ..|.++|. .++.|.+||+.|.+..-|
T Consensus 126 ~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLL 203 (279)
T KOG2462|consen 126 AKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLL 203 (279)
T ss_pred ccCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHh
Confidence 355678899999999999999999998876 3456999999985 45667775 569999999999999999
Q ss_pred HHHHHhhCCc-ceeccccchhccChhHHHHHHHHhCCc-ccccccCcccccChHHHHHHHHH
Q psy13164 124 TEHKKRHQGI-RYKCDLCSKEYFHKGYLTDHKKIHQGI-RYKCNLCSKEFLRKDILIEHKKI 183 (193)
Q Consensus 124 ~~h~~~h~~~-~~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~C~~C~~~F~~~~~L~~H~~~ 183 (193)
+-|+++|+|+ ||.|++|+++|...++|+.||++|.+. +|+|..|+++|...+.|.+|...
T Consensus 204 QGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 204 QGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred hcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 9999999998 999999999999999999999999996 99999999999999999999754
No 2
>KOG2462|consensus
Probab=99.91 E-value=3.2e-25 Score=161.42 Aligned_cols=108 Identities=22% Similarity=0.476 Sum_probs=98.2
Q ss_pred CCCccCCCCccc-------chhhhhhc---CCCceecccccccccChhHHHHHHHhhCCcceeccccchhccChhHHHHH
Q psy13164 84 SINYNCQQSYKV-------GKLNKILH---RGIRYKCDLCSKEYFHKGSLTEHKKRHQGIRYKCDLCSKEYFHKGYLTDH 153 (193)
Q Consensus 84 ~~~~~C~~c~~~-------~~~~~~~~---~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~C~~C~~~f~~~~~l~~H 153 (193)
...|+|++|++. .+|+.+|- ..+.+.|+.|++.|.....|..|+++|.- ++.|.+|||.|.+.+.|+.|
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l-~c~C~iCGKaFSRPWLLQGH 206 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTL-PCECGICGKAFSRPWLLQGH 206 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCC-CcccccccccccchHHhhcc
Confidence 344999999984 46666663 35669999999999999999999999996 89999999999999999999
Q ss_pred HHHhCCc-ccccccCcccccChHHHHHHHHHcCCCCCCCC
Q psy13164 154 KKIHQGI-RYKCNLCSKEFLRKDILIEHKKIHQGIRFKCD 192 (193)
Q Consensus 154 ~~~h~~~-~~~C~~C~~~F~~~~~L~~H~~~h~~~~~~~c 192 (193)
+|+|+|+ ||.|..|+++|..+++|+.|+.+|.+.|.|.|
T Consensus 207 iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC 246 (279)
T KOG2462|consen 207 IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQC 246 (279)
T ss_pred cccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccC
Confidence 9999998 99999999999999999999999999999887
No 3
>KOG1074|consensus
Probab=99.60 E-value=2.2e-16 Score=129.96 Aligned_cols=38 Identities=16% Similarity=0.223 Sum_probs=32.7
Q ss_pred CCcccchhHhhccCchhhcccccccccCCCCccCCCCcc
Q psy13164 56 NDAVTRDCLEFFKSHDSTLKNESDHERRSINYNCQQSYK 94 (193)
Q Consensus 56 ~~~~c~~c~~~f~~~~~~~~h~~~~~~~~~~~~C~~c~~ 94 (193)
.+.+|.+|.++|.+.+.|..|.+.|.. ++||+|.+|+.
T Consensus 352 ~khkCr~CakvfgS~SaLqiHlRSHTG-ERPfqCnvCG~ 389 (958)
T KOG1074|consen 352 FKHKCRFCAKVFGSDSALQIHLRSHTG-ERPFQCNVCGN 389 (958)
T ss_pred ccchhhhhHhhcCchhhhhhhhhccCC-CCCeeeccccc
Confidence 455799999999999999999988874 88999999974
No 4
>KOG3608|consensus
Probab=99.57 E-value=3e-15 Score=112.80 Aligned_cols=130 Identities=20% Similarity=0.368 Sum_probs=93.8
Q ss_pred CCcccchhHhhccCchhhcccccccccCCCCccCCCCcc-------cchhhhh-hcCCCceecccccccccChhHHHHHH
Q psy13164 56 NDAVTRDCLEFFKSHDSTLKNESDHERRSINYNCQQSYK-------VGKLNKI-LHRGIRYKCDLCSKEYFHKGSLTEHK 127 (193)
Q Consensus 56 ~~~~c~~c~~~f~~~~~~~~h~~~~~~~~~~~~C~~c~~-------~~~~~~~-~~~~~~~~C~~C~~~f~~~~~l~~h~ 127 (193)
.+|.|..|.+-|.++..|..|+..|- ..|+|+.|+. +..|++. |...+||+|+.|+..|.+...|.+|.
T Consensus 236 n~fqC~~C~KrFaTeklL~~Hv~rHv---n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~ 312 (467)
T KOG3608|consen 236 NSFQCAQCFKRFATEKLLKSHVVRHV---NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHV 312 (467)
T ss_pred CchHHHHHHHHHhHHHHHHHHHHHhh---hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHH
Confidence 35666666666666666666665553 2366776654 3455544 34467888888888888888888888
Q ss_pred HhhCCcceeccc--cchhccChhHHHHHHHHhC-Cc---ccccccCcccccChHHHHHHHHHcCCCC
Q psy13164 128 KRHQGIRYKCDL--CSKEYFHKGYLTDHKKIHQ-GI---RYKCNLCSKEFLRKDILIEHKKIHQGIR 188 (193)
Q Consensus 128 ~~h~~~~~~C~~--C~~~f~~~~~l~~H~~~h~-~~---~~~C~~C~~~F~~~~~L~~H~~~h~~~~ 188 (193)
..|...-|.|.. |...|.+...+.+|++-+. |. +|.|-.|++.|++..+|.+|++.-+|-+
T Consensus 313 ~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~ 379 (467)
T KOG3608|consen 313 QVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFR 379 (467)
T ss_pred HhccccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhccc
Confidence 888865688877 8888888888888887654 43 6888889999988888888887655544
No 5
>KOG3576|consensus
Probab=99.57 E-value=7.6e-16 Score=107.78 Aligned_cols=111 Identities=26% Similarity=0.480 Sum_probs=86.7
Q ss_pred CCCcccchhHhhccCchhhcccccccccCCCCccCCCCcccchhhhhhcCCCceecccccccccChhHHHHHHHhhCCc-
Q psy13164 55 GNDAVTRDCLEFFKSHDSTLKNESDHERRSINYNCQQSYKVGKLNKILHRGIRYKCDLCSKEYFHKGSLTEHKKRHQGI- 133 (193)
Q Consensus 55 ~~~~~c~~c~~~f~~~~~~~~h~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~- 133 (193)
...+.|..|++.|.-...|.+|++-|.. -+.+.|..||+.|.....|++|+++|+|.
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~----------------------vkr~lct~cgkgfndtfdlkrh~rthtgvr 172 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSD----------------------VKRHLCTFCGKGFNDTFDLKRHTRTHTGVR 172 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccH----------------------HHHHHHhhccCcccchhhhhhhhccccCcc
Confidence 3455566666666555555555554442 34478999999999999999999999998
Q ss_pred ceeccccchhccChhHHHHHHHHhCCc------------ccccccCcccccChHHHHHHHHHcCCC
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKKIHQGI------------RYKCNLCSKEFLRKDILIEHKKIHQGI 187 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~h~~~------------~~~C~~C~~~F~~~~~L~~H~~~h~~~ 187 (193)
||.|..|+++|++.-.|..|++.-+|. -|.|..||..-.....+..|+..|+.-
T Consensus 173 pykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 173 PYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPF 238 (267)
T ss_pred ccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCC
Confidence 899999999999999999999865553 288999999988888899999887653
No 6
>KOG3576|consensus
Probab=99.53 E-value=1.6e-15 Score=106.12 Aligned_cols=82 Identities=32% Similarity=0.630 Sum_probs=75.9
Q ss_pred CCceecccccccccChhHHHHHHHhhCCc-ceeccccchhccChhHHHHHHHHhCCc-ccccccCcccccChHHHHHHHH
Q psy13164 105 GIRYKCDLCSKEYFHKGSLTEHKKRHQGI-RYKCDLCSKEYFHKGYLTDHKKIHQGI-RYKCNLCSKEFLRKDILIEHKK 182 (193)
Q Consensus 105 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~-~~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~C~~C~~~F~~~~~L~~H~~ 182 (193)
...|.|..|++.|.....|.+|++.|... .+.|..||+.|.....|++|+++|+|. ||+|..|+++|+++..|..|++
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHH
Confidence 34599999999999999999999999987 799999999999999999999999998 9999999999999999999987
Q ss_pred HcCC
Q psy13164 183 IHQG 186 (193)
Q Consensus 183 ~h~~ 186 (193)
.-+|
T Consensus 195 kvhg 198 (267)
T KOG3576|consen 195 KVHG 198 (267)
T ss_pred HHcC
Confidence 5333
No 7
>KOG1074|consensus
Probab=99.52 E-value=3.3e-15 Score=123.22 Aligned_cols=54 Identities=24% Similarity=0.535 Sum_probs=50.3
Q ss_pred eccccchhccChhHHHHHHHHhCCc-ccccccCcccccChHHHHHHHHHcCCCCC
Q psy13164 136 KCDLCSKEYFHKGYLTDHKKIHQGI-RYKCNLCSKEFLRKDILIEHKKIHQGIRF 189 (193)
Q Consensus 136 ~C~~C~~~f~~~~~l~~H~~~h~~~-~~~C~~C~~~F~~~~~L~~H~~~h~~~~~ 189 (193)
.|..||+.|.+++.|..|+++|+|. ||.|.+|++.|..+.+|+.||.+|.+..|
T Consensus 881 ~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~ 935 (958)
T KOG1074|consen 881 VCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQP 935 (958)
T ss_pred hhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCC
Confidence 8999999999999999999999997 99999999999999999999999988664
No 8
>KOG3623|consensus
Probab=99.50 E-value=4.5e-15 Score=120.83 Aligned_cols=106 Identities=24% Similarity=0.446 Sum_probs=85.1
Q ss_pred cccchhHhhccCchhhcccccccccCCCCccCCCCcccchhhhhhcCCCceecccccccccChhHHHHHHHhhCC-----
Q psy13164 58 AVTRDCLEFFKSHDSTLKNESDHERRSINYNCQQSYKVGKLNKILHRGIRYKCDLCSKEYFHKGSLTEHKKRHQG----- 132 (193)
Q Consensus 58 ~~c~~c~~~f~~~~~~~~h~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~----- 132 (193)
..|.+|+..+....++..|..-.+.+. +..|.|..|..+|.+...|.+||.+|..
T Consensus 211 ltcpycdrgykrltslkeHikyrhekn--------------------e~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa 270 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKN--------------------EPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQA 270 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhC--------------------CCCCcchhhhhhhhhHHHHHHHHHhhcCCCccc
Confidence 356666666666556655544433211 2238899999999999999999998853
Q ss_pred ---------cceeccccchhccChhHHHHHHHHhCCc-ccccccCcccccChHHHHHHHHH
Q psy13164 133 ---------IRYKCDLCSKEYFHKGYLTDHKKIHQGI-RYKCNLCSKEFLRKDILIEHKKI 183 (193)
Q Consensus 133 ---------~~~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~C~~C~~~F~~~~~L~~H~~~ 183 (193)
+.|+|.+|||+|..+..|+-|+|+|.|+ ||.|+.|.++|..+..+..|+..
T Consensus 271 ~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 271 ISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred ccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 2599999999999999999999999998 99999999999999998888753
No 9
>KOG3608|consensus
Probab=99.47 E-value=3.7e-14 Score=106.96 Aligned_cols=139 Identities=22% Similarity=0.372 Sum_probs=88.4
Q ss_pred CCCCcccchhHhhccCchhhccccccccc-CCCCccCCCCcccch---hhhhhcCC--CceecccccccccChhHHHHHH
Q psy13164 54 NGNDAVTRDCLEFFKSHDSTLKNESDHER-RSINYNCQQSYKVGK---LNKILHRG--IRYKCDLCSKEYFHKGSLTEHK 127 (193)
Q Consensus 54 ~~~~~~c~~c~~~f~~~~~~~~h~~~~~~-~~~~~~C~~c~~~~~---~~~~~~~~--~~~~C~~C~~~f~~~~~l~~h~ 127 (193)
++....|..||..|++...+..|.+.... ...+|.|..|.+.+. ..+.|... ..|+|+.|+.+....+.|..|+
T Consensus 204 ~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~ 283 (467)
T KOG3608|consen 204 NEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHI 283 (467)
T ss_pred CCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHH
Confidence 33444577777777766666666554432 234577777766432 22222221 2377777777777777777777
Q ss_pred Hh-hCCc-ceeccccchhccChhHHHHHHHHhCCccccccc--CcccccChHHHHHHHHHcC-CCC--CCCC
Q psy13164 128 KR-HQGI-RYKCDLCSKEYFHKGYLTDHKKIHQGIRYKCNL--CSKEFLRKDILIEHKKIHQ-GIR--FKCD 192 (193)
Q Consensus 128 ~~-h~~~-~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~--C~~~F~~~~~L~~H~~~h~-~~~--~~~c 192 (193)
+. |... ||+|..|.+.|.+.+.|.+|..+|...-|+|.. |..+|++...|++|++-++ |.. +|.|
T Consensus 284 r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~C 355 (467)
T KOG3608|consen 284 RYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYAC 355 (467)
T ss_pred HhhhccCCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceee
Confidence 65 4443 777877777777777777777777754677776 7777777777777776544 533 4554
No 10
>KOG3623|consensus
Probab=99.46 E-value=1.4e-14 Score=118.03 Aligned_cols=75 Identities=37% Similarity=0.799 Sum_probs=72.2
Q ss_pred ceecccccccccChhHHHHHHHhhCCc-ceeccccchhccChhHHHHHHHHhCCc-ccccccCcccccChHHHHHHH
Q psy13164 107 RYKCDLCSKEYFHKGSLTEHKKRHQGI-RYKCDLCSKEYFHKGYLTDHKKIHQGI-RYKCNLCSKEFLRKDILIEHK 181 (193)
Q Consensus 107 ~~~C~~C~~~f~~~~~l~~h~~~h~~~-~~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~C~~C~~~F~~~~~L~~H~ 181 (193)
.|.|+.|+++|...+.|.+|.--|+|. ||+|.+|.|+|..+..|.-|+|.|.|+ ||+|..|+++|..+..+..||
T Consensus 894 myaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 894 MYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred cchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 499999999999999999999999998 999999999999999999999999998 999999999999999988886
No 11
>PHA00733 hypothetical protein
Probab=99.09 E-value=8.2e-11 Score=79.05 Aligned_cols=80 Identities=20% Similarity=0.304 Sum_probs=64.3
Q ss_pred CceecccccccccChhHHHHH------HHhhCCcceeccccchhccChhHHHHHHHHhCCcccccccCcccccChHHHHH
Q psy13164 106 IRYKCDLCSKEYFHKGSLTEH------KKRHQGIRYKCDLCSKEYFHKGYLTDHKKIHQGIRYKCNLCSKEFLRKDILIE 179 (193)
Q Consensus 106 ~~~~C~~C~~~f~~~~~l~~h------~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~F~~~~~L~~ 179 (193)
+++.|.+|...|.+...|..+ +..+...||.|..|++.|.+...|..|++.| ..+|.|..|+++|.....|..
T Consensus 39 ~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~~C~~CgK~F~~~~sL~~ 117 (128)
T PHA00733 39 KRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT-EHSKVCPVCGKEFRNTDSTLD 117 (128)
T ss_pred hhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC-CcCccCCCCCCccCCHHHHHH
Confidence 457788888777776655554 3334444899999999999999999999976 347999999999999999999
Q ss_pred HHHHcCC
Q psy13164 180 HKKIHQG 186 (193)
Q Consensus 180 H~~~h~~ 186 (193)
|+...++
T Consensus 118 H~~~~h~ 124 (128)
T PHA00733 118 HVCKKHN 124 (128)
T ss_pred HHHHhcC
Confidence 9987665
No 12
>PHA02768 hypothetical protein; Provisional
Probab=99.08 E-value=4.5e-11 Score=66.89 Aligned_cols=42 Identities=24% Similarity=0.555 Sum_probs=29.2
Q ss_pred eeccccchhccChhHHHHHHHHhCCcccccccCcccccChHHH
Q psy13164 135 YKCDLCSKEYFHKGYLTDHKKIHQGIRYKCNLCSKEFLRKDIL 177 (193)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~F~~~~~L 177 (193)
|.|+.||+.|....+|..|+++|+ .+|+|..|++.|...+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~-k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN-TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC-CcccCCcccceeccccee
Confidence 667777777777777777777776 467777777777665544
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.06 E-value=2.9e-10 Score=92.83 Aligned_cols=126 Identities=19% Similarity=0.344 Sum_probs=82.0
Q ss_pred CCcccchhHhhccCchhhcccccccccCCCCccCCC--CcccchhhhhhcCCCceecccccccccChhHHHHHHHhhCCc
Q psy13164 56 NDAVTRDCLEFFKSHDSTLKNESDHERRSINYNCQQ--SYKVGKLNKILHRGIRYKCDLCSKEYFHKGSLTEHKKRHQGI 133 (193)
Q Consensus 56 ~~~~c~~c~~~f~~~~~~~~h~~~~~~~~~~~~C~~--c~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~ 133 (193)
....|.-|..... ...+..|.....+ ..-.|+. |+.+.. .......+.|+.|+..|. ...|..|+..|+ .
T Consensus 406 ~~V~C~NC~~~i~-l~~l~lHe~~C~r--~~V~Cp~~~Cg~v~~---r~el~~H~~C~~Cgk~f~-~s~LekH~~~~H-k 477 (567)
T PLN03086 406 DTVECRNCKHYIP-SRSIALHEAYCSR--HNVVCPHDGCGIVLR---VEEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH-E 477 (567)
T ss_pred CeEECCCCCCccc-hhHHHHHHhhCCC--cceeCCcccccceee---ccccccCccCCCCCCccc-hHHHHHHHHhcC-C
Confidence 3446888876653 3445566544432 2245653 666542 111223367888888875 566888888875 4
Q ss_pred ceeccccchhccChhHHHHHHHHhCCc-ccccccCcccccC----------hHHHHHHHHHcCCCCCCCC
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKKIHQGI-RYKCNLCSKEFLR----------KDILIEHKKIHQGIRFKCD 192 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~C~~C~~~F~~----------~~~L~~H~~~h~~~~~~~c 192 (193)
++.|+ ||+.+ ....|..|+.+|.+. ++.|..|++.|.. .+.|..|..++ |.+++.|
T Consensus 478 pv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C 544 (567)
T PLN03086 478 PLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPC 544 (567)
T ss_pred CccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEc
Confidence 78888 88654 557888888888776 8888888888742 35788887775 7777666
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.89 E-value=6.8e-10 Score=62.15 Aligned_cols=43 Identities=23% Similarity=0.609 Sum_probs=39.4
Q ss_pred ceecccccccccChhHHHHHHHhhCCcceeccccchhccChhHH
Q psy13164 107 RYKCDLCSKEYFHKGSLTEHKKRHQGIRYKCDLCSKEYFHKGYL 150 (193)
Q Consensus 107 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~C~~C~~~f~~~~~l 150 (193)
.|.|+.||+.|.+..+|..|+++|+ .++.|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~-k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN-TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC-CcccCCcccceeccccee
Confidence 3899999999999999999999999 589999999999877765
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.86 E-value=5.2e-09 Score=85.63 Aligned_cols=109 Identities=17% Similarity=0.357 Sum_probs=82.3
Q ss_pred ccc--hhHhhccCchhhcccccccccCCCCccCCCCccc------chhhhhhcCCCceecccccccccChhHHHHHHHhh
Q psy13164 59 VTR--DCLEFFKSHDSTLKNESDHERRSINYNCQQSYKV------GKLNKILHRGIRYKCDLCSKEYFHKGSLTEHKKRH 130 (193)
Q Consensus 59 ~c~--~c~~~f~~~~~~~~h~~~~~~~~~~~~C~~c~~~------~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~h 130 (193)
.|. .|+..|. ...+..| +.|+.|++. ..|.++++ .++.|+ |+..+ ....|..|+..|
T Consensus 435 ~Cp~~~Cg~v~~-r~el~~H----------~~C~~Cgk~f~~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~th 499 (567)
T PLN03086 435 VCPHDGCGIVLR-VEEAKNH----------VHCEKCGQAFQQGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQAST 499 (567)
T ss_pred eCCcccccceee-ccccccC----------ccCCCCCCccchHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhcc
Confidence 465 3888773 3334444 578888763 45666664 779999 99755 668899999988
Q ss_pred CCc-ceeccccchhccC----------hhHHHHHHHHhCCcccccccCcccccChHHHHHHHHH
Q psy13164 131 QGI-RYKCDLCSKEYFH----------KGYLTDHKKIHQGIRYKCNLCSKEFLRKDILIEHKKI 183 (193)
Q Consensus 131 ~~~-~~~C~~C~~~f~~----------~~~l~~H~~~h~~~~~~C~~C~~~F~~~~~L~~H~~~ 183 (193)
... ++.|..|++.|.. ...|..|.......++.|..||+.|..+ .|..|+..
T Consensus 500 Cp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vrlr-dm~~H~~~ 562 (567)
T PLN03086 500 CPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRSVMLK-EMDIHQIA 562 (567)
T ss_pred CCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCCeeeeh-hHHHHHHH
Confidence 877 8999999999852 3589999998755599999999999876 56778754
No 16
>PHA00733 hypothetical protein
Probab=98.81 E-value=4.7e-09 Score=70.57 Aligned_cols=56 Identities=23% Similarity=0.392 Sum_probs=49.4
Q ss_pred cCCCceecccccccccChhHHHHHHHhhCCcceeccccchhccChhHHHHHHHHhCC
Q psy13164 103 HRGIRYKCDLCSKEYFHKGSLTEHKKRHQGIRYKCDLCSKEYFHKGYLTDHKKIHQG 159 (193)
Q Consensus 103 ~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 159 (193)
++..+|.|..|++.|.+...|..|++.|. .+|.|..|+++|.....|..|+...++
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~-~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYTE-HSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcCC-cCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 34678999999999999999999999873 379999999999999999999987554
No 17
>KOG3993|consensus
Probab=98.67 E-value=1.4e-08 Score=78.86 Aligned_cols=22 Identities=23% Similarity=0.561 Sum_probs=18.3
Q ss_pred cccccCcccccChHHHHHHHHH
Q psy13164 162 YKCNLCSKEFLRKDILIEHKKI 183 (193)
Q Consensus 162 ~~C~~C~~~F~~~~~L~~H~~~ 183 (193)
|.|.+|.-.|.++..|.+|...
T Consensus 459 f~~ky~~atfyss~~ltrhin~ 480 (500)
T KOG3993|consen 459 FTCKYCPATFYSSPGLTRHINK 480 (500)
T ss_pred cccccchHhhhcCcchHhHhhh
Confidence 7888888888888888888654
No 18
>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=98.65 E-value=2.2e-08 Score=47.97 Aligned_cols=24 Identities=42% Similarity=0.827 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCc-ccccccCccccc
Q psy13164 149 YLTDHKKIHQGI-RYKCNLCSKEFL 172 (193)
Q Consensus 149 ~l~~H~~~h~~~-~~~C~~C~~~F~ 172 (193)
+|.+|+++|+|+ ||.|+.|+++|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 467777777776 778888877775
No 19
>PHA00616 hypothetical protein
Probab=98.64 E-value=1.5e-08 Score=54.02 Aligned_cols=32 Identities=25% Similarity=0.278 Sum_probs=18.8
Q ss_pred ccccccCcccccChHHHHHHHHHcCCCCCCCC
Q psy13164 161 RYKCNLCSKEFLRKDILIEHKKIHQGIRFKCD 192 (193)
Q Consensus 161 ~~~C~~C~~~F~~~~~L~~H~~~h~~~~~~~c 192 (193)
||+|..||+.|...+.|..|++.|+|++++.|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 35566666666666666666666666555443
No 20
>KOG3993|consensus
Probab=98.61 E-value=6.8e-09 Score=80.59 Aligned_cols=79 Identities=29% Similarity=0.617 Sum_probs=61.6
Q ss_pred eecccccccccChhHHHHHHHhhCCc-ceeccccchhccChhHHHHHHHHhCCc--------------------------
Q psy13164 108 YKCDLCSKEYFHKGSLTEHKKRHQGI-RYKCDLCSKEYFHKGYLTDHKKIHQGI-------------------------- 160 (193)
Q Consensus 108 ~~C~~C~~~f~~~~~l~~h~~~h~~~-~~~C~~C~~~f~~~~~l~~H~~~h~~~-------------------------- 160 (193)
|.|..|...|.....|.+|.-.-.-. -|+|++|+|.|+-..+|..|.|.|.-+
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~r 347 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAER 347 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccc
Confidence 77888888888888777776443333 478888888888888888887777421
Q ss_pred --------ccccccCcccccChHHHHHHHHHcCC
Q psy13164 161 --------RYKCNLCSKEFLRKDILIEHKKIHQG 186 (193)
Q Consensus 161 --------~~~C~~C~~~F~~~~~L~~H~~~h~~ 186 (193)
-|.|..|++.|.....|+.|+.+|+.
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 18999999999999999999988763
No 21
>PHA00732 hypothetical protein
Probab=98.38 E-value=2.1e-07 Score=57.00 Aligned_cols=48 Identities=29% Similarity=0.551 Sum_probs=31.4
Q ss_pred ceecccccccccChhHHHHHHHh-hCCcceeccccchhccChhHHHHHHHHhCC
Q psy13164 107 RYKCDLCSKEYFHKGSLTEHKKR-HQGIRYKCDLCSKEYFHKGYLTDHKKIHQG 159 (193)
Q Consensus 107 ~~~C~~C~~~f~~~~~l~~h~~~-h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 159 (193)
||.|..|++.|.+...|..|++. |. ++.|..|++.|. .+..|.+++..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT--LTKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC--CCccCCCCCEeC---ChhhhhcccCC
Confidence 36677777777777777777764 43 346777777776 36666655433
No 22
>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=98.36 E-value=3.4e-07 Score=43.77 Aligned_cols=24 Identities=38% Similarity=0.841 Sum_probs=19.2
Q ss_pred HHHHHHHhhCCc-ceeccccchhcc
Q psy13164 122 SLTEHKKRHQGI-RYKCDLCSKEYF 145 (193)
Q Consensus 122 ~l~~h~~~h~~~-~~~C~~C~~~f~ 145 (193)
+|..|+++|+++ ||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 477888888887 788888888875
No 23
>PHA00616 hypothetical protein
Probab=98.27 E-value=4e-07 Score=48.61 Aligned_cols=38 Identities=16% Similarity=0.218 Sum_probs=26.4
Q ss_pred ceeccccchhccChhHHHHHHHHhCCc-ccccccCcccc
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKKIHQGI-RYKCNLCSKEF 171 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~C~~C~~~F 171 (193)
||+|+.||+.|...+.|..|++.|+|. ++.|..--..|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~y~~f 39 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEYFYIYF 39 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeEEEEEE
Confidence 567778888888788888888777776 66665433333
No 24
>PHA00732 hypothetical protein
Probab=98.26 E-value=6e-07 Score=54.97 Aligned_cols=47 Identities=28% Similarity=0.498 Sum_probs=39.2
Q ss_pred ceeccccchhccChhHHHHHHHH-hCCcccccccCcccccChHHHHHHHHHcC
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKKI-HQGIRYKCNLCSKEFLRKDILIEHKKIHQ 185 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~C~~C~~~F~~~~~L~~H~~~h~ 185 (193)
||.|..|++.|.+...|..|++. |. ++.|+.|++.|.+ |..|.++..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~~---l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT--LTKCPVCNKSYRR---LNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC--CCccCCCCCEeCC---hhhhhcccC
Confidence 58899999999999999999984 65 3689999999984 777876543
No 25
>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=98.16 E-value=1.5e-06 Score=40.29 Aligned_cols=23 Identities=43% Similarity=0.847 Sum_probs=15.2
Q ss_pred cccccCcccccChHHHHHHHHHc
Q psy13164 162 YKCNLCSKEFLRKDILIEHKKIH 184 (193)
Q Consensus 162 ~~C~~C~~~F~~~~~L~~H~~~h 184 (193)
|.|+.|++.|..+..|..|++.|
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 45666777777777777666653
No 26
>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=98.09 E-value=6.1e-06 Score=46.88 Aligned_cols=48 Identities=29% Similarity=0.595 Sum_probs=27.9
Q ss_pred eeccccchhccChhHHHHHHHH-hCCc--ccccccCcccccChHHHHHHHHHcC
Q psy13164 135 YKCDLCSKEYFHKGYLTDHKKI-HQGI--RYKCNLCSKEFLRKDILIEHKKIHQ 185 (193)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~-h~~~--~~~C~~C~~~F~~~~~L~~H~~~h~ 185 (193)
|.|++|++ ..+...|..|... |... .+.|++|...+. .+|..|+..++
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 56667776 3445566666553 4432 566777766543 36666766644
No 27
>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=97.95 E-value=6.8e-06 Score=37.96 Aligned_cols=22 Identities=36% Similarity=0.801 Sum_probs=12.5
Q ss_pred eeccccchhccChhHHHHHHHH
Q psy13164 135 YKCDLCSKEYFHKGYLTDHKKI 156 (193)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~ 156 (193)
|.|+.|++.|.+...|..|++.
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 4555555555555555555554
No 28
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.93 E-value=6.8e-06 Score=52.73 Aligned_cols=73 Identities=21% Similarity=0.436 Sum_probs=21.1
Q ss_pred ecccccccccChhHHHHHHHhhCCcceeccccchhccChhHHHHHHHHhCCcccccccCcccccChHHHHHHHHHc
Q psy13164 109 KCDLCSKEYFHKGSLTEHKKRHQGIRYKCDLCSKEYFHKGYLTDHKKIHQGIRYKCNLCSKEFLRKDILIEHKKIH 184 (193)
Q Consensus 109 ~C~~C~~~f~~~~~l~~h~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~F~~~~~L~~H~~~h 184 (193)
+|..|+..|.+...|..|+...++.... ....+.....+..+++.-....+.|..|++.|.+...|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~---~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP---DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ---------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccc---cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 4889999999999999999765553211 111222333444444433333689999999999999999999874
No 29
>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=97.81 E-value=1.7e-05 Score=36.81 Aligned_cols=23 Identities=35% Similarity=0.824 Sum_probs=13.4
Q ss_pred cccccCcccccChHHHHHHHHHc
Q psy13164 162 YKCNLCSKEFLRKDILIEHKKIH 184 (193)
Q Consensus 162 ~~C~~C~~~F~~~~~L~~H~~~h 184 (193)
|.|+.|++.|.+...|..|+++|
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 45666666666666666666654
No 30
>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=97.80 E-value=1.3e-05 Score=38.62 Aligned_cols=25 Identities=36% Similarity=0.700 Sum_probs=18.4
Q ss_pred ccccccCcccccChHHHHHHHHHcC
Q psy13164 161 RYKCNLCSKEFLRKDILIEHKKIHQ 185 (193)
Q Consensus 161 ~~~C~~C~~~F~~~~~L~~H~~~h~ 185 (193)
||.|..|++.|.+...|..|++.|.
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 4677777777777777777777664
No 31
>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=97.71 E-value=7e-05 Score=42.47 Aligned_cols=48 Identities=29% Similarity=0.582 Sum_probs=38.3
Q ss_pred eecccccccccChhHHHHHHHh-hCCc--ceeccccchhccChhHHHHHHHHhC
Q psy13164 108 YKCDLCSKEYFHKGSLTEHKKR-HQGI--RYKCDLCSKEYFHKGYLTDHKKIHQ 158 (193)
Q Consensus 108 ~~C~~C~~~f~~~~~l~~h~~~-h~~~--~~~C~~C~~~f~~~~~l~~H~~~h~ 158 (193)
|.|+.|++ ..+...|..|... |... .+.|++|...+. .+|..|+..++
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 89999999 5567789999765 5554 599999998654 48999998754
No 32
>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=97.57 E-value=7.1e-05 Score=34.57 Aligned_cols=23 Identities=30% Similarity=0.804 Sum_probs=11.8
Q ss_pred eeccccchhccChhHHHHHHHHh
Q psy13164 135 YKCDLCSKEYFHKGYLTDHKKIH 157 (193)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~h 157 (193)
|.|+.|++.|.+...|..|+++|
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 45555555555555555555544
No 33
>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=97.52 E-value=6.4e-05 Score=41.07 Aligned_cols=29 Identities=17% Similarity=0.252 Sum_probs=18.5
Q ss_pred ccccccCcccccChHHHHHHHHHcCCCCC
Q psy13164 161 RYKCNLCSKEFLRKDILIEHKKIHQGIRF 189 (193)
Q Consensus 161 ~~~C~~C~~~F~~~~~L~~H~~~h~~~~~ 189 (193)
|..|++|+..+.+..+|++|+.++++.+|
T Consensus 24 PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 77788888888777788888777776664
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.46 E-value=0.0001 Score=47.22 Aligned_cols=24 Identities=25% Similarity=0.225 Sum_probs=0.0
Q ss_pred ccchhHhhccCchhhccccccccc
Q psy13164 59 VTRDCLEFFKSHDSTLKNESDHER 82 (193)
Q Consensus 59 ~c~~c~~~f~~~~~~~~h~~~~~~ 82 (193)
+|..|+..|.+...+..|+...+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~ 24 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHG 24 (100)
T ss_dssp ------------------------
T ss_pred Cccccccccccccccccccccccc
Confidence 488999999999999999877664
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.42 E-value=0.00014 Score=34.09 Aligned_cols=24 Identities=42% Similarity=0.796 Sum_probs=17.3
Q ss_pred cccccCcccccChHHHHHHHHHcC
Q psy13164 162 YKCNLCSKEFLRKDILIEHKKIHQ 185 (193)
Q Consensus 162 ~~C~~C~~~F~~~~~L~~H~~~h~ 185 (193)
|.|..|++.|...+.|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 467777777777777777777654
No 36
>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=97.40 E-value=0.00012 Score=35.09 Aligned_cols=23 Identities=39% Similarity=0.888 Sum_probs=11.7
Q ss_pred eecccccccccChhHHHHHHHhh
Q psy13164 108 YKCDLCSKEYFHKGSLTEHKKRH 130 (193)
Q Consensus 108 ~~C~~C~~~f~~~~~l~~h~~~h 130 (193)
|.|..|++.|.+...|..|++.|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 44555555555555555555444
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.96 E-value=0.00072 Score=31.56 Aligned_cols=24 Identities=33% Similarity=0.753 Sum_probs=15.1
Q ss_pred eeccccchhccChhHHHHHHHHhC
Q psy13164 135 YKCDLCSKEYFHKGYLTDHKKIHQ 158 (193)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~h~ 158 (193)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 356666666666666666666553
No 38
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.94 E-value=0.00024 Score=53.92 Aligned_cols=22 Identities=27% Similarity=0.668 Sum_probs=18.5
Q ss_pred cccccccCcccccChHHHHHHH
Q psy13164 160 IRYKCNLCSKEFLRKDILIEHK 181 (193)
Q Consensus 160 ~~~~C~~C~~~F~~~~~L~~H~ 181 (193)
+||.|.+|++++.+...|+-|.
T Consensus 397 KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 397 KPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CceeccccchhhccCccceecc
Confidence 3799999999999988887764
No 39
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.76 E-value=0.00053 Score=52.16 Aligned_cols=51 Identities=35% Similarity=0.748 Sum_probs=43.1
Q ss_pred CCCceeccc--ccccccChhHHHHHHHh-hCC-------------------cceeccccchhccChhHHHHHH
Q psy13164 104 RGIRYKCDL--CSKEYFHKGSLTEHKKR-HQG-------------------IRYKCDLCSKEYFHKGYLTDHK 154 (193)
Q Consensus 104 ~~~~~~C~~--C~~~f~~~~~l~~h~~~-h~~-------------------~~~~C~~C~~~f~~~~~l~~H~ 154 (193)
+++||+|++ |.+++.+...|+-|+.- |.. +||+|.+|+|.+.+...|+-|+
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 358999987 99999999999999764 310 3899999999999999999884
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.74 E-value=0.00089 Score=31.30 Aligned_cols=22 Identities=27% Similarity=0.753 Sum_probs=14.7
Q ss_pred cccccCcccccChHHHHHHHHH
Q psy13164 162 YKCNLCSKEFLRKDILIEHKKI 183 (193)
Q Consensus 162 ~~C~~C~~~F~~~~~L~~H~~~ 183 (193)
|.|..|++.|.+...|..|++.
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 4566777777777777766654
No 41
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.71 E-value=0.0011 Score=30.72 Aligned_cols=22 Identities=45% Similarity=0.623 Sum_probs=11.6
Q ss_pred cccccCcccccChHHHHHHHHHc
Q psy13164 162 YKCNLCSKEFLRKDILIEHKKIH 184 (193)
Q Consensus 162 ~~C~~C~~~F~~~~~L~~H~~~h 184 (193)
|+|+.|+.... ...|..|++.|
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 45666665555 55666666554
No 42
>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=96.59 E-value=0.0018 Score=35.54 Aligned_cols=26 Identities=19% Similarity=0.314 Sum_probs=16.2
Q ss_pred ceeccccchhccChhHHHHHHHHhCC
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKKIHQG 159 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 159 (193)
|..|++|+..+.+..+|.+|+.++++
T Consensus 24 PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred CCCCCcchhhccchhhHHHHHHHHhc
Confidence 67777787777777777777765544
No 43
>PRK04860 hypothetical protein; Provisional
Probab=96.49 E-value=0.0019 Score=45.09 Aligned_cols=37 Identities=27% Similarity=0.792 Sum_probs=29.7
Q ss_pred ceeccccchhccChhHHHHHHHHhCCc-ccccccCcccccCh
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKKIHQGI-RYKCNLCSKEFLRK 174 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~C~~C~~~F~~~ 174 (193)
+|.|. |++ ....+.+|.++|++. +|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 68887 887 567788888888887 79999998887643
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.47 E-value=0.0019 Score=30.17 Aligned_cols=22 Identities=27% Similarity=0.744 Sum_probs=14.5
Q ss_pred eeccccchhccChhHHHHHHHH
Q psy13164 135 YKCDLCSKEYFHKGYLTDHKKI 156 (193)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~ 156 (193)
|.|..|++.|.+...|..|++.
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 4566677777777777666654
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.15 E-value=0.0041 Score=28.71 Aligned_cols=21 Identities=43% Similarity=0.599 Sum_probs=9.3
Q ss_pred eeccccchhccChhHHHHHHHH
Q psy13164 135 YKCDLCSKEYFHKGYLTDHKKI 156 (193)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~ 156 (193)
|.|+.|+.... ...|..|++.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 34555554444 4455555544
No 46
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.83 E-value=0.0083 Score=28.08 Aligned_cols=20 Identities=40% Similarity=0.908 Sum_probs=14.1
Q ss_pred ccccCcccccChHHHHHHHHH
Q psy13164 163 KCNLCSKEFLRKDILIEHKKI 183 (193)
Q Consensus 163 ~C~~C~~~F~~~~~L~~H~~~ 183 (193)
.|+.||+.| ....|..|+.+
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHHh
Confidence 577788888 55677777654
No 47
>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=95.83 E-value=0.0023 Score=30.53 Aligned_cols=22 Identities=32% Similarity=0.664 Sum_probs=15.7
Q ss_pred cccccCcccccChHHHHHHHHH
Q psy13164 162 YKCNLCSKEFLRKDILIEHKKI 183 (193)
Q Consensus 162 ~~C~~C~~~F~~~~~L~~H~~~ 183 (193)
|.|..|++.|.+...|..|++.
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 5677777777777777777653
No 48
>PRK04860 hypothetical protein; Provisional
Probab=95.56 E-value=0.009 Score=41.78 Aligned_cols=37 Identities=27% Similarity=0.772 Sum_probs=31.9
Q ss_pred ceecccccccccChhHHHHHHHhhCCc-ceeccccchhccCh
Q psy13164 107 RYKCDLCSKEYFHKGSLTEHKKRHQGI-RYKCDLCSKEYFHK 147 (193)
Q Consensus 107 ~~~C~~C~~~f~~~~~l~~h~~~h~~~-~~~C~~C~~~f~~~ 147 (193)
+|.|. |+. ...++.+|.++|.+. +|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 59998 987 677899999999997 89999999988654
No 49
>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=95.02 E-value=0.0054 Score=29.22 Aligned_cols=22 Identities=32% Similarity=0.659 Sum_probs=14.9
Q ss_pred eeccccchhccChhHHHHHHHH
Q psy13164 135 YKCDLCSKEYFHKGYLTDHKKI 156 (193)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~ 156 (193)
|.|..|++.|.+...+..|+++
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 5677777777777777766653
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=94.08 E-value=0.037 Score=27.88 Aligned_cols=23 Identities=26% Similarity=0.459 Sum_probs=17.2
Q ss_pred ccccccCcccccChHHHHHHHHH
Q psy13164 161 RYKCNLCSKEFLRKDILIEHKKI 183 (193)
Q Consensus 161 ~~~C~~C~~~F~~~~~L~~H~~~ 183 (193)
+|.|..|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 56788888888877777777653
No 51
>KOG1146|consensus
Probab=92.93 E-value=0.023 Score=51.27 Aligned_cols=129 Identities=14% Similarity=0.131 Sum_probs=84.1
Q ss_pred cCCCCcccchhHhhccCchhhcccccccccCCCCccCCCCcccchhhhh------hcCCCceecccccccccChhHHHHH
Q psy13164 53 NNGNDAVTRDCLEFFKSHDSTLKNESDHERRSINYNCQQSYKVGKLNKI------LHRGIRYKCDLCSKEYFHKGSLTEH 126 (193)
Q Consensus 53 ~~~~~~~c~~c~~~f~~~~~~~~h~~~~~~~~~~~~C~~c~~~~~~~~~------~~~~~~~~C~~C~~~f~~~~~l~~h 126 (193)
.....++|..|+..++....|..|++..+..... ..|.....|.+. -.+.++|.|..|...+..+.+|.+|
T Consensus 461 S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~---~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsih 537 (1406)
T KOG1146|consen 461 SFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS---AYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIH 537 (1406)
T ss_pred cccccccCCccchhhhhHHHhhhcccccccccch---hHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHH
Confidence 3346778888888888888888888774432222 233222222111 1235679999999999999999999
Q ss_pred HHh--hCC-----------------------------------------c-ceeccccchhccChhHHHHHHHH-hCCc-
Q psy13164 127 KKR--HQG-----------------------------------------I-RYKCDLCSKEYFHKGYLTDHKKI-HQGI- 160 (193)
Q Consensus 127 ~~~--h~~-----------------------------------------~-~~~C~~C~~~f~~~~~l~~H~~~-h~~~- 160 (193)
+.. |.. + +|.|..|+.......+|+.||.. ++-.
T Consensus 538 lqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmtss~~s~~ 617 (1406)
T KOG1146|consen 538 LQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTASPSSSP 617 (1406)
T ss_pred HHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhccccccccCCCCCC
Confidence 864 311 2 37888888887777788777753 3333
Q ss_pred ccccccCcccccChHHHHHHHHHc
Q psy13164 161 RYKCNLCSKEFLRKDILIEHKKIH 184 (193)
Q Consensus 161 ~~~C~~C~~~F~~~~~L~~H~~~h 184 (193)
|.-+-.++..+.....+..+.+.+
T Consensus 618 p~~~Lq~~it~~l~~~~~~~~~lp 641 (1406)
T KOG1146|consen 618 PSLVLQQNITSSLASLLGGQGRLP 641 (1406)
T ss_pred hHHHhhhcchhhccccccCcCCCC
Confidence 466666777776666666665555
No 52
>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=92.92 E-value=0.082 Score=26.57 Aligned_cols=23 Identities=22% Similarity=0.446 Sum_probs=18.1
Q ss_pred ceeccccchhccChhHHHHHHHH
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKKI 156 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~ 156 (193)
+|.|..|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57788888888888888888763
No 53
>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=92.01 E-value=0.35 Score=31.47 Aligned_cols=25 Identities=24% Similarity=0.503 Sum_probs=23.1
Q ss_pred ccc----ccCcccccChHHHHHHHHHcCC
Q psy13164 162 YKC----NLCSKEFLRKDILIEHKKIHQG 186 (193)
Q Consensus 162 ~~C----~~C~~~F~~~~~L~~H~~~h~~ 186 (193)
|.| ..|+....+...|+.|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 999 9999999999999999998765
No 54
>KOG2186|consensus
Probab=90.86 E-value=0.19 Score=37.38 Aligned_cols=46 Identities=22% Similarity=0.535 Sum_probs=32.0
Q ss_pred eecccccccccChhHHHHHHHhhCCcceeccccchhccChhHHHHHHH
Q psy13164 108 YKCDLCSKEYFHKGSLTEHKKRHQGIRYKCDLCSKEYFHKGYLTDHKK 155 (193)
Q Consensus 108 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~C~~C~~~f~~~~~l~~H~~ 155 (193)
|.|..||.... +..+..|+.+-++..|.|..|++.|.. ..+..|..
T Consensus 4 FtCnvCgEsvK-Kp~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHhccCCeeEEeeccccccc-chhhhhhh
Confidence 67777877543 344666777777767888888888876 56666754
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=90.19 E-value=0.2 Score=25.07 Aligned_cols=10 Identities=40% Similarity=1.119 Sum_probs=5.1
Q ss_pred eecccccccc
Q psy13164 108 YKCDLCSKEY 117 (193)
Q Consensus 108 ~~C~~C~~~f 117 (193)
|.|..||..+
T Consensus 2 ~~C~~CGy~y 11 (33)
T cd00350 2 YVCPVCGYIY 11 (33)
T ss_pred EECCCCCCEE
Confidence 4555555543
No 56
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.05 E-value=0.051 Score=43.72 Aligned_cols=54 Identities=28% Similarity=0.560 Sum_probs=30.2
Q ss_pred ceecccccccccChhHHHHHHH--hhCCc---ceecc--ccchhccChhHHHHHHHHhCCc
Q psy13164 107 RYKCDLCSKEYFHKGSLTEHKK--RHQGI---RYKCD--LCSKEYFHKGYLTDHKKIHQGI 160 (193)
Q Consensus 107 ~~~C~~C~~~f~~~~~l~~h~~--~h~~~---~~~C~--~C~~~f~~~~~l~~H~~~h~~~ 160 (193)
++.|..|...|.....+..|.. .|.+. ++.|+ .|++.|.....+..|..+|++.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~ 349 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSI 349 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCC
Confidence 3555556666666655655555 45443 45555 4666666555555555555543
No 57
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.77 E-value=0.063 Score=43.19 Aligned_cols=59 Identities=31% Similarity=0.508 Sum_probs=52.9
Q ss_pred ceeccccchhccChhHHHHHHH--HhCCc---ccccc--cCcccccChHHHHHHHHHcCCCCCCCC
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKK--IHQGI---RYKCN--LCSKEFLRKDILIEHKKIHQGIRFKCD 192 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~--~h~~~---~~~C~--~C~~~F~~~~~L~~H~~~h~~~~~~~c 192 (193)
++.|..|...|.....+..|.+ .|.+. ++.|+ .|++.|.....+..|..+|++.++..+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccc
Confidence 5889999999999999999999 78876 89999 799999999999999999998876543
No 58
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=88.54 E-value=0.073 Score=39.68 Aligned_cols=24 Identities=21% Similarity=0.297 Sum_probs=12.2
Q ss_pred ceeccccchhccChhHHHHHHHHh
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKKIH 157 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~h 157 (193)
++.|+.||........|..-.|+|
T Consensus 209 ~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 209 PIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCcccccccceeeeecc
Confidence 566666665554444444333333
No 59
>KOG1146|consensus
Probab=88.53 E-value=0.14 Score=46.46 Aligned_cols=116 Identities=14% Similarity=0.126 Sum_probs=60.7
Q ss_pred CcccchhHhhccCchhhccccccccc---CCCCccCCCCcccchhh---hhhcCCCceecccccccccChhHHHHHHHhh
Q psy13164 57 DAVTRDCLEFFKSHDSTLKNESDHER---RSINYNCQQSYKVGKLN---KILHRGIRYKCDLCSKEYFHKGSLTEHKKRH 130 (193)
Q Consensus 57 ~~~c~~c~~~f~~~~~~~~h~~~~~~---~~~~~~C~~c~~~~~~~---~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~h 130 (193)
...|..|...|........+-+.... ....+.|..+..+..-. .+.....+|.|..|...|.....|..|++.
T Consensus 1228 gl~~~~~e~~f~~~~~~~~~a~~~~~~~~~sGe~~c~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~k- 1306 (1406)
T KOG1146|consen 1228 GLLPNALEQPFPQEPEPTATAPPKPPELPASGEGECGAVDELLTPSFGISTLDVTHRYLCRQCKMAFDGEAPLTAHQRK- 1306 (1406)
T ss_pred cccHHhhhcCccCcccccccCCCCCCcCcCCCcchhhhccccccCccceeecccchhHHHHHHHhhhcchhHHHHHHHH-
Confidence 34566677777766666555433211 12225566665542211 122233458888888888888888877621
Q ss_pred CCcceeccccchhccChhHHHHHHHHhCCc-ccccccCcccccChHHHHHHHHH
Q psy13164 131 QGIRYKCDLCSKEYFHKGYLTDHKKIHQGI-RYKCNLCSKEFLRKDILIEHKKI 183 (193)
Q Consensus 131 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~-~~~C~~C~~~F~~~~~L~~H~~~ 183 (193)
|.+.+.......-|+..+... .| |..|...|.....|..|+++
T Consensus 1307 ---------~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~ 1350 (1406)
T KOG1146|consen 1307 ---------FCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRS 1350 (1406)
T ss_pred ---------HHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHH
Confidence 112222222222233333332 34 66666666666666666665
No 60
>KOG2231|consensus
Probab=87.89 E-value=0.8 Score=39.24 Aligned_cols=116 Identities=16% Similarity=0.325 Sum_probs=67.8
Q ss_pred cccchhHhhcc---------------CchhhcccccccccCCCCccCCCCcc----------------cchhhhhh-cCC
Q psy13164 58 AVTRDCLEFFK---------------SHDSTLKNESDHERRSINYNCQQSYK----------------VGKLNKIL-HRG 105 (193)
Q Consensus 58 ~~c~~c~~~f~---------------~~~~~~~h~~~~~~~~~~~~C~~c~~----------------~~~~~~~~-~~~ 105 (193)
..|.+|+..|. +-..|..|+...|.. +.|..|.. +..|++.- .+.
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~~---~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~ 176 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHKL---HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDD 176 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhhh---hccccccccceeeeeeeehehHHHHHHHHhcCCCcc
Confidence 45777777763 455677788766643 55666542 12222111 101
Q ss_pred C----ceecccccccccChhHHHHHHHhhCCcceecccc------chhccChhHHHHHHHHhCCcccccc--cCc-----
Q psy13164 106 I----RYKCDLCSKEYFHKGSLTEHKKRHQGIRYKCDLC------SKEYFHKGYLTDHKKIHQGIRYKCN--LCS----- 168 (193)
Q Consensus 106 ~----~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~C~~C------~~~f~~~~~l~~H~~~h~~~~~~C~--~C~----- 168 (193)
. .-.|..|...|.....|..|++.++. .|..| +..|.....|..|-+.++ |.|. .|.
T Consensus 177 ~s~rGhp~C~~C~~~fld~~el~rH~~~~h~---~chfC~~~~~~neyy~~~~dLe~HfR~~H---flCE~~~C~~~~f~ 250 (669)
T KOG2231|consen 177 ESCRGHPLCKFCHERFLDDDELYRHLRFDHE---FCHFCDYKTGQNEYYNDYDDLEEHFRKGH---FLCEEEFCRTKKFY 250 (669)
T ss_pred ccccCCccchhhhhhhccHHHHHHhhcccee---heeecCcccccchhcccchHHHHHhhhcC---ccccccccccceee
Confidence 0 14688899999998989988876655 44444 345666788888888654 4554 343
Q ss_pred ccccChHHHHHHHH
Q psy13164 169 KEFLRKDILIEHKK 182 (193)
Q Consensus 169 ~~F~~~~~L~~H~~ 182 (193)
..|.....|.+|-+
T Consensus 251 ~~~~~ei~lk~~~~ 264 (669)
T KOG2231|consen 251 VAFELEIELKAHNR 264 (669)
T ss_pred ehhHHHHHHHhhcc
Confidence 23344445555544
No 61
>KOG2893|consensus
Probab=87.14 E-value=0.18 Score=37.26 Aligned_cols=41 Identities=32% Similarity=0.709 Sum_probs=22.0
Q ss_pred cccccccccChhHHHHHHHhhCCcceeccccchhccChhHHHHH
Q psy13164 110 CDLCSKEYFHKGSLTEHKKRHQGIRYKCDLCSKEYFHKGYLTDH 153 (193)
Q Consensus 110 C~~C~~~f~~~~~l~~h~~~h~~~~~~C~~C~~~f~~~~~l~~H 153 (193)
|=.|++.|....-|..|++.. .|+|.+|-|...+...|..|
T Consensus 13 cwycnrefddekiliqhqkak---hfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAK---HFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhhc---cceeeeehhhhccCCCceee
Confidence 445666666665555554432 35566666555555555444
No 62
>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=86.24 E-value=0.44 Score=31.02 Aligned_cols=12 Identities=33% Similarity=0.708 Sum_probs=5.9
Q ss_pred ccccccCccccc
Q psy13164 161 RYKCNLCSKEFL 172 (193)
Q Consensus 161 ~~~C~~C~~~F~ 172 (193)
|..|+.||..|.
T Consensus 26 PivCP~CG~~~~ 37 (108)
T PF09538_consen 26 PIVCPKCGTEFP 37 (108)
T ss_pred CccCCCCCCccC
Confidence 444555555543
No 63
>KOG2231|consensus
Probab=85.17 E-value=1.5 Score=37.64 Aligned_cols=47 Identities=21% Similarity=0.463 Sum_probs=22.9
Q ss_pred eeccccchhccChhHHHHHHHHhCCcccccccC------cccccChHHHHHHHHHc
Q psy13164 135 YKCDLCSKEYFHKGYLTDHKKIHQGIRYKCNLC------SKEFLRKDILIEHKKIH 184 (193)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C------~~~F~~~~~L~~H~~~h 184 (193)
-.|..|...|.....|.+|++.++ |.|..| +.-|..-..|..|.+.+
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h---~~chfC~~~~~~neyy~~~~dLe~HfR~~ 235 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDH---EFCHFCDYKTGQNEYYNDYDDLEEHFRKG 235 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccce---eheeecCcccccchhcccchHHHHHhhhc
Confidence 355555555555555555555432 223333 33444445555555543
No 64
>KOG2186|consensus
Probab=84.82 E-value=0.7 Score=34.50 Aligned_cols=50 Identities=22% Similarity=0.419 Sum_probs=39.8
Q ss_pred ceeccccchhccChhHHHHHHHHhCCcccccccCcccccChHHHHHHHHHcC
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKKIHQGIRYKCNLCSKEFLRKDILIEHKKIHQ 185 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~F~~~~~L~~H~~~h~ 185 (193)
-|.|..||-... ...+.+|+..-++.-|.|..|++.|.. .....|...-+
T Consensus 3 ~FtCnvCgEsvK-Kp~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 3 FFTCNVCGESVK-KPQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred EEehhhhhhhcc-ccchHHHHHhccCCeeEEeeccccccc-chhhhhhhhcc
Confidence 478999998765 456778998888888999999999987 66777876433
No 65
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=83.54 E-value=0.82 Score=35.80 Aligned_cols=75 Identities=28% Similarity=0.484 Sum_probs=43.2
Q ss_pred eeccc--ccccccChhHHHHHHHhhCCcceeccccc---hh------ccChhHHHHHHHHhC-C---c-ccccccCcccc
Q psy13164 108 YKCDL--CSKEYFHKGSLTEHKKRHQGIRYKCDLCS---KE------YFHKGYLTDHKKIHQ-G---I-RYKCNLCSKEF 171 (193)
Q Consensus 108 ~~C~~--C~~~f~~~~~l~~h~~~h~~~~~~C~~C~---~~------f~~~~~l~~H~~~h~-~---~-~~~C~~C~~~F 171 (193)
|.|+. |..+......|..|.+..++ .+.|.+|- +. ..++..|..|.-... + + --.|..|...|
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~-~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~F 230 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHG-FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYF 230 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC-cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhcccee
Confidence 66754 55555556677777776555 34555443 22 234455565654321 1 1 23577777777
Q ss_pred cChHHHHHHHHH
Q psy13164 172 LRKDILIEHKKI 183 (193)
Q Consensus 172 ~~~~~L~~H~~~ 183 (193)
..-..|..|+|.
T Consensus 231 YdDDEL~~HcR~ 242 (493)
T COG5236 231 YDDDELRRHCRL 242 (493)
T ss_pred cChHHHHHHHHh
Confidence 777777777765
No 66
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.43 E-value=1.2 Score=29.19 Aligned_cols=76 Identities=18% Similarity=0.346 Sum_probs=43.4
Q ss_pred ceecccccccccChhHHHHHHHhhCC--------cc-------eeccccchhccChhHHHHHHHHhCCcccccccCcccc
Q psy13164 107 RYKCDLCSKEYFHKGSLTEHKKRHQG--------IR-------YKCDLCSKEYFHKGYLTDHKKIHQGIRYKCNLCSKEF 171 (193)
Q Consensus 107 ~~~C~~C~~~f~~~~~l~~h~~~h~~--------~~-------~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~F 171 (193)
|..|+.|+-+......|.+.. |+- .+ -.|--|...|........-. .-...+|+|+.|...|
T Consensus 15 P~~CpiCgLtLVss~HLARSy--HHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~-~~~~~~y~C~~C~~~F 91 (112)
T TIGR00622 15 PVECPICGLTLILSTHLARSY--HHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDE-LKDSHRYVCAVCKNVF 91 (112)
T ss_pred CCcCCcCCCEEeccchHHHhh--hccCCCcccccccccccCCCCcccCcCCCCCCcccccccc-cccccceeCCCCCCcc
Confidence 456777777766666665431 111 01 13777888776543211000 1111278888888888
Q ss_pred cChHHHHHHHHHcC
Q psy13164 172 LRKDILIEHKKIHQ 185 (193)
Q Consensus 172 ~~~~~L~~H~~~h~ 185 (193)
=..-....|..+|.
T Consensus 92 C~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 92 CVDCDVFVHESLHC 105 (112)
T ss_pred ccccchhhhhhccC
Confidence 77777777777764
No 67
>KOG4173|consensus
Probab=83.06 E-value=0.53 Score=34.00 Aligned_cols=73 Identities=18% Similarity=0.461 Sum_probs=45.6
Q ss_pred eeccc--ccccccChhHHHHHHHhhCCcceeccccchhccChhHHHHHHHHhCC----------c-cccccc--Cccccc
Q psy13164 108 YKCDL--CSKEYFHKGSLTEHKKRHQGIRYKCDLCSKEYFHKGYLTDHKKIHQG----------I-RYKCNL--CSKEFL 172 (193)
Q Consensus 108 ~~C~~--C~~~f~~~~~l~~h~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~----------~-~~~C~~--C~~~F~ 172 (193)
+.|+. |...|.....+..|..+-++ -.|..|.+.|.+...|..|+.-.+. . -|+|-. |+..|.
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~--~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFk 157 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHG--NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFK 157 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc--chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhh
Confidence 55655 66667666666666544222 2677777777777777777654322 1 267743 777777
Q ss_pred ChHHHHHHHH
Q psy13164 173 RKDILIEHKK 182 (193)
Q Consensus 173 ~~~~L~~H~~ 182 (193)
+...-..|+-
T Consensus 158 T~r~RkdH~I 167 (253)
T KOG4173|consen 158 TSRDRKDHMI 167 (253)
T ss_pred hhhhhhhHHH
Confidence 7766666654
No 68
>KOG2482|consensus
Probab=82.94 E-value=4 Score=32.10 Aligned_cols=56 Identities=29% Similarity=0.547 Sum_probs=38.5
Q ss_pred ceeccccchhc-cChhHHHHHHH-HhC---Ccc-------------------cccccCcccccChHHHHHHHHH--cCCC
Q psy13164 134 RYKCDLCSKEY-FHKGYLTDHKK-IHQ---GIR-------------------YKCNLCSKEFLRKDILIEHKKI--HQGI 187 (193)
Q Consensus 134 ~~~C~~C~~~f-~~~~~l~~H~~-~h~---~~~-------------------~~C~~C~~~F~~~~~L~~H~~~--h~~~ 187 (193)
..+|..|...+ .+.+.+..|+- .|. |.| +.|-.|.+.|+.+..|+.||+. |...
T Consensus 144 slqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrri 223 (423)
T KOG2482|consen 144 SLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRRI 223 (423)
T ss_pred eeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCccc
Confidence 47888887554 34455666664 332 223 8899999999999999999986 5443
Q ss_pred CC
Q psy13164 188 RF 189 (193)
Q Consensus 188 ~~ 189 (193)
.|
T Consensus 224 nP 225 (423)
T KOG2482|consen 224 NP 225 (423)
T ss_pred CC
Confidence 34
No 69
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=82.71 E-value=1.8 Score=33.98 Aligned_cols=121 Identities=16% Similarity=0.183 Sum_probs=73.2
Q ss_pred Ccccc--hhHhhccCchhhcccccccccCCCCccCCCCcc---cch---------hhhhhc----CCCc----eeccccc
Q psy13164 57 DAVTR--DCLEFFKSHDSTLKNESDHERRSINYNCQQSYK---VGK---------LNKILH----RGIR----YKCDLCS 114 (193)
Q Consensus 57 ~~~c~--~c~~~f~~~~~~~~h~~~~~~~~~~~~C~~c~~---~~~---------~~~~~~----~~~~----~~C~~C~ 114 (193)
.|.|. .|..+......+..|.+..+.. +.|.+|.. .+. -.+.|. .+.. -.|..|.
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~---~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~ 227 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGF---VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCK 227 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCc---EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhcc
Confidence 44443 4555555566777787765543 67777753 111 112221 1111 3588999
Q ss_pred ccccChhHHHHHHHhhCCcceeccccc----hhccChhHHHHHHHHhCCccccccc--Cc----ccccChHHHHHHHHH
Q psy13164 115 KEYFHKGSLTEHKKRHQGIRYKCDLCS----KEYFHKGYLTDHKKIHQGIRYKCNL--CS----KEFLRKDILIEHKKI 183 (193)
Q Consensus 115 ~~f~~~~~l~~h~~~h~~~~~~C~~C~----~~f~~~~~l~~H~~~h~~~~~~C~~--C~----~~F~~~~~L~~H~~~ 183 (193)
..|-.-..|..|++..+..-+.|..-+ .-|.+-..|.+|.+.- .|.|.. |. ..|.....|..|+..
T Consensus 228 ~~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~---hy~ct~qtc~~~k~~vf~~~~el~~h~~~ 303 (493)
T COG5236 228 IYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRNA---HYCCTFQTCRVGKCYVFPYHTELLEHLTR 303 (493)
T ss_pred ceecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhcC---ceEEEEEEEecCcEEEeccHHHHHHHHHH
Confidence 999999999999998777434443322 3466677777777632 255543 32 468888888888765
No 70
>KOG2785|consensus
Probab=82.68 E-value=3.9 Score=32.56 Aligned_cols=74 Identities=18% Similarity=0.272 Sum_probs=42.6
Q ss_pred ceecccccccccChhHHHHHHHhhCCcceeccccchhccChhHHHHHHHHhCCcccccccCc---ccccChHHHHHHHHH
Q psy13164 107 RYKCDLCSKEYFHKGSLTEHKKRHQGIRYKCDLCSKEYFHKGYLTDHKKIHQGIRYKCNLCS---KEFLRKDILIEHKKI 183 (193)
Q Consensus 107 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~---~~F~~~~~L~~H~~~ 183 (193)
|-.|-.|+..+.+...-..||..+++. |.-.. .-......|...+..-.+.-|.|-.|+ +.|.+..+.+.||..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~Hgf-fIPdr--eYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGF-FIPDR--EYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCC-cCCch--HhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 355666777766666666677666652 11000 011222333344443333347888888 888888888888865
No 71
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=82.49 E-value=0.74 Score=25.80 Aligned_cols=25 Identities=12% Similarity=0.340 Sum_probs=15.5
Q ss_pred CCceecccccccccChhHHHHHHHh
Q psy13164 105 GIRYKCDLCSKEYFHKGSLTEHKKR 129 (193)
Q Consensus 105 ~~~~~C~~C~~~f~~~~~l~~h~~~ 129 (193)
+.-++|+.|+..|.....+.+|...
T Consensus 15 E~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 15 EEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred ceeeeCCchhHHHHHhHHHHHHhhH
Confidence 3446666666666666666666543
No 72
>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=82.16 E-value=3.8 Score=26.58 Aligned_cols=26 Identities=23% Similarity=0.447 Sum_probs=22.8
Q ss_pred ceec----cccchhccChhHHHHHHHHhCC
Q psy13164 134 RYKC----DLCSKEYFHKGYLTDHKKIHQG 159 (193)
Q Consensus 134 ~~~C----~~C~~~f~~~~~l~~H~~~h~~ 159 (193)
.|.| ..|+..+.+...+..|++.++|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3899 9999999999999999987654
No 73
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=81.02 E-value=1.9 Score=24.57 Aligned_cols=9 Identities=33% Similarity=0.899 Sum_probs=5.2
Q ss_pred ceeccccch
Q psy13164 134 RYKCDLCSK 142 (193)
Q Consensus 134 ~~~C~~C~~ 142 (193)
+|.|+.||.
T Consensus 48 ~Y~CP~CGF 56 (59)
T PRK14890 48 PYTCPKCGF 56 (59)
T ss_pred ceECCCCCC
Confidence 566666653
No 74
>PHA00626 hypothetical protein
Probab=79.84 E-value=1.4 Score=24.83 Aligned_cols=11 Identities=27% Similarity=0.470 Sum_probs=6.1
Q ss_pred eeccccccccc
Q psy13164 108 YKCDLCSKEYF 118 (193)
Q Consensus 108 ~~C~~C~~~f~ 118 (193)
|.|+.||..|+
T Consensus 24 YkCkdCGY~ft 34 (59)
T PHA00626 24 YVCCDCGYNDS 34 (59)
T ss_pred eEcCCCCCeec
Confidence 55555555543
No 75
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=79.50 E-value=1.6 Score=23.42 Aligned_cols=9 Identities=44% Similarity=1.209 Sum_probs=3.9
Q ss_pred eeccccccc
Q psy13164 108 YKCDLCSKE 116 (193)
Q Consensus 108 ~~C~~C~~~ 116 (193)
|.|..||..
T Consensus 3 Y~C~~Cg~~ 11 (44)
T smart00659 3 YICGECGRE 11 (44)
T ss_pred EECCCCCCE
Confidence 444444443
No 76
>KOG2785|consensus
Probab=79.20 E-value=2 Score=34.16 Aligned_cols=73 Identities=19% Similarity=0.231 Sum_probs=44.6
Q ss_pred CCCCcccchhHhhccCchhhcccccccccCCCC---ccCCCCcccchh-hhhhcCCCceeccccc---ccccChhHHHHH
Q psy13164 54 NGNDAVTRDCLEFFKSHDSTLKNESDHERRSIN---YNCQQSYKVGKL-NKILHRGIRYKCDLCS---KEYFHKGSLTEH 126 (193)
Q Consensus 54 ~~~~~~c~~c~~~f~~~~~~~~h~~~~~~~~~~---~~C~~c~~~~~~-~~~~~~~~~~~C~~C~---~~f~~~~~l~~h 126 (193)
...+-.|..|+..+.+......||..+|.-..| |.-+.-|-+.-. .++ ...+.|-.|+ +.|.+....+.|
T Consensus 163 e~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV---~~~~~CL~CN~~~~~f~sleavr~H 239 (390)
T KOG2785|consen 163 ELIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKV---GIGFICLFCNELGRPFSSLEAVRAH 239 (390)
T ss_pred ccCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHh---ccCceEEEeccccCcccccHHHHHH
Confidence 334577999999999999999999988763222 222222222111 111 2235565565 777777777888
Q ss_pred HHh
Q psy13164 127 KKR 129 (193)
Q Consensus 127 ~~~ 129 (193)
|..
T Consensus 240 M~~ 242 (390)
T KOG2785|consen 240 MRD 242 (390)
T ss_pred Hhh
Confidence 764
No 77
>KOG2482|consensus
Probab=79.14 E-value=3.9 Score=32.16 Aligned_cols=22 Identities=32% Similarity=0.578 Sum_probs=17.0
Q ss_pred cccccCcccccChHHHHHHHHH
Q psy13164 162 YKCNLCSKEFLRKDILIEHKKI 183 (193)
Q Consensus 162 ~~C~~C~~~F~~~~~L~~H~~~ 183 (193)
-.|-.|....-+...|..||.+
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~ 301 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKI 301 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHH
Confidence 3677888888778888888875
No 78
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=78.01 E-value=2 Score=23.60 Aligned_cols=10 Identities=40% Similarity=0.976 Sum_probs=5.1
Q ss_pred eeccccchhc
Q psy13164 135 YKCDLCSKEY 144 (193)
Q Consensus 135 ~~C~~C~~~f 144 (193)
-.|..|++.+
T Consensus 19 a~C~~C~~~l 28 (50)
T smart00614 19 AKCKYCGKKL 28 (50)
T ss_pred EEecCCCCEe
Confidence 4455555544
No 79
>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=77.65 E-value=1.7 Score=29.44 Aligned_cols=22 Identities=36% Similarity=0.697 Sum_probs=8.1
Q ss_pred cccccCcccccChHHHHHHHHHcCC
Q psy13164 162 YKCNLCSKEFLRKDILIEHKKIHQG 186 (193)
Q Consensus 162 ~~C~~C~~~F~~~~~L~~H~~~h~~ 186 (193)
..|-+||+.|.. |.+|++.|+|
T Consensus 73 i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-
T ss_pred eEEccCCcccch---HHHHHHHccC
Confidence 334445554443 2445544443
No 80
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=77.02 E-value=0.42 Score=35.23 Aligned_cols=41 Identities=22% Similarity=0.578 Sum_probs=22.6
Q ss_pred ceecccccccccChhHHHHHHHh-h---------CCc------ceeccccchhccCh
Q psy13164 107 RYKCDLCSKEYFHKGSLTEHKKR-H---------QGI------RYKCDLCSKEYFHK 147 (193)
Q Consensus 107 ~~~C~~C~~~f~~~~~l~~h~~~-h---------~~~------~~~C~~C~~~f~~~ 147 (193)
...|+.|+..|....-.....+. . .+. .+.|+.||.++...
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 35677777776655433322221 1 111 26899999876644
No 81
>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=76.53 E-value=0.94 Score=23.95 Aligned_cols=9 Identities=44% Similarity=1.405 Sum_probs=3.5
Q ss_pred eeccccccc
Q psy13164 108 YKCDLCSKE 116 (193)
Q Consensus 108 ~~C~~C~~~ 116 (193)
|+|..||..
T Consensus 6 y~C~~Cg~~ 14 (42)
T PF09723_consen 6 YRCEECGHE 14 (42)
T ss_pred EEeCCCCCE
Confidence 333344433
No 82
>PF12907 zf-met2: Zinc-binding
Probab=75.53 E-value=1.6 Score=22.87 Aligned_cols=32 Identities=25% Similarity=0.510 Sum_probs=16.4
Q ss_pred cccccCccccc---ChHHHHHHHHH-cCCCCCCCCC
Q psy13164 162 YKCNLCSKEFL---RKDILIEHKKI-HQGIRFKCDL 193 (193)
Q Consensus 162 ~~C~~C~~~F~---~~~~L~~H~~~-h~~~~~~~c~ 193 (193)
+.|.+|...|. ....|..|... |.+..+..||
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~~CF 37 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTFEECF 37 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHHHcC
Confidence 35666665553 33456666553 4444454443
No 83
>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=75.51 E-value=2.1 Score=22.71 Aligned_cols=20 Identities=30% Similarity=0.461 Sum_probs=9.0
Q ss_pred cccccCcccccC----hHHHHHHH
Q psy13164 162 YKCNLCSKEFLR----KDILIEHK 181 (193)
Q Consensus 162 ~~C~~C~~~F~~----~~~L~~H~ 181 (193)
..|..|++.+.. .++|..|+
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHH
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhh
Confidence 445555555433 24555555
No 84
>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=75.41 E-value=1.9 Score=21.64 Aligned_cols=9 Identities=22% Similarity=0.818 Sum_probs=4.4
Q ss_pred eeccccccc
Q psy13164 108 YKCDLCSKE 116 (193)
Q Consensus 108 ~~C~~C~~~ 116 (193)
|.|..||..
T Consensus 3 ~~C~~CG~i 11 (34)
T cd00729 3 WVCPVCGYI 11 (34)
T ss_pred EECCCCCCE
Confidence 445555543
No 85
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=75.31 E-value=2.7 Score=23.96 Aligned_cols=11 Identities=36% Similarity=0.930 Sum_probs=6.3
Q ss_pred Ccceeccccch
Q psy13164 132 GIRYKCDLCSK 142 (193)
Q Consensus 132 ~~~~~C~~C~~ 142 (193)
+.+|.|+.||.
T Consensus 48 g~~Y~Cp~CGF 58 (61)
T COG2888 48 GNPYRCPKCGF 58 (61)
T ss_pred CCceECCCcCc
Confidence 34666666653
No 86
>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=73.89 E-value=1.3 Score=22.92 Aligned_cols=10 Identities=30% Similarity=1.271 Sum_probs=4.7
Q ss_pred eecccccccc
Q psy13164 108 YKCDLCSKEY 117 (193)
Q Consensus 108 ~~C~~C~~~f 117 (193)
|+|..|+..|
T Consensus 6 y~C~~Cg~~f 15 (41)
T smart00834 6 YRCEDCGHTF 15 (41)
T ss_pred EEcCCCCCEE
Confidence 4444455444
No 87
>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=73.71 E-value=2.8 Score=21.40 Aligned_cols=10 Identities=20% Similarity=0.860 Sum_probs=4.6
Q ss_pred eeccccchhc
Q psy13164 135 YKCDLCSKEY 144 (193)
Q Consensus 135 ~~C~~C~~~f 144 (193)
..|+.|+..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 4455444443
No 88
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=73.17 E-value=2.1 Score=30.14 Aligned_cols=22 Identities=27% Similarity=0.826 Sum_probs=12.9
Q ss_pred ceecccccccccChhHHHHHHHhhCCc-ceeccccc
Q psy13164 107 RYKCDLCSKEYFHKGSLTEHKKRHQGI-RYKCDLCS 141 (193)
Q Consensus 107 ~~~C~~C~~~f~~~~~l~~h~~~h~~~-~~~C~~C~ 141 (193)
.|.|+.||.+ +.+. |..||+||
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCC
Confidence 4667777653 2333 56677666
No 89
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=72.70 E-value=3.3 Score=21.18 Aligned_cols=11 Identities=18% Similarity=0.869 Sum_probs=5.3
Q ss_pred ceecccccccc
Q psy13164 107 RYKCDLCSKEY 117 (193)
Q Consensus 107 ~~~C~~C~~~f 117 (193)
..+|+.|+..|
T Consensus 25 ~vrC~~C~~~f 35 (37)
T PF13719_consen 25 KVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCcEe
Confidence 34555555444
No 90
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=72.19 E-value=2.3 Score=26.34 Aligned_cols=11 Identities=27% Similarity=0.966 Sum_probs=5.8
Q ss_pred eeccccchhcc
Q psy13164 135 YKCDLCSKEYF 145 (193)
Q Consensus 135 ~~C~~C~~~f~ 145 (193)
|.|..||..|.
T Consensus 54 W~C~kCg~~fA 64 (89)
T COG1997 54 WKCRKCGAKFA 64 (89)
T ss_pred EEcCCCCCeec
Confidence 55555555543
No 91
>KOG2893|consensus
Probab=71.23 E-value=1.8 Score=32.15 Aligned_cols=43 Identities=7% Similarity=0.014 Sum_probs=32.8
Q ss_pred eeEEEecccccCCCccccccCCCCcccchhHhhccCchhhccc
Q psy13164 34 YEVTVKEESYEGDSINVEENNGNDAVTRDCLEFFKSHDSTLKN 76 (193)
Q Consensus 34 ~~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~f~~~~~~~~h 76 (193)
-+||-|..+|....++.......-|+|.+|.+.+.+--.|..|
T Consensus 11 pwcwycnrefddekiliqhqkakhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQKAKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred ceeeecccccchhhhhhhhhhhccceeeeehhhhccCCCceee
Confidence 4688888888888888888888888888887776666666555
No 92
>PF14353 CpXC: CpXC protein
Probab=70.34 E-value=3.7 Score=27.44 Aligned_cols=49 Identities=18% Similarity=0.314 Sum_probs=27.5
Q ss_pred eecccccccccChhH--------HHHHHHhhCCc--ceeccccchhccChhHHHHHHHH
Q psy13164 108 YKCDLCSKEYFHKGS--------LTEHKKRHQGI--RYKCDLCSKEYFHKGYLTDHKKI 156 (193)
Q Consensus 108 ~~C~~C~~~f~~~~~--------l~~h~~~h~~~--~~~C~~C~~~f~~~~~l~~H~~~ 156 (193)
..|+.|+..|..... -..-.++-.|. .+.|+.||..|.-...+.-|...
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcCC
Confidence 368888877643311 11112233444 58888888887766665555443
No 93
>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=69.04 E-value=4.7 Score=18.84 Aligned_cols=19 Identities=21% Similarity=0.683 Sum_probs=11.7
Q ss_pred ccccCcccccChHHHHHHHH
Q psy13164 163 KCNLCSKEFLRKDILIEHKK 182 (193)
Q Consensus 163 ~C~~C~~~F~~~~~L~~H~~ 182 (193)
.|+.|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 477777776 4455666654
No 94
>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=67.78 E-value=2.1 Score=23.61 Aligned_cols=10 Identities=30% Similarity=1.291 Sum_probs=3.9
Q ss_pred eecccccccc
Q psy13164 108 YKCDLCSKEY 117 (193)
Q Consensus 108 ~~C~~C~~~f 117 (193)
|+|..|+..|
T Consensus 6 y~C~~Cg~~f 15 (52)
T TIGR02605 6 YRCTACGHRF 15 (52)
T ss_pred EEeCCCCCEe
Confidence 3344444333
No 95
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=67.26 E-value=3.4 Score=36.24 Aligned_cols=9 Identities=22% Similarity=0.641 Sum_probs=4.8
Q ss_pred ccccccCcc
Q psy13164 161 RYKCNLCSK 169 (193)
Q Consensus 161 ~~~C~~C~~ 169 (193)
|..|+.||.
T Consensus 475 p~~Cp~Cgs 483 (730)
T COG1198 475 PQSCPECGS 483 (730)
T ss_pred CCCCCCCCC
Confidence 455555554
No 96
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=66.92 E-value=4.8 Score=27.72 Aligned_cols=12 Identities=42% Similarity=1.035 Sum_probs=7.0
Q ss_pred eeccccchhccC
Q psy13164 135 YKCDLCSKEYFH 146 (193)
Q Consensus 135 ~~C~~C~~~f~~ 146 (193)
|.|+.|+..|..
T Consensus 100 Y~Cp~C~~~y~~ 111 (147)
T smart00531 100 YKCPNCQSKYTF 111 (147)
T ss_pred EECcCCCCEeeH
Confidence 566666655553
No 97
>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=66.69 E-value=6.5 Score=27.49 Aligned_cols=29 Identities=10% Similarity=0.463 Sum_probs=17.1
Q ss_pred eeccccchhccChhHHHHHHHHhCCcccccccCcccc
Q psy13164 135 YKCDLCSKEYFHKGYLTDHKKIHQGIRYKCNLCSKEF 171 (193)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~F 171 (193)
|.|+.|+..|+....+. .-|.|+.||...
T Consensus 110 Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 110 FICPNMCVRFTFNEAME--------LNFTCPRCGAML 138 (158)
T ss_pred EECCCCCcEeeHHHHHH--------cCCcCCCCCCEe
Confidence 66666666666555543 136676666543
No 98
>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=66.51 E-value=4.5 Score=27.38 Aligned_cols=24 Identities=29% Similarity=0.616 Sum_probs=15.1
Q ss_pred ceeccccchhccChhHHHHHHHHhCCc
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKKIHQGI 160 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~h~~~ 160 (193)
...|.+||+.|.. |.+|++.|+|-
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S
T ss_pred eeEEccCCcccch---HHHHHHHccCC
Confidence 4789999998864 58899988764
No 99
>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=66.43 E-value=4.1 Score=27.24 Aligned_cols=12 Identities=0% Similarity=-0.033 Sum_probs=5.9
Q ss_pred ceeccccchhcc
Q psy13164 134 RYKCDLCSKEYF 145 (193)
Q Consensus 134 ~~~C~~C~~~f~ 145 (193)
|..|+.||..|.
T Consensus 26 p~vcP~cg~~~~ 37 (129)
T TIGR02300 26 PAVSPYTGEQFP 37 (129)
T ss_pred CccCCCcCCccC
Confidence 445555554443
No 100
>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=66.04 E-value=3.9 Score=28.62 Aligned_cols=32 Identities=9% Similarity=0.432 Sum_probs=24.0
Q ss_pred CCceecccccccccChhHHHHHHHhhCCcceeccccchhc
Q psy13164 105 GIRYKCDLCSKEYFHKGSLTEHKKRHQGIRYKCDLCSKEY 144 (193)
Q Consensus 105 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~C~~C~~~f 144 (193)
..-|.|+.|+..|+....+. ..|.|+.||...
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME--------LNFTCPRCGAML 138 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH--------cCCcCCCCCCEe
Confidence 45589999998887776664 268999999653
No 101
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=65.85 E-value=3.2 Score=29.71 Aligned_cols=29 Identities=14% Similarity=0.580 Sum_probs=15.8
Q ss_pred eeccccchhccChhHHHHHHHHhCCcccccccCcccc
Q psy13164 135 YKCDLCSKEYFHKGYLTDHKKIHQGIRYKCNLCSKEF 171 (193)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~F 171 (193)
|.|+.|+..|+.-..+. ..|.|+.||...
T Consensus 118 Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L 146 (178)
T PRK06266 118 FFCPNCHIRFTFDEAME--------YGFRCPQCGEML 146 (178)
T ss_pred EECCCCCcEEeHHHHhh--------cCCcCCCCCCCC
Confidence 66666666655544432 136666666543
No 102
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=65.55 E-value=2 Score=32.30 Aligned_cols=81 Identities=23% Similarity=0.458 Sum_probs=47.2
Q ss_pred cCCCceecccccccccChhHHHHHHHhh---CCcceeccccchhccChhHH-------HHHHHHh-----CCcccccccC
Q psy13164 103 HRGIRYKCDLCSKEYFHKGSLTEHKKRH---QGIRYKCDLCSKEYFHKGYL-------TDHKKIH-----QGIRYKCNLC 167 (193)
Q Consensus 103 ~~~~~~~C~~C~~~f~~~~~l~~h~~~h---~~~~~~C~~C~~~f~~~~~l-------~~H~~~h-----~~~~~~C~~C 167 (193)
++++.|+|..|..... ...--.|+..- ..+.|.|..|.+.- +.+-| ..|.+.- .++++.|+.|
T Consensus 138 hGGrif~CsfC~~flC-EDDQFEHQAsCQvLe~E~~KC~SCNrlG-q~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKC 215 (314)
T PF06524_consen 138 HGGRIFKCSFCDNFLC-EDDQFEHQASCQVLESETFKCQSCNRLG-QYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKC 215 (314)
T ss_pred CCCeEEEeecCCCeee-ccchhhhhhhhhhhhccccccccccccc-chhhhheeeeehhhhhhhcccccccCCCCCCCCC
Confidence 5667799999997443 33344465542 22357777666432 11222 3455432 2348999999
Q ss_pred cccccChHHHHHHHHHcC
Q psy13164 168 SKEFLRKDILIEHKKIHQ 185 (193)
Q Consensus 168 ~~~F~~~~~L~~H~~~h~ 185 (193)
+........|..-.|+|.
T Consensus 216 g~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 216 GYETQETKDLSMSTRSHK 233 (314)
T ss_pred CCcccccccceeeeecch
Confidence 988776666655555554
No 103
>KOG4167|consensus
Probab=64.82 E-value=2.3 Score=36.81 Aligned_cols=25 Identities=28% Similarity=0.587 Sum_probs=22.3
Q ss_pred ceeccccchhccChhHHHHHHHHhC
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKKIHQ 158 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~h~ 158 (193)
-|.|.+|+|.|.....++.||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 3899999999999999999999885
No 104
>PF15269 zf-C2H2_7: Zinc-finger
Probab=64.70 E-value=6.2 Score=21.09 Aligned_cols=21 Identities=38% Similarity=0.605 Sum_probs=12.8
Q ss_pred cccccCcccccChHHHHHHHH
Q psy13164 162 YKCNLCSKEFLRKDILIEHKK 182 (193)
Q Consensus 162 ~~C~~C~~~F~~~~~L~~H~~ 182 (193)
|+|-+|.....-++.|..||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 556666666666666666654
No 105
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=64.34 E-value=3.6 Score=22.09 Aligned_cols=8 Identities=25% Similarity=0.924 Sum_probs=3.5
Q ss_pred eecccccc
Q psy13164 108 YKCDLCSK 115 (193)
Q Consensus 108 ~~C~~C~~ 115 (193)
..|+.||.
T Consensus 22 ~~Cp~CG~ 29 (46)
T PRK00398 22 VRCPYCGY 29 (46)
T ss_pred eECCCCCC
Confidence 34444443
No 106
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=64.34 E-value=5.5 Score=20.22 Aligned_cols=9 Identities=22% Similarity=0.818 Sum_probs=4.0
Q ss_pred eeccccchh
Q psy13164 135 YKCDLCSKE 143 (193)
Q Consensus 135 ~~C~~C~~~ 143 (193)
.+|..|+..
T Consensus 26 v~C~~C~~~ 34 (36)
T PF13717_consen 26 VRCSKCGHV 34 (36)
T ss_pred EECCCCCCE
Confidence 444444443
No 107
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=63.69 E-value=4.5 Score=22.23 Aligned_cols=10 Identities=50% Similarity=1.235 Sum_probs=5.2
Q ss_pred eecccccccc
Q psy13164 108 YKCDLCSKEY 117 (193)
Q Consensus 108 ~~C~~C~~~f 117 (193)
|.|..|+..|
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 5555555544
No 108
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=63.29 E-value=2.9 Score=29.10 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=7.8
Q ss_pred eecccccccccChhH
Q psy13164 108 YKCDLCSKEYFHKGS 122 (193)
Q Consensus 108 ~~C~~C~~~f~~~~~ 122 (193)
++|+.||.+|.....
T Consensus 29 ~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 29 RECLACGKRFTTFER 43 (154)
T ss_pred eeccccCCcceEeEe
Confidence 555555555554433
No 109
>KOG4167|consensus
Probab=59.85 E-value=2.5 Score=36.55 Aligned_cols=24 Identities=29% Similarity=0.621 Sum_probs=22.4
Q ss_pred cccccCcccccChHHHHHHHHHcC
Q psy13164 162 YKCNLCSKEFLRKDILIEHKKIHQ 185 (193)
Q Consensus 162 ~~C~~C~~~F~~~~~L~~H~~~h~ 185 (193)
|.|..|++.|..-..+..||++|.
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHH
Confidence 999999999998889999999986
No 110
>KOG3408|consensus
Probab=59.02 E-value=6.2 Score=26.09 Aligned_cols=23 Identities=26% Similarity=0.564 Sum_probs=16.8
Q ss_pred ccccccCcccccChHHHHHHHHH
Q psy13164 161 RYKCNLCSKEFLRKDILIEHKKI 183 (193)
Q Consensus 161 ~~~C~~C~~~F~~~~~L~~H~~~ 183 (193)
.|.|..|.+-|.....|..|.++
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhc
Confidence 47777777777777777777654
No 111
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=58.92 E-value=1.8 Score=24.43 Aligned_cols=36 Identities=14% Similarity=0.138 Sum_probs=19.3
Q ss_pred ccchhHhhccCchhhcccccccccCCCCccCCCCcc
Q psy13164 59 VTRDCLEFFKSHDSTLKNESDHERRSINYNCQQSYK 94 (193)
Q Consensus 59 ~c~~c~~~f~~~~~~~~h~~~~~~~~~~~~C~~c~~ 94 (193)
.|.+|++.+.-......-.+-.+++...|.|+.|..
T Consensus 4 kC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~ 39 (56)
T PF09963_consen 4 KCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKE 39 (56)
T ss_pred EEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHH
Confidence 577777776543332222223334455577777754
No 112
>PRK04023 DNA polymerase II large subunit; Validated
Probab=58.75 E-value=10 Score=34.36 Aligned_cols=11 Identities=27% Similarity=0.712 Sum_probs=7.1
Q ss_pred ccccccCcccc
Q psy13164 161 RYKCNLCSKEF 171 (193)
Q Consensus 161 ~~~C~~C~~~F 171 (193)
++.|+.|+..-
T Consensus 663 ~y~CPKCG~El 673 (1121)
T PRK04023 663 EDECEKCGREP 673 (1121)
T ss_pred CCcCCCCCCCC
Confidence 46677777644
No 113
>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=56.84 E-value=5.4 Score=19.76 Aligned_cols=8 Identities=25% Similarity=0.937 Sum_probs=3.3
Q ss_pred eecccccc
Q psy13164 108 YKCDLCSK 115 (193)
Q Consensus 108 ~~C~~C~~ 115 (193)
.+|+.||.
T Consensus 18 irC~~CG~ 25 (32)
T PF03604_consen 18 IRCPECGH 25 (32)
T ss_dssp SSBSSSS-
T ss_pred EECCcCCC
Confidence 34555543
No 114
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=56.15 E-value=6.2 Score=33.16 Aligned_cols=8 Identities=25% Similarity=0.758 Sum_probs=3.9
Q ss_pred ceeccccc
Q psy13164 134 RYKCDLCS 141 (193)
Q Consensus 134 ~~~C~~C~ 141 (193)
|..|+.|+
T Consensus 253 ~~~Cp~C~ 260 (505)
T TIGR00595 253 PKTCPQCG 260 (505)
T ss_pred CCCCCCCC
Confidence 34455554
No 115
>KOG4173|consensus
Probab=55.28 E-value=7.9 Score=28.20 Aligned_cols=46 Identities=20% Similarity=0.517 Sum_probs=36.6
Q ss_pred eeccc--cchhccChhHHHHHHHHhCCcccccccCcccccChHHHHHHHH
Q psy13164 135 YKCDL--CSKEYFHKGYLTDHKKIHQGIRYKCNLCSKEFLRKDILIEHKK 182 (193)
Q Consensus 135 ~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~F~~~~~L~~H~~ 182 (193)
|.|+. |...|.+...+..|-.+-+| -.|..|.+.|.+...|..|+.
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~--~sCs~C~r~~Pt~hLLd~HI~ 127 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHG--NSCSFCKRAFPTGHLLDAHIL 127 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc--chhHHHHHhCCchhhhhHHHH
Confidence 88887 77888888877777654333 479999999999999998875
No 116
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=54.44 E-value=14 Score=19.37 Aligned_cols=24 Identities=25% Similarity=0.369 Sum_probs=13.9
Q ss_pred cccccCcccccC--hHHHHHHHHHcC
Q psy13164 162 YKCNLCSKEFLR--KDILIEHKKIHQ 185 (193)
Q Consensus 162 ~~C~~C~~~F~~--~~~L~~H~~~h~ 185 (193)
-.|+.||..|.. ...-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 467777766643 345555666553
No 117
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=52.18 E-value=7.5 Score=26.25 Aligned_cols=22 Identities=27% Similarity=0.327 Sum_probs=13.0
Q ss_pred eeccccchhccChhHHHHHHHHhCC
Q psy13164 135 YKCDLCSKEYFHKGYLTDHKKIHQG 159 (193)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~h~~ 159 (193)
..|.++|+.|. .|++|+.+|.|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccC
Confidence 55666666654 35666666554
No 118
>KOG3507|consensus
Probab=52.15 E-value=5.7 Score=22.59 Aligned_cols=28 Identities=18% Similarity=0.379 Sum_probs=14.7
Q ss_pred ccCCCCcccchhhhhhcCCCceeccccccccc
Q psy13164 87 YNCQQSYKVGKLNKILHRGIRYKCDLCSKEYF 118 (193)
Q Consensus 87 ~~C~~c~~~~~~~~~~~~~~~~~C~~C~~~f~ 118 (193)
|.|..|+.-....+. -.++|..||....
T Consensus 21 YiCgdC~~en~lk~~----D~irCReCG~RIl 48 (62)
T KOG3507|consen 21 YICGDCGQENTLKRG----DVIRCRECGYRIL 48 (62)
T ss_pred EEeccccccccccCC----CcEehhhcchHHH
Confidence 666666654332222 2366777775443
No 119
>PRK14873 primosome assembly protein PriA; Provisional
Probab=50.44 E-value=9 Score=33.43 Aligned_cols=8 Identities=13% Similarity=0.380 Sum_probs=5.2
Q ss_pred cCCCCccc
Q psy13164 88 NCQQSYKV 95 (193)
Q Consensus 88 ~C~~c~~~ 95 (193)
.|..|+..
T Consensus 385 ~C~~Cg~~ 392 (665)
T PRK14873 385 ACARCRTP 392 (665)
T ss_pred EhhhCcCe
Confidence 56666665
No 120
>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=48.88 E-value=9.2 Score=18.62 Aligned_cols=8 Identities=25% Similarity=0.667 Sum_probs=3.5
Q ss_pred ceeccccc
Q psy13164 134 RYKCDLCS 141 (193)
Q Consensus 134 ~~~C~~C~ 141 (193)
-+.|+.|+
T Consensus 19 ~~vCp~C~ 26 (30)
T PF08274_consen 19 LLVCPECG 26 (30)
T ss_dssp SEEETTTT
T ss_pred EEeCCccc
Confidence 34444443
No 121
>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=47.60 E-value=12 Score=25.72 Aligned_cols=18 Identities=22% Similarity=0.564 Sum_probs=11.3
Q ss_pred ceeccccchhccChhHHH
Q psy13164 134 RYKCDLCSKEYFHKGYLT 151 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~ 151 (193)
-+.|+.||+.|...+.+.
T Consensus 124 f~~C~~C~kiyW~GsH~~ 141 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGSHWR 141 (147)
T ss_pred EEECCCCCCEecccccHH
Confidence 367777777776655544
No 122
>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=47.41 E-value=16 Score=27.02 Aligned_cols=23 Identities=22% Similarity=0.589 Sum_probs=17.8
Q ss_pred ceeccccchhccChhHHHHHHHH
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKKI 156 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~ 156 (193)
.|.|..|+|.|.....+..|+..
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHH
T ss_pred EECCCCCCcccCChHHHHHHHhh
Confidence 58888888888888888888875
No 123
>KOG0696|consensus
Probab=46.41 E-value=8.3 Score=31.64 Aligned_cols=57 Identities=25% Similarity=0.451 Sum_probs=34.5
Q ss_pred CCceecccccccccChhHHHHHHHhhCCcceeccccchhccChhHHHHHH-HHhCCc-ccccccCcc
Q psy13164 105 GIRYKCDLCSKEYFHKGSLTEHKKRHQGIRYKCDLCSKEYFHKGYLTDHK-KIHQGI-RYKCNLCSK 169 (193)
Q Consensus 105 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~C~~C~~~f~~~~~l~~H~-~~h~~~-~~~C~~C~~ 169 (193)
...|+|..|.. ..|.+.|.-..|.|+-=++.+.+...-..|. ..|+-. |-=|..||.
T Consensus 71 KQGfQCqvC~f--------vvHkrChefVtF~CPGadkg~dtDdpr~kHkf~~~tYssPTFCDhCGs 129 (683)
T KOG0696|consen 71 KQGFQCQVCCF--------VVHKRCHEFVTFSCPGADKGPDTDDPRSKHKFKIHTYSSPTFCDHCGS 129 (683)
T ss_pred cCceeeeEEee--------hhhhhhcceEEEECCCCCCCCCCCCcccccceeeeecCCCchhhhHHH
Confidence 34478888764 4577777666777777666666655555553 234433 555666654
No 124
>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=46.03 E-value=9.8 Score=28.08 Aligned_cols=25 Identities=24% Similarity=0.582 Sum_probs=20.0
Q ss_pred ccccccCcccccChHHHHHHHHHcC
Q psy13164 161 RYKCNLCSKEFLRKDILIEHKKIHQ 185 (193)
Q Consensus 161 ~~~C~~C~~~F~~~~~L~~H~~~h~ 185 (193)
.|.|+.|+|.|.-..-.+.|+..-+
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred EECCCCCCcccCChHHHHHHHhhcC
Confidence 6999999999999999999988643
No 125
>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=44.27 E-value=11 Score=17.63 Aligned_cols=9 Identities=33% Similarity=0.921 Sum_probs=4.4
Q ss_pred ccccCcccc
Q psy13164 163 KCNLCSKEF 171 (193)
Q Consensus 163 ~C~~C~~~F 171 (193)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 345555544
No 126
>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=41.64 E-value=12 Score=17.18 Aligned_cols=7 Identities=29% Similarity=1.151 Sum_probs=3.4
Q ss_pred eeccccc
Q psy13164 108 YKCDLCS 114 (193)
Q Consensus 108 ~~C~~C~ 114 (193)
|.|+.||
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 4444444
No 127
>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=40.37 E-value=15 Score=21.38 Aligned_cols=9 Identities=33% Similarity=1.239 Sum_probs=2.9
Q ss_pred ecccccccc
Q psy13164 109 KCDLCSKEY 117 (193)
Q Consensus 109 ~C~~C~~~f 117 (193)
.|..|++.|
T Consensus 11 ~C~~C~~~F 19 (69)
T PF01363_consen 11 NCMICGKKF 19 (69)
T ss_dssp B-TTT--B-
T ss_pred cCcCcCCcC
Confidence 455666655
No 128
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=40.12 E-value=21 Score=18.53 Aligned_cols=16 Identities=31% Similarity=0.713 Sum_probs=6.9
Q ss_pred eecccccccccChhHH
Q psy13164 108 YKCDLCSKEYFHKGSL 123 (193)
Q Consensus 108 ~~C~~C~~~f~~~~~l 123 (193)
..|+.|+..+-....|
T Consensus 20 d~C~~C~G~W~d~~el 35 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGEL 35 (41)
T ss_pred EECCCCCeEEccHHHH
Confidence 3444444444444333
No 129
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=40.11 E-value=18 Score=23.22 Aligned_cols=12 Identities=17% Similarity=0.578 Sum_probs=5.7
Q ss_pred eeccccchhccC
Q psy13164 135 YKCDLCSKEYFH 146 (193)
Q Consensus 135 ~~C~~C~~~f~~ 146 (193)
++|..||..|..
T Consensus 3 H~CtrCG~vf~~ 14 (112)
T COG3364 3 HQCTRCGEVFDD 14 (112)
T ss_pred ceeccccccccc
Confidence 344445544444
No 130
>KOG2593|consensus
Probab=39.54 E-value=22 Score=29.02 Aligned_cols=35 Identities=23% Similarity=0.494 Sum_probs=19.3
Q ss_pred CCceecccccccccChhHHHHHHHhhC-Ccceeccccch
Q psy13164 105 GIRYKCDLCSKEYFHKGSLTEHKKRHQ-GIRYKCDLCSK 142 (193)
Q Consensus 105 ~~~~~C~~C~~~f~~~~~l~~h~~~h~-~~~~~C~~C~~ 142 (193)
...|.|+.|.+.|.....++ ..-- ...|.|..|+.
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGG 161 (436)
T ss_pred cccccCCccccchhhhHHHH---hhcccCceEEEecCCC
Confidence 34577777777766544333 1111 11577777763
No 131
>PRK05580 primosome assembly protein PriA; Validated
Probab=37.96 E-value=17 Score=31.81 Aligned_cols=9 Identities=22% Similarity=0.615 Sum_probs=4.6
Q ss_pred ceeccccch
Q psy13164 134 RYKCDLCSK 142 (193)
Q Consensus 134 ~~~C~~C~~ 142 (193)
|..|+.||.
T Consensus 421 ~~~Cp~Cg~ 429 (679)
T PRK05580 421 PKACPECGS 429 (679)
T ss_pred CCCCCCCcC
Confidence 445555543
No 132
>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=37.96 E-value=24 Score=19.84 Aligned_cols=7 Identities=43% Similarity=1.084 Sum_probs=3.0
Q ss_pred ecccccc
Q psy13164 109 KCDLCSK 115 (193)
Q Consensus 109 ~C~~C~~ 115 (193)
.|+.||.
T Consensus 24 ~Cp~CGa 30 (54)
T TIGR01206 24 ICDECGA 30 (54)
T ss_pred eCCCCCC
Confidence 4444443
No 133
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.17 E-value=7.2 Score=22.37 Aligned_cols=11 Identities=18% Similarity=0.347 Sum_probs=6.2
Q ss_pred CCCCccCCCCc
Q psy13164 83 RSINYNCQQSY 93 (193)
Q Consensus 83 ~~~~~~C~~c~ 93 (193)
+...|.|++|.
T Consensus 28 PIrtymC~eC~ 38 (68)
T COG4896 28 PIRTYMCPECE 38 (68)
T ss_pred CceeEechhhH
Confidence 34456666664
No 134
>KOG3408|consensus
Probab=36.88 E-value=23 Score=23.55 Aligned_cols=23 Identities=22% Similarity=0.496 Sum_probs=20.6
Q ss_pred ceeccccchhccChhHHHHHHHH
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKKI 156 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~ 156 (193)
.|-|..|.+-|.....|..|.++
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhc
Confidence 59999999999999999999875
No 135
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=36.22 E-value=36 Score=23.96 Aligned_cols=18 Identities=28% Similarity=0.678 Sum_probs=12.3
Q ss_pred ceeccccchhccChhHHH
Q psy13164 134 RYKCDLCSKEYFHKGYLT 151 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~ 151 (193)
-+.|+.||+.|.-.+++.
T Consensus 130 f~~C~~CgkiYW~GsHw~ 147 (165)
T COG1656 130 FYRCPKCGKIYWKGSHWR 147 (165)
T ss_pred eeECCCCcccccCchHHH
Confidence 467888887777666554
No 136
>KOG2593|consensus
Probab=36.18 E-value=34 Score=27.98 Aligned_cols=35 Identities=26% Similarity=0.588 Sum_probs=24.1
Q ss_pred ceeccccchhccChhHHHHHHHHhCC-cccccccCcccc
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKKIHQG-IRYKCNLCSKEF 171 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~h~~-~~~~C~~C~~~F 171 (193)
.|.|+.|.+.|+..-.++ ..-.. ..|.|..|+-..
T Consensus 128 ~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGGEL 163 (436)
T ss_pred cccCCccccchhhhHHHH---hhcccCceEEEecCCCch
Confidence 599999999997654432 33222 269999998643
No 137
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=36.02 E-value=56 Score=21.03 Aligned_cols=37 Identities=5% Similarity=0.107 Sum_probs=29.7
Q ss_pred ceecccccccccChhHHHHHHHhhCCcceeccccchh
Q psy13164 107 RYKCDLCSKEYFHKGSLTEHKKRHQGIRYKCDLCSKE 143 (193)
Q Consensus 107 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~C~~C~~~ 143 (193)
.|.|+.-+..|.+...+...+......-|.|...|+.
T Consensus 3 Vf~i~~T~EiF~dYe~Y~~R~~~y~~~vwtC~~TGk~ 39 (102)
T PF10537_consen 3 VFYIPFTGEIFRDYEEYLKRMILYNQRVWTCEITGKS 39 (102)
T ss_pred eEEeCCCCcccCCHHHHHHHHHHHhCCeeEEecCCCC
Confidence 4778888889999888888877776667899888864
No 138
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=35.18 E-value=20 Score=28.00 Aligned_cols=48 Identities=21% Similarity=0.447 Sum_probs=29.3
Q ss_pred eccccchhccChhHHHHHHHHhCCcccccccCcccccChHHHHHHHHHc
Q psy13164 136 KCDLCSKEYFHKGYLTDHKKIHQGIRYKCNLCSKEFLRKDILIEHKKIH 184 (193)
Q Consensus 136 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~F~~~~~L~~H~~~h 184 (193)
.|-.|...|.....-..-. .-+..+|+|..|...|-.--....|...|
T Consensus 364 ~Cf~CQ~~fp~~~~~~~~~-~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 364 HCFVCQGPFPKPPVSPFDE-STSSGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred cceeccCCCCCCCCCcccc-cccccceechhhhhhhhhhhHHHHHHHHh
Confidence 3666776666543321111 11122799999999998777777777666
No 139
>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=34.58 E-value=11 Score=23.61 Aligned_cols=11 Identities=36% Similarity=1.099 Sum_probs=6.5
Q ss_pred eeccccchhcc
Q psy13164 135 YKCDLCSKEYF 145 (193)
Q Consensus 135 ~~C~~C~~~f~ 145 (193)
|.|..|++.|.
T Consensus 54 W~C~~C~~~~A 64 (90)
T PF01780_consen 54 WKCKKCGKKFA 64 (90)
T ss_dssp EEETTTTEEEE
T ss_pred eecCCCCCEEe
Confidence 66666665553
No 140
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=34.15 E-value=31 Score=19.25 Aligned_cols=8 Identities=38% Similarity=0.418 Sum_probs=3.7
Q ss_pred hHHHHHHH
Q psy13164 148 GYLTDHKK 155 (193)
Q Consensus 148 ~~l~~H~~ 155 (193)
..|..|+.
T Consensus 24 ~~l~~H~~ 31 (60)
T PF02176_consen 24 KELDDHLE 31 (60)
T ss_dssp CCHHHHHH
T ss_pred HHHHHHHH
Confidence 34444544
No 141
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=33.86 E-value=33 Score=18.87 Aligned_cols=11 Identities=27% Similarity=0.860 Sum_probs=6.2
Q ss_pred eeccccccccc
Q psy13164 108 YKCDLCSKEYF 118 (193)
Q Consensus 108 ~~C~~C~~~f~ 118 (193)
+.|..||..|.
T Consensus 5 l~C~dCg~~Fv 15 (49)
T PF13451_consen 5 LTCKDCGAEFV 15 (49)
T ss_pred EEcccCCCeEE
Confidence 55666665554
No 142
>KOG2907|consensus
Probab=33.48 E-value=21 Score=23.32 Aligned_cols=10 Identities=20% Similarity=0.557 Sum_probs=5.3
Q ss_pred cchhHhhccC
Q psy13164 60 TRDCLEFFKS 69 (193)
Q Consensus 60 c~~c~~~f~~ 69 (193)
|..||..+..
T Consensus 10 C~~CG~ll~~ 19 (116)
T KOG2907|consen 10 CSDCGSLLEE 19 (116)
T ss_pred hhhhhhhccc
Confidence 5566655433
No 143
>KOG2807|consensus
Probab=33.39 E-value=61 Score=25.62 Aligned_cols=24 Identities=29% Similarity=0.681 Sum_probs=18.8
Q ss_pred ccccccCcccccChHHHHHHHHHc
Q psy13164 161 RYKCNLCSKEFLRKDILIEHKKIH 184 (193)
Q Consensus 161 ~~~C~~C~~~F~~~~~L~~H~~~h 184 (193)
.|.|..|...|=.--....|...|
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred cEEchhccceeeccchHHHHhhhh
Confidence 689999999887776666777666
No 144
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=33.28 E-value=19 Score=18.57 Aligned_cols=13 Identities=31% Similarity=0.810 Sum_probs=10.4
Q ss_pred ccccccCcccccC
Q psy13164 161 RYKCNLCSKEFLR 173 (193)
Q Consensus 161 ~~~C~~C~~~F~~ 173 (193)
||.|..|+..|=.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 7888888888854
No 145
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=32.17 E-value=23 Score=23.26 Aligned_cols=10 Identities=40% Similarity=0.943 Sum_probs=4.7
Q ss_pred eecccccccc
Q psy13164 108 YKCDLCSKEY 117 (193)
Q Consensus 108 ~~C~~C~~~f 117 (193)
..|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (115)
T TIGR00100 71 CECEDCSEEV 80 (115)
T ss_pred EEcccCCCEE
Confidence 4455555443
No 146
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.91 E-value=27 Score=22.71 Aligned_cols=11 Identities=18% Similarity=0.220 Sum_probs=6.8
Q ss_pred ceeccccchhc
Q psy13164 134 RYKCDLCSKEY 144 (193)
Q Consensus 134 ~~~C~~C~~~f 144 (193)
|..|++||+.|
T Consensus 26 PiVsPytG~s~ 36 (129)
T COG4530 26 PIVSPYTGKSY 36 (129)
T ss_pred ccccCcccccc
Confidence 56666666665
No 147
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=30.83 E-value=26 Score=22.98 Aligned_cols=10 Identities=30% Similarity=0.295 Sum_probs=4.7
Q ss_pred eecccccccc
Q psy13164 108 YKCDLCSKEY 117 (193)
Q Consensus 108 ~~C~~C~~~f 117 (193)
+.|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 4455555433
No 148
>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=30.80 E-value=21 Score=22.79 Aligned_cols=20 Identities=20% Similarity=0.419 Sum_probs=12.4
Q ss_pred HHHhCCcccccccCcccccC
Q psy13164 154 KKIHQGIRYKCNLCSKEFLR 173 (193)
Q Consensus 154 ~~~h~~~~~~C~~C~~~F~~ 173 (193)
+..+.|.+++|..||..|..
T Consensus 72 ~~l~~g~~~rC~eCG~~fkL 91 (97)
T cd00924 72 MWLEKGKPKRCPECGHVFKL 91 (97)
T ss_pred EEEeCCCceeCCCCCcEEEE
Confidence 34455557777777777643
No 149
>PLN02294 cytochrome c oxidase subunit Vb
Probab=30.68 E-value=15 Score=26.02 Aligned_cols=23 Identities=17% Similarity=0.450 Sum_probs=16.9
Q ss_pred HHHHHHhCCcccccccCcccccC
Q psy13164 151 TDHKKIHQGIRYKCNLCSKEFLR 173 (193)
Q Consensus 151 ~~H~~~h~~~~~~C~~C~~~F~~ 173 (193)
..++..+.|+|..|+.||..|..
T Consensus 131 v~Wf~L~kGkp~RCpeCG~~fkL 153 (174)
T PLN02294 131 VVWFWLEKGKSFECPVCTQYFEL 153 (174)
T ss_pred eEEEEecCCCceeCCCCCCEEEE
Confidence 34456677778889999988854
No 150
>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=30.38 E-value=30 Score=18.07 Aligned_cols=8 Identities=25% Similarity=0.663 Sum_probs=3.0
Q ss_pred eecccccc
Q psy13164 108 YKCDLCSK 115 (193)
Q Consensus 108 ~~C~~C~~ 115 (193)
+.|..||.
T Consensus 20 ~vC~~CG~ 27 (43)
T PF08271_consen 20 LVCPNCGL 27 (43)
T ss_dssp EEETTT-B
T ss_pred EECCCCCC
Confidence 34444443
No 151
>KOG2071|consensus
Probab=30.06 E-value=31 Score=29.42 Aligned_cols=25 Identities=24% Similarity=0.476 Sum_probs=18.3
Q ss_pred ccccccCcccccChHHHHHHHHHcC
Q psy13164 161 RYKCNLCSKEFLRKDILIEHKKIHQ 185 (193)
Q Consensus 161 ~~~C~~C~~~F~~~~~L~~H~~~h~ 185 (193)
|-+|..||.+|........||-+|-
T Consensus 418 pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 418 PNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cchhcccccccccchhhhhHhhhhh
Confidence 5778888888887777666666554
No 152
>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=29.45 E-value=33 Score=17.43 Aligned_cols=8 Identities=50% Similarity=1.364 Sum_probs=3.8
Q ss_pred Cceecccc
Q psy13164 106 IRYKCDLC 113 (193)
Q Consensus 106 ~~~~C~~C 113 (193)
..|.|..|
T Consensus 28 qryrC~~C 35 (36)
T PF03811_consen 28 QRYRCKDC 35 (36)
T ss_pred EeEecCcC
Confidence 33555544
No 153
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=29.40 E-value=26 Score=22.58 Aligned_cols=22 Identities=36% Similarity=0.738 Sum_probs=16.1
Q ss_pred ccccccCcccccChHHHHHHHH
Q psy13164 161 RYKCNLCSKEFLRKDILIEHKK 182 (193)
Q Consensus 161 ~~~C~~C~~~F~~~~~L~~H~~ 182 (193)
.+-|..|.+-|.+...|..|.+
T Consensus 55 qhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhc
Confidence 4667777777777777777764
No 154
>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=28.36 E-value=19 Score=18.92 Aligned_cols=13 Identities=38% Similarity=0.933 Sum_probs=7.9
Q ss_pred ccccccCcccccC
Q psy13164 161 RYKCNLCSKEFLR 173 (193)
Q Consensus 161 ~~~C~~C~~~F~~ 173 (193)
|+.|..|+..|=.
T Consensus 13 ~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 13 PFKCKHCGKSFCL 25 (43)
T ss_dssp HEE-TTTS-EE-T
T ss_pred CeECCCCCcccCc
Confidence 6888888888843
No 155
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=28.32 E-value=27 Score=24.25 Aligned_cols=33 Identities=27% Similarity=0.905 Sum_probs=18.2
Q ss_pred ceeccccchhccChhHHHHHHHHhCCcccccccCccc
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKKIHQGIRYKCNLCSKE 170 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~ 170 (193)
+|.|. |+..|.+. .+|-..-.|+.|.|..|+-.
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~~YrC~~C~gk 149 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGEVYRCGKCGGK 149 (156)
T ss_pred eEEee-cCCccchh---hhcccccccceEEeccCCce
Confidence 57777 77664432 23333333445777777643
No 156
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=28.22 E-value=37 Score=18.69 Aligned_cols=8 Identities=38% Similarity=0.991 Sum_probs=3.5
Q ss_pred cccccccc
Q psy13164 110 CDLCSKEY 117 (193)
Q Consensus 110 C~~C~~~f 117 (193)
|..|++.|
T Consensus 5 C~~C~~~F 12 (57)
T cd00065 5 CMGCGKPF 12 (57)
T ss_pred CcccCccc
Confidence 44444444
No 157
>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=27.98 E-value=35 Score=17.61 Aligned_cols=10 Identities=20% Similarity=0.913 Sum_probs=4.3
Q ss_pred Cceecccccc
Q psy13164 106 IRYKCDLCSK 115 (193)
Q Consensus 106 ~~~~C~~C~~ 115 (193)
+.+.|..|+.
T Consensus 23 ~~w~C~~C~~ 32 (40)
T PF04810_consen 23 KTWICNFCGT 32 (40)
T ss_dssp TEEEETTT--
T ss_pred CEEECcCCCC
Confidence 4455555554
No 158
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=27.58 E-value=46 Score=17.94 Aligned_cols=9 Identities=33% Similarity=0.958 Sum_probs=4.6
Q ss_pred eeccccccc
Q psy13164 108 YKCDLCSKE 116 (193)
Q Consensus 108 ~~C~~C~~~ 116 (193)
+.|+.|+..
T Consensus 21 ~vC~~Cg~~ 29 (52)
T smart00661 21 FVCRKCGYE 29 (52)
T ss_pred EECCcCCCe
Confidence 455555543
No 159
>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=27.03 E-value=24 Score=19.53 Aligned_cols=12 Identities=25% Similarity=0.708 Sum_probs=6.3
Q ss_pred ccccCcccccCh
Q psy13164 163 KCNLCSKEFLRK 174 (193)
Q Consensus 163 ~C~~C~~~F~~~ 174 (193)
.|+.|++.|..-
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 899999998643
No 160
>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=26.92 E-value=46 Score=17.70 Aligned_cols=7 Identities=43% Similarity=1.549 Sum_probs=3.6
Q ss_pred eeccccc
Q psy13164 108 YKCDLCS 114 (193)
Q Consensus 108 ~~C~~C~ 114 (193)
|+|..|.
T Consensus 38 ~~C~~C~ 44 (46)
T PF12760_consen 38 YRCKACR 44 (46)
T ss_pred EECCCCC
Confidence 5555554
No 161
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=26.85 E-value=39 Score=18.58 Aligned_cols=9 Identities=33% Similarity=1.036 Sum_probs=4.6
Q ss_pred ccccccCcc
Q psy13164 161 RYKCNLCSK 169 (193)
Q Consensus 161 ~~~C~~C~~ 169 (193)
++.|..|+.
T Consensus 37 R~~CGkCgy 45 (51)
T COG1998 37 RWACGKCGY 45 (51)
T ss_pred eeEeccccc
Confidence 455555553
No 162
>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=26.45 E-value=95 Score=17.88 Aligned_cols=9 Identities=33% Similarity=0.933 Sum_probs=4.5
Q ss_pred eeccccccc
Q psy13164 108 YKCDLCSKE 116 (193)
Q Consensus 108 ~~C~~C~~~ 116 (193)
|.|+.||..
T Consensus 47 ~~C~~Cg~~ 55 (69)
T PF07282_consen 47 FTCPNCGFE 55 (69)
T ss_pred EEcCCCCCE
Confidence 455555544
No 163
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=26.34 E-value=36 Score=23.28 Aligned_cols=31 Identities=29% Similarity=0.882 Sum_probs=16.8
Q ss_pred ceecccccccccChhHHHHHHHhhCC-cceeccccchhc
Q psy13164 107 RYKCDLCSKEYFHKGSLTEHKKRHQG-IRYKCDLCSKEY 144 (193)
Q Consensus 107 ~~~C~~C~~~f~~~~~l~~h~~~h~~-~~~~C~~C~~~f 144 (193)
.|.|..|+..+.. +. .+.. ..|.|..|+..+
T Consensus 112 ~y~C~~C~~~~~~------~r-r~~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYLR------VR-RSNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCce------Ec-cccCcceEEcCCCCCEE
Confidence 4777777765431 11 1122 357777777554
No 164
>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=26.28 E-value=50 Score=27.52 Aligned_cols=26 Identities=23% Similarity=0.414 Sum_probs=18.0
Q ss_pred ceeccccchhccChhHHHHHHH-HhCC
Q psy13164 134 RYKCDLCSKEYFHKGYLTDHKK-IHQG 159 (193)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~-~h~~ 159 (193)
-|.|+.|.+.|.....+..|+. .|.+
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 3677777777777777777776 3544
No 165
>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=26.14 E-value=12 Score=20.77 Aligned_cols=25 Identities=24% Similarity=0.587 Sum_probs=12.6
Q ss_pred CceecccccccccChhHHHHHHHhh
Q psy13164 106 IRYKCDLCSKEYFHKGSLTEHKKRH 130 (193)
Q Consensus 106 ~~~~C~~C~~~f~~~~~l~~h~~~h 130 (193)
..|.|+.|...|-..-.+..|...|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CeEECCCCCCccccCcChhhhcccc
Confidence 3488888888887766666555544
No 166
>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=25.97 E-value=17 Score=17.36 Aligned_cols=9 Identities=56% Similarity=1.161 Sum_probs=4.6
Q ss_pred ccccCcccc
Q psy13164 163 KCNLCSKEF 171 (193)
Q Consensus 163 ~C~~C~~~F 171 (193)
.|..|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 344555555
No 167
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.90 E-value=33 Score=22.66 Aligned_cols=10 Identities=30% Similarity=0.889 Sum_probs=4.7
Q ss_pred eecccccccc
Q psy13164 108 YKCDLCSKEY 117 (193)
Q Consensus 108 ~~C~~C~~~f 117 (193)
+.|..|+..|
T Consensus 72 ~~C~~Cg~~~ 81 (117)
T PRK00564 72 LECKDCSHVF 81 (117)
T ss_pred EEhhhCCCcc
Confidence 4455555433
No 168
>PRK04351 hypothetical protein; Provisional
Probab=25.05 E-value=38 Score=23.45 Aligned_cols=31 Identities=32% Similarity=0.897 Sum_probs=18.3
Q ss_pred eecccccccccChhHHHHHHHhhCCcceeccccchhcc
Q psy13164 108 YKCDLCSKEYFHKGSLTEHKKRHQGIRYKCDLCSKEYF 145 (193)
Q Consensus 108 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~C~~C~~~f~ 145 (193)
|.|..|+..+.+. +.+-...|.|..|+..+.
T Consensus 113 Y~C~~Cg~~~~r~-------Rr~n~~~yrCg~C~g~L~ 143 (149)
T PRK04351 113 YECQSCGQQYLRK-------RRINTKRYRCGKCRGKLK 143 (149)
T ss_pred EECCCCCCEeeee-------eecCCCcEEeCCCCcEee
Confidence 7887788655321 122223688888876554
No 169
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=24.85 E-value=24 Score=31.51 Aligned_cols=11 Identities=36% Similarity=0.703 Sum_probs=0.0
Q ss_pred ceeccccchhc
Q psy13164 134 RYKCDLCSKEY 144 (193)
Q Consensus 134 ~~~C~~C~~~f 144 (193)
-|.|+.|+...
T Consensus 680 ~~~Cp~C~~~~ 690 (900)
T PF03833_consen 680 VYVCPDCGIEV 690 (900)
T ss_dssp -----------
T ss_pred ceecccccccc
Confidence 36677666543
No 170
>KOG2272|consensus
Probab=24.28 E-value=82 Score=23.95 Aligned_cols=20 Identities=5% Similarity=-0.076 Sum_probs=12.6
Q ss_pred CCCCcccchhHhhccCchhh
Q psy13164 54 NGNDAVTRDCLEFFKSHDST 73 (193)
Q Consensus 54 ~~~~~~c~~c~~~f~~~~~~ 73 (193)
-..-+.|++|.+.+.+...+
T Consensus 96 Hp~CF~Cd~Cn~~Lad~gf~ 115 (332)
T KOG2272|consen 96 HPACFRCDLCNKHLADQGFY 115 (332)
T ss_pred CcccchhHHHHHHHhhhhhH
Confidence 34456788888776654443
No 171
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=24.19 E-value=61 Score=17.79 Aligned_cols=9 Identities=22% Similarity=0.885 Sum_probs=4.7
Q ss_pred eeccccccc
Q psy13164 108 YKCDLCSKE 116 (193)
Q Consensus 108 ~~C~~C~~~ 116 (193)
+.|..|+.+
T Consensus 38 ~~C~~Cgyt 46 (50)
T PRK00432 38 WHCGKCGYT 46 (50)
T ss_pred EECCCcCCE
Confidence 555555543
No 172
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=23.33 E-value=25 Score=17.69 Aligned_cols=8 Identities=38% Similarity=0.953 Sum_probs=3.8
Q ss_pred eccccccc
Q psy13164 109 KCDLCSKE 116 (193)
Q Consensus 109 ~C~~C~~~ 116 (193)
.|..|+..
T Consensus 22 ~C~~C~Y~ 29 (35)
T PF02150_consen 22 ACRTCGYE 29 (35)
T ss_dssp EESSSS-E
T ss_pred CCCCCCCc
Confidence 45555544
No 173
>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=23.03 E-value=40 Score=17.20 Aligned_cols=11 Identities=36% Similarity=0.878 Sum_probs=5.6
Q ss_pred ceecccccccc
Q psy13164 107 RYKCDLCSKEY 117 (193)
Q Consensus 107 ~~~C~~C~~~f 117 (193)
.|+|..||...
T Consensus 6 ~YkC~~CGniV 16 (36)
T PF06397_consen 6 FYKCEHCGNIV 16 (36)
T ss_dssp EEE-TTT--EE
T ss_pred EEEccCCCCEE
Confidence 38888888754
No 174
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.88 E-value=31 Score=20.85 Aligned_cols=9 Identities=33% Similarity=1.139 Sum_probs=5.3
Q ss_pred eeccccccc
Q psy13164 108 YKCDLCSKE 116 (193)
Q Consensus 108 ~~C~~C~~~ 116 (193)
|.|..|+..
T Consensus 13 Y~c~~cg~~ 21 (82)
T COG2331 13 YECTECGNR 21 (82)
T ss_pred EeecccchH
Confidence 566666654
No 175
>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=22.78 E-value=76 Score=16.23 Aligned_cols=11 Identities=45% Similarity=1.156 Sum_probs=3.8
Q ss_pred ccccccCcccc
Q psy13164 161 RYKCNLCSKEF 171 (193)
Q Consensus 161 ~~~C~~C~~~F 171 (193)
+|-|..|+..|
T Consensus 3 ryyCdyC~~~~ 13 (38)
T PF06220_consen 3 RYYCDYCKKYL 13 (38)
T ss_dssp S-B-TTT--B-
T ss_pred Ceeccccccee
Confidence 35577777776
No 176
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=22.36 E-value=64 Score=17.82 Aligned_cols=8 Identities=38% Similarity=1.186 Sum_probs=3.2
Q ss_pred eeccccch
Q psy13164 135 YKCDLCSK 142 (193)
Q Consensus 135 ~~C~~C~~ 142 (193)
+.|..||.
T Consensus 29 W~C~~Cgh 36 (55)
T PF14311_consen 29 WKCPKCGH 36 (55)
T ss_pred EECCCCCC
Confidence 34444433
No 177
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the COG1773 Rubredoxin [Energy production and conversion]
Probab=22.29 E-value=44 Score=18.88 Aligned_cols=13 Identities=31% Similarity=0.907 Sum_probs=8.9
Q ss_pred ceecccccccccC
Q psy13164 107 RYKCDLCSKEYFH 119 (193)
Q Consensus 107 ~~~C~~C~~~f~~ 119 (193)
.|+|..||..|.-
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 3778888877643
No 179
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.28 E-value=41 Score=22.80 Aligned_cols=12 Identities=33% Similarity=0.753 Sum_probs=6.4
Q ss_pred eecccccccccC
Q psy13164 108 YKCDLCSKEYFH 119 (193)
Q Consensus 108 ~~C~~C~~~f~~ 119 (193)
+.|..||..|..
T Consensus 71 ~~C~~CG~~~~~ 82 (135)
T PRK03824 71 LKCRNCGNEWSL 82 (135)
T ss_pred EECCCCCCEEec
Confidence 555555555443
No 180
>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=21.74 E-value=56 Score=17.28 Aligned_cols=12 Identities=25% Similarity=0.866 Sum_probs=7.8
Q ss_pred ccccCcccccCh
Q psy13164 163 KCNLCSKEFLRK 174 (193)
Q Consensus 163 ~C~~C~~~F~~~ 174 (193)
.|..|++.|+..
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 467777777654
No 181
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=21.22 E-value=25 Score=19.73 Aligned_cols=8 Identities=25% Similarity=0.721 Sum_probs=3.9
Q ss_pred ceeccccc
Q psy13164 134 RYKCDLCS 141 (193)
Q Consensus 134 ~~~C~~C~ 141 (193)
|+.|+.|.
T Consensus 28 PlyCpKCK 35 (55)
T PF14205_consen 28 PLYCPKCK 35 (55)
T ss_pred cccCCCCC
Confidence 44555544
No 182
>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=21.13 E-value=65 Score=15.53 Aligned_cols=11 Identities=36% Similarity=1.150 Sum_probs=4.4
Q ss_pred eeccccccccc
Q psy13164 108 YKCDLCSKEYF 118 (193)
Q Consensus 108 ~~C~~C~~~f~ 118 (193)
|.|+.|+..+-
T Consensus 14 Y~Cp~C~~~~C 24 (30)
T PF04438_consen 14 YRCPRCGARYC 24 (30)
T ss_dssp EE-TTT--EES
T ss_pred EECCCcCCcee
Confidence 56666655443
No 183
>KOG0717|consensus
Probab=20.92 E-value=57 Score=27.12 Aligned_cols=22 Identities=27% Similarity=0.581 Sum_probs=18.7
Q ss_pred cccccCcccccChHHHHHHHHH
Q psy13164 162 YKCNLCSKEFLRKDILIEHKKI 183 (193)
Q Consensus 162 ~~C~~C~~~F~~~~~L~~H~~~ 183 (193)
+-|..|+++|.+-..|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7799999999999888888653
No 184
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.90 E-value=41 Score=22.64 Aligned_cols=13 Identities=46% Similarity=1.063 Sum_probs=11.4
Q ss_pred ccccccCcccccC
Q psy13164 161 RYKCNLCSKEFLR 173 (193)
Q Consensus 161 ~~~C~~C~~~F~~ 173 (193)
+|.|..|++.|..
T Consensus 53 RyrC~~C~~tf~~ 65 (129)
T COG3677 53 RYKCKSCGSTFTV 65 (129)
T ss_pred ccccCCcCcceee
Confidence 7999999999964
No 185
>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=20.78 E-value=40 Score=21.22 Aligned_cols=13 Identities=15% Similarity=0.641 Sum_probs=8.3
Q ss_pred ceeccccchhccC
Q psy13164 134 RYKCDLCSKEYFH 146 (193)
Q Consensus 134 ~~~C~~C~~~f~~ 146 (193)
.|.|..|++.|..
T Consensus 53 IW~C~~C~~~~AG 65 (91)
T TIGR00280 53 IWTCRKCGAKFAG 65 (91)
T ss_pred EEEcCCCCCEEeC
Confidence 4677777766643
No 186
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=20.44 E-value=56 Score=16.35 Aligned_cols=8 Identities=25% Similarity=0.688 Sum_probs=4.4
Q ss_pred eecccccc
Q psy13164 108 YKCDLCSK 115 (193)
Q Consensus 108 ~~C~~C~~ 115 (193)
+.|+.|+.
T Consensus 23 ~vC~~Cg~ 30 (34)
T PF14803_consen 23 LVCPACGF 30 (34)
T ss_dssp EEETTTTE
T ss_pred eECCCCCC
Confidence 55555554
No 187
>PTZ00448 hypothetical protein; Provisional
Probab=20.39 E-value=71 Score=25.73 Aligned_cols=23 Identities=13% Similarity=0.447 Sum_probs=18.2
Q ss_pred ccccccCcccccChHHHHHHHHH
Q psy13164 161 RYKCNLCSKEFLRKDILIEHKKI 183 (193)
Q Consensus 161 ~~~C~~C~~~F~~~~~L~~H~~~ 183 (193)
.|.|..|+..|......+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57788888888877777778765
No 188
>KOG1842|consensus
Probab=20.07 E-value=66 Score=26.58 Aligned_cols=26 Identities=19% Similarity=0.445 Sum_probs=21.4
Q ss_pred ceecccccccccChhHHHHHHHh-hCC
Q psy13164 107 RYKCDLCSKEYFHKGSLTEHKKR-HQG 132 (193)
Q Consensus 107 ~~~C~~C~~~f~~~~~l~~h~~~-h~~ 132 (193)
.|.|++|...|.+...|..|... |.+
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~ 41 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFE 41 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhccc
Confidence 48899999999999999999865 554
Done!